BB2280 Molecular Modeling 7.5 credits

Molekylär modellering

  • Educational level

    Second cycle
  • Academic level (A-D)

    D
  • Subject area

    Biotechnology
  • Grade scale

    A, B, C, D, E, FX, F

Course offerings

Autumn 17 for single courses students

  • Periods

    Autumn 17 P2 (7.5 credits)

  • Application code

    10010

  • Start date

    30/10/2017

  • End date

    2018 week: 3

  • Language of instruction

    English

  • Campus

    AlbaNova

  • Number of lectures

    18 (preliminary)

  • Number of exercises

  • Tutoring time

    Daytime

  • Form of study

    Normal

  • Number of places *

    Min. 7

    *) The Course date may be cancelled if number of admitted are less than minimum of places.

  • Course responsible

    Murugan Natarajan Arul <murugan@kth.se>

  • Teacher

    Murugan Natarajan Arul <murugan@kth.se>

    Mårten Ahlquist <ahlqui@kth.se>

    Stefan Knippenberg <sknippen@kth.se>

  • Target group

    SAP students

Autumn 17 for programme students

Intended learning outcomes

Today, computer simulations are an important tool for the study of chemical processes in such different systems as isolated molecules, fluids, polymers, solid state, and biological macromolecules, like proteins and DNA.  The enormous development of computer hard drive space means that the molecular modeling field is developing very quickly. 

The goal with this course is to provide an overview of the methods and techniques which are used within modern molecular modeling.  Basic theory will be covered and applications within chemistry, biochemistry and medicinal chemistry will be discussed.

Course main content

The course consists of both theoretical lectures and practical computer exercises. The following topics will be discussed:

  • Basic quantum chemistry: Molecular orbital theory, semi-empirical methods
  • Basic density functional theory (DFT)
  • Molecular mechanics and molecular dynamics
  • Monte Carlo methods
  • Energy minimization and potential energy surfaces
  • QM/MM methods
  • Solvation and surrounding effects
  • Theoretical methods in drug discovery: Docking, protein structure prediction, QSAR
  • Simulation of chemical reactions in solution
  • Modelling of enzymatic catalysis
  • Field trip to pharmaceutical company

Eligibility

Admission requirements for programme students at KTH:
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 of these must be within the fields of Numerical Analysis and Computer Sciences, 20 credits of Chemistry, possibly including courses in Chemical Measuring Techniques and 20 credits of Biotechnology or Molecular Biology.

Admission requirements for independent students:
A total of 20 university credits (hp) in Biotechnology or Molecular Biology. 20 university credits (hp) of Chemistry, possibly including courses in Chemical Measuring Techniques , as well as 20 university credits (hp) in Mathematics,  Numerical Analysis and Computer Sciences, 5 of these must be within the fields of Numerical Analysis and Computer Sciences. Documented proficiency in English corresponding to English B.

Recommended prerequisites

Basic classes in chemistry and mathematics för K och BIO.

Literature

Andrew R. Leach: Molecular Modelling, Principles and Applications, 2ed, samt utdelat material.

Examination

  • LAB1 - Laboratory Work, 1.5, grade scale: A, B, C, D, E, FX, F
  • TEN1 - Examination, 6.0, grade scale: A, B, C, D, E, FX, F

Requirements for final grade

Examination (TEN1, 6,0 credits, grading scale A-F) and Lab courses (LAB1, 1,5 credits, grading scale A-F).

Offered by

BIO/Biotechnology

Examiner

Mårten Ahlquist <ahlqui@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: Autumn 2016.
Examination information valid from: Autumn 2007.