CECAM-ICTP School on Molecular Dynamics and its Applications to Biological Systems
International Center for Theoretical Physics (ICTP, Trieste, Italy)
Graduate students in Physics or Chemistry typically have a solid background in stat-mech and condensed-matter physics but little knowledge of the numerical algorithms and concepts that are the bedrock for any theoretical work in such areas. A similar gap is often found in graduate students coming from developing countries, where numerical skills are still limited due to low availability of computational resources.
It is our aim to fill this cultural gap by proposing a joint school with the International Center for Theoretical Physics (ICTP), an institution in Trieste working specifically with developing countries. The activity will be organized in three weeks: a 2-week School devoted to an introduction to molecular dynamics simulation techniques for people without previous programming experience, and a 1-week workshop presenting the latest achievements in computer modeling of biological systems lectured by world-renowned scientists. With the CECAM-IT-SISSA-SNS Node we propose to cover the fees for undergraduate students coming from the usual CECAM basin, while ICTP will provide support for students coming from developing countries.
To our knowledge, this makes the activity quite unique:
- The school is mainly tailored to beginners, at variance with most other schools in the CECAM program, which are typically targeted to students/young researchers with a working knowledge of specific methods.
- The last week of the activity, which will be a workshop, will make the students appreciate the versatility, the generality and "the beauty" of the techniques which have learned by attending the school.
- Carrying on the activity in collaboration with ICTP will be an important cultural "plus", fostering future collaborations and scientific contacts with developing countries.
The purposes of this event is three-fold:
- Providing undergraduate students with a basic but detailed overview of the theoretical foundations of classical molecular dynamics methods.
- Providing the basics for writing and running in practice simple molecular simulations.
- Giving an overview of the domains of the most exciting and up-to-date applications in the realm of biological systems.
At the end of the event the students will have acquired a first-hand experience with numerical simulations for a broad range of scientific contexts, will be aware of the challenges and open problems in computational physics, and will be able to write simple codes for simulating systems of their interest and carry out the pertinent data analysis.
The School has a 10year-old tradition in Trieste at SISSA, with an impressive rate of success in terms of applications and attendance. For the first time, the School will be coorganized by SISSA and the International Center for Theoretical Physics (ICTP), the world-renowned center in Trieste whose mission is to promote Physics and Science in developing countries. This proposal, then, attempts to capitalise on the already existing strong school in atomistic simulations that has been organised by SISSA through CECAM in the past years and the half-a-century experience in promoting high-level education in developing countries of ICTP.
TOPICS for the SCHOOL (Weeks 1+2, September 7-18 2020)
Days 1-2, Sept 7-8 2020
- Introduction to programming and shell scripting.
Days 3-6, Sept 9-10-11-14 2020
- Introduction to Molecular Dynamics
- Integrating the equations of motion
- Thermostats and barostats
- Long-range forces
- Estimating errors
Days 7-10, Sept 15-16-17-18 2020
- Introduction to enhanced sampling methods
- Rare events
- Biased sampling: umbrella sampling and metadynamics
- Transition path sampling
- Data Science Techniques for molecular simulations
TOPICS for the SCHOOL (Week 3, September 21-25 2020)
Applications of Molecular Dynamics to Biology
- 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: random walks and Langevin equations
*** Notes from the Organizers ***
1) Due to uncertainty related to the current covid-19 epidemics, the weeks 1&2 of the School originally scheduled on the dates Sept. 7-18 2020 have been cancelled and the event postponed to 2021.
New dates are not available yet. Those interested to apply to the School are invited to check regularly the CECAM website for further notice.
2) The week 3 of the School, originally planned as a Workshop with introductory lectures on the dates Sept. 21-25 2020, will be adapted into a DIGITAL EVENT. The dates will remain the same as originally planned.
For more information on this event and the rules to apply, please check at the following link: https://www.cecam.org/workshop-details/990
Giovanni Bussi (Scuola Internazionale Superiore di Studi Avanzati) - Organiser
Ali Hassanali (ICTP) - Organiser
Alessandro Laio (SISSA) - Organiser
Alessandra Magistrato (CNR-IOM@SISSA) - Organiser
Cristian Micheletti (SISSA) - Organiser
Alejandro Rodriguez Garcia Rodriguez Garcia (International Centre for Theoretical Physics) - Organiser
Edgar Roldan (International Center for Theoretical Physics (ICTP, Trieste, Italy)) - Organiser
Angelo Rosa (SISSA Trieste) - Organiser
Angelo Rosa (Scuola Internazionale Superiore di Studi Avanzati (SISSA)) - Organiser