J. Bardhan

发表

Predicting Solvation Free Energies and Thermodynamics in Polar Solvents and Mixtures Using a Solvation-Layer Interface Condition

M. Knepley, A. Tabrizi, S. Goossens, 2016, 1611.02150.

Comparison of three-dimensional poisson solution methods for particle-based simulation and inhomogeneous dielectrics.

R. Eisenberg, C. Fiegna, J. Bardhan, 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

Rapid Bounds on Electrostatic Energies Using Diagonal Approximations of Boundary-integral Equations

J. Bardhan, 2010 .

A Curved Panel Integration Technique for Molecular Surfaces

Jacob K. White, Jaydeep P. Bardhan, Bruce Tidor, 2005 .

Discretization of the induced-charge boundary integral equation.

Dirk Gillespie, Jaydeep P Bardhan, Robert S Eisenberg, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

Mihai Anitescu, Jaydeep P Bardhan, M. Anitescu, 2009, The Journal of chemical physics.

Numerical solution of boundary-integral equations for molecular electrostatics.

Jaydeep P Bardhan, J. Bardhan, 2009, The Journal of chemical physics.

Interpreting the Coulomb-field approximation for generalized-Born electrostatics using boundary-integral equation theory.

Jaydeep P Bardhan, J. Bardhan, 2008, The Journal of chemical physics.

Multi-wavelength anomalous diffraction using medium-angle X-ray solution scattering (MADMAX).

Diane J. Rodi, L. Makowski, R. Fischetti, 2012, Biophysical journal.

Cost and Quality Implications of Discrepancies Between Admitting and Discharge Diagnoses

R. Mcnutt, J. Bardhan, T. Johnson, 2012, Quality management in health care.

2 Background 2 . 1 Mean-field theory and a general Landau – Ginzburg Hamiltonian

J. Bardhan, Baihua Ren, 2017 .

Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators

M. Knepley, J. Bardhan, P. Brune, 2015, Molecular Based Mathematical Biology.

Streaming current and wall dissolution over 48 h in silica nanochannels.

S. Pennathur, H. Bruus, J. Bardhan, 2011, Journal of colloid and interface science.

WAXS studies of the structural diversity of hemoglobin in solution.

Diane J. Rodi, C. Ho, L. Makowski, 2011, Journal of molecular biology.

Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson-Boltzmann Solvent.

Amir Saman Molavi Tabrizi, M. Knepley, S. Goossens, 2017, Journal of chemical theory and computation.

Biomolecular electrostatics simulation with a parallel FMM-based BEM, using up to 512 GPUs

Matthew G. Knepley, Lorena A. Barba, Jaydeep P. Bardhan, 2010 .

Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary Conditions

Matthew G. Knepley, Jaydeep P. Bardhan, M. Knepley, 2014, The Journal of chemical physics.

Solvation thermodynamics of neutral and charged solutes using the solvation‐layer interface condition continuum dielectric model

Amir Saman Molavi Tabrizi, M. Knepley, S. Goossens, 2018, International Journal of Quantum Chemistry.

A Nonlinear Boundary Condition for Continuum Models of Biomolecular Electrostatics

M. Knepley, J. Bardhan, D. A. Tejani, 2015, 1505.06968.

Multiscale models and approximation algorithms for protein electrostatics

M. Knepley, J. Bardhan, 2015, 1512.08408.

Hospital Care May Not Affect the Risk of Readmission

R. Mcnutt, J. Bardhan, T. Johnson, 2012, Quality management in health care.

Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture From Small Angle X-Ray Scattering Intensity Measurements

Murat Akçakaya, Deniz Erdogmus, Dana H. Brooks, 2015, IEEE Transactions on Signal Processing.

Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase.

David D. L. Minh, Deniz Erdoğmuş, D. Brooks, 2017, Biochemistry.

A Simple Electrostatic Model for the Hard-Sphere Solute Component of Nonpolar Solvation

J. Bardhan, C. D. Cooper, 2020, 2005.13019.

Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model.

S. Lustig, J. Bardhan, S. Jamali, 2022, Journal of chemical theory and computation.

Comparison of 3-D Poisson solution methods for particle-based simulation and inhomogeneous dielectrics

R. Eisenberg, C. Fiegna, J. Bardhan, 2012 .

Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling

M. Knepley, J. Bardhan, Thomas S Klotz, 2017, 1708.06028.

Efficiently accounting for ion correlations in electrokinetic nanofluidic devices using density functional theory.

Dirk Gillespie, Jaydeep P Bardhan, Sumita Pennathur, 2011, Journal of colloid and interface science.

A "Reverse-Schur" Approach to Optimization With Linear PDE Constraints: Application to Biomolecule Analysis and Design.

Jacob K. White, Jaydeep P Bardhan, Jacob K White, 2009, Journal of chemical theory and computation.

Biomolecular electrostatics—I want your solvation (model)*

Jaydeep P. Bardhan, J. Bardhan, 2012 .

Simulated x-ray scattering of protein solutions using explicit-solvent models.

Lee Makowski, Benoît Roux, Jaydeep P Bardhan, 2009, The Journal of chemical physics.

Biomolecular Electrostatics Simulation by an FMM-based BEM on 512 GPUs pdf

Matthew G. Knepley, Lorena A. Barba, Jaydeep P. Bardhan, 2010, ArXiv.

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules.

Lee Makowski, Jaydeep Bardhan, Sanghyun Park, 2009, Journal of applied crystallography.

A fast solver for nonlocal electrostatic theory in biomolecular science and engineering

Jaydeep P. Bardhan, Andreas Hildebrandt, A. Hildebrandt, 2011, 2011 48th ACM/EDAC/IEEE Design Automation Conference (DAC).

Gradient models in molecular biophysics: progress, challenges, opportunities

Jaydeep P Bardhan, J. Bardhan, 2013, Journal of the mechanical behavior of materials.

Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces.

Jacob K. White, Bruce Tidor, Jaydeep P Bardhan, 2007, The Journal of chemical physics.

FFTSVD: A Fast Multiscale Boundary-Element Method Solver Suitable for Bio-MEMS and Biomolecule Simulation

Jacob K. White, Jaydeep P. Bardhan, Bruce Tidor, 2006, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.

Efficient numerical algorithms for surface formulations of mathematical models for biomolecule analysis and design

Jaydeep P. Bardhan, J. Bardhan, 2006 .

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.

Lee Makowski, Pavel Jungwirth, Jaydeep P Bardhan, 2012, The Journal of chemical physics.

Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding

Jaydeep P Bardhan, Amelia B Kreienkamp, Lucy Y Liu, 2013, Molecular Based Mathematical Biology.

Mathematical Analysis of the BIBEE Approximation for Molecular Solvation: Exact Results for Spherical Inclusions

Matthew G. Knepley, Jaydeep P. Bardhan, M. Knepley, 2011, The Journal of chemical physics.

Efficient optimization of electrostatic interactions between biomolecules

Jacob K. White, Jaydeep P. Bardhan, Bruce Tidor, 2007, 2007 46th IEEE Conference on Decision and Control.

An Accurate Surface Formulation for Biomolecule Electrostatics in Non-Ionic Solutions

B. Tidor, M. Altman, J. Bardhan, 2005, 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference.

Analytical Nonlocal Electrostatics Using Eigenfunction Expansions of Boundary-Integral Operators pdf

Matthew G. Knepley, Peter R. Brune, Jaydeep P. Bardhan, 2012, ArXiv.

Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns

Matthew G. Knepley, Lorena A. Barba, Jaydeep P. Bardhan, 2010, Comput. Phys. Commun..

Fast methods for simulation of biomolecule electrostatics

Jacob K. White, Jaydeep P. Bardhan, Bruce Tidor, 2002, IEEE/ACM International Conference on Computer Aided Design, 2002. ICCAD 2002..

Generalising the mean spherical approximation as a multiscale, nonlinear boundary condition at the solute–solvent interface

M. Knepley, A. Tabrizi, J. Bardhan, 2016, 1607.04257.

Fast Solvers for Molecular Science and Engineering

Jaydeep P. Bardhan, J. Bardhan, 2012, IEEE Design & Test of Computers.

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

Jaydeep P Bardhan, J. Bardhan, 2011, The Journal of chemical physics.

Boundary-Integral and Boundary-Element Methods for Biomolecular Electrostatics: Progress, Challenges, and Important Lessons from CEBA 2013

Jaydeep P. Bardhan, J. Bardhan, 2015 .

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

Lorena A. Barba, Jaydeep P. Bardhan, Christopher D. Cooper, 2013, Comput. Phys. Commun..

Accurate solution of multi‐region continuum biomolecule electrostatic problems using the linearized Poisson–Boltzmann equation with curved boundary elements

Jacob K. White, Jaydeep P. Bardhan, Bruce Tidor, 2009, J. Comput. Chem..

Accelerating protein coordinate conversion using GPUs

Jaydeep P. Bardhan, Miriam Leeser, Mahsa Bayati, 2014, 2014 IEEE High Performance Extreme Computing Conference (HPEC).

Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics

Matthew G. Knepley, Jaydeep P. Bardhan, M. Knepley, 2015, 1512.08406.

High‐performance transformation of protein structure representation from internal to Cartesian coordinates

Miriam Leeser, Mahsa Bayati, Jaydeep P Bardhan, 2020, J. Comput. Chem..

GPU implementation of reverse coordinate conversion for proteins

Jaydeep P. Bardhan, Miriam Leeser, Mahsa Bayati, 2015, 2015 IEEE High Performance Extreme Computing Conference (HPEC).

Drag reduction and the Vogel exponent of a flexible beam in transient shear flows

S. Lustig, J. Bardhan, S. Jamali, 2022, Physics of Fluids.

Computational science and re-discovery: open-source implementations of ellipsoidal harmonics for problems in potential theory pdf

Matthew G. Knepley, Jaydeep P. Bardhan, M. Knepley, 2012, ArXiv.

Dirichlet Priors for MAP Inference of Protein Conformation Abundances from SAXS

Murat Akçakaya, Deniz Erdogmus, Dana H. Brooks, 2018, J. Signal Process. Syst..

Fast Methods for Biomolecule Charge Optimization

S. S. Kuo, B. Tidor, M. Altman, 2002 .

Wavelet Analysis for Molecular Dynamics by Berend

J. Bardhan, A. Ismail, C. Rinderspacher, 2015 .

Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase.

David D. L. Minh, Deniz Erdoğmuş, D. Brooks, 2017, Biochemistry.