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Tytuł artykułu

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

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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

Bibliografia

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  • [11] S. Jo, M. Vargyas, J. Vasko-Szedlar, B. Roux, and W. Im, PBEQ-Solver for online visualization of electrostatic potential of biomolecules, Nucleic Acids Research 36 (2008), W271–W275. [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 Equations by 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 equation in 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 electrostatic equations in biomolecules – Applications in biotechnology, Biotech. Annu. Rev. 9 (2003), 315–395.
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  • [18] W. Rocchia, E. Alexov, and B. Honig, Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions, J. Phys. Chem. B 105 (2001), 6507–6514.
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  • [20] D. Xie, New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics, Journal of Computational Physics, 275 (2014), 294–309.
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  • [24] Y. Zhou, M. Feig, and G. Wei, Highly accurate biomolecular electrostatics in continuum dielectric environments, Journal of Computational 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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