6 EC
Semester 2, period 5
5254BISI6Y
| Owner | Master Chemistry (joint degree) |
| Coordinator | dr. Jocelyne Vreede |
| Part of | Master Chemistry (joint degree), track Molecular Sciences, Master Computational Science (Joint Degree), |
Molecular dynamics is a powerful tool to investigate the structure and dynamics of biologically relevant molecules such as proteins, DNA and lipids in atomistic detail. The insight from MD simulation yields quantitative predictions and a 'molecular movie' of important processes that helps experimentalists interpret their results. Such simulations can also be used to predict effects of e.g. point mutations. This course provides an introduction to biomolecular simulation using molecular dynamics, and enhanced sampling methodology to study biomolecular processes.
This course consists of lectures which will cover the following topics: 1) the basics of molecular dynamics, 2) the structural analysis of biomolecules, e.g. through NMR and crystallography, 3) multiscale modeling of biomolecular systems 4) the problem of rare events in conformational changes.
In addition to the lectures there will be a practical tutorial consisting of theoretical exercises as well as computer problems. The course ends with doing a small project including a real simulation on a biomolecular system.
Tutorials on canvas
Lectures that explain relevant concepts, theory and applications
Computer practicals that provide the students with hands-on experience in performing molecular simulations on biomolecules.
During the project, the students will work on a biomolecular system independently, applying the knowledge from the lectures and computer practicals.
Activity | Number of hours |
Computerpracticum | 14 |
Hoorcollege | 14 |
Zelfstudie | 140 |
This programme does not have requirements concerning attendance (TER part B).
| Item and weight | Details |
|
Final grade |
Examination consists of 5 assignments on canvas and the written report of a project the students will work on during the course. For the grade: 50% is based on the average grade for the assignments and 50% is based on the written report of the project.
Contact the course coordinator to make an appointment for inspection.
The assignments will be discussed during laptop lectures following the deadline of handing in the assignment. To discuss the project report grade, make an appointment with the coordinator.
During the course the students will do tutorials to learn to use the various software packages and approaches. Each tutorial comes with an assignment that has to be handed in individually via canvas before the specified deadline. The assignment will be graded and will be discussed during the next laptop lecture.
The students work individually on a project during the course. They have to write a report for that project, which will be graded.
The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl
| Weeknummer | Topics |
| 1 | Structure of biomolecules |
| 2 | Force fields |
| 3 | Molecular dynamics |
| 4 | Sampling |
| 5 | Biased sampling |
| 6 | Transition path sampling |
| 7 | Coarse graining |
The topics are also given on the schedule on datanose.
The schedule for this course is published on DataNose.
Recommended prior knowledge: thermodynamics, statistical mechanics, biochemistry.
Contact the course coordinator for questions.