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IMA Annual Program Year Workshop
Mathematics of DNA Structure, Function, and Interactions
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 |
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
Download full schedule »| Sunday | Monday | Tuesday | Wednesday | Thursday | Friday | |||
|---|---|---|---|
| Sunday September 16, 2007 | |||
| Structure & Elasticity (David Swigon chair) | |||
| 8:30am-9:00am | Registration and coffee | EE/CS 3-176 | |
| 9:00am-9:15am | Welcome to the IMA | Douglas Arnold (University of Minnesota) | EE/CS 3-180 |
| 9:15am-10:15am | DNA mechanics: Deformation and recognition | Richard Lavery (Centre National de la Recherche Scientifique (CNRS)) | EE/CS 3-180 |
| 10:15am-10:45am | Coffee | EE/CS 3-176 | |
| 10:45am-11:45am | Structure and dynamics of the four-way DNA junction | David Lilley (University of Dundee) | EE/CS 3-180 |
| 11:45am-1:45am | Lunch | ||
| 1:45pm-2:45pm | Conformational statistics of DNA | Gregory Chirikjian (Johns Hopkins University) | EE/CS 3-180 |
| 2:45pm-3:15pm | Coffee | EE/CS 3-176 | |
| 3:15pm-4:15pm | Supercoiled minicircle DNA to probe topoisomerase-DNA interactions | Lynn Zechiedrich (Baylor College of Medicine) | EE/CS 3-180 |
| 4:15pm-4:45pm | Second Chances Discussion | EE/CS 3-180 | |
| 4:45pm-5:00pm | A new twist step-parameter coupled to the chirality of the global structure of DNA | Irwin Tobias (Rutgers University) | EE/CS 3-180 |
| 5:00pm-5:15pm | Smallest containers enclosing random equilateral polygons | Eric Rawdon (University of St. Thomas) | EE/CS 3-180 |
| 5:15pm-5:30pm | 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 University) | EE/CS 3-180 |
| Monday September 17, 2007 | |||
| Topology I (De Witt Sumners chair) | |||
| 8:30am-9:00am | Coffee | EE/CS 3-176 | |
| 9:00am-10:00am | 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 |
| 10:00am-10:30am | Coffee | EE/CS 3-176 | |
| 10:30am-11:30am | Breaking DNA double helix by bending stress | Alexander Vologodskii (New York University) | EE/CS 3-180 |
| 11:30am-1:30pm | Lunch | ||
| 1:30pm-2:30pm | Tangle analysis of protein-DNA complexes | Isabel Darcy (University of Iowa) | EE/CS 3-180 |
| 2:30pm-3:00pm | Coffee | EE/CS 3-176 | |
| 3:00pm-4:00pm | Closing the loop on protein-DNA interactions | Stephen Levene (University of Texas at Dallas) | EE/CS 3-180 |
| 4:00pm-4:30pm | Second Chances Discussion | EE/CS 3-180 | |
| 4:30pm-4:40pm | Group Pictures | EE/CS 3-180 | |
| 4:45pm-6:15pm | Lind Hall 400 | ||
| Tuesday September 18, 2007 | |||
| Chromatin & Packing (Wilma Olson chair) | |||
| 8:30am-9:00am | Coffee | EE/CS 3-176 | |
| 9:00am-10:00am | The genomic code for nucleosome positioning | Jonathan Widom (Northwestern University) | EE/CS 3-180 |
| 10:00am-10:30am | Coffee | EE/CS 3-176 | |
| 10:30am-11:30am | Nucleosome dynamics probed by torsional manipulation of single chromatin fibers | Ariel Prunell (Institut Jacques Monod) | EE/CS 3-180 |
| 11:30am-1:30pm | Lunch | ||
| 1:30pm-2:30pm | Torque in stretched and twisted DNA | John Marko (Northwestern University) | EE/CS 3-180 |
| 2:30pm-3:00pm | Coffee | EE/CS 3-176 | |
| 3:00pm-4:00pm | 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 |
| 4:00pm-4:30pm | Second Chances Discussion | EE/CS 3-180 | |
| 6:30pm-8:30pm | Workshop Dinner | Kikugawa at Riverplace
43 Main St. SE. Minneapolis, MN 55414 (612) 378-3006 | |
| Wednesday September 19, 2007 | |||
| Single-Molecules & Motors & Enzymes (Steve Harvey chair) | |||
| 8:30am-9:00am | Coffee | EE/CS 3-176 | |
| 9:00am-10:00am | Real-time observation of bacteriophage T4 gp41 helicase reveals unwinding mechanism | Vincent Croquette (École Normale Supérieure) | EE/CS 3-180 |
| 10:00am-10:30am | Coffee | EE/CS 3-176 | |
| 10:30am-11:30am | Helicase unwinding of dsDNA: velocity, processivity, and collective effects | Meredith Betterton (University of Colorado) | EE/CS 3-180 |
| 11:30am-1:30pm | Lunch | ||
| 1:30pm-2:30pm | 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 (UCLA)) | EE/CS 3-180 |
| 2:30pm-3:00pm | Coffee | EE/CS 3-176 | |
| 3:00pm-3:30pm | Second Chances Discussion | EE/CS 3-180 | |
| 3:30pm-3:45pm | Macroscopic modeling of a circular rod with twist and bend in a viscous fluid | | EE/CS 3-180 |
| 3:45pm-4:00pm | Assessing the ability of continuum solvation models to accurately model nucleic acid electrostatics | Nathan Baker (Washington University School of Medicine) | EE/CS 3-180 |
| 4:00pm-4:15pm | Geometric flows on biological surfaces | Guowei Wei (Michigan State University) | EE/CS 3-180 |
| 4:15pm-4:30pm | 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 | |||
| Transcription Regulation & Biology (Craig Benham chair) | |||
| 8:30am-9:00am | Coffee | EE/CS 3-176 | |
| 9:00am-10:00am | Chromatin compaction as a topological problem | Andrew Travers (MRC Laboratory of Molecular Biology) | EE/CS 3-180 |
| 10:00am-10:30am | Coffee | EE/CS 3-176 | |
| 10:30am-11:30am | Lysogeny maintenance: a matter of looping | Laura Finzi (Emory University) | EE/CS 3-180 |
| 11:30am-1:30pm | Lunch | ||
| 1:30pm-2:30pm | Design, analysis, and modeling of protein-DNA loops | Jason Kahn (University of Maryland) | EE/CS 3-180 |
| 2:30pm-3:00pm | Coffee | EE/CS 3-176 | |
| 3:00pm-4:00pm | Approaches to understanding the origin and management of DNA stiffness | James Maher (Mayo Clinic) | EE/CS 3-180 |
| 4:00pm-4:30pm | Second Chances Discussion | EE/CS 3-180 | |
| 4:30pm-4:45pm | 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 |
| 4:45pm-5:00pm | Molecular seismology: An inverse problem in nanobiology | Erik Boczko (Vanderbilt University) | EE/CS 3-180 |
| 5:00pm-5:15pm | 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 |
| 5:15pm-5:30pm | 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 | |||
| Topology II (Dorothy Buck chair) | |||
| 8:30am-9:00am | Coffee | EE/CS 3-176 | |
| 9:00am-10:00am | Difference topology: Analysis of DNA architecture in complex DNA-protein assemblies | Makkuni Jayaram (University of Texas at Austin) | EE/CS 3-180 |
| 10:00am-10:30am | Coffee | EE/CS 3-176 | |
| 10:30am-11:30am | 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 |
| 11:30am-12:15pm | Second Chances + Closing Discussion | EE/CS 3-180 | |
Participants
| NAME | DEPARTMENT | AFFILIATION |
|---|---|---|
| Pranav Agarwal | Department of Electrical Engineering | University of Minnesota |
| Tanuj Aggarwal | Department of Electrical Engineering | University of Minnesota |
| Ramzi Alsallaq | Institute of Molecular Biophysics | Florida State University |
| Douglas Arnold | Institute for Mathematics and its Applications | University of Minnesota |
| 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 |
| Peter 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, Davis |
| Meredith Betterton | Department of Physics | University of Colorado |
| Yermal 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 Braun | Department of Mathematical Sciences | University of Delaware |
| Dorothy Buck | Department of Mathematics | Imperial College London |
| Gregory Buck | Department of Mathematics | Saint Anselm College |
| Maria-Carme 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 Chirikjian | Department of Mechanical Engineering | Johns Hopkins University |
| Bernard 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 Darcy | Department of Mathematics | University of Iowa |
| Melanie DeVries | Mathematics Department | University of Iowa |
| Yuanan Diao | Department of Mathematics & Statistics | University of North Carolina - Charlotte |
| 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 |
| 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 |
| Peter Hinow | Department of Mathematics | University of Minnesota |
| Xia Hua | Department of Mathematics | Massachusetts Institute of Technology |
| Richard James | Department of Aerospace Engineering and Mechanics | University of Minnesota |
| Makkuni Jayaram | Department of Molecular Genetics & Microbiology | University of Texas at Austin |
| Tiefeng Jiang | School of Statistics | University of Minnesota |
| Jason Kahn | Department of Chemistry and Biochemistry | 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 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 & 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 |
| 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 |
| Roger 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 at Austin |
| John Marko | Departments of Biochemistry, Molecular Biology & Cell Biology and Physics | Northwestern University |
| Kyle McQuisten | Department of Mathematics | University of Iowa |
| Ezra Miller | School of Mathematics | University of Minnesota |
| Willard Miller | Institute for Mathematics and its Applications | University of Minnesota |
| Kenneth Millett | Department of Mathematics | University of California, Santa Barbara |
| Hyeyoung Moon | Department of Mathematics | 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 |
| Duane Nykamp | School of Mathematics | University of Minnesota |
| Isamu Ohnishi | Department of Mathematical and Life Sciences | Hiroshima University |
| Wilma Olson | Department of Chemistry and Chemical Biology | Rutgers University |
| John Oprea | Department of Mathematics | Cleveland State University |
| Hans 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, Santa Barbara |
| 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 Applications | 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 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 | 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 |
| Annika Wedemeier | Biophysics of Macromolecules Department | German Cancer Research Center |
| Guowei Wei | Department of Mathematics | Michigan State University |
| Shimon Weiss | Department of Chemistry and Biochemistry | University of California, Los Angeles (UCLA) |
| 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 Zhurkin | Laboratory of Cell Biology | National Cancer Institute |
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