Related papers: Size limits sensitivity in all kinetic schemes
Many-body systems can have multiple equilibria. Though the energy of equilibria might be the same, still systems may resist to switch from an unfavored equilibrium to a favored one. In this paper we investigate occurrence of such phenomenon…
The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small…
The nonequilibrium stationary state of an exclusive genetic switch is considered. The model comprises two competing species and a single binding site which, when bound to by a protein of one species, causes the other species to be…
Classical reaction dynamics suggests transport through an index-1 saddle is organized not just by flux, but by local symplectic width scales of bounded proxy neighborhoods near the bottleneck. We investigate if a related geometric effect…
The sensitivity (i.e. dynamic response) of complex networked systems has not been well understood, making difficult to predict whether new macroscopic dynamic behavior will emerge even if we know exactly how individual nodes behave and how…
Sensory adaptation enables organisms to adjust their perception in a changing environment. A paradigm is bacterial chemotaxis, where the output activity of chemoreceptors is adapted to different baseline concentrations via receptor…
There are problems with defining the thermodynamic limit of systems with long-range interactions; as a result, the thermodynamic behavior of these types of systems is anomalous. In the present work, we review some concepts from both…
We introduce a simple nonequilibrium model for a driven diffusive system with nonconservative reaction kinetics which exhibits ergodicity breaking and hysteresis in one dimension. These phenomena can be understood through a description of…
We consider three models of evolving interfaces intimately related to the weakly asymmetric simple exclusion process with $N$ particles on a finite lattice of $2N$ sites. Our Model 1 defines an evolving bridge on $[0,1]$, our Model 1-w an…
A nonlinear dynamical system model that approximates a microscopic Gibbs field model for the yielding of a viscoplastic material subjected to varying external stress recently reported in [1] is presented. The predictions of the model are in…
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…
In the framework of statistical mechanics the properties of macroscopic systems are deduced starting from the laws of their microscopic dynamics. One of the key assumptions in this procedure is the ergodic property, namely the equivalence…
Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitate adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
Nanothermodynamics extends standard thermodynamics to facilitate finite-size effects on the scale of nanometers. A key ingredient is Hill's subdivision potential that accommodates the non-extensive energy of independent small systems,…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium…
We investigate the equilibrium state of the model of Peng, \textit{et al.} for molecular breeding. In the model, a population of DNA sequences is successively culled by removing the sequences with the lowest binding affinity to a particular…
Conformational changes are observed in many enzymes, but their role in catalysis is highly controversial. Here we present a theoretical model that illustrates how rigid catalysts can be fundamentally limited and how a conformational change…