Jaydeep P. Bardhan

ORCID

Publication Activity (10 Years)

Years Active: 2002-2021
Publications (10 Years): 4

Top Venues

CoRR

HPEC

ISBI

IEEE Des. Test Comput.

Massachusetts Institute of Technology, Cambridge, MA, USA (PHD)

Education History

Massachusetts Institute of Technology, Cambridge, MA, USA

PHD

Publications

Jaydeep P. Bardhan, Mary Ann E. Leung, Eileen Martin, Amanda Randles
DOE Computational Science Graduate Fellowship Research Showcase. Comput. Sci. Eng. 23 (6) (2021)
Mahsa Bayati, Miriam Leeser, Jaydeep P. Bardhan
High-performance transformation of protein structure representation from internal to Cartesian coordinates. J. Comput. Chem. 41 (24) (2020)
A. Emre Onuk, Murat Akçakaya, Jaydeep P. Bardhan, Deniz Erdogmus, Dana H. Brooks, Lee Makowski
Dirichlet Priors for MAP Inference of Protein Conformation Abundances from SAXS. J. Signal Process. Syst. 90 (2) (2018)
Biel Roig-Solvas, Jaydeep P. Bardhan, Deniz Erdogmus, Dana H. Brooks, Lee Makowski
A framework to optimize protein structure from solution scattering using ADMM and an elastic subdomain network. ISBI (2016)
A. Emre Onuk, Murat Akçakaya, Jaydeep P. Bardhan, Deniz Erdogmus, Dana H. Brooks, Lee Makowski
Maximum a posteriori estimation of relative abundances of protein conformations. MLSP (2015)
Mahsa Bayati, Jaydeep P. Bardhan, Miriam Leeser
GPU implementation of reverse coordinate conversion for proteins. HPEC (2015)
A. Emre Onuk, Murat Akçakaya, Jaydeep P. Bardhan, Deniz Erdogmus, Dana H. Brooks, Lee Makowski
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. 63 (20) (2015)
Christopher D. Cooper, Jaydeep P. Bardhan, Lorena A. Barba
A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers. Comput. Phys. Commun. 185 (3) (2014)
Jaydeep P. Bardhan, Matthew G. Knepley
Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary Conditions. CoRR (2014)
Mahsa Bayati, Jaydeep P. Bardhan, David M. King, Miriam Leeser
Accelerating protein coordinate conversion using GPUs. HPEC (2014)
Jaydeep P. Bardhan
Fast Solvers for Molecular Science and Engineering. IEEE Des. Test Comput. 29 (3) (2012)
Jaydeep P. Bardhan, Matthew G. Knepley, Peter R. Brune
Analytical Nonlocal Electrostatics Using Eigenfunction Expansions of Boundary-Integral Operators CoRR (2012)
Jaydeep P. Bardhan, Matthew G. Knepley
Computational science and re-discovery: open-source implementations of ellipsoidal harmonics for problems in potential theory CoRR (2012)
Jaydeep P. Bardhan, Matthew G. Knepley
Mathematical Analysis of the BIBEE Approximation for Molecular Solvation: Exact Results for Spherical Inclusions CoRR (2011)
Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley, Lorena A. Barba, Tsuyoshi Hamada
Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns. Comput. Phys. Commun. 182 (6) (2011)
Jaydeep P. Bardhan, Andreas Hildebrandt
A fast solver for nonlocal electrostatic theory in biomolecular science and engineering. DAC (2011)
Rio Yokota, Tsuyoshi Hamada, Jaydeep P. Bardhan, Matthew G. Knepley, Lorena A. Barba
Biomolecular Electrostatics Simulation by an FMM-based BEM on 512 GPUs CoRR (2010)
Michael D. Altman, Jaydeep P. Bardhan, Jacob K. White, Bruce Tidor
Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements. J. Comput. Chem. 30 (1) (2009)
Jaydeep P. Bardhan, Michael D. Altman, Jacob K. White, Bruce Tidor
Efficient optimization of electrostatic interactions between biomolecules. CDC (2007)
Michael D. Altman, Jaydeep P. Bardhan, Bruce Tidor, Jacob K. White
FFTSVD: A Fast Multiscale Boundary-Element Method Solver Suitable for Bio-MEMS and Biomolecule Simulation. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 25 (2) (2006)
Shihhsien S. Kuo, Michael D. Altman, Jaydeep P. Bardhan, Bruce Tidor, Jacob K. White
Fast methods for simulation of biomolecule electrostatics. ICCAD (2002)

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Publication Activity (10 Years)

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Jaydeep P. Bardhan