(151a) A Hybrid Fluctuating Hydrodynamics and Molecular Dynamics Approach for Simulation of Biomolecular Systems

A Hybrid Fluctuating Hydrodynamics and Molecular Dynamics
Approach for Simulation of Biomolecular Systems

To
go beyond the accessible time- and length-scales of atomistic simulation while
retaining the essential forces for representing biomolecular systems, such as
solvation, hydrophobicity, interfacial phenomena, and hydrodynamics
interactions, we develop a hybrid fluctuating hydrodynamics and molecular
dynamics (hybrid FHD/MD) simulation method. The hybrid FHD/MD method is also
multiphysics in nature as field and particulate variables are hybridized in the
simulation model. We will discuss the devised approaches of mixing particles
and fields to achieve this hybridization. The ability to represent important
phenomena such as the Stoke's law, hydrodynamic relaxation, solvation free
energy, and hydrodynamic collapse at the same time by the simulation model will
also be illustrated. The inter-domain coupling between enzyme protomers in
protein dynamics will be employed as an application example to illustrate how
this method can be used to obtain insights and dynamics information that are
difficult to acquire otherwise.