论文标题
质量转换方法:一种用于模拟混合化学反应网络的混合技术
The mass-conversion method: a hybrid technique for simulating well-mixed chemical reaction networks
论文作者
论文摘要
存在几种模拟化学反应网络代表的生物学和物理系统的方法。粒子数量少的系统经常被建模为离散的马尔可夫跳跃过程,通常通过随机模拟算法(SSA)模拟。 SSA虽然准确,但通常不适合大量个体的系统,并且随着反应频率的增加而变得过高的昂贵。通常使用普通的微分方程确定性地对大型系统进行建模,从而为计算效率和分析障碍性牺牲准确性和随机性。在本文中,我们提出了一种新型的杂种技术,用于对大型化学反应网络进行准确有效的模拟。我们将这种技术称为“质量转换方法”,通过同时使用这两种技术模拟反应网络,将离散状态的马尔可夫跳跃过程与普通微分方程的系统融为一体。网络中的单个分子在任何给定时间都完全由一个策略表示,并且可能会根据粒子密度切换其管理状态。通过这种方式,我们使用较便宜的连续性方法和低拷贝数的物种对高拷贝数进行建模,并使用更昂贵的离散态随机方法来保留以低拷贝数来保留随机波动的影响。与类似方法一样,动机是保留优势,同时减轻每种方法的不足。我们通过比较从我们的方法和精确的随机模拟获得的平均轨迹来证明我们方法的性能和准确性,这些测试问题表现出不同程度的连接性和复杂性。
There exist several methods for simulating biological and physical systems as represented by chemical reaction networks. Systems with low numbers of particles are frequently modelled as discrete-state Markov jump processes and are typically simulated via a stochastic simulation algorithm (SSA). An SSA, while accurate, is often unsuitable for systems with large numbers of individuals, and can become prohibitively expensive with increasing reaction frequency. Large systems are often modelled deterministically using ordinary differential equations, sacrificing accuracy and stochasticity for computational efficiency and analytical tractability. In this paper, we present a novel hybrid technique for the accurate and efficient simulation of large chemical reaction networks. This technique, which we name the mass-conversion method, couples a discrete-state Markov jump process to a system of ordinary differential equations by simulating a reaction network using both techniques simultaneously. Individual molecules in the network are represented by exactly one regime at any given time, and may switch their governing regime depending on particle density. In this manner, we model high copy-number species using the cheaper continuum method and low copy-number species using the more expensive, discrete-state stochastic method to preserve the impact of stochastic fluctuations at low copy number. The motivation, as with similar methods, is to retain the advantages while mitigating the shortfalls of each method. We demonstrate the performance and accuracy of our method for several test problems that exhibit varying degrees of inter-connectivity and complexity by comparing averaged trajectories obtained from both our method and from exact stochastic simulation.