Domain decomposition for implicit solvation models

Domain decomposition for implicit solvation models.

This article is the first of a series of papers dealing with domain decomposition algorithms for implicit solvent models. We show that, in the framework of the COSMO model, with van der Waals molecular cavities and classical charge distributions, the electrostatic energy contribution to the solvation energy, usually computed by solving an integral equation on the whole surface of the molecular ...

Computational protein design is a challenge for implicit solvation models.

Increasingly complex schemes for representing solvent effects in an implicit fashion are being used in computational analyses of biological macromolecules. These schemes speed up the calculations by orders of magnitude and are assumed to compromise little on essential features of the solvation phenomenon. In this work we examine this assumption. Five implicit solvation models, a surface area-ba...

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics.

Explicit / Implicit Conservative Galerkin Domain Decomposition Procedures for Parabolic Problems

Several domain decomposition methods for approximating solutions of parabolic problems are given. These methods rely on implicit Galerkin procedures in the subdomains and explicit flux calculation on the inter-domain boundaries. The procedures are conservative both in the subdomains and across inter-domain boundaries. A priori error bounds and experimental results are presented.

Quality meshing of implicit solvation models of biomolecular structures

This paper describes a comprehensive approach to construct quality meshes for implicit solvation models of biomolecular structures starting from atomic resolution data in the Protein Data Bank (PDB). First, a smooth volumetric electron density map is constructed from atomic data using weighted Gaussian isotropic kernel functions and a two-level clustering technique. This enables the selection o...