用于监测具有噪声和建模误差的基因调控过程的非线性软件传感器

Environmental Disorder Regulation of Invasion and Genetic Loss

Many physical and natural systems, including the population of species, evolve in habitats with spatial stochastic variations of the individuals' motility. We study here the effect of those fluctuations on invasion and genetic loss. A Langevin equation for the \textit{position} and \textit{border} of the invasion front is obtained. A striking result is that small/large fluctuations of diffusivity suppress/intensify genetic loss. Our findings reveal the potential role of environmental fluctuations as a regulating factor for genetic loss and provide a simple explanation for the regional differen…

Effects of restrained degradation on gene expression and regulation

The effects of carrying capacity of environment $K$ for degradation (the $K$ effect for short) on the constitutive gene expression and a simple genetic regulation system, are investigated by employing a stochastic Langevin equation combined with the corresponding Fokker-Planck equation for the two stochastic systems subjected to internal and external noises. This $K$ effect characterizes the limited degradation ability of the environment for RNA or proteins, such as insufficient catabolic enzymes. The $K$ effect could significantly change the distribution of mRNA copy-number in constitutive ge…

Models of chromosome architecture and connection with the regulation of genetic expression

Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space. Furthermore, functional structures can result from the particular folding of the chromosome. Such phenomena have in common to result from the binding of divalent proteins that can bridge regions sometimes far away on the DNA sequence. The physical system consisting of the chromosome interacting with divalent proteins can be very complex. As such, most of the mechanism…

Ensembles, Dynamics, and Cell Types: Revisiting the Statistical Mechanics Perspective on Cellular Regulation

Genetic regulatory networks control ontogeny. For fifty years Boolean networks have served as models of such systems, ranging from ensembles of random Boolean networks as models for generic properties of gene regulation to working dynamical models of a growing number of sub-networks of real cells. At the same time, their statistical mechanics has been thoroughly studied. Here we recapitulate their original motivation in the context of current theoretical and empirical research. We discuss ensembles of random Boolean networks whose dynamical attractors model cell types. A sub-ensemble is the cr…

Likelihood for transcriptions in a genetic regulatory system under asymmetric stable Lévy noise

This work is devoted to investigating the evolution of concentration in a genetic regulation system, when the synthesis reaction rate is under additive and multiplicative asymmetric stable Lévy fluctuations. By focusing on the impact of skewness (i.e., non-symmetry) in the probability distributions of noise, we find that via examining the mean first exit time (MFET) and the first escape probability (FEP), the asymmetric fluctuations, interacting with nonlinearity in the system, lead to peculiar likelihood for transcription. This includes, in the additive noise case, realizing higher likelihood…

基于Poisson过程划分的基因表达随机模型的蛋白质精确分布

Exact protein distributions for stochastic models of gene expression using partitioning of Poisson processes

基因表达的随机性引起遗传相同细胞群体中蛋白质水平的波动。这种波动会导致克隆群体中的表型变异，因此使用随机模型定量基因表达中的噪声具有相当大的兴趣。然而，获得精确的蛋白质分布的分析结果一直是一个棘手的任务，但最简单的模型。在这里，我们调用的泊松过程的分区属性开发的映射，显着简化了随机模型的分析基因表达。映射导致精确的蛋白质分布，使用基于启动子的调节模型中的mRNA分布的结果。使用这种方法，我们推导出精确的分析结果的稳态和时间依赖的分布的基本2阶段模型的基因表达。此外，我们展示了映射如何导致精确的蛋白质分布的基本模型，包括转录后和翻译后调控的影响的扩展。这项工作中开发的方法是广泛适用的，可以有助于定量了解随机性的基因表达及其调控。