Highlights of Biological Physics (DBIO) Talks @ APS 2022 March Meeting
American Physics Society (APS) March meeting is one of the largest physics meetings in the world. In 2022, the meeting will take place in Chicago.
To help the community quickly catch up on the work presented in this conference, Paper Digest Team processed all accepted papers, and generated one highlight sentence (typically the main topic) for each paper. Readers are encouraged to read these machine generated highlights / summaries to quickly get the main idea of each paper. Based in New York, Paper Digest is dedicated to producing high-quality text analysis results that people can acturally use on a daily basis. In the past 4 years, we have been serving users across the world with a number of exclusive services on ranking, search, tracking and review. This month we feature Literature Review Generator, which automatically generates literature review around any topic.
If you do not want to miss any interesting academic paper, you are welcome to sign up our free daily paper digest service to get updates on new papers published in your area every day. You are also welcome to follow us on Twitter and Linkedin to get updated with new conference digests.
Paper Digest Team
team@paperdigest.org
TABLE 1: Highlights of Biological Physics (DBIO) Talks @ APS 2022 March Meeting
| Paper | Author(s) | |
|---|---|---|
| 1 | DBIO Short Course: The Physics of Biological Movement Across Scales Related Papers Related Patents Related Grants Related Orgs Related Experts Details |
|
| 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 … |
|
| 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 |