Modern questions of biological science are becoming increasingly quantitative and microscopic, and increasingly approachable by physical models and computer simulations. This workshop is focused at the interface where molecular and cellular biology meet the mathematical and computational sciences. We will explore both principles and methodologies, particularly those that are rooted in physics and rigorous mathematics, in addition to applications to biological problems. Research topics will include the computational folding of proteins and other biomolecules, ligand docking, biological networks, heterogeneous dynamics, and complex systems. Speakers will be encouraged to present new work, and to identify important unsolved problems and opportunities at this interface.
| Schedule |
| Monday | Tuesday | Wednesday | Thursday | Friday | |
|
Monday, January 14
|
Morning Theme: Force fields & simulations
Afternoon Theme: Design, predictions, and optimization |
| 8:15a-9:00a |
Registration and coffee |
|
EE/CS 3-176 |
| 9:00a-9:15a |
Welcome to the IMA |
Douglas N. Arnold (University of Minnesota) |
EE/CS 3-180 |
| 9:15a-9:45a |
Assessing the performance of Poisson-Boltzmann continuum solvation
models
|
Nathan A. Baker (Washington University School of Medicine) |
EE/CS 3-180 |
| 9:50a-10:20a |
Simple models for simulating replica exchange simulations of protein folding and binding
|
Ronald M. Levy (Rutgers University) |
EE/CS 3-180 |
| 10:25a-10:55a |
Alpha-helical topology and tertiary structure prediction of
globular proteins
|
Christodoulos A. Floudas (Princeton University) |
EE/CS 3-180 |
| 10:55a-11:40a |
Coffee |
|
EE/CS 3-176 |
| 11:40a-12:10p |
Challenges in generation of conformational ensembles for peptides and small proteins
|
Carlos L. Simmerling (SUNY) |
EE/CS 3-180 |
| 12:15p-12:30p |
What is a transition path?
|
Robert D. Skeel (Purdue University) |
EE/CS 3-180 |
| 12:30p-2:00a |
Lunch |
|
|
| 2:00p-2:30p |
Engineering protein structure and function with theoretical protein design
|
Jeffery G. Saven (University of Pennsylvania) |
EE/CS 3-180 |
| 2:35p-2:50p |
Modeling ensembles of transmembrane beta-barrel proteins
|
Jérôme Waldispühl (Massachusetts Institute of Technology) |
EE/CS 3-180 |
| 2:55p-3:25p |
Coffee |
|
EE/CS 3-176 |
| 3:25p-3:40p |
Exact methods for simplified protein models
|
Rolf Backofen (Albert-Ludwigs-Universität Freiburg) |
EE/CS 3-180 |
| 3:40p-4:10p |
Discussion forum |
|
EE/CS 3-180 |
| 4:10p-4:25p |
Group Photo |
|
|
| 4:30p-6:00p |
Reception and Poster Session
Lind Hall 400
|
|
Tuesday, January 15
|
Morning Theme: Systems modeling
Afternoon Theme: Conformational exploration, routes, and searching |
| 8:30a-9:00a |
Coffee |
|
EE/CS 3-176 |
| 9:00a-9:30a |
Simulation methods for stochastic chemical systems that arise from a random time change representation
|
David F. Anderson (University of Wisconsin) |
EE/CS 3-180 |
| 9:35a-10:05a |
Coarse-grained parameterizations of biomolecular
systems
|
Peter R. Kramer (Rensselaer Polytechnic Institute) |
EE/CS 3-180 |
| 10:10a-10:40a |
From chemical reaction systems to cellular states: A
computational approach
|
Hong Qian (University of Washington) |
EE/CS 3-180 |
| 10:40a-11:10a |
Coffee |
|
EE/CS 3-176 |
| 11:10a-11:40a |
Computational experiments in coarse-graining atomistic simulations
|
Yannis G. Kevrekidis (Princeton University) |
EE/CS 3-180 |
| 11:40a-1:30p |
Lunch |
|
|
| 1:30p-2:00p |
Using motion planning to study molecular motions
|
Nancy M. Amato (Texas A & M University) |
EE/CS 3-180 |
| 2:05p-2:35p |
Geometrical methods for the efficient exploration of protein conformation space
|
Evangelos A. Coutsias (University of New Mexico) |
EE/CS 3-180 |
| 2:40p-3:10p |
Network models for protein dynamics and allostery: Application to GroEL-GroES
|
Ivet Bahar (University of Pittsburgh) |
EE/CS 3-180 |
| 3:10p-3:40p |
Coffee |
|
EE/CS 3-176 |
| 3:40p-4:10p |
Structural control of motions?
|
Robert L. Jernigan (Iowa State University) |
EE/CS 3-180 |
| 4:15p-4:45p |
The network of sequence flow between protein structures
|
Ron Elber (University of Texas) |
EE/CS 3-180 |
| 4:50p-5:20p |
Discussion forum |
|
EE/CS 3-180 |
|
Wednesday, January 16
|
Morning Theme: Nonequilibrium & single molecules
Afternoon Theme: Nucleic acids & genomes |
| 8:30a-9:00a |
Coffee |
|
EE/CS 3-176 |
| 9:00a-9:30a |
Exploring global energy landscape of lattice protein models via Monte Carlo methods
|
Samuel Kou (Harvard University) |
EE/CS 3-180 |
| 9:35a-10:05a |
Mathematical models of folded and unfolded protein ensembles
|
Gregory S. Chirikjian (Johns Hopkins University) |
EE/CS 3-180 |
| 10:10a-10:25a |
Current issues in understanding complex biological networks
|
Hans G. Othmer (University of Minnesota) |
EE/CS 3-180 |
| 10:30a-11:15a |
Coffee |
|
EE/CS 3-176 |
| 11:15a-11:45a |
Improving nonequilibrium free energy estimates by enhancing phase space overlap
|
Christopher Jarzynski (University of Maryland) |
EE/CS 3-180 |
| 11:45a-2:00a |
Lunch |
|
|
| 2:00p-2:30p |
The electrostatic free energy landscape for nucleic acid folding - beyond the Poisson-Boltzmann equation
|
Shi-Jie Chen (University of Missouri) |
EE/CS 3-180 |
| 2:35p-2:50p |
Annotated tertiary interactions in RNA structures reveal new interactions, correlations in motifs and composite motifs
|
Christian E. Laing (New York University) |
EE/CS 3-180 |
| 2:50p-3:20p |
Coffee |
|
EE/CS 3-176 |
| 3:20p-3:35p |
Mapping evolutionary pathways of HIV-1 drug resistance using
conditional selection pressure
|
Christopher J. Lee (University of California) |
EE/CS 3-180 |
| 3:40p-4:10p |
Discussion forum |
|
EE/CS 3-180 |
|
Thursday, January 17
|
Morning Theme: Protein folding & low-resolution modeling
Afternoon Theme: Protein design and interactions |
| 8:30a-9:00a |
Coffee |
|
EE/CS 3-176 |
| 9:00a-9:30a |
Free energies and kinetics of protein folding from coarse master equations
|
Gerhard Hummer (National Institutes of Health (NIH)) |
EE/CS 3-180 |
| 9:35a-10:05a |
Entropic and enthalpic barriers in cooperative protein folding
|
Hue-Sun Chan (University of Toronto) |
EE/CS 3-180 |
| 10:10a-10:40a |
The energy landscape for folding and molecular motors
|
José Nelson Onuchic (University of California, San Diego) |
EE/CS 3-180 |
| 10:40a-11:25a |
Coffee |
|
EE/CS 3-176 |
| 11:25a-11:55a |
Transition states in protein folding
|
Thomas Weikl (Max Planck Institute for Colloids and Interfaces) |
EE/CS 3-180 |
| 12:00p-12:15p |
Probing the diversity of unfolding pathways by simulated thermal denaturation
|
Andrew J. Rader (Indiana University-Purdue University) |
EE/CS 3-180 |
| 12:30p-2:00a |
Lunch |
|
|
| 2:00p-2:30p |
Structure-based maximal affinity model predicts small-molecule druggability
|
Alan C. Cheng (Amgen Cambridge Research Center) |
EE/CS 3-180 |
| 2:35p-2:50p |
Cluster optimization in protein docking
|
Julie C. Mitchell (University of Wisconsin) |
EE/CS 3-180 |
| 2:50p-3:20p |
Coffee |
|
EE/CS 3-176 |
| 3:20p-3:50p |
Multistage optimization for protein-protein docking
|
Sandor Vajda (Boston University) |
EE/CS 3-180 |
| 3:55p-4:25p |
Discussion forum |
|
EE/CS 3-180 |
| 6:30p-8:30p |
Workshop Dinner |
|
Caspian Bistro
2418 University Ave SE
Minneapolis, MN 55414
612-623-1133 |
|
Friday, January 18
|
| Theme: Big Simulations of atomically detailed models |
| 8:30a-9:00a |
Coffee |
|
EE/CS 3-176 |
| 9:00a-9:30a |
The limitations of temperature replica exchange (T-REMD) for
protein folding
|
Jed W. Pitera (IBM Research Division) |
EE/CS 3-180 |
| 9:35a-10:05a |
Simulations on BlueGene of a fast folding mutant of lambda(6-85)
|
William Swope (IBM) |
EE/CS 3-180 |
| 10:05a-10:50a |
Coffee |
|
EE/CS 3-176 |
| 10:50a-11:20a |
Simulations of peptide folding and dynamics
|
Krzysztof Kuczera (University of Kansas) |
EE/CS 3-180 |
| 11:25a-11:55a |
Discussion forum |
|
EE/CS 3-180 |
| 11:55a-12:10p |
Concluding remarks |
Ken A. Dill (University of San Francisco), Sorin Istrail (Brown University) |
EE/CS 3-180 |
| Name | Department | Affiliation |
|---|
| Hoda Abdel-Aal Bettley | Pharmacy Department | University of Manchester |
| Nancy M. Amato | Department of Computer Science | Texas A & M University |
| David F. Anderson | Department of Mathematics | University of Wisconsin |
| Douglas N. Arnold | School of Mathematics | University of Minnesota |
| Rolf Backofen | Institute of Computer Science | Albert-Ludwigs-Universität Freiburg |
| Ivet Bahar | Department of Computational Biology | University of Pittsburgh |
| Nathan A. Baker | Department of Biochemistry and Molecular Biophysics | Washington University School of Medicine |
| Daniel J. Bates | Institute for Mathematics and its Applications | University of Minnesota |
| John Baxter | Institute for Mathematics and its Applications | University of Minnesota |
| Yermal Sujeet Bhat | Institute for Mathematics and its Applications | University of Minnesota |
| Victor Bloomfield | Department of Biochemistry | University of Minnesota |
| Jamie Blundell | Department of Physics | University of Cambridge |
| Khalid Boushaba | Department of Mathematics | Iowa State University |
| Maria-Carme T. Calderer | School of Mathematics | University of Minnesota |
| Hannah Callender | Institute for Mathematics and its Applications | University of Minnesota |
| Hue-Sun Chan | Department of Biochemistry | University of Toronto |
| Shi-Jie Chen | Department of Physics | University of Missouri |
| Alan C. Cheng | | Amgen Cambridge Research Center |
| Gregory S. Chirikjian | Department of Mechanical Engineering | Johns Hopkins University |
| Ludovica Cecilia Cotta-Ramusino | Institute for Mathematics and its Applications | University of Minnesota |
| Evangelos A. Coutsias | Department of Mathematics and Statistics | University of New Mexico |
| Lenore J. Cowen | Department of Computer Science | Tufts University |
| Isabel K. Darcy | Department of Mathematics | University of Iowa |
| Yuanan Diao | Department of Mathematics and Statistics | University of North Carolina - Charlotte |
| Ken A. Dill | Department of Pharmaceutical Chemistry | University of San Francisco |
| Yang Ding | Department of Biology | Boston College |
| Ron Elber | Department of Chemistry and Biochemistry | University of Texas |
| Claus Ernst | Department of Mathematics | Western Kentucky University |
| Elisenda Feliu | Facultat de Matemàtiques | University of Barcelona |
| Christodoulos A. Floudas | Department of Chemical Engineering | Princeton University |
| Anant Godbole | Department of Mathematics | East Tennessee State University |
| Laura Rocio Gonzalez-Ramirez | Department of Mathematics | CINVESTAV |
| Jason E. Gower | Institute for Mathematics and its Applications | University of Minnesota |
| Sergei Grudinin | | INRIA Rhone-Alpes Research Unit |
| Esfandiar Haghverdi | School of Informatics | Indiana University |
| Omar Haq | Computational Biology and Molecular Biopphysics | Rutgers University |
| Milena Hering | Institute for Mathematics and its Applications | University of Minnesota |
| Peter Hinow | Institute for Mathematics and its Applications | University of Minnesota |
| Kenneth Hinson | Department of Mathematics | University of North Carolina - Charlotte |
| Xia Hua | Department of Mathematics | Massachusetts Institute of Technology |
| Gerhard Hummer | Laboratory of Chemical Physics | National Institutes of Health (NIH) |
| Sorin Istrail | Department of Computer Science | Brown University |
| Filip Jagodzinski | Department of Computer Science | University of Massachusetts |
| Richard D. James | Department of Aerospace Engineering and Mechanics | University of Minnesota |
| Christopher Jarzynski | Department of Chemistry and Biochemistry | University of Maryland |
| Robert L. Jernigan | Baker Ctr for Bioinformatics and Biological Statistics | Iowa State University |
| Tiefeng Jiang | Department of Statistics | University of Minnesota |
| Christopher Kauffman | Department of Computer Science | University of Minnesota |
| Yiannis N. Kaznessis | Department of Chemical Engineering and Materials Science | University of Minnesota |
| Yannis G. Kevrekidis | Department of Chemicial Engineering | Princeton University |
| Abdul Qayyum Masud Khaliq | Department of Mathematical Sciences | Middle Tennessee State University |
| Soojeong Kim | Department of Mathematics | University of Iowa |
| Debra Knisley | Department of Mathematics | East Tennessee State University |
| Dmitry A. Kondrashov | Department of Biological Sciences | University of Chicago |
| Samuel Kou | Department of Statistics | Harvard University |
| Dmytro Kozakov | Department of Biomedical Engineering | Boston University |
| Peter R. Kramer | Department of Mathematical Sciences | Rensselaer Polytechnic Institute |
| Krzysztof Kuczera | Department of Molecular Biosciences | University of Kansas |
| Christian E. Laing | Department of Mathematics, Chemistry | New York University |
| Fumei Lam | Department of Computer Science | Brown University |
| Juan C. Latorre | Department of Mathematical Sciences | Rensselaer Polytechnic Institute |
| Audrey Lee | Computer Science Department | University of Massachusetts |
| Christopher J. Lee | Department of Chemistry and Biochemistry | University of California, Los Angeles |
| Michael Levitt | Department of Cell Biology | Stanford University |
| Ronald M. Levy | Chemistry and Chemical Biology | Rutgers University |
| Robert Michael Lewis | Department of Mathematics | College of William and Mary |
| Anton Leykin | Institute for Mathematics and its Applications | University of Minnesota |
| Timothy Lezon | Department of Computational Biology | University of Pittsburgh |
| Florence J. Lin | Department of Mathematics | University of Southern California |
| Andy Lorenz | Department of Biology | Boston College |
| Roger Lui | Department of Mathematical Sciences | Worcester Polytechnic Institute |
| Laura Lurati | Institute for Mathematics and its Applications | University of Minnesota |
| Christopher Michael Maloney | Department of Computer Science | Brown University |
| Yi Mao | Department of Mathematics | Michigan State University |
| Ezra Miller | School of Mathematics | University of Minnesota |
| Kenneth C. Millett | Department of Mathematics | University of California, Santa Barbara |
| Julie C. Mitchell | Departments of Mathematics and Biochemistry | University of Wisconsin |
| Alejandro Morales Valencia | Department of Computational Sciences | University of Guadalajara |
| Antonio Mucherino | Departimento di Matematica | Seconda Università di Napoli |
| Chitra Narayanan | Department of Biochemistry | Rutgers University |
| Junalyn Navarra-Madsen | Department of Mathematics and Computer Science | Texas Woman's University |
| Timothy Newman | Department of Physics | Arizona State University |
| Duane Nykamp | School of Mathematics | University of Minnesota |
| David J. Odde | Department of Biomedical Engineering | University of Minnesota |
| Charles W. O'Donnell | Electrical and Computer Engineering Department | Massachusetts Institute of Technology |
| José Nelson Onuchic | Department of Physics | University of California, San Diego |
| Hans G. Othmer | Department of Mathematics | University of Minnesota |
| Sefika Banu Ozkan | Department of Physics | Arizona State University |
| Sanghyun Park | Mathematics and Computer Science Division | Argonne National Laboratory |
| Ioannis Paschalidis | Department of Electrical and Computer Engineering,and Center for Information and Systems Engineering (CISE) | Boston University |
| Bobby Philip | Computer and Computational Sciences Division | Los Alamos National Laboratory |
| Jed W. Pitera | Almaden Research Center | IBM Research Division |
| Andrea Pugliese | Dipartimento di Matematica | Università di Trento |
| Hong Qian | Department of Applied Mathematics | University of Washington |
| Terrance Quinn | Department of Mathematical Sciences | Middle Tennessee State University |
| Andrew J. Rader | Physics Department | Indiana University-Purdue University |
| Subramanian Ramamoorthy | School of Informatics | University of Edinburgh |
| Rahul Ravindrudu | Department of Computer Science | Iowa State University |
| Eric J. Rawdon | Department of Mathematics | University of St. Thomas |
| Stephane Redon | Inovallée | INRIA Rhône-Alpes |
| Shantanu Roy | Institute of Physics | Universität Basel |
| Anchanee Sangcharoen | Institute of Molecular Biology and Genetics | Mahidol University |
| Jeffery G. Saven | Department of Chemistry | University of Pennsylvania |
| Deena Schmidt | Institute for Mathematics and its Applications | University of Minnesota |
| Tamara Schmidt-Hegge | | University of Minnesota |
| Brigitte Servatius | Department of Mathematics | Worcester Polytechnic Institute |
| Chehrzad Shakiban | Institute of Mathematics and its Application | University of Minnesota |
| Yang Shen | Department of Biomedical Engineering | Boston University |
| Carlos L. Simmerling | Department of Chemistry | SUNY |
| Zachariah Sinkala | Department of Mathematical Sciences | Middle Tennessee State University |
| Robert D. Skeel | Department of Computer Science | Purdue University |
| Carlos Sosa | Supercomputing Institute | University of Minnesota |
| Andrew M. Stein | Institute for Mathematics and its Applications | University of Minnesota |
| Ileana Streinu | Department of Computer Science | Smith College |
| Weitao Sun | Department of Computer Science | New Mexico State University |
| Vladimir Sverak | School of Mathematics | University of Minnesota |
| William Swope | Almaden Research Center | IBM |
| Michael Tomasini | | Rutgers University |
| Erkan Tüzel | Institute for Mathematics and its Applications | University of Minnesota |
| George Vacek | Department of Life and Materials Sciences | Hewlett Packard |
| Sandor Vajda | Department of Biomedical Engineering | Boston University |
| Jérôme Waldispühl | Applied Mathematics Department | Massachusetts Institute of Technology |
| Jin Wang | Department of Chemistry, Physics and Applied Mathematics | SUNY |
| Zhian Wang | Institute for Mathematics and its Applications | University of Minnesota |
| Guowei Wei | Department of Mathematics | Michigan State University |
| Thomas Weikl | Department of Theory and Bio-Systems | Max Planck Institute for Colloids and Interfaces |
| Lauren Wickstrom | Department of Biochemistry and Structural Biology | SUNY |
| Sebastian Will | Institute of Computer Science | Albert-Ludwigs-Universität Freiburg |
| Di Wu | Department of Mathematics | Western Kentucky University |
| Zhijun Wu | Department of Mathematics | Iowa State University |
| Jiaan Yang | | MicrotechNano |
| Sichun Yang | Department of Biochemistry and Molecular
Biology
| University of Chicago |
| Ya-xiang Yuan | Institute of Computational Mathematics and Scientific/Engineering Computing | Chinese Academy of Sciences |
| Adam Zemla | Computing Applications and Research | Lawrence Livermore National Laboratory |
| Hongchao Zhang | Institute for Mathematics and its Applications | University of Minnesota |
| Carol L. Ecale Zhou | Computing Applications and Research | Lawrence Livermore National Laboratory |
