GRC 2004 Comp Chem Review Russell talks about GRC Computational Chemistry 2004 mol_sims Discussion Group GT Schools of Biology and Chemistry et al July.

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Presentation transcript:

GRC 2004 Comp Chem Review Russell talks about GRC Computational Chemistry 2004 mol_sims Discussion Group GT Schools of Biology and Chemistry et al July 20, 2004

GRC 2004 Comp Chem Review 2 Requests Philippe Hunenberger (ETH) “New schemes for evaluating electrostatic interactions in molecular systems under periodic boundary conditions” Algorithms for GROMOS electrostatic force field determination, in next Rev. of that software

GRC 2004 Comp Chem Review 3 Hunenberger (p2)

GRC 2004 Comp Chem Review 4 Hunenberger (p3)

GRC 2004 Comp Chem Review 5 Requests Anthony Stone (Cambridge University) "Ab initio calculation of intermolecular potential energy surfaces"

GRC 2004 Comp Chem Review 6 Jiali Gao Jiali Gao (U. Minn.) [Michael Zerner Memorial Lecture] "Dynamics of Enzymatic Reactions from Combined QM/MM Simulations"

GRC 2004 Comp Chem Review 7

8 Protein Phenomena Session Joan Shea: “Role of Frustration in Chaperonin- Mediated Protein Folding”: –How cellular environments affect protein folding –Effects on protein folding: pH, temp, crowding –Aggregates of mis-folded proteins in diseases like Parkinson’s –Chaperonins recognize misfolded proteins by exposed hydrophobic patches –GroEL: 10sec time for ATP hydrolysis

GRC 2004 Comp Chem Review 9 Joan Shea (p2) Three theories to how chaperone –1) Populating trapped states –2) Passive mechanism (inefficient b/c protein aggregates; “Folding in the cage”) –3) Non-cycling single GroEL, prot. outside cavity, no confinement effects T_m > T_f: –Temp of min folding time greater than folding temp

GRC 2004 Comp Chem Review 10 Matthew Tirrell Matthew Tirrell (U. Calif. Santa Barbara) "Frontiers of Computational Chemistry: Ideas from the National Research Council Report" Edited two books: –Beyond the Molecular Frontier –National Security and Homeland Defense: Challenges for the Chemical Sciences in the 21st Century (2002) Office of Information and Communications

GRC 2004 Comp Chem Review 11

GRC 2004 Comp Chem Review 12

GRC 2004 Comp Chem Review 13 End Requests … now for the good stuff

GRC 2004 Comp Chem Review 14 Maria Kurnikova Maria Kurnikova (Carnegie-Mellon University) "Hierarchical Methods for Modeling Membrane Protein Structure and Function"

GRC 2004 Comp Chem Review 15 Maria Kurnikova (p2)

GRC 2004 Comp Chem Review 16

GRC 2004 Comp Chem Review 17 Yuko Okamoto Yuko Okamoto (Institute for Molecular Science, Okazaki, Aichi, Japan) "Protein Force Fields: Comparisons and Improvements" Replica-Exchange MD (REMD) –MUCAREM, REMUCA

GRC 2004 Comp Chem Review 18

GRC 2004 Comp Chem Review 19 Martin Head-Gordon Faster methods for electron correlation? New MP2 methods? Pulay-Saebo Model BSSE – Basis Set Superposition Error Resolution of Identity function smaller than all possible products DFT does not do dispersion Martin Head-Gordon (U. Calif. Berkeley) "Localized orbitals and fast correlation methods"

GRC 2004 Comp Chem Review 20 Questions Can Density Functional Theory (DFT) fold proteins? Self-interaction of DFT is hopeless? Fast Multipole vs. Ewald? GAMESS-US vs. GAMESS-UK?

GRC 2004 Comp Chem Review 21