Experimental diffusion-weighted MRI measurements of a fiber phantom were compared to signals generated using a Monte-Carlo diffusion simulation. The diffusion simulation was combined with a...Show moreExperimental diffusion-weighted MRI measurements of a fiber phantom were compared to signals generated using a Monte-Carlo diffusion simulation. The diffusion simulation was combined with a generally applicable MRI simulation. We performed simulations for square packed and random packed cylinders that model the fibers. Good agreement was found between the simulated signal and the measured signal for a specific random packing type (the relative error was 0.09+-0.06). Follow-up simulations that use larger system sizes are needed to improve the accuracy. The simulation method presented here can be used to study changes in microstructural properties and to compare the efficiency of different MRI protocols in detecting these changes.Show less
TNO is developing a carbon-contamination-insensitive EUV power sensor that uses the photo-electric effect to distinguish in- from out-of-band EUV photons. The central question of this MSc research...Show moreTNO is developing a carbon-contamination-insensitive EUV power sensor that uses the photo-electric effect to distinguish in- from out-of-band EUV photons. The central question of this MSc research project was to verify if the EUV power sensor signal can be purified by suppressing the out-of-bound secondary electron signal using an electrostatic barrier, and, if so, which potential difference suffices. To this end, we designed a Secondary Electron Energy Distribution (SEED) analyzer to characterize the e-beam-induced secondary electron emission of gold and carbon targets. It was shown that the SEED analyzer allows filtering of electrons on their kinetic energy and could perform SE yield measurements as well as SE energy distribution measurements. However, systematic errors occurred in the form of secondary electron emission of the grid inside the SEED analyzer, leakage current flow, a loss of emitted electrons through the SEED analyzer’s opening and deflection of electrons due to lack of a field-free region. The SE yield measurement results were in good agreement with literature, after estimating the effect of the systematic errors. The SE energy distribution of both target materials were obtained and show similarities to experimental data reported in literature. However, the absence of a field-free region during the measurements causes a small mismatch between our acquired SE energy distribution and the reference data.Show less
This thesis investigates acoustic phenomena associated with the presence of a synthetic gauge field in a mechanical metamaterial. Such fields minimally couple to the momentum of phonons in a low...Show moreThis thesis investigates acoustic phenomena associated with the presence of a synthetic gauge field in a mechanical metamaterial. Such fields minimally couple to the momentum of phonons in a low energy limit, which leads to acoustic analogs of some of the effects of a gauge field in an electronic system, such as Landau quantization. We develop two strategies for realizing a pseudo-magnetic field in a metamaterial based on the honeycomb lattice. In the first strategy, we consider deformations of the lattice that result from applied boundary stress. In the second strategy, we use nonuniform patterning of the local material stiffness. We then explore physical phenomena associated with a constant pseudo-magnetic field. We provide evidence for the existence of a mechanical Landau-level spectrum in this metamaterial. We then focus on the zeroth Landau level and show that the corresponding modes are localized in the bulk of the system and exist mostly on one sublattice. Following recent insights into similar physical systems, we investigate topologically robust sound modes along domain walls in the bulk of the metamaterial. Further, by introducing dissipation, we test selective enhancement of the domain-wall-bound topological sound mode, a feature that could potentially be exploited for the design of acoustic couplers, rectifiers, and sound amplification by stimulated emission of radiation (SASERs) -- mechanical devices analogs to lasers.Show less
The nucleosome consists of a short stretch of DNA wrapped around a protein cylinder, and is the fundamental unit of chromatin, which compacts the DNA into the cell nucleus. The nucleosome is known...Show moreThe nucleosome consists of a short stretch of DNA wrapped around a protein cylinder, and is the fundamental unit of chromatin, which compacts the DNA into the cell nucleus. The nucleosome is known to transiently partially unwrap or 'breathe' \textit{in vitro}, exposing DNA which would otherwise be sterically inaccessible to enzymes. Breathing is investigated for its potential importance \textit{in vivo} in both essential DNA processes, and in higher-order chromatin organisation. In this thesis we present a two-parameter physical statistical model of the breathing process based on steric enzyme accessibility, the energetics of the bent DNA molecule, and the adsorption of the DNA upon the proteins. We estimate the elastic energy using Monte Carlo simulations of a coarse-grained model of the nucleosomal DNA, and we fit the model to the available experimental results. We find in agreement with experimental studies that site accessibility decays exponentially toward the centre sites, and that highly asymmetric breathing behaviour is possible due to the very sensitive dependence of breathing upon energy distribution, and in turn, sequence.Show less
In this thesis, we probe the bending stiffness of origami metamaterials, to investigate under which conditions origami can be described as continuum media. The Miura Ori pattern was bent using two...Show moreIn this thesis, we probe the bending stiffness of origami metamaterials, to investigate under which conditions origami can be described as continuum media. The Miura Ori pattern was bent using two mechanical tests: three point bending test and cantilever bending. Our origami metamaterials at rest can be characterised by the opening angle between adjacent plates, which specifies how much the structure is folded. We varied two things, the width and the opening angle. The bending stiffness of the Miura Ori sheet at different widths showed significant deviations from continuum classical elastic theory. These deviations differed in behaviour and this was dependant on the opening angle of the sheet. When the Miura Ori sheets were almost flat folded, an continuum mechanical behaviour was seen when the width was small. The deviations were seen when the width increased. When the sheets were opened, possible finite size effects were determined that corresponded to Cosserat elasticity. Tests showed that the bending stiffness increased with the opening angle. This contradicts previously made theoretical predictions.Show less
The aim of this study was to computationally resolve nucleosome dynamics and chromatin structure. To achieve this we ran Monte Carlo simulations of a base pair level model of a mononucleosome....Show moreThe aim of this study was to computationally resolve nucleosome dynamics and chromatin structure. To achieve this we ran Monte Carlo simulations of a base pair level model of a mononucleosome. Additionally, we developed a graphical user interface for generating a chromatin structure with realistic linker DNA, which enabled us to calculate linking number and writhe for different chromatin structures. The force extension curve of our simulated mononucleosome shows similar behaviour to force spectroscopy experiments.Show less
An indispensable ingredient for nanoscale imaging within the field of Magnetic Resonance Force Microscopy (MRFM) is a radiofrequency (RF) source. Conventional RF-sources constitute a significant...Show moreAn indispensable ingredient for nanoscale imaging within the field of Magnetic Resonance Force Microscopy (MRFM) is a radiofrequency (RF) source. Conventional RF-sources constitute a significant impediment for MRFM experiments at extreme low temperatures and consequently form a major obstacle towards the single-spin measurement. In this thesis we have introduced a non-trivial method where an intrinsic property of an MRFM force sensor is exploited for the generation of an ultra-low dissipative RF-field. Using MRFM as a probe for local nuclear magnetic resonance (NMR) experiments on copper nuclei at millikelvin temperatures, we have demonstrated that the correct implementation of this feature resulted in an amplification of the NMR signal by more than a factor 2. Based on these findings, we propose an adjusted design of the force sensor that could contribute towards a significantly improved imaging sensitivity as established in MRFM experiments to date.Show less
We have investigated the technical feasibility of a novel concept within the scientific field of magnetic resonance force microscopy (MRFM), in which a cantilever is used as a force sensor on the...Show moreWe have investigated the technical feasibility of a novel concept within the scientific field of magnetic resonance force microscopy (MRFM), in which a cantilever is used as a force sensor on the one hand and a radio frequency (rf) source on the other. By driving a magnet-tipped cantilever at a higher resonance mode, the rotational motion of the magnetic tip generates an oscillating magnetic field. In this way the cantilever can serve as an ultra-low dissipative rf source with an rf frequency corresponding to the specific higher mechanical resonance mode of the cantilever. In this work we have tested this idea for an attonewton-sensitivity silicon cantilever with a high magnetic gradient cobalt nanomagnet attached at the cantilever's free end. Using frequency-shift cantilever magnetometry, we found that the nanomagnet's remanent magnetisation is 0.83 tesla. When the nanomagnet is close enough to a spin-containing sample, we have calculated that the nanomagnet's magnetisation - even at zero applied magnetic field - can mechanically generate an rf field of the order millitesla. This implies that the protocol for adiabatic rapid passage can be conducted without the use of an rf wire as a radio frequency source, which eliminates a major dissipation channel that constitutes an obstacle to date for lower working temperatures in high resolution 3D-imaging experiments with MRFM.Show less
Metamaterials exhibit exotic properties derived from their geometric structures. A procedure has recently been developed to build reconfigurable structures from convex polyhedra. While initally...Show moreMetamaterials exhibit exotic properties derived from their geometric structures. A procedure has recently been developed to build reconfigurable structures from convex polyhedra. While initally characterized as rigid, we found that some of these structures possess multiple stable configurations. In the present study we develop numerical tools to simulate all possible deformations that can be applied to these structures, mapping the corresponding energy landscape. We use the simulation to identify the additional stable configurations and study their dependence on key physical parameters. Based on the results found, we explain the mechanism behind the observed multistability and suggest its validity as fundamental ingredient for a general designing rule. Finally, we explore the possibility of implementing our results into the development of a reconfigurable, multistable and multifunctional 3D material.Show less
In a quantum network, interconnected nodes use shared entangled states as a resource for communication. The nitrogen-vacancy (NV) centre in diamond is a promising candidate for the realization of a...Show moreIn a quantum network, interconnected nodes use shared entangled states as a resource for communication. The nitrogen-vacancy (NV) centre in diamond is a promising candidate for the realization of a such a node. It provides a solid state qubit that can be initialized and read out optically and manipulated via microwave pulses. However, for any practical implementation, control mechanisms that maintain the resonance of the excitation and emission frequencies need to be in place. Additionally, to guarantee phase stability as required for long distance entanglement, it is necessary to realize a frequency stabilized excitation laser. We demonstrate an autonomous routine for the optimization of excitation and emission frequencies, that recovers resonance conditions automatically when sudden jumps in the emission frequencies occur. Furthermore, an optical setup for the stabilization of excitation frequencies in a Pound-Drever-Hall scheme is presented. An upper bound on the excitation linewidth of 1.7 kHz is measured, yielding a phase deviation lower than 5 over a distance of 1 km. These developments will be essential in the development of a stand-alone quantum node involving the NV centre, on the road to a global quantum internet.Show less
In order to filter out unwanted noise or known factors from correlation matrices, we use maximum entropy models to generate spectra of correlation matrices, which we utilise for this purpose....Show moreIn order to filter out unwanted noise or known factors from correlation matrices, we use maximum entropy models to generate spectra of correlation matrices, which we utilise for this purpose. Furthermore, we relate them to widely used one-factor models justifying their use and presenting ways to relate the postulated one-factor models to empirical data. We improve further by adding signatures of sign projections of rectangular matrices and present a method to compare them to their corresponding weighted signatures. Finally, we make a small step towards a new definition of covariances that would filter out new types of noise.Show less
The gross domestic product is no longer as widely accepted as an indicator of economical performance as it once was, so the search for a replacement or additional indicators has begun. It was shown...Show moreThe gross domestic product is no longer as widely accepted as an indicator of economical performance as it once was, so the search for a replacement or additional indicators has begun. It was shown by Hidalgo and Hausmann, and in later research by Pietronero and others, that the network of international trade carries intrinsical information about economical competitiveness. This idea is based on the observation that strong economies have diverse production capabilities. We have been able to reproduce their results. However, we found that in deciding what trade links are relevant for the analysis, the filter of choice (the revealed comparative advantage) is flawed, as it lacks any statistical justification. We have devised a way to choose only the relevant trade links, justified by Fermi-Dirac statistics through the application of the concept of entropy on the network. With this technique, we show that although the basic idea is still valid, the results by previous authors have to be revised. More importantly, with this new statistical information, we are able to provide countries with an advice on investment strategies for particular industries.Show less
In this work, we investigate methods to determine the average length for cotunneling in self-assembled gold nanoparticle arrays spaced with alkanethiols. Cotunneling currents can be as low as 10 fA...Show moreIn this work, we investigate methods to determine the average length for cotunneling in self-assembled gold nanoparticle arrays spaced with alkanethiols. Cotunneling currents can be as low as 10 fA, requiring the development of robust measurement techniques to lower the noise floor. We present a comparison of different methods for finding the effective cotunneling length N. Preliminary findings on a variety of arrays indicate the onset of the cotunneling regime, but that there is no distinction in N between choice of alkanethiol in the array.Show less
Domain wall manipulation in ferromagnets shows great promise for the development of fast and efficient computer memory devices. In particular, chromium dioxide has a half-metal characteristic that...Show moreDomain wall manipulation in ferromagnets shows great promise for the development of fast and efficient computer memory devices. In particular, chromium dioxide has a half-metal characteristic that holds the potential for reducing the heat produced from reading or writing memory bits. To reliably control the motion of domain walls, CrO2 nanowires are created with geometric anisotropy that acts as a potential well to ”pin” domain walls to fixed sites. Each wire was grown using selective-area growth to avoid the creation of random pinning sites from crystal disorder. This process is sensitive to many different factors in the creation of the SiO2 mask. Different effects can interfere with each other, including the proximity effect from electron beam lithography and a sensitivity to the levels of oxygen in the doped SiO2. This thesis presents methods of correction for individual effects, as well as initial results of domain wall mechanics in CrO2 nanowires. Using MFM measurements, I show the static pinning of a domain wall at the predicted pinning location. Magnetoresistance measurements of CrO2 wires ranging from 700 nm to 900 nm wide show that, at this scale, the dominant influence on the domain wall mechanics remains the magnetocrystalline anisotropy, instead of shape anisotropy as desired.Show less
METIS, one of the E-ELT's first instruments, will not offer classical chopping and nodding. If this is not solved then the residual background on reduced observations will be of the same order or...Show moreMETIS, one of the E-ELT's first instruments, will not offer classical chopping and nodding. If this is not solved then the residual background on reduced observations will be of the same order or larger than potential science targets. For this reason an investigation has been started to understand and quantify the nature and source of the residuals in order to infer whether or not it is possible to reduce the background and reach the shot noise limit. To answer this question we have developed a specialized observing plan that allows us to look at the relation between the background residuals and various variables like the chop throw, chop frequency, chop direction, telescope altitude, filter and rotation angle. This plan has been executed on both the VLT and the GTC using the VISIR and CANARICAM IR instruments respectively. From the analysis of this data we have discovered that contrary to what is believed in the literature the high order residuals are likely to be caused by the telescope and that they are stable over time but not over rotation angle, while the gradient is caused by the atmosphere and is not constant over time. Using this theory we have found a new way of reducing the background without nodding that, for chopping throws below 10"", gives nearly identical results when compared to classical chopping and nodding. We believe that with this method we have found a solution for the challenge stated above but conclude that more rigorous follow-up observations are needed.Show less
At the end of 2015 two collaborations ATLAS and CMS reported the diphoton excess at the invariant mass 750 GeV. In this work we consider the extension of the Standard Model where this peak can be...Show moreAt the end of 2015 two collaborations ATLAS and CMS reported the diphoton excess at the invariant mass 750 GeV. In this work we consider the extension of the Standard Model where this peak can be explained. This model involves a heavy scalar particle and a light scalar particle (axion) that come from the Peccei-Quinn symmetry breaking. Using different experimental data we find the allowed parameter space of the model. We study the possibility to search for the light axion of this model at the intensity frontier experiments and show that, unfortunately, SHiP and NA62 experiments will not be sensitive to the model. At the end we show that this model of 750 GeV excess can be falsified at √(s) = 13 TeV LHC run. We make quantitative predictions for new decay channels involving gauge bosons and one photon plus missing energy.Show less
