Workshop Programme

for period 3-7 September

Topological Aspects of DNA Function and Protein Folding

3-7 September

Timetable

Monday 03 September
08:30-09:00	Registration	TOD
09:00-09:10	Welcome from John Toland	TOD
09:10-09:50	Schlick, T (New York University)	TOD
	Chromatin Compaction: A Modeling Exploration of Fiber Hetergeoneity and Linker Histone Influence	Sem 1
09:50-10:10	Morning Coffee	TOD
10:10-10:50	Jayaram, M (University of Texas at Austin, USA)	TOD
	The topological equivalence of the yeast chromosome centromere and the yeast plasmid partitioning locus	Sem 1
10:50-11:30	Lieberman Aiden, E (Harvard University, USA)	TOD
	How the genome folds	Sem 1
11:30-12:10	Mirny, L (Massachusetts Institute of Technology, USA)	TOD
	The role of topological constraints on condensed polymers and DNA in human cells	Sem 1
12:30-13:30	Lunch at Wolfson Court	TOD
13:30-14:10	Nicodemi, M (University of Naples Federico II, Italy)	TOD
	Large scale organization of chromatin	Sem 1
14:10-14:50	Levene, S (University of Texas at Dallas, USA)	TOD
	All Good Things Must Bend: the Energetics of DNA Shape and Flexibility in Biological Assemblies	Sem 1
14:50-15:20	Afternoon Tea and Poster Session	TOD
15:20-15:40	Giorgetti, L (Institut Curie, Paris)	TOD
	Structure meets function at the mouse X chromosome inactivation center	Sem 1
15:40-16:00	Maggioni, F (University of Bergamo, Italy)	TOD
	Modeling chromatin fibre folding for human embryonic stem cells and cancer cells	Sem 1
16:00-16:20	Rosa , A (SISSA, Trieste, Italy)	TOD
	Three-dimensional conformations of entangled ring polymers in solution	Sem 1
16:20-17:00	Kleckner, N (Harvard University, USA)	TOD
	How E.coli organizes and segregates its chromosome	Sem 1
17:00-18:00	Drinks Reception and Poster Session	TOD
18:00-18:30	Dinner at Wolfson Court	TOD

Tuesday 04 September
08:30-09:10	Jackson, S (University of Cambridge)	TOD
	A tangled problem: the structure,function and folding of knotted proteins	Sem 1
09:10-09:50	Micheletti, C (SISSA, Trieste, Italy)	TOD
	Knotted and unknotted proteins: a comparative study (*)	Sem 1
09:50-10:10	Morning Coffee	TOD
10:10-10:50	Cieplak, M (Polish Academy of Sciences, Warsaw)	TOD
	Topological features in stretching of proteins	Sem 1
10:50-11:30	Sulkowska , J (University of California, San Diego, USA)	TOD
	Conservation of complex knotting and slipknotting patterns in proteins	Sem 1
11:30-11:50	Kister, A (Rutgers University, New Jersey, USA)	TOD
	Amino acid patterns for protein folding	Sem 1
11:50-12:10	Szymczak, P (University of Warsaw, Poland)	TOD
	How to untie it-translocation of a knotted protein through a pore	Sem 1
12:30-13:30	Lunch at Wolfson Court	TOD
13:30-14:10	Virnau, P (Johannes Gutenberg-Universität Mainz, Germany)	TOD
	Computer simulations of knotted DNA and proteins	Sem 1
14:10-14:50	Ishihara, K (Imperial College London)	TOD
	Knots confined to tubes in the simple cubic lattice	Sem 1
14:50-15:20	Afternoon Tea and Poster Session	TOD
15:20-15:40	Cifra, P (Slovak Academy of Sciences, Bratislava)	TOD
	Simulations of cyclic and linear DNA chains moderately and strongly confined in nanochannels	Sem 1
15:40-16:00	Deguchi, T (Ochanomiu University, Tokyo, Japan)	TOD
	Diffusion dynamics of circular DNA mini-rings in solution	Sem 1
16:00-16:20	Narros, A (Universität Wien, Austria)	TOD
	Influence of topology in coarse-graining of polymer solutions	Sem 1
16:20-17:00	Millett, K (University of California, Santa Barbara, USA)	TOD
	Locating knots and slipknots in open and closed macromolecules	Sem 1
17:00-17:40	Rawdon, E (University of St Thomas, Minnesota, USA)	TOD
	Knotting of open chains, closed chains and proteins	Sem 1
18:00-18:30	Dinner at Wolfson Court	TOD

Wednesday 05 September
08:30-09:10	Benham, C (University of California, Davis, USA)	TOD
	Superhelically Driven Structural Transitions in Genomic DNA - Theoretical Analyses, Genomic Distributions and Roles in Regulation	Sem 1
09:10-09:50	Dorman, C (Trinity College Dublin, Ireland)	TOD
	Co-operative roles for DNA supercoiling and nucleoid-associated proteins in the regulation of bacterial transcription	Sem 1
09:50-10:10	Morning Coffee	TOD
10:10-10:50	Travers, A (University of Cambridge)	TOD
	Chromosomes as topological machines-the role of DNA thermodynamics	Sem 1
10:50-11:30	Zechiedrich, L (Baylor College of Medicine, Houston, Texas, USA)	TOD
	How DNA topology and DNA length affect the body's defense against nucleic acids of invading organisms in the blood	Sem 1
11:30-11:50	Chirikjian, G S (Johns Hopkins University)	TOD
	Twisted paths in Euclidean groups: Keeping track of total orientation while traversing DNA	Sem 1
11:50-12:10	Cortini, R (Imperial College London)	TOD
	Chiral effects in DNA supercoiling	Sem 1
12:30-13:30	Lunch at Wolfson Court	TOD
13:30-14:10	Maddocks, J (EPFL, Lausanne, Switzerland)	TOD
	Sequence-Dependent Coarse-Grain Descriptions of DNA: models, methods and simulations	Sem 1
14:10-14:50	Zakrzewska, K (BPC, Paris, France)	TOD
	DNA recognition studied by molecular simulations	Sem 1
14:50-15:20	Afternoon Tea and Poster Session	TOD
15:20-15:40	Baxter, J (University of Sussex)	TOD
	The yeast Pif1 family helicase RRM3 promotes DNA unwinding during replisome swivelling	Sem 1
15:40-16:00	Hanke, A (University of Texas at Brownsville, USA)	TOD
	Denaturation transition of stretched DNA in the presence of DNA-binding ligands	Sem 1
16:00-16:20	Bohr, J (DTU, Denmark)	TOD
	Twist neutrality and topological aspects of nucleosomal DNA	Sem 1
16:20-17:00	Swigon, D (University of Pittsburgh, USA)	TOD
	Dynamics of DNA supercoiling and knotting	Sem 1
17:00-17:40	Olson, W (Rutgers University, New Jersey, USA)	TOD
	Simulated looping propensities of protein-decorated DNA	Sem 1
17:40-19:00	Poster Session	TOD
19:30-22:00	Conference Dinner at Christ's College	TOD

Thursday 06 September
09:10-09:50	Maxwell, A (John Innes Centre, Norwich)	TOD
	DNA topology and the mechanism of type II DNA topoisomerases	Sem 1
09:50-10:10	Morning Coffee	TOD
10:10-10:50	Mondragon, A (Northwestern University, Chicago, USA)	TOD
	Mechanistic studies of type IA topoisomerases	Sem 1
10:50-11:30	Soteros, C (University of Saskatchewan, Canada)	TOD
	Knot statistics and knot reduction for a lattice polygon model of local strand passage	Sem 1
11:30-11:50	Schvartzman, J (CIB, Madrid, Spain)	TOD
	Topo IV is the topoisomerase that knots and unknots sister duplexes during DNA replication	Sem 1
11:50-12:10	Sulkowski , P (University of Amsterdam / Caltech / University of Warsaw)	TOD
	Topological recursion and classification of multi-stranded biopolymer configurations	Sem 1
12:30-13:30	Lunch at Wolfson Court	TOD
13:30-14:10	Dietler, G (EPFL, Lausanne, Switzerland)	TOD
	DNA in confined geometries: topology effects	Sem 1
14:10-14:50	Brackley, C (University of Edinburgh)	TOD
	A generic non-specific mechanism for the clustering of DNA and chromosome binding proteins	Sem 1
14:50-17:40	Free Afternoon	TOD
18:00-18:30	Dinner at Wolfson Court	TOD

Friday 07 September
08:30-09:10	Colloms, S (University of Glasgow)	TOD
	Topology of Xer site-specific recombination	Sem 1
09:10-09:50	Grainge, I (University of Newcastle, Australia)	TOD
	Simplification of topology during Xer-mediated recombination	Sem 1
09:50-10:10	Morning Coffee	TOD
10:10-10:50	Darcy, I (University of Iowa, USA)	TOD
	Tangle analysis of protein-DNA complexes	Sem 1
10:50-11:30	Vazquez, M (San Francisco State University, USA)	TOD
	DNA unknotting and unlinking	Sem 1
11:30-11:50	Scharein, R (Hypnagogic Software, Canada)	TOD
	TopoICE and other software tools for investigating topological problems in DNA	Sem 1
11:50-12:10	Summary/Closing Remarks	TOD
12:30-13:30	Lunch at Wolfson Court	TOD
18:00-18:30	Dinner at Wolfson Court	TOD

Other Seminars

Seminars in the University
National and International Scientific Research Meetings