Related papers: Molecular Distributions in Gene Regulatory Dynamic…
In this paper we study the interplay between stochastic gene expression and system design using simple stochastic models of auto-activation and auto-inhibition. Using the Poisson Representation, a technique whose particular usefulness in…
In a previous work, we presented a model that integrates cancer cell differentiation and immunotherapy, analysing a particular therapy against cancer stem cells by cytotoxic cell vaccines. As every biological system is exposed to random…
Gene expression and its regulation is a nonequilibrium stochastic process. Different molecules are involved in several biochemical steps in this process with low copies. It is observed that the stochasticity in biochemical processes is…
We present the numerical estimation of noise parameter induced in the dynamics of the variables by random particle interactions involved in the stochastic chemical oscillator and use it as order parameter to detect the transition from…
Bistable biological regulatory systems need to cope with stochastic noise to fine-tune their function close to bifurcation points. Here, we study stability properties of this regime in generic systems to demonstrate that cooperative…
We review the mathematical formalism underlying the modelling of stochasticity in biological systems. Beginning with a description of the system in terms of its basic constituents, we derive the mesoscopic equations governing the dynamics…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
The problem of determining the mathematical model of the dynamics of multi-dimensional control systems in the presence of noise under the condition that the correlation functions cannot be found. Known statistical dynamics of linear systems…
Stochasticity in gene expression can result in fluctuations in gene product levels. Recent experiments indicated that feedback regulation plays an important role in controlling the noise in gene expression. A quantitative understanding of…
The processes, resulting in the transcription of RNA, are intrinsically noisy. It was observed experimentally that the synthesis of mRNA molecules is driven by short, burst-like, events. An accurate prediction of the protein level often…
Chemical reactions in cell are subject to intense stochastic fluctuations. An important question is how the fundamental physiological behavior of cell is kept stable against those noisy perturbations. In this paper a stochastic model of…
In this paper, we consider discrete-time non-linear stochastic dynamical systems with additive process noise in which both the initial state and noise distributions are uncertain. Our goal is to quantify how the uncertainty in these…
Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Bursting in gene expression is known to impact cell-fate in diverse systems ranging from latency in HIV-1…
While noise is generally associated with uncertainties and often has a negative connotation in engineering, living organisms have evolved to adapt to (and even exploit) such uncertainty to ensure the survival of a species or implement…
We analyze general two-species stochastic models, of the kind generally used for the study of population dynamics. We show that the conditions for the stochastic (microscopic) model to display approximate sustained oscillatory behavior are…
Noise in gene expression, either due to inherent stochasticity or to varying inter- and intracellular environment, can generate significant cell-to-cell variability of protein levels in clonal populations. We present a theoretical…
We study an excitable active rotator with slowly adapting nonlinear feedback and noise. Depending on the adaptation and the noise level, this system may display noise-induced spiking, noise-perturbed oscillations, or stochastic busting. We…
The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule…
Modelling the dynamics of dense granular media is a long standing challenge and essential to many natural phenomena and technological applications. Here, we trace back puzzling experimental observation of detailed-balanced steady states to…
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,…