Freie-Energie-Simulationen in der Physik von Biomolekülen und weicher Materie
Free Energy Simulations in Soft Matter and Biomolecular Physics
Modul PH8130
Basisdaten
PH8130 ist ein Semestermodul in auf das unregelmäßig angeboten wird.
Das Modul ist Bestandteil der folgenden Kataloge in den Studienangeboten der Physik.
- Fachliche Qualifizierungsmodule für Doktorand(inn)en der Physik (Seminare)
Soweit nicht beim Export in einen fachfremden Studiengang ein anderer studentischer Arbeitsaufwand ("Workload") festgelegt wurde, ist der Umfang der folgenden Tabelle zu entnehmen.
| Gesamtaufwand | Präsenzveranstaltungen | Umfang (ECTS) |
|---|---|---|
| 90 h | 38 h | 3 CP |
Inhaltlich verantwortlich für das Modul PH8130 ist Martin Zacharias.
Inhalte, Lernergebnisse und Voraussetzungen
Inhalt
Content:
- Overview of classical atomistic Molecular Dynamics (MD) simulations and the computer-assisted determination of biomolecular binding free energies
- Hands-on exercises for calculating a binding free energy with
* Alchemical methods
* Pathway methods (Umbrella sampling and non-equilibrium pulling)
Lernergebnisse
After successful completion of the module the students are able to plan, setup and perform free energy calculations using MD simulations. The students will know the theoretical basis, methodology, advantages and disadvantages of the most important methods for the calculation of a (bio)molecular binding free energy with MD simulations. They can independently carry out and analyze binding free-energy calculations for a target-ligand complex using a common MD simulation package and can assess the reliability of the results. Finally, they can report the results in a manner compatible with publication in a research journal.
list of all the learning outcome:
1. Understanding the theory and practice of free energy simulations
2. Setup of computer simulations of large biomolecular systems
3. Anaylsis of MD simulations
4. Extraction of free energy changes and other thermodynamic quantities
5. Setup of alchemical changes in MD simulations
6. Calculation of relative and absolute binding free energies
Voraussetzungen
Preconditions:
- Basic knowledge in classical mechanics and statistical thermodynamics, familiarity with Unix-like operating systems and shell scripting and/or python programming are of advantage.
Lehrveranstaltungen, Lern- und Lehrmethoden und Literaturhinweise
Lehrveranstaltungen und Termine
| Art | SWS | Titel | Dozent(en) | Termine | Links |
|---|---|---|---|---|---|
| VI | 2.5 | Free Energy Simulations in Soft Matter and Biomolecular Physics |
Zacharias, M.
Mitwirkende: Reif, M. |
Mo, 09:00–17:00, PH 1151 |
Lern- und Lehrmethoden
Learning and Teaching Methods:
- Introductory powerpoint presentation including interactive explanations on the blackboard or virtual whiteboard
- Hands-on computer exercises
- Working in small teams
- Interactive discussion and immediate feedback
Medienformen
Media:
Powerpoint presentation, blackboard or virtual whiteboard, written instructions in the form of a tutorial booklet
Literatur
Literature:
- Reference manual for the employed simulation package (will be provided as a download/link)
- D. Frenkel, B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, Academic Press. 2014
- Mark E. Tuckerman, Statistical Mechanics: Theory and Molecular Simulation, Oxford Graduate Press, 2016