Conference Program
 
COMPUTATIONAL CHEMISTRY

October 8-13, 2006
Les Diablerets Conference Center
Les Diablerets, Switzerland

Chair:
Wilfred F. Van Gunsteren

Vice Chair:
Jed W. Pitera

The GRC on Computational Chemistry has been held every second year since 1986. The chair is alternatingly a scientist from academia and from industry. Because computational chemistry represents too diverse a field of research to cover within 5 days, the conferences focus on different areas from year to year. In 2006 the focus will be on methodology for (bio)molecular modeling and simulation: quantum-mechanics and dynamics, hybrid QM/MM, force-field development, coarse-graining, sampling methods. Furthermore, applications in drug design, treatment of complex systems such as membranes, simulation of reactions, etc. will also be discussed. Most of the past conferences were held in New England, only the 1998 one took place in Oxford, UK. In order to encourage European participation but also as an incentive to visit Europe, the 2006 conference will be held in Switzerland at a beautiful location in the Swiss Alps, Les Diablerets, easily reachable by train or car from Geneva.

The format is the usual GRC one: speakers should talk about unpublished work, with plenty of time reserved for discussion, participants will be a mix of researchers from industry and academia, of different ages, backgrounds, and from different countries. Poster sessions will offer participants the opportunity to show their work and to initiate discussion.


CONTRIBUTORS

Novartis
Genentech Inc fund.


SUNDAY
4:00 pm - 9:00 pmArrival and Check-in
6:00 pmDinner
7:30 pm - 7:40 pmWelcome / Introductory comments (from the GRC site staff and Wilfred F. van Gunsteren)
7:40 pm - 9:30 pm FORCE FIELDS, POLARIZATION
7:40 pm - 7:45 pmDiscussion Leader: Wilfred F. van Gunsteren (ETH Zürich, Zürich, Switzerland)
7:45 pm - 8:15 pm Alexander D. MacKerell (University of Maryland, Baltimore, USA)
"Polarizable empirical force field based on the classical Drude oscillator model"
8:15 pm - 8:25 pmDiscussion
8:25 pm - 8:55 pm Jay W. Ponder (Washington University Medical School, St. Louis, USA)
"Polarizable force fields: Perspective and personal experience"
8:55 pm - 9:05 pmDiscussion
9:05 pm - 9:25 pm Robert Woods (University of Georgia, Athens, USA)
"Approaches to deriving internally-consistent atomic polarizabilities for use in classical simulations"
9:25 pm - 9:30 pmDiscussion
9:30 pmReception
MONDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm QUANTUM METHODS
(Session in remembrance of Michael Zerner)
9:00 am - 9:15 amDiscussion Leader: Walter Thiel (Max-Planck-Institute, Mülheim, Germany)
9:15 am - 9:45 am Richard A. Friesner (University of Columbia, New York, USA)
"A New Approach To Density Functional Thermochemistry: Empirical Localized Orbital Corrections"
9:45 am - 10:00 amDiscussion
10:00 amGroup Photo / Coffee break
10:30 am - 11:00 am Jürg Hutter (University of Zürich, Zürich, Switzerland)
"Large scale density functional calculations with the Gaussian and augmented-plane wave method"
11:00 am - 11:15 amDiscussion
11:15 am - 11:45 am Dirk Bakowies (ETH Zürich, Zürich, Switzerland)
"Ab initio thermochemistry without empirical corrections"
11:45 am - 12:00 pmDiscussion
12:00 pm - 12:20 pm Reinhold F. Fink (University of Würzburg, Würzburg, Germany)
"Retaining the excitation degree perturbation theory: A well defined multi-reference configuration electron structure method"
12:20 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pm REACTIONS
7:30 pm - 7:45 pmDiscussion Leader: Adrian Mulholland (University of Bristol, Bristol, UK)
7:45 pm - 8:15 pm Arieh Warshel (University of Southern California, Los Angeles, USA)
"Recent advances in simulation of biological functions"
8:15 pm - 8:25 pmDiscussion
8:25 pm - 8:55 pm Bernhard H. Schlegel (Wayne State University, Detroit, USA)
"Exploring potential energy surfaces for biochemical reactions"
8:55 pm - 9:05 pmDiscussion
9:05 pm - 9:25 pm Hans Martin Senn (Max-Planck-Institute, Mülheim, Germany)
"Enzymatic halogenation in the fluorinase: Insights from QM and QM/MM calculations"
9:25 pm - 9:30 pmDiscussion
9:30 pmBar, Poster Session
TUESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm BIOMOLECULAR MODELING
(Session in remembrance of Peter Kollman)
9:00 am - 9:15 am Discussion Leader: Alan E. Mark (University of Queensland, Brisbane, Australia)
9:15 am - 9:45 am Ken A. Dill (University of California, San Francisco, USA)
"Speeding up conformational searching in all-atom folding models"
9:45 am - 10:00 amDiscussion
10:00 amCoffee break
10:30 am - 11:00 am Liu Haiyan (University of Science and Technology, Hefei, China)
"Using free energy surfaces to guide the improvement of models for biomolecular simulations"
11:00 am - 11:15 amDiscussion
11:15 am - 11:45 am Bernard R. Brooks (National Institutes of Health, Bethesda, USA)
"Multi-scale methods for examining macromolecular systems"
11:45 am - 12:00 pmDiscussion
12:00 pm - 12:20 pm Hans-Jörg Limbach (Nestlé Research Center, Lausanne, Switzerland)
"Simulations of malto-oligomer water mixtures"
12:20 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pm DRUG DESIGN, DOCKING
7:30 pm - 7:45 pm Discussion Leader: Peter W. Kenny (AstraZeneca, Cheshire, United Kingdom)
7:45 pm - 8:15 pm Andrew Leach (GlaxoSmithKline Med. Res. Centre, Stevenage, United Kingdom)
"Virtual screening: theory and practice"
8:15 pm - 8:25 pmDiscussion
8:25 pm - 8:55 pm Terry Stouch (J. Computer-Aided Molecular Design, USA)
"Drug design, water, and solvation"
8:55 pm - 9:05 pmDiscussion
9:05 pm - 9:25 pm Andreas H. Göller (Bayer HealthCare AG, Wuppertal, Germany)
"Modelling protein-mediated oxidation of small molecules: A mixed quantum-mechanics and descriptor-based approach"
9:25 pm - 9:30 pmDiscussion
9:30 pmBar, Poster Session
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm SEARCHING, ELECTROSTATICS, FREE ENERGY
9:00 am - 9:15 am Discussion Leader: Philippe H. Hünenberger (ETH Zürich, Zürich, Switzerland)
9:15 am - 9:45 am Andrew E. Torda (University of Hamburg, Germany)
"Statistical scoring functions - not haunted by the ghost of Herrn Boltzmann"
9:45 am - 10:00 amDiscussion
10:00 amCoffee break
10:30 am - 11:00 am Paul Tavan (Ludwig-Maximilian University Munich, Germany)
"Electrostatics of proteins in solvent continua: Newtons third law marries qE-forces. A progress report"
11:00 am - 11:15 amDiscussion
11:15 am - 11:45 am Johan Aqvist (University of Uppsala, Uppsala, Sweden)
"Free energy calculations on the ribosome"
11:45 am - 12:00 pmDiscussion
12:00 pm - 12:20 pm Chris Oostenbrink (Free University of Amsterdam, Amsterdam, The Netherlands)
"Efficient free energy calculations from biomolecular simulations: methodology and applications"
12:20 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:00 pm - 7:30 pmBusiness Meeting
(Nominations for the next Vice Chair; Fill out Conference Evaluation Forms; Discuss future Site & Scheduling preferences; Election of the next Vice Chair)
7:30 pm - 9:30 pm COARSE-GRAINING
7:30 pm - 7:45 pm Discussion Leader: Bojan Zagrovic (ETH Zürich, Zürich, Switzerland)
7:45 pm - 8:15 pm Julian C. Shillcock (Max-Planck-Institute, Potsdam, Germany)
"Mesoscopic simulations of actin filaments, lipid vesicles and nanoparticles"
8:15 pm - 8:25 pmDiscussion
8:25 pm - 8:55 pm Siewert-Jan Marrink (University of Groningen, Groningen, The Netherlands)
"Membrane proteins in action"
8:55 pm - 9:05 pmDiscussion
9:05 pm - 9:25 pm Christine Peter (Max-Planck-Institute, Mainz, Germany)
"Multiscale modeling of photoactive liquid crystalline systems"
9:25 pm - 9:30 pmDiscussion
9:30 pmBar, Poster Session
THURSDAY
7:30 am - 8:30 amBreakfast
8:30 am - 9:00 amBusiness Meeting (continued...)
9:00 am - 12:30 pm APPLICATIONS, MEMBRANES
9:00 am - 9:15 am Discussion Leader: David Beveridge (Wesleyan University, Connecticut, USA)
9:15 am - 9:45 am Gerhard Hummer (National Institutes of Health, Bethesda, USA)
"Protein dynamics: from nanoseconds to microseconds and beyond"
9:45 am - 10:00 amDiscussion
10:00 amCoffee break
10:30 am - 11:00 am Benoit Roux (University of Chicago, Chicago, USA)
"Computation of absolute (standard) binding free energies"
11:00 am - 11:15 amDiscussion
11:15 am - 11:45 am Olle Edholm (Royal Institute of Technology, Stockholm Sweden)
"Monitoring long time dynamic processes in lipid bilayers by molecular dynamics simulations"
11:45 am - 12:00 pmDiscussion
12:00 pm - 12:20 pm Yuji Takaoka (Taisho Pharmaceutical Co., Saitama, Japan)
"Molecular dynamics simulation of phospholipid bilayer membrane under hydrostatic pressure control and surface tension"
12:20 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pm QUANTUM DYNAMICS
7:30 pm - 7:45 pm Discussion Leader: Bill Swope (IBM, San Jose, USA)
7:45 pm - 8:15 pm Irene Burghardt (Ecole Normale Superieure, Paris, France)
"Photochemistry and non-adiabatic quantum dynamics: multiconfigurational methods and effective-mode models for large systems"
8:15 pm - 8:25 pmDiscussion
8:25 pm - 8:55 pm Sara Bonella (University of Rome, La Sapienza, Italy)
"Mixed quantum classical dynamics for systems with many degrees of freedom: Linearization methods and time correlation functions"
8:55 pm - 9:05 pmDiscussion
9:05 pm - 9:25 pm Yolanda A. Small (The Pennsylvania State University, Pennsylvania, USA)
"Hydrogen bonding pathways and hydrogen transfer in dihydrorotate dehydrogenase"
9:25 pm - 9:30 pmDiscussion
9:30 pmBar, Poster Session
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDeparture

Last Updated: October 11, 2006