Kaisa_2012_3_photo by Veikko Somerpuro

Enrol
18.12.2019 at 08:00 - 7.1.2020 at 23:59

Timetable

Description

Master's Programme in Materials Research is responsible for the course.

Modules where the course belong to:

  • MATR300 Advanced Studies in Materials Research
    Optional for:
    1. Study Track in Computational Materials Physics
    2. Study Track in Medical Physics and Biophysics
    3. Study Track in Electronics and Industrial Physics
  • TCM300 Advanced Studies in Theoretical and Computational Methods

The course is available to students from other degree programmes.

  • Familiarity with the Linux operating system.
  • Basic understanding of coding (e.g., with C or Python) would be an asset but not compulsory.
  • Understanding of computer simulation methods through more basic/intermediate courses would be useful but not compulsory.

Those interested in extending the understanding of biological systems should consider, for instance, also courses MATR331 Introduction to Biological Physics and MATR332 Physics of Biological Systems that are highly recommended. Additionally, other courses in computer simulation techniques such as MATR325 Molecular dynamics simulations and MATR326 Tools of high performance computing (as examples) would be useful in training.

  • Students will have an understanding of the theoretical bases of simulation methods.
  • They will know areas of applications and limitations of these methods.
  • In practice, students will be able to run simulations of individual biomolecules and more complex systems comprised of numerous biomolecules.
  • They will know and be able to use the most common software packages employed in biomolecular simulations.

First or second year of Master's studies.

Given every second year in the autumn term.

  • Basis of molecular dynamics simulations
  • Empirical force fields for bio-simulations
  • Introduction to quantum mechanical methods
  • Quantum mechanical calculations used for force field parameterization
  • Algorithms used in bio-simulations
  • Building up simulation systems
  • Analysis of trajectories obtained in MD simulations
  • Free energy calculations (umbrella sampling, thermodynamic integration)
  • Algorithms used to improve sampling (coarse graining, replica exchange, thermodynamic integration, metadynamics)
  • Continuum electrostatic calculations
  • Hybrid QM/MM techniques in bio-simulations
  • Lecture notes
  • GROMACS manual (www.gromacs.org)
  • Supplementary literature
    • Andrew R. Leach: Molecular Modelling. Principles and Applications
    • Peter Atkins, Ronald Friedman: Molecular Quantum Mechanics

Lectures and exercises (individual work).

Final grade is based on exam (75%) and exercises (25%).

Exercises and exam.