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
The theoretical description of fermionic system with strong interaction is a very challenging open problem in physics. The most notable (but far from the only) experimental realization of this... Show moreThe theoretical description of fermionic system with strong interaction is a very challenging open problem in physics. The most notable (but far from the only) experimental realization of this type of systems are the cuprate superconductors which have zero electric resistivity. Even if onehas a good microscopic model for the description of these materials it is very hard to translate it to macroscopic observables which in principle can be experimentally checked. The problem is that in case of a relevant interaction one can not Taylor expand in the coupling constant in the low-energy regime in which we are most interested. On the other hand, because of the fermion sign problem Monte Carlo numerical techniques (which are succesful with bosonic models) do not work for fermions at finite density. This thesis is devoted to the applications of several methods to the research area described above. The common theme of these techniques is that they are (partly) motivated from high-energy physics: the research area which deals with particle physics, string theory etc. Show less
The nature of the Dark Matter is one of the biggest open questions in modern cosmology and particle physics. The work in this thesis concerns a search for the observational effects of one... Show moreThe nature of the Dark Matter is one of the biggest open questions in modern cosmology and particle physics. The work in this thesis concerns a search for the observational effects of one particular class of hypothetical Dark Matter particles, namely those that are allowed to decay. In decaying, X-ray photons are emitted and should be observable. One part of the thesis details the discovery of a potential Dark Matter decay signal in X-ray spectra of galaxies and galaxy clusters, and the subsequent efforts to identify its origin. To this end archival data and new observations are compared to the respective Dark Matter masses of the observed objects. Interpretations of the signal as an instrumental effect, or due to regular astrophysical processes are unsatisfactory. Although the Dark Matter interpretation remains plausible, definitive conclusions about the origin of the signal can not be drawn yet and will require measurements by next generation observatories. The last chapter of the thesis contains the proof-of-concept of a novel technique to search for such weak signals that combines increased statistical power with the ability to determine the physical origin of a signal, while avoiding some of the disadvantages of traditional methods. Show less
Parkinson’s disease is a neurodegenerative disease characterized by the presence of abnormal deposits of aggregated proteins in the brain tissue, known as Lewy bodies. The major components of Lewy... Show moreParkinson’s disease is a neurodegenerative disease characterized by the presence of abnormal deposits of aggregated proteins in the brain tissue, known as Lewy bodies. The major components of Lewy bodies are aggregated forms of a small presynaptic protein known as α-synuclein (α-syn). In this thesis we report on the intricacies of α-syn aggregation. Using an array of biophysical techniques we were able to observe the formation of the earliest α-syn oligomeric species – relatively stable dimers and tetramers – which are more easily formed than commonly assumed. Fluorescent labelling was shown to significantly affect the morphology of α-syn aggregates, which limits the applicability of this technique. From the growth kinetics of α-syn fibrillar seeds we conclude that the elongation of fibrils proceeds by a different mechanism than primary nucleation. Further, we studied the effect of solution conditions and surface effects on the growth of the α-syn aggregates. Using total internal reflection microscopy and confocal fluorescence imaging we observed the elongation of individual fibrils in real time, showing that this process proceeds by leaps and bounds. Show less
By combining low-energy electron microscopy (LEEM) with pulsed laser deposition (PLD), we have created a unique set-up to study the first stages of growth of complex metal oxides. We... Show more By combining low-energy electron microscopy (LEEM) with pulsed laser deposition (PLD), we have created a unique set-up to study the first stages of growth of complex metal oxides. We demonstrate this by investigating the growth of SrTiO3 (STO) and LaAlO3 (LAO) on STO in real-time. We follow growth by monitoring the intensity and the full-width-half-maximum (FWHM) of the specular diffracted beam at various energies. For layer-by-layer growth, we find the anticipated intensity peaks at the completion of each layer, and an oscillatory FWHM with the maximum at half-layer coverage. In the LAO on STO case, for optimal growth conditions and a LAO thickness above the critical thickness of 4 unit cells the interface between the band insulators shows conductivity. We obtain an electronic fingerprint of the growing material, by measuring the intensity of the specular beam as a function of energy at regular intervals during growth. Extending this fingerprint with the intensity dependence on the momentum parallel to the surface allows us to extract the band dispersion of unoccupied electron states of the sample surface. Significant differences in the unoccupied band structure develop between samples which are conducting and non-conducting. Show less
This work covers two closely related topics: a theoretical study on the origins of friction and an experimental study on the growth of graphene. Both fundamental studies are focusing on the atomic... Show moreThis work covers two closely related topics: a theoretical study on the origins of friction and an experimental study on the growth of graphene. Both fundamental studies are focusing on the atomic processes involved. The study on friction treats the dissipation that takes places at one single friction contact. We show that the current explanations result in a discrepancy that we solve by evalutation of the mass involved: this mass is orders of magnitude smallar than assumed. The very small and dynamic mass at a friction contact forms an efficient channel of dissipation. This explanation allows us to understand and predict the friction behavior of surfaces at both the small and large scale. The study of graphene growth investigates the growth process of graphene at the atomic scale with a Scannning Tunneling Microscope in situ. We use our high- and, variable-temperature STM to determine the lowest nucleation temperature of graphene on Ir(111). Additionaly, individual steps that follow up each other during growth are clarified and presented. The graphene film closure is studied as well, which showed that graphene introduces internal strain in order to prevent local lattice defects. Our results are important for the improvement of the quality of graphene. Show less
We present a novel strategy to overcome this limitation and create programmable me chanical metamaterials, where the response of a single structure is determined and can be changed by the... Show more We present a novel strategy to overcome this limitation and create programmable me chanical metamaterials, where the response of a single structure is determined and can be changed by the amount of lateral confinement. Show less
A foam is not a homogeneous material, but consists of a large number of small air bubbles. The whole is more than the sum of its parts: even though the behavior of a single bubble is easy... Show more A foam is not a homogeneous material, but consists of a large number of small air bubbles. The whole is more than the sum of its parts: even though the behavior of a single bubble is easy to understand, their collective behavior is much more complicated and completely different. The reason for this is that a deformation of the whole is only reflected partially in the deformation of individual bubbles. Instead, a large part of the deformation is reflected in a change in the structure of the foam. In this thesis, we investigate this change in structure. In the first part of this thesis, we use a simple microscopic computer model to simulate the response of a foam when it is deformed by a tiny amount, and measure how far we need to deform the foam until it is irreversibly deformed. In the second part of this thesis, we focus on an experiment, where we measure the response of a two-dimensional foam when it is deformed at the edges. We observe that the response of bubbles in the center of the foam qualitatively depends on how densely the bubbles are packed together. Show less
The Lead Zeppelin is a small piece of Lead that is made to float in a magnetic field. At low temperatures - 4.2 K in this thesis, the boiling point of Helium - Lead is a superconductor, and... Show more The Lead Zeppelin is a small piece of Lead that is made to float in a magnetic field. At low temperatures - 4.2 K in this thesis, the boiling point of Helium - Lead is a superconductor, and acts as a ‘mass on a spring’, where the spring is formed by the magnetic field. As such, it is incredibly sensitive to externally applied forces. Other techniques are already capable of measuring forces in the range of zeptoNewtons; the Lead Zeppelin has the potential to be even more sensitive. The development of such increasingly sensitive force sensors paves the way to all sorts of interesting experiments, such as probing the quantum mechanics of heavy objects. At this moment, the Lead Zeppelin is already so sensitive that the motion of the laboratory, which is only a few nanometers at 10 Hz, is picked up so easily that it dominates the Lead Zeppelin. Show less
