论文标题
分段确定性生化仿真的推送方法
Push-forward method for piecewise deterministic biochemical simulations
论文作者
论文摘要
在搅拌良好的反应器条件下,大量分子和频繁反应,可以通过一组普通微分方程(ODE)来模拟生化网络。当某些分子物种数量少,改变它们的反应很少发生时,这不再是强大的表示。在这种情况下,离散的随机事件会触发生化网络平滑确定性动力学的变化。分段确定的马尔可夫过程(PDMP)非常适合描述这种情况。尽管PDMP模型现在在生物学中已建立,但这些模型在计算上仍然具有挑战性。以前,我们已经引入了推动方向方法,以通过使用相应的半群的分析表达式来计算PDMPS的确定性ODE流量如何通过确定性的ODE流量来扩展概率度量。在本文中,我们提供了一种更通用的仿真算法,该算法也适用于非整合系统。该方法可用于具有基本生物学,生物技术和生物计算的应用的生化模拟。这项工作是CMSB2019会议上介绍的工作的扩展版本。
A biochemical network can be simulated by a set of ordinary differential equations (ODE) under well stirred reactor conditions, for large numbers of molecules, and frequent reactions. This is no longer a robust representation when some molecular species are in small numbers and reactions changing them are infrequent. In this case, discrete stochastic events trigger changes of the smooth deterministic dynamics of the biochemical network. Piecewise-deterministic Markov processes (PDMP) are well adapted for describing such situations. Although PDMP models are now well established in biology, these models remain computationally challenging. Previously we have introduced the push-forward method to compute how the probability measure is spread by the deterministic ODE flow of PDMPs, through the use of analytic expressions of the corresponding semigroup. In this paper we provide a more general simulation algorithm that works also for non-integrable systems. The method can be used for biochemical simulations with applications in fundamental biology, biotechnology and biocomputing.This work is an extended version of the work presented at the conference CMSB2019.