BM122: Bioinformatics IV: Modelling and simulation of biological systems (5 ECTS)

STADS: 0104141

Level


Teaching period

Spring semester.

Teacher responsible
Email: ptr@bmb.sdu.dk

Additional teachers
hgp@mip.sdu.dk

Timetable
Show entire timetable
Show personal time table for this course.

Prerequisites:
None

Academic preconditions:
BM131 - Introduction to bioinformatics, DM01 Structured programming and MM02 Linear algebra must be passed.

Course introduction
The course gives an introduction to modelling and simulation of biological systems and will provide students with an overview of computational methods relevant to solve complex problems of a biomolecular nature.

Main topics covered in the course are:
1) biomolecular structure and modelling,
2) simulation techniques, and
3) optimisation techniques.

Expected learning outcome
Upon completion of the course the student must be able to

• Explain the fundamental theoretical and computational principles that form the basis for molecular dynamics and biomolecular structure determination.
• Explain and describe bonded and non-boned interactions in biomolecular systems.
• Explain methods for constrained molecular dynamics.
• Describe the various ensembles (micro-canonical, canonical) used in molecular dynamics.
• Derive the classical mechanical equations of motion for a biomolecular system and explain how to numerically solve the equations of motion.
• Assess and evaluate the accuracy and usability of the various computational methods in the study of biomolecular systems.
• Implement a molecular dynamics program that can be used to simulate a biomolecular system.
• Describe and apply local and global optimizations methods in the study of biomolecular systems.
• Describe and explain protein structure and nucleic acids structure.
• Describe and explain protein folding and misfolding.
• Implement a computer program that can determine protein structures using a combination of techniques from molecular dynamics and optimization.

Subject overview
• Biomolecular structure and modelling
• Computational challenges
• Protein folding and misfolding
• Practical applications
• Protein structure
• Nucleic acids structure
• Computational approaches to biomolecular structure
• Force fields
• Molecular dynamics
• Optimisation
• Basic methods
• Global optimization methods
• Application: Protein structure determination

Literature

• Tamar Schlick: Molecular Modeling and Simulation, Springer, 2002.
• Udvalgte artikler og noter. .

Syllabus
See syllabus.

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam
None

Assessment and marking:
A final project and oral examination. The project may be done in groups of two or three students. The oral examination is individual and consists of a presentation of the final project lasting max. 30 min. The presentation will be followed by questions related to the project and the course topics. Internal examination by instructors. Marks according to the 7-point marking scale.

Expected working hours
The teaching method is based on three phase model.

Forelæsninger (20 timer), derudover projektarbejde.
Educational activities

Language
This course is taught in Danish.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.