Related papers: The effect of phenotypic selection on stochastic g…
A dynamical mean-field theory is developed to analyze stochastic single-cell dynamics of gene expression. By explicitly taking account of nonequilibrium and nonadiabatic features of the DNA state fluctuation, two-time correlation functions…
Stochastic kinetic models of genetic expression are able to describe protein fluctuations. A comparative study of the canonical and a feedback model is given here by using stochastic simulation methods. The feedback model is skeleton model…
Biochemical reaction networks are subjected to large fluctuations attributable to small molecule numbers, yet underlie reliable biological functions. Most theoretical approaches describe them as purely deterministic or stochastic dynamical…
In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may…
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 consider a stochastic model of transcription factor (TF)-regulated gene expression. The model describes two genes: Gene A and Gene B which synthesize the TFs and the target gene proteins respectively. We show through analytic…
We study the effects of demographic stochasticity on the long-term dynamics of biological coevolution models of community assembly. The noise is induced in order to check the validity of deterministic population dynamics. While mutualistic…
The degree to which population fluctuations arise from variable adult survival relative to variable recruitment has been debated widely for marine organisms. Disentangling these effects remains challenging because data generally are not…
Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical population genetics…
Speciation is of fundamental importance to understanding the huge diversity of life on Earth. In contrast to current phenomenological models, we develop a biophysically motivated approach to study speciation involving the co-evolution of…
The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous…
A demographic Allee effect occurs when individual fitness, at low densities, increases with population density. Coupled with environmental fluctuations in demographic rates, Allee effects can have subtle effects on population persistence…
Environmental changes greatly influence the evolution of populations. Here, we study the dynamics of a population of two strains, one growing slightly faster than the other, competing for resources in a time-varying binary environment…
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including…
The intrinsic stochasticity of gene expression can lead to large variability of protein levels across a population of cells. Variability (or noise) in protein distributions can be modulated by cellular mechanisms of gene regulation; in…
Gene expression is significantly stochastic making modeling of genetic networks challenging. We present an approximation that allows the calculation of not only the mean and variance but also the distribution of protein numbers. We assume…
Reversibility of state transitions is intensively studied topic in many scientific disciplines over many years. In cell biology, it plays an important role in epigenetic variation of phenotypes, known as phenotypic plasticity. More…
Under low concentrations of antibiotics causing DNA damage, \textit{Escherichia coli} bacteria can trigger stochastically a stress response known as the SOS response. While the expression of this stress response can make individual cells…
We investigate two stochastic models of a growing population subject to selection and mutation. In our models each individual carries a fitness which determines its mean offspring number. Many of these offspring inherit their parent's…
The phenotypic equilibrium, i.e. heterogeneous population of cancer cells tending to a fixed equilibrium of phenotypic proportions, has received much attention in cancer biology very recently. In previous literature, some theoretical models…