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IMA Annual Program Year Workshop

Mathematics of DNA Structure, Function, and Interactions

September 16-21, 2007
Organizers:
Craig John Benham Mathematics, University of California, Davis
Stephen Harvey Biology, Georgia Institute of Technology
Wilma K. Olson Chemistry and Chemical Biology, Rutgers University
De Witt L. Sumners Mathematics, Florida State University
David Swigon Mathematics, University of Pittsburgh

Schedule Participants Program Application Feedback
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Abstracts and Talk Materials Dining Guide
Tutorial: Mathematics of Nucleic Acids, September 15, 2007
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Description:

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. This workshop will concentrate on the role of modern mathematics in elucidating the relationship between DNA structure and function.

Schedule

Week 1: Sunday | 
Week 2: Monday | Tuesday | Wednesday | Thursday | Friday | 
  Sunday, September 16
Structure & Elasticity (David Swigon chair)
8:30a-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-10:15a DNA mechanics: Deformation and recognition Richard Lavery (Centre National de la Recherche Scientifique (CNRS)) EE/CS 3-180
10:15a-10:45a Coffee   EE/CS 3-176
10:45a-11:45a Structure and dynamics of the four-way DNA junction David M.J. Lilley (University of Dundee) EE/CS 3-180
11:45a-1:45a Lunch    
1:45p-2:45p Conformational statistics of DNA Gregory S. Chirikjian (Johns Hopkins University) EE/CS 3-180
2:45p-3:15p Coffee   EE/CS 3-176
3:15p-4:15p Supercoiled minicircle DNA to probe topoisomerase-DNA interactions Lynn Zechiedrich (Baylor College of Medicine) EE/CS 3-180
4:15p-4:45p Second Chances Discussion   EE/CS 3-180
4:45p-5:00p A new twist step-parameter coupled to the chirality of the global structure of DNA Irwin Tobias (Rutgers University) EE/CS 3-180
5:00p-5:15p Smallest containers enclosing random equilateral polygons Eric Rawdon (University of St. Thomas) EE/CS 3-180
5:15p-5:30p 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 D. Coleman (Rutgers University) EE/CS 3-180
  Monday, September 17
Topology I (De Witt Sumners chair)
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-10:00a 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
10:00a-10:30a Coffee   EE/CS 3-176
10:30a-11:30a Breaking DNA double helix by bending stress Alexander Vologodskii (New York University) EE/CS 3-180
11:30a-1:30p Lunch    
1:30p-2:30p Tangle analysis of protein-DNA complexes Isabel K. Darcy (University of Iowa) EE/CS 3-180
2:30p-3:00p Coffee   EE/CS 3-176
3:00p-4:00p Closing the loop on protein-DNA interactions Stephen D. Levene (University of Texas at Dallas) EE/CS 3-180
4:00p-4:30p Second Chances Discussion   EE/CS 3-180
4:30p-4:40p Group Pictures   EE/CS 3-180
4:45p-6:15p Reception and Poster Session
Lind Hall 400
On the association of proteins to circular DNA: modeling the facilitated rate of association Ramzi Alsallaq (Florida State University)
Mathematical methods to study the relative position of chromosomes during interphase in human cells F. Javier Arsuaga (San Francisco State University)
Chicken and yeast nucleosomal DNA sequences differ at the ends: A possible relation to the linker histone binding Feng Cui (National Institutes of Health)
Free energy simulation studies of sharp DNA bending using a global restraint of space-invariant internucleotides rotation axis Jeremy Curuksu (Jacobs University)
Generating a tangle table for DNA protein complex modeling Melanie DeVries (University of Iowa)
Modelling DNA unknotting by type II topoisomerases Xia Hua (Massachusetts Institute of Technology)
Mariel Vazquez (San Francisco State University)
DNA solitons as an explanation for codon bias Alex Kasman (College of Charleston)
A tangle analysis of a DNA-protein complex which binds four DNA segments Soojeong Kim (University of Iowa)
Nucleosome and chromatin structure and dynamics studied by fluorescence techniques and computer modeling Jörg Langowski (Deutsches Krebsforschungszentrum (Cancer Research)(DKFZ))
Macroscopic modeling of a circular rod with twist and bend in a viscous fluid Sookkyung Lim (University of Cincinnati)
Tangle models for recombinase action Kyle McQuisten (University of Iowa)
Polynomial invariants, knot distances and topoisomerase action Hyeyoung Moon (University of Iowa)
Signature curves in classifying DNA supercoils Chehrzad Shakiban (University of Minnesota)
Developing computer software for detecting fluorescent chromosome labels Lawrence Varela (San Francisco State University)
Modelling diffusional transport in the interphase cell nucleus Annika Wedemeier (German Cancer Research Center)
Geometric flows on biological surfaces Guowei Wei (Michigan State University)
A DNA base-pair step parameter database Guohui Zheng (Rutgers University)
  Tuesday, September 18
Chromatin & Packing (Wilma Olson chair)
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-10:00a The genomic code for nucleosome positioning Jonathan Widom (Northwestern University) EE/CS 3-180
10:00a-10:30a Coffee   EE/CS 3-176
10:30a-11:30a Nucleosome dynamics probed by torsional manipulation of single chromatin fibers Ariel Prunell (Institut Jacques Monod) EE/CS 3-180
11:30a-1:30p Lunch    
1:30p-2:30p Torque in stretched and twisted DNA John F. Marko (Northwestern University) EE/CS 3-180
2:30p-3:00p Coffee   EE/CS 3-176
3:00p-4:00p A novel 'Kink-and-Slide' mechanism of DNA folding in chromatin. Implications for nucleosome positioning and p53-DNA binding Victor B. Zhurkin (National Cancer Institute) EE/CS 3-180
4:00p-4:30p Second Chances Discussion   EE/CS 3-180
6:30p-8:30p Workshop Dinner   Kikugawa at Riverplace
43 Main St. SE. Minneapolis, MN 55414
(612) 378-3006 
  Wednesday, September 19
Single-Molecules & Motors & Enzymes (Steve Harvey chair)
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-10:00a Real-time observation of bacteriophage T4 gp41 helicase reveals unwinding mechanism Vincent Croquette (École Normale Supérieure) EE/CS 3-180
10:00a-10:30a Coffee   EE/CS 3-176
10:30a-11:30a Helicase unwinding of dsDNA: velocity, processivity, and collective effects Meredith Betterton (University of Colorado) EE/CS 3-180
11:30a-1:30p Lunch    
1:30p-2:30p Single molecule probing of dynamic conformation, molecular interactions and dynamic localizations in-vitro, in live cells and in organisms Shimon Weiss (University of California) EE/CS 3-180
2:30p-3:00p Coffee   EE/CS 3-176
3:00p-3:30p Second Chances Discussion   EE/CS 3-180
3:30p-3:45p Macroscopic modeling of a circular rod with twist and bend in a viscous fluid Sookkyung Lim (University of Cincinnati) EE/CS 3-180
3:45p-4:00p Assessing the ability of continuum solvation models to accurately model nucleic acid electrostatics Nathan A. Baker (Washington University School of Medicine) EE/CS 3-180
4:00p-4:15p Geometric flows on biological surfaces Guowei Wei (Michigan State University) EE/CS 3-180
4:15p-4:30p 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
Transcription Regulation & Biology (Craig Benham chair)
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-10:00a Chromatin compaction as a topological problem Andrew Travers (MRC Laboratory of Molecular Biology) EE/CS 3-180
10:00a-10:30a Coffee   EE/CS 3-176
10:30a-11:30a Lysogeny maintenance: a matter of looping Laura Finzi (Emory University) EE/CS 3-180
11:30a-1:30p Lunch    
1:30p-2:30p Design, analysis, and modeling of protein-DNA loops Jason D. Kahn (University of Maryland) EE/CS 3-180
2:30p-3:00p Coffee   EE/CS 3-176
3:00p-4:00p Approaches to understanding the origin and management of DNA stiffness James Maher (Mayo Clinic) EE/CS 3-180
4:00p-4:30p Second Chances Discussion   EE/CS 3-180
4:30p-4:45p 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
4:45p-5:00p Molecular seismology: An inverse problem in nanobiology Erik Boczko (Vanderbilt University) EE/CS 3-180
5:00p-5:15p 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 University) EE/CS 3-180
5:15p-5:30p Exploring salt-mediated electrostatics in the association of TATA binding proteins to DNA with a combined molecular mechanics/Poisson-Boltzmann approach Marcia O. Fenley (Florida State University) EE/CS 3-180
  Friday, September 21
Topology II (Dorothy Buck chair)
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-10:00a Difference topology: Analysis of DNA architecture in complex DNA-protein assemblies Makkuni Jayaram (University of Texas) EE/CS 3-180
10:00a-10:30a Coffee   EE/CS 3-176
10:30a-11:30a 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
11:30a-12:15p Second Chances + Closing Discussion   EE/CS 3-180

LIST OF CONFIRMED PARTICIPANTS

Name Department Affiliation
Pranav Agarwal Electrical Engeneering University of Minnesota
Tanuj Aggarwal Electrical Engeneering University of Minnesota
Ramzi Alsallaq Institute of Molecular Biophysics Florida State University
Douglas N. Arnold Institute for Mathematics and its Applications University of Minnesota
F. Javier Arsuaga Department of Mathematics San Francisco State University
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
Peter W. Bates Department of Mathematics Michigan State University
John Baxter Institute for Mathematics and its Applications University of Minnesota
Craig Benham Department of Biomedical Engineering University of California
Meredith Betterton Department of Physics University of Colorado
Yermal Sujeet Bhat Institute for Mathematics and its Applications University of Minnesota
John Bida Biochemistry Department Mayo Clinic
Betul Bilgin   University of Minnesota
Victor Bloomfield Department of Biochemistry University of Minnesota
Erik Boczko Department of Biomedical Informatics Vanderbilt University
Richard J. Braun Department of Mathematical Sciences University of Delaware
Dorothy E. Buck Department of Mathematics Imperial College London
Gregory Buck Department of Mathematics Saint Anselm College
Maria-Carme T. Calderer School of Mathematics University of Minnesota
Hannah Callender Institute for Mathematics and its Applications University of Minnesota
Shi-Jie Chen Department of Physics University of Missouri
Gregory S. Chirikjian Department of Mechanical Engineering Johns Hopkins University
Bernard D. Coleman School of Engineering Rutgers University
Vincent Croquette Departement de Physique École Normale Supérieure
John Crow   University of Minnesota
Feng Cui   National Institutes of Health
Jeremy Curuksu School of Engineering and Science Jacobs University
Luke Czapla Department of Chemistry and Chemical Biology Rutgers University
Isabel K. Darcy Department of Mathematics University of Iowa
Melanie DeVries Mathematics Department University of Iowa
Yuanan Diao Department of Mathematics and Statistics University of North Carolina - Charlotte
Claus Ernst Department of Mathematics Western Kentucky University
Marcia O. Fenley Department of Physics Florida State University
Laura Finzi Department of Physics Emory University
Anant Godbole Department of Mathematics East Tennessee State University
Jason E. Gower Institute for Mathematics and its Applications University of Minnesota
Steve Harvey School of Biology Georgia Institute of Technology
Christine E. Heitsch School of Mathematics Georgia Institute of Technology
Milena Hering Institute for Mathematics and its Applications University of Minnesota
Peter Hinow Institute for Mathematics and its Applications University of Minnesota
Xia Hua Department of Mathematics Massachusetts Institute of Technology
Richard D. James Department of Aerospace Engineering and Mechanics University of Minnesota
Makkuni Jayaram Department of Molecular Genetics & Microbiology University of Texas
Tiefeng Jiang Department of Statistics University of Minnesota
Jason D. Kahn Department of Chemistry and Bio-Chemistry University of Maryland
George Karypis Department of Computer Science and Engineering University of Minnesota
Alex Kasman Department of Mathematics College of Charleston
Christopher Kauffman Department of Computer Science University of Minnesota
Christine A Kelley Department of Mathematics Ohio State University
Soojeong Kim Department of Mathematics University of Iowa
Debra Knisley Department of Mathematics East Tennessee State University
Mark Kon Department of Mathematics and Statistics Boston University
Christian E. 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 D. Levene Department of Molecular and Cellular Biology University of Texas at Dallas
Anton Leykin Institute for Mathematics and its Applications University of Minnesota
David M.J. 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
Roger Y. Lui Department of Mathematical Sciences Worcester Polytechnic Institute
Laura Lurati Institute for Mathematics and its Applications University of Minnesota
James Maher   Mayo Clinic
Jennifer Mann Department of Mathematics University of Texas
John F. Marko Departments of Biochemistry, Molecular Biology & Cell Biology and Physics Northwestern University
Kyle McQuisten Department of Mathematics University of Iowa
Ezra Miller Department of Mathematics University of Minnesota
Willard Miller Jr. Institute for Mathematics and its Applications University of Minnesota
Kenneth C. Millett Department of Mathematics University of California
Hyeyoung Moon Department of Mathematics University of Iowa
Maria Giovanna Mora Department of Mathematics International School for Advanced Studies (SISSA/ISAS)
Tolkynay Myrzakul Physics Department 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
Duane Nykamp School of Mathematics University of Minnesota
Isamu Ohnishi Department of Mathematical and Life Sciences Hiroshima University
Wilma K. Olson Department of Chemistry and Chemical Biology Rutgers University
John Oprea Department of Mathematics Cleveland State University
Hans G. Othmer Department of Mathematics University of Minnesota
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
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
George Rublein Department of Mathematics College of William and Mary
Deena Schmidt Institute for Mathematics and its Applications University of Minnesota
Chehrzad Shakiban Institute of Mathematics and its Application University of Minnesota
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
De Witt L. Sumners Department of Mathematics Florida State University
Vladimir Sverak School of Mathematics University of Minnesota
David Swigon Department of Mathematics University of Pittsburgh
Irwin Tobias Department of Chemistry and Chemical Biology Rutgers University
Andrew Travers Department of Cell Biology MRC Laboratory of Molecular Biology
Erkan Tüzel Institute for Mathematics and its Applications University of Minnesota
Lawrence Varela 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
Annika Wedemeier Biophysics of Macromolecules Department German Cancer Research Center
Guowei Wei Department of Mathematics Michigan State University
Shimon Weiss Department of Chemistry and Bio-Chemistry University of California
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
Guohui Zheng Department of Chemistry and Chemical Biology Rutgers University
Victor B. Zhurkin Laboratory of Cell Biology National Cancer Institute

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