Related papers: Stochastic Simulations of Genetic Switch Systems
Many biochemical processes can successfully be described by dynamical systems allowing some form of switching when, depending on their initial conditions, solutions of the dynamical system end up in different regions of state space…
A single gene, regulating its own expression via a positive feedback loop, constitutes a common motif in gene regulatory networks and signalling cascades. Recent experiments on the development of competence in the bacterial population…
We present a self-consistent field approximation to the problem of the genetic switch composed of two mutually repressing/activating genes. The protein and DNA state dynamics are treated stochastically and on equal footing. In this approach…
We study a biological autoregulation process, involving a protein that enhances its own transcription, in a parameter region where bistability would be present in the absence of fluctuations. We calculate the rate of fluctuation-induced…
We study long-range interacting systems driven by external stochastic forces that act collectively on all the particles constituting the system. Such a scenario is frequently encountered in the context of plasmas, self-gravitating systems,…
We study by mean-field analysis and stochastic simulations chemical models for genetic toggle switches formed from pairs of genes that mutually repress each other. In order to determine the stability of the genetic switches, we make a…
The state of many physical, biological and socio-technical systems evolves by combining smooth local transitions and abrupt resetting events to a set of reference values. The inclusion of the resetting mechanism not only provides the…
Stochastic reaction networks are mathematical models frequently used in, but not limited to, biochemistry. These models are continuous-time Markov chains whose transition rates depend on certain parameters called rate constants, which…
Gene expression has a stochastic component owing to the single molecule nature of the gene and the small number of copies of individual DNA binding proteins in the cell. We show how the statistics of such systems can be mapped on to quantum…
A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…
Recently, several theoretical and experimental studies have been undertaken to probe the effect of stochasticity on gene expression (GE). In experiments, the GE response to an inducing signal in a cell, measured by the amount of…
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…
Cell-fate transition can be modeled by ordinary differential equations (ODEs) which describe the behavior of several molecules in interaction, and for which each stable equilibrium corresponds to a possible phenotype (or 'biological…
Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…
Single-cell data reveal the presence of biological stochasticity between cells of identical genome and environment, in particular highlighting the transcriptional bursting phenomenon. To account for this property, gene expression may be…
Stochastic simulation has been a powerful tool for studying the dynamics of gene regulatory networks, particularly in terms of understanding how cell-phenotype stability and fate-transitions are impacted by noisy gene expression. However,…
Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks (GRNs). In this view, different phenotypes are associated with alternative states…
Recent experiments at the level of a single cell have shown that gene expression occurs in abrupt stochastic bursts. Further, in an ensemble of cells, the levels of proteins produced have a bimodal distribution. In a large fraction of…
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 investigate the transient nonequilibrium dynamics of a molecular junction biased by a finite voltage and strongly coupled to internal vibrational degrees of freedom. Using two different, numerical exact techniques, diagrammatic Monte…