Workshop I: Multiscale Modeling in Soft Matter and Bio-Physics - IPAM

Workshop I: Multiscale Modeling in Soft Matter and Bio-Physics

Part of the Long Program Bridging Time and Length Scales in Materials Science and Bio-Physics
September 26 - 30, 2005

Schedule

All times in this Schedule are Pacific Time (PT)

Monday, September 26, 2005

Morning Session

From atomistic detail to (macro) molecular motion
08:00-08:50
Check-In/Light Breakfast (Hosted by IPAM)
08:50-09:00
Welcome and Opening Remarks
09:00-09:50
Klaus Schulten (University of Illinois at Urbana-Champaign)
Multiscale simulations of DNA-protein, and protein-lipid complexes
09:50-10:20
Break
10:20-11:10
Joel Ireta (Universidad Autonoma Metropolitana)
IInfinite polypeptides: An approach to study the secondary structure of proteins
11:10-12:00
Joan-Emma Shea (UC Santa Barbara)
Design of Inhibitors of Alzheimer Amyloid-ß Peptide Aggregation

Afternoon Session

12:00-14:00
Lunch (on your own)
The coarse-graining approach: new methods and perspectives
14:00-14:50
William Gelbart (UCLA)
Chain translocation in a biological context
14:50-15:40
John Maddocks (École Polytechnique Fédérale de Lausanne (EPFL))
Parametrizations of Coarse-Grain Sequence-Dependent Models of DNA Mechanics
15:40-16:10
Break
16:10-17:00
Alexander Lyubartsev (University of Stockholm)
Invese Monte Carlo method for determination of effective potentials for coarse-grained models
17:00-19:00
Wine & Cheese Reception and Poster Session

Tuesday, September 27, 2005

Morning Session

Multiscaling and collective behaviors: insights from analytical theories
08:30-08:50
Continental Breakfast
09:00-09:50
Michael Schick (University of Washington)
A comparison of two routes to membrane fusion
09:50-10:20
Break
10:20-11:10
Anatoly Kolomeisky (Rice University)
Growth Dynamics of Cytoskeleton Proteins: Multiscale Theoretical Analysis
11:10-12:00
Steve Plotkin (University of British Columbia)
How do many-body interactions and transition state structure determine how a protein folds?

Afternoon Session

12:00-14:00
Lunch (on your own)
Water interactions and hydrophobic effect: an intrinsically multiscale problem
14:00-14:50
Monte Pettitt (University of Houston)
Hydrophobicity at different length scales
14:50-15:40
Philip Pincus (UC Santa Barbara)
Multi-Scale Views of the Hydrophobic Interaction
15:40-16:10
Break
Emerging techniques to combine multiple resolutions
16:10-17:00
Daniel Zuckerman (University of Pittsburgh)
Exploring Algorithm Space: Resolution Exchange Simulation and Other Exchange Variants
17:00-17:50
Zan Luthey-Schulten (University of Illinois at Urbana-Champaign)
Using Evolutionary Concepts to Study the Function and Folding of Proteins

Wednesday, September 28, 2005

Morning Session

From atomistic detail to (macro) molecular motion
08:30-09:00
Continental Breakfast
09:00-09:50
Angel Garcia (Rensselaer Polytechnic Institute)
Theoretical Studies of Pressure effects on folding/unfolding of proteins
09:50-10:20
Break
10:20-11:10
Mark Tuckerman (New York University)
Enhanced conformational sampling via novel variable transformation and very large time-step molecular dynamics
11:10-12:00
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Afternoon Session

12:00-18:00
Excursion to the Getty Center: lunch and afternoon visit

Thursday, September 29, 2005

Morning Session

Water interactions and hydrophobic effect: an intrinsically multiscale problem
08:30-08:50
Continental Breakfast
09:00-09:50
Jeffery Saven (University of Pennsylvania)
Solvation and the design and engineering of folding molecules
09:50-10:20
Break
10:20-11:10
Ken Dill (University of California, San Francisco)
Statistical mechanical models of water and aqueous solvation
11:10-12:00
Nathan Baker (Washington University in St. Louis)
Multiscale methods for biomolecular electrostatics and diffusion

Afternoon Session

12:00-14:00
Lunch (on your own)
Multiscaling and collective behaviors: insights from analytical theories
14:00-14:50
Alexander Grosberg (University of Minnesota, Twin Cities)
How proteins find their target on DNA? Delbruck model revisited
14:50-15:40
Peter Wolynes (University of California, San Diego (UCSD))
Recent Successes of Energy Landscape Theory of Protein Folding
15:40-16:10
Break
16:10-17:00
David Wales (University of Cambridge)
Navigating the Energy Landscape: Pathways and Rates
17:00-17:50
Mrs. Bruinsma (Institute for Pure and Applied Mathematics)
Physical Models of Viruses

Friday, September 30, 2005

Morning Session

Emerging techniques to combine multiple resolutions
08:30-08:50
Continental Breakfast
09:00-09:50
Steve Nielsen (University of Texas at Dallas)
Coarse grained to atomistic mapping algorithm: a tool for multiscale simulations
09:50-10:20
Break
10:20-11:10
Mike Thorpe (Arizona State University)
Flexibility in Biomolecules: Beyond Molecular Dynamics
11:10-12:00
Kurt Kremer (Max Planck Institute for Polymer Research)
Linking Structure and Properties: Multiscale Simulations of Macromolecules

Afternoon Session

12:00-14:00
Lunch (on your own)
14:00-14:50
Arieh Warshel (University of Southern California)
Multiscale Modeling of Biological Functions
14:50-15:40
Panel Discussion
15:40-16:10
Break
16:10-17:50
Panel Discussion
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