We offer students opportunities to do a project work, a bachelor thesis or a master thesis. We are looking for highly motivated students with an interest to work at the interface of cell biology, biophysics and biochemistry. Further working fileds are data simulation and the improvement of microscopy setups. If you are interested and for further information, don't hesitate to contact us.

Thesis opportunities include, but are not limited to the following subjects:

Master thesis

 

 

 

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Electrostatics_side_3.5kT

Most cellular proteins are covalently modified in the course of their existence, whereby these modifications are often dynamically regulated. One modification whose function is still largely unclear is palmitoylation, i.e. the coupling of a protein with a fatty acid chain. One obvious explanation is that palmitoylation allows a protein to be recruited to the cell membrane in order to perform its function there. Surprisingly, however, a large number of trans-membrane proteins are affected by palmitoylation. Also, proteins that are relevant for cancer seem to be more frequently palmitoylated.

In this Master's project, we want to pursue a new idea as to why palmitoylation might be important. To this end, molecular dynamics simulations will be carried out on proteins in various membrane models. The work will be carried out in close collaboration with Prof. Thomas Stockner, Medical University of Vienna. 

Field: Technical Physics, Biomedical Engineering

Anderluh A, Hofmaier T, Klotzsch E, Kudlacek O, Stockner T, Sitte HH, Schütz GJ (2017) Direct PIP2 binding mediates stable oligomer formation of the serotonin transporter., opens an external URL in a new window Nature Communications 8: 14089

 

Logo TU Wien und des IAP

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Logo TU Wien IAP

Contact for TU Wien

Prof. Gerhard Schütz
Head of the Biophysics research unit
+43 1 58801 13480
gerhard.schuetz@tuwien.ac.at

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© MedUni Wien

MedUni Wien

Collaboration partner MedUni Vienna
Prof. Thomas Stockner
Medical University of Vienna
+43 1 40160 31215
thomas.stockner@meduniwien.ac.at

The Zimmer lab at the University of Vienna, opens an external URL in a new window is probing neuronal network dynamics in the brains of small animals like fish and nematode worms using advanced volumetric and real-time fluorescence microscopy techniques. These approaches require sophisticated and coordinated control over various components like lasers, cameras, stages, filter wheels, etc. Similar components need to be controlled in the Schütz lab at the TU Wien, opens in new window for performing single molecule fluorescence microscopy techniques, where dynamic imaging and superresolution microscopy are used to gain insights into general aspects of membrane biophysics, neuroscience and immunology.

Master Thesis Hardware Control

© TU Wien

Master Thesis Hardware Control

Your tasks:

  • Discussing and participating in different experiments and microscopy development.
  • Developing and building a microcontroller based I/O board.
  • Developing and integrating software for experimental control.
  • Publish your work as open-source and open-hardware.
[Translate to English:] Hardware Control

© TU Wien

Master Thesis Hardware Control

Motivation:

  • Participating and understanding of a variety of biophysical experiments.
  • Learning and working with a modern ECAD program (KiCad).
  • Programming micro controllers. (Arduino, C)
  • Interest in automation.
[Translate to English:] Hardware Control

© TU Wien

Master Thesis Hardware Control

Benefits:

  • Getting knowledge about state of the art fluorescence microscopy techniques and experiments in cell biology and neuroscience.
  • Specific tasks with close mentoring and regular discussions about progress and outcome.
  • Diverse and comprehensive techniques and lab work.
  • Contributing hard/software development for a large imaging community.
  • The master project is full time and will be supported by a stipend of ~€490 / Month.

 

Contact:

 

Logo Universität Wien

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Logo Universität Wien

Supervisor:
University of Vienna
Dipl.-Ing. Lukas Hille
Department of Neuroscience and Developmental Biology
Lukas.Hille@univie.ac.at

Logo TU Wien und des IAP

© TU WIEN - IAP

Logo TU Wien IAP

TU Wien
Dr. Mario Brameshuber
Institute of Applied Physics
brameshuber@iap.tuwien.ac.at 

picture of an Fluorescence microscopes

© TU Wien

Fluorescence microscope

Joint project with Prof. Radu Grosu, Faculty of Informatics

Biological cells react dynamically to biochemical and biophysical stimuli provided by their environment, such as the presence and spatial organization of specific ligands, the dynamical behavior of the matrix or its rigidity. Typically, microscopists have to observe attentively the experiment and intervene manually, whenever appropriate. In this project, we will go beyond the state of the art by developing an autonomous microcopy system, which enables the automated interpretation of cell biological images, and – based on a set of user-defined rules – a corresponding response exerted on the cell by the microscopy system. We will employ machine learning methods to automate the image interpretation and control the hardware response.

Field: Technical Physics, Biomedical Engineering, Data Science, Informatic

Bachelor or Master Thesis

picture of an Cryostat container

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Cryostat container

Fluorescent dyes behave differently at room temperature and low (cryogenic) temperatures. Performing super resolution microscopy at low temperatures requires a full understanding of the fluorescent dyes properties. In this project, we will examine the behaviour of different dyes at low temperatures and will characterize its photoblinking/photoswitching capabilities, establishing a library of dyes suitable for cryo super resolution microscopy.

Field: Technical Physics, Biomedical Engineering, Technical Chemistry

Scientific illustration shows CHO cells incubated on an EM grid

© TU Wien

CHO cells incubated on a EM grid

Cryofixation is considered an ideal fixation technique for biological structures. It combines complete immobilization with total preservation of the live state of the cell. In this project we will evaluate different parameters and protocols for criofixating a variety of cell lines, with the aim of designing an optimized protocol for their study with super resolution microscopy.

Field: Technical Physics, Biomedical Engineering, Technical Chemistry

Bachelor thesis

picture shows the illustration of a construction of an automatic focus holding system for cryo-super-resolution microscopy.

© TU Wien

Construction of an automatic focus holding system for cryo-super-resolution microscopy

Super resolution microscopy measurements often take from few minutes to several tens of minutes for a single measurement to be done. In such long measurements, the focus of the optical system may move, which means we often need manual repositioning of the objective. In this project we will construct an automated system that continuously tracks the position of the focus and repositions the objective using a piezoelectric positioner.

Field: Technical Physics, Technical Chemistry

Scientific illustration of the concept of the drift correction method

© TU Wien

Concept of the drift correction method

Typical super resolution microscopy measurements take several tens of minutes. During these long measuring times, the microscope can suffer from mechanical drift, which deteriorates the final resolution of the images. To attain the potential resolution of tens of nms, the mechanical drift needs to be corrected. In this project, we will design a strategy for drift correction based on tracking the displacement of fixed fiducial markers distributed all over the field of view. Their individual trajectories will be analysed and used to correct the movement of the whole system, and, this way, obtain a drift-corrected image.

Field: Technical Physics, Biomedical Engineering, Technical Chemistry