An analytical model to estimate the time taken for cytoplasmic reactions for stochastic simulation of complex biological systems

P. Ghosh, Samik Ghosh, K. Basu, Sajal K. Das, S. Daefler
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引用次数: 18

Abstract

The complexity of biological systems motivates the use of a computer or "in silico" stochastic event based modeling approach to better identify the dynamic interactions of different processes in the system. This requires the computation of the time taken by different events in the system based on their biological functions and corresponding environment. One such important event is the reactions between the molecules inside the cytoplasm of a cell where the reaction environment is highly chaotic. We present a mathematical formulation for the estimation of the reaction time between two molecules within a cell based on the system state assuming that the reactant molecules enter the system one at a time to initiate reactions. We derive expressions for the average and second moment of the time for reaction to be used by our stochastic event-based simulation. Unlike rate equations, the proposed model does not require the assumption of concentration stability for multiple molecule reactions. The reaction time estimate is considered to be a random variable that suits the stochastic event based simulation method.
复杂生物系统随机模拟中估计细胞质反应所需时间的分析模型
生物系统的复杂性促使人们使用计算机或基于“计算机”随机事件的建模方法来更好地识别系统中不同过程的动态相互作用。这就需要根据系统中不同事件的生物功能和相应的环境来计算它们所花费的时间。其中一个重要事件是细胞细胞质内分子之间的反应,而反应环境是高度混乱的。我们提出了一个数学公式,用于估计细胞内两个分子之间的反应时间,基于系统状态,假设反应物分子一次一个进入系统引发反应。我们导出了反应时间的平均力矩和第二力矩的表达式,用于基于随机事件的模拟。与速率方程不同,该模型不需要假设多分子反应的浓度稳定。反应时间估计被认为是一个随机变量,适合基于随机事件的模拟方法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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