Motivations and scopes
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, concepts and unresolved problems that are the bedrock for any theoretical work in such areas. A similar gap becomes especially dramatic in graduate students coming from developing countries, where numerical skills are still limited due to low availability of computational resources.
In order to fill this cultural gap and motivated further by the necessity of envisioning new methods of communicating Science in the present and future covid-19 era, we present the first CECAM-IT-SISSA-SNS / ICTP DIGITAL EVENT.
The event is organized by the CECAM-IT-SISSA-SNS Node at SISSA (www.sissa.it) in collaboration with the International Center for Theoretical Physics (ICTP, www.ictp.it). Both institutions are located in Trieste (Italy) and represent two leading research centers specifically dedicated to promote education and research of young people at pre-doctoral level.
The present activity will last one week (5 working days), with e-lectures being given remotely by local SISSA/ICTP experts and international renowned experts from some amongst the most prestigious institutions around the world. These e-lectures will aim at introducing the novice to the latest achievements in computer modeling of biological systems.
To our knowledge, this makes the activity rather unique:
- The event is mainly tailored to beginners, at variance with most other events of this kind scheduled in the CECAM program or around the world, which are typically targeted to students/young researchers with a working knowledge of specific methods.
- The event will make the students appreciate the versatility, the generality and the elegance of the numerical techniques involved in the analysis and solution of complex biologically-motivated problems.
- Carrying on the activity in collaboration with ICTP will be an important cultural "plus", fostering future collaborations and scientific contacts with developing countries.
At the end of the event the attendants will have acquired a first-hand experience with numerical simulations for a broad range of scientific contexts and will be prepared on the challenges and open problems in computational physics.
The event goes on the path of a firmly established, 10year-old tradition of Schools in Trieste, a tradition which has been blessed by an impressive rate of success in terms of applications and attendance. For the first time in this long tradition and especially motivated by the crisis of the covid-19 epidemics, the event will be coorganized fully online and in joint collaboration between the CECAM Node located in SISSA and the ICTP. As such, the event can capitalise on the strong experience in education and research about atomistic simulations performed at these two partner institutions.
- 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
Outline of the event (in construction)
Day 1 (September, 7)
- Students will get a very short introduction to what MD is and what can be done with it.
- They will also receive the video links of lectures that they are supposed to listen to. Lectures will include a very basic overview and general notions about MD simulations which will introduce the students to the general language that they will hear about in the workshop.
- On the same day, the students will get introduced to the simple MD code and the exercises that they should begin after going through the online lectures.
Day 5 (September, 12)
- The students will get a tutorial in VMD.
- Mid through the second week the solution of the exercise will be shared with the students.