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Physics of Genes 2

Module PH2288

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.

Module version of SS 2020 (current)

There are historic module descriptions of this module. A module description is valid until replaced by a newer one.

Whether the module’s courses are offered during a specific semester is listed in the section Courses, Learning and Teaching Methods and Literature below.

available module versions
SS 2020SS 2019

Basic Information

PH2288 is a semester module in German or English language at Master’s level which is offered in summer semester.

This module description is valid from SS 2019 to WS 2021/2.

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 60 h 5 CP

Responsible coordinator of the module PH2288 is Friedrich Simmel.

Content, Learning Outcome and Preconditions


1. Biophysics of DNA-binding proteins

2. Searching for binding sites

3. Biophysics of transcription

4. Biophysics of translation

5. Transcriptional regulation

6. Traffic and traffic jams on DNA

7. Regulatory RNA

8. Gene circuit motifs

Optional: information theory, CRISPR technology,
chromatin remodeling, epigenetics

Learning Outcome

After successful completion of the module, students can: 1. Understand and quantitatively describe gene expression processes from a biophysical point of view 2. Follow lectures on the quantitative biology of gene expression and synthetic biology and participate in relevant scientific discussions. 3. Starting from the foundations laid in the lecture, independently educate themselves through literature research 4. Design and model simple gene circuits using computer programs


Knowledge in biophysics, biochemistry and molecular biology. Attending the lecture Physics of Genes 1 is helpful.

Courses, Learning and Teaching Methods and Literature

Learning and Teaching Methods

The learning content is presented in the thematically structured lecture.
In scientific discussions the students are involved and the independent application
of the basics is promoted on the basis of concrete problems. In the exercise, the
learning content is deepened and practiced by discussing specific problems
of biophysics of gene expression or synthetic biology and related tasks.
Moreover, in the exercises special literature will be read and discussed in detail.


The lecture will be held via PowerPoint presentation, sometimes supported by blackboard. A script for the lecture will be provided via moodle. Tasks and technical literature are issued for the exercises.


Vologodskii, Biophysics of DNA, Cambridge University Press

Phillips, Kondev, Theriot, Garcia, Physical Biology of the Cell, Garland Science

Alon, Systems Biology, CRC Press

More literature (scientific publications) will be provided and discussed in the lecture

Module Exam

Description of exams and course work

There will be an oral exam of 25 minutes duration. Therein the achievement of the competencies given in section learning outcome is tested exemplarily at least to the given cognition level using comprehension questions and sample calculations.

For example an assignment in the exam might be:

  • Formulate a simple mathematical model for a gene expression process (transcription + translation)
  • What are the possibilities for producing a genetic "AND" gate?
  • How does CRISPR / Cas9 find its binding target? Discuss the process from a biophysical perspective.

In the exam no learning aids are permitted.

Exam Repetition

The exam may be repeated at the end of the semester.

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