移动边界上和移动边界内随机反应扩散系统的模拟
Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries
摘要：
细胞内的化学反应通常被认为发生在固定大小的隔间内。不用说，细胞和它们的区室是高度动态的。因此，这种严格的假设可能并不反映生物化学的现实，并可能高度偏离模拟研究的结论。在这项工作中，我们提出了一个直观的算法，基于粒子的扩散和移动边界上，点粒子和球形粒子。我们首先基准在适当的情况下，我们提出的随机方法对偏微分方程的解决方案，并进一步证明，移动边界可以引起超扩散运动以及时间不均匀的反应速率。最后，我们进行了一个数值实验，表示光漂白的扩散荧光蛋白在酿酒酵母细胞分裂，以证明移动边界可能会导致重要的影响，在以前发表的研究中被忽视。
英文摘要：
Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and can highly bias conclusions from simulation studies. In this work, we present an intuitive algorithm for particle-based diffusion in and on moving boundaries, for both point particles and spherical particles. We first benchmark in appropriate scenarios our proposed stochastic method against solutions of partial differential equations, and further demonstrate that moving boundaries can give rise to super diffusive motion as well as time-inhomogeneous reaction rates. Finally, we conduct a numerical experiment representing photobleaching of diffusing fluorescent proteins in dividing Saccharomyces cerevisiae cells to demonstrate that moving boundaries might cause important effects neglected in previously published studies.
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