Fast methods for simulation of biomolecule electrostatics. - Shihhsien S. Kuo; Michael D. Altman; Jaydeep P. Bardhan; Bruce Tidor; Jacob K. White 001 (ICCAD, 2002)

FFTSVD: A Fast Multiscale Boundary-Element Method Solver Suitable for Bio-MEMS and Biomolecule Simulation. - Michael D. Altman; Jaydeep P. Bardhan; Bruce Tidor; Jacob K. White 001 (IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2006)

Efficient numerical algorithms for surface formulations of mathematical models for biomolecule analysis and design. - Jaydeep P. Bardhan (2006)

Efficient optimization of electrostatic interactions between biomolecules. - Jaydeep P. Bardhan; Michael D. Altman; Jacob K. White 001; Bruce Tidor (CDC, 2007)

Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements. - Michael D. Altman; Jaydeep P. Bardhan; Jacob K. White 001; Bruce Tidor (J. Comput. Chem., 2009)

Biomolecular Electrostatics Simulation by an FMM-based BEM on 512 GPUs - Rio Yokota; Tsuyoshi Hamada; Jaydeep P. Bardhan; Matthew G. Knepley; Lorena A. Barba (CoRR, 2010)

A fast solver for nonlocal electrostatic theory in biomolecular science and engineering. - Jaydeep P. Bardhan; Andreas Hildebrandt 001 (DAC, 2011)

Mathematical Analysis of the BIBEE Approximation for Molecular Solvation: Exact Results for Spherical Inclusions - Jaydeep P. Bardhan; Matthew G. Knepley (CoRR, 2011)

Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns. - Rio Yokota; Jaydeep P. Bardhan; Matthew G. Knepley; Lorena A. Barba; Tsuyoshi Hamada (Comput. Phys. Commun., 2011)

Computational science and re-discovery: open-source implementations of ellipsoidal harmonics for problems in potential theory - Jaydeep P. Bardhan; Matthew G. Knepley (CoRR, 2012)

Analytical Nonlocal Electrostatics Using Eigenfunction Expansions of Boundary-Integral Operators - Jaydeep P. Bardhan; Matthew G. Knepley; Peter R. Brune (CoRR, 2012)

Fast Solvers for Molecular Science and Engineering. - Jaydeep P. Bardhan (IEEE Des. Test Comput., 2012)

Accelerating protein coordinate conversion using GPUs. - Mahsa Bayati; Jaydeep P. Bardhan; David M. King; Miriam Leeser (HPEC, 2014)

Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary Conditions. - Jaydeep P. Bardhan; Matthew G. Knepley (CoRR, 2014)

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers. - Christopher D. Cooper; Jaydeep P. Bardhan; Lorena A. Barba (Comput. Phys. Commun., 2014)

GPU implementation of reverse coordinate conversion for proteins. - Mahsa Bayati; Jaydeep P. Bardhan; Miriam Leeser (HPEC, 2015)

Maximum a posteriori estimation of relative abundances of protein conformations. - A. Emre Onuk; Murat Akçakaya; Jaydeep P. Bardhan; Deniz Erdogmus; Dana H. Brooks; Lee Makowski (MLSP, 2015)

Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture From Small Angle X-Ray Scattering Intensity Measurements. - A. Emre Onuk; Murat Akçakaya; Jaydeep P. Bardhan; Deniz Erdogmus; Dana H. Brooks; Lee Makowski (IEEE Trans. Signal Process., 2015)

A framework to optimize protein structure from solution scattering using ADMM and an elastic subdomain network. - Biel Roig-Solvas; Jaydeep P. Bardhan; Deniz Erdogmus; Dana H. Brooks; Lee Makowski (ISBI, 2016)

Dirichlet Priors for MAP Inference of Protein Conformation Abundances from SAXS. - A. Emre Onuk; Murat Akçakaya; Jaydeep P. Bardhan; Deniz Erdogmus; Dana H. Brooks; Lee Makowski (J. Signal Process. Syst., 2018)

High-performance transformation of protein structure representation from internal to Cartesian coordinates. - Mahsa Bayati; Miriam Leeser; Jaydeep P. Bardhan (J. Comput. Chem., 2020)

DOE Computational Science Graduate Fellowship Research Showcase. - Jaydeep P. Bardhan; Mary Ann E. Leung; Eileen Martin; Amanda Randles (Comput. Sci. Eng., 2021)