Voulgarakis Nikolaos K, Shang Barry Z, Chu Jhih-Wei
Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, USA and Department of Mathematics, Washington State University, Richland, Washington 99372, USA.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Aug;88(2):023305. doi: 10.1103/PhysRevE.88.023305. Epub 2013 Aug 27.
The development of a hybrid fluctuating hydrodynamics (FHD) and molecular dynamics (MD) simulation method that combines the molecular dynamics of moving particles with the fluctuating hydrodynamics of solvent fields on Eulerian grid cells is presented. This method allows resolution of solute-solvent interfaces and realization of excluded volumes of particles in the presence of hydrodynamic coupling. With these capabilities, we show that the ubiquitous forces mediated by the solvent, hydrophobicity and hydrodynamics, can be linked in a mesoscopic simulation. The strategies we devise to overcome the numerical issues of mixing variables in the Eulerian and Lagrangian coordinate systems, i.e., using a pair of auxiliary fluids to realize the excluded volumes of particles and assigning collocating gridding systems on solutes to interface with solvent fields, are also presented. Simulation results show that the hybrid FHD and MD method can reproduce the solvation free energies and scaling laws of particles dynamics for hydrophobes of different sizes. The collapse of two hydrophobic particles was also simulated to illustrate that the hybrid FHD and MD method has the potential to be generally applied to study nanoscale self-assembly and dynamics-structure-function relationships of biomolecules.
本文提出了一种混合波动流体动力学（FHD）和分子动力学（MD）模拟方法，该方法将移动粒子的分子动力学与欧拉网格单元上溶剂场的波动流体动力学相结合。这种方法能够解析溶质 - 溶剂界面，并在存在流体动力耦合的情况下实现粒子的排除体积。借助这些能力，我们表明，由溶剂介导的普遍存在的力、疏水性和流体动力学，可以在介观模拟中联系起来。我们还介绍了为克服欧拉坐标系和拉格朗日坐标系中混合变量的数值问题而设计的策略，即使用一对辅助流体来实现粒子的排除体积，并在溶质上分配并置网格系统以与溶剂场界面连接。模拟结果表明，混合FHD和MD方法可以重现不同尺寸疏水物的溶剂化自由能和粒子动力学的标度律。还模拟了两个疏水粒子的聚集，以说明混合FHD和MD方法有潜力普遍应用于研究生物分子的纳米级自组装以及动力学 - 结构 - 功能关系。
