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Workshop Programme

for period 3-7 September

Topological Aspects of DNA Function and Protein Folding

3-7 September


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-Universitšt 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 (Universitšt 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

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