Stud.IP Uni Oldenburg
University of Oldenburg
26.02.2021 22:21:14
5.04.4528 Lecture: Computational Biophysics - Details
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General information

Course number 5.04.4528
Semester Wintersemester 2020/2021
Current number of participants 7
Home institute Institute of Physics
Courses type Lecture in category Teaching
First date Wed , 21.10.2020 12:00 - 14:00, Room: (online)
Type/Form V
Participants angestrebte Lernergebnisse:
The students will learn about the physical models and computational approaches used for atomistic simulations of complex macromolecular structures. Concrete examples will include proteins, DNA, membranes, as well as their composites. The course will include hands-on training with the simulation software packages NAMD and VMD, where the following topics will be addressed:
• using computational biophysics programs VMD and NAMD;
• applications of VMD and NAMD in modern research enabled by high-performance computing;
• force fields and parameterizing new molecules;
• modeling nucleic acid systems;
• simulating membrane proteins and ion channels
Pre-requisites Knowledge of basic Physics courses (classical mechanics, electrodynamics, statistical mechanics, introductory quantum mechanics). Some knowledge of Linux operating system and scripting luangages (Python, and/or Tcl). Knowledge of data-analysis programs (Excel, Origin, xmgrace) is recommended.
Lehrsprache englisch
ECTS points 3

Course location / Course dates

(online) Wednesday: 12:00 - 14:00, weekly (14x)


The course will explore physical models and computational approaches used for the simulations of macromolecular systems. A mixture of lectures and hands-on tutorials will serve to provide a roadmap for setting investigations of macro-molecular structure and dynamics at the atomic level of detail. The course is based on practical exercises with the biophysical programs NAMD and VMD. In particular, the case studies of various biological systems will be discussed. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling and molecular dynamics on parallel computers