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
The reuse of agent-based models (ABM) is widely recognized to have a number of benefits. Not only is it often economical to reuse models, it can also be a great methodological test and tool for...Show moreThe reuse of agent-based models (ABM) is widely recognized to have a number of benefits. Not only is it often economical to reuse models, it can also be a great methodological test and tool for theory-building. However, reuse, like replication, of ABM is still rare in archaeology, and little critical discussion exists on the topic. This thesis aims to open up a discussion regarding the reuse of ABM in archaeology, its potential, and its limitations. It features a reapplication of Brughmans and Poblome’s well-studied MERCURY ABM to a new case study and data-set: Sigillata in the Roman West as seen through Römisch-Germanisches Zentralmuseum’s Samian Research database. In this process, new insights are gained into the MERCURY model, and challenges to reimplementing and reusing the ABM are identified. The thesis concludes by discussing the general challenges to and potential of ABM reuse in archaeology as gauged from the reapplication exercise.Show 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
This thesis provides a philosophical discussion of the implementation of virtual and augmented reality in the cultural heritage sector. In particular, the paper critically investigates the ways in...Show moreThis thesis provides a philosophical discussion of the implementation of virtual and augmented reality in the cultural heritage sector. In particular, the paper critically investigates the ways in which digital technologies attempt to simulate and approximate materiality.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
The main issue that this thesis aims to address is the marginalised position of the affective dimension in theoretical texts or the academic form. By means of an exploration into Severo Sarduy’s...Show moreThe main issue that this thesis aims to address is the marginalised position of the affective dimension in theoretical texts or the academic form. By means of an exploration into Severo Sarduy’s essay “Simulation” (La Simulacíon, 1982), this thesis aims to demonstrate the potential that lies in the employment of the affective dimension in theoretical writing- and reading processes. The analysis focuses on affective strategies in Sarduy’s essay or, in other words, the means in which the reader is incorporated into the text to fulfill an important role in the making of meaning of the text. This thesis aims to emphasise the ways in which the affective dimension is utilised to communicate the ontological perspective of Sarduy’s text as well as it aspires to show how these affective strategies have the ability to criticise and to mobilise change by providing a different kind of knowledge in academic discourses.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
Research master thesis | Archaeology (research) (MA/MSc)
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HomininSpace is an agent based modelling and simulation environment for moving hominin groups through a large scale geographical landscape. Changing carrying capacity in a reconstructed...Show moreHomininSpace is an agent based modelling and simulation environment for moving hominin groups through a large scale geographical landscape. Changing carrying capacity in a reconstructed paleoclimate is the ultimate driving force behind dispersal in HomininSpace. Changing temperatures and precipitation levels influence the carrying capacity of the landscape, and are assumed to be the most influential parameter in the mobility of ancient hominins in the underlying model. This research combines for the first time an environmental reconstruction driven by the results from isotopic measurements with a year by year demographic model for Neandertal groups moving through North-west Europe. The Neandertals utilize the energy levels from the environment in the form of the meat from large herbivores. The aim is to assess conceptual models underlying the behavior of Middle Pleistocene hominins in fluctuating climatic conditions, including severe stress-inducing environments. The research contributes to understanding past hominin behaviors regarding mobility strategy, dispersal and occupation history within changing environments. Two major types of behavior driving movement were identified and are implemented in the simulations: a dynamic mobility and a static mobility. Dynamic mobility can be best described as hominins following their preferred habitat. Static mobility is an implementation of the source and sink model, where populations stay in the same area and suffer from local extinction when the climate deteriorates and are replenished from remote source locations when conditions improve. Simulations were run from 131 ky BP to 50 ky BP. For 14.948 grid cells (148 x 101) in each of 81.000 timesteps climatic parameters are reconstructed, including elevation, temperature (yearly average, warmest and coldest month values) and precipitation levels. From these values a (grid-based) environment is reconstructed through which groups of hominins move, driven by the inferred abundance of large herbivores, representing the energy levels stored in the local environment. For each simulation different parameters can be set through the user interface implementing different models and hypotheses about hominin behavior. Output of the simulation processes include density maps of hominin presence, density maps identifying areas where hominins died and statistical information on hominin groups including sizes, composition, foraging ranges, resource deficiencies, and ages. Simulations can be started, paused and restarted at any point in time. Results can further include a log file with the key characteristics of the simulation, debug information at a desired level, screen dumps in different formats and a playable movie from snapshots at indicated intervals. Movement patterns of the simulated hominins are matched against archaeological dating information on Neandertal material taken from the literature. This data is collected in a comprehensive database which includes site name and GPS location, material dated, date assigned including accuracy and dating method, reference to the literature, and a confidence level. The archaeological data are included as Checkpoints in Space and Time of which 75 individual sites are included. Simulation results are summarized in key values allowing assessment of the level of agreement between model and archaeology on different aspects.Show less
