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Conference on Molecular Aspects of Cell Biology: A Perspective from Computational Physics | (smr 2169)
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  • Monday, 11 October 2010
    • 08:00 - 08:50 Registration and Administrative Matters - Adriatico Guest House, Lower Level 1
      • 08:00 Registration and Administrative Matters - Adriatico Guest House, Lower Level 1 50'
    • 08:50 - 09:00 Opening Remarks
      • 08:50 Opening Remarks 10'
        Speaker: P. CARLONI and S. PANTANO (Directors of this Event)
    • 09:00 - 09:50 Post-translational Regulation of Protein Function by Acetylation: Many Occurences, Few Rules
      • 09:00 Post-translational Regulation of Protein Function by Acetylation: Many Occurences, Few Rules 50'
        Speaker: M. GIACCA (ICGEB, Trieste, Italy)
        Material: lecture notes
    • 09:50 - 11:00 Structural insights into inherited human prion diseases: An experimental and computational approach
      • 09:50 Structural insights into inherited human prion diseases: An experimental and computational approach 1h10'
        Speaker: G. LEGNAME (SISSA, Dept. of Neurobiology, Trieste, Italy)
        Material: Abstract G. LEGNAME
    • 11:00 - 11:15 Coffee/tea Break
      • 11:00 Coffee/tea Break 15'
    • 11:15 - 12:05 Tackling Large Macromolecular Complexes: The Interplay of Electron Microscopy and Protein Crystallography
      • 11:15 Tackling Large Macromolecular Complexes: The Interplay of Electron Microscopy and Protein Crystallography 50'
        Speaker: S. ONESTI (Sincrotrone, Trieste, Italy)
        Material: Abstract S. ONESTI lecture notes
    • 12:05 - 12:55 Multi-scale Combinatorial Docking of the Proteome for Functional Predictions
      • 12:05 Multi-scale Combinatorial Docking of the Proteome for Functional Predictions 50'
        Speaker: R. NUSSINOV (SAIC Frederick, Cancer Research, Nanobiology, Frederick, U.S.A.)
    • 12:55 - 14:00 Lunch break
      • 12:55 Lunch break 1h5'
    • 14:00 - 14:20 Registration continuation - Adriatico Guest House, Lower Level 1
      • 14:00 Registration continuation - Adriatico Guest House, Lower Level 1 20'
    • 14:20 - 15:10 Allostery and Conformational Control of Ubiquitination in the Cullin-RING E3 Ligase Machinery
      • 14:20 Allostery and Conformational Control of Ubiquitination in the Cullin-RING E3 Ligase Machinery 50'
        Speaker: R. NUSSINOV (SAIC Frederick, Cancer Research, Nanobiology, Frederick, U.S.A.)
    • 15:10 - 16:00 From Cells Level and Continuum Mechanics - Multiscale Aspects in Biology and Medical Physics
      • 15:10 From Cells Level and Continuum Mechanics - Multiscale Aspects in Biology and Medical Physics 50'
        Speaker: S. ROLLER (GRS Lab. of Applied Supercomputing in Engg., Aachen, Germany)
    • 15:50 - 16:10 Break
      • 15:50 Break 20'
    • 16:10 - 17:30 Hands-on Session on Molecular Visualization (VMD)
      Location: Adriatico Guest House - Eklund Informatics Lab (Lower Level 1)
      • 16:10 Hands-on Session on Molecular Visualization (VMD) 1h20'
        Speaker: S. PANTANO (Institut Pasteur de Montevideo, Uruguay)
    • 18:00 - 19:30 Get-together Welcome Reception at Adriatico Guest House Cafeteria
      Location: Adriatico Guest House Cafeteria
      • 18:00 Get-together Welcome Reception at Adriatico Guest House Cafeteria 1h30'
  • Tuesday, 12 October 2010
    • 09:00 - 09:50 From in silico Demystification of GPCR Structure to the Design of New GPCR Ligands: The Human A3 Adenosine Receptor as a Key Study
      • 09:00 From in silico Demystification of GPCR Structure to the Design of New GPCR Ligands: The Human A3 Adenosine Receptor as a Key Study 50'
        Speaker: S. MORO (Univ. of Padova, Dept. Pharmaceutical Sciences, MMS, Padova, Italy)
        Material: Abstract S. MORO lecture notes
    • 09:50 - 10:40 Classical and QM/MM Simulations of G-protein-coupled Receptors
      • 09:50 Classical and QM/MM Simulations of G-protein-coupled Receptors 50'
        Speaker: S. VANNI (Lab. Computational Chem. & Biochem., BCH 4118 EPF Lausanne, Switzerland)
        Material: lecture notes
    • 10:40 - 11:00 Coffee/tea Break
      • 10:40 Coffee/tea Break 20'
    • 11:00 - 11:50 Insights into the Structural Determinants of Bitter Taste Receptors from a Combined in silico and in vitro Study
      • 11:00 Insights into the Structural Determinants of Bitter Taste Receptors from a Combined in silico and in vitro Study 50'
        Speaker: A. GIORGETTI (Univ. of Verona, Biotechnology, Verona, Italy)
        Material: Abstract A. GIORGETTI lecture notes
    • 11:50 - 12:40 Modelling Biological Processes on Multiple Scales
      • 11:50 Modelling Biological Processes on Multiple Scales 50'
        Speaker: S. ROLLER (GRS Lab. of Applied Supercomputing in Engg., Aachen, Germany)
    • 12:40 - 14:30 Lunch break
      • 12:40 Lunch break 1h50'
    • 14:30 - 17:00 Hands-on Session on Structural Bioinformatics
      Location: Adriatico Guest House - Eklund Informatics Lab (Lower Level 1)
      • 14:30 Hands-on Session on Structural Bioinformatics 2h30'
        Speaker: A. GIORGETTI (Univ. of Verona, Biotechnology, Verona, Italy)
        Material: lecture notes
    • 17:00 - 17:30 POSTER SESSION
      Location: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)
      • 17:00 POSTER SESSION 30'
  • Wednesday, 13 October 2010
    • 09:00 - 10:20 Allosterism in MutS Proteins and How DNA Mismatch Recognition Signals Repair: Molecular Dynamics Simulations
      • 09:00 Allosterism in MutS Proteins and How DNA Mismatch Recognition Signals Repair: Molecular Dynamics Simulations 1h20'
        Speaker: D. BEVERIDGE (Wesleyan Univ., Dept. of Chemistry, Middletown, U.S.A.)
        Material: Abstract D.L. BEVERIDGE
    • 10:20 - 10:40 Coffee/tea Break
      • 10:20 Coffee/tea Break 20'
    • 10:40 - 11:30 Protein DNA Recognition Mechanisms
      • 10:40 Protein DNA Recognition Mechanisms 50'
        Speaker: R. LAVERY (Inst. of Biology & Chemical Proteins, Molecular Biostructure, Lyon, France)
        Material: Abstract R. LAVERY (I)
    • 11:30 - 12:15 Simplified Models to Simulate DNA Dynamics
      • 11:30 Simplified Models to Simulate DNA Dynamics 45'
        Speaker: S. PANTANO (Institut Pasteur de Montevideo, Uruguay)
        Material: lecture notes
    • 12:15 - 12:30 Participants' Presentations
      • 12:15 Participants' Presentations 15'
    • 12:30 - 14:30 Lunch break
      • 12:30 Lunch break 2h0'
    • 14:30 - 17:00 Hands-on Session on Molecular Dynamics Simulation
      Location: Adriatico Guest House - Eklund Informatics Lab (Lower Level 1)
      • 14:30 Hands-on Session on Molecular Dynamics Simulation 2h30'
        Speaker: A. VARGIU (CNR-IOM UOS of Cagliari, Univ. of Cagliari, Physics, Monserrato, Italy)
    • 17:00 - 17:30 POSTER SESSION - Voting the Best Posters (from participants and speakers)
      Location: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)
      • 17:00 POSTER SESSION - Voting the Best Posters (from participants and speakers) 30'
  • Thursday, 14 October 2010
    • 09:00 - 09:50 Coarse-grain Approaches to Modeling Biological Macromolecules
      • 09:00 Coarse-grain Approaches to Modeling Biological Macromolecules 50'
        Speaker: R. LAVERY (Inst. of Biology & Chemical Proteins, Molecular Biostructure, Lyon, France)
        Material: Abstract R. LAVERY (II)
    • 09:50 - 10:40 3D Modeling of Large Protein Complexes and the Genome
      • 09:50 3D Modeling of Large Protein Complexes and the Genome 50'
        Speaker: F. ALBER (Univ. of Southern California, Biological Sciences, Los Angeles, U.S.A.)
    • 10:40 - 11:00 Coffee/tea Break
      • 10:40 Coffee/tea Break 20'
    • 11:00 - 11:50 DNA Packaging in Viral Capsids: A Computational Approach
    • 11:50 - 12:40 Participants' Presentations
      • 11:50 Participants' Presentations 50'
    • 12:40 - 14:30 Lunch break
      • 12:40 Lunch break 1h50'
    • 14:30 - 15:20 Accuracy and Precision in Atomistic Molecular Dynamics Simulations
      • 14:30 Accuracy and Precision in Atomistic Molecular Dynamics Simulations 50'
        Speaker: S. PIANA AGOSTINETTI (D.E. Shaw Research, New York, U.S.A.)
        Material: Abstract S. PIANA AGOSTINETTI
    • 15:20 - 16:10 Structural and Computational Studies of a Bacterial Pentameric Ligand-gated Ion Channel
      • 15:20 Structural and Computational Studies of a Bacterial Pentameric Ligand-gated Ion Channel 50'
        Speaker: M. DELARUE (Institut Pasteur, Structural Biology & Chemistry, Paris, France)
    • 16:10 - 16:30 Break
      • 16:10 Break 20'
    • 16:30 - 17:20 A Kinetic View of Viral RNA in Single Live Cells in Real Time
      • 16:30 A Kinetic View of Viral RNA in Single Live Cells in Real Time 50'
        Speaker: A. MARCELLO (ICGEB, Molecular Virology Laboratory, Trieste, Italy)
        Material: Abstract A. MARCELLO lecture notes
    • 17:20 - 18:00 POSTER SESSION
      Location: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)
      • 17:20 POSTER SESSION 40'
  • Friday, 15 October 2010
    • 09:00 - 09:50 Applications of Metadynamics Simulations to Biological Systems
      • 09:00 Applications of Metadynamics Simulations to Biological Systems 50'
        Speaker: A. BARDUCCI (ETH Zurich, Computational Science Lab., Lugano, Switzerland)
    • 09:50 - 10:40 Characterizing the kinetics of complex biochemical processes by bias-exchange metadynamics
      • 09:50 Characterizing the kinetics of complex biochemical processes by bias-exchange metadynamics 50'
        Speaker: A. LAIO (SISSA, Trieste, Italy)
    • 10:40 - 11:00 Coffee/tea break
      • 10:40 Coffee/tea break 20'
    • 11:00 - 11:50 Genome Organization and Assembly of RNA Viruses: Where Structure Meets Function
      • 11:00 Genome Organization and Assembly of RNA Viruses: Where Structure Meets Function 50'
        Speaker: R. TWAROCK (Univ. of York, Dept. Mathematics, York, U.K.)
        Material: Abstract R. TWAROCK
    • 12:00 - 14:00 Lunch break
      • 12:00 Lunch break 2h0'
    • 14:00 - 14:50 Coffee Chemistry
      • 14:00 Coffee Chemistry 50'
        Speaker: L. NAVARINI (AromaLab, Illycaffe' S.p.A., Trieste, Italy)
        Material: Abstract L. NAVARINI
    • 14:50 - 15:40 Role and Perspective of ab initio Molecular Dynamics for Molecular Medicine
      • 14:50 Role and Perspective of ab initio Molecular Dynamics for Molecular Medicine 50'
        Speaker: P. CARLONI (SISSA Trieste and GRS Lab. of Comput.Biophy., Juelich, Germany)
    • 15:40 - 16:00 Break
      • 15:40 Break 20'
    • 16:00 - 16:20 Talk by the First Winner of the Poster Competition
      • 16:00 Talk by the First Winner of the Poster Competition 20'
    • 16:20 - 16:40 Talk by the Second Winner of the Poster Competition
      • 16:20 Talk by the Second Winner of the Poster Competition 20'
    • 16:40 - 17:00 Huntingtin: Stability and Interaction with Molecular Partners from Computational Biophysics Studies
      • 16:40 Huntingtin: Stability and Interaction with Molecular Partners from Computational Biophysics Studies 20'
        Speaker: G. ROSSETTI (SISSA, Statistical & Biological Physics Sector, Trieste, Italy)
    • 17:00 - 17:30 FINAL REMARKS / CERTIFICATES
      • 17:00 FINAL REMARKS / CERTIFICATES 30'
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