We will present a continuum modeling framework based on unstructured mesh to study molecular solvation in aqueous salt solution in both equilibrium and non-equilibrium states. Unstructured mesh allows employment of well-established finite element/boundary element methods and packages to achieve high computational speed, accuracy and expandability. We developed a robust molecular surface mesh generation software, TMSmesh, to handle complex and arbitrarily large biomolecular systems in PDB, which allows applying FEM/BEM to continuum molecular modeling for general biomolecular systems, especially for large-scale and complicate systems. With the surface mesh and our latest version of AFMPB combining a parallel adaptive new version fast multipole method and BEM, we can successfully compute the PB electrostatics of a virus molecule with more than one million atoms and with more than ten million triangles in the surface mesh. For nonlinear PB cases and more general non-equilibrium electro-diffusion processes described by the Poisson-Nernst-Planck equations, we resort to a parallel adaptive finite element method, and the PB can be treated as a special case of PNP model. PNP modeling tracks particle diffusion and time information, and allows convenient incorporation of more physical effects such as size effects and ion-ion correlations in the model. Examples of non-equilibrium simulation will be given on the diffusion controlled substrate-enzyme encounter dynamics and on ionic flow through an ion channel. In addition, we also specifically designed a visualization system, VCMM, to facilitate continuum modeling based on unstructured mesh, which is not supported by usual visual systems in molecular modeling community. VCMM is a comprehensive system for visualizing and analyzing data from generic continuum molecular modeling. It can visual molecule, mesh (especially unstructured mesh), and numerical results all at once.      With these highly technical approaches and a complete set of specific/unique software from different areas, the continuum modeling platform is shown as an emerging powerful tool in computer simulation world. Our ongoing project can be seen at: www.continuummodel.org.

Unstructured mesh based continuum modeling of molecular solvation in both equilibrium and non-equilibrium aqueous salt solution

248th National Meeting (2014)

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