Jaydeep P. Bardhan

According to our database, Jaydeep P. Bardhan authored at least 22 papers between 2002 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2021

DOE Computational Science Graduate Fellowship Research Showcase.

Jaydeep P. Bardhan, Mary Ann E. Leung, Eileen Martin, Amanda Randles

Comput. Sci. Eng., 2021

2020

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

Mahsa Bayati, Miriam Leeser, Jaydeep P. Bardhan

J. Comput. Chem., 2020

2018

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

2016

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

Proceedings of the 13th IEEE International Symposium on Biomedical Imaging, 2016

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

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

Proceedings of the 25th IEEE International Workshop on Machine Learning for Signal Processing, 2015

GPU implementation of reverse coordinate conversion for proteins.

Mahsa Bayati, Jaydeep P. Bardhan, Miriam Leeser

Proceedings of the 2015 IEEE High Performance Extreme Computing Conference, 2015

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

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

Jaydeep P. Bardhan, Matthew G. Knepley

CoRR, 2014

Accelerating protein coordinate conversion using GPUs.

Mahsa Bayati, Jaydeep P. Bardhan, David M. King, Miriam Leeser

Proceedings of the IEEE High Performance Extreme Computing Conference, 2014

2012

Fast Solvers for Molecular Science and Engineering.

Jaydeep P. Bardhan

IEEE Des. Test Comput., 2012

Analytical Nonlocal Electrostatics Using Eigenfunction Expansions of Boundary-Integral Operators

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

CoRR, 2012

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

Jaydeep P. Bardhan, Matthew G. Knepley

CoRR, 2012

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

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

Jaydeep P. Bardhan, Matthew G. Knepley

CoRR, 2011

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

Jaydeep P. Bardhan, Andreas Hildebrandt

Proceedings of the 48th Design Automation Conference, 2011

2010

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

2009

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, Bruce Tidor

J. Comput. Chem., 2009

2007

Efficient optimization of electrostatic interactions between biomolecules.

Jaydeep P. Bardhan, Michael D. Altman, Jacob K. White, Bruce Tidor

Proceedings of the 46th IEEE Conference on Decision and Control, 2007

2006

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

Jaydeep P. Bardhan

PhD thesis, 2006

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

IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2006

2002

Fast methods for simulation of biomolecule electrostatics.

Shihhsien S. Kuo, Michael D. Altman, Jaydeep P. Bardhan, Bruce Tidor, Jacob K. White

Proceedings of the 2002 IEEE/ACM International Conference on Computer-aided Design, 2002