Literature DB >> 20370108

An efficient algorithm for classical density functional theory in three dimensions: ionic solutions.

Matthew G Knepley1, Dmitry A Karpeev, Seth Davidovits, Robert S Eisenberg, Dirk Gillespie.   

Abstract

Classical density functional theory (DFT) of fluids is a valuable tool to analyze inhomogeneous fluids. However, few numerical solution algorithms for three-dimensional systems exist. Here we present an efficient numerical scheme for fluids of charged, hard spheres that uses O(N log N) operations and O(N) memory, where N is the number of grid points. This system-size scaling is significant because of the very large N required for three-dimensional systems. The algorithm uses fast Fourier transforms (FFTs) to evaluate the convolutions of the DFT Euler-Lagrange equations and Picard (iterative substitution) iteration with line search to solve the equations. The pros and cons of this FFT/Picard technique are compared to those of alternative solution methods that use real-space integration of the convolutions instead of FFTs and Newton iteration instead of Picard. For the hard-sphere DFT, we use fundamental measure theory. For the electrostatic DFT, we present two algorithms. One is for the "bulk-fluid" functional of Rosenfeld [Y. Rosenfeld, J. Chem. Phys. 98, 8126 (1993)] that uses O(N log N) operations. The other is for the "reference fluid density" (RFD) functional [D. Gillespie et al., J. Phys.: Condens. Matter 14, 12129 (2002)]. This functional is significantly more accurate than the bulk-fluid functional, but the RFD algorithm requires O(N(2)) operations.

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Year:  2010        PMID: 20370108      PMCID: PMC2856503          DOI: 10.1063/1.3357981

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


  9 in total

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Authors:  W Nonner; L Catacuzzeno; B Eisenberg
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2.  Density functional theory of charged, hard-sphere fluids.

Authors:  Dirk Gillespie; Wolfgang Nonner; Robert S Eisenberg
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-09-19

3.  Multigrid Monte Carlo method. Conceptual foundations.

Authors: 
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Authors: 
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6.  Density functional theory for hard-sphere mixtures: the White Bear version mark II.

Authors:  Hendrik Hansen-Goos; Roland Roth
Journal:  J Phys Condens Matter       Date:  2006-08-24       Impact factor: 2.333

Review 7.  Fundamental measure theory for hard-sphere mixtures: a review.

Authors:  Roland Roth
Journal:  J Phys Condens Matter       Date:  2010-01-27       Impact factor: 2.333

8.  (De)constructing the ryanodine receptor: modeling ion permeation and selectivity of the calcium release channel.

Authors:  Dirk Gillespie; Le Xu; Ying Wang; Gerhard Meissner
Journal:  J Phys Chem B       Date:  2005-08-18       Impact factor: 2.991

9.  Energetics of divalent selectivity in a calcium channel: the ryanodine receptor case study.

Authors:  Dirk Gillespie
Journal:  Biophys J       Date:  2007-10-19       Impact factor: 4.033

  9 in total
  4 in total

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Journal:  Lab Chip       Date:  2017-01-31       Impact factor: 6.799

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Authors:  Guo-Wei Wei
Journal:  J Theor Comput Chem       Date:  2013-12       Impact factor: 0.939

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Journal:  J Mech Behav Mater       Date:  2013-12

4.  Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: theory, simulations, and experiments.

Authors:  Zaven Ovanesyan; Bharat Medasani; Marcia O Fenley; Guillermo Iván Guerrero-García; Mónica Olvera de la Cruz; Marcelo Marucho
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

  4 in total

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