Browsing by Author "Voulgarakis, Nikolaos K."

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Dynamic mesoscale model of dipolar fluids via fluctuating hydrodynamics
(2014-11-07)
Persson, Rasmus A. X.
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Voulgarakis, Nikolaos K.
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Chu, Jhih-Wei
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生物科技學系
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生物資訊及系統生物研究所
Fluctuating hydrodynamics (FHD) is a general framework of mesoscopic modeling and simulation based on conservational laws and constitutive equations of linear and nonlinear responses. However, explicit representation of electrical forces in FHD has yet to appear. In this work, we devised an Ansatz for the dynamics of dipole moment densities that is linked with the Poisson equation of the electrical potential phi in coupling to the other equations of FHD. The resulting phi-FHD equations then serve as a platform for integrating the essential forces, including electrostatics in addition to hydrodynamics, pressure-volume equation of state, surface tension, and solvent-particle interactions that govern the emergent behaviors of molecular systems at an intermediate scale. This unique merit of phi-FHD is illustrated by showing that the water dielectric function and ion hydration free energies in homogeneous and heterogenous systems can be captured accurately via the mesoscopic simulation. Furthermore, we show that the field variables of phi-FHD can be mapped from the trajectory of an all-atom molecular dynamics simulation such that model development and parametrization can be based on the information obtained at a finer-grained scale. With the aforementioned multiscale capabilities and a spatial resolution as high as 5 angstrom, the phi-FHD equations represent a useful semi-explicit solvent model for the modeling and simulation of complex systems, such as biomolecular machines and nanofluidics. (C) 2014 AIP Publishing LLC.
Linking hydrophobicity and hydrodynamics by the hybrid fluctuating hydrodynamics and molecular dynamics methodologies
(2013-08-27)
Voulgarakis, Nikolaos K.
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Shang, Barry Z.
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Chu, Jhih-Wei
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生物科技學系
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生物資訊及系統生物研究所
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.