Research Results from High Performance Computing

From WakeDEAC

Contents

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Research Groups

This listing is not complete and, although the groups are listed by discipline, collaborations exist between the groups and some research interests overlap.

Biophysics and Biomedical Engineering Computational Mathematics and Computer Science Quantum Chemistry Numeric Relativity, Astrophysics Condensed Matter
Alexander Research Group Plemmons Research Group Salam Research Group Cook Research Group Holzwarth Research Group
Salsbury Research Group Swofford Research Group Eric Carlson Research Group Kerr Research Group
Fetrow Research Group Paul Anderson Research Group Matthews Research Group
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Student Participation

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Doctoral Students

  • Yonas Abraham, "Electronic states near surfaces -- a) Analysis of calculation methods using semi-infinite boundary conditions; b) Sensitive detection using laser photoelectron spectroscopy", PhD Physics (2004)
  • Blythe Ashcraft, "Carbon-Hydrogen Stretching Vibrational Transitions:Experimental and Computational Studies", PhD Chemistry (2007)
  • Doug Bonessi, PhD Physics (expected 2008)
  • Jason Bates, Physics graduate student (2007-Present)
  • Michael Budiman, PhD Chemistry (2006)
  • Kevin Conley, "A Dirac All-Electron Basis and Spin-Orbit Coupled Projector Implementation of the Projector Augmented Wave Method for Atomic Systems", PhD Physics (2008)
  • Andrew Graham, "Nucleation Rates for One-Dimensional Stochastic Systems with Asymmetric Quartic Potentials, Brownian Noise and Damping", PhD Physics (1999)
  • Jason Grigsby, Physics graduate student (2003-Present)
  • William Hirsch, Physics graduate student (2002-Present)
  • William Hodge, PhD Physics (expected 2008)
  • Brian Kolb, Physics graduate student (2006-Present)
  • Guanghui Lei. Physics graduate student (1998-2004)
  • Matthew Rave, "Aspects of Berry's Phase in Solid State Physics", PhD Physics (2007)
  • Yuan Shen, Biomedical Engineering graduate student, at Virginia Tech (2007-present)
  • Ping Tang, "Computational Research on Lithium-Ion Battery Materials", PhD Physics (2006)
  • Haiyong Xu, Biomedical Engineering graduate student (2007-present)
  • Xiao Xu, Physics graduate student (2005-Present)
  • Ye Yuan, Physics graduate student (2004-Present)
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Masters Research Candidates

  • Donghui Chen, Mathematics (2007-present)
  • David Evanich, MS Physics "Aspects of Parametric Resonance in Chaotic Inflation" (2006)
  • Jason Fye,MS Computer Science "Elucidation of Transcriptional Regulatory Relationships via Information Theoretic Clustering and Consensus Nucleotide Motif Extraction" (2008)
  • Ryan Huff, MS Computer Science "Active site profiling for identification of functional sites in protein sequences and stuctures" (2005)
  • M. Graham Lopez, MS Computer Science "A Computational Method to explore the time-evolution of protein cavities" (2008)
  • Amy Olex, MS Computer Science "Development of novel microarray analysis tools and application to a dendritic cell maturation time course experiment" (2007)
  • Edward Pryor, MS Computer Science "PASSS: Protein Active Site Structure Search" (2006)
  • Huan Tan, MS Computer Science "Active Site Profile Scoring With Protein Features" (2006)
  • Yuhe Wang, Chemistry (Spring 2008 to present)
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Undergraduate Research Students

  • Douglas Agopsowicz, Physics (2002-2003)
  • Shane Ahlers, Biology (Spring 2005- Spring 2007)
  • Ivan Azarov, Physics (Summer 2003)
  • Nick Babladelis, Chemistry (Spring 2007 - Spring 2008)
  • Jillian Bjerke, Physics (Fall 2007 - Spring 2008)
  • Domonique Bulls, Biology, from NC A&T (Summer 2008)
  • Matthew Caudill, Physics, Honors Thesis, "Testing the Black Hole's Spin in Black-Hole Binary Initial Data" (2005)
  • Paul Wilson Cauley, Physics (Fall 2008 - Spring 2009)
  • Dominique Collins, Applied Mathematics, from NC A&T (Summer 2008)
  • Nicholas Dellaripa, Physics (Spring, Summer 2007)
  • Zach Dexter, Physics, HS Student (Summer 2006)
  • Lisa Federico, Chemistry (2005)
  • Nikki Garcia, Chemistry (Summer 2007 to present)
  • Sam Glover, Biology, from UNC (Fall 2006-Present)
  • Matt Gottbrecht, Physics, (Fall 2007-present)
  • David Harrington, Physics, from Southern Adventist (Summer 2006)
  • David Harris, Physics, from UNC (Summer 2007, 2008)
  • Michael Hicks, Biology, Honors Thesis, "Molecular modeling of mammalian carboxylesterases provides insight into CPT-11 activation" (2005)
  • Jared Hill, Physics (Summer 2003 - Spring 2007)
  • Margaret Hurt, Chemistry (Spring 2007 to present)
  • Briana Keeling, Physics (2003-2004)
  • Sarah Klyap, Physics (Spring 2007 - Spring 2008 )
  • Audra Lemley, Chemistry, Honors Thesis,"Analysis of long range interactions in eglin c using molecular dynamics simulations" (2007)
  • Camilo Mateus, Biology, (Fall 2007-present)
  • George Martin, Physics (2004-2005)
  • Megan McCormick, Biology (Fall 2005)
  • Ashley Spooner, Biology (Fall 2005-Spring 2006)
  • John Tumbleston, Physics, from Elon University (Summer 2005)
  • Mary Beth Ward, Biology (Spring 2007-Present)
  • Lee Watkins, Physics ( Spring 2007 - Spring 2008)
  • Andrew Wilson, Physics (Fall 2006 - Spring 2008 )
  • Sarah Yocum, Biology, Honors Thesis, "Analysis of functional sites of enolase, crotonase, and dehalogenase protein families" (2005)
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First Year Rotation Graduate Students

  • Akash Das, Biochemistry, " Molecular dynamic simulation reveals deviation from the fully folded conformation around peroxidatic cysteine in the reduced structure ofTryparedoxin Peroxidase" (2004)
  • Michael Murray, Biochemistry, "Simulation of the Thermal UnfoldingPathway of Two Homologous ProteaseInhibitors at Multiple Temperatures" (2005)
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Grant Awards

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2009

  1. NIH NCI R01 (PI: F. Salsbury) "Targeting the MSH2-dependent Cell Death Pathway" May 1 2009 - Feb 28 2014
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2008

  1. Translational Science Institute (Co-PI's: F. Salsbury, K. Scarpinato, S.B. King. WFU Reynolda Campus and School of Medicine) "Drug Design for Targeted Therapy of Chemoresistant Tumors"
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2007

  1. Golfers Against Cancer, (Co-PI's: F. Salsbury, K. Scarpinato, T. Hollis. WFU Reynolda Campus and School of Medicine) "Multi-investigator Projects in Cancer Research."
  2. NSF DMR-0705239 (PI: N. A. W. Holzwarth; WFU Reynolda Campus) "First principles simulations of battery materials", Dec. 15, 2007-Nov. 30, 2008.
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2006

  1. NSF PHY-0556292 (PI: P.R. Anderson; WFU Reynolda Campus). "Studies of Classical and Quantum Effects in Gravity", July 2006 - June 2009.
  2. NSF PHY-055617 (PI: G.B. Cook; WFU Reynolda Campus). "Quasiequilibrium BH-BH and NS-BH binary initial data," November 2006 - October 2009.
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2005

  1. NIH NIGMS RO1 GM075304 (PI: J. Fetrow, Co-PIs, D. John, S. Thomas, E. Allen, L. Poole, and L. Daniel; WFU Reynolda Campus and School of Medicine). "Algebraic and Statistical Models of Redox Signaling", April 2005 - March 2009.
  2. NIH NCI R21 CA112145 (PI:L. Poole, Co-PIs, J. Fetrow, B. King, :L. Daniel; WFU Reynolda Campus and School of Medicine). "Profiling of Redox-Sensitive Signaling Proteins", May 2005 - April 2007.
  3. NSF MCB-0517343 (PI: J. Fetrow, Co-PIs, F. Salsbury and, L. Poole; WFU Reynolda Campus and School of Medicine). "Integrated Process for Functional Site Feature Analysis", August 2005 - July 2008.
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2004

  1. NSF Award (PI: N.A.W. Holzwarth; WFU Reynolda Campus). "Computational Study of Transition Metal Phosphate Materials", August 2004 - July 2007.
  2. NSF ITR (PI: N.A.W. Holzwarth; WFU Reynolda Campus). "ITR - Computational Tools for Detailed Simulations of Materials", September 2004 - August 2009.
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2003

  1. WFU Research Award (PI: Robert L. Swofford; Reynolda Campus). "Experimental measurements combined with computations provide new information about chemical bond strengths", Fall 2003 - Fall 2004.
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2002

  1. NSF Award (PI: G.B. Cook; WFU Reynolda Campus). "Improved Initial Data for Black-Hole Binaries", June 2002 - May 2004.
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Peer-Reviewed Publications

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2008

  1. F. R. Salsbury, S. T. Knutson, L. B. Poole and J. S. Fetrow, "Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid," Protein Science 17 299-312(2008).
  2. J.D. Grigsby and G.B. Cook, "Measuring eccentricity in binary black-hole initial data," Phys. Rev. D 77 044011 (2008).
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2007

  1. M. Boyle, D.A. Brown, L.E. Kidder, A.H. Mroue, H.P. Pfeiffer, M.A. Scheel, G.B. Cook and S.A. Teukilsky, "High-accuracy comparison of numerical relativity simulations with post-Newtonian expansions," Phys. Rev. D 76, 124038 (2007).
  2. M. H. Knaggs, F. R. Salsbury, M. H. Edgell, J. S. Fetrow. Insights into CheY relaxation and relaxation derived from molecular dynamics simulations. Biophys J .2062-2079 Mar 15 2007
  3. S. W. Paine and A. Salam. "A Computational Study of the Keto-Enol Equilibria of Sulphur Substituted Analogues of Hydroxycyclopropenone", J. Mol. Struct. (THEOCHEM) 814, 105-112 (2007).
  4. G.B. Cook and B.F. Whiting, "Approximate Killing Vectors on S2," Phys. Rev. D 76, 041501(R) (2007).
  5. Yaojun A. Du and N. A. W. Holzwarth, "Li Ion Diffusion Mechanisms in the Crystalline Electrolyte γ-Li3PO4", Journal of the Electrochemical Society 154, A999-A1004 (2007).
  6. Ping Tang, N. A. W. Holzwarth, and Yaojun A. Du, "Comparison of the electronic structures of four crystalline phases of FePO4", Phys. Rev. B 76, 174118 (2007)
  7. Yaojun A. Du and N. A. W. Holzwarth, "Mechanisms of Li+ diffusion in crystalline Li3PO4 electrolytes from first principles", Phys. Rev. B 76, 174302 (2007)
  8. Budiman, M.E., Knaggs, M.H., Fetrow, J.S., and Alexander, R.W. (2007) Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase. Proteins: Structure, Function, and Bioinformatics 68: 670-689.
  9. Paul R. Anderson, Emil Mottola, and Ruslan Vaulin, Stress tensor from the trace anomaly in Reissner-Nordström spacetimes, Physical Review D 76, 124028 (2007).
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2006

  1. E.E. Allen, J.S. Fetrow, L.W. Daniel, S.J. Thomas, D.J. John. Algebraic dependency models of protein signal transduction networks from time-series data. J. Theor. Biol. 238 (2): 317-330 JAN 21 2006
  2. F. R. Salsbury Jr. An analysis of errors in Stil's equation for macromolecular electrostatic solvation energies. Molecular Physics, April 20, 104, 1311 (2006)
  3. J.S. Fetrow, S.T. Knutson, and M.H. Edgell. Mutations in α-helical solvent exposed sites of eglin c have long-range effects: evidence from molecular dynamics simulations. Proteins, May 1, 63, 356-72 (2006).
  4. Yonas Abraham and N. A. W. Holzwarth, "A method for calculating electronic structures near surfaces of semi-infinite crystals ", Phys. Rev. B 73, 035412 (2006).
  5. Y. Ma and A. Salam, On chiral selectivity of enantiomers using a circularly polarized pulsed laser under resonant and off-resonant conditions. Chem Phys 324, 367-375 (2006).
  6. Y. Ma and A. Salam, Calculation of electronic circular dichroism spectra by rotating wave approximation. Chem Phys 324, 622-630 (2006).
  7. F. R. Salsbury Jr., J. Clodfelter, M. Gentry, T. Hollis and K. D. Scarpinato, The molecular mechanism of DNA damage recognition by MutS homologs and its distinction from mismatch binding", Nucleic Acids Research 2006 34(8):2173-2185
  8. S. W. Paine and A. Salam, “Computational Study of Keto-Enol Equilibria of Tropolone in Gas and Aqueous Solution Phase”, Chem. Phys. 331, 61-66 (2006)
  9. Y. Ma and A. Salam, “Controlling State Populations of Enantiomers of Real Chiral Molecules by Using a Circularly Polarized Pulsed Laser”, Chem. Phys. Lett. 431, 247-252 (2006).
  10. M. Caudill, G.B. Cook, J.D. Grigsby, and H.P. Pfeiffer, "Circular orbits and spin in black-hole initial data," Phys. Rev. D 74 064011 (2006).
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2005

  1. E.E. Allen, J.S. Fetrow, L.W. Daniel, S.J. Thomas, D.J. John. Algebraic dependency models of protein signal transduction networks from time-series data. J. Theor. Biol. 2005 Jul 4. Epub ahead of print.
  2. Huff RG, Bayram E, Tan H, Knutson ST, Knaggs MH, Richon AB, Santago P, Fetrow JS Chemical and structural diversity in cyclooxygenase protein active sites CHEMISTRY & BIODIVERSITY 2 (11): 1533-1552 2005
  3. M. J. Rave and W. C. Kerr. Berry's Phase for an Electron in a Periodic Potential without Inversion Symmetry. Euro. Phys. Jour. B, 45, 473 (2005)
  4. W. C. Kerr, M. J. Rave and L. A. Turski. The Phase Space Dynamics of Semi-Classical Spin-1/2 Bloch Electrons. Physical Review Letters 94, 176403 (2005)
  5. Paul R. Anderson, R. Balbinot, and A. Fabbri. Cutoff Anti de SitterSpace/Conformal-Field-Theory Duality and the Quest for Braneworld Black Holes. Phys. Rev. Lett. 94, 061301
  6. S. W. Paine, A. J. Kresge, and A. Salam, An ab initio and density functional theory study of keto-enol equilibria of hydroxycyclopropenone in gas and aqueous solution phase. J. Phys. Chem. A 109, 4149 (2005).
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2004

  1. K. Drotschmann, R. P. Topping, J. E. Clodfelter, and F. R. Salsbury, Jr. Mutations in the Nucleotide-binding Domain of MutS Homologs Uncouple Cell Death from Cell Survival. DNA Repair, 3 (7):729-742
  2. L. R. Thomas, A. Henson, J. C. Reed, F. R. Salsbury, Jr., and A. Thorburn. Direct Binding of FADD to the TRAIL Receptor DR5 is Regulated by the Death Effector Domain of FADD. J. Bio. Chem. 279, 31
  3. M. S. Lee, F. R. Salsbury, Jr., and C. L. Brooks, III. Constant pH-molecular Dynamics using Continuous Titration Coordinate, Proteins: Structure, Function and Bioinformatics. Proteins: Struct Funct Bioinform 56 (4):738-752
  4. M.S. Lee, F. R. Salsbury, Jr., and M. A. Olson. An Efficient Hybrid Implicit/Explicit Solvent Method for Biomolecular Simulations that Uses A Generalized Born Reaction Field and Multigrid Enhancements. J. Comp. Chem. 25:1967-7198
  5. E. Bayram, P. Santago II, R. Harris, Y. Xiao, A.J. Clauset, and J.D. Schmitt. Genetic Algorithms and Self-Organizing Maps: A Powerful Combination for Modeling Complex QSAR and QSPR Problems. Journal of Computer-Aided Molecular Design. 18:483-493
  6. G.B. Cook and H.P. Pfeiffer, "Excision boundary conditions for black hole initial data," Phys. Rev. D 70, 104016 (2004).
  7. W. C. Kerr and A. J. Graham. Nucleation Rate of Critical Droplets on an Elastic String in a \phi^6 Potential. Phys. Rev. E 70, 066103
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2003

  1. Ping Tang and N. A. W. Holzwarth. Electronic structures of FePO_4, LiFePO_4, and related materials. Physical Review B 68, 165107 (2003)
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2002

  1. Jason D. Weibel, Charles F. Jackels, and Robert L. Swofford, "Experimental and ab initio investigation of the O-H overtone vibration in ethanol" J. Chem. Phys. 117, 4245-4254 (2002)
  2. Harald P. Pfeiffer, Gregory B. Cook, and Saul A. Teukolsky, "Comparing initial-data sets for binary black holes," Phys. Rev. D 66 024047 (2002).
  3. A J Graham and W C Kerr, "Solution of Kramers' problem for a moderately to heavily damped elastic string", Phys Rev E 65, 016106
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2001

  1. Yonas B. Abraham, N. A. W. Holzwarth, R. T. Williams, G. Eric. Matthews, and Alan R. Tackett, "The electronic structure of oxygen related defects in PbWO4 and CaMoO4 crystals" Phys. Rev. B64, 245109 (2001)
  2. A. R. Tackett, N. A. W. Holzwarth, and G. E. Matthews, "A Projector Augmented Wave (PAW) code for electronic structure calculations, Part I: atompaw for generating atom-centered functions and PartII: pwpaw for periodic solids in a plane wave basis." Computer physics Communications 135 329-347, 348-376 (2001)
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2000

  1. Harald P. Pfeiffer, Saul A. Teukolsky, and Gregory B. Cook, "Quasi-circular orbits for spinning binary black holes," Phys. Rev. D 62 104018 (2000).
  2. Lawrence E. Kidder, Mark A. Scheel, Saul A. Teukolsky, Eric D. Carlson and Gregory B. Cook, "Black hole evolution by spectral methods," Phys. Rev. D 62 084032 (2000).
  3. Y. Abraham, N. A. W. Holzwarth, and R. T. Williams, "Electronic Structure and Optical Properties of CdMoO_4 and CdWO_4 ", Phys. Rev. B 62, 1733-1741 (2000)
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International, National and Regional Presentations

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2008

  1. J. Fetrow, "From molecular function to biological mechanism: feature analysis of protein functional sites" Indiana University School of Medicine, Center for Computational Biology and Bioinformatics, Feb 25, 2008,
  2. J. Fetrow, "Feature analysis of functional sites in proteins", Keystone Conference: Computer-Aided Drug Design, April 1 2008
  3. W. Hodge, "The One-Hole, One-Dimensional Hubbard Model at U = ∞" 2008 APS March Meeting in New Orleans, LA, March 2008.
  4. N. A. W. Holzwarth, "Simulation of Li ion diffusion near electrolyte-metal interface -- Li3PO4 and Li" 2008 APS March Meeting in New Orleans, LA, March 2008.
  5. Y. A. Du, "Li ion migration in Li3PO4 electrolytes: Effects of O vacancies and N substitutions" 213th Biannual Meeting of the Electrochemical Society in Phoenix, AZ May 18-22, 2008.
  6. N. A. W. Holzwarth, "Simulations of Li ion diffusion in the electrolyte material -- Li3PO4" Workshop on Pseudopotentials and the Quantum Theory of Materials" in Austin, TX Apr. 9-11 2008 in honor of J. R. Chelikowsky.
  7. X. Xu, "Projector Augmented Wave Formulation of Optimized Effect Potential Density Functional Theory -- PAW-OEP" 20th Annual Workshop on Recent Developments in Electronic Structure Methods at the University of Illinois at Urbana-Champaign, June 17-20, 2008.
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2007

  1. A. Salam, "Molecular Quantum Electrodynamical Theory of Chiroptical Phenomena", Invited Seminar, Rowland Institute, Harvard University, Cambridge, Massachusetts, 19 April, 2007.
  2. G.B. Cook, "The role of diagnostics in evaluating initial-data sets," Invited talk, Numerical Relativity Meets 3rd Post-Newtonian Workshop, Washington University of St. Louis. February 8-11
  3. F.R Salsbury Jr, "Computational Modeling of a DNA Mismatch Repair Enzyme", Invited talk, Symposium Speaker, Biophysical Society Annual Meeting. Baltimore MD. March 3-7
  4. G. Eric Matthews, N.A.W. Holzwarth, George Martin, Briana Keeling, and Douglas Agopsowicz, "Accelerating self consistent field convergence by rubber sheeting of initial electronic wave functions.", 2007 March Meeting of the American Physical Society.
  5. Xiao Xu, Yaojun A. Du., and N. A. W. Holzwarth, "Simulated electrolyte-metal interfaces Li_3PO_4 and Li" 2007 March Meeting of the American Physical Society
  6. Yaojun A. Du., and N. A. W. Holzwarth, "Li-ion diffusion mechanisms in crystalline Li_3PO_4 electrolytes" 2007 March Meeting of the American Physical Society
  7. William Hodge, N. A. W. Holzwarth and W. C. Kerr, "Pair State Analysis of the Hubbard Hamiltonian in One-Dimension" 2007 March Meeting of the American Physical Society
  8. R. W. Alexander. "Dissecting long-range communication in methionyl-tRNA synthetase". Washington & Lee College, Chemistry department, March 22, 2007
  9. Amy Olex, "Additional limitations of the clustering validation method figure of merit", 45th ACM Southeast Conference. Winston-Salem, NC, March 23-24, 2007.
  10. Eddie Pryor, "PDBSQL: A Storage Engine for Macromolecular Data", 45th ACM Southeast Conference. Winston-Salem, NC, March 23-24, 2007.
  11. Edward Allen, "The Shuffle Index and Evaluation of Models of Signal Transduction Pathways", 45th ACM Southeast Conference. Winston-Salem, NC, March 23-24, 2007.
  12. R. W. Alexander. "Dissecting long-range communication in methionyl-tRNA synthetase". Ohio State University, Microbiology department, April 5, 2007
  13. F. R. Salsbury J., Invited talk. "Two Studies in Physics-based Modeling of Protein Dynamics and Function." CUNY, New York, New York, 20 April 2007.
  14. G.B. Cook, "Approximate Killing Vectors and Black-Hole Diagnostics," Contributed talk, 10th Eastern Gravity Meeting, Cornell University. May 31-June 1
  15. J.D. Grigsby, "Effective Potentials and Eccentric Orbits," Contributed talk, 10th Eastern Gravity Meeting, Cornell University. May 31-June 1
  16. Budiman, M.E., Knaggs, M.H., McKinney, W., Brown, C.L., Fetrow, J.S., and Alexander, R.W. "Computational and experimental dissection of enzyme allostery" 2007 Gordon Research Conference on BioOrganic Chemistry, June 10-15, 2007, Andover, NH.
  17. Xiao Xu and N. A. W. Holzwarth, "Projector Augmented Wave Formulation of Exact Exchange Density Functional Theory -- PAW-EXX", 19th Annual Workshop on Recent Developments in Electronic Structure Methods, June 13-15, 2007, Raleigh, NC.
  18. Yaojun Du and N. A. W. Holzwarth, "Li ion diffusion mechanisms in Li3PO4 electrolytes", 19th Annual Workshop on Recent Developments in Electronic Structure Methods, June 13-15, 2007, Raleigh, NC.
  19. G.B. Cook, "Approximate Killing Vectors for Computing Spin in Black-Hole Initial Data and Evolutions," Contributed talk, 18th International Conference on General Relativity & Gravitation, Sydney, Australia. July 8-13.
  20. Y. Yuan, M. Knaggs, L. Poole, J. Fetrow, and F.R. Salsbury. Structural Origins of the Peroxidatic Cysteine pKa Shift of the Tryparedoxin Peroxidase from Trypanosoma cruzi. 21st Symposium of the Protein Sociey, Boston July 21-25
  21. F. Salsbury Jr., S. Knutson, M. Ward, L. Poole and J. Fetrow. Analysis of Sulfenic Acid Posttranslational Modification Sites in Protein Structures: A Mechanism Involved in Redox Signaling.21st Symposium of the Protein Sociey, Boston July 21-25
  22. F. Salsbury Jr. Computational Studies of Long Range Communication in Proteins. University of Delaware, Department of Chemistry, Invited Colloquium Speaker, September 14th
  23. N. Babladelis, and R. W. Alexander,Symposium on RNA Biology VII, October 19-20, 2007, Chapel Hill, NC. “Computational and experimental dissection of tRNA aminoacylation.”
  24. S. J. Thomas, W. H. Turkett Jr., F. R. Salsbury Jr., S. T. Knutson, L. B. Poole and J. S. Fetrow, Analysis and Characterization of Reactive Cysteines in Protein Structures and Within Cellular Signal Transduction Networks. Microsoft eScience Workskop at RENCI. Chapel Hill, NC, October 21-23
  25. R. W. Alexander, Southeast Regional Meeting of the American Chemical Society, October 24-27, 2007, Greenville, SC. “Computational and experimental dissection of tRNA aminoacylation.”
  26. R. W. Alexander, 22nd tRNA Workshop, November 1-6, 2007, Uppsala, Sweden “Computational and experimental dissection of ARS:tRNA interaction networks”
  27. N. A. W. Holzwarth "Simulations of Li ion diffusion in the electrolyte Li3PO4", SESAPS, Nashville, TN, November 9, 2007.
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2006

  1. J.S. Fetrow and D.J. John. Bioinformatics and computing curriculum: A new model for interdisciplinary courses. SIGCSE 2006 Houston TX, March 1-5
  2. R. W. Alexander. "Dissecting long-range communication in methionyl-tRNA synthetase". University of Delaware, Chemistry & Biochemistry Department, March 6, 2006
  3. R. W. Alexander. "Dissecting long-range communication in methionyl-tRNA synthetase". Johns Hopkins University, Chemistry Department, March 7, 2006
  4. Y. Abraham and N.A.W. Holzwarth. "Surface electronic structure of H/Li(110) -- an application of the semi-infinite method," 2006 APS March Meeting, Baltimore, MD. March 13
  5. P. Tang and N. A. W. Holzwarth "Comparison of the electronic structures of four crystalline phases of FePO_4" 2006 APS March Meeting, Baltimore, MD. March 15
  6. W. B. Hodge, N. A. W. Holzwarth and W. C. Kerr "Pair State Analysis of the Hubbard Hamiltonian in One-Dimension" 2006 APS March Meeting, Baltimore, MD. March 15
  7. G.B. Cook, "Status of Initial Data for Binary Black Hole Collisions" 2006 APS April Meeting Dallas, Texas. April 23.
  8. A. Salam. "Rotating Wave Approximation Calculation of Circular Dichroism". 3th South East Theoretical Chemistry Association Meeting, Emory University, Atlanta, Georgia, May 20.
  9. G.B. Cook, "Circular Orbits and Spin in Black-Hole Initial Data," Numerical Relativity Seminar at the California Institute for Technolocy, Pasadena, CA. June 7.
  10. M.H. Knaggs., Y. Yuan, L. B. Poole, F. R. Salsbury and J. S. Fetrow. Active site asymmetry in typical and atypical peroxiredoxin dimers, 2006 Gordon Research Conference on Thiol-Based Redox Signaling June 18-24
  11. F.R. Salsbury Jr., S. T. Knutson, L. B. Poole, and J. S. Fetrow, Methods to Identify Cysteines Modifiable to Sulfenic Acid in Proteins, 2006 Gordon Research Conference on Thiol-Based Redox Signaling, June 18-24
  12. N. A. W. Holzwarth,“State of the art, developments and perspectives of electronic structure calculations in the frame of the Projector Augmented-Wave (PAW) method" Invited talk, Lyon, France, 12-14 June 2006.
  13. Ping Tang, Y. Du, X. Xu, and N. A. W. Holzwarth. “Electronic Structures of Four Crystalline Phases of FePO4.” 8th Annual Workshop on Recent Developments in Electronic Structure Methods, Ohio State University, 22-25 June 2006.
  14. Y. Du, X. Xu and N. A. W. Holzwarth. “Li-ion Diffusion Mechanisms in g-Li3PO4 Electrolytes.” 8th Annual Workshop on Recent Developments in Electronic Structure Methods, Ohio State University, 22-25 June 2006.
  15. P. R. Anderson, M. Binkley, H. Calderon, W. A. Hiscock, E. Mottola, and R. Vaulin, "Effects of quantized fields on the spacetime geometries of static spherically symmetric black holes."Eleventh Marcel Grossmann Meeting, Berlin, July 2006
  16. G.B. Cook, "Circular Orbits and Spin in Black-Hole Initial Data," Gravity Theory Seminar at the University of Maryland. September 29.
  17. Budiman, M.E., Knaggs, M.H., Fetrow, J.S., and Alexander, R.W. "Using molecular dynamics to predict communication networks in methionyl-tRNA synthetase" 2006 International Conference of Aminoacyl-tRNA Synthetases, October 1-6, 2006, San Diego, CA.
  18. F.R Salsbury Jr, "Computational Modeling of DNA Repair Enzymes", Invited talk, Carolina Biophysics Symposium. Raleigh, NC. November 1-3
  19. Y. Yuan, M. H. Knaggs, L. B. Poole, J. S. Fetrow, and F. R. Salsbury Jr. "Electrostatic Analysis of pKa Shifts and Oligomerization effects in Tryparedoxin Peroxidase"Carolina Biophysics Symposium. Raleigh, NC. November 1-3
  20. J .S. Fetrow "Structure, dynamics, and redox signaling from bacteria to eukaryotes:�the peroxiredoxin protein family" University of Richmond.
  21. R. W. Alexander. "Dissecting long-range communication in methionyl-tRNA synthetase". UNC-Chapel Hill, Chemistry department, November 8, 2006
  22. G.B. Cook, "Inspiral, merger and ring-down of equal-mass black-hole binaries," Physics Department Colloquium, North Carolina State University, Raleigh, NC. November 20.
[edit]

2005

  1. F. R. Salsbury, Jr., S. A. Knutson, L. A. Poole and J. S. Fetrow. Electrostatic Calculation of pKa Shifts in Proteins. 2005 Biophysical Society Meeting, Long Beach, CA
  2. Paul Anderson. Asymptotic Behavior of the Stress-Energy Tensor for Scalar Fields in the Boulware State in Schwarzschild Spacetimes. 8th Eastern Gravity Meeting, Winston-Salem, March 18-19, 2005
  3. G.B. Cook. Black-Hole Binary Initial Data. 8th Eastern Gravity Meeting, held in Winston-Salem on March 18-19, 2005
  4. Matthew Caudill. Testing the Black Hole's Spin in Black-Hole Binary Initial Data. 8th Eastern Gravity Meeting, Winston-Salem, March 18-19, 2005
  5. Jason Grigsby. Are We Finding Circular Orbits? 8th Eastern Gravity Meeting, Winston-Salem, March 18-19, 2005
  6. Yonas Abraham and N. A. W. Holzwarth A method for calculating surface electronic structures using semi-infinite boundary conditions, March APS 2005 Meeting, Los Angeles
  7. N. A. W. Holzwarth, P. Tang, F. R. Salsbury, Jr., and J. Qualls. The electronic structure of zeta-BEDT-TTF PF6; a comparison of self-consistent field and Hubbard model analyses., March APS 2005 Meeting, Los Angeles
  8. P. Tang and N. A. W. Holzwarth Comparison of the electronic structures of four crystalline forms of FePO4. March APS 2005 Meeting, Los Angeles
  9. Paul Anderson. Infrared efects on the stress-energy of static black holes. Black Holes V meeting, Banff, Canadar, May 14-17, 2005
  10. G.B. Cook. Black-Hole Binary Initial Data. Frontiers of Gravitational Wave Physics. Yukawa Institute for Theoretical Physics, Kyoto University, Japan. July 2005
  11. G.B. Cook. Getting the Spin Right In Black-Hole Binaries. Post-YKIS2005 Scientific Program on Gravity and Cosmology. Yukawa Institute for Theoretical Physics, Kyoto University, Japan, July 2005
  12. M. H. Knaggs, F. R. Salsbury, Jr., M. H. Edgell, and J. S. Fetrow. Insights into early events in CheY relaxation from active to inactive form from MD simulation. Protein Society National Meeting, August 2005
  13. R. W. Alexander. "Dissecting long-range communication in methionyl-tRNA synthetase". NC State University, Biochemistry department, September 22, 2005
  14. G.B. Cook. Black-Hole Binary Initial Data: Getting the Spin Right. CTA Seminar on Theoretical Astrophysics and General Relativity, University of Illinois at Urbana-Champaign, Oct. 2005
  15. G.B. Cook. Black-Hole Binary Initial Data: Getting the Spin Right. Numerical Relativity 2005: Compact Binaries. NASA Goddard Space Flight Center, Nov. 2005
  16. A. Salam, “On the Interaction of Circularly Polarized Light With Chiral Molecules: A Rotating- Wave Approximation Study”. Invited Seminar , Department of Applied Chemistry, Osaka University, Osaka, Japan on 26 December, 2005.
[edit]

2004

  1. S. W. Paine and A. Salam. Computational Study of Tautomerism in Hydroxycyclopropenone. Abstract accepted and poster presented at 44th Sanibel Symposium on Atomic, Molecular, Biophysical and Condensed Matter Theory, St. Augustine, FL, 28 Feb - 5 Mar, 2004
  2. A. Salam, “Recent Theoretical Studies of Molecular Chirality”, Invited Departmental Seminar at Department of Biological and Chemical Sciences, University of the West Indies, Cave Hill Campus, PO Box 64, Bridgetown, Barbados, 10 Mar, 2004.
  3. F.R. Salsbury, Jr., and J. Hill. Developments in Local and Nonlocal Functionals in Magnetic Field Density Functional Theory. American Physical Society Spring Meeting, Montreal, Canada, March 2004
  4. M. J. Rave and W. C. Kerr. Exact calculation of Berry's phase for an electron in a simple 1-D System. BAPS 49, 1431 (2004) American Physical Society Spring Meeting, Montreal, March 2004
  5. W. B. Hodge, N. A. W. Holzwarth, W. C. Kerr. Pair State Analysis of the Hubbard Hamiltonian in One-Dimension. BAPS 49, 257 (2004) American Physical Society Spring Meeting, Montreal, March 2004
  6. F. R. Salsbury, Jr., and M. S. Lee. Constant-pH Molecular dynamics: Principles and Applications. American Physical Society Spring Meeting, Montreal, March 2004
  7. E. Bayram, P. Santago II, R. Harris, Y.D. Xiao, J.C. Aaron, J.D. Schmitt. Genetic Algorithms and Self-Organizing Maps: A Powerful Combination for Modeling Complex QSAR and QSPR Problems. The 227th American Chemical Society National Meeting, 2004
  8. J.D. Schmitt, R. Harris; E. Bayram, Y.D. Xiao, P. Santago II. Coupling Feature Reduction with Self-Organizing Maps for Drug Discovery. The 227th American Chemical Society National Meeting, 2004
  9. Y.D. Xiao, E. Bayram, R. Harris, P. Santago II, J.D. Schmitt. Use of Simulated Annealing with Supervised Self-Organizing Maps for QSAR and QSPR Studies. The 227th American Chemical Society National Meeting, 2004
  10. K. Drotschmann, J. E. Clodfelter, R. P. Topping and F. R. Salsbury, Jr. Separation of function mutants in MutS homologs uncouple cell death from cell survival. American Association for Cancer Research National Meeting, March 2004
  11. A. Salam, “Recent Semi-Classical and Quantum Electrodynamical Studies of Molecular Chirality”, Invited Departmental Seminar at Department of Chemistry, University of Tennessee, Knoxville, Tennessee, 2 July, 2004.
  12. S. A. Knutson, F. R. Salsbury, Jr., L. A. Poole, and J. S. Fetrow. Sequence, Structure, and Electrostatic Analysis of Sites of Cysteine Sulfenic Acid Modification in Proteins. 2004 Gordon Research Conference, Enzymes, Coenzymes, & Metabolic Pathways
  13. Paul Anderson. Asymptotic Behavior of the Stress-Energy Tensor for Scalar Fields in the Boulware State in Schwarzschild Spacetimes. Talk given at the 14th Midwest Relativity Meeting held in Milwaukee on Oct. 15-16, 2004
  14. F. R. Salsbury, Jr. Constant-pH Molecular Dynamics. Invited Seminar: Old Dominion University Department of Chemistry, October 2004
[edit]

2003

  1. F. R. Salsbury, Jr. and M. S. Lee. Macromolecular Simulations with New Generalized Born Methods. American Physical Society National Meeting, Austin TX, March 2003
  2. M. J. Rave and W. C. Kerr. Berry Phase Effects in a Generalized Kronig-Penney Model. BAPS 48, 272 (2003). American Physical Society National Meeting, Austin TX, March 2003
  3. G. Lei, S. N. Kerr, W. C. Kerr. Propagation of Nonlinear Schroedinger Solitons in an Electron-Phonon System. BAPS 48, 276 (2003). American Physical Society National Meeting, Austin TX, March 2003
  4. M. S. Lee, F. R. Salsbury, Jr., C. L. Brooks, III. New trends in generalized Born implicit solvent methods. American Chemical Society National Meeting, March 2003
  5. R. Swofford. Using C-H and O-H overtone spectra to evaluate models of bond dissociation. SouthEast Theoretical Chemists Association, annual meeting, Clemson University, May 2003
  6. Gregory B. Cook. Generating Initial Data for Interacting Compact Binaries. Gravitational Interaction of Compact Objects, Kavli Institute for Theoretical Physics, Santa Barbara CA, May 2003
  7. Gregory B. Cook. Generating Binary Black Hole Initial Data. Numerical Relativity Seminar, California Institute of Technology, May 2003
  8. R. Swofford. Studying Bond Strengths using overtone spectroscopy and Computational Models. Chemistry Department Seminar, UNC-Wilmington, September, 2003
  9. R. Swofford. C-H overtones and Computed potenetial energy surfaces: New insights into bond strengths. SouthEast Regional Meeting of the American Chemical Society, Atlanta, November 2003
[edit]

2002

  1. S. N. Kerr, G. Lei, W. C. Kerr. Reusable C++ Code for an Electron-Phonon Simulation. OOPSLA '02 Companion: Conference on Object-Oriented Programming, Systems, Languages, and Applications, 4-8 November 2002, Seattle WA, pp. 74-75
  2. G. Lei, S. N. Kerr, and W. C. KerrComputer Simulation of Disordered Electron-Phonon Systems.” American Physical Society, Indianapolis, IN, March 2002.
  3. W C Kerr, and A J Graham, "Nucleation Rates in an Extended System with a Symmetric Local Potential" American Physical Society, Indianapolis, IN, March 2002.
[edit]

2001

  1. N. A. W. Holzwarth, The Structure of an Oxygen Vacancy in Crystalline CaMo4., March 2001 American Physical Society, Seattle, WA, March 12-16, 2001.
  2. G Lei, W C Kerr, D Marshburn ,Interaction of Sine-Gordon Solitons with Impurities. March 2001 Meeting of the American Physical Society, Seattle, WA, March 12-16, 2001.
  3. Y. Abrams and N. A. W. Holzwarth, The Electronic Structure ofOxygen Related Defects in PbWO4 and CaMoO4 Crystals, 13th Annual Workshop of Recent Developments in Electronic Structure Algorithms, Princeton, NJ, 15-18 June 2001.
  4. P. Tang and N. A. W. Holzwarth, Comparison of the Electronic Structure of Three Phases of the Organic Conducting Material (BEDT-TTF)PF6. 13th Annual Workshop of Recent Developments in Electronic Structure Algorithms, Princeton, NJ, 15-18 June 2001.
[edit]

Acknowledgments

  • Acknowledging the use of the cluster in your research for computations performed after January 2008. 
Computations were performed on the Wake Forest University DEAC cluster,
a centrally managed resource with support provided in part by the University.
Retrieved from "http://www.deac.wfu.edu/index.php?title=Research_Results_from_High_Performance_Computing"