Background

Dr. T. P. Straatsma is the Group Leader for Scientific Computing in the National Center for Computational Sciences, a division that houses the Oak Ridge Leadership Computing Facility, at Oak Ridge National Laboratory, and Adjunct Faculty member in the Chemistry Department of the University of Alabama in Tuscaloosa. He earned his Ph.D. in Mathematics and Natural Sciences from the University of Groningen, the Netherlands. After a postdoctoral associate appointment, followed by a faculty position in the Department of Chemistry at the University of Houston, he moved to Pacific Northwest National Laboratory (PNNL), as co-developer of the NWChem computational chemistry software, established a program in computational biology, and was group leader for computational biology and bioinformatics. Straatsma served as Director for the Extreme Scale Computing Initiative at PNNL, focusing on developing science capabilities for emerging petascale computing architectures. He was promoted to Laboratory Fellow, the highest scientific rank at the Laboratory.

In 2013 he joined Oak Ridge National Laboratory, where, in addition to being Group Leader for Scientific Computing, he is the Lead for the Center for Accelerated Application Readiness, and Lead for the Applications Working Group in the Institute for Accelerated Data Analytics and Computing, focusing on preparing scientific applications for the next generation pre-exascale and exascale computer architectures.

Straatsma has been a pioneer 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. In particular, his expertise is in the evaluation of thermodynamic properties from large scale molecular simulations, having been involved since the mid-1980s, in the early development of thermodynamic perturbation and thermodynamic integration methodologies. His research interests also include the design of efficient implementations of these methods on modern, complex computer architectures, from the vector processing supercomputers of the 1980s to the massively parallel and accelerated computer systems of today. Since 1995, he is a core developer of the massively parallel molecular science software suite NWChem and responsible for its molecular dynamics simulation capability. Straatsma has co-authored nearly 100 publications in peer-reviewed journals and conferences, was the recipient of the 1999 R&D 100 Award for the NWChem molecular science software suite, and was recently elected Fellow of the American Association for the Advancement of Science.

PUBLICATIONS

1. J. P. M. Postma, H. J. C. Berendsen and T. P. Straatsma, “Intramolecular vibrations from molecular simulations of liquid water”, Journal de Physique, C7, 31-40 (1984).
2. T. P. Straatsma, H. J. C. Berendsen and A. J. Stam, “Estimation of statistical errors in molecular simulation calculations”, Mol. Phys., 57, 89-95 (1986).
3. T. P. Straatsma, H. J. C. Berendsen and J. P. M. Postma, “Free energy of hydrophobic hydration. A molecular dynamics study of noble gases in water”, J. Chem. Phys., 85, 6720-6727 (1986).
4. T. P. Straatsma, “Free energy evaluation by molecular dynamics simulations. Analysis of a perturbation method and a thermodynamic integration technique”, Ph.D. thesis, University of Groningen, the Netherlands (1987).
5. H. J. C. Berendsen, J. R. Grigera and T. P. Straatsma, “The missing term in effective pair potentials”, J. Phys. Chem., 91, 6269-6271 (1987).
6. T. P. Straatsma and H. J. C. Berendsen, “Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations”, J. Chem. Phys., 89, 5876-5886 (1988).
7. T. P. Straatsma and J. A. McCammon, “Treatment of rotational isomers in free energy evaluations. Analysis of the evaluation of free energy differences by molecular dynamics simulations of systems with isomeric states”, J. Chem. Phys., 90, 3300-3304 (1989).
8. T. P. Straatsma and J. A. McCammon, “Treatment of rotational isomers in free energy calculations II. Molecular dynamics simulation study of 18-crown-6 in aqueous solution as an example of systems with large numbers of rotational isomeric states”, J. Chem. Phys., 91, 3631-3637 (1989).
9. T. P. Straatsma and J. A. McCammon, “Free energy thermodynamic integrations in molecular dynamics simulations using a noniterative method to include electronic polarization”, Chem. Phys. Lett., 167, 252-254 (1990).
10. T. P. Straatsma and J. A. McCammon, “ARGOS, a vectorized molecular dynamics program”, J. Comp. Chem., 11, 943-951 (1990).
11. T. P. Straatsma and J. A. McCammon, “Molecular dynamics simulations with interaction potentials including polarization. Development of a noniterative method and application to water”, Molecular Simulation, 5, 181-192 (1990).
12. T. P. Straatsma and J. A. McCammon, “Free energy evaluation from molecular dynamics simulations using force fields including electronic polarization”, Chem. Phys. Lett., 177, 433-440 (1991).
13. T. P. Straatsma and J. A. McCammon, “Multiconfiguration thermodynamic integration”, J. Chem. Phys., 95, 1175-1188 (1991).
14. T. P. Straatsma and J. A. McCammon, “Theoretical calculations of relative affinities of binding”, Methods in Enzymology, 22, 497-511 (1991).
15. T. P. Straatsma and J. A. McCammon, “Computational Alchemy”, Ann. Rev. Phys. Chem., 43, 407 (1992).
16. T. P. Straatsma, M. Zacharias and J. A. McCammon, “Holonomic constraint contributions to free energy differences from thermodynamic integration molecular dynamics simulations”, Chem. Phys. Lett., 196, 297 (1992).
17. M. Zacharias, T. P. Straatsma, J. A. McCammon and F. A. Quiocho, “Inversion of receptor binding preferences by mutagenesis: Free energy thermodynamic integration studies on sugar-binding to L-arabinose binding proteins”, Biochemistry, 32, 7428 (1993).
18. T. P. Straatsma, M. Zacharias and J. A. McCammon, “Free energy difference calculations in biomolecular systems”, in “Computer Simulation of Biomolecular Systems”, edited by W. F. van Gunsteren et al., ESCOM, Leiden, 1993, p. 349-367.
19. T. P. Straatsma, “HIV-1 proteinase inhibitor binding. The effect of active site conformational restraints on calculated free energies of ligand binding”, NATO ASI Series, C426, 495-513 (1994).
20. M. K. Gilson, T. P. Straatsma, J. A. McCammon, D. R. Ripoll, C. H. Faerman, P. H. Axelsen, I. Silman and J. L. Sussman, “Open “back door” in a molecular dynamics simulation of acetylcholinesterase”, Science, 263, 1276-1278 (1994).
21. M. Zacharias, T. P. Straatsma and J. A. McCammon, “Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration”, J. Chem. Phys., 100, 9025-9031 (1994).
22. T. P. Straatsma and J. A. McCammon, “Treatment of rotational isomers III. The use of biasing potentials”, J. Chem. Phys., 101, 5032-5039 (1994).
23. M. Zacharias and T. P. Straatsma, “Path dependence of free energy components in thermodynamic integration”, Molecular Simulation, 14, 417-423 (1995).
24. T. P. Straatsma, “Free energy by molecular simulation”, in “Reviews in Computational Chemistry”, Vol. IX, edited by K. B. Lipkowitz and D. B. Boyd, pp. 81-127.
25. S. T. Wlodek, J. Antosiewicz, J. A. McCammon, T. P. Straatsma, M. K. Gilson, J. M. Briggs, C. Humblet and J. L. Sussman, “Binding of tacrine and 6-Chlorotacrine by Acetylcholinesterase”, Biopolymers, 38, 109-117 (1996).
26. T. J. Marrone, T. P. Straatsma, J. M. Briggs, D. K. Wilson, F. A. Quiocho and J. A. McCammon, “Theoretical Study of Inhibition of Adenosine Deaminase by (8R)-Coformycin and (8R)-Deoxycoformycin”, J. Med. Chem., 39, 277-284 (1996).
27. M. D. Paulsen and T. P. Straatsma, “Chlorinated ethanes in aqueous solution: Parameterization based on Thermodynamics of Hydration”, Chem. Phys. Lett., 259, 142-145 (1996).
28. C. N. Hodge, T. P. Straatsma, J. A. McCammon and A. Wlodawer, “Rational design of HIV protease inhibitors”, in Structural biology of viruses, edited by W. Chiu, R. M. Burnett and R. L. Garcea, Oxford University Press, New York, NY, 1998, pp. 451-473.
29. R. A. Kutteh and T. P. Straatsma, “Molecular dynamics with general holonomic constraints and application to internal coordinate constraints”, In Reviews in Computational Chemistry, Vol. XII, edited by K. B. Lipkowitz and D. B. Boyd, pp. 75-136, (1998).
30. T. P. Straatsma, “NWChem molecular dynamics simulation”, in Proceedings High Performance Computing Systems and Applications, 1998,
31. V. Helms, E. F. Y. Hom, T. P. Straatsma, J. A. McCammon, P. Langhoff, “Exciting Green Fluorescent Protein”, ACS symposium series, 712, 288-295 (1998).
32. T. P. Straatsma, “Free energy simulations”, in “Encyclopedia of Computational Chemistry”, edited by P. von Rague Schleyer, 1999, pp. 1083-1089.
33. V. Helms, T. P. Straatsma and J. A. McCammon, “Internal dynamics of Green Fluorescent”, Protein.J. Phys. Chem. B, 103, 3263-3269 (1999).
34. S. Tara, T. P. Straatsma and J. A. McCammon, “Acetylcholinesterase unliganded and complexed with huperzine A: A comparison of molecular dynamics simulations”, Biopolymers, 50, 35-43 (1999).
35. R. D. Lins, J. M. Briggs, T. P. Straatsma, H. A. Carlson, J. Greenwald, S. Choe and J. A. McCammon, “Molecular Dynamics Studies on the HIV-1 Integrase Catalytic Domain”, Biophys. J., 76, 2999-3011 (1999).
36. S. Tara, V. Helms, T. P. Straatsma, P. Taylor and J. A. McCammon, “Molecular Dynamics of Mouse Acetylcholinesterase Complexed with Huperzine A”, Biopolymers, 50, 347-359 (1999).
37. D. A. Dixon, T. H. Dunning, M. Dupuis, D. F. Feller, D. K. Gracio, R. J. Harrison, D. R. Jones, R. A. Kendall, J. A. Nichols, K. L. Schuchardt and T. P. Straatsma, “Computational Chemistry in the Environmental Molecular Sciences Laboratory”, in “High Performance Computing”, Ed. R.J. Allan, M.J. Guest, A.D. Simpson, D.S. Henty, and D.A. Nicole, Kluwer Academic, Plenum, New York, p. 215-228 (1999).
38. T. P. Straatsma and V. Helms, “Molecular Dynamics Module of NWChem – Design and Application in Protein Simulations”, in “Proceedings Molecular Dynamics on Parallel Computers”,, 2000, pp. R. Esser, P. Grassberger, J. Grotendorst, M. Lewerenz, editors, World Scientific Pub. Co.
39. T. P. Straatsma, M. Philippopoulos and J. A. McCammon, “NWChem: Exploiting Parallelism in Molecular Simulations”, Computer Physics Communications, 128, 377-385 (2000).
40. R. D. Lins, T. P. Straatsma and J. M. Briggs, “Similarities in the HIV-1 and ASV integrase active sites upon metal cofactor binding”, Biopolymers, 53, 308-315 (2000).
41. R. A. Kendall, E. Apra, D. E. Bernhold, E. J. Bylaska, M. Dupuis, G. I. Fann, R. J. Harrison, J. Ju, J. A. Nichols, J. Nieplocha, T. P. Straatsma, T. L. Windus and A. T. Wong, “High performance computational chemistry: An overview of NWChem, a distributed parallel application”, Comp. Phys. Comm., 128, 260-283 (2000).
42. J. Nieplocha, J. Ju and T. P. Straatsma, “A Multiprotocol Communication Support for the Global Address Space Programming Model on the IBM SP”, Lecture Notes in Computer Science, 1900, 718 (2000).
43. H. Resat, T. P. Straatsma, D. A. Dixon, and J. H. Miller, “The arginine finger of RasGAP helps Gln61 align the nucleophilic water in GAP-stimulated hydrolysis of GTP”, Proc. Natl. Acad. Sciences, USA, 98, 6033-6038 (2001).
44. T. P. Straatsma and J. A. McCammon, “Load balancing of molecular dynamics simulation with NWChem”, IBM Systems Journal, 40, 328-341 (2001).
45. R. D. Lins and T. P. Straatsma, “Computer simulations of the lipopolysaccharide membrane of Pseudomonas aeruginosa”, Biophysical Journal, 81, 1037-1046 (2001).
46. T. A. Soares, J. H. Miller, and T. P. Straatsma, “Revisiting the Structural Flexibility of the Complex p21ras-GTP: The Catalytic Conformation of the Molecular Switch II”, Proteins: Structure, Function and Genetics, 45, 297-312 (2001).
47. T. A. Soares, R. D. Lins, T. P. Straatsma, and J. M. Briggs, “Internal Dynamics and Ionization States of the Macrophage Migration Inhibitory Factor: Comparison Between Wild Type and Mutant Forms”, Biopolymers, 65, 313-323 (2002).
48. R. M. Shroll, and T. P. Straatsma, “Molecular Structure of the Outer Bacterial Membrane of Pseudomonas aeruginosa via Classical Simulation”, Biopolymers, 65, 395-407 (2002).
49. R. M. Shroll, and T. P. Straatsma, “Molecular Dynamics Simulations of the Goethite-Water Interface”, Molecular Simulation, 29, 1-11 (2003).
50. R. M. Shroll, and T. P. Straatsma, “Molecular Basis for Microbial Adhesion to Geochemical Surfaces: Computer Simulation of Pseudomonas aeruginosa Adhesion to Goethite”,Biophysical Journal, 84, 1765-1772 (2003).
51. D. M. A. Smith, M. Dupuis, E. R. Vorpagel, and T. P. Straatsma, “Characterization of Electronic Structure and Properties of a bis(Histidine) Heme Model Complex”, Journal of the American Chemical Society, 125, 2711-2717 (2003).
52. R. C. Rittenhouse, W. K. Apostoluk, J. H. Miller, and T. P. Straatsma, “Characterization of the Active Site of DNA polymerase-beta by Molecular Dynamics and Quantum Chemical Calculation”, Proteins, Structure, Function, and Genetics, 53(3), 667-682 (2003).
53. J. H. Miller, C.-C. P. Fan-Chiang, T. P. Straatsma, and M. A. Kennedy, “8-Oxoguanine Enhances Bending of DNA that Favors Binding to Glycosylases”, Journal of the American Chemical Society, 125, 6331-6336 (2003).
54. T. L. Windus, E. J. Bylaska, M. Dupuis, S. Hirata, L. Pollack, D. M. Smith, T. P. Straatsma, and E. Apra, “NWChem: New functionality”, Lecture Notes in Computer Science, 2660, 168-177 (2003).
55. T. P. Straatsma, “Molecular Basis for Microbial Adhesion to Geochemical Surfaces: Computer Simulations of Pseudomonas aeruginosa Adhesion to Geothite”, Abstracts of Paper of the American Chemical Society 225, U805-806 (2003).
56. T. L. Windus, E. Apra, S. Hirata, E. J. Bylaska, and T. P. Straatsma, ”High Performance Computing with NWChem”, Abstracts of Paper of the American Chemical Society 226, U424 (2003).
57. A. R. Felmy, C. Liu, and T. P. Straatsma, “The importance of diffusion at the microbe-mineral interface: Electrical double layer effects and the impact on precipitation/dissolution”, Geochimica et Cosmochimica Acta, 69(10), A171, (2005).
58. C. F. Wong, J. Kua, Y. Zhang, T. P. Straatsma, and J. A. McCammon, “Molecular Docking of Balanol to Dynamics Snapshots of Protein Kinase A”, Proteins Structure, Function and Bioinformatics 61(4), 850-858 (2005).
59. D. M. A. Smith, M. Dupuis, and T. P. Straatsma, “Multiplet Splittings and Other Properties from Density Functional Theory: An Assessment in Iron-Porphyrin Systems”, Molecular Physics, 108, 273-278 (2005).
60. T. P. Straatsma, “Scalable Molecular Dynamics”, Journal of Physics: Conference Series, 16, 287-299 (2005).
61. T. P. Straatsma, “Molecular Modeling of Complex Biological Systems: Microbial Membranes”, Abstracts of Papers of the American Chemical Society, 230, U1295-U1296 (2005).
62. C. S. Oehmen, T. P. Straatsma, G. Anderson, G. Ohr, B. M. Webb-Robertson, D. R. Jones, “Challenges Facing Integrative Biological Science in the Post-Genomic Era”, Journal of Biological Systems, 14(2), 275-293 (2006).
63. D. M. A. Smith, K. M. Rosso, M. Dupuis, M. Valiev, and T. P. Straatsma, “Electronic Coupling between Heme Electron-Transfer Centers and Its Decay with Distance Depends Strongly on Relative Orientation”, Journal of Physical Chemistry B, 110, 15582-15588 (2006).
64. T. P. Straatsma, “Lipopolysaccharide Membranes and Membrane Proteins of Pseudomonas aeruginosa Studied by Computer Simulation”, Lecture Series on Computer and Computational Sciences, 7B, 519-525 (2006).
65. W. Gu, T. Frigato, T. P. Straatsma, and V. Helms, “Dynamic Simulation of the Protonation Equilibrium of Solvated Acetic Acid”, Angewandte Chemie International Edition, 46, 2939-2943 (2007).
66. W. Gu, T. Frigato, T. P. Straatsma, and V. Helms, “Dynamisches Protonierungsgleichgewicht der in Wasser gelösten Essigsäure”, Angewandte Chemie, 119, 2997-3001 (2007).
67. T. A. Soares, M. A. Osman, and T. P. Straatsma, “Molecular Dynamics of Organophosphorous Hydrolase Bound to the Nerve Agent Soman”, Journal of Chemical Theory and Computation, 3(4), 1569-1579 (2007).
68. T. A. Soares and T. P. Straatsma, “Towards Simulations of Outer Membrane Proteins in Lipopolysaccharide Membranes”, International Conference of Computational Methods in Sciences and Engineering. 2007, American Institute of Physics Conference Proceedings 963(2), 1375-1378 (2007).
69. T. P. Straatsma, “Data Intensive Analysis of Biomolecular Simulations”, International Conference of Computational Methods in Sciences and Engineering. American Institute of Physics Conference Proceedings 963(2), 1379-1382 (2007).
70. T. P. Straatsma, “Data-intensive computing laying foundation for biological breakthroughs”, DOE Pulse 237, June 18, 2007.
71. N. F. Samatova, A. Gorin, E. Uberbacher, T. Karpinets, B.-H. Park, C. Pan, T. P. Straatsma, W. Cannon, H. Resat, R. D. Lins, and C. Oehmen, “Data-Driven Computing for Biological Systems” SciDAC Review 5, 10-25 (2007).
72. C. S. Oehmen, H. J. Sofia, D. J. Baxter, E. Szeto, P. Hugenholtz, N. C. Kyrpides, V. M. Markowitz, and T. P. Straatsma, “Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond”, submitted, (2007).
73. K. M. Rosso, S. N. Kerisit, M. Valiev, D. M. A. Smith, N. A. Deskins, S. Yanina, N. S. Wigginton, T. P. Straatsma, and M. Dupuis. “Computational Bioelectrochemistry for Cytochrome-electrode Interfaces.” Abstracts of Papers of the American Chemical Society, 234, 247, (2007).
74. R. D. Lins, E. R. Vorpagel, M. Guglielmi, and T. P. Straatsma, “Computer Simulations of Uranyl Uptake by the Rough Lipopolysaccharide Membrane of Pseudomonas aeruginosa” Biomacromolecules, 9, 29-35 (2008).
75. T. A. Soares, T. P. Straatsma, and R. D. Lins, “Influence of the B-band O-antigen Chain in the Structure and electrostatics of the Lipopolysaccharide Membrane of Pseudomonas aeruginosa”, Journal of the Brazilian Chemical Society, 19(2) 312-320 (2008).
76. T. A. Soares and T. P. Straatsma, “Assessment of the Convergence of Molecular Dynamics Simulations of Lipopolysaccharide Membranes”, Molecular Simulation, 34(3), 295-307 (2008).
77. B. H. Lower, R. D. Lins, Z. Oestreicher, T. P. Straatsma, M. F. Hochella, L. Shi, and S. K. Lower, “In Vitro Evolution of a Peptide with a Hematite Binding Motif That May Constitute a Natural Metal-Oxide Binding Archetype”, Environmental Science and Technology, 42(10), 3821-3827 (2008).
78. E. S. Peterson, E. G. Stephan. A. L. Corrigan, R. D. Lins, T. A. Soares, R. E. Scarberry, L. K. Williams, S. J. Rose, C. Lai, T. J. Critchlow and T. P. Straatsma, “Northwest Trajectory Analysis Capability: A Platform for Enhancing Computational Biophysics Analysis”, Proceedings of the International Conference on Bioinformatics & Computational Biology, Las Vegas, NV, July 14-17, 2008.
79. F. Sieker, T. P. Straatsma, S. Springer, and M. Zacharias, ”Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: A molecular dynamics simulation study”, Molecular Immunology, 45, 3714-3722, (2008).
80. D. E. B. Gomes. R. D. Lins, P. G. Pascutti, T. P. Straatsma, and T. A. Soares, “Molecular Models to Emulate Confinement Effects on the Internal Dynamics of Organophosphorous Hydrolase”, Lecture Notes in Bioinformatics, 5167, 68-78 (2008).
81. E. D. Franca, L. C. Freitas, T. P. Straatsma, and R. D. Lins, “Characterization of Chitin and Chitosan Fiber Structure in Aqueous Solution”, Journal of Chemical Theory and Computing, 4(12), 2141-2149 (2008).
82. O. V. Oliveira, L. C. Freitas, T. P. Straatsma, and R. D. Lins, “Interaction between the CBM of Cel9A from Thermobifida fusca and Cellulose Fibers”, Journal of Molecular Recognition, 22, 38-45 (2009).
83. C. Boschek, D. Apiyo, T. A. Soares, H. Engelmann, N. Pefaur, T. P. Straatsma, and C. L. Baird. “Engineering an ultra-stable affinity reagent based on Top7”, Protein Engineering Design and Selection, 22(5), 325-332 (2009).
84. 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).
85. 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).
86. 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).
87. 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, 1(6), 888-894 (2011).
88. D. M. A. Smith, T. P. Straatsma and T. C. Squier, “Molecular dynamics study of calmodulin-target complexes”, Biophysical Journal 100, 150-150 (2011).
89. 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).
90. 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).
91. D. M. A. Smith, T. P. Straatsma, and T. C. Squier, “DFT classical force field development and molecular dynamics of [NiFe] hydrogenase”, Abstr. Papers Am. Chem. Soc., 243, 331 (2012).
92. 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).
93. D. M. A. Smith, T. P. Straatsma, and T. C. Squier, “Retention of Conformational Entropy upon Calmodulin Binding to Target Peptides Is Driven by Transient Salt Bridges”, Biophys. J., 103(7), 1576-1584 (2012).
94. D. G. Chavarria-Miranda, K. Agarwal, and T. P. Straatsma, “Scalable PGAS Metadata Management on Extreme Scale Systems”, Proceedings of the 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid May, 2013), Delft, the Netherlands, pp103-111, (2013).
95. 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).
96. M. Chen, T. P. Straatsma, and D. A. Dixon, “Molecular and Dissociative Adsorption of Water on (TiO2)n Clusters, n=1−4”, J. Phys. Chem. A, 119(46), 11406-11421 (2015).
97. M. Chen, T. P. Straatsma, Z. Fang, and D. A. Dixon, “A Structural and Electronic Property Study of (ZnO)n, n ≤ 168: The Transition from Zinc Oxide Molecular Clusters to Ultra-Small Nanoparticles”, J. Phys. Chem. C, accepted. DOI: 10.1021/acs.jpcc.6b06730

R&D Activities Contributions

Center for Accelerated Application Readiness (CAAR) - In preparation for next-generation supercomputer Summit, the Oak Ridge Leadership Computing Facility (OLCF) selected 13 partnership projects into its Center for Accelerated Application Readiness (CAAR)…

Accelerated Data Analytics and Computing Institute (ADAC) - The Accelerated Data Analytics and Computing Institute has been established to explore potential future collaboration among UT-Battelle, LLC (UT-Battelle), the Swiss Federal Institute of Technology,…

Exascale Computing Project – NWChemEx - The NWChemEx project will redesign the architecture of NWChem to work with the pre-exascale and exascale computers to be deployed at U.S. Department of Energy…

Highlights