KE824: Biomolecular Simulations (5 ECTS)
STADS: 10007201Level
Master's level course approved as PhD course
Teaching period
The course is offered in the spring semester.
Teacher responsible
Email: hkhandel@sdu.dkTimetable
| Group | Type | Day | Time | Classroom | Weeks | Comment |
|---|---|---|---|---|---|---|
| Common | I | Thursday | 12-13 | U26b | 5 | |
| Common | I | Thursday | 10-11 | U26b | 6 | |
| Common | I | Thursday | 10-12 | U26b | 7,9 | |
| Common | I | Thursday | 12-14 | U26b | 8 | |
| H1 | TL | Monday | 14-17 | U26b | 10 | |
| H1 | TL | Tuesday | 10-13 | U26b | 11 | |
| H1 | TL | Tuesday | 12-15 | U26b | 12 | |
| H1 | TL | Wednesday | 12-15 | U26b | 16-17 | |
| H1 | TL | Thursday | 12-15 | U26b | 13-14 | |
| H1 | TL | Thursday | 11-14 | U26b | 18 | |
| H1 | TL | Friday | 12-14 | U26b | 9 |
Show personal time table for this course.
Prerequisites:
None
Academic preconditions:
Students taking the course are expected to:
- Have knowledge of basic physics chemistry and mathematics
- Be able to use computers
Course introduction
The aim of the course is to enable the student to understand and implement the particle-based molecular simulations of complex biological systems such as proteins, membranes and nucleotides, and interactions between them. In addition, the course aims to inculcate a quantitative understanding of biomolecular interactions, as well as to encourage and emphasize the importance of interdisciplinary research, which is important in regard to understanding molecular interactions in biological systems
Furthermore, the students will learn to run simulations on the ABACUS 2.0 supercomputer
The course builds on the knowledge acquired in courses like molecular modelling, and gives an academic basis for studying the topics modelling, nanotechnology, biochemistry, medicinal chemistry that are part of the degree.
In relation to the competence profile of the degree it is the explicit focus of the course to:
- 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
The learning objective of the course is that the student demonstrates the ability to:
- 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
Subject overview
The following main topics are contained in the course:
- 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
- Andrew Leach: Molecular Modelling: Principles and Applications.
Website
This course uses e-learn (blackboard).
Prerequisites for participating in the exam
None
Assessment and marking:
- A combination of a project report and an MC-test will constitute to the mark with 50% and 50% respectively. Internal marking, 7-mark scale. (5 ECTS). (100072029).
A closer description of the exam rules will be posted under 'Course Information' on Blackboard.
Expected working hours
The teaching method is based on three phase model.
Intro phase: 20 hours
Skills training phase: 30 hours, hereof:
- Tutorials: 30 hours
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.
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.
Language
This course is taught in English.
Course enrollment
See deadline of enrolment.
Tuition fees for single courses
See fees for single courses.
