Research Phase and Master's Thesis in the M.Sc. Biomedical Engineering and Medical Physics

Are you interested in the prospects to manipulate biological structures with magnetic fields to intervene in central cellular processes relevant in biomedicine? Then you should be interested in this joint Master’s project between the Bucher Lab https://www.bucherlab.org/ and Westmeyer Lab https://www.westmeyerlab.org/ on using quantum technology based on nitrogen-vacancy (NV-)centers [1,2] to characterize and optimize biomagnetic nanostructures [3,4] in living mammalian cells.

Summary

NV-magnetometry to characterize and optimize biomagnetic nanostructures in mammalian cells

Your Profile

● an excellent and recent Bachelors's degree in (bio-)physics, biochemistry, biological engineering, biomedical engineering, or related academic programs,

● genuine interest in the powerful applications of NV-centers (https://en.wikipedia.org/wiki/Nitrogen-vacancy_center)

● previous experience with microscopy and mammalian cell culture,

● the ability to be self-motivated and work with an interdisciplinary team of bioengineers, biochemists, neuroscientists, and data scientists,

● excellent English language and organizational skills. ● an openness and mobility to collaborate with our partners at Max Planck Institutes, MIT, Caltech, and the University of Washington.

References:

[1] Bucher, D.B., Glenn, D.R., Park, H., Lukin, M.D., Walsworth, R.L., 2020. Hyperpolarization-Enhanced NMR Spectroscopy with Femtomole Sensitivity Using Quantum Defects in Diamond. Physical Review X 10, 021053. https://doi.org/10.1103/PhysRevX.10.021053

[2] Bucher, D.B., Craik, D.P.L.A., Backlund, M.P., Turner, M.J., Dor, O.B., Glenn, D.R., Walsworth, R.L., 2019. Quantum diamond spectrometer for nanoscale NMR and ESR spectroscopy. Nat Protoc 14, 2707–2747. https://doi.org/10.1038/s41596-019-0201-3

[3] Sigmund, F., Massner, C., Erdmann, P., Stelzl, A., Rolbieski, H., Desai, M., Bricault, S., Wörner, T.P., Snijder, J., Geerlof, A., Fuchs, H., Hrabe de Angelis, M., Heck, A.J.R., Jasanoff, A., Ntziachristos, V., Plitzko, J., Westmeyer, G.G., 2018. Bacterial encapsulins as orthogonal compartments for mammalian cell engineering. Nat Commun 9, 1990. https://doi.org/10.1038/s41467-018-04227-3

[4] Sigmund, F., Pettinger, S., Kube, M., Schneider, F., Schifferer, M., Schneider, S., Efremova, M.V., Pujol-Martí, J., Aichler, M., Walch, A., Misgeld, T., Dietz, H., Westmeyer, G.G., 2019. Iron-Sequestering Nanocompartments as Multiplexed Electron Microscopy Gene Reporters. ACS Nano 13, 8114–8123. https://doi.org/10.1021/acsnano.9b03140

Dark-field radiography exploits the scattering of X-rays to visualize structures below the resolution limit. Currently, several initial clinical patient studies are underway on a worldwide first prototype we recently realized at Klinikum rechts der Isar. Within the framework of this project, the special algorithms for image post-processing of these first clinical data will be further optimized and used together with the participating radiologists for the evaluation of better direction of lung diseases.

Character of thesis work: mainly computational physics & image processing

For more information, please contact: Rafael Schick (rafael.schick@tum.de) or Franz Pfeiffer (franz.pfeiffer@tum.de).

Dark-field radiography is a novel X-ray imaging technique that is being tested for the first time in clinical patient studies on a worldwide first prototype recently completed by us at the TUM Klinikum rechts der Isar. Within the scope of this project, Monte Carlo based Compton simulations will be developed, which will allow an exact modelling of the Compton scattering and thus a better correction of the image artifacts.

Character of thesis work: experimental physics (50%) & computational physics (50%).

For more information, please contact: Theresa Urban (theresa.urban@tum.de) or Franz Pfeiffer (franz.pfeiffer@tum.de).

Comparisons of magnetic coils for inductive nerve stimulation are challenging and are mostly based on simulations. Those simulations rely on approximations and assumptions and often ignore issues like skin effect or proximity effect. Further, such calculations are time consuming and limited in accuracy and resolution. To determine the spatial field distribution along a nerve, we want to design a device that scans the electric field induced by a coil on a millimeter scale.

Character of thesis work:

Literature research on different field measurement methods and evaluate suitability; Design and construction of the device, including custom circuits and measurement environment; Evaluation of the device and exemplary measurement for different coil designs.

Question and tasks:

What methods are suitable to evaluate the electric field on a millimeter scale? Design and built the device; Determine the spatial field distribution for different coil designs; Investigate ohmic losses for solid coil wire and high frequency litz wire.

You should bring:

Interest in literature research, hardware design, experimental setup design.

Using phase-contrast as alternative imaging contrast for X-rays can considerably improve the imaging results for biomedical specimens. This project will focus on the development of an algorithmic framework for a high-sensitivity and high-resolution grating-based phase-contrast micro-tomography setup at the Munich Compact Light Source for investigating soft-tissue biomedical samples, such biopsies. 

Character of thesis work: mainly computational (image processing/ reconstruction)  

For more information, please contact: Martin Dierolf (martin.dierolf@tum.de), Johannes Brantl (johannes.brantl@tum.de), or Franz Pfeiffer (franz.pfeiffer@tum.de)

Regression of the diaphragm muscle during artificial respiration leads to severe problems with breathing for many patients. To avoid such regression, stimulation of the phrenic nerve is a promising solution. Magnetic stimulation of the phrenic nerve has been demonstrated. However, devices are too large and complex and hence, optimization is required. We want to adapt parameters like pulse shape and coil design to stimulate the phrenic nerve with minimum energy. Further, we want to evaluate the possibility of electric stimulation and compare it to the magnetic approach. Those problems can be addressed using simulations. To verify our results, we want to design an experimental setup involving the stimulation of the sciatic nerve in the forearm.

Character of thesis work:

Extensive literature research on different simulation approaches; Extend and adapt a software environment to implement simulations for magnetic and electric simulation; Calculate field data using FEM and similar methods; Data processing using python; Design an experimental setup to verify simulations;

Question and Tasks:

What is the optimal configuration to stimulate the phrenic nerve? How are magnetic and electric stimulation different on a cellular level and how can they be simulated? How precise are our simulations? How can we verify our results?

You should bring:

Basic data science skills, ideally familiar with python and git; Good understanding of field theory; Interest in literature research

Hybrid pixel photon-counting detectors have been developed in the past in high-energy physics and are currently used in various medical imaging applications. They offer higher spatial resolution and additional energy resolution and therefore have significant potential for future improvements in radiography and CT. This work will investigate some basic physical properties of the detectors and, in particular, explore the response of such detectors to oblique radiation, which is very important for some spectral imaging applications.

The project is carried out in close collaboration with external partners from industry.

Character of the work: experimental physics (70%) & image processing (30%).

For more information, please contact: Daniel Berthe (daniel.berthe@tum.de) or Franz Pfeiffer (franz.pfeiffer@tum.de)