Dr. Tjerk Straatsma
Dr. Tjerk P. Straatsma is an internationally recognized scientist with more than 30 years of experience in the development, efficient implementation and application of advanced modeling and simulation methods as key scientific tools in the study of chemical and biomolecular systems, complementing analytical theories and experimental studies. His research focuses on the development of computational techniques that provide unique and detailed atomic level information that is difficult or impossible to obtain by other methods, and that contributes to the understanding of the properties and function of these systems.
His research interests are in the combination of the design of efficient implementations of these methods on modern, complex computer architectures, including the vector processing supercomputers of the 1980s and the massively parallel computer systems of today. He has applied biomolecular simulation methods to study a variety of systems of interest, such as microbial membrane mediated geochemical processes at mineral surfaces, material and signal transport processes across microbial membranes, and complex enzymatic reactions that involve combined electron and proton transfer steps.
Dr. Straatsma joined Oak Ridge National Laboratory in 2013, where he manages the Scientific Computing group in the National Center for Computational Sciences. This center is the site for the Oak Ridge Leadership Computing Facility and houses the largest supercomputer for open science in the United States. Prior to joining ORNL, Dr. Straatsma was a Laboratory Fellow at Pacific Northwest National Laboratory, and Director for the eXtreme Scale Computing Initiative to build the capabilities needed to enable scientific advancements and breakthroughs in selected domain sciences through computational modeling and simulation on next-generation, extreme-scale computers. He established the Computational Biology and Bioinformatics research group and was co-developer of the NWChem massively parallel computational chemistry software suite.
In 2013, Dr. Straatsma was appointed Adjunct Professor in the Department of Chemistry at the University of Alabama, where he is collaborating with Prof. David A. Dixon, Robert Ramsey Professor of Chemistry, on a variety of computational chemistry projects, including an Energy Frontiers Research Center studying acid gas absorption on metal organic framework materials and an INCITE project focused on actinide chemistry.
T. P. Straatsma and T. A. Soares, “Characterization of the Outer Membrane Protein OprF of Pseudomonas aeruginosa in a Lipopolysaccharide Membrane by Computer Simulation”, Proteins: Structure, Function, and Bioinformatics, 74, 475-488 (2009).
T. A. Soares, C. B. Boschek, D. Apiyo, C. Baird, and T. P. Straatsma “Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions”, Journal of Molecular Graphics and Modelling, 28(8), 755-765 (2010).
M. Valiev, E. J. Bylaska, N. Govind, K. Kowalski, T. P. Straatsma, H. J. J. van Dam, D. Wang, J. Nieplocha, E. Apra, T. L. Windus, and W. A. de Jong “NWChem: A comprehensive and scalable open- source solution for large scale molecular simulations”, Computer Physics Communications 181(9), 1477-1489 (2010).
H. J. J. van Dam, W. A. de Jong, E. J. Bylaska, N. Govind, K. Kowalski, T. P. Straatsma, and M. Valiev,
“NWChem: scalable parallel computational chemistry” Computational Molecular Science, Wiley Interdisciplinary Reviews, in preparation (2010).
D. M. A. Smith, T. P. Straatsma and T. C. Squier, “Molecular dynamics study of calmodulin-target complexes”, Biophysical Journal 100, 150-150 (2011).
N. Govind, E. J. Bylaska, W. A. de Jong, K. Kowalski, T. P. Straatsma, M. Valiev, and H. J. J. van Dam,“NWChem”, Encyclopedia of Parallel Computing, 14, 1345-1353 (2011).
T. P. Straatsma, E. J. Bylaska, H. J. J. van Dam, N. Govind, W. A. de Jong, K. Kowalski and M. Valiev,“Advances in Scalable Computational Chemistry: NWChem”, Annual Reports of Computational Chemistry, 7, 151-177 (2011).
D. M. A. Smith, Y. J. Xiong, T. P. Straatsma, K. M. Rosso, T. C. Squier, “Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase, Journal of Chemical Theory and Computation, 8 (6), 2103-2114 (2012).
T. P. Straatsma and D. G. Chavarría-Miranda, “On Eliminating Synchronous Communication in Molecular Dynamics Simulation to Improve Scalability”, Computer Physics Communications, 84, 2634-2640 (2013).