Synthetic Biology 1
Module version of WS 2020/1
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 2022/3||WS 2021/2||WS 2020/1||WS 2019/20||WS 2015/6|
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 workload||Contact hours||Credits (ECTS)|
|150 h||40 h||5 CP|
Responsible coordinator of the module PH2228 in the version of WS 2020/1 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
4. Molecular networks
5. Chemical kinetics
6. Dynamical Systems
7. Stochastic Dynamics
8. Synthetic gene circuits
9. Artificial cells
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)
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.
The exam may be repeated at the end of the semester.