Pratul K. Agarwal, Ph. D.


Contact Information

Phone: +1 (865) 574-7184
Email: agarwalpk(AT)ornl.gov
Mail: 1 Bethel Valley Road
Oak Ridge National Laboratory
Oak Ridge, TN 37830, USA

Curriculum vitae
Agarwal

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 (Specialty Editor: Biochemistry)
Lead High Performance Computing (HPC) Working Group,
IMAG and MSM Consortium, NIH

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
  • Workshop on the Future of BioMolecular Simulations: From Ab Initio to Nano-molecular Machines, 11-12th December 2006, Oak Ridge National Laboratory
  • International Workshop on Bio-molecular Simulations on Future Computing Architectures, 16-17th September 2010, Oak Ridge National Laboratory
  • Workshop on Bio-catalysis, 26th May 2011, Denver

  • Funding Profile


    CURRENT

    Agency: National Institutes of Health (NIH), NIGMS
    Title: R01: Conformational sub-states in enzyme catalysis: Applications to ribonuclease.
    Role: PI (Multi-PI R01 with Dr. Chakra Chennubhotla, Pittsburgh, and Dr. Nicholas Doucet, INRS/Quebec.)
    Amount: $ 2,576,912 ($ 953,870 to PKA)
    Period: 04/01/2014 - 03/31/2019
    Description: Development and application 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 ribonuclease A.

    PENDING

    Agency: National Institutes of Health (NIH), Pioneer Award Proposal
    Title: Fever: Effects and benefits at the molecular level
    Role: PI
    Amount: $2,500,000
    Period: 09/01/2014 - 07/31/2019
    Description: Developing computational models for biomolecular systems from host and pathogens, to investigate the role of elevated temperature on the mechanism of biomolecular function.

    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: Department of Energy (DOE), Advanced Scientific Computing Research (ASCR)
    Title: Investigation of Cellulose Degrading Protein Machines: Enabling Technologies for Petascale Biomolecular Simulations
    Role: PI
    Amount: $819,623
    Period: 01/01/2007 - 12/31/2009
    Description: Development of high performance computing software and simulation strategies for large biomolecular complexes.
    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.
    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: $300,000
    Period: 02/01/2011 - 09/30/2012
    Description: Focus on characterizing and developing strategies to overcome the impact of OS jitter on science applications.
    Agency: ORNL Technology Transfer Program
    Title: Maturation funds for optimizing enzyme engineering approach
    Role: PI
    Amount: $60,000
    Period: 02/21/2012 - 12/31/2012
    Description: Optimization of the enzyme engineering approach through conformational modulation.

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