Literature DB >> 22723750

Comparing the Predictions of the Nonlinear Poisson-Boltzmann Equation and the Ion Size-Modified Poisson-Boltzmann Equation for a Low-Dielectric Charged Spherical Cavity in an Aqueous Salt Solution.

Alexander R J Silalahi1, Alexander H Boschitsch, Robert C Harris, Marcia O Fenley.   

Abstract

The ion size-modified Poisson Boltzmann equation (SMPBE) is applied to the simple model problem of a low-dielectric spherical cavity containing a central charge, in an aqueous salt solution to investigate the finite ion size effect upon the electrostatic free energy and its sensitivity to changes in salt concentration. The SMPBE is shown to predict a very different electrostatic free energy than the nonlinear Poisson-Boltzmann equation (NLPBE) due to the additional entropic cost of placing ions in solution. Although the energy predictions of the SMPBE can be reproduced by fitting an appropriatelysized Stern layer, or ion-exclusion layer to the NLPBE calculations, the size of the Stern layer is difficult to estimate a priori. The SMPBE also produces a saturation layer when the central charge becomes sufficiently large. Ion-competition effects on various integrated quantities such the total number of ions predicted by the SMPBE are qualitatively similar to those given by the NLPBE and those found in available experimental results.

Entities:  

Year:  2010        PMID: 22723750      PMCID: PMC3378335          DOI: 10.1021/ct1002785

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  20 in total

1.  Mg(2+) binding to tRNA revisited: the nonlinear Poisson-Boltzmann model.

Authors:  V K Misra; D E Draper
Journal:  J Mol Biol       Date:  2000-06-09       Impact factor: 5.469

2.  Counterion distribution around DNA probed by solution X-ray scattering.

Authors:  R Das; T T Mills; L W Kwok; G S Maskel; I S Millett; S Doniach; K D Finkelstein; D Herschlag; L Pollack
Journal:  Phys Rev Lett       Date:  2003-05-08       Impact factor: 9.161

3.  Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation.

Authors:  Alexander H Boschitsch; Marcia O Fenley
Journal:  J Comput Chem       Date:  2004-05       Impact factor: 3.376

4.  A new outer boundary formulation and energy corrections for the nonlinear Poisson-Boltzmann equation.

Authors:  Alexander H Boschitsch; Marcia O Fenley
Journal:  J Comput Chem       Date:  2007-04-15       Impact factor: 3.376

5.  Inter-DNA attraction mediated by divalent counterions.

Authors:  Xiangyun Qiu; Kurt Andresen; Lisa W Kwok; Jessica S Lamb; Hye Yoon Park; Lois Pollack
Journal:  Phys Rev Lett       Date:  2007-07-20       Impact factor: 9.161

6.  Importance of partially unfolded conformations for Mg(2+)-induced folding of RNA tertiary structure: structural models and free energies of Mg2+ interactions.

Authors:  Dan Grilley; Vinod Misra; Gokhan Caliskan; David E Draper
Journal:  Biochemistry       Date:  2007-08-18       Impact factor: 3.162

7.  Comparison of exclusion volume corrections to the Poisson-Boltzmann equation for inhomogeneous electrolytes.

Authors:  L B Bhuiyan; C W Outhwaite
Journal:  J Colloid Interface Sci       Date:  2008-12-03       Impact factor: 8.128

8.  Counterion-induced condesation of deoxyribonucleic acid. a light-scattering study.

Authors:  R W Wilson; V A Bloomfield
Journal:  Biochemistry       Date:  1979-05-29       Impact factor: 3.162

9.  Phospholipid-based artificial viruses assembled by multivalent cations.

Authors:  Guillaume Tresset; Wun Chet Davy Cheong; Yan Ling Shireen Tan; Jérôme Boulaire; Yeng Ming Lam
Journal:  Biophys J       Date:  2007-05-04       Impact factor: 4.033

10.  Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations.

Authors:  Richard Owczarzy; Bernardo G Moreira; Yong You; Mark A Behlke; Joseph A Walder
Journal:  Biochemistry       Date:  2008-04-19       Impact factor: 3.162

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  11 in total

1.  The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations.

Authors:  Serdal Kirmizialtin; Alexander R J Silalahi; Ron Elber; Marcia O Fenley
Journal:  Biophys J       Date:  2012-02-21       Impact factor: 4.033

2.  Formulation of a new and simple nonuniform size-modified Poisson-Boltzmann description.

Authors:  Alexander H Boschitsch; Pavel V Danilov
Journal:  J Comput Chem       Date:  2012-02-27       Impact factor: 3.376

3.  Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation.

Authors:  Robert C Harris; Alexander H Boschitsch; Marcia O Fenley
Journal:  J Chem Phys       Date:  2014-02-21       Impact factor: 3.488

4.  Mean-field description of ionic size effects with nonuniform ionic sizes: a numerical approach.

Authors:  Shenggao Zhou; Zhongming Wang; Bo Li
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2011-08-01

5.  Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.

Authors:  Marcia O Fenley; Robert C Harris; Travis Mackoy; Alexander H Boschitsch
Journal:  J Comput Chem       Date:  2014-11-27       Impact factor: 3.376

6.  Competitive adsorption and ordered packing of counterions near highly charged surfaces: From mean-field theory to Monte Carlo simulations.

Authors:  Jiayi Wen; Shenggao Zhou; Zhenli Xu; Bo Li
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2012-04-26

7.  Ionic Size Effects: Generalized Boltzmann Distributions, Counterion Stratification, and Modified Debye Length.

Authors:  Bo Liu; Pei Liu; Zhenli Xu; Shenggao Zhou
Journal:  Nonlinearity       Date:  2013-10-01

8.  Progress in developing Poisson-Boltzmann equation solvers.

Authors:  Chuan Li; Lin Li; Marharyta Petukh; Emil Alexov
Journal:  Mol Based Math Biol       Date:  2013-03-01

9.  Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers.

Authors:  Nuo Wang; Shenggao Zhou; Peter M Kekenes-Huskey; Bo Li; J Andrew McCammon
Journal:  J Phys Chem B       Date:  2014-12-11       Impact factor: 2.991

Review 10.  Molecular Mean-Field Theory of Ionic Solutions: A Poisson-Nernst-Planck-Bikerman Model.

Authors:  Jinn-Liang Liu; Bob Eisenberg
Journal:  Entropy (Basel)       Date:  2020-05-14       Impact factor: 2.524

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