Performance characterization of molecular dynamics techniques for biomolecular simulations. - Sadaf R. Alam; Jeffrey S. Vetter; Pratul K. Agarwal; Al Geist (PPoPP, 2006)

Performance Evaluation of a Scalable Molecular Dynamics Simulation Framework on a Massively-Parallel System. - Sadaf R. Alam; Pratul K. Agarwal; Jeffery A. Kuehn (BIBE, 2007)

On the Path to Enable Multi-scale Biomolecular Simulations on PetaFLOPS Supercomputer with Multi-core Processors. - Sadaf R. Alam; Pratul K. Agarwal (IPDPS, 2007)

Using FPGA Devices to Accelerate Biomolecular Simulations. - Sadaf R. Alam; Pratul K. Agarwal; Melissa C. Smith; Jeffrey S. Vetter; David Caliga (Computer, 2007)

Throughput Improvement of Molecular Dynamics Simulations Using Reconfigurable Computing. - Sadaf R. Alam; Pratul K. Agarwal; Jeffrey S. Vetter; Melissa C. Smith (Scalable Comput. Pract. Exp., 2007)

Experimental Evaluation of Molecular Dynamics Simulations on Multi-core Systems. - Sadaf R. Alam; Pratul K. Agarwal; Scott S. Hampton; Hong Ong (HiPC, 2008)

Impact of multicores on large-scale molecular dynamics simulations. - Sadaf R. Alam; Pratul K. Agarwal; Scott S. Hampton; Hong Ong; Jeffrey S. Vetter (IPDPS, 2008)

Performance characteristics of biomolecular simulations on high-end systems with multi-core processors. - Sadaf R. Alam; Pratul K. Agarwal; Jeffrey S. Vetter (Parallel Comput., 2008)

Energy efficient biomolecular simulations with FPGA-based reconfigurable computing. - Ananth Nallamuthu; Melissa C. Smith; Scott S. Hampton; Pratul K. Agarwal; Sadaf R. Alam (Conf. Computing Frontiers, 2010)

Towards microsecond biological molecular dynamics simulations on hybrid processors. - Scott S. Hampton; Pratul K. Agarwal; Sadaf R. Alam; Paul S. Crozier (HPCS, 2010)

Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations. - Scott S. Hampton; Sadaf R. Alam; Paul S. Crozier; Pratul K. Agarwal (SC, 2010)

An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations. - Arvind Ramanathan; Pratul K. Agarwal; Maria G. Kurnikova; Christopher James Langmead (J. Comput. Biol., 2010)

Realization of User Level Fault Tolerant Policy Management through a Holistic Approach for Fault Correlation. - Byung H. Park; Thomas J. Naughton; Pratul K. Agarwal; David E. Bernholdt; Al Geist; Jennifer L. Tippens (POLICY, 2011)

QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin. - Andrej J. Savol; Virginia M. Burger; Pratul K. Agarwal; Arvind Ramanathan; Chakra S. Chennubhotla (Bioinform., 2011)

Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble. - Virginia M. Burger; Arvind Ramanathan; Andrej J. Savol; Christopher B. Stanley; Pratul K. Agarwal; Chakra S. Chennubhotla (Pacific Symposium on Biocomputing, 2012)

Performance modeling of microsecond scale biological molecular dynamics simulations on heterogeneous architectures. - Pratul K. Agarwal; Scott S. Hampton; Jeffrey D. Poznanovic; Arvind Ramanathan; Sadaf R. Alam; Paul S. Crozier (Concurr. Comput. Pract. Exp., 2013)

Application health monitoring for extreme-scale resiliency using cooperative fault management. - Pratul K. Agarwal; Thomas J. Naughton; Byung H. Park; David E. Bernholdt; Joshua Hursey; Al Geist (Concurr. Comput. Pract. Exp., 2020)

Evolutionary Dynamics and Functional Differences in Clinically Relevant Pen β-Lactamases from Burkholderia spp. - Jing Gu; Pratul K. Agarwal; Robert A. Bonomo; Shozeb M. Haider (J. Chem. Inf. Model., 2025)