KE824: Biomolecular Simulations (5 ECTS)

STADS: 10007201

Level
Master's level course

Teaching period
The course is offered in the spring semester.
4th quarter

Teacher responsible
Email: hkhandel@memphys.sdu.dk

Additional teachers
mip@sdu.dk

Timetable
Show entire timetable
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:
Oral exam 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 after 2nd quarter.

Expected working hours
The teaching method is based on three phase model.
Skills training phase: 50 hours, hereof:
 - Tutorials: 36 hours
 - Other: 14 forelæsninger (lectures) hours
Skills training phase: 50 hours, hereof:
 - Tutorials: 36 hours
 - Other: 14 forelæsninger (lectures) 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.