We successfully produce Josephson junctions by stacking NbSe2 flakes, where the twist angle and strain are responsible for a weak link. Field sweep measurements are taken to characterize these...Show moreWe successfully produce Josephson junctions by stacking NbSe2 flakes, where the twist angle and strain are responsible for a weak link. Field sweep measurements are taken to characterize these devices. These measurements highlight the importance of the direction of the applied magnetic field. Prompted by this, simulations of the critical current given an arbitrarily shaped interface area are presented and compared to measurements.Show less
There is a demand for high bandwidth down links from space to earth. A cubesat in a GEO could function as a relatively cheap access point to a high bandwidth communication channel with earth. This...Show moreThere is a demand for high bandwidth down links from space to earth. A cubesat in a GEO could function as a relatively cheap access point to a high bandwidth communication channel with earth. This thesis explores new ways to increase the bandwidth by identifying bottlenecks in the GEO- Earth communication channel and how to circumvent them. The diffrac- tion limit causes large beam spreading at GEO distance, holding back ad- vanced modulation techniques due to the inability to capture the whole wave front. In this case, a modulation scheme using only a few bits should be chosen, allowing to modulate as fast as possible. The low signal inten- sity can be detected with more sensitivity by making use of a quantum enhanced receiver. From GEO to Earth, data rates around 50 Gbps are possible. Additionally, the atmosphere introduces spatial incoherence. To mitigate the effects of the atmosphere, a modulation scheme should be chosen that exploits modulation vectors which are orthogonal to the spa- tial dimension, such as polarization or wavelength. This gives a modula- tion scheme with many degrees of freedom. To deal with the complexity, a variational auto-encoder deep neural network is used to act as the modu- lator and demodulator. The variational distribution is chosen to match the noise introduced by an atmospheric channel. Using this scheme, we were able to find encodings that increase the density of symbols in phase space relative to the noise. This approach is especially promising in a bandwidth limited channel.Show less
The application of denoising machine learning to STM data has several advantages, such as improving data quality, aiding visual interpretation of data, and speeding up measurement time. With...Show moreThe application of denoising machine learning to STM data has several advantages, such as improving data quality, aiding visual interpretation of data, and speeding up measurement time. With experimental data, the absence of a ground truth poses a problem for traditional supervised learning techniques. In this work, state-of-the art self-supervised machine learning techniques are applied to reduce noise in quasiparticle interference data of overdoped cuprates, using only the noisy measurements. The machine learning methods are shown to outperform traditional denoising methods. Further ideas to improve and generalize the denoising of quasiparticle interference data are proposed.Show less
We use the large-volume cosmological hydrodynamical FLAMINGO simulations to identify dissociated clusters of galaxies by a visual inspection. This dissociation is seen between the dark matter and...Show moreWe use the large-volume cosmological hydrodynamical FLAMINGO simulations to identify dissociated clusters of galaxies by a visual inspection. This dissociation is seen between the dark matter and gas components of two merging galaxy clusters: the dark matter regions pass through each other while the gas components collide and get stuck in the middle between the dark matter regions. A first selection removes low-mass haloes with M200c < 1014.5 M⊙ to conform to what is observationally possible. After this, selections of certain parameters are used to try to select a large amount of dissociated clusters. Based on just offsets between the centres of potential, mass, and X-ray luminosity, about 5% of the objects that satisfy the specific conditions are dissociated, while 20% of all dissociated objects are included. In a different selection, based on angles between CoM velocities, mass ratios, and offsets, about 20% are dissociated while 15% of the total amount is selected. Properties of all dissociated haloes are analysed and reveal that slightly different constraints on the offsets, velocity angles, and other parameters might provide better results. Nevertheless, it is still very difficult to find a definitive selection that only picks out the dissociated clusters. Finally, the X-ray luminosity–mass relation is also analysed and reveals that dissociated clusters have a slightly higher X-ray luminosity. This is explained by the presence of hot gas, which exists because of the collision of the gas components that significantly heats up the gas. This hot gas emits more X-rays than cold gas so the X-ray luminosity is expected to be higher in dissociated clusters than in relaxed clusters that have not recently undergone a merging event.Show less
To better understand tumor progression and metastasis, it is important to investigate the mechanical properties of its cellular components. Tumors generally consist of cancer cells and healthy...Show moreTo better understand tumor progression and metastasis, it is important to investigate the mechanical properties of its cellular components. Tumors generally consist of cancer cells and healthy cells, whose interactions are fundamental for their structure and functionality. It has been shown that in co-cultured spheroids, cells rearrange themselves and completely separate. To closely mimic the tumor micro-environment in-vitro, hetero-spheroids containing both cancer cells and fibroblasts were used. The forces generated during cell-cell interaction and their cell sorting were studied. The interaction between the two cell types was probed with cell-sized (15-30 μm) microparticles. Different seeding-times and number ratios were investigated. No significant difference in the stress fields applied by the two different cell types during their interaction was found. However, it was observed that there is a critical number ratio between 1:3 and 1:6, above which the two cell types tend to completely separate. Below the critical ratio, there were intermixed areas of both cell lines. These cell clusters tend to merge over time, however no complete phase separation of the two cell types was observed for a period of one week. These results show that there is a favourable rearrangement of the cells consisting tumor-like structures. This cell type separation could indicate the next steps towards understanding the clustering and detachment of the cancer cells from the primary tumor, during metastasis.Show less
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
