KJM5630 – Multi-scale Molecular Modeling
Course description
Schedule, syllabus and examination date
Course content
The course is designed to give students in chemistry and related subjects an introduction to the theory for molecular modeling, and use of modeling as a fundamental conceptual approach in molecular-based research. Considerable emphasis will be placed on practical use of modeling and an understanding of the methods which extends beyond purely operational skills. The aim is to give the students the sufficient background to independently evaluate choice of methods and reliability of results in molecular modeling.
Learning outcome
When you have completed this course, you can
- understand the theoretical connection between statistical and quantum mechanics, and computer modelling
- understand how macroscopic thermodynamic quantities, including endo/exoergonic processes or reaction rates, can be derived from microscopic mechanical properties
- understand how molecular models at different scales and resolutions can be used to describe different (bio)chemical and (bio)physical phenomena
- master the fundamental algorithms used in molecular modelling, including molecular dynamics, Monte Carlo, and advanced enhanced sampling techniques
- explain strengths and weaknesses of different models (including ab initio, molecular mechanics, QM/MM, coarse grained).
- evaluate the accuracy of performed calculations
- present results from computational studies in both oral and written form
Admission to the course
Students who are admitted to study programmes at UiO must each semester register which courses and exams they wish to sign up for in Studentweb.
Students enrolled in other Master's Degree Programmes can, on application, be admitted to the course if this is cleared by their own study programme.
If you are not already enrolled as a student at UiO, please see our information about admission requirements and procedures. Nordic citizens and applicants residing in the Nordic countries may apply to take this course as a single course student.
Recommended previous knowledge
KJM2600 – Physical chemistry II - quantum chemistry and spectroscopy (continued), KJM3300 – Physical Chemistry II (discontinued) (new Physical Chemistry III), MAT1050 – Mathematics for Applications 1, MAT1060 – Mathematics for applications 2, IN-KJM1900 – Introduction to Programming for Chemists, or equivalent courses
Overlapping courses
- 10 credits overlap with KJM9630 – Multi-scale Molecular modeling (discontinued).
Teaching
The course consists of 30 hours of lectures and 32 hours of computer lab (eight sessions/reports). To take the exam, all eight reports must be approved. You also have to give an oral presentation of one of the eight practical exercises. The presentation has to be approved. Three of the reports count 50 % in all of the final evaluation. You will be informed at the beginning of the semester which reports influence your final grade. Approved exercises are only valid the semester they are written.
The first lecture/group exercise is mandatory. If you are unable to join, you must notify the student administration at the Department of Chemistry before the first lecture/group exercise starts. If you fail to register as an active student for the course in either of these ways, you will lose access to the course for the given semester.
Examination
Three reports from the practical exercises count 50 % in all of the final evalutation. You will be informed at the beginning of the semester which reports influence your final grade. Final oral exam counts 50 % of the final grade. To take the exam, all eight reports must be approved. You also have to give an oral presentation of one of the eight practical exercises. The presentation has to be approved.
Approved exercises are only valid the semester they are written.
Language of examination
The examination text is given in English, and you must submit your response in English.
Grading scale
Grades are awarded on a scale from A to F, where A is the best grade and F is a fail. Read more about the grading system.
Resit an examination
This course offers both postponed and resit of examination. Read more:
More about examinations at UiO
- Use of sources and citations
- Special exam arrangements due to individual needs
- Withdrawal from an exam
- Illness at exams / postponed exams
- Explanation of grades and appeals
- Resitting an exam
- Cheating/attempted cheating
You will find further guides and resources at the web page on examinations at UiO.