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 | Tuesday | Wednesday | Thursday | Friday |
|
Monday, May 18
|
Morning Chair: Daan Frenkel (University of Cambridge)
Afternoon Chair: Giovanni Ciccotti (Università di Roma "La Sapienza") |
| 8:15am-9:00am |
Registration and coffee |
|
EE/CS 3-180 |
| 9:00am-9:15am |
Welcome to the IMA |
Fadil Santosa (University of Minnesota) |
EE/CS 3-180 |
| 9:15am-9:55am |
Coupled atomistic-continuum methods for fluids
|
Weiqing Ren (New York University) |
EE/CS 3-180 |
| 9:55am-10:15am |
Discussion |
|
EE/CS 3-180 |
| 10:15am-10:45am |
Break |
|
EE/CS 3-176 |
| 10:45am-11:25am |
Dynamics and thermodynamics of large conformational rearrangements in confined polymers
|
Dmitrii E. Makarov (University of Texas) |
EE/CS 3-180 |
| 11:25am-11:45am |
Discussion |
|
EE/CS 3-180 |
| 11:45am-2:00pm |
Lunch |
|
|
| 2:00pm-2:40pm |
Coarse-graining molecular dynamics for crystalline solids
|
Xiantao Li (Pennsylvania State University) |
EE/CS 3-180 |
| 2:40pm-3:00pm |
Discussion |
|
EE/CS 3-180 |
| 3:00pm-3:40pm |
Adaptive kinetic Monte Carlo for simulating dynamics in atomic systems
|
Graeme Henkelman (University of Texas) |
EE/CS 3-180 |
| 3:40pm-4:00pm |
Discussion |
|
EE/CS 3-176 |
| 4:00pm-6:30pm |
Reception and Poster Session
Poster submissions welcome from all participants
Instructions
Lind Hall 400
|
|
Tuesday, May 19
|
Morning Chair: Ron Elber
(University of Texas)
Afternoon Chair: Tamar Schlick (New York University)
|
| 8:30am-9:00am |
Coffee |
|
EE/CS 3-176 |
| 9:00am-9:40am |
Modeling organic-inorganic interfaces across different scales: Modeling concepts and Applications
|
Luigi Delle Site (Max-Planck Institut für Polymerforschung) |
EE/CS 3-180 |
| 9:40am-10:00am |
Discussion |
|
EE/CS 3-180 |
| 10:00am-10:40am |
Benard convection by dynamical nonequilibrium molecular dynamics
|
Giovanni Ciccotti (Università di Roma "La Sapienza") |
EE/CS 3-180 |
| 10:40am-11:00am |
Discussion |
|
EE/CS 3-180 |
| 11:00am-11:30am |
Break |
|
EE/CS 3-176 |
| 11:30am-12:10pm |
Free-energy methods to study conformational transitions and
ligand binding to flexible targets
|
Francesco Luigi Gervasio (Eidgenössische TH Zürich) |
EE/CS 3-180 |
| 12:10pm-12:30pm |
Discussion |
|
EE/CS 3-180 |
| 12:30pm-2:00pm |
Lunch |
|
|
| 2:00pm-2:40pm |
Energy landscapes of clusters, glasses, and biomolecules
|
David John Wales (University of Cambridge) |
EE/CS 3-180 |
| 2:40pm-3:00pm |
Discussion |
|
EE/CS 3-180 |
| 3:00pm-3:15pm |
Break |
|
EE/CS 3-176 |
| 3:15pm-3:55pm |
Algorithms for millisecond-scale simulation on Anton, a
specialized molecular Dynamics machine
|
Ron Dror (D. E. Shaw Research) |
EE/CS 3-180 |
| 3:55pm-4:15pm |
Discussion |
|
EE/CS 3-180 |
|
Wednesday, May 20
|
1:00pm-3:00pm Chair: Benedict Leimkuhler
(University of Edinburgh)
3:30pm-5:30pm Chair: Tamar Schlick (New York University) |
| 1:00pm-1:40pm |
Folding landscape of RNA from single molecule trajectories
|
Devarajan Thirumalai (University of Maryland) |
EE/CS 3-180 |
| 1:40pm-2:00pm |
Discussion |
|
EE/CS 3-180 |
| 2:00pm-2:40pm |
Markov state models for biomolecular dynamics: Theory and applications
|
Christof Schütte (Freie Universität Berlin) |
EE/CS 3-180 |
| 2:40pm-3:00pm |
Discussion |
|
EE/CS 3-180 |
| 3:00pm-3:30pm |
Break |
|
EE/CS 3-176 |
| 3:30pm-4:10pm |
Coarse-grained molecular simulation of soft matter and
interfaces
|
Michael Philip Allen (University of Warwick) |
EE/CS 3-180 |
| 4:10pm-4:30pm |
Discussion |
|
EE/CS 3-180 |
| 4:30pm-5:10pm |
Hybrid field-based models of cell membranes and proteins
for signaling applications
|
Ravi Radhakrishnan (University of Pennsylvania) |
EE/CS 3-180 |
| 5:10pm-5:30pm |
Discussion |
|
EE/CS 3-180 |
| 5:30pm-5:40pm |
Group photo |
|
|
|
Thursday, May 21
|
Morning Chair: Weinan E
(Princeton University)
Afternoon Chair: Christof Schütte (Freie Universität Berlin) |
| 8:30am-9:00am |
Coffee |
|
EE/CS 3-176 |
| 9:00am-9:40am |
Protein path sampling: Bring your algorithm and your
model
|
Daniel M. Zuckerman (University of Pittsburgh) |
EE/CS 3-180 |
| 9:40am-10:00am |
Discussion |
|
EE/CS 3-180 |
| 10:00am-10:40am |
Generating, sampling, and analyzing the dynamical pathways of folding proteins with rare event techniques
|
Peter Bolhuis (Universiteit van Amsterdam) |
EE/CS 3-180 |
| 10:40am-11:00am |
Discussion |
|
EE/CS 3-180 |
| 11:00am-11:30am |
Break |
|
EE/CS 3-176 |
| 11:30am-12:10pm |
Theory and modeling of reactive events
|
Eric Vanden-Eijnden (New York University) |
EE/CS 3-180 |
| 12:10pm-12:30pm |
Discussion |
|
EE/CS 3-180 |
| 12:30pm-2:00pm |
Lunch |
|
|
| 2:00pm-2:40pm |
Computing slow reaction rates in molecular systems
|
Eric Felix Darve (Stanford University) |
EE/CS 3-180 |
| 2:40pm-3:00pm |
Discussion |
|
EE/CS 3-180 |
| 3:00pm-3:15pm |
Break |
|
EE/CS 3-176 |
| 3:15pm-3:55pm |
Rheological properties of polymer melt between rapidly
oscillating plates: an application of multiscale modeling
|
Ryoichi Yamamoto (Kyoto University) |
EE/CS 3-180 |
| 3:55pm-4:15pm |
Discussion |
|
EE/CS 3-180 |
| 6:30pm-8:30pm |
Workshop dinner |
|
Pagoda Restaurant
1417 4th St. SE
Minneapolis, MN
612-378-4710 |
|
Friday, May 22
|
| Chair: Robert D. Skeel (Purdue University) |
| 8:30am-9:00am |
Coffee |
|
EE/CS 3-176 |
| 9:00am-9:40am |
Milestoning
|
Ron Elber (University of Texas) |
EE/CS 3-180 |
| 9:40am-10:00am |
Discussion |
|
EE/CS 3-180 |
| 10:00am-10:30am |
Break |
|
EE/CS 3-176 |
| 10:30am-11:10am |
Flexible control of the ensemble
|
Benedict Leimkuhler (University of Edinburgh) |
EE/CS 3-180 |
| 11:10am-11:30am |
Discussion |
|
EE/CS 3-180 |
| 11:30am-11:40am |
Closing remarks |
|
EE/CS 3-180 |
| Name | Department | Affiliation |
|---|
| Carlo Adamo | Laboratoire d'Electrochimie et de Chimie Analytique | École Nationale Supérieure de Chimie de Paris |
| Michael Philip 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 A. 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 J. Braams | Chemistry Department | Emory University |
| Peter Brune | Department of Computer Science | University of Chicago |
| Sun Young Bu | Department of Mathematics | University of North Carolina |
| Maria-Carme T. Calderer | School of Mathematics | University of Minnesota |
| Hannah Callender | Institute for Mathematics and its Applications | University of Minnesota |
| Maria Kourkina Cameron | Department of Mathematics | Courant Institute of Mathematical Sciences |
| Xianjin Chen | Institute for Mathematics and its Applications | University of Minnesota |
| 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 Felix 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 |
| Weinan E | Department of Mathematics and Applied Computational Mathematics | Princeton University |
| Robert S. Eisenberg | Department of Molecular Biophysics and Physiology | Rush University Medical Center |
| Ron Elber | Department of Chemistry and Biochemistry | University of Texas |
| James W. Evans | Department of Mathematics | Iowa State University |
| Meredith Catherine 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 Luigi 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 | University of Texas |
| Mark S. Herman | Institute for Mathematics and its Applications | University of Minnesota |
| Peter Hinow | Institute for Mathematics and its Applications | University of Minnesota |
| Jingfang Huang | Department of Mathematics | University of North Carolina |
| Yunkyong Hyon | Institute for Mathematics and its Applications | University of Minnesota |
| Olexandr Isayev | Department of Chemistry | Case Western Reserve University |
| Ivaylo N. Ivanov | Department of Chemistry & Biochemistry | University of California, San Diego |
| Mark Iwen | Institute for Mathematics and its Applications | University of Minnesota |
| Alexander Izzo | Department of Mathematics and Statistics | Bowling Green State University |
| Srividhya Jeyaraman | Institute for Mathematics and its Applications | University of Minnesota |
| Lijian Jiang | Institute for Mathematics and its Applications | University of Minnesota |
| 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 |
| Robert Krasny | Department of Mathematics | University of Michigan |
| Krzysztof Kuczera | Department of Molecular Biosciences | University of Kansas |
| Juan C. Latorre | Department of Mathematics and Computer Science | Freie Universität Berlin |
| Kah Chun Lau | Department of Chemistry | George Washington University |
| Claude Le Bris | Ecole Nationale des Ponts et Chaussées (ENPC) | CERMICS |
| Chiun-Chang Lee | Department of Mathematics | National Taiwan University |
| Young-Ju Lee | Department of Mathematics | Rutgers University |
| 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 | | Pennsylvania State University |
| Xiantao Li | Department of Mathematics | Pennsylvania State University |
| Yongfeng Li | Institute for Mathematics and its Applications | University of Minnesota |
| Hai Lin | Department of Chemistry | University of Colorado |
| Tai-Chia Lin | Department of Mathematics | National Taiwan University |
| Yuchun Lin | Department of Mathematics and Statistics | University of North Carolina - Charlotte |
| Chun Liu | Institute for Mathematics and its Applications | University of Minnesota |
| Gang Lu | Department of Physics and Astronomy | California State University |
| Mitchell Luskin | School of Mathematics | University of Minnesota |
| Dmitrii E. Makarov | Department of Chemistry and Biochemistry | University of Texas |
| Thérèse E. 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 E. Markland | Physical and Theoretical Chemistry Department | University of Oxford |
| Vasileios Maroulas | Institute for Mathematics and its Applications | University of Minnesota |
| Kevin W. Mclaughlin | Department of Chemistry | University of Wisconsin - River Falls |
| David A. Micha | Departments of Chemistry and of Physics | University of Florida |
| Thomas F Miller | Department of Chemistry | California Institute of Technology |
| David Do Le Minh | Laboratory of Chemical Physics | National Institutes of Health |
| Kimiya Minoukadeh | CERMICS - ENPC | Ecole Nationale des Ponts et Chaussees |
| Peter A. Monson | Department of Chemical Engineering | University of Massachusetts |
| Abdul Rehaman Moughal Shahi | Department of Physical Chemistry | 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 C. 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 |
| Weiqing Ren | Courant Institute of Mathematical Sciences | New York University |
| Karsten Reuter | Fritz-Haber-Institut | Max-Planck-Institut |
| Adrian E. Roitberg | Department of Chemistry | University of Florida |
| Fadil Santosa | Institute for Mathematics and its Applications | University of Minnesota |
| Carlos F. 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 |
| Tamar Schlick | Courant Institute of Mathematical Sciences | New York University |
| Christof Schütte | Department of Mathematics and Computer Science | Freie Universität Berlin |
| L. Ridgway Scott | Department of Computer Science | University of Chicago |
| Tsvetanka Sendova | Institute for Mathematics and its Applications | University of Minnesota |
| Sami Shahin | Mathematics and Computer Science Department | Southwest Minnesota State University |
| Yuk Sham | Center for Drug Design | University of Minnesota |
| Juanfang Shen | Department of Mathematics | Purdue University |
| Robert D. Skeel | Department of Computer Science | Purdue University |
| Adnan Sljoka | Department of Mathematics | York University |
| Daniel B. Smith | Department of Mathematics | University of Pittsburgh |
| Gabriel Stoltz | CERMICS | École Nationale des Ponts-et-Chaussées (ENPC) |
| Huan Sun | Department of Mathematics | Pennsylvania State University |
| Devarajan Thirumalai | Department of Chemistry and Biochemistry | University of Maryland |
| Donald G. Truhlar | Supercomputer Institute and Department of Chemistry | University of Minnesota |
| Erkan Tüzel | Institute for Mathematics and its Applications | University of Minnesota |
| Steven M. 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 John Wales | Department of Chemistry | University of Cambridge |
| Zhian Wang | Institute for Mathematics and its Applications | University of Minnesota |
| Stephen Wiggins | School of Mathematics | University of Bristol |
| Wei Xiong | Institute for Mathematics and its Applications | University of Minnesota |
| Xiang Xu | Department of Computational and Applied Mathematics | Pennsylvania State University |
| Ryoichi Yamamoto | Department of Chemical Engineering | Kyoto University |
| Ke Yang | Department of Chemistry | University of Minnesota |
| Xiao Yi | Department of Ecology, Evolution and Behavior | University of Minnesota |
| Darrin M. York | Department of Chemistry | University of Minnesota |
| Chensong Zhang | Department of Mathematics | Pennsylvania State University |
| Chunfeng Zhao | Institute of Biocomplexity and Informatics | University of Calgary |
| Ruijun Zhao | Department of Computer Sciences | Purdue University |
| Guishan Zheng | Deparment of Chemistry and Chemical Biology | Harvard University |
| Weigang Zhong | Institute for Mathematics and its Applications | University of Minnesota |
| Daniel M. Zuckerman | Department of Computational Biology | University of Pittsburgh |
