Eutopia Academy for students and post-docs on tools in computational biophysics

Organizers: Davide Michieletto, Samuela Pasquali, Pawel Dabrowski-Tumanski

We are proud to launch the EUTOPIA Academy, a series of online events for software training dedicated to all members of the network (especially early career investigators) who are looking to learn specific pieces of software that are relevant for the investigation of topological signatures. The aim of these events is to go through these software in detail and step-by-step, from download to execution.

The Academy will be held on-line, each last Thursday and Friday of the month, February-June 2021. The link to the on-line event will be provided to all registered participants. The registration form will be sent via the Eutopia mailing list before each event. Alternatively, please ask directly to the organizers.

The plan of the Academy:

25-26 February 2021 – Molecular Dynamics and LAMMPS:
Lecturer: Davide Michieletto
• Basics of MD, theory and simulations in LAMMPS (including simulation of knotted polymers);
• Visualization in VMD
• Simple analysis with C++ codes
• Tricks and tweaks for LAMMPS
Material: you find the material of the course here

25-26 March 2021 – Analysis of the MD results:
Lecturers: Marco Giulini, Samuela Pasquali, Pawel Dabrowski-Tumanski
• Introduction to Python
• Python-based analysis of trajectories
• Structure and trajectory visualization
• Troubleshooting
Material: TBA

29-30 April 2021 – All atom simulations:
Lecturers: TBA
• Running all atom simulations
• Analyzing the DNA elasticity
• Emulating AFM images
Material: TBA

27-28 May 2021 – Topological analysis:
Lecturer: TBA
• KnotPlot
• Topoly
• KymoKnot
• KnotoID
• …
Material: TBA

24-25 June 2021 – Analysis of experimental data:
• In preparation