Brno, Czech Republic

Multiscale Modelling Methods

when 14 July 2024 - 27 July 2024
language English
duration 2 weeks
credits 4 EC
fee EUR 750

Delve into the realm of computer simulations: we are living in an era, where (super)computers continue to grow the possibilities of simulating molecular and biomolecular systems with unprecedented scale and precision. However, the key to unlocking these simulations are in the adept to use of accurate models and theoretical approaches.

In this course we provide essential theoretical foundations of computational chemistry, emphasizing the critical understanding of the limitations of employed approximations. The classes are designed to guide you through the world of molecular modeling methods, tackling fields ranging from the complexities of supramolecular chemistry to structural biology.

Theoretical lectures will be complemented by practical sessions exercising typical simulation techniques in each discipline.

Additionally, course offers opportunity for those participants interested in presenting their projects in a poster session (chance to showcase your passion for the field).

As a bonus, participants of this course will gain an exclusive key to MetaCentrum, the Czech national supercomputing center for a duration of three months.
This programme is designed as a part of our Intensive 2 Week Summer School, where multiple courses from a wide variety of Masaryk University study programmes and departments will be offered. These courses will be arranged in an intensive and dynamic form, each working day there will be an academic session. In the afternoon and evenings students come together from across disciplines to enjoy everything Brno has to offer!

In addition to the academics, daily cultural and social programming will be offered, including the option of a one-day excursion to Vienna.

Course leader

Petr Kulhánek, Tomáš Trnka

Target group

This course is targeted for students enrolled in chemistry or physics studies of bachelor, master and early stage doctoral levels.

Course aim

Topics included:

1) Basics from phenomenological and statistical thermodynamics.
2) Physical foundations of interaction within and between atoms.
3) How to build suitable models ranging from small to very large biomolecular systems.
4) Chemistry models include quantum mechanics (QM), molecular mechanics (MM), and their hybrid versions, particularly QM/MM.
5) Sampling techniques for the free energy calculation, employing an ideal gas model and potential of mean force (PMF) methods, including umbrella sampling, adaptive biasing force, and their accelerated versions by a multiple-walker approach.
6) Impact of collective variables on calculated free energies.
7) How to simulate biomolecular systems properly.
8) Impact of pH on ionizable groups and reconstruction of experimentally unresolved protein structure parts.
9) Protein structure prediction by machine learning methods (AlphaFold, ESMFold). Docking to prepare protein/substrate complexes.
10) Simulations employing ReaxFF reactive force field.

Fee info

EUR 750: All students will receive a tuition waiver due to outside funding. Fees include:

- Tuition fees

- Accommodation in Brno (14-27 July)

- Opening and Closing receptions

- Culture activities around Brno

- Day trip to Vienna

- 24/7 support

- Social programme

Students should budget an additional €200-500 depending on their spending habits for food (breakfast, lunch, dinner) and fun "optional" activities in Brno.
EUR 700: €50 discount for students from partner universities

Register for this course
on course website