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Content and learning outcomes
Course contents
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
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 Disposition
No information inserted
Literature and preparations
Specific prerequisites
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.
Equipment
No information inserted
Literature
Andrew R. Leach: Molecular Modelling, Principles and Applications, 2ed, samt utdelat material.
Examination and completion
If the course is discontinued, students may request to be examined during the following two academic years.
Grading scale
A, B, C, D, E, FX, F
Examination
- LAB1 - Laboratory Work, 1,5 hp, betygsskala: A, B, C, D, E, FX, F
- TEN1 - Written exam, 6,0 hp, betygsskala: A, B, C, D, E, FX, F
Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.
The examiner may apply another examination format when re-examining individual students.
Other requirements for final grade
Examination (TEN1, 6,0 credits, grading scale A-F) and Lab courses (LAB1, 1,5 credits, grading scale A-F).
Opportunity to complete the requirements via supplementary examination
No information inserted
Opportunity to raise an approved grade via renewed examination
No information inserted
Examiner
Ethical approach
- All members of a group are responsible for the group's work.
- In any assessment, every student shall honestly disclose any help received and sources used.
- In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.
Further information
Course web
Further information about the course can be found on the Course web at the link below. Information on the Course web will later be moved to this site.
Course web BB2280Offered by
Main field of study
Biotechnology
Education cycle
Second cycle
Add-on studies
No information inserted
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.