KE824: Biomolecular Simulations

The Study Board for Science

Teaching language: English
EKA: N540034102
Assessment: Second examiner: Internal
Grading: 7-point grading scale
Offered in: Odense
Offered in: Spring
Level: Master's level course approved as PhD course

STADS ID (UVA): N540034101
ECTS value: 5

Date of Approval: 20-10-2025


Duration: 1 semester

Version: Approved - active

Comment

If there are fewer than 12 students enrolled, the course may. be held with another teaching form. 

Entry requirements

None

Academic preconditions

Students taking the course are expected to:
  • Have knowledge of basic physics chemistry and mathematics
  • Be able to use computers

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.

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. 

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

Content

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 Applica-tions.
See itslearning for syllabus lists and additional literature references.

Examination regulations

Exam element a)

Timing

Spring

Tests

Portfolio

EKA

N540034102

Assessment

Second examiner: Internal

Grading

7-point grading scale

Identification

Full name and SDU username

Language

Normally, the same as teaching language

Examination aids

All aids allowed

ECTS value

5

Additional information

Portfolio: A combination of a project report and an MCQ-test will constitute to the mark with 50% and 50% respectively.

The re-exam will consist of the report and a oral exam. 

Indicative number of lessons

50 hours per semester

Teaching Method

Planned lessons:
Total number of planned lessons: 50
Hereof:
Common lessons in classroom/auditorium: 20
Team lessons in classroom: 30

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.

Other planned teaching 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.

Teacher responsible

Name E-mail Department
Himanshu Khandelia hkhandel@sdu.dk Kemi og Farmaci

Timetable

Administrative Unit

Fysik, kemi og Farmaci

Team at Registration

NAT

Offered in

Odense

Recommended course of study

Transition rules

Transitional arrangements describe how a course replaces another course when changes are made to the course of study. 
If a transitional arrangement has been made for a course, it will be stated in the list. 
See transitional arrangements for all courses at the Faculty of Science.