A robust numerical algorithm for studying biomolecular transport processes
A robust numerical algorithm for studying biomolecular transport processes
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DOI：
10.1006/jtbi.2003.3200
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发表时间：
2003-04-21
影响因子：
2
通讯作者：
Elston, TC
中科院分区：
文献类型：
--
作者：
Wang, HY;Peskin, CS;Elston, TC
我们提出了一个数值算法，非常适合于生物分子的运输过程的研究。在该算法中，连续马尔可夫过程离散为一个跳跃过程，并从连续系统的局部解导出跳跃率。因此，该算法有两个优点比标准的数值方法：（1）它保留了详细的平衡过程，（2）它能够处理不连续的潜力。该算法的公式还允许我们计算有效扩散系数或等效的随机参数。我们提供了几个简单的例子来说明如何实现该算法。复制本文中给出的结果所需的所有MATLAB函数文件都可以从www.amath.une.edu/Faculty/telston/matlab_functions获得。(C)2003爱思唯尔科技有限公司版权所有。
We present a numerical algorithm that is well suited for the study of biomolecular transport processes. In the algorithm a continuous Markov process is discretized as a jump process and the jump rates are derived from local solutions of the continuous system. Consequently, the algorithm has two advantages over standard numerical methods: (1) it preserves detailed balance for equilibrium processes, (2) it is able to handle discontinuous potentials. The formulation of the algorithm also allows us to calculate the effective diffusion coefficient or, equivalently, the randomness parameter. We provide several simple examples of how to implement the algorithm. All the MATLAB functions files needed to reproduce the results presented in the article are available from www.amath.une.edu/Faculty/telston/matlab_functions. (C) 2003 Elsevier Science Ltd. All rights reserved.