BB2540 Multiscale Modelling in Chemistry and Biology 10.0 credits
Flerskalig modellering i kemi och biologi
The current course is aimed at providing students with basic knowledge of multi-scale modeling. In this course, you will learn some fundamental concepts and important methods in multi-scale modeling. You will also learn how to use some widely-used modeling tools to calculate the properties of some molecular systems at different scales.
Education cycleSecond cycle
Main field of studyBiotechnology
Grading scaleA, B, C, D, E, FX, F
At present this course is not scheduled to be offered.
Intended learning outcomes
After the course, you should be able to
- outline the purpose and functions of multi-scale modeling;
- give examples of different types of intermolecular interactions;
- describe the fundamental concepts and important approaches in relation to a modeling scale;
- choose an appropriate modeling tool for a given property of a molecular system, with respect to the modeling scale, and apply the modeling tool to calculate the property;
- combine modeling tools at different scales to model a complex biological phenomenon;
- explain how the modeling approaches at different scales interrelate.
Course main content
1. Introduction to Multi-scale modelling
2. Review of underlying electronic structure calculations
3. Modelling intermolecular interactions
4. Methods for atomistic scale simulations
5. Introduction to currently used molecular dynamics simulation softwares
6. Meso-scale simulation methods
7. Application of multi-scale modeling to protein structure and folding
8. Computer exercises
At least 150 credits from grades 1, 2 and 3 of which at least 100 credits from years 1 and 2, and bachelor's work must be completed.
The 150 credits should include a minimum of 20 credits within the fields of Mathematics, Numerical Analysis and Computer Sciences, 5 credits of these must be within the fields of Numerical Analysis and Computer Sciences.
BB2280 Molecular modelling
Andrew R. Leach,“Molecular Modeling, Principles and Applications”, 2nd edition;
Lecture notes and handouts will be distributed after each lecture.
- LAB1 - Laboratory Work, 2.0, grading scale: P, F
- PRO1 - Project 1, 1.5, grading scale: A, B, C, D, E, FX, F
- PRO2 - Project 2, 1.5, grading scale: A, B, C, D, E, FX, F
- TEN1 - Examination, 3.0, grading scale: A, B, C, D, E, FX, F
- UPG1 - Home Assignment, 2.0, grading scale: P, F
Requirements for final grade
To pass the course, you should
- attend the lectures and fulfill 10 course assignments (UPG1; 2 credits);
- fulfill 4 computational labs on multi-scale modeling (LAB1; 2 credits);
- complete the written examination which covers the fundamental knowledge in multi-scale modeling (TEN1; 3 credits);
- fulfill 2 projects by applying the knowledge learned from the “Multi-scale modeling” course to solve some practical problems in chemistry and biology (PRO1 and PRO2, together 3 credits).
CBH/Theoretical Chemistry and Biology
Yaoquan Tu, email@example.com
Hans Ågren <firstname.lastname@example.org>
Students are required to sign up at least two weeks in advance for examination.
The course is given provided at least seven students are admitted.
Course syllabus valid from: Spring 2012.
Examination information valid from: Spring 2019.