Pratul K. Agarwal, Ph. D.
Contact Information
Curriculum vitae 
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Current Appointments
| Senior R&D Scientist | Computer Science and Mathematics Division, Oak Ridge National Laboratory (ORNL) |
| Joint Faculty Member | Dept. of Biochemistry, Molecular and Cellular Biology, University of Tennessee, Knoxville |
| Academic Editor | PLoS ONE |
| Editorial Board Member | Microbial Cell Factories |
| Editor | WebmedCentral plus (Speciality Editor: Biochemistry) |
| Lead | High Performance Computing
(HPC) Working Group, IMAG and MSM Consortium |
Education
| B. Tech. (1995) | Indian Institute of Technology-Delhi, New Delhi, India (Biochemical Engineering and Biotechnology) |
| M. Tech. (1997) | Indian Institute of Technology-Delhi, New Delhi, India (Biochemical Engineering and Biotechnology) |
| Ph. D. (2002) | The Pennsylvania State University, University Park, PA Thesis Advisor: Prof. Sharon Hammes-Schiffer |
Positions and Employment
| 2002-2005 | Post-doctoral Research Associate, Computer Science and Mathematics Division, ORNL |
| 2005-2007 | Associate R&D Scientist, Computational Biology Institute & Computer Science and Mathematics Division, ORNL |
| 2005-2010 | Adjunct Faculty, Graduate Program in Genome Science and Technology, University of Tennessee, Knoxville |
| 2007-2011 | Adjunct Faculty, Department of Biochemistry, Cellular and Molecular Biology University of Tennessee, Knoxville |
| 2008-2011 | R&D Scientist, Computational Biology Institute & Computer Science and Mathematics Division, ORNL |
Awards and Honors
| 2005 | Research featured in President's Information Technology Advisory Committee's Report to the President (George W. Bush), "Computational Sciences: Ensuring America's Competitiveness""Protein Dynamics and Function" |
| 2006-2007 | DOE's INCITE computing time allocation on Cray XT4 (1.5 million hours) "Next generation simulations in biology" |
| 2007 | Research Featured on cover of Journal IEEE Computer |
| 2009 | Research Featured on cover of Journal of Physical Chemistry B |
| 2010 | Outstanding Paper Award at the International Conference on High Performance Computing and Simulation (HPCS) 2010, Caen, France. |
| 2010 | Key Contributor Award, UT-Battelle Partnerships Awards |
| 2011 | Research Featured on cover of Journal of Physical Chemistry B |
| 2011 | Distinguished Contributor Award (June 2011), Computing and Computational Science Directorate, ORNL |
| 2011 | DOE's ALCC computing time allocation on Cray XT5 supercomputer (4.0 million hours) "Understanding the factors that affect the efficiency of bio-catalytic processes" |
| 2011 | Research/Image featured on the cover of PLoS Biology |
| 2012 | DOE's ALCC computing time allocation on Cray XK6 supercomputer (5.0 million hours) "Designing Bio-inspired Catalysts for Energy Harvesting & Renewable Energy" |
Professional Services
| Panelist & Proposal Reviewer | NIH, NSF, EPA, DTRA, Petroleum Research Fund, Swiss National Supercomputing Centre, Swiss High Performance and High Productivity Computing (HP2C), Italian Ministry of Health |
| Manuscript Reviewer (Journals and Conferences) |
Amino Acids, Biochemical Engineering Journal, Biochemistry, Biomacromolecules, Biophysical Journal, Chemical Physics Letters, HiBB (High Performance Bioinformatics and Biomedicine), HiCOMB (International Workshop on High Performance Computational Biology), HPCS (International Conference on High Performance Computing and Simulation), International Journal of Biological Macromolecules, Journal of the American Chemical Society, The Journal of Biochemistry, Journal of Chemical Information and Modeling, Journal of Chemical Physics, Journal of Chemical Theory and Computation, Journal of Parallel and Distributed Computing, Journal of Physical Chemistry, Microbial Cell Factories, The Journal of Physical Chemistry Letters, PLoS Computational Biology, PLoS ONE, Proceedings of the Royal Society A, Proteins (Proteins: Structure, Function and Bioinformatics), Protein Science, Spectroscopy Letters, Systems Biology and Medicine |
| Chief Organizer |
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Funding Profile
COMPLETED
| Agency: | Battelle Memorial Institute |
| Title: | A Novel Approach to Enzyme Engineering |
| Role: | PI |
| Amount: | $160,000 |
| Period: | 03/01/2007 - 06/30/2009 |
| Description: | Maturation funds for developing technology for enzyme
engineering. |
| Agency: | Laboratory Directed Research and Development (LDRD), ORNL |
| Title: | Mapping the Protein Structure, Dynamics and Function Landscape |
| Role: | PI |
| Amount: | $391,000 |
| Period: | 10/01/2007 - 09/30/2010 |
| Description: | Joint computational-neutron scattering to explore protein
structure, dynamics and function (with Dr. Dean Myles and Dr. Ken Herwig). |
| Agency: | National Institutes of Health (NIH), NIGMS |
| Title: | Accelerating Biomolecular Simulations on Reconfigurable Computing Hardware (R21GM083946) |
| Role: | PI |
| Amount: | $409,447 |
| Period: | 08/15/2008 - 06/30/2011 (with 1 year no cost extension) |
| Description: | Biomolecular simulations software development for
graphical processing units (GPUs) and Field-Programmable Gate Arrays (FPGAs). |
| Agency: | Laboratory Directed Research and Development (LDRD), ORNL |
| Title: | High Throughput Computational Screening Approach for Systems Medicine |
| Role: | PI |
| Amount: | $610,000 |
| Period: | 10/01/2008 - 09/30/2011 |
| Description: | Developing high throughput computational approach for allosteric site prediction and chemical compound library screening against the discovered targets. |
CURRENT
| Agency: | Department of Energy, Office of Science |
| Title: | Improvement of Fault Tolerance in Systems (CIFTS) |
| Role: | Investigator (PI: Pete Beckman, Argonne National Laboratory) |
| Period: | 10/01/2006 - 09/30/2012 |
| Description: | The major goals of this project are to develop fault
tolerant software for next generation HPC architecture. |
| Agency: | National Center for Computational Sciences |
| Title: | Application porting and optimization for LCF3 |
| Role: | Investigator |
| Amount: | $200,000 |
| Period: | 02/01/2011 - 09/30/2012 |
| Description: | Focus on characterizing and developing strategies to overcome the impact of OS jitter on science applications. |
PENDING
| Agency: | National Institutes of Health (NIH) |
| Title: | (R01) Accelerating biomolecular simulation and analysis on future computational architectures |
| Role: | PI |
| Amount: | $1,813,312 |
| Period: | 04/01/2013 - 03/31/2018 |
| Description: | Development and optimization of biomolecular simulations
software (molecular dynamics and molecular docking) on current and future
computer hardware. Emphasis on GPUs as well as many-core CPUs and the ARM processor. |
| Agency: | Multi-agency call (NIH/DOE and others) |
| Title: | (R01) Multi-scale modeling framework for biomolecular characterization: Applications for bio-inspired light energy harvesting and technologies for renewable energy |
| Role: | PI |
| Amount: | $2,328,819 |
| Period: | 04/01/2012 - 03/31/2017 |
| Description: | Development of multi-scale modeling framework and strategies
for enabling identification and characterization of rare inter-mediates and
conformational transitions associated with protein function. Applications to enzyme
cellulase and RuBisCO. |
