NCBR002 From Supramolecular Chemistry to Structural Biology by Multiscale Modelling Methods

Faculty of Science
Spring 2023
Extent and Intensity
1/2/0. 4 credit(s). Type of Completion: k (colloquium).
Taught in person.
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Jan Novotný, Ph.D. (lecturer)
Ing. Tomáš Trnka, Ph.D. (lecturer)
doc. Mgr. Karel Kubíček, PhD. (lecturer)
RNDr. Miroslav Krepl, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites (in Czech)
SOUHLAS
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
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.
Learning outcomes
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.
Syllabus
  • 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
Teaching methods
lectures, tutorials, and practical exercises in the computer room, followed by discussion about individual problems
Assessment methods
oral exam
Language of instruction
English
Further comments (probably available only in Czech)
The course can also be completed outside the examination period.
The course is taught only once.
The course is taught: in blocks.
Teacher's information
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.

  • Enrolment Statistics (recent)
  • Permalink: https://is.muni.cz/course/sci/spring2023/NCBR002