A constrained variational model of biomolecular solvation and its numerical implementation
A constrained variational model of biomolecular solvation and its numerical implementation
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生物分子溶剂化的约束变分模型及其数值实现
DOI：
10.1016/j.camwa.2021.12.009
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发表时间：
2022
影响因子：
2.9
通讯作者：
Chen, Zhan
中科院分区：
文献类型：
--
作者：
Shao, Yuanzhen;Hawkins, Elizabeth;Wang, Kai;Chen, Zhan
具有光滑界面的生物分子的变分溶剂化模型作为隐式溶剂模型框架中溶质-溶剂界面的一种有效而可靠的表示方法，在过去的十年里引起了人们的广泛关注。这项工作旨在为基于几何流动的光滑界面计算溶剂化模型(GFBSS)及其所涉及的计算处理提供坚实的数学支持。为此，我们通过显式地包含两个物理约束来改进GFBSS模型：(1)新的基于实验的区域分解；(2)描述最优扩散溶质-溶剂边界的特征函数的双边障碍。结果表明，所得到的约束模型在数学上是适定的。此外，为了克服包含这些约束带来的挑战，我们提出了一族广义约束能量泛函，其变量满足非极性分子的AQ-Laplacian方程。广义模型预测的溶剂化自由能收敛于所提出的约束模型的自由能。最重要的是，广义模型与以前的无约束GFBSS模型之间的数值差异可以忽略不计。这表明，新提出的约束溶剂化模型与以前的非约束溶剂化模型在溶剂化自由能的计算和预测上是等价的。我们的模型验证、数值实现和溶剂化能量收敛已通过几个常见的生物分子建模任务进行了演示。
Variational based solvation models of biomolecules with smooth interface have drawn attentions in the past decade since they have been developed as an efficient and reliable representation of solute-solvent interfaces in the framework of implicit solvent models. This work aims at providing solid mathematical supports for a promising geometric flow based computational solvation model with smooth interface (GFBSS) and its involved computational treatments. For this purpose, we improve the GFBSS model by explicitly including two physical constraints: (1) a novel experimental based domain decomposition, and (2) a two-sided obstacle for the characteristic function describing the optimal diffuse solute-solvent boundary. It is shown that the resulting constrained model is mathematically well-posed. Further, to overcome the challenges arising from including these constraints, we propose a family of generalized constrained energy functionals whose variations satisfy aq-Laplacian type equation for nonpolar molecules. The solvation free energies predicted by the generalized models converge to that of the proposed constrained one. Most importantly, the numerical difference between the generalized models and the previous unconstrained GFBSS model is negligible. It implies that the newly proposed constrained solvation model and the previous unconstrained one are equivalent to each other in terms of the solvation free energy calculation and prediction. Our model validation, its numerical implementation, and solvation energy convergence have been demonstrated using several common biomolecular modeling tasks.
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影响因子：
8.6
作者：
Koehl P;Orland H;Delarue M
通讯作者：
Delarue M
DOI：
10.1063/1.4812839
发表时间：
2013-07
期刊：
The Journal of chemical physics
影响因子：
--
作者：
Yanxiang Zhao;Y. Kwan;Jianwei Che;Bo Li;J. McCammon
通讯作者：
Yanxiang Zhao;Y. Kwan;Jianwei Che;Bo Li;J. McCammon
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
DOI：
10.1016/j.bbapap.2006.08.007
发表时间：
2006-11
期刊：
Biochimica et biophysica acta
影响因子：
--
作者：
A. Warshel;P. K. Sharma;Mitsunori Kato;W. W. Parson-W.
通讯作者：
A. Warshel;P. K. Sharma;Mitsunori Kato;W. W. Parson-W.
当 p 变为 1 时 p-拉普拉斯方程解的行为
影响因子：
1.1
作者：
A. Mercaldo;S. S. D. León;C. Trombetti
通讯作者：
C. Trombetti