The theory describing physics at the highest energy scales likely contains extra dimensions, whose internal degrees of freedom result in many massive field and particles. At accelerator experiments... Show moreThe theory describing physics at the highest energy scales likely contains extra dimensions, whose internal degrees of freedom result in many massive field and particles. At accelerator experiments these fields and particles generally decouple from the low energy physics. However, in cosmology gravity couples everything, thereby invalidating the decoupling assumption. In this thesis we have shown that massive particles and field that do not decouple during cosmological inflation will generate corrections, which lead to possibly observable features in the Cosmic Microwave Background. Furthermore, in specific setups where the massive particles and fields do decouple their stability can still be affected by the low energy physics energy scale Show less
Although the extracellular matrix (ECM) is the key determinant of the mechanical behavior and stability of tissue, remarkably little is known on this tissue component. Most biomedical research on... Show moreAlthough the extracellular matrix (ECM) is the key determinant of the mechanical behavior and stability of tissue, remarkably little is known on this tissue component. Most biomedical research on the human aorta focuses on biochemical analysis of tissues or the properties of specific cells in the aorta. We show that a physics-based approach can yield important complementary insight. By measuring the mechanical response of the ECM by AFM and imaging it with multi-photon microscopy, we show that the spatial organization of the network structure of collagen fibers plays an important role. First we show how aneurysms, a local dilatation of the arterial wall, are caused by profound defects in collagen network. The collagen fibers in het healthy aorta are organized in a loose braiding of collagen ribbons, while the aneurysmatic tissue show dramatically altered collagen architectures with loss of the collagen knitting. Evaluation by AFM shows how this altered network could explain the failure of the tissue. In a follow-up study, we examine the effects of enzymatic digestion of the ECM of the aortic wall. By starting with real tissue and selectively removing different elements, we are able to measure the contribution of the different constituents of the ECM to the mechanical properties of the whole tissue. We also show how the content of neutrophils is able to mimic the observed change in mechanical response from a healthy aorta to an aneurysm. Finally we will show first results on the disease of atherosclerosis, another common vascular disease. The collagen structure of the cap changes during the growth of the atherosclerotic plaque and we discuss its mechanical implications. This study gives key insights in the failure mechanism of two common pathologies and provides biomedical researchers a new, physics-oriented view to organs, with implications for the study of wound healing, myocardial infarction and cancer cell migration. Show less
The MiniGRAIL detector is a cryogenic 68 cm diameter spherical gravitational wave antenna made of CuAl(6%) alloy with a mass of 1400 Kg and a resonance frequency of 2.9 kHz. Unlike other types of... Show moreThe MiniGRAIL detector is a cryogenic 68 cm diameter spherical gravitational wave antenna made of CuAl(6%) alloy with a mass of 1400 Kg and a resonance frequency of 2.9 kHz. Unlike other types of gravitational wave detectors, a single sphere is capable of determining direction and polarization of GW signal, because it has five degenerate modes of oscillation that interact with gravitational waves. This thesis is focused on building the full acquisition system and preparation of MiniGRAIL for a scientific run, with a full read-out configuration at millikelvin temperatures. We have also performed a test run to evaluate the calibration procedure we developed. During the run we have reached a peak strain sensitivity of 3E-20 Hz^(-1/2) at 4.2K. For current system configuration and thermodynamic temperature of the sphere of 20 mK, the estimated peak sensitivity level is 2E-22 Hz^(-1/2) and the minimal detectable Fourier amplitude of gravitational wave burst of 1E-22. In the last chapter of the thesis we present a SQUID-based scheme to measure the displacement of a nanomechanical resonator at cryogenic temperature. We demonstrate its potential by cooling an ultrasoft silicon cantilever to a noise temperature of 25 mK, corresponding to a subattonewton thermal force noise of 0.5 aN/Hz^(1/2). Show less
This thesis describes the development of a combined high-pressure/ultrahigh-vacuum flow reactor for the study of model catalysts by means of surface x-ray diffraction and grazing incidence small... Show moreThis thesis describes the development of a combined high-pressure/ultrahigh-vacuum flow reactor for the study of model catalysts by means of surface x-ray diffraction and grazing incidence small angle scattering. The system was used to measure a stability diagram for the different oxide phases (surface oxide, bulk-like oxides) that exist on Pd(100) during catalytic CO oxidation at near ambient pressures. As soon as an oxide was present the reactivity of the surface was found to be mass transfer limited by the flux of CO molecules reaching the surface. Experiments on spontaneous reaction oscillations of the CO oxidation rate on Pd(100) reveal that a high density of steps strongly alters the stability of the thin, catalytically active palladium oxide film. It is shown that stabilization of the metal, caused by the steps and consequent destabilization of the oxide, is at the heart of the well-known reaction rate oscillations exhibited during CO oxidation at atmospheric pressure. Lastly reaction oscillations on supported Pd nanoparticles are shown to be accompanied by shape changes of the particles consistent with the formation and removal of a thin palladium oxide film on the particles. Show less
The interfacing of biomolecules to nanostructures, electrode surfaces and/or optical components constitutes the new discipline of bioelectronics. It is based on electron transfer between a protein... Show moreThe interfacing of biomolecules to nanostructures, electrode surfaces and/or optical components constitutes the new discipline of bioelectronics. It is based on electron transfer between a protein and an electrode, and can be monitored by amperometric techniques. The integration of biomolecules with electronics has strong potential for applications in a variety of functional devices, ranging from biosensors to solar cells. In this thesis we explore the possibilities of constructing a bio-electronic device for solar energy conversion by surface-assembly of photosynthetic pigment-protein complexes on a gold electrode. Optical excitation of the photosynthetic pigments gives rise to charge separation in the so-called reaction center complex. Energy conversion is completed by subsequent electron transfer to the electrode, generating a light-induced electric current. The data shows that light-harvesting complexes can be immobilized directly on a gold surface and on various SAM surfaces whilst retaining their full optical functionality. All energy transferring reactions still take place and are similar to those observed for the detergent-solubilized proteins. Furthermore it is shown that LH1 complexes exhibit a remarkable photostability, even under ambient conditions. These findings demonstrate the possibility of interfacing a fully functional energy transferring protein complex to a conducting substrate in the presence of oxygen, with the capacity of converting light into electrical energy. Show less
The influence of temperature on various elastic properties of DNA is analyzed close to elastic instabilities. The buckling transition under compression is interpreted as decreasing. Under torsion a... Show moreThe influence of temperature on various elastic properties of DNA is analyzed close to elastic instabilities. The buckling transition under compression is interpreted as decreasing. Under torsion a first order phase transition is described ending in an important multi-plectoneme phase that changes to a line of critical points in the infinite chain limit. Show less
This thesis presents scanning tunneling spectroscopy (STS) measurements of the spatial distribution of the density of states (DOS) of materials where electron correlations play a role. In the... Show moreThis thesis presents scanning tunneling spectroscopy (STS) measurements of the spatial distribution of the density of states (DOS) of materials where electron correlations play a role. In the manganite La0.67Ca0.33MnO3, the measurements show that flat films with atomically smooth terraces are electronically homogeneous, while rough films with no apparent terraces are electronically inhomogeneous and respond to applied magnetic fields in a way consistent with the percolation model of colossal magnetoresistance. The flat surfaces appear to have an electronic structure different from the bulk due to the change in symmetry at the surface. In La0.5Sr0.5CoO3 films the thickness drives the electronic homogeneity. A film thinner than a critical thickness t__ was electronically inhomogeneous, while a film thicker than t__ was found to be electronically homogeneous. Both films were rough, indicating that surface morphology plays no role here. STS measurements of the DOS of a ferromagnetic/superconducting bilayer (CuNi alloy/Nb) were performed to probe the phase of the superconducting order parameter induced in the ferromagnet. DOS measurements varied from deeply gapped (zero phase) to flat, with no reproducible signs of inverted spectra (_ phase). The seeming anticorrelation between film morphology and spectral character suggests the presence of Ni-clusters in the CuNi layer. STM/S measurements of the quasiparticle DOS of a ferromagnetic/superconducting bilayer (CuNi alloy/Nb) were performed to probe the zero and pi phases of the order parameter induced in the ferromagnet. DOS measurements on one bilayer varied from deeply gapped (zero phase) to flat, with occasional but irreproducible inverted spectra (pi phase). The seeming anticorrelation between film morphology and spectral character suggests the presence of Ni-clusters in the CuNi layer. Show less
The electronic structure of transition-metal sites can be probed by electron-paramagnetic-resonance (EPR) spectroscopy. The study of high-spin transition-metal sites benefits from EPR spectroscopy... Show moreThe electronic structure of transition-metal sites can be probed by electron-paramagnetic-resonance (EPR) spectroscopy. The study of high-spin transition-metal sites benefits from EPR spectroscopy at frequencies higher than the standard 9.5 GHz. However, high-frequency EPR is a developing field. In particular it is still difficult to achieve the sensitivity needed to study high-spin transition-metal sites in proteins and enzymes. In this thesis we show that high-quality EPR spectra of mM frozen solutions of high-spin Fe3+ proteins can be obtained at 275.7 GHz in continuous-wave mode using a single-mode cavity. This new possibility is exploited in the study of the high-spin transition-metal sites in the proteins rubredoxin, desulforedoxin and human serum transferrin. Moreover, a multi-frequency EPR study of a high-spin Fe2+ imidodiphosphinate complex and a pulsed ENDOR study at 94.9 GHz of a high-spin Co2+ imidodiphosphinate complex are described. Finally, another spectroscopic technique, namely resonance-Raman spectroscopy, is employed to establish the configuration of spheroidene in the photosynthetic reaction center of Rhodobacter sphaeroides. Show less
Resistive switching memories have gained an increased interest due to the possibilities for downscaling of memory devices down to a few nanometers. These memories consist of a resistive material... Show moreResistive switching memories have gained an increased interest due to the possibilities for downscaling of memory devices down to a few nanometers. These memories consist of a resistive material sandwiched between two metal electrodes, and applying a voltage between them induces resistance switching. In this thesis we study the specific case when switching is due to the reversible formation of a conductive path that connects and disconnects the electrodes. We investigate the electrical conductance properties and transport mechanisms in solid electrolyte memory devices, to gain a fundamental understanding of conductance switching. Our model system consists of Ag2S thin films with a Ag bottom electrode and a Pt AFM or STM tip as top electrode. We present a quantitative analysis of the steady state transport that leads up to resistance switching. We discuss the relation between stoichiometry and resistance changes in the material, and the necessity of Ag supersaturation prior to nucleation and switching. We also discuss the possible presence of two distinct switching mechanisms in Ag2S. Our findings could be extended to other semiconductor materials with mobile donors or acceptors. Show less
A dynamic vortex line traces out a world sheet in spacetime. This thesis shows that the information of all its dynamic behaviour is completely contained in the world sheet. Furthermore a... Show moreA dynamic vortex line traces out a world sheet in spacetime. This thesis shows that the information of all its dynamic behaviour is completely contained in the world sheet. Furthermore a mathematical framework for order–disorder phase transitions in terms of the proliferation of such vortex world sheets is presented, leading to the prediction of quantized vortex lines of electric current in phase-disordered superconductors. Show less
Superconducting correlations can penetrate in a ferromagnet via proximity effect but over a very short length of the order of a few nanometers because ferromagnetic exchange field tries to align... Show moreSuperconducting correlations can penetrate in a ferromagnet via proximity effect but over a very short length of the order of a few nanometers because ferromagnetic exchange field tries to align the antiparallel spins of electrons in a Cooper pair. Theoretically, it was suggested that rather a long-range proximity effect can occur if spin-triplet (with parallel spins) Cooper pairs are generated at the interface that requires a magnetic inhomogeneity (spin-active interface). Experimentally, it was first observed at the Delft University using CrO2 (a half metallic ferromagnet). In these devices the induced supercurrent was not both well controlled and well understood. We have provided new evidence that supercurrents can flow through CrO2 films, deposited on sapphire substrates, over a length of 1_m. The analysis shows that these films exhibit six-fold magnetic-anisotropy that might provide the required spin-active interface. Still, low reproducibility suggests a weak control over the spin-active interface. Such a control appears better with an artificially created spin-active interface, using an additional ferromagnetic layer of Ni (2nm) with CrO2. From investigations, it suggests that there are other scattering phenomena (different spin dependent magnetic scattering from different magnetic layers) or magnetic moment disorder at the interface involved to generate the odd-frequency spin-triplet supercurrent. Show less
Light is a ubiquitous carrier of information. This information can be encoded in the intensity, direction, frequency and polarisation of the light and, which was described more recently, in its... Show moreLight is a ubiquitous carrier of information. This information can be encoded in the intensity, direction, frequency and polarisation of the light and, which was described more recently, in its orbital angular momentum. Although creating light beams with orbital angular momentum is relatively easy, measuring this property has proven to be difficult. In this thesis we present two fundamental methods to solve this problem. First, we show that by analysing the interference pattern behind a multi-pinhole interferometer, we can determine the phase and amplitude of the light impinging the pinholes, making it possible to determine the orbital angular momentum of the incoming light beam. A multi-pinhole interferometer can be scaled to arbitrary sizes, making it suitable for studying optical fields that stretch out over large distances, that can be expected in, for instance, astrophysics. The second method is based on transforming the helical wave fronts that are associated with light beams with orbital angular momentum to distinguishable, titled wave fronts that can be easily sorted by a lens. This method works for single photons, making it a key piece in a high-dimensional optical communication scheme. This thesis provides theory, simulations and measurements on both detection methods. Show less
In this thesis we investigate diverse aspects of spatial coherence of light. Non-classical fields containing two photons can be generated by a nonlinear optical process known as spontaneous... Show moreIn this thesis we investigate diverse aspects of spatial coherence of light. Non-classical fields containing two photons can be generated by a nonlinear optical process known as spontaneous parametric down conversion (SPDC). Among the questions we consider are: What is so special about spatial entanglement? How is it revealed in the fourth-order correlations? What are the differences between a highly entangled and a classically correlated state? How can the number of modes be manipulated and measured? For a two-photon system, we measure both intensities and two-photon correlations. To get deeper insights into how coherence affects interference, we also investigate completely classical sources. Show less
In eukaryotic cells, genomic DNA is organized in chromatin fibers composed of nucleosomes as structural units. A nucleosome contains 1.7 turns of DNA wrapped around a histone octamer and is... Show moreIn eukaryotic cells, genomic DNA is organized in chromatin fibers composed of nucleosomes as structural units. A nucleosome contains 1.7 turns of DNA wrapped around a histone octamer and is connected to the adjacent nucleosomes with linker DNA. The folding of chromatin fibers effectively increases the compaction of genomic DNA, but it remains accessible for enzymatic reactions. This apparent paradox motivates a detailed study of the dynamics of chromatin. A structural model at the molecular level will shed light on how cells regulate the compaction and dynamics of genomic DNA. This thesis presents the results of an experimental study on the dynamics of chromatin higher-order folding. Using magnetic tweezers, we observed force-dependent structural changes within chromatin fibers at the single nucleosome level. Show less
This dissertation is about transport and electronic properties of two types of electronic states occuring at the edges, which are protected by symmetry between positive and negative energies. One... Show moreThis dissertation is about transport and electronic properties of two types of electronic states occuring at the edges, which are protected by symmetry between positive and negative energies. One type of these states is shown to occur universally in graphene. It is also described how another type of edge states, Majorana fermions, can be used for topological quantum computation. Show less
Optical frequency conversion is important nonlinear process for generating coherent radiation in spectral regions where there are no convenient laser sources. For example, nonlinear processes are... Show moreOptical frequency conversion is important nonlinear process for generating coherent radiation in spectral regions where there are no convenient laser sources. For example, nonlinear processes are used to generate ultraviolet radiation for biomedical applications or mid-infrared radiation in the wavelength range of 3–12 μm for remote sensing of atmosphere. Besides these practical applications, frequency conversion can be used to create entangled photon pairs in quantum optics experiments to test the fundamental laws of quantum mechanics. This thesis describes an experimental investigation of second harmonic generation in III-V semiconductor photonic structures. These nanostructures have both wavelength and subwavelength dimensions. In particular, ensembles of aligned gallium phosphide nanowires and two-dimensional aluminum gallium arsenide photonic crystal slabs with a square lattice of holes are studied. In both cases, the III-V semiconductor material provides a large second-order nonlinearity, while the special arrangement of dielectric material of the nanostructure introduces additional dispersion. This extra dispersion can be used to phase match the nonlinear process in order to make frequency conversion efficient. We demonstrate that it is possible to resonantly couple to leaky modes of a photonic crystal slab at both the fundamental and second harmonic frequency and enhance the second harmonic signal ~10,000 times. Show less
This thesis describes the construction of a second generation high-pressure, high-temperature scanning tunneling microscope, the ReactorSTM, with which the surfaces of catalysts can be studied... Show moreThis thesis describes the construction of a second generation high-pressure, high-temperature scanning tunneling microscope, the ReactorSTM, with which the surfaces of catalysts can be studied under relevant reaction conditions. Furthermore, the thesis describes three separate catalytic systems at ~ 1 bar, and elevated temperatures. Firstly, NO reduction on Pt(100), in which a mathematical model for the reaction mechanism, following Langmuir-Hinshelwood kinetics, is proposed. Secondly, CO oxidation, in which the Pt(110) surface is atomically resolved at high p, T. Thirdly, the thesis describes a successful pilot experiment about the hydrodesulphurization of thiophene, which is catalytically activated by molybdenum disulphide nano-crystallites on an Au(111) support. Show less
This thesis is devoted to the effects of disorder on two-dimensional systems of Dirac fermions. Disorder localizes the usual electron system governed by the Schroedinger equation. The influence of... Show moreThis thesis is devoted to the effects of disorder on two-dimensional systems of Dirac fermions. Disorder localizes the usual electron system governed by the Schroedinger equation. The influence of disorder on Dirac fermions is qualitevely different. We concentrate on a random mass term in the Dirac equation. We have discovered that Dirac fermions in graphene are localized by a random mass, without any transition into metallic state. The situation is entirely different for Dirac fermions in a p-wave superconductor. There electrostatic disorder appears in the Dirac equation as a random mass, which localizes the excitation, but only if the disorder is relatively weak. For large mass fluctuations a transition into metallic state appears. This qualitatively different response to disorder in graphene and in p-wave superconductors is explained by the appearance of Majorana bound states, which allow for resonant tunneling and metallic state. Electrostatic disorder in a d-wave superconductor represented as random vector potential in the Dirac equation. We look at the transmission of Dirac fermions for electrostatic potential with long- and short-range fluctuations. We study the interplay of electrical and mechanical properties of suspended graphene by calculating the correction to the conductivity due to its deformation by a gate electrode. Show less
By tuning control parameters like pressure, magnetic field or doping, a fermionic system can be driven to a state with vanishing Fermi energy and power law behavior in many observables. Such... Show moreBy tuning control parameters like pressure, magnetic field or doping, a fermionic system can be driven to a state with vanishing Fermi energy and power law behavior in many observables. Such fermionic quantum critical states have been identified in systems including heavy fermions, cuprates and pnictides. We study the superconducting transition in such systems. We propose that the superconducting instability, which is marginal in Fermi liquids, becomes relevant, leading naturally to a high transition temperature. This picture has been verified numerically in the 2-dimensional Hubbard model by using the Dynamical Cluster Approximation. We also propose tunneling experiments which can distinguish our mechanism from others. Show less
In this thesis we present a new method to simulate realistic three-dimensional networks of biopolymers under shear. These biopolymer networks are important for the structural functions of cells and... Show moreIn this thesis we present a new method to simulate realistic three-dimensional networks of biopolymers under shear. These biopolymer networks are important for the structural functions of cells and tissues. We use the method to analyze these networks under shear, and consider the elastic modulus, the non-affinity during deformation, the normal modes and the density of states. We expand our analysis to composite networks consisting of stiff and floppy filaments. In the final chapter of the thesis we incorporate the thermal and viscous interactions of the surrounding medium in the calculations, and present the results of the simulations of the shear frequency dependence of the network response. We find that non-affine reorientations are important for understanding the network response. These non-affine reorientations make the networks relatively soft under shear and delay the onset of stiffnening. In composite networks non-affine reorientations allow for an intricate interplay between the stiff and floppy filaments. The frequency-dependent response shows a transition from a soft, non-affine regime at low frequencies to a stiff, close-to-affine response at high frequencies. Show less
