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Conference: From DNA-Inspired Physics to Physics-Inspired Biology | (smr 2038)
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  • Monday, 1 June 2009
    • 08:30 - 09:30 REGISTRATION / ADMINISTRATIVE FORMALITIES 
      (Leonardo da Vinci Building - reception area)
      • 08:30 REGISTRATION / ADMINISTRATIVE FORMALITIES 1h0'
    • 09:30 - 10:50 SESSION 1 - OPENING SESSION 
      CHAIR:  Alexei KORNYSHEV

Greetings from ICTP
      • 09:30 SESSION 1 - OPENING SESSION 1h20'
    • 09:35 - 09:50 Preamble: can one always judge the book by its cover?
      • 09:35 Preamble: can one always judge the book by its cover? 15'
        Speaker: Alexei KORNYSHEV (Imperial College London, U.K.)
    • 09:50 - 10:20 From disciplinary borders to frontiers of science
      • 09:50 From disciplinary borders to frontiers of science 30'
        Speaker: Arturo FALASCHI (SNS, Pisa & ICGE, Trieste, Italy)
        Material: abstract lecture notes
    • 10:20 - 10:50 The devil in the details: how DNA structure, sequence and counterions drive biology
      • 10:20 The devil in the details: how DNA structure, sequence and counterions drive biology 30'
        Speaker: Lynn ZECHIEDRICH (Baylor College, Houston, U.S.A.)
        Material: abstract
    • 10:50 - 11:20 Coffee Break
      Location: Leonardo da Vinci Building, Lobby
      • 10:50 Coffee Break 30'
    • 11:20 - 11:50 Approaches to understanding the origin and management of DNA stiffness
      • 11:20 Approaches to understanding the origin and management of DNA stiffness 30'
        Speaker: Jim MAHER (Mayo Clinic College, Rochester, U.S.A.)
        Material: abstract lecture notes
    • 11:20 - 12:50 SESSION 2 - DNA MECHANICS 
      CHAIR:  Jorge LANGOWSKI
      • 11:20 SESSION 2 - DNA MECHANICS 1h30'
    • 11:50 - 12:20 DNA micromechanics and macromolecular organization
      • 11:50 DNA micromechanics and macromolecular organization 30'
        Speaker: Wilma OLSON (Rutgers University, U.S.A.)
        Material: abstract lecture notes
    • 12:20 - 12:50 Nanomechanics of single and double stranded DNA
      • 12:20 Nanomechanics of single and double stranded DNA 30'
        Speaker: Piotr MARSZALEK (Duke University, Durham, U.S.A.)
        Material: abstract lecture notes
    • 12:50 - 15:00 Lunch Break
      Location: Leonardo da Vinci Building Cafeteria
      • 12:50 Lunch Break 2h10'
    • 15:00 - 15:30 Multi-scale modelling of sequence-dependent DNA mechanics
      • 15:00 Multi-scale modelling of sequence-dependent DNA mechanics 30'
        Speaker: John MADDOCKS (EPFL, Lausanne, Switzerland)
        Material: abstract lecture notes
    • 15:00 - 16:00 SESSION 3 - DNA MECHANICS 
      CHAIR:  Jorge LANGOWSKI
      • 15:00 SESSION 3 - DNA MECHANICS 1h0'
    • 15:30 - 16:00 Geometry and mechanics of condensed DNA: Toroids and beyond
      • 15:30 Geometry and mechanics of condensed DNA: Toroids and beyond 30'
        Speaker: Evgueni STAROSTIN (University College London, U.K.)
        Material: abstract lecture notes
    • 16:00 - 16:30 Coffee Break
      Location: Leonardo da Vinci Building, Lobby
      • 16:00 Coffee Break 30'
    • 16:30 - 17:00 Electrostatic interactions between DNA double helices
      • 16:30 Electrostatic interactions between DNA double helices 30'
        Speaker: Sergey LEIKIN (NIH, Bethesda, U.S.A.)
        Material: lecture notes
    • 16:30 - 18:15 SESSION 4 - DNA STRUCTURE, INTERACTIONS AND AGGREGATION 
      CHAIR:  Adrian PARSEGIAN
      • 16:30 SESSION 4 - DNA STRUCTURE, INTERACTIONS AND AGGREGATION 1h45'
    • 17:00 - 17:30 Generalizations and ramifications induced by counterion structure in the strong and weak-coupling electrostatic interactions between macromolecules
      • 17:00 Generalizations and ramifications induced by counterion structure in the strong and weak-coupling electrostatic interactions between macromolecules 30'
        Speaker: Rudi PODGORNIK (University of Ljubljana, Slovenia)
        Material: abstract lecture notes
    • 17:30 - 18:00 Counterion-mediated DNA-DNA interactions
      • 17:30 Counterion-mediated DNA-DNA interactions 30'
        Speaker: Brian TODD (Purdue University, West Lafayette, U.S.A.)
        Material: abstract lecture notes
    • 18:00 - 18:15 Correlations and helical coherence in DNA structure: "straightening" the helix upon crystal packing
      • 18:00 Correlations and helical coherence in DNA structure: "straightening" the helix upon crystal packing 15'
        Speaker: Aaron WYNVEEN (University of Duesseldorf, Germany)
        Material: abstract lecture notes
    • 19:00 - 21:00 WELCOME RECEPTION
      Location: Leonardo da Vinci Building Terrace
      • 19:00 WELCOME RECEPTION 2h0'
  • Tuesday, 2 June 2009
    • 09:00 - 09:30 Simulations of DNA condensation
      • 09:00 Simulations of DNA condensation 30'
        Speaker: Malek KHAN (Uppsala University, Sweden)
        Material: abstract lecture notes
    • 09:00 - 10:30 SESSION 5 - DNA STRUCTURE, INTERACTIONS AND AGGREGATION 
      CHAIR: Richard LAVERY
      • 09:00 SESSION 5 - DNA STRUCTURE, INTERACTIONS AND AGGREGATION 1h30'
    • 09:30 - 09:45 Mediating role of Alkaline earth metal ions in electrostatics of DNA: The long-range effects of solvent dielectric saturation
      • 09:30 Mediating role of Alkaline earth metal ions in electrostatics of DNA: The long-range effects of solvent dielectric saturation 15'
        Speaker: Sergei GAVRYUSHOV (RAS, Engelhardt Institute of Molecular Biology, Moscow, Russia)
        Material: abstract lecture notes
    • 09:45 - 10:00 How does helical structure influence correlation forces between DNA?
      • 09:45 How does helical structure influence correlation forces between DNA? 15'
        Speaker: Dominic LEE (Max-Planck-Institute for Complex Systems, Dresden, Germany)
        Material: abstract lecture notes
    • 10:00 - 10:15 DNA from the polymer physics point of view: Topology and dimensionality effects
      • 10:00 DNA from the polymer physics point of view: Topology and dimensionality effects 15'
        Speaker: Giovanni DIETLER (EPFL, Laussane, Switzerland)
        Material: abstract lecture notes
    • 10:15 - 10:30 Kinetics of force-induced DNA melting
      • 10:15 Kinetics of force-induced DNA melting 15'
        Speaker: Ioulia ROUZINA (University of Minnesota, Minneapolis, U.S.A.)
        Material: abstract lecture notes
    • 10:30 - 11:00 Coffee Break
      Location: Leonardo da Vinci Building, Lobby
      • 10:30 Coffee Break 30'
    • 11:00 - 11:30 How can two homologous needles find each other in the genomic haystack?
      • 11:00 How can two homologous needles find each other in the genomic haystack? 30'
        Speaker: Adi BARZEL (University of Tel Aviv, Israel)
        Material: abstract lecture notes
    • 11:00 - 12:45 SESSION 6 - RECOGNITION OF HOMOLOGOUS GENES 
      CHAIR:  Jim MAHER
      • 11:00 SESSION 6 - RECOGNITION OF HOMOLOGOUS GENES 1h45'
    • 11:30 - 12:00 Is recognition between homologous DNA double helices an intrinsic property of DNA?
      • 11:30 Is recognition between homologous DNA double helices an intrinsic property of DNA? 30'
        Speaker: Geoff BALDWIN (Imperial College London, U.K.)
        Material: abstract
    • 12:00 - 12:30 Single molecule studies of homolog pairing
      • 12:00 Single molecule studies of homolog pairing 30'
        Speaker: Mara PRENTISS (Harvard University, Cambridge, U.S.A.)
        Material: lecture notes
    • 12:30 - 12:45 Homology recognition funnel
      • 12:30 Homology recognition funnel 15'
        Speaker: Alexei KORNYSHEV (Imperial College London, U.K.)
        Material: abstract lecture notes
    • 12:45 - 15:00 Lunch Break
      Location: Leonardo da Vinci Building Cafeteria
      • 12:45 Lunch Break 2h15'
    • 15:00 - 15:30 Conformation and dynamics of single molecules of DNA in solution
      • 15:00 Conformation and dynamics of single molecules of DNA in solution 30'
        Speaker: Adam COHEN (Harvard University, Cambridge, U.S.A.)
        Material: abstract lecture notes
    • 15:00 - 18:30 SESSION 7 - CONFORMATIONAL DYNAMICS, SUPERCOILING AND PACKING 
      CHAIR:  David BENSIMON
      • 15:00 SESSION 7 - CONFORMATIONAL DYNAMICS, SUPERCOILING AND PACKING 3h30'
    • 15:30 - 16:00 Dynamics of supercoiled DNA: some recent insights from single-molecule experiments
      • 15:30 Dynamics of supercoiled DNA: some recent insights from single-molecule experiments 30'
        Speaker: Aurelien CRUT (LASIM, Villeurbanne, France)
        Material: abstract lecture notes
    • 16:00 - 16:30 Compactness and apparent circularization of ssRNA
      • 16:00 Compactness and apparent circularization of ssRNA 30'
        Speaker: Avinoam BEN-SHAUL (Hebrew University of Jerusalem, Israel)
        Material: abstract lecture notes
    • 16:30 - 17:00 Coffee Break
      Location: Leonardo da Vinci Building, Lobby
      • 16:30 Coffee Break 30'
    • 17:00 - 17:30 DNA supercoiling and the lambda bacteriophage epigenetic switch
      • 17:00 DNA supercoiling and the lambda bacteriophage epigenetic switch 30'
        Speaker: Laura FINZI (Emory University, Atlanta, U.S.A.)
        Material: abstract lecture notes
    • 17:30 - 18:00 Computer simulations of DNA supercoiling at the atomic level
      • 17:30 Computer simulations of DNA supercoiling at the atomic level 30'
        Speaker: Sarah HARRIS (University of Leeds, U.K.)
        Material: abstract lecture notes
    • 18:00 - 18:30 Unravelling the organization of bacterial chromatin
      • 18:00 Unravelling the organization of bacterial chromatin 30'
        Speaker: Remus DAME (Leiden University, Leiden & VU, Amsterdam, The Netherlands)
        Material: abstract
  • Wednesday, 3 June 2009
    • 09:00 - 09:30 The organization and topology of chromatin
      • 09:00 The organization and topology of chromatin 30'
        Speaker: Andrew TRAVERS (MRC-LMB, Cambridge, U.K.)
        Material: abstract lecture notes
    • 09:00 - 12:30 SESSION 8 - CONFORMATIONAL DYNAMICS, SUPERCOILING AND PACKING 
      CHAIR:  Wilma OLSON
      • 09:00 SESSION 8 - CONFORMATIONAL DYNAMICS, SUPERCOILING AND PACKING 3h30'
    • 09:30 - 10:00 Stacking plates and wedges: the physics of DNA compaction
      • 09:30 Stacking plates and wedges: the physics of DNA compaction 30'
        Speaker: Helmut SCHIESSEL (University of Leiden, The Netherlands)
        Material: abstract
    • 10:00 - 10:30 DNA and chromatin dynamics studied by single molecule methods and computer modelling
      • 10:00 DNA and chromatin dynamics studied by single molecule methods and computer modelling 30'
        Speaker: Jorg LANGOWSKI (GSRC, Heidelberg, Germany)
        Material: abstract
    • 10:30 - 11:00 Coffee Break
      Location: Leonardo da Vinci Building, Lobby
      • 10:30 Coffee Break 30'
    • 11:00 - 11:30 DNA, chromatin and remodeling factors
      • 11:00 DNA, chromatin and remodeling factors 30'
        Speaker: David BENSIMON (ENS, Paris, France)
    • 11:30 - 12:00 DNA and chromatin dynamics: Discovery of a novel ATP-dependent DNA rewinding motor
      • 11:30 DNA and chromatin dynamics: Discovery of a novel ATP-dependent DNA rewinding motor 30'
        Speaker: James KADONAGA (UCSD, La Jolla, U.S.A.)
        Material: abstract lecture notes
    • 12:00 - 12:30 Modelling chromatin with explicit ions: ion correlation effects and like charge attraction. Comparison with new experiments
      • 12:00 Modelling chromatin with explicit ions: ion correlation effects and like charge attraction. Comparison with new experiments 30'
        Speaker: Lars NORDENSKIOLD (Nanyang Technological University, Singapore)
        Material: abstract lecture notes
    • 12:30 - 12:45 Modeling the hysteretic behavior of chromatin fibers under magnetic tweezers: why are nucleosomes left handed?
      • 12:30 Modeling the hysteretic behavior of chromatin fibers under magnetic tweezers: why are nucleosomes left handed? 15'
        Speaker: Maria BARBI (Universite Pierre et Marie Curie, Paris,France)
        Material: abstract
    • 12:45 - 15:00 Lunch Break
      Location: Leonardo da Vinci Building Cafeteria
      • 12:45 Lunch Break 2h15'
    • 15:00 - 15:30 DNA ejection from bacterial and mammalian viruses
      • 15:00 DNA ejection from bacterial and mammalian viruses 30'
        Speaker: William GELBART (UCLA, Los Angeles, U.S.A.)
        Material: abstract
    • 15:00 - 16:30 SESSION 9 - DNA COMPACTIZATION IN VIRUSES 
      CHAIR:  Helmut SCHIESSEL
      • 15:00 SESSION 9 - DNA COMPACTIZATION IN VIRUSES 1h30'
    • 15:30 - 16:00 Menagerie of viruses: diverse chemical sequences or simple electrostatics?
      • 15:30 Menagerie of viruses: diverse chemical sequences or simple electrostatics? 30'
        Speaker: Murugappan MUTHUKUMAR (University of Massachusetts, Amherst, U.S.A.)
        Material: abstract
    • 16:00 - 16:30 DNA structure and phase transitions in the bacteriophage capsid
      • 16:00 DNA structure and phase transitions in the bacteriophage capsid 30'
        Speaker: Francoise LIVOLANT (CNRS, Orsay, France)
        Material: abstract
    • 16:30 - 17:00 Coffee Break
      Location: Leonardo da Vinci Building, Lobby
      • 16:30 Coffee Break 30'
    • 17:00 - 17:30 Charge transport of cancer-related genes
      • 17:00 Charge transport of cancer-related genes 30'
        Speaker: Rudolf ROEMER (University of Warwick, Coventry, U.K.)
        Material: abstract
    • 17:00 - 18:00 SESSION 10 - FEATURE PRESENTATION 
      CHAIR:  Helmut SCHIESSEL
      • 17:00 SESSION 10 - FEATURE PRESENTATION 1h0'
    • 17:30 - 19:30 POSTER FAIR - Wellcome Trust Prizes for the best works of young participants 
      POSTER GALLERY (behind the Main Lecture Hall)

refreshments available
      Location: Leonardo da Vinci Building, Lobby
      • 17:30 POSTER FAIR - Wellcome Trust Prizes for the best works of young participants 2h0'
  • Thursday, 4 June 2009
    • 09:00 - 09:30 Mechanisms of direct and indirect readout
      • 09:00 Mechanisms of direct and indirect readout 30'
        Speaker: Loren WILLIAMS (Georgia Tech., Atlanta, U.S.A.)
        Material: abstract lecture notes
    • 09:00 - 13:00 SESSION 11 - DNA-PROTEIN INTERACTION AND RECOGNITION 
      CHAIR:  Laura FINZI
      • 09:00 SESSION 11 - DNA-PROTEIN INTERACTION AND RECOGNITION 4h0'
    • 09:30 - 10:00 A singular view of DNA transactions
      • 09:30 A singular view of DNA transactions 30'
        Speaker: Gijs WUITE (VU, Amsterdam, The Netherlands)
        Material: abstract lecture notes
    • 10:00 - 10:30 Single-molecule manipulation of DNA
      • 10:00 Single-molecule manipulation of DNA 30'
        Speaker: Ching-Hwa KIANG (Rice University, Houston, U.S.A.)
        Material: abstract lecture notes
    • 10:30 - 11:00 Coffee Break
      Location: Leonardo da Vinci Building, Lobby
      • 10:30 Coffee Break 30'
    • 11:00 - 11:30 DNA mechanics and protein-DNA recognition
      • 11:00 DNA mechanics and protein-DNA recognition 30'
        Speaker: Richard LAVERY (BCP, Lyon, France)
        Material: abstract
    • 11:30 - 12:00 How proteins find their Targets on DNA
      • 11:30 How proteins find their Targets on DNA 30'
        Speaker: Anatoly KOLOMEISKY (Rice University, Houston, U.S.A.)
        Material: abstract lecture notes
    • 12:00 - 12:30 Topoisomerase I equilibrates metastable secondary structure in relaxed supercoiled DNA's
      • 12:00 Topoisomerase I equilibrates metastable secondary structure in relaxed supercoiled DNA's 30'
        Speaker: Michael SCHURR (University of Washington, Seattle, U.S.A.)
        Material: lecture notes
    • 12:30 - 12:45 Binding of HU-proteins and DNA elasticity
      • 12:30 Binding of HU-proteins and DNA elasticity 15'
        Speaker: Yitzhak RABIN (Bar Ilan University, Ramat-Gan, Israel)
        Material: abstract lecture notes
    • 12:45 - 13:00 The effect of HU on DNA looping
      • 12:45 The effect of HU on DNA looping 15'
        Speaker: Luke CZAPLA (University of Uppsala, Sweden)
        Material: abstract
    • 13:00 - 14:30 Lunch Break
      Location: Leonardo da Vinci Building Cafeteria
      • 13:00 Lunch Break 1h30'
    • 14:30 - 18:30 Group and Project Meetings Networking
      • 14:30 Group and Project Meetings Networking 4h0'
    • 18:30 - 22:30 CONFERENCE DINNER
      • 18:30 CONFERENCE DINNER 4h0'
  • Friday, 5 June 2009
    • 09:00 - 09:30 Subtitles of nanoconfined DNA 
      (talk presented by Marc EMANUEL)
      • 09:00 Subtitles of nanoconfined DNA 30'
        Speaker: Theo ODIJIK (TU Delft, The Netherlands)
    • 09:00 - 12:00 SESSION 12 - DNA IN CONFINEMENT 
      CHAIR:  Sergey LEIKIN
      • 09:00 SESSION 12 - DNA IN CONFINEMENT 3h0'
    • 09:30 - 10:00 DNA capture in nanoscale pores - How does it happen?
      • 09:30 DNA capture in nanoscale pores - How does it happen? 30'
        Speaker: Amit MELLER (Boston University, U.S.A.)
        Material: abstract
    • 10:00 - 10:30 Origin of the electrophoretic force on DNA in solid state nanopores
      • 10:00 Origin of the electrophoretic force on DNA in solid state nanopores 30'
        Speaker: Serge LEMAY (TU Delft, The Netherlands)
        Material: abstract
    • 10:30 - 11:00 Coffee Break
      Location: Leonardo da Vinci Building, Lobby
      • 10:30 Coffee Break 30'
    • 11:00 - 11:30 Amphiphile-DNA complexes: adsorption, delivery and release
      • 11:00 Amphiphile-DNA complexes: adsorption, delivery and release 30'
        Speaker: Yan LEVIN (IF-UFRGS, Porto Alegre, Brazil)
        Material: abstract lecture notes
    • 11:30 - 12:00 Backtracking by RNA polymerase: single molecule experiments vs theory
      • 11:30 Backtracking by RNA polymerase: single molecule experiments vs theory 30'
        Speaker: Stephen GRILL (Max-Planck-Institute for Complex Systems, Dresden, Germany)
        Material: abstract
    • 12:00 - 14:30 Lunch Break
      Location: Leonardo da Vinci Building Cafeteria
      • 12:00 Lunch Break 2h30'
    • 14:30 - 15:00 What is it like to be a molecular robot based on DNA?
      • 14:30 What is it like to be a molecular robot based on DNA? 30'
        Speaker: Milan STOJANOVIC (Columbia University, New York, U.S.A.)
        Material: abstract
    • 14:30 - 16:00 SESSION 13 - SMART DNA 
      CHAIR:  Rudi PODGORNIK
      • 14:30 SESSION 13 - SMART DNA 1h30'
    • 15:00 - 15:30 Synthetic DNA Holliday junctions as controllable nanoswitch systems
      • 15:00 Synthetic DNA Holliday junctions as controllable nanoswitch systems 30'
        Speaker: Andrew MOUNT (University of Edinburgh, U.K.)
        Material: abstract
    • 15:30 - 16:00 On the theory of cholesteric ordering in solutions of macromolecules
      • 15:30 On the theory of cholesteric ordering in solutions of macromolecules 30'
        Speaker: Mikhail OSIPOV (University of Stratchclyde, U.K.)
        Material: abstract
    • 16:00 - 16:30 Coffee Break
      Location: Leonardo da Vinci Building, Lobby
      • 16:00 Coffee Break 30'
    • 16:30 - 18:15 SESSION 14 - PANEL-LED GENERAL DISCUSSION 
      PANEL CHAIR:  Adrian PARSEGIAN

PANEL MEMBERS - T.B.C.
      • 16:30 SESSION 14 - PANEL-LED GENERAL DISCUSSION 1h45'
    • 18:15 - 18:30 CLOSING SESSION
      • 18:15 CLOSING SESSION 15'
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