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2020 – today
- 2021
[j9]Jaydeep P. Bardhan
, Mary Ann E. Leung, Eileen Martin, Amanda Randles:
DOE Computational Science Graduate Fellowship Research Showcase. Comput. Sci. Eng. 23(6): 5-8 (2021)- 2020
- [j8]Mahsa Bayati, Miriam Leeser, Jaydeep P. Bardhan:
High-performance transformation of protein structure representation from internal to Cartesian coordinates. J. Comput. Chem. 41(24): 2104-2114 (2020)
2010 – 2019
- 2018
- [j7]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): 167-174 (2018) - 2016
- [c7]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: 145-149 - 2015
- [j6]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): 5383-5394 (2015) - [c6]Mahsa Bayati, Jaydeep P. Bardhan, Miriam Leeser:
GPU implementation of reverse coordinate conversion for proteins. HPEC 2015: 1-6 - [c5]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: 1-5 - 2014
- [j5]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): 720-729 (2014) - [c4]Mahsa Bayati, Jaydeep P. Bardhan, David M. King, Miriam Leeser:
Accelerating protein coordinate conversion using GPUs. HPEC 2014: 1-6 - [i5]Jaydeep P. Bardhan, Matthew G. Knepley:
Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary Conditions. CoRR abs/1409.7418 (2014) - 2012
- [j4]Jaydeep P. Bardhan:
Fast Solvers for Molecular Science and Engineering. IEEE Des. Test Comput. 29(3): 40-48 (2012) - [i4]Jaydeep P. Bardhan, Matthew G. Knepley:
Computational science and re-discovery: open-source implementations of ellipsoidal harmonics for problems in potential theory. CoRR abs/1204.0267 (2012) - [i3]Jaydeep P. Bardhan, Matthew G. Knepley, Peter R. Brune:
Analytical Nonlocal Electrostatics Using Eigenfunction Expansions of Boundary-Integral Operators. CoRR abs/1208.3866 (2012) - 2011
- [j3]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): 1272-1283 (2011) - [c3]Jaydeep P. Bardhan, Andreas Hildebrandt:
A fast solver for nonlocal electrostatic theory in biomolecular science and engineering. DAC 2011: 801-805 - [i2]Jaydeep P. Bardhan, Matthew G. Knepley:
Mathematical Analysis of the BIBEE Approximation for Molecular Solvation: Exact Results for Spherical Inclusions. CoRR abs/1109.0651 (2011) - 2010
- [i1]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 abs/1007.4591 (2010)
2000 – 2009
- 2009
- [j2]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): 132-153 (2009) - 2007
- [c2]Jaydeep P. Bardhan, Michael D. Altman, Jacob K. White, Bruce Tidor:
Efficient optimization of electrostatic interactions between biomolecules. CDC 2007: 4563-4569 - 2006
- [b1]Jaydeep P. Bardhan:
Efficient numerical algorithms for surface formulations of mathematical models for biomolecule analysis and design. Massachusetts Institute of Technology, Cambridge, MA, USA, 2006 - [j1]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): 274-284 (2006) - 2002
- [c1]Shihhsien S. Kuo, Michael D. Altman, Jaydeep P. Bardhan, Bruce Tidor, Jacob K. White:
Fast methods for simulation of biomolecule electrostatics. ICCAD 2002: 466-473
Coauthor Index
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