FCB3204 Molecular Modeling 7.5 credits

The course comprises approximately 200 full-time study hours and is co-read with the course BB2280. The course elements include lectures with in-depth reading and reflective analysis that form the basis for the design and implementation of an individual project where a research problem is formulated and studied (PRO1, approximately 160 full-time study hours). Computer exercises are also included (LAB1, approximately 40 full-time study hours).

The practical content of the course includes computer exercises based on the course's subject focus and an individual project related to the course's theoretical foundations. The project is based on a research question and is based on selected research articles. The project must encounter the theoretical foundations and the skills acquired in the computer exercises with the student’s research topic leading to an original work in the form of a written report. The theoretical basis for the research question must be obtained and a project plan must be prepared before the design and implementation phase begins

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

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]

Eligible for studies at the third-cycle level.

BB2280, or equivalent knowledge from another course.

Announced at course start.

If the course is discontinued, students may request to be examined during the following two academic years.

• 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.

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).

Mårten Ahlquist

• 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.

If the course is discontinued, the student is given the opportunity to be examined on the course for another two academic years.