Lectures

Session 1: Potential Design

“Evaluating Coarse-Grained Protein Structures”
Bob Jernigan, Iowa State University

“Using NMR Data to Evaluate and Improve Empirical Force Fields”
Carlos Simmerling, State University of New York

“1Djury: Fast and Accurate Method for Protein Model Quality Assessment”
Jarek Meller, University of Cincinnati

Session 2: Simulations of Systems in Equilibrium

“Simulations of Small Globular Proteins”
Ulrich H.E. Hansmann, Michigan Technological Institute

“Novel Stochastic-Dynamical Sampling Methods”
Ben Leimkuhler, University of Edinburgh

“X-Pol Potential: From Lifson Molecular Mechanics to a Quantal Force Field for Biomolecular Simulations”
Jiali Gao, University of Minnesota

“A goal-oriented adaptive finite element method for the Poisson-Boltzmann equation”
Steve Bond, University of Illinois at Urbana-Champaign

Session 3: Advances in Hardware and Software

“Millisecond-Long Molecular Simulations of Proteins on the Anton Machine”
D.E. Shaw, D.E. Shaw Research, LLC

“Structure and Parallelization of N-Body Solvers”
Robert Skeel, Purdue University

“Challenges and Opportunities in Simulations of Biomolecular Systems at Petascale and Beyond”
L.V. Kale, University of Illinois at Urbana-Champaign

TBA
Keshav Pingali, ICES, The University of Texas at Austin

Session 4: Soft Matter

“Multiscale Simulation of Biomolecular Assemblies”
Greg Voth, University of Utah

“Computer simulations of protein translocation”
Dmitrii Makarov, UT-Austin

Session 5: Protein Folding and Protein-Protein Interactions

“Molecular Dynamics of T. aquaticus MutS: Interdomain Communication and Allosterism”
David Beveridge, Wesleyan University

“Recent Successes of the Energy Landscape Theory of Protein Folding”
Peter Wolynes, University of California, San Diego

“Calculation of Folding Pathways and Native Structures of Proteins”
Harold Scheraga, Cornell University

“New Approaches to Drug Discovery and Cancer Metabolomics”
Jeff Skolnick, Georgia Tech

Session 6: Nucleic Acids

“Coarse-grained Approaches for Simulating the Chromatin Fiber”
Tamar Schlick, New York University

“Micromechanical Study of DNA-Protein Interactions and Chromosome Structure”
John Marko, Northwestern University

“Analysis, Prediction, and Design of Viral RNA Secondary Structures”
Christine Heitsch, Georgia Tech

“Perils and Promise in Simulation of RNA-Ligand Interaction”
Thomas Cheatham, University of Utah

“The Writhe: A Macromolecular Shape Descriptor”
De Witt Sumners, Florida State University

Session 7: Kinetics and Mechanism

“Theory and Modeling of Reactive Events”
Eric Vanden-Eijnden, Courant Institute

“Insights from All-Atom Simulations of Protein Folding on the Millisecond Timescale and Beyond”
Vijay Pande, Stanford University

“Generalized Replica Exchange Method: Optimal combination of generalized ensemble methods and replica exchange method”
John Straub, Boston University

“Computing Reaction Rates in the Presence of Multiple Energy Barriers”
E. Darve, Stanford

TBA
Giovanni Ciccotti, University of Rome

“Calculating Ion Permeation through Protein Channels”
Rob Coalson, University of Pittsburgh