Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: A review
Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: A review
复制标题
用于生物分子建模的基于微分几何的溶剂化和电解质传输模型：综述
DOI：
--
复制
发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Nathan A. Baker
中科院分区：
文献类型：
--
作者：
G. Wei;Nathan A. Baker
本章回顾了微分几何为基础的溶剂化和电解质运输的生物分子溶剂化，在过去的十年中已经发展起来。这些方法的一个关键组成部分是微分几何的表面理论，适用于溶剂-溶质边界。在这些方法中，溶剂-溶质边界由变分原理确定，该变分原理确定感兴趣的主要物理观测量，例如，生物分子表面积、封闭体积、静电势、离子密度、电子密度等。最近，微分几何理论已被用于定义将生物分子的微观（溶质）域与宏观（溶剂）域分开的表面。在这些方法中，微观领域与原子或量子力学的描述建模，而连续介质力学模型（包括流体力学，弹性力学，和连续介质静电）应用于宏观领域。这种多物理场描述是通过能量泛函形式主义和所得的欧拉-拉格朗日方程来集成的，用于导出不同溶剂化和输运过程的各种控制偏微分方程;例如，用于溶剂-溶质界面的Laplace-Beltrami方程、用于静电势的Poisson或Poisson-Boltzmann方程、用于离子密度的Nernst-Planck方程和用于溶质电子密度的Kohn-Sham方程。这些模型已进行了广泛的验证，超过数百个分子，包括蛋白质和离子通道，并在溶剂化能量，电压-电流曲线和密度分布方面的实验数据进行了比较。我们还提出了一个新的量子模型的电解质运输。
This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In these approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.
登录
查看更多内容
影响因子：
5.5
作者：
Cheng, Li-Tien;Xie, Yang;Dzubiella, Joachim;McCammon, J. Andrew;Che, Jianwei;Li, Bo
通讯作者：
Li, Bo
影响因子：
2.4
作者：
Wei GW
通讯作者：
Wei GW
影响因子：
3.4
作者：
Chen, Hanning;Wu, Yujie;Voth, Gregory A.
通讯作者：
Voth, Gregory A.
DOI：
10.1073/pnas.86.21.8382
发表时间：
1989-11
影响因子：
11.1
作者：
Ruth S. Spolar;J. Ha;Record Mt
通讯作者：
Ruth S. Spolar;J. Ha;Record Mt
溶剂化自由能几何流计算中参数简并和分子形状关系的起源。
DOI：
10.1063/1.4832900
发表时间：
2013
期刊：
The Journal of chemical physics
影响因子：
--
作者：
Daily,MichaelD;Chun,Jaehun;Heredia-Langner,Alejandro;Wei,Guowei;Baker,NathanA
通讯作者：
Baker,NathanA