Highlights of Biological Physics (DBIO) Talks @ APS 2022 March Meeting
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TABLE 1: Highlights of Biological Physics (DBIO) Talks @ APS 2022 March Meeting
Paper | Author(s) | |
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1 | DBIO Short Course: The Physics of Biological Movement Across Scales Related Papers Related Patents Related Grants Related Orgs Related Experts Details |
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2 | A Mathematical Analysis of Learning in Both Biological and Artificial Neural Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The unification of these fields will likely enable us to exploit the power of complex systems analysis, developed in theoretical physics and applied mathematics, to elucidate the design principles governing neural systems, both biological and artificial, and deploy these principles to develop better algorithms in machine learning. |
Surya Ganguli; |
3 | Intrinsic and Parameter-less Gain Control in Rate Coding By Spiking Neurons Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we propose a biophysical mechanism for contrast adaptation that does not rely on changes in internal state. |
Nirag Kadakia ; Will Rosenbluth ; Thierry Emonet; |
4 | Neural Network Model of Nonlinear Bayesian Learning Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Previous work from our group revealed that this process, in the context of pitch compensation in songbirds learning to sing, can be modeled by a Bayesian filter with non-Gaussian probability distributions. |
Camilla Li ; Ilya Nemenman; |
5 | Desynchronous and Decentralized Learning In A Physical Network Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we take the system one step closer to its biological inspiration by relaxing the global clock requirement, allowing individual edges of the network to update randomly and independently. |
Jacob Wycoff ; Sam Dillavou ; Menachem Stern ; Andrea Liu ; Douglas Durian; |
6 | Merging Kalman Filtering with The Information Bottleneck Technique for Optimal State Inference Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present the analytic solution to one-dimensional stimuli, and observe several regimes for the sensory model as a function of correlation time and resource constraints. |
Vedant Sachdeva ; Thierry Mora ; Arvind Murugan ; Stephanie Palmer ; Aleksandra Walczak; |
7 | A Theory of Weight Distribution-constrained Learning Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Motivated by this, we developed a theory of learning in neural networks that incorporates both sign and distribution constraints. |
Weishun Zhong ; Ben Sorscher ; Daniel Lee ; Haim Sompolinsky; |
8 | Biophysical Learning : Training Flow Networks Via Chemical Signaling Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work explores how modifications in a physical system using locally available information can give rise to emergent global functionality. |
Vidyesh Rao Anisetti ; Benjamin Scellier ; Siddhartha Mishra ; Jennifer Schwarz; |
9 | How Physics-informed Neural Networks Improve Image Segmentation Performance Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: An alternative approach is the use of data augmentation, using a physics-informed neural network, to supplement training. |
Daniela Koch; |
10 | Exploring The Landscape of Collective Modes Using IB-RG Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In another domain, the information bottleneck approach (IB) describes the best probabilistic compression of an input variable X under a pre-defined “relevance” variable Y. Recent theoretical work has shown that IB can be imposed on RG, allowing one to define the notion of large-scale structure probed by the RG flow [1]. |
Adam Kline; |
11 | Energy-Based Models Capture Pairwise and Higher-Order Interactions in Protein Sequence Data Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present a unifying approach for inferring two of the most important structural units of proteins: pairwise contacts, and higher-order strongly correlated units, known as sectors. |
Peter Fields ; Vudtiwat Ngampruetikorn ; Stephanie Palmer ; David Schwab; |
12 | Learning in Gene Regulatory Networks: Dimensionality Reduction By Master Regulators Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will present a computational framework to describe such adaptation inspired by learning models of the brain. |
Naama Brenner; |
13 | Memory Formation in Adaptive Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we show that adaptation dynamics allow a network to memorize the position of an applied load within its network morphology. |
Komal Bhattacharyya ; David Zwicker ; Karen Alim; |
14 | The Route to Chaos of Reinforcement Learning in Routing Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we show that collective behaviors of reinforcement learning agents can be driven away from the Nash equilibrium. |
Jakub Bielawski ; Thiparat Chotibut ; Fryderyk Falniowski ; Michal Misiurewicz ; Georgios Piliouras; |
15 | Molecular Implementations of Positive and Negative Feedback Inform Robustness in Biological Oscillator Motifs Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Biological oscillators like the cell cycle, the circadian sleep-wake cycle, etc. are vital to an organism’s survival. Biochemical oscillator circuits are typically classified … |
Chaitra Agrahar ; Michael Rust; |
16 | Metabolic Pathway Design Using Active Subspaces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I formulated a differential equation model of this system to compare five candidate strains with different enzyme concentrations in the MCP. |
Andre Archer ; Taylor Nichols ; Niall Mangan ; Danielle Tullman-Ercek; |
17 | Building Synthetic Circuits to Achieve Cascading Cell Fate Transitions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Previously, we proposed a cascading bistable switches (CBS) mechanism for epithelial to mesenchymal transition (EMT). |
Xiaojun Tian ; Rong Zhang ; Hanah Goetz ; Juan Melendez-Alvarez ; Jiao Li ; Tian Ding ; Xiao Wang; |
18 | Identifying Mechanisms of Gene Circuit Evolution That Elicit Mammalian Drug Resistance Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Recently we used synthetic gene circuits harboring positive feedback (PF) and negative feedback (NF) regulation to tune mammalian drug resistance transgene (DRT) expression noise. |
Joseph Cohen ; Mu; Ph.D; Quanhua ; Yiming Wan ; Farquar; Ph.D; Kevin ; Gabor Balazsi; |
19 | The Role of Energy Dissipation in Shaping Eukaryotic Transcriptional Regulation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this deficit, we developed a framework for modelling non-equilibrium regulation and used it to define underlying parameter regimes that set limits for cooperativity in various regulatory schemes, thereby discovering a trade-off between energy dissipation and cooperativity. |
Zheng Diao ; Caleb Bashor ; Oleg Igoshin; |
20 | Advancing The Frontiers of Design-driven Medicine: Engineering Programmable Cell-based Therapies and Diagnostics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will present recent advances made toward achieving the vision of design-driven engineering of novel mammalian cellular functions. |
Joshua Leonard; |
21 | Dynamics of DNA Methylation and Persistence of Epigenetic Memory Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We examine a theoretical model of this process by considering a one-dimensional lattice where each site can either be methylated (1) or unmethylated (0). |
Sagnik Ghosh ; Arnab Datta ; Colin Kunze ; Jane Kondev ; Ahmad Khalil; |
22 | Deciphering The Influence of Genome Architecture in A Minimized Bacterial Genome Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Probabilistic interactions of RNA polymerase with DNA dictate transcription, the process which evolves the bacterial transcriptome composed of rRNA, tRNA, mRNA, and sRNA. The … |
Troy Brier ; Pratap Venepally ; John Glass ; Zaida (Zan) Luthey-Schulten; |
23 | A Novel Riboswitch Design for Integrative, Functional RNA Detection in Mammalian Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we propose a strategy for detection of mRNA or short RNAs by trigger-specific control of mammalian translation. |
Rafał Krzysztoń ; Yiming Wan ; Julia Petreczky ; Gabor Balazsi; |
24 | The State of Water in Lipidic Mesophase Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here I will present our recent studies on water under soft confining media provided by lipidic mesophase (LMP). |
Yang Yao ; Sara Catalini ; Bence Kutus ; Johannes Hunger ; Tao Zhou ; Paolo Foggi ; George Floudas ; Raffaele Mezzenga; |
25 | Leveraging Evolutionary Trade-offs and Phage Selection Pressure to Alter Bacterial Infections Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present examples of phages that have evolved to kill target bacteria while selecting for phage resistance that coincides with phenotypic traits that are beneficial to biomedicine. |
Paul Turner; |
26 | AI-driven Predictions of Binding Trends of SARS-CoV-2 Variants from Atomistic Simulations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The aim of our study is to leverage machine learning approaches to address this challenge and estimate binding affinity trends between two proteins using short atomistic simulations. |
Sara Capponi; |
27 | Evolutionary Tradeoff of Enterovirus A71 Thermostability and Cell Entry Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This study examines Enterovirus A71, normally the cause of Hand, Foot, and Mouth Disease but more recently more severe diseases such as encephalitis and acute flaccid paralysis, through the lens of evolutionary selection, molecular mechanisms, and animal models. |
Benjamin Catching ; Ming Yeh ; Sara Capponi ; Raul Andino ; Simone Bianco; |
28 | Inferring Polygenic Selection for HIV Escape from T Cell Responses Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we build a model describing this polygenic immune selection. |
Yirui Gao ; John Barton; |
29 | Modeling Time-series of Noisy Two-cycle Ecological Oscillators Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We will present forecast skill results for the three developed models (two-state, three-state and continuous-state) and a machine learning forecasting tool. |
Vahini Reddy Nareddy ; Jonathan Machta ; Karen Abbott ; Shadi Esmaeili-Wellman ; Alan Hastings; |
30 | Dynamics of Viral Mutation and Evolution Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We discuss our model of viral-host interaction, and the dynamics that is introduced by the multiple forces acting on the virus in that system. |
Greyson Lewis; |
31 | Diversity-generating Host-disease Coevolution with Adaptive Immunity Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find with a simple stochastic population dynamics model that viruses experience a changing fitness that both drives and reigns in diversity: new virus mutants that escape immune targeting have high fitness and experience selective dynamics associated with low diversity, while established virus clones experience immune targeting and lose their fitness advantage, going extinct following neutral dynamics associated with high diversity. |
Madeleine Bonsma-Fisher ; Sidhartha Goyal; |
32 | The Scales of Viral-host Co-evolution Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will show that co-evolution between immune systems and viruses in a finite-dimensional antigenic space can be described by an antigenic wave pushed forward and canalized by host-pathogen interactions. |
Aleksandra Walczak; |
33 | Predicted Adaptation of Microbial Population Growth Deceleration in Feast-and-famine Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we give a model for co-culture experiments between two strains competing for a single limiting resource where cell growth slows down with nutrient concentration. |
Justus Fink ; Michael Manhart; |
34 | Preventing Co-infection: A Viral Strategy with Short-term Benefits and Long-term Drawbacks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that genetic drift is suppressed when co-infection is allowed, which in turn facilitates the fixation of beneficial mutations and the removal of deleterious ones. |
Michael Hunter ; Diana Fusco; |
35 | Enhanced Biodiversity in Time-dependent Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we show that including a periodic time dependence in a generic population dynamics model can enhance the biodiversity of the system. |
Tom Burkart ; Erwin Frey; |
36 | Time to Fixation in Changing Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we study the properties of the conditional fixation time defined as the time to fixation of a new mutant that is destined to fix in a finite, randomly mating diploid population with intermediate dominance that is evolving in a periodically changing environment. |
Sachin Kaushik; |
37 | Metabolic Preferences of Marine Copiotrophs Are Explained By The Structure of Central Metabolism Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We found that the metabolic niches were oriented along a primary axis corresponding to the relative preference for sugars (i.e., glycolytic substrates) and organic and amino acids (i.e., gluconeogenic substrates). |
Matti Gralka ; Otto Cordero; |
38 | Bayesian Nonparametrics in Multi-particle Superresolved Tracking Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have overcome the limitations of existing algorithms by employing a fully self-consistent Bayesian-nonparametrics framework where all aforementioned steps are treated simultaneously. |
Zeliha Kilic ; Steve Presse ; Ioannis Sgouralis; |
39 | Inference of C. Elegans Neural Network Structure from Calcium Flurescence Time Series Data with Reservoir Computing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we train a particular kind of machine learning architechture, called "reservoir computing", on publicly available whole-brain calcium imaging time series datasets from C. elegans. |
Amitava Banerjee ; Sarthak Chandra ; Edward Ott; |
40 | Towards Interpretable Imputation of Missing Observations with Time Slice Synthetic Minority Oversampling Technique Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To deal with these issues, we developed a simple yet novel non-parametric time series imputation technique with the goal of constructing an irregular time series that is uniform across every sample in a data set. |
Andrew Baumgartner; |
41 | Graph Neural Networks for Multicellular Dynamics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we propose a generic machine learning approach capable of learning various multicellular dynamics from recorded experimental videos. |
Ming Han ; John Devany ; Margaret Gardel ; Vincenzo Vitelli; |
42 | Sociophysics of Subjective Pain: Robust Cluster Assignment Based on Sparsely and Irregularly Sampled Data from A Dynamical System Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce and test a variety of methods for comparing irregularly and sparsely sampled trajectories, with the goal of providing a rigorous basis for defining clusters and assigning trajectories to them. |
Gary Nave ; Swati Padhee ; Kumar Utkarsh ; Amanuel Alambo ; Tanvi Banerjee ; Nirmish Shah ; Daniel Abrams; |
43 | Learning The Shape of The Protein Universe with 3D-equivariant Holographic Convolutional Neural Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we introduce holographic convolutional neural networks (H-CNNs) that take atomic coordinates of a protein structure as input and, through 3D equivariant transformations that respect the rotational symmetries in data, learn interpretable models of protein micro-environments reflecting the underlying biophysics. |
Michael Pun ; Andrew Ivanov ; Quinn Bellamy ; Colin LaMont ; Jakub Otwinowski ; Armita Nourmohammad; |
44 | Machine Learning Continuum Models for Cellular Force Generation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we show how machine learning can be used to build continuum models that relate protein distributions to forces. |
Matthew Schmitt ; Jonathan Colen ; Stefano Sala ; Margaret Gardel ; Patrick Oakes ; Vincenzo Vitelli; |
45 | EMBED: A Low Dimensional Reconstruction of Gut Microbiome Dynamics Based on Ecological Normal Modes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To that end, we develop EMBED: Essential Microbiome Dynamics; a matrix factorization method that embeds longitudinal microbiome abundance data onto a series of lower dimensional Boltzmann Distributions. |
Mayar Shahin ; Purushottam Dixit ; Brian Ji; |
46 | Parameter Estimation from Stochastic Processes Applied to Neural Dynamics and Aging Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: H. H. Strey, Estimation of parameters from time traces originating from an Ornstein-Uhlenbeck process. Phys Rev E 100, 062142 (2019). H. H. Strey, R. Kumar, L. Mujica-Parodi, … |
Helmut Strey ; Lilianne Mujica-Parodi ; Uri Alon ; Yifan Yang; |
47 | Salient Projections Over Maximum Projections: Improving Deep-learning Detection and Segmentation During Invasion of Cell-dense Spheroids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we present on a highly adaptable deep-learning module which accepts 3D inputs to propogate 3D spatial latent embeddings as inputs to 2D instance segmentation neural networks. |
Christopher Eddy; |
48 | Non-linear Interpolation for Genetic Fitness Prediction Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we propose a stochastic non-linear interpolation method using Bézier’s method [2]. |
Kai Shimagaki ; John Barton; |
49 | Multi-Model Analysis of De Novo Antimicrobial Peptide Design Via Variational Autoencoder Latent Sampling Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work develops a comparison of generative deep learning models used widely in the field of chemical compound discovery as an application to de novo AMP generation. |
Samuel Renaud ; Ré Mansbach; |
50 | Learning The Forces in Active Matter from The Trajectories: A Graph-neural-network Approach Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose a graph-neural-network-based scheme that learns the interactions between particles and the active forces to predict the correct particle dynamics. |
Miguel Ruiz-Garcia ; Miguel Barriuso Gutierrez ; Luca Ghiringhelli ; Chantal Valeriani; |
51 | Active Nematics and Topological Defects in Colonies of Gliding Bacteria Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that these new holes and layers form at topological defects where the cell orientation field is undefined, and is driven by the bacteria acting as an active nematic liquid crystal through cell motility and substrate friction. |
Katherine Copenhagen; |
52 | Mechanical Stress Fluctuations in Myxococcus Xanthus Monolayers Revealed By Traction Force Microscopy Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using traction force microscopy, we map out the spatial distribution of forces exerted by M. xanthus cells on a soft hydrogel substrate and link the position of defects to the distribution of stresses. |
Endao Han ; Katherine Copenhagen ; Joshua Shaevitz; |
53 | Capillary Attraction Facilitates Bacterial Collective Dynamics: Experiment Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we use surface profilometry to quantify the water meniscus that wets surface-attached cells, and show that the capillary attraction mediated by these menisci shapes the structure and dynamics of M. xanthus group motility. |
Matthew Black ; Chenyi Fei ; Sebastian Gonzales La Corte ; Ricard Alert ; Ned Wingreen ; Joshua Shaevitz; |
54 | Capillary Attraction Facilitates Bacterial Collective Dynamics: Theory Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we developed a computational model to study the role of capillary forces in this process. |
Chenyi Fei ; Matthew Black ; Sebastian Gonzalez La Corte ; Ricard Alert ; Joshua Shaevitz ; Ned Wingreen; |
55 | A Mechanism for Migrating Bacterial Populations to Non-genetically Adapt to New Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Through theory and simulations, we predict that expanding populations non-genetically adapt their phenotype compositions to migrate effectively through multiple physical environments. |
Henry Mattingly ; Thierry Emonet; |
56 | Roughening Instability of Growing Three-dimensional Bacterial Colonies in Complex Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we describe a morphological instability exhibited by large dense colonies of bacteria growing in 3D. |
Alejandro Martinez-Calvo ; Tapomoy Bhattacharjee ; R. Konane Bay ; Anna Hancock ; Ned Wingreen ; Sujit Datta; |
57 | Topological Traps Control Material Flux in Self-organizing Active Filament Spirals Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Utilizing a novel active matter system of filamentous cyanobacteria spread on two-dimensional agar, we explore the role of topology in controlling material flux in self-organizing systems. |
Xingting Gong ; Manu Prakash; |
58 | Active Decentralized Transport in Biological Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we combine experimental data from real Physarum networks with simulations of the active mechanism that drives flow. |
Adam Dionne ; Henrik Ronellenfitsch; |
59 | Collective Dynamics of Active Filaments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We explore the patterns they form by tuning the key physical parameters such as the bending stiffness, activity, and reversal rate at low density of filaments. |
Leila Abbaspour; |
60 | Microphase Separation in Scalar Active Matter Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a microscopic model inspired by the bacteria Neisseria Meningitidis in which diffusive agents feel intermittent attractive forces determined by an internal variable that switches stochastically. |
Henry Alston ; Thibault Bertrand; |
61 | Active Noise of Chlorella in Photosynthesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here in our study, taking Chlorella Vulgaris as an example, we observed the “active color noises” produced by microalgae due to the external photoactivation which then affects their dynamical behaviors correspondingly. |
Jin Tae Park ; Yitan Li ; Song Liu ; Steve Granick; |
62 | Bioluminescent Breaking Waves Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we go beyond single-cell analysis and present a lab-scale model of bioluminescent breaking waves. |
Maziyar Jalaal ; Nico Schramma ; Sophie Beck ; Tanguy Sarafian; |
63 | Trajectory Analysis of Single Microswimmer Behaviour Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose novel motility measures to deduce how swimming behaviour changes and adapts in response to increasing physical confinement, light stimulation and sudden chemical perturbations. |
Hannah Laeverenz Schlogelhofer ; Samuel Bentley ; Vasileios Anagnostidis ; Fabrice Gielen ; Kirsty Wan; |
64 | Dynamic Kinetic Stability: Toward The Physicalization of Biology Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk I will describe the recent discovery of a previously unrecognized kinetic dimension in chemical space, one offering new insights into the life phenomenon seemingly unavailable through traditional thermodynamic considerations. |
Addy Pross ; Robert Pascal; |
65 | How Informational Sequences Emerge from Random Templated Ligation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: [1,2] we studied a general problem of heteropolymers capable of template-assisted ligation based on Watson-Crick-like hybridization. |
Sergei Maslov ; Alexei Tkachenko ; Dieter Braun ; Patrick Kudella ; Annalena Salditt; |
66 | Computer Simulations of Non-Enzymatic Template-Directed RNA Synthesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present simulations that incorporate melting, reannealing, primer extension, and ligation. |
Paul Higgs; |
67 | Towards A Statistical Mechanics of Biochemistry Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here I introduce a more generalizable concept of biochemical universality, akin to the kind found in physics. |
Sara Walker; |
68 | Life Originated When Physical Chemistry “discovered” Survival of The Fittest Dynamics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have developed a dynamical model that shows that simple random peptide syntheses could have led to peptide chains that elongate, collapse and sometimes fold and catalyze. |
Ken Dill ; Charles Kocher; |
69 | Effective Temperature and Activity Induced Memory Effects of A Passive Particle in An Active Bath Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present an overview of the properties of a system of a passive particle immersed in a bath of active particles with translational inertia. |
Jeanine Shea ; Gerhard Jung ; Friederike Schmid; |
70 | Collective Dynamics of Quincke Rollers with Fully Resolved Hydrodynamics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We report our successful simulations on the collective motions of Quincke rollers, which depends on the strength of dipole moment induced on a particle, the area fraction of particles, and the strength of interparticle attraction, with fully resolving the hydrodynamics of the system. |
Shun Imamura ; Kohei Sawaki ; John Molina ; Ryoichi Yamamoto; |
71 | Dynamics of Active Rings in Porous Media Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that the activity of individual beads differently affects the dynamical and conformal properties of the ring polymer depending on the pore size of the media, flexibility, and stiffness of the polymer. |
Rajarshi Chakrabarti ; Tapomoy Bhattacharjee ; Subhasish Chaki ; Ligesh Theeyancheri; |
72 | Phase Behaviour of Active Nanoparticles in Block Copolymer Melts Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work we explore the co-assembly of active nanoparticles within block copolymer melts in two- and three-dimensions finding single-particle and collective behaviour due to the interplay between colloidal directed motion and block copolymer morphology. |
Javier Diaz ; Ignacio Pagonabarraga ; Andrei Zvelindovsky ; Marco Pinna; |
73 | Disordered Boundaries Destroy Bulk Phase Separation in Scalar Active Matter Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that disordered boundaries destroy bulk phase separation in scalar active systems in dimension d <3. |
Yariv Kafri; |
74 | Pulsating Active Particles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: It is known that cells in biological tissues interact and give rise to collective behavior such as size oscillation and wave propagation: we explore the physical mechanisms underlying this collective behavior by introducing a novel class of active matter, where the activity is the ability to change an internal degree of freedom at the single-particle level, which can be eventually related to the particle size. |
Alessandro Manacorda ; Étienne Fodor; |
75 | Tension-Controlled Collective Dynamics in Active Solids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we show how mechanical tension can serve as a general mechanism for switching between different collective dynamics in active solids. |
Paul Baconnier ; Dor Shohat ; Olivier Dauchot; |
76 | Dynamics of Self-propelled Particles Over A Periodic Potential Landscape Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We report a systematic study of self-propelled particles (SPPs) over a periodic potential landscape. |
Penger Tong ; Yan Wen ; Zhihao Li ; Haiqin Wang ; Jing Zheng ; Jinyao Tang ; Pik-Yin Lai ; Xinpeng Xu; |
77 | The Anomalous Transport of Tracers in Active Baths Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We derive the exact long-time dynamics of a tracer immersed in a one-dimensional active bath. |
Omer Granek ; Yariv Kafri ; Julien Tailleur; |
78 | Using Phase Field Models to Simulate The Full Chemohydrodynamics of Passive and Active Colloids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have recently developed a method using phase field models that performs full chemohydrodynamics simulations of such dense and unsteady systems and incorporates colloidal particles as highly viscous fluid phases. |
Douglas Tree ; Qinyu Zhu; |
79 | Experiments on Single-molecular Energetics of Biological Molecular Motor Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that the F 1-motor achieves 100% thermodynamic efficiency at the stalled state. |
Shoichi Toyabe; |
80 | The Lawnmower: An Artificial Protein-based Burnt-bridge Molecular Motor Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Inspired by biology, we have synthesized and characterized a protein-based microscale motor we dub the lawnmower. |
Nancy Forde ; Chapin Korosec ; Paul M.G. Curmi ; Heiner Linke; |
81 | Single-molecule Studies of KIF1A Motion and Force Generation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To test the importance of neck linker docking in KIF1A force generation, we introduced the V8M and Y89D disease mutations. |
Arne Gennerich; |
82 | Signaling and Mechanics in Mitotic Spindle Assembly Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk I will introduce our recent theoretical modeling in both the signaling and mechanical aspects of spindle assembly. |
Jing Chen; |
83 | Adaptation and Evolution in Flagellar Motors Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a model for torque generation in the E. coli flagellar motor rooted in this new structural understanding. |
Jasmine Nirody; |
84 | Neural Circuits for Dynamics-based Segmentation of Time Series Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present two algorithms for performing this segmentation task that are biologically plausible, which we define as acting in a streaming setting and all learning rules being local. |
Tiberiu Tesileanu ; Siavash Golkar ; Samaneh Nasiri ; Anirvan Sengupta ; Dmitri Chklovskii; |
85 | Recording Neural Activity in Freely Behaving Animals with A Random Access Two Photon Microscopy Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: By implementing acousto-optic deflectors and a custom-designed compact dispersion compensator [1], we developed a random-access two-photon tracking microscope capable of recording activity from neurons in unrestrained freely behaving Drosophila larvae without motion artifacts. |
Akihiro Yamaguchi ; Akihiro Yamaguchi ; Paul McNulty ; Rui Wu ; Jason Wolk ; Marc Gershow; |
86 | Volumetric, Multi-neuronal Imaging in Freely Behaving Drosophila Larvae Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The Gershow Lab is occupied with trying to answer how living brains make decisions, and we use Drosophila larvae to answer this profound question. |
Paul McNulty; |
87 | Building Emergent Representation of Neural States Using Dynamical Models Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we develop a deep-learning framework that can reduce the complex dynamics across the different spatial and temporal scales to stereotyped brain states through fitting our data and associating points in time to differing basins of attraction. |
Josuan Calderon ; Gordon Berman; |
88 | Unveiling The Dynamics and Structure of Drifting Neural Representations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we explore the hypothesis that neural representations optimize a representational objective with a degenerate solution space, and noisy synaptic updates drive the network to explore this (near-)optimal space causing representational drift. |
Shanshan Qin; |
89 | A Simple Theory of Stochastic Dynamics Near Stable Fixed Points Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Specifically, we introduce a simple approach to deriving analytical expressions for the noise power spectrum and coherency spectrum (and their corresponding correlation functions) in terms of rational polynomial functions and identify compact formulas for certain polynomial coefficients. |
Shivang Rawat ; Stefano Martiniani; |
90 | Stimulation-induced Long-lasting Desynchronization of Plastic Neuronal Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that CRS-induced synaptic reshaping is affected by the statistics of neuronal responses to individual stimuli and their spatio-temporal pattern [1,2]. |
Justus Kromer ; Ali Khaledi-Nasab ; Peter Tass; |
91 | Closed-loop Targeted Optogenetic Stimulation of C. Elegans Populations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a worm tracking setup for closed-loop tracking and optogenetic stimulation of multiple C. elegans worms. |
Mochi Liu ; Sandeep Kumar ; Anuj Sharma ; Andrew Leifer; |
92 | Temperature Mediated Transitions in Neuronal Activity Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present a mathematical model developed for studying the influence of temperature on neuronal behavior. |
Epaminondas Rosa ; Rosangela Follmann ; Manuela Burek; |
93 | Autocorrelations in Homeostatic Spiking Neural Networks As A Result of Emergent Bistable Activity Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Using a neuromorphic processor, we emulate networks of excitatory and inhibitory leaky integrate and fire neurons with spiking rates regulated by homeostatic plasticity. The … |
Johannes Zierenberg ; Benjamin Cramer ; Markus Kreft ; Sebastian Billaudelle ; Vitali Karasenko ; Aron Leibfried ; Eric Müller ; Philipp Spilger ; Johannes Weis ; Johannes Schemmel ; Viola Priesemann; |
94 | Effects of Suppressing Inhibitory Synaptic Strength on The Dynamics of A Network of Spiking Neurons: A Computational Study Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have found that the responses of individual neurons within a network to such a suppression of inhibition is heterogeneous: the firing rate of some neurons increases as expected but the firing fate of the other neurons decreases or remains unchanged. |
Emily S.C. Ching ; H.Y. Li ; G.M. Cheng; |
95 | Comparison of The Synchronization Transition of The Kuramoto Model on Fruit-fly Versus A Large Human Connectome Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: The Kuramoto equation has been solved numerically on the 21.662 node fruit-fly [1] and the 804.113 node human connectomes. While the fly neural connectome resembles to a … |
Geza Odor ; Gustavo Deco ; Jeffrey Kelling; |
96 | Geometry and Genetics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: The application of quantitative methods to biological problems faces the choice of how much detail to include and the generality of the conclusions. Both routine data analysis and … |
Eric Siggia; |
97 | Inferring The Molecular Mechanisms That Guide Developmental Bifurcations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work demonstrates how dynamical systems theory enables inferring molecular-scale mechanisms from cell-scale state changes. |
Simon Freedman ; Addison Howe ; Sidhartha Goyal ; Madhav Mani; |
98 | Cell Fate Specification and Transitions in Multicellular Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have developed a generalized model of multicellular gene expression which accounts for intracellular and intercellular gene regulation. |
Matthew Smart ; Anton Zilman; |
99 | Sensing and Making Sense of Fluctuating Cellular States Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work reveals a new mechanism of cell fate decision making. |
Felix Meigel ; Lina Hellwig ; Philipp Mergenthaler ; Steffen Rulands; |
100 | To Biofilm or Not To Biofilm: A Biophysical Threshold for Biofilm Formation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this issue, here, we develop a generally-applicable biophysical model that captures essential features of the interplay between motility-mediated dispersal and biofilm formation. |
Sujit Datta ; Jenna Ott ; Selena Chiu ; Daniel Amchin ; Tapomoy Bhattacharjee; |
101 | Stochastic Dynamics of Cell Shape During Cell Fate Transitions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a pipeline to quantify and analyse cell shapes as cells undergo the epithelial-to-mesenchymal transition (EMT). |
Wolfram Pönisch ; Iskra Yanakieva ; Aki Stubb ; Guillaume Salbreux ; Ewa Paluch; |
102 | Designing and Decoding Transcription Factor Screening Experiments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We map this to a communication problem in which a cell acts as a noisy parity bit informing us about the presence of a programming set. |
Forrest Sheldon; |
103 | Label-free Cell Tracking Enables Collective Motion Phenotyping in Epithelial Monolayers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce an AI-based pipeline to segment and track cell nuclei from phase-contrast images. |
Shuyao Gu ; Rachel Lee ; Zackery Benson ; Chenyi Ling ; Michele Vitolo ; Stuart Martin ; Joe Chalfoun ; Wolfgang Losert; |
104 | Systems-level Interdependence in Organelle Biogenesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we have characterized the systems-level patterns of interdependence in organelle biogenesis using Saccharomyces cerevisiae as a model system. |
Kiandokht Panjtan Amiri ; Deepthi Kailash ; Shankar Mukherji; |
105 | Multigenerational Memory in Cell Size Homeostasis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work provides new insights into the impact of the environment on cell homeostasis. |
Motasem ElGamel ; Harsh Vashistha ; Hanna Salman ; Andrew Mugler; |
106 | Volume Segregation Programming in A Nematode’s Early Embryogenesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Combining knowledge about the fate specification induced by asymmetric division and the anti-correlation between cell cycle length and cell volume in Caenorhabditis elegans, we propose a minimal model to simulate lineage initiation by altering cell volume segregation ratio in each division, and quantify the derived pattern’s performance in proliferation speed, fate diversity, and space robustness. |
Guoye Guan; |
107 | ANDOR and Beyond: Dynamically Switchable Logic Gates As Modules for Flexible Information Processing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We here propose a small set of effective modules that are capable of performing different logical operations based on the basin of attraction in which the system resides or is steered to. |
Carl Modes ; Mohammadreza Bahadorian; |
108 | Universal Biofilm Height Dynamics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Through interferometry, we can capture their height dynamics with nanometer precision. |
Pablo Bravo ; Siu Lung Ng ; Brian Hammer ; Peter Yunker; |
109 | Bacteriophage-driven Spatial Structuring of Pseudomonas Aeruginosa Biofilms Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will identify the conditions under which phage-induced aggregation occurs and discuss their relevance to human infections. |
Robert Edmiston ; Hemaa Selvakumar ; Joshua Weitz ; Stephen Diggle ; Jennifer Curtis; |
110 | A Computational Model of Interface Formation in Bacterial Colonies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present an agent-based model to predict patterns formed by motile and matrix-producing cells in growing Bacillus subtilis colonies. |
Joseph Larkin ; Gürol Süel ; Alan Gillman ; Jake McCool ; Caelan Brooks ; Andrew Mugler; |
111 | Confinement-induced Self-organization in Growing Bacterial Colonies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will describe our recent theoretical and experimental efforts toward understanding the origin of these fascinating examples of self-organisation in growing active matter. |
Luca Giomi; |
112 | Growth of Bacterial Biofilms at Interfaces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using Vibrio cholerae as a model biofilm former, we investigate the growth of biofilms at the interface between a glass and a gel substrate. |
Japinder Nijjer ; Thomas Henzel ; Changhao Li ; qiuting zhang ; Sulin Zhang ; Tal Cohen ; Jing Yan; |
113 | A Segmentation Clock Patterns Cellular Differentiation in A Bacterial Biofilm Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Unexpectedly, we find that gene expression underlying the nitrogen stress response of a developing Bacillus subtilis biofilm becomes organized into a ring-like pattern. |
Kwang-Tao Chou ; Dong-yeon Lee ; Jian-geng Chiou ; Leticia Galera-Laporta ; San Ly ; Jordi Garcia-Ojalvo ; Jian-geng Chiou ; Gürol Süel; |
114 | Impact of Spatial Structure on Heteroresistance Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We examine this using white-light interferometry and confocal microscopy. |
Adam Krueger ; Pablo Bravo ; Gabi Steinbach ; Aawaz Pokhrel ; David Weiss ; Peter Yunker; |
115 | An Agent-Based Model of Spatially Structured Bacterial Populations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Future work can extend the model to test the effectiveness of "drug sanctuaries," in which the use of certain drugs is restricted for certain patches and/or times to suppress the emergence of resistance. |
Louis Nemzer; |
116 | Spreading Rates of Bacteria Colonies Depend on Substrate Stiffness and Permeability Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we report the use of synthetic polyacrylamide hydrogels with tunable stiffness and controllable pore size to assess the effects of substrate mechanics on biofilm development. |
Merrill Asp ; Minh-Tri Ho Thanh ; Alison Patteson; |
117 | Mechanophysiology of Bacterial Microcolonies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We will show how the internal and external forces shaping Type IV pili mediated microcolonies can alter the physiology of the bacteria within these microcolonies. |
Nicolas Biais; |
118 | Exploring Bacterial Swarm Development Through Smart Microscopy Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, I will describe how we take advantage of this system to investigate biological and biophysical processes in a developing bacterial swarm, following its changes as the community expands over several orders of magnitude in space. |
Hannah Jeckel ; Konstantin Neuhaus ; Kazuki Nosho ; Knut Drescher; |
119 | Quinary Structure Modulates Protein Sequence Stability in Vivo Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we compare the sequence, stability, and kinetics of consensus PGK and four extant PGK sequences. |
Caitlin Davis ; Martin Gruebele; |
120 | Optimizing Kinetics of Hetero-subunit Assembly Using Differentiable Models Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We exploit efficient automatic differentiation of kinetic models to ‘discover’ assembly pathways that can maximize yield while avoiding errors and traps. |
Adip Jhaveri; |
121 | Nature of Size Fluctuations in Filamentous Cytoskeletal Structures Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using a master equation approach, we find that length fluctuations, small deviations in length produced by stochastic addition, and removal of building blocks/fragments during filament assembly and disassembly, are Gaussian independent of the nature of feedback. |
Aldric Rosario ; Shane McInally ; Bruce Goode ; Jane Kondev; |
122 | Predicting Timescales of DNA Mediated Protein Assembly Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we implemented a reaction-diffusion model to simulate proteins binding and forming higher-order complexes on chromatin. |
Mankun Sang ; Margaret Johnson; |
123 | Active Nuclear Transport in Living Cells: Dynamics and Steady-state Profiles of Cargo Concentrations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, a physical model of this mechanism is described that allows us to determine the temporal and spatial distributions of transport receptors and cargo proteins within the nucleus, and their role in the regulation of other cellular processes such as chromatin remodeling and transcription is discussed. |
Alex Rautu ; Michael Shelley; |
124 | Acentrosomal Spindles Assemble from Branching Nucleation Near Chromosomes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Motors serve to self-organize these chromosomal branched networks into proper spindles, which we rationalize using a model of opposing motors. |
Bernardo Gouveia ; Sagar Setru ; Joshua Shaevitz ; Howard Stone ; Sabine Petry; |
125 | The Roles of Stoichiometric Crowding and Protein-protein Interactions in Accelerating Translation Elongation Rates in E. Coli Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we extend our representative E. coli cytoplasm by incorporating attractions between EF-Tu–GFP–tRNA and ribosomal L7/L12 subunits, which are hypothesized to ‘pre-load’ ternary complexes onto ribosomes. |
Jennifer Hofmann ; Roseanna Zia; |
126 | LIM Domain Proteins Localize to Strained Actin, Focal Adhesions and Adherens Junctions in A Tension-dependent Manner Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we show that several members of the LIM family including Zyxin, Paxillin, FHL-2 and LIMD1 bind to SFs, FAs or AJs in a contractility-dependent manner. |
Shailaja Seetharaman ; Jonathan Winkelman ; Yvonne Beckham ; Margaret Gardel; |
127 | Measuring Weak Protein-Protein Interactions Using A Mechanically Transduced Immunosorbent Assay Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a novel technique that leverages the fundamental concept of friction to produce a mechanical signal that correlates to binding potential. |
Joshua Steimel ; Christopher Petell ; Joe Harrison ; Brian Strahl ; Michael Pappas; |
128 | Evolutionary Advantage of A Dissociative Search Mechanism in DNA Mismatch Repair Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we study the probability that these complexes locate a given target site via a semi-analytic, Monte Carlo calculation that tracks the association and dissociation of the sliding complexes. |
Kyle Crocker ; James London ; Andres Medina ; Richard Fishel ; Ralf Bundschuh; |
129 | Steps of Actin Filament Branch Formation By Arp2/3 Complex Investigated with Coarse-grained Molecular Dynamics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We applied the C-alpha based model Kim and Hummer that retains amino-acid level information and allows coarse-grained molecular dynamics simulations in implicit solvent, with globular domains represented as rigid bodies and flexible regions allowed to fluctuate. |
Dimitrios Vavylonis ; Shuting Zhang; |
130 | Overlooked Transcription Factor Crosslinking and Steric Forces Can Coordinate Chromatin and TAD Organization Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, I investigate how steric forces between TFs expand and isolate genomic regions, while individually modeled crosslinking proteins condense other regions. |
Adam Lamson ; Wen Yan ; Alex Rautu ; Michael Shelley; |
131 | Understanding The Unfolding Mechanisms of ??D Crystallin Using Molecular Dynamics Simulations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our findings can help to predict potential drug targets, which will help γD-crystallin to retain its native conformation and provide an economically viable solution to treat cataracts. |
DEEPSHIKHA GHOSH ; Kandarp Sojitra ; Manish Agarwal ; Mithun Radhakrishna; |
132 | How Immune Cells Respond to Physical Cues – The Role of Cytoskeletal Dynamics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Together, these studies reveal how different regulators of signaling work in concert with the cytoskeleton to control the immune response. |
Arpita Upadhyaya; |
133 | Identifying Mechanisms of Non-muscle Myosin II Filament Assembly and Amplification Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Taken together, we propose a model whereby increased actin network density during retraction events acts as a kinetic trap for myosin monomers, resulting in filament nucleation. |
Melissa Quintanilla ; Huini Wu ; Kem Sochacki ; Matthew Akamatsu ; Jeremy Rotty ; Farida Korobova ; James Bear ; Justin Taraska ; Jordan Beach ; Patrick Oakes; |
134 | In Vitro Light-controlled Patterns and Force Generation for Synthetic Cytoskeletal Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: By understanding simple contractile force-generating protein networks, our work offers insight into design and control of artificial cytoskeletons in synthetic and living cells. |
Xiangting Lei ; Tuhin Chakrabortty ; Jerry Honts ; Saad Bhamla; |
135 | The Effect of Ionic Strength in Microtubule Tactoid Formation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Cell division via mitosis is one of the most important biological processes to sustain life. Microtubules, along with their associated proteins, crosslinkers, and enzymes, play a … |
Prashali Chauhan ; Hong Beom Lee ; Sumon Sahu ; Niaz Goodbee ; Ruell Branch ; Jennifer Schwarz ; Jennifer Ross; |
136 | The Effects of Ionic Strength in MAP65 Binding to Microtubules Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Specifically we have used NaCl in buffer to determine the binding time and diffusion of single MAP65 on microtubules using total internal reflection (TIRF) microscopy. |
Hong Beom Lee ; Prashali Chauhan ; Niaz Goodbee ; Ruell Branch ; Sumon Sahu ; Jennifer Schwarz ; Jennifer Ross; |
137 | Motor-free Contractility in Active Gels Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we propose a motor-free mechanism that generates contraction in biopolymer networks. |
Sihan Chen ; Tomer Markovich ; Frederick MacKintosh; |
138 | Tunable Non-Equilibrium Dynamics of Motor-Driven Cytoskeleton Composites Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we create in vitro actin-microtubule networks driven by myosin-II minifilaments and quad-headed kinesin clusters, and use multi-color confocal microscopy to image the active composites. |
Daisy Achiriloaie ; Christopher Currie ; Maya Hendija ; Ryan McGorty ; Jennifer Ross ; Moumita Das ; Michael Rust ; Janet Sheung ; Rae Robertson-Anderson; |
139 | Actin-microtubule Networks As Time-varying Rigidly Percolating Double Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present results from Langevin Dynamics simulations of a model that combines two structure-function frameworks: a double network (DN) made of a network of stiff filaments (microtubules) interacting with a network of flexible filaments (actin), and rigidity percolation theory. |
Moumita Das ; Pancy Lwin ; Jonathan Michel ; Lauren Melcher ; Michael Rust ; Jennifer Ross ; Rae Robertson-Anderson; |
140 | Competition Between Severing and Tubulin Induced Repair of Microtubules Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Based on this observation, we propose a model for microtubule severing as a competition between the processes of damage spreading and repair. |
Chloe Shiff ; Jane Kondev ; Lishibanya Mohapatra; |
141 | Laser Ablation Reveals How The Mitotic Spindle Reshapes The Fission Yeast Nucleus Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To test the mechanical interactions between the envelope and spindle, we use targeted laser ablation to sever the spindle and to rupture the envelope, and examine the ensuing responses by live cell confocal fluorescence microscopy. |
Mary Elting ; Parsa Zareiesfandabadi ; Abhimanyu Sharma ; Marc Begley ; Gautam Dey; |
142 | Active Restructuring of Actin-Microtubule Composites By Kinesin and Myosin Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we investigate the active dynamics and restructuring of actin-microtubule composites driven by kinesin motors and myosin II minifilaments. |
Christopher Currie ; Daisy Achiriloaie ; Janet Sheung ; Jennifer Ross ; Moumita Das ; Michael Rust ; Rae Anderson; |
143 | Differential Robustness of Neural Networks in A Regenerative Brain Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we develop a platform to continuously measure planarian behavior throughout neural regeneration. |
Samuel Bray ; Bo Wang ; Livia Wyss ; Chew Chai; |
144 | Dynamic Switch Between ON and OFF Responses in An Olfactory Receptor Neuron Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we demonstrate existence of a third response modality in the Drosophila olfactory receptor neuron (ORN) ab2A, whose polarity is inverted from excitatory to inhibitory when stimulated with a single odorant of a certain type. |
Mahmut Demir ; Srinivas Gorur-Shandilya ; Thierry Emonet; |
145 | Deep Learning Diagnostic Analysis of The Kinematic Movement Data Recorded from Individuals with Neurodevelopmental Disorders Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have used Deep Learning ML techniques to analyze the kinematic movement patterns of individuals with Neurodevelopmental disorders (NDD). |
Khoshrav Doctor ; Di Wu ; Aditya Phadnis ; Martin Plawecki ; John Nurnberger Jr. ; Jorge Jose; |
146 | Hebbian Learning of Orientation-selective Receptive Fields with Monotonic Fall-off of Input Correlations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we study a two-layer network model with Hebbian development of the feedforward connectivity. |
Bettina Hein ; Francesco Fumarola ; Kenneth Miller; |
147 | A Spiking Network Model of Prefrontal Cortex Activity During Strategic Behavior Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we analyze under what conditions a metastable network of spiking neurons can exhibit strategic behavior. |
Tianshu Li ; Giancarlo La Camera; |
148 | Chemosensory Diversity Is Invariant to Background Stimuli in Chemotactic E. Coli Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we explored how sensitivity to one stimulus varies in the presence of different background stimuli. |
Jeremy Moore ; Keita Kamino ; Thomas Shimizu ; Thierry Emonet; |
149 | Investigating The Effects of Arousal on Auditory Processing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that perturbations that increase external input heterogeneity modulate stimulus decoding in a way that is consistent with the effect of arousal in auditory cortex, with intermediate perturbation strengths yielding the best performance. |
Evangelia Papadopoulos ; Michael Wehr ; Luca Mazzucato; |
150 | Mobile Defects Born from An Energy Cascade Shape The Locomotive Behavior of A Headless Animal Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we introduce a non-neuromuscular model system which is complex enough to teach us something new but also simple enough for us to understand. |
Manu Prakash ; Matthew Bull; |
151 | Extracting Multi-neuron and Dendritic Activities from A Freely Behaving Drosophila Larva Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study the decision-making process in Drosophila larva by simultaneously recording behavior and neural activity in a freely moving larva. |
Rui Wu ; Paul McNulty ; Doycho Karagyozov ; Mirna Skanata ; Marc Gershow; |
152 | An Excitatory Plasticity Rule for The Formation of Neural Clusters in Populations of Spiking Neurons Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Motivated by obtaining a minimal learning rule which relies only on local ingredients, we propose an excitatory plasticity rule combined with a homeostatic mechanism that keeps the neural activity close to a desired level. |
Xiaoyu Yang ; Giancarlo La Camera; |
153 | Analyzing Dynamics of Calcium and Actin in Primary Cortical Rat Astrocytes of Differing Cytoskeletal Architectures Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We employ data analytic algorithms to demonstrate differences (or lack there of) in the dynamics of these different astrocyte phenotypes. |
Nicholas Mennona ; Wolfgang Losert ; Sylvester Gates ; Kate O’Neill; |
154 | Controlled Gating of MS Channels in Bacterial Cells in Vivo Using A Mechanical Load Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We here present a new experimental approach to characterize gating activity of Mscs in bacteria in vivo. |
renata garces ; Octavio Albarran ; Samantha Miller ; Christoph Schmidt; |
155 | Fibration Symmetries of Integrated Bio-network in A Hypergraph Representation of E.coli Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we consider a hypergraph representation to model the integrated network of metabolites, and TFs, where dynamical features of metabolism are retained. |
Kuang Liu ; Luis Alvarez ; Stefan Wuchty ; Hernan Makse; |
156 | Functional Analysis of Metabolism: A Global Approach Unravels Fluxes and Protein Allocation in E. Coli Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We developed a novel framework that allows to disentangle flux and proteome components associated with the production of energy and of individual biosynthetic precursors. |
Matteo Mori ; Chuankai Cheng ; Terence Hwa; |
157 | Mechanism-based Disease Similarity: with Random Walks Starting from A Set of Disease Genes, Traveling Through The Protein-protein Interaction Network, and Then Back Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk the similarity measure and classification algorithm used by DeCoaD are presented and the resulting human disease network is explored. |
Yikuo Yu ; Mehdi Hamaneh; |
158 | Soft Coral Network Diversity Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Quantifying the morphology and morphogenesis of branching biological structures has recently progressed in systems across taxa. Our group focused on finding principles that govern … |
Natalia Rodriguez; |
159 | Principles of Gene Regulation Quantitatively Connect DNA to RNA and Proteins in Bacteria Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we performed absolute transcriptomic and proteomic analysis for E. coli across many conditions, obtaining a plethora of results on promoters and mRNAs characteristics that clash with conventional expectations: the majority of mRNAs exhibit similar translational efficiencies, while the promoter strengths are vastly different across genes. |
Matteo Mori ; Rohan Balakrishnan ; Igor Segota ; Zhongge Zhang ; Christina Ludwig ; Ruedi Aebersold ; Terence Hwa; |
160 | Analytical Descriptions of Fundamental Constraints in Protein Synthesis and Microbial Growth Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce a low-dimensional model which investigates this principle, generating novel analytical expressions that define key properties of microbial growth (e.g. translation rate and ribosome content) and explore how they depend on major physiological parameters (e.g. maximal translation rate and metabolic output). |
Griffin Chure ; Jonas Cremer; |
161 | Bacterial Adaptation to Changing Conditions – An Eco-physiological Case Study with The Gut Bacterium Escherichia Coli Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: By combing experiments and theory we show how competition between genes for the limited protein synthesis capacity constrains growth during the transition. |
Jonas Cremer ; Terence Hwa ; Rohan Balakrishnan; |
162 | Top-down Identification of Keystone Species in The Microbiome Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we propose a top-down identification framework, which detects keystones by their total influence on the rest of the species. |
Guy Amit ; Amir Bashan; |
163 | Cell Cycle Phase Inheritance Models to Reveal Biological Oscillators That Drive The Cell Cycle Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce a general stochastic matrix model of abstract cell-cycle factors that are inherited from the mother to daughter cell. |
Fern Hughes ; Alexis Barr ; Philipp Thomas; |
164 | Shell Proteins’ Roles in Bacterial Microcompartment Assembly Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we use atomistic simulations to measure a vast range of interaction strengths including a multitude of different bending interactions between pairs of Pdu shell proteins. |
Curt Waltmann ; Carolyn Mills ; Nolan Kennedy ; Danielle Tullman-Ercek ; Monica Olvera De La Cruz; |
165 | Bottom-up Synthetic Embryology for Understanding Early Human Development Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will describe our effort in using human pluripotent stem cells (hPSCs) to develop tractable experimental models of the peri-implantation embryonic development and neurulation. |
Jianping Fu; |
166 | Large-scale Cortex-core Structure Formation in Brain Organoids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Brain organoids recapitulate a number of brain properties, including neuronal diversity. However, do they recapitulate brain shape? Using a hydrodynamic description for cell … |
Ahmad Borzou ; J. Schwarz ; J. Schwarz; |
167 | A Morphogenetic Action Principle for Thin Tissues and The Origins of Anisotropic Growth Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose that nature settles on the ‘simplest’ growth patterns. |
Dillon Cislo ; Boris Shraiman; |
168 | Epithelial Tissue As A Self-sculpting, Viscoelastic Slab Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: With the importance of the third dimension in mind, we have developed a self-sculpting, three-dimensional model of epithelia whose dynamics are driven by active forces on its surface. |
XinXin Du ; Michael Shelley; |
169 | In Morphogenesis Tissue Geometry Controls Cellular Morphology Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we develop a statistical mechanics framework that considers the random migration and stochastic morphological change in cells while satisfying homeostatic condition and demonstrate, by theoretical predictions and experimental validations, that the geometrical constraints imposed by the mould is the primary factor that determines cell morphology, specifically the cell orientational ordering. |
Shuvrangsu Das ; Juan Alberto Panadero Pérez ; Jamie Concannon ; Patrick McGarry ; Vikram Deshpande; |
170 | Butterfly Scale Morphogenesis: Wrinkling on The Micron Scale Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk I will present recent measurements of in-vivo butterfly scale development exhibiting wrinkling. |
Jan Totz ; Anthony McDougal ; Mathias Kolle; |
171 | Mechanical Mechanisms That Contribute to Left-right Asymmetry During The Development of The Zebrafish Embryo Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we perform specific perturbations to alter the drag forces and test this hypothesis directly. |
Paula Sanematsu ; Emma Retzlaff ; Debadrita Pal ; Michael Bates ; Heidi Hehnly ; Jeffrey Amack ; Lisa Manning; |
172 | Active Nematic Defects and Epithelial Morphogenesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Inspired by recent experiments that highlight the role of nematic defects in the morphogenesis of epithelial tissues, we develop a minimal framework to study the dynamics of an active curved surface driven by its nematic texture. |
Farzan Vafa ; L Mahadevan; |
173 | Physical Limits on Size Precision in Growing Organs and Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this question theoretically, we investigate fundamental physical limits on setting the size of growing organs. |
Daniel McCusker ; David Lubensky; |
174 | Improved Solid Mechanic Model of Aortic Dissection Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We create a more realistic model of aortic dissection progression via a semiautomatic segmentation and meshing workflow, followed by separation of the complex surfaces of the true and false lumens as well as the flap geometry. |
Sanjeev Dhara ; Nabeel Rasheed ; Kameel Khabaz ; Nhung Nguyen ; Kathleen Cao ; Cheong Jun Lee ; Ross Milner ; Luka Pocivavsek; |
175 | A Growth-Based Computational Model of Aortic Dissection Morphogenesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We used a finite element analysis (FEA) computational model of the aorta’s complex geometry and anisotropic fiber composition (with the Ogden-Gasser-Holzapfel constitutive model) that incorporates pressurization and growth to predict shape change of aortic dissections over time. |
Kameel Khabaz ; Luka Pocivavsek ; Nhung Nguyen ; Janet Kang ; Seth Sankary ; Kathleen Cao ; Gordon Kindlmann ; Ross Milner; |
176 | Surface Geometry Analysis of Pathological Aortas for Endovascular Aortic Repair Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The goal of this project is to compare the surface geometry, specifically the curvedness and shape index of aortas that demonstrated successful remodeling after EVAR and aortas with persistent Type 1A endoleaks. |
Junsung Kim ; Alyssa Varsanik ; Blessing Nnate ; Kameel Khabaz ; Nhung Nguyen ; Luka Pocivavsek; |
177 | A Case Study to Predict Endoleaks with Aortic Geometry Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To treat this condition, physicians use an endovascular aortic repair (EVAR) technique to implant a stent in the affected region. |
Blessing Nnate; |
178 | Revealing The Origin of Multiphasic Dynamic Behaviors in Cyanobacteriochrome Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we integrate femtosecond-resolved fluorescence and transient-absorption methods and unambiguously showed the significant solvation dynamics occurring at the active site from a few to hundreds of picoseconds. |
Dongping Zhong; |
179 | Photoswitching of Terahertz Structural Dynamics in The Photosynthesis Photo Protective Orange Carotenoid Protein Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We examine how structural vibrations may actuate the transition using anisotropic terahertz microspectroscopy (ATM). |
Jeffrey Mckinney ; Deepu George ; Yanting Deng ; Robert Thompson ; Cheryl Kerfeld ; Xing Liu ; Tod Romo ; Alan Grossfield ; Andrea Markelz; |
180 | Probing Protein Motions for Sequence Fidelity Control or Information Detection Along DNA Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have combined kinetic modeling with all-atom molecular dynamics (MD) simulation to show most critical residue motions supporting the nucleotide ‘recognition’ and selectivity, from phage T7 to SARS-CoV-2 viral replication. |
Jin Yu; |
181 | Directional Information Flow As A Tool for Analyzing Protein Allostery Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We used transfer entropy to develop a workflow for generating causal protein networks based on residue fluctuations and applied it to study allosteric communication in the SARS-CoV-2 main protease, a protein that binds allosteric ligands at various sites. |
Remy Yovanno ; Albert Lau; |
182 | Photo-response of Photoreceptor Proteins Based on Graphene Field Effect Transistors Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: A detection method can be developed based on optical properties of biomolecules that generate electrical readout. |
Yifei Wang ; Ho Vinh ; Leslie Howe ; Rosalie Dohmen ; Wouter Hoff ; Vinh Nguyen; |
183 | From Quantum Connectivity to Biological Networks: A Window Into Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will present a multidisciplinary approach for characterizing side-chain based protein structure networks. |
Saraswathi Vishveshwara; |
184 | Crystal Symmetry Effects on Protein Anisotropic Absorption Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Anisotropic Terahertz Microspectroscopy provides a method of measuring these vibrations. |
Alexander McNulty-Romaguera ; Jeffrey Mckinney ; Deepu George ; Xiaotong Zhang ; Jason Benedict ; Tod Romo ; Alan Grossfield ; Andrea Markelz; |
185 | Quantifying Viscous Coupling Between Global Diffusion and Conformational Dynamics from Simulated Protein Trajectories Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a Langevin equation of motion in the body-fixed frame which explicitly quantifies the instantaneous coupling, via inertial and viscous forces, between the molecule’s global diffusion and its internal conformational fluctuations. |
Jesse Hall ; Marina Guenza; |
186 | Unified Free Energy Landscapes of Μ-conotoxins Reveal Prefolding Predictors of Folding Pathway Classification Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we employ the composite diffusion map approach to study the unified free energy surface of pre-folded equilibrium. |
Ré Mansbach ; Lara Patel ; Gnana Gnanakaran; |
187 | A Many-body Effect Renders Universal Sub-diffusion of Water on The Surface of Different Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Instead, we showed that, the power law of diffusive motion of hydration water is independent of the underlying protein and this independence results from the inter-water interaction, which has been rarely considered in the past when describing the diffusion of interfacial water. |
Song Li; |
188 | Mechanics of Cytoplasmic Dynein Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using single-molecule imaging methods, we presented a robust mechanistic model of how dynein steps along microtubules and generates force. |
Ahmet Yildiz; |
189 | Effects of Motor Mobility in Cargo Transport Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we investigate the effects of network complexity and cargo surface properties on a cargos ability to get across a network. |
Nimisha Krishnan ; Jennifer Ross; |
190 | VESICLE TRANSPORTATION OF ZYMOGEN GRANULE BY MYOSIN; FORCE MEASURING THE STEPPING BY OPTICAL TWEEZER Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To understand which molecular motor exerted a force on ZGs, myosin inhibitor, PCIP and TIP, were used in this study. |
Takeshi Sakaomto ; Takeshi Sakaomto; |
191 | Heterogeneity in Single Motor Velocity Leads to Enhanced Velocity of Membrane-bound Cargoes Carried By Teams of Molecular Motors Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we show using Brownian dynamics simulations that the underlying heterogeneity in single motor velocities is essential for the above mechanism and hence the cargo speedup. |
Niranjan Sarpangala ; Ajay Gopinathan; |
192 | Spiraling Galaxies of Microtubules Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Analysis of a coarse-grained model shows that the system is controlled by a combination of microtubule density and cell size, and the collective organization of microtubule bending by hydrodynamics. |
Michael Shelley ; Jesse Gatlin ; Gokberk Kabacaoglu ; ABDULLAH BASHAR SAMI ; David Stein; |
193 | ALENS: Towards The Cellular-scale Simulation of Motor-driven Cytoskeletal Assemblies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present aLENS, a novel computational framework to surmount the limits of conventional simulation methods. |
Wen Yan ; Saad Ansari ; Adam Lamson ; Matt Glaser ; Meredith Betterton ; Michael Shelley; |
194 | ATP Consumption in An Actin-myosin Network: Response Functions in An NADH Assay Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present the regimes of contraction, as well as identifying the optimal conditions to maximize contraction efficiency in a freely contracting actin network. |
Francis Cavanna; |
195 | Modeling The Collective Motion of Microtubules Driven By Mobile Kinesin Motors Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We control the degree of overlap of microtubules using a modified Weeks–Chandler–Anderson potential and show that depending on the degree of overlap and the flexibility of the chains, our model predicts that gliding assays transition between an active polar state and an active nematic state. |
Madhuvanthi Athani ; Fabian Jan Schwarzendahl ; Fereshteh Memarian ; Ajay Gopinathan ; Linda Hirst ; Kinjal Dasbiswas ; Daniel Beller; |
196 | Effect of Microtubule Length on Topological Defect Dynamics and Morphology in Active Nematics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using fluorescence microscopy, we investigate the self-organization of GMPCPP stabilized microtubules into patterns in active nematic, looking to see how the resulting defect dynamics and morphologies vary as the length of microtubules is increased from 1 to 10 micrometers. |
Derek Hammar ; Fereshteh Memarian ; Linda Hirst; |
197 | The Mammalian Meiotic Spindle: A Living Material Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will present data and analysis that suggests that many aspects of the large-scale structure and long-time dynamics of meiotic spindles in living cells can be understood via a relatively simple continuum picture in which the spindle is modeled as an active liquid crystal. |
Colm Kelleher ; Marta Venturas ; Daniel Needleman; |
198 | Self-organization of Microtubules and Motors Drive Large-scale Intracellular Flows in Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a quantitative study of streaming in Drosophila oocytes that combines PIV of 3D time-lapse movies, with biophysical modeling and simulation. |
Reza Farhadifar ; Sayantan Dutta ; Gokberk Kabacaoglu ; Wen Lu ; Vladimir Gelfand ; Stanislav Shvartsman ; Michael Shelley; |
199 | Learning Control Laws for Activity-induced Patterns of Cytoskeletal Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We use reinforcement learning (RL) to probe the role of fluctuations in structure modulation in cytoskeletal networks. |
Laura Tociu ; Carlos Floyd ; Yuqing Qiu ; Suriyanarayanan Vaikuntanathan ; Alexandra Lamtyugina; |
200 | Steady-state Directional Flow in Active Model Cytoskeletal Network Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We here use a model system of water-in-oil emulsion droplets composed of Xenopus egg extract that contains all the ingredients for active cytoskeletal assembly. |
Jianguo Zhao ; Charlie Duclut ; Rahil Golipour ; An Pham ; Behzad Golshaei ; Chonglin Guan ; Mingru Li ; Rudolf Oldenbourg ; James Harden ; Frank Jülicher ; Christoph Schmidt; |
201 | Polymers in Two-dimensional Bacterial Turbulence Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we experimentally investigate the effects of polymer additives on the collective dynamics of swarming Serratia marcescens in quasi-2D liquid films. |
Ranjiangshang Ran ; David Gagnon ; Paulo Arratia; |
202 | Crossing and Non-crossing Dictates The Collective Swimming of Bacteria Under Two-dimensional Confinement Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that the emergent collective phase formed by bacteria has two different symmetries depending on the gap thickness of the Hele-Shaw cell. |
Dipanjan Ghosh ; Xiang Cheng; |
203 | Play. Pause. Rewind. Measuring Local Entropy Production and Extractable Work in Active Matter Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce a local measure of entropy production and a numerical protocol to estimate it. |
Stefano Martiniani ; Buming Guo ; Sunghan Ro ; Aaron Shih ; Trung Phan ; Robert Austin ; Dov Levine ; Paul Chaikin; |
204 | Rheotaxis of E.Coli in Viscoelastic Shear Thinning Fluids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our study focuses on the description of E. coli’s rheotaxis in Carbomethylcellulose and Xantham Gum solutions. |
Bryan O Maldonado ; Quentin Brosseau ; Paulo Arratia; |
205 | Active Transport of Particles Within Biopolymer Solutions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We integrated a standard optical microscope with a pair of coils, which can be used to create uniform magnetic field and field gradient. |
Wyatt Gage ; Ashis Mukhopadhyay; |
206 | Braiding Dynamics in Active Nematics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: In active matter systems, energy consumed at the small scale by individual agents gives rise to emergent flows at large scales. For 2D active nematic microtubule systems, these … |
Spencer Smith ; Kevin Mitchell ; Linda Hirst ; Dimitrius Khaladj ; Ruozhen Gong ; Zoe Boysen; |
207 | Confinement Effects on The Collective Behavior of Active Matter Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using this method, we simulate dense active colloidal dispersions in strongly confined geometries and observe transitions in their collective behavior dependent on the interplay between the propulsion characteristics and the confinement. |
Ian Madden ; Erik Luijten; |
208 | Weakly Active Particles Near Boundaries: Towards Solving The Boundary Value Problem for Active Particles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we focus particularly on weakly active particles confined on a line and in a wedge-shaped region, and absorbing onto a sphere. |
Michael Wang; |
209 | Novel Dynamical Features of Chiral Active Particles in Crowded Lattices Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To this end, we perform particle-based simulations to investigate the transport properties of chiral active particles (CAPs) in a complex, crowded environment. |
Chung Wing Chan ; Rui Zhang; |
210 | Frustrating Active Flows Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work explains how the local strategies used by active flows to resolve geometrical frustration determine the large scale morphology of their flow fields. |
Amelie Chardac ; Camille Jorge ; Alexis Poncet ; Denis Bartolo; |
211 | Doi-Peliti Field Theory of Free Active Ornstein-Uhlenbeck Particles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We derive a Doi-Peliti field theory for free active Ornstein-Uhlenbeck particles, or, equivalently, free inertial Brownian particles, and present a way to diagonalise the quadratic part of the action and calculate the propagator. |
Marius Bothe ; Gunnar Pruessner; |
212 | Active Nematic Obstacle Courses Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This talk will present our recent findings in channels with different obstacle configurations and imposed boundary conditions. |
Ryan Keogh ; Tyler Shendruk ; Sumesh Thampi ; Santhan Chandragiri ; Tapio Ala-Nissila; |
213 | Multiparticle Collision Dynamics Simulations of Squirmers in A Nematic Fluid Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Considering both nematodynamic effects (anisotropic viscosity and elasticity) and thermal fluctuations, in the present study, we couple the nematic MPCD algorithm with a molecular dynamics (MD) scheme for the squirmer. |
Shubhadeep Mandal ; Marco Mazza; |
214 | Spontaneous Rotation of Polar Active Particles in A Colloidal Suspension Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we demonstrate a generic active mechanism that leads to their spontaneous chiralization through a symmetry-breaking instability. |
Marco De Corato ; Ignacio Pagonabarraga ; Giovanniantonio Natale; |
215 | Kelvin-Helmholtz Instability in Two Dimensional Semi-bounded Active Yukawa Liquids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In the present work, considering a two-dimensional semi-bounded cartesian domain, we systematically investigate the effect of activity, internal drives at the smallest scales of the system, on the growth, evolution, and saturation of KH instability, using Molecular Dynamics simulation[1], wherein a Yukawa liquid is used as a prototype. |
Soumen Karmakar ; Rajaraman Ganesh; |
216 | Memorizing Without Overfitting: Over-parameterization in Machine Learning, Physics and Biology Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this presentation, we analyze the generalization properties of two-layer neural networks to showcase some of the new, unaccounted-for behaviors that arise in these "over-parameterized" models that are not present in classic statistics. |
Jason Rocks; |
217 | When Are Neural Networks Kernel Learners? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We demonstrate that this can indeed happen due to a phenomenon we term silent alignment, which requires that the NTK of a network evolves in eigenstructure while small in overall scale. |
Alexander Atanasov ; Blake Bordelon ; Cengiz Pehlevan; |
218 | Teaching A Material to Be Adaptive Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Evolution in time-varying environments naturally leads to adaptable biological systems that can easily switch functionalities. Advances in the synthesis of … |
Martin Falk ; Jiayi Wu ; Vedant Sachdeva ; Sidney Nagel ; Arvind Murugan; |
219 | Information Theory of High Dimensional Linear Regression Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We consider randomized ridge regression in the thermodynamic limit where we send the numbers of model parameters and data points to infinity while fixing the ratio. |
Vudtiwat Ngampruetikorn ; David Schwab; |
220 | Learning Out of Equilibrium in Physical Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Going beyond the critical learning rate, we find non-equilibrium learning oscillations but the network can still learn allosteric tasks at much greater rates. |
Menachem Stern ; Sam Dillavou ; Marc Miskin ; Douglas Durian ; Andrea Liu; |
221 | Learning Continuous Chaotic Attractors with A Reservoir Computer Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose a theoretical mechanism of this abstraction by combining ideas from differentiable generalized synchronization and feedback dynamics. |
Lindsay Smith ; Jason Kim ; Zhixin Lu ; Danielle Bassett; |
222 | Learning Nonequilibrium Control Forces to Characterize Dynamical Phase Transitions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we propose a machine learning algorithm that samples rare trajectories and estimates the associated large deviation functions using a many-body control force by leveraging the flexible function representation provided by deep neural networks, importance sampling in trajectory space, and stochastic optimal control theory. |
Jiawei Yan ; Hugo Touchette ; Grant Rotskoff; |
223 | A Bayesian Approach to Hyperbolic Embeddings Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose a novel, physics based model of embedding uncertainty within this Bayesian framework which improves both performance and interpretability of the model. |
Anoop Praturu ; Tatyana Sharpee; |
224 | A Symbolic Systen That Synthesises An Internal Model of An Algebraic Theory of The Data and Prior Knowlwedge Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we propose an approach inspired in Model Theory that combines the mathematical transparency of symbolic systems with the ability to learn internal models with no use of optimization. |
Gonzalo de Polavieja; |
225 | Optimal Learning Despite A Hundred Distracting Directions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present results on principled choices of measure which avoid this issue, and lead to unbiased posteriors. |
Michael Abbott ; Benjamin Machta; |
226 | Memory, Prediction and Computation in The Kuramoto Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work offers an insight into the emergence of computation from the collective behaviors of large dynamical systems. |
Chanin Kumpeerakij ; David Schwab ; Thiparat Chotibut ; Vudtiwat Ngampruetikorn; |
227 | Friend or Foe: The Potential of Transposable Element Tuning Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose a model in which TnpB increases the efficiency of successful reinsertion of excised TEs. |
Davneet Kaur ; Thomas Kuhlman; |
228 | A Plasmid System with Tunable Copy Number Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we demonstrate two methods we’ve developed that allow for finely-tuned control of ColE1 plasmid copy number: a plasmid with an anhydrotetracycline-inducible copy number, and a massively parallel assay that is used to generate a continuous spectrum of ColE1-based copy number variants. |
Miles Rouches ; Louis Cortes ; Yasu Xu ; Guillaume Lambert; |
229 | Developing A Genetic Toggle Switch in Arabidopsis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We used a forward engineering approach by first analyzing synthetically designed repressors in plant protoplasts[1]. |
Tessema Kassaw ; Wenlong Xu ; Christopher Zalewski ; Katherine Kiwimagi ; Ron Weiss ; Mauricio Antunes ; Ashok Prasad ; June Medford; |
230 | Noise and Tunability of A Programmable CRISPR Platform for Gene Network Regulation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we adapted a negative-feedback synthetic gene circuit to precisely regulate the Cas13d effector expression. |
Yiming Wan ; Rafal Krzyszton ; Joseph Cohen ; Damiano Coraci ; Gabor Balazsi; |
231 | Factors That Affect The Bistability of Programmable CRISPR-based Toggle Switches in Escherichia Coli Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We found that by carefully matching promoter strength and the copy number of toggle swtich construct, we are able to see bistabilty in the cell. |
Yasu Xu; |
232 | Computational Investigation of Cell Shape Changes Driven By Actomyosin Contractility Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To overcome experimental limits and thus perform extensive parametric studies, we developed a novel agent-based model for a minimal cell-like structure comprised of discrete actomyosin cortex, osmotic pressure, and cell membrane simplified into a triangulated mesh. |
Fahmida Sultana Laboni ; Makito Miyazaki ; Taeyoon Kim; |
233 | Identification of Pathological Nodes in The Protein-protein Interaction Network Maps of Triple Negative Breast Cancer Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study we analyzed PPI networks in Triple Negative Breast Cancer (TNBC) to delineate the hot-spot nodes and the related reactive protein interfaces. |
Nandakumar Yellapu; |
234 | CRISPR-mediated Imaging of Three-dimensional Genomic Loci in Live Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we report an improved LiveFISH method that could target non-repetitive genomic loci of choice. |
Yanyu Zhu ; Mengting Han ; Xueqiu Lin ; Haifeng Wang ; Lei Stanley Qi; |
235 | Synthetic Biology Tools to Create Electroactive Biofilms Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this need, we have adapted several synthetic biology constructs to enable light-induced gene expression within the bacteria Shewanella oneidensis. |
James Boedicker; |
236 | AI-based Analysis of Microbial Ecological Dynamics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we develop an AI-based approach that can predict the conditional probability distribution of a quantitative function/behavior with a limited number of observations per input condition (initial composition and the environment factors). |
Shangying Wang ; Simone Bianco; |
237 | Dynamical Model for A Bistable Contractile Molecular Injection System Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Drawing from recent structural evidence for the conformation changes at the molecular level, we model this molecular machine using a simplified geometry of inextensible filaments inspired by chebyshev nets. |
Noah Toyonaga; |
238 | Inferring Gene Regulation from Static Snapshots of Gene Expression Variability Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show how static population snapshots of gene expression reporters can be used to infer causal and dynamic properties of gene regulatory networks without using perturbations. |
Euan Joly-Smith ; Jerry Zitong Wang ; Fotini Papazotos ; Paige Allard ; Laurent Potvin-Trottier ; Andreas Hilfinger; |
239 | Acid Stress and Cross-feeding Provide A Dynamic Mechanism of Microbial Coexistence Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Despite the ubiquity of microbial diversity observed across environments, mechanisms of cooperativity that enable species coexistence beyond the classical limit of … |
Avaneesh Narla ; Kapil Amarnath ; Sammy Pontrelli ; Jiajia Dong ; Tolga Caglar ; Brian Taylor ; Julia Schwartzman ; Uwe Sauer ; Otto Cordero ; Terence Hwa; |
240 | Community Assembly in Time-Varying Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Thus, our work suggests distinct ecological principles for coexistence in fluctuating environments. |
Avaneesh Narla ; Terence Hwa ; Arvind Murugan; |
241 | A Minimal Model of Cross-feeding in Microbial Communities Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a minimal model of bacterial cross-feeding that enables us to establish biophysical rules underlying these non-linear phenomena. |
Daniel Amchin ; Alejandro Martinez-Calvo ; Hongbo Zhao ; Carolina Trenado Yuste ; Sujit Datta; |
242 | Complementary Resource Preferences Spontaneously Emerge in Diauxic Microbial Communities Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Overall, our work provides testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microbes. |
Zihan Wang ; Sergei Maslov; |
243 | Structure-function Landscape of A Closed Microbial Ecosystem Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In a previous study, we established closed microbial ecosystems (CES) as models of nutrient cycling in ecosystems. |
Luis de Jesus Astacio ; Chandana Gopalakrishnappa ; Seppe Kuehn; |
244 | Modeling Multi-trophic Ecosystems with Consumer Resource Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: MacArthur’s consumer-resource model describes the ecological dynamics of a simple two trophic-layer ecosystem where consumers compete for a pool of resources (e.g herbivores compete for plants). |
Zhijie Feng ; Pankaj Mehta ; Robert Marsland ; Maria Yampolskaya; |
245 | Learning and Control for Evolutionary Processes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we show that studying a deterministic analog of a stochastic system highlights the tradeoff between control and learning. |
Obinna Ukogu ; Colin LaMont ; Ceyhun Eksin ; Armita Nourmohammad; |
246 | Coarse-graining Ecological Dynamics in The Face of Unkown Microscopic Details Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, building on the theoretical framework of resource competition, we introduce an eco-evolutionary model that allows organisms to be described at an arbitrary level of detail, enabling us to formally study the hierarchy of possible coarse-grained descriptions. |
Jacob Moran ; Mikhail Tikhonov; |
247 | Pinpoint Ecological Niches and Metabolic Essentiality of Microbial Communities Using Both Metagenomics and Metaproteomics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we propose to compare the network degree and redundancy of each protein between the genomic content network obtained from metagenome and the protein content network obtained from metaproteome. |
Tong Wang ; Leyuan Li ; Daniel Figeys ; Yang-Yu Liu; |
248 | A PDE Model for Protocell Evolution and The Origin of Chromosomes Via Multilevel Selection Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To model this phenomenon, we consider a simple protocell composed of two types of genes: a “fast gene” with an advantage for gene-level self-replication and a “slow gene” that confers an advantage for protocell-level reproduction. |
Daniel Cooney ; Fernando Rossine ; Dylan Morris ; Simon Levin; |
249 | Robust Altruism By Similarity in Multifaceted Phenotypes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study the evolution of altruistic behavior under a model where individuals choose to cooperate with each other by comparing a set of always-visible continuous tags, and find the generic maintenance of robust cooperation when individuals carry more than one tag. |
Linnea Bavik ; Rohan Mehta ; Daniel Weissman; |
250 | Sequence-Dependent Backbone Dynamics and Membrane Association of Intrinsically Disordered Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will report advances from our computational and experimental studies of ChiZ, a membrane protein that contains an intrinsically disordered N-terminal region (NT) and is a component of the cell division machinery in Mycobacterium tuberculosis. |
Huan-Xiang Zhou; |
251 | Assessing The Ability of Molecular Dynamics Force Fields to Capture Conformational Dynamics of Amino Acid Residues in Water Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We here assess Amber ff19SB & ff14SB, OPLS-AA/M, and CHARMM36m with respect to their capacity to capture intrinsic conformational dynamics of a guest amino acid residue x of unblocked GxG in water. |
Brian Andrews ; Shuting Zhang ; Reinhard Schweitzer-Stenner ; Brigita Urbanc; |
252 | The Dark Side of The Low and High Temperature Denaturation of Myoglobin Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We derive an exact thermodynamic expression for cold denaturation and give a better approximation than exists in the literature for predicting cold denaturation temperatures in the two-state model. |
Robert Austin ; Trung Phan ; Ramzi Khuri; |
253 | Quantification of The Molar Degree of Folding/unfolding Using A Scaling Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, a scaling model is discussed to quantify the molar degree of folding and to define the unfolded state. |
Greg Beaucage; |
254 | Beyond 3 Å-1: Total X-ray Scattering and Atomic Pair Distribution Function (PDF) Analysis to Determine The High-resolution Structure of Protein and Polysaccharide in Aqueous Solutions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, for the first time, by taking advantage of high-energy wide-angle X-ray scattering (WAXS) at 11-ID-B at the Advanced Photon Source, Argonne National Laboratory, we reliably collected WAXS profiles of several types of biomacromolecules including protein and polysaccharide in aqueous solutions up to ≈ 20 Å -1. |
Jiahui Chen ; Olaf Borkiewicz ; Alexander Grishaev ; Fan Zhang ; Uta Ruett ; Igor Levin; |
255 | Local Interactions and Transient Secondary Structures Govern Backbone Dynamics of Intrinsically Disordered Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: 1 To define general rules governing sequence-dependent backbone dynamics, we performed molecular dynamics simulations on eight IDPs. |
Souvik Dey ; Matthew MacAinsh ; Huan-Xiang Zhou; |
256 | Exploring SANS As A Novel Approach to Investigate Protein Stability with Hydrogen-Deuterium Exchange Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Due to the very large difference of the neutron scattering cross section between H and D, techniques such as small angle neutron scattering (SANS), can offer an alternate approach to monitoring HDX. |
Roisin Donnelly ; Yun Liu ; Norman Wagner; |
257 | Aggregation of Amphipathic Peptides Into Amyloid-like Fibrils Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we perform all-atom molecular dynamics simulations in explicit solvent to study the aggregation of amphipathic peptides. |
Sharareh Jalali ; Yanxing Yang ; Farbod Mahmoudinobar ; Shaneen Singh ; Bradley Nilsson ; Cristiano Dias; |
258 | A Transferable Explicit-Solvent Polarizable Coarse-Grained Model for Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we present a transferrable CG forcefield with an explicit representation of the environment for accurate simulations with proteins. |
Pei-Yin Lee ; Abhilash Sahoo; |
259 | Characterization of Amyloid Fibril Bundling in Hen Egg White Lysozyme Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Amyloids are proteins that, in their misfolded conformations, self-assemble into non-branching rigid fibrils. Growth of these fibrils involves both primary and secondary … |
Olivia Williams ; Martin Muschol ; Kanchana Karunarathne ; Nabila Bushra; |
260 | How to Probe Intrinsically Disordered Proteins and Protein Unfolding Using Advanced FT-IR Technology? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we report how temperature-resolved and time-resolved Fourier transform infrared (FT-IR) techniques were employed to study intrinsically disordered proteins and protein folding. |
Aihua Xie; |
261 | Binding of Amyloid-like Peptides to Lipid Bilayers: Effects of Ions and Lipid Content Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we perform all-atom molecular dynamics simulations to provide an understanding at the atomic level of peptide-bilayer interactions and their modulation by Ca 2+ and selected lipids. |
Yanxing Yang ; Sharareh Jalali ; Bradley Nilsson ; Cristiano Dias; |
262 | Hidden Order in An Intrinsically Disordered Protein Region Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Previously, we presented evidence of glassy dynamics in a model intrinsically disordered protein region (IDR) system, suggesting that it contains hidden regions of order. |
Ian Morgan ; Omar Saleh ; Roy Beck ; Gil Rahamim ; Joachim Dzubiella ; Upayan Baul; |
263 | Non-liquid Behavior of Coalescing Droplets of Liquid-like Cellular Aggregates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We conduct numerical simulations of droplet coalescence using both standard particulate models and vertex models meant to more accurately represent the dynamics and mechanics of dense cellular matter. |
Haicen Yue ; Daniel Sussman ; Justin Burton; |
264 | Learning Developmental Mode Dynamics from Single-cell Trajectories Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we have combined mode decomposition ideas that have proved successful in condensed matter and fluid physics with sparse dynamical systems inference to learn interpretable biophysical models from single-cell imaging data. |
Nicolas Romeo ; Alasdair Hastewell ; Alexander Mietke ; Jorn Dunkel; |
265 | Models of Galvanotaxis: Coupling Cell Migration and Shape Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We developed a coarse-grained phenomenological model that qualitatively captures these keratocyte behaviors and fits experimental data on response to a field being turned on. |
Ifunanya Nwogbaga ; Brian Camley; |
266 | Mechanical Routes to Cell Extrusion in 3D Cellular Monolayers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We utilize a phase-field model of a three-dimensional cell layer to study the interplay of cell extrusion with cell-cell and cell-substrate interactions. |
Siavash Monfared ; Guruswami Ravichandran ; Jose Andrade ; Amin Doostmohammadi; |
267 | Dynamics of An Expanding Cell Monolayer Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we consider an expansion of a dense monolayer of cells: a collective multicellular phenomenon, where cells divide, grow, and maintain contacts with their neighbors. |
Evgeniy Khain; |
268 | How Short-Range Forces Generate Long Range Order in Extreme Tissue Deformations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We use Hydra mouth opening as an in vivo biomechanics model for extreme tissue deformations. |
Tapan Goel ; Ellen Adams ; Cassidy Tran ; Trevor Rowe ; Johanna Schubert ; Patrick Diamond ; Eva-Maria Collins; |
269 | Scaling Entangled Active Matter Locomotion Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Motivated by these observations, we model individual organisms as active polymers that attract each other to form a collective. |
Chantal Nguyen ; Saad Bhamla ; Orit Peleg; |
270 | Topological Defects Reveal Signatures of Odd Elasticity in A Living Chiral Crystal Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we investigate the mechanics and dynamics of topological defects in these living chiral crystals. |
Yuchao Chen ; Yu-Chen Chao ; Junang Li ; Alexander Mietke ; Tzer Han Tan ; Jorn Dunkel ; Nikta Fakhri; |
271 | Gradients in Surface Tension Drive Global Flows in Cell Aggregates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Analysis of deformation fields allows us to evaluate the magnitude of the surface tension perturbation, which we find to be proportional to the aggregate size and correlated to the pre-strain of cells at the surface. |
Vikrant Yadav ; Sulaiman Yousafzai ; Sorosh Amiri ; Robert Styles ; Eric Dufresne ; Michael Murrell; |
272 | Active Mechanics of Starfish Oocytes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we address this question in vivo using the meiotic surface contraction wave of starfish oocytes. |
Peter Foster ; Sebastian Fürthauer ; Nikta Fakhri; |
273 | Non-equilibrium Shape Fluctuations in Living Cells Report Driving Forces and Organelle Mechanics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a theoretical description and measure the bending stiffness of MTs in vivo, finding general agreement with published in vitro data. |
Kengo Nishi ; Sufi Raja ; An Pham ; Ronit Freeman ; Antonina Roll-Mecak ; Frederick MacKintosh ; Christoph Schmidt; |
274 | Principles of Cellular Behavior: A Unicellular Walker Controlled By A Microtubule-based Finite State Machine Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we demonstrate finite state machine-like processing embodied in cells using the walking behavior of Euplotes eurystomus, a ciliate that walks across surfaces using fourteen motile appendages (cirri). |
Ben Larson ; Jack Garbus ; Jordan Pollack ; Wallace Marshall; |
275 | Active Nematics on Deformable Surfaces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We describe the numerical solution of the resulting Euler-Lagrange equations for biologically relevant case studies such as for shape changes in the manifold of contractile cytoskeleton network undergoing cell division and for shape changes in a monolayer of microtubules and kinesin enclosed in a lipid vesicle. |
Waleed Mirza ; Marino Arroyo ; Alejandro Torres-Sánchez ; Guillermo Vilanova; |
276 | Curvature Induces Active Matter Velocity Waves in Rotating Multicellular Spheroids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study 3D collective migration in a mammary cell spheroid, which represents a common and conceptually simple curved geometry. |
Tom Brandstätter ; David Brückner ; Yulong Han ; Ricard Alert ; Ming Guo ; Chase Broedersz; |
277 | A Competitive Advantage Through Fast Dead Matter Elimination in Confined Cellular Aggregates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that passive by-products of the processes maintaining homeostasis can significantly alter fitness, enabling cell types with lower homeostatic pressure to outcompete those with higher homeostatic pressure. |
Yoav Pollack ; Yoav Pollack ; Philip Bittihn ; Ramin Golestanian; |
278 | Odor Motion Detection By An Olfactory System Aids Navigation of Complex Odor Plumes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using a virtual reality setup to decouple wind from odor signal, we find that flies detect odor motion from the temporal correlations of the odor signal between its two antennae, in a computation similar to motion detection in vision. |
Nirag Kadakia ; Mahmut Demir ; Brenden Michaelis ; Matthew Reidenbach ; Damon Clark ; Thierry Emonet; |
279 | Quantifying Structure in Immune Receptor Epitope Maps Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In my talk I will introduce an analytical framework to quantify structure in recent high-throughput measurements of such maps. |
Andreas Mayer; |
280 | 2022 Early Career Award for Biological Physics: Organization and Encoding of Memory in Evolving Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will discuss how statistics and dynamics of stimuli should determine the optimal memory encoding strategies in biological networks. |
Armita Nourmohammad; |
281 | Conventional and Unconventional T Cell Receptor Recognition Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here I will discuss approaches to deconstruct this complexity, utilizing TCR distance-based analysis and novel methods for integrating TCR sequence and single cell gene expression data. |
Paul Thomas; |
282 | Sequential and Efficient Neural-population Coding of Complex Task Information Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We suggest that neural circuits can implement time-dependent encodings in a simple way using random sequential dynamics as a temporal scaffold. |
Sue Ann Koay ; Adam Charles ; Stephan Thiberge ; Carlos Brody ; David Tank; |
283 | Effect of Geometric Complexity on Intuitive Model Selection Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Occam’s razor is the principle stating that, all else being equal, simpler explanations for a set of observations are to be preferred to more complex ones. This idea can be made … |
Eugenio Piasini ; Vijay Balasubramanian ; Joshua Gold; |
284 | Functional Imaging and Quantification of Multi-neuronal Olfactory Responses in C. Elegans Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we studied the ensemble-level representation of odor identity in the nematode C. elegans. |
Albert Lin; |
285 | Biomechanical and Ionic Excitability Within Developing Brain Cell Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work shows that pharmacologically perturbing actin impacts the functional communication as measured by calcium in the developing neural networks – suggesting new avenues to understanding the impact of biomechanical elements in neural communication. |
Sylvester Gates ; Wolfgang Losert; |
286 | Functional Connectivity in The C. Elegans Brain Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will present functional connectivity measurements in C. elegans obtained via sequential optogenetic stimulation of individual neurons and simultaneous whole-brain imaging of neural activity as a first step towards probing the relationship between neuroanatomy and neural function. |
Francesco Randi ; Anuj Sharma ; Sophie Dvali ; Andrew Leifer; |
287 | Recurrent Activity in Neuronal Avalanches Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To explain these observations, we adapted a model of structural weakening in materials. |
Tyler Salners; |
288 | Evidence of Quasicritical Dynamics Across The Life Span: A MEG Study Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We analyzed the Cambridge Centre for Ageing and Neuroscience (Cam-CAN) resting-state magnetoencephalography (MEG) dataset –the largest neuroimaging cohort available to date— in light of a new theoretical framework known as Quasicriticality. |
Leandro Fosque ; John Beggs ; Gerardo Ortiz ; Marzieh Zare ; Abolfazl Alipour ; Rashid Williams-García ; Mahdi Sarikhani; |
289 | Simpler Models of Neuronal Activity Via Compression of Interactions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In condensed matter physics, simple models often work, quantitatively, but simplifications rest in part in the pairwise and local microscopic interactions. |
Luisa Ramirez ; William Bialek; |
290 | Universal Scaling in Neural Activity: A Renormalization-group Perspective Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To shed further light on these issues, here we analyze activity recordings of thousands of individual neurons across regions in the mouse brain. |
Guillermo Barrios Morales ; Miguel Muñoz ; Serena di Santo; |
291 | A Novel Modeling Approach to Identify Groups of Coordinated Neurons Which Accounts for High-order Neural Correlations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we proposed a novel approach that is based on modeling groups of coordinated neurons with minimally complex spin models. |
Clelia de Mulatier ; Jean-Hugues Lestang ; Songhan Zhang ; Lalitta Suriya-Arunroj ; Yale Cohen ; Vijay Balasubramanian; |
292 | Full-stack Inference of Low-dimensional Effective Models Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In the present work, we recover both model parameters and input sequences from noisy observations of a Wilson-Cowan model driven by unobserved stochastic inputs. |
Alexandre René ; Andre Longtin; |
293 | Mapping Transcriptomic Vector Fields of Single Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we introduce an analytical framework dynamo, that infers absolute RNA velocity, reconstructs continuous vector-field functions that predict future cell fates, employs differential geometry to extract underlying regulatory networks, and ultimately predicts optimal reprogramming paths and perturbation outcomes. |
Xiaojie Qiu ; Yan Zhang ; Ivet Bahar ; Vijay Sankaran ; Jianhua Xing ; Jonathan Weissman; |
294 | Landscape-inspired Order Parameters for Classifying Cell Fate Using Single-cell RNA-seq Data Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that we can use a spin-glass inspired epigenetic landscape model of cell identity to classify cell type quickly and accurately from scRNA-seq measurements using “order parameters” derived from single cell expression atlases (for example, the Mouse Cell Atlas). |
Maria Yampolskaya ; Jason Rocks ; Pankaj Mehta; |
295 | Features of Gene Regulatory Dynamics on Minimally Frustrated Topologies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we analyze the ODEs-based dynamics of gene regulation on networks with minimally frustrated topologies and find that they exhibit stable states that vary mostly along a single principal component, a property that is key to establishing and maintaining cell types. |
Shubham Tripathi ; David Kessler ; Herbert Levine; |
296 | Glassy Fluctuations in Gene Regulatory Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work highlights the possibility that long-lived noise could be a carrier of biological information. |
Fabrizio Olmeda ; Yiteng Dang ; Fabian Rost ; Steffen Rulands; |
297 | Master Regulators As Order Parameters of Gene Expression States Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The model is applied to gene expression data in the context of hematopoiesis. |
Andreas Kraemer; |
298 | Individual and Collective Events in Cell Competition Dynamics Using A Cellular Potts Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we develop a Cellular Potts model for cell competition using parameters determined from cultured epithelial cells. |
Logan Carpenter ; Daniel Gradeci ; Shiladitya Banerjee; |
299 | Growth Dynamics of Bacterial Cell Cycles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using time-lapse microscopy of Escherichia coli and a variety of mutants and drug treatments, we explore the relation between the reduced growth rate at a population level and the distribution of cell-cycle durations. |
Teresa Lo; |
300 | Utilizing Massively Parallel CRISPRi Assays to Investigate Persistence During Antibiotic Exposure Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that the CRISPRi can replace the function of the toxin-antitoxin systems, inhibiting the cells metabolism and improving survival under certain antibiotics. |
Keiran Stevenson ; Guillaume Lambert; |
301 | Covariance Structure in Sizes and Numbers Shows That Membrane-bound Organelles Grow in A More Correlated Manner When Cellular Growth Rate Is Limited Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Among the fundamental questions in system cell biology is how the cell coordinates synthesis of its components to grow and self-replicate, in correspondence with its environment. … |
Shixing Wang ; Shankar Mukherji; |
302 | Reversibiliy and Cell Division Dynamics of Elongated Escherichia Coli Cells Obtained at High Pressure Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have studied the dynamics of cell division of a population of heterogeneous morphology of Escherichia coli cells obtained after the application of high hydrostatic pressure. |
Steven Murray ; Aidan Glaser Schoff ; Albert Libchaber ; Pradeep Kumar; |
303 | Dynamics of Colonization and Phenotypic Adaptations of Commensal Gut Bacteria in Larval Zebrafish Populations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We address this using larval zebrafish, an established model vertebrate system, implementing an imaging-based assay to study the dynamics of colonization by fluorescently labelled bacteria native to the zebrafish gut. |
Vivek Ramakrishna ; Raghuveer Parthasarathy; |
304 | Stochastic Induction Dynamics of The Lac Operon Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We observe that the feedback loop activation is stochastic, and days can separate the activation of cells growing in separated chamber when gene expression is tuned down. |
Louis Cortes; |
305 | Competition Between Two Cell Types Under Cell Cycle Regulation with Apoptosis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we report on extensions of this model to multiple cell types. |
Jintao Li ; Simon Schnyder ; Ryoichi Yamamoto ; Matthew Turner; |
306 | Interactions and Structure of Native Gut Microbiome of C. Elegans Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: From in vitro data, we observed a range of inter-species interactions, and colonizing the gut with individual species revealed intestinal populations that increase over time, consistent with a simple Lotka-Volterra-type model for saturating growth. |
Satya Spandana Boddu ; K. Michael Martini ; Megan Taylor ; Ilya Nemenman ; Nic Vega; |
307 | Compromising Matrix Structure to Make Biofilm Bacteria Easier to Eat Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To remedy this, we use polymer-specific enzyme treatments matched to the dominant polymer produced by a bacterial strain—these treatments cause changes in the bulk mechanical properties of the biofilm, aiding phagocytosis and leading to higher engulfment rates. |
Isabella Chavez; |
308 | Spatially Localized Adhesin Sharing Confers Ecological Stability in V. Cholerae Biofilms Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, using Vibrio cholerae as the model biofilm-former, we show that biofilm adhesins are indeed susceptible to cheater exploitation, and the evolutionary stability of adhesin production depends on the spatial structure of biofilms and the flow conditions in the environment. |
Jung-Shen Tai ; Saikat Mukherjee ; Rich Olson ; Jeffrey Tithof ; Carey Nadell ; Jing Yan ; Thomas Nero; |
309 | Irvin Oppenheim Award (2022): Microbial Diversity and Competition for Resources in A Model Seasonal Ecosystem Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we focus on consumer-resource models subject to serial dilutions. |
Amir Erez; |
310 | On The Sizes of Gut Bacterial Aggregates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Analyzing imaging data for eight different bacterial strains examined in isolation in the larval zebrafish gut, we find a common family of cluster size distributions that decay approximately as power laws with exponents close to -2, becoming shallower for large clusters in a strain-dependent manner. |
Raghuveer Parthasarathy ; Deepika Sundarraman ; Brandon Schlomann; |
311 | Oxygen Dynamics in A Vertically Stratified Microbial Community Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study the dynamics by which the topmost stratum, corresponding to aerobic heterotrophy, emerges in homogenized salt marsh sediment. |
Benjamin Roque ; Alexander Petroff; |
312 | The Physics of Sessile Droplets Rediscovered in Bacterial Biofilms Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will present our newest results showing that the growth of surface attached bacterial colonies can be captured by the physics of sessile droplets. |
Gabi Steinbach ; Peter Yunker ; Aawaz Pokhrel ; Brian Hammer ; Siu Lung Ng; |
313 | Stochastic Effects in Quorum Sensing Mediated By Extracellular Vesicles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present here a fully stochastic reaction-diffusion model of QS that accounts for fluctuations in both freely diffusing and vesicle-bound AI molecules. |
Brian Weaver ; Christoph Haselwandter ; James Boedicker; |
314 | High-throughput Assays Show Timescale of Phagocytic Success Depends on Target Toughness Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Rapid data collection allows us to extend our study to neutrophils isolated from the whole blood of three healthy adult volunteers. |
Marilyn Wells; |
315 | Bacterial Foraging in Patchy Landscapes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Interpreting trajectories using the ideal chain model of polymer physics allowed us to decipher the diversity of foraging behaviors in response to the topology of the habitat and local patch/corridor occupancy. |
Miles Wetherington; |
316 | High Dimensional Geometry of Fitness Landscapes Identifies Master Regulators of Evolution and The Microbiome Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we develop a geometric formalism that allows us to quantify interactions at high dimensionality in genetics and the microbiome. |
Will Ludington ; Michael Joswig ; Holger Eble ; Lisa Lamberti; |
317 | Coupling Between Spatial Structure and Heterogeneous Antibiotic Responses Through Self-generated Nutrient Gradients in Microbial Populations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we observe the response of spatially extended microcolonies of tetracycline-resistant E. coli to precisely defined dynamic drug regimens in a custom microfluidic device. |
Philip Bittihn ; Mirjana Stevanovic ; Thomas Boukéké-Lesplulier ; Lukas Hupe ; Jeff Hasty ; Daniel Schultz; |
318 | Active Bulging Promotes Biofilm Formation in A Bacterial Swarm Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we studied cell-fluid interaction in bacterial colonies and the consequence of such interaction on biofilm development. |
Siyu Liu ; Ye Li ; Daniel Kearns ; Yilin Wu; |
319 | Molecular Cutting Machine: Katanin Microtubule Severing Enzyme Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our recent work on katanin has revealed surprising results including that katanin is inhibited by the presence of free tubulin, katanin can depolymerize microtubules lacking the carboxy-terminal tail, and katanin only mildly disrupts cell division, even when tethered directly to the kinetochore. |
Jennifer Ross; |
320 | Exploring Secondary Structural Transitions in Microtubule Severing Motors with Machine Learning Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To characterize changes to the secondary structure of the protomers, we developed a centroid-based clustering method applied directly to the Ramachandran plot to analyze structural changes occurring in simulations . |
Amanda Macke ; Ruxandra Dima ; Maria Kelly; |
321 | Motor Guidance By Long-range Communication Through The Microtubule Highway Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we report that microtubules can physically couple motor movement in the absence of short-range interactions. |
Shane Fiorenza ; Meredith Betterton ; Sithara Wijeratne ; Radhika Subramanian; |
322 | Microtubule Studies on Lattice Dynamics and Severing Machine Guided Regulation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Utilizing Machine Learning techniques, we found that features related to the energetics of the lattice are crucial to distinguish between the four kinetic states. |
Maria Kelly ; Ruxandra Dima ; Valeri Barsegov; |
323 | A Magnetic Tweezers-Based Study of DNA-Histone Interactions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We report data from single-molecule forcemediated DNAcore histone assembly and disassembly processes using horizontal magnetic tweezers. |
Santosh Gaire ; Roberto Jr Fabian ; Ian Pegg ; Abhijit Sarkar; |
324 | DNA Supercoiling Drives A Transition Between Collective Modes of Gene Synthesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To underpin the mechanism behind this drastic transition, we developed a continuum deterministic model for transcription under torsion with two novel features: (1) the number of RNAPs on the gene affects the torsional stress experienced by individual RNAPs and (2) transcription factors, when bound to the DNA, block the diffusion of supercoils at the promoter. |
Purba Chatterjee ; Sangjin Kim ; Nigel Goldenfeld; |
325 | Atomically Precise Control Over Rotation of A Rare-earth Molecular Motor Complex on Au(111) Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work demonstrates that charged counterions can be used to control dynamics of rare-earth molecular systems on materials surfaces. |
Saw Hla ; Tolulope Michael Ajayi ; Vijay Singh ; Sanjoy Sarkar ; Shaoze Wang ; Sineth Premarathna ; Xinyue Cheng ; Fahimeh Movahedifar ; Larry Curtiss ; Anh Ngo ; Eric Masson; |
326 | Modelling The Step Size Distribution of Myosin VI Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have developed a single model that allows us to study this multifaceted stepping behavior. |
Riina Tehver; |
327 | ROCK Dependent Volume Regulation of Cell Shape in Confluent Epithelial Tissue Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we describe the role of ROCK dependent volume regulation of confluent renal epithelial tissue It is well studied that single cells typically recover their volume in hyperosmotic conditions in under an hour. |
Theresa Chmiel ; Margaret Gardel; |
328 | Torques Within Microtubule Bundles Generate The Curved Shape of The Mitotic Spindle Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To answer this, we introduce a mean-field approach, in which we describe the dominating forces and torques at the poles, in order to model he entire spindle. |
Arian Ivec ; Maja Novak ; Monika Trupinić ; Ivana Ponjavić ; Iva Tolić ; Nenad Pavin; |
329 | Why Exercise Builds Muscles: Titin Mechanosensing Controls Skeletal Muscle Growth Under Load Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, I will explain how the opening of kinase domain of the muscle molecule titin under load provides a possible explanation for muscle growth following resistance training. |
Neil Ibata; |
330 | Active Viscoelastic Composites Generate Self-regulating Asters with Programmable Lifetimes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we introduce an active cytoskeletal composite material whose viscoelasticity is controlled by the actin filament concentration. |
John Berezney ; Bruce Goode ; Seth Fraden ; Zvonimir Dogic; |
331 | Tuning Cellular Contractility By Assembly of Subcellular Actomyosin Structures Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To this end, we aim to quantitatively characterize how actomyosin assemblies remodel in cells leading to varying levels of contractility. |
Wen-hung Chou ; Mehdi Molaei ; Huini Wu ; Jordan Beach ; Patrick Oakes ; Margaret Gardel; |
332 | Force Chains Lead to Long Range Percolation of Forces Produced By Myosin Motors in A Disordered Cytoskeleton Network Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We model myosin motors as force dipoles embedded in a random fiber network with linear elastic elements that have both bending and stretching moduli. |
Abhinav Kumar ; David Quint ; Kinjal Dasbiswas; |
333 | Mechanical Coupling Between The Actomyosin and Microtubule Systems During T-cell Activation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that microtubule growth dynamics is modulated by actin nucleators. |
Ivan Rey Suarez ; Arpita Upadhyaya; |
334 | Effects of Disorder on The Topological Properties of Microtubules Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we employ a model to demonstrate that the charge distribution and lattice-like configuration of the microtubule additionally allow for electronic topological edge modes. |
Varsha Subramanyan ; Saraswathi Vishveshwara ; Smitha Vishveshwara; |
335 | Optimal Control and Design of Cytoskeleton-based Dynamic Biomaterials Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using active nematics as an exemplar, I outline how the inverse problem toolset combined with a dynamical systems view of active matter enables both exogenous and endogenous material control. |
Michael Norton; |
336 | Characterizing Cytoquakes, Heavy-tailed Fluctuations in The Actomyosin Cortex, Using Super-resolved Micropost Arrays Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using high-resolution measurements of fluctuations in the cortex via arrays of flexible microposts, we find that the distributions of sizes of these cortical fluctuations are well-modeled by exponentially truncated Lévy distributions for multiple cell types and substrate stiffnesses. |
Shankar Sivarajan ; Yu Shi ; Katherine Xiang ; John Crocker ; Daniel Reich; |
337 | Roles of The Cytoskeletal Structure in Neurite Outgrowth Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To investigate the mechanisms of neurite elongation, we constructed an agent-based model that consists of essential cytoskeletal elements with consideration of their mechanical properties and mechanical interactions. |
Donghyun Yim ; Kyle Miller ; Daniel Suter ; Taeyoon Kim; |
338 | Dynamic Behaviour of Microtubules Around The Critical Temperature and Effect of The Electric Field Produced By These Vibrations on Its Environment Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we study the microtubule as a ferroelectric system. |
NGANFO WILLY ANISET; |
339 | Organization and Dynamics of Crosslinked Actin Networks Under Confinement Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We employ coarse-grained computer simulations to study the dynamics and organization of semiflexible actin filaments as we vary as the system shape, the number and type of crosslinking proteins, and the length of filaments. |
Oghosa Akenuwa; |
340 | Regulation of F-actin Size Heterogeneity By Formin and Capping Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our study quantitatively predicts how heterogeneity in actin filament size can be regulated by tuning nucleation and growth rates. |
Deb Banerjee ; Shiladitya Banerjee; |
341 | Life at The Bottom: NMR and MRI at 6.5 MT Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We will discuss signal acquisition approaches and hardware methods to improve attainable SNR in the Johnson-noise-dominated Larmor frequency of 276 kHz (6.5 mT) [1,2]. |
Matthew Rosen; |
342 | Imaging Néel Relaxation of Superparamagnetic Nanoparticles Using Diamond Magnetic Microscopy Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we report progress on the use of diamond magnetic microscopy to study the magnetic relaxation dynamics of single SPIONs and characterize their heterogeneity. |
Bryan Richards ; Nate Ristoff ; Abdelghani Laraoui ; Ilja Fescenko ; Joshua Damron ; Nazanin Mosavian ; Janis Smits ; Andrey Jarmola ; Pauli Kehayias ; Maziar Saleh Ziabari ; Andrew Mounce ; Dale Huber ; Victor Acosta; |
343 | Developing A Magnetic Resonance Spectroscopy Instrument for Use in Consumer Health Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We describe early development efforts of such a device including methods to increase signal to noise using novel filtering techniques, simulations of the device performance and design of the magnet. |
Gil Travish; |
344 | Magnetic Particle Imaging Using A Single Sided Field Free Line Scanner Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work we show imaging simulations that make use of the FBP method, which demonstrates the viability of our scanner, and present experimental images of one dimensional phantoms. |
Alexey Tonyushkin ; Christopher McDonough ; David Newey; |
345 | Non-negative Least Squares Using Multi-regularization and A Gaussian Basis, with Application to Magnetic Resonance Relaxometry Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Accordingly, we have developed a multiple regularization (MultiReg) approach to solving the FEFK by incorporating a linear combination of solutions corresponding to a set of values. |
Richard Spencer ; Chuan Bi ; Yvonne M. Ou ; Wenshu Qian ; Kenneth Fishbein ; Mustapha Bouhrara; |
346 | Magnetic Resonance Imaging of Cancer Turns 45: How It Works, How We Use It Today, and Future Outlook Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This presentation will review the physical fundamentals of MRI signal and contrast, provide a clinical overview of the techniques used in current radiology practice, and highlight current, ongoing research for the future development of MRI in human health. |
David Jordan; |
347 | The Physical Basis of Using MRI for Cancer Detection Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will review the history of MRI development and discuss the possible physical mechanism behind the relaxation time changes between normal cells and cancer cells. |
Donald Chang; |
348 | Highly Sensitive and High Throughput Magnetic Resonance Thermometry Using Superparamagnetic Nanoparticles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We describe an approach for highly sensitive and high throughput MR thermometry that is not susceptible to motional artifacts. |
Darshan Chalise ; David Cahill; |
349 | Enhancing NMR Sensitivity for Near-surface NV Centers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, I discuss a survey of fabrication treatments we have tested to improve the sensing performance of shallow NV centers for surface NMR, including high-temperature annealing, chemical termination, advanced cleaning methods, and co-implantation. |
Erika Janitz ; Tianqi Zhu ; John Abendroth ; Konstantin Herb ; Viraj Damle ; Jan Rhensius ; Gabriel Puebla Hellmann ; Christian Degen; |
350 | Room Temperature Hyperpolarization of 13C in Diamond at 3.34 T Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we use microwave-induced dynamic nuclear polarization (DNP) of the P1 centers to enhance the NMR signals of natural abundance 13C nuclei at 3.34 T at room temperature. |
Chandrasekhar Ramanathan ; Daphna Shimon; |
351 | Assessing Protein Corona Formation on Hard and Polymeric Nanoparticles – Towards Understanding Biocompatibility, Biodistribution, and Efficacy Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Herein, we present a multimodal study of protein corona composition and dynamics, first on ‘hard’ nanoparticles: spherical polystyrene nanoparticles and high aspect ratio single-walled carbon nanotubes (SWCNTs). |
Markita Landry; |
352 | Human Airway Mucus: Cactus-like Conformations of Associative Polymers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: A unique "cactus" model resulting from loops of different orders is proposed. |
Scott Danielsen ; Michael Rubinstein; |
353 | Role of Active and Thermal Fluctuations in Biopolymer Dynamics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We develop a theoretical framework for predicting the combined influence of active and Brownian forces in biopolymer dynamics. |
Ashesh Ghosh ; Andrew Spakowitz; |
354 | A Mean-field Theory to Predict Statistics of Semiflexible Biomolecules Due to Inhomogeneous Forces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In our work, we modify an existing analytically tractable mean-field approach to account for the heterogeneity in tension for electric fields. |
Ananya Mondal ; Greg Morrison; |
355 | Nanopore Chip with Self-Aligned Transverse Tunneling Junction for Biomolecule Detection and Sequencing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we report a new strategy for fabricating a solid-state nanopore with transverse tunneling junction integrated inside a nanofluidic channel, where DNA molecules can be enriched and straightened to pass through the nanopore between the electrodes. |
Sanjana Mukherjee ; Yuan Wang ; Joshua Sadar ; Ching-Wei Tsao ; Quan Qing; |
356 | Unexpected Fluorescence in Peptide Amphiphile Micelles for Molecular-recognition Sensing Applications Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work will present the design, characterization, and functionality of this newly discovered and versatile AIE material. |
Whitney Fowler; |
357 | Bayesian Inference of Chromatin Looping Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We developed a Bayesian inference algorithm to detect sustained contacts in two-particle tracking experiments, thereby uncovering the dynamics of chromatin loops. |
Simon Grosse-Holz ; Hugo Brandão ; Michele Gabriele ; Asmita Jha ; Claudia Cattoglio ; Tsung-Han Hsieh ; Leonid Mirny ; Christoph Zechner ; Anders Hansen; |
358 | Extreme Elastic Properties of Mechanosensory Chordotonal Organs in Drosophila Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we study the lateral pentascolopidial organ (lch5), a type of chordotonal organ (ChO), of Drosophila larvae. |
Xiaoxuan Jian ; Chonglin Guan ; Kengo Nishi ; Christian Kreis ; Oliver Baeumchen ; Martin Göpfert ; Christoph Schmidt; |
359 | A Coarse-grain Elastic Lattice Polymer Model of Bacterial Chromosomes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this context, we studied an elastic lattice polymer model for tightly double-folded ring polymers. |
Elham Ghobadpour ; Ralf Everaers ; Ivan Junier; |
360 | Modulation of DNA Entanglements By Nucleoid Associated Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will report on recent results we obtained using particle tracking microrheology on entangled solutions of large lambda-DNA functionalized by IHF/HNS proteins. |
Davide Michieletto; |
361 | Mechanical Properties Of Peptide Nucleic Acids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We argue that the neutral backbones of the PNA make it less stiff than dsDNA and dsRNA. |
Khadka Chhetri ; Akshara Sharama ; Supriyo Naskar ; Prabal Maiti; |
362 | Stochastic Dynamics of Coupled DNA Loci on A Compacted Chromosome Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using a live imaging assay to simultaneously measure positions of pairs of enhancers and promoters in thousands of nuclei of the developing fly embryo, we analyze the two-point correlations of these DNA loci. |
David Brückner ; Lev Barinov ; Hongtao Chen ; Thomas Gregor; |
363 | Dynamic Bridging Explains Sub-diffusive Movement of Chromosomal Loci Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, using polymer simulations we investigate the role of DNA bridging in determining the dynamics of chromosomal loci. |
Srikanth Subramanian ; Sean Murray; |
364 | Associative Memory of Knowledge Structures and Sequences Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we focus on the task of storage and recall of structured knowledge in long term memory. |
Julia Steinberg ; Haim Sompolinsky; |
365 | Error-driven Input Modulation: Solving The Credit Assignment Problem Without A Backward Pass Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we propose to replace the backward pass with a second forward pass in which the input signal is modulated based on the network’s error. |
Giorgia Dellaferrera ; Gabriel Kreiman; |
366 | Robust Sequential Retrieval of Memories in Interaction-modulated Neural Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We identify three requirements for sequential retrieval: a destabilization of the present memory, a directional bias towards the next memory in the sequence, and a separation of timescales. |
Lukas Herron ; BingKan Xue ; Pablo Sartori; |
367 | Working Memory Via Combinatorial Persistent States Atop Chaos in A Random Multivariate Network Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work thus reveals a chaotic network that can nonetheless retain any of a combinatorially large number of memories, shedding new light on how distributed dynamics could support WM. |
Rich Pang; |
368 | Dynamical Phases and Computation in Nonlinear Networks with Correlated Couplings Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The statistics of fixed points and chaos in different parameter regimes can be studied using random matrix methods and dynamic mean-field theory. |
Daniel Wennberg ; Atsushi Yamamura ; Surya Ganguli ; Hideo Mabuchi; |
369 | Structured Neural Codes Enable Sample Efficient Learning Through Code-Task Alignment Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To identify how inductive biases are implemented in and shaped by neural codes, we study sample-efficient learning of arbitrary stimulus-response maps from arbitrary neural population codes with biologically-plausible readouts. |
Blake Bordelon ; Cengiz Pehlevan; |
370 | Capacity of Group-invariant Linear Readouts from Equivariant Representations: How Many Objects Can Be Linearly Classified Under All Possible Views? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We address this gap by providing a generalization of Cover’s Function Counting Theorem that quantifies the number of linearly separable and group-invariant binary dichotomies that can be assigned to equivariant representations of objects. |
Matthew Farrell ; Blake Bordelon ; Shubhendu Trivedi ; Cengiz Pehlevan; |
371 | Signal Representation and Learning in Random Feedback Neural Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we study nonlinear feedback networks trained to generate a sinusoidal signal, and analyze how learning performance is shaped by the interplay between internal network dynamics and target properties. |
Lee Susman; |
372 | Understanding Multi-pass Stochastic Gradient Descent Via Dynamical Mean-field Theory Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have applied dynamical mean-field theory to derive a full description of the learning curves of SGD and of its performances in prototypical models. |
Francesca Mignacco; |
373 | Nested Canalizing Functions Minimize Sensitivity and Simultaneously Promote Criticality Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We prove that nested canalizing functions are the minimum-sensitivity Boolean functions for any given activity ratio and we characterize the sensitivity boundary which has a nontrivial fractal structure. |
Alkan Kabakcioglu ; Hamza Coban; |
374 | The Physics of Interactions in Soft Robotics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Soft robotics is a relatively young field of robotics that takes advantage of soft materials and compliant structures to improve robot interactions with their surrounding … |
Cecilia Laschi; |
375 | Worm Omega Turn Modeling and Its Limbless Robot Implementation Via Geometric Mechanics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work focuses on an omega shaped turning motion of the mm-long nematode worm C. elegans that allows large and rapid reorientation in natural environments (e.g., rotting fruit). |
Tianyu Wang ; Baxi Chong ; Kelimar Diaz ; Yuelin Deng ; Ruijie Fu ; Hang Lu ; Howie Choset ; Daniel Goldman; |
376 | Locomotion Planning and Control for Discretely-soft Bodied Legged Robots Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we present two geometric motion planning frameworks for an autonomous, discretely soft, closed kinematic chain articulated, insect-sized quadrupedal robot with electroadhesive feet – CLARI (Compliant Legged Articulated Robotic Insect). |
Hari Krishna Hari Prasad ; Kaushik Jayaram; |
377 | Snake Robot Uses Vertical Bending with Force Feedback Control to Traverse Large Obstacles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To understand how to effectively utilize vertical bending, we use a snake robot to test two hypotheses: (1) With large height variation, vertical bending alone can generate substantial propulsion; (2) With force feedback, propulsion can be better maintained. |
Qiyuan Fu ; Chen Li; |
378 | A Modular Approach to Discrete Differential Geometry-based Simulation of Soft Robots Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a numerical simulator for articulated soft robots inspired by a discrete differential geometry-based computational framework. |
Mohammad Khalid Jawed ; Yayun Du ; Mrunmayi Mungekar; |
379 | Coordinating Tiny Limbs and Long Bodies: Geometric Mechanics of Diverse Undulatory Lizard Locomotion Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Study of a limbed/undulatory robophysical model demonstrates that a traveling wave is beneficial when thrust is generated by body-environment interaction. |
Baxi Chong ; Tianyu Wang ; Eva Erickson ; Philip Bergmann ; Daniel Goldman; |
380 | Bio-inspired Sensing and Control of Soft Slithering Bodies in 3D Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a bio-inspired neural architecture for learning closed-loop controls in slithering soft bodies, realized through coupled oscillators and reinforcement learning. |
Xiaotian Zhang ; Tixian Wang ; Andrew Dou ; Prashant Mehta ; Mattia Gazzola; |
381 | Enhancing Manueverability Via Gait Design Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we propose both local and global gait morphing algorithms for modulating a nominal gait to provide efficient, single-parameter steering control. |
Siming Deng ; Ross Hatton ; Noah Cowan; |
382 | Granulobot: From Granular Matter to Self-assembling and Reconfigurable Robotics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce Granulobot, a soft robotic platform that uses the rich properties of granular matter to propose new resilient capabilities. |
Baudouin Saintyves ; Matthew Spenko ; Heinrich Jaeger; |
383 | Manipulating Propulsive Forces with Mulitple Fins: Understanding How The Relative Location, Phase Relationship, Compliance and Flapping Frequency of Fins Affect The Swimming Forces and Associated Flows Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Fish produce swimming and maneuvering forces through the coordinated motions of their body and fins. To achieve a locomotory task, fish will typically use multiple fins … |
Anthony Mignano; |
384 | Mismatch of Body Undulation and Limb Waves Enables Robust Centipede Locomotion Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We studied body-limb coordination in centipedes via a robophysical model (L=70 cm, 8 leg pairs), programmed to generate retrograde waves for both the body and limbs. |
Juntao He ; Tianyu Wang ; Baxi Chong ; Kelimar Diaz ; Eva Erickson ; Daniel Goldman; |
385 | Studying Force Generation and Control in Snakes Using A Sensorized Robot Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To begin to understand this, we created a 12-segment robot with each segment instrumented with 3 sheet contact sensors capable of measuring normal contact forces at 30 Hz. |
Divya Ramesh ; Qiyuan Fu ; Chen Li; |
386 | Emergence of Undulation Gait Based on Embodied Position Controller and Filter Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Therefore, we come up with two research questions: 1. |
Longchuan Li ; Shugen Ma ; Isao Tokuda; |
387 | Combinatorics in Evolution: from Rule-based Systems to The Thermodynamics of Selectivities Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study we use a rule-based model to generate "all possible" solutions to a biological problem of sugar-phosphate conversion, deriving the natural dissipaton costs and information geometry that constitute fitness criteria and separability of solutions. |
Eric Smith ; Harrison Smith ; Jakob Andersen; |
388 | Thermally Induced Habitat for The Emergence of Life – Enrichment of Phosphorus, Divalent Salts and Compact Oligomer Folds Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show how ubiquitous heat fluxes through rock fractures implement a physical solution to this problem: Thermal convection and thermophoresis together are able to separate calcium from phosphorus and thus use ubiquitous but otherwise inert apatite as a phosphate source. |
Christof Mast ; Dieter Braun ; Thomas Matruex ; Paula Aikkila ; Bettina Scheu ; Don Dingwell ; Kris Le Vay ; Hannes Mutschler; |
389 | A Robust Transition to Homochirality in Complex Chemical Reaction Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, using random matrix theory, we show that large non-equilibrium reaction networks can undergo a generic and robust phase transition towards a homochiral state as a consequence of the fact that they contain a large number of chiral species. |
Gabin Laurent ; David Lacoste ; Pierre Gaspard; |
390 | How The Drive for Survival of The Fittest Might Have Arisen from A Physico-chemical Ratcheting Process Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We seek the roots of SoF in prebiotic physical chemistry of simple molecules. |
Charles Kocher ; Ken Dill; |
391 | Evolutionary Dynamics: A Stochastic Thermodynamics Perspective Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this presentation, we introduce a general model of reproduction–variation–selection dynamics. |
Riccardo Rao ; Stanislas Leibler; |
392 | Spatial Patterns in Winning Mediated Thermodynamic Strategy Evolution Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: For a parameterized rock-paper-scissors game, we find a condition under which stationary local communities form, for which the domain sizes scale with the size of the system. |
Andrew Belmonte ; Connor Olson; |
393 | Dynamical Mean-field Theory: from Ecosystems to Reaction Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To connect these phenomena, in this work we find a reaction network whose large-scale behavior precisely recovers the random Lotka-Volterra model considered recently. |
Eric De Giuli ; Camille Scalliet; |
394 | It Doesn’t Always Pay to Be Fit: Success Landscapes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we discuss a form of landscape in evolutionary biology which takes into account (1) initial growth rates, (2) mutation rates, (3) resource consumption by organisms, and (4) cyclic changes in the resources with time. |
Trung Phan ; Gao Wang ; Tuan Do ; Ioannis Kevrekidis ; Sarah Amend ; Emma Hammarlund ; Kenneth Pienta ; Joel Brown ; Liyu Liu; |
395 | Dynamics of Bacterial Replisomes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In my talk, I will present a theoretical connection between the dynamics of replisomes and the distribution of DNA abundance in an exponentially growing bacterial population. |
Simone Pigolotti ; Deepak Bhat ; Samuel Hauf ; Charles Plessy ; Yohei Yokobayashi; |
396 | Modeling Circadian Clocks in Real Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We use a dynamical systems model of circadian clocks and real-world weather data to study tradeoffs in parameters in these systems, and to understand potential relationships between geography and underlying parameters and structure in circadian clocks. |
Caroline Holmes ; Stephanie Palmer; |
397 | Global Constraints Within The Developmental Program of The Drosophila Wing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We develop a mathematical approach that enables a robust description of biologically salient phenotypic variation. |
Vasyl Alba ; James Carthew ; Richard Carthew ; Madhav Mani; |
398 | Mechanical Feedback in Drosophila Embryonic Development Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We address this in the D. melanogaster embryo, combining in-toto imaging, (opto-)genetic perturbations, and quantitative modeling. |
Nikolas Claussen ; Matthew Lefebvre ; Hannah Gustavson ; Noah Mitchell ; Stefano De Renzis ; Boris Shraiman ; Sebastian Streichan; |
399 | Physical Mechanisms of Tissue Compartmentalization and Internalization in The Drosophila Embryo Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To study the role of myosin cables at the MEB, we simulated the internalization using a vertex model. |
Gonca Erdemci-Tandogan ; Jessica Yu ; Negar Balaghi ; Veronica Castle ; Rodrigo Fernandez-Gonzalez; |
400 | Symmetry Breaking in Tissue Flow During Early Drosophila Morphogenesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: With this combination of experimental and modeling approaches, we aim to systematically unravel how organized multicellular dynamics emerge from genetic, mechanical, and geometric "information" during morphogenesis. |
Emily Gehrels ; Bandan Chakrabortty ; Matthias Merkel ; Thomas Lecuit; |
401 | In Vivo Measurements of Embryonal Tissue Mechanics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We here study the process of dorsal closure (DC) in Drosophila melanogaster embryos. |
Behzad Golshaei ; Chonglin Guan ; An Pham ; Janice Crawford ; Daniel Kiehart ; Christoph Schmidt; |
402 | Multi-scale Mechanical Interactions Across Layers Drive Folding Morphogenesis in The Gut Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, leveraging the Drosophila midgut as a model system, we use light-sheet microscopy, genetics, computer vision, and tissue cartography to reconstruct in toto shape dynamics of a developing organ in vivo. |
Noah Mitchell ; Dillon Cislo ; Suraj Shankar ; Yuzheng Lin ; Boris Shraiman ; Sebastian Streichan; |
403 | Electrical Cues Regulate Hydrostatic Pressure and Swelling in Cysts and Organoids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we show that electrical cues can drive the swelling of homotypic epithelial cysts and intestinal organoids. |
Isaac Breinyn ; Gawoon Shim ; Daniel Cohen; |
404 | Docking of Fire Ant Rafts Using Pseudopods Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this experimental study, we observe how ant rafts identify potentially docking sites and extend multiple "planks" to simultaneously anchor the raft and release ants ashore. |
Hungtang Ko ; Keyana Komilian ; Leo Hollingworth ; Elliot Willner ; David Hu; |
405 | Machine Learning Drosophila Embryogenesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we show that deep neural networks can learn to map between the time-varying distribution of myosin motors and the cellular flows occurring in developing Drosophila embryos. |
Jonathan Colen ; Noah Mitchell ; Nikolas Claussen ; Marion Raich ; Sebastian Streichan ; Vincenzo Vitelli; |
406 | Sensing The Fly Embryo’s Transcription Factors Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: It may thus be possible to view the complex enhancer logic that "reads" the transcription factor concentrations as implementing a solution to an information theoretical optimization problem. |
Marianne Bauer ; Mariela Petkova ; Thomas Gregor ; Eric Wieschaus ; William Bialek; |
407 | A Spontaneous Strain Mediated Mechanical Model of The Drosophila Wing Disc Eversion Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have analyzed the spatial distribution of individual cell properties, such as apical area, and how these patterns change during eversion. |
Abhijeet Krishna ; Jana Fuhrmann ; Charlie Duclut ; Frank Jülicher ; Natalie Dye ; Carl Modes; |
408 | A Mechano-chemical Coupling Drives Fountain Streaming and Nuclear Positioning in Drosophila Embryos Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that a two-fluid model, considering a water-like incompressible phase (sol) and an active elasto-viscous actin network (gel), captures the experimentally observed sol flows and the uniform nuclei spreading by cell cycle seven independently of natural variations in the initial nuclei position. |
Claudio Hernandez Lopez ; Stefano Di Talia ; Alberto Puliafito; |
409 | Cellular Compartmentalisation and Receptor Promiscuity As A Strategy for Accuracy and Robustness in Positional Inference During Morphogenesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using multiple signalling mechanisms in development as motivation, we show how cells may utilise multiple tiers of processing (compartmentalisation) and parallel branches (multiple receptor types), together with feedback control, to bring about fidelity in morphogenetic decoding of their positions within a developing tissue. |
Krishnan Iyer ; Chaitra Prabhakara ; Madan Rao ; Satyajit Mayor; |
410 | Modeling Helical Shape Formation in Bacteria Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Motivated by recent experiments on H. pylori showing that cell wall synthesis is not uniform, we investigate the possible mechanism of helix formation induced by elastic heterogeneity. |
Luyi Qiu ; Cesar Pastrana ; Ulrich Gerland ; Shahaf Armon ; Ariel Amir; |
411 | Inferring The Stochastic Dynamics of Bacterial Growth and Shape Fluctuations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose a physical model that explains this phenomenon based on heterogeneous patterning of cell growth. |
Kurt Cylke ; Shiladitya Banerjee; |
412 | Conservative Interactions in Protein Evolution Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose that such conservative interactions is important for efficient protein production. |
Wouter Hoff; |
413 | On The Role of Multiple States in Allostery Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study this question by introducing and analyzing a simplified model of protein allostery under a diversity of physical and evolutionary constraints. |
Eric Rouviere ; Olivier Rivoire ; Rama Ranganathan; |
414 | Quantifying Protein Interactions in A Living Organism Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we demonstrate a pipeline to study such protein interactions in different tissues of live zebrafish larvae. |
Aniket Ravan ; Yann Chemla ; Martin Gruebele; |
415 | Many Sequence-diverse Protein Domains Switch Between Α-helix and Β-sheet Folds Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this question, we developed a sequence-based predictor, which suggested that thousands of proteins from this superfamily switch folds. |
Lauren Porter; |
416 | Preferential Exclusion and Hydration Dynamics in Compatible Osmolyte Solutions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Compatible osmolytes are a broad class of small organic molecules employed by living systems to combat environmental stress by enhancing native protein structure. The molecular … |
Christina Othon ; Nimesh Shukla ; Erika Taylor ; Brianna Bembenek; |
417 | Quantifying Tubulin Heterodimer Assembly in Vitro and Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present a new method to quantify protein-protein weak interactions in living cells. |
Yuhan Wang ; Mahima Unnikrishnan ; Brooke Ramsey ; Catherine Murphy ; Martin Gruebele; |
418 | Comparison of Α-conotoxin Free Energy Landscapes Via Simulation and Dimensionality Reduction Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We construct different low-dimensional models to compare their free energies and explore how we can transform between them with minimal additional simulation time. |
Ré Mansbach ; Natalya Watson; |
419 | A Superstatistical Variational Model for Categorical Data: Applications to Protein Sequence Variation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To that end, we present a variational data-driven model rooted in superstatistics that leverages the pre-existing information present in natural sequences for generative purposes; and thus can sample new protein sequences from the inferred latent space. |
Hoda Akl ; Purushottam Dixit ; Xiaochuan Zhao; |
420 | A Mechanochemical Protein Model Reveals The Principles of Molecular Discrimination Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a genetic-mechano-chemical model of evolving protein-ligand interactions which offers a mechanistic understanding of molecular discrimination: More difficult discrimination tasks require more collective and precise interplay of structure, forces and dynamics. |
John McBride ; Tsvi Tlusty ; Jean-Pierre Eckmann; |
421 | Modeling Sequence-space Exploration and Emergence of Epistatic Signals in Protein Evolution Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we build upon recent progress in reconstructing data-driven fitness landscapes for families of homologous proteins, to propose stochastic models of experimental protein evolution. |
Francesco Zamponi; |
422 | Microtubule Capture and En-Route Interactions in Retrograde Cargo Transport Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using a mix of analytical modeling, numeric simulations, and quantitative analysis of in vivo imaging data, we explore several aspects of retrograde cargo capture and delivery in narrow cellular projections such as fungal hyphae and neuronal axons. |
Elena Koslover; |
423 | Trafficking Mechanics of Inter-Synaptic Vesicle Exchange Support in Synaptic Transmission Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this presentation we will discuss evidence that the structure of the actin presynaptic cytoskeleton, through the ARP2/3 branching complex, is important for vesicle capture. |
Mason Parkes ; Michael Gramlich; |
424 | Distinguishing Neurotransmitter Carrying Pause Mechanics During Axonal Trafficking Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We distinguish vesicles undergoing axonal transport, and use a computational approach to characterize motor-driven motion from pausing. |
Mason Parkes ; Nathan Landers ; Michael Gramlich; |
425 | Modeling Intra-cellular Insulin Transport Dynamics in Pancreatic Beta Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will discuss the role of cytoskeletal-mediated transport (by microtubules) in regulating insulin dynamics in pancreatic cells. |
William Holmes; |
426 | Intracellular Cargo Transport Time Statistics That Result from Competing Transport Mechanisms Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We consider intracellular transport of cargo when molecular motor-driven transport along microtubules is directed towards the target in the interior of the cell. |
Oleg Kogan ; Ajay Gopinathan ; Niranjan Sarpangala; |
427 | Optimal Cytoskeletal Filament Dynamics for Intracellular Transport Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we study the transport of cargo carried by myosin motors on a dynamic actin network. |
Ajay Gopinathan ; Imtiaz Ali; |
428 | A Slowing of Neurofilament Transport and An Increase in Neurofilament Influx Both Contribute to The Radial Growth of Axons During Development Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To explore the relative contribution of these two mechanisms, we developed a computational model that simulates NF transport and axon growth. |
Rawan Nowier ; Anthony Brown ; Peter Jung; |
429 | Molecular Quakes and Neurofilament Movement Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we show that this can be explained by the stochastic and reversible association of NF sidearms with neighboring NFs. |
Sijan Regmi ; Peter Jung ; Anthony Brown; |
430 | Mitochondrial Distribution in Neurons: Interplay of Transport and Morphology Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using mathematical modeling, we show that specific scaling laws for dendritic branching patterns enable robust self-organization of the mitochondrial population for a range of transport behaviors, to maintain equitable distribution across subtrees while still allowing for increased densities at distal tips. |
Anamika Agrawal ; Eavan Donovan ; Nicole Liberman ; Erin Barnhart ; Elena Koslover; |
431 | Image-based Model of Diffusion on The Endoplasmic Reticulum Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We use a coarse-grained model of random walks on networks to efficiently simulate the diffusion of biomolecules along the endoplasmic reticulum (ER). |
Thomas Fai ; Ying Zhang ; Lachlan Elam; |
432 | Protein Dispersion and Facilitated Diffusion in The Endoplasmic Reticulum Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We describe a new model for cargo loading and sorting at ER exit sites, relying on `facilitated diffusion’ of secretory cargo to a region of weak binding surrounding a narrow exit site neck. |
Zubenelgenubi Scott ; Laura Westrate ; Elena Koslover; |
433 | Long Lived Protein Demixing in Flagella Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I describe a simple physical model of combined directed transport and diffusion that leads to diffusional uncoupling of the flagellar tip from the cell body over time scales that are exponential in the length of the flagellum. |
Arnab Datta; |
434 | Large Deformations in The Cytoplasm and Cytoskeleton Plasticity Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will describe the physics of large cytoplasm deformations. |
Sijie Sun ; David Weitz; |
435 | DBIO Business Meeting & Town Hall Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: DBIO Business Meeting & Town Hall Tuesday, March 15, 2022 6:15 PM-9:00 PM … |
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436 | Collective Sensing in The Slime Mold Physarum Polycephalum Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that, indeed, the ability to detect and follow the environmental gradient improves with the size of the slime mold. |
Albert Kao ; Andrew Berdahl; |
437 | Competition for Fluctuating Resources Reproduces Statistics of Species Abundance Over Time Across Wide-ranging Microbiotas Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work unifies numerous time series patterns under one model, clarifies their origins, and provides a framework to infer parameters of effective resource competition from longitudinal studies of microbial communities. |
Kerwyn Huang; |
438 | Weight Distribution in Honey Bee Swarms Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that the structure of the swarm is non-homogeneous. |
Olga Shishkov ; Claudia Chen ; Claire Madonna ; Alexander Lawson ; Kaushik Jayaram ; Orit Peleg; |
439 | Coordination Without Communication in Fire-Ant Excavation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To understand such scaling and motivate how such rate modulation emerges without global control avoiding deleterious traffic clogs, we use a cellular automata model with multiple tunnels. |
Ram Avinery ; Kehinde Aina ; Carl Dyson ; Hui-Shun Kuan ; Meredith Betterton ; Michael Goodisman ; Daniel Goldman; |
440 | A Deep Learning Approach to Quantify Aggression Between Competing Ant Colonies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we assembled a deep learning pipeline to track posture sequences of individual ants and infer their behavioral ‘states’ through high-resolution video. |
Kevin Do ; Amisha Jain ; Robert Riehn; |
441 | Inferring Collective Dynamics in Groups of Social Mice Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will address this question in social mice, where we infer statistical physics models for the collective dynamics for groups of 15 mice, housed and location-tracked over multiple days in a controlled environment (the Eco-HAB [Puścian et al. 2016]). |
Xiaowen Chen ; Maciej Winiarski ; Alicja Puścian ; Ewelina Knapska ; Thierry Mora ; Aleksandra Walczak; |
442 | Signatures of Irreversibility in Microscopic Models of Flocking Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigate how the interplay of alignment interaction and self-propulsion in Vicsek-like dynamics leads to the breakdown of detailed balance and constrains asymmetries in the steady-state distribution of the many-body system. |
Federica Ferretti ; Caroline Holmes ; Jordan Shivers ; Simon Grosse-Holz ; Irene Giardina ; Aleksandra Walczak ; Thierry Mora; |
443 | Synchronization Dynamics of Firefly-LED Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using controlled density experiments where small groups of fireflies are exposed to rhythmic, controlled LED flashes in dark tents, we examine the range of artificial flash frequencies that produce aligned phase responses from the fireflies. |
Owen Martin ; Orit Peleg ; Raphael Sarfati ; Julie Hayes; |
444 | The Exploitative Segregation of Plant Roots: A Game-theoretical Framework for Belowground Plant Interactions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The exploitative segregation of plant roots: a game-theoretical framework for belowground plant interactions. |
Ricardo Martinez Garcia ; Ciro Cabal ; Aurora de Castro ; Fernando Valladares ; Stephen Pacala ; Gabriel Andreguetto Maciel; |
445 | Identifying Interaction Epochs in Social Behavior: Contest Phases in Pairwise Zebrafish Fights Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present our work in identifying these phases in adult zebrafish fights on multiple timescales. |
Liam O’Shaughnessy ; Tatsuo Izawa ; Joshua Shaevitz ; Greg Stephens; |
446 | Empirical Social Triad Statistics Can Be Explained with Dyadic Homophylic Interactions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we attempt to explain this phenomenon by a different approach where agents do not know information about triangles in the update of their relations and opinions. |
TUAN PHAM ; Jan Korbel ; Rudolf Hanel ; Stefan Thurner; |
447 | SubCellular Model to Study Bacterial – Fungal Interaction Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we focus on interactions between P.flourescens and the fungi L.bicolor. |
Alireza Ramezani ; Jolene Britton ; Francesco Pancaldi ; Kevin Tsai ; Dale Pelletier ; Mark Alber ; William Cannon; |
448 | Using Molecular Simulation to Interpret Weak Cryo-EM Density for The Spike Protein Post-fusion Complex Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we use our cryo_fit method to produce structural ensembles of the spike protein complex, including the fusion peptide, highly consistent with the strong and weak density observed experimentally. |
Karissa Sanbonmatsu ; Chang-Shung Tung; |
449 | Sterically Confined Rearrangements of SARS-CoV-2 Spike Protein Control Cell Invasion Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To provide an initial mechanistic description of the pre-to-post rearrangement, an all-atom model with simplified energetics was used to perform thousands of simulations in which the protein transitions between the prefusion and postfusion conformations. |
Esteban Dodero Rojas; |
450 | Helium-ion Microscopy Reveals An Intra-cytoplasmic Route for SARS-CoV-2 Cell-cell Transmission Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We used scanning Helium-ion microscopy to study the virion propagation process in in-vitro culture of Vero E6 cells infected with mNeonGreen-SARS-CoV-2. |
Antonio Merolli ; Leila Kasaei ; Santhamani Ramasamy ; Afsal Kolloli ; Ranjeet Kumar ; Selvakumar Subbian ; Leonard Feldman; |
451 | Extracellular Vimentin As A Target Against SARS-CoV-2 Host Cell Invasion Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present results indicating that extracellular vimentin may serves as an important binding partner for the SARS-CoV-2 spike protein by showing that antibodies against vimentin reduced SARS-CoV-2 pseudoviral infection of ACE2-expressing cells. |
Maxx Swoger ; Łukasz Suprewicz ; Sarthak Gupta ; Danielle Germann ; Paul Janmey ; J. Schwarz ; Robert Bucki ; Alison Patteson; |
452 | Binding Mechanism of SARS-CoV(-2) Into HACE2 Receptor Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, three important binding regions between SARS-CoV(-2) and hACE2 have been detected. |
Narayan Adhikari ; Bidhya Thapa ; Rajendra Koirala ; Shyam Khanal ; Jhulan Powrel ; Lokendra Dhami ; Lalit Dhami; |
453 | Modeling Within-host SARS-CoV-2 Dynamics and The Relationship Between Viral Load and A Person’s Infectiousness Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The models we studied compared the roles of target-cell limitation versus the roles of the innate and the adaptive immune response as well as the role of spatial infection in the LRT. |
Alan Perelson; |
454 | Effect of Diurnal Temperature Range on SARS-CoV-2 Lifetime Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This study provides a framework, based on the rate law and Arrhenius equation, for modeling virus lifetime in an environment with a time-varying temperature profile. |
Te Faye Yap ; Colter Decker ; Daniel Preston; |
455 | A Model Based on Mobility Data Explains Localization-delocalization Properties in The Spread of Diseases Among Communities Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigate the modes of propagation of an epidemic across a network of communities. |
Guillaume Le Treut; |
456 | Inferring The Effects of Mutations on SARS-CoV-2 Transmission from Genomic Surveillance Data Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we describe a Bayesian inference method to infer the effects of mutations on viral transmission. |
John Barton ; Brian Lee ; Syed Ahmed ; Elizabeth Finney ; Ahmed Quadeer ; Muhammad Sohail ; Matthew McKay; |
457 | Back Projection Methods for The Refinement of SARS-Cov-2 Sequence Data Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this issue, we apply an adapted back projection to our time series data. |
Elizabeth Finney ; John Barton ; Brian Lee ; Syed Faraz Ahmed ; Ahmed Abdul Quadeer ; Muhammad Saqib Sohail ; Matthew McKay; |
458 | Critical Behavior of The Diffusive Susceptible-infected-recovered Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: By performing numerical simulations on a square lattice, we show that diffusion for all agents in the susceptible-infected-recovered model constitutes a singular perturbation, which induces asymptotically novel dynamical and stationary critical behavior distinct from the non-diffusive model. |
Shengfeng Deng ; Geza Odor; |
459 | A New Evolutionary Perspective on Drug(g)ability Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this seminar, I unpack this ambiguity, and introduce new metrics that quantify the likelihood that (i) a given drug is effective across alleles, and that (ii) alleles are treatable by a panel of drugs. |
Brandon Ogbunu; |
460 | Stability Criteria for The Consumption and Exchange of Essential Resources Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we model an arbitrarily large system of consumers governed by Liebig’s law, where species require and deplete multiple resources, but each consumer’s growth rate is only limited by a single one of these multiple resources. |
Theo Gibbs ; Yifan Zhang ; Zachary Miller ; James O’Dwyer; |
461 | High-dimensional Characterization of Phototroph-heterotroph Interactions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work presents a new view of how the chemical environment impacts phototroph-heterotroph interactions. |
Chandana Gopalakrishnappa ; Zeqian Li ; Seppe Kuehn; |
462 | Genomic Structure Predicts Metabolite Dynamics in Microbial Communities Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. |
Karna Gowda ; Derek Ping ; Madhav Mani ; Seppe Kuehn; |
463 | Unique Functional Structure of The Yellowstone Hot Spring Microbial Mats Revealed By Multi-omics Studies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using a multi-omics dataset, including metagenomic data of samples across various environmental parameters, metatranscriptomic data of full diel cycles, and single-cell sequencing data, we extensively studied the mats’ community composition, genomic structure, and metabolic activities. |
Zeqian Li ; Amanda Shelton ; Frederick De St Pierre Bunbury ; Arthur Grossman ; Devaki Bhaya ; Feiqiao Yu ; Seppe Kuehn; |
464 | Constrained Proteome Allocation Affects Coexistence in Models of Competitive Microbial Communities Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we reconsider one of the theoretical frameworks most commonly used to model population dynamics in competitive ecosystems, MacArthur’s consumer-resource model, in light of experimental evidence showing how proteome allocation affects microbial growth. |
Leonardo Pacciani-Mori; |
465 | Alternative Sources of Information for Adaptation to Varying Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we demonstrate a different type of strategy that utilizes an internal source of information to improve performance. |
BingKan Xue ; Leo Law; |
466 | Nutrient Availability Controls Coupling Between Algae and Bacteria Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our study shows that when the frequency of externally supplied nutrients is low, phototrophs control bacterial community assembly, but when nutrients are supplied frequently, bacterial community assembly is decoupled from the phototroph. |
Kaumudi Prabhakara ; Derek Ping ; Seppe Kuehn; |
467 | Environment Complexity and Nativeness Control The Level of Coarse-graining at Which Community Assembly Is Reproducible Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address such questions, we built a theoretical framework where a microscopic "ground truth" based on consumer-resource dynamics can be systematically compared to a hierarchy of coarse-grained descriptions. |
Mikhail Tikhonov ; Jacob Moran ; Ryan McGee; |
468 | How Bet-hedging Species Survive Competition in Fluctuating Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that, when both environmental and demographic fluctuations are considered, there are three contributions to the extinction risk. |
XIAO ZHOU ; BingKan Xue; |
469 | Ecological Diversification of Rapidly Adapting Populations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this gap, we study the dynamics of a simple class of consumer resource models in which individuals acquire mutations that alter their resource uptake rates. |
Daniel Wong ; Benjamin Good; |
470 | How Does Ecological Diversity Develop Against Competitive Exclusion? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we use a mechanistic model that observes metabolic constraints, and bridge the regimes for essential and alternative resources. |
Ga Ching Lui ; Sidhartha Goyal; |
471 | Phenotypic Heterogeneity Facilitates Survival While Hindering The Evolution of Drug Resistance Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We develop deterministic and stochastic population models that incorporate resource competition to quantitatively investigate the transition from non-genetic to genetic resistance during the exposure to static and cidal drugs. |
Joshua Guthrie ; Daniel Charlebois; |
472 | Using Core Packing to Assess The Quality of NMR Structures Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this question, we have analyzed all NMR structures deposited in the Protein DataBank (PDB) that contain the restraints used to generate NMR model structures. |
Alex Grigas ; Lynne Regan ; Corey O’Hern; |
473 | Proteins – A Celebration of Consilience Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present an interdisciplinary framework that aims to marry ideas from Plato and Darwin and demonstrates an astonishing consilience between disciplines in describing proteins. |
Tatjana Skrbic ; Trinh Hoang ; Achille Giacometti ; Amos Maritan ; Jayanth Banavar; |
474 | Impact of Water-Protein Interactions on Protein Dynamics(Nguyen Q. Vinh, Department of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061) Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In response, we have employed a broad-band megahertz to terahertz spectroscopy with ultrahigh precision, assisted by molecular dynamics simulations, to investigate the dynamics of water molecules within hydration shells of proteins as well as the collective vibrational motions of hydrated proteins, which are vital to protein conformation and functionality. |
Vinh Nguyen; |
475 | Atomistic and Coarse-grained Molecular Dynamics Study of Peptide-lipid Membrane Dissociation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To this end, the PMFs of three Wimley-White pentapeptides (Ac-WLXLL, with guest residues X=R,I and L) interacting with two different lipid bilayers (zwitterionic POPC and charged POPG) are calculated using the umbrella sampling method. |
Ryan Smith ; Ioan Kosztin; |
476 | Photo-Switching in Crystalline OCP Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we report the conditions to achieve crystal phase photoswitching. |
Robert Thompson ; Andrea Markelz ; Timothy Lafave ; Deepu George ; Jeffrey Mckinney; |
477 | Structural Dynamics of Prefusion Spike Protein of SARS-CoV-2 and Its Variants: Insights from Molecular Dynamics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This study provides insight into the dynamic behavior of the spike protein of different SARS-CoV-2 variants, which is key to identifying targets for the development of novel vaccines and therapeutic agents. |
Mortaza Derakhshani Molayousefi ; Ugochi Isu ; Mahmoud Moradi; |
478 | Temperature Sensitive Contact Analysis Directs Hyperactive Enzyme Design Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In order to reveal the residue level interactions encoding enzymatic activities, we employed Hamiltonian Replica Exchange Molecular Dynamics (HREMD) to sample the conformational ensemble across temperature of the disordered catalytic loops of these 4 EIC homologs. |
Dan Burns; |
479 | Characterizing Hydration Dynamics and Collective Motions of Hemoglobin in Aqueous Solutions Using High Sensitivity Dielectric Spectroscopy Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Hemoglobin, the dominant component of mammals’ red blood cells, is the oxygen and carbon-dioxide transport protein. Hemoglobin physically performs its function by changing the … |
Huong Hoang ; Vinh Nguyen; |
480 | Assignment of Protein Collective Structural Vibrations Steering Conformational Change Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present strategies to assign the spectrally observed bands with structural displacements based on normal mode ensemble analysis (NMEA). |
Xing Liu ; Andrea Markelz; |
481 | Quality Assessment of Computational Models of Protein-protein Interfaces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we describe novel methods to determine whether computational models of protein-protein interfaces are experimentally accurate or not. |
Grace Meng ; Alex Grigas ; Lynne Regan ; Corey O’Hern; |
482 | Monte Carlo Simulations Reveal Limitations of The Single-reaction-coordinate Picture Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We consider a slightly more realistic situation in which elements of the chain backbone move in the continuum and are subject to nearest-neighbor bond-bending costs and to long-range interactions that account for excluded volume effects, hydrophobic attraction, and electrostatics. |
Sudeep Adhikari ; Kevin Beach; |
483 | Non-ergodic Internal Dynamics of A Globular Protein Observed Over Fourteen Orders in Time Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Analysis of MD trajectories reveals that observed heterogeneity derives from the high-dimensional complex energy landscape. |
Liang Hong ; Jun Li; |
484 | Locomotion of Flagellated Bacteria: From The Swimming of Single Bacteria to The Collective Motion of Bacterial Swarm Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Together, our study sheds light onto the puzzling motile behaviors of bacteria in complex fluids and provides new insights into the collective swimming of bacterial suspensions relevant to a wide range of microbiological and biomedical processes. |
Xiang Cheng; |
485 | Formation of Active Two-Dimensional Fluids By Multicellular Magnetotactic Bacteria Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We characterize a new phase of active matter composed of Multicellular Magnetotactic Bacteria (MMB). |
Alexander Petroff ; Pradeep Kumar ; Benjamin Roque ; Alejandra Rosselli-Calderon; |
486 | Continuum Kinetic Modeling of Active Turbulence Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we discuss active turbulence in a continuum kinetic model of a suspension of extensile particles — an example of an active nematic fluid. |
Scott Weady ; Michael O’Brien ; Blakesley Burkhart ; Michael Shelley; |
487 | Statistical Topology of Streamlines in A Time-invariant 2D Flow Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To investigate this question, we introduce a framework for studying ensembles of two-dimensional time-invariant flow fields. |
Boris Veytsman ; Mason Kamb ; Janie Byrum ; Greg Huber ; Guillaume Le Treut ; Shalin Mehta ; David Yllanes; |
488 | Cilia Coordination Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, I will analyze cilia coordination in in-silico experiments and theoretical models reflecting two extremes of pairs and infinite numbers cilia. |
Eva Kanso; |
489 | Cilia Metasurfaces for Electronically Programmable Surface-driven Microfluidic Manipulation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We report here active metasurfaces of electronically-actuated artificial cilia that can create arbitrary flow patterns in liquids near a surface. |
Wei Wang ; Qingkun Liu ; Ivan Tanasijevic ; Michael Reynolds ; Alejandro Cortese ; Marc Miskin ; Alyosha Molnar ; Eric Lauga ; Paul McEuen ; Itai Cohen; |
490 | Self-similar Clustering of Beads in A Bacterial Suspension Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We explore this coarsening dynamics by varying the radius and surface fraction of the beads and the bacterial concentration. |
Julien Bouvard ; Harold Auradou ; Frederic Moisy; |
491 | Resistive Force Theory and Wave Dynamics in Swimming Flagellar Apparatus Isolated from C. Reinhardtii Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we use freely swimming intact flagellar apparatus isolated from a wall-less strain of Chlamydomonas to investigate wave dynamics. |
Azam Gholami ; Albert Bae ; Samira Goli Pozveh; |
492 | Metachronal Coordination in The Larvae of The Coral Acropora Millepora Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present the first detailed biophysical study of motility in the multiciliated larvae of the common reef coral A. millepora. |
Rebecca Poon ; Hannah Laeverenz Schlogelhofer ; Emelie Brodrick ; Jamie Craggs ; Gaspar Jekely ; Kirsty Wan; |
493 | Ciliary Chemosensitivity Is Enhanced By Cilium Geometry and Motility Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigate whether locating chemoreceptors on cilia provides sensitivity advantages and whether motile sensory cilia have further advantages. |
David Hickey ; Andrej Vilfan ; Ramin Golestanian; |
494 | Local Metachronal Synchronization in Cilia Carpets Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Beyond a characteristic noise strength, we observe an abrupt loss of global synchronization even in finite systems, characterized by local synchronized patches. |
Benjamin Friedrich ; Anton Solovev; |
495 | Rate-Dependent Damage and Fracture of Dynamic Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This presentation will discuss a theoretical framework, a.k.a., the transient network theory (TNT) that provides a useful tool to track the chain conformation space of a dynamic polymer network. |
Franck Vernerey; |
496 | Energy Dissipation After Chain Scission in Polymer Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will describe our simulations attempting to uncover how the energy dissipated depends on the polymer strand length, the network volume fraction, and defect concentration in the network. |
Han Zhang ; Ziyu Ye ; Robert Riggleman; |
497 | Fracture Mechanics of Polymers: Plastics and Elastomers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this presentation we examine a unifying framework for fracture of polymers. |
Shi-Qing Wang ; Travis Smith ; Chaitanya Ramanand Gupta ; Zehao Fan; |
498 | Mechanical Effects of Topological Entanglement and Knotting of Linear Chains in A Melt Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We use tools from topology, the Gauss linking integral and the Jones polynomial, to measure entanglement in polymer melts of linear chains using computer simulations. |
Eleni Panagiotou; |
499 | Understanding Elasticity of Polydisperse Polymer Networks By A Stochastic Method Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Classical theory, like affine and phantom models, is well established and has enjoyed great success, with an assumption that the network comprises only of monodisperse polymer chains. |
Weikang Xian ; Amitesh Maiti ; Andrew Saab ; Ying Li; |
500 | Engineering The Toughness of Silicone Elastomers: Theory and Experiments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work uses a combination of simulations and experiments to enable the design of silicone elastomers with improved fracture properties compared with existing commercial elastomers. |
Akash Arora ; Rocky Zhu ; Jon Degroot ; Eric Joffre ; Zachary Kean ; Steven Arturo; |
501 | Fracture, Fatigue, and Friction of Polymers in Which Entanglements Greatly Outnumber Cross-links Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We demonstrate that such polymers resolve a long-standing conflict: crosslinks stiffen polymers but embrittle them. |
Junsoo Kim ; Guogao Zhang ; Meixuanzi Shi ; Zhigang Suo; |
502 | Controlling Topology and Mechanical Properties of Polymer Networks Through Kinetics of Gelation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We gelled model poly(ethyl glycidyl ether) networks with two organoaluminum-based catalysts, and investigated the relationship between rate of gelation, network architecture, and mechanical properties. |
Aaliyah Dookhith ; Nathaniel Lynd ; Costantino Creton ; Gabriel Sanoja; |
503 | Effects of Crosslink Homogeneity on The High Strain Behavior of Elastic Polymer Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we address this problem using a double network approach, in which the network of interest is swollen in a mixture of monomer and cross linkers that is then polymerized to generate a secondary network that helps dissipate stress, delay fracture, and "lock" the first network in a higher strain state. |
Victoria Kong ; Thomas Staunton ; Jennifer Laaser; |
504 | A Molecular-Level Theory for Predicting Rheological Behavior of Dynamically Associating Polymer Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To that end, we present a new theory that incorporates experimentally controllable molecular-level parameters (concentration, chain length, unbinding rate) to fully capture the rheological behavior of physically associating gels. |
Pamela Cai ; Andrew Spakowitz ; Sarah Heilshorn ; Matthew Webber ; Brad Krajina; |
505 | Controlling Network Relaxation and Modulus with Dynamic Covalent Chemistry and Salt Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Polymer networks with dynamic bonds are a promising route to sustainable materials, but many questions remain about the relationships between molecular structure and dynamics or … |
Christopher Evans ; Brian Jing ; Seongon Jang; |
506 | Dynamic Covalent Polymer Networks Under Supersonic Micro-Projectile Impact Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Dynamic bonding brings new features to polymeric materials, including new modes of energy dissipation and self-healing under quasi-static deformation. The behavior of dynamically … |
Zhen Sang ; Qing Zhou ; Wenpeng Shan ; Hongkyu Eoh ; Jinho Hyon ; Frank Gardea ; Svetlana Sukhishvili ; Edwin Thomas; |
507 | Inferring Long Timescale Dynamics in Animal Behavior Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we take a different approach, fitting dynamical models to long behavioral sequences from fruit flies and rodents. |
Gordon Berman; |
508 | Sensorimotor Transformations Underlying Spider Web-making Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present an assay and algorithms for real-time tracking of limb movements and web structure produced by the orb-weaver Uloborus diversus. |
Abel Corver ; Andrew Gordus; |
509 | Characterizing Social Impairments in Rat Models of ASD Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We extend a recently developed technique for 3D kinematic tracking of single animals (DANNCE) to capture the 3D poses of freely interacting animals by tracking animal identity and refining keypoint labeling networks to maintain accuracy during touching and occlusion. |
Ugne Klibaite ; Jesse Marshall ; Timothy Dunn ; Diego Aldarondo ; Bence Olveczky; |
510 | Hierarchical Timescales of Free Behavior Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we use a Recurrent Neural Network (RNN) based modeling approach to create representations of animal behavior at multiple timescales. |
Kanishk Jain ; Tomaso Muzzu ; Elena Menichini ; Jakob Macke ; Aman Saleem ; Gordon Berman; |
511 | Long Timescale Structure in Drosophila Behavior Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find rich features across timescales and present details of the dynamics of behavior across the lifespan of a fly. |
Scott Wolf ; Grace McKenzie-Smith ; Joshua Shaevitz; |
512 | Why Do Octopuses Camouflage When Asleep? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To that end, we study octopus camouflage behavior. |
Leenoy Meshulam ; Aditi Pophale ; Kazumichi Shimizu ; Sam Reiter; |
513 | Decoding Locomotion from Population Neural Activity in Moving C. Elegans Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We report that population activity more accurately decodes locomotion than any single neuron. |
Kelsey Hallinen ; Xinwei Yu ; Ross Dempsey ; Monika Scholz ; Ashley Linder ; Francesco Randi ; Anuj Sharma ; Joshua Shaevitz ; Andrew Leifer; |
514 | Monitoring Odor Landscape to Study Learned Olfactory Navigation in C. Elegans Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we investigate butanone-odor associative learning using an odor chamber to precisely measure the odor concentration experienced by worms during odor-guided navigation. |
Kevin Chen ; Rui Wu ; Marc Gershow ; Andrew Leifer; |
515 | Hunting, Scavenging, and Kleptoparasitism: A Fitness-maximising Approach to Predicting Predator Foraging Strategy Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we use an energetics-based computational model to investigate how a focal predator’s interactions with potential prey and other predators constrain the use of these strategies. |
Ritwika Vallomparambath PanikkasserySu ; Ajay Gopinathan ; Justin D. Yeakel; |
516 | Synchronized Locomotion Improves Spatial Accessibility in Ant Colonies and in Oscillating Active Particles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: By using a combination of multiple image analysis techniques, we show that inactive ants act as immobile obstacles to moving ants and that, compared with asynchronous movement, synchronized activity reduces the likelihood that active ants will encounter clusters of inactive ants that impede access to regions of the nest. |
Grant Doering ; Carmen Lee ; Kari Dalnoki-Veress; |
517 | Ant Cooperative Transport of Large Flexible Objects Under Constraint Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Therefore, we question the validity of the existing model for the case of a large soft object and study how ants still manage efficient transport despite limited communication. |
Atanu Chatterjee ; Hillel Aharoni ; ofer feinerman; |
518 | Decoding The Specificity of The T Cell Repertoire: From Random Energy Models to Coarse-grained Structure-based Prediction Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Motivated by a statistical random energy model of TCR-antigen interactions, we describe the development of a structure-based, supervised machine learning model to resolve relevant TCR-antigen pairs from large immune repertoires and putative antigen lists. |
Jason George; |
519 | Probing T Cell Thymic Maturation Through Repertoire Sequencing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: From high-throughput sequencing of different repertoires FACS-sorted in the thymus provided, we use inference techniques to learn interpretable models for the selected features informative about the maturation cascade. |
Francesco Camaglia ; Erez Greenstein ; Benjamin Chain ; Nir Friedman ; Aleksandra Walczak ; Thierry Mora; |
520 | Quantifying Shapes and Dynamics of Migrating T Cells in 3D Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using multi-scale wavelet analysis we show that these form a continuum, albeit with some frequently repeated (‘stereotyped’) motifs. |
Henry Cavanagh ; Robert Endres ; Maté Biro ; Daryan Kempe; |
521 | Cytotoxic T Lymphocyte Activation Signals Modulate Cytoskeletal Dynamics and Mechanical Force Generation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We hypothesized that IL-12 modulates cytoskeletal dynamics at the IS, thus potentiating CTL function. |
Aashli Pathni ; Altug Ozcelikkale ; Ivan Rey-Suarez ; Lei Li ; Scott Davis ; Nate Rogers ; Zhengguo Xiao ; Arpita Upadhyaya; |
522 | Modeling The Proinflammatory Microenvironment and Immune Response Dynamics During Infection Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Focusing on these key PME cytokines, which are found to modulate the in vivo response to Ft, we developed in silico and in vitro models to investigate the role of PME in macrophage activation and outcome of infection. |
Elebeoba May; |
523 | The Lifecycle of A B Cell Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce a stochastic telegraph process to model the B-cell lifecycle by capturing the entry and exit of B cells from GCs and constraining the accumulation of mutations to the GC residents only. |
Zachary Montague ; Armita Nourmohammad; |
524 | How Slow Delivery Antigen Modulates Immunodominance Upon Immunization for Difficult Pathogens Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We developed a computational model to study the competition of B cells targeting two different epitopes on the same antigen, with immunodominance hierarchy imposed by the differences in naive B cell precursor frequency and affinity. |
Leerang Yang ; Arup Chakraborty; |
525 | Immune Cells Use Active Tugging Forces to Rank Affinity and Accelerate Evolution Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we study the stochastic process of antigen extraction using theory and simulations. |
Hongda Jiang ; Shenshen Wang; |
526 | Immune Training By Evolving Antigens Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will present a framework for identifying key determinants of the mode and fate of viral-immune coevolution, by linking molecular recognition and eco-evolutionary dynamics. |
Shenshen Wang ; Jiming Sheng; |
527 | Search and Localization Dynamics of The CRISPR-Cas9 System Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce a model of facilitated diffusion for Cas9 and fit its parameters to single-molecule experiments. |
Qiao Lu ; Simone Pigolotti ; Deepak Bhat ; Darya Stepanenko; |
528 | Microrheology of Pseudomonas Aeruginosa Biofilms Grown in Wound Beds Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To understand collagen interactions with biofilms, we study biofilms grown from a range of mutant strains of PAO1 P. aeruginosa that lack polysaccharide components of extra polymeric substance. |
Gordon Christopher ; Vernita Gordon ; Kendra Rumbaugh ; Minhaz Rahman ; Liyun Wang ; Derek Fleming; |
529 | How Surface Fluidity Impacts The Mechanics of Biofilm Adhesion Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We will present results on the dependence of biofilm formation versus the brush height ranging from 500 nm to 10 μm. |
Katherine Powell ; Jessica Faubel ; Robert Edmiston ; Ellen Park ; Jennifer Curtis; |
530 | Bayesian Estimation of Pseudomonas Aeruginosa Viscoelastic Properties Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: For this purpose, we developed a mathematical model to study the rheological behavior of components of three biofilms: P. aeruginosa PAO1, isogenic PAO1ΔwspF, and their mucoid variant PAO1mucA22. |
Mohammad Nooranidoost ; NG Cogan ; M. Yousuff Hussaini; |
531 | Microgels from Food Waste As A Tool to Understand Microbe Interactions with Hierarchical Fiber Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work focuses on demystifying the structure-function relationships of indigestible fibrous biomaterials and the effects of structural hierarchy on toxin binding and microbial interactions. |
Symone Alexander; |
532 | Live Imaging Reveals Connections Between Aggregation and Competition Among A Pair of Gut Bacterial Species Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We focus on the role of physical factors such as spatial structure on inter-species competition, examining a pair of bacterial species native to the zebrafish gut, namely Aeromonas (AE) and Enterobacter (EN), that both form dense aggregates with similar spatial distributions in the intestine. |
Deepika Sundarraman ; Jarrod Smith ; Jade Kast ; Karen Guillemin ; Raghuveer Parthasarathy; |
533 | Role of Surface Interactions in Bacterial Biofilms Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we use interferometry to look at the three-dimensional surface morphology of biofilms and investigate the effect of different surface friction and adhesive forces. |
Aawaz Pokhrel ; Gabi Steinbach ; Siu Lung Ng ; Peter Yunker; |
534 | Rheology of The Environment Regulates Bacterial Growth Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work thus reveals a new mechanism, beyond mechanosensing, by which mechanics modulates microbial behavior. |
Anna Hancock ; Sujit Datta; |
535 | Self-organized Canals Enable Long Range Directed Material Transport in A Biofilm Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we discover that a large-scale and temporally evolving channel system spontaneously develops in the bacterial colony. |
Shiqi LIU ; Ye Li ; Yingdan Zhang ; Zi Jing SENG ; Haoran Xu ; Liang Yang ; Yilin Wu; |
536 | Global Conformational Changes and Their Allosteric Control By Ubiquitin Regulate Protein Degradation of The 26S Proteasome Molecular Machine Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We found that ubiquitin binding to an allosteric trigger affects the proteasome switching between engagement-competent and processing-competent states, and accelerates motor engagement of the substrate for faster, more efficient degradation. |
Andreas Martin ; Zaw Htet ; Erik Jonsson ; Erika Lopez-Alfonzo ; Ken Dong ; Jared Bard; |
537 | Asymmetric Conformational Dynamics of The ClpB Disaggregase Nanomachine Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We performed molecular dynamics simulations of the ClpB disaggregation machine, a AAA+ motor with a double ring hexameric structure that contains two nucleotide binding domains per protomer. |
Ashan Dayananda ; Ruxandra Dima ; George Stan; |
538 | A General Bayesian Framework for Learning Molecular Kinetics From Single Photon Arrivals Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a new unifying Bayesian framework for analyzing conformational dynamics of molecules from single photon traces generated by multi-color Forster Resonance Energy Transfer (FRET) setups under continuous and pulsed illumination. |
Ayush Saurabh ; Steve Presse ; Ioannis Sgouralis; |
539 | Ambigrammatic Viruses Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I shall discuss some observations on the structure of the genetic code which explain how this ‘ambigrammatic’ property can evolve, and which can distinguish different explanations of why it offers a reproductive advantage. |
Michael Wilkinson; |
540 | Impact of The Localization of The RNA Binding Domain of Protein Shells on The Stability of Virus Particles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we investigate by means of computer simulations and scaling theory the impact of spatial localization of the RNA binding domains on the stability of viral shells. |
Mohammadamin Safdari ; Yinan Dong ; Paul Van der Schoot ; Roya Zandi; |
541 | Ionic Propulsion in A Non-motile Dinoflagellate Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using high-resolution vertical tracking microscopy along with molecular perturbations we describe a coordinated order of magnitude volume increase that takes place in under 15 minutes to rapidly decrease sedimentation speed after cell division. |
Adam Larson; |
542 | Quantitative in Vivo Measurement of Fork Velocity By Deep Sequencing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we demonstrate a novel approach to measuring the locus-dependent in vivo replication fork velocity by deep sequencing and test a number of mechanisms for replication slowdown, including transcription-replication conflicts. |
Dean Huang ; Paul Wiggins; |
543 | Accessibility Patterns and Folding Frustration in Long Telomeric Overhangs Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present single molecule experimental and computational modeling studies investigating accessibility and folding landscape of human telomeric overhangs that contain 4-28 repeats of GGGTTA (G-Tract) sequence. |
Hamza Balci ; sajad shiekh ; Golam Mustafa ; Eric Yokie ; Mohammed Hoque ; John Portman; |
544 | Insertions and Deletions Affect RNA-protein Interactions Through RNA Secondary Structure Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we show that insertions and deletions in an RNA have an even stronger effect on protein-RNA interactions in their vicinity and that this effect grows with the length of the insertion or deletion. |
Ralf Bundschuh ; Carlos Owusu Ansah; |
545 | Conformational Dynamics of The Grp94 Molecular Chaperone in Protein Remodeling Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To investigate how conformational changes of Grp94 are coupled to protein remodeling, we performed all-atom biased molecular dynamics simulations and probed the effects of allostery imparted onto a model client protein. |
John Paul Alao ; Molly Wynveen ; IK Obaseki ; Katherine Connors ; Quynh Nguyen ; Alex Tam ; ANDREA KRAVATS; |
546 | New Paradigms for Bacteria Sensing The World: Molecular Mechanisms of Mechanosensation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study cell survival in environments fluctuating in osmolyte concentrations using Bacillus Subtilis as a model system. |
David Gomez; |
547 | Investigating Structural Stability of Transmembrane Ligand-Appended Pillar[n]ene (LAP) Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Artificial water channels are synthetic, transmembrane molecules inspired by aquaporins and offer a scalable solution for biological membrane applications. |
Tyler Duncan ; Harekrushna Behera ; Manish Kumar ; Venkatraghavan Ganesan; |
548 | Building An Artificial Neuron with Simple Hydrophobic Nanopores: A One Component Memristor Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Ion-based neuromorphic systems are a developing reseach topic[2] and by using hydrophobic gating in ion-channels[2] as a building block and the HH model as a description of their behaviour we study a simple model hydrophobic nanopore and it’s ability to generate neuron-like pulses. |
Goncalo Paulo ; Alberto Gubbiotti ; Alberto Giacomello; |
549 | Are Cell Membranes Electrorheological Fluids? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using giant vesicles as an in-vitro membrane model system, we explore the effects of electric field on membrane mechanical properties. |
Petia Vlahovska ; Hammad Faizi ; Rumiana Dimova; |
550 | Electromechanics of Lipid Bilayers: A Dimensionally Reduced Theory Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To derive an electromechanical theory for lipid bilayers, we propose a new dimension reduction approach. |
Yannick Omar ; Zachary Lipel ; Kranthi Mandadapu; |
551 | Applications of Dimensionally Reduced Theory of Lipid Bilayers: Fluctuation Spectra and Shear-induced Hydrodynamic Instabilities Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Typically, a direct two-dimensional approach is used in order to obtain a computationally and analytically tractable theory. |
Zachary Lipel ; Yannick Omar ; Kranthi Mandadapu; |
552 | Functional and Functionalized Membranes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will provide a perspective on the basic mechanisms how physical membrane properties can affect diseases, and the therapeutic potential of changing membrane properties to target certain diseases. |
Maikel Rheinstadter; |
553 | Electrostatic Interactions in Symmetric and Asymmetric Charged Free-standing Membranes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this presentation, we will discuss recent advances in our lab applying a novel technique to create free-standing charge asymmetric membranes with controlled composition on either membrane leaflet. |
Peter Beltramo ; Oscar Zabala-Ferrera ; Paige Liu; |
554 | Understanding The Effect of Foreign Particles on Membrane Elasticity in Lipid Vesicles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: At salt concentrations identical to oceanic conditions experienced by marine life, we observed an increase in bending elasticity of model lipid membranes along with an increase in bilayer thickness. |
Sudipta Gupta; |
555 | X-ray Studies of Free Floating and Supported Bilayers Formed from Cholesterol Phospholipid Mixtures Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have used small angle x-ray scattering (SAXS) and x-ray reflectivity (XRF) to study the structure of bilayers comprised of varying mixtures of DPPC and Cholesterol in both the supported geometry (on top of single crystal Si-111 substrates) and as free floating liposomes. |
Larry Lurio ; Jyotsana Lal ; Michael Vega ; Elizabeth Gaillard ; Gobind Basnet ; Evguenia Karapetrova ; Soenke Seifert; |
556 | A Dynamic Model for Cell Membrane Growth in A Genetically Minimal Cell Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: After developing these expected "production goals" of the cellular economy, we have constructed a dynamic kinetic model linking lipid metabolism and membrane protein insertion via the Sec system to cell membrane growth utilizing theoretical and experimentally determined values for lipid headgroup membrane surface area contribution. |
David Bianchi ; Zane Thornburg ; Nataliya Safranova ; Kim Wise ; James Saenz ; John Glass ; Zaida Luthey-Schulten; |
557 | Non-ideality in Lipid Mixtures, A Molecular Dynamics Study Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigate in this work binary lipid bilayers using the SPICA coarse-grained molecular dynamics model. |
Fabrice Thalmann ; Lisa Berezovska; |
558 | Red Blood Cell Membrane in Low Reynolds Flow and A Vorticity-based Characterization of Shapes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce an alternative phase-field model formulation of two-dimensional cells that solves the vorticity and the stream function that simplifies the numerical implementation [1]. |
Andreu Gallen; |
559 | Hypofractionated Brain Radiosurgery Utilizing Quasi Dynamic Dose Painting Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this paper, the first-time clinical implementation of QDDP for hypofractionated radiosurgery of large lesions is presented. |
Lijun Ma; |
560 | X-ray Nanothermometry to Improve Anticancer Thermal Therapies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we investigate the potential of X-ray absorption spectroscopy technique to determine in situ the temperature reached in gold and iron oxide-based nanoparticles under therapeutic photoactivated hyperthermia [3, 4]. |
Ana Espinosa ; German R. Castro ; Javier Reguera ; Carlo Castellano ; Javier Castillo ; Rosalía López-Méndez ; Julio Camarero ; Claire Wilhelm ; Miguel Ángel García ; Álvaro Muñoz-Noval; |
561 | Is 11B(p,α)2α Nuclear Reaction Contributing in Proton Therapy? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study we present a series of simulations in an effort to quantify the enhancement of the dose in the target volume originating from the p + 11B → 3α nuclear reaction. |
Panagiota Galanakou ; Theodora Leventouri ; Wazir Muhammad; |
562 | Evaluation of Dosimetric Uncertainties in Diminutive MLC Fields By “Fixed Virtual Cone Technique” Using Measurements and Monte Carlo Simulations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose a virtual cone technique defined by a fixed field size to mimic a physical cone. |
Taindra Neupane ; Charles Shang ; Wazir Muhammad ; Theodora Leventouri; |
563 | A Novel Method of Quantitative Comparison of The Benefit and The Risk of Hydrogen and Select Heavy Ions Radiotherapy on Breast Cancer Tumor Using SRIM Ion Transport Code Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we present a new way of quantifying the relative radiation dose given to cancerous and healthy tissues on the radiation path. |
Nnaemeka Nnamani ; Gigi Zeng ; Jenna Hacket; |
564 | Development of The Web-based Simulation Platform for GMicroMC Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Method: We proposed to establish two servers: a web server for storing static files and an application server for performing GPU-based gMicroMC simulation. |
Parvat Sapkota ; Thomas Shipman ; Edward Gonzales ; Yujie Chi; |
565 | Signal Optimization in Mesh-based X-ray Phase and Dark Field Imaging Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our method employs a single, low-cost wire mesh that does not need precise alignment and relaxes the coherence requirement on the source. |
Uttam Pyakurel ; Laila Hassan ; Carolyn MacDonald ; Jonathan Petruccelli; |
566 | Low-dose High-resolution TOF-PET Using Ionization-activated Multi-state Low-Z Detector Media Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose PET scanners using low atomic number media that undergo a persistent local change of state along the paths of the Compton recoil electrons. |
Joao Shida; |
567 | Deep High Resolution 4D Ultrafast Ultrasound Imaging with 2D Matrix Arrays Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we propose a novel probe design to provide unprecedented spatial resolution in ultrasound imaging, from three spatial dimensions up to 4D (x,y,z,t) when imaging media on ultrafast time scales. |
Hanna Bendjador ; Josquin Foiret ; Robert Wodnicki ; Katherine Ferrara; |
568 | Uptake of Carbon Nanodots Into Human Acute Myeloid Leukemia (AML) Cells in Comparison to Primary Hematopoietic Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Carbon nanodots (CNDs) are a promising class of nanoparticles. These carbon based, nanometer-sized particles offer a broad spectrum of potential biomedical applications like … |
Cathrin Nollmann ; Thomas Heinzel ; Rainer Haas; |
569 | Evaluation of Sperm Selection Efficiency in Abnormal Semen Sample Using Rheotaxis-based Microfluidic Device Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have developed a rheotaxis-based microfluidic device that washes out the raw semen sample from any dead or less motile sperm. |
Afrouz Ataei ; A.W.C Lau ; Waseem Asghar; |
570 | Robustness of Diffuse Reflectance Spectra Analysis By The Inverse Adding-doubling Algorithm Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We assessed the effect of fixing model parameters on the accuracy and robustness of a GPU-accelerated two-layer inverse adding-doubling (IAD) algorithm by calculating RMSE and MAE for estimated parameters and fitted spectra. |
Tadej Tomanič ; Luka Rogelj ; Matija Milanic; |
571 | The Phenomenon Cancer Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The presentation provides the theoretical part of the research project The Phenomenon Cancer with the King Saud University. |
Christina Pospisil; |
572 | Delbruck Prize (2022): Resource Allocation for Bacteria Growth: Laws and Mechanisms Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will briefly recount how we embarked on the path of top-down phenomenological studies, exhibit the striking universality of the law of ribosome allocation across diverse bacterial lineages, and describe a recent study establishing how this law is implemented molecularly via simple regulatory processes [10, 11]. |
Terence Hwa; |
573 | Optimality and Microbial Growth Strategies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We proposed, much at the same time as Terry Hwa did when he introduced proteome reallocation, that protein costs must be weighted against the functional benefits of specific growth strategies. |
Bas Teusink; |
574 | Precision in Protein Production: Requirements and Mechanism Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will discuss our research that is focused on elucidating the physiological requirements and mechanistic basis of the precise rates of protein production. |
Gene-Wei Li; |
575 | Esther Hoffman Beller Lectureship (2022): Growth-rate Dependent Action of Cell-wall Targeting Antibiotics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have investigated experimentally the efficacy of the cell wall targeting antibiotic mecillinam, which is used to treat urinary tract infections, for bacteria growing under different conditions. |
Rosalind Allen ; Rebecca Brouwers ; Sharareh Tavaddod ; Leonardo Mancini ; Elizabeth Tatham ; Pietro Cicuta ; Waldemar Vollmer; |
576 | Characterizing Failure Behavior of Ductile Glassy Polymers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we apply concepts familiar fracture mechanics, e.g., stress intensification ahead of crack, and show how ductile glassy polymers shows brittle response when the combination of nominal load and crack size defines a threshold toughness. |
Travis Smith ; Shi-Qing Wang; |
577 | Fracture Behavior of Elastomers: Case of EPDM Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this presentation, we show, based on ethylene-propylene diene monomer (EPDM) rubbers (acquired from Lion Elastomers), how the new approach compares with the Rivlin-Thomas method and indicate that a different framework may offer more effective instructions on how to improve mechanical characteristics of polymers. |
Zehao Fan ; Shi-Qing Wang; |
578 | Dynamic Properties of Filled Elastomers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Proton MQ NMR spectroscopy method is used to measure the crosslink density of the composites. |
Deboleena Dhara ; Md. Anisur Rahman ; Eric Ruzicka ; Zaid Abbas ; Akshay Karekar ; Nikolaos Kalafatakis ; Dimitris Vlassopoulos ; Kay Saalwaechter ; Brian Benicewicz ; Sanat Kumar; |
579 | Spatially-resolved Dynamics of Poly Vinyl Alcohol Gels Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we stretch poly(vinyl alcohol) gels and study the resulting dynamics parallel and perpendicular to the direction of deformation using dynamic small angle light scattering. |
Sujata Dhakal ; Daniel Estrin ; Hobart Chen ; Svetlana Morozova; |
580 | Dilute Surfactant Induced Swelling and Dissolution of Hydrophobically Crosslinked Hydrogels Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Non-covalently crosslinked hydrogels can exhibit toughness and mechanical adaptability associated with biological tissues, but interactions with molecules in the environment can … |
Bryan Vogt ; Siyuan Li ; Robert Weiss; |
581 | Design and Characterization of A Programmable Self Regulation Hybrid Material System: Wrinkled Hydrogels and Plasmonic Nanoparticl Lattices Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this research, a self-regulating system of wrinkle-patterned hydrogel with tunable feedback cycle timescales will be presented where wrinkled pattern senses humidity variation and plasmonic nanoparticle (PNP) lattice regulates through the plasmonic heating. |
Zeynab Mousavikhamene ; Young-Ah Lucy Lee ; Abhishek Kottaram Amrithanath ; Suzanne M. Neidhart ; Sridhar Krishnaswamy ; George Schatz ; Teri Odom; |
582 | Contraction Response of A Polyelectrolyte Hydrogel Structure to A Spatially Non-uniform Electric Field Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study the shape fluctuations of a semi-infinite polyelectrolyte hydrogel slab to transient and spatially nonuniform sinusoidal electric fields by using extensive coarse-grained molecular dynamics simulations. |
Aykut Erbas ; Ekrem Bahceci; |
583 | Reversing Fatigue Damage in Self- Healing Vitrimer and Its Composites Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We report a vitrimeric system which is prepared using epoxy resin and adipic acid with a suitable catalyst. |
Mithil Kamble ; Dong Wang ; Nikhil Koratkar ; Catalin Picu; |
584 | Using Thiol-Thioester Bond Exchange to Elucidate The Interplay Between Crystallinity and Dynamic Bond Exchange in Semi-Crystalline Polymer Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Coupled with microscopy and x-ray scattering, we present a rationale for these observations and how dynamic bonds can be harnessed in polymer networks to control both rheology and structure. |
Alexa Kuenstler ; Christopher Bowman; |
585 | Shear Banding in Entangled Polymers: Stress Plateau, Banding Location, and Lever Rule Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using molecular dynamics simulation, we study shear banding of entangled polymer melts under steady shear. |
Zhen-Gang Wang ; Yongjin Ruan ; Yuyuan Lu ; Lijia An; |
586 | Tuning Mechanical Properties of A Stretchable Hydrogel System Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a hydrogel system capable of mimicking some of these properties. |
Santanu Kundu ; Rosa Maria Badani Prado ; Anandavalli Varadarajan ; Katherine Elmore ; Satish Mishra; |
587 | Microstructure and Dynamics of Nanocellulose Network: Insights Into The Deformational Behaviors Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our study provides fundamental insights into deformational mechanisms of CNC films at a molecular level, aiding in the tailored design of cellulose-based materials for their mechanical performance. |
Zhaofan Li ; Wenjie Xia; |
588 | Theory and Simulation for Elasticity of Slide-ring Gels Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We develop single-chain analytical models designed to quantitatively describe the sliding effects on the elasticity of slide-ring gels and test these models by simulations. |
Danyang Chen ; Liel Sapir ; Sergey Panyukov ; Michael Rubinstein; |
589 | Principled Understanding of Dynamic Multi-legged Locomotion in Complex Terrain Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Research on dynamic multi-legged locomotion on relatively flat, rigid surfaces significantly advanced our understanding of how animals walk and run and provided foundations for multi-legged robots that do so dynamically, stably, and efficiently. |
Chen Li; |
590 | A Mode Map Model to Predict State Transitions of Multi-legged Robots Within Obstacle Fields Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Inspired by the agile movements achievable by humans and animals through actively engaging obstacles, we (i) investigate how robot gaits affect robot dynamics during repeated contact with obstacles, and (ii) seek locomotion strategies that exploit the "disturbances" caused by robot-obstacle contacts to produce desired trajectories. |
Haodi Hu ; Matthew Kvalheim ; Feifei Qian; |
591 | Locomotion in Granular Media: A Geomechanical Perspective on Symmetry Breaking Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This study investigates the correlation between underground locomotion and the symmetricity of cyclic body shape changes from a geomechanics perspective. |
Sichuan Huang ; Junliang Tao; |
592 | Reducing Model Fidelity for Statistical Path Characterization of An Insect-scale Robot Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we explore a modelling technique for an insect scale, robotic locomotor that abstracts the complex leg and foot-ground interactions by leveraging past experimental data. |
Henry Cerbone ; Perrin Schiebel ; Robert Wood; |
593 | A Multi-legged Robot Traverses Heterogeneous 3-D Terrain Via Locomotor Transitions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our recent research studied distinct locomotor challenges abstracted from such terrain—traversing large bumps, gaps, pillars, and flexible beams, and self-righting—and discovered strategies to overcome them (Othayoth et al. 2020, Proc. |
Jonathan Mi ; Yaqing Wang ; Qihan Xuan ; Chen Li; |
594 | Planning of Obstacle-aided Navigation for Multi-legged Robots Using A Sampling-based Method Over Directed Graphs Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we develop a method that allows multi-legged robots to achieve desired dynamics by taking advantage of their interactions with obstacles. |
Kaustav Chakraborty ; Matthew Kvalheim ; Feifei Qian; |
595 | A Novel Insect Scale Autonomous Soft Quadrupedal Robot for Locomotion Through 3D Complex Terrain Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose to extend this idea with hypothesizing body compliance of soft bodied animals and robots as an alternate yet equally effective strategy to squeeze through cluttered obstacles. |
Heiko Kabutz ; Kaushik Jayaram; |
596 | Low Slip Bipedal Locomotion on Granular Slopes Via Cleated Foot Interaction Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We achieve stable locomotion on uphill/downhill granular slopes of ±10 degrees, slipping at each step at most 10% of its step length. |
Deniz Kerimoglu ; Daniel Goldman; |
597 | Robophysical and Simulation Modeling of How Leg Posture Affects Vibration Sensing in Orb Weaving Spiders Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we developed a robophysical model spider to test whether this is true in a real system. |
Eugene Lin ; Yishun Zhou ; Andrew Gordus ; Chen Li; |
598 | Robophysics-inspired Biology Experiments to Study Gait Control for Obstacle Negotiation in Canines Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We explore how gait types and environment structure influence the way quadrupedal animals, here dogs, negotiate obstacles. |
Michelle Joyce ; Simon Wilshin ; Andrew Spence; |
599 | SLIP-Inspired Hopping on Yielding Terrain Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We recently addressed these challenges using direct-collocation trajectory optimization, informed by resistive force theory (RFT), discovering hopping gaits for a monopod that closely resemble the spring-loaded inverted pendulum (SLIP) motions characteristic of running animals. |
Daniel Lynch ; Kevin Lynch ; Paul Umbanhowar; |
600 | Passive Mechanical Limb Features Facilitate Rough Terrain Locomotion of An Insect-scale Robot Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We observed two primary sources of performance degradation: colliding with features during the swing phase, which could halt or even reverse forward motion, and jamming of the limb tip in local minima. |
Perrin Schiebel ; Pierre-Louis Lechere ; Robert Wood; |
601 | Force Sensing Facilitates Traversal in Cluttered Beams with Interaction Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To test this hypothesis, we developed a physics model of a robot capable of environmental force sensing propelled forward to traverse beams. |
Qihan Xuan ; Yaqing Wang ; Chen Li; |
602 | Free Energy Transduction in Chemical Reaction Networks from Enzymes to Metabolism Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will rigorously define energy transduction in open chemical reaction networks (CRNs). |
Massimiliano Esposito; |
603 | Performance Bounds, Trade-offs, and Scaling for Collective Motor-driven Transport Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using stochastic thermodynamics, we derive a series of bounds that constrain the performance (including velocity, precision, and efficiency) of a broad class of these collective transport systems for any number of motors. |
David Sivak ; Matthew Leighton; |
604 | Learning Regulation from The Ground Up: Combining Natural Selection, Thermodynamics and Data Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This makes model building a physics-based model a very hard problem. |
Mark Alber ; William Cannon ; Sam Britton ; Jolene Britton; |
605 | Scaling Relations of Energy Dissipation Rate in Nonequilibrium Reaction Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To quantify how energy dissipation is associated across scales, we develop a coarse-graining process in the state space and a corresponding renormalization procedure for reaction rates, an approach conceptually inspired by the real space renormalization group. |
Qiwei Yu ; Dongliang Zhang ; Yuhai Tu; |
606 | Algebra for Large Macromolecular Complexes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Their combinatorial complexity, however, has hindered their theoretical study using the standard methods of statistical physics. |
Rebecca Rousseau ; Justin Kinney; |
607 | Decomposing The Local Arrow of Time in Interacting Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that the local evidence for the arrow of time, which is the entropy production for thermodynamic systems, can be decomposed. |
Christopher Lynn ; Caroline Holmes ; William Bialek ; David Schwab; |
608 | Information Transmission By Heterogeneous Cell Populations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Information theory provides a natural framework to quantify how much does the cell know about its extracellular environment; the so-called channel capacity represents the upper limit of the information transmitted through any signaling network channel. |
Andrew Goetz ; Hoda Akl ; Purushottam Dixit; |
609 | Functional Universality in Slow-growing Microbial Communities Arises from Thermodynamic Constraints Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Overall, the work demonstrates how universal thermodynamic constraints may constrain community metabolism and explain observed functional convergence in microbial communities. |
Ashish George ; Tong Wang ; Sergei Maslov; |
610 | Life Without Oxygen: The Energy Saving Mechanisms of Anaerobic Gut Bacteria Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a study on the energy saving mechanisms of Bacteroides thetaiotaomicron, a representative gut organism which is surprisingly energy efficient for an anaerobe. |
Vadim Patsalo ; Brian Taylor ; Hiroyuki Okano ; Zhongge Zhang ; James Williamson ; Terence Hwa; |
611 | 3D Diffusion in Live Escherichia Coli Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We use GEMs ranging in size from 20 to 50 nm, similar in scale to ribosomes and other complexes in the cell. |
Diana Mendez ; Benjamin Bratton ; Joseph Sheehan ; Liam Holt ; Zemer Gitai ; Joshua Shaevitz; |
612 | In Vitro Cell Cycle Oscillations Exhibit A Robust and Hysteretic Response to Changes in Cytoplasmic Density Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we study how a cell cycle oscillator comprising cyclin-dependent kinase (CDK1) responds to cytoplasmic density changes by systematically diluting or concentrating a cycling Xenopus egg cytoplasm in cell-like microfluidic droplets. |
Franco Tavella ; Qiong Yang ; Minjun Jin ; Shiyuan Wang; |
613 | Ornstein-Uhlenbeck Models of Phenotypic Selection and Cellular Evolution Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we generalize the OU process to model stochastic protein level fluctuations in single cells that can divide or die. |
Gabor Balazsi ; Amr Ibrahim ; Yiming Wan; |
614 | Metabolic Fitness Landscapes Predict The Evolution of Antibiotic Resistance Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we develop a fitness model that predicts growth rates of common resistance mutants from their effects on cell metabolism. |
Fernanda Pinheiro ; Omar Warsi ; Dan Andersson ; Michael Lässig; |
615 | Noisy Metabolism Can Drive The Evolution of Microbial Cross-feeding Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we introduce a novel theory for the evolution of cross-feeding, which we term noise-averaging cooperation (NAC). |
Jaime Lopez ; Ned Wingreen; |
616 | Emergent Evolutionary Forces in Spatial Models of Luminal Growth in The Human Gut Microbiota Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we describe a mathematical framework which demonstrates how evolutionary forces emerge from simple models of growth in the intestinal lumen. |
Olivia Ghosh ; Benjamin Good; |
617 | Inheritance of Broadcast Enzymes Enables High Dispersal of Chitin-associated Marine Bacteria Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We studied the degradation of chitin by a marine bacterium of the Vibrio species. |
Ghita Guessous ; Terence Hwa; |
618 | Effect of Migration on Host-Parasitoid Outbreaks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we introduce a simple discrete time model for a host-parasitoid system with spatial coupling. |
Appilineni Kushal; |
619 | Evolutionary Dynamics of Branching Cellular Populations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we develop a basic theory of the evolutionary dynamics of branching populations with tip-driven growth. |
Maxim Lavrentovich ; Adam Bryant; |
620 | Slow Expanders Invade By Forming Dented Fronts in Microbial Colonies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We developed a theory of sector geometry that accounts for both local and global competitions and describes all possible sector shapes. |
Hyunseok Lee ; Jeffrey Gore ; Kirill Korolev; |
621 | Spatial Structure Alters The Allele Frequency Spectrum Produced By Hitchhiking Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We use mathematical modeling and simulations to find the unfolded allele-frequency-spectrum (AFS) left by hitchhiking in the genomic region of a sweep in a population occupying a one-dimensional range. |
Jiseon Min ; Michael Desai ; Daniel Weissman; |
622 | Validity of Pioneer Dominance in Range Expansions with Long-range Dispersal Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We used continuous space, individual-based simulations to ascertain when it is valid to use such models. |
Nathan Villiger ; Jayson Paulose; |
623 | Population-level Properties from Single-cell Statistics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will show that under mild and sensible assumptions, models of growth and division have independent effects on the population dynamics: models of single-cell growth determine the population growth rate independent of the details of cell division, and models of division and cell-size regulation determine the population cell-size distribution independent of details of cellular growth. |
Farshid Jafarpour ; Yaïr Hein; |
624 | Phage-host Dynamics During Spatial Expansions Modulate The Rate of Genetic Diversity Loss Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that during viral expansions, this effective density dependent dispersal alters the shape of genetic drift, or random sampling of offspring, and subsequently the rate of loss of genetic diversity. |
Nikhil Krishnan ; Kirill Korolev ; Diana Fusco; |
625 | Population Genetics in Microchannels Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigate the population genetics of bacteria Escherichia coli proliferating in microchannels with open ends. |
Anzhelika Koldaeva ; Simone Pigolotti ; Amy Shen ; Hsieh-Fu Tsai; |
626 | Effect of Environmental Heterogeneity on Mutation-selection Balance During Range Expansions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We consider a system with mutation and selection where individuals with deleterious alleles have an advantage in isolated patches, but a disadvantage everywhere else. |
Wolfram Moebius ; Thomas Tunstall ; Tim Rogers; |
627 | Chromatin Constrains The Formation, Diffusion, and Coarsening of Phase-separated Condensates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We utilized an optogenetic strategy to examine how chromatin influences droplet coarsening in the nucleus. |
Ned Wingreen; |
628 | Chromatin Organization: The Role of Microphase Separation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Based on recent experiments and simulations showing that chromatin phase separates from the nucleoplasm, we propose a minimal, block copolymer model for chromatin in which each type of block experiences different solvent conditions which can also be regulated by soluble molecules. |
Omar Adame-Arana ; Gaurav Bajpai ; Samuel Safran; |
629 | The Polymer Model of Constitutive Heterochromatin Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We develop a simple model containing spherical particles and a single chain polymer to represent proteins and chromatin. |
Ramin Basir ; Vivek Shenoy; |
630 | Modeling The Competition Between The RAD 51 and The RPA in Binding to The Single-stranded DNA Using A One-dimensional Lattice Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Therefore, we have developed a dynamic lattice model to model the competition between RAD51 and RPA molecules binding to the single-stranded DNA. |
Ali Tabei ; Aaron Kirchman; |
631 | Mesoscale Modeling of The Dynamics of Phase-separated Chromatin Compartments in Eukaryotic Nucleus Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In order to understand and disentangle the complex interplay of forces that contribute to the emergent patterns of organization and dynamics, we have devised a phenomenological field-theoretic model of nucleus as a multi-phase condensate of liquid chromatin types. |
Rabia Laghmach ; Michele Di Pierro ; Davit Potoyan; |
632 | Mechanical Force Derived from Transcriptional Activity Can Induce Local Order and Frozen Motion in Interphase Chromosome Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To understand this phenomenon, we investigated, using polymer simulations, how mechanical force derived from transcriptional activity affects the dynamic properties of interphase chromosome. |
Sucheol Shin ; Hyun Woo Cho ; Guang Shi ; Dave Thirumalai; |
633 | Resolving Chromatin Landscapes Around Nuclear Condensates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work provides new insights into the complex interplay between biomolecular condensates and chromatin topologies. |
Jan-Hendrik Spille ; Ganesh Pandey ; Aishwarya Katiki ; Saurabh Priyadarshi ; Filmon Medhanie ; Amy Kenter; |
634 | Single Molecule Tracking Reveals Distinct Mobility States That Contribute to The Dynamics and Function of Nuclear Receptors Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We used SMT in concert with a machine-learning based classification algorithm to directly measure the intranuclear dynamics of nuclear receptors. |
Kaustubh Wagh ; Rikke AM Jensen ; R. Louis Schiltz ; Ville Paakinaho ; Susanne Mandrup ; Diego Presman ; Arpita Upadhyaya ; Gordon Hager; |
635 | Compressing Cell Nuclei: From Nonlinear Mechanics to Nontrivial Shapes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have developed a Brownian-dynamics-based model of a nucleus subjected to uniaxial compression. |
Sarthak Gupta ; Edward Banigan ; Alison Patteson ; J. Schwarz; |
636 | Phase Separation in Sequence and Space: Coupling Folding Landscape of Chromatin with Epigenetics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose a model wherein the polymer is modelled as a matrix of contacts between sites (nucleosomes); additionally, each site carries a binary variable denoting its epigenetic state. |
Amogh Sood ; Bin Zhang; |
637 | Nonlinear Mechanics of Human Mitotic Chromosomes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that under increasing mechanical load, chromosomes exhibit nonlinear stiffening behavior, distinct from classical polymer models. |
Janni Harju ; Anna Meijering ; Kata Sarlós ; Christian Nielsen ; Hannes Witt ; Emma Kerklingh ; Guus Haasnoot ; Anna Bizard ; Iddo Heller ; Ying Liu ; Erwin Peterman ; Ian Jackson ; Gijs Wuite ; Chase Broedersz; |
638 | Enzymatic Activity in Chromatin Organization Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we construct a polymer physics model following the mechanistic scheme of Topoisomerase-II, an enzyme resolving topological constraints of chromatin, and investigate its role on interphase chromatin organization. |
Rakesh Das ; Takahiro Sakaue ; G. V. Shivashankar ; Jacques Prost ; Tetsuya Hiraiwa; |
639 | Elastic Interactions in Confinement Direct Cell Motility Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a physical model of durotaxis where cells are described as motile agents that exert contractile, traction forces on the underlying substrate. |
Subhaya Bose ; Arvind Gopinath ; Kinjal Dasbiswas; |
640 | Matrix-mediated Symmetry Breaking of Single Cells in A Three-dimensional Space Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This study highlights the utility of our approach in understanding biophysical mechanisms of cellular symmetry breaking in a 3D space with potential implications in directing cell fate decision. |
Ik Sung Cho ; Sing-Wan Wong ; Stephen Lenzini ; Jae-Won Shin; |
641 | Brittle-to-ductile Cell Escape from A Two-dimensional Spheroid Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To determine how the geometry and the rheology of the spheroid affects how cells escape a tumor, we construct and study a minimal computational model in two dimensions for the outer edge of a spheroid that allows us to connect larger-scale geometric and rheological properties of the spheroid to the shapes of individual cells. |
Tara Finegan ; M. Lisa Manning ; J. Schwarz; |
642 | Multidimensional Mechano-tomography of Biological Cells: Novel Modes and Machine Learning Data Analysis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will describe our solution which is based on a substantial reduction of the dimension of the data space by using so-called surface parameters. |
Igor Sokolov ; Maxim Dokukin ; Renato Aguliera ; Nadezda Makarova; |
643 | Chemo-mechanical Diffusion Waves Orchestrate Collective Oscillations of Immune Cell Podosomes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we develop a chemo-mechanical model for both oscillatory growth of individual podosomes and wave-like dynamics in podosome clusters. |
Ze Gong ; Koen van den Dries ; Alessandra Cambi ; Vivek Shenoy; |
644 | Vimentin Intermediate Filaments Increases Collective Cell Migration Through Extracellular Matrix Network Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that loss of vimentin significantly impairs the ability of the spheroid to collectively expand through collagen networks and remodel the collagen network. |
Minh-Tri Ho Thanh; |
645 | Cell-Induced Dynamic Remodeling of An Extracellular Matrix Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we significantly improved the model to simulate dynamic remodeling of ECM driven by cells under more physiologically relevant conditions. |
Taeyoon Kim ; Brandon Slater; |
646 | A Multiscale Theory for Opposing Durotactic Regimes in Mesenchymal Cell Migration Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To discern the underlying parameters of this rich behavior we developed a multiscale single-cell model for mesenchymal migration: At the sub-cellular scale, our framework translates the coupling between the viscoelastic substrate, chemical signaling pathways involving Rac and Rho GTPases, the intracellular dynamics of actomyosin complexes and microtubules to the emergent chemo-mechanical forces. |
C. Nadir Kaplan; |
647 | Active Regulation of Contractility and Ion Transport Drives "nuclear Piston" Mechanism of 3D Migration in Tumor Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To quantitatively understand the biophysical mechanisms governing this pressure driven migration mode, we developed a model that considers the translocation of the nucleus driven by actomyosin contractility through Nesprin links. |
Zhaoqiang Song ; Vivek Shenoy ; Ryan Petrie; |
648 | Mechanotransduction of Matrix Remodeling-directed Lineage Specification Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Together, our work reveals a mechanism where stem cells sense the preexisting amount of their surrounding matrix, and build a new one to direct lineage specification. |
Sing-Wan Wong ; Prerak Gupta ; Ik Sung Cho ; Jae-Won Shin; |
649 | Does Cellular Ability to Adapt Fast Varying Forces Determine The Biphasic Vs Monotonic Behaviour of Actin Retrograde Flow with Substrate Stiffness? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a theoretical model for cell-matrix adhesions at the leading edge of a crawling cell and address a puzzling observation of the biphasic versus monotonic relationship of the retrograde flow with increasing substrate rigidity. |
Rumi De ; Partho Sakha De; |
650 | Hermitian and Non-Hermitian Topological Phenomena in Active Matter Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that it is protected by the topological structure associated with exceptional points in complex-valued band structures and is thus immune to disorder or impurities. |
Yuto Ashida ; Kazuki Sone ; Takahiro Sagawa; |
651 | Towards A Topological Classification of Molecules and Chemical Reactions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I outline a topological classification of molecules and their chemical reactions, proposing that changes in topological invariants of molecules measure strong non-adiabatic couplings along the reaction path. |
Lukas Muechler; |
652 | Protected Edge Currents in Stochastic and Biological Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In particular, we will introduce stochastic networks in molecular configuration space that enable different phenomena from a global clock, stochastic growth and shrinkage, to synchronization. |
Evelyn Tang; |
653 | Topological Band Theory of Thermal Diffusion and Rock-paper-scissors Games Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this paper, we report the emergence of topological edge modes in classical diffusion systems[3] and systems described by the evolutionary game theory[4,5,6]. |
Yoshida Tsuneya; |
654 | Looking at Protein Interactions from The "Top" Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Herein we propose an approach that uses all the best available empirical data to capture the essential structural features of dynamic protein interactions network in mammalian whole cell lysate. |
Mihaela Sardiu; |
655 | Manipulating Light and Color with Soft and Structured Matter Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Investigations of nature’s most fascinating light manipulation strategies can inspire design concepts for synthetic, hierarchically structured, functional optical materials and … |
Mathias Kolle; |
656 | Combining Experimental and Simulation Approaches to Model Color Generation in Colloidal Assemblies Under Spherical Confinement Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we present a robust method of performing optical modeling using experimental and simulation tools that includes a) extraction of structural information from colloidal assemblies using scattering techniques, b) reconstruction of the assemblies using the previously developed CREASE method, and c) optical simulation of the reconstructed structures using finite-difference time-domain calculations to produce reflectance profiles that match the experimental reflectance spectra. |
Anvay Patil ; Christian Heil ; Arthi Jayaraman ; Ali Dhinojwala; |
657 | Liquid Collection on Welwitschia-Inspired Wavy Surfaces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we propose an omniphilic wavy surface design, inspired by Welwitschia mirabilis, that possesses the requisite characteristics for efficient liquid collection: a low energy barrier for nucleation and fast liquid transport. |
Christian Machado ; Kyoo-Chul Park ; Yuehan Yao ; Joanna Aizenberg ; Emma Feldman; |
658 | Mechanically Self-adaptable Materials, A Novel Bio-inspired Pathway for Overcoming Fatigue Failure Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Building upon our previous work demonstrating proportional mineral deposition as a function of a stress using piezoelectric scaffold [1], we report a bioinspired pathway for next generation materials with improved fatigue resistance. |
Mostafa Omar ; Bohan Sun ; Sung Hoon Kang; |
659 | Field Driven Transition of Artificial Membraneless Organells: from Spheres to Discoids to Prolate Ellipsoids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Inspired by such non-classical shapes in natural systems, we studied external field driven shape transitions in one of the ubiquitous biological materials: membraneless organelles (MLOs). |
Aman Agrawal ; Anusha Vonteddu ; Jack Douglas ; Alamgir Karim; |
660 | Effect of Wettability on Fog Collection on A Cylindrical Wire Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we conduct experiments using individual wires – the primarily components of conventional fog-collection systems. |
LEYUN FENG ; Youhua Jiang ; Kyoo-Chul Park; |
661 | Mechanical Metamaterial Based on Cellular Structures Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce an amorphous mechanical metamaterial inspired by how cells pack in biological tissues. |
Xinzhi Li ; Dapeng(Max) Bi; |
662 | Bioinspired Dopamine-functionalized Polymers for Enhanced Adhesion in Construction Applications Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The primary goal of this work was to focus our efforts on incorporating mussel-inspired adhesives for building and construction materials, with an emphasis on concrete. |
Travis Thornell ; Erik Alberts ; Ashvin Fernando ; Gilbert Kosgei ; Emily Asenath-Smith ; Charles Weiss ; Lee Moores; |
663 | Bioinspired Liquid-infused Materials for Self-healing and Self-stiffening Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We will present our characterization of piezoelectric properties, liquid-infusion capability as well as self-healing and self-stiffening capability. |
Bohan Sun ; Mostafa Omar ; Sung Hoon Kang; |
664 | Collective Behavior Triggers Chemomechanical Oscillations in Active Hydrogels Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we demonstrate that the quorum sensing response of an assembly of soft small BZ hydrogels (smaller than their critical size to oscillate on their own) can trigger their chemomechanical oscillations. |
Baptiste Blanc ; Johnson Agyapong ; Ian Hunter ; Ali Agvhami ; Seth Fraden; |
665 | Thermodynamic Law for Control of Biopolymer Reorganization Through Energy Consumption Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we address the interplay between structure and energy dissipation in a model system which transitions between aster-like and bundle-like configurations of actin filaments, which interact through the action of myosin molecular motors. |
Alexandra Lamtyugina ; Yuqing Qiu ; Etienne Fodor ; Aaron Dinner ; Suriyanarayanan Vaikuntanathan; |
666 | Spatiotemporal Control of Mechanical Phase Transition in 3D Active Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we demonstrate that active networks composed of molecular motors and biopolymers exhibit an activity-controlled phase transition from an active liquid that spontaneously bends in-plane to an active solid that spontaneously buckles out-of-plane. |
Bibi Najma; |
667 | Wetting, Speed, and Contact Geometry in Cell-cell Collisions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We build a phase-field model for two-body collisions, in which cells are treated as continuously deformable objects. |
Pedrom Zadeh ; Brian Camley; |
668 | Modeling Evolution of Firefly-like Signal Vocabularies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigate how flash sequences can co-evolve to be distinguishable by developing a "vocabulary generator" model. |
Chantal Nguyen ; Isabella Huang ; Orit Peleg; |
669 | Socially Isolated Bumblebees Display Frequent Antennation and Close Interactions Compared to Socially Reared Bumblebees Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We observed the behavior of age-matched bees from extra-hive isolated and grouped rearing conditions and hive reared bees. |
Grace McKenzie-Smith ; Z. Yan Wang ; Hyo Jin Cho ; Talmo Pereira ; Sarah Kocher ; Joshua Shaevitz; |
670 | Modeling Ant Pontoon Bridging Using A Robophysical Active Matter System Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To begin to robophysically model the bridge formation behavior we use BOBbots [Li et al, Sci. |
Noah Egan ; Shengkai Li ; Ram Avinery ; Haolin Zeng ; Takao Sasaki ; Daniel Goldman; |
671 | Spatiotemporal Patterns of Flash Synchrony in Firefly Mating Swarms Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using stereoscopic reconstructions of swarms, we investigate how individual flash motifs and the structure of social interactions induce collective flash patterns of various kinds. |
Raphael Sarfati ; Julie Hayes ; Orit Peleg; |
672 | Larval Zebrafish Exhibit Collective Circulation in Confined Spaces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We report our analysis of a new observation for this well-studied species: in circular confinement and at sufficiently high densities, the larvae collectively circle rapidly alongside the boundary. |
Haider Zaki ; Enkeleida Lushi ; Kristen Severi; |
673 | An Agent Based Force Vector Model of Human Social Influence Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: A force vector model gives the effect of each agent on all other agents. |
G Maclay ; Moody Ahmad; |
674 | Third-party Restoration and Annihilation of Attractor Basins in A Dynamical Model of Coordination Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work explores a phenomenon whereby a dyad of oscillators, which would be only monostable in isolation, can exhibit bistable coordination when embedded in a larger system. |
Joseph McKinley ; Mengsen Zhang ; Alice Wead ; Christine Williams ; Emmanuelle Tognoli ; Christopher Beetle; |
675 | The Physics of Team Formation: Modeling The Catalysis of Collaboration at In-Person and Virtual Conferences Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we present a new nonlinear dynamical model for the origin of scientific collaborations at conferences, inspired by the physics of catalytic processes. |
Emma Zajdela ; Daniel Abrams ; Richard Wiener ; Andrew Feig; |
676 | Causality Analysis of Synchronized 2D Neuron Monolayer Network Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we aim to understand how communication would play a role in the chemosesing process by using statistical causality analysis. |
Guanyu Li ; Bo Sun ; Andrew Mugler ; Ryan LeFebre ; Patrick Chappell ; Alia Starman; |
677 | Escaping Confinement: How Bacteria Reshape Their Surroundings to Enable Migration Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, by monitoring the dynamics of 3D-printed populations of Escherichia coli and Vibrio Cholerae in jammed hydrogel matrices, we demonstrate how bacteria can in turn reshape their surroundings to promote their active motion and dispersal. |
R. Konane Bay ; Hao Nghi Luu ; Sujit Datta; |
678 | A Noise Model Allows Quantitative Interpretation of Immune Responses at Repertoire Scale Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we have built a mechanistic statistical model, which we validated against replicate data, that captures the multiple steps in the measurement process. |
Christopher Joel Russo ; Andreas Mayer ; Ned Wingreen; |
679 | Evolution of Covid-like Viruses Under The Influence of Therapeutics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present our study of the role of therapeutics in three critical phases of the viral life cycle: infection, reproduction process, and fecundity. |
Pancy Lwin ; Moumita Das ; Barbara Jones; |
680 | Spatial and Temporal Stability of UV-C Sources Power Density in 254 Nm Fluorescent Tubes Versus 260-280 Nm Light-Emitting Diodes for Pathogen Eradication for Reliable UV-C Sterilization Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, the PD of identical 253.7 nm UV-C fluorescent tubes are found to average variation of 25% if measured weekly for three short 60 s sterilization cycles. |
Yash Soni ; Kush Patel ; Ashwin Suresh ; Ajay Taduri ; Shreyash Prakash ; Nimith Gurijala ; Vishesh Amin ; Siddarth Jandhyala ; Pranav Penmatcha ; Aarush Thinakaran ; Wesley Peng ; Sri Swaminathan ; Hemanth Yalahanka ; Nicole Herbots; |
681 | Bad Vibrations: Quantum Tunnelling in The Context of SARS-CoV-2 Infection Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose that quantum biology might offer essential new insights into the problem, especially with regards to the important first step of virus-host invasion. |
Francesco Petruccione ; Betony Adams ; Ilya Sinayskiy; |
682 | Functional Proteins Synthesis, Refolding and Surface Active Palladium Nano-thin-film Sensors Development for Virus Sensing and Anti-infectious Drugs Screening Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: In COVID-19 pandemics era, a rapid, specific and sensitive sensing platform is highly desired. By combining molecular biology, thermodynamics nanotechnology processes, both virus … |
Chia-Ching Chang ; Chia-Yu Chang ; Lik-Voon Kiew ; Sheng-Yu Huang ; Pei-Wen Wang ; Yen-Chen Chen ; Yi-Xuan Huang ; Shin-Ru Shih ; Dar-Bin Shieh; |
683 | Rational Policy Design for Epidemics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study the optimal control of an epidemic by governments and individuals using a Hamiltonian approach. |
Simon Schnyder ; John Molina ; Ryoichi Yamamoto ; Matthew Turner; |
684 | Nash Neural Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce Nash Neural Networks (N 3) to learn the cost functions that determine how rational individuals behave within a differential game with a Nash equilibrium. |
John Molina ; Simon Schnyder ; Matthew Turner ; Ryoichi Yamamoto; |
685 | A New Approach for Extracting Network Information from Protein Dynamics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Thus, we apply this inverse approach to the dynamics of protein dihedral angles, a system of internal coordinates that avoids the structural alignment artifacts. |
Jenny Liu ; Sinan Keten ; Luis A; |
686 | Toward A Minimal DNA Origami for Seeding Tiled DNA Nanotube Bundles and Patterning Silos Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using DNA origami, a self-assembly method for building arbitrary and highly addressable structures out of DNA, we designed what we believe to be the shortest possible seed for nucleating tiled DNA nanotubes from either end; 75% the size of the smallest seed described in the literature. |
Sarah Webster ; Deborah Fygenson; |
687 | Nanoscale Characterization of DNA Binding on Gold Nanostars Via Quantitative EELS Spectral Imaging Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: By combining quantitative scanning transmission electron microscopy (STEM) and electron energy loss spectroscopy (EELS) spectral mapping, we find a twofold increase in ligand density with respect to increase in surface curvature, indicating corressponding higher DNA binding. |
Sang hyun Bae ; Kwahun Lee ; Teri Odom ; Pinshane Huang ; Susanna Monti; |
688 | Optimizing Communication Speeds in DNA Origami Nanodevices Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, a kinetic theory to estimate the stepping rate constant of communicating DNA origami nanostructures of arbitrary lengths is introduced. |
Sebastian Sensale ; Pranav Sharma ; Gaurav Arya; |
689 | Self-Assembly of Nanoscale Architectures with DNA Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk I will discuss recent work towards this goal using DNA as a nanoscale, programmable building block [1-4]. |
Grigory Tikhomirov; |
690 | Seeing The Forces: Single Avalanching Upconverting Nanoparticles As Ultrasensitive Local Force Transducers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: It has recently been demonstrated that ensembles of upconverting nanoparticles (UCNPs) exhibit changes in their emission spectra due to applied stress [1, 2]. Avalanching UCNPs … |
Natalie Fardian-Melamed ; Changhwan Lee ; Hye Sun Park ; Ayelet Teitelboim ; Kevin WC Kwock ; Tom Darlington ; Bruce Cohen ; Emory Chan ; Sang Hwan Nam ; Yung Doug Suh ; P. James Schuck; |
691 | Grafted Polymer Architecture As A Tool to Inform Mechanisms of Polymer-Cell Membrane Interactions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we seek to study the mechanisms of polymer-lipid interactions by leveraging known structure-property relationships of graft polymers. |
Joseph Hassler ; Adelyn Crabtree ; Frank Bates ; Benjamin Hackel ; Timothy Lodge; |
692 | Fabrication Strategies of Peptide Rigid Rods with Computationally Designed Coiled-coils Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The presentation will discuss results from bundlemer building blocks with a wide range of charge characteristics that all have the same size, shape (i.e., nanocylinders that are 2 by 4 nanometers), and functionality to be linked together to form rigid rod polymers. |
Yi Shi ; Rui Guo ; Jeffery Saven ; Christopher Kloxin ; Darrin Pochan; |
693 | Nanoparticles Functionalized with Bundlemers and Bundlemer Rods Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: By incorporating substrate-binding terminal residues, we can design bundlemers to assemble with preferred orientation on a substrate to produce bundlemer brushes through either a grafting to approach, e.g., coupling bundlemer rods directly to a substrate through functionalized termini, or a grafting from approach, e.g., using a template layer of bundlemers as reaction sites for subsequent bundlemer coupling or assembly. |
Matthew Langenstein ; Darrin Pochan; |
694 | Polymer Nanoparticle Hydrogels: Physical Hydrogels with Extreme Extensibility Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We explore how these physically crosslinked materials exhibit functional yield stress values and gel-like properties across most frequencies depending on component stoichiometry. |
Abigail Grosskopf ; Eric Appel; |
695 | Citric Acid-modified Hydroxyapatite Nanoparticles As An Antibiotic Protein Carrier Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We observed that a higher concentration of CA leads to a greater negative surface charge of HAp NPs, which increases lysozyme loading capacity while maintaining its biological function during the adsorption/release process. |
Ruibo Hu ; Nita Sahai; |
696 | Biomimetic Porous Calcium Phosphate Nanoparticles with Lithium Ions Incorporation Induce Osteogenic Stem Cell Differentiation in Vitro and in Vivo Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here in, we have developed a novel type of CP nanoparticles (CaP), by mimicking bone forming precursors particles involved in bone mineralisation process. |
Sara Romanazzo ; Iman Roohani; |
697 | Using Phytoglycogen Nanoparticles to Improve The Water Solubility of Bioactive Compounds Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have explored improving the solubility of the insoluble carotenoid astaxanthin (ASX) through association with PG as a gateway to enhanced bioavailability. |
Nicholas van Heijst ; Michael Grossutti ; Jay Leitch ; Ciaran Henry ; John Dutcher; |
698 | A Molecular View of Liquid-Liquid Phase Separation of Disordered Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have recently developed a computational framework to elucidate the sequence determinants of protein liquid-liquid phase separation (LLPS) and apply it to many different IDPs of interest using coarse-grained molecular dynamics simulations. |
Gregory Dignon; |
699 | Liquid State Theory Study of The Microstructure and Phase Behavior of Protein Condensates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we use polymer integral equation theory (PRISM), which describes globally disordered structural correlations over a wide range of length scales in melts and solutions, to study the internal organization of protein condensates. |
Guang Shi ; Kenneth Schweizer; |
700 | Phase Separation Vs Aggregation Behavior for Model Disordered Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we present how sequence distribution, sticker fraction and chain length impact the formation of finite-size aggregates which can preempt macroscopic phase separation for some sequences. |
Ushnish Rana ; Cliff Brangwynne ; Athanassios Panagiotopoulos; |
701 | Nucleation in Multicomponent Liquid Mixtures Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we investigate the nucleation of a new droplet inside a multiphase system. |
Josep Bataller i Umbert ; Mikko Haataja ; Sheng Mao ; Andrej Kosmrlj; |
702 | Thermodynamic Stability and Critical Points in Multicomponent Mixtures with Structured Interactions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we consider such solutions with non-random interactions, characterized in terms of a pairwise interaction matrix of variable rank. |
Isabella Graf ; Benjamin Machta; |
703 | Material Properties of Rubisco-EPYC1 Condensates in An Algal Pyrenoid Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We developed a coarse-grained model for interacting Rubisco and EPYC1, with bonding properties derived from experiments, to understand the dynamics and material properties of Rubisco-EPYC1 condensates. |
Trevor GrandPre ; Yaojun Zhang ; Andrew Pyo ; Benjamin Weiner ; Ned Wingreen; |
704 | Sequence and Stoichiometry Dependence of Surface Properties of Biomolecular Condensates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using MD simulations, we discovered that the sequence and stoichiometry of heterotypic interaction domains determine the interface entropy, which in turn strongly influences the surface properties of the condensates, suggesting a mechanism of biological regulation. |
Andrew Pyo ; Yaojun Zhang ; Ned Wingreen; |
705 | Concentration-dependent Structure, Diffusion and Viscosity in A Model Macromolecular Crowder Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: A living biological cell has multiple macromolecules that occupy 30-40% of the total volume, or more. This phenomenon is known as macromolecular crowding. Crowding conditions can … |
Anand Yethiraj ; Yun Liu ; Venketesh Thrithamara Ranganathan; |
706 | On The Interplay Between Phase Separation and Aggregation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To this end, we propose a theory for a multicomponent mixture that contains aggregates of different sizes. |
Giacomo Bartolucci ; Thomas Michaels ; Christoph Weber; |
707 | Dynamics of Intrinsically Disordered Proteins and Their Droplet-like Aggregates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We describe a novel model (constructed with Lukasz Mioduszewski) that is a generalization of the so-called Go-like model, originally designed for structured proteins, and based on the concept of contact interactions between amino acids. |
Marek Cieplak ; Łukasz Mioduszewski; |
708 | Phase Behavior and Kinetics in Systems with Random Interactions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will revisit this model using theory and computer simulations. |
Martin Girard; |
709 | Computational Design of Amino-acid Sequence Variations That Modulate The Liquid-liquid Phase Separation of Intrinsically Disordered Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose a set of experimentally-testable amino-acid sequence variations of intrinsically disordered proteins that can either promote or inhibit their phase separation. |
Maria Maristany ; Jerelle Joseph ; Rosana Collepardo-Guevara ; Aleks Reinhardt; |
710 | Lack of Neighbor Exchanges From Modulating Epithelial Cell Movement Through Division and Substrate Stiffness Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We explore the interplay between these two origins of active stress in epithelia by using cells whose cell cycle is stalled and by modifying the extracellular matrix to which the model tissue is attached. |
Ayanna Matthews ; Margaret Gardel ; Sidney Nagel; |
711 | Effect of Compression on Tumor Fluidity and Invasion Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we developed a 3D in vitro model to study tumor spheroids under mechanical compression. |
Mrinal Pandey ; Young Joon Suh ; Minha Kim ; Hannah Davis ; Jeffrey Segall ; Mingming Wu; |
712 | Rheology of The Cellular Vertex Model with External and Internal Dissipation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we show that extending the model to include dissipation due to relative motion of cells with respect to each other has non-trivial effects on rheology in the linear regime. |
Sijie Tong ; Rastko Sknepnek ; Andrej Kosmrlj; |
713 | Vimentin Intermediate Filament Networks Are Required for Compression Stiffening of Cells and Protection of Nuclei from Compressive Stress Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: These results provide a new framework by which to understand the mechanical responses of cells and point to a central role of intermediate filaments in response to compression |
Paul Janmey ; Alison Patteson ; Katarzyna Pogoda; |
714 | Epithelial Monolayer Response to Boundary Mechanical Perturbations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have examined this question using a continuum model that couples mechanical deformations of the tissue to contractile activity of the cells. |
Toshi Parmar ; Liam Dow ; Beth Pruitt ; M Cristina Marchetti; |
715 | Nanofibril-mediated Hierarchical Fracture Resistance of Bone Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This versatile approach enables quantifying the relationship between toughness and microstructure in various complex material systems and provides direct insight for designing biomimetic composites. |
Guy German; |
716 | Microstructure-Based Constitutive Model of Nuclear Lamina Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we developed a microstructure-based model of lamina networks with orientation and initial length distributions of lamin filaments obtained from experimental imaging. |
Ottman Tertuliano; |
717 | E2 and Gamma Distributions in Polygonal Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Based on analysis of 99 polygonal tessellations with a wide variety of physical origins, this work demonstrates the ubiquity of an exponential distribution in the squared norm of the deformation tensor E2, which directly leads to the ubiquitous presence of gamma distributions in the polygon aspect ratio, as recently demonstrated by Atia et al. [Nat. |
Nima Mostafazadeh; |
718 | Reentrant Rigidity Percolation in Correlated Elastic Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We model structurally correlated, dilute Kagome lattice-based networks and compute their linear response to simple shear. |
Ran Li ; Hao Lin ; Seyedsajad Moazzeni ; Zhenru Zhou ; Kenneth Irvine ; Consuelo Ibar ; Liping Liu ; Andrew N. Norris; |
719 | Cells-ECM Mechanical Interaction: Taking Advantage of Nonlinearities for Mechanosensing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Following this idea, we use a fiber network model to perform numerical experiments mimicking cells probing locally the ECM’s mechanical response. |
Jonathan Michel ; Thomas Wyse Jackson ; Gabriel von Kessel ; Lawrence Bonassar ; Itai Cohen ; Moumita Das; |
720 | A Tensegrity Framework to Study Force Balance in Tissues Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present a tensegrity system of the largest reflection, the Falx cerebri, which sits between the left and right hemispheres of the cerebrum. |
Estelle Berthier ; Pierre Ronceray ; Chase Broedersz; |
721 | Nuclear Membrane Three Orders Magnitude Faster Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We detect fluctuations of cell nucleus envelope over the exceptionally broad spatiotemporal resolution. |
Allyson Ryan ; Carl Modes; |
722 | Noise-driven Phenomena on The Dynamics of Levitated Nanoparticles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we will discuss some of our work with trapped nanoparticles dispersed in different media, including water, air, and vacuum. |
Raul Rica; |
723 | Active Matter Under Control Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Indeed, existing equilibrium thermodynamics is an inadequate foundation to build a framework of control for active systems due to the constant consumption of fuel. |
Luke Davis ; Etienne Fodor; |
724 | Non-monotonic Skewness and Arcsine Laws in Non-equilibrium Steady States Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we employ a model NESS stochastic system, which comprises of a colloidal microparticle, optically trapped in a viscous fluid and externally driven by a temporally correlated colored noise. |
Raunak Dey ; Sreekanth Manikandan ; Avijit Kundu ; Biswajit Das ; Supriya Krishnamurthy ; Ayan Banerjee; |
725 | Anomalous Cooling Without Metastability Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we show that anomalous relaxation can be observed in a potential that has only a single local minimum. |
John Bechhoefer ; David Tam ; Avinash Kumar ; Raphaël Chétrite; |
726 | Effective Thermal Equilibrium Induced By Crosslinking Proteins in Polymer Chromosome Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To explain the mechanism behind this emergent clustering behavior, we derive an effective thermal equilibrium that captures both the average force and fluctuations induced by the stochastically switching force, accurately predicting the mean transition time between stable configurations. |
Katherine Newhall ; Ben Walker; |
727 | Statistical Mechanics of Thermalized Odd Elastic Membranes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: We are interested in studying the mechanical properties of thermalized ‘odd’ elastic membranes using statistical mechanics. Recently, generalizations of isotropic elastic … |
Mohamed El Hedi Bahri ; Andrej Kosmrlj ; Siddhartha Sarkar ; Daniel Alejandro Matoz-Fernandez ; Alex Ban; |
728 | Critical Dynamics of The Antiferromagnetic O(3) Nonlinear Sigma Model with Conserved Total Magnetization Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study the near-equilibrium critical dynamics of the O(3) nonlinear sigma model describing isotropic antiferromagnets with a conserved total magnetization. |
Louie Hong Yao ; Uwe Tauber; |
729 | Confidence Bounds for The Jarzynski Estimator Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The determination of free energy differences using this relationship plays a crucial role in the study of physical, chemical, and biological systems at small scales. |
Sivaraman Rajaganapathy ; cailong hua ; Murti Salapaka; |
730 | Stochastic Thermodynamics of Separation Process in Space and Time: from Kinetic Proofreading to Chromatography Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work provides a unified description of various separations: kinetic proofreading as separation in the chemical space, distillation tower as a spatial separation, and chromatography as separation in the time domain. |
Sa Hoon Min ; Zhiyue Lu; |
731 | Every Raindrop Is Exceptional Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The talk will discuss how large-deviation theory and extreme value statistics can give a quantitative description of rainfall, including recent results on the growth history of those ‘lucky’ microscopic droplets which grow to become raindrops. |
Michael Wilkinson ; Marc Pradas ; Christian Salas ; Michael Wilkinson; |
732 | Spontaneous Chiral Symmetry Breaking in A Random, Driven Chemical System Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we examine this question within a model of randomly-generated complex chemical networks and show that chiral symmetry breaking may occur spontaneously and generically by harnessing energy sources from external environmental drives. |
William Piñeros; |
733 | Bona Fide Stochastic Resonance Without Periodic Forcing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We report on the synchronization of Brownian particles in nanoscale bistable potentials in the presence of correlated Poisson noise, with mean interval τ P and correlation time τ c , mimicking an active bath. |
Govind Paneru ; Tsvi Tlusty ; Hyuk Kyu Pak; |
734 | Ubiquitous Power Law Intensity Distributions in The Self-excited Nonlinear Hawkes Processes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we present its asymptotic solutions using the field master equation approach previously introduced by the authors. |
Kiyoshi Kanazawa ; Didier Sornette; |
735 | The Cost-performance Tradeoffs in Biochemical Clocks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present a series of work on how biochemical clocks can utilize free energy to reduce phase fluctuations, enhance response sensitivity and achieve synchronization between molecular clocks. |
Yuansheng Cao; |
736 | Optimization of Lysogeny Frequency for Temperate Phages Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We suggest to apply the game-theoretic bet-hedging strategy introduced by Kelly to derive the optimal lysogenic fraction of the total population of phages. |
Kim Sneppen; |
737 | Non-genetic Variability in Microbes: Benefits and Detriments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Building on it, we will connect single-cell variability to the population growth, showing that in contrast to the dogma growth-rate fluctuations may lower the population growth. |
Ariel Amir; |
738 | Transport in Insect Respiratory Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a model of perfusion-based transport on a network, analyzing the oxygen concentration field predicted by this model when applied to our data set of hundreds of terminal cells. |
Tatyana Gavrilchenko ; Lena Barrett ; Pauline Hansen ; Stanislav Shvartsman; |
739 | The Optimal Checkpoint Strategy Predicts Experimental Checkpoint Override Times Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To uncover laws governing the dynamics of error-correction systems, we derived a general theory of optimal checkpoint strategies, balancing the trade-off between risk and self-replication opportunity. |
Sahand Rahi; |
740 | Stimulus-responsive Surfaces for Controlled Cell Adhesion During Mammalian Cell Culture Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have designed a fast, simple platform for on-demand cell detachment that uses transparent, biocompatible composite surfaces to trigger cell detachment in response to simple external stimuli without the need for trypsinization. |
Caroline McCue ; Kripa Varanasi; |
741 | Thermodynamics of Active Field Theories: Informatic Vs Thermodynamic Entropy Production Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk I will discuss a widely used measure of irreversibility we refer to as informatic entropy production and describe how it relates to the underlying energy dissipation or thermodynamic entropy production. |
Tomer Markovich ; Etienne Fodor ; Elsen Tjhung ; Michael Cates; |
742 | Melting of A Two Dimensional Crystal Driven Far from Equilibrium Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We explore this question by introducing a small fraction of magnetic spinners to our system of charged particles confined to a water-oil interface. |
Ankit Vyas ; stefano sacanna ; Andrew Hollingsworth ; Rodrigo Guerra ; Paul Chaikin; |
743 | Light-activated Kinesin Tune Defect Density and Nematic Speed Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To control the flow and suppress turbulence we developed a 2D active nematic system consisting of microtubule bundles driven by light-activated kinesin motor clusters. |
Zahra Zarei ; John Berezney ; Zvonimir Dogic ; Seth Fraden; |
744 | Mixing of Active and Passive Fluids in Microtubule-kinesin Active Fluid System Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To overcome this challenge, we introduced microtubule-kinesin active fluid to power the active mixing process. |
Teagan Bate ; Kun-Ta Wu; |
745 | Motile Particles Without Inertia Form Caustics in Vortical Flows Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that self-propelled particles (SPPs) with no inertia display similar behaviour thanks to the persistence of their motion in the direction of their intrinsic orientation. |
Rahul Chajwa ; Sriram Ramaswamy ; Rama Govindarajan; |
746 | Shape-Evolving Structured Liquids Via Ferromagnetic Active Particles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we employed ferromagnetic active swimmers with relatively large momentum. |
Paul Kim ; Thomas Russell; |
747 | Collective Motion of Interacting Swimmers in Impure Flows Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We utilize the Brinkman approximation to capture the effect of sparse and stationary obstacles that are represented via a single resistance parameter. |
Yasser Almoteri ; Enkeleida Lushi; |
748 | Interfacial Flow Fields Generated By A Pusher Bacterium Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study Pseudomonas aeruginosa PA01 in the pusher mode at aqueous-hexadecane interfaces. |
Jiayi Deng ; Mehdi Molaei ; Nicholas Chisholm ; Kathleen Stebe; |
749 | Collective Motion of Torque-dipolar Micro-swimmers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a model and simulations for micro-swimmers that take into account the counter-rotation of the body and flagella, as seen in motile bacteria or spermatozoa. |
Enkeleida Lushi; |
750 | Mixing with Acitivity: Transport of Swimming Bacteria in Time-periodic Flows Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will discuss recent experiemnts on the mixing of a passive scalar (dye) in dilute suspensions of swimming Escherichia coli in experiments using a two-dimensional (2D) time-periodic flow. |
Paulo Arratia ; Ranjiangshang Ran ; Quentin Brosseau ; Boyang Qin; |
751 | Activity-induced Microswimmer Interactions and Cooperation in One-dimensional Environment Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we confine catalytic microswimmers along one-dimensional paths and demonstrate that they, too, show a variety of cooperative behaviours. |
Stefania Ketzetzi ; Melissa Rinaldin ; Pim Dröge ; Joost de Graaf ; Daniela Kraft; |
752 | Active Particles in External Fields Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we discuss how the boundary conditions on the particle can crucially alter the particle dynamics in the viscosity gradients. |
Vaseem Shaik ; Gwynn Elfring; |
753 | Microfluidic SANS Study of The Lamellar-to-MLV Transition in Model Surfactant System of Varying Membrane Bending Rigidity Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we investigate the flow response of a model surfactant system, Sodium Dodecyl Sulfate (SDS)/octanol/brine, in the lamellar phase and, specifically, the mechanism and conditions required for the formation of MLVs. |
Liva Donina ; Joao Cabral; |
754 | Flow Fluctuations in Confined Bacterial Suspension Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose a Langevin-type equation with reflective boundary conditions, where a colored noise term models the flow generated by the bacterial suspension and is characterized by two parameters: its amplitude and correlation time. |
Cristian Villalobos Concha ; Maria Luisa Cordero ; Rodrigo Soto; |
755 | Calculation of Effective Properties of Composite Materials with Periodic Microstructures Using The Asymptotic Homogenization Method Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The current work aims at implementing the proposed AHM method to structures with aligned spheroidal inclusions of various aspect ratios and conductivity ratios, thus providing a more generalized approach to predict the effective electrical conductivity. |
Easwar Kumar ; Anubhab Roy ; Arockiarajan A; |
756 | Microporous Nanoparticle Emulsion Thermosets for Multi-material, Multifunctional Porous Nanocomposites Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have developed microporous nanoparticle emulsion thermosets (MiNET), a new class of nanocomposites made from epoxies and nanoparticles, a liquid porogen, and a small quantity of surfactant. |
Yogin Patel ; Michael Grzenda ; Arielle Marie Gamboa ; Molla Hasan ; Charm Nicholas ; Jonathan Singer; |
757 | Spontaneous "wave Ripples" Through Sequential Wrinkling Interference Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we report the formation of `sand ripple’ patterns by the sequential superposition of non-orthogonal surface waves excited by the spontaneous buckling of polymeric bilayers. |
Luca Pellegrino ; Joao Cabral ; Annabelle Tan; |
758 | Deformations of Compliant Textured Surfaces Due to Surface Stress Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We develop a microfabrication technique to produce compliant textures with large amplitude and extend these investigations to compliant textures with higher aspect ratio, h/w ~ 1. |
Lebo Molefe ; John Kolinski; |
759 | Flexible Fibrillar Surface Array Morphology As A Function of Inter-Fibril Interactions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We use fluorescent microscopy to monitor the evolution of these structures as a function of ambient pH, salinity, and dissolved polymer. |
Demi Moed ; Alfred Crosby; |
760 | Self-Assembly of 2D Host-Guest Pore Networks Via Entropy Compartmentalization Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we show that athermal binary mixtures of simple concave star particles and convex polygon guest particles form HG networks. |
Tobias Dwyer ; Timothy Moore ; Joshua Anderson ; Sharon Glotzer; |
761 | Size-dependent Polarizability of Mesoscopic Ionic Clusters During Assembly Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using coarse-grained simulations, we demonstrate that the ionic polarizability of electrically neutral ionic clusters, and hence their induced-dipole interactions, vary as charged particles aggregate into the clusters during assembly. |
Trung Nguyen ; Felipe Jimenez ; Monica Olvera De La Cruz; |
762 | Viscosity Metamaterials Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we introduce a new class of metamaterials- viscosity metamaterials- created by applying acoustic perturbations to a shear thickening suspension. |
Prateek Sehgal ; Meera Ramaswamy ; Itai Cohen ; Brian Kirby; |
763 | Perylene-based Self-Assembly of Chloroplast-like Lamellae for Artificial Photosynthesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we report a self-assembled structure composed of multi-perylene bisimides (PBIs) and a polyoxometalate (POM) catalyst as a guest, building highly ordered three-dimensional (3D) non-covalent assembled lamellas in water. |
Vasilis Petropoulos ; Mattia Russo ; Francesco Rigodanza ; Luca Moretti ; Thomas Gobbato ; Andrea Sartorel ; Maurizio Prato ; Giulio Cerullo ; Marcella Bonchio ; Margherita Maiuri; |
764 | Bundlemers-peptide Nanoparticles for Hierarchical Material Assembly Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using this tunability, we have used bundlemers as macromonomers to create stiff and extremely high aspect ratio supramolecular polymers through covalent chemistry between the neighboring bundlemer ends. |
Darrin Pochan; |
765 | Capsids Under Compression Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk we use dynamical Monte Carlo simulations to investigate icosahedral shells undergoing compression between two parallel walls. |
Botond Tyukodi ; Farzaneh Mohajerani ; Michael Hagan; |
766 | Microscale Mechanics and Structural Organization of Cross-linked Actin Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We actively drive a microsphere 10 micrometers through cross-linked actin networks at a constant speed and measure the resistive force that the network exerts on the bead during and following strain. |
Michael Dwyer ; Bekele Gurmessa; |
767 | The Use of First-axillary Steering Muscles in Drosophila Roll Control Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We now seek to elucidate the underlying mechanisms of neural control within the wing motor system which make this possible. |
Brianna Ludlow ; Samuel Whitehead ; Han Kheng Teoh ; Deepika Gupta ; Erica Ehrhardt ; Wyatt Korff ; Michael Dickinson ; David Stern ; Gwyneth Card ; Itai Cohen; |
768 | Elucidating The Role of Tergopleural Muscles in Fruit Fly’s Pitch Stability Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To elucidate the neuromuscular underpinnings of this flight control reflex, we perform behavioral assays in which freely flying flies are simultaneously subjected to external mechanical torques and acute, targeted neuronal manipulations. |
Han Kheng Teoh ; Samuel Whitehead ; Kemper Ludlow ; Deepika Gupta ; Erica Ehrhardt ; Wyatt Korff ; Gwyneth Card ; Michael Dickinson ; David Stern ; Itai Cohen; |
769 | Neuromechanics of Gait Adaptation in The Nematode C. Elegans Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We compare measured phase lags to a resistive force theory model, which allows cross-taxa comparisons to previously studied systems, such as the cm-scale sandfish lizard, which locomotes through granular terrain. |
Christopher Pierce ; Baxi Chong ; Kelimar Diaz ; Hang Lu ; Daniel Goldman; |
770 | A Minimal, Biomimetic, Add-on Model for C. Elegans Swimming in A Natural Environment Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In order to better understand C. elegans locomotion, we develop a minimal “add-on” model (the opposite of a knockout model) for the C. elegans central pattern generator (CPG) (c.f. Xu et al. 2018, Wen et al. 2012). |
Anshul Singhvi ; C. Evelyn Lee ; Susannah Zhang ; Jenny Magnes ; Harold Hastings; |
771 | Spectral Mode Dynamics of C. Elegans Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we present a general method for learning motor programs in a spectral representation. |
Alex Cohen ; Alasdair Hastewell ; Sreeparna Pradhan ; Steven Flavell ; Jorn Dunkel; |
772 | Water Surface Swimming Dynamics in Centipedes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Centipedes use body and limb coordination to navigate diverse terrains. In terrestrial environments, the animals use body travelling wave and limb-stepping waves for locomotion. … |
Kelimar Diaz ; Steven Tarr ; Daniel Goldman; |
773 | Gait Transitions in Centipede Locomotion on Complex Terrains Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Centipedes locomote in diverse environments via propagation of coordinated travelling waves of body and limb flexion. To study centipede body-limb coordination and control on … |
Eva Erickson ; Kelimar Diaz ; Tianyu Wang ; Baxi Chong ; Juntao He ; Daniel Goldman; |
774 | Walking on A Membrane: How to Measure Ground Contact Forces for Small Animals Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show a new method to measure spatially distributed in vivo loads that uses the deformation of a thin sheet to back-calculate the applied traction; reminiscent of traction force microscopy but with some notable differences. |
Yue Guan ; Madhusudhan Venkadesan; |
775 | Simulation of Snakes Using Vertical Body Bending to Traverse Terrain with Large Height Variation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, to understand how vertical bending generates propulsion, we developed a dynamic simulation of a snake traversing a wedge (height ≈ 0.05 body length, slope = 27°) and a half cylindrical obstacle (height ≈ 0.1 body length). |
Yifeng Zhang ; Qihan Xuan ; Qiyuan Fu ; Chen Li; |
776 | Statistical Fingerprints of Immune Selection of Tumor Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will describe computational methods that can be used to infer immune selection effects from data, based on quantitative analysis of TCRs sequences. |
Yuval Elhanati; |
777 | Distinguishing Multicellular from Unicellular Sources of Antifungal Resistance Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we develop a general pipeline for mechanistic drug response interpretation based on growth curve analysis and modeling for two Saccharomyces cerevisiae genetic backgrounds: TBR1 (multicellular, clumping wild-type and unicellular AMN1 deletion mutant) and BY4742 (unicellular wild-type and unicellular AMN1 deletion mutant). |
Lesia Guinn ; Evan Lo ; Gabor Balazsi; |
778 | Exploring The Dynamical Phases of Tumor-immune Interaction Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We built a simplified dynamical system modeling these interactions, and try to map distinct dynamical states to biological observations. |
Youyuan Deng ; Herbert Levine; |
779 | Predicting Clonal Evolution in Cancer Under Immune Selection Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we develop a biophysically grounded neoantigen quality model, which quantifies the immunogenicity of tumor neoantigens. |
Marta Luksza; |
780 | Effect of Flow on Chemical Sensing for Directed Cell Migration Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study we analyze cancer cell migration in response to the simultaneous presence of fluid flow and a chemical attractant. |
Soutick Saha ; Hye-ran Moon ; Bumsoo Han ; Andrew Mugler; |
781 | Statistical Dynamics of Tumor Initiation and Progression Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this challenge we analyzed cellular dynamics in human colorectal cancer samples by following the fate of distinct tumor cells in vivo. |
Sidhartha Goyal ; Sumaiyah Rehman ; Catherine O’Brien; |
782 | Incorporating The Role of A Biomarker in A Mathematical Model to Study Drug Resistance Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, our previously reported mathematical model of cancer dynamics in the presence of drug resistance is expanded to incorporate one possible role of a biomarker. |
Mitra Shojania Feizabadi; |
783 | Mathematical Model for Karyotype Evolution Describing Mouse Pretumor and Tumor Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: By developing a mathematical model, that includes chromosome mis-segregation, apoptosis and proliferation, we study karyotype evolution over multiple generations. |
Lucija Tomašić ; Ivana Ban ; Marianna Trakala ; Iva Tolić ; Nenad Pavin; |
784 | Decomposition of Deterministic and Stochastic Growth Rates Within Cell Lineages Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Cell growth rates exhibit cell-intrinsic cell-to-cell variability, which influences cell and population fitness from bacteria to cancer. Cell-to-cell growth variability arises, at … |
Joon Ho Kang ; Ethan Levien ; Ariel Amir ; Scott Manalis ; Teemu Miettinen; |
785 | Cancer Cell Migration Directed By Mechanochemical Dual Guidance Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we quantified the effectiveness of ROCK-inhibitors (Y27632) and Rho-activators (CN03) on the cell migration directionality in presence of mechanochemical dual guidance. |
Pedram Esfahani ; Bo Sun ; Herbert Levine; |
786 | How Cytoskeletal Forces Alter Nuclear Protein and Chromatin Distributions During Confined Cell Migration Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We address here the mechanism of nucleus pulling during cell translocation through openings smaller than the nuclear diameter. |
Sirine Amiri; |
787 | Overcoming Physical Obstacles: A Collective Microbial Solution to A Shared Problem Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using time-lapse microscopy on expanding biofilms of B. subtilis crashing against populations of E. coli of variable density and width, we find that the biofilm population exhibits different collective strategies to bypass the barrier on its path, often requiring coordination of cell behaviour across thousands of cells. |
Diana Fusco; |
788 | The Role of Quenched Noise in The Evolution of Populations Undergoing Range Expansions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To study the interactions between these two regimes of noise, we conduct multi-species Eden model simulations of population growth in heterogeneous landscapes, and we analyze the results through the "lenses" of population genetics and geometric optics. |
Jimmy Gonzalez ; Daniel Beller ; Jayson Paulose ; Wolfram Möbius; |
789 | Modelling Finger-like Pattern Formation in A Bacteria Colony Growing at An Interface Using Dynamical Self-consistent Field Theory Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study this pattern formation phenomenon by simulating a dynamical self-consistent field theory. |
Robert Wickham ; Drake Lee; |
790 | Calibrating Active Forces of Gliding Bacteria Through Self-buckling Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Adapting Euler’s self-buckling theory to the properties of self-propelling filaments, we derive the active force density from the critical length and an independent calibration of the bending rigidity. |
Maximilian Kurjahn ; Stefan Karpitschka; |
791 | A Phase Diagram for Bacterial Swarming Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present new experiments of swarming Bacillus subtilis mutants with different aspect ratios and at different densities. |
Avraham Beer; |
792 | Self-organization of Bacterial Colonies Through Quorum Sensing and Motility Regulation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk I will discuss how the regulation of motility allows bacterial colonies to self-organize in space and time. |
Julien Tailleur ; Yongfeng Zhao ; Agnese Curatolo ; Nan Zhou ; Chenli Liu ; Adrian Daerr ; Jiandong Huang ; Alberto Dinelli ; Jérémy O’Byrne ; Peter Sollich; |
793 | Co-existence and Extinction Due to Surfing Viral Infections in A Spatially Expanding Bacterial Colony Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we investigate the dynamics of the spread of the infection due to a phage-lambda during the range expansion of an E coli colony; the phages "surf" the front of the growing bacterial colony by hitchhiking on E coli that are advected due to growth of the bacteria in the colony, resulting in an anisotropic spread of the phages — ballistically in the direction of colony growth and diffusively in the lateral direction (occurring over timescales of many hours and millimetric length scales). |
Godwin Stephenson ; Amit Nadig ; Toshi Parmar ; Vijay Krishnamurthy ; Namiko Mitarai ; Sandeep Krishna ; Shashi Thutupalli; |
794 | Cellular Sensing Governs The Stability of Chemotactic Fronts Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will theoretically show that the stability of such chemotactic fronts to morphological perturbations is determined by limitations in the ability of individual cells to sense and respond to the chemical gradient. |
Ricard Alert ; Sujit Datta; |
795 | Bacteria Bioluminesce in Response to Fluid Shear Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we combine imaging and rheology experiments to show that bacteria indeed emit light in response to shear within seconds of stimulation. |
Sumit Kumar Birwa ; Raymond Goldstein ; Nuno Oliveira; |
796 | Light-induced Phase Separation and Pattern Formation By Phototactic Micro-algae Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here I will present our results on the quantitative characterization of the patterns as well as the simple model we developed in order to rationalise our observations. |
Raphael Jeanneret ; Nicolas Desprat ; Isabelle Eisenmann; |
797 | Phototaxis of The Dominant Marine Pico-eukaryote Micromonas Sp.: from Population to Single Cell Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Single-cell tracking experiments detail thoroughly the way Micromonas sp. |
Marco Polin ; Richard Henshaw ; Raphael Jeanneret; |
798 | Microbial Narrow-escape Is Facilitated By Wall Interactions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, using the model microalgae Chlamydomonas reinhardtii, we combine experiments and simulations to achieve a tractable realization of the classical Brownian narrow escape problem in the context of active confined matter. |
Antoine Allard ; Mathieu Souzy ; Jean-Francois Louf ; Idan Tuval ; Marco Polin; |
799 | How Encounters at The Microscale Prime Microbial Ecosystems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: A variety of physical mechanisms can drive these interactions, including diffusion, active swimming, gravitational settling and turbulent mixing, and the concept of encounter rates provide a unifying framework to describe them. |
Jonasz Slomka ; Roman Stocker; |
800 | Label-free Composition Determination for Biomolecular Condensates with An Arbitrary Number of Components Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we describe a label-free method to measure the shape and composition of micron-sized condensates based on quantitative phase microscopy and the physics of sessile droplets. |
Patrick McCall; |
801 | A Background Enzymatic Active Bath Affects Liquid-Liquid Phase Separation of Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We will use urease, an exothermic and kinetically fast enzyme that converts urea to carbon dioxide and ammonia, as the background enzyme. |
Kevin Ching ; Diego Luna ; Kavita Sarathy ; Nicholas Sawyer ; Jennifer Schwarz ; Jennifer Ross; |
802 | Liquid-liquid Phase Separation and Coarsening in An Active Fluid Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In my talk, I will show that active flows yield short-time superdiffusive motion and long-time diffusive motion, and that this motion accelerates droplet coarsening compared to a passive network. |
Jeremy Laprade ; William Rogers ; Guillaume Duclos; |
803 | Effect of ATP on Phase Separation in FUS Condensates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we used all-atom simulations to elucidate, at the microscopic level, how ATP affects FUS phase separation. |
Nick Weaver ; David Winogradoff ; Kumar Sarthak ; Aleksei Aksimentiev; |
804 | Nucleotide-dependent Dynamics and Material Properties of A Model Biomolecular Condensate Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We identify two distinct modes for nucleotide-dependent regulation of condensate material state and demonstrate tunable dynamics dependent on nucleotide concentration. |
Sebastian Coupe ; Nikta Fakhri; |
805 | Non-coding RNAs Could Fine-tune Transcription of Proximal Genes By Modulating Dynamics of Transcriptional Condensates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using a free energy functional that takes into account the interactions between the different molecular species, we modeled the dynamics of concentration fields using Model B dynamics for the stable protein and non-coding RNA coupled to a reaction-diffusion equation for the transcribed mRNA that pushes the system far away from equilibrium. |
Pradeep Natarajan ; Arup Chakraborty ; Mehran Kardar ; Krishna Shrinivas; |
806 | Physical Principles Underlying Regulation of Size Distributions of Intracellular Condensates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We demonstrate that these power laws are due to a preferential attachment or “rich get richer” effect. |
Daniel Lee ; Chang-Hyun Choi ; David Sanders ; Joshua Riback ; Lien Beckers ; Cliff Brangwynne ; Ned Wingreen; |
807 | Non-equilibrium Phase Separation in Mixtures of Catalytically Active Particles: Size Dispersity and Screening Effects Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we analytically study a model describing the phase separation of a mixture of such catalytically active particles. |
Vincent Ouazan-Reboul ; Jaime Agudo-Canalejo ; Ramin Golestanian; |
808 | Chemical Reaction Kinetics in Phase Separated Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The theory of phase separation determines how condensates form in living cells. |
Sudarshana Laha ; Jonathan Bauermann ; Patrick McCall ; Frank Julicher ; Christoph Weber; |
809 | Active Droplets Supplied with Energy and Matter Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work reveals that life-like processes such as metabolism and division can emerge in simple non-equilibrium systems that combine the physics of phase separation and chemical reactions. |
Jonathan Bauermann ; Christoph Weber ; Frank Julicher; |
810 | Molecular Assembly Lines in Active Droplets Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific sequence of assembly steps. |
Tyler Harmon ; Frank Julicher; |
811 | Quantitative Reaction-Diffusion Dynamics in Liquid Condensates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We recently introduced a precise way of measuring intra-droplet diffusion rates based on a spatially resolved phase separation model. |
Lars Hubatsch ; Stefano Bo ; Basusree Ghosh ; Marc Karnat ; Hari Singh ; T-Y Tang ; Anthony Hyman ; Christoph Weber; |
812 | Mesoscale Properties of Non-equilibrium Liquid-liquid Phase Separation with Molecular Production and Degradation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Motivated by cellular LLPS, we present a theoretical framework for the analysis of out-of-equilibrium LLPS, where the phase-separating molecules are constantly synthesized and degraded. |
Dan Deviri ; Amit Kumar ; Omar Adame-Arana ; Samuel Safran; |
813 | Physical Limits to Membrane Curvature Sensing By A Single Protein Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using continuum models of fluctuating membranes, we investigate whether it is feasible for a protein to sense deviations in bilayer lipid densities as a proxy for local curvature to infer the membrane’s overall shape. |
Indrajit Badvaram ; Brian Camley; |
814 | Lipid Bilayer Fluctuations in Silico: Statistical Improvements and Systematic Corrections Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We in particular discuss systematic effects connected with: (1) interpolation of height and directional fields; (2) normalization and averaging of lipid directors; (3) determining small-scale cutoffs. |
Muhammed Erguder ; Markus Deserno; |
815 | Mechanical Properties of Pseudomonas Aeruginosa Outer Membrane Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work aims to develop an accurate in silico model of P. aeruginosa outer membrane using all-atom molecular dynamics and characterize its mechanical properties. |
Emad Pirhadi ; Jeffrey Schertzer ; Xin Yong; |
816 | Formation of Buds, Pearls, and Tubes in Membranes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, using continuum models, I will elaborate on continuum models that can help us obtain insight into the parameter spaces necessary to obtain these shapes and particularly, how membrane tension can play a critical role in determining the outcome of these shapes. |
Padmini Rangamani; |
817 | Coupled Evolution of Viral Protein Density and Membrane Shape in Coronavirus Assembly Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To quantitatively understand the dynamics of this process, we propose a generalized analytical model that accounts for the key physical features. |
Joseph McTiernan ; Ajay Gopinathan; |
818 | Erythro-PmBs: A Novel Polymyxin B Delivery System Using Antibody-Conjugated Hybrid Erythrocyte Liposomes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a novel PmB delivery system constructed by conjugating hybrid erythrocyte liposomes with bacterial antibodies to combine a high loading efficiency with guided delivery. |
Hannah Krivic ; Sebastian Himbert ; Ruthie Sun ; Maikel Rheinstadter; |
819 | Sterol Conjugated Lipids for Improved Liposomal Stability Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Liposomal nanoparticles are outstanding candidates for vaccine and drug delivery applications. However, the liposomal stability under physiological conditions is a major … |
Teshani Kumarage ; Wally Borden ; Haden Scott ; John Katsaras ; Rana Ashkar; |
820 | Viral Fusion Peptide Interactions with Lipid Bilayers Studied By Neutron Scattering Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: The HIV-1 virus infects a target cell through a process that begins with binding to the surface of the cell membrane and then fusing with it. Key to the process is a short … |
William Heller ; Piotr Zolnierczuk; |
821 | Dependence of Protein-induced Lipid Bilayer Thickness Deformations on Protein Shape Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We describe here a boundary value method for the straightforward calculation of protein-induced bilayer thickness deformations for arbitrary protein shapes. |
Carlos Alas ; Christoph Haselwandter; |
822 | How Pinning Influences The Dynamics of Cell Membranes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that: (a) for small frame tension the internal tension decreases as pinning increases, (b) The internal tension and the fluctuating tension are approximately equal, (c) how the pinned points are distributed affects the spectrum at small wavenumbers but has no significant effect on the internal tension. |
Dhrubaditya MITRA; |
823 | Spontaneous Lipid Nano Tubulation Driven By Automotive Passive Nanoparticles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, the role of the membrane phase has been varied to analyze its effect on the properties of LNTs such as tube length, tube stiffness, and growth kinetics such as tubulation and retraction time scale. |
Roobala Chelladurai ; Anurag Chaudhury ; Jaydeep Basu; |
824 | Multiscale Geometry and Mechanics of Lipid Monolayer Collapse Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a general lipid monolayer collapse phase diagram, which shows that wrinkling, folding, crumpling, shear banding, and vesiculation are a continuous set of mechanical states that can be approached by either tuning monolayer composition or temperature. |
Angelo Rosario Carotenuto ; Nhung Nguyen ; Kathleen Cao ; Anna Gaffney ; Alan Waring ; Ka Yee Lee ; David Owen ; Massimiliano Fraldi ; Luca Deseri ; Luka Pocivavsek; |
825 | A Tutorial Model for The Role of Superspreaders in Pandemic Outbreaks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will give a simple implementation of this idea suitable for an undergraduate-level project. |
Phil Nelson; |
826 | Modeling The Impact of Social Distancing and Targeted Vaccination on The Spread of COVID-19 Through A Real City-Scale Contact Network Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We use mobile device data to construct empirical interpersonal physical contact networks in the city of Portland, Oregon, both before and after social distancing measures were enacted during the COVID-19 pandemic. |
Gavin Hartnett; |
827 | A Continuous Commuter Model for The Spread of Infectious Disease Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The localized nature of daily commutes allows us to derive a continuous, spatially resolved SIR model with diffusion that is independent of the exact form of the commuting probabilities. |
Aaron Winn ; Eleni Katifori ; Adam Konkol; |
828 | S-I-R and Disease Spreading in Active Matter Models Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we examine S-I-R (Susceptible-Infected-Recovered) dynamics on an active matter assembly of run-and-tumble disks. |
Cynthia Reichhardt ; Peter Forgacs ; Andras Libal ; Charles Reichhardt; |
829 | Front Propagation in A System of Weakly Connected Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we will discuss a model for the spread of an epidemic in a system of weakly connected patches, where the disease dynamics of each patch occurs on a network. |
Madhavan Iyengar ; Evgeniy Khain; |
830 | Spreading Dynamics of An Infection in A Growing Population Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work reveals the complex interplay between population growth and front propagation. |
Rory Claydon; |
831 | Recovery of Resonant Stochastic Fluctuations in An Interacting-particle System-based Contagion Model Coupled with Social Mimicry: Comparative Analysis of The Effect of Event Ordering in Their Corresponding Agent Based Models Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we show the presence and non-trivial nature of differences between various parametrizations of a coupled network-IPS contagion model, with an emphasis on two types of scheduling algorithms: a fully randomized model and a priority random model. |
Santiago Núñez-Corrales; |
832 | A Seascape Origin of Richards Growth Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we find that Richards-like growth laws emerge naturally from generic analytical growth rules in a distributed population, upon inclusion of {\bf (i)} migration (spatial diffusion) amongst different locales, and {\bf (ii)} stochasticity in the growth rate, also known as “seascape noise.” |
Bertrand Ottino-Loffler ; Mehran Kardar ; Daniel Swartz; |
833 | Structure and Information Dynamics of Pro- and Anti-Vaccine Interaction Networks in Twitter Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we present a study of all vaccine-related conversations between Twitter users in Chile during a six-month period that includes most of the mass vaccination efforts in that country. |
Cristian Huepe; |
834 | Theoretical and Numerical Analysis of A Locally Nonchaotic Energy Barrier Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In the current research, we investigate a billiard-type model system, in which elastic particles randomly move across a locally nonchaotic energy barrier between an upper plateau and a lower plain. |
Yu Qiao ; Zhaoru Shang; |
835 | Choosing Optimal Reservoir Computers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: One conventional design rule that I show is not always true is that reservoir computers function best at the edge of stability, or the “edge of chaos”. |
Thomas Carroll; |
836 | Non-equilibrium Hydrodynamic Fluctuations in Binary Fluids During Effusion Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This talk will describe the structure of hydrodynamic fluctuations that emerges when the fluid is driven out of equilibrium by confinement between reservoirs of varying concentrations in the presence of an effusive membrane. |
Ishan Srivastava ; Daniel Ladiges ; Andrew Nonaka ; John Bell ; Alejandro Garcia; |
837 | Characterizing Irreversibility in Noise-driven Dynamical Systems with Stream Functions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk we apply the stream function technique to the following systems: two masses moving in one spatial dimension and coupled by a linear or nonlinear spring with each mass driven by a distinct thermal noise source; and a nonlinear tunnel diode circuit model driven by multiple noise sources. |
Stephen Teitsworth ; John Neu; |
838 | Dynein-Inspired Multilane Exclusion Process with Open Boundary Conditions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Motivated by the sidewise motions of dynein motors shown in experiments, we use a variant of the exclusion process to model the multistep dynamics of dyneins on a cylinder with open ends. |
Priyanka Priyanka ; Uwe Tauber ; Riya Nandi; |
839 | Enhancing Associative Memory Recall in Non-equilibrium Materials Through Activity Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce activity into the system as AOUP noise which breaks detailed balance and takes the system out of equilibrium. |
Agnish Behera ; Madan Rao ; Srikanth Sastry ; Suriyanarayanan Vaikuntanathan; |
840 | Simulation Studies of A Particle-Based Molecular Motor Toy Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will introduce a particle-based toy model for an "information ratchet", a motor that rectifies thermal noise into directed motion. |
Alex Albaugh ; Geyao Gu ; Ray Fu ; Todd Gingrich; |
841 | Optimizing A Chemically-Fueled Molecular Motor Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We will discuss strategies for that dynamical optimization. |
Geyao Gu ; Alex Albaugh ; Ray Fu ; Todd Gingrich; |
842 | Anomalous Fluctuations of Extremes in Many-Particle Diffusion Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: By introducing a shared environment, we find three scaling regimes relating to the KPZ equation for the variance of the maximally displaced particle, contrary to the Einstein diffusion model which predicts a single scaling regime. |
Jacob Hass ; Eric Corwin ; Ivan Corwin ; Aileen Carroll-Godfrey; |
843 | Transport Regimes of Underdamped Brownian Particles in ATilted Washboard Potential Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: In this work, a Runge-Kutta numerical solution to the Langevin equation is computed for a tilted washboard potential. The parameter-space of temperature, tilt, and well-depth is … |
Jarrod Schiffbauer ; Marygrace Prinster ; Trey Jiron; |
844 | Modeling and Analysis of Systems with Nonlinear Functional Dependence on Random Quantities Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk we explore a class of differential equations where evolution depends nonlinearly on a random or effectively-random quantity, and we argue that these equations may exhibit finite-time stochastic behavior in line with an equivalent Ito process, which is of great utility for their numerical simulation and theoretical analysis. |
David Sabin-Miller ; Daniel Abrams; |
845 | Scaling Study of Diffusion in Dynamic Crowded Spaces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we study diffusive motion in a space with a high density of moving obstacles in one, two and three dimensions. |
David Yllanes ; Harry Bendekgey ; Greg Huber; |
846 | Using Tensor Network States to Describe Periodically Driven Multiparticle Brownian Ratchets Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a novel approach for computing these currents for a time-periodic 1D ratchet discretized on a periodic-boundary-condition lattice. |
Nils Strand; |
847 | Characterizing Noise-induced Lifetime of A Phase State in A Kerr Nonlinear Resonator Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We compare the suitability of several mathematical methods to characterize the lifetime of two-level systems. |
Deividas Sabonis ; Alexander Eichler ; Gabriel Margiani ; Sebastián Guerrero ; Toni Heugel ; Christian Marty ; Thomas Gisler ; Raphael Pachlatko ; Nicholas Bousse ; Thomas Kenny ; Oded Zilberberg ; Gabrielle Vukasin ; Hyun-Keun Kwon ; James Miller ; Suchita Agrawal ; Christian Degen ; Ramasubramanian Chitra; |
848 | Universal Corrections to Reaction-diffusion Dynamics Above The Upper Critical Dimension Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will discuss how a Bose gas representation, which maps the real-time dynamics of the reactants to the imaginary-time evolution of an interacting Bose gas, can be used to determine corrections to the late-time scaling above the upper critical dimension, where mean-field theory sets the leading order. |
Johannes Hofmann; |
849 | Synchronization and Enhanced Catalysis of Mechanically Coupled Enzymes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find conditions under which the enzymes can synchronize their catalytic steps, and discover that the coupling can lead to a significant enhancement in their overall catalytic rate. |
Jaime Agudo-Canalejo ; Tunrayo Adeleke-Larodo ; Pierre Illien ; Ramin Golestanian; |
850 | Using Knowledge-based Neural Ordinary Differential Equations to Learn Complex Dynamics and Chaos Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, I will present a universal learning framework for extracting predictive models of nonlinear systems based on observations. |
M. Ani Hsieh; |
851 | DBIO Dissertation Award (2021): Physics of Behavior Across Scales Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we introduce a unifying formalism that bridges between these scales. |
Antonio Carlos Costa; |
852 | Machine-Learning-Guided Discovery of 19F MRI Agents Enabled By Automated Copolymer Synthesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Modern polymer science suffers from the curse of multidimensionality. The large chemical space imposed by including combinations of monomers into a statistical copolymer … |
Olexandr Isayev; |
853 | An Interpretable Model for Polydiketoenamine Recyclability Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we identify design rules for recyclable PDK chemistries using an interpretable model. |
Rithwik Ghanta ; Kristin Persson ; Max Venetos ; Alexander Epstein ; Brett Helms ; Jeremy Demarteau ; Hai Wang; |
854 | Measuring Mechanical Properties at High-throughput Using Centrifugation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we develop a high-throughput colorimetric screening method for adhesion using a common laboratory centrifuge, multiwell plates, and microparticles. |
Muzhou Wang ; Yusu Chen ; Qifeng Wang ; Carolyn Mills ; Johanna Kann ; Kenneth Shull ; Danielle Tullman-Ercek; |
855 | Benchmarking Machine Learning Models for Polymer Informatics: An Example of Glass Transition Temperature Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The three major components in setting up an ML model are structure representations, feature representations, and ML algorithms. |
Ying Li ; Lei Tao ; Vikas Varshney; |
856 | Data-efficient Machine Learning Mimicking Human Intelligence in Fundamental Materials Science Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will give an introduction on data-efficient machine learning that mimics human intelligence in terms of creating digital counterpart of fundamental materials science concepts. |
Jian Yang ; Teresa Karjala ; Ellen Du ; Kyle Hart ; Babli Kapur ; YuanQiao Rao; |
857 | Using Transfer Learning to Leverage Prior Knowledge in The Prediction of Adhesive Free Energies Between Polymers and Surfaces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we demonstrate a transfer learning (TL) technique with a deep neural network (DNN) to improve the accuracies of ML models trained on small datasets when a larger database from a related system is available. |
Jiale Shi ; Yamil Colón ; Jonathan Whitmer; |
858 | Briding The Scale-Gap: Transfer Learning for Fudamental Polymer Properties Using Molecular-Dynamics Simulation Data Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we will discuss our recent effort to tackle the above challenge by combining MD simulation and transfer learning (TL). |
Umi Yamamoto ; Masahiro Kitabata; |
859 | Active Learning of Many-Body Transferable Coarse Grained Interactions in Polymers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we extend the idea of Gaussian process based on-the-fly active learning schemes applied to all-atom systems to coarse-grained applications of hydrocarbon liquids. |
Blake Duschatko ; Jonathan Vandermause ; Nicola Molinari ; Boris Kozinsky; |
860 | Phase Behavior Predictions of Binary Linear Polymer Solutions Using Machine Learning Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we show that a curated experimental data set consisting of 14 linear polymers and 46 solvents can be used to train machine learning models (random forest, XGBoost, and deep neural networks) to predict the cloud point temperature to within 3 °C, and capture various phase behaviors, ranging from upper and lower critical solubility curves, pressure effects (isopleths), and closed-loop behavior. |
Jeffrey Ethier ; Rohan Casukhela ; Joshua Latimer ; Matthew Jacobsen ; Richard Vaia; |
861 | Unsupervised Learning of Sequence-specific Aggregation Behavior for Model Copolymers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The machine learning algorithm we develop is able to classify the global aggregate structure directly using descriptions of the local environments. |
Antonia Statt ; Devon Kleeblatt ; Wesley Reinhart; |
862 | Molecular Dynamics Simulations Combined with Gaussian Process Regression to Investigate Block Copolymer Orientation in Thin Films Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This AE loop iterates to build a robust model of the system. |
Suwon Bae ; Marcus Noack ; Kevin Yager; |
863 | Microstructural Descriptors for Data-driven Prediction of Energetics and Structures of Polymer Mesophases Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we develop a set of sensitive lower-order microstructural descriptors for species density fields, which are generalizations of those previously designed for characterizing two-phase heterogeneous materials and are physically interpretable. |
Duyu Chen ; Yao Xuan ; Kris Delaney ; Hector Ceniceros ; Glenn Fredrickson; |
864 | Accelerating Langevin Field-Theoretic Simulation with Semantic Segmentation Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In order to accelerate the L-FTS, we introduce deep learning (DL). |
Daeseong Yong ; Jaeup Kim; |
865 | Emergent Behavior of Growing Bacterial Communities in Polymeric Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that, when the polymer is sufficiently concentrated, the cells grow in striking “cable-like” morphologies—in stark contrast to the compact morphologies that arise in the conventionally-studied polymer-free case. |
Sebastian Gonzalez La Corte ; Sujit Datta ; Ned Wingreen ; Tapomoy Bhattacharjee; |
866 | Mammalian Sperm Navigation in Response to Biochemical Factors Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, using microfluidic experimentation as well as theoretical and computational modeling, we explore bull sperm motion in response to pharmacological agonists to identify whether biochemical factors modulate sperm navigation. |
Meisam Zaferani ; Susan Suarez ; Alireza Abbaspourrad; |
867 | Evaporating Droplet Dynamics Enhances Bacterial Pathogenesis on Fomites Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This study demonstrates that dried bacterial morphologies (formed within minutes) on organic and inorganic surfaces, significantly contribute to enhanced pathogenesis of fomites that can last up to several days. |
Saptarshi Basu; |
868 | Geometry-driven Trapping and Escaping of Bacteria in Arrays of Micropillars Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we investigate a potential geometry-based abstraction of such interactions by considering bacteria of varying sizes in pillar arrays with given geometries. |
Pooja Chopra ; David Quint ; Ajay Gopinathan ; Bin Liu; |
869 | A Rheological Interpretation of Chirality-switching Vortices in Viscoelastic Active Fluids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Previous work has shown that a hydrodynamic model coupling active and viscoelastic stresses can reproduce the vortical states with globally oscillating chirality. |
Paarth Gulati ; Suraj Shankar ; M Cristina Marchetti; |
870 | Controlling Speed of Bacterial Active Droplets in A Nematic Environment Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigate the effect of the viscosity of the droplet medium on the propulsion speed of the droplets. |
Hend Baza ; Yuhan Wang ; Holly Matthews ; Oleg Lavrentovich; |
871 | Active Particle Transport in Disordered Porous Media Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Fluid suspensions of motile microswimmers such as bacteria and active colloids are often observed in porous environments, but the complexity of the medium geometry and its effect on particle dynamics makes the study of their transport properties challenging. |
Akhil Varma ; David Saintillan; |
872 | Locally Induced Analog Casimir Force from A Self-propelling Vibrating Robot Boat Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Inspired by the wave-mediated dynamics of surface-bouncing droplets, we study the motion and wave-field dynamics of a 5.9 cm radius, 8.8 cm tall, eccentric motor-driven vibrating robot boat on the surface of a 4 cm deep pool of water. |
Steven Tarr ; Enes Aydin ; Daniel Goldman; |
873 | Active Nematic Defect Control Via Variations in Oil Sublayer Thickness Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we develop a method to curve the surface of an isotropic oil layer via the wetting of cylindrical microfabricated pillars. |
Dimitrius Khaladj ; Linda Hirst; |
874 | Fluctuations in Pedestrian Dynamics Routing Choices Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work we analyse the role of fluctuations, related to pedestrians individual variability, in the emergent behaviors observed in crowd flows subject to binary path choices. |
Alessandro Gabbana ; Federico Toschi ; Alessandro Corbetta; |
875 | C. Elegans Motility in Self-healing Gels Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Together, our results will present an approach to maintain and image nematodes in 3D and harvest them from this medium for further processing. |
Saheli Dey ; Tapomoy Bhattacharjee; |
876 | Analysis of Steered Molecular Dynamics Study of Sickle Hemoglobin Protein in Water Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The study of sickled hemoglobin protein using nano scale molecular dynamics(NAMD) is performed for analyzing the binding mechanism and stability of protein. |
Jhulan Powrel ; Narayan Adhikari; |
877 | Understanding The Thermodynamic Driving Forces for Directed Motion at The Nanoscale Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have utilized theory and simulation to understand the influence of specific binding interactions and catalysis in driving molecular chemotaxis. |
Kathleen Krist ; William Noid; |
878 | Microtubules’ Dynamic Apolar Lane Formation and Long-Range Order on A Supported Lipid Bilayer Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this project, we studied MT-based active matter on a supported lipid bilayer. |
Fereshteh Memarian ; Niranjan Sarpangala ; Fabian Jan Schwarzendahl ; Joseph Lopes ; Madhuvanthi Athani ; Daniel Beller ; Kinjal Dasbiswas ; Ajay Gopinathan ; Linda Hirst; |
879 | What Is The Correct Physical Picture of Reflectin Protein Self-assembly? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This talk explores and weighs the evidence for several novel hypotheses of reflectin assembly mechanisms, including the free energy of the proteins’ association with lipid bilayers and the bilayers’ corresponding physical phases; the evidence for true patchy-colloid physics in reflectins; the possibility of a surface-induced phase transition; and the possible role of flexible metal coordination. |
Alison Sweeney ; Anjana Rajkumar-Kammath ; Irem Altan ; Charles Lomba; |
880 | Sensing The Shape of A Cell: Reaction-diffusion and Energy Minimization Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study polarity arising from Rho GTPase proteins cycling between active membrane-bound forms and inactive cytosolic forms – a wave-pinning reaction-diffusion process. |
Amit Singh ; Travis Leadbetter ; Brian Camley; |
881 | Robust Pattern Formation in Reaction-diffusion Systems in The Presence of Heterogeneity Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To demonstrate these results in our augmented model, we show that adding a continuous gradient in the intrinsic activator and inhibitor length scales leads to discrete steps in the emergent scale of the formed pattern. |
Anna Rasmussen ; Mikail Khona ; Sarthak Chandra ; Ila Fiete ; Mehran Kardar; |
882 | Ballistic Deposition with Memory:a New Universality Class of Surface Growth with A New Dynamical Scaling Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: By studying the statistics of surfaces in this model, we obtain three independent critical exponents: the growth exponent $\beta =5/4$, the roughening exponent $\alpha = 2$, and the new (size) exponent $\gamma = 3/4$. |
Ahmed Roman ; Ruomin Zhu ; Ilya Nemenman; |
883 | Mechanochemical Coupling Enables Propagating Patterns Without Diffusion Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We demonstrate that depending on key parameters, for example the threshold in activation of cell’s mechanical response or the shell thickness, the mechanochemical feedback gives rise to qualitatively different deformation patterns such as ridges and spots that are robust to changes in shell geometry. |
Andrei Zakharov ; Kinjal Dasbiswas; |
884 | Towards A Quantitative Understanding of Spontaneous Mitotic Waves Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Instead, we explore a known spatial coordination mechanism: waves. |
Owen Puls ; Qiong Yang; |
885 | Honeycomb Formation Under Geometric Frustration Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we study how bees collectively adapt their environment to regulate and heal the honeycomb structure. |
Golnar Fard ; Francisco Lopez Jimenez ; Orit Peleg; |
886 | Frustrated Frustules: Geometric Frustration in Diatom Frustules Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In our work we investigate the intricate arrangement of the microstructure pattern of the diatom C.granii and related species. |
Maria Feofilova ; Eric Dufresne; |
887 | Biological Pattern Formation in Spatio-temporally Fluctuating Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The study of biological pattern-forming systems has revealed generic features that promote robustness with respect to variations between cells or populations in morphogen and protein production rates. |
Philip Pearce ; Mohit Dalwadi; |
888 | Directing Protein-based Patterns with Advective Bulk Flow Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work demonstrates how hydrodynamic flow can be used to control protein-based pattern formation and to gain insight into the underlying pattern forming mechanisms. |
Fridtjof Brauns ; Jerney Finzgar ; Sabrina Meindlhumer ; Cees Dekker ; Erwin Frey; |
889 | Organizing Principles Shared Between Intracellular Protein Patterns and Intracellular Condensates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We show that similar concepts underlie both cellular self-organization processes and that these parallels allow us to use the same basic approaches to understand liquid-liquid phase separation and protein pattern formation. |
Henrik Weyer ; Fridtjof Brauns ; Tobias Roth ; Erwin Frey; |
890 | Reconstructing Spatiotemporal Protein Patterns in Heterogeneous Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We will discuss multiscale patterns of the Min protein system, a paradigmatic model for pattern formation, in a spatially heterogeneous setup. |
Laeschkir Würthner ; Fridtjof Brauns ; Grzegorz Pawlik ; Jacob Halatek ; Jacob Kerssemakers ; Cees Dekker ; Erwin Frey; |
891 | Smart Microscopic Robots Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we report the creation of microscopic robots that meet this standard. |
Paul McEuen; |
892 | Why Does A Viscous Friction Ansatz Give Accurate Multi-contact Coulomb Friction Predictions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We previously presented a geometric connection model for friction-dominated multi-legged locomotion with slipping using a Coulomb-viscous friction ansatz. |
Ziyou Wu ; Shai Revzen; |
893 | Biologically Inspired Actuation Via Electromagnetic Motors Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We explore the benefits of implementing biologically inspired actuation in electromagnetic motors by means of a proportional-integral-differential (PID) controller. |
Jake McGrath; |
894 | Mapping An Outdoor Odor Plume Using A Mobile Chemical Sensor Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our analysis shows that for higher wind speeds, whiff durations decrease and encounter frequency increases at greater distances from the source. |
Arunava Nag; |
895 | Bulk Electrochemical Actuators for Microscopic Robots and Microscale Medical Tools Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We demonstrate microscopic electrically controllable actuators fabricated using CMOS compatible methods exhibiting a larger work density than any offered actuator technology. |
Jacob Pelster ; Qingkun Liu ; Wei Wang ; Michael Reynolds ; Itai Cohen ; Paul McEuen; |
896 | Uncovering The Mechanisms of Wing Damage Compensation in Insect Flight Using Control Theory and Robophysics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using system identification techniques, we found that wing damage subtly reduced flight performance. |
Wael Salem ; Benjamin Cellini ; Heiko Kabutz ; Hari Krishna Hari Prasad ; Bo Cheng ; Kaushik Jayaram ; Jean-Michel Mongeau; |
897 | Simultaneous Leg Impacts Lead to A Differentiable Flow Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present experimental validation of this finding on a 3-legged hopping robot with springy legs by showing that all 6=3! |
Marion Anderson ; Shai Revzen; |
898 | Performance Trade-offs in A Latch-mediated Spring Actuated Robotic Jumper Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we experimentally investigate robotic jumpers designed with an integrated latch-mediated spring actuation (LaMSA) system. |
Tanvi Krishnan ; Sathvik Divi ; Ryan St. Pierre ; Sarah Bergbreiter ; Mark Ilton; |
899 | Incorporating A Time History of Ambient Wind Improves Odor Plume Tracking Success in Simulated Flying Agents Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In our study, we gave our agents a memory of wind direction which it uses along with “surge and cast” to generate a collection of finite candidate routes. |
TAMZEED ELAHI ; Floris van Breugel; |
900 | Enabling Power and Control Autonomy for Insect Scale Robo-Physical Models Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we have devised modular and scalable solutions for our insect scale robo-physical model CLARI (compliant legged articulated robot insect). |
William McDonnell ; Kaushik Jayaram; |
901 | Accelerating Multi-contact Modeling Using A GPU Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we report on advances we made in GPU acceleration of this computation, with the goal of demonstrating brute-force trajectory planning for a hexapedal robot with slipping. |
Advait Deshpande ; Ziyou Wu ; Shai Revzen; |
902 | Self-organized Robotic Locomotion By Closing The Propriosensory Feedback Loop Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigate how motion primitives are generated for wheeled and hexapod-type robots using a simple neural controller with propriosensory feedback. |
Bulcsú Sándor ; Michael Nowak ; Claudius Gros; |
903 | Simple Motions As Templates for Generating Gait Spaces of Robophysical Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work attempts to mathematically describe the complete set of motions of a broad class of models using fundamental concepts from the fields of nonlinear dynamics and topology. |
Nelson Rosa ; Maximilian Raff ; C. David Remy; |
904 | Sensitive Thermometry Through Criticality in Voltage-coupled TRP Channels Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we propose a theoretical model wherein sensitivity arises due to the diverging susceptibility close to a critical point. |
Isabella Graf ; Sarah Veatch ; Benjamin Machta; |
905 | Tissue Confinement Governs Cell Size Regulation in Epithelium Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce a concept of tissue confinement which describes the extent to which spatial constraints suppress cell growth in different tissues. |
John Devany ; Martin Falk ; Liam Holt ; Arvind Murugan ; Margaret Gardel; |
906 | Identifying Key Network Features Coordinating Robust Collective Signaling Oscillations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work sheds light on the basic principles in single-cell signaling networks that drive robust population oscillations in biochemically-coupled systems. |
Chuqiao Huyan ; Alexander Golden ; Xinwen Zhu ; Pankaj Mehta ; Allyson Sgro; |
907 | Modeling Collective Cell Migration on Substrates with Topological Defects Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose two potential mechanisms that can lead to increased density at the defect core: first, collective spiraling motion driven by coherent migration, and second, the regulation of proliferation by cell area and aspect ratio. |
Kurmanbek Kaiyrbekov ; Brian Camley; |
908 | Synchrony and Causality in Stimulated Communicating Cell Populations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we investigate the relationships between cell-cell communication, synchrony, and causality using a simple excitable-response model to describe experiments performed in monolayers of kisspeptin neurons stimulated by time-varying ATP concentrations. |
Ryan LeFebre ; Guanyu Li ; Patrick Chappell ; Bo Sun ; Andrew Mugler; |
909 | Developmentally Driven Formation and Dissolution of Living Chiral Crystals Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce a minimal hydrodynamic model that is fully parameterized by experimental measurements of single embryos and can quantitatively describe the stability, formation and rotation of emerging living crystals. |
Alexander Mietke ; Tzer Han Tan ; Junang Li ; Yuchao Chen ; Hugh Higinbotham ; Peter Foster ; Shreyas Gokhale ; Jörn Dunkel ; Nikta Fakhri; |
910 | Optical Flow-based Characterization of Serotonergic Modulation of Crayfish Hindgut Motility Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To explore this relationship further, we study a simple crayfish model and capture its hindgut motility under denervation and serotonergic excitation. |
Spandan Pathak ; Norma Peña-Flores ; Phillip Alvarez ; Jenna Feeley ; Wolfgang Losert ; Jens Herberholz; |
911 | The Role of Positional Information in Collective Gradient Sensing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We apply maximum likelihood estimation to study gradient sensing accuracy when cells have limited positional information. |
Emiliano Perez Ipina ; Brian Camley; |
912 | Self Tuned Criticality Amplifies Signals in Bacterial Chemotaxis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we propose a model where chemoreceptors act as the edges for the percolation of activity between signaling proteins. |
Derek Sherry ; Samuel Bryant ; Thierry Emonet ; Isabella Graf ; Benjamin Machta; |
913 | Relating Division, Migration, and Cell Signaling During Collective Cell Migration Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The ERK signaling pathway is key for many forms of cell-cell signaling, and here we study the interplay between ERK signaling, collective migration, and tissue proliferation in epithelia. |
Kevin Suh ; Daniel Cohen ; Jared Toettcher ; Richard Thornton; |
914 | Tunning to Criticality in The Cochlea with Local Information Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work suggests a new perspective on the hearing mechanism: Instead of individual hair cells being critical, their concerted individual action tunes the whole cochlea to a critical point revealing a collective organization principle in the inner ear. |
Asheesh Momi ; Julian Rubinfien ; Isabella Graf ; Benjamin Machta; |
915 | Defining "success" for Pairwise Maximum Entropy Models Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Despite their ubiquity, deciding whether these models "work" remains a challenge. |
Leenoy Meshulam ; Jeffrey Gauthier ; Carlos Brody ; David Tank ; William Bialek; |
916 | Higher Accuracy Due to Higher Speeds in Copying Information Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We derive conditions under which proofreading mechanisms can evolve under selection for higher speed alone, without any pressure to reduce mutation rates. |
Riccardo Ravasio ; Kabir Husain ; Marco Ribezzi-Crivellari ; Arvind Murugan; |
917 | Evolution of Mutation Rates Is Determined By Short Term Costs and Long Term Benefits in Proofreading Polymerases Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we study the evolution of mutation rates in proofreading polymerases using a self-replicating plasmid system in yeast. |
Vedant Sachdeva ; Kabir Husain ; Riccardo Ravasio ; Wanqiang Liu ; Benjamin Good ; Arvind Murugan; |
918 | Signatures of An Evolutionary Capacitor from A High-resolution Luria-Delbruck Assay Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Pre-existing genetic diversity drives adaptation, but the factors that determine standing genetic variation in a population remain poorly understood. The chaperone Hsp90 has been … |
Kabir Husain ; David Pincus ; Arvind Murugan; |
919 | Inferring Epistasis from Deep Mutational Scanning Data Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a method drawing on previous theoretical advances in population genetics [1] to interpret not only the functional effects of single genetic variants but also the epistasis effects from DMS data. |
Zhenchen Hong ; John Barton; |
920 | Dynamics of Bacterial Recombination in The Human Gut Microbiome Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we will show how the broad range of timescales within the human gut microbiota provides new opportunities to measure individual recombination events directly, leveraging nonparametric approaches that require minimal population genetic assumptions. |
Zhiru Liu ; Benjamin Good; |
921 | Core Genes Can Have Higher Recombination Rates Than Accessory Genes Within Global Microbial Populations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we apply a non-phylogenetic approach to infer homologous recombination rates in the core and accessory genome (genes present in all strains and only a subset of strains, respectively) using >100,000 whole genome sequences from 12 microbial species. |
Asher Preska Steinberg ; Mingzhi Lin ; Edo Kussell; |
922 | Hybridization Driven By Selection Is A Major Source of Genetic Diversity in A Natural Bacterial Population Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this question, we used single cell genomics to sequence a large, unbiased sample from a population of thermophilic cyanobacteria. |
Gabriel Birzu ; Devaki Bhaya ; Daniel Fisher; |
923 | Eco-evolutionary Response of Complex Ecosystems to Changing Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We explore this eco-evolutionary feedback via a consumer-resource model to account for evolution. |
Jim Wu ; David Schwab ; Anne-Florence Bitbol; |
924 | Effects of Light and Nutrients on The Growth of Algal Cells Revealed By A Microfluidic Platform Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this presentation, we systematically studied the growth kinetics of Chlamydomonas reinhardtii, under a light intensity gradient, a nitrogen (N) concentration gradient, and combined light and N gradients. |
Fangchen Liu ; Larissa Gaul ; Mohammad Yazdani ; Beth Ahner ; Mingming Wu; |
925 | Acetate Inhibits Bacterial Growth By Shrinking The Metabolite Pool Size Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present a quantitative physiological study of E. coli under acetate stress, complemented by proteomic and metabolomic analysis. |
Brian Taylor ; Vadim Patsalo ; Joshua Rabinowitz ; Yihui Shen ; Terence Hwa ; Hiroyuki Okano ; James Williamson ; Zhongge Zhang; |
926 | Population Dynamics of Mitochondrial Genomes in Saccharomyces Cerevisiae Reveal Tightly Constrained Mutational Trajectories and A Simple Relationship Between Genome Content and Replicative Fitness Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this, we utilize long read single-molecule sequencing to track the mutational trajectories of mtDNA in Saccharomyces cerevisiae (budding yeast). |
Christopher Nunn ; Sidhartha Goyal; |
927 | Spontaneous Mutations Emerge As Drivers of De Novo Gene Birth in A Minimal Evolutionary Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose here that spontaneous mutations are potential drivers of gene birth. |
Somya Mani ; Tsvi Tlusty; |
928 | Chromatin Network Retards Droplet Coalescence Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our study suggests that nucleoli-chromatin interactions facilitate droplets’ nucleation but hinder their coarsening due to the coupled motion between droplets and the chromatin network: as droplets coalesce, the chromatin network becomes increasingly constrained. |
Bin Zhang; |
929 | Rheological Properties of Chromatin and Nuclear Microenvironment in Living Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we use genomic-locus tracking and polymer models to characterize the viscoelasticity of chromatin and the surrounding nuclear environment. |
Yu-Chieh Chung ; Madhoolika Bisht ; Li-Chun Tu; |
930 | Active Dynamics of Chromosome Polymers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we propose an active polymer model for chromosomes, where microscopic activity leads to non-equilibrium fluctuations at the coarse-grained length scales. |
Sumitabha Brahmachari ; Tomer Markovich ; Fred MacKintosh ; Jose Onuchic; |
931 | Phase Separation and Correlated Motions in Motorized Genome Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we studied the impact of non-equilibrium activities on the structural dynamics and organization of the human genome. |
Zhongling Jiang ; Bin Zhang; |
932 | When Motors Collide: How Transcription and Loop-extruding Cohesins Organize Chromatin Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We analyze chromosome conformation capture (Hi-C) data near active genes, including in conditions in which cohesin dynamics or transcription are perturbed. |
Edward Banigan ; Wen Tang ; Aafke van den Berg ; Roman Stocsits ; Gordana Wutz ; Hugo Brandão ; Georg Busslinger ; Jan-Michael Peters ; Leonid Mirny; |
933 | Limited Spreading Enzyme Stabilizes Epigenetic Memory Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We introduce a minimal biophysical model stylizing chromatin and its dynamics through the cell cycle, in which modifying enzymes "spread" marks between nearby histones and marked histones experience self-attraction. |
Jeremy Owen ; Dino Osmanovic ; Leonid Mirny; |
934 | 4D Chromosome Organization: Combining Polymer Physics, Knot Theory and High Performance Computing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk I will present a novel data-driven modeling approach, 4DHiC, and demonstrate a number of possibilities that this method holds. |
Anna Lappala ; Jeannie Lee ; Kevin Tan ; Karissa Sanbonmatsu; |
935 | Nucleosome-scale Structure Drives Linker Histone Enrichment in Heterochromatin in Silico Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work we introduce a multi-scale polymer model for chromatin which captures both megabase-scale phase separation and nucleosome-scale physics, explicitly accounting for the effects of both DNA linker length and H1 binding. |
Aria Coraor ; Juan De Pablo; |
936 | Differential Regulation of Alternative Promoters Emerges from Unified Kinetics of Enhancer-promoter Interaction Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using a theoretical model to relate promoter activity to enhancer states, we show that the two promoters follow common transcription kinetics driven by sequential Bcd binding at the two enhancers. |
Heng Xu; |
937 | Mesoscale Mixing of Chromosomes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we present our simulations of how the extent of chromosome mixing dynamics changes over time, as a function of the chromosome volume fraction, self-interactions, and binding to the lamina. |
Gaurav Bajpai ; Samuel Safran; |
938 | Impact of Cytosolic Crowders on The Morphology of Bacterial Chromosomes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Motivated by such observation, we consider a "feather-boa" type model of chromosome in the presence of non-additive crowders, encapsulated inside cylindrical confinement. |
Amit Kumar ; Pinaki Swain ; Bela Mulder ; Debasish Chaudhuri; |
939 | Changes in Biomechanical Properties of Neuronal Cells Measured By Combined Atomic Force and Fluorescence Microscopy Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find a power law relationship between cell elastic modulus and volume, and propose a simple model, based on elastic properties of biopolymer networks, that predicts the observed relationship. |
Cristian Staii; |
940 | Development of A 3D Microfluidic Platform for Dynamic Compression of Tumor Spheroids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we have developed a high-throughput microfluidic platform to study tumor spheroids under well-controlled dynamic compressive loads. |
Young Joon Suh ; Mrinal Pandey ; Jeffrey Segall ; Mingming Wu; |
941 | Flow and Forces on A Rigid Osteocyte Immersed in Bone: Effects of The Flow Network and Pericellular Matrix Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study we use a two-dimensional model of a rigid osteocyte in a canalicular network to consider the questions of how the number of canaliculi and pericellular matrix may affect force generation on the osteocyte. |
Jared Barber ; Luoding Zhu ; Hiroki Yokota ; Sungsoo Na; |
942 | Extracellular Matrix Viscoelasticity and Its Impact on Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using hydrogels with tunable viscoelasticity for 3D cell culture, we have found that matrix viscoelasticity regulates the morphogenesis of pluripotent stem cells, cell migration, and cell division. |
Ovijit Chaudhuri; |
943 | Probing Mechanical Interactions Between Lamellipodia and Surrounding Mechanical Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To better understand the mechanical interactions, we developed an agent-based model of a branched actin network consisting of F-actin and Arp2/3 with myosin motors and an underlying substrate. |
June Hyung Kim ; Taeyoon Kim; |
944 | Cell Spreading and Migration on Viscoelastic Substrates: A Bio-chemo-mechanical Multiscale Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The proposed framework takes into account the feedback between the biochemical and biomechanical events and integrates the motor-clutch model at the sub-cellular scale with the cell structural analysis at the global level. |
Wenya Shu ; C. Nadir Kaplan; |
945 | Hydraulics of Cellular Extension and Contraction in Lacrymaria Olor Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our current work provides a new approach for exploring extreme dynamical shape changes in eukaryotic cells. |
Samhita Banavar ; Eliott Flaum ; Manu Prakash; |
946 | Topological Brakes in An Ultrafast Giant Cell Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To study cellular adaptations under extreme forces, we study the ultrafast contractions (50% body length contraction within 5-10 msec, peak acceleration 15g) in Spirostomum ambiguum, a giant single cell organism, as a model system. |
Ray Chang ; Manu Prakash; |
947 | Hyaluronan-rich Biomimetic Glycocalyx Mechanically Drives Focal Adhesion Dynamics and Cell Shape Deformation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Given the range of biological processes that involve HA-rich glycocalyx, from synaptogenesis to cell migration and division to immune cell interactions, this work provides critical insight into the mechanoresponse of cells exposed to their own changing glycocalyx or that of others. |
Yu Jing ; Jessica Faubel ; Katherine Powell ; Shlomi Cohen ; Jennifer Curtis; |
948 | Nanotopographic Surfaces Alter Actin Dynamics in Primary Rat Astrocytes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We characterize astrocytes’ responses to these mechanical cues and use micron-scale alterations in actin dynamics to understand the cellular-level response to changes in the extracellular microenvironment. |
Kate O’Neill ; Emanuela Saracino ; Tamara Posati ; Roberto Zamboni ; Valentina Benfenati ; Wolfgang Losert; |
949 | Deciphering Vimentin-Microtubule Interactions in Cell Polarity Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using wild-type and vimentin- null mice embryonic fibroblast (mEF), we found that vimentin null cells exhibit lower expression of the centrosome protein CEP215 compared to wild-type cells. |
Renita Saldanha; |
950 | A Mathematical Model of Chemotactic Endothelial Cell Migration in A Fibrin-based Hydrogel Extracellular Matrix Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a phase field model and experiments to study the collective EC migration considering the chemotactic and the mechanotactic stimuli. |
Ferré ; Josep Torres; |
951 | Stick-slip Model of Cell Crawling Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will discuss a theoretical model combining the stochasticity of cell-substrate adhesion and linear cell visco-elastic mechanics, in which the force-sensitive unbinding of adhesion bonds leads to a stick-slip dynamics. |
Pierre Sens; |
952 | Soft, Biologically Inspired Materials for Neuromorphic Memristors and Memcapacitors Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This talk will describe the development and characterization of neuromorphic elements for brain-inspired computing such as memristors and memcapacitors assembled from soft materials like lipids, polymers, peptides, proteins, and redox-active molecules. |
Charles Collier; |
953 | Machine Learning Approach to Identify Critical Configurations for Strong Electronic Coupling Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we develop an automated method to calculate electronic coupling that considers the effect of polarization and hence gives a more accurate description. |
Puja Agarwala ; Shane Donaher ; Baskar Ganapathysubramanian ; Enrique Gomez ; Scott Milner; |
954 | The Use of Small Angle Neutron Scattering Data to Support Dark Field Data Analysis in Far-field Interferometry Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: One limitation is that it provides a sample-averaged view of the structure, making the study of heterogeneous materials difficult with SANS alone. |
Caitlyn Wolf ; Youngju Kim ; Peter Bajcsy ; Paul Kienzle ; Daniel Hussey ; Katie Weigandt; |
955 | High-throughput Microrheology of Polymer Solutions and Gels Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we report a new method for extracting microrheology information using differential dynamic microscopy (DDM). |
Matthew Helgeson ; Yimin Luo ; Alexandra Bayles ; Yuekun Heng ; Maneesh Gupta ; Todd Squires ; Megan Valentine ; Matthew Helgeson; |
956 | Predicting The Glass Transition of Complex Polymers Via Integration of Machine Learning, Theory and Molecular Simulations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we establish an integrated framework based on machine learning (ML) and molecular simulations to predict T g for a diverse set of CPs and other polymers with a drastic difference in their chemical structures. |
Wenjie Xia ; Amirhadi Alesadi ; Zhaofan Li ; Zhiqiang Cao ; Xiaodan Gu; |
957 | Diverse Property-spectrum of Flavors of Polyolefins: A Data Analysis Study Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Such data analysis studies are useful (1) to obtain a comprehensive understanding of the sources of property value variations, and (2) improving existing machine learning models for property prediction by incorporating features in the fingerprint (i.e., representation of polymers) derived from key features known to affect properties. |
Arunkumar Rajan ; Oliver Hvidsten ; Chiho Kim ; Rampi Ramprasad; |
958 | Machine Learning Discovery of Multi-Functional Polyimides Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Aiming to discover high-performance polyimides, we utilize computational methods of machine learning (ML) techniques and molecular dynamics (MD) simulations. |
Lei Tao ; Jinlong He ; Vikas Varshney ; Ying Li ; Wei Chen; |
959 | HI Vs AI: Designing Solvent-free Brush Networks with Tissue-like Mechanical Properties Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We developed a design strategy of solvent-free networks made by crosslinking brush-like strands which is based on a theoretical model of the nonlinear network deformation and Machine Learning approach. |
Andrey Dobrynin ; Sergei Sheiko ; Anastasia Stroujkova; |
960 | Illuminating Stress and Failure in Polyethylene with A Neural Network Potential Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have thus trained a neural network potential (NNP) based on the SCAN density functional potential energy surface which yields energies within 1 meV/atom of the ab-initio results yet is several orders of magnitude more efficient. |
Mark Dellostritto ; Simona Percec ; Michael Klein; |
961 | Machine Learning-based Study of Mechanical Properties of Dynamically Crosslinked Polymer Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we utilize Molecular Dynamics (MD) simulations to investigate the relationship between polymer network configuration and the resulting mechanical properties of crosslinked polymer composites. |
Mehdi Zanjani ; Alexandra Filiatraut; |
962 | Application of Machine-learned Constitutive Relations for Well-entangled Polymer Melt Flows Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this presentation, we will use benchmark Multi-Scale simulation results to present a detailed error analysis of our ML predictions and their computational efficiency. |
Souta Miyamoto ; John Molina ; Takashi Taniguchi; |
963 | Machine Learning Parametrization of A Coarse-grained Epoxy Model at Varying Crosslink Density Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: A persistent challenge in molecular modeling of thermoset polymers is capturing the effects of chemical composition and degree of crosslinking (DC) on dynamical and mechanical properties with high computational efficiency. |
Andrea Giuntoli ; Nitin Hansoge ; Anton van Beek ; Zhaoxu Meng ; Wei Chen ; Sinan Keten; |
964 | Identifying Accelerated Ageing Pathways for Cross-Linked Polyethylene Pipes Using Principal Component Analysis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We used infrared (IR) microscopy to build a database of high-spatial resolution spectra of cross-sections of pipes subjected to different types of accelerated ageing. |
Michael Grossutti ; Melanie Hiles ; Joseph D’Amico ; William Wareham ; Benjamin Morling ; Scott Graham ; John Dutcher; |
965 | The Multi-scale Nature of Leaf Growth – Fluctuations, Timescales and Adaptation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We try to expose the characteristics of the growth field dynamics by measuring the evolving leaf surface with high spatio-temporal resolution. |
Eran Sharon; |
966 | Benchmarking Growth – How Fast Do Plant Cells Expand During Development? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In our meta-analysis, we aim to standardise the growth rate data presented in several articles in order to make a direct comparison between studies of the same plant organ. |
Viraj Alimchandani ; Anne-Lise Routier ; Elvis Branchini; |
967 | The Impact of Pathogenic and Abiotic Stress on Nutrient Cycling Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In Part 1 of this talk, we describe ongoing efforts to characterize the relationship between pathogens, hosts, and the microbiome using genomics and ecological modeling. |
Benjamin Weiner; |
968 | Leaf Voltage Differences Induced By Fluctuating Light: A Proxy for The Electron Transport? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The aim of this study is to correlate these voltage differences with the photosynthetic electron transport, as a new direct method for carbon assimilation measurements of several plant organs and to unravel plant interactions with the natural environment. |
Nicole Salvatori; |
969 | GIWAXS Reveals Interactions Between Cellulose and Matrix Polysaccharides in Plant Primary Cell Walls Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we used grazing incidence wide angle X-ray scattering (GIWAXS) to investigate the effect of defective cell wall biosynthesis on the nanoscale organization of cellulose in primary cell walls. |
Sintu Rongpipi ; William Barnes ; Oskar Siemianowski ; Dan Ye ; Joshua Del Mundo ; Sydney Duncombe ; Xiaoran Xin ; Chenhui Zhu ; Michael Toney ; Ying Gu ; Charles Anderson ; Enrique Gomez ; Esther Gomez; |
970 | In Vitro Experiments and Kinetic Models of Pollen Hydration Show That MSL8 Is Not A Simple Tension-gated Osmoregulator Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We found that a mathematical model wherein MSL8 acts as a simple tension-gated osmoregulator does not replicate this behavior. |
Elizabeth Haswell ; Anders Carlsson ; Kari Miller ; Wanda Strychalski ; Masoud Nickaeen; |
971 | Parallelized Plant Morphogenesis in A Controlled Microfluidic Environement Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To quantify this process we developed a microfluidic system to follow several individuals growing in parallel under the same controlled conditions. |
Valentin LAPLAUD ; Arezki Boudaoud ; Stephanie Drevensek; |
972 | The Unique Transfusion Tissue in Conifer Needles: The Bridge Between Production and Transport. II. Transport Efficiency Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We argue that this is related to the way sugars are loaded into the phloem for efficient sugar transport. |
Tomas Bohr ; Henning Poulsen ; Carsten Gundlach ; Sean Marker ; Chen Gao ; Alexander Schulz; |
973 | The Unique Transfusion Tissue in Conifer Needles: The Bridge Between Production and Transport. I. Structure and Function Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have studied the needles of P. pinaster using X-ray tomography on living needles and by TEM. |
Sean Marker ; Tomas Bohr ; Alexander Schulz ; Chen Gao ; Carsten Gundlach ; Henning Friis Poulsen; |
974 | How Memory Shapes Shoot Gravitropism Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we aim to determine the memory kernel underlying shoot gravitropism. |
Mathieu Rivière ; Hugo Chauvet-Thiry ; Bruno Moulia ; Yasmine Meroz; |
975 | Probing Time-dependent Gravitropic Response in Rice Roots Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present results from experiments in which rice roots ( O. sativa) are rotated between 0 and 90 degrees, with respect to gravity, at various frequencies. |
Madison Hales ; Aradhya Rajanala ; Isaiah Taylor ; Philip Benfey ; Daniel Goldman; |
976 | A Mechano-Sensing Mechanism for Waving in Plant Roots Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose a mechano-sensing model for root-waving, based on a combination of friction induced by gravitropism, the elasticity of the root and the anchoring of the root to the agar by thin hairs, and demonstrate its relevance to previously obtained experimental results. |
Ido Regev ; Zhenwei Zhang ; Danie van Ophem ; Raghunath Chelakkot ; Naftali Lazarovitch; |
977 | Modeling Plant Root circumnutation using Cellular Simulation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We develop a numerical simulation using a DEM (Discrete Element Modeling) approach to model plant roots to study circumnutation as an emergent property of cell level behaviors. |
Aradhya Rajanala ; Mingyuan Zhu ; Isaiah Taylor ; Christopher Pierce ; Madison Hales ; Philip Benfey ; Daniel Goldman; |
978 | Root Growth Response to Rigid Obstacles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our research aims at studying the impact of mechanical stress on a primary root growing inside a soft homogeneous soil and encountering a single rigid obstacle such as a stone or a hard pan. |
Manon Quiros ; Evelyne Kolb ; Marie-Béatrice Bogeat-Triboulot ; Etienne Couturier; |
979 | Waving and Skewing of Arabidopsis Thaliana Roots Results from Mechanical Interactions with The Substrate Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a novel numerical solver based on a Cosserat rod integrator and a quasi-static integration scheme, which allows to quantitatively investigate how growing rod-like organs mechanically interact with their environment, for the first time. |
Amir Porat ; Yashraj Bhosale ; Arman Tekinalp ; Mattia Gazzola ; Yasmine Meroz; |
980 | Sloppy Model Analysis of Bifurcations in Biochemical Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This paper shows how sloppy analysis can apply directly to bifurcations, including the normal-form of all major types and multi-parameter multi-variable systems with no obvious simplifying reparameteriziation. |
Christian Anderson ; Mark Transtrum; |
981 | Excitable Mechanics Embodied in A Walking Cilium Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, studying an animal without neurons or muscles, we report analogous excitable and multistable dynamics embedded in the physics of a ‘walking’ cilium. |
Matthew Bull ; Laurel A. Kroo ; Manu Prakash; |
982 | Evolution of Schooling and Exploration Strategies in The Mexican Tetra Fish Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk I will present results on the collective dynamics of groups of fish from surface and cave populations and discuss the implications of the observed inter-population differences on the way each population explores its environment. |
Yaouen Fily ; Adam Patch ; Alexandra Paz ; Karla Holt ; Erik Duboué ; Alex Keene ; Johanna Kowalko; |
983 | Riding The CAMP Wave: Maximizing Cell Migration By Slow Chemoattractant Waves Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This study may help us devise strategies to maximize cell migration efficiency. |
Aravind Rao Karanam; |
984 | Cellular Crowd Control: Improving External Control of Collective Cell Migration By Modulating Existing Cell-cell Coordination Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we investigate two major questions: 1) how much does the strength of an endogenous collective behavior in a tissue limit our ability to control its collective cell migration, and 2) how can we circumvent such limitations? |
Gawoon Shim ; Daniel Cohen ; Danelle Devenport; |
985 | Cellular Integration of Physical and Biochemical Damage Signals in The Generation of Tissue-level Wound Responses Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have developed a computational model to test the plausibility of multiple hypothesized mechanisms driving these calcium signals and to further understand the underlying biology. |
Aaron Stevens ; James O’Connor ; Andrew Pumford ; Hannah Kim ; Caroline Howell ; Lila Nassar ; Shane Hutson ; Andrea Page-McCaw; |
986 | A Celluar Potts Model for Collective Cell Migration Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present two applications of the Cellular Potts Model (CPM) to describe different collective migration patterns that are experimentally observed: 1) coherent rotational motion during aggregation of social amoeba Dictyostelium discoideum cells and, 2) distinct invasion modes of cancer cells embedded in extracellular matrix (ECM). |
Man Ho Tang ; Wouter-Jan Rappel ; Stephanie Fraley ; William Leineweber ; Sural Ranamukhaarachchi ; Alyssa Walker; |
987 | Computational Model for Migration of Human Osteoblasts in Direct Current Electric Field Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a computational model that takes into account cell interactions and describes cell migration in direct current electric field. |
Jonathan Dawson ; Tina Sellmann ; Katrin Porath ; Rainer Bader ; Ursula van Rienen ; Revathi Appali ; Rüdiger Köhling; |
988 | Collective Curvature Sensing and Fluidity in Three-dimentional Multicellular Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose a physical mechanism in which cells naturally form hexagonally organized clusters to minimize free energy, where the size of these clusters is limited by an elastic bending energy penalty induced by substrate curvature. |
Wenhui Tang ; Dapeng(Max) Bi ; Ming Guo; |
989 | Collective Contact Guidance Triggers Polar Laning of Turbulent Epithelial Monolayers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we show that, when plated on subcellular grooves, a confluent monolayer of human bronchial epithelial cells spontaneously organizes into supracellular alternating millimeter-long polar lanes that migrate in antiparallel directions. |
Mathilde Lacroix ; Bart Smeets ; Carles Blanch-Mercader ; Samuel Bell ; Caroline Giuglaris ; Jacques Prost ; pascal silberzan; |
990 | 3D Porous Liquid Crystal Elastomer Scaffolds As Cell Supports for Long-term Tissue Cultures Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: I will present mechanically tunable, biocompatible, and biodegradable liquid crystal elastomers and elastomers with a porous structure that have been made to specifically address the needs of two distinctive cell lines. |
Senay Ustunel ; Marianne Prévôt ; Grace Rohaley ; Robert Clements ; Elda Hegmann; |
991 | Enhanced Strength and Shape Memory in Microgel Filled Biopolymer Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that this combination of material components synergistically enhances the system material properties. |
Vignesh Subramaniam ; Thomas Angelini; |
992 | E-cadherin Substrates Alter The Biophysics of Collective Cell Migration and Proliferation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigate this by patterning zones of E-cadherin – a key cell-cell adhesion protein – and collagen on culture surfaces and explore how this ‘cell-mimetic’ biomaterial influences collective cell behaviors in macro-scale epithelial monolayers. |
Youn Kyoung Cho ; Kevin Suh ; Daniel Cohen; |
993 | Effect of Extracellular Matrix Age on Disease Progression Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk I will present our research in understanding biophysical and biochemical changes in the native tissue matrix with age and our efforts to create engineered tissue models that possess these variables to study myocardial infarction and breast cancer progression. |
Pinar Zorlutuna; |
994 | Cas Nucleases Binding Selectivity Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To further build upon previously established knowledge of CRISPR binding activity, selectivity and efficiency, we study analytical solutions to first passage times which can be successfully exploited to model binding affinity, and precision, across several Cas nucleases. |
Pete Rigas; |
995 | Topology-dependent Hole Transfer in G-quadruplex By Molecular Dynamics and Density Functional Theory Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we investigate such effects, by a combination of classical simulations of the structure and dynamics and quantum calculations of electronic couplings. |
Samprita Nandi ; Angel-Emilio Villegas Sanchez ; Colin Coane ; Angana Ray ; Rosa Di Felice; |
996 | The Mesoscale Order of Nacreous Pearls Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: By characterizing the entire structure of pearls (~3 mm) in cross-section at high resolution, we show nacre has medium-range mesoscale periodicity. |
Robert Hovden ; Jiseok Gim ; Alden Koch ; Laura Otter ; Benjamin Savitzky ; Sveinung Erland ; Lara Estroff ; Dorrit Jacob; |
997 | Enhancing Sustainability of Palm-Leaf Foodware By Secretion of Surface Wax Layer Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study diffusion of water through the sheath using mass gain measurements and in situ observations of water transport. |
Debapriya Pinaki Mohanty ; Anirudh Udupa ; Mysore Dayananda ; Srinivasan Chandrasekar; |
998 | Electrospray Deposition As An Efficient Alternative to Coat Medical Devices Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We envision SLED as being a replacement for dip or conventional-spray coating, where its greatest advantage would be the potential for much higher materials utilization. |
Sarah Park ; Lin Lei ; Catherine Nachtigal ; Emran Lallow ; Maria Atzampou ; Alex Liu ; Jeffrey Zahn ; Hao Lin ; Jonathan Singer; |
999 | Antibacterial Activity of Pulsed Laser Synthesized Silver Nanoparticles Combined with Methylene Blue for Prosthetic Joint Infection Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, methylene blue (MB) functionalized silver nanoparticles (Ag NPs) are used as an effective photodynamic therapy (PDT) agent for prosthetic joint infection (PJI). |
Somon Hakimov ; Salizhan Kylychbekov ; Shreya Neupane ; Simran Banga ; Ali Oguz Er; |
1000 | Heat Transfer Through Functionalized Carbon Nanotubes for Photothermal Therapy of Cancer Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We use Dissipative Particle Dynamics with energy conservation (DPDe) package from Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) in order to study heat transfer from CNTs to the cell and surrounding medium. |
Delaram Nematollahi ; Kieran Mullen ; Dimitrios Papavassiliou; |
1001 | Polyethylene Oxide Doped with Nano Cobalt Cerium Dioxide Nanocomposite As An Antimicrobial Surface Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we propose an innovative idea by using doping method in doping a polymeric surface with nano cobalt cerium dioxide (CeO 2:Co) forming a multifunctional polymeric nanocomposite complex. |
Ahmad Alsaad ; A Ahmad ; Q Al-Bataineh; |
1002 | Polymorphism, Structure, and Nucleation of Cholesterol.H2O at Aqueous Interfaces and in Pathological Media: Revisited from A Computational Perspective Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We revisit the important issues of polymorphism, structure, and nucleation of cholesterol.H 2O using first principles calculations based on dispersion-augmented density functional theory. |
Margarita Shepelenko ; Anna Hirsch ; Neta Varsano ; Fabio Beghi ; Lia Addadi ; Leeor Kronik ; Leslie Leiserowitz; |
1003 | Single Molecule Force Spectroscopy of Telomeric H3.3 Variant Nucleosomes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Understanding how histone protein variants affect the dynamics of nucleosome unwinding is key for developing a mechanistic model of their role in chromatin maintenance and disease. |
Brian Dawes ; Daniel Jackson ; Rachel Flynn ; Maria Kamenetska; |
1004 | Effects of Macromolecular Crowding on Protein-mediated Looping in DNA Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We have investigated the crowding effects of Dextran 70 (Dx70), as well as bovine serum albumin (BSA), at various concentrations, on protein-mediated DNA looping through tethered particle motion experiments, using 831 bp-long DNA and the lac repressor protein (LacI). |
Dylan Collette ; David Dunlap ; Laura Finzi; |
1005 | Simplifying Protein Collective Vibrational Assignment Through Symmetry Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We examine crystal symmetry effects on the anisotropic spectra for hen egg white lysozyme crystals (HEWL). |
Deepu George ; Jeffrey Mckinney ; Yanting Deng ; Alexander McNulty-Romaguera ; Xiaotong Zhang ; Jason Benedict ; Tod Romo ; Alan Grossfield ; Andrea Markelz; |
1006 | Regulation of Gene Expression By Transcription Factor Clustering Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we show that this apparent heterogeneity arises out of accumulation of the TFs into submicron clusters. |
Rahul Munshi ; Michal Levo ; Eric Wieschaus ; Thomas Gregor; |
1007 | Optical Detection of Structural Alteration of Brain Tissues in Progressive Alzheimer’s Diseases Using Partial Wave Spectroscopy (PWS) Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Alzheimer disease (AD) is the most common form of dementia, characterized pathologically by amyloid plaques and neurofibrillary tangles. One of the earliest overt signs of AD is a … |
Pinki Chahal ; Fatemah Alharthi ; Pardeep shukla ; Prakash Adhikari ; Radhakrishna Rao ; Mohammad Moshahid khan ; Prabhakar Pradhan; |
1008 | Multiscale Molecular Dynamics Simulations of Amyloidogenic Protein Binding and Folding on Lipid Rafts Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work will allow us to have a better understanding of the physics of protein interactions and folding on nanostructured surfaces, and propose new protein structures for future anti-aggregation drug development to treat amyloid diseases. |
Kwan Cheng ; Thuong Pham; |
1009 | Anti-apoptotic Condensates of Extremotolerance-related Proteins Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Phase-separated macromolecular assemblies have long been implicated in biological tolerance to environmental stress, from prototypical stress granules to the gel-like or glassy … |
Dan Nguyen ; Mike Veling ; Nicole Thadani ; Michela Oster ; Nathan Rollins ; Kelly Brock ; Neville Bethel ; David Baker ; Jeffrey Way ; Debora Marks ; Roger Chang ; Pamela Silver; |
1010 | Receptor-mediated Signaling Through A Prewetting Phase-transition Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we develop a theory of these phenomena through Monte-Carlo simulations and a minimal Landau theory. |
Mason Rouches ; Sarah Veatch ; Benjamin Machta; |
1011 | Interface Resistance of Biomolecular Condensates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work highlights the underappreciated role of interface resistance on condensate exchange dynamics. |
Yaojun Zhang ; Andrew Pyo ; Cliff Brangwynne ; Ned Wingreen; |
1012 | Non-specific Adhesive Forces Reorganize The Cytoskeleton Around Membrane-less Organelles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we study the interactions of stress granules, a phase-separated protein-RNA droplet in the cytosol, with the heterogeneous networks of the cytoskeleton. |
Thomas Boeddeker ; Kathryn Rosowski ; Robert Style ; Eric Dufresne; |
1013 | Pattern Formation of Liquid Condensates at Surfaces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Strikingly, for small systems or molecules that can be sufficiently densified on the membrane, we report the emergence of condensates continuously oscillating between two opposite membranes. |
Xueping Zhao; |
1014 | Nanomechanical Crowding at The Interface Between RNA and Soft Surfaces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we introduce a multiscale approach which couples a tractable RNA coarse-grained model with an elastic energy component. |
Horacio Guzman ; Simon Poblete; |
1015 | Theoretical Model of Efficient Phagocytosis Driven By Curved Membrane Proteins and Active Cytoskeleton Forces Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study the process of phagocytosis by considering a simplified coarse grained model of a three-dimensional vesicle, having uniform adhesion interaction with a particle, in the presence of curved membrane proteins and active cytoskeleton forces. |
Raj Sadhu; |
1016 | Polymer Architecture Orchestrates The Segregation and Spatio-temporal Organization of Replicating E. Coli Chromosomes in Slow Growth Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We propose that cross-links (plausibly induced by SMC proteins) at crucial positions along the contour is enough to provide sufficient entropic forces for segregation within experimentally observed time scales. |
Debarshi Mitra; |
1017 | Microtubule Deacetylation Enables in Vivo Collective Cell Migration By Tuning Cell Stiffness in Relation to Substrate Stiffness Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We discover that the reduction in neural crest cell stiffness and consequently its migration is triggered by microtubule deacetylation mediated by Piezo1. |
Abdul Malmi Kakkada ; Christian Marchant ; Jaime Espina ; Elias Barriga; |
1018 | Modulation of Cell Signals with Nanotopography Through Cytoskeleton Actuation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we explore how aligned nanoridges guide cell migration by modulating the regulatory signal-transduction excitable network (STEN) coupled with the cytoskeleton excitable network (CEN). |
Qixin Yang ; Yuchuan Miao ; Matt Hourwitz ; Minxi Hu ; Quan Qing ; Peter Devreotes ; John Fourkas ; Wolfgang Losert; |
1019 | In The Blink of An Eye: Modeling Structural Transformations During The Ultrafast Contraction of A Single-celled Organism Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, we will discuss light microscopy measurements that allow for detailed quantification of the myoneme mesh structure. |
Carlos Floyd ; Xiangting Lei ; Jerry Honts ; Suriyanarayanan Vaikuntanathan ; Aaron Dinner ; Saad Bhamla; |
1020 | How Rigid Is A Microtubule? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address these questions, we use the freely fluctuating filaments method in combination with bootstrapping to investigate whether purification, labeling, age, or the presence of MAPs alter stabilized, microtubule mechanics. |
Taviare Hawkins; |
1021 | Deciphering The Origins of Heterogeneity in Biological Tissues Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To do so, we compare monolayers of randomly seeded cells to cloned cells, where both experience the same physical packing effect, but different genetic heterogeneity distributions. |
Alexandra Bermudez ; Junxiang Huang ; Zachary Gonzalez ; Dapeng Bi ; Neil Lin; |
1022 | Mechanical Basis for Epithelialization Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our work suggests that cell density is the primary factor in cell-cell border development and that cell-cell adhesion is subordinate. |
Christian Cammarota ; Nicole Dawney ; Mimi Jüng ; Dan Bergstralh; |
1023 | No Large-scale Demixing Due to Differences in Diffusivity at High Densities Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigate whether this demixing persists at higher densities. |
Erin McCarthy ; Ojan Damavandi ; M. Lisa Manning; |
1024 | Measuring Mechanical Heterogeneities in Live Epithelia Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we develop a method to visualize the heterogenous modulus distribution in live epithelial monolayers by integrating a cell stretcher, light microscopy, and artificial intelligence (AI)-based inference. |
Zachary Gonzalez ; Alexandra Bermudez ; Bao Zhao ; Xuanqing Liu ; Ethan Salter ; Khalid Jawed ; Cho-Jui Hsieh ; Neil Lin; |
1025 | Alignment of Tractions Between Neighboring Cells in A Monolayer Causes More Persistent Migration and Faster Wound Closure Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To address this gap in understanding, we use both wound geometry and HB-EGF to systematically perturb the persistence of migration. |
Kelly Vazquez ; Jacob Notbohm; |
1026 | The Mechanics of Cephalic Furrow Formation in The Drosophila Embryo Investigated Using Anadvanced Vertex Model Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To identify mechanical forces that drive CFF we have developed an advanced 2D vertex model that incorporates membrane curvature into the system description. |
Redowan Ahmed Niloy ; Michael Holcomb ; Jeffrey Thomas ; Jerzy Blawzdziewicz; |
1027 | Mechanical Boundaries in 3D Models for Confluent Tissue Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigate possible mechanisms for the creation and stabilization of these boundaries using an extended 3D Vertex model with features specific to stratified epithelia, such as additional heterotypic tension at interfaces between cells of different types. |
Elizabeth Lawson-Keister ; Tao Zhang ; Lisa Manning; |
1028 | Emergent Order in A Three-dimensional Vertex Model for Organoids Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: To make quantitative predictions regarding the morphology and rheology of a developing organoid, we construct and study a three-dimensional vertex model. |
Tao Zhang ; J. Schwarz; |
1029 | UNDERSTANDING PROTEIN COMPLEX ASSEMBLY THROUGH GRAND CANONICAL MAXIMUM ENTROPY MODELING Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we aim to model these clusters of coarse-grained protein assemblies from multiple subunits through the constraints of interactions among the subunits and the chemical potential of each subunit. |
Margaret Cheung; |
1030 | Epithelial-to-mesenchymal Transition Proceeds Through Directional Destabilization of Multidimensional Attractor Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We established a quantitative experimental-theoretical framework to formulate the problem as transitions between nonequilibrium attractors. |
Jianhua Xing ; Weikang Wang ; Dante Poe ; Yaxuan Yang ; Thomas Hyatt; |
1031 | Cellular Organization in Lab-evolved and Extant Multicellular Species Obeys A Maximum Entropy Law Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We find that despite large differences in cellular organization, the free space associated with individual cells in both organisms closely fits a modified gamma distribution, consistent with maximum entropy predictions originally developed for granular materials. |
Thomas Day ; Seyed Alireza Zamani Dahaj ; Peter Yunker ; Raymond Goldstein ; William Ratcliff ; Stephanie Hoehn; |
1032 | Development of A Vessel-on-a-chip Model for Study of Hb-based Artificial Oxygen Carriers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work presents oxygen transport in transfusion of artificial oxygen carriers. |
Babak Mosavati; |
1033 | Using X-ray Scattering to Investigate Effects of E-cigarette Additives on Pulmonary Membrane Structure Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study we use Small- and Wide-Angle X-ray Scattering (SAXS & WAXS) to investigate how the structure of the pulmonary surfactant membranes is altered by the addition of these e-cigarette chemical flavorings. |
Alauna Wheeler ; Jocelyn Ochoa ; Rayner Hernandez Perez ; Linda Hirst; |
1034 | Exploring Cooperative Treadmilling and Protrusion Growth in Fire Ant Rafts Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we observe the collective morphogenesis of fire ant rafts docked to stationary, vertical rods. |
Robert Wagner ; Franck Vernerey; |
1035 | Will More Data Rather Than More Samples Improve Spectroscopic Analysis? Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we explore the use of submultiple data collection to improve multivariate curve resolution – alternating least squares methods to separate the infrared spectra of buffer and protein, objectively, from protein solution spectra. |
Curtis Meuse ; Sabrina Hafiz ; Michaela Staab ; Kenneth Rubinson; |
1036 | An Atomistic Model Of The Human Stratum Corneum: Permeation Through The Long Periodicity Phase. Effect of A Pro-penetrant Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present a simulation model of the LPP with a mixture of three ceramides (Ceramides 1, 2, and 3), cholesterol, and lignoceric acid and we investigate whether the use of solute-penetration enhancers (known as pro-penetrant) (ex. |
Christian Jorgensen ; Fabien Léonforte ; Gustavo Luengo ; Sébastien Gregoire ; Bruno Biatry ; Peter Olmsted ; Ann Detroyer; |
1037 | Dense-core Vesicle Fusion Kinetics As A Function of SNARE Isoforms Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We investigated how timescale of the fusion event vary in dense-core vesicle fusion through assessing the roles of SNARE isoforms. |
Xiaojia Xu ; Sathish Ramakrishnan; |
1038 | Asymmetric Branching Scale Factors As Features in Neuronal and Glial Cell-Type Classification Using Machine Learning Methods Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In previous work, we constructed a biophysical theory that establishes a correspondence between neuron structure and function as mediated by principles such as time or power minimization, using undetermined Lagrange multipliers to predict scaling ratios for axon and dendrite sizes across branching levels. |
Paheli Desai-Chowdhry ; Van Savage ; Alexander Brummer; |
1039 | Patterns of Growth and Thickness in The Cerebral Cortex Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will cover both our models of cortical folding and our analysis of folded cortical geometries. |
Maria Holland; |
1040 | Aortic Shape Space Topology Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using over 150 computed tomography scans from patients with normal and dissected aortas, we show that aortic classification is optimally performed in a scale space defined by topologic invariants rather than geometric ones. |
Luka Pocivavsek ; Enrique Cerda ; Kameel Khabaz ; Seth Sankary ; Karen Yuan ; Janet Kang ; Nhung Nguyen ; Kathleen Cao ; Cheong Jun Lee ; Ross Milner ; Gordon Kindelmann; |
1041 | Agent-based Modelling of Vasculogenesis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present an agent-based model of vascular network formation in which single cell properties like cellular adhesion, anisotropic propulsion and the presence of multiple cell types and proliferation can lead to a variety of network morphologies that we compare quantitatively with i n vitro experiments. |
Suraj Sahu ; Suzzane Sindi ; Ajay Gopinathan ; Kara McCloskey ; Jose Zamora ; Mikahl Banwarth-Kuhn; |
1042 | Optimizing Multicellular Network Formation on Elastic Substrates Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Motivated by the transport functions of biological networks, we characterize our simulated force dipole networks in terms of a percolation order parameter and morphological features such as junctions, branches, and rings and show how they depend on substrate mechanics, cell density and noise. |
Patrick Noerr ; Kinjal Dasbiswas ; Ajay Gopinathan ; Farnaz Golnaraghi; |
1043 | Flow Facilitated Hierarchical Pattern Formation in Biological Transport Networks Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study a model where tube radius grows in proportional to local fluid flow velocity, shear rate, or flux, and show that it may facilitate the formation of hierarchical network patterns, reminiscent of some biological networks. |
Deng Pan ; Ahmad Zareei ; Ariel Amir; |
1044 | Live-imaging and Optogenetic Dissection of Transcriptional Repression in Living Embryos Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we utilized optogenetics and live-imaging tools to analyze transcriptional repression in the early fruit fly embryo. |
Jiaxi Zhao ; Nicholas Lammers ; Hernan Garcia; |
1045 | Non-linear Dynamics in Contact-based Pattern Formation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We consider spatial probability distributions that represent the chance of encountering and exchanging signals with a given cell. |
Tim Dullweber ; Dr. Adrian Jacobo ; Prof. Albert James Hudspeth ; Dr. Anna Erzberger; |
1046 | Patterning of Membrane Adhesion Under Hydraulic Stress Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Together with a theoretical model and a computational framework, we explore the length- and time-scales relevant to this process. |
Alejandro Torres Sánchez ; Celine Dinet ; Margarita Staykova ; Marino Arroyo; |
1047 | Matter Exchange As A Physical Mechanism for Pattern Formation in Membranes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we consider a theoretical phase-field model to describe the composition of a two-dimensional membrane exchanging matter with a reservoir. |
Nirvana Caballero ; Karsten Kruse ; Thierry Giamarchi; |
1048 | Mechanics of Functionally Graded Panicum Miliaceum Seedcoat with Sutural Tessellation Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: The goal of this study is to quantify the functionally graded mechanical properties of the seedcoat under different levels of humidity. |
Richard Nash ; Yaning Li; |
1049 | Contact-breaking, Pore-space Patterning and Network Formation in Spongy Mesophyll Development Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We develop a two-dimensional computational model of discrete, deformable particles to mimic the developmental process from confluent mesophyll progenitor cells to porous, network-like mature cells with highly non-spherical shapes. |
John Treado ; Adam Roddy ; Craig Brodersen ; Mark Shattuck ; Corey O’Hern; |
1050 | Discretizing The Dragonfly Wing: Fluid Flow and Strucutral Analysis Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, I study the interplay between flow and mechanics. |
Sherwood Martineau ; Henrik Ronellenfitsch; |
1051 | Circular and Spiral-like Crack Patterns of Desiccated Bacterial Deposits Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we report desiccation crack patterns of drying suspensions of Escherichia coli ( E. coli) with different swimming behaviors. |
Xiaolei Ma ; Zhengyang Liu ; Tianyi Lin ; Wei Zeng ; Xin Tian ; Xiang Cheng; |
1052 | Phase Transitions in Bacterial Populations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: This work will not only inform how and when antibiotic resistance mutations are likely to evolve but will more broadly investigate evolutionary rescue during critical phase transition population collapse. |
R. Fredrik Inglis; |
1053 | Dynamics, Stability, and Robustness of Minimal-change Trajectories to Increased Multicellular Size Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We developed simulations to interrogate the minimal changes that can be made to cellular and growth morphologies to facilitate branch entanglement. |
Thomas Day ; Peter Yunker ; William Ratcliff ; Seyed Alireza Zamani Dahaj ; G. Ozan Bozdag ; Anthony Burnetti; |
1054 | Stable Coexistence Through Dynamic Adaptation of A Shared Resource Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: As a case study, we analyze an ecological system with exploitative competition between two predators feeding on a single prey. |
Zachary Jackson ; BingKan Xue; |
1055 | Phase Transitions, Hysteresis and Memory in Microbial Ecologies Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present a layered ecological model where the evolutionary forces which hone the adaptation mechanisms at the molecular level are enacted through interactions among distinct populations that grow and compete across an ecology of localized patches. |
Antun Skanata ; Edo Kussell; |
1056 | In Search of Universality in The Short-Time Dynamics of Systems of Coupled Ecological Oscillators Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we use the Short Time Critical Dynamics (STCD) approach to explore the universality of the time evolution of the order parameter of these models at a much shorter timescale before they reach equilibrium. |
Shadi Esmaeili-Wellman ; Alan Hastings ; Karen Abbott ; Jonathan Machta ; Vahini Reddy Nareddy; |
1057 | Jamming Phase Diagram for Active Deformable Particles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we implement the active, deformable particle model (ADPM) in two dimensions, in which explicitly deformable particles are modeled as polygons with small disks at the vertices whose locations are determined by a shape-energy function that includes particle compressibility, contractility, and curvature energies. |
Francesco Arceri ; Corey O’Hern ; Mark Shattuck ; Dong Wang ; John Treado ; Yuxuan Cheng; |
1058 | Configurational Fingerprints of Multicellular Living Systems Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we develop configurational fingerprints of particulate and multicellular assemblies, and extract volumetric and shear order parameters based on this fingerprint to quantify the system disorder. |
Haiqian Yang ; Adrian Pegoraro ; Yulong Han ; Wenhui Tang ; Rohan Abeyaratne ; Dapeng(Max) Bi ; Ming Guo; |
1059 | Cell Junctions and Spatiotemporal Patterns of Motion in Cell Monolayers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Building on our previous work, in this presentation we will discuss the collective spatiotemporal patterns of motion in monolayers, focusing on how different classes of cell-cell junctions control transitions between different regimes of collective motion. |
Steven Chisolm ; Thomas Angelini ; Vignesh Subramaniam ; Kyle Schulze ; Emily Guo; |
1060 | Light-Sensitive Self-Organization in Plant Cells Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this study, we aim to establish a new framework to investigate the dynamics of active biological systems featuring intriguing dynamical phase transitions. |
Nico Schramma ; Cintia Perugachi Israels ; Maziyar Jalaal; |
1061 | Oscillation in Cell Cycle Times in Drosophila Abdomen Modeled As Cell Phase Synchronization Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: As a simple explanation for such oscillations, we propose that neighbouring cells have synchronous cycles. |
Riya Nandi ; Andrea Cairoli ; John Williamson ; Ana Ferriera ; Anna Ainslie ; John Davis ; Nicolas Tapon ; Guillaume Salbreux; |
1062 | Diffusion in Coulomb Plasmas Across Coupling Regimes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In previous work we focused on screening lengths typical for white dwarf astrophysics and developed a simple empirical model for diffusion for use in stellar evolution codes. |
Ian Freeman ; Matthew Caplan; |
1063 | Generalized Sheath Criterion for Multi-species Weakly Ionized Plasmas Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In the current work, this criterion has been extended to systems with multiple species including effects such as electron inertia and electrical fields. |
Sadasivan Shankar; |
1064 | Electromagnetic Modeling of A Plasma-filled Resonator for Diagnostics Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, the author presents an approach to numerical simulations of plasmas in microwave resonators, including the effects of photo-ionization and multiple resonant modes, as they develop in time. |
Andrey Semichaevsky; |
1065 | Driven-dissipative Electron Transport in A Quantized Conducting Array Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We study driven-dissipative electron transport in a quantized conducting array of coupled two-level electron sites with a Markovian quantum master equation approach [2] that includes Coulomb interactions, electron tunneling, radiative recombination and non-radiative thermal relaxation [2]. |
Felipe Recabal ; Felipe Herrera; |
1066 | Visualization of Spatially Confined Air Plasma in Macro (mm) Tubes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: The spatially confined nanosecond pulse laser induced air plasma generated in a rectangular glass tube is visualized through shadowgraphy and self-emission, to understand the role … |
NAGARAJU GUTHIKONDA ; D.P.S.L. Kameswari ; Sai Shiva S ; Elle Manikanta ; S Sree Harsha ; V.R. Ikkurthi ; P. Prem Kiran; |
1067 | Estimating Ionospheric Scintillation S4 from ROTI Over The Indian Region Using GPS Data Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Ionospheric irregularities can be assessed through the rate of change of total electron content (TEC) indicated by ROT, which can be derived from a dual-frequency GNSS receiver at … |
Chandan Kapil ; Gopi Seemala; |
1068 | Coarse-grained Simulations Elucidate The Role of Inositol Hexakisphosphate (IP6) in HIV-1 Mature Viral Capsid Self-assembly Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we adopted a Coarse-Graining approach to study the structural basis of CA and IP6 interaction during maturation since it is difficult to effectively address the implicated time and length scale using a fine-grained atomistic model. |
Manish Gupta ; Gregory Voth; |
1069 | Tools for Local Elasticity Calculations and Their Applications to Simulations of Lipid Biomembranes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here I will present our development and implementation of the tools for the elasticity calculations in an open-source library MDstress and the GROMACS-LS post-processing analysis code. |
Andrew Lewis ; Benjamin Himberg ; Juan Vanegas; |
1070 | Towards A Model for Charge-driven Protein Reconstitution Using Dynamical Self-consistent Field Theory Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We extend neutral polymeric dynamical self-consistent field theory (dSCFT) to include charge interactions, salt, and solvent. |
Sylvia Luyben ; Robert Wickham; |
1071 | Dynamical Self-consistent Field Theory Simulation of Dendritic Phytoglycogen Nanoparticles Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: 1 We use dynamical self-consistent field theory (dSCFT) to simulate the dynamical evolution of a PG nanoparticle solubilized in water. |
Benjamin Morling ; Sylvia Luyben ; John Dutcher ; Robert Wickham; |
1072 | Iterative Steady-state Restarting of Weighted Ensemble Simulations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Recent work has shown that history-augmented Markov models (haMSMs) can provide estimates of steady state from transient, unconverged WE data; additionally, a new WE simulation can be initialized using structures from the initial simulation, weighted according to steady state. |
John Russo ; Jeremy Copperman ; Daniel Zuckerman; |
1073 | Dynamic Density Functional Theory of Multicomponent Cellular Membranes Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. |
Liam Stanton ; Tomas Oppelstrup ; Helgi Ingolfsson ; Michael Surh ; Felice Lightstone ; James Glosli; |
1074 | Modeling The Cell Cycle of The Minimal Bacterial Cell JCVI-syn3A Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our whole-cell kinetic model predicts a membrane growth rate based on the synthesis and incorporation of lipids and membrane proteins. |
Madeline Stover ; Zane Thornburg ; David Bianchi ; Troy Brier ; Benjamin Gilbert ; James Saenz ; Clyde Hutchison III ; John Glass ; Zaida Luthey-Schulten; |
1075 | Coarse-grained Simulations of RNAs Allowing for Conformational Transitions of The Sugar Pucker Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Accordingly, we have developed a coarse-grained RNA force field to include transitions between the two sugar pucker states in order to accurately reproduce RNA structures and thermodynamics. |
Yiheng Wu ; Riccardo Alessandri ; Aria Coraor ; Tobin Sosnick ; Juan De Pablo; |
1076 | Building Stimuli-Responsive Nanoparticle Assemblies In Polymer Matrix and Solutions Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In the present work, we used electrostatics to tune these stimuli-responsive transitions in solutions. |
Pothukuchi Rajesh Pavan ; Mithun Radhakrishna; |
1077 | Rational Discovery of Cardiolipin-selective Small Molecules By Coarse-grained High-throughput Simulations Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We make use of efficient coarse-grained free-energy calculations in combination with active learning to streamline the identification of relevant physical and chemical properties that determine selectivity towards a given biomolecular target. |
Bernadette Mohr ; Kirill Shmilovich ; Isabel Kleinwächter ; Dirk Schneider ; Andrew Ferguson ; Tristan Bereau; |
1078 | Simulating The Molecular Processes of Living Matter – What Is Missing from Current Models Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we discuss the significance of these challenges as well as the preliminary methodological work that has been conducted. |
Ilpo Vattulainen; |
1079 | Determining Partitioning and Transport Coefficients for Hydrophobic Chemicals in Polydimethylsiloxane (PDMS)-based Devices Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we measure and model chemical-PDMS interactions, accounting for chemical partitioning across the PDMS interface mediated by free energy differential and internal diffusion in bulk PDMS. |
Nathaniel Hermann ; Shane Hutson ; Lisa McCawley ; Dmitry Markov; |
1080 | Order-of-Magnitude Tuning of Microbial Growth Rates Through Photo-Excitation Growth Spectroscopy Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we describe a novel method, called Photo-Excitation Growth Spectroscopy (PhotoExGS), that combines broadband supercontinuum excitation and real-time laser probes of microbial growth in highly controlled environments. |
Mehmet Kilinc ; Jacky Wan ; Thomas Kuhlman ; Nathaniel Gabor; |
1081 | Input-response Function for Spatiotemporally Modulated Input Transcription Factor and Target Gene Outputs Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We found the target genes showing differential transcriptional activity in response to acute TF concentration perturbations in time and space. |
Anand Singh ; Ping Wu ; Sergey Ryabichko ; João Raimundo ; Michael Swan ; Eric Wieschaus ; Jared Toettcher ; Thomas Gregor; |
1082 | Automated Detection and Identification of Membrane Proteins in Atomic Force Microscopy Images Using Machine Learning Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we present a workflow for the automated detection and identification of membrane proteins in a previously recorded stack of AFM images. |
Creighton Lisowski ; Dylan Weaver ; Gavin King ; Ioan Kosztin; |
1083 | Approaches to Peptide Photodissociation for Single-Molecule Protein Sequencing Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We analyze the feasibility of using light to fragment a peptide into its constituent amino acids before identifying them by mass spectrometry (MS) for the purpose of single-molecule protein sequencing. |
Derek Stein; |
1084 | Biocompatible Surface Functionalization Architecture for A Diamond Quantum Sensor Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we introduce a general strategy to tackle this challenge. |
Mouzhe Xie ; Xiaofei Yu ; Lila Rodgers ; Daohong Xu ; Ignacio Chi Durán ; Adrien Toros ; Niels Quack ; Nathalie de Leon ; Peter Maurer; |
1085 | Enhanced Nonenzymatic Glucose Detection Through The Synergy of Cu and Ni in A Co-sputtered Heteroatomic Thin Film Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this work, we report the synthesis and characterization of nickel (Ni) and copper (Cu) heteroatomic thin films using RF magnetron sputtering technique. |
Brianna Barbee ; Baleeswaraiah Muchharla ; Wei Cao ; Hani E. Elsayed-Ali ; Adetayo Adedeji ; Abdennaceur Karoui ; Kishor Kumar Sadasivuni ; Bijandra Kumar; |
1086 | Direct Measurement of Single Molecule DNA Bend-stiffness with Nano-magnetic Torque Balance Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using magPI, a novel approach for measuring the position and orientation of magnetic nanoparticle probes, we perform a torque-balance measurement on short dsDNA molecules to directly measure the DNA bending free energy. |
Isaac Shelby ; Zeeshawn Kazi ; Kai-Mei Fu ; Paul Wiggins; |
1087 | Quantifying Out-of-equilibrium Transcriptional Bursting in Living Fly Embryos Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here, we present an optimized two-photon microscope to measure gene activity of individual loci in living fly embryos. |
Po-Ta Chen ; Benjamin Zoller ; Michal Levo ; Thomas Gregor; |
1088 | Tuning Cell Division Machinery in Oocytes Using Light Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: The process of cell division relies on the coordination of chemical and mechanical signals in response to cell cycle cues. During early developmental processes in starfish egg … |
Jinghui Liu ; Tzer Han Tan ; S. Zachary Swartz ; Nikta Fakhri; |
1089 | FRET Based Biosensors for CBRN Threat Detection Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: Advanced sensor capabilities for the simultaneous on-site detection of chemical, biological, and radiological/nuclear (CBRN) threats would significantly limit the risk of exposure … |
Steven Demers ; Kaitlin Lawrence ; Ashlee Swindle ; Wendy Kuhne ; Candace Langan; |
1090 | Anatomical Study of Cells and Tissues Using Helium Ion Microscopy Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We report our specific experience in employing HeIM based correlative microscopy on cells (Vero E6, Schwann cells and oligodendrocytes) and tissue (brain, nerve, retina, kidney). |
Leila Kasaei ; Antonio Merolli ; Hussein Hijazi ; Viacheslav Manichev ; Leonard Feldman; |
1091 | Using Neutron and X-ray Reflectivity to Investigate The Interfacial Structure of Cell Monolayers Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We extend our work to x-rays because they provide a rich set of tools to probe the structure and interactions of cellular monolayers. |
Kathleen Cao ; Ann Junghans ; Tanvi Subramanian ; Anna Gaffney ; Adam Lam ; Wei Bu ; Binhua Lin ; Mark Schlossman ; Jaroslaw Majewski ; Ka Yee Lee ; Luka Pocivavsek; |
1092 | 3D Tracking of Continuous Nanoscale Objects in Complex Environments Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Here we describe our recent development of a multi-modal structured illumination (SIM) and ODT microscope based on a digital micromirror device. |
Peter Brown ; Douglas Shepherd; |
1093 | Onset of Lipid-nanoparticle Cooperative Association in Biomembranes: Role of Nanoparticle Charge and Membrane Stiffness Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Our recent study with multi-component phase-segregated Floating Lipid Monolayers as a model using X-ray scattering reveals that the Cationic nanoparticles have a preferential binding to one of the phases. |
Anurag Chaudhury ; Wei Bu ; Maximilian Skoda ; Koushik Debnath ; Nikhil Jana ; Jaydeep Basu; |
1094 | Shear-driven Solidification and Nonlinear Elasticity in Epithelial Tissues Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: Using a minimal cell-based computational model, we investigate the constitutive relation of confluent tissues under simple shear deformation. |
Dapeng Bi; |
1095 | Active T1 Transitions in Dynamic Tissues Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We describe and explain these findings using cell based arguments and through the lens of a continuum description of the tissue as an anisotropic active material. |
Frank Julicher ; Charlie Duclut ; Joris Paijmans ; Mandar Inamdar ; Carl Modes; |
1096 | Rigidity Phase Transitions in Embryo Development: from Identification to Function Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In this talk, I will present how rigidity percolation theory can identify in vivo rigidity phase transitions with high spatiotemporal precision during zebrafish morphogenesis. |
Nicoletta Petridou; |
1097 | Simple Animals Stretch Our Physical Understanding of Cilia, Sticky Cells and Tissue Rheology Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We report the discovery of abrupt, bulk epithelial tissue fractures and healing induced by the organism’s own motility that cause dramatic shape changes and physiological asexual division. |
Vivek Nagendra Prakash; |
1098 | Collective Mechanical Signaling Through Cell-Cell Contacts Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: In our work we have conducted a single-cell level spatiotemporal analysis of how local mechanical shear propagates change in cell morphology throughout an epithelium. |
Liam Dow; |
1099 | Magnetic Nanoparticle Clusters Delivering Antibiotics to E Coli. Through High Viscous Non-Newtonian Fluid Using A Magnetic Field Related Papers Related Patents Related Grants Related Orgs Related Experts Details Abstract: The purpose of this experiment is to expand the biomedical applications of magnetic particles and antibiotics, through the oscillating of magnetic particle clusters through high … |
River Gassen; |
1100 | Nuclear Membrane Three Orders Magnitude Faster Related Papers Related Patents Related Grants Related Orgs Related Experts Details Highlight: We detect fluctuations of cell nucleus envelope over the exceptionally broad spatiotemporal resolution. |
Kisung Lee ; Sun-Min Yu ; Steve Granick; |