相关论文: Epigenetic Ratchet: Spontaneous Adaptation via Sto…

We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…

A general class of stochastic gene expression models with self regulation is considered. One or more genes randomly switch between regulatory states, each having a different mRNA transcription rate. The gene or genes are self regulating…

Phase variation, or stochastic switching between alternative states of gene expression, is common among microbes, and may be important in coping with changing environments. We use a theoretical model to assess whether such switching is a…

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…

We introduce a stochastic model that describes the quasi-static dynamics of an electric transmission network under perturbations introduced by random load fluctuations, random removing of system components from service, random repair times…

Genetic algorithms are a well-known example of bio-inspired heuristic methods. They mimic natural selection by modeling several operators such as mutation, crossover, and selection. Recent discoveries about Epigenetics regulation processes…

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…

The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…

The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a…

Stochastic oscillations in individual cells are usually characterized by a non-monotonic power spectrum with an oscillatory autocorrelation function. Here we develop an analytical approach of stochastic oscillations in a minimal hybrid…

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…

Gene expression in cells is stochastic, yet differentiation is robust. We propose a mechanism in which frustrated genes with weakly stable intermediate expression undergo noise-driven switching between basins of attraction, followed by…

Signal-processing molecules inside cells are often present at low copy number, which necessitates probabilistic models to account for intrinsic noise. Probability distributions have traditionally been found using simulation-based approaches…

Cells adapt to different conditions by altering a vast number of components, which is measurable using transcriptome analysis. Given that a cell undergoing steady growth is constrained to sustain each of its internal components, the…

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 study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…

Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…

Spontaneous switching events in most characterized genetic switches are rare, resulting in extremely stable epigenetic properties. We show how simple arguments lead to theories of the rate of such events much like the absolute rate theory…

The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…

Response time-delay is an ubiquitous phenomenon in biological systems. Here we use a simple stochastic population model with time-delayed switching-rate conversion to quantitatively study the biological influence of the response time-delay…