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.

  • Educational level

    Second cycle
  • Academic level (A-D)

  • Subject area

    Biotechnology
  • Grade scale

    A, 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

Eligibility

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.

Recommended prerequisites

BB2280 Molecular modelling

Literature

Andrew R. Leach,“Molecular Modeling, Principles and Applications”, 2nd edition;

Lecture notes and handouts will be distributed after each lecture.

Examination

  • LAB1 - Laboratory Work, 2.0, grade scale: P, F
  • PRO1 - Project 1, 1.5, grade scale: A, B, C, D, E, FX, F
  • PRO2 - Project 2, 1.5, grade scale: A, B, C, D, E, FX, F
  • TEN1 - Examination, 3.0, grade scale: A, B, C, D, E, FX, F
  • UPG1 - Home Assignment, 2.0, grade 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).

Offered by

BIO/Biotechnology

Contact

Yaoquan Tu, tu@theochem.kth.se

Examiner

Hans Ågren <hagren@kth.se>

Supplementary information

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.

Version

Course syllabus valid from: Spring 2012.
Examination information valid from: Spring 2012.