In this report, the possibilities of identifying a specific t neutrino signature using KM3NeT, a neutrino telescope with an instrumented volume of multiple cubic kilometers, are investigated. When...Show moreIn this report, the possibilities of identifying a specific t neutrino signature using KM3NeT, a neutrino telescope with an instrumented volume of multiple cubic kilometers, are investigated. When uniquely identified, these neutrinos can offer a unique view on the universe with little to no background. We study the ‘Double Bang’ signature of the t neutrino interaction and reconstruct these events with a reconstruction algorithm designed for single showers. Using this algorithm, the two particle showers in this event are reconstructed as a single shower. By looking at the differences in reconstruction performance between these events and single shower events, a first indication of the relevant parameters for the identification of t neutrinos is given.Show less
In eukaryotes, three quarters of the DNA is wrapped around histone proteins, forming a string of nucleosomes. This organization condenses the DNA considerably, and at the same time restricts it...Show moreIn eukaryotes, three quarters of the DNA is wrapped around histone proteins, forming a string of nucleosomes. This organization condenses the DNA considerably, and at the same time restricts it accessibility for DNA binding proteins. Conformational dynamics of the nucleosome, like partial release of the DNA, called nucleosome breathing, plays an important part in regulating this accessibility of the genetic information. To study the wrapping and unwrapping in DNA breathing we followed the Förster Resonance Energy Transfer of a pair of fluorophores placed in the nucleosome, in time. We selected a single nucleosome immobilized on glass from an image acquired by a scanning confocal microscopy. Data acquisition and analysis software was developed to record and process time trace of individual nucleosomes with sub ms resolution. Although we can now reach the required temporal resolution to resolve nucleosome breathing, we did not observe it. A large fraction of the nucleosomes did not show FRET after surface immobilization suggesting partial disassembly, which prevented statistical analysis of large numbers of nucleosomes.Show less
To sense the movement or piling up of single charges, a system interacting strongly with these charges is required. An available system, having these properties, is a single electron transistor ...Show moreTo sense the movement or piling up of single charges, a system interacting strongly with these charges is required. An available system, having these properties, is a single electron transistor (SET). The electric fi eld caused by the charge, strongly changes the resistance of the SET. Yet experiments opt for a less invasive charge sensor. Such a proposed charge sensor is a single fluorescent dye molecule. The distinguishable zero phonon lines (ZPL's) of the fluorescence of the molecules shifts strongly by the Stark e ffect. The lineshift of each molecule can be tracked with an excitation laser, allowing to observe the change in charging. Tracking the ZPL's of multiple molecules allows the observation of slow charge movement. The optical charge sensing method needs to be tested on devices fabricated on a glass substrate. In particular devices, which exhibit single electron charging. These devices have been constructed with electron beam lithography (EBL). Nanoparticles, representing an island to hold the charge, have been trapped between nano-electrodes using dielectrophoresis. The nanogaps have been created by electromigration or by EBL. Eventually, nano-electrodes were also fabricated on glass by coating the glass with a 1,5 nm Cr layer. This coating was removed afterwards with plasma etching. The project focused on the fabrication of the devices. The deposition of fluorescent dye molecules and tracking the lineshifts was left for subsequent experiments. A fluorescence microscope, also necessary for the lineshift measurements, was used to observe quantum dots. Proposed experiments with quantum dots are the tracking of the movement of quantum dots in a strong alternating electric fi eld or the eff ect of a high electric field on the fluorescence of a quantum dot in a nano-electrode junction.Show less
We seek to study the in uence of substrate geometry on di usion of substrate attached particles by building a model system in which colloidal particles are attached to a supported lipid bilayer on...Show moreWe seek to study the in uence of substrate geometry on di usion of substrate attached particles by building a model system in which colloidal particles are attached to a supported lipid bilayer on TPA suitable material. We test a variety of lipid compositions and polyelectrolyte cushioning with respect to lipid mobility. Our experimental e orts show that DOPC/DOPE-PEG2000 uid lipid bilayers on glass and ORMOCER can be created. DNA linkers with cholesterol anchors are adsorbed in this bilayer and polystyrene colloids coated with complementary DNA linkers are coupled to the linkers in the bilayer. We show that the colloids di use in a two dimensional fashion on a glass substrate.Show less
Accessibility to nucleosomal dna is an important factor in transcription and gene expression. During transcription, rna polymerase exerts a force on the nucleosome under which the nucleosome...Show moreAccessibility to nucleosomal dna is an important factor in transcription and gene expression. During transcription, rna polymerase exerts a force on the nucleosome under which the nucleosome unwraps, and, as recently shown experimentally, this can happen asymmetrically. In this thesis, we show, using computer simulations of sequence-dependent coarse-grained dna, what causes this asymmetry. We will also show a proof of concept that we can design dna sequences that unwrap in a predetermined way.Show less
Chiral phases of nematic structures in liquid crystals are generally produced by either chiral molecules or by doping a system of achiral LC molecules with chiral constituents. However, a chiral...Show moreChiral phases of nematic structures in liquid crystals are generally produced by either chiral molecules or by doping a system of achiral LC molecules with chiral constituents. However, a chiral nematic phase may also emerge in geometrically confined nematics with achiral constituents. It has recently been shown that spontaneous chirality emerges for a nematic in a torus with parallel anchoring for a particular choice of the aspect ratio. Experimental evidence suggests that a chiral phase can also be observed for perpendicular anchoring conditions, however, an analytical minimisation of the Frank free energy suggests otherwise. Nevertheless, analytical calculations show that a chiral vortex structure can be observed for very thin capillary lengths.Show less
The simplest form of dipole interaction between an atom and a single photon field mode, is described by the vacuum Rabi model. Strong atom-photon coupling, which is described by the simpler Jaynes...Show moreThe simplest form of dipole interaction between an atom and a single photon field mode, is described by the vacuum Rabi model. Strong atom-photon coupling, which is described by the simpler Jaynes-Cummings model, has been achieved in many platforms, such as cavity and circuit quantum electrodynamics (QED) and has brought a lot of success towards experimental quantum information processing over the past years. The full Rabi model dynamics can only be obtained in the so-called ultra-strong and deep-strong coupling regimes where the interaction coupling strength is comparable or higher than the natural system frequencies. However, due to our inability to achieve such high coupling strengths, these regimes remain largely unexplored in the lab. In this thesis, we investigate the possibility of reaching these regimes in a circuit QED setup, by means of a recently proposed analog-digital quantum simulation. Following a detailed numerical model of the proposed scheme, where we include the most important experimental limitations, we demonstrate the feasibility of the proposal using a transmon coupled to a 2D superconducting resonator, for a certain range of design parameters. Moreover, we show that the Wigner function representation of the resonator state in phase space is instrumental in order to probe the signature of deep-strong coupling in the system. Following these results, we design a device that will enable us to carry out the experiment with high fidelity measurements and perform direct Wigner tomography inside the resonator.Show less
We study the dynamics of a charged spinning particle in a Reissner-Nordström geometry using the hamiltonian formalism. We use covariant instead of canonical momentum and a worldline along which the...Show moreWe study the dynamics of a charged spinning particle in a Reissner-Nordström geometry using the hamiltonian formalism. We use covariant instead of canonical momentum and a worldline along which the spin tensor is covariantly constant. We find the equations of motion as well as the constants of motion and give a full characterization of the circular orbits for a minimal hamiltonian. We study the spin and charge dependence of the innermost stable circular orbit. In the last part we introduce a non-minimal hamiltonian, including spin-spin interaction and an interaction between the spin tensor and the electromagnetic field. We show that the conserved quantities that we found with the minimal hamiltonian are still constants of motion.Show less
The construction of the supersymmetric non-linear sigma model is presented. This model is then applied to the symmetry group SU(2N). The thesis considers the gauging of different subgroups of SU(2N...Show moreThe construction of the supersymmetric non-linear sigma model is presented. This model is then applied to the symmetry group SU(2N). The thesis considers the gauging of different subgroups of SU(2N), whereupon the particle spectrum of the theory is determined. The thesis concludes with an outline on how to proceed.Show less
Electromigration in bismuth is studied as a way to create bismuth(111) bilayers. Temperature-dependent electromigration measurements have been performed and a model incorporating Joule heating is...Show moreElectromigration in bismuth is studied as a way to create bismuth(111) bilayers. Temperature-dependent electromigration measurements have been performed and a model incorporating Joule heating is used to describe those. An activation energy for diffusion between 100 and 180meV is found. Furthermore, in-situ electromigration experiments have been performed in a scanning electron microscope. This allowed us to link events in the conductance traces of bismuth constrictions during electromigration to visual features. Specifically, remerging of the bismuth electrodes was found to cause increases in conduction.Show less
The working temperature is a limiting factor for improving the sensitivity of Magnetic Resonance Force Microscopy towards imaging of a single nuclear spin. In this report we take a step in lowering...Show moreThe working temperature is a limiting factor for improving the sensitivity of Magnetic Resonance Force Microscopy towards imaging of a single nuclear spin. In this report we take a step in lowering the working temperature by reducing the energy loss of the radio frequent source, using a superconducting NbTiN microwire. A cryogenic calorimeter with 100 nW resolution at 4 Kelvin is developed to investigate the power dissipation of the detection chip, giving new insights on the current design. The use of a NbTiN microwire enables to keep the mixing chamber of a dilution refrigerator at 10mK. The presence of flux vortices penetrating the NbTiN material seems to play an active role in the energy losses. Improvements are proposed on the design of the detection chip to reduce the power dissipation further for future experiments.Show less
Results of a six-month-long internship in cosine Science & Computing BV are presented. Data of a full-field Fringe Reflection Technique measurements of Silicone Pore Optics components for...Show moreResults of a six-month-long internship in cosine Science & Computing BV are presented. Data of a full-field Fringe Reflection Technique measurements of Silicone Pore Optics components for ATHENA X-ray observatory were used for least-square fitting and evaluation of surface quality. Basic forward ray tracing was used to evaluate the components’ performance in X-rays: half-energy width and point-spread function were calculated. The best-fitting surface parameters and optical performance were compared with manufacturer’s specifications and X-ray measurements performed in Berlin Electron Storage Ring Society for Synchrotron Radiation (BESSY). Even though the FRT measurements exhibited nanometer height accuracy of local surface features, constant discrepancies of the measured figure parameters were noticed. However, a correspondence between axial slope deviations measured with FRT and X-rays was found for a silicon plate of SPO stack.Show less
A recent paper [DeCamp et al 2015] reported dynamical effects of defect orientation in experiments with planar nematic liquid crystals. The numerical determination of defect orientations was...Show moreA recent paper [DeCamp et al 2015] reported dynamical effects of defect orientation in experiments with planar nematic liquid crystals. The numerical determination of defect orientations was complicated by the absence of a rigorous definition of defect orientation in the paper. In this thesis I will introduce rigorously a defect orientation which can be easily determined numerically. I will show that defect orientation is a significant factor in the dynamics of defect annihilations with most notably an orthogonal velocity component not documented in the literature.Show less
Most vital processes in our body including tissue formation, wound healing and immune response are dependent on directed cell migration, which is mediated by chemical and mechanical stimuli....Show moreMost vital processes in our body including tissue formation, wound healing and immune response are dependent on directed cell migration, which is mediated by chemical and mechanical stimuli. Dysfunctions in directed migration can have severe consequences, such as tumor formation and metastasis. We studied the combined effect of both chemical and topographical stimuli on the model organism Dictyostelium discoideum, which exhibits amoeboid migration similar to that of higher eukaryotes. A chemotactic gradient was introduced by the diffusion of cyclic adenosine monophosphate (cAMP) in a microfluidic chamber and a topotactic gradient was established by use of a polydimethylsiloxane (PDMS) micro-pillar array of variable pillar density. Establishing both gradients in a quasi-3D environment mimics a controllable natural setting that D. discoideum cells encounter during the aggregation competent state. We then observed live cell migration of 2000 cells in different configurations of the combined gradients using spinning disk confocal fluorescence microscopy. We distinguished directed cellular runs from non-directed random migration through high resolution motion analysis. This analysis helped characterizing the combined chemotactic and topotactic effects on cell migration. We found that different configurations of both gradients, individually and combined, can increase or suppress cell velocity and amplify or weaken directionality in migration.Show less
Quantum computing promises to deliver exponential speed-up over classical machines in solving specific problems. However, quantum information is susceptible to decoherence and errors, and fault...Show moreQuantum computing promises to deliver exponential speed-up over classical machines in solving specific problems. However, quantum information is susceptible to decoherence and errors, and fault-tolerant quantum computing (FTQC) is the only realistic approach. In FTQC, operations are performed on logical qubits which are encoded in physical qubits such that errors are correctable or trackable. Specifically, in the repetition code for quantum error correction (QEC), qubits are encoded in Greenberger-Horne-Zeilinger (GHZ)-type states to be protected from bit-flip or phase-flip errors. It is important not to leave the protected subspace at any time to meet the basic requirement for FTQC. Previous demonstrations of the repetition code in various physical systems have circumvented this requirement, detecting errors at the cost of decoding the logical qubit. Using five superconducting qubits in circuit quantum electrodynamics, we demonstrate quantum bit-flip error detection at the logical-qubit level by stabiliser measurements for the first time. These stabilisers are assessed by their ability to generate GHZ-type entanglement: projecting a maximal superposition state into the subspaces being stabilised, while maintaining the coherence within each. To further characterise the error detection, we intentionally apply errors on all qubits and assess the fidelities both in the encoded subspace and at the logical-qubit level. Although current fidelities of the stabiliser measurements preclude improvements by error detection over idling, this demonstration is a critical step towards larger codes based on stabiliser measurements in the paradigm of FTQC.Show less
In this thesis, the necessary elements to build up a quantum switch, the central element in a quantum random access memory, are proposed and analyzed. A network with quantum switches at its nodes...Show moreIn this thesis, the necessary elements to build up a quantum switch, the central element in a quantum random access memory, are proposed and analyzed. A network with quantum switches at its nodes forms the bifurcation path that leads an address register from a root node to an array of memory cells, activating, quantum coherently, only the quantum switches that the register encounters in its path to the memory cells. Transmon qubits and SQUIDs are used to design a superconducting device capable of routing a register of microwave photons through a bifurcation network, allowing for superposition of paths. In order to give rise to all the required interactions between the device and the address register, a non-linear capacitor, composed of two plates with carbon nanotubes in between, is introduced into the transmon. The dynamic operation of the quantum switch is analyzed using Langevin equations and a scattering approach, and probabilities of reflection and transmission of photons by (or through) the switch are computed, both for single- and two-photon processes. Computations show that, with parameters taken from up-to-date similar devices, probabilities of success are above 94%. Applications of quantum random access memories are discussed, as well as other applications of quantum switches. Also, solutions are proposed to the challenges that emerge during the study of the dynamics of the quantum switch.Show less
