Pre-registered Posters 2004

Gordon Research Conference on Computational Chemistry

* = Presenter on multi-author posters.

1. Conformational Energetics of Ace-Alan-Nme Peptides.
Robert Abel* and Adrian Roitberg
Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, FL

2. Density Dependence of the Diffusion Coefficient of Alkali Metals.
G. A. Adebayo*, B. C. Anusionwu, A. N. Njah, B. Mathew and O.A.T. Fabamise, Abdus Salam ICTP, Trieste, Italy
Dept. of Physics, Univ. of Agric, Abk, Nigeria, Dept. of Physics, Fed. Univ. of Technology, Owerri, Nigeria

3. Molecular Simulation of Protein Adsorption to Polymer Surfaces.
Madhuri Agashe* (1), Vivek Raut (2), Steven Stuart (2), Robert Latour (1)
(1) Department of Bioengineering, Clemson University, Clemson, SC, (2) Department of Chemistry, Clemson University, Clemson, SC

4. B3LYP/6-311++G** geometry optimization of the chair forms of alpha- and beta mannopyranose.
Michael Appell*, J. L. Willett and Frank A. Momany
National Center for Agricultural Research, USDA, Peoria, IL

5. Atomization energies from ab initio calculations without empirical corrections.
Dirk Bakowies*
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zurich, Switzerland

6. Integration of photosynthetic protein molecular complexes in solid-state electronic devices.
Marc Baldo* (1), Rupa Das (1), Patrick J. Kiley(1), Francesco Stellacci (2), Nikolai Lebedev (3), Barry D. Bruce (4), Shuguang Zhang(5)
Massachusetts Institute of Technology, Cambridge, MA

7. Recent Advances in Bioinformatics and Chemical Information Science Utilizing the TAE Method.
Curt Breneman*, N. Sukumar, Bill Katt, Matt Sundling, Qiong Luo, Dechuan Zhuang
Department of Chemistry, Rensselaer Polytechnic Institute, Troy, NY

8. Rate constants for the abstraction reactions RO2+C2H6, R=H, CH3 and C2H5.
Hans-Heinrich Carstensen* and Anthony M. Dean
Chemical Engineering Department, Colorado School of Mines, Golden, CO

9. MD/NMR Characterization of Internal Motions of Peptide Toxins.
David Chatfield*, Cassian D'Cunha and Ashish Gairola
Florida International University, Miami, FL

10. The Importance of Accurate Charges in Molecular Docking: Quantum Mechanical/Molecular Mechanical (QM/MM) Approach.
Art E. Cho* (1), Victor Guallar (2), Bruce J. Berne (1), and Richard Friesner (1)
(1) Center for Biomolecular Simulations, Columbia University, New York, NY (2) Department of Biochemistry and Molecular Biophysics, Columbia University

11. Constructing master equation models of protein folding and dynamics from atomistic simulation.
John D. Chodera* (1), William Swope (2), Jed W. Pitera (2), and Ken A. Dill (1)
(1) University of California at San Francisco, San Francisco, CA, (2) IBM Almaden Research Center, San Jose, CA

12. Protein dynamics in amorphous glass environments.
Joseph E. Curtis* (1), Dan A. Neumann (1), and Douglas J. Tobias (2)
(1) NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and (2) Institute of Surface and Interface Science and Department of Chemistry, University of California, Irvine, CA

13. Scalable implementation of the 3D-FFT kernel to support the P3ME method on massively parallel machines such as Blue Gene/L Supercomputer.
Maria Eleftheriou*, Blake Fitch and Robert Germain
IBM T. J. Watson Research Center, Yorktown Hts., NY

14. Modeling Molecular Polarizabilities.
Denny Elking*, Michael Kennerty, Sarah Tschampel, and Robert J. Woods
Complex Carbohydrate Research Center, University of Georgia, Athens, GA

15. Molecular Dynamics Study of Polarizability Anisotropy Relaxation in Solution.
M. Dolores Elola* and Branka M. Ladanyi
Department of Chemistry, Colorado State University, Fort Collins, CO

16. Toward a finite temperature intrinsic reaction coordinate - a combination of multi-dimensional free energy probing and one-dimensional umbrella sampling.
Bernd Ensing* (1), Alessandro Laio (2), Fransesco L. Gervasio (2), Michele Parrinello (2) and Michael L. Klein (1)
(1) Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, (2) Computational Science and Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Lugano, Switzerland

17. Cluster Analysis for Evaluating Computational Chemistry Methods.
Tulay Ercanli and Donald B. Boyd*
Department of Chemistry, Indiana University-Purdue University at Indianapolis, Indianapolis, IN

18. DFT Study of Imidazole pKa in Cu Complexes: Implications in the Proton Pumping Mechanism of Cytochrome c Oxidase.
Elisa Fadda* and Regis Pomes
Structural Biology and Biochemistry, The Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada

19. A Generalized Born Model for Heterogeneous Dielectric Environments Applied to Biological Membranes.
Michael Feig* (1) and Seiichiro Tanizaki
(1) Department of Biochemistry, Michigan State University, East Lansing, MI

20. Dynamic Insight into the Equilibrium Behavior of Arachidonate Bound to COX-1 and COX-2.
Kristina Furse* (1), Derek Pratt (1,2), Ned Porter (1) and Terry Lybrand (1)
Center for Structural Biology, Vanderbilt University, Nashville, TN

21. Modeling capillary phenomena in porous glasses and sol-gel materials.
Lev D. Gelb*, Rafael Salazar, Niny Z. Rao, Brian C. Barnes
Department of Chemistry, Washington University in St. Louis, St. Louis, MO

22. Methods for Modeling Metals: Completing the General Force Field.
Kevin E. Gilbert* and Benjamin P. Hay
Serena Software, Bloomington, IN, Pacific Northwest National Laboratory, Richland, WA

23. Refinements of anisotropic, separable, polarizable molecular mechanics. Towards a reproduction of each individual contribution of the Hartree-Fock intermolecular interaction energies. Applications to multiply hydrogen-bonded complexes and to complexes of polycoordinated divalent cations.
Nohad Gresh*, Jean-Philip Piquemal, Claude Giessner-Prettre
(JPP, CGP) Laboratoire de Chimie Theorique, Universite Pierre-et-Marie-Curie (NG), Laboratoire de Pharmacochimie Moleculaire et Cellulaire, Universite Rene-Descartes, Paris, France

24. Conformational Preferences of Solvated Alanine Dipeptide Determined from Simulations with a Polarizable Force Field.
Alan Grossfield*, Pengyu Ren and Jay W. Ponder
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO

25. QM/MM Simulations on Macrophomate Synthase: Diels-Alder versus Michael-Aldol Reaction Mechanism.
Cristiano Ruch Werneck Guimaraes*, Marina Udier-Blagovic, and William L. Jorgensen
Department of Chemistry, Yale University, New Haven, CT

26. Development of an improved four-site Water model for bio-molecular simulations: TIP4P-EW.
Hans Horn* (1), William C. Swope (1), Jed W. Pitera (1), Jeffry D. Madura (2), Thomas J. Dick (2), Greg L. Hura (3), Teresa Head-Gordon (3)
(1) IBM Almaden Research Center, San Jose, CA, (2) Duquesne University, Pittsburgh, PA, (3) University of California, Berkeley, CA

27. Structure and Dynamics of Phospholamban in Solution and in Membrane Bilayer: Computer Simulations.
Yao Houndonougbo* (1), Krzysztof Kuczera (1), and Gouri Jas (1)
Higuchi Biosciences Center, University of Kansas, Lawrence, KS., (2) Department of Chemistry and Department of Molecular Biosciences, University of Kansas, Lawrence, KS

28. Pathways of Nitrobenzene reduction by Iron (II) compounds. A DFT Study.
Olexandr Isayev* (1), Leonid Gorb (1), Igor Zilberberg (2) and Jerzy Leszczynski (1)
(1) Computational Center for Molecular Structure and Interaction, Jackson State University, Jackson, MS 39217, (2) Boreskov Institute of Catalysis, Novosibirsk 630090, Russia

29. Effect of ions on the dipole moment and electronic properties of water: An ab initio molecular dynamics study.
Ivaylo Ivanov* (1), Simone Raugei (2) and Michael L. Klein (1)
(1) Department of Chemistry, University of Pennsylvania, Philadelphia, PA, (2) SISSA, Via Beirut 4, 34014 Trieste, Italy

30. Calculation of Absolute Binding Free Energies for FKBP Ligands.
Guha Jayachandran* (1), Michael R. Shirts (2), Christopher D. Snow (3), and Vijay S. Pande (2,3,4)
(1) Computer Science Department, Stanford University, (2) Chemistry Department, Stanford University, (3) Biophysics Program, Stanford University, (4) Structural Biology Department, Stanford University, Stanford, CA

31. Accurate Prediction of pKa Values in Water with a Polarizable Force Field.
George A. Kaminski*
Department of Chemistry, Central Michigan University, Mount Pleasant, MI

32. On the Mode of Inhibition of alpha-Mannosidases by Mannostatin A and Aminocyclopentitetrol.
Sameer P Kawatkar*, Robert J. Woods, Geert-Jan Boons
Complex Carbohydrates Research Center, University of Georgia, Athens, GA

33. Gemini Surfactants at the Air/Water Interface: A Molecular Dynamics study.
Ekta Khurana*, Steven O. Nielsen, Michael L. Klein
Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, PA

34. Predictions of membrane protein structures by molecular simulations in generalized ensemble.
Hironori Kokubo* (1) and Yuko Okamoto (1,2)
(1) Institute for Molecular Science, Okazaki, Aichi, Japan, (2) The Graduate University for Advanced Studies, Okazaki, Aichi, Japan

35. Quantum Mechanical Models of the Vanadium Dependent Haloperoxidases.
Joslyn Yudenfreund Kravitz*, Heather A. Carlson and Vincent L. Pecoraro
Department of Chemistry, University of Michigan (all) and College of Pharmacy, University of Michigan (Carlson only), Ann Arbor, MI

36. Hydrophobic hydration: A comparison of TIP4P-Ew with other water model.
Peter Krouskop* (1), Aliaksei Krukau (2), Dietmar Paschek (2), and Jeffry Madura (1)
(1) Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA, (2) Department of Physical Chemistry, University of Dortmund, Dortmund, Germany

37. Molecular Orbital Theory Study on Surface Complexation Structures of Bacterial Extracellular DNA to Fe-hydroxides.
Kideok D. Kwon*, James D. Kubicki
Dept. of Geosciences, Pennsylvania State University, University Park, PA

38. Searching for the minimum energy path in the sulfuryl transfer reaction catalyzed by human Estrogen sulfotransferase.
Ping Lin* and Lee G. Pedersen
Department of Chemistry, University of North Carolina at Chapel Hill, NC

39. A Combined QM/MM study on the N-terminal Auto-cleavage of SARS Coronavirus Main Proteinase.
Shuhua Ma* and Jiali Gao
Department of Chemistry, University of Minnesota, Minneapolis, MN

40. What is your Confidence in your Predictions?: Assessing and Ensuring Prediction Confidence with Virtual Screening Models.
Charles J. Manly*, Daniel Severance, Joseph Ochterski
Neurogen Corporation, Branford, CT

41. Sampling Heterogeneous Response of Protein Structure to Residue Protonation and Cofactor Oxidation by Multi-Conformation Continuum Electrostatics (MCCE).
Junjun Mao*, Yifan Song, Marilyn Gunner
Department of Physics, City College of New York, New York, NY

42. Low Earth Orbit for Theorists O (3P) + graphite by Two Approaches.
Natasa Mateljevic* and J.C. Tully
Yale University, New Haven, CT

43. Protein Behavior Under Mass-Spectroscopy Conditions.
Tim Meyer*, Xavier de la Cruz, and Modesto Orozco
University of Freiburg, University of Barcelona, Barcelona, Spain

44. Permeation and Gating in Proteins: Kinetic Monte Carlo Reaction Path Following.
Gennady V. Miloshevsky* and Peter C. Jordan
Department of Chemistry, Brandeis University, Waltham, MA

45. Localization of the Antimitotic Peptide and Depsipeptide Binding Site on Beta-tubulin.
Arpita Mitra* and David Sept
Center for Computational Biology, Washington University in St. Louis, St. Louis, MO

46. Discrete-state Constant pH Molecular Dynamics in Generalized Born Implicit Solvent.
John Mongan* (1,2), David A. Case (1,3) and J. Andrew McCammon (1,2,4,5)
(1)The Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, (2) Bioinformatics Program, University of California at San Diego, (3) Department of Molecular Biology, The Scripps Research Institute, (4) Department of Chemistry and Biochemistry, University of California at San Diego, (5) Howard Hughes Medical Institute

47. Effects of Enzyme Dynamics on Haloalkane Dehalogenase Catalyzed Reaction: Combined QM/MM Study.
Kwangho Nam*, Xavier Prat-Resina, Mireia Garcia-Viloca, Lakshmi S. Devi-Kesavan, and Jiali Gao
Department of Chemistry, University of Minnesota, Minneapolis, MN

48. A Dynamic Explanation of Catalysts by hPNP through QM/MM and QM/MM-MD Methods.
Sara Nunez*, Vern L. Schramm and Steven D. Schwartz
Albert Einstein College of Medicine, New York, NY

49. Incorporating variable dielectric environments into the Generalized Born model.
Alexey Onufriev*, Grigori Sigalov, Peter Scheffe
Computer Science Department, Virginia Tech, Blacksburg, VA

50. Many relative free energies of base pairing and stacking from a few simulations of DNA.
Chris Oostenbrink* and Wilfred van Gunsteren
Physical Chemistry, Swiss Federal Institute of Technology, Zurich, Switzerland

51. Detailed balance and equilibrium in mixed quantum-classical molecular dynamics.
Priya V. Parandekar* and John C. Tully
Department of Chemistry, Yale University, New Haven, CT

52. Polarizable Potentials for Proteins: Development and Application to Small Proteins/Peptides In Polarizable Solvent.
Sandeep Patel* and Charles L. Brooks, III
The Scripps Research Institute, Department of Molecular Biology, La Jolla, CA

53. Vibrational Circular Dichroism: Absolute Configuration Determination.
Linda Phillips*, Steve Gozo, and Jack Gougoutas
Bristol-Myers Squibb Company, Princeton, NJ

54. Binding of the VCA domains of WASp to Arp2/3 complex and Actin.
Aravind R. Rammohan* (1), Andrew C. Michaels (1) and David Sept (1,2)
(1) Biomedical Engineering, (2) Center for Computational Biology, Washington University St. Louis, MO

55. The AMOEBA Polarizable Atomic Multipole Force Field for Proteins Model and Parameterization.
Pengyu Ren* and Jay W. Ponder
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO

56. Reactions with implications in biology: The role of Melatonin as a free radical scavenger; Julia E. Rice* (1), Cesar Mejia (2), Timothy Lee (3), Martin Head-Gordon (2)
(1) IBM Almaden Research Center, San Jose, CA, (2) Dept. of Chemistry, Univ. California at Berkeley, Berkeley, CA, (3) NASA Ames Research Center, Moffett Field, CA

57. Free energy calculations for enzymatic reactions.
Thomas H. Rod*, Patrik Rydberg, and Ulf Ryde
Department of Theoretical Chemistry, Lund University, Lund, Sweden

58. Force-field parameters based on Protein Data Bank.
Yoshitake Sakae* (1) and Yuko Okamoto (2,3)
(1) Graduate School of Science and Center for Quantum Life Sciences, Hiroshima University, Japan, (2) Department of Theoretical Studies, Institute for Molecular Science, Japan, (3) Department of Functional Molecular Science, The Graduate University for Advanced Studies, Japan

59. Trans Influence in Six Coordinate Co2+ with Biologic Ligands: A DFT Study.
Ann Schmiedekamp*
Pennsylvania State University, Abington College, Abington, PA

60. Electron Propagator Calculations of Photoionization Cross Sections and Angular Dependencies.
G.M. Seabra* (1), I. Kaplan (2), J.V. Ortiz (1) and V.G. Zakrzewski (1)
(1) Department of Chemistry, Kansas State University, Manhattan, KS

61. Hydration free energies using a series of water models: A test case for efficient free energy methods.
Michael R. Shirts* and Vijay S. Pande
Stanford University, Stanford, CA

62. Temperature Dependence of Helix Stability Study by Replica Exchange Simulations.
Kun Song* (1), Neils Andersen (2), Carlos Simmerling (1)
(1) Chemistry Department, Stony Brook University, (2) Chemistry Department, University of Washington, Seattle, WA

63. Can ab initio calculations help in combinatorial library design?.
David Spellmeyer*
IBM Almaden Research Center, San Jose, CA

64. Coarse-grain molecular dynamics simulations of hydraphile cation translocation across a lipid bilayer.
Goundla Srinivas* and Michael L Klein
Department of Chemistry, University of Pennsylvania, Philadelphia, PA

65. Diffusion Calculations of Simulated Lipid-Cholesterol Bilayers.
Frank Suits* (1), Michael C. Pitman (1), Scott E. Feller (2)
(1) IBM T. J. Watson Research Center, Yorktown Heights, NY, (2) Department of Chemistry, Wabash College, Crawfordsville, IN

66. Optimized Radii for PB Continuum Solvent Calculations.
Jessica M.J. Swanson*, Stewart Adcock, and J. Andrew McCammon (1)
Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, and (1)Department of Pharmacology, University of California at San Diego, La Jolla, CA

67. Controlling Reactivity within Nanoporous Carbons: Monte Carlo Simulations.
C. Heath Turner*
University of Alabama, Department of Chemical and Biological Engineering, Tuscaloosa, AL

68. Interaction of halothane with alpha, delta-subunits of acetylcholine receptor: A molecular dynamics study.
Satyavani Vemparala* and Michael L. Klein
University of Pennsylvania, Philadelphia, PA

69. Hierarchical Database Screenings for HIV-1 Reverse Transcriptase Using a Pharmacophore Model, Rigid Docking, Solvation Docking and MM-PB/SA.
Junmei Wang*, Xinshan Kang, Irwin D. Kuntz and Peter A. Kollman
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA

70. Principal Mode Analysis: Where Chemometrics and Physical Chemistry Meet.
Ralph A. Wheeler*, Haitao Dong, and Scott E. Boesch
Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK

71. Ab initio QM/MM studies of enzyme reactions.
Yingkai Zhang*
Department of Chemistry, New York University, New York, NY

72. Performance comparison of Ewald and P3ME methods on Blue Gene/L supercomputer.
Yuri Zhestkov*, Maria Eleftheriou, Blake G. Fitch, Aleksandr Rayshubskiy, Robert S. Germain
IBM T. J. Watson Research Center, Yorktown Hts., NY


Additional Posters

73. Isotropic Periodic Simulation Method.
X. Wu and Bernie R. Brooks*
National Institutes of Health, Bethesda, MD

74. Molecular Simulations and Information Theory.
G. La Penna* (1,2), A. Perico (1), S. Morante (3), and G.C. Rossi (3)
(1) National Research Council, Institute for Macromolecular Studies, Genova, Italy, (2) Magnetic Resonance Center, Florence, Italy, (3) Department of Physics, University of Rome - Tor Vergata and INFM, Rome, Italy


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