Flexible single molecule simulation of reaction-diffusion processes
Flexible single molecule simulation of reaction-diffusion processes
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DOI：
10.1016/j.jcp.2011.02.020
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发表时间：
2011-05-10
影响因子：
4.1
通讯作者：
Lotstedt, Per
中科院分区：
文献类型：
--
作者：
Hellander, Stefan;Lotstedt, Per
开发了一种算法，以模拟微观水平的单分子的运动和反应。分子在溶剂中扩散并相互反应或聚合物，分子可以解离。此类模拟引起了人们的关注在分子生物学中。该算法与Van Zon和Ten Wolde的Green功能反应动力学（GFRD）算法相似，在该算法中，可以通过计算概率密度函数（PDF），然后从分布函数进行采样来进行更长的时间步骤。我们对PDF的计算比GFRD复杂得多，并且更灵活。 PDF的部分微分方程的解分为两个步骤，以简化计算。采样无需在两个分子和分子聚合物相互作用的两个坐标方向上分裂误差，并且在第三方向上近似。 PDF是从分析解决方案或数值离散化获得的。分析了由于操作员分裂，系统分配和数值近似值而引起的误差。该方法应用于最多四个反应的三个不同系统。与其他介观和宏观模型的比较表现出极好的一致性。 （c）2011 Elsevier Inc.保留所有权利。
An algorithm is developed for simulation of the motion and reactions of single molecules at a microscopic level. The molecules diffuse in a solvent and react with each other or a polymer and molecules can dissociate. Such simulations are of interest e.g. in molecular biology. The algorithm is similar to the Green's function reaction dynamics (GFRD) algorithm by van Zon and ten Wolde where longer time steps can be taken by computing the probability density functions (PDFs) and then sample from the distribution functions. Our computation of the PDFs is much less complicated than GFRD and more flexible. The solution of the partial differential equation for the PDF is split into two steps to simplify the calculations. The sampling is without splitting error in two of the coordinate directions for a pair of molecules and a molecule-polymer interaction and is approximate in the third direction. The PDF is obtained either from an analytical solution or a numerical discretization. The errors due to the operator splitting, the partitioning of the system, and the numerical approximations are analyzed. The method is applied to three different systems involving up to four reactions. Comparisons with other mesoscopic and macroscopic models show excellent agreement. (C) 2011 Elsevier Inc. All rights reserved.