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Prediction of multiple dry–wet transition pathways with a mesoscale variational approach

The Journal of chemical physics, 2021-09, Vol.155 (12), p.124110-124110

2021

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LS-VISM: A software package for analysis of biomolecular solvation

Journal of computational chemistry, 2015-05, Vol.36 (14), p.1047-1059

2015

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Binary Level Set Method for Variational Implicit Solvation Model

SIAM journal on scientific computing, 2023-10, Vol.45 (5), p.B618-B645

2023

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Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

The Journal of chemical physics, 2016-08, Vol.145 (5), p.054114-054114

2016

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Application of the level-set method to the implicit solvation of nonpolar molecules

The Journal of chemical physics, 2007-08, Vol.127 (8), p.084503-084503

2007

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Variational Problems and Partial Differential Equations on Implicit Surfaces

Journal of computational physics, 2001-12, Vol.174 (2), p.759-780

2001

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Zebrafish Model-Based Assessment of Indoxyl Sulfate-Induced Oxidative Stress and Its Impact on Renal and Cardiac Development

Antioxidants, 2022-02, Vol.11 (2), p.400

2022

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A Second-Order-Accurate Symmetric Discretization of the Poisson Equation on Irregular Domains

Journal of computational physics, 2002-02, Vol.176 (1), p.205-227

2002

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Redistancing by flow of time dependent eikonal equation

Journal of computational physics, 2008-04, Vol.227 (8), p.4002-4017

2008

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Fast Sweeping Algorithms for a Class of Hamilton--Jacobi Equations

SIAM journal on numerical analysis, 2003-01, Vol.41 (2), p.673-694

2003

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Explicit-solute implicit-solvent molecular simulation with binary level-set, adaptive-mobility, and GPU

Journal of computational physics, 2023-01, Vol.472, p.111673, Article 111673

2023

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Identification of Protein–Ligand Binding Sites by the Level-Set Variational Implicit-Solvent Approach

Journal of chemical theory and computation, 2015-02, Vol.11 (2), p.753-765

2015

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Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding

Journal of chemical theory and computation, 2021-04, Vol.17 (4), p.2465-2478

2021

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Numerical methods for solvent Stokes flow and solute-solvent interfacial dynamics of charged molecules

Journal of computational physics, 2018-12, Vol.374, p.533-549

2018

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Variational Implicit Solvation with Poisson–Boltzmann Theory

Journal of chemical theory and computation, 2014-04, Vol.10 (4), p.1454-1467

2014

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Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

Frontiers in molecular biosciences, 2018-02, Vol.5, p.13-13

2018

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Variational implicit-solvent predictions of the dry–wet transition pathways for ligand–receptor binding and unbinding kinetics

Proceedings of the National Academy of Sciences - PNAS, 2019-07, Vol.116 (30), p.14989-14994

2019

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“Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins

The journal of physical chemistry. B, 2017-07, Vol.121 (27), p.6538-6548

2017

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Interfaces and hydrophobic interactions in receptor-ligand systems:A level-set variational implicit solvent approach

The Journal of chemical physics, 2009-10, Vol.131 (14), p.144102-144102-10

2009

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Heterogeneous Hydration of p53/MDM2 Complex

Journal of chemical theory and computation, 2014-03, Vol.10 (3), p.1302-1313

2014

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Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation

Journal of chemical theory and computation, 2012-02, Vol.8 (2), p.386-397

2012

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Level-set minimization of potential controlled Hadwiger valuations for molecular solvation

Journal of computational physics, 2010-11, Vol.229 (22), p.8497-8510

2010

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Binary Level-Set Shape Optimization Model and Algorithm for Volumetric Modulated Arc Therapy in Radiotherapy Treatment

SIAM journal on scientific computing, 2013-01, Vol.35 (6), p.B1321-B1340

2013

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Numerical Treatment of Stokes Solvent Flow and Solute–Solvent Interfacial Dynamics for Nonpolar Molecules

Journal of scientific computing, 2016-05, Vol.67 (2), p.705-723

2016

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Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules

Journal of chemical theory and computation, 2009-02, Vol.5 (2), p.257-266

2009

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Prediction of multiple dry–wet transition pathways with a mesoscale variational approach

LS-VISM: A software package for analysis of biomolecular solvation

Binary Level Set Method for Variational Implicit Solvation Model

Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

Application of the level-set method to the implicit solvation of nonpolar molecules

Variational Problems and Partial Differential Equations on Implicit Surfaces

Zebrafish Model-Based Assessment of Indoxyl Sulfate-Induced Oxidative Stress and Its Impact on Renal and Cardiac Development

A Second-Order-Accurate Symmetric Discretization of the Poisson Equation on Irregular Domains

Redistancing by flow of time dependent eikonal equation

Fast Sweeping Algorithms for a Class of Hamilton--Jacobi Equations

Explicit-solute implicit-solvent molecular simulation with binary level-set, adaptive-mobility, and GPU

Identification of Protein–Ligand Binding Sites by the Level-Set Variational Implicit-Solvent Approach

Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding

Numerical methods for solvent Stokes flow and solute-solvent interfacial dynamics of charged molecules

Variational Implicit Solvation with Poisson–Boltzmann Theory

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

Variational implicit-solvent predictions of the dry–wet transition pathways for ligand–receptor binding and unbinding kinetics

“Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins

Interfaces and hydrophobic interactions in receptor-ligand systems:A level-set variational implicit solvent approach

Heterogeneous Hydration of p53/MDM2 Complex

Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation

Level-set minimization of potential controlled Hadwiger valuations for molecular solvation

Binary Level-Set Shape Optimization Model and Algorithm for Volumetric Modulated Arc Therapy in Radiotherapy Treatment

Numerical Treatment of Stokes Solvent Flow and Solute–Solvent Interfacial Dynamics for Nonpolar Molecules

Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules

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