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Conference on Knots and other Entanglements in Biopolymers: Topological and Geometrical Aspects of DNA, RNA and Protein Structures | (smr 1963)
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  • Monday, 15 September 2008
    • 08:00 - 09:15 -
      • 08:00 - 1h15'
    • 09:30 - 10:00 Welcome address
    • 10:00 - 11:00 Life -- A result of evolution or design? + 15' discussion 
      The lecture will discuss the probability issues and, in particular, the Levithal paradox
      • 10:00 Life -- A result of evolution or design? + 15' discussion 1h0'
        Speaker: Peter Schuster (President Austrian Academy of Sciences)
        Material: recording
    • 11:05 - 11:50 Evolutionary Optimisation of Proteins on a Fitness Landscape with Entangled Traits
      • 11:05 Evolutionary Optimisation of Proteins on a Fitness Landscape with Entangled Traits 45'
        Speaker: Erich Bornberg-Bauer (University of Muenster)
        Material: recording
    • 11:50 - 12:35 Capturing knots in polymers and proteins
      • 11:50 Capturing knots in polymers and proteins 45'
        Speaker: Peter Virnau (Johannes Gutenberg-Universität Mainz)
        Material: recording
    • 12:35 - 14:15 Lunch
      • 12:35 Lunch 1h40'
    • 14:15 - 15:00 Stretching of proteins and dynamics of knots
      • 14:15 Stretching of proteins and dynamics of knots 45'
        Speaker: Marek Cieplak (Polish Academy of Sciences)
        Material: recording
    • 15:00 - 15:45 The Folding Pathways of Knotted Proteins
      • 15:00 The Folding Pathways of Knotted Proteins 45'
        Speaker: Sophie Jackson (University of Cambridge)
        Material: abstract recording
    • 15:45 - 16:00 Break
      Location: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)
      • 15:45 Break 15'
    • 16:00 - 16:45 Disentangling the folding mechanics of a knotted protein: kinetics vs thermodynamics 
      No recording is available for this lecture due to copyright restrictions.
      • 16:00 Disentangling the folding mechanics of a knotted protein: kinetics vs thermodynamics 45'
        Speaker: Stefan Wallin (Lund University)
    • 16:45 - 17:30 Protein topology and knots
      • 16:45 Protein topology and knots 45'
        Speaker: William Taylor (The National Institute for Medical Research London)
        Material: recording
    • 19:00 - 20:30 Welcome drink
      Location: Adriatico Guest House (Terrace)
      • 19:00 Welcome drink 1h30'
  • Tuesday, 16 September 2008
    • 09:00 - 09:45 An Electrostatic/Geometric Mechanism for Compact Chromatin Stabilization Revealed by Mesoscale Modeling 
      No recording is available for this lecture due to copyright restrictions.
      • 09:00 An Electrostatic/Geometric Mechanism for Compact Chromatin Stabilization Revealed by Mesoscale Modeling 45'
        Speaker: Tamar Schlick (New York University)
        Material: abstract
    • 09:45 - 10:30 DNA replication fork repair by RecG protein: A propagating front model
    • 10:30 - 10:55 Coffee break
      Location: Adriatico Guest House (Terrace)
      • 10:30 Coffee break 25'
    • 11:00 - 11:45 Interplay of DNA supercoiling and catenation during the segregation of sister duplexes
      • 11:00 Interplay of DNA supercoiling and catenation during the segregation of sister duplexes 45'
        Speaker: Jorge Schvartzman (Centro de Investigaciones Biológicas (CSIC) Madrid)
        Material: abstract recording
    • 11:45 - 12:30 Single DNA molecule micromanipulation: a tool to investigate replication enzymes
      • 11:45 Single DNA molecule micromanipulation: a tool to investigate replication enzymes 45'
        Speaker: Vincent Croquette (Ecole Normale Supérieure Paris)
        Material: abstract recording
    • 12:30 - 13:45 Lunch
      • 12:30 Lunch 1h15'
    • 13:45 - 14:30 DNA tangles
    • 14:30 - 15:15 Modeling DNA unlinking by Xer recombination
      • 14:30 Modeling DNA unlinking by Xer recombination 45'
        Speaker: Mariel Vazquez (San Francisco State University)
        Material: abstract recording
    • 15:15 - 15:30 Break
      Location: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)
      • 15:15 Break 15'
    • 15:30 - 16:15 Computer Simulations of DNA Topology at the Atomic Level
    • 16:15 - 17:00 The statistical mechanics of how recognition of local DNA juxtaposition geometry may underlie the disentangling actions of type-II topoisomerases
      • 16:15 The statistical mechanics of how recognition of local DNA juxtaposition geometry may underlie the disentangling actions of type-II topoisomerases 45'
        Speaker: Hue Sun Chan (University of Toronto)
        Material: recording
  • Wednesday, 17 September 2008
    • 09:00 - 09:45 Monte Carlo simulation on the conformational statistics of worm-like DNA chains: effect of DNA juxtaposition and topoisomerase action
      • 09:00 Monte Carlo simulation on the conformational statistics of worm-like DNA chains: effect of DNA juxtaposition and topoisomerase action 45'
        Speaker: Zhirong Liu (Peking University)
        Material: abstract recording
    • 09:45 - 10:30 The effect of knotting on the shape of polymers
      • 09:45 The effect of knotting on the shape of polymers 45'
        Speaker: Kenneth Millett (University of California at Santa Barbara)
        Material: recording
    • 10:30 - 10:55 Coffee break
      Location: Adriatico Guest House (Terrace)
      • 10:30 Coffee break 25'
    • 11:00 - 11:45 Topological signatures of the thermodynamics of knotted polymer rings
      • 11:00 Topological signatures of the thermodynamics of knotted polymer rings 45'
        Speaker: Attilio Stella (Università degli Studi di Padova)
        Material: Presentation slides recording
    • 11:45 - 12:30 Polymers, polygons and pattern theorems
    • 12:30 - 13:45 Lunch
      • 12:30 Lunch 1h15'
    • 13:45 - 15:15 Poster session
      Location: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)
      • 13:45 Poster session 1h30'
    • 15:15 - 15:30 Break
      Location: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)
      • 15:15 Break 15'
    • 15:30 - 16:15 Bullied no more- DNA takes an active role in biology
      • 15:30 Bullied no more- DNA takes an active role in biology 45'
        Speaker: Lynn Zechiedrich (Baylor College of Medicine Houston)
        Material: recording
    • 16:15 - 17:00 DNA knotting in spooling like conformations in bacteriophages
      • 16:15 DNA knotting in spooling like conformations in bacteriophages 45'
        Speaker: Javier Arsuaga (San Francisco State University)
        Material: abstract recording
  • Thursday, 18 September 2008
    • 09:00 - 09:45 DNA supercoiling inhibits DNA knotting
      • 09:00 DNA supercoiling inhibits DNA knotting 45'
        Speaker: Andrzej Stasiak (Université de Lausanne)
        Material: recording
    • 09:45 - 10:30 Entanglement Complexity of Systems of Self-Avoiding Walks in Lattice Tubes
      • 09:45 Entanglement Complexity of Systems of Self-Avoiding Walks in Lattice Tubes 45'
        Speaker: Christine Soteros (University of Saskatchewan)
        Material: Presentation slides recording
    • 10:30 - 10:55 Coffee break
      Location: Adriatico Guest House (Terrace)
      • 10:30 Coffee break 25'
    • 11:00 - 11:45 Knotting in stretched polymers
      • 11:00 Knotting in stretched polymers 45'
        Speaker: Carla Tesi (Università di Bologna)
        Material: recording
    • 11:45 - 12:30 Writhe Descriptors for Macromolecular Structure
      • 11:45 Writhe Descriptors for Macromolecular Structure 45'
        Speaker: De Witt Sumners (Florida State University Tallahassee)
        Material: abstract recording
    • 12:30 - 14:15 Lunch
      • 12:30 Lunch 1h45'
    • 14:15 - 15:00 Predicting RNA pseudoknot folding and ribosomal frameshifting
      • 14:15 Predicting RNA pseudoknot folding and ribosomal frameshifting 45'
        Speaker: Shi-Jie Chen (University of Missouri Columbia)
        Material: recording
    • 15:00 - 15:45 Pseudoknots in RNA
      • 15:00 Pseudoknots in RNA 45'
        Speaker: Henri Orland (CEA Gif-sur-Yvette)
        Material: recording
    • 15:45 - 16:00 Break
      Location: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)
      • 15:45 Break 15'
    • 16:00 - 16:20 Molecular Dynamics simulation of hepatitis C virus IRES IIId domain. Effects of mutations in electrostatic and structural properties
      • 16:00 Molecular Dynamics simulation of hepatitis C virus IRES IIId domain. Effects of mutations in electrostatic and structural properties 20'
        Speaker: Angel Gonzalez (Pontificia Universidad Catolica de Chile)
        Material: recording
    • 16:20 - 16:40 Dodging the crisis of folding proteins with knots
      • 16:20 Dodging the crisis of folding proteins with knots 20'
        Speaker: Joanna I. Sulkowska (The University of California, San Diego)
        Material: recording
    • 16:40 - 17:00 Modeling filament kinematics for proteic coding and viral spooling
      • 16:40 Modeling filament kinematics for proteic coding and viral spooling 20'
        Speaker: Francesca Maggioni (University of Bergamo)
        Material: Presentation slides recording
  • Friday, 19 September 2008
    • 09:00 - 09:45 Soft Entropic forces between approaching polymers with prescribed topology: possible implications on the physics of interphase chromosomes
      • 09:00 Soft Entropic forces between approaching polymers with prescribed topology: possible implications on the physics of interphase chromosomes 45'
        Speaker: Enzo Orlandini (Istituto Nazionale di Fisica Nucleare Padova)
    • 09:45 - 10:30 Scaling aspects in the probability of random knots and links and the dynamics of ring polymers in solution
      • 09:45 Scaling aspects in the probability of random knots and links and the dynamics of ring polymers in solution 45'
        Speaker: Tetsuo Deguchi (Ochanomizu University Tokyo)
        Material: abstract
    • 10:30 - 10:55 Coffee break
      Location: Adriatico Guest House (Terrace)
      • 10:30 Coffee break 25'
    • 11:00 - 11:45 Structural motifs of biomolecules
      • 11:00 Structural motifs of biomolecules 45'
        Speaker: Trinh Xuan Hoang (Pennsylvania State University)
        Material: abstract recording
    • 11:45 - 12:05 Statistical properties of intrinsically curved polymers
      • 11:45 Statistical properties of intrinsically curved polymers 20'
        Speaker: Surya K. Ghosh (Indian Institute of Technology Bombay)
    • 12:05 - 12:25 Topological methods for measuring the entanglement of polymers
      • 12:05 Topological methods for measuring the entanglement of polymers 20'
        Speaker: Eleni Panagiotou (National Technical University, Athens)
        Material: recording
    • 12:25 - 12:45 Numerical simulations of DNA catenanes: energetic and topological influence of supercoiling
      • 12:25 Numerical simulations of DNA catenanes: energetic and topological influence of supercoiling 20'
        Speaker: Guillaume Witz (Ecole Polytechnique Fédérale de Lausanne)
        Material: recording
    • 12:45 - 14:15 Lunch
      • 12:45 Lunch 1h30'
    • 14:15 - 15:00 Confined biopolymers: DNA packaging and chromosome territories
      • 14:15 Confined biopolymers: DNA packaging and chromosome territories 45'
        Speaker: Davide Marenduzzo (University of Edinburgh)
        Material: recording
    • 15:00 - 15:45 Size, Shape and Correlations of Topologically Constrained DNA
      • 15:00 Size, Shape and Correlations of Topologically Constrained DNA 45'
        Speaker: Giovanni Dietler (Ecole Polytechnique Fédérale de Lausanne)
        Material: recording
    • 15:45 - 16:00 Concluding remarks
      • 15:45 Concluding remarks 15'
        Speaker: Cristian Micheletti (SISSA, Trieste)
        Material: recording