We investigate how radiation pressure can be used to influence the mechanical motion of a micro-mirror suspended from springs. This trampoline resonator is part of an optical Fabry-Perot cavity. By... Show moreWe investigate how radiation pressure can be used to influence the mechanical motion of a micro-mirror suspended from springs. This trampoline resonator is part of an optical Fabry-Perot cavity. By tuning the laser frequency with respect to the optical resonance, we are able to optically cool the mechanical motion of the resonator. When combining this optical cooling with cryogenic cooling techniques, we are able to bring the mechanical resonator close to the quantum mechanical ground state. This is a requirement for future experiments to investigate the fundamentals of quantum mechanics. Show less
In this work the reconstruction of a tau neutrino signal in the KM3NeT detector is discussed. Tau neutrinos leave a two shower signature in the detector, which is a unique signature among all... Show moreIn this work the reconstruction of a tau neutrino signal in the KM3NeT detector is discussed. Tau neutrinos leave a two shower signature in the detector, which is a unique signature among all neutrino interactions. By identifying and reconstructing these tau signatures the KM3NeT detector will be able to distinguish all three neutrino flavors. In addition, cosmic tau neutrinos suffer significantly less from atmospheric backgrounds, makign them ideal messengers for cosmic events. The presented reconstruction is the first tau reconstruction for the KM3NeT detector and resulted in a total expected observation rate of half a tau event per year for one unit of the KM3NeT detector. Show less
We investigate the buildup of galaxies from various vantage points. The first two chapters focus on the stellar content of galaxies, especially the distribution of stellar masses at birth and... Show moreWe investigate the buildup of galaxies from various vantage points. The first two chapters focus on the stellar content of galaxies, especially the distribution of stellar masses at birth and potential variations therein in various galactic environments. We find that in some cases these inferred variations can be due to an underestimation of model and measurement errors. Furthermore, we infer the consequences of these proposed variations on the interpretation of galaxy properties and galaxy formation processes. Chapters 3 and 4 focus on the buildup of galaxies in time through mergers and in-situ star formation. We test and improve observational models that aim to trace galaxies though cosmic time, by applying them to cosmological hydrodynamical simulations, for which we have access to the full history and evolution of galaxies since the beginning of time. The fifth chapter focusses on the buildup of galaxy morphology. We follow the buildup of morphological components in a cosmological simulation, which leads us to conclude that galaxy formation is a three-phase process, consisting of an early, rather disorganised, phase, followed by a phase in which stars are formed primarily in an organised rotating disk, and ending in a late phase of merger-driven spheroid formation. Show less
Shape and biological function are tightly connected. Physical descriptions are used to connect the shape of a biological system with its function. One system investigated here is the dendritic... Show moreShape and biological function are tightly connected. Physical descriptions are used to connect the shape of a biological system with its function. One system investigated here is the dendritic spine, which is the connection between neurons. The dendritic spine is mimicked in an artificial system. In this way, I was able to show that the shape of the dendritic spine is important in memory and learning. The shape of a cell itself is governed by its actin cytoskeleton. I showed that a simple model can be used to describe the shape of adherent cells. An adherent cell attaches itself at discrete points to the substrate. The edge of the cell in between these points can be described as a part of an ellipse. I show that all edges of a single cell can all be described with a single ellipse. On a small scale, the shape of the membrane of a cell changes with changing lipid content. I used light to change the lipid content, triggering phase unmixing in an artificial lipid membrane. I show that various important parameters change significantly. Show less
In this thesis, classes of strongly interacting quantum field theories, have been studied. A non-perturbative method applied to these theories are gauge/gravity duality or holographic duality,... Show moreIn this thesis, classes of strongly interacting quantum field theories, have been studied. A non-perturbative method applied to these theories are gauge/gravity duality or holographic duality, which map a system of quantum field theory to a theory of gravity in higher dimensions. This thesis focused on the transport coefficients which govern the low energy excitations of these systems. Show less
The thesis describes experimental steps towards reduction of friction on the macroscopic scale by scenarios of thermo- and superlubricity well-known on the nanoscale. The friction study involves... Show moreThe thesis describes experimental steps towards reduction of friction on the macroscopic scale by scenarios of thermo- and superlubricity well-known on the nanoscale. The friction study involves experiments on tailored Si nanopillar arrays, micropatterned Diamond-Like Carbon coating and high-quality graphene. Show less
In mechanical metamaterials, large deformations can occur in systems which are topological from the point of view of linear waves. The interplay between such nonlinearities and topology affects... Show moreIn mechanical metamaterials, large deformations can occur in systems which are topological from the point of view of linear waves. The interplay between such nonlinearities and topology affects wave propagation. Beyond perfectly periodic systems, defects provide a way to modify and control the properties of metamaterials, and can also interact with both nonlinearities and the bulk topology. To investigate these, we explore the wave propagation in three mechanical models, i.e.~solitary waves in topological rotor chains, lattice waves in twisted kagome networks, and transverse shock waves in flexible strings. Show less
The four possible segments A, T, C and G that link together to form DNA molecules, and with their ordering encode genetic information, are not only different in name, but also in their physical and... Show moreThe four possible segments A, T, C and G that link together to form DNA molecules, and with their ordering encode genetic information, are not only different in name, but also in their physical and chemical properties. The result is that DNA molecules with different sequences have different physical behavior. For instance, one sequence may lead to a very flexible DNA molecule, another to a very stiff one. A DNA molecule with a given sequence may be straight, or intrinsically curved. This leads to an interplay between the information stored in a DNA molecule on one hand, and the physical properties of that molecule on the other. This is of great importance in our cells, where lengths of DNA far longer than the size of the cells that contain them need to be significantly folded up. The research presented in this thesis looks at how we can model this interplay, what its effects can be, and whether nature has made use of it to encode mechanical signals into real genomes. Show less
The lipid membrane is a basic structural component of all living cells. Embedded in this nanometer-thin barrier, membrane proteins shape the membrane and at the same time respond to the shape... Show moreThe lipid membrane is a basic structural component of all living cells. Embedded in this nanometer-thin barrier, membrane proteins shape the membrane and at the same time respond to the shape of the membrane. This two-way interaction gives rise to a force between membrane-deforming objects that is mediated by the membrane. In this thesis, this effect is measured by employing micron-sized colloidal particles. In Chapters 2 and 3, methods for extracting local forces from video images of colloidal particles are described. Then, in Chapter 4, the development of colloidal particles that strongly attach to specific lipid membranes is described. These are then used in Chapters 5 and 6, in which membrane-mediated forces and assembly pathways between membrane-attached colloidal particles are investigated and quantified. Finally, in Chapters 7 and 8, the preparation of micron-sized oil droplets is studied and their use as lipid monolayer support is demonstrated. The results from this thesis contribute to fundamental microbiological questions about forces between membrane proteins, as well as to the understanding of the toxicity of microplastics. Show less
We study the interplay of topology and geometry with chirality for several passive and active systems, employing both analytical and numerical methods. In chapter 1, we explain how nematic liquid... Show moreWe study the interplay of topology and geometry with chirality for several passive and active systems, employing both analytical and numerical methods. In chapter 1, we explain how nematic liquid crystals confined in toroidal geometries undergo structural phase transitions depending on the slenderness of the confining toroid. In chapter 2, we consider a system of active polar swimmers that align with their neighbors. When confined in the right geometry, the system will self-assemble into a state with topologically protected chiral acoustic modes. The chirality in this system manifests itself as a temporal one, rather than a spatial chirality. Chapter 3 shows how systems of Yukawa charged active spinning dimers self-assemble into a crystal phase with spatiotemporal order, a liquid phase or a glass phase depending on the density. Depending on the phase and the confinement geometry of these systems of actively spinning dimers, the system will allow for rigid body rotations or edge currents. Finally, in chapter 4 we introduce a novel method of doing molecular dynamics on curved surfaces by developing a symplectic integrator. We present preliminary results on two-dimensional crystal melting in the presence of curvature. We find that the crystal may melt inhomogeneously. Show less
In the early nineties, Sidles (1991) came with a solution to combine the force microscopy techniques sensitive to atoms with that of magnetic resonance techniques: Magnetic Resonance Force... Show moreIn the early nineties, Sidles (1991) came with a solution to combine the force microscopy techniques sensitive to atoms with that of magnetic resonance techniques: Magnetic Resonance Force Microscopy (MRFM) was born. The technique was promising, big steps were taken, and the holy grail of atomic resolution imaging of biological tissues seemed within an arm’s reach. Unfortunately, the last steps are the most difficult. The technique is experimentally challenging and so far, the images of biological structures are no better than those obtained by other conventional techniques. In order to be an attractive technique, MRFM needs to be scientifically relevant while the technique is further improved towards the holy grail of imaging biological structures on the nanometer scale. In this thesis, we show how MRFM can usefully contribute to the field of condensed-matter. Show less
Gold nanorods are biocompatible nanoparticles that present an excellent two-photon signal that can be used to get high spatial resolution inside living cells. Gold nanorods are photostable and... Show moreGold nanorods are biocompatible nanoparticles that present an excellent two-photon signal that can be used to get high spatial resolution inside living cells. Gold nanorods are photostable and therefore can be followed inside cells for long time, with possible applications as trackers in live cells. We explored the use of gold nanorods as labels for single-particle tracking in live cells, both not functionalized and functionalized with nuclear localization signal for nuclear targeting. For single-particle tracking we used mean square displacement analysis, after characterizing the limitations of this analysis with simulations. We also tested the acquisition of excitation spectra of single gold nanorods for sensing applications. Show less
The thesis describes the use of electron paramagnetic resonance (EPR) spectroscopy, in continuous wave and pulse modes, to address the interaction of α-Synuclein (αS) with membranes and the... Show moreThe thesis describes the use of electron paramagnetic resonance (EPR) spectroscopy, in continuous wave and pulse modes, to address the interaction of α-Synuclein (αS) with membranes and the aggregation of αS. The protein, αS, associated with Parkinson’s disease, plays its role by interacting with vesicles/membranes in nerve cells in the brain. We investigate, specifically, the interaction of αS with small unilamellar vesicles mimicking the inner mitochondrial membrane and the neuronal plasma membrane (chapter 2). Also, the influence of phosphorylation of αS at positions 87 and 129, mimicked by the mutations S87A, S129A (nonphosphorylated) and S87D, S129D (phosphorylated) on membrane binding is investigated (chapter 3). One of the peculiar properties of αS is to form amyloid fibrils. In the fibril, the protein chain of αS is folded into a β-sheet structure. We investigate how αS is folded in the fibrils (chapter 4 and 5). The chapter 6 focuses on peptides that help in membrane fusion. Using two small helical peptides, K and E, which act as zippers in the membrane-fusion model, we investigate the orientation of K and E in the zipper. Show less
Surface plasmons (SPs) are surface waves at the interface between a dielectric and a good metal, and are formed by the interaction between light and the free electrons at the metal-dielectric... Show moreSurface plasmons (SPs) are surface waves at the interface between a dielectric and a good metal, and are formed by the interaction between light and the free electrons at the metal-dielectric interface. They provide strong field confinement for optical fields, opening new possibilities for enhanced light-matter interaction. We combine SPs with a semiconductor gain layer and a resonator for SPs to create a SP-laser. The resonator for SPs is created by scattering on an array of holes in the gold film, i.e., a metal hole array. In this thesis, we describe experiments on SP propagation and SP lasing in active two-dimensional metal hole arrays operating at telecom wavelengths. A resonator for SPs is created by scattering on an array of holes in the gold film. We have studied such active hole arrays with square and hexagonal lattice symmetries both below and above their lasing threshold. We have investigated the role of the symmetry of the lattice on the SP propagation and SP lasing. We have explored the laser frequencies and the feedback mechanism of these SP lasers, and observed the spatial profile and direction of the emitted laser beams. Show less
The thesis mainly contributes to the characterization of Majorana fermions as they appear in the Condensed Matter context. Large attention is devoted to discuss signatures in the density of... Show moreThe thesis mainly contributes to the characterization of Majorana fermions as they appear in the Condensed Matter context. Large attention is devoted to discuss signatures in the density of states and transport observables of unpaired Majorana zero modes confined in chaotic and superconducting billiards. The final chapter concerns magnetic adatoms, promising small logic units future computer technologies. In particular, an analysis on the relation between the symmetries of isolated nanomagnets and their magnetic stability is performed. Show less
A plasma is an ionized gas with very low electrical resistivity. As such, magnetic field lines are 'frozen in' and move with the fluid. Magnetic field lines that are linked, knotted and... Show moreA plasma is an ionized gas with very low electrical resistivity. As such, magnetic field lines are 'frozen in' and move with the fluid. Magnetic field lines that are linked, knotted and tangled, cannot be undone by the fluid motions. In this thesis we investigate how this linking and knottedness influences the plasma dynamics through numerical simulations. One of the main results is the identification of a novel, self-organizing equilibrium, where every field line is linked with every other one. In such a structure all the field lines lie on toroidal magnetic surfaces, and the entire structure resembles the famous topological structure of the Hopf fibration. This magnetic equilibrium is localized, and kept in balance by a finite external pressure. Through resistive effects the structure slowly expands while the magnetic energy is dissipated. This research, and the novel structures identified have implications for nuclear fusion research and the study of astrophysical plasma phenomena. Show less
The main focus of this Thesis is the behaviour of two-dimensional materials,namely (anti)-ferromagnetic materials in the first two chapters, which showtopological phases, and energetic square ice... Show moreThe main focus of this Thesis is the behaviour of two-dimensional materials,namely (anti)-ferromagnetic materials in the first two chapters, which showtopological phases, and energetic square ice in the third and fourth chapter.The magnetic materials are of interest in part due to foreseen practical applicationsin which skyrmions can act as data carriers for which we have shownthat skyrmions can exist in the ground state. Energetic square ice is of theoreticalinterest due to its anomalous behaviour at the infinite-order phasetransition and as a purely mathematical analytically solvable model. We usedthis model to test the order parameter we constructed that, by definition, canbe used to detect these infinite-order phase transitions. We also show agreementbetween conjectured and known properties for energetic square icewith special boundaries and show the existence of oscillations that go beyondcurrent theories. Show less
Gold nanorods are ideal candidates for complementing fluorophores in labelling applications. The presence of the surface plasmon resonance generates large absorption and scattering cross sections,... Show moreGold nanorods are ideal candidates for complementing fluorophores in labelling applications. The presence of the surface plasmon resonance generates large absorption and scattering cross sections, thus making the detection of single nanoparticles possible under a light microscope. The plasmon of gold nanorods depends on the ratio between their width and length and covers the range between 540nm for spheres and even above 800nm for elongated particles, thus almost the entire visible and near-infrared spectrum. The surface plasmon presents great opportunities in (bio-)sensing, enhanced spectroscopies, photothermal therapy and for concentrating light below the diffraction limit. Show less
Since the discovery of enzymes as biological catalysts, the mechanism of enzymatic reactions has been a key question to enzymologists. Elucidating the reaction kinetics and the nature of enzymatic... Show moreSince the discovery of enzymes as biological catalysts, the mechanism of enzymatic reactions has been a key question to enzymologists. Elucidating the reaction kinetics and the nature of enzymatic intermediates are necessary to understand such reactions. An important challenge in these studies is the limited lifetime of such intermediates, usually on the time scale of milliseconds to seconds. Therefore, a suited trapping method is required. Rapid freeze-quench (RFQ) is a proven technique to trap the intermediates on the time scale of milliseconds. The RFQ technique has been mostly combined with electron paramagnetic resonance (EPR) spectroscopy to reveal the nature of the paramagnetic intermediates involved in enzymatic reactions. In this thesis, we improve and extend the combination of conventional RFQ technique with EPR spectroscopy up to a microwave frequency of 275 GHz to trap and characterize the intermediates involved in the enzymatic reduction of O2 by small laccase (SLAC). Show less
Complex systems, from financial markets to the brain, exhibit heterogeneous structures and non-stationary dynamics. These characteristics manifest themselves in the diversity of the elements in a... Show moreComplex systems, from financial markets to the brain, exhibit heterogeneous structures and non-stationary dynamics. These characteristics manifest themselves in the diversity of the elements in a system, and in the changing behaviour over time. Capturing and understanding this heterogeneity via appropriate models, can have important implications not only for science, but also for societal challenges like predicting the next financial crisis or developing advanced brain imaging techniques. In this thesis, we use the maximum-entropy approach to introduce a new class of statistical models, which captures part of the observed structural and/or temporal heterogeneity in the system. The models are applied to various real-world complex systems, and are used to address different problems. Show less
