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Description In recent years the problem of biomolecular knotting has attracted more and more interest across different scientific disciplines. This is largely due to the advancement of single-molecule manipulation techniques, which have provided unprecedented quantitative insight into the ubiquity of various form of topological entanglement, especially knots, in biomolecules.
The wealth of available experimental data has, in turn, accelerated much activity on the theoretical and modelling side aimed at understanding the general mechanisms that govern the dynamic formation of knots and links in biopolymers as well as understanding their biological implications.

The workshop will focus on:

1) the active and passive molecular mechanisms adopted by living organisms to deal with the self- and mutual-entanglement that inevitably arises in the "molecules of life" (DNA, RNA and proteins) inside the crowded cellular environment;

2) the significant advancements in the design of synthetic molecular constructs capable of attaining novel topologies, particularly knotted ones;

3) soft-matter systems where the knotted or linked structures are not of molecular origin.

Material

Workshop on Knots and Links in Biological and Soft Matter Systems | (smr 2881)
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  • Monday, 26 September 2016
    • 08:30 - 17:50 Monday, 26 September 2016
      Location: Leonardo Building - Budinich Lecture Hall
      • 08:30 Registration & Administrative Formalities 1h40' ( Leonardo Building Lobby ) 
        Slot reserved for Participants not staying in ICTP Guesthouses & Invited Speakers.
Participants staying in ICTP Guesthouses are registered upon check-in at the Guesthouse Reception desks.
Registered visitors funded by the ICTP must go directly to the Operations Office,  E. Fermi building, ground floor (Mon, Tue & Fri, 8:30-12:00/13:30-14:30) to collect their dues.
      • 10:10 Opening and Welcome 10'
      • 10:20 What Knot to Make 50'
        Speaker: David Leigh (The University of Manchester)
        Material: Video
      • 11:10 Energy Landscapes of Knotted Clusters 50'
        Speaker: Mark Miller (Durham University)
        Material: Video
      • 12:00 Lunch break 2h0' ( Leonardo Building - Cafeteria )
      • 14:00 Pathways of Unlinking by Local Reconnection 50'
        Speaker: Mariel Vazquez (UC Davis)
        Material: Video
      • 14:50 Knotting-Unknotting Paths in Polymers 50'
        Speaker: Henri Orland (CEA, Saclay)
        Material: Video
      • 15:40 Coffee Break 30' ( Leonardo Building - Terrace )
      • 16:10 Knots and Coarse-grained Models for DNA, Polymers and Proteins 50'
        Speaker: Peter Virnau (J. Gutenberg-Universität, Mainz)
        Material: Video
      • 17:00 Design of Patchy Polymers: Biomimetic Self-Knotting Chains 50'
        Speaker: Ivan Coluzza (University of Vienna)
        Material: Video
  • Tuesday, 27 September 2016
    • 09:00 - 21:50 Tuesday, 27 September 2016
      Location: Leonardo Building - Budinich Lecture Hall
      • 09:00 Exotic Linking in Liquid Crystals 50'
        Speaker: Randall Kamien (University of Pennsylvania)
        Material: Video
      • 09:50 Knotted Nematic Braids in Confined Liquid Crystals 50'
        Speaker: Slobodan Zumer (University of Ljubljana)
        Material: Video
      • 10:40 Coffee Break 30' ( Leonardo Building - Terrace )
      • 11:10 Evidence for a Topological Glass in Ring Polymers 50'
        Speaker: Matthew Turner (Warwick University)
        Material: Video
      • 12:00 Lunch break 2h0' ( Leonardo Building - Cafeteria )
      • 14:00 Topological Friction and Electrophoretic Patterns of DNA Knots 50'
        Speaker: Davide Marenduzzo (Edinburgh University)
        Material: Video
      • 14:50 Pulling and Tightening Protein Knots Using Optical Tweezers and Cellular Degradation Machines 50'
        Speaker: Sophie Jackson (University of Cambridge)
        Material: Video
      • 15:40 Science for Sustainable Development 30'
        Speaker: Max Paoli - Third World Academy of Sciences
        Material: Video
      • 16:10 Coffee Break 30' ( Leonardo Building - Terrace )
      • 16:40 Poster Session 1h50' ( Leonardo Building - Gallery behind Budinich Lecture Hall )
      • 19:00 Reception 2h0' ( Leonardo Building - Terrace )
  • Wednesday, 28 September 2016
    • 09:00 - 18:50 Wednesday, 28 September 2016
      Location: Leonardo Building - Budinich Lecture Hall
      • 09:00 Beyond the Static Structural Models of Watson and Crick: Dynamic Supercoiling Drives DNA Metabolism 50'
        Speaker: Lynn Zechiedrich (Baylor College of Medicine, Houston)
        Material: Video
      • 09:50 Generation of Supercoils in Nicked and Gapped DNA Drives DNA Unknotting and Postreplicative Decatenation 50'
        Speaker: Dusan Racko (Université de Lausanne)
        Material: Video
      • 10:40 Coffee Break 30' ( Leonardo Building - Terrace )
      • 11:10 Vortex Knots Cascade by HOMFLYPT Polynomial 50'
        Speaker: Renzo Ricca (University of Milan-Bicocca)
        Material: Video
      • 12:00 Global Theory of Knots in Nematic Liquid Crystals 50'
        Speaker: Gareth Alexander (Warwick University)
        Material: Video
      • 12:50 GROUP PHOTO 10' ( Leonardo Building - Main entrance )
      • 13:00 Lunch break 1h50' ( Leonardo Building - Cafeteria )
      • 14:50 FREE AFTERNOON 3h10'
  • Thursday, 29 September 2016
    • 09:00 - 17:50 Thursday, 29 September 2016
      Location: Leonardo Building - Budinich Lecture Hall
      • 09:00 How Topology and Confinement Affect the Geometry of Random Knots 50'
        Speaker: Yuanan Diao (UNC Charlotte)
        Material: Video
      • 09:50 Knot Probabilities of Ring Polymers with Excluded Volume and the Hydrodynamic Properties of Graph-Shaped Topological Polymers 50'
        Speaker: Tetsuo Deguchi (Ochanomizu University)
        Material: Video
      • 10:40 Coffee Break 30' ( Leonardo Building - Terrace )
      • 11:10 Really Small Knots: The Action of Topoisomerase IV and Glueball Decay 50'
        Speaker: Eric Rawdon (U. of St. Thomas, Minnesota)
        Material: Video
      • 12:00 Lunch break 2h0' ( Leonardo Building - Cafeteria )
      • 14:00 DNA Unlinking 50'
        Speaker: Dorothy Buck (Imperial College, London)
      • 14:50 Statistical Properties of DNA in Various Topological Configurations 50'
        Speaker: Giovanni Dietler (EPFL, Lausanne)
        Material: Video
      • 15:40 Coffee Break 30' ( Leonardo Building - Terrace )
      • 16:10 Dynamics of Knotted Proteins and Entangled Neurotoxic Peptides 50'
        Speaker: Marek Cieplak (Polish Academy of Sciences)
        Material: Video
      • 17:00 Geometry of Spaces of Curves and Knots 50'
        Speaker: Jason Cantarella (University of Georgia, USA)
        Material: Video
  • Friday, 30 September 2016
    • 09:00 - 14:30 Friday, 30 September 2016
      • 09:00 Function of Knotted Protein and Lassoprot: Server Analyzing Biopolymers with Lassos 50'
        Speaker: Joanna Sulkowska (University of Warsaw)
        Material: Video
      • 09:50 Knots and Defect Constellations in Cholesteric Droplets 50'
        Speaker: Simon Copar (University of Ljubljana)
        Material: Video
      • 10:40 Coffee Break 30' ( Leonardo Building - Terrace )
      • 11:10 Linking in Systems with One-dimensional Periodic Boundaries 50'
        Speaker: Kenneth Millett (UC Santa Barbara)
        Material: Video
      • 12:00 Self Entangled Surfaces 50'
        Speaker: Stuart Whittington (Toronto University)
        Material: Video
      • 12:50 Flash talks by presenters of Prized posters - Q & A 30'
        Material: Video
        • Mousumi Beto (IISc Bangalore) "DNA Based Antiviral Strategy in the Inhibition of Viral RNA Replication in Liver Cells" 5'
        • Davide Michieletto (U. Edinburgh) "Kinetoplast DNA as a Network of Linked Rings at its Critical Point" 5'
        • Wanda Niemyska (U. Warsaw) "Complex Lasso Topology in Proteins" 5'
        • Antonio Suma (SISSA, Trieste) "Pore Translocation of Knotted Chains" 5'
      • 13:20 Concluding Remarks 20'
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