(329h) A Hybrid Fluctuating Hydrodynamics and Molecular Dynamics (Hybrid FHD/MD) Simulation Methods

The development of a hybrid FHD/MD simulation method that combines the molecular dynamics of moving particles with the fluctuating hydrodynamics of solvent fields on grid cells fixed in space 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 showed that the ubiquitous forces mediated by the solvent, hydrophobicity and hydrodynamics, can be linked in a mesoscopic simulation. The strategies we devised to overcome the numerical issues of mixing Eulerian and Lagrangian variables: using an auxiliary fluid to fill in the volumes excluded by particles and assigning collocating griding systems on solutes to interface with solvent fields, are also discussed. Simulation results show that the hybrid FHD/MD method can reproduce the solvation free energies and scaling laws of particles dynamics for hydrophobes of difference sizes. The collapse of two hydrophobic particles was also simulated to illustrate that the hybrid FHD/MD method has the potential to be generally applied to study nano-scale self-assembly and dynamics-struction-function relationships of biomolecules.