Scientific Calendar Event
GO TO SCIENTIFIC CALENDAR



  • Europe/Rome
  • English
  • Administration
Description
The workshop is live-streamed on the ICTP Condensed Matter and Statistical Physics YouTube page at the following link:

There continues to be a growing community of scientists in both the developed and developing world, interested in and working on applications of molecular dynamics techniques to understand biological systems. This is highly relevant for problems in health and medicine.

The topics of this workshop is relevant in diverse contexts, from basic science, where molecular modelling and simulations have become indispensable tools even to interpret and design experiments, to applicative avenues such as health and medicine where advanced MD simulation techniques are used for insilico drug screening. This workshop is aimed at bringing together world experts working in a broad range of topics related to bio-molecular simulations which will expose both young and advanced researchers to the state-of-the-art in the field.

Topics:
  • Quantum Mechanics in Biology: Enzyme Catalysis
  • Protein Dynamics/Protein Folding 
  • Drug Design 
  • Protein Structure Prediction
  • DNA/RNA Dynamics/Folding 
  • Coarse-grain simulations of nucleic acids & chromatin 
  • Multi-scale computer simulations for polymer melts 
  • Spectroscopy: Excited State Dynamics in Biology
  • Stochastic processes in biophysics
Speakers:
M. BONOMI, Institut Pasteur - CNRS, France
M.E. CASIDA, University of Grenoble, France
M. CERIOTTI, Swiss Federal Institutes of Technology Lausanne (EPFL), Switzerland
B. CHENG, Trinity College Cambridge University, UK
G. COLOMBIO, Università di Pavia, Italy
M. DE VIVO, Istituto Italiano di Tecnologia, Italy
R. EICHHORN, The Nordic Institute for Theoretical Physics, Sweden
R. EVERAERS, École Normale Supérieure de Lyon, France
G. HUMMER, Max Planck Institute of Biophysics, Germany
V. KAILA, Stockholm University, Sweden
L. KAMMERLIN, Uppsala Biomedical Center, Sweden
S. KHALID, University of Southampton, UK
E. ROSTA, King's College London, UK
L. ROVIGATTI, Sapienza University of Rome, Italy
K. SEKIMOTO, Université Paris Diderot, France
S. WOLF, Albert Ludwigs University, Germany

Material

ICTP-SISSA-CECAM Workshop on Molecular Dynamics and its Applications to Biological Systems | (smr 3483)
Go to day
  • Monday, 21 September 2020
    • 09:15 - 12:15 Introductory Lectures - morning session 
      Chair: Angelo Rosa (SISSA, Italy)
      • 09:15 RNA Dynamics Using Molecular Modeling and Experimental Data 45'
        Speaker: Giovanni BUSSI (SISSA, Italy)
        Material: Slides Video
      • 10:00 Martingale Stochastic Thermodynamics 45'
        Speaker: Edgar ROLDAN (ICTP, Italy)
        Material: Video
      • 10:45 Advanced Sampling Techniques for Atomistic Simulations 45'
        Speaker: Alessandro LAIO (SISSA, Italy)
        Material: Video
      • 11:30 QM/MM Simulations in Enzymatic Systems and Drug Discovery 45'
        Speaker: Alessandra MAGISTRATO (SISSA, Italy)
    • 14:00 - 17:00 Introductory Lectures - aftenoon session 
      Chair: Giovanni Bussi (SISSA, Italy)
      • 14:00 Spontaneous and Designed Molecular Knotting 45'
        Speaker: Cristian MICHELETTI (SISSA, Italy)
      • 14:45 Clustering of Molecular Data 45'
        Speaker: Alex RODRIGUEZ (ICTP, Italy)
        Material: Video
      • 15:30 Why the Solvent Bath Matters in Biology 45'
        Speaker: Ali HASSANALI (ICTP, Italy)
      • 16:15 Chromosome Folding: Lessons from Polymer Physics 45'
        Speaker: Angelo ROSA (SISSA, Italy)
        Material: Video
  • Tuesday, 22 September 2020
    • 09:15 - 11:00 Advanced Lectures, PART 1 - morning session 
      Chair: Ali Hassanali (ICTP, Italy)
      • 09:15 Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy 45'
        Speaker: Massimiliano BONOMI (Institut Pasteur - CNRS, France)
      • 10:00 Break 15'
      • 10:15 Our Experience with TD-DFT and TD-DFTB in Biological, Bio-inspired, and Other Photoprocesses 45'
        Speaker: Mark E. CASIDA (University of Grenoble, France)
        Material: Slides Video
    • 14:00 - 15:45 Advanced Lectures, PART 1 - afternoon session 
      Chair: Giovanni Bussi (SISSA, Italy)
      • 14:00 Equivariant Representations for Atomistic Machine Learning 45'
        Speaker: Michele CERIOTTI (Swiss Federal Institutes of Technology Lausanne (EPFL), Switzerland)
        Material: Slides Video
      • 14:45 Break 15'
      • 15:00 Modelling Water with the Help of Machine Learning 45'
        Speaker: Bingqing CHENG (Trinity College Cambridge University, UK)
        Material: Video
  • Wednesday, 23 September 2020
    • 09:15 - 11:00 Advanced Lectures, PART 2 - morning session 
      Chair: Alessandro Laio (SISSA, Italy)
      • 09:15 Studying Protein Dynamics with an Eye to Molecular Design 45'
        Speaker: Giorgio COLOMBO (Università di Pavia, Italy)
        Material: Video
      • 10:00 Break 15'
      • 10:15 Metal-Aided Enzymatic Processing of DNA and RNA 45'
        Speaker: Marco DE VIVO (Istituto Italiano di Tecnologia, Italy)
        Material: Video
    • 14:00 - 15:45 Advanced Lectures, PART 2 - afternoon session 
      Chair: Cristian Micheletti (SISSA, Italy)
      • 14:00 Brownian Dynamics Simulations with Hard-Body Interactions: Exact Numerical Treatment 45'
        Speaker: Ralf EICHHORN (The Nordic Institute for Theoretical Physics, Sweden)
        Material: Slides Video
      • 14:45 Break 15'
      • 15:00 Understanding the Large Scale Structure of Interphase Nuclei in Drosophila for Different Stages of the Embryonic Development 45'
        Speaker: Ralf EVERAERS (École Normale Supérieure de Lyon, France)
        Material: Video
  • Thursday, 24 September 2020
    • 09:15 - 11:00 Advanced Lectures, PART 3 - morning session 
      Chair: Alessandra Magistrato (SISSA, Italy)
      • 09:15 Molecular Simulations in Times of Covid-19 45'
        Speaker: Gerhard HUMMER (Max Planck Institute of Biophysics, Germany)
        Material: Video
      • 10:00 Break 15'
      • 10:15 Elucidating Mechanisms of Biological Energy Conversion by Simulations Across Scales 45'
        Speaker: Ville KAILA (Stockholm University, Sweden)
        Material: Video
    • 14:00 - 15:45 Advanced Lectures, PART 3 - afternoon session 
      Chair: Alejandro Rodriguez Garcia (ICTP, Italy)
      • 14:00 Bacterial Cell Envelopes: Incorporating Biological Complexity in Molecular Dynamics Simulation Studies 45'
        Speaker: Syma KHALID (University of Southampton, UK)
        Material: Video
      • 14:45 Break 15'
      • 15:00 Using Molecular Simulations to Trace the Role of Conformational Dynamics in Enzyme Evolution 45'
        Speaker: Lynn KAMERLIN (Uppsala Biomedical Center, Sweden)
        Material: Slides
  • Friday, 25 September 2020
    • 09:15 - 11:00 Advanced Lectures, PART 4 - morning session 
      Chair: Edgar Roldan (ICTP, Italy)
      • 09:15 Progressive Quenching and Hidden Martingale Process 45'
        Speaker: Ken SEKIMOTO (Université Paris Diderot, France)
        Material: Video
      • 10:00 Break 15'
      • 10:15 Designer Protein Assemblies with Tunable Phase Diagrams in Living Cells 45'
        Speaker: Lorenzo ROVIGATTI (Università di Roma La Sapienza, Italy)
        Material: Video
    • 14:00 - 15:45 Advanced Lectures, PART 4 - afternoon session 
      Chair: Angelo Rosa (SISSA, Italy)
      • 14:00 Irreversible Monte Carlo Methods to Sample Biomolecular Simulations 45'
        Speaker: Edina ROSTA (King's College London, UK)
        Material: Video
      • 14:45 Break 15'
      • 15:00 Protein-Ligand Dynamics on Multi-Second Timescales from Sub-µs Atomistic Simulations 45'
        Speaker: Steffen WOLF (Albert Ludwigs University, Germany)
        Material: Video
GO TO SCIENTIFIC CALENDAR