论文标题
计算翻译框架通过特殊拓扑及其长期动态标识生化反应网络
Computational translation framework identifies biochemical reaction networks with special topologies and their long-term dynamics
论文作者
论文摘要
在随机模型中的确定性模型和固定分布中,稳态描述了生化系统的长期行为。可以在有限的情况下(例如线性或有限状态系统)获得分析解决方案,因为它通常需要求解许多耦合方程。有趣的是,当基础网络具有特殊拓扑(称为弱可逆性(WR)和零缺乏症(ZD))时,可以轻松获得分析解决方案,并且动力学定律遵循质量动力学的广义形式。但是,这种所需的拓扑条件在大多数情况下都不符合。因此,提出了在保留原始动力学时将网络转换为具有WR和ZD的。然而,这种方法是有限的,因为手动在大量候选人中获得所需的网络翻译是具有挑战性的。在这里,我们证明了翻译后具有WR和ZD的必要条件,并且基于这些条件,我们开发了一个用户友好的计算软件包,该计算软件包朝向Z,该计算软件包自动,有效地通过WR和ZD自动识别了翻译的网络。这使我们可以定量检查翻译后获得WR和ZD的可能性,具体取决于物种和反应的数量。重要的是,我们还描述了如何使用包装来分析确定性模型的稳态和随机模型的固定分布。朝向Z提供了分析生化系统的有效工具。
Long-term behaviors of biochemical systems are described by steady states in deterministic models and stationary distributions in stochastic models. Obtaining their analytic solutions can be done for limited cases, such as linear or finite-state systems, as it generally requires solving many coupled equations. Interestingly, analytic solutions can be easily obtained when underlying networks have special topologies, called weak reversibility (WR) and zero deficiency (ZD), and the kinetic law follows a generalized form of mass-action kinetics. However, such desired topological conditions do not hold for the majority of cases. Thus, translating networks to have WR and ZD while preserving the original dynamics was proposed. Yet, this approach is limited because manually obtaining the desired network translation among the large number of candidates is challenging. Here, we prove necessary conditions for having WR and ZD after translation, and based on these conditions, we develop a user-friendly computational package, TOWARDZ, that automatically and efficiently identifies translated networks with WR and ZD. This allows us to quantitatively examine how likely it is to obtain WR and ZD after translation depending on the number of species and reactions. Importantly, we also describe how our package can be used to analytically derive steady states of deterministic models and stationary distributions of stochastic models. TOWARDZ provides an effective tool to analyze biochemical systems.