Conference Program
 
Computational Chemistry
New Computational Tools For 21st Century Chemistry
July 27 - August 1, 2008
Mount Holyoke College
South Hadley, MA
Chair:
Jed W. Pitera

Vice Chair:
Walter Thiel

The Computational Chemistry GRC has been held biennially since 1986, with chairs alternating between academia and industry. The conference draws a mix of participants from industry, academia, and government covering the full spectrum of computational chemistry -- from ab initio quantum chemistry and quantum dynamics through classical simulation of liquids, biopolymers and materials to docking, virtual screening, and cheminformatics. The 2008 Conference will keep to the traditional GRC format: talks and posters will focus on new, unpublished work; extensive time will be set aside for discussion; and poster sessions will allow participants to show their work and discuss it in detail.

The 2008 conference program will focus on new computational chemistry methods for industrial applications in drug discovery, materials science, and nanotechnology. In addition to general sections on quantum mechanics (topics such as dispersion and local hybrid methods in DFT), classical simulation (focusing on sampling methods and free energy calculations), and cheminformatics, special sections are planned for “Physical Methods in Docking”, “Open Boundary Multiscale Modelling” and “Biomolecular Electrostatics”.


Contributors

SUNDAY
2:00 pm - 11:00 pmArrival and Check-in
6:00 pmDinner
7:30 pm - 7:40 pmWelcome / Introductory Comments by GRC Site Staff
7:40 pm - 8:30 pm Keynote Session: Simulating Rates of Biological Processes
Discussion Leader: Jed W. Pitera (IBM Research)
7:40 pm - 8:20 pm J. Andrew McCammon (UCSD)
"Rate Processes in Biophysics: From the Molecule to the Cell"
8:20 pm - 8:40 pm Discussion
8:40 pm - 9:30 pm Biomolecular Electrostatics I
Discussion Leader: Darrin York (U. Minnesota)
8:40 pm - 9:15 pm Nathan Baker (Washington University - St. Louis)
"Assessing the performance of continuum models for nonpolar solvation"
9:15 pm - 9:30 pm Discussion
9:30 pm - 10:30 pm Reception
MONDAY
7:30 am - 8:30 amBreakfast
8:45 amGroup Photo
9:15 am - 12:30 pm Biomolecular Electrostatics II
9:15 am - 9:35 amDiscussion Leader: Darrin York (U. Minnesota)
9:45 am - 10:10 am Jana Khandogin (U. Oklahoma)
"Electrostatic interactions in the unfolded states of proteins"
10:10 am - 10:20 am Discussion
10:20 am Coffee Break
10:50 am - 11:25 am Matt Jacobson (University of California, San Francisco)
"Electrostatic switches in proteins"
11:25 am - 11:40 am Discussion
11:40 am - 12:15 pm Celeste Sagui (NCSU)
"Accurate electrostatics for organic molecules"
12:15 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session A
6:00 pmDinner
7:30 pm - 9:30 pm Open Boundary Multiscale Modelling
7:30 pm - 7:45 pmDiscussion Leader: William Swope (IBM Research)
7:45 pm - 8:10 pm Donald Truhlar (U. Minnesota)
"Open Boundary approaches for QM/MM calculations"
8:10 pm - 8:20 pm Discussion
8:20 pm - 8:45 pm Luigi Delle Site (MPI-Polymers, Mainz)
"The Adaptive Resolution Simulation Scheme (AdResS): Basic Principles and Applications"
8:45 pm - 8:55 pm Discussion
8:55 pm - 9:20 pm Bernd Ensing (U. Amsterdam)
"Construction of an adaptive atomistic / coarse-grained molecular dynamics method"
9:20 pm - 9:30 pm Discussion
TUESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm Statistics and Sampling
9:00 am - 9:20 amDiscussion Leader: David Kofke (SUNY-Buffalo)
9:20 am - 9:55 am Wei Yang (Florida State University)
"Quantitative Alchemical Free Energy Simulations: Are We There Yet?"
9:55 am - 10:10 am Discussion
10:10 am Coffee Break
10:30 am - 11:10 am Aaron Dinner (University of Chicago)
"Automated analysis of path sampling simulations reveals a mechanism for DNA damage detection"
11:10 am - 11:25 am Discussion
11:25 am - 12:15 pm Daniel Zuckerman (University of Pittsburgh)
"A blind, automated procedure for estimating the effective sample size of a molecular simulation"
12:15 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session A
6:00 pmDinner
7:30 pm - 9:30 pm Advances in Quantum Chemistry
Discussion Leader: Walter Thiel (MPI-Mülheim)
7:30 pm - 8:00 pmTakao Tsuneda (U. Tokyo)
"Long-range corrected density functional theory and its progress"
8:00 pm - 8:10 pm Discussion
8:10 pm - 8:40 pm Julia Rice (IBM Research)
"A unified theory of periodic boundary condition QM/MM"
8:40 pm - 8:50 pm Discussion
8:50 pm - 9:20 pm Valentino Cooper (Rutgers)
"Applications of the van der Waals density functional: DNA and metal organic framework materials"
9:20 pm - 9:30 pm Discussion
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm Advances in (Bio)molecular Simulation
9:00 am - 9:20 amDiscussion Leader: Alan Grossfield (U. Rochester)
9:20 am - 9:55 am Terry P. Lybrand (Vanderbilt)
"Molecular simulation of cyclooxygenase-inhibitor complexes: Insights into inhibitor binding and selectivity"
9:55 am - 10:10 am Discussion
10:10 am Coffee Break
10:30 am - 11:10 am Juan de Pablo (University of Wisconsin, Madison)
"Coarse Grain Simulations of Complex Materials - Polymers, Copolymers and Liquid Crystals"
11:10 am - 11:25 am Discussion
11:25 am - 12:15 pm Modesto Orozco (IRB Barcelona)
"From atomistic to genomic scale simulations"
12:15 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session B
6:00 pmDinner
7:30 pm - 9:30 pm Industrial Applications of Computational Chemistry
7:30 pm - 7:45 pmDiscussion Leader: Terry Stouch (Springer/JCAMD)
7:45 pm - 8:20 pm Theresa Johnson (Pfizer)
"Data, data everywhere and not a drop of information: Leveraging high quality internal kinase data into usable information"
8:20 pm - 8:30 pm Discussion
8:30 pm - 9:05 pm Alice Glättli (BASF)
"Molecular Modelling for Crop Protection"
9:05 pm - 9:20 pm Discussion
THURSDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm Computation of Spectroscopic Observables
9:00 am - 9:10 amDiscussion Leader: Jed Pitera (IBM Research)
9:10 am - 9:50 am Alexei Stuchebrukhov (University of California, Davis)
"Computational studies of redox-driven proton pump cytochrome c oxidase"
9:50 am - 10:05 am Discussion
10:05 am Coffee Break
10:35 am - 10:55 am Stefano Tonzani (Northwestern University)
"A practical approach for DNA spectra and dynamics in solution"
10:55 am - 11:05 am Discussion
11:05 am - 11:25 am Deniz Sezer (MPI-Biophysics)
"Calculation of ESR spectra from MD simulations"
11:25 am - 11:35 am Discussion
11:35 am - 12:15 pmAndrei Tokmakoff (MIT)
"Simulations of the Infrared Spectroscopy of Water and Proteins"
12:15 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session B
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 Physical Methods in Docking and Drug Discovery
Discussion Leader: Michelle Lamb (Astra-Zeneca)
7:30 pm - 8:10 pm Geoff Skillman (Openeye)
"SAMPL: A true(r) test of modeling"
8:00 pm - 8:10 pm Discussion
8:10 pm - 8:40 pm Iris Antes (MPI-Informatik)
"Inclusion of protein flexibility in molecular docking"
8:40 pm - 8:50 pm Discussion
8:50 pm - 9:20 pm B. Woody Sherman (Schrödinger)
"Accurate treatment of protein flexibility, polarized charges, and explicit waters in docking and scoring"
9:20 pm - 9:30 pm Discussion
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDeparture