Sayyidmousavi Alireza, Rohlf Katrin
Author to whom any correspondence should be addressed.
Phys Biol. 2018 May 9;15(4):046007. doi: 10.1088/1478-3975/aabc35.
In the present study, an off-lattice particle-based method called the reactive multi-particle collision (RMPC) dynamics is extended to model reaction-diffusion systems with reactive boundary conditions in which the a priori diffusion coefficient of the particles needs to be maintained throughout the simulation. To this end, the authors have made use of the so-called bath particles whose purpose is only to ensure proper diffusion of the main particles in the system. In order to model partial adsorption by a reactive boundary in the RMPC, the probability of a particle being adsorbed, once it hits the boundary, is calculated by drawing an analogy between the RMPC and Brownian Dynamics. The main advantages of the RMPC compared to other molecular based methods are less computational cost as well as conservation of mass, energy and momentum in the collision and free streaming steps. The proposed approach is tested on three reaction-diffusion systems and very good agreement with the solutions to their corresponding partial differential equations is observed.
在本研究中，一种名为反应性多粒子碰撞（RMPC）动力学的非格点粒子方法被扩展，用于对具有反应边界条件的反应扩散系统进行建模，其中在整个模拟过程中需要保持粒子的先验扩散系数。为此，作者使用了所谓的浴粒子，其目的仅是确保系统中主要粒子的适当扩散。为了在RMPC中对反应边界的部分吸附进行建模，通过将RMPC与布朗动力学进行类比，计算粒子一旦撞击边界就被吸附的概率。与其他基于分子的方法相比，RMPC的主要优点是计算成本较低，以及在碰撞和自由流动步骤中质量、能量和动量的守恒。所提出的方法在三个反应扩散系统上进行了测试，并观察到与它们相应的偏微分方程的解有很好的一致性。
