Offer for the Research Phase (BIO)

To assist you in finding topics for the research phase, a platform is available. The potential supervisors in the Professional Profile Physics publish suitable topics with short descriptions that can be done in their group. The list thus provides an insight into possible topics for the final thesis in the Master's degree program in BIO. If you are interested in a topic, please contact the research group. 

The list is not complete, so it is also worth asking the working groups directly. The exact titles and descriptions can of course be modified by the supervisor.

Temporarily, topics may also be announced in a Moodle course.

Research Group
Associate Professorship of Theory of Biological Networks (Prof. Alim)
Supervisor
Prof. Dr. Karen Alim
Description
Can we recreate the origins of life on earth in the lab? Hydrothermal vents at the ocean floor are theorised as a possible setting for the emergence of life. These structures contain intricate fluid flow pathways, and thermal- and chemical gradients which makes them ideal as a reaction chamber for synthesising the molecules necessary for the emergence of life. In this project, you will use our microfluidic channel setup to experimentally simulate a prebiotic hydrothermal vent. Through fluorescence microscopy, you will investigate how particles interact with and diffuse through a mineral wall. You will learn about microscopy, microfluidics, fluid flow, and data analysis in Python. Task 1: Perform microfluidic experiments to simulate mineral membranes of hydrothermal vents. Task 2: Quantify the diffusion of small molecules across the mineral membrane using fluorescence microscopy. Task 3: Characterise the interaction of fluorescent beads with the mineral membrane through experiments and fluid dynamics.
Research Fields
Biological Physics (Experiment) (100%)

Research Group
Chair of Cellular Biophysics (Prof. Bausch)
Supervisor
Prof. Dr. Andreas Bausch
Description
A droplet microfluidics set up will be improved to manipulate cell culture environments for the differentiation of stem cells. By emulsifying 100micron sized droplets, cells are encapsulated in hydrogles and their growth observed. In the project different strategies to parallize the application of drugs to the cell culture will be developed and tested.
Research Fields

Research Group
Chair of Physics of Synthetic Biological Systems (Prof. Simmel)
Supervisor
Prof. Dr. Friedrich Simmel
Description
DNA origami enables the construction of nanoscale devices with precise control over structure and function. This project aims to develop a DNA origami-based turbine that converts linear into rotational motion by transmitting torque between two axes. This project will explore the mechanical properties of the turbine system and study the response to external actuation such as fluid flow or electric fields. The project involves designing chiral DNA origami structures, verifying their assembly using AFM and TEM, and developing a microfluidic or electric field-based measurement setup. Using TIRFM, we will observe and analyze rotational behavior to quantify torque transmission at the nanoscale.
Research Fields
Biological Physics (Experiment) (100%)

Research Group
Chair of Physics of Synthetic Biological Systems (Prof. Simmel)
Supervisor
Prof. Dr. Friedrich Simmel
Description
Molecular devices that have an anisotropic periodic potential landscape can be operated as Brownian motors. When the potential landscape is cyclically switched with an external force, such devices can harness random Brownian fluctuations to generate a directed motion. Recently, directed Brownian motor-like rotatory movement was demonstrated with an electrically switched DNA origami rotor with designed ratchet-like obstacles. In this follow-up project, we want to investigate how a rational design of anisotropic energy landscapes can enforce a biased rotary motion. The experimental work includes the fabrication of DNA origami rotors and their characterization via single-molecule TIRFM (total internal reflection fluorescence microscopy). Tasks: 1. Design and fabrication of DNA origami nanostructures 2. Verification of structural integrity via AFM/TEM 3. Assessment of diffusional energy landscapes via TIRFM 4. Measuring ratcheting behavior during electric actuation 5. Screening of governing parameters driving the directional motion Related references https://doi.org/10.1016/j.bpj.2022.08.046 https://doi.org/10.1021/acs.nanolett.4c00675 https://doi.org/10.1038/s41586-022-04910-y
Research Fields
Biological Physics (Experiment) (100%)

Research Group
Associate Professorship of Theory of Biological Networks (Prof. Alim)
Supervisor
Prof. Dr. Karen Alim
Description
The slime mold Physarum polycephalum is able to sense and migrate toward food, substrate and light from afar thanks to its ability to maintain directionality. How the organism maintains and control its directionality despite its peristaltic shuttle flow mixing up its interior is unclear. Previous studies have found the nuclei trafficking under peristaltic flow plays an essential role. In particular, we hypothesize that when nuclei get trapped in Physarum’s tube walls, they become a waypoint of information exchange. The idea is that the kinetics of nuclei trapping and untrapping enables formation of chemical gradients patterning down directionality. In this project, you will model nuclei trapping-untrapping and chemical signal concentration emitted by nuclei numerical and search for conditions allowing for patterns. You will learn to program in matlab and about flows and transport in peristaltic flow. Task 1 Implement trapping and untrapping kinetics in our numerical model of nuclei dynamics in a single tube Task 2 Identify the key physical parameters of your model from the analytical equations Task 3 Explore chemical patterns while exploring the phase space of your key physical parameters.
Research Fields
Biological Physics (Theory) (100%)

Research Group
Associate Professorship of Theory of Biological Networks (Prof. Alim)
Supervisor
Prof. Dr. Karen Alim
Description
The complex behavior of the giant cell Physarum polycephalum finds its origin in the versatile transformation of liquid cytoplasm to gel-like actin-myosin meshwork making up the tube walls and vice versa. These active mechanics allow the organism to recycle its’ gel-like tubes at its rear and move it in its fluid form to the front, where it grows. Also, responding to stimuli like food, touch, or light, a change in cytoplasm viscosity seems to initiate the response. Yet, what are the mechanical properties of the liquid cytoplasm, and how much do they change upon stimulation? Do the mechanical properties of the cytoplasm change with the location in the cell? The measure of the mechanical properties of cells is challenging, but one can probe their visco-elasticity by tracking injected micron-sized beads - a technique called microrheology.You will measure the mechanical properties of cytoplasm extracts and grown Physarum, and quantify how they change upon stimulation by passive and active microrheology. Task 1: Establish cytoplasm extraction following previous work in the literature. Task 2: Perform passive microrheology on cytoplasmic droplets without and with stimulation (light, food, drugs) and analyze your data quantitatively. Task 3: Establish active microrheology to extract cytoplasm viscosity in different parts of Physarum’s network.
Research Fields
Biological Physics (50%)
Soft Matter Physics (50%)

Research Group
Chair of Physics of Synthetic Biological Systems (Prof. Simmel)
Supervisor
Prof. Dr. Friedrich Simmel
Description
The self-assembly of DNA origami tiles enables the formation of 2D lattices with well-defined spatial arrangements. This project focuses on constructing a system in which DNA origami-based four-arm rotors are embedded within a lattice and interact through sequence-specific DNA interactions. By controlling these interactions, the system can serve as a model for statistical physics frameworks like the Ising model and its generalizations. The objective is to investigate how the collective behavior of rotors emerges under different conditions. Experimental work will involve the fabrication of DNA origami lattice structures and their characterization using atomic force microscopy (AFM) or electron microscopy (SEM / TEM). Specifically designed rotors will then be assembled onto the lattice to study interaction dynamics via AFM or fluorescence microscopy. Finally, acquired microscopy images will be analyzed to quantify spatial correlations and dynamic behavior. Tasks: Assemble 2D DNA origami lattices to precisely position rotors within a controlled environment via two approaches – top down and bottom up. Design DNA origami rotors with specific interaction schemes. Characterize collective rotor behavior under varying conditions. Analyze microscopy data to quantify interaction-driven patterns and structural organization.
Research Fields
Nanostructures (Experiment) (50%)
Biological Physics (50%)

Research Group
Chair of Cellular Biophysics (Prof. Bausch)
Supervisor
Prof. Dr. Andreas Bausch
Description
One sever limitation in organoid research is the lack of blood support structures in cell culture conditions. to this end different approaches were envisioned to form capillaries in cell cultures to not only suplement media exchange but also to introduce important crosstalk between the cells. In this project a microfluidic setup will be constructed to self organize a vasculator to connect heart organoids with.
Research Fields

Potential supervisors can manage their own offer of Research Phase topics via the application “Thesis” in the Digital School Services. They can find more information on thesis management in the NAT wiki.