Jaydeep P. Bardhan

22 papers A* 1A 1Journal 14Unranked 5
YearRankTypeTitle / Venue / Authors
2021 J jnl
DOE Computational Science Graduate Fellowship Research Showcase.
Comput. Sci. Eng.
Jaydeep P. Bardhan, Mary Ann E. Leung, Eileen Martin, Amanda Randles
2020 J jnl
High-performance transformation of protein structure representation from internal to Cartesian coordinates.
J. Comput. Chem.
Mahsa Bayati, Miriam Leeser, Jaydeep P. Bardhan
2018 J jnl
Dirichlet Priors for MAP Inference of Protein Conformation Abundances from SAXS.
J. Signal Process. Syst.
A. Emre Onuk, Murat Akçakaya, Jaydeep P. Bardhan, Deniz Erdogmus, Dana H. Brooks, Lee Makowski
2016 — conf
A framework to optimize protein structure from solution scattering using ADMM and an elastic subdomain network.
ISBI
Biel Roig-Solvas, Jaydeep P. Bardhan, Deniz Erdogmus, Dana H. Brooks, Lee Makowski
2015 J jnl
Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture From Small Angle X-Ray Scattering Intensity Measurements.
IEEE Trans. Signal Process.
A. Emre Onuk, Murat Akçakaya, Jaydeep P. Bardhan, Deniz Erdogmus, Dana H. Brooks, Lee Makowski
2015 — conf
GPU implementation of reverse coordinate conversion for proteins.
HPEC
Mahsa Bayati, Jaydeep P. Bardhan, Miriam Leeser
2015 — conf
Maximum a posteriori estimation of relative abundances of protein conformations.
MLSP
A. Emre Onuk, Murat Akçakaya, Jaydeep P. Bardhan, Deniz Erdogmus, Dana H. Brooks, Lee Makowski
2014 J jnl
A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers.
Comput. Phys. Commun.
Christopher D. Cooper, Jaydeep P. Bardhan, Lorena A. Barba
2014 — conf
Accelerating protein coordinate conversion using GPUs.
HPEC
Mahsa Bayati, Jaydeep P. Bardhan, David M. King, Miriam Leeser
2014 J jnl
Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary Conditions.
CoRR
Jaydeep P. Bardhan, Matthew G. Knepley
2012 J jnl
Analytical Nonlocal Electrostatics Using Eigenfunction Expansions of Boundary-Integral Operators
CoRR
Jaydeep P. Bardhan, Matthew G. Knepley, Peter R. Brune
2012 J jnl
Computational science and re-discovery: open-source implementations of ellipsoidal harmonics for problems in potential theory
CoRR
Jaydeep P. Bardhan, Matthew G. Knepley
2012 J jnl
Fast Solvers for Molecular Science and Engineering.
IEEE Des. Test Comput.
Jaydeep P. Bardhan
2011 A* conf
A fast solver for nonlocal electrostatic theory in biomolecular science and engineering.
DAC
Jaydeep P. Bardhan, Andreas Hildebrandt
2011 J jnl
Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns.
Comput. Phys. Commun.
Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley, Lorena A. Barba, Tsuyoshi Hamada
2011 J jnl
Mathematical Analysis of the BIBEE Approximation for Molecular Solvation: Exact Results for Spherical Inclusions
CoRR
Jaydeep P. Bardhan, Matthew G. Knepley
2010 J jnl
Biomolecular Electrostatics Simulation by an FMM-based BEM on 512 GPUs
CoRR
Rio Yokota, Tsuyoshi Hamada, Jaydeep P. Bardhan, Matthew G. Knepley, Lorena A. Barba
2009 J jnl
Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements.
J. Comput. Chem.
Michael D. Altman, Jaydeep P. Bardhan, Jacob K. White, Bruce Tidor
2007 — conf
Efficient optimization of electrostatic interactions between biomolecules.
CDC
Jaydeep P. Bardhan, Michael D. Altman, Jacob K. White, Bruce Tidor
2006 — —
Efficient numerical algorithms for surface formulations of mathematical models for biomolecule analysis and design.
Jaydeep P. Bardhan
2006 J jnl
FFTSVD: A Fast Multiscale Boundary-Element Method Solver Suitable for Bio-MEMS and Biomolecule Simulation.
IEEE Trans. Comput. Aided Des. Integr. Circuits Syst.
Michael D. Altman, Jaydeep P. Bardhan, Bruce Tidor, Jacob K. White
2002 A conf
Fast methods for simulation of biomolecule electrostatics.
ICCAD
Shihhsien S. Kuo, Michael D. Altman, Jaydeep P. Bardhan, Bruce Tidor, Jacob K. White