Topological Problems in Molecular Biology

American Mathematical Society Central Section

Special Session and lead-in Workshop

University of Iowa,

Iowa City IA

March 16-20, 2011

Figures:  Data provided by Sarah Harris, visualized with Swiss-PdbViewer.

Sponsors:

         Mathematics Department, University of Iowa, NSF VIGRE Grant #002242

Integrated DNA Technologies

This year's AMS Spring Central Sectional meeting will be held at the University of Iowa. We are organizing a Special Session, "Topological Problems in Molecular Biology". In connection with the Special Session, we also are organizing an associated Workshop to begin Wednesday evening March 16: so the combined activity will run from Wednesday evening March 16 through Sunday morning March 20. The Workshop will include tutorials in several areas, hands-on software demos, as well as research talks; the Special Session will include research talks and a special panel discussing open problems and future research directions. We are planning the workshop to include tutorials in several areas, hands-on sofware demos, as well as research talks, and a panel on open problems and future research directions.

Click here for actual schedule

NEW: Registration form

NEW: Submit poster abstract (deadline Feb 18)

Tentative schedule

The conference starts Wednesday March 16. We will have a very basic tutorial on Molecular Biology for mathematics graduate students with no biology background at 3:30pm on 3/16. The main part of the conference will start with a conference dinner (including 1-2 talks) at 6pm (?) on Wednesday March 16 . The conference will end at noon on Sunday March 20.

Panel on open problems and future research directions

(Saturday afternoon?)
Jon Simon , Department of Mathematics, University of Iowa
Joanna Sulkowska , Center for Theoretical Biological Physics, University of California San Diego
De Witt Sumners , Department of Mathematics, Florida State University
Stu Whittington , Department of Chemistry, University of Toronto
Lynn Zechiedrich , Department of Molecular Virology and Microbiology, Baylor College of Medicine.

Software demonstrations

(Thursday afternoon?)
3DNA, Andrew Colasanti , Chemistry Department, Rutgers
LinKnot, Radmila Sazdanovic , Department of Mathematics, University of Pennsylvania
KnotPlot, Rob Scharein , Hypnagogic Software

Tutorial Speakers

Topological models of DNA, Dorothy Buck , Department of Mathematics Department of Mathematics, Imperial College London
Polymers, Stephen D Levene , Department of Molecular and Cell Biology, University of Texas at Dallas
DNA geometry and energetics, Sarah Harris , School of Physics and Astronomy, University of Leeds
Protein knotting and tangling, Joanna Sulkowska , Center for Theoretical Biological Physics, University of California San Diego
Chromatin, Yongli Zhang , Department of Cell Biology Yale University School of Medicine

Additional Speakers (tentative)

Angela Angeleska , Department of Mathematics, The University of Tampa
Ken Baker , Department of Mathematics, University of Miami
Elizabeth Denne , Department of Mathematics and Statistics, Smith College
Yuanan Diao , Department of Mathematics, University of North Carolina Charlotte
Claus Ernst , Department of Mathematics, Western Kentucky University
Alexander Grosberg, Department of Physics, New York University
Andreas Hanke , Department of Physics and Astronomy, University of Texas at Brownsville
Sophie Jackson , Department of Chemistry, University of Cambridge
Makkuni Jayaram , Molecular Genetics & Microbiology, University of Texas at Austin
Natasha Jonoska , Department of Mathematics, University of South Florida
Alex J. Levine , Department of Chemistry, UCLA
Erez Lieberman-Aiden , Harvard Society of Fellows, Harvard University
Matt Mastin , Department of Mathematics, University of Georgia
Anthony Montemayor , Department of Mathematics, Western Kentucky University
Jeff Noel, The Center for Theoretical Biological Physics and the Department of Physics, University of California at San Diego
Candice Price, Department of Mathematics, University of Iowa
Eric Rawdon , Department of Mathematics, University of St. Thomas.
Massa Shoura , Department of Molecular and Cell Biology, University of Texas at Dallas
Chris Soteros , Department of Mathematics and Statistics, University of Saskatchewan
Mariel Vazquez , Department of Mathematics, San Francisco State University
Uta Ziegler , Computer Science Department, Western Kentucky University

Registration and Local Information:

Registration Fees: There is no registration for the pre-workshop. All participants are requested to register with the AMS for the AMS meeting. The registration desk will be located in the Iowa Memorial Union and will be open Friday, March 18, 12:00 p.m. - 4:00 p.m. and Saturday, March 19, 7:30 a.m - 4:00 p.m. Registration fees are US$50 for AMS members, US$70 for nonmembers (To be confirmed: speakers may register at the AMS members rate if they not in a mathematics department); and US$5 for students, unemployed mathematicians, and emeritus members. Fees are payable on site by cash, check, or credit card.

Hotel: A block of rooms have been reserved at the Iowa House Hotel, conveniently located adjoining the Iowa Memorial Union. You may call the Iowa House Hotel at 319-335-3513 to reserve a room. Be sure to tell the reservation clerk you are reserving one of the rooms set aside for the "Math meeting" in March, 2011. Rates are US$85 single/double and includes parking, wireless Internet, and continental breakfast. This hotel is on the University of Iowa campus and is the main hotel for our visitors. Registration and the poster session will be held in the same building as this hotel.

Airport: The closest airport is The Eastern Iowa Airport ~ Cedar Rapids (CID). It is 22 miles from UI. Info on airport shuttles will appear later. CID is a relatively small airport, so flights fill up quickly. For best flight times and prices, book early.

For additional local information including more hotels, see
UI math department conference website
AMS conference website

Meeting Scope

Intro to Topological Problems in Molecular Biology Workshop. Ernst and Sumners used tools from abstract knot theory in the late 1980's to determine the topology of the protein-DNA reactions involving the recombinases Tn3 resolvase and phage lambda integrase. Their techniques have since been extended and applied by both mathematicians and biologists to study a variety of protein-DNA complexes. How DNA is packed inside cells affects how genes are regulated. DNA packing often involves a variety of proteins. For example, chromatin is a complex structure of DNA bound to many proteins. Understanding its structure is a very interesting topological problem that is biologically important. Knot theory is also used to study protein folding. Proteins are long, linear polymer chains of amino-acids. The 1-dimensional primary sequence of amino acids dictates the three-dimensional folded shape of a protein molecule and, ultimately, its biological function. Any sufficiently long random chain, including a protein chain, is expected to become knotted with high probability. The fact that few knotted protein structures have been found suggests that biological proteins have folded structures that avoid the formation of knots. Understanding the differences between knotted and unknotted protein structures may therefore provide valuable clues to the underlying principles of the protein folding problem. Moreover, understanding protein knotting could improve our understanding of protein misfolding, which is the molecular basis for several well-known diseases, including sickle-cell disease, bovine spongiform encephalopathy (mad-cow disease), scrapie, and Alzheimer's disease. This special session will bring together mathematicians, biologists, and other scientists. Participants will include those not currently working at the interface of math and biology in order to facilitate new collaborations. We will include a panel discussion on open problems of interest to biologists and topologists. The pre-workshop before the AMS meeting which will include several tutorials, hands-on sofware demos, and research talks. We encourage students, post-docs, and researchers (both estabished and new to this field) to attend both the pre-workshop and the AMS meeting.

Organizers

Isabel Darcy, Department of Mathematics, University of Iowa
Stephen D Levene,Department of Molecular and Cell Biology, University of Texas at Dallas
Jon Simon , Department of Mathematics, University of Iowa