Topic 127

biophysics stochastic dynamics model rate experimental mathematical experiments theoretical time mechanism experimentally cell motors size diffusion division force systems single noise fluctuations mechanical theory cells motion processes kinetic cellular collective reaction flagellar physical find derive process coli concentration simulations length motility between density mean parameters observed growth rates distributions equation switching kinetics transition it bacterial explained show on times speed number how constant gradients intracellular switch measurements geometry distribution velocity equilibrium swimming dimensional simulation motor chemical which can mechanics biological steady shape migration probability forces active quantitatively kinesin parameter stochasticity dependence analytical bacteria state consistent theoretically cycle intrinsic us statement

236 items. Top items listed below.

A Parallel Ratchet-Stroke Mechanism Leads to an Optimum Force for Molecular Motor Function. 127 38 8

A stochastic model of gene expression with polymerase recruitment and pause release 127 38

Connecting actin polymer dynamics across multiple scales 127 38 8

Dynamics of chromosomal target search by a membrane-integrated one-component receptor 127 8 3

Control of filament length by a depolymerizing gradient 127 38 8

Flagellar dynamics reveal large fluctuations and kinetic limit in the Escherichia coli chemotaxis network 127 38 8

Size regulation of multiple organelles competing for a shared subunit pool 127 38 8

A theoretical framework to study the influence of electrical fields on mesenchymal stem cells 172 127 38 18

Drag-induced directionality switching of kinesin-5 Cin8 revealed by cluster-motility analysis 127 38 8

New mathematical modelling tools for co-culture experiments: when do we need to explicitly account for signalling molecules? 127 38 18 4

Biological Noise in an Organelle Size Control System 127 38

Role of cell polarity dynamics and motility in pattern formation due to contact dependent signalling 55 38 8

Conformational state switching and pathways of chromosome dynamics in cell cycle 7

Following the footprints of variability during filopodia growth 127 38 8

Predicting global dynamics of spatial microbial communities from local interaction rules 158 99 38 17 5

Stable tug-of-war between kinesin-1 and cytoplasmic dynein upon different ATP and roadblock concentrations 127 55 8

Uncovering modeling features of viral replication dynamics from high-throughput single-cell virology experiments 38 21 4

Virus-host interactions shape viral dispersal giving rise to distinct classes of travelling waves in spatial expansions 127 38 21 5

Roles of motor on-rate and cargo mobility in intracellular transport 127 8

Biological network growth in complex environments - a computational framework 38 18 4

Division stochasticity can be transmitted to protein expression through chromosome replication 127 38 21 5

Cell proliferation and migration explain pore bridging dynamics in 3D printed scaffolds of different pore size 127 38 18

The kinesin-8 Kip3 depolymerizes microtubules with a collective force-dependent mechanism 127 55 8

Coordination between E. coli Cell Size and Cell Cycle Mediated by DnaA 127 38 8

Coordinating cell polarization and morphogenesis through mechanical feedback 127 38 8

Cell cycle-dependent active stress drives epithelia remodeling 127 55 38 20 18 3

Four different mechanisms for switching cell polarity 127 38 8

Cell size statistics in cell lineages and population snapshots with different growth regimes and division strategies. 127 38 5

Queuing models of gene expression: Analytical distributions and beyond 127 38

Single depolymerizing and transport kinesins stabilize microtubule ends 127 55 8 3

Embryonic Tissues as Active Foams 127 38 8

Abundant proteins contribute strongly to noise in the growth rate of optimally growing bacteria 185 127 38 21 5

Multiscale mechanical model for cell division orientation in developing biological systems 127 38 18 8

Novel tunable spatio-temporal patterns from a simple genetic oscillator circuit 38 18

Viscoelastic relaxation of collagen networks provides a self-generated directional cue during collective migration 127 55 38 8

Phenotypic delay in the evolution of bacterial antibiotic resistance: mechanistic models and their implications 185 21 5

Sticking around: Optimal cell adhesion patterning for energy minimization and substrate mechanosensing 127 38 18 8

Spatial segregation and cooperation in radially expanding microbial colonies under antibiotic stress 127 38 12 5

Processivity of molecular motors under vectorial loads 127 55 8

Transcription factor binding dynamics shape noise across biological processes 134 31 9 3

Origin of diverse phosphorylation patterns in the ERBB system 127 38

First-principles prediction of the information processing capacity of a simple genetic circuit 38 4

The role of replication-removal spatial correlations and cellular replicative lifespan in corneal epithelium homeostasis 127 38 20 18 8

Generalizing HMMs to Continuous Time for Fast Kinetics: Hidden Markov Jump Processes 127 38 18 4

Epithelial Tissues as Active Solids: From Nonlinear Contraction Pulses to Rupture Resistance 127 38 18 8

Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology 31 8

Kinetic control of stationary flux ratios for a wide range of biochemical processes 127 38 8

Dual Role of Cell-Cell Adhesion In Tumor Suppression and Proliferation Due to Collective Mechanosensing 127 38 14 3

Continuous Rate Modelling of bacterial stochastic size dynamics 127 38 18

Traveling fronts in self-replicating persistent random walks with multiple internal states 127 38 8

A first-takes-all model of centriole copy number control 127 38 8

Nutrient-dependent trade-offs between ribosomes and division protein synthesis control bacterial cell size and growth 158 127 38 12 8

The Response of Bacterial Flagellar Motor to Stepwise Increase in NaCl Concentration 127 8

Chemotactic Migration of Bacteria in Porous Media 127 38 18 8

Theory of mechano-chemical patterning and optimal migration in cell monolayers 127 38 18 8

Theoretical analysis of neural crest cell migration 127 38 20 8

Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions 38 8

A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data 38 8

Transfer function for YAP/TAZ nuclear translocation revealed through spatial systems modeling 38 18 8

Mechanical memory in cells emerges from mechanotransduction with transcriptional feedback and epigenetic plasticity 127 38 18

Hierarchical modeling of mechano-chemical dynamics of epithelial sheets across cells and tissue 127 38 18 8

Kinetics of self-assembly of inclusions due to lipid membrane thickness interactions 127 78 38 8

Diffusion of kinesin motors on cargo can enhance intracellular transport 127 8

Cell-scale biophysical determinants of cell competition in epithelia 127 38 18

Effects of spatial heterogeneity on bacterial genetic circuits 7

Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system 38

Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication 127 38 4

Efficacy of information transmission in cellular communication 127 38 18 8

Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment 21 5

Kinetic analysis reveals the rates and mechanisms of protein aggregation in a multicellular organism 78 38 8

Extrinsic noise acts to lower protein production at higher translation initiation rates 127 49 38

A hybrid stochastic-deterministic approach to explore multiple infection and evolution in HIV 38 21

Urn models for regulated gene expression yield physically intuitive solutions for probability distributions of single-cell counts 127 38

Molecular switch architecture drives response properties 127 38

Extensions of the worm-like-chain model to tethered active filaments under tension 127 55 18 8

Single-cell growth inference of Corynebacterium glutamicum reveals asymptotically linear growth 127 38

Frequency domain analysis of fluctuations of mRNA and protein copy numbers within a cell lineage: theory and experimental validation 127 38 18

Exploring the Sequence Fitness Landscape of a Bridge Between Protein Folds 149 91 38 8 4

Programming cell growth into different cluster shapes using diffusible signals 38 18

Single-cell characterization of the eukaryotic transcription cycle using live imaging and statistical inference 18 4

Role of combined cell membrane and wall mechanicalproperties regulated by polarity signals in cell budding 127 8

Phase separation of tunable biomolecular condensates predicted by an interacting particle model 38 18 8 4

Paradoxical relationships between active transport and global protein distributions in neurons 82 38 8

From Hi-C Contact Map to Three-dimensional Organization of Interphase Human Chromosomes 127 38 4

Modelling FtsZ nucleation, hydrolysis and treadmilling activity with Monte Carlo methods 127 38 8

A spatial model of the plant circadian clock reveals design principles for coordinated timing under noisy environments 155 38

Dynamical phase diagram of an auto-regulating gene in fast switching conditions 127 38

Constrained proteome allocation affects coexistence inmodels of competitive microbial communities 99 38 17 5

Membrane tension can enhance adaptation to maintain polarity of migrating cells 127 38

The Roles of Space and Stochasticity in Computational Simulations of Cellular Biochemistry: Quantitative Analysis and Qualitative Insights 38 4

Disentangling intrinsic and extrinsic gene expression noise in growing cells 127 38 18 4

Ca2+ release via IP3Rs increases RyR mediated Ca2+ spark frequency in ventricular cardiomyocytes without altering spark amplitude and duration 127 38 3

Quantifying the dynamics of viral recombination during free virus and cell-to-cell transmission in HIV-1 infection 41 21

Scale invariance during bacterial reductive division observed by an extensive microperfusion system 127 38 18

Protein diffusion on membrane domes, tubes and pearling structures 127 78 38 8

Intrinsic disorder in the T cell receptor creates cooperativity and controls ZAP70 binding 149 8

Tissue failure propagation as mediated by circulatory flow 127 38 18 8

Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments 21 5

Power-law behaviour of transcription factor dynamics at the single-molecule level implies a continuum affinity model 127 38 8

Molecular height measurement by cell surface optical profilometry (CSOP) 78 8