结合布朗动力学和格林函数反应动力学的各向异性粒子多尺度模拟
Multiscale simulations of anisotropic particles combining Brownian Dynamics and Green's Function Reaction Dynamics
摘要：
例如，细胞生物化学网络或自组装软物质中的复杂反应扩散过程的建模可以通过采用多尺度算法来极大地加速，该多尺度算法将介观格林函数反应动力学（GFRD）方法与显式随机布朗、朗之万或确定性分子动力学相结合以在微观尺度下处理反应物[A. Vijaykumar，P.G. Bolhuis和P.R. Ten Wolde，J. Chem. Phys. { \bf 43}，21：214102（2015）]。在这里，我们扩展了这种多尺度BD-GFRD方法，包括取向动力学，这是至关重要的描述各向异性的相互作用，往往普遍存在于生物分子系统。我们说明了新的算法，使用一个简单的补丁粒子模型。在对算法进行验证后，我们讨论了它的性能。旋转BD-GFRD多尺度方法将为大规模模拟例如蛋白质信号网络开辟可能性。
英文摘要：
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic Molecular Dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P.G. Bolhuis and P.R. ten Wolde, J. Chem. Phys. {\bf 43}, 21: 214102 (2015)]. Here we extend this multiscale BD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm we discuss its performance. The rotational BD-GFRD multiscale method will open up the possibility for large scale simulations of e.g. protein signalling networks.
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