View of San Francisco from Twin Peaks

View of San Francisco from Twin Peaks

Program

Wednesday afternoon
Genentech Hall Auditorium, UCSF Mission Bay campus

1:30pm
Registration
1:45pm
Welcome
2:00–2:40pm
Plenary Speaker
James Berger, mcb.berkeley.edu/index.php?option=com_mcbfaculty&name=bergerj University of California at Berkeley, USA. Understanding a DNA disentangling machine: the structural mechanisms of type II topoisomerases
2:50–3:10pm
Hue Sun Chan, University of Toronto, Canada. Selective segment passages at hooked and twisted juxtapositions consistently rationalize the decatenating, unknotting, and supercoil-suppressing actions of type-II topoisomerases
3:15pm
Coffee Break
3:40–4:00pm
Greg Buck, (http://www.anselm.edu/academic/mathematics/), Saint Anselm College. Modeling Topoisomerase II Search, Recognition, and Action
4:05–4:25pm
Lynn Zechiedrich, (www.bcm.edu/labs/zechiedrich/?PMID=1623), Baylor College of Medicine at Texas, USA. Supercoiled minicircle DNA: a superior substrate for the study of DNA structure and topoisomerase-DNA interactions
4:30–4:50pm
Alexander Vologodskii, New York University, USA. How Conformational Properties of Long DNA Molecules Depend on Their Topology?
4:55–5:15pm
Andrzej Stasiak, (www.unil.ch/cig/page50667_en.html), University of Lausanne, Switzerland. Topological considerations of chromosomal territories.

Thursday Morning
Rock Hall Auditorium, UCSF Mission Bay campus

9:00am
Registration
9:30–10:10am
Plenary Speaker
Carla Tesi, (www.bo.infn.it/pinazza/Mainardi/mariacarlatesi.html), Università di Bologna, Italy. Mathematical models of entangled macromolecules
10:15–10:35am
Janse van Rensburg, (www.math.yorku.ca/Who/Faculty/Rensburg/), York University, Canada Monte Carlo Sampling of Knotted Lattice Polygons.
10:40am
Coffee Break
11:05–11:25am
Christine Soteros, (math.usask.ca/~soteros/) University of Saskatchewan, Canada. Entanglement Complexity of lattice models of polymers: knotting and linking probabilities.
11:30–11:50am
Enzo Orlandini, (www.pd.infn.it/~orlandin) Universita di Padova, Italy. Interplay between writhe and knotting in swollen and compact lattice polygons.
11:55–12:15pm
Rob Scharein, San Francisco State University, USA Modeling type II topoisomerase unknotting action by random strand passage on cubic lattice knots
12:20–2:00pm
Lunch Break

Thursday Afternoon
Genentech Hall Auditorium, UCSF Mission Bay campus

2:00–2:40pm
Plenary Speaker
John Marko, (markolab.bmbcb.northwestern.edu/marko/), Northwestern University, USA Micromechanical study of chromosome organization
2:50–3:10pm
Davide Marenduzzo, (www.ph.ed.ac.uk/~dmarendu/DMarenduzzo.html), University of Edinburgh, Scotland. Entropic repulsion in biopolymers: possible implications on the physics of interphase chromosomes.
3:15pm
Coffee Break
3:40–4:00pm
Cristian Micheletti, (people.sissa.it/~michelet/), Coarse-grained Simulations of DNA knotting in confined geometries.
4:05–4:25pm
Julia Yeomans, (www-thphys.physics.ox.ac.uk/people/JuliaYeomans/home.html), Oxford University, UK. Modeling the dynamics of knotted polymers.
4:30–4:50pm
Valentin Rybenkov, (cheminfo.ou.edu/faculty/vvr.html), University of Arkansas, USA. DNA organization by bacterial condensin MukBEF.
4:55–5:15pm
Giovanni Dietler, (people.epfl.ch/giovanni.dietler), Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland. DNA Properties in 2 Dimensions.
6:00–9:00pm
Poster Session and Reception, Fisher Banquet Room East, Rutter Community Center, UCSF Mission Bay campus
Special guest: Judit Camacho, Executive Director, SACNAS
The two best posters will be awarded travel scholarships to the 2009 SACNAS conference. Up to four posters will be selected to deliver short talks on the Sunday afternoon session.

Friday morning
Genentech Hall Auditorium, UCSF Mission Bay campus

9:00am
Registration
9:30–10:10am
Plenary Speaker
David Sherratt, (www.bioch.ox.ac.uk/aspsite/research/brochure/Sherratt/), University of Oxford, UK. DNA unlinking solutions.
10:15–10:35am
Koya Shimokawa, (www.rimath.saitama-u.ac.jp/lab.en/kshimoka/index-e.html), Saitama University, Japan. Tangle analysis of DNA catenane unlinking by the Xer/FtsK system.
10:40am
Coffee Break
11:05–11:25am
Jorge B. Schvartzman, Centro de Investigaciones Biologias Madrid, Spain. Interplay of DNA Supercoiling and Catenation During the Segregation of Sister Duplexes.
11:30–11:50am
Hugo Cabrera-Ibarra, (sipicyt.ipicyt.edu.mx:7779/web/curriculaInvestigador_new.Portada?p_cvePersonal=39), (IPICYT) Analyzing the products of some enzymes.
11:55–12:15pm
Marcelo E. Tolmasky, California State University at Fullerton, USA. XerCD-mediated recombination at mwr sites is hypersensitive to DNA supercoiling.
12:20–1:45pm
Lunch Break

Friday afternoon
Genentech Hall Auditorium, UCSF Mission Bay campus

2:00–2:20pm
Marcelo Nollman, University of California Berkeley Mechanism of chromosomal segregation by SpoIIIE/FtsK.
2:25–2:45pm
Anca Segall, San Diego State University DNA repair inhibitors and topoisomerase induced damage
2:50–3:10pm
Ian Grainge, University of Oxford, UK. Control of Xer recombination by the FtsK DNA translocase.
3:15pm
Coffee Break
3:40–4:00pm
Dorothy Buck, (www3.imperial.ac.uk/people/d.buck), Imperial College London, UK. DNA Knots and Links arising from Protein Actions
4:05–4:25pm
Sonia Trigueros, (nanomed.bioch.ox.ac.uk/index.php?option=com_content&view=article&id=20&Itemid=6), Oxford University, UK. DNA Conformation and Biomolecular Motors: New Nanomedicine Research Targets.
4:30–4:50pm
Craig Benham, (genomics.ucdavis.edu/benham/benham.php), University of California Davis, USA. Roles of Topologically Driven DNA Structural Transitions in Regulation
4:55–5:15pm
Sean Colloms, (www.gla.ac.uk:443/ibls/staff/grants.php?who=PGedeS), University of Glasgow, Scotland.

Saturday morning
Science 210, San Francisco State University main campus

7:30am
Registration and Coffee
8:30–9:30am
Plenary Speaker
John Luecke, (www.ma.utexas.edu/users/luecke/), University of Texas at Austin, USA. Knot Theoretic Analysis of Difference Topology Experiments on a Protein-DNA complex. [AMS abstract No. 1049-57-85]
9:30–10:00am
Makkuni Jayaram, (www.biosci.utexas.edu/mgm/people/faculty/profiles/jayaram.htm), University of Texas at Austin, USA. Analyzing DNA Transposition and Recombination by Difference Topology. [AMS abstract No. 1049-03-41]
10:00–10:30am
Isabel K. Darcy, (www.math.uiowa.edu/~idarcy/), University of Iowa, USA. Tangle analysis of protein-DNA complexes. [AMS abstract No. 1049-57-53]
10:30–11:00am
Stephen D. Levene, (www.utdallas.edu/biology/faculty/research/levene.html), University of Texas at Dallas, USA. New Mechanistic Insights into Flp and Cre Recombination from DNA Loop-closure Kinetics. [AMS abstract No. 1049-92-150]
11:00am
AMS plenary
12:00–2:00pm
Lunch Break

Saturday afternoon
Science 210, San Francisco State University main campus

2:00–2:45pm
AMS plenary
3:00–4:00pm
Plenary Speaker
Todd Yeates, (www.doe-mbi.ucla.edu/~yeates/), University of California at Los Angeles, USA. Finding and Designing Novel Knotted Protein Structures.
4:00-4:30pm
Eric J. Rawdon, (george.math.stthomas.edu/rawdon/index.php), University of St. Thomas at Minnesota, USA. Measuring the size and shape of knotted polymers. [AMS abstract No. 1049-57-52]
4:30–5:00pm
Kenneth C. Millett, (www.math.ucsb.edu/~millett/KM.html), University of California at Santa Barbara, USA. Knots, Ephmeral Knots and Slipknots in Random Walks and Equilateral Polygons. [AMS abstract No. 1049-57-62 ]
5:00–5:30pm
De Witt Sumners, (www.math.fsu.edu/~sumners/), Florida State University, USA. The Writhe of Oriented Polygonal Graphs. [AMS abstract No. 1049-57-121]
6:30–9:00
Conference Dinner, Okazu Ya, 1735 Taraval Street, San Francisco

Sunday morning
Science 210, San Francisco State University main campus

7:30am
Coffee
8:30–9:30am
Plenary Speaker
Alexander Y. Grosberg, (www.physics.nyu.edu/Grosberg/) New York University, New York USA Self-avoiding knots. [AMS abstract No. 1049-54-83]
9:30–10:00am
Yuanan Diao, (www.math.uncc.edu/index.php/people/full-time-faculty/277-diao-yuanan-.html), University of North Carolina at Charlotte USA. The Ropelengths of Knots Are Almost Linear in Terms of Their Crossing Numbers: Part 1. [AMS abstract No. 1049-57-76]
10:00–10:30am
Claus Ernst, (www.wku.edu/~claus.ernst/), Western Kentucky University, USA The Ropelengths of Knots Are Almost Linear in Terms of Their Crossing Numbers: Part 2. [AMS abstract No. 1049-57-77]
10:30–11:00am
Tetsuo Deguchi, (researchers.ao.ocha.ac.jp/3640461595_en.html), Ochanomizu University, Japan. A chain of linked ring polymers in solution via Brownian dynamics. [AMS abstract No. 1049-82-82]
11:00–12:00pm
AMS plenary
12:00–2:00pm
Lunch Break

Sunday afternoon
Science 210, San Francisco State University main campus

2:00–2:45pm
AMS plenary
3:00–3:15pm
Soojeong Kim, University of Iowa. 4-string tangle analysis of DNA-protein complexes. [AMS abstract No. 1049-57-208 ]
3:15–3:30pm
TBA (this talk will be selected from the poster session)
3:30–3:45pm
Mahshid Atapour, York University. Exponential Growth of the Number of n-edge Linked Clusters in Z3 and the Consequences in Entanglement Percolation. [AMS abstract No. 1049-05-187]
3:45–4:00pm
TBA (this talk will be selected from the poster session)
4:00–4:15pm
Teresita Ramirez-Rosas, University of California, Santa Barbara. Upper Bound for the Ropelength of a Trefoil Knot. [AMS abstract No. 1049-54-192]
4:15–4:30pm
TBA (this talk will be selected from the poster session)
4:30–4:45pm
Rocco Varela, University of California at San Francisco. A fast ergodic algorithm for generating ensembles of equilateral random polygons. [AMS abstract No. 1049-54-125]