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Synthetic Biology 1

Module PH2228

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 WS 2015/6

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
WS 2022/3WS 2021/2WS 2020/1WS 2019/20WS 2015/6

Basic Information

PH2228 is a semester module in German or English language at Master’s level which is offered in winter semester.

This Module is included in the following catalogues within the study programs in physics.

  • Specific catalogue of special courses for Biophysics
  • Focus Area Bio-Sensors in M.Sc. Biomedical Engineering and Medical Physics
  • Complementary catalogue of special courses for condensed matter physics
  • Complementary catalogue of special courses for nuclear, particle, and astrophysics
  • Complementary catalogue of special courses for Applied and Engineering Physics
  • Mandatory Modules in Master Program Matter to Life

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 PH2228 in the version of WS 2015/6 was Friedrich Simmel.

Content, Learning Outcome and Preconditions


The module Synthetic Biology 1 lays the foundations for understanding current research in synthetic biology,
especially synthetic gene "circuits"

This includes an introduction to the fundamentals of molecular biology as well as quantitative aspects. Content items are:

1. Historical Introduction
2. Biomolecules
3. Bionanoscience
4. Molecular networks
5. Chemical kinetics
6. Dynamical Systems
7. Stochastic Dynamics
8. Synthetic gene circuits
9. Artificial cells

Learning Outcome

After successful completion of the module the students are able to:

  • understand gene expression gene regulatory processes.
  • have an overview of current research topics in synthetic biology.
  • know how to quantitatively describe gene expression and gene regulation.
  • construct basic gene circuits (theoretically).
  • undestand nonlinear dynamics and dynamical systems applied to synthetic biological systems.


Basic knowledge in Biophysics and Biochemistry (e.g. PH0020, PH2013 or PH8106)

Courses, Learning and Teaching Methods and Literature

Courses and Schedule

VO 2 Synthetic Biology 1 Simmel, F. Thu, 12:00–14:00, ZNN 0.001
UE 2 Exercise to Synthetic Biology 1
Responsible/Coordination: Simmel, F.
Tue, 16:00–18:00, ZNN 2.003

Learning and Teaching Methods

The lecture introduces basic concepts and discusses them scientifically using a variety of examples from current research. The students should try to understand and penetrate these examples in moredetail at home. Here, the students should actively apply the contents of the lecture,

In addition, the students will use corresponding textbooks (or sections in the textbooks) as well as special literature to deepen the knowledge necessary for the contents of the lecture.


Media/powerpoint presentation and occasional work on the blackboard, transparencies, additional literature, online tools for biophysics/synthetic biology. Literature will be provided via moodle.


  • R. Milo & R. Phillips: Biology by the Numbers, Taylor & Francis, (2016)
  • R. Phillips, J. Kondev, J. Theriot & H. Garcia: Physical Biology of the Cell, Taylor & Francis, (2012)
  • U. Alon: Systems Biology, Taylor & Francis, (2006)
  • B. Alberts, A. Johnson, D. Morgan, M. Raff, K. Roberts & P. Walter: Molecular Biology of the Cell, Norton & Company, (2014)
  • S.H. Strogatz: Nonlinear Dynamics and Chaos, Westview Press, (2014)

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:

  • Describe a possibility to create logic gates.
  • How can one create genetic oscillators?
  • Describe different possibilities of circuit wiring.
  • Describe the Poincare-Bendixson theorem.
  • Write down differential equations for simple gene expression.
  • Explain the importance of cooperativity in gene regulation.

Exam Repetition

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

Current exam dates

Currently TUMonline lists the following exam dates. In addition to the general information above please refer to the current information given during the course.

Exam to Synthetic Biology 1
Tue, 2024-02-20, 10:00 till 12:00 Dummy-Termin. Wenden Sie sich zur individuellen Terminvereinbarung an die/den Prüfer(in). Anmeldung für Prüfungstermin vor 23.03.2024. // Dummy date. Contact examiner for individual appointment. Registration for exam date before 2024-Mar-23. till 2024-01-15 (cancelation of registration till 2024-02-13)
Mon, 2024-04-08, 10:00 till 12:00 Dummy-Termin. Wenden Sie sich zur individuellen Terminvereinbarung an die/den Prüfer(in). Anmeldung für Prüfungstermin zwischen 25.03.2024 und 20.04.2024. // Dummy date. Contact examiner for individual appointment. Registration for exam date between 2024-Mar-25 and 2024-Apr-20. till 2024-01-15 (cancelation of registration till 2024-04-01)
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