KE824: Biomolecular Simulations
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Entry requirements
Academic preconditions
Students taking the course are expected to:
- Have knowledge of basic physics chemistry and mathematics
- Be able to use computers
Course introduction
- Give the competence to run state of the art molecular simulations on large supercomputers
- Give skills to run particle-based simulations for different length scales of liquid systems, such as proteins, membranes and nucleotides, the cluster computers. The students will be able to dig useful information out of these simulations and use it to interpret experimental data. Students will learn to apply scientific computing methods to solve research problems
- Give knowledge and understanding of biomolecular interactions
Expected learning outcome
- identify the need of implementing a molecular simulation to address a biological problem
- to explain a limited set of fundamentals of statistical mechanics (phase space, sampling, ergodic hypothesis, probability density)
- to setup, implement and analyze a molecular dynamics simulation containing various types of (bio)molecules interacting with each other, and compare the output to experimental data
- is able to use supercomputers to run simulations
Content
- short introduction to statistical mechanics
- molecular dynamics simulation
- analysis of molecular dynamics simulations
- tutorials on the following topics: simulations of a (1) Lennard jones fluid (2) ethanol (3) protein in water (4) lipid membranes (5) coarse grained simulations and (6) specific topics of interest to students
- introduction to disspative particle dynamics, monte-carlo simulations
Literature
See itslearning for syllabus lists and additional literature references.
Examination regulations
Exam element a)
Timing
Tests
Portfolio
EKA
Assessment
Grading
Identification
Language
Examination aids
A closer description of the exam rules will be posted in itslearning
ECTS value
Additional information
Indicative number of lessons
Teaching Method
- Intro phase: 20 hours
- Training phase: 30 hours, hereof: tutorials: 30 hours
The teaching will be ~ 20% lecture based, and the rest lab exercise based, because the objective of the course is to make the students familiar with running simulations. The lectures will provide a fundamental basis of running the simulations.
Educational activities
The students are expected to become familiar with the fundamentals of both statistical mechanics and molecular dynamics, specific reading will be provided in class. Also, the students will be responsible for becoming familiar with visualization software (VMD) on their own. Tutorials will be provided for these.
Most importantly, the students are expected to continually work on the home assignments.