General information
| Course name | Lecture: Theoretical and Computational Biophysics |
| Subtitle | |
| Course number | 530257 |
| Semester | WiSe 2023/24 |
| Current number of participants | 31 |
| expected number of participants | 30 |
| Home institute | III. Physikalisches Institut - Biophysik |
| Courses type | Lecture in category Teaching |
| First date | Monday, 23.10.2023 16:00 - 17:30, Room: (HS3, A.00.105 (Fakultät Physik)), (C.00.106 (Fakultät Physik)) |
| Type/Form | |
| Participants | Bachelor Students \(Semester 5 and higher) Master Students \(Semester 1) |
| Pre-requisites |
This combined lecture and hands-on computer tutorial focuses on the basics of computational biophysics and deals with questions like "How can the particle dynamics of thousands of atoms be described precisely?" or "How does a sequence alignment algorithm function?" The aim of the lecture is to develop a physical understanding of those "nano maschines" by using modern concepts of non-equilibrium thermodynamics and computer simulations of the dynamics on an atomistic scale. Moreover, the lecture shows (by means of examples) how computers can be used in modern biophysics, e.g. to simulate the dynamics of biomolecular systems or to calculate or refine a protein structure. No cell could live without the highly specialized macromolecules. Proteins enable virtually all tasks in our bodies, e.g. photosynthesis, motion, signal transmission and information processing, transport, sensor system, and detection. The perfection of proteins had already been highly developed two billion years ago. The following topics will be introduced and discussed: Protein structure and function, physics of protein dynamics, relevant intermolecular interactions, principles of molecular dynamics simulations, numeric integration, influence of approximations, efficient algorithms, parallel programing, methods of electrostatics, protonation balances, influence of solvents, protein structure determination (NMR, X-ray), principal component analysis, normal mode analysis, functional mechanisms in proteins, bioinformatics: sequence comparison, protein structure prediction, homology modeling, and hands-on computer simulation. The course focuses on the basic concepts and techniques of computational biophysics, addressing questions such as "How can the dynamics, the statistical mechanics, and the quantum mechanics of biological macromolecules -- consisting of thousands of atoms -- be described sufficiently accurately to quantitatively understand their function?", or "How do sequence alignment algorithms work?". The main aim of the lecture is to acquire a fundamental physical understanding of these "nano-machines" through modern non-equilibrium thermodynamics concepts and computer simulations of their dynamics at the atomistic level. Moreover, we will demonstrate the use of computers in modern biophysics, e.g. to derive and refine protein structures from experimental data and, ultimately, to understand the function of these biological nano-machines. Without these highly specialised macromolecules, no cell would survive. In fact, virtually all tasks in our bodies, e.g. photosynthesis, motion, signal transmission and information processing, transport, sensor system, and detection, are performed or driven by proteins, which have been optimized and perfected by evolution over the past two billion years. The summer term lecture "Biomolecular Physics and Simulations" is recommendedin the following semester for interested students to get more insight into concepts and methods. Doctoral students of the Göttinger Graduate School for Neurosciences, Biophysics and Molecular Biosciences \(GGNB) are welcome to participate and receive 2 Credits for this methods course \(Biophysics, Bioinformatics and Statistics). Basic knowledge in physics preferred, programing skills are not required. Lecture "Introcution to Biophysics" is recommended but not prerequisite. |
