Three-phase Model of Visco-elastic Incompressible Fluid Flow and its Computational Implementation [0.03%]
黏弹性不可压缩流体三相流模型及其计算实现方法研究
Shixin Xu,Mark Alber,Zhiliang Xu
Shixin Xu
Energetic Variational Approach is used to derive a novel thermodynamically consistent three-phase model of a mixture of Newtonian and visco-elastic fluids. The model which automatically satisfies the energy dissipation law and is Galilean i...
Fast Simulation of Lipid Vesicle Deformation Using Spherical Harmonic Approximation [0.03%]
基于球面调和逼近的脂质体形变快速模拟
Michael Mikucki,Yongcheng Zhou
Michael Mikucki
Lipid vesicles appear ubiquitously in biological systems. Understanding how the mechanical and intermolecular interactions deform vesicle membranes is a fundamental question in biophysics. In this article we develop a fast algorithm to comp...
DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes [0.03%]
DelPhi网络服务器：用于生物大分子及其复合物静电计算的全面在线工具集
Subhra Sarkar,Shawn Witham,Jie Zhang et al.
Subhra Sarkar et al.
Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra servi...
In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor [0.03%]
人绒毛膜促性腺激素受体结合人催乳素和人的生长激素的pH依赖性的一项计算机模拟研究
Lin Wang,Shawn Witham,Zhe Zhang et al.
Lin Wang et al.
Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in si...
Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants [0.03%]
利用Delphi的能力并采用特定氨基酸相对介电常数来模拟蛋白质的构象重排
Lin Wang,Zhe Zhang,Walter Rocchia et al.
Lin Wang et al.
Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrost...
A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore [0.03%]
一种求解纳米孔道离子电流的稳定化有限元方法（修改型Poisson-Nernst-Planck方程）
Jehanzeb Hameed Chaudhry,Jeffrey Comer,Aleksei Aksimentiev et al.
Jehanzeb Hameed Chaudhry et al.
The conventional Poisson-Nernst-Planck equations do not account for the finite size of ions explicitly. This leads to solutions featuring unrealistically high ionic concentrations in the regions subject to external potentials, in particular...
An Interface-Fitted Finite Element Level Set Method with Application to Solidification and Solvation [0.03%]
适用于固体固化和溶剂化的拟合界面有限元水平集方法及其应用
Bo Li,John Shopple
Bo Li
A new finite element level set method is developed to simulate the interface motion. The normal velocity of the moving interface can depend on both the local geometry, such as the curvature, and the external force such as that due to the fl...
Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model [0.03%]
像电荷溶剂化模型揭示反应场对分子间力和力矩的影响
Wei Song,Yuchun Lin,Andrij Baumketner et al.
Wei Song et al.
We recently developed the Image-Charge Solvation Model (ICSM), which is an explicit/implicit hybrid model to accurately account for long-range electrostatic forces in molecular dynamics simulations [Lin et al., J. Chem. Phys., 131, 154103, ...
Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation [0.03%]
连续体中质子输运的量子动力学 第1部分：基本理论框架
Duan Chen,Guo-Wei Wei
Duan Chen
Proton transport is one of the most important and interesting phenomena in living cells. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane protein...
Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution [0.03%]
基于泊松-玻尔兹曼的电荷分布描述及其生物大分子溶液体系中的模型依赖性
Sergio Decherchi,José Colmenares,Chiara Eva Catalano et al.
Sergio Decherchi et al.
The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular gra...