Over the last few decades, several methods have been explored and applied to circumvent the Abbe-Rayleigh diffraction limit, probably most importantly, stochastic super-resolution fluorescence...Show moreOver the last few decades, several methods have been explored and applied to circumvent the Abbe-Rayleigh diffraction limit, probably most importantly, stochastic super-resolution fluorescence microscopy methods. Another possibility, relying only on linear classical optics, is to exploit optical superoscillations, and is far less explored to date. In this project we explore the use of optical vortices for super-resolution far-field imaging. For this, we investigate strongly focused optical fields using a number of theoretical methods, we implement an experiment where a micro-pinhole is scanned through the focus, and, explore spin-orbit interactions of strongly focused optical fields. We find that our micron-sized pinhole is able to discern structures much smaller than its own size and leads to an enhancement of the spin-orbit interaction. Our method can be implemented as a simple and fast tool for characterizing the intensity distribution of a focused field with high resolution.Show less
We characterized an alternatively designed, low-cost “electron bombarding based” silicon L-shell radiation source, to be applied for metrology in the Extreme Ultra Violet Lithography process. The...Show moreWe characterized an alternatively designed, low-cost “electron bombarding based” silicon L-shell radiation source, to be applied for metrology in the Extreme Ultra Violet Lithography process. The design of the source enables adjustable focusing of the electrons on the target. A transmission grating spectrometer as well as a silicon drift detector were used to determine the radiation spectrum. In our electron-based source, we found that the maximum source power input was 80 W. Experiments with the grating spectrometer showed that for electrons with an energy of 5 kV, the source produced a power of 2 * 10^(-6) W/sr and the conversion efficiency amounts to 8 * 10^(-8)/sr for radiation around 13.5 nm. Regarding spectrum detection, the sensitivity of the silicon drift detector appeared too low to measure the silicon L peak. A decreased signal of silicon L-shell radiation was observed associated with the growing of carbon K peak.Show less
In this research, we aim to achieve sub-mK effective electron measurements to better analyze effects that occur at these very low temperatures. We do this by using a Faraday cage, through which we...Show moreIn this research, we aim to achieve sub-mK effective electron measurements to better analyze effects that occur at these very low temperatures. We do this by using a Faraday cage, through which we send a signal using sets of inductors. In order to test this, we define an effective frequency range for our signal by analyzing the theoretical electrical side effects that occur in our system. We perform multiple room temperature tests on our system within the defined frequency range, and work towards testing the effectiveness of our system at millikelvin temperatures as well.Show less
Phase-based conductivity mapping using MRI data contains an assumption of locally constant complex permittivity and use of a differential operator which result in significant inaccuracies at tissue...Show morePhase-based conductivity mapping using MRI data contains an assumption of locally constant complex permittivity and use of a differential operator which result in significant inaccuracies at tissue boundaries and amplification of noise in data. This work focuses on the implementation of an iterative model-based nonlinear optimization algorithm that aims to surpass these rising inaccuracies. The algorithm is designed to optimize conductivity maps using phase data acquired from MRI. In addition to optimization, the algorithm focuses on regularization which further improves the optimized outcome of the conductivity maps. Successful results are demonstrated using both simulated as well as phantom data. The comparison between results of a conventional phase-based conductivity mapping and the iterative algorithm shows improved accuracy for the latter. In addition, the model-based algorithm possesses potential for reduced acquisition time as it is capable of reconstructing accurate conductivity maps with relatively low SNR. In the future, experiments on in-vivo data can be performed. Additionally, to improve the accuracy of the conductivity maps even further, implementation of optimal methods to determine regularization parameters and regularization functions is possible.Show less
The nucleosome core particle is at the lowest level of DNA compaction, a mechanism that enables the DNA to fit inside the cell nucleus. Multiple nucleosomes, connected to each other like beads on a...Show moreThe nucleosome core particle is at the lowest level of DNA compaction, a mechanism that enables the DNA to fit inside the cell nucleus. Multiple nucleosomes, connected to each other like beads on a string, can stack tightly together to form the chromatin fiber. The compact form of this structure hinders external proteins and enzymes from accessing the nucleosomal DNA and using them in fundamental DNA processes. Nucleosome breathing is a process in which access is facilitated by the transient unwrapping of the nucleosome, thereby exposing the otherwise occluded DNA. This thesis investigates the nucleosome breathing mechanism in a dinucleosome system, a sub-structure of the chromatin fiber where two identical nucleosomes with varying DNA sequence are connected by a piece of linker DNA of varying length. The accessibility of the nucleosomal binding sites is modelled through a statistical model, expressing the breathing process in terms of the adsorption energy of the binding sites and the elasticity of the bent DNA in a dinucleosome configuration. The elastic energy of the bent linker DNA and nucleosomal DNA during the breathing process is estimated through a Monte-Carlo simulation. The results make clear that binding sites in such a dinucleosome structure are much more accessible than binding sites in a mononucleosome. Our findings show that the length of the linker DNA and the sequence of the nucleosomes are a determining factor of the dinucleosome configuration, thereby suggesting that these parameters play an important role in regulating the accessibility of higher order structures such as the chromatin fiber.Show less
Fabry-Perot cavities are generally used in cavity QED. Due to technical restraints it is prudent to evaluate the ability to create open micro cavities in the weakly coupled regime. We have focussed...Show moreFabry-Perot cavities are generally used in cavity QED. Due to technical restraints it is prudent to evaluate the ability to create open micro cavities in the weakly coupled regime. We have focussed on building the foundation for the weakly coupled cavity by charactarizing a macroscopic cavity in detail. We analyse the cavity effects, for the fundamental and higher order modes. Using the primary mode of a plane-curved mirror cavity we found the Free Spectral Range in multiple ways, and looking at transmission spectra as a function of wavelenght we found a spectrum of transmission peaks with a predictable mode ordering. Thus the cavity was found to be consistent with theory. The system has been improved upon by presenting an extensive model for modematching. The model is capable of determining the coupling efficiency after introducing a lens with any focal length and possible position. With the model we were able to find a setup configurations with near unity coupling efficiency to the fundamental mode of the cavity.Show less
The chiral-induced spin selectivity effect (the CISS effect) is the effect where the electron transmission yield through chiral molecules depends on the spin orientation of the electron. The CISS...Show moreThe chiral-induced spin selectivity effect (the CISS effect) is the effect where the electron transmission yield through chiral molecules depends on the spin orientation of the electron. The CISS effect has been demonstrated. However, to formulate a model describing the effect, quantitative testing is required. Therefore, we want to make samples where single chiral molecules are embedded in a host matrix, a self-assembling monolayer of insulating thiols. Consequently, we want to measure the tunneling current through these single chiral molecules by using STM with a ferromagnetic tip. With a coil around the ferromagnetic tip, we can change the magnetization and thus the spin polarization in situ. In the framework of the project, we aim to measure chiral-induced spin selectivity in single chiral molecules. In this thesis specifically methods of sample and STM tip fabrication are discussed. Our work proposes the first steps towards quantitative testing of chiral-induced spin selectivity.Show less
The Specific Absorption Rate (SAR) is a limiting factor to all MRI-scans. Especially at ultra-high magnetic fields (≥ 7 Tesla), it imposes a significant constraint in the design of pulse sequences....Show moreThe Specific Absorption Rate (SAR) is a limiting factor to all MRI-scans. Especially at ultra-high magnetic fields (≥ 7 Tesla), it imposes a significant constraint in the design of pulse sequences. Due to interpatient variability and the complicated structure of human anatomy, it is difficult to accurately determine the exact SAR-distribution for individual patients. Computational simulations using high-resolution human body models can be used to estimate the SAR, but such models are not available for individual patients in a clinical setting. Here, a method for developing a personalized model for estimating SAR in the head using parallel transmission at 7 Tesla is proposed based on clustered segmentation of tissues. We found that by segmenting all the tissues in the head into fat, cerebrospinal fluid (CSF), grey matter, and bone, the peak-SAR can be determined with an error of less than 2.8 % of the overall peak-SAR. This result is shown to be reproducible for subjects of different ages and genders. Methods for the automated segmentation of this mapping in individual patients based on T1w-images, quantitative T1-mapping, and ultra-short TE-scans are proposed and tested experimentally. Using the proposed method, it should be possible to operate scanners closer to the true SAR-limits due to improved estimations of the actual patient-specific SAR.Show less
In this thesis, we characterize and test a new MiM cavity for use in the Bouwmeester Optomechanics group. The cavity seems stable over time, though alignment offers some issues. The tip/tilt...Show moreIn this thesis, we characterize and test a new MiM cavity for use in the Bouwmeester Optomechanics group. The cavity seems stable over time, though alignment offers some issues. The tip/tilt alignment of the membrane was achieved to within 700 arcs eventually however. We also explore the use of finesse measurements to determine the absorbance of our membranes. We conclude that optical ring down measurements are preferable in our system and suspect that the PSG4 membranes have higher absorbance as compared to later generations. We present a scheme to determine the thermal gradient of our membrane in-situ, without any modifications required to the principle of the system. We do find, however, that the measurement is very sensitive to drift of the laser detuning. Finally, we explore the observed short term drift in our mechanical mode frequencies. We suspect the thermal expansion of some part of the system of adding additional strain to the membranes, and in doing so raising their mode frequencies, though the exact pathway remains unclear.Show less
DNA, the carrier of genetic information is compacted into nucleosomes, which regulate access to that DNA. These nucleosomes are themselves folded into a higher order structure called chromatin....Show moreDNA, the carrier of genetic information is compacted into nucleosomes, which regulate access to that DNA. These nucleosomes are themselves folded into a higher order structure called chromatin. Little is known of the effect of this chromatin structure on the conformational dynamics of nucleosomes. Here we introduce a single-pair F¨orster Resonance Energy Transfer (spFRET) method that allows for quantitative measurement of nucleosome structure in folded fibers through both Fluorescence Correlation Spectroscopy (FCS) and burst analysis. Preliminary experiments determined optimal measurement concentrations and methods of excitation. However, measurements on reconstituted chromatin fibers showed poor signal-to-noise. We propose several improvements to enable the study of chromatin dynamics, such as nucleosome breathing. We expect the work outlined in this thesis to contribute to greater understanding of both nucleosome and chromatin structure, and how these regulate the accessibility of DNA to other molecules and proteins.Show less
Two-dimensional crystals on curved surfaces have been in the research spotlight for a long time. In the soft matter area, extensive work has been done towards addressing fundamental questions on...Show moreTwo-dimensional crystals on curved surfaces have been in the research spotlight for a long time. In the soft matter area, extensive work has been done towards addressing fundamental questions on stress screening via topological defects. However, experimental colloidal crystallization on non-zero Gaussian curvature surfaces has only been reported using interfaces. Despite the success of those systems, a self-limitation arises when creating different-shaped surfaces. As a result, all previous reported experiments have used manifolds homeomorphic to a sphere. In this thesis, we provide an experimental set-up for 2D colloidal crystallization on arbitrary 3D surfaces. In particular we obtained toroidal crystals with different aspect ratios, by using depletion interaction and 3D micro-printed structures. We first investigate the suitable parameters for 2D crystallization on 3D surfaces. Experiments with two different depletants: pNIPAM nanoparticles and polyethylene glycol(PEO) on a flat surface are conducted. While pNIPAM particles yield unexpected results, the PEO system results in a hexagonal crystal as expected. We extend the experiment to 3D printed tori as surfaces, resulting in toroidal crystals. We qualitatively analyse different aspect ratio tori and compare a "flat" torus with typical one. The obtained crystals exhibit vacancies, disclinations, and scars on the top part of the structure to alleviate the stress induced by the curvature. Although results are only analyzed qualitatively in this thesis, our toroidal crystals provide a proof of principle for the proposed experimental set-up.Show less
This work presents a study of two types of spin-triplet Josephson junctions that are characterised by superconducting quantum interference and Shapiro step measurements. The first type of system is...Show moreThis work presents a study of two types of spin-triplet Josephson junctions that are characterised by superconducting quantum interference and Shapiro step measurements. The first type of system is a cobalt/niobium disk where long-range triplets are generated by the spin texture of a ferromagnetic vortex. The second system is a mesoscopic ring of Sr2RuO4, which is expected to host intrinsic Josephson junctions by the presence of chiral domain walls. For the cobalt/niobium disk, two supercurrent channels have been found surprisingly close to the edges of the disk by quantum interferometry measurements while indications of 0-pi segments have been found by the observation of half-integer Shapiro steps. Two rings with different inner and outer radii of Sr2RuO4 are shown to behave as Josephson junctions. The configurations of these junctions depend on the ring dimensions and the temperature. These findings make a convincing case for the presence of chiral domains in Sr2RuO4.Show less
An important goal in soft matter physics is to steer microscale self-assembly processes. Here we show linear structures made of colloids and the energy landscape that describes the angular mobility...Show moreAn important goal in soft matter physics is to steer microscale self-assembly processes. Here we show linear structures made of colloids and the energy landscape that describes the angular mobility. It was done by functionalizing isotropic and anisotropic colloids with a lipid bilayer and insert DNA linkers that have a specific binding group. The DNA linkers are fully mobile along the particle surface and colloids functionalized with DNA linkers are able to form flexible polymers. Specifically, we looked at polymers consisting of four monomers: tetramers and found very mobile clusters that had an averaged joint mobility of 154 +- 3 deg2/s. In the energy landscape that we experimentally and theoretically found, we can conclude the preferred angles are 180/180 degrees. For polymers made of two dumbbell particles we found a mobile bilayer, but no mobile clusters were found. Our tunable tetramers could be the design for a model of controlled self-assembly in even larger structures and define the cluster properties.Show less
In this thesis, we investigate the mechanical interplay between a cell’s shape and its actin cytoskeleton organisation. We combine theoretical work with numerical simulations and experimental data...Show moreIn this thesis, we investigate the mechanical interplay between a cell’s shape and its actin cytoskeleton organisation. We combine theoretical work with numerical simulations and experimental data to investigate this behaviour. The actin cytoskeleton is modelled using a liquid crystal framework and is combined with a model for the cell contour that has stress fibers apply a directed stress on the edge. We describe a feedback mechanism where the orientation of stress fibers is a competition between alignment with the cell edge and with one another, and where the shape of the cell edge is dependent on the contractile force exerted along the direction of the nearby stress fibers. We show that we can accurately reproduce the shape and anisotropic actin cytoskeleton structure of cells on micropillar arrays, as well as the emergence of topological defects.Show less
Electrical properties tomography (ETP) enables find the electrical properties of tissues in a non-invasive method by using the magnetic fields of an MRI scanner. EPT can be used in clinic to assess...Show moreElectrical properties tomography (ETP) enables find the electrical properties of tissues in a non-invasive method by using the magnetic fields of an MRI scanner. EPT can be used in clinic to assess lesions in the breast. Still, there is a lot of variance between inter-subject conductivity values. In this project, we studied the effect of SNR, which we varied by receiving the signal with different coils. The effect of the pulse sequence was investigated by scanning a phantom and a healthy volunteer with a 3D turbo spin echo (TSE), a 3D balanced steady state free precession (bSSFP) and additionally the healthy volunteer was scanned with a 2D TSE. Lastly, we studied the effect of noise-smoothing operations by pre-processing the data with a Gaussian filter with a standard deviation of 2 pixels and post-processing with a 5x5 pixel median filter. We found that the noise does not affect the mean value of the conductivity. Also, the noise can be smoothed with the operations described above. Artifacts caused by acquisition does influence the values that we obtained. From the sequences that were used, we found that the 2D TSE resulted in the best conductivity map. In the future, we hope to differentiate benign from malignant tumors in breast data by applying this sequence in the clinic, such that histology of the tumoral tissue can be abolished.Show less
The problem of the cosmological constant together with the tension in the observations of the present value of the Hubble parameter has brought about the search of alternative theories to the...Show moreThe problem of the cosmological constant together with the tension in the observations of the present value of the Hubble parameter has brought about the search of alternative theories to the Standard Model of Cosmology. One of the most promising ones is Modified Gravity. In this thesis, we explore scalar-tensor theories that are invariant under weakly broken galileon (WBG) transformations. We have derived the background cosmology and found attractor solutions that track a De Sitter Universe at late times, solving the coincidence problem and preventing from fine tuning issues. We have implemented the model into EFTCAMB, an Einstein- Boltzmann solver that employs the effective field theory of dark energy, and computed the power spectrum of temperature-temperature CMB anisotropies and the matter power spectrum. Our results, based on the theoretical predictions, are promising. While being compatible with LCDM at small scales, WBG can lower the ISW tail of the TT models on the CMB power spectrum, making it potentially favoured by observations.Show less
This thesis project studies a membrane-in-the-middle setup for optomechanics experiments with the goal of improving its stability. A strong focus is laid on the redesign of the cavity as well as a...Show moreThis thesis project studies a membrane-in-the-middle setup for optomechanics experiments with the goal of improving its stability. A strong focus is laid on the redesign of the cavity as well as a mechanically robust sample positioning system, as this was the limiting factor in the existing setup. Finite element analysis is used to assure the mechanical stability of the new design. Furthermore, the challenges of the Pound-Drever-Hall locking technique are better understood by characterizing the cavity locking on both the old and new setup in comparison. Besides separately investigating the electronic components involved and the impact of electronic filtering, gain-phase-measurements reveal information about their behavior in a closed feedback loop. The stability of the lock is closely linked to the mechanical stability of the setup. Especially vibrations coupling into the optical system via the chip holder with the membrane can be strong enough to cause instability of the feedback loop. Therefore a clever design is needed where their impact can be minimized.Show less
Building on the discovery that a Weyl superconductor in a magnetic field supports chiral Landau level motion along the vortex lines, we investigate its transport properties out of equilibrium. We...Show moreBuilding on the discovery that a Weyl superconductor in a magnetic field supports chiral Landau level motion along the vortex lines, we investigate its transport properties out of equilibrium. We show that the vortex lattice carries an electric current between two normal metal contacts at a voltage difference. This current is proportional to the square of the renormalized charge of Weyl fermions in the superconducting Landau level. Because the charge renormalization is energy dependent, a nonzero thermoelectric coefficient appears even in the absence of energy-dependent scattering processes.Show less
Multiple external tuning parameters affecting the different Charge Density Wave (CDW) phase transitions in few-layer 1T-TaS2 have been reported in literature. The formation of CDWs still lacks a...Show moreMultiple external tuning parameters affecting the different Charge Density Wave (CDW) phase transitions in few-layer 1T-TaS2 have been reported in literature. The formation of CDWs still lacks a predictive theory, so understanding may be gained from experiments on the effects favoring or suppressing CDW transitions. In this project we performed electronic transport measurements on ~ 100nm thin 1T-TaS2 at 1.55K to 290K. Flakes of 1T-TaS2 were exfoliated and stamped on top of Au contacts to form a Hall bar. The Charge Density Wave transition is observed between T = 100K and 160K with a relaxation time in the range of hours. Consequently, the transition can be suppressed by fast cooling and we find a range of metastable states, that are supposedly coexisting spatially separated domains of NC- and C-CDW. Under application of a magnetic field, the change of sign of the Hall voltage at the transition is confirmed. Both CDW phases show positive magnetoresistance along the channel with similar shape, whilst the effect is more pronounced in the C-CDW phase. The magnetoresistance effect is attributed to Weak Anti Localization, which would also explain a decrease in resistivity seen in the supercooled NC-CDW phase at low temperature. The slow transition and the magnitude of resistivity increase, that is about two times lower than reported in literature, may be caused by defects in the crystal hindering long-range CDW order.Show less
Quasi-periodic Hamiltonians have a fractal density of states with a hierarchical structure of bands. One pathway to controllably creating quasi-periodic Hamiltonian is stacking layers of graphene...Show moreQuasi-periodic Hamiltonians have a fractal density of states with a hierarchical structure of bands. One pathway to controllably creating quasi-periodic Hamiltonian is stacking layers of graphene twisted with incommensurate angles. Nevertheless, due to the weakness of the inter-layer coupling, the fractality in these type of systems remains to be observed. We investigate the fractality of graphene quasicrystals numerically. To achieve this, we develop an algorithm to compute the fractal dimension of the density of states. Using this approach, we demonstrate that increasing the value of inter-layer coupling of dodecagonal graphene does generate fractal density of states. Finally, we propose a four-layer system that utilizes the flat band appearing in the twisted bilayer graphene at the magic twist angles TBLG together with the dodecagonal stacking as a pathway towards observing fractal density of states.Show less
