Improvements in continuum modeling for biomolecular systems

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

中国物理B ›› 2016, Vol. 25 ›› Issue (1): 18705-018705.doi: 10.1088/1674-1056/25/1/018705

所属专题： TOPICAL REVIEW — 8th IUPAP International Conference on Biological Physics

• TOPICAL REVIEW—8th IUPAP International Conference on Biological Physics • 上一篇下一篇

Improvements in continuum modeling for biomolecular systems

Yu Qiao(乔瑜) and Ben-Zhuo Lu(卢本卓)

State Key Laboratory of Scientific and Engineering Computing, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing 100190, China

收稿日期:2015-05-08 修回日期:2015-07-22 出版日期:2016-01-05 发布日期:2016-01-05
通讯作者: Ben-Zhuo Lu E-mail:bzlu@lsec.cc.ac.cn
基金资助:
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.

Improvements in continuum modeling for biomolecular systems

Yu Qiao(乔瑜) and Ben-Zhuo Lu(卢本卓)

State Key Laboratory of Scientific and Engineering Computing, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing 100190, China

Received:2015-05-08 Revised:2015-07-22 Online:2016-01-05 Published:2016-01-05
Contact: Ben-Zhuo Lu E-mail:bzlu@lsec.cc.ac.cn
Supported by:
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.

摘要/Abstract

摘要：

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.

关键词: Poisson-Boltzmann equation, Poisson-Nernst-Planck equations, ionic size effects, density functional theory

Abstract:

Key words: Poisson-Boltzmann equation, Poisson-Nernst-Planck equations, ionic size effects, density functional theory

中图分类号: (Theory, modeling, and computer simulation)

87.15.A-

乔瑜, 卢本卓. Improvements in continuum modeling for biomolecular systems[J]. 中国物理B, 2016, 25(1): 18705-018705.

Yu Qiao(乔瑜) and Ben-Zhuo Lu(卢本卓). Improvements in continuum modeling for biomolecular systems[J]. Chin. Phys. B, 2016, 25(1): 18705-018705.

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Improvements in continuum modeling for biomolecular systems

Improvements in continuum modeling for biomolecular systems

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