Geometric flow for biomolecular solvation
Nathan Baker, Knowledge Discovery and Informatics, Battelle Pacific Northwest Laboratories (April 26, 2011)
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Implicit solvent models are important components of modern biomolecular simulation methodology due to their efficiency and dramatic reduction of dimensionality. However, such models are often constructed in an ad hoc manner with an arbitrary decomposition and specification of the polar and nonpolar components. In this talk, we review current implicit solvent models and suggest a new free energy functional which combines both polar and nonpolar solvation terms in a common self-consistent framework. Upon variation, this new free energy functional yields the traditional Poisson-Boltzmann equation as well as a new geometric flow equation. We describe numerical methods for solving these equations and comment on future research directions in this area.
This work was performed in collaboration with Dennis Thomas, Jaehun Chun, Zhan Chen, and Guowei Wei.