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OnderzoekZernike (ZIAM)QISDSchlathölter Group

MSc and BSc projects

There are always exciting opportunities for talented Master and Bachelor students in our team. Below, you find 2 BSc projects for spring 2018 as well as two example MSc projects, currently available. More MSc and BSc projects with similar focus are always possible. For more information, please contact Thomas Schlathölter.

BSc project 2018: Self assembled DNA complexes studied in an ion trap
Sketch of a G-quadruplex.
Sketch of a G-quadruplex.

Besides the well-known double helix structure, DNA can assume a variety of 3D conformations. For instance, telomere DNA which is found in the protective end-caps of our chromosomes is known to form the so-called G-quadruplex structure. Generally, G-quadruplex structures can form from DNA sequences rich in guanine (G) in a self-assembling manner: 4 G bases bond to form a square planar structure called a guanine tetrad. Stacks of these tetrads form, and their excess negative charge is compensated by positive ions (see figure on the left).

For our experimental studies on the fundamental mechanisms underlying radiotherapy, we need to prepare G-quadruplex DNA in ionic form, bring it into the gas phase and trap it in a radiofrequency ion trap. In this project, experimental strategies will be compared that aim at constructing self-assembled G-quadruplexes containing different metal counterions and to collect these in an ion trap.

The experiments will be done in collaboration with PhD students using an experimental setup designed and constructed by our group.

BSc project 2018: H2 formation on polycyclic aromatic hydrocarbon molecules

Molecular hydrogen is the most abundant molecule of our Universe. H2 formation on Polycyclic Aromatic Hydrocarbon (PAH) cations is considered a potentially important route towards molecular hydrogen formation in the interstellar medium (ISM). Hydrogen interaction with PAHs furthermore is a model system for hydrogen-graphene interactions, the latter being key for future graphene-based hydrogen storage appliactions.

We have recently found that for coronene cations (C24H12 +), sequential H attachment involves well defined adsorption sites. Along this sequence, "magic numbers" of attached H atoms are observed to be particularly stable [1]. The process competes with H2 abstraction, where an incoming H atom reacts with a previously attached H atom, to form a free H2 molecule.

Until now, attachment and abstraction reactions have only been studied for coronene cations. In this project, the process will be investigated for the significantly smaller pyrene molecule (C16H10). Pyrene cations will be produced be collected in a radiofrequency ion trap and exposed to H atoms form a thermal H source. To distinguish between attachment and abstraction reaction, experiments will be carried out using C16 1H+ cations which are exposed to 2H (deuterium) atoms. The different mass of the otherwise identical H isotopes allows to distinguish both processes and quantitatively analyze the interaction processes.

[1] S. Cazaux, L. Boschman, N. Rougeau, G. Reitsma, R. Hoekstra, D. Teillet-Billy, S. Morisset, M. Spaans & T. Schlathölter, Nature Scientific Reports 6 (2016) 19835

MSc projects: Hydrogenation of polycyclic aromatic hydrocarbons
Coronene in space
Coronene in space

The understanding of hydrogen attachment to carbonaceous surfaces is essential to a wide variety of research fields and technologies such as hydrogen storage for transportation, precise localization of hydrogen in electronic devices and the formation of cosmic H2. For coronene cations as prototypical Polycyclic Aromatic Hydrocarbon (PAH) molecules, our group has experimentally uncovered the existence of particularly stable systems with “magic” numbers of H atoms attached. For these closed-shell cations, further hydrogenation requires large changes in molecular structure associated with high energetic barriers. Controlling specific hydrogenation pathways would provide the possibility to tune the location of hydrogen attachment and the stability of the system. In an Astronomical context, our findings indicate that PAH hydrogenation is probably an important channel for the formation of cosmic H2.

In the course of this project you will develop novel strategies, to bring large PAH cations into the gas phase and trap these ions in a radiofrequency ion trap. The interaction of hydrogen and deuterium atoms with PAH cations will then be experimentally studied as a function of temperature, exposure time, PAH size and other parameters. Eventually, you will compare the obtained experimental data with quantum chemical calculations.

MSc projects: Soft X-ray and heavy ion interactions with gas-phase DNA
Our RF ion-trap at the FLASH facility in Hamburg
Our RF ion-trap at the FLASH facility in Hamburg

The concept of radiotherapy for tumor control is based on the idea of killing cancerous cells by means of ionizing radiation, while simultaneously sparing healthy surrounding tissues. This implies delivery of high doses to tumour volumes while minimising dose deposition into surrounding healthy tissues. To increase the contrast between dose to tumor and healthy tissue so-called radiosensitizers are enriched in the tumor. Heavy metal nanoparticles are the most recent group of radiosensitizers, for which the clinical potential is currently investigated. Currently, the underlying mechanisms on a molecular level are not fully understood for X-ray irradiation and even more ambiguous for proton or heavy ion therapy. The investigation of this issue in macroscopic systems (in vivo and in vitro) is difficult because of the complexity of the systems and because timescales range from the fs-scale of primary ionization and excitation processes over ms timescales of diffusion limited radical chemistry up to second and even year timescales of biological processes and biological endpoints.

In our group, we are investigating the most fundamental processes of radiation action on DNA on a molecular level, i.e. on sub-nanometer length-scales and on few femtosecond time-scales. In the course of this project, you will use a radiofrequency ion trap, to prepare a well defined target of gas-phase DNA ions. You will then study the interaction of soft X-rays with these targets during an experimental campaign (typically two weeks) either at the synchrotron BESSY II (Berlin) or SOLEIL (Paris).

Last modified:20 March 2018 3.11 p.m.