Parafermionic zero-modes are zero-energy excitations with peculiar mutual statistics, which can be realized at the edge of the Fractional Quantum Hall Effect sample. We came up with several...Show moreParafermionic zero-modes are zero-energy excitations with peculiar mutual statistics, which can be realized at the edge of the Fractional Quantum Hall Effect sample. We came up with several protocols for adiabatic quantum pumping with parafermions, which allow to test the statistics of Fractional Quantum Hall quasiparticles and observe universal noise in the pumping current. That is, the noise takes a specific value which is essentially given by universal constants, and is robust with respect to changes in many system parameters.Show less
Gold nanorods (GNRs) have unique optical properties. GNRs can be excited in the near-infrared range and their photoluminescence is bright and stable. Because of this, GNRs have a large range of...Show moreGold nanorods (GNRs) have unique optical properties. GNRs can be excited in the near-infrared range and their photoluminescence is bright and stable. Because of this, GNRs have a large range of possible applications, including use as labels or as biosensors. For these kinds of applications, it is important to be able to determine a GNR’s properties with high accuracy. Here we characterize single gold nanorods by five properties: their 3D position, plasmon resonance and orientation. The position of GNRs is determined with a sub-nanometer error in x, y and a 3 nm error in z. The surface plasmon resonance wavelength and the orientation of GNRs are determined with errors of <0.1 nm and 0.1 deg respectively. This is achieved by applying a four-dimensional fit to a stack of two-photon photoluminescence images. The methods presented in this thesis can be used to improve accuracy in the aforementioned applications of GNRs.Show less
Next to its well–known helix structure, double stranded DNA can form alternative structures that might have biological importance. For example, in guanine–rich DNA sites of the c–MYC promotor a...Show moreNext to its well–known helix structure, double stranded DNA can form alternative structures that might have biological importance. For example, in guanine–rich DNA sites of the c–MYC promotor a second order structure called a G–Quadruplex has been found. In the G–Quadruplex, one strand of the DNA forms a stack of 4 interacting guanines. In this thesis we study the formation of G–Quadruplexes in double–stranded DNA using a combination of F¨oster Resonance Energy Transfer (FRET) and multiplex Magnetic Tweezers (MT). Moreover, a two–state model was developed which describes the probability to form a G–Quadruplex in double–stranded DNA. Using this model we calculated how the extension and the FRET efficiency depends on force, twist and the sequence of the DNA. Because the synthesis of double–stranded DNA containing a G–Quadruplex site proved challenging, the experimental data could not be compared to the outcomes of the two–state model. Based on simulations we conclude that adding a 3–bp mismatch to the DNA tether next to the G4 site is required for the formation of a G–Quadruplex in dsDNA. Our findings may be relevant for understanding a link with transcription and/or replication.Show less
We will discuss non-local solutions to some of the problems of the standard model of cosmology, L cold dark matter (LCDM), focusing on two models of gravity and their applications to cosmology. The...Show moreWe will discuss non-local solutions to some of the problems of the standard model of cosmology, L cold dark matter (LCDM), focusing on two models of gravity and their applications to cosmology. The first comes from modifying the Einstien-Hilbert action by including an m2R 1 2 R term and the second by including an m2 1 R term. Both models posses self-accelerating solutions. I will demonstrate that their background cosmology is consistent with data, and testable primarily through the equation of state of our universe’s effective stress-energy tensor. At the perturbative level, these models have more galaxy clustering and weak lensing, so they are be highly testable using up coming cosmological surveys. My contribution to this work is the perturbation theory of the m2 1 R model and the recovery of these results for the m2R 1 2 R model.Show less
A hinge specifically designed for continuous friction measurements during ice skating was tested and used. The hinge can handle large vertical normal forces to simulate the weight of a real person...Show moreA hinge specifically designed for continuous friction measurements during ice skating was tested and used. The hinge can handle large vertical normal forces to simulate the weight of a real person on a skate, and is very flexible in the horizontal direction, so it deforms under a friction force. Two sensors on the hinge measure the deformation. Friction measurements were done with a part of a real skate, with varying temperatures, skating speeds and normal forces on the skate. A clear dependence of friction on temperature was found. Friction coefficients for an ice temperature of -20 C and air temperature of -10 C varied between 0.04 and 0.1, and coefficients for an ice temperature of -10 C and air temperature of -6 C varied from 0.006 to 0.016. The temperature of the skate was held at -10 C for both cases. The results also suggest friction dependence on skating speed and normal force, but this has to be verified. During the calibration of the setup it was found that the vertical force, controlled by air pressure, could be determined up to a factor of 2. Furthermore there was a large variation (up to a factor 2) in friction coefficients from measurements under the same circumstances, on the same ice layer. These could have been caused by changing humidity in the setup, as this was not monitored during the measurements. The setup works, but needs to be improved for more precise friction measurements. A humidity sensor in the setup is recommended.Show less
In this thesis we are going to study the mechanical properties of a chromatin fiber. Chromatin is the second compaction stage of DNA, after the wrapping of DNA around histones proteins to form...Show moreIn this thesis we are going to study the mechanical properties of a chromatin fiber. Chromatin is the second compaction stage of DNA, after the wrapping of DNA around histones proteins to form nucleosomes. Specifically we are going to analyze how its behaviour under external stresses is going to change with the variation of the linker DNA length, the DNA segment that links two adjacent nucleosomes. We will be able to do it at a single-molecule level thanks to the use of magnetic tweezers, an apparatus that can exert forces and torques directly to individual molecules.Show less
This work examines the network structure of illicit marketplaces that operate on the darknet. These on-line marketplaces are crawled to obtain data of inter-user communications and this data is...Show moreThis work examines the network structure of illicit marketplaces that operate on the darknet. These on-line marketplaces are crawled to obtain data of inter-user communications and this data is parsed in a network structure and its physical properties are analysed. The Configuration Model is used as a null model to investigate the patterns in these networks to reveal information about their topology. This information is applied to interpret the behaviour of users within these illegal marketplaces.Show less
The structure of chromatin fibers has been researched in different salt conditions with Magnetic tweezers. The drag force on the tether as a result of flowing in a new buffer into the flow cell...Show moreThe structure of chromatin fibers has been researched in different salt conditions with Magnetic tweezers. The drag force on the tether as a result of flowing in a new buffer into the flow cell resulted in structural changes of the chromatin and disassembly of the histone octamer. In a new flow cell design, the drag force was eliminated by changing the buffer conditions by diffusion through a permeable membrane made from PEG-DA 400. Furthermore, double stranded DNA was unzipped using Magnetic tweezers and the position of the melting force was correlated with the G-C content calculated from the sequence.Show less
It has been a long term goal of physicists to control macroscopic quantum superposition states - cat states - since these connect to a number of open fundamental questions in physics: the...Show moreIt has been a long term goal of physicists to control macroscopic quantum superposition states - cat states - since these connect to a number of open fundamental questions in physics: the transition from the quantum to the classical world, the quantum measurement problem, and the area between quantum physics and theory of general relativity. Optomechanics has been identified as a method for generating cat states, however, this is yet to be achieved. The scientific community has developed increasingly improved optomechanical systems. About a decade ago, a promising optomechanical system has been demonstrated that consists of a high-stress silicon nitride membrane in the middle of a Fabry-Pérot cavity. This project concerns the development of a membrane-in-the-middle device for our lab. Our main focus lies on developing an understanding about the connection between system design and optomechanical performance. In addition, we demonstrate optomechanics for our device, and show that the initial optomechanical parameters are good. The availability of clearly defined methods for improving upon the current system parameters implies that we are moving in the right direction towards quantum optomechanical experiments.Show less
High-fidelity single photon sources are required for quantum information technologies and fundamental research. Recently near-unity single photon purity and near-unity indistinguishability have...Show moreHigh-fidelity single photon sources are required for quantum information technologies and fundamental research. Recently near-unity single photon purity and near-unity indistinguishability have been shown in resonantly pumped quantum dots embedded in an optical cavity. In this thesis we provide a theoretical framework and experimental results on polarization non-degenerate self-assembled InAs/GaAs quantum dots inside a polarization non-degenerate cavity, and show that by filtering the polarization the brightness of the single photon source can be enhanced. We furthermore describe the resulting output light analytically as a mixture of single photons and coherent light and derive a simple expression for the purity of the single photon source. Lastly we present pulsed measurements of this quantum dot-cavity system, and show that the purity of the single photon source is 98%.Show less
Describing the motion of natural fragments in human tissue is crucial for lethality and vulnerability studies. The motion of small compact fragments is simulated by small cubes, cylinders and FSPs....Show moreDescribing the motion of natural fragments in human tissue is crucial for lethality and vulnerability studies. The motion of small compact fragments is simulated by small cubes, cylinders and FSPs. Two models that describe the penetration of these small compact fragment are ICARUS and WTI. However, bigger elongated fragments are also released during explosions. Describing the motion of elongated natural fragments is done by implementing the angle dependency in the presented area. This angle is found by solving the conservation of momentum. The developed model “Velocity Retardation of Elongated Cylinders” (VREC) solves the conservation of momentum and uses the angle to calculate the velocity retardation. The model is validated by comparing the expected velocity retardation with experimental data obtained from shooting tumbling cylinders at gelatin. The velocity retardation from the experimental data was similar to the velocity retardation calculated by VREC, while the velocity retardation calculated by ICARUS did not accurately describe the velocity retardation of the elongated cylinders at low or high impact angles. ICARUS did describe the penetration of cylinders with impact angles between 30o and 60o accurately. For small compact fragments, both models, VREC and ICARUS, describe the penetration accurately.Show less
B0 magnetic field non-uniformity is the cause of a large amount of image artifacts in MRI. B0 inhomogeneities arise due to magnetic susceptibility differences between tissues. In particular, the 9...Show moreB0 magnetic field non-uniformity is the cause of a large amount of image artifacts in MRI. B0 inhomogeneities arise due to magnetic susceptibility differences between tissues. In particular, the 9 ppm magnetic susceptibility difference between air and tissue generate disturbances in the B0 main field near the skin. We study the B0 passive shimming approach of covering the skin with a susceptibility-matching material from both an experimental and a mathematical viewpoint. In the experimental study, a lightweight and simple to shape pyrolytic graphite composite foam is used to compensate for the field inhomogeneities in the region of the neck. We experimentally demonstrate that the pyrolytic graphite foam improves the uniformity of the static field in a phantom and in vivo at 3T. In the numerical study, we aim for a design of a neck shim which efficiently homogenizes the B0 field while being practically implementable. We propose a level set optimization method as an approach to find the optimum design for a neck shim. Simulations prove that the proposed method is able to solve the topological optimization problem while preserving the imposed constraints.Show less
We describe a complete strategy to numerically compute the collapse of a massless U(1) charged scalar field into a black brane final state in 4+1-dimensional anti-de Sitter space. We implement this...Show moreWe describe a complete strategy to numerically compute the collapse of a massless U(1) charged scalar field into a black brane final state in 4+1-dimensional anti-de Sitter space. We implement this strategy to investigate the formation of scalar hair, corresponding to a superconducting order parameter in a dual conformal field theory. We show that the approach to the final state takes the form of damped oscillations, with the degree of damping being strongly dependent on the temperature of the final state, as well as on the near-boundary shape of the initial distribution.Show less
Α-synuclein is a small 14 kDa protein, which is believed to play a role in the Parkinson’s disease. The aggregation process of α-synuclein could be the reason for the death of the neural cells in...Show moreΑ-synuclein is a small 14 kDa protein, which is believed to play a role in the Parkinson’s disease. The aggregation process of α-synuclein could be the reason for the death of the neural cells in the human brain during the disease. In order to understand this aggregation process, we need to set up a method for measuring the small aggregates of α-synuclein. This report will show the results of burst analysis, Fluorescence Correlation Spectroscopy in solution and in gel. Using the last method, we can find a size dependence on the diffusion coefficient of -1.64. FCS in gel could be performed for finding the early events in α-synuclein aggregation (monomer, dimer and tetramer)Show less
We look at a mechanical metamaterial whose stiffness does not scale inversely proportional to its length. We perform tensile tests to study the relation between the length and the stiffness of the...Show moreWe look at a mechanical metamaterial whose stiffness does not scale inversely proportional to its length. We perform tensile tests to study the relation between the length and the stiffness of the metamaterial. We find two regimes for the stiffness, which are separated by a characteristic length. We explain the cause of this length and show that we can alter its value. Lastly we set up a model that simulates the behavior of the metamaterial in tension and can reproduce the experimental data.Show less
Van der Waals materials such as graphene are layered materials that can be created in single atom thickness. In most cases there is more than one way to stack subsequent layers, often leading to...Show moreVan der Waals materials such as graphene are layered materials that can be created in single atom thickness. In most cases there is more than one way to stack subsequent layers, often leading to domains of different stackings. In this work stacking domains in few layer stacks of graphene and \mos are studied using Low Energy Electron Microscopy. From dark field LEEM measurements on few layer epitaxial graphene on SiC it is concluded that two different types of domains exists: domains created from nucleation during growth and triangular stress domains induced from lattice mismatch with the underlying SiC. A detailed comparison between epitaxial and quasi-freestanding graphene is made. As part of this comparison deintercalation of the latter to reform the former is performed. The hydrogen diffusion out of the material occurring here is studied and linked to defects in the material and aforementioned stacking domains. For MoS2 no domains were analysed within the scope of this project, but a comparison of flatness for different substrates is made and using muLEED measurements a method to determine the number of layers is demonstrated and the two different orientations of the 2H polytype are experimentally identified.Show less
Colloidal particles at a liquid-liquid interface can order into interesting structures. In this work poly(methyl methacrylate) colloids with a core-shell structure have been synthesized and studied...Show moreColloidal particles at a liquid-liquid interface can order into interesting structures. In this work poly(methyl methacrylate) colloids with a core-shell structure have been synthesized and studied. They have been clustered to create anisotropic particles with regular shapes. Their structure is optimal for studies at water-oil interface with both bright field and confocal microscopy. The stability of the colloids has been tested in aqueous and organic media with single and clustered particles. Both single spherical particles and clusters have been observed at an water-oil interface. A computational project related to self-assembly problem in virus-like protein capsid is presented inShow less
