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Master and Bachelorprojects

Coordinator:Dr. Raoul Frese, T128, 020-5987263

Our Bachelor and Master projects are open for all students from the VU and other universities. They are meant to introduce you to science and will hopefully let you experience that science in the area of Biophysics is fascinating and very exciting. The research is performed under supervision of a PhD student or a postdoc and a member of our scientific staff, below you find a description of some of our projects. Raoul Frese can help you find a project according to your level and interest. You can also contact the supervisors of specific projects below directly.

Especially students within the three following masters programs are encouraged to perform their Bachelor or Master research with us.  

  • Physics of Life (Specialization within the Medical Natural Science Master)
  • Biological Physics (Specialization within the Biomolecular Science Master)
  • Biophysics (Specialization within the Amsterdam Physical Sciences Master)

From sunlight to fuel

Up to now, solar energy can only be converted into electricity. Our research aims at the construction of new materials where sunlight is directly stored in a fuel.
We study molecules that have been designed to mimic the ability of biological photosynthesis to utilize photons to split water molecules into oxygen and hydrogen. Their performance and efficiency predominantly depend on the primary reactions after absorption of light. These you will study by applying ultrafast time-resolved spectroscopy. Your results will be used to drive novel molecular designs.


Molecular eyes – biopolymers that transform light into biological information

Light active molecules embedded in biopolymers can trigger a response that may induce growth of a plant or anxiety in a mouse.
We want to understand the molecular processes femtoseconds after light absorption and the resulting structural changes on much slower timescales that determine life style decisions.
In this project you will employ light spectroscopic methods to follow events right after absorption of a photon to the activity of the effector domain in the biopolymer. Techniques include visible, infrared and raman spectroscopy in combination with isotope labeling.

Building a superresolution microscope

Optical microscopy is an extremely valuable tool in many scientific fields. However, its spatial resolution is limited by diffraction. We are building a new type of microscope, based on stimulated emission depletion (STED), to overcome the diffraction limit. With this microscope, we will study ultrastructure of photosynthetic membranes and neuronal vesicle transport.

You will be working in close collaboration with a postdoctoral researcher, and are free to focus on one or more disciplines/subjects: (i) optics and electronics to build the setup; (ii) informatics for the software to control the setup; (iii) biophysics for the superresolution microscopy experiments.


Energy migration in photosynthetic membranes

After a photon is absorbed by a chlorophyll molecule, its energy hops to neighboring chlorophylls, and so on, until it reaches the photosynthetically active chlorophyll. The rate and distance of energy covered by this “hopping” process is important for understanding photosynthesis, but it is largely unknown.

Occasionally the energy of two absorbed photons will end up on the same chlorophyll molecule. In that case one of the energy quanta is annihilated, which can be observed as a loss of excited states. In this project we plan to use annihilation phenomena to study “hopping” behavior in photosynthetic membranes.

 You will build a system to measure laser power-dependent annihilation, and use this to study hopping in several types of photosynthetic membranes.


How fast do atoms move in proteins?

To observe vibrations of molecules spectroscopically, mid infrared light is needed which is invisible for our eyes and hard to detect. Using a non-linear optical crystal, we translate the infrared light to the visible region; following energy conservation, we use 800nm + 500nm -> 690nm. Thus the 690 nm wavelength of light can be observed and is easily detected with simple instruments. Using this technique you will investigate ultrafast vibrational dynamics. Movements of atoms and bonds can be observed with 200 femtosecond time resolution.


Linking blinking with quenching in different single light-harvesting complexes

Single-photon counters allow the tracking of spectroscopic processes of individual molecules down to millisecond timescales. Single-molecule spectroscopy has revealed that apart from changing their colour when you shine light on them, biological molecules can also “blink”, i.e., turn their fluorescence emission “on” and “off” at any random time. What is even more intriguing is that plants are designed to tune these blinking properties by a regulation mechanism known as nonphotochemical quenching (NPQ), in which excess energy is harmlessly dissipated as heat. In this project you will get the opportunity to track the spectral fluctuations from these systems in real time for a variety of light-harvesting complexes. This will provide a vital step to resolving the long-standing, hot debate of which type of complex is the most efficient energy quencher.


Measuring the fluorescence lifetime of single light-harvesting complexes

Single-molecule spectroscopy (SMS) has led to the discovery of intriguing phenomena that are masked by standard ensemble-averaging techniques. Not only are detectors nowadays sensitive enough to detect the individual photons, but sophisticated techniques have also been developed to push back the boundaries of the shortest time-scales that can be accessed for the fluorescence from these small objects. One such a technique is known as Time Correlated Single Photon Counting (TCSPC). This technique plays a major role to ensure that the illuminated object is indeed a single quantum-coupled system. The aim of this project is to develop a simple script in LabVIEW that would apply this technique to single light-harvesting complexes by measuring their fluorescence lifetimes. This will provide a crucial step in characterizing the rapid fluorescence fluctuations from these complexes.

Protection by heat generation

Excess light in photosynthesis is just an example of how too much of a good thing can be extremely harmful. In order to cope with the deleterious effects of excess light photosynthetic organisms have developed remarkable photoprotective strategies where the excess energy absorbed by the system is dissipated as heat. In this project the process will be investigated in diatoms, one of the major groups of algae, by ultrafast spectroscopy.


Ultrafast vibrations

Experimental investigation of (bio)molecular vibrations on the quantum time scale (10-14s). The recent advent in Stimulated Raman experiments brings new insight into molecular vibrational dynamic on the femtosecond scale. It brings new alternative to already established femto-IR spectroscopy by its different selection rules and easier experimental realization. The topic is suited for students who are interested in biophysics and have positive attitude towards experiments and innovative thinking. Fresh nature of the method brings unique opportunity to combine technical and/or programming skills with bit of theoretical work in future development and application of brand new method. Project can be based on programming software for instrument operation (for computer oriented students), characterizing system performance (for physicists) or application of method in study of complex molecules (for biophysicists or physical chemists).


Photoactive proteins – PYP

In our group we study the photophysics of several photoactive proteins, which act as light sensors, energy converters, proton pumps or molecular transporters, to unravel the molecular mechanism. For example, PYP, LOV or BLUF proteins act as signal transducers: the absorption of a photon induces a structural change of the protein that act as a signal for partner proteins. These reactions can be followed by triggering the protein with a short laser pulse and probing the progress with a second, delayed laser pulse in the UV-vis-nearIR-midIR spectral range. In PYP we study a very early stage in its reaction, namely the effect of the strength of a single hydrogen bond between the chromophore and an amino acid, on the outcome of the isomerization reaction.
Aim: perform ultrafast spectroscopic measurements on site selective mutants of PYP, in collaboration with the PhD student.


Protein behavior in artificial nanodisc membranes

In this project you will study the behavior of photosynthetic light-harvesting or reaction center proteins that are assembled in lipid nanodiscs: little artificial membranes that ideally only fit one protein each. With these nanoscale photosynthetic models, we can control the effects of aggregation and simulate the flexibility of individual proteins inside a membrane. One of the aims is to use light-harvesting nanodisc models to understand the unresolved mechanism of non-photochemical quenching.

The protein nanodisc-architectures will be characterized with different spectroscopic techniques, including time-resolved fluorescence spectroscopy or single-molecule fluorescence microscopy. This project is highly interdisciplinary with links to (bio)physics, physical chemistry and biochemistry. Biology-oriented students are also welcome to focus on the preparation and biochemical analysis of the protein-nanodiscs.


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