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Our recent paper on Engineering a Hyper-catalytic Enzyme by Photoactivated Conformation Modulation published in The Journal of Physical Chemistry Letters, is covered in news by Science Daily, HPC Wire, and Biofuels Digest (April 2012).

PUBLICATIONS

Citation Summary: Google Scholar citation report

Peer-Reviewed Articles Reports Patents Talks
  1. Agarwal P.K.; Bhattacharya S.K., "Construction of a multi RE module: Exploitation of mechano-chemistry of restriction endonucleases", Biotechnology & Bioengineering (1999) 65, 233-239.
  2. Agarwal, P.K.; Webb, S.P.; Hammes-Schiffer, S. "Computational Studies of the Mechanism for Proton and Hydride Transfer in Liver Alcohol Dehydrogenase", J. Am. Chem. Soc. (2000) 122, 4803-4812.
  3. Webb, S.P.; Agarwal, P.K.; Hammes-Schiffer, S. "Combining Electronic Structure Methods with Calculation of Hydrogen Vibrational Wavefunctions: Application to Hydride Transfer Catalyzed by Liver Alcohol Dehydrogenase", J. Phys. Chem. B (2000) 104, 8884-8894.
  4. Billeter, S.R.; Webb, S.P.; Iordanov, T.; Agarwal, P.K.; Hammes-Schiffer, S. "Hybrid Approach for Including Electronic and Nuclear Quantum Effects in Molecular Dynamics Simulations of Hydrogen Transfer Reactions in Enzymes", J. Chem. Phys. (2001) 114, 6925-6936.
  5. Billeter, S.R.; Webb, S.P.; Agarwal, P.K.; Iordanov, T.; Hammes-Schiffer, S. "Hydride Transfer in Liver Alcohol Dehydrogenase: Quantum Dynamics, Kinetic Isotope Effects, and the Role of Enzyme Motion", J. Am. Chem. Soc. (2001) 123, 11262-11272.
  6. Agarwal, P.K.; Billeter, S.R.; Rajagopalan, P.T.R.; Benkovic, S.J.; Hammes-Schiffer, S. "Network of Coupled Promoting Motions in Enzyme Catalysis", Proc. Natl. Acad. Sci. USA (2002) 99, 2794-2799.
  7. Agarwal, P.K.; Billeter, S.R.; Hammes-Schiffer, S. "Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis", J. Phys. Chem. B (2002) 106, 3283-3293.
  8. Watney, J. B.; Agarwal, P. K.; Hammes-Schiffer, S.; "Effect of mutation on enzyme motion in dihydrofolate reductase", J. Am. Chem. Soc. (2003) 125, 3745-3750.
  9. Agarwal, P. K.*; "Computational studies of the mechanism of cis/trans isomerization in HIV-1 catalyzed by cyclophilin A", Proteins: Struct. Funct. Bioinformatics (2004) 56, 449-463.
  10. Agarwal, P. K.*; Geist A.; Gorin A.; "Protein Dynamics and Enzymatic Catalysis: Investigating the Peptidyl-Prolyl Cis-Trans Isomerization Activity of Cyclophilin A", Biochemistry (2004) 43, 10605-10618.
  11. Agarwal, P. K.*, "Role of Protein Dynamics in Reaction Rate Enhancement by Enzymes", J. Am. Chem. Soc. (2005) 127, 15248-15246.
  12. Agarwal, P. K.*, "Enzymes: An integrated view of structure, dynamics and function", Invited Review Article: Microbial Cell Factories. (2006) 5:2.
  13. Alam, S. R.*; Agarwal, P. K.*; Vetter, J. S.; Geist A., 'Performance characterization of bio-molecular simulations using molecular dynamics', Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming. (2006) 59-68.
  14. Agarwal, P. K.*; Alam, S. R., "Biomolecular Simulations on Petascale: Promises and Challenges", J. Physics Conference Series (2006) 46, 327-333.
  15. Alam, S. R.; Agarwal, P. K.; Smith, M. C.; Vetter, J. S.; Calliga, D. "Using FPGA Devices to Accelerate Biomolecular Simulations", Cover Feature, IEEE Computers (2007) 40, 66-73.
  16. Agarwal, P. K.*; Alam, S. R.; Geist A, "Simulating Biomolecules on Petascale Supercomputers". Invited book chapter. Petascale Computing: Algorithms and Applications, Edited by David A. Bader, CRC Press (2007).
  17. Alam, S. R.; Agarwal, P. K.;, "On the Path to Enable Multi-scale Biomolecular Simulations on PetaFLOPS Supercomputer with Multi-core Processors", Proceedings of the IEEE International Workshop on High Performance Computational Biology (HiCOMB 2007), in conjunction with IPDPS, (2007), 1-8
  18. Alam, S. R.; Agarwal, P. K.; Vetter, J. S.; Smith, M. C., "Throughput Improvement of Molecular Dynamics Simulations Using Reconfigurable Computing.", Scalable Computing: Practice and Experience (2007), 8(4), 395-410.
  19. Alam, S. R.; Agarwal, P. K.; Kuehn, J. A., "Performance Evaluation of a Scalable Molecular Dynamics Simulation Framework on a Massively-Parallel System.", In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE, (2007), 1459-1466.
  20. Alam, S. R.; Agarwal, P. K.; Vetter, J. S., "Performance characteristics of biomolecular simulations on high-end systems with multi-core processors", Parallel Computing (2008) 34, 640-651.
  21. Alam, S. R.; Agarwal, P. K.; Hampton, S. S.; Hong Ong, "Experimental Evaluation of Molecular Dynamics Simulations on Multi-core Systems.", Proceedings of the annual IEEE International Conference on High Performance Computing (HiPC) (2008) 1-11.
  22. Alam, S. R.; Agarwal, P. K.; Hampton, S. S.; Hong Ong; Vetter, J. S., "Impact of multicores on large-scale molecular dynamics simulations", Proceedings of the IEEE International Symposium on Parallel and Distributed Processing (IPDPS) (2008) 1-7.
  23. Ramanathan, A.; Agarwal, P. K.*,"Computational identification of slow conformational fluctuations in proteins", Journal Cover, J. Phys. Chem. B (2009) 113 (52), 16669-16680.
  24. Ramanathan, A.; Agarwal, P. K.; Kurnikova, M.; Langmead, C.J. "An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations", J. Comput. Biol. (2010) 17(3), 309-324.
  25. Nallamuthu, A.; Smith, M. C.; Hampton, S. S.; Agarwal, P. K.; Alam, S. R., "Energy efficient biomolecular simulations with FPGA-based reconfigurable computing", Proceedings of the 7th ACM international conference on Computing frontiers (2010) 83-84.
  26. Hampton, S. S.; Agarwal, P. K.*; Alam, S. R.; Crozier, P. S. "Towards microsecond biological molecular dynamics simulations on hybrid processors", Outstanding Paper Award, Proceedings of International Conference on High Performance Computing and Simulation (2010) 98-107.
  27. Hampton, S. S.; Alam, S. R.; Crozier, P. S.; Agarwal, P. K.*, "Optimal utilization of heterogeneous resources for biomolecular simulations" In the Proceedings of International Conference for High Performance Computing, Networking, Storage and Analysis (SC' 10), New Orleans, LA (2010). 1-11.
  28. Kamath, G.; Howell, E. E.; Agarwal, P. K.*, "The Tail Wagging the Dog: Insights into Catalysis in R67 Dihydrofolate Reductase", Biochemistry (2010) 49, 9078-9088.
  29. Ramanathan, A.; Savol, A.; Langmead, C. J.; Agarwal, P. K.*; Chennubhotla, C. S.*, "Discovering conformational sub-states relevant to protein function", PLoS ONE (2011) 6(1): e15827.
  30. Borreguero, J. M.; He, J.; Meilleur, F.; Weiss, K.; Brown, C. M.; Myles, D. A. A.; Herwig, K. W.; Agarwal, P. K., "Redox-Promoting Protein Motions in Rubredoxin", Journal Cover. J. Phys. Chem. B. (2011), 115 (28), 8925-8936.
  31. Park, B. H.; Naughton, T. J.; Agarwal, P. K.; Bernholdt, D. E.; Geist, A.; Tippens., J. L., "Realization of User Level Fault Tolerant Policy Management through a Holistic Approach for Fault Correlation", In the Proceedings of IEEE International Symposium on Policies for Distributed Systems and Networks (POLICY 2011) (2011).
  32. Savol, A. J.; Burger, V. M.; Agarwal, P. K.; Ramanathan, A. R.; Chennubhotla, C. S., "QAARM: Quasi-anharmonic auto-regressive model reveals molecular recognition pathways in ubiquitin". Bioinformatics (2011), 27(13), i52-i60.
  33. Burger, V. M.; Ramanathan, A. R.; Savol, A. J.; Stanley, C.; Agarwal, P. K.; Chennubhotla, C. S., "Quasi-anharmonic analysis reveals intermediate states in the nuclear co-activator receptor binding domain ensemble". Pacific Symposium on Biocomputing 2012 (2012).
  34. Ramanathan, A.; Agarwal, P. K.*,"Evolutionarily Conserved Linkage between Enzyme Fold, Flexibility, and Catalysis.", PLoS Biology (2011), 9(11), e1001193.
  35. Agarwal, P. K.*; Schultz, C.; Kalivreteno, A.; Ghosh, B.; Sheldon, B., "Engineering a hyper-catalytic enzyme by photo-activated conformation modulation", J. Phys. Chem. Lett. (2012), 3, 1142-1146.
  36. Heredia, A.; Meunier, V.; Bdikin, I. K.; Gracio, J.; Balke, N.; Jesse, S.; Tselev, A.; Agarwal, P. K. ; Sumpter, B. G.; Kalinin, S. V.; Kholkin, A. L., "Nanoscale Ferroelectricity in Crystalline gamma-Glycine" Advanced Functional Materials (2012), 22, 2996-3003.
  37. Ramanathan, A.; Savol, A. J.; Agarwal, P. K.; Chennubhotla, C. S., "Event Detection And Sub-state Discovery From Bio-molecular Simulations Using Higher-Order Statistics: Application To Enzyme Adynelate Kinase", Proteins: Structure, Function and Bioinformatics, (2012), 80 (11), 2536.2551.
  38. Agarwal, P. K.*; Hampton S. S.; Poznanovic, J.; Ramanathan, A.; Alam, S. R; Crozier, P. S., "Performance modeling of microsecond scale biological molecular dynamics simulations on heterogeneous architectures",Concurrency and Computation: Practice and Experience (2012). In Press.
  39. Ramanathan, A.; Savol, A.; Burger, V.; Quinn S.; Agarwal, P. K.; Chennubhotla, C., "Statistical Inference for Big Data Problems in Molecular Biophysics", In Proceedings of Big Learning 2012
  40. Agarwal, P. K.*, "Role of Protein Motions in Function", Physics of Life Reviews (2013), 10 (1), 35-36.
  41. Agarwal, P. K.*; Naughton, T. J.; Alam, S. R.; Park, B. H.; Bernholdt, D. E.; Hursey, J. J.; Geist, A., "Application Self-health Monitoring for Extreme-scale Resiliency using Cooperative Fault Management", Concurrency and Computation: Practice and Experience (2012). Under Revision.
  42. Ramanathan, A.; Savol, A.; Burger, V.; Chennubhotla, C. S.*; Agarwal, P. K.*, "Protein Conformational Populations and Functionally Relevant Sub-states", Accounts of Chemical Research (2013). Under Review.
  43. Agarwal, P. K.*, "A Biophysical Model of Enzyme Catalysis" (2013), Submitted.
  1. Protein Dynamics and Function: PITAC Report to the President of United States on Computational Science: Ensuring America's Competitiveness (June 2005), page 83.
  2. Vibrations may be Key to Protein Functions: DOE Advanced Scientific Computing Research FY 2004 Accomplishment.
  3. Evaluation of the SGI Altix 3700 at Oak Ridge National Laboratory.
  4. Cray X1 Evaluation Status Report, Proceedings of the 46th Cray User Group Conference, Knoxville TN, May 17-20, 2004.
  1. Fast computational methods for mechanism of protein folding and prediction of protein structure from primary sequence, Inventor: Pratul K. Agarwal, US Patent # 7,983,887, Issued 07/19/2011.
  2. Identification and Modification of Dynamically Active Protein Residues, Inventor: Pratul K. Agarwal, US Patent # 8,417,461 B2, Issued 04/09/2013.
  1. Invited Seminar: University of Tennessee (Genome Science and Technology program seminar), Knoxville TN, Jan. 18th, 2006, Enzymes: An integrated view of structure, dynamics and function.
  2. Invited Seminar: NIST (Physics Division Seminar) Gaithersburg MD, April 18th, 2006, Protein Vibrations Promoting Enzyme Catalysis.
  3. University of Minnesota (Supercomputing Institute and Department of Chemistry seminar), Minneapolis MN, May 31st and Jun. 2nd 2006, Protein Vibrations Promoting Enzyme Catalysis.
  4. Invited Seminar: IBM Inc., Rochester MN, Jun 1st 2006, Next generation simulations in biology.
  5. Invited Talk: NanoFocUL workshop, ORNL, Oak Ridge TN, Aug. 29th 2006, Multi-scale modeling of enzymes.
  6. Invited Seminar: Vanderbilt University, (Dept. Chemical Engineering seminar), Nashville, TN, Sep. 4th 2006, Multi-scale modeling of enzyme catalysis.
  7. Workshop on the Future of BioMolecular Simulations: From Ab Initio to Nano-molecular Machine, Oak Ridge TN, Dec. 11th 2006, Biomolecular Simulations on Petascale: Promises and challenges.
  8. Invited Seminar.University of Cincinnati, Cincinnati, OH, 15th March 2007, Protein vibrations promote enzyme catalysis: An integrated view of enzyme structure, dynamics and function.
  9. CERMACS 2007 (ACS regional meeting), Covington KY, 23rd May 2007, Evolution of enzyme fold: Role of protein dynamics in enzyme catalysis.
  10. VII European Symposium of the Protein Society, Stockholm (Sweden), 15th May 2007, Protein vibrations promote enzyme catalysis: An integrated view of enzyme structure, dynamics and function.
  11. Argonne National Laboratory, Argonne, IL, 30th Aug. 2007, Towards A Fault Tolerant Molecular Dynamics Application.
  12. Invited Seminar: Carnegie Mellon University, Pittsburgh, PA, 17th September, 2007, Evolutionary linkage between enzyme structure, dynamics and function.
  13. Invited Seminar: HPC user's forum, Santa Fe 27th Sept. 2007, Biomolecular Simulations with HPC: Implications for Bio-ethanol.
  14. DOE BER, Germantown MD, Dec 17th 2007, Multi-scale Modeling of Enzymes: Implications of low cost ethanol.
  15. Protein Dynamics Workshop, Tarrytown NY, May 2nd 2008, Evolution of Enzyme Fold: Linking Protein Dynamics and Catalysis.
  16. Workshop in Trend, Technologies and Collaborative Opportunities (WTTC) 2008, Bangkok Thailand, June 9th 2008, High Performance Simulations in Biology: Implications for Health, Energy and Environment.
  17. Workshop in Trend, Technologies and Collaborative Opportunities (WTTC) 2008, Phuket Thailand, June 11th 2008, High Performance Simulations in Biology: Implications for Health, Energy and Environment.
  18. 236th Annual Meeting of the American Chemical Society, Philadelphia PA, August 19th 2008, An Integrated View of Enzyme Structure, Dynamics and Function.
  19. 236th Annual Meeting of the American Chemical Society, Philadelphia PA, August 20th 2008, Evolution of Enzyme Fold: Linking Protein Dynamics and Catalysis
  20. Invited Seminar: St. Jude Children's Research Hospital, Memphis, TN, November 25th, 2008, Evolution of enzyme fold: Linking protein dynamics and catalysis.
  21. Biophysical Society 53rd Annual Meeting, Boston, MA, March 3rd, 2009, Evolution of enzyme fold: Linking protein dynamics and catalysis.
  22. ACS 238th National Meeting, Washington, DC, August 17, 2009, Linking enzyme structure, dynamics, and catalysis.
  23. LAMMPS Users Workshop, Sandia National Laboratories, Albuquerque, NM, Feb 26th 2010, GPU-enabled biomolecular simulations with LAMMPS.
  24. Outstanding Paper Award: International Conference on High Performance Computing and Simulation (HPCS) 2010, Caen, France, July 1st 2010, Towards Microsecond Biological Molecular Dynamics Simulations on Hybrid Processors.
  25. University of Tennessee, Knoxville, Department of Biochemistry, Cellular and Molecular Biology (BCMB) Retreat, Knoxville, 20th August 2010, The Tail Wagging the Dog: Insights into Catalysis in R67 Dihydrofolate Reductase.
  26. American Chemical Society 240th National Meeting, Boston, MA, August 22nd 2010, Biomolecular simulations in heterogeneous computing architectures.
  27. Workshop on force field development, CNMS, ORNL, Oak Ridge, TN, Sept. 15th 2010, Linking Protein Flexibility to Enzyme Catalysis.
  28. Bio-molecular Simulations on Future Computing Architectures, ORNL, Oak Ridge, TN, Sept. 15th 2010, Optimal biomolecular simulations on future computing architectures.
  29. SC10, Intl. Conf. for High Performance Computing, Networking, Storage and Analysis, New Orleans, LA., November 14th 2010, Molecular Biophysics in Cloud: Promises and Challenges .
  30. SC10, Intl. Conf. for High Performance Computing, Networking, Storage and Analysis, New Orleans, LA., November 18th 2010, Optimal utilization of heterogeneous resources for biomolecular simulations.
  31. Zing Conference on Biocatalysis, Puerto Morelos, Mexico, December 11th 2010, Evolutionary Conserved Linkage Between Enzyme Fold, Flexibility, and Catalysis.
  32. ACS 241st National Meeting, Anaheim, CA, March 31, 2011, Non-homologous enzymes catalyzing same chemistry: Insights into linkage between enzyme fold, flexibility and catalysis
  33. Workshop on Biocatalysis, Denver, CO, May 26th, 2011, Computational Bio-catalysis for Renewable Energy and Environmental Research
  34. Titan Summit, Oak Ridge, TN, August 17th, 2011, Next Generation Simulations of Bio-molecules
  35. Zing Conference on Enzymes, Coenzymes and Metabolic Pathways, Xcaret, Mexico, November 20th 2011, Role of enzyme dynamics: Engineering hypercatalytic enzymes by conformation modulation.
  36. Next-Gen Kinase Inhibitors, Boston, MA, June 5th 2012, Discovering and characterizing allosteric sites for novel drug design.
  37. Best Poster Award: GRC Medicinal Chemistry, New London, NH, August 9th 2012, Discovering and characterizing allosteric sites for novel drug design.
  38. ACS 244th National Meeting, Philadelphia, PA, August 19 2012, Learning from and manipulating enzymes for better catalysis.
  39. ACS 244th National Meeting, Philadelphia, PA, August 19 2012, Unraveling the mystery of solvent-protein thermodynamical coupling: Insights from enzyme catalysis in organic solvents.
  40. ACS 244th National Meeting, Philadelphia, PA, August 20 2012, Engineering hyper-catalytic enzyme by photo-activated conformation modulation.
  41. Invited Seminar: BiG Seminar Series, University of North Carolina, Charlotte, Setember 21 2012, Using Computations to Understand and Manipulate the Working of Biomolecules .
  42. Drug Design 2012 Conference, Oxofrd, United Kingdom, September 28th, 2012, Discovering and Characterizing Allosteric Sites for Novel Drug Design.
  43. Invited Talk: 10th Discovery on Target, Allosteric Modulators Series, Boston MA, October 3rd, 2012. Biophysical Approach to Allosteric Site Discovery and Characterization of Kinases.
  44. Invited Talk: Novartis Institutes for BioMedical Research, Cambridge MA, October 4th, 2012. Biophysical Approach to Allosteric Site Discovery and Characterization of Kinases.
  45. Invited Talk: Zing Conference on Mathematical and Computational Medicine, Xcaret, Mexico, December 4th 2012, Biophysical Approach to Allosteric Site Discovery and Characterization of Kinases.
  46. Zing Conference on Biocatalysis, Xcaret, Mexico, December 6th 2012, Engineering Hyper-catalytic Enzymes through Conformation Modulation.
  47. Invited Speaker: 13th Annual Symposium of PROTEO, the Quebec Network for Research on Protein Structure, Function and Engineering. Montreal, Canada, May 17th 2013. Protein Dynamics and Conformational Sub-states in Enzyme Catalysis.

    48. Upcoming:
  48. Invited Speaker: 2nd Conference Conference on Dynamics in Enzymatic Catalysis, Telluride, CO, July 29th-August 2nd, 2013.
  49. Invited Speaker: Modeling and Computational Design Symposium, Society for Industrial Micorbiology and Biotechnology (SIMB) Conference 2013, San Diego, CA, August 11-15th 2013.
  50. Invited Speaker: International Symposium on Cyclophilins and other Foldases: Cell Signaling Catalysts and Drug Targets, Halle (Salle), Germany, September 19th-21st 2013.
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