Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems

The Journal of Chemical Physics
Miroslav HodakJ Bernholc

Abstract

A hybrid computational method intended for simulations of biomolecules in solution is described. The ab initio Kohn-Sham (KS) density functional theory (DFT) method is used to describe the chemically active part of the system and its first solvation shells, while a frozen-density orbital-free (FDOF) DFT method is used to treat the rest of the solvent. The molecules in the FDOF method have fixed internal structures and frozen electron densities. The hybrid method provides a seamless description of the boundary between the subsystems and allows for the flow of molecules across the boundary. Tests on a liquid water system show that the total energy is conserved well during molecular dynamics and that the effect of the solvent environment on the KS subsystem is well described. An initial application to copper ion binding to the prion protein is also presented.

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Citations

Sep 11, 2012·The Journal of Chemical Physics·Piotr de Silva, Tomasz A Wesolowski
Sep 8, 2011·The Journal of Chemical Physics·Francesco Aquilante, Tomasz A Wesołowski
Dec 3, 2008·The Journal of Chemical Physics·Juan Maria Garcia LastraTomasz A Wesolowski
Sep 8, 2010·The Journal of Chemical Physics·Jason D GoodpasterThomas F Miller
Nov 3, 2010·The Journal of Chemical Physics·S LaricchiaF Della Sala
Jun 30, 2009·Proceedings of the National Academy of Sciences of the United States of America·Miroslav HodakJ Bernholc
Feb 2, 2010·Prion·Miroslav Hodak, Jerzy Bernholc
Apr 24, 2015·The Journal of Chemical Physics·Szymon ŚmigaFabio Della Sala
Feb 23, 2012·Scientific Reports·Frisco RoseJerzy Bernholc
Jan 20, 2016·Journal of Computational Chemistry·Eric G KratzG Andrés Cisneros
Aug 30, 2014·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Sapana Vitthal Shedge, Tomasz A Wesolowski
Oct 17, 2018·Physical Chemistry Chemical Physics : PCCP·Niccolò RicardiTomasz A Wesolowski
Aug 6, 2016·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Daniel J Cole, Nicholas D M Hine
Apr 30, 2015·Chemical Reviews·Tomasz A WesolowskiXiuwen Zhou

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Software Mentioned

RATTLE
KS ultrasoft

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