Related papers: Stochastic dynamics of adhesion clusters under sha…
We study time continuous branching processes with exponentially distributed lifetimes, with two types of cells that proliferate according to binary fission. A range of possible system dynamics are considered, each of which is characterized…
Collective oscillation of cells in a population has been reported under diverse biological contexts and with vastly different molecular constructs. Could there be common principles similar to those that govern spontaneous oscillation in…
We study molecular dynamics within populations of diffusively coupled cells under the assumption of fast diffusive exchange. As a technical tool, we propose conditions on boundedness and ultimate boundedness for systems with a singular…
We simulate the collision of atomic clusters with a weakly attractive surface using molecular dynamics in a regime between soft-landing and fragmentation, where the cluster undergoes large deformation but remains intact. As a function of…
In this article, we study the kinetics of reversible ligand binding to receptors on a spherical cell surface using a self-consistent stochastic theory. Binding, dissociation, diffusion and rebinding of ligands are incorporated into the…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
We investigate a class of stochastic aggregation processes involving two types of clusters: active and passive. The mass distribution is obtained analytically for several aggregation rates. When the aggregation rate is constant, we find…
We present a stochastic model which describes fronts of cells invading a wound. In the model cells can move, proliferate, and experience cell-cell adhesion. We find several qualitatively different regimes of front motion and analyze the…
The one-dimensional contact process is analyzed by a cluster approximation. In this approach, the hierarchy of rate equations for the densities of finite length empty intervals are truncated under the assumption that adjacent intervals are…
The coherent dynamics of bubble clusters in liquid are of fundamental and industrial importance and are elusive due to the complex interactions of disordered bubble oscillations. Here we introduce and demonstrate unsupervised learning of…
Contact between fluctuating, fluid-lubricated soft surfaces is prevalent in engineering and biological systems, a process starting with adhesive contact, which can give rise to complex coarsening dynamics. One representation of such a…
This chapter provides a pedagogical introduction and overview of spatial and temporal correlation and fluctuation effects resulting from the fundamentally stochastic kinetics underlying chemical reactions and the dynamics of populations or…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
In many cellular signaling pathways, key components form clusters at the cell membrane. Although much work has focused on the mechanisms behind such cluster formation, the implications for downstream signaling remain poorly understood.…
Motivated by rolling adhesion of white blood cells in the vasculature, we study how cells move in linear shear flow above a wall to which they can adhere via specific receptor-ligand bonds. Our computer simulations are based on a Langevin…
We propose a generic model to describe the mechanical response and failure of systems which undergo a series of stick-slip events when subjected to an external load. We model the system as a bundle of fibers, where single fibers can…
Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial…
Populations are made up of an integer number of individuals and are subject to stochastic birth-death processes whose rates may vary in time. Useful quantities, like the chance of ultimate fixation, satisfy an appropriate difference…
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…
Stochastic chemical reaction or population dynamics in finite systems often terminates in an absorbing state. Yet in large spatially extended systems, the time to reach species extinction (or fixation) becomes exceedingly long. Tuning…