Computational Biology of the Cell - The Next Decade

Program

Lectures held in the Beckman Auditorium, Room 1025 (first floor, west end of building) of the Beckman Institute

MONDAY, September 21, 2009

11:45-1:00	Registration and lunch
1:00-1:15	Klaus Schulten and Tamer Başar (Director, Beckman Institute), "Welcome" (gallery)

Session I: General Challenges (gallery) - Chair, Martin Gruebele

1:15-1:45	Michael L. Klein “Computer Simulation: Challenges for the Next Decade and Beyond”
1:45-2:15	J. Andrew McCammon “Prospects for Enhanced Sampling in Molecular Dynamics”
2:15-2:45	Petros Koumoutsakos “Computational Biology = ? + Biology”
2:45-3:05	DISCUSSION
3:05-3:30	BREAK (Beckman Garden or Room 1005)

Session II: Towards Subcellular and Cellular Assemblies and Processes (gallery, gallery) - Chair, Ido Golding

3:30-4:00	Helmut Grubmüller “Simulation of Life at the Meso-scale”
4:00-4:30	Chris Chipot "Gliding on Multidimensional Free Energy Landscapes Using Time-dependent Biases on Collective Variables" Gerhard Hummer's lecture was moved to Wednesday at 11:00 am
4:30-5:00	Gregory Voth “Systematic Multiscale Modeling of Biomolecular Systems”
5:00-5:20	DISCUSSION
5:20-5:45	BREAK (garden or 1005)
5:45-6:15	Steve Harvey “The Puzzle of Viral Packaging: What We Know, and What Still Puzzles Us”
6:15-6:45	Charles L. Brooks “Building Virus Capsids: from Design Principles Assembly Mechanisms”
6:45-7:05	DISCUSSION
7:05-7:30	RECEPTION
7:30-	DINNER [Klaus Schulten dinner talk, “Can Modelers be Nice to Each Other?" (gallery)]

TUESDAY, September 22, 2009

Session III: Milliseconds and Beyond (gallery, gallery) - Chairs, Thom Dunning and Wen-Mei Hwu

8:30-9:00	David E. Shaw “Unsupported Speculation on Future Opportunities and Challenges for Millisecond-Scale Molecular Dynamics Simulations”
9:00-9:30	Laxmikant Kale “Challenges and Opportunities in Simulations of Biomolecular Systems Beyond Petascale”
9:30-10:00	Angel E. Garcia “Microsecond Simulations of the Detailed folding/unfolding Thermodynamics of Proteins”
10:00-10:20	DISCUSSION
10:20-10:45	BREAK (garden or 1005)
10:45-11:15	Vijay Pande “A Paradigm Shift for Simulation: Viewing Simulations from a Statistical Perspective”
11:15-11:45	Benoit Roux “Treatment of Slow and Complex Conformational Transitions”
11:45-12:15	Zaida Luthey-Schulten “Challenges in Simulating RNA Systems”
12:15-12:35	DISCUSSION
12:35-1:45	LUNCH

Session IV: The Big Picture (gallery) - Chair, Steve Sligar

1:45-2:15	Jeffrey Skolnick “New Approaches to Drug Discovery and Cancer Metabolomics”
2:15-2:45	Valerie Daggett “Dynameomics”
2:45-3:15	Thorsten Ritz “Can We Use Physics to find Laws of Biology? Towards Quantifying Biological Function in the Context of Evolutionary Constraints”
3:15-3:35	DISCUSSION
3:35-4:00	BREAK (garden or 1005)

Session V: Hand in Hand With Experiment (gallery) - Chair, Taekjip Ha

4:00-4:30	Angela Gronenborn “Structural Studies of HIV-1 capsid: Synergy Between cryo-EM, NMR and X-ray”
4:30-5:00	Andrej Sali “Computational Integration of Diverse Structural and Kinetic Data for Visualizing Macromolecular Assemblies and Processes”
5:00-5:30	Dave Thirumalai “Universality and Specificity in Protein Folding”
5:30-6:00	Olga Dudko “Single Molecules Under Force: Kinetics of Rupture in 1D and Beyond”
6:00-6:20	DISCUSSION
6:20-6:50	RECEPTION
6:50-	DINNER

WEDNESDAY, September 23, 2009

Session VI: Special Systems (gallery) - Chair, Greg Timp

9:00-9:30	Richard W. Pastor “Why Pure Lipid Systems Remain Challenging”
9:30-10:00	Emad Tajkhorshid “Simulating The Art of Active Transport Across the Cellular Membrane”
10:00-10:30	Alek Aksimentiev “Molecular Modeling in Nanobiotechnology”
10:30-11:00	Break (in garden or 1005)
11:00-11:30	Gerhard Hummer “Protein-Protein Binding: from Encounter Complexes to Multi-Protein Assemblies”
11:30-12:00	Klaus Schulten “Molecular Assembly and Teamwork - Bridge Between Inanimate and Animate Matter”
12:00-1:00	LUNCH

Note: program subject to change.