KE824: Biomolecular Simulations (5 ECTS)
STADS: 10007201Level
Master's level 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 | Monday | 14-16 | U26b | 06 | |
| Common | I | Monday | 12-14 | U26b | 07 | |
| Common | I | Monday | 12-13 | U26b | 08,13,16,18,20 | |
| Common | I | Thursday | 14-15 | U26b | 11 | |
| H1 | TE | Monday | 14-16 | U26b | 10,12 | |
| H1 | TE | Tuesday | 08-10 | U26b | 20 | |
| H1 | TE | Wednesday | 12-14 | U26b | 07 | |
| H1 | TE | Wednesday | 14-16 | U26b | 08,19,21 | |
| H1 | TE | Wednesday | 12-13 | U26b | 12,16,18 | |
| H1 | TE | Wednesday | 16-18 | U26b | 17 | |
| H1 | TE | Thursday | 15-16 | U26b | 11 | |
| H1 | TE | Thursday | 12-14 | U26b | 15 |
Show personal time table for this course.
Prerequisites:
None
Academic preconditions:
Bachelor of Science.
Course introduction
The course aims to enable students to understand and implement particle-based molecular simulations of complex biological systems such as proteins, membranes and nucleotides, and interactions between them. The course aims to inculcate a quantitative comprehension of biomolecular interactions, and encourage and emphasize the importance of cross-disciplinary research. The aim is to train Masters and PhD level students in state-of-the-art biomolecular simulations.
Expected learning outcome
Students will be able to run particle-based simulations at various length scales for liquid systems of interest, such as proteins, membranes and nucleotides, on computing clusters. Students will be able to extract useful information from these simulations, and use it to interpret experimental data. Students will thus learn to apply scientific computing methods to solve research problems.
Subject overview
Atomistic molecular dynamics, Coarse-grained MD and Dissipative Particle Dynamics (DPD) of biological systems such as membranes, proteins and nucleotides like DNA, Fundamentals of Statistical Mechanics. Analysis of 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:
Written report based on project assignment. Grading according to the Danish 7 mark scale. Internal second examiner. Students will implement simulations on a system of THEIR research interest, and make a report and presentation on the simulations.
Rexam in the same exam period or immediately thereafter. The exam mode for the reexamination may differ from the ordinary exam.
Expected working hours
The teaching method is based on three phase model.
Intro phase: 20 hours
Skills training phase: 30 hours, hereof:
- Laboratory exercises: 30 hours
Educational activities
Language
This course is taught in English.
Course enrollment
See deadline of enrolment.
Tuition fees for single courses
See fees for single courses.
