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Description An ICTP-SISSA-CECAM Virtual Meeting

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.
 
This virtual gathering is aimed at bringing together both current students and alumni of SISSA and ICTP working in the broad area of atomistic simulations as applied to biological systems. This event will include introductory lectures to various aspects of biomolecular simulations, research talks by alumni working both in academia and industry and highlights of the research at SISSA and ICTP delivered by young researchers. This virtual activity is structured to enhance informal social interactions which will take place through the gather.town platform.

Registration: There is no registration fee.

Material

ICTP-SISSA-CECAM Workshop on Molecular Dynamics and its Applications to Biological Systems | (smr 3627)
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  • Monday, 13 September 2021
    • 10:30 - 11:00 Welcome by the Organisers
      Conveners: Ali HASSANALI (ICTP, Italy), Angelo ROSA (SISSA, Italy)
    • 11:00 - 17:00 ICTP & SISSA PI's 
      Platform: Zoom
      • 11:00 Chromosome folding: Lessons from polymer physics 40'
        Speaker: Angelo ROSA (SISSA, Italy)
        Material: Video
      • 11:40 Why the solvent bath matters in Biology 40'
        Speaker: Ali HASSANALI (ICTP, Italy)
        Material: Video
      • 12:20 Enhanced sampling in Molecular Dynamics: Why is it necessary? 40'
        Speaker: Alessadro LAIO (SISSA, Italy)
        Material: Video
      • 13:00 Lunch 1h0'
      • 14:00 Questions & Answers session 2h0' 
        Platform: Gather town
      • 16:00 Poster Session 1h0' 
        Platform: Gather town
        Material: Booklet Poster Presenters
  • Tuesday, 14 September 2021
    • 10:20 - 16:00 ICTP & SISSA PI's 
      Platform: Zoom
      • 10:20 Clustering Molecular Data 40'
        Speaker: Alejandro GARCIA RODRIGUEZ (ICTP, Italy)
        Material: Video
      • 11:00 From natural to synthetic molecular knots 40'
        Speaker: Cristian MICHELETTI (SISSA, Italy)
        Material: Video
      • 11:40 RNA dynamics from molecular simulations and solution experiments 40'
        Speaker: Giovanni BUSSI (SISSA, Italy)
        Material: Video
      • 12:20 QM/MM Simulations in Enzymatic Systems and Drug Discovery 40'
        Speaker: Angelo SPINELLO (SISSA, Italy)
      • 13:00 Lunch 1h0'
      • 14:00 Questions & Answers session 2h0' 
        Platform: Gather town
  • Wednesday, 15 September 2021
    • 10:00 - 15:00 Plenary Speaker Talk & ICTP/SISSA PhD Students & Postdocs 
      Platform: Zoom
      • 10:00 Transition path sampling and analysis of complex activated (bio)molecular processes 1h30'
        Speaker: Peter BOLHUIS (Amsterdam University, The Netherlands)
        Material: Slides Video
      • 11:30 Break 15'
      • 11:45 Self-assembly of molecules with non-trivial topology 30'
        Speaker: Matteo BECCHI (SISSA, Italy)
      • 12:15 Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles 30'
        Speaker: Mattia BERNETTI (SISSA, Italy)
        Material: Video
      • 12:45 Break 1h15'
      • 14:00 Estimating high-dimensional free energies without collective variables 30'
        Speaker: Matteo CARLI (SISSA, Italy)
        Material: Video
      • 14:30 Using machine learning to improve RNA force fields 30'
        Speaker: Thorben FRÖHLKING (SISSA, Italy)
        Material: Video
  • Thursday, 16 September 2021
    • 11:00 - 17:00 ICTP & SISSA PhD Students & Postdocs 
      Platform: Zoom
      • 11:00 The information imbalance, a tool to quantify the relative information content of feature spaces 30'
        Speaker: Aldo GLIELMO (SISSA, Italy)
      • 11:30 NKCC1 ion cotransporter: four ions, one channel 30'
        Speaker: Pavel JANOS (SISSA, Italy)
        Material: Video
      • 12:00 Ultrafast electron-ion dynamics around conical intersections: the key role of the strong hydrogen bond 30'
        Speaker: Uriel MORZAN (ICTP, Italy)
        Material: Video
      • 12:30 A computational model for melts of polymer ring with unconstrained topology 30'
        Speaker: Mattia Alberto UBERTINI (SISSA, Italy)
        Material: Video
      • 13:00 Break 1h0'
      • 14:00 Poster Session 3h0' 
        Platform: Gather town
  • Friday, 17 September 2021
    • 11:00 - 16:15 ICTP & SISSA Alumni Talks 
      Platform: Zoom
      • 11:00 My first job 1h0'
        Speaker: Andrea CESARI (Allianz, Italy)
      • 12:00 Communication pathways in an IgG4 antibody: a multiscale study 1h0'
        Speaker: Raffaello POTESTIO (Trento University, Italy)
        Material: Video
      • 13:00 Break 1h0'
      • 14:00 Water-triggered, irreversible conformational change of SARS-CoV-2 main protease on passing from the solid state to aqueous solution 1h0'
        Speaker: Narjes ANSARI (IIT, Italy)
      • 15:00 Ligand binding and peptide design using molecular simulations 1h0'
        Speaker: Pilar COSSIO (Max Planck Institute, Colombia)
      • 16:00 Closing remarks 15'
        Speaker: Ali HASSANALI (ICTP, Italy)
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