We have developed a stereo video rig able to track particles in three dimensions to study the gas-like phase of an experimental granular media system driven by contact charge electrophoresis. We...Show moreWe have developed a stereo video rig able to track particles in three dimensions to study the gas-like phase of an experimental granular media system driven by contact charge electrophoresis. We use the stereo set-up to simultaneously capture the granular media gas-like 2D dynamics and the particle motion in the perpendicular driven direction. We find that melting of the crystalline order happens when two particles anti-synchronize their oscillation phase, attract due to opposite sign charges, and collide. The repeated occurrence of such events establish a sustained mechanism of energy injection from the driven direction to the XY plane, resulting in a stationary dilute gas-like phase. We explore the change in dynamics upon an increase of the driving field and find that the dynamics of the gas-like phase are unchanged if re-normalized by the period of oscillation in the driven direction. The developed stereo system has proved itself as a robust and crucial advance in the experimental techniques used to explore the physics of driven media, opening the door to perform experiments fully capturing both the driven and horizontal dynamics.Show less
The chromatin fiber, formed by nucleosomes attached together by linker DNA, organizes into higher-order structures such as chromatin domains and chromosomes. The domains’ compaction level plays a...Show moreThe chromatin fiber, formed by nucleosomes attached together by linker DNA, organizes into higher-order structures such as chromatin domains and chromosomes. The domains’ compaction level plays a role in the regulation of transcription and depends on chromatin folding and aggregation mechanisms. However, the relation between conformational changes of the fibers and their aggregation has not been clearly resolved yet. Here, we test in vitro conditions that favor or prevent the aggregation of chromatin fibers with linker DNA lengths of 20 bp, 25 bp, 50 bp, and 55 bp and use fluorescent correlation spectroscopy to analyze the mobility of the aggregates and their constituents. Our results show that chromatin fibers with 25, 50 and 55 bp linker DNA form micron-sized aggregates in the presence of mono and divalent cation salts. The auto-correlation and cross-correlation models yielded diffusion times in the order of seconds for early-stage aggregation. The protocols and results obtained can provide a starting point for further research on the aggregation mechanism of chromatin and its impact on DNA transcription.Show less
Inelastic electron tunneling spectroscopy (IETS) is a tool used to research the vibrational modes in a tunneling junction. This report describes the setup of a cryogenic scanning tunneling...Show moreInelastic electron tunneling spectroscopy (IETS) is a tool used to research the vibrational modes in a tunneling junction. This report describes the setup of a cryogenic scanning tunneling microscope (STM). Potentially this STM can be used in the research to the edge modes of graphene edge junctions. Gold samples were used for the calibration of the z stage of the setup by using two different methods (histogram based/line cut based). Experiments at cryogenic temperatures seemed to have difficulties measuring topographic images at 77K. These difficulties are most likely caused by condensation of atmospheric gasses still present in the system. To solve this problem, a heater is required to prevent material condensing on the sample or tip. In order to implement IETS in the system it is proposed to used a combination of a heater and thermometer in order to keep the system clean.Show less
Over the years, the development of large-scale structure simulations has given us more and more cluster samples from which we can infer cosmological information via cluster counts. As a matter of...Show moreOver the years, the development of large-scale structure simulations has given us more and more cluster samples from which we can infer cosmological information via cluster counts. As a matter of fact, we can use this probes to constraint some cosmological parameters like the matter density Ωm or the amplitude of density fluctuations at 8 Mpc h−1, σ8. However, this kind of data analysis is heavily affected by systematic errors of astrophysical kind. A recent proxy has been proposed to overcome this difficulties: the cluster sparsity, defined as the ratio of different halo mass definitions. In this thesis we will test this observable on the halo catalogue of the new simulation FLAMINGO, studying its property in a fullhydrodynamics simulation for the first time. We will test its dependence on different cosmologies, showing that the effects of baryonic matter are almost an order of magnitude higher than the differences between two valid cosmologies (in this case Planck-18 and DES). Finally, we will use the hot gas particles included in FLAMINGO to perform a mock X-ray measurement of the sparsity in order to predict the systematics that could affect a real-life observation. We find that indeed a significant bias affects the halo mass, while the sparsity is way less biased and is actually compatible with accurate values extracted from the simulation. We conclude that the sparsity does seem as a reliable and effective proxy for cosmological constraints.Show less
In this thesis we study the behaviour of scalar and fermion fields on a curved spacetime. Specifically, this is done for the pp-wave metric. This corresponds to the curvature of spacetime...Show moreIn this thesis we study the behaviour of scalar and fermion fields on a curved spacetime. Specifically, this is done for the pp-wave metric. This corresponds to the curvature of spacetime associated with the gravitational wave of a light wave that solves the Einstein-Maxwell equations. The results for the analytical solution of the scalar field, as well as its quantization have been reproduced. As an extention, the fermion field has been quantized. In case of a Majorana fermion, anticommutation relations have been found. Furthermore, the Green’s functions in this scenario for the scalar and fermion fields have also been obtained.Show less
The main goal of this project is to study the conductivity of pentacene thin films in the herringbone standing-up (HSU) phase as a function of layer count and to investigate the role of film...Show moreThe main goal of this project is to study the conductivity of pentacene thin films in the herringbone standing-up (HSU) phase as a function of layer count and to investigate the role of film defects in the charge transport through these pentacene layers. To grow these films, atomically flat and spatially uniform substrates are required, for which hexagonal boron-nitride (hBN) is used. Several techniques to clean these substrates are tested and multiple growth experiments are performed on our samples. We also develop a very general approach, which we have named the Laplace conductivity algorithm, to extract local conductivities on a sample from experimental potential maps. This algorithm is tested using simulations, with very promising results being achieved.Show less
Active particles that transform energy into directed or persistent motion show collective behavior and self-organization. One type of self-organization is in the form of crystal structures. However...Show moreActive particles that transform energy into directed or persistent motion show collective behavior and self-organization. One type of self-organization is in the form of crystal structures. However, an active crystal with tunable properties has not been achieved. Inspired by an experiment in which vibrated polar discs form ordered domains, and an experiment in which metallic spheres, that move by contact charge electrophoresis, form a passive crystal, we create active particles in the shape of a cylinder composed of a metallic and a dielectric part, that move thanks to Quincke rotation on the dielectric side and an electrostatic force on the metallic side due to an external electric field. We study the behavior of these particles by characterizing the persistence of their motion, their ability to repel each other, and by studying their instantaneous speed as a function of the electric field and their size. Our results suggest that the particles have the potential to form an active crystal and seem to be compatible with the passive crystal existent at our lab.Show less
The repositioning of nucleosomes in DNA plays a vital role in accessing the encoded information. This repositioning can be induced through remodelers sitting on the DNA wrapped around the histone...Show moreThe repositioning of nucleosomes in DNA plays a vital role in accessing the encoded information. This repositioning can be induced through remodelers sitting on the DNA wrapped around the histone cores. These introduce twist defects which can propagate through the nucleosomal DNA and escaping on one end which leads to single base pair repositioning of the nucleosome. However the precise dynamics at play here and how it interacts with the larger DNA sequence are not fully clear. Here we will demonstrate some of the properties of the twist defects on the wrapped DNA and how this affects the nucleosome repositioning along a sequence. This is done through setting up a Monte-Carlo Markov chain for the rigid base pair model. We find that a build-up of twists occurs on hard to traverse DNA regions and that this causes multiple steps in quick succession. We also see that the positional preference of the nucleosome with remodeler is less sensitive to the global landscape as opposed to free nucleosome repositioning. This quick succession of steps may explain an earlier work by Sabantsev et al. where this effect was seen in an experiment without an explanation. The current work can be used as guidance for future studies investigating the dynamics of simultaneous defects around the nucleosome.Show less
