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Systems Biophysics

Module PH2006

This module handbook serves to describe contents, learning outcome, methods and examination type as well as linking to current dates for courses and module examination in the respective sections.

Basic Information

PH2006 is a semester module in German or English language at Master’s level which is offered in summer semester.

If not stated otherwise for export to a non-physics program the student workload is given in the following table.

Total workloadContact hoursCredits (ECTS)
150 h 40 h 5 CP

Responsible coordinator of the module PH2006 is Friedrich Simmel.

Content, Learning Outcome and Preconditions


The course provides an introduction to the biophysical basis of engineered and natural biological systems and networks. Special attention is given to applications in synthetic biology.

- Biochemical kinetics
- Biochemistry and biophysics of gene transcription
- Transcriptional regulatory motifs
- Signalling
- Biochemical circuits as dynamical systems
- Stochastic dynamics of gene regulation
- Networks
- Oscillations
- Quorum Sensing
- Morphogenesis
- Metabolic Control Theory

Learning Outcome

After successful completion of this module, the student is able

1) To understand and explain the physical principles of gene regulation and gene transcription
2) to understand and explain the basic physics of signal transduction
3) to understand and explain the physical basis of biological pattern formation
4) to understand and explain self-organization phenomena on the basis of nonlinear and stochastic dynamics and network theory
5) to understand modern developments in the field of synthetic biology


The course has no special requirements beyond that of the masters program. We recommend a basic knowledge of molecular biophysics and biochemistry, and statistical physics.

Courses, Learning and Teaching Methods and Literature

Courses and Schedule

VO 2 Systems Biophysics Simmel, F. singular or moved dates

Learning and Teaching Methods

Lecture, beamer presentation, blackboard calculations, discussions


Das Modul besteht aus einer Vorlesung (2 SWS) und einem thematisch verbundenen Seminar (2 SWS). Die Inhalte der Vorlesungen werden durch Tafelvorträge, Beamer-Präsentationen oder Lehrfilme vermittelt. Zusätzlich wird den Studierenden ein begleitendes Vorlesungsskript zugänglich gemacht. Die Studierenden ergänzen die Informationen aus Vorlesung und Skript durch die Arbeit mit zusätzlicher Literatur und wissenschaftlichen Fachartikeln. Für das Seminar bereitet jede(r) Teilnehmer/in unter Anleitung eines wissenschaftlichen Mitarbeiters einen Vortrag von 20-30 Minuten über ein spezifisches Gebiet der Systembiophysik vor, an den sich eine etwa 20-minütige Dsikussionsrunde anschließt. Auf einer begleitenden Webseite werden Lernmaterialien zur Verfügung gestellt: Vorlesungsskript und Verweise auf ergänzende Literatur.


Biophysics textbooks - Beard & Qian: Chemical biophysics (Cambridge, 2008), Sneppen & Zocchi: Physics in Molecular Biology (Cambridge, 2005), R. Phillips et al: Physical Biology of the Cell (Garland Science, 2008)..
Standard textbooks of molecular biology - Alberts, Molecular biology (Garland Science, 2008)
Specifically - U. Alon: Systems Biology (Chapman & Hall / CRC, 2007), E. Klipp et al, Systems Biology (Wiley-Blackwell, 2009).

Module Exam

Description of exams and course work

In an oral exam the learning outcome is tested using comprehension questions and sample problems.

In accordance with §12 (8) APSO the exam can be done as a written test. In this case the time duration is 60 minutes.

Exam Repetition

The exam may be repeated at the end of the semester. There is a possibility to take the exam in the following semester.

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