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2014 | 2 | 1 |
Tytuł artykułu

A Poisson-Boltzmann Equation Test Model for Protein in Spherical Solute Region and its Applications

Treść / Zawartość
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. Several numerical algorithms and program packages have been developed but verification and comparison between them remains an interesting topic. In this paper, a PBE test model is presented for a protein in a spherical solute region, along with its analytical solution. It is then used to verify a PBE finite element solver and applied to a numerical comparison study between a finite element solver and a finite difference solver. Such a study demonstrates the importance of retaining the interface conditions in the development of PBE solvers.
Twórcy
autor
  • Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201-0413, USA
autor
  • Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201-0413, USA
autor
  • Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201-0413, USA, dxie@uwm.edu
Bibliografia
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  • [3] N.A. Baker, D. Sept, M. Holst, and J. A. McCammon, The adaptive multilevel finite element solution of the Poisson-Boltzmannequation on massively parallel computers, IBM Journal of Research and Development 45 (2001), 427–438.
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  • [7] W. Geng, S. Yu, and G. Wei, Treatment of charge singularities in implicit solvent models, The Journal of chemical physics 127(2007), 114106.[WoS]
  • [8] M. Holst, J.A. McCammon, Z. Yu, Y. Zhou, and Y. Zhu, Adaptive finite element modeling techniques for the Poisson-Boltzmannequation, Communications in computational physics 11 (2012), no. 1, 179.[WoS]
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  • [14] A. Logg, G. N. Wells, and J. Hake, DOLFIN: A C++/Python finite element library, Automated Solution of Differential Equationsby the Finite Element Method, Lect. Notes Comput. Sci. Eng., vol. 84, Springer, Heidelberg, 2012, pp. 173–225.
  • [15] B. Lu, Y. Zhou, M.J. Holst, and J.A. McCammon, Recent progress in numerical methods for the Poisson-Boltzmann equationin biophysical applications, Commun. Comput. Phys. 3 (2008), no. 5, 973–1009.
  • [16] M.T. Neves-Petersen and S.B. Petersen, Protein electrostatics: A review of the equations and methods used to model electrostaticequations in biomolecules – Applications in biotechnology, Biotech. Annu. Rev. 9 (2003), 315–395.
  • [17] A. Nicholls and B. Honig, A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation, J. Comp. Chem. 12 (1991), 435–445.[Crossref]
  • [18] W. Rocchia, E. Alexov, and B. Honig, Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectricconstants and multivalent ions, J. Phys. Chem. B 105 (2001), 6507–6514.
  • [19] J.Waldén, On the approximation of singular source terms in differential equations, Numerical Methods for Partial DifferentialEquations 15 (1999), no. 4, 503–520.
  • [20] D. Xie, New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecularelectrostatics, Journal of Computational Physics, 275 (2014), 294–309.
  • [21] D. Xie and S. Zhou, A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation,BIT Num. Math. 47 (2007), 853–871.
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  • [23] S. Yu, W. Geng, and G. Wei, Treatment of geometric singularities in implicit solvent models, The Journal of Chemical Physics126 (2007), 244108.[WoS]
  • [24] Y. Zhou, M. Feig, and G. Wei, Highly accurate biomolecular electrostatics in continuum dielectric environments, Journal ofComputational Chemistry 29 (2008), no. 1, 87–97.[WoS]
Typ dokumentu
Bibliografia
Identyfikatory
Identyfikator YADDA
bwmeta1.element.doi-10_2478_mlbmb-2014-0006
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