276330 A Hybrid Fluctuating Hydrodynamics and Molecular Dynamics Approach for Simulation of Biomolecular Systems

Monday, October 29, 2012: 3:15 PM
411 (Convention Center )
Jhih-Wei Chu, Chemical Engineering, University of California, Berkeley, Berkeley, CA and Nikolaos Voulgarakis, Chemical Engineering, University of California Berkeley, Berkeley, CA

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.


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See more of this Session: Model Development for Biomolecular Systems
See more of this Group/Topical: Engineering Sciences and Fundamentals