Author: de Victoria, AL CA Kieslich; AK Rizos; E Krambovitis; D Morikis;

Title: Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties

Journal: BMC BIOPHYSICS

Year: 2012

Volume: 5


Author: M Holst; JA McCammon; Z Yu; YC Zhou; Y Zhu;

Title: Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation

Journal: COMMUNICATIONS IN COMPUTATIONAL PHYSICS

Year: 2012

Volume: 11

Page: 179 - 214


Author: DX Xie; LR Scott;

Title: A new boundary integral equation for molecular electrostatics with charges over whole space

Journal: BIT NUMERICAL MATHEMATICS

Year: 2011

Volume: 51

Page: 1051 - 1071


Author: A Manzin; O Bottauscio; DP Ansalone;

Title: Application of the Thin-Shell Formulation to the Numerical Modeling of Stern Layer in Biomolecular Electrostatics

Journal: JOURNAL OF COMPUTATIONAL CHEMISTRY

Year: 2011

Volume: 32

Page: 3105 - 3113


Author: RD Gorham; CA Kieslich; A Nichols; NU Sausman; M Foronda; D Morikis;

Title: An Evaluation of Poisson-Boltzmann Electrostatic Free Energy Calculations through Comparison with Experimental Mutagenesis Data

Journal: BIOPOLYMERS

Year: 2011

Volume: 95

Page: 746 - 754


Author: Q Cai; X Ye; J Wang; R Luo;

Title: Dielectric boundary force in numerical Poisson-Boltzmann methods: Theory and numerical strategies

Journal: CHEMICAL PHYSICS LETTERS

Year: 2011

Volume: 514

Page: 368 - 373


Author: MV Basilevsky; AV Odinokov; EA Nikitina; NC Petrov;

Title: The dielectric continuum solvent model adapted for treating preferential solvation effects

Journal: JOURNAL OF ELECTROANALYTICAL CHEMISTRY

Year: 2011

Volume: 660

Page: 339 - 346


Author: JP Bardhan;

Title: Nonlocal continuum electrostatic theory predicts surprisingly small energetic penalties for charge burial in proteins

Journal: JOURNAL OF CHEMICAL PHYSICS

Year: 2011

Volume: 135


Author: MJ Hsieh; R Luo;

Title: Exploring a coarse-grained distributive strategy for finite-difference Poisson-Boltzmann calculations

Journal: JOURNAL OF MOLECULAR MODELING

Year: 2011

Volume: 17

Page: 1985 - 1996


Author: RC Harris; JH Bredenberg; ARJ Silalahi; AH Boschitsch; MO Fenley;

Title: Understanding the physical basis of the salt dependence of the electrostatic binding free energy of mutated charged ligand-nucleic acid complexes

Journal: BIOPHYSICAL CHEMISTRY

Year: 2011

Volume: 156

Page: 79 - 87


Author: AW Lange; JM Herbert;

Title: A simple polarizable continuum solvation model for electrolyte solutions

Journal: JOURNAL OF CHEMICAL PHYSICS

Year: 2011

Volume: 134


Author: A Helgadottir; F Gibou;

Title: A Poisson-Boltzmann solver on irregular domains with Neumann or Robin boundary conditions on non-graded adaptive grid

Journal: JOURNAL OF COMPUTATIONAL PHYSICS

Year: 2011

Volume: 230

Page: 3830 - 3848


Author: AH Boschitsch; MO Fenley;

Title: A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids

Journal: JOURNAL OF CHEMICAL THEORY AND COMPUTATION

Year: 2011

Volume: 7

Page: 1524 - 1540


Author: A Manzin; DP Ansalone; O Bottauscio;

Title: Numerical Modeling of Biomolecular Electrostatic Properties by the Element-Free Galerkin Method

Journal: IEEE TRANSACTIONS ON MAGNETICS

Year: 2011

Volume: 47

Page: 1382 - 1385


Author: ZL Xu; W Cai; XL Cheng;

Title: Image Charge Method for Reaction Fields in a Hybrid Ion-Channel Model

Journal: COMMUNICATIONS IN COMPUTATIONAL PHYSICS

Year: 2011

Volume: 9

Page: 1056 - 1070


Author: RD Gorham; CA Kieslich; D Morikis;

Title: Electrostatic Clustering and Free Energy Calculations Provide a Foundation for Protein Design and Optimization

Journal: ANNALS OF BIOMEDICAL ENGINEERING

Year: 2011

Volume: 39

Page: 1252 - 1263


Author: CA Kieslich; D Morikis; JF Yang; D Gunopulos;

Title: Automated Computational Framework for the Analysis of Electrostatic Similarities of Proteins

Journal: BIOTECHNOLOGY PROGRESS

Year: 2011

Volume: 27

Page: 316 - 325


Author: ZL Xu; XL Cheng; HZ Yang;

Title: Treecode-based generalized Born method

Journal: JOURNAL OF CHEMICAL PHYSICS

Year: 2011

Volume: 134


Author: MCA Kropinski; BD Quaife;

Title: Fast integral equation methods for the modified Helmholtz equation

Journal: JOURNAL OF COMPUTATIONAL PHYSICS

Year: 2011

Volume: 230

Page: 425 - 434


Author: CA Kieslich; RD Gorham; D Morikis;

Title: Is the rigid-body assumption reasonable? Insights into the effects of dynamics on the electrostatic analysis of barnase-barstar

Journal: JOURNAL OF NON-CRYSTALLINE SOLIDS

Year: 2011

Volume: 357

Page: 707 - 716


Author: B Li; XL Cheng; ZF Zhang;

Title: DIELECTRIC BOUNDARY FORCE IN MOLECULAR SOLVATION WITH THE POISSON-BOLTZMANN FREE ENERGY: A SHAPE DERIVATIVE APPROACH

Journal: SIAM JOURNAL ON APPLIED MATHEMATICS

Year: 2011

Volume: 71

Page: 2093 - 2111


Author: ZL Xu; W Cai;

Title: Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations

Journal: SIAM REVIEW

Year: 2011

Volume: 53

Page: 683 - 720


Author: C Bajaj; SC Chen; A Rand;

Title: AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN-BASED MOLECULAR ELECTROSTATICS

Journal: SIAM JOURNAL ON SCIENTIFIC COMPUTING

Year: 2011

Volume: 33

Page: 826 - 848


Author: MX Chen; BZ Lu;

Title: TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique

Journal: JOURNAL OF CHEMICAL THEORY AND COMPUTATION

Year: 2011

Volume: 7

Page: 203 - 212


Author: K Chae; BJ Gonong; SC Kim; CA Kieslich; D Morikis; S Balasubramanian; EM Lord;

Title: A multifaceted study of stigma/style cysteine-rich adhesin (SCA)-like Arabidopsis lipid transfer proteins (LTPs) suggests diversified roles for these LTPs in plant growth and reproduction

Journal: JOURNAL OF EXPERIMENTAL BOTANY

Year: 2010

Volume: 61

Page: 4277 - 4290


Author: B Lu; MJ Holst; JA McCammon; YC Zhou;

Title: Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutions

Journal: JOURNAL OF COMPUTATIONAL PHYSICS

Year: 2010

Volume: 229

Page: 6979 - 6994


Author: FN Hwang; SR Cai; YL Shao; JS Wu;

Title: Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional Poisson-Boltzmann equation in numerical simulation of colloidal particle interactions

Journal: COMPUTER PHYSICS COMMUNICATIONS

Year: 2010

Volume: 181

Page: 1529 - 1537


Author: YC Shu; CC Chang; YS Chen; CY Wang;

Title: Electro-osmotic flow in a wavy microchannel: Coherence between the electric potential and the wall shape function

Journal: PHYSICS OF FLUIDS

Year: 2010

Volume: 22


Author: G Lamm; GR Pack;

Title: Counterion Condensation and Shape Within Poisson-Boltzmann Theory

Journal: BIOPOLYMERS

Year: 2010

Volume: 93

Page: 619 - 639


Author: EH Yap; T Head-Gordon;

Title: New and Efficient Poisson-Boltzmann Solver for Interaction of Multiple Proteins

Journal: JOURNAL OF CHEMICAL THEORY AND COMPUTATION

Year: 2010

Volume: 6

Page: 2214 - 2224


Author: AS Cheung; CA Kieslich; JF Yang; D Morikis;

Title: Solvation Effects in Calculated Electrostatic Association Free Energies for the C3d-CR2 Complex and Comparison with Experimental Data

Journal: BIOPOLYMERS

Year: 2010

Volume: 93

Page: 509 - 519


Author: J Wang; R Luo;

Title: Assessment of Linear Finite-Difference Poisson-Boltzmann Solvers

Journal: JOURNAL OF COMPUTATIONAL CHEMISTRY

Year: 2010

Volume: 31

Page: 1689 - 1698


Author: S Weggler; V Rutka; A Hildebrandt;

Title: A new numerical method for nonlocal electrostatics in biomolecular simulations

Journal: JOURNAL OF COMPUTATIONAL PHYSICS

Year: 2010

Volume: 229

Page: 4059 - 4074


Author: A Singharoy; AM Yesnik; P Ortoleva;

Title: Multiscale analytic continuation approach to nanosystem simulation: Applications to virus electrostatics

Journal: JOURNAL OF CHEMICAL PHYSICS

Year: 2010

Volume: 132


Author: X Ye; J Wang; R Luo;

Title: A Revised Density Function for Molecular Surface Calculation in Continuum Solvent Models

Journal: JOURNAL OF CHEMICAL THEORY AND COMPUTATION

Year: 2010

Volume: 6

Page: 1157 - 1169


Author: MV Basilevsky; FV Grigoriev; EA Nikitina; J Leszczynski;

Title: Implicit Electrostatic Solvent Model with Continuous Dielectric Permittivity Function

Journal: JOURNAL OF PHYSICAL CHEMISTRY B

Year: 2010

Volume: 114

Page: 2457 - 2466


Author: P Koehl; M Delarue;

Title: AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation

Journal: JOURNAL OF CHEMICAL PHYSICS

Year: 2010

Volume: 132


Author: ZL Xu;

Title: Treecode algorithm for pairwise electrostatic interactions with solvent-solute polarization

Journal: PHYSICAL REVIEW E

Year: 2010

Volume: 81


Author: Q Cai; MJ Hsieh; J Wang; R Luo;

Title: Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers

Journal: JOURNAL OF CHEMICAL THEORY AND COMPUTATION

Year: 2010

Volume: 6

Page: 203 - 211


Author: MO Fenley; M Mascagni; J McClain; ARJ Silalahi; NA Simonov;

Title: Using Correlated Monte Carlo Sampling for Efficiently Solving the Linearized Poisson-Boltzmann Equation Over a Broad Range of Salt Concentration

Journal: JOURNAL OF CHEMICAL THEORY AND COMPUTATION

Year: 2010

Volume: 6

Page: 300 - 314


Author: AJ Christlieb; CB Macdonald; BW Ong;

Title: PARALLEL HIGH-ORDER INTEGRATORS

Journal: SIAM JOURNAL ON SCIENTIFIC COMPUTING

Year: 2010

Volume: 32

Page: 818 - 835


Author: J Wang; CH Tan; E Chanco; R Luo;

Title: Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics

Journal: PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Year: 2010

Volume: 12

Page: 1194 - 1202


Author: PH Qin; ZL Xu; W Cai; D Jacobs;

Title: Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules

Journal: COMMUNICATIONS IN COMPUTATIONAL PHYSICS

Year: 2009

Volume: 6

Page: 955 - 977


Author: ZL Xu; W Cai;

Title: Fast Spectral Collocation Method for Surface Integral Equations of Potential Problems in a Spheroid

Journal: COMMUNICATIONS IN COMPUTATIONAL PHYSICS

Year: 2009

Volume: 6

Page: 625 - 638


Author: M Baptista; R Schmitz; B Dunweg;

Title: Simple and robust solver for the Poisson-Boltzmann equation

Journal: PHYSICAL REVIEW E

Year: 2009

Volume: 80


Author: JP Bardhan; RS Eisenberg; D Gillespie;

Title: Discretization of the induced-charge boundary integral equation

Journal: PHYSICAL REVIEW E

Year: 2009

Volume: 80


Author: PJ Li; H Johnston; R Krasny;

Title: A Cartesian treecode for screened coulomb interactions

Journal: JOURNAL OF COMPUTATIONAL PHYSICS

Year: 2009

Volume: 228

Page: 3858 - 3868


Author: Q Cai; J Wang; HK Zhao; R Luo;

Title: On removal of charge singularity in Poisson-Boltzmann equation

Journal: JOURNAL OF CHEMICAL PHYSICS

Year: 2009

Volume: 130


Author: W Cai; ZL Xu; A Baumketner;

Title: A new FFF-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation

Journal: JOURNAL OF COMPUTATIONAL PHYSICS

Year: 2008

Volume: 227

Page: 10162 - 10177