The course provides knowledge and skills in the field of molecular modeling corresponding to the third cycle.
Course memo Autumn 2022
Du hittar kurs-PM för nyare kursomgångar på sidan Kurs-PM.
Course presentation
Headings denoted with an asterisk ( * ) is retrieved from the course syllabus version Autumn 2021
Content and learning outcomes
Course contents
The course's theoretical content includes:
- Introduction to 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
- Modeling of enzymatic catalysis
Intended learning outcomes
After completion of the course the student shall be able to
- demonstrate in-depth knowledge and analytical ability in molecular modeling adequate for the level of educational level of the course, and critically review others' work in the field [LAB1, PRO1]
- demonstrate good ability to explain and analyze complex concepts in molecular modeling based on relevant research literature, and in a pedagogical way communicate the knowledge in writing and orally [PRO1]
- be able to reflect on and describe how scientific issues in the field's research can contribute to sustainable societal development [PRO1]
Detailed plan
| Lecture 1 (31 Oct) | Introduction + Potential energy surfaces | |
| Lecture 2 (1 Nov) | Molecular Mechanics | |
| Lecture 3 (2 Nov) | Molecular dynamics | |
| Lecture 4 (7 Nov) | Solvation models | |
| Lecture 5 (8 Nov) | Introduction to QM | |
| Lecture 6 (9 Nov) | Hartree-Fock, Basis sets | |
| Lecture 7 (14 Nov) | Correlated Methods | |
| Lecture 8 (15 Nov) | Density Functional Theory | |
| Lecture 9 (16 Nov) | No lecture | |
| Lecture 10 (21 Nov) | Qualitative Structure Activity Relation (QSAR) in Drug Discovery | |
| Lecture 11 (22 Nov) | Molecular Docking in Drug Discovery | |
| Lecture 12 (23 Nov) | Applications of Molecular Modeling | |
| Lecture 13 (28 Nov) | Research paper presentation | Mandatory to present one paper |
|
Lecture 14 (29 Nov) |
Research paper presentation | |
|
Lecture 15 (30 Nov) |
Research paper presentation | |
| Lecture 16 (TBA) | Invited lecture | |
| Lecture 17 (After X-Mas) | Summary and repetion |
Preparations before course start
Recommended prerequisites
BB2280, or equivalent knowledge from another course.
Literature
Announced at course start.
Support for students with disabilities
Students at KTH with a permanent disability can get support during studies from Funka:
Examination and completion
Grading scale
P, F
Examination
- LAB1 - Laboratory work, 1.5 credits, Grading scale: P, F
- PRO1 - Project, 6.0 credits, Grading scale: P, 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.
Grading criteria are specified in the course PM.
Other requirements for final grade
Required for final grade: 90% attendance at lectures, written critical reflection for selected scientific articles, approved written project report and completed oral project presentation (PRO1); and attendance on computer exercises and completed exercise reports (LAB1).
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
No information inserted
Contacts
Round Facts
Start date
31 Oct 2022
Course offering
- Autumn 2022-50917
Language Of Instruction
English