KJM5631 – Multi-Scale Molecular Modeling
Course content
The course is designed to give students in chemistry and related subjects an introduction to the theory for molecular modeling, and the use of modeling as a tool in chemical research. Considerable emphasis will be placed on the practical use of modeling and an understanding of the methods which extends beyond purely operational skills. The aim is to give the students sufficient background to independently evaluate the choice of methods and reliability of results in molecular modeling.
Learning outcome
After completing the course, you are able to
- Explain the theoretical connection between statistical mechanics, quantum mechanics, and computer modeling.
- Explain how macroscopic thermodynamic quantities, including free-energy profiles and reaction rates, can be derived from microscopic mechanical properties
- Describe how?molecular models at different scales and resolutions can be used to describe different (bio)chemical and (bio)physical phenomena
- Describe and usethe fundamental algorithms used in molecular modeling, including molecular dynamics, as well as more advanced enhanced sampling techniques.
- Discuss the strengths and weaknesses of different models,?including ab initio, molecular mechanics, QM/MM, coarse grained, and mesoscale.
- Evaluate the accuracy of performed calculations
- Present results from computational studies in both oral and written form
Admission to the course
Students admitted at UiO must?apply for courses?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.
Nordic citizens and applicants residing in the Nordic countries may?apply to take this course as a single course student.
If you are not already enrolled as a student at UiO, please see our information about?admission requirements and procedures for international applicants.
Recommended previous knowledge
KJM2601 – Fysikalsk kjemi II - kvantekjemi og spektroskopi, KJM3300 – Physical Chemistry II (discontinued), MAT1050 – Mathematics for Applications 1, MAT1060 – Mathematics for applications 2, IN-KJM1900 – Introduction to Programming for Chemists, or equivalent courses.
Teaching
The course duration is one semester. The teaching 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.
Approved presentation and reports 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 % of the final evaluation. You will be informed at?the beginning of the semester which reports will influence your final grade.
- Final oral exam counts 50 % of the final grade.
This course has mandatory exercises that must be approved before you can sit the final exam.
It will also be counted as one of the three attempts to sit the exam for this course, if you sit the exam for? the following course: KJM9631 – Multi-scale Molecular modeling
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
Students who can document a valid reason for absence from the regular examination are?offered a postponed examination at the beginning of the next semester.
Re-scheduled examinations are not offered to students who withdraw during, or did not pass the original examination.
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.