Improvements in continuum modeling for biomolecular systems

doi:10.1088/1674-1056/25/1/018705

Abstract

Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of the biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress.

Keywords: Poisson-Boltzmann equation Poisson-Nernst-Planck equations ionic size effects density functional theory

Received: 08 May 2015
Revised: 22 July 2015
Accepted manuscript online:

PACS:

87.15.A-

(Theory, modeling, and computer simulation)

Fund:

Project supported by the National Natural Science Foundation of China (Grant No. 91230106) and the Chinese Academy of Sciences Program for Cross & Cooperative Team of the Science & Technology Innovation.

Corresponding Authors: Ben-Zhuo Lu
E-mail: bzlu@lsec.cc.ac.cn

Cite this article:

Yu Qiao(乔瑜) and Ben-Zhuo Lu(卢本卓) Improvements in continuum modeling for biomolecular systems 2016 Chin. Phys. B 25 018705

[1]	Lu B, Zhou Y, Holst M and McCammon J 2008 Commun. Comput. Phys. 3 973
[2]	Baker N 2005 Biomolecular Applications of Poisson-Boltzmann Methods (Hoboken: John Wiley & Sons, Inc.) pp. 349-379
[3]	Fogolari F, Brigo A and Molinari H 2002 J. Mol. Recognit. 15 377
[4]	Gilson M, Davis M, Luty B and McCammon J 1993 J. Phys. Chem. 97 3539
[5]	Sharp K and Honig B 1990 J. Phys. Chem. 94 7684
[6]	Lu B, Zhou Y, Huber G, Bond S, Holst M and McCammon J 2007 J. Chem. Phys. 127 135102
[7]	Tu B, Chen M, Xie Y, Zhang L, Eisenberg B and Lu B 2013 J. Comput. Chem. 34 2065
[8]	Xie Y, Cheng J, Lu B and Zhang L 2013 Mol. Based. Math. Biol. 1 90
[9]	Pods J, Schönke J and Bastian P 2013 Biophys. J. 105 242
[10]	Lu B and Zhou Y 2011 Biophys. J. 100 2475
[11]	Vlachy V 1999 Annu. Rev. Phys. Chem. 50 145
[12]	Netz R and Orland H 2000 Eur. Phys. J. E 1 203
[13]	Bazant M, Storey B and Kornyshev A 2011 Phys. Rev. Lett. 106 046102
[14]	Borukhov I, Andelman D and Orland H 1997 Phys. Rev. Lett. 79 435
[15]	Chu V, Bai Y, Lipfert J, Herschlag D and Doniach S 2007 Biophys. J. 93 3202
[16]	Silalahi A, Boschitsch A, Harris R and FenleyM2010 J. Chem. Theory Comput. 6 3631
[17]	Qiao Y, Tu B and Lu B 2014 J. Chem. Phys. 140 174102
[18]	Li B, Liu P, Xu Z and Zhou S 2013 Nonlinearity 26 2899
[19]	Liu J 2013 J. Comput. Phys. 247 88
[20]	Gillespie D, Nonner W and Eisenberg R 2002 J. Phys.: Condens. Matter 14 12129
[21]	Ji S and Liu W 2012 J. Dyn. Differ. Equat. 24 955
[22]	Meng D, Zheng B, Lin G and SushkoM2014 Commun. Comput. Phys. 16 1298
[23]	Knepley M, Karpeev D, Davidovits S, Eisenberg R and Gillespie D 2010 J. Chem. Phys. 132 124101
[24]	Hyon Y, Eisenberg B and Liu C 2011 Commun. Math. Sci. 9 459
[25]	Li H and Lu B 2014 J. Chem. Phys. 141 024115
[26]	Allahyarov E, Gompper G and Löwen H 2004 Phys. Rev. E 69 041904
[27]	Qiao Y, Lu B and Chen M 2016 J. Statistical Physics (in press)
[28]	Dzubiella J, Swanson J and McCammon J 2006 Phys. Rev. Lett. 96 087802
[29]	Zhao Y, Kwan Y, Che J, Li B and McCammon J 2013 J. Chem. Phys. 139 024111
[30]	Wei G 2013 J. Theor. Comput. Chem. 12 1341006
[31]	Li C, Li L, Petukh M and Alexov E 2013 Mol. Based. Math. Biol. 1 42
[32]	Fogolari F and Briggs J 1997 Chem. Phys. Lett. 281 135
[33]	Li B 2009 SIAM J. Math. Anal. 40 2536
[34]	Jadhao V, Solis F J and Olvera de la Cruz M 2013 Phys. Rev. E 88 022305
[35]	Borukhov I, Andelman D and Orland H 2000 Electrochim. Acta 46 221
[36]	Harris R, Boschitsch A and Fenley M 2014 J. Chem. Phys. 140 075102
[37]	Evans R 2009 Lectures at 3rd Warsaw School of Statistical Physics, Kazimierz Dolny 27
[38]	Rosenfeld Y 1989 Phys. Rev. Lett. 63 980
[39]	Rosenfeld Y, Levesque D and Weis J 1990 J. Chem. Phys. 92 6818
[40]	Roth R, Evans R, Lang A and Kahl G 2002 J. Phys.: Condens. Matter 14 12063
[41]	Roth R 2010 J. Phys.: Condens. Matter 22 063102
[42]	Yu Y and Wu J 2002 J. Chem. Phys. 117 10156
[43]	Jiang J, Cao D, Jiang D and Wu J 2014 J. Phys.: Condens. Matter 26 284102
[44]	Goos H and Mecke K 2009 Phys. Rev. Lett. 102 018302
[45]	Kierlik E and Rosinberg M 1990 Phys. Rev. A 42 3382
[46]	Lin G, Liu W, Yi Y and Zhang M 2013 SIAM J. Appl. Dyn. Syst. 12 1613
[47]	Horng T, Lin T, Liu C and Eisenberg B 2012 J. Phys. Chem. B 116 11422
[48]	Hasted J, Ritson D and Collie C 1948 J. Chem. Phys. 16 1
[49]	Abrashkin A, Andelman D and Orland H 2007 Phys. Rev. Lett. 99 077801
[50]	Gan Z and Xu Z 2011 Phys. Rev. E 84 016705
[51]	Kjellander R and Mitchell J 1992 Chem. Phys. Lett. 200 76
[52]	Kjellander R 2001 Distribution Function Theory of Electrolytes and Electrical Double Layers (Heidelberg: Springer Netherlands) pp. 317- 366
[53]	Tan Z and Chen S 2005 J. Chem. Phys. 122 044903
[54]	Tan Z and Chen S 2009 Predicting Electrostatic Forces in RNA Folding pp. 465-487
[55]	Ikeguchi M and Doi J 1995 J. Chem. Phys. 103 5011
[56]	Beglov D and Roux B 1995 J. Chem. Phys. 103 360
[57]	Vrbka L, Lund K, Kalcher I, Dzubiella J, Netz R and Kunz W 2009 J. Chem. Phys. 131 15109
[58]	Giambasu G, Luchko T, Herschlag D, York D and Case D 2014 Biophys. J. 106 883
[59]	Zwanikken J W and Olvera de la Cruz M 2013 Proc. Natl. Acad. Sci. USA 110 5301
[60]	Moreira A and Netz R 2000 Europhys. Lett. 52 705
[61]	Avdeev S and Martynov G 1986 Colloid J. USSR 48 535
[62]	Xu Z and Maggs A 2014 J. Compt. Phys. 275 310
[63]	Chern I, Liu J and Wang W 2003 Methods Appl. Anal. 10 309
[64]	Zhou Y, Zhao S, Feig M and Wei G 2006 J. Comput. Phys. 213 1
[65]	Geng W, Yu S and Wei G 2007 J. Chem. Phys. 127 114106
[66]	Wang C,Wang J, Cai Q, Li Z, Zhao H and Luo R 2013 Comput. Theor. Chem. 1024 34
[67]	Geng W and Jacob F 2013 Comput. Phys. Commun. 184 1490
[68]	Yokota R, Bardhan J, Knepley M, Barba L and Hamada T 2011 Comput. Phys. Commun. 182 1272
[69]	Zhang B, Peng B, Huang J, Pitsianis N, Sun X and Lu B 2015 Comput. Phys. Commun. 190 173

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