Molecular Simulations: Algorithms, Analysis, and Applications

May 18 - 22, 2009

Content

Overview

Organizers:

Weinan E	Princeton University
Ron Elber	The University of Texas at Austin
Daan Frenkel	University of Cambridge
Tamar Schlick	New York University

This workshop will bring together mathematicans, chemists, physicists, biologists and researchers from other disciplines whose work pertains to statistical mechanics and molecular dynamics used in simulations of biomolecular, chemical, and liquid or solid state systems. We will consider key aspects of molecular simulations--numerical algorithms, mathematical analysis and applications--paying special attention to problems that call for new methodologies or mathematics.

Relevant topics include sampling methods, methods for free energy calculation, reaction pathways and reaction rates, long-time integration, geometric integrators, trajectory analysis, stochastic and Monte Carlo methods, and Car-Parrinello dynamics. Numerical methodologies, mathematical theory, and applications will be discussed.

Schedule

Monday, May 18, 2009

12:01 am	Morning Chair: Daan Frenkel (University of Cambridge) Afternoon Chair: Giovanni Ciccotti (Università di Roma La Sapienza)
8:15 am - 9:00 am	Registration and coffee	EE/CS 3-180
9:00 am - 9:15 am	Welcome to the IMA Fadil Santosa (University of Minnesota, Twin Cities)	EE/CS 3-180
9:15 am - 9:55 am	Coupled atomistic-continuum methods for fluids	EE/CS 3-180
9:55 am - 10:15 am	Discussion	EE/CS 3-180
10:15 am - 10:45 am	Break	EE/CS 3-176
10:45 am - 11:25 am	Dynamics and thermodynamics of large conformational rearrangements in confined polymers Dmitrii Makarov (The University of Texas at Austin)	EE/CS 3-180
11:25 am - 11:45 am	Discussion	EE/CS 3-180
11:45 am - 2:00 pm	Lunch
2:00 pm - 2:40 pm	Coarse-graining molecular dynamics for crystalline solids Xiantao Li (The Pennsylvania State University)	EE/CS 3-180
2:40 pm - 3:00 pm	Discussion	EE/CS 3-180
3:00 pm - 3:40 pm	Adaptive kinetic Monte Carlo for simulating dynamics in atomic systems Graeme Henkelman (The University of Texas at Austin)	EE/CS 3-180
3:40 pm - 4:00 pm	Discussion	EE/CS 3-176
4:00 pm - 6:30 pm	Reception and Poster Session Poster submissions welcome from all participants Instructions	Lind 400

Tuesday, May 19, 2009

12:01 am	Morning Chair: Ron Elber (University of Texas) Afternoon Chair: Tamar Schlick (New York University)
8:30 am - 9:00 am	Coffee	EE/CS 3-176
9:00 am - 9:40 am	Modeling organic-inorganic interfaces across different scales: Modeling concepts and Applications Luigi Delle Site (Max-Planck Institut für Polymerforschung)	EE/CS 3-180
9:40 am - 10:00 am	Discussion	EE/CS 3-180
10:00 am - 10:40 am	Benard convection by dynamical nonequilibrium molecular dynamics Giovanni Ciccotti (Università di Roma La Sapienza)	EE/CS 3-180
10:40 am - 11:00 am	Discussion	EE/CS 3-180
11:00 am - 11:30 am	Break	EE/CS 3-176
11:30 am - 12:10 pm	Free-energy methods to study conformational transitions and ligand binding to flexible targets Francesco Gervasio (Eidgenössische TH Zürich)	EE/CS 3-180
12:10 pm - 12:30 pm	Discussion	EE/CS 3-180
12:30 pm - 2:00 pm	Lunch
2:00 pm - 2:40 pm	Energy landscapes of clusters, glasses, and biomolecules David Wales (University of Cambridge)	EE/CS 3-180
2:40 pm - 3:00 pm	Discussion	EE/CS 3-180
3:00 pm - 3:15 pm	Break	EE/CS 3-176
3:15 pm - 3:55 pm	Algorithms for millisecond-scale simulation on Anton, a specialized molecular Dynamics machine Ron Dror (D. E. Shaw Research)	EE/CS 3-180
3:55 pm - 4:15 pm	Discussion	EE/CS 3-180

Wednesday, May 20, 2009

12:01 am	1:00pm-3:00pm Chair: Benedict Leimkuhler (University of Edinburgh) 3:30pm-5:30pm Chair: Tamar Schlick (New York University)
1:00 pm - 1:40 pm	Folding landscape of RNA from single molecule trajectories Devarajan Thirumalai (University of Maryland)	EE/CS 3-180
1:40 pm - 2:00 pm	Discussion	EE/CS 3-180
2:00 pm - 2:40 pm	Markov state models for biomolecular dynamics: Theory and applications Christof Schütte (Freie Universität Berlin)	EE/CS 3-180
2:40 pm - 3:00 pm	Discussion	EE/CS 3-180
3:00 pm - 3:30 pm	Break	EE/CS 3-176
3:30 pm - 4:10 pm	Coarse-grained molecular simulation of soft matter and interfaces Michael Allen (University of Warwick)	EE/CS 3-180
4:10 pm - 4:30 pm	Discussion	EE/CS 3-180
4:30 pm - 5:10 pm	Hybrid field-based models of cell membranes and proteins for signaling applications Ravi Radhakrishnan (University of Pennsylvania)	EE/CS 3-180
5:10 pm - 5:30 pm	Discussion	EE/CS 3-180
5:30 pm - 5:40 pm	Group photo

Thursday, May 21, 2009

12:01 am	Morning Chair: Weinan E (Princeton University) Afternoon Chair: Christof Schütte (Freie Universität Berlin)
8:30 am - 9:00 am	Coffee	EE/CS 3-176
9:00 am - 9:40 am	Protein path sampling: Bring your algorithm and your model Daniel Zuckerman (University of Pittsburgh)	EE/CS 3-180
9:40 am - 10:00 am	Discussion	EE/CS 3-180
10:00 am - 10:40 am	Generating, sampling, and analyzing the dynamical pathways of folding proteins with rare event techniques Peter Bolhuis (Universiteit van Amsterdam)	EE/CS 3-180
10:40 am - 11:00 am	Discussion	EE/CS 3-180
11:00 am - 11:30 am	Break	EE/CS 3-176
11:30 am - 12:10 pm	Theory and modeling of reactive events Eric Vanden-Eijnden (New York University)	EE/CS 3-180
12:10 pm - 12:30 pm	Discussion	EE/CS 3-180
12:30 pm - 2:00 pm	Lunch
2:00 pm - 2:40 pm	Computing slow reaction rates in molecular systems Eric Darve (Stanford University)	EE/CS 3-180
2:40 pm - 3:00 pm	Discussion	EE/CS 3-180
3:00 pm - 3:15 pm	Break	EE/CS 3-176
3:15 pm - 3:55 pm	Rheological properties of polymer melt between rapidly oscillating plates: an application of multiscale modeling Ryoichi Yamamoto (Kyoto University)	EE/CS 3-180
3:55 pm - 4:15 pm	Discussion	EE/CS 3-180
6:30 pm - 8:30 pm	Workshop dinner

Friday, May 22, 2009

12:01 am	Chair: Robert D. Skeel (Purdue University)
8:30 am - 9:00 am	Coffee	EE/CS 3-176
9:00 am - 9:40 am	Milestoning Ron Elber (The University of Texas at Austin)	EE/CS 3-180
9:40 am - 10:00 am	Discussion	EE/CS 3-180
10:00 am - 10:30 am	Break	EE/CS 3-176
10:30 am - 11:10 am	Flexible control of the ensemble Benedict Leimkuhler (University of Edinburgh)	EE/CS 3-180
11:10 am - 11:30 am	Discussion	EE/CS 3-180
11:30 am - 11:40 am	Closing remarks	EE/CS 3-180

Participants

Name	Department	Affiliation
Carlo Adamo	Laboratoire d'Electrochimie et de Chimie Analytique	École Nationale Supérieure de Chimie de Paris
Michael Allen	Department of Physics	University of Warwick
Manuel Athenes	Service de Recherches de Métallurgie Physique	Commissariat à l'Energie Atomique (CEA)-Centre d'Études Nucléaires de Grenoble (CEN)
Henry Boateng	Department of Mathematics	University of Michigan
Peter Bolhuis	Department of Chemistry	Universiteit van Amsterdam
Stephen Bond	Department of Computer Science	University of Illinois at Urbana-Champaign
Nawaf Bou-Rabee	Department of Mathematics	New York University
Bastiaan Braams	Chemistry Department	Emory University
Peter Brune	Department of Computer Science	University of Chicago
Sun Young Bu	Department of Mathematics	University of North Carolina, Chapel Hill
Carme Calderer	School of Mathematics	University of Minnesota, Twin Cities
Hannah Callender	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Maria Cameron	Department of Mathematics	Courant Institute of Mathematical Sciences
Xianjin Chen	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Giovanni Ciccotti	Department of Physics	Università di Roma La Sapienza
Ilaria Ciofini	Laboratoire d'Electrochimie et de Chimie Analytique	École Nationale Supérieure de Chimie de Paris
Rosana Collepardo-Guevara	Physical and Theoretical Chemistry Laboratory	University of Oxford
Grazia Cottone	Dipartimento di Scienze Fisiche ed Astronomiche	Università di Palermo
Eric Darve	Department of Mechanical Engineering	Stanford University
Luigi Delle Site		Max-Planck Institut für Polymerforschung
Daniel Dix	Department of Mathematics	University of South Carolina
Ron Dror		D. E. Shaw Research
Olivier Dubois	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Weinan E	Department of Mathematics and Applied Computational Mathematics	Princeton University
Robert Eisenberg	Department of Molecular Biophysics and Physiology	Rush University Medical Center
Ron Elber	Department of Chemistry and Biochemistry	The University of Texas at Austin
James Evans	Department of Mathematics	Iowa State University
Meredith Foley	Department of Chemistry	New York University
Christopher Fraser	Department of Computer Science	University of Chicago
Daan Frenkel	Institute for Atomic and Molecular Physics	University of Cambridge
Weihua Geng	Department of Mathematics	University of Michigan
Francesco Gervasio	Department of Chemistry and Applied Biosciences	Eidgenössische TH Zürich
Scott Habershon	Physical and Theoretical Chemistry Laboratory	University of Oxford
Amir Haji-Akbari	Department of Chemical Engineering	University of Michigan
Carsten Hartmann	Institut für Mathematik	Freie Universität Berlin
Graeme Henkelman	Department of Chemistry and Biochemistry	The University of Texas at Austin
Mark Herman	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Peter Hinow	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Jingfang Huang	Department of Mathematics	University of North Carolina, Chapel Hill
YunKyong Hyon	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Olexandr Isayev	Department of Chemistry	Case Western Reserve University
Ivaylo Ivanov	Department of Chemistry & Biochemistry	University of California, San Diego
Mark Iwen	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Alexander Izzo	Department of Mathematics & Statistics	Bowling Green State University
Srividhya Jeyaraman	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Lijian Jiang	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Segun Jung	Department of Computational Biology	New York University
Gerhard Kahl	Institute for Theoretical Physics	Technische Universität Wien
Hiqmet Kamberaj	Center for Drug Design	University of Minnesota, Twin Cities
Markus Keel	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Robert Krasny	Department of Mathematics	University of Michigan
Krzysztof Kuczera	Department of Molecular Biosciences	University of Kansas
Juan Latorre	Department of Mathematics and Computer Science	Freie Universität Berlin
Kah Chun Lau	Department of Chemistry	George Washington University
Claude Le Bris		CERMICS
Chiun-Chang Lee	Department of Mathematics	National Taiwan University
Young Ju Lee	Department of Mathematics	Rutgers, The State University Of New Jersey
Frédéric Legoll	LAMI	École Nationale des Ponts-et-Chaussées
Benedict Leimkuhler	School of Mathematics	University of Edinburgh
Tony Lelievre	CERMICS	Ecole Nationale des Ponts et Chaussees
Kun Li		The Pennsylvania State University
Xiantao Li	Department of Mathematics	The Pennsylvania State University
Yongfeng Li	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Hai Lin	Department of Chemistry	University of Colorado Denver
Tai-Chia Lin	Department of Mathematics	National Taiwan University
Yuchun Lin	Department of Mathematics & Statistics	University of North Carolina
Chun Liu	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Gang Lu	Department of Physics and Astronomy	California State University
Mitchell Luskin	School of Mathematics	University of Minnesota, Twin Cities
Dmitrii Makarov	Department of Chemistry and Biochemistry	The University of Texas at Austin
Thérèse Malliavin	Biologie structurale et chimie	Centre National de la Recherche Scientifique (CNRS)
Paul Maragakis		D. E. Shaw Research
Luca Maragliano	Department of Biochemistry and Molecular Biology	University of Chicago
Thomas Markland	Physical and Theoretical Chemistry Department	University of Oxford
Vasileios Maroulas	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Kevin Mclaughlin	Department of Chemistry	University of Wisconsin - River Falls
David Micha	Departments of Chemistry and of Physics	University of Florida
Thomas Miller III	Department of Chemistry	California Institute of Technology
David Minh	Laboratory of Chemical Physics	National Institutes of Health
Kimiya Minoukadeh	CERMICS - ENPC	Ecole Nationale des Ponts et Chaussees
Peter Monson	Department of Chemical Engineering	University of Massachusetts
Abdul Rehaman Moughal Shahi	BAD ADDRESS	Université de Genève
Kwangho Nam	Department of Chemistry and Chemical Biology	Harvard University
Emad Noorizadeh	The Maxwell Institute and School of Mathematics	University of Edinburgh
Albert Pan	Department of Biochemistry and Molecular Biology	University of Chicago
Malgorzata Peszynska	Department of Mathematics	Oregon State University
Matej Praprotnik		National Institute of Chemistry
Ravi Radhakrishnan	Department of Bioengineering	University of Pennsylvania
Neeraj Rai	Department of Chemistry	University of Minnesota, Twin Cities
Weiqing Ren	Courant Institute of Mathematical Sciences	New York University
Karsten Reuter	Fritz-Haber-Institut	Max-Planck-Institut
Adrian Roitberg	Department of Chemistry	University of Florida
Fadil Santosa	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Carlos Sanz-Navarro	Centre d'Investigacions en Nanociència i Nanotecnologia	Autonomous University of Barcelona
Srikanth Sastry	Department of Throretical Science	Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR)
Arnd Scheel	School of Mathematics	University of Minnesota, Twin Cities
Tamar Schlick	Courant Institute of Mathematical Sciences	New York University
Christof Schütte	Fachbereich Mathematik und Informatik	Freie Universität Berlin
L. Ridgway Scott	Department of Computer Science	University of Chicago
Tsvetanka Sendova	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Sami Shahin	Mathematics and Computer Science Department	Southwest Minnesota State University
Yuk Sham	Center for Drug Design	University of Minnesota, Twin Cities
Juanfang Shen	Department of Mathematics	Purdue University
Robert Skeel	Department of Computer Science	Purdue University
Adnan Sljoka	Department of Mathematics	York University
Daniel Smith	Department of Mathematics	University of Pittsburgh
Gabriel Stoltz	CERMICS	École Nationale des Ponts-et-Chaussées (ENPC)
Huan Sun	Department of Mathematics	The Pennsylvania State University
Devarajan Thirumalai	Department of Chemistry and Biochemistry	University of Maryland
Donald Truhlar	Supercomputer Institute and Department of Chemistry	University of Minnesota, Twin Cities
Erkan Tüzel	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Steven Valone	Material Science and Technology Division	Los Alamos National Laboratory
Eric Vanden-Eijnden	Courant Institute of Mathematical Sciences	New York University
Carlos Vega de las Heras	Department of Physical Chemistry	Universidad Complutense de Madrid
Maddalena Venturoli	Courant Institute of Mathematical Sciences	New York University
Rodolphe Vuilleumier	Département de Chimie	École Normale Supérieure
David Wales	Department of Chemistry	University of Cambridge
Zhian Wang	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Stephen Wiggins	Department of Mathematics	University of Bristol
Wei Xiong	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Xiang Xu	Department of Computational and Applied Mathematics	The Pennsylvania State University
Ryoichi Yamamoto	Department of Chemical Engineering	Kyoto University
Ke Yang	Department of Chemistry	University of Minnesota, Twin Cities
Xiao Yi	Department of Ecology, Evolution and Behavior	University of Minnesota, Twin Cities
Darrin York	Department of Chemistry	University of Minnesota, Twin Cities
Chensong Zhang	Department of Mathematics	The Pennsylvania State University
Chunfeng Zhao	Institute of Biocomplexity and Informatics	University of Calgary
Ruijun Zhao	Department of Computer Science	Purdue University
Guishan Zheng	Department of Chemistry and Chemical Biology	Harvard University
Weigang Zhong	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Daniel Zuckerman	Department of Computational Biology	University of Pittsburgh