The study looked at how regression to the mean affects the results of diabetes Type II medication effectiveness using data from the Netherlands Epidemiology of Obesity (NEO) study. This research...Show moreThe study looked at how regression to the mean affects the results of diabetes Type II medication effectiveness using data from the Netherlands Epidemiology of Obesity (NEO) study. This research showed that RTM can happen before and after starting medication. In simulations where there was no treatment effect, the HbA1c levels before starting medication were unexpectedly lower than the true average. This suggests that choosing different times to compare in the study can really change how effective the medication seems. When applying the same methods to the real NEO study data, there were some big differences compared to the simulations. For example, the estimated average HbA1c level before starting medication in the NEO study was higher than what was found using certain statistical models. This points out some possible issues with these methods and shows how complex the NEO study data is. The findings suggest that RTM is an important factor to consider in studies about medication effectiveness. Because the NEO study data is so complex, future research might need more detailed methods to properly understand RTM and how it affects the results. Expanding the types of scenarios studied, including different criteria for when treatment starts, and looking at more patient data could help give a fuller picture of RTM and improve how we evaluate medication effectiveness in real-world studiesShow less
In this thesis, the potential of Chemical Exchange Saturation Transfer to image brain metabolites is presented. The Bloch-McConnell equations are simulated and the optimal parameters are found to...Show moreIn this thesis, the potential of Chemical Exchange Saturation Transfer to image brain metabolites is presented. The Bloch-McConnell equations are simulated and the optimal parameters are found to be 3.5uT, tsat = 1s for glutamate and 3uT, tsat = 1.5s for creatine. Furthermore, multiple quantification methods, including MTR asymmetry, Lorentzian fits and spinlock fits are evaluated for quantifying CEST signal from glutamate and creatine. The quantification methods are tested on the Bloch-McConnell simulations, 2-pool phantoms, 3-pool phantoms and in vivo.Show less
Active particles can be used to model various biological processes like groups of bacteria or even flocks of birds. Until now, the shape of active prolate ellipsoids has not been optimized to make...Show moreActive particles can be used to model various biological processes like groups of bacteria or even flocks of birds. Until now, the shape of active prolate ellipsoids has not been optimized to make these particles move in a straight line. This is particularly interesting because a straight moving particle can be used as a basis to model these biological systems. Simulations were done to optimize the shape of prolate ellipsoids for straightness of path and four variables are defined that quantify this. The paths of active prolate ellipsoids with a long semi axis of 5 μm and a short semi axis between 1 and 4.9 μm were simulated in C, and the straightness of path was compared using the variables. The simulations suggest that particles with a larger short semi axis follow straighter paths, although this needs to be supported by empirical results.Show less
Gastrulation is a crucial stage for embryonic development of multicellular animals. During this process, the structure of embryos for the rest of the development is determined. When trying to...Show moreGastrulation is a crucial stage for embryonic development of multicellular animals. During this process, the structure of embryos for the rest of the development is determined. When trying to emulate this process in vitro, a wide variety of shapes arises. We have developed a mathematical model that tries to describe this variety in shapes. The model we have used is based on the Cellular Potts Model. In order to run simulations of this stochastic model, we have used Tissue Simulation Toolkit. A method for improving the efficiency of this code is discussed in this thesis. Next, we have studied a published model for convergent extension which globally assigns directional cues and causes ovoid shapes. Consequently, we studied a variation of this model that uses local directional cues. This enabled us to achieve non-ovoid shapes, as are present for in vitro gastruloids, as well. Different methods for analyzing the shapes that arise from these simulations are discussed as well. From these methods, we have looked at the sorting kinetics for different models. We have also studied a variation on Elliptic Fourier Analysis. This method eventually aided us to describe the shapes from our simulations quantitatively. An attempt to compare these simulations with in vitro data has been made henceforth, which gave us a parameter range that seems to best fit experimental data.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
This thesis is concerned with the design of numerical methods for solving the Schrödinger equation for a system of two-electrons in a double quantum dot. Theoretical background is presented for the...Show moreThis thesis is concerned with the design of numerical methods for solving the Schrödinger equation for a system of two-electrons in a double quantum dot. Theoretical background is presented for the physics of a two-electron quantum dot. Implementation of the double dot system is via the QuTiP library is discussed and a numerical approach for the treatment of the system using the density matrix formalism is presentedShow less
We describe a method to increase the critical temperature of BCS superconductors. The method is based on altering the electronic properties of a thin film of a superconductor by periodically...Show moreWe describe a method to increase the critical temperature of BCS superconductors. The method is based on altering the electronic properties of a thin film of a superconductor by periodically fabricating holes in the crystal lattice. We use a MATLAB simulation to demonstrate that certain patterns enhance the coupling between electrons and phonons, which increases the transition temperature. In this project we attempted to improve the simulation such that it executes faster and is compatible with hexagonal structures.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
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
This thesis consists of two parts, one part describes the heating of a gold nanosphere and the forming of a vapor bubble as a result of this. The first part consist mainly of theory and there are...Show moreThis thesis consists of two parts, one part describes the heating of a gold nanosphere and the forming of a vapor bubble as a result of this. The first part consist mainly of theory and there are no measurement results to support the theory, the second part describes a Matlab simulation of a random walk of a ATTO 647N molecule close to a gold nanorod that is being placed in an electromagnetic field. The simulation uses the MNPBEM toolbox to calculate the electric field generated by the gold nanorod and a random walk for the movement of the molecule.Show less
