Program

User Meeting Program (May 25-27)

User meeting will start on May 25, in the morning, and will end on May 27, lunchtime. All the talks will be in room 005 (ground floor). The lunch breaks and poster sessions on Thursday and Friday will be in the foyer of the Aula Magna (in the garden). If you are looking for the program of the Tutorial you should look at this page.

Talks will last 25 minutes + 5 minutes for questions.


May 25, Thursday:

  • 8:30 Special bus from Piazza Oberdan. Normal ticket needed!
  • 8:30-9:30 Registration
  • 9:30-10:00 Bernd Ensing - Chemistry with PLUMED
  • 10:00-10:30 Fabio Pietrucci - Developing graph theory-inspired collective variables for a broad spectrum of chemical reactions and phase transitions
  • 10:30-11:00 Coffee break
  • 11:00-11:30 Tomáš Kubař - QM/MM simulation of proton transfer with PLUMED
  • 11:30-12:00 Alessandro Barducci - Structural and thermodynamic characterization of Hsp70 chaperones as unfolding machines
  • 12:00-12:30 Azade Yazdan Yar - Interaction of Simulated Body Fluid (SBF) ions with a rutile surface: Linking bioactivity​ and free energy calculations
  • 12:30-16:00 Lunch break, including poster session
  • 16:00-16:30 Jan Domanski - Sampling challenges in studying membrane helix-helix dimerization
  • 16:30-17:00 Federico Comitani - Identifying Cryptic Pockets in FGFRs with Enhanced Sampling Simulations
  • 17:00-17:30 Daniele Di Marino - A Comprehensive Description of the Homo and Heterodimerization Mechanism of the Chemokine Receptors CCR5 and CXCR4
  • 17:30-18:30 Discussion: How to improve PLUMED documentation (chair: Gareth Tribello)
  • 19:00 Special bus from SISSA. Normal ticket needed!


May 26, Friday:

  • 8:30 Special bus from Piazza Oberdan. Normal ticket needed!
  • 9:00-9:30 Michele Ceriotti - Bridging the gap between atomistic and mesoscopic models of nucleation
  • 9:30-10:00 Gabriele Sosso - Forward Flux Sampling Simulations of Heterogeneous Ice Nucleation: a PLUMED Story
  • 10:00-10:30 Matteo Salvalaglio - Studying concentration-driven processes with finite-sized molecular simulations
  • 10:30-11:00 Coffee break
  • 11:00-11:30 Alessandro Laio - Estimating the free energy without collective variables
  • 11:30-12:00 Toni Giorgino - PLUMED's collective variables in the High Throughput Molecular Dynamics analysis environment
  • 12:00-12:30 Luca Donati - Metadynamics on path space
  • 12:30-16:00 Lunch break, including poster session
  • 15:30-16:00 Francesco Colizzi - Chasing the regulation of Adenylate Cyclase by G-proteins with coevolution-driven molecular simulations
  • 16:00-16:30 Matteo Masetti - Simulating transition metal trafficking: the activation of urease
  • 16:30-17:00 Markéta Paloncýová - Role of Enzyme Flexibility in Ligand Access and Egress to Active Site
  • 17:00-18:00 Discussion: How to contribute to PLUMED (chair: Giovanni Bussi)
  • 18:00-19:00 Concert in Aula Magna
  • 19:20 Special bus from SISSA. Normal ticket needed!


May 27, Saturday:

  • 9:00-9:30 Joan Clark-Nicolas - Implementation and testing of the JEDI collective variable to explore protein druggability
  • 9:30-10:00 Omar Valsson - VES Code: Module for Performing Variationally Enhanced Sampling Simulations within PLUMED
  • 10:00-10:30 Vojtěch Spiwok - Flying Gaussian Method
  • 10:30-11:00 Coffee break
  • 11:00-12:30 Discussion: How should PLUMED evolve (chair: Max Bonomi)