Mathematics of DNA Structure, Function, and Interactions

September 16 - 21, 2007

Mathematics of Molecular and Cellular Biology

Content

Overview

Organizers:

Craig Benham	University of California
Steve Harvey	Georgia Institute of Technology
Wilma Olson	Rutgers, The State University of New Jersey
De Witt Sumners	Florida State University
David Swigon	University of Pittsburgh

Cellular DNA is a long, thread-like molecule with remarkably complex topology. Enzymes that manipulate and control the geometry and topology of cellular DNA perform many important cellular processes,including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity. The understanding of the biological importance of RNA in cellular metabolism is rapidly developing, and structural properties and principles of RNA folding are being worked out. This workshop will concentrate on the role of modern mathematics in elucidating the relationship between nucleic acid structure and function.

Schedule

Sunday, September 16, 2007

12:01 am	Structure & Elasticity (David Swigon chair)
8:30 am - 9:00 am	Registration and coffee	EE/CS 3-176
9:00 am - 9:15 am	Welcome to the IMA Douglas Arnold (University of Minnesota, Twin Cities)	EE/CS 3-180
9:15 am - 10:15 am	DNA Mechanics: Deformation and Recognition Richard Lavery (Centre National de la Recherche Scientifique (CNRS))	EE/CS 3-180
10:15 am - 10:45 am	Coffee	EE/CS 3-176
10:45 am - 11:45 am	Structure and Dynamics of the Four-way DNA Junction David Lilley (University of Dundee)	EE/CS 3-180
11:45 am - 1:45 am	Lunch
1:45 pm - 2:45 pm	Conformational Statistics of DNA Gregory Chirikjian (Johns Hopkins University)	EE/CS 3-180
2:45 pm - 3:15 pm	Coffee	EE/CS 3-176
3:15 pm - 4:15 pm	Supercoiled Minicircle DNA to Probe Topoisomerase-DNA Interactions Lynn Zechiedrich (Baylor College of Medicine)	EE/CS 3-180
4:15 pm - 4:45 pm	Second Chances Discussion	EE/CS 3-180
4:45 pm - 5:00 pm	A New Twist Step-parameter Coupled to the Chirality of the Global Structure of DNA Irwin Tobias (Rutgers, The State University Of New Jersey )	EE/CS 3-180
5:00 pm - 5:15 pm	Smallest Containers Enclosing Random Equilateral Polygons Eric Rawdon (University of St. Thomas)	EE/CS 3-180
5:15 pm - 5:30 pm	On Problems in DNA Elasticity in Which Electrostatic Forces, the Sequence Dependence of Elastic Properties and the Impenetrability of the DNA Molecule Must all be Taken into Account Bernard Coleman (Rutgers, The State University of New Jersey)	EE/CS 3-180

Monday, September 17, 2007

12:01 am	Topology I (De Witt Sumners chair)
8:30 am - 9:00 am	Coffee	EE/CS 3-176
9:00 am - 10:00 am	Local Selection Rules that can Determine Specific Pathways of DNA Unknotting by Type II DNA Topoisomerases Andrzej Stasiak (University of Lausanne)	EE/CS 3-180
10:00 am - 10:30 am	Coffee	EE/CS 3-176
10:30 am - 11:30 am	Breaking DNA Double Helix by Bending Stress Alexander Vologodskii (New York University)	EE/CS 3-180
11:30 am - 1:30 pm	Lunch
1:30 pm - 2:30 pm	Tangle Analysis of Protein-DNA Complexes Isabel Darcy (The University of Iowa)	EE/CS 3-180
2:30 pm - 3:00 pm	Coffee	EE/CS 3-176
3:00 pm - 4:00 pm	Closing the Loop on Protein-DNA Interactions Stephen Levene (University of Texas at Dallas)	EE/CS 3-180
4:00 pm - 4:30 pm	Second Chances Discussion	EE/CS 3-180
4:30 pm - 4:40 pm	Group Pictures	EE/CS 3-180
4:45 pm - 6:15 pm	Reception and Poster Session	Lind 400

Tuesday, September 18, 2007

12:01 am	Chromatin & Packing (Wilma Olson chair)
8:30 am - 9:00 am	Coffee	EE/CS 3-176
9:00 am - 10:00 am	The Genomic Code for Nucleosome Positioning Jonathan Widom (Northwestern University)	EE/CS 3-180
10:00 am - 10:30 am	Coffee	EE/CS 3-176
10:30 am - 11:30 am	Nucleosome Dynamics Probed by Torsional Manipulation of Single Chromatin Fibers Ariel Prunell (Institut Jacques Monod)	EE/CS 3-180
11:30 am - 1:30 pm	Lunch
1:30 pm - 2:30 pm	Torque in Stretched and Twisted DNA John Marko (Northwestern University)	EE/CS 3-180
2:30 pm - 3:00 pm	Coffee	EE/CS 3-176
3:00 pm - 4:00 pm	A Novel 'Kink-and-Slide' Mechanism of DNA Folding in Chromatin. Implications for Nucleosome Positioning and p53-DNA Binding Victor Zhurkin (National Cancer Institute)	EE/CS 3-180
4:00 pm - 4:30 pm	Second Chances Discussion	EE/CS 3-180
6:30 pm - 8:30 pm	Workshop Dinner

Wednesday, September 19, 2007

7:00 am - 9:00 pm	Single-Molecules & Motors & Enzymes
8:30 am - 9:00 am	Coffee	EE/CS 3-176
9:00 am - 10:00 am	Real-time Observation of Bacteriophage T4 gp41 Helicase Reveals Unwinding Mechanism Vincent Croquette (École Normale Supérieure)	EE/CS 3-180
10:00 am - 10:30 am	Coffee	EE/CS 3-176
10:30 am - 11:30 am	Helicase Unwinding of dsDNA: Velocity, Processivity, and Collective Effects Meredith Betterton (University of Colorado)	EE/CS 3-180
11:30 am - 1:30 pm	Lunch
1:30 pm - 2:30 pm	Single Molecule Probing of Dynamic Conformation, Molecular Interactions and Dynamic Localizations In-vitro, in Live Cells and in Organisms Shimon Weiss (University of California, Los Angeles)	EE/CS 3-180
2:30 pm - 3:00 pm	Coffee	EE/CS 3-176
3:00 pm - 3:30 pm	Second Chances Discussion	EE/CS 3-180
3:30 pm - 3:45 pm	Macroscopic Modeling of a Circular Rod with Twist and Bend in a Viscous Fluid Sookkyung Lim (University of Cincinnati)	EE/CS 3-180
3:45 pm - 4:00 pm	Assessing the Ability of Continuum Solvation Models to Accurately Model Nucleic Acid Electrostatics Nathan Baker (Washington University School of Medicine)	EE/CS 3-180
4:00 pm - 4:15 pm	Geometric Glows on Biological Surfaces Guowei Wei (Michigan State University)	EE/CS 3-180
4:15 pm - 4:30 pm	Nucleosome and Chromatin Structure and Dynamics Studied by Fluorescence Techniques and Computer Modeling Jörg Langowski (Deutsches Krebsforschungszentrum (Cancer Research)(DKFZ))	EE/CS 3-180

Thursday, September 20, 2007

12:01 am	Transcription Regulation & Biology (Craig Benham chair)
8:30 am - 9:00 am	Coffee	EE/CS 3-176
9:00 am - 10:00 am	Chromatin Compaction as a Topological Problem Andrew Travers (MRC Laboratory of Molecular Biology)	EE/CS 3-180
10:00 am - 10:30 am	Coffee	EE/CS 3-176
10:30 am - 11:30 am	Lysogeny Maintenance: A Matter of Looping Laura Finzi (Emory University)	EE/CS 3-180
11:30 am - 1:30 pm	Lunch
1:30 pm - 2:30 pm	Design, Analysis, and Modeling of Protein-DNA Loops Jason Kahn (University of Maryland)	EE/CS 3-180
2:30 pm - 3:00 pm	Coffee	EE/CS 3-176
3:00 pm - 4:00 pm	Approaches to Understanding the Origin and Management of DNA Stiffness James Maher (Mayo Clinic)	EE/CS 3-180
4:00 pm - 4:30 pm	Second Chances Discussion	EE/CS 3-180
4:30 pm - 4:45 pm	Mathematical Methods to Study the Relative Position of Chromosomes During Interphase in Human Cells F. Javier Arsuaga (San Francisco State University)	EE/CS 3-180
4:45 pm - 5:00 pm	Molecular Seismology: An Inverse Problem in Nanobiology Erik Boczko (Vanderbilt University)	EE/CS 3-180
5:00 pm - 5:15 pm	The Effect of the Nucleoid Protein HU on the Structure, Flexibility, and Ring-closure Properties of DNA Deduced from Monte Carlo Simulation Luke Czapla (Rutgers, The State University Of New Jersey )	EE/CS 3-180
5:15 pm - 5:30 pm	Exploring Salt-mediated Electrostatics in the Association of TATA Binding Proteins to DNA with a Combined Molecular Mechanics/Poisson-Boltzmann Approach Marcia Fenley (Florida State University)	EE/CS 3-180

Friday, September 21, 2007

12:01 am	Topology II (Dorothy Buck chair)
8:30 am - 9:00 am	Coffee	EE/CS 3-176
9:00 am - 10:00 am	Difference Topology: Analysis of DNA Architecture in Complex DNA-protein Assemblies Makkuni Jayaram (The University of Texas at Austin)	EE/CS 3-180
10:00 am - 10:30 am	Coffee	EE/CS 3-176
10:30 am - 11:30 am	The Mathematics of Site-specific Recombination: 1. Difference Topology Experiments and the Mu Tranpososome; 2. DNA Unlinking by XerCD/FtsK Mariel Vazquez (San Francisco State University)	EE/CS 3-180
11:30 am - 12:15 pm	Second Chances + Closing Discussion	EE/CS 3-180

Participants

Name	Department	Affiliation
Pranav Agarwal	Department of Electrical Engineering	University of Minnesota, Twin Cities
Tanuj Aggarwal	Department of Electrical Engineering	University of Minnesota, Twin Cities
Ramzi Alsallaq	Institute of Molecular Biophysics	Florida State University
Douglas Arnold	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
F. Javier Arsuaga	Department of Mathematics	San Francisco State University
Nathan Baker	Department of Biochemistry and Molecular Biophysics	Washington University School of Medicine
Daniel Bates	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Peter Bates	Department of Mathematics	Michigan State University
John Baxter	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Craig Benham	Department of Biomedical Engineering	University of California
Meredith Betterton	Department of Physics	University of Colorado
Yermal Bhat	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
John Bida	Biochemistry Department	Mayo Clinic
Betul Bilgin		University of Minnesota, Twin Cities
Victor Bloomfield	Department of Biochemistry	University of Minnesota, Twin Cities
Erik Boczko	Department of Biomedical Informatics	Vanderbilt University
Richard Braun	Department of Mathematical Sciences	University of Delaware
Dorothy Buck	Department of Mathematics	Imperial College London
Gregory Buck	Department of Mathematics	Saint Anselm College
Carme Calderer	School of Mathematics	University of Minnesota, Twin Cities
Hannah Callender	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Shi-Jie Chen	Department of Physics	University of Missouri
Gregory Chirikjian	Department of Mechanical Engineering	Johns Hopkins University
Bernard Coleman	School of Engineering	Rutgers, The State University of New Jersey
Vincent Croquette	Departement de Physique	École Normale Supérieure
John Crow		University of Minnesota, Twin Cities
Feng Cui		National Institutes of Health
Jeremy Curuksu	School of Engineering and Science	Jacobs University
Luke Czapla	Department of Chemistry and Chemical Biology	Rutgers, The State University Of New Jersey
Isabel Darcy	Department of Mathematics	The University of Iowa
Melanie DeVries	Mathematics Department	The University of Iowa
Yuanan Diao	Department of Mathematics & Statistics	University of North Carolina
Claus Ernst	Department of Mathematics	Western Kentucky University
Marcia Fenley	Institute of Molecular Biophysics	Florida State University
Laura Finzi	Department of Physics	Emory University
Anant Godbole	Department of Mathematics	East Tennessee State University
Jason Gower	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Steve Harvey	School of Biology	Georgia Institute of Technology
Christine Heitsch	School of Mathematics	Georgia Institute of Technology
Milena Hering	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Peter Hinow		University of Minnesota, Twin Cities
Xia Hua	Department of Mathematics	Massachusetts Institute of Technology
Richard James	Department of Aerospace Engineering and Mechanics	University of Minnesota, Twin Cities
Makkuni Jayaram	Department of Molecular Genetics & Microbiology	The University of Texas at Austin
Tiefeng Jiang	School of Statistics	University of Minnesota, Twin Cities
Jason Kahn	Department of Chemistry and Biochemistry	University of Maryland
George Karypis	Department of Computer Science and Engineering	University of Minnesota, Twin Cities
Alex Kasman	Department of Mathematics	College of Charleston
Christopher Kauffman	Department of Computer Science	University of Minnesota, Twin Cities
Christine Kelley	Department of Mathematics	The Ohio State University
Soojeong Kim	Department of Mathematics	The University of Iowa
Debra Knisley	Department of Mathematics	East Tennessee State University
Mark Kon	Department of Mathematics & Statistics	Boston University
Christian Laing	Department of Mathematics, Chemistry	New York University
Jörg Langowski	Division of Biophysics of Macromolecules	Deutsches Krebsforschungszentrum (Cancer Research)(DKFZ)
Richard Lavery	Laboratoire de Biochimie Théorique	Centre National de la Recherche Scientifique (CNRS)
Stephen Levene	Department of Molecular and Cellular Biology	University of Texas at Dallas
Anton Leykin	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
David Lilley	The Nucleic Acid Structure Research Group	University of Dundee
Sookkyung Lim	Department of Mathematical Sciences	University of Cincinnati
Chun-Chi Lin	Department of Mathematics	National Taiwan Normal University
Maggie Linak	CEMS	University of Minnesota, Twin Cities
Roger Lui	Department of Mathematical Sciences	Worcester Polytechnic Institute
Laura Lurati	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
James Maher		Mayo Clinic
Jennifer Mann	Department of Mathematics	The University of Texas at Austin
John Marko	Departments of Biochemistry, Molecular Biology & Cell Biology and Physics	Northwestern University
Kyle McQuisten	Department of Mathematics	The University of Iowa
Ezra Miller	School of Mathematics	University of Minnesota, Twin Cities
Willard Miller Jr.	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Kenneth Millett	Department of Mathematics	University of California
Hyeyoung Moon	Department of Mathematics	The University of Iowa
Maria Giovanna Mora	Department of Mathematics	International School for Advanced Studies (SISSA/ISAS)
Tolkynay Myrzakul	Department of Physics	Kazakh Al-Farabi State National University
Junalyn Navarra-Madsen	Department of Mathematics and Computer Science	Texas Woman's University
Timothy Newman	Department of Physics	Arizona State University
Olalla Nieto Faza	Department of Chemistry	University of Minnesota, Twin Cities
Duane Nykamp	School of Mathematics	University of Minnesota, Twin Cities
Isamu Ohnishi	Department of Mathematical and Life Sciences	Hiroshima University
Wilma Olson	Department of Chemistry and Chemical Biology	Rutgers, The State University of New Jersey
John Oprea	Department of Mathematics	Cleveland State University
Hans Othmer	Department of Mathematics	University of Minnesota, Twin Cities
Jinhae Park	Department of Mathematics	Purdue University
Ariel Prunell	Genome Biology	Institut Jacques Monod
Teresita Ramirez-Rosas	Department of Mathematics	University of California
Graham Randall	Department ofStructural & Computational Biology and Molecular Biophysics	Baylor College of Medicine
Huzefa Rangwala	Department of Computer Science	University of Minnesota, Twin Cities
Eric Rawdon	Department of Mathematics	University of St. Thomas
Dale Rolfsen	Department of Mathematics	University of British Columbia
Ioulia Rouzina	Biochemistry, Molecular Biology and Biophysics	University of Minnesota, Twin Cities
George Rublein	Department of Mathematics	College of William and Mary
Deena Schmidt	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Chehrzad Shakiban	Institute of Mathematics and its Applications	University of Minnesota, Twin Cities
Koya Shimokawa	Department of Mathematics	Saitama University
David Snyder	Department of Mathematics	Texas State University-San Marcos
Andrzej Stasiak	Laboratoire d'Analyse Ultrastructurale	University of Lausanne
Andrew Stein	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
De Witt Sumners		Florida State University
Vladimir Sverak	School of Mathematics	University of Minnesota, Twin Cities
David Swigon	Department of Mathematics	University of Pittsburgh
Irwin Tobias	Department of Chemistry and Chemical Biology	Rutgers, The State University Of New Jersey
Andrew Travers	Department of Cell Biology	MRC Laboratory of Molecular Biology
Erkan Tüzel	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Lawrence Varela	Department of Computer Science	San Francisco State University
Tanya Vassilevska	Center for Applied Scientific Computing	Lawrence Livermore National Laboratory
Mariel Vazquez	Department of Mathematics	San Francisco State University
Alexander Vologodskii	Department of Chemistry	New York University
Haiyan Wang	Department of Mathematical Sciences and Applied Computing	Arizona State University
Zhian Wang	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Annika Wedemeier	BAD ADDRESS	German Cancer Research Center
Guowei Wei	Department of Mathematics	Michigan State University
Shimon Weiss	Department of Chemistry and Biochemistry	University of California, Los Angeles
Jonathan Widom	Department of Chemistry	Northwestern University
Peng Wu		Rockefeller University
Zhijun Wu	Department of Mathematics	Iowa State University
Yanji Xu		Minnesota Supercomputing Institute
Lynn Zechiedrich	Department of Molecular Virology & Microbiology, Biochemistry & Molecular Biology	Baylor College of Medicine
Hongchao Zhang	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Guohui Zheng	Department of Chemistry and Chemical Biology	Rutgers, The State University Of New Jersey
Victor Zhurkin	Laboratory of Cell Biology	National Cancer Institute