Differential geometry based solvation model I: Eulerian formulation

Z Chen, NA Baker, GW Wei - Journal of computational physics, 2010 - Elsevier
formulation. However, this approach does not work directly in our formulation because no
sharp solvent–… Additionally, for practical purpose, we need an appropriate Eulerian formulation

Minimization and Eulerian formulation of differential geormetry based nonpolar multiscale solvation models

Z Chen - Computational and Mathematical Biophysics, 2016 - degruyter.com
… Second, we present an Eulerian formulation of differential geometry based nonpolar solvation
model … and Eulerian formulations. Third, we look into the distinction between phase field …

Differential geometry based solvation model. III. Quantum formulation

Z Chen, GW Wei - The Journal of chemical physics, 2011 - pubs.aip.org
… By using the Euler-Lagrange variation, we derive a system of three coupled governing
equations, ie, the generalized Poisson-Boltzmann equation for the electrostatic potential, the …

Pseudo‐time‐coupled nonlinear models for biomolecular surface representation and solvation analysis

S Zhao - International Journal for Numerical Methods in …, 2011 - Wiley Online Library
model for biomolecular surface representation and solvation analysis. Based on the Eulerian
formulation, the … In explicit solvent models, the solvent is represented in molecular or atomic …

Operator splitting ADI schemes for pseudo-time coupled nonlinear solvation simulations

S Zhao - Journal of Computational Physics, 2014 - Elsevier
… In Section 2, we first introduce the pseudo-transient solvation model in the Eulerian
formulation. The proposed time splitting ADI schemes will then be formulated for solving the …

[HTML][HTML] Parameter optimization in differential geometry based solvation models

B Wang, GW Wei - The Journal of chemical physics, 2015 - pubs.aip.org
… Our DG-based solvation models have been implemented in the Eulerian formulation, where
the solvent-solute interface is embedded in the three-dimensional (3D) Euclidean space …

Variational approach for nonpolar solvation analysis

Z Chen, S Zhao, J Chun, DG Thomas… - The Journal of …, 2012 - pubs.aip.org
… been carried out to practically implement differential geometry based solvation models in the
Eulerian representation, 45 Lagrangian representation, 46 and quantum formulation. These …

Parameterization of a geometric flow implicit solvation model

DG Thomas, J Chun, Z Chen, G Wei… - Journal of …, 2013 - Wiley Online Library
… of the implicit solvent model (surface tension, dielectric coefficient, solvent pressure, etc.) and
do … For Eulerian formulations of the geometric flow problem,[6] S varies smoothly across the …

A solvation‐free‐energy functional: A reference‐modified density functional formulation

T Sumi, A Mitsutake, Y Maruyama - Journal of computational …, 2015 - Wiley Online Library
solvated state in solution and the unsolvated state in vacuum, that is, ΔG solv .1, 2 We can
categorize the phenomena of solvation … the solute from the pure solvent to the solution system …

Differential geometry based solvation model II: Lagrangian formulation

Z Chen, NA Baker, GW Wei - Journal of mathematical biology, 2011 - Springer
… required by the Eulerian representation in solvation analysis. … Eulerian and Lagrangian
formalisms of the solvation model. … the differential geometry based solvation model. The present …