NCBR002 From Supramolecular Chemistry to Structural Biology by Multiscale Modelling Methods

Přírodovědecká fakulta
jaro 2023
Rozsah
1/2/0. 4 kr. Ukončení: k.
Vyučováno prezenčně.
Vyučující
RNDr. Petr Kulhánek, Ph.D. (přednášející)
Mgr. Jan Novotný, Ph.D. (přednášející)
Ing. Tomáš Trnka, Ph.D. (přednášející)
doc. Mgr. Karel Kubíček, PhD. (přednášející)
RNDr. Miroslav Krepl, Ph.D. (přednášející)
Garance
RNDr. Petr Kulhánek, Ph.D.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Předpoklady
SOUHLAS
Omezení zápisu do předmětu
Předmět je otevřen studentům libovolného oboru.
Cíle předmětu
Computer simulations have become a valuable tool for expanding our knowledge in many areas. The steadily increasing performance of supercomputers or even desktop computers allows us to simulate bigger systems more accurately. However, proper predictions can only be obtained if correct models and theoretical approaches are employed. Therefore, this course aims to provide essential foundations for performing computer simulations and ways to avoid typical errors from misunderstanding employed approximations. The lectures will span various molecular modelling methods addressing problems from supramolecular chemistry to structural biology. The course will comprise theoretical lectures complemented by practical sessions exercising typical simulation techniques in each discipline.
Výstupy z učení
After completing the course, students will:
be familiar with work in the Linux environment in supercomputing centres
know how to run molecular simulations on supercomputers
understand the fundamentals of molecular modelling
be familiar with the three pillars of molecular modelling: models, chemistry models, and sampling techniques
know the fundamentals of quantum chemistry methods and molecular mechanics
know how to simulate molecular systems in time
know how to perform free energy calculations
be familiar with the interpretation of data.
By achieving these learning outcomes, students should gain a solid foundation in molecular modelling simulations and be equipped to apply these techniques in their future study and research.
Osnova
  • Scope of Summer School
  • History I (1687-1926)
  • WOLF Cluster
  • Infinity / Software
  • Software for Molecular Modelling I (warm up)
  • Supramolecular Chemistry
  • Basics of Thermodynamics
  • Equilibrium
  • Modelling Overview
  • Supercomputing I
  • Statistical Thermodynamics
  • Laboratory Notebooks
  • Macrocycles
  • Macrocycles/Build Models
  • Applications of NMR in Supramolecular Chemistry
  • Quantum Mechanics Foundations
  • Macrocycles/Characterise Models
  • Structure
  • Potential Energy Surface
  • Quantum Mechanics
  • 3D Printing
  • Molecular Mechanics
  • PES: Energy Differences
  • Molecular Dynamics
  • Molecular Dynamics - Tips
  • ReaxFF
  • Protein Structure
  • Crystallography Basics
  • Protein Structure Prediction
  • Structure Comparison, ColabFold: Analysing Results, Monomer Prediction: Summary
  • CryoEM
  • PES: Transition Structure
  • RNA Splicing by Computer Simulations
  • SCM Applications: Materials
  • Nucleic Acid Simulations
  • Free Energy Calculations
  • Round Table Discussion
Výukové metody
lectures, tutorials, and practical exercises in the computer room, followed by discussion about individual problems
Metody hodnocení
oral exam
Vyučovací jazyk
Angličtina
Informace učitele
https://wolf.ncbr.muni.cz/bluezone/2023/fsc2sb-m3
The web site is available for registered students only (e-INFRA account is required and registration into the summer school internal area is required).
The school is held in the computer classroom 118/C04 at University Campus Bohunice every working day from 9:00 to 15:00 from 10th to 21th July, 2023.

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