M.Sc./M.Ed. Seminar: Biophysics

08.128.785 Dynamics of Biophysical Systems


Summer term 2017, Begin: Apr. 18.

Times: Tuesday 15:45-17:15,
Place: IMB Mainz, Ackermannweg 4, Meeting room 1.624 (1st floor)

Seminar available through video conferencing at KIP, Uni Heidelberg
Lecturers: Dr. Udo Birk, Prof. Dr. Christoph Cremer, Dr. Stefan Legewie
The language used throughout the course will be English, unless otherwise specified.
This course will be taught at the post-baccalaureate level. A basic knowledge in electromagnetics/optics and in digital signal processing could be very helpful. These are subject of our course on Modelling with Matlab.

In this seminar, some of the apparently obvious but on closer look not so trivial questions related to modelling and control of complex biophysical systems, i.e. dynamics of biomechanical and biochemistry in solid state biophysics will be discussed. Discussions will be stimulated and augmented by regular presentations of recent research papers.

Students actively participating will give a presentation focusing on one of the particular problems encountered in "real" biophysical systems, i.e. in the presence of complex factors in addition to a well-defined linear response. For example, the interaction of regulatory mechanisms and signalling pathways, and also influence of noise on quantitative modelling, of motion, of fluctuating output etc. will be discussed. Since the aim of a model descriptor is (at least in a physics environment) to obtain quantitative data, with predictive features, problems related to model quantization and digitization, as well as to system stability are a further important focus of this seminar.

These general topics will be amended by more specialized presentations on problems related to fluorescence imaging such as e.g. photophysics of fluorophores, and to superresolution microscopy.

Aim of this seminar is to provide the students with the opportunity to prepare for oral examinations by providing a discussion forum for state-of-the art experimental biophysics methods. At the same time, topics of the seminar presentations will illustrate the enormous potential that biophysics has for your future career.

M.Sc. Physics course

Jogustine entry for this course at the University of Mainz

Course material

Will be handed out during the lectures/course

Preliminary program

Date 1. Technical Presentation by 2. Journal Article by
18.04. General outline of the course
Registration for seminar talks
UB --- ---
26.04. Discussion NN NN
03.05. Polymer models UB NN
10.05. How to efficiently make molecules blink AS NN
17.05. Effects of Illumination in Fluorescence Microscopy: Forces, Damage, and Polarization NN NN
24.05. Out-of-focus suppression in SMLM NN NN
31.05. Structured Illumination Microscopy FS NN
07.06. Photoswitching AS NN
14.06. Multiblinking in Localization Microscopy AG NN
21.06. Winter break

28.06. Winter break

05.07. Discussion

12.07. Focus field distribution JvH NN
19.07. Multi-photon absorption and fluorescence JvH NN
26.07. Motion artefacts in biomedical imaging FS NN
02.08. Discussion

Additional topics for the talks could be:
- Spatially Modulated Illumination
- Optical Tomography
- Superresolution in biology
- Sampling and digitization
- How to construct a microscope objective lens
- Interaction of light and biological tissue
- Effects of Illumination in Fluorescence Microscopy: Forces, Damage, and Polarization
- Stimulated Emission in real experiments
- Numerical Aperture: How it defines image quality