Related papers: Stochastic dynamics of adhesion clusters under sha…
Discrete time, spatially extended models play an important role in ecology, modelling population dynamics of species ranging from micro-organisms to birds. An important question is how 'bottom up', individual-based models can be…
Conventional studies of biomolecular behaviors rely largely on the construction of kinetic schemes. Since the selection of these networks is not unique, a concern is raised whether and under which conditions hierarchical schemes can reveal…
In an experimental study of single enzyme reactions, it has been proposed that the rate constants of the enzymatic reactions fluctuate randomly, according to a given distribution. To quantify the uncertainty arising from random rate…
We report a study of the phase behavior of multiple-occupancy crystals through simulation. We argue that in order to reproduce the equilibrium behavior of such crystals it is essential to treat the number of lattice sites as a constraining…
A model is proposed to study the process of hypoxia-induced angiogenesis in cancer cells. The model accounts for the role played by the vascular endothelial growth factor (VEGF)-A in regulating the oxygen intake. VEGF-A is dynamically…
The adhesive dynamics of a one-dimensional aggregating gas of point particles is rigorously described. The infinite hierarchy of kinetic equations for the distributions of clusters of nearest neighbours is shown to be equivalent to a system…
The dynamical arrest of gels is the consequence of a well defined structural phase transition, leading to the formation of a spanning cluster of bonded particles. The dynamical glass transition, instead, is not accompanied by any clear…
The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of…
Spatial self-similarity is a hallmark of critical phenomena. We study the dynamic process of percolation, in which bonds are incrementally added to an initially empty lattice until the system becomes fully occupied. By tracking the gap --…
Three-dimensional molecular dynamics simulations of dissipative particles (~ 10^6) are carried out for studying the clustering kinetics of granular media during cooling. The inter-connected high particle density regions are identified,…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
T cell receptor signaling must operate reliably under tight time constraints. While assuming quite different mechanisms, two prominent models of T cell receptor activation, kinetic segregation and kinetic proofreading, both introduce a…
The effects of a stochastic reset, to its initial configuration, is studied in the exactly solvable one-dimensional coagulation-diffusion process. A finite resetting rate leads to a modified non-equilibrium stationary state. If in addition…
We propose a one-dimensional nonlocal stochastic model of adsorption and desorption depending on one parameter, the adsorption rate. At a special value of this parameter, the model has some interesting features. For example, the spectrum is…
Finite time convergence to functionally important target states is a key component of many biological processes. We previously found that the terminal approach phase of such dynamics exhibits universal types of stochastic dynamics that…
We analyze zero-lag and cluster synchrony of delay-coupled non-smooth dynamical systems by extending the master stability approach, and apply this to networks of adaptive threshold-model neurons. For a homogeneous population of excitatory…
This paper studies a novel approach for approximating the behavior of compartmental spreading processes. In contrast to prior work, the methods developed describe a dynamics which bound the exact moment dynamics, without explicitly…
Epithelial cell clusters often move collectively on a substrate. Mechanical signals play a major role in organizing this behavior. There are a number of experimental observations in these systems which await a comprehensive explanation.…
Population structure can have a significant effect on evolution. For some systems with sufficient symmetry, analytic results can be derived within the mathematical framework of evolutionary graph theory which relate to the outcome of the…
Cell-cell adhesion is one the most fundamental mechanisms regulating collective cell migration during tissue development, homeostasis and repair, allowing cell populations to self-organize and eventually form and maintain complex tissue…