University of Minnesota
University of Minnesota
http://www.umn.edu/
IMA Web
Mathematics of Materials and Macromolecules: Multiple Scales, Disorder, and Singularities, September 2004 - June 2005

IMA Workshop:

Experiments in Physical Biology

Part I: May 2-6, 2005
Part II: May 16-19, 2005

Organizers:

John H. Maddocks
Institut de Mathématiques Bernoulli (IMB)
FSB (School of Basic Sciences)
EPFL (Swiss Federal Institute of Technology)
John.Maddocks@epfl.ch
http://lcvmsun9.epfl.ch/~jhm/

Robert Phillips
Mechanical Engineering and Applied Physics
California Institute of Technology (Caltech)
phillips@aero.caltech.edu
http://www.me.caltech.edu/faculty/phillips.html

Schedule
Program Application Feedback
Participants
   Part II
Dining Guide Maps
Talk Materials (Part I) Abstracts
John H. Maddocks Introductory tutorial on the basics of DNA April 28, 2005

Organizers
John H. Maddocks
    John.Maddocks@epfl.ch
Institut de Mathématiques Bernoulli (IMB)
FSB (School of Basic Sciences)  
EPFL (Swiss Federal Institute of Technology)
Robert Phillips
    phillips@aero.caltech.edu
Mechanical Engineering and Applied Physics   California Institute of Technology (Caltech)
Presenters for Part I
Zev Bryant Department of Biochemistry
Stanford University
Nikolaus P. Ernsting Department of Chemistry
Humboldt University, Berlin
Nicholas Hud School of Chemistry and Biochemistry
Georgia Institute of Technology
Jason D. Kahn Department of Chemistry and Biochemistry
University of Maryland
M. Thomas Record, Jr. Department of Chemistry
University of Wisconsin
Robert Schleif Department of Biology
Johns Hopkins University
Jonathan Widom Department of Biochemistry, Molecular Biology and Cell Biology
Northwestern University
Presenters for Part II
Sarah Keller Department of Chemistry
University of Washington
Deborah Leckband Department of Chemical and Biomolecular Engineering
University of Illinois - Urbana-Champaign
Thomas D. Pollard Molecular, Cellular & Developmental Biology
Yale University
Paul Selvin Department of Physics
University of Illinois - Urbana-Champaign

Abstract: The analysis of biological systems is becoming increasingly quantitative. The emergence of quantitative biology is due in no small part to significant advances in structural biology and single molecule biophysics. The advent of these various techniques has led to a situation in which experimental data has advanced at a much more rapid pace than the models aiming to respond to that data. The aim of this symposium will be to permit experimental leaders in quantitative biology to present in a tutorial fashion the basis of these quantitative insights and to argue for the types of mathematical models needed to respond to these experiments.

This symposium will take place during two different one week periods and will involve a relatively small number of speakers in a relaxed atmosphere to encourage maximal discussion.

WORKSHOP SCHEDULE (PART I - MAY 2-6)
Monday Tuesday
MONDAY, MAY 2
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00-10:15 Coffee and Registration

Reception Room EE/CS 3-176

10:15-10:30 Douglas N. Arnold and Organizers Welcome and Introduction
10.30-12:30 Nikolaus P. Ernsting
Humboldt University, Berlin
Molecular probes for DNA structure and dynamics

Slides: Part I    Part II

12:30
Lunch Break
2:30-4:30 Nicholas Hud
Georgia Institute of Technology
DNA condensation
TUESDAY, MAY 3
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:30-10:30 Nikolaus P. Ernsting
Humboldt University, Berlin
Molecular probes for DNA structure and dynamics

Slides: Part I    Part II

10:30-11:00 Coffee Break Reception Room EE/CS 3-176
11.00-1:00 Jason D. Kahn
University of Maryland
DNA bending, twisting, and looping in the control of transcription
1:00
Lunch Break
2:30-4:30 Jonathan Widom
Northwestern University
Sequence-dependent DNA mechanics in very small DNA circles and nucleosomes
4:30-6:00
Reception
400 Lind Hall
WEDNESDAY, MAY 4
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:30-10:30 Nicholas Hud
Georgia Institute of Technology
DNA condensation
10:30-11:00 Coffee Break Reception Room EE/CS 3-176
11:00-12:00 Jason D. Kahn
University of Maryland
DNA bending, twisting, and looping in the control of transcription
12:00-1:00 Jonathan Widom
Northwestern University
Sequence-dependent DNA mechanics in very small DNA circles and nucleosomes
1:00
Lunch Break
2:30-4:30 Zev Bryant
Stanford University
Single molecule mechanics of DNA
THURSDAY, MAY 5
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:30-10:30 Zev Bryant
Stanford University
Single molecule mechanics of DNA
10:30-11:00 Coffee Break Reception Room EE/CS 3-176
11:00-1:00 Robert Schleif
Johns Hopkins University
DNA looping: biology and mechanisms
1:00
Lunch Break
2:30-4:30 M. Thomas Record, Jr.
University of Wisconsin
Wrapping of DNA on protein surfaces
FRIDAY, MAY 6
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:30-10:30 Robert Schleif
Johns Hopkins University
DNA looping: biology and mechanisms
10:30-11:00 Coffee Break Reception Room EE/CS 3-176
11:00-12:00 M. Thomas Record, Jr.
University of Wisconsin
Large-scale conformational changes in RNA polymerase and promoter DNA in transcription initiation
Monday Tuesday
WORKSHOP SCHEDULE (PART II - MAY 16-19)
Monday Tuesday
MONDAY, MAY 16
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
8:30-9:00 Coffee and Registration Reception Room EE/CS 3-176

9:00-9:30 Robert Phillips
California Institute of Technology
Introduction and overview
9:30-11:00 Deborah Leckband
University of Illinois - Urbana-Champaign
Biological adhesion: molecules to tissues
11:00-11:30
coffee
Reception Room EE/CS 3-176
11:30-12:00 questions/discussion
12:00
lunch
1:30-3:00 Deborah Leckband
University of Illinois - Urbana-Champaign
Biological adhesion: dynamics, organization, and function
3:00-3:30
coffee
Reception Room EE/CS 3-176
3:30-4:00 questions/discussion
TUESDAY, MAY 17
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00-9:30 coffee Reception Room EE/CS 3-176
9:30-11:00 Paul Selvin
University of Illinois - Urbana-Champaign
Molecular motors I

Publications

11:00-11:30
coffee
Reception Room EE/CS 3-176
11:30-12:00 questions/discussion
12:00-1:30
lunch
1:30-3:00 Paul Selvin
University of Illinois - Urbana-Champaign
Molecular motors II, DNA haplotyping, and ion channels

Publications

3:00-3:30
coffee
Reception Room EE/CS 3-176
3:30-4:00 questions/discussion
4:15
Reception
400 Lind Hall
WEDNESDAY, MAY 18
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00-9:30 coffee Reception Room EE/CS 3-176
9:30-11:00 Sarah L. Keller
University of Washington
A gentle introduction to lipid membranes and resulting miscibility phase diagrams
11:00-11:30 coffee Reception Room EE/CS 3-176
11:30-12:00 questions/discussion
12:00-1:30
lunch
1:30-3:00 Sarah L. Keller
University of Washington
Seeing spots: experimentally determining lipid miscibility phase diagrams in free-floating vesicles, supported membranes, and monolayers at an air-water interface
3:00-3:30 coffee Reception Room EE/CS 3-176
3:30-4:00 questions/discussion
THURSDAY, MAY 19
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00-9:30 coffee Reception Room EE/CS 3-176
9:30-11:00 Thomas D. Pollard
Yale University
Quantitative analysis of actin-based cellular motility and cytokinesis
11:00-11:30 coffee Reception Room EE/CS 3-176
11:30-12:00
questions/discussion
12:00-1:00
lunch
1:00-2:30 Thomas D. Pollard
Yale University
Research frontiers and opportunities
2:30 Concluding remarks by Robert Phillips
Monday Tuesday

PART I: MAY 2-6, 2005 LIST OF CONFIRMED PARTICIPANTS

Name Department Affiliation
Arnaud Amzallag DMA Swiss Federal Institute of Technology at Lausanne (EPFL)
Irene Arias Applied Mathematics III Polytechnic University Catalonia
Douglas N. Arnold Institute for Mathematics and its Applications University of Minnesota
Donald G. Aronson Institute for Mathematics and its Applications University of Minnesota
Marino Arroyo Mathematica de Catalunya Polytechnic University of Catalunya
Thomas C. Bishop Center for Bioenvironmental Research Tulane University
Zev Bryant Department of Molecular and Cell Biology University of California - Berkeley
Maria-Carme T. Calderer School of Mathematics University of Minnesota
Thomas Cheatham Medical Chemistry / Pharmaceutics University of Utah
Qianyong Chen Institute for Mathematics and its Applications University of Minnesota
Rustum Choksi Department of Mathematics Simon Fraser University
Ludovica Cecilia Cotta-Ramusino SB-IMB-LCVMM Swiss Federal Institute of Technology at Lausanne (EPFL)
Antonio DeSimone Applied Mathematics SISSA-Italy
Antonio Di Carlo Department of Studies on Structures Universita` degli Studi Roma Tre
Brian DiDonna Institute for Mathematics and its Applications University of Minnesota
Ryan S. Elliott   University of Michigan
Nikolaus Ernsting Institut für Chemie Humboldt University of Berlin
Ralf Everaers   Max-Planck-Institut for Physics of Complex Sys
Wayne Falk Oral Science University of Minnesota
Eugene C. Gartland Jr. Department of Mathematical Sciences Kent State University
Robert Gulliver School of Mathematics University of Minnesota
Leesa Maree Heffler Institut de Mathematiques Bernoulli Swiss Federal Institute of Technology Lausanne
Chun-Hsiung Hsia Department of Mathematics Indiana University
Nicholas Hud School of Chemistry and Biochemistry Georgia Institute of Technology
Chris Hunter Department of Chemistry University of Sheffield
Richard D. James Department of Aerospace Engineering and Mechanics University of Minnesota
Paul Jardine Department of Diagnostic/Biological Sciences University of Minnesota
Robert L. Jerrard Department of Mathematics University of Toronto
Sookyung Joo Institute for Mathematics and its Applications University of Minnesota
Nara Jung Department of Mathematics University of Toronto
Jason Kahn Department of Chemistry and Biochemistry University of Maryland
Chiu Yen Kao Institute for Mathematics and its Applications University of Minnesota
David Kinderlehrer Department of Mathematics Carnegie Mellon University
Richard Kollar   University of Minnesota
Matthias Kurzke Institute for Mathematics and its Applications University of Minnesota
Filip Lankas Bernoulli Institute for Mathematics Swiss Federal Institute of Technology (EPFL)
Richard Lavery Laboratoire de Biochimie Theorique CNRS
Frederic Legoll   University of Minnesota
Benedict Leimkuhler Department of Mathematics and Computer Science University of Leicester
Stephen Levene Molecular & Cell Biology University of Texas - Dallas
Debra Lewis Institute for Mathematics and its Applications University of Minnesota
Xiantao Li   University of Minnesota
Chun Liu Department of Mathematics Pennsylvania State University
Hailiang Liu Department of Mathematics Iowa State University
Mitchell Luskin School of Mathematics University of Minnesota
John H. Maddocks Institut de Mathématiques Bernoulli Swiss Federal Institute of Technology Lausanne
Karsten Matthies Institut fuer Mathematik I Freie University Berlin
Julie C. Mitchell Departments of Mathematics and Biochemistry University of Wisconsin - Madison
Sharareh Noorbaloochi Department of Electrical Engineering University of Minnesota
Duane Nykamp School of Mathematics University of Minnesota
Peter Palffy-Muhoray Liquid Crystal Institute Kent State University
Peter Philip Institute for Mathematics and its Application University of Minnesota
Robert Phillips Division of Engineering California Institute of Technology
Andrew Pohorille   NASA Ames Research Center
Ashok Prasad Physics Department Brandeis University
M. Thomas Record Department of Chemistry University of Wisconsin - Madison
Rolf Ryham Department of Mathematics Pennsylvania State University
Arnd Scheel Institute for Mathematics and its Applications University of Minnesota
Robert Schleif Department of Biology Johns Hopkins University
Tim P. Schulze Department of Mathematics University of Tennessee
George R Sell School of Math University of Minnesota
Tien-Tsan Shieh Department of Mathematics Indiana University
Shagi-Di Shih Department of Mathematics University of Wyoming
Valery P. Smyshlyaev   University of Bath-UK
Jiri Sponer Institute of Biophysics Czechoslovakian Academy of Sciences
Peter J. Sternberg Department of Mathematics Indiana University
Vladimir Sverak School of Mathematics University of Minnesota
Alain B. Tchagang Control Science & Dynamical Systems University of Minnesota
Luciano Teresi Mathematical Structures of Materials Physics Universita` degli Studi Roma Tre
Florian Theil Mathematics Institute University of Warwick
Stephen J. Watson ESAM Northwestern University
Jonathan Widom Department of Biochemistry, Molecular Biology and Cell Biology Northwestern University
Jie Yan Department of Physics University of Illinois - Chicago
Aaron Nung Kwan Yip Department of Mathematics Purdue University
Krystyna Zakrzewska Laboratoire de Biochimie Théorique CNRS
Yongli Zhang Department of Physics University of California - Berkeley

PART II: MAY 16-19, 2005 LIST OF CONFIRMED PARTICIPANTS

Name Department Affiliation
Amandine Aftalion Laboratoire Jacques-Louis Lions Universite Pierre et Maris Curie (Paris VI)
Irene Arias Applied Mathematics III Polytechnic University Catalonia
Douglas N. Arnold Institute for Mathematics and its Applications University of Minnesota
Donald G. Aronson Institute for Mathematics and its Applications University of Minnesota
Marino Arroyo Mathematica de Catalunya Polytechnic University of Catalunya
Mary C. Boyce Mechanical Engineering Massachusetts Institute of Technology
Maria-Carme T. Calderer School of Mathematics University of Minnesota
Qianyong Chen Institute for Mathematics and its Applications University of Minnesota
Ae-Gyeong Cheong Center for Advanced Engineering and Films Clemson University
Vassilios Christopoulos Department of Computer Science and Engineering University of Minnesota
Antonio DeSimone Applied Mathematics SISSA-Italy
Antonio Di Carlo Department of Studies on Structures Universita` degli Studi Roma Tre
Brian DiDonna Institute for Mathematics and its Applications University of Minnesota
Qiang Du Department of Mathematics Pennsylvania State University
Yuhua Duan Chemical Engineering and Materials Science University of Minnesota
Ryan S. Elliott   University of Michigan
Wayne Falk Oral Science University of Minnesota
Eugene C. Gartland Jr. Department of Mathematical Sciences Kent State University
Alexander Grosberg Department of Physics and Astronomy University of Minnesota
Robert Gulliver School of Mathematics University of Minnesota
Mikko P. Haataja Mechanical and Aerospace Engineering Princeton University
Hazem Hamdan School of Mathematics University of Minnesota
Mandar M. Inamdar Applied Mechanics California Institute of Technology
Richard D. James Department of Aerospace Engineering and Mechanics University of Minnesota
Robert L. Jerrard Department of Mathematics University of Toronto
Sookyung Joo Institute for Mathematics and its Applications University of Minnesota
Hem Raj Joshi Mathematics and Computer Science Xavier University
Nara Jung Department of Mathematics University of Toronto
Chiu Yen Kao Institute for Mathematics and its Applications University of Minnesota
Sarah L. Keller Department of Chemistry University of Washington
Daniel Kern apt. 204 University of Nevada - Las Vegas
David Kinderlehrer Department of Mathematics Carnegie Mellon University
Richard Kollar   University of Minnesota
Matthias Kurzke Institute for Mathematics and its Applications University of Minnesota
Deborah Leckband Department of Chemical and Biomolecular Engineering University of Illinois - Urbana-Champaign
Frederic Legoll   University of Minnesota
Benedict Leimkuhler Department of Mathematics and Computer Science University of Leicester
Debra Lewis Institute for Mathematics and its Applications University of Minnesota
Xiantao Li   University of Minnesota
Chun Liu Department of Mathematics Pennsylvania State University
Hailiang Liu Department of Mathematics Iowa State University
Mitchell Luskin School of Mathematics University of Minnesota
Marc Q. Ma Department of Computer Science New Jersey Institute of Technology
Karsten Matthies Institut fuer Mathematik I Freie University Berlin
Bagisa Mukherjee Department of Mathematics Penn State Worthington Scranton
Jinhae Park School of Mathematics University of Minnesota
Eric Lee Peterson Physics Department California Institute of Technology
Peter Philip Institute for Mathematics and its Application University of Minnesota
Robert Phillips Division of Engineering California Institute of Technology
Harald Pleiner 55021 Mainz Max Planck Institute for Polymer Research
Thomas D. Pollard Molecular, Cellular & Developmental Biology Yale University
Alejandro Rey Department of Chemical Engineering McGill University, Canada
Rolf Ryham Department of Mathematics Pennsylvania State University
Arnd Scheel Institute for Mathematics and its Applications University of Minnesota
Tim P. Schulze Department of Mathematics University of Tennessee
George R Sell School of Math University of Minnesota
Paul Selvin Department of Physics University of Illinois - Urbana-Champaign
Vivek Shenoy Division of Engineering Brown University
Tien-Tsan Shieh Department of Mathematics Indiana University
Shagi-Di Shih Department of Mathematics University of Wyoming
Valery P. Smyshlyaev   University of Bath-UK
Peter J. Sternberg Department of Mathematics Indiana University
Vladimir Sverak School of Mathematics University of Minnesota
Alain B. Tchagang Control Science & Dynamical Systems University of Minnesota
Luciano Teresi Mathematical Structures of Materials Physics Universita` degli Studi Roma Tre
Florian Theil Mathematics Institute University of Warwick
Stephen J. Watson ESAM Northwestern University
Aaron Nung Kwan Yip Department of Mathematics Purdue University

 

  Mathematics of Materials and Macromolecules: Multiple Scales, Disorder, and Singularities, September 2004 - June 2005