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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

NameDepartmentAffiliation
Douglas N. ArnoldSchool of Mathematics University of Minnesota
Daniel J. BatesInstitute for Mathematics and its Applications University of Minnesota
John BaxterInstitute for Mathematics and its Applications University of Minnesota
Yermal Sujeet BhatInstitute for Mathematics and its Applications University of Minnesota
Jamie BlundellDepartment of Physics University of Cambridge
Maria-Carme T. CaldererSchool of Mathematics University of Minnesota
Hannah CallenderInstitute for Mathematics and its Applications University of Minnesota
Larry Carson 3M
Alessandro CembranDepartment of Chemistry University of Minnesota
Patrick L ColemanDepartment of Biotechnology 3M
Ludovica Cecilia Cotta-RamusinoInstitute for Mathematics and its Applications University of Minnesota
Isabel K. DarcyDepartment of Mathematics University of Iowa
Yuanan DiaoDepartment of Mathematics and Statistics University of North Carolina - Charlotte
Oguz C. DurumericDepartment of Mathematics University of Iowa
Christodoulos A. FloudasDepartment of Chemical Engineering Princeton University
Ece Cazibe GaffarogullariDepartment of Chemistry University of Minnesota
Andrew GilletteDepartment of Mathematics University of Texas
Laura Rocio Gonzalez-RamirezDepartment of Mathematics CINVESTAV
Jason E. GowerInstitute for Mathematics and its Applications University of Minnesota
Esfandiar HaghverdiSchool of Informatics Indiana University
Omar HaqComputational Biology and Molecular Biopphysics Rutgers University
Milena HeringInstitute for Mathematics and its Applications University of Minnesota
Peter HinowInstitute for Mathematics and its Applications University of Minnesota
Kimberly Jean HuerterDepartment of Mathematics University of Iowa
Filip JagodzinskiDepartment of Computer Science University of Massachusetts
Tiefeng JiangDepartment of Statistics University of Minnesota
Abdul Qayyum Masud KhaliqDepartment of Mathematical Sciences Middle Tennessee State University
Soojeong KimDepartment of Mathematics University of Iowa
Debra KnisleyDepartment of Mathematics East Tennessee State University
Patrice KoehlDepartment of Computer Science Genome Center University of California, Davis
Peter R. KramerDepartment of Mathematical Sciences Rensselaer Polytechnic Institute
Christian E. LaingDepartment of Mathematics, Chemistry New York University
Juan C. LatorreDepartment of Mathematical Sciences Rensselaer Polytechnic Institute
Audrey LeeComputer Science Department University of Massachusetts
Michael LevittDepartment of Cell Biology Stanford University
Robert Michael LewisDepartment of Mathematics College of William and Mary
Anton LeykinInstitute for Mathematics and its Applications University of Minnesota
Roger LuiDepartment of Mathematical Sciences Worcester Polytechnic Institute
Laura LuratiInstitute for Mathematics and its Applications University of Minnesota
Ezra MillerSchool of Mathematics University of Minnesota
Kenneth C. MillettDepartment of Mathematics University of California, Santa Barbara
Alejandro Morales ValenciaDepartment of Computational Sciences University of Guadalajara
Naoto Morikawa GENOCRIPT
Antonio MucherinoDepartimento di Matematica Seconda Università di Napoli
Junalyn Navarra-MadsenDepartment of Mathematics and Computer Science Texas Woman's University
Timothy NewmanDepartment of Physics Arizona State University
Duane NykampSchool of Mathematics University of Minnesota
David J. OddeDepartment of Biomedical Engineering University of Minnesota
Hans G. OthmerDepartment of Mathematics University of Minnesota
Bobby PhilipComputer and Computational Sciences Division Los Alamos National Laboratory
Candice PriceDepartment of Mathematics University of Iowa
Rahul RavindruduDepartment of Computer Science Iowa State University
Eric J. RawdonDepartment of Mathematics University of St. Thomas
Shantanu RoyInstitute of Physics Universität Basel
Deena SchmidtInstitute for Mathematics and its Applications University of Minnesota
Tamara Schmidt-Hegge University of Minnesota
Brigitte ServatiusDepartment of Mathematics Worcester Polytechnic Institute
Chehrzad ShakibanInstitute of Mathematics and its Application University of Minnesota
Atilla SitDepartment of Mathematics Iowa State University
Daniel B. SmithDepartment of Mathematics University of Pittsburgh
Andrew M. SteinInstitute for Mathematics and its Applications University of Minnesota
Ileana StreinuDepartment of Computer Science Smith College
Vlad SukhoyDepartment of Mathematics Iowa State University
Weitao SunDepartment of Computer Science New Mexico State University
Vladimir SverakSchool of Mathematics University of Minnesota
Michael Tomasini Rutgers University
Alex TropshaSchool of Pharmacy University of North Carolina
Erkan TüzelInstitute for Mathematics and its Applications University of Minnesota
Zhian WangInstitute for Mathematics and its Applications University of Minnesota
Steven WojtkiewiczDepartment of Civil Engineering University of Minnesota
Di WuDepartment of Mathematics Western Kentucky University
Zhijun WuDepartment of Mathematics Iowa State University
Chuan XueDepartment of Mathematics University of Minnesota
Ya-xiang YuanInstitute of Computational Mathematics and Scientific/Engineering Computing Chinese Academy of Sciences
Hongchao ZhangInstitute for Mathematics and its Applications University of Minnesota
Likun ZhengMathematics Department University of Minnesota