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IMA Tutorial

Mathematics of Proteins

January 10-11, 2008
Organizers:
Michael Levitt Computational Structural Biology, Stanford University Medical School
Patrice Koehl Computer Science and Genome Center, University of California, Davis

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Abstracts and Talk Materials Dining Guide

Description:

The molecular basis of life rests on the activity of biological macro-molecules, mostly nucleic acids and proteins. A perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities. In this workshop, we will explore the connection between the biological activities of proteins and mathematics. We will focus on geometry and topology. More specifically we will cover the importance of shape, how to generate measures or features that describe protein structures, and how these measures can be used to classify protein structures and to model their energetics of proteins. In addition, we will describe recent input from Mathematics into fundamental problems in the structural biology of proteins, focusing on protein folding and protein-protein interactions.

Schedule
Thursday | Friday | 
  Thursday, January 10
8:15a-8:50a Registration and coffee   EE/CS 3-176
8:50a-9:00a Welcome to the IMA Douglas N. Arnold (University of Minnesota) EE/CS 3-180
9:00a-10:00a Lecture 1: Fundamental forces and molecular architecture Michael Levitt (Stanford University) EE/CS 3-180
10:00a-10:30a Break   EE/CS 3-176
10:30a-11:30a The geometry of biomolecular solvation. Part 1: Hydrophobicity Patrice Koehl (University of California) EE/CS 3-180
11:30a-1:30p Lunch    
1:30p-2:30p Part 2: Electrostatics Patrice Koehl (University of California) EE/CS 3-180
2:30p-3:00p Break   EE/CS 3-176
3:00p-4:00p Lecture 2: Simulating molecular motion Michael Levitt (Stanford University) EE/CS 3-180
4:00p-4:30p Second chances Patrice Koehl (University of California), Michael Levitt (Stanford University) EE/CS 3-180
  Friday, January 11
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-10:00a Part 3: Protein shape descriptors Patrice Koehl (University of California) EE/CS 3-180
10:00a-10:30a Break   EE/CS 3-176
10:30a-11:30a Lecture 3: Simulating protein folding Michael Levitt (Stanford University) EE/CS 3-180
11:30a-2:00p Lunch    
2:00p-2:30p Geometric simulation of protein flexibility Ileana Streinu (Smith College) EE/CS 3-180
2:30p-3:00p Knot theory and proteins Isabel K. Darcy (University of Iowa) EE/CS 3-180
3:00p-3:30p Break   EE/CS 3-176
3:30p-4:00p An introduction to multigrid techniques Bobby Philip (Los Alamos National Laboratory) EE/CS 3-180

LIST OF CONFIRMED PARTICIPANTS

Name Department Affiliation
Douglas N. Arnold Institute for Mathematics and its Applications University of Minnesota
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
Jamie Blundell Department of Physics University of Cambridge
Maria-Carme T. Calderer School of Mathematics University of Minnesota
Hannah Callender Institute for Mathematics and its Applications University of Minnesota
Larry Carson   3M
Alessandro Cembran Department of Chemistry University of Minnesota
Patrick L Coleman Department of Biotechnology 3M
Ludovica Cecilia Cotta-Ramusino Institute for Mathematics and its Applications University of Minnesota
Isabel K. Darcy Department of Mathematics University of Iowa
Yuanan Diao Department of Mathematics and Statistics University of North Carolina - Charlotte
Oguz C. Durumeric Department of Mathematics University of Iowa
Christodoulos A. Floudas Department of Chemical Engineering Princeton University
Ece Cazibe Gaffarogullari Department of Chemistry University of Minnesota
Andrew Gillette Department of Mathematics University of Texas
Laura Rocio Gonzalez-Ramirez Department of Mathematics CINVESTAV
Jason E. Gower Institute for Mathematics and its Applications University of Minnesota
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
Kimberly Jean Huerter Department of Mathematics University of Iowa
Filip Jagodzinski Department of Computer Science University of Massachusetts
Tiefeng Jiang Department of Statistics University of Minnesota
Abdul 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
Patrice Koehl Department of Computer Science Genome Center University of California
Peter R. Kramer Department of Mathematical Sciences Rensselaer Polytechnic Institute
Christian E. Laing Department of Mathematics, Chemistry New York University
Juan Latorre Department of Mathematical Sciences Rensselaer Polytechnic Institute
Audrey Lee Computer Science Department University of Massachusetts
Michael Levitt Department of Cell Biology Stanford University
Robert Michael Lewis Department of Mathematics College of William and Mary
Anton Leykin Institute for Mathematics and its Applications University of Minnesota
Roger Y. Lui Department of Mathematical Sciences Worcester Polytechnic Institute
Laura Lurati Institute for Mathematics and its Applications University of Minnesota
Ezra Miller School of Mathematics University of Minnesota
Kenneth C. Millett Department of Mathematics University of California
Alejandro Morales Valencia Department of Computational Sciences University of Guadalajara
Naoto Morikawa   GENOCRIPT
Antonio Mucherino Departimento di Matematica Seconda Università di Napoli
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 Odde Department of Biomedical Engineering University of Minnesota
Hans G. Othmer Department of Mathematics University of Minnesota
Bobby Philip Computer and Computational Sciences Division Los Alamos National Laboratory
Candice Price Department of Mathematics University of Iowa
Rahul Ravindrudu Department of Computer Science Iowa State University
Eric J. Rawdon Department of Mathematics University of St. Thomas
Shantanu Roy Institute of Physics Universität Basel
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
Atilla Sit Department of Mathematics Iowa State University
Daniel Smith Department of Mathematics University of Pittsburgh
Andrew Stein Institute for Mathematics and its Applications University of Minnesota
Ileana Streinu Department of Computer Science Smith College
Vlad Sukhoy Department of Mathematics Iowa State University
Weitao Sun Department of Computer Science New Mexico State University
Vladimir Sverak School of Mathematics University of Minnesota
Michael Tomasini   Rutgers University
Alex Tropsha School of Pharmacy University of North Carolina
Erkan Tüzel Institute for Mathematics and its Applications University of Minnesota
Zhian Wang Institute for Mathematics and its Applications University of Minnesota
Steven Wojtkiewicz Department of Civil Engineering University of Minnesota
Di Wu Department of Mathematics Western Kentucky University
Zhijun Wu Department of Mathematics Iowa State University
Chuan Xue Department of Mathematics University of Minnesota
Ya-xiang Yuan Institute of Computational Mathematics and Scientific/Engineering Computing Chinese Academy of Sciences
Hongchao Zhang Institute for Mathematics and its Applications University of Minnesota
Likun Zheng Math Department University of Minnesota