Literature DB >> 18376903

Simulating prescribed particle densities in the grand canonical ensemble using iterative algorithms.

Attila Malasics1, Dirk Gillespie, Dezso Boda.   

Abstract

We present two efficient iterative Monte Carlo algorithms in the grand canonical ensemble with which the chemical potentials corresponding to prescribed (targeted) partial densities can be determined. The first algorithm works by always using the targeted densities in the kT log(rho(i)) (ideal gas) terms and updating the excess chemical potentials from the previous iteration. The second algorithm extrapolates the chemical potentials in the next iteration from the results of the previous iteration using a first order series expansion of the densities. The coefficients of the series, the derivatives of the densities with respect to the chemical potentials, are obtained from the simulations by fluctuation formulas. The convergence of this procedure is shown for the examples of a homogeneous Lennard-Jones mixture and a NaCl-CaCl(2) electrolyte mixture in the primitive model. The methods are quite robust under the conditions investigated. The first algorithm is less sensitive to initial conditions.

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Year:  2008        PMID: 18376903     DOI: 10.1063/1.2839302

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


  9 in total

1.  Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids.

Authors:  Bob Eisenberg; Yunkyong Hyon; Chun Liu
Journal:  J Chem Phys       Date:  2010-09-14       Impact factor: 3.488

2.  Volume exclusion in calcium selective channels.

Authors:  Dezso Boda; Wolfgang Nonner; Douglas Henderson; Bob Eisenberg; Dirk Gillespie
Journal:  Biophys J       Date:  2008-01-16       Impact factor: 4.033

3.  Synthetic nanopores as a test case for ion channel theories: the anomalous mole fraction effect without single filing.

Authors:  Dirk Gillespie; Dezso Boda; Yan He; Pavel Apel; Zuzanna S Siwy
Journal:  Biophys J       Date:  2008-04-04       Impact factor: 4.033

4.  Analyzing the components of the free-energy landscape in a calcium selective ion channel by Widom's particle insertion method.

Authors:  Dezso Boda; Janhavi Giri; Douglas Henderson; Bob Eisenberg; Dirk Gillespie
Journal:  J Chem Phys       Date:  2011-02-07       Impact factor: 3.488

5.  Current and selectivity in a model sodium channel under physiological conditions: Dynamic Monte Carlo simulations.

Authors:  Eva Csányi; Dezso Boda; Dirk Gillespie; Tamás Kristóf
Journal:  Biochim Biophys Acta       Date:  2011-11-04

6.  Simulations of calcium channel block by trivalent cations: Gd(3+) competes with permeant ions for the selectivity filter.

Authors:  Attila Malasics; Dezso Boda; Mónika Valiskó; Douglas Henderson; Dirk Gillespie
Journal:  Biochim Biophys Acta       Date:  2010-08-07

7.  Protein structure and ionic selectivity in calcium channels: selectivity filter size, not shape, matters.

Authors:  Attila Malasics; Dirk Gillespie; Wolfgang Nonner; Douglas Henderson; Bob Eisenberg; Dezso Boda
Journal:  Biochim Biophys Acta       Date:  2009-10-07

8.  Tuning transport properties of nanofluidic devices with local charge inversion.

Authors:  Yan He; Dirk Gillespie; Dezsö Boda; Ivan Vlassiouk; Robert S Eisenberg; Zuzanna S Siwy
Journal:  J Am Chem Soc       Date:  2009-04-15       Impact factor: 15.419

9.  Ionic selectivity in L-type calcium channels by electrostatics and hard-core repulsion.

Authors:  Dezso Boda; Mónika Valiskó; Douglas Henderson; Bob Eisenberg; Dirk Gillespie; Wolfgang Nonner
Journal:  J Gen Physiol       Date:  2009-05       Impact factor: 4.086

  9 in total

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