Related papers: Bridging Time Scales in Cellular Decision Making w…
Stem cells, through their ability to produce daughter stem cells and differentiate into specialized cells, are essential in the growth, maintenance, and repair of biological tissues. Understanding the dynamics of cell populations in the…
The macroscopic behaviour of active matter arises from nonequilibrium microscopic processes. In soft materials, active stresses typically drive macroscopic shape changes, which in turn alter the geometry constraining the microscopic…
Noise caused by fluctuations at the molecular level is a fundamental part of intracellular processes. While the response of biological systems to noise has been studied extensively, there has been limited understanding of how to exploit it…
A simulation approach to the stochastic growth of bacterial towers is presented, in which a non-uniform and finite nutrient supply essentially determines the emerging structure through elementary chemotaxis. The method is based on cellular…
We study a stochastic multiscale spatial gene network. These naturally arise in molecular biology. In our model, the reactants are subject to on-site reactions on both scales and diffusion on the continuous scale only, although diffusion on…
We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the…
We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under1 quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady…
Heterogeneity in gene expression across isogenic cell populations can give rise to phenotypic diversity, even when cells are in homogenous environments. This diversity arises from the discrete, stochastic nature of biochemical reactions,…
Multicellular collective migration is a ubiquitous strategy of cells to translocate spatially in diverse tissue environments to accomplish a wide variety of biological phenomena, viz. embryonic development, wound healing, and tumor…
Mathematical models are vital interpretive and predictive tools used to assist in the understanding of cell migration. There are typically two approaches to modelling cell migration: either micro-scale, discrete or macro-scale, continuum.…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the…
Based on symmetry consideration of migration and shape deformations, we formulate phenomenologically the dynamics of cell crawling in two dimensions. Forces are introduced to change the cell shape. The shape deformations induce migration of…
Understanding how fluctuations propagate across spatial scales is central to our understanding of inanimate matter from turbulence to critical phenomena. In contrast to physical systems, biological systems are organized into a hierarchy of…
A perturbation framework is developed to analyze metastable behavior in stochastic processes with random internal and external states. The process is assumed to be under weak noise conditions, and the case where the deterministic limit is…
Lipid bilayer membranes are the fundamental biological barriers that permit life. The bilayer dynamics largely participates in orchestrating cellular workings and is characterized by substantial stability together with extreme plasticity…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
We develop a stochastic framework for viral population dynamics at the cellular level that explicitly incorporates the replication cycle with random stage durations. The model is formulated as a structured birth-death process coupled with a…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
We derive a physiologically structured multiscale model for biofilm development. The model has components on two spatial scales, which induce different time scales into the problem. The macroscopic behavior of the system is modeled using…