Literature DB >> 16161566

High-order discretization schemes for biochemical applications of boundary element solvation and variational electrostatic projection methods.

Brent A Gregersen1, Darrin M York.   

Abstract

A series of high-order surface element discretization schemes for variational boundary element methods are introduced. The surface elements are chosen in accord with angular quadrature rules for integration of spherical harmonics. Surface element interactions are modeled by Coulomb integrals between spherical Gaussian functions with exponents chosen to reproduce the exact variational energy and Gauss's law for a point charge in a spherical cavity. The present work allows high-order surface element expansions to be made for variational methods such as the conductorlike screening model for solvation and the variational electrostatic projection method for generalized solvent boundary potentials in molecular simulations.

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Year:  2005        PMID: 16161566     DOI: 10.1063/1.1899146

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  4 in total

1.  Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models.

Authors:  Kin-Yiu Wong; Yuqing Xu; Darrin M York
Journal:  J Comput Chem       Date:  2014-05-20       Impact factor: 3.376

2.  VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.

Authors:  Erich R Kuechler; Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2016-04-28       Impact factor: 3.488

3.  Radiative transfer equation modeling by streamline diffusion modified continuous Galerkin method.

Authors:  Feixiao Long; Fengyan Li; Xavier Intes; Shiva P Kotha
Journal:  J Biomed Opt       Date:  2016-03       Impact factor: 3.170

4.  Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation.

Authors:  Hong Gu; Shuming Zhang; Kin-Yiu Wong; Brian K Radak; Thakshila Dissanayake; Daniel L Kellerman; Qing Dai; Masaru Miyagi; Vernon E Anderson; Darrin M York; Joseph A Piccirilli; Michael E Harris
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-22       Impact factor: 11.205

  4 in total

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