Frazier Zachary, Alber Frank
Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA.
J Comput Biol. 2012 Jun;19(6):606-18. doi: 10.1089/cmb.2012.0027.
Particle-based Brownian dynamics simulations offer the opportunity to not only simulate diffusion of particles but also the reactions between them. They therefore provide an opportunity to integrate varied biological data into spatially explicit models of biological processes, such as signal transduction or mitosis. However, particle based reaction-diffusion methods often are hampered by the relatively small time step needed for accurate description of the reaction-diffusion framework. Such small time steps often prevent simulation times that are relevant for biological processes. It is therefore of great importance to develop reaction-diffusion methods that tolerate larger time steps while maintaining relatively high accuracy. Here, we provide an algorithm, which detects potential particle collisions prior to a BD-based particle displacement and at the same time rigorously obeys the detailed balance rule of equilibrium reactions. We can show that for reaction-diffusion processes of particles mimicking proteins, the method can increase the typical BD time step by an order of magnitude while maintaining similar accuracy in the reaction diffusion modelling.
基于粒子的布朗动力学模拟不仅提供了模拟粒子扩散的机会，还提供了模拟它们之间反应的机会。因此，它们为将各种生物学数据整合到生物过程的空间明确模型中提供了机会，例如信号转导或有丝分裂。然而，基于粒子的反应扩散方法通常受到准确描述反应扩散框架所需的相对较小时间步长的阻碍。如此小的时间步长往往会妨碍与生物过程相关的模拟时间。因此，开发能够容忍更大时间步长同时保持相对高精度的反应扩散方法非常重要。在这里，我们提供了一种算法，该算法在基于BD的粒子位移之前检测潜在的粒子碰撞，同时严格遵守平衡反应的详细平衡规则。我们可以表明，对于模拟蛋白质的粒子的反应扩散过程，该方法可以将典型的BD时间步长提高一个数量级，同时在反应扩散建模中保持相似的精度。
