SoSe 2023 Biomolecular Physics and Simulations

Lecture series and practical course by Bert de Groot and Helmut Grubmüller.

Course description

This combined lecture and hands-on computer tutorial (University Module B.Phy.5649.Mp: Biomolekulare Physik und Simulationen) offers the possibility to deepen the knowledge about theory and computer simulations of biomolecular systems, particularly proteins, and can be understood as continuation of the lecture “Theoretical and Computational Biophysics” (usually taking place in the previous winter term).

Whereas the winter term lecture “Theoretical and Computational Biophysics” emphasized the principles of running and analyzing simple atomistic force field-based simulations, this advanced course will broaden our view and introduce concepts and methods particularly required to understand biomolecular function, namely thermodynamic quantities such as free energies and affinities. Further, inclusion of quantum mechanical simulation techniques will allow to also simulate chemical reactions, e.g., in enzymes.

During the exercises, the knowledge presented in the lecture will be applied to practical examples to further deepen and strengthen the understanding. By completing homework sets, which will be distributed after each lecture, additional aspects of the addressed topics during the lecture shall be worked out. The homework sets will be collected during the corresponding exercises.

Examination requirements: Basic knowledge and understanding of the material covered in the course such as: Free energy calculations,  Rate Theory, Non-equilibrium thermodynamics, Quantum mechanical methods (Hartree-Fock and Density Functional Theory), enzymatic catalysis; “hands-on” computational calculations and simulations

Participation in the winter term lecture "Theoretical and Computational Biophysics" is recommended but not prerequisite.

Time and Place

Mondays, 16:00-17:30

The course alternates between two rooms in the Physics Faculty: Lectures take place in a lecture hall and the hands-on computer tutorials take place in a PC-Pool room, both Friedrich-Hund-Platz 1, 37077 Göttingen.

Organisation

To conduct the hands-on computer tutorial, you need access to the CIP-Pool computers at the Physics Faculty. If you do not possess such an account yet, please contact the local CIP-Pool Administrator office in room C.00.101 or write an Email to: support@cip.physik.uni-goettingen.de or contact the tutor.

Info on Homework: Completing it is voluntary (keine Prüfungsvorleistung), but will help you to “digest” and understand the teaching content better. Will be corrected by tutor, please ask questions during the practical. You have one week time to complete it.

Examinations are scheduled at the end of the lecturing period and will be arranged upon individual appointment. Contact our department office to arrange an individual appointment and also register in Flexnow (Modul B.Phy.5648 Theoretical and Computational Biophysics) You can conduct the exam it with either lecturer: Bert de Groot or Helmut Grubmüller.

Granted credits: Undergraduate Students: Modul B.Phy.5649/5648: 4 Credits (compulsory examination)
PhD Candidates (GGNB Students, Matter to Life Students): 2 Credits (optional examination)