For more than 65 years, scientists have been fascinated by the idea to miniaturize electrical circuits toward the smallest length scales. One particular way is inspired by nature itself,... Show moreFor more than 65 years, scientists have been fascinated by the idea to miniaturize electrical circuits toward the smallest length scales. One particular way is inspired by nature itself, specifically to assemble electrical components and switches from atoms and molecules. The molecules typically used have dimensions of the scale of a few nanometers (1 nanometer = 0,000000001 meter). The scientific research area that represents the study of electrical currents through molecules is called "molecular charge transport" or "molecular electronics". In this thesis, I have performed fundamental research on charge transport through various molecules. Specifically, I have investigated a special type of molecule that has the ability to change its spin state. To test these functional molecules, I have used a more robust type of molecular device that enables me to bridge the size gap mentioned above. This thesis has led to two important new insights. First, the properties of a switchable molecular device can be strongly enhanced artificially by making use of a charge transport mechanism called multiple inelastic cotunneling. Second, we show that the spin transition phenomenon can take place in a molecular-nanoparticle ensemble. Show less
DNA-hosted silver clusters (Ag:DNAs) have attracted a lot of attention due to their small size (~20 atoms), wide range of applications in chemistry and biology, and sequence-dependent optical... Show moreDNA-hosted silver clusters (Ag:DNAs) have attracted a lot of attention due to their small size (~20 atoms), wide range of applications in chemistry and biology, and sequence-dependent optical tunability. Most of the previous studies are focused on the ensemble of emitters in solution. However, little is known about the optical properties of individual emitters, which is a crucial step towards understanding of their real nature, otherwise lost in ensemble averaging. We show that the excitation and emission spectra of individual emitters are broad even at 1.7 K (FWHM ~25 nm). Also, polarization measurements indicate that the excitation is not strongly dependent on the polarization of excitation light, whereas the emission is highly linearly polarized. Furthermore, from time-resolved measurements, we can conclude that the emission of single emitters can be fitted with single exponential decay curve, whereas the emitters organized with nanometer precision on the DNA scaffolds show double–exponential decay. This indicates the interaction between densely packed Ag:DNAs. Finally, we show that the DNA tubes can be used as a nano-contact glue between the colloidal particles functionalized with short DNA strands. Show less
Polymers are the main building blocks of many biological systems, and thus polymer models are important tools for our understanding. One such biological system is the large scale organisation of... Show morePolymers are the main building blocks of many biological systems, and thus polymer models are important tools for our understanding. One such biological system is the large scale organisation of chromatin. A key question here, is how during cell division the chromosomes can separate without entanglement and knotting. One proposal is that this achieved by a specific spatial organisation of the chromosomes, known as the "fractal globule". Using Monte Carlo simulations, we found that fractal globules are unstable and thus cannot represent the biological system without further ingredients. Another proposal is that topological effects cause spatial separation of the chromosomes. These topological effects can be studied using simulations of nonconcatenated ring polymers. Using a compute device called the Graphics Processing Unit, very detailed and long simulations were carried out. From these a picture emerged in which ring polymers behave much slower than was found in previous studies. A second biological system studied here is the folded state of the protein. This is modeled by the Hamiltonian walk. Here, instead of simulations, we exactly enumerated all Hamiltonian walks of the 4x4x4 cube. Interestingly, simulations show that for larger systems many more walks exist than previously estimated. Show less
Although the Standard Model of elementary particles successfully describes the Universe up to the smallest known scales, we know that there exists a number of observational phenomena, which do not... Show moreAlthough the Standard Model of elementary particles successfully describes the Universe up to the smallest known scales, we know that there exists a number of observational phenomena, which do not find explanation in the framework of this theory. Among these problems are Neutrino Oscillations, Dark Matter and the Baryon Asymmetry of the Universe. In this thesis, we are studying the Neutrino Minimal Standard Model (nuMSM), a minimalistic extension of the Standard Model, which can explain all these three phenomena simultaneously, by adding only three right-handed neutrinos to the known three left-handed neutrinos. It is shown that the two heavier sterile neutrinos with masses below the mass of pi-meson, could have been present in such large amounts in the early Universe that they spoil the otherwise excellent agreement between the Standard-Model prediction of light nuclei production during the Big-Bang Nucleosynthesis and the astrophysical observations. In this way, masses of sterile neutrinos are excluded from below, which reduces the potentially interesting parameter space for future accelerator searches. Another effect of sterile neutrinos in the early Universe that is studied is the production of large-scale magnetic fields due to the so-called Chiral Magnetic Effect. Show less
Ewing sarcoma (ES) is a special type of bone cancer, first described by Dr. James Ewing in his paper __Diffusive endothelioma of bone__. Today Ewing sarcoma represents the second most common bone... Show moreEwing sarcoma (ES) is a special type of bone cancer, first described by Dr. James Ewing in his paper __Diffusive endothelioma of bone__. Today Ewing sarcoma represents the second most common bone cancer among adolescents and young adults. Contrary to the positive achievement in treatment of localized tumors, the long-term (5-years) survival for Ewing sarcoma patients with metastasis, however, remain below the 30% mark. In this thesis a report on experimental work aiming for a better understanding of the mechanisms underlying Ewing sarcoma metastasis is presented. Two distinct mechanisms are investigated: (1) a biochemical approach in which the initial steps in the CXCR4 signaling cascade are followed, and (2) a biophysical approach in which the guidance of Ewing sarcoma metastasis by the stiffness of their microenvironment is demonstrated. The results presented in this thesis provide deeper insights into the mechanisms controlling signaling of the chemokine receptor CXCR4 and into the role of the micro-environment in Ewing sarcoma cells behavior.Through various experimental approaches it was shown that both biochemical and biophysical guidance control how Ewing sarcoma develops into its distinct metastatic phenotype. Show less
Gaussian random fields pervade all areas of science. However, it is often the departures from Gaussianity that carry the crucial signature of the nonlinear mechanisms at the heart of diverse... Show moreGaussian random fields pervade all areas of science. However, it is often the departures from Gaussianity that carry the crucial signature of the nonlinear mechanisms at the heart of diverse phenomena, ranging from structure formation in condensed matter and cosmology to biomedical imaging. The standard test of non-Gaussianity is to measure higher-order correlation functions. This work takes a different route. It is shown how geometric and topological properties of Gaussian fields, in particular the statistics of extrema and umbilical points, are modified by the presence of a non-Gaussian perturbation. The resulting discrepancies give an independent way to detect and quantify non-Gaussianities. Both local and nonlocal mechanisms that generate non-Gaussian fields are considered, both statically and dynamically through nonlinear diffusion. The effects of coarse-graining are also investigated. Show less
In this thesis novel techniques are described which are developed to analyze or predict the efficacy of pharmacotherapy for pain. In Chapter 2 an overview is presented on recent pharmacokinetic... Show moreIn this thesis novel techniques are described which are developed to analyze or predict the efficacy of pharmacotherapy for pain. In Chapter 2 an overview is presented on recent pharmacokinetic pharmacodynamic (PKPD) modeling in acute and chronic pain. Chapter 3 describes the analgesic effect of a capsaicin patch in diabetic painful neuropathy (DPN) pain patients. A longitudinal population PD analysis is performed. In Chapter 4 a subgroup analysis is performed on pooled data from 4 multicenter trials on the effect of capsaicin 8% patch in post herpetic neuralgia (PHN). Apart from longitudinal and mixture analyses, covariates are examined to identify predictors of efficacy. In Chapter 5 the analgesic effect of orodispersible oxycodone versus orodispersible paracetamol for the management of breakthrough pain is quantified using a novel pharmacodynamic model. ________________________________Finally, Chapter 6 describes the effect of tapentadol versus morphine on conditional pain modulation (CPM) in healthy volunteers. A difference in CPM engagement between these two __opioids__ might proof the difference in mechanisms of action between the classical mu opioid receptor (MOR) agonist and the combined MOR-noradrenalin reuptake inhibitor (NRI) compound. Show less
We first investigate the microscopic working principle of the nanowire superconducting single-photon detectors (SSPDs), and we find that the edge of the nanowire is much more sensitive than the... Show moreWe first investigate the microscopic working principle of the nanowire superconducting single-photon detectors (SSPDs), and we find that the edge of the nanowire is much more sensitive than the central part. The experimental results agree quantitatively with the theory based on a photon-assisted vertex- entry model. We then explore its potential to be used as a probe for near-field detection. Our calculations show that the SSPDs have a much higher signal collection efficiency than the conventional near-field optical microscopy, and that their spacial resolution can reach 20 nm. With photon number resolving ability, a SSPD fabricated on a micro-pillar can be used to investigate the quantum information of the optical near-field at subwavelength scales. Show less
The thesis is devoted to applications of the anti de Sitter/Conformal field theory correspondence (AdS/CFT, also called holography) to various problems in different areas of theoretical physics. We... Show moreThe thesis is devoted to applications of the anti de Sitter/Conformal field theory correspondence (AdS/CFT, also called holography) to various problems in different areas of theoretical physics. We make use of AdS/CFT to get insights into the physics of superconductors, quark-gluon plasma, and to study properties of quantum field theories on non-causal backgrounds. In the first part of the thesis we construct a holographic model of a Bardeen-Cooper-Schrieffer-like superconductor and demonstrate that the Cooper instability of Fermi-liquids can be naturally described in holographic terms. We show that both the superconducting phase and the BEC/BCS crossover appear naturally. In the second part we address the problem of quark-gluon plasma formation in heavy ion collisions. We study the effect of finite chemical potential on this process and calculate physical properties of the resulting deconfined state. The third part is dedicated to study of evolution of a quantum system with violated causality. Using AdS/CFT we can map the complicated and poorly defined non-causal quantum dynamics onto a classical spacetime with closed timelike curves. Doing that we have derived the Green's function of the QFT and demonstrated that evolution of a quantum system can be consistent and non-pathological even at broken causality. Show less
Topological superconductors are a novel type of superconductors that carry Majorana particles at their boundary. These surface states are equal superpositions of electrons and holes, and hence are... Show moreTopological superconductors are a novel type of superconductors that carry Majorana particles at their boundary. These surface states are equal superpositions of electrons and holes, and hence are their own anti-particles. There has been a recent surge of theoretical and experimental effort to realize these special particles in the lab. While first observations support the theoretical predictions, fail-safe experimental evidence for Majoranas is still needed. Part of the challenge is that due to their vanishing charge they are not easily detected electrically. The topic of this thesis is the proposal and study of electrical signatures of Majoranas that are present in spite of their charge neutrality. By applying scattering and random matrix theory we first examine their generic properties. With the tool of numerical simulations we then put our predictions to test on realistic systems. Show less
Quantum dots (QDs) are nm-size semiconductor structures that hold promise for applications in quantum information. One important requirement, however, is to achieve near-unity interaction between... Show moreQuantum dots (QDs) are nm-size semiconductor structures that hold promise for applications in quantum information. One important requirement, however, is to achieve near-unity interaction between photons and (singly charged) QDs. For this purpose, we make use of oxide-apertured micropillars that confine light in a small volume and thereby enhance the interaction. A QD transition coupled to the cavity mode can turn a transmittive cavity into a reflective one, and this property can be used to create entanglement between the spatial state of a photon and the spin state of a charge in the QD. This thesis consists of two parts: 1) in the first part we demonstrate techniques to monitor and fine tune the oxide aperture size and shape. By controlling the oxide shape we show we can fabricate polarization degenerate microcavities. 2) In the second part, perform cryogenic experiments with such a QD-cavity system. We investigate neutral and singly charged QDs as function of polarization and find this offers a way to assess the QD coherence. Next, we demonstrate a novel effect where charges around the QDs have a strong feedback with the QD properties. Finally, we present a homodyne detection technique of the QD coherence and phase shift. Show less
The research contained in this thesis lies at the interface between quantum phyiscs, nanotechnology and the theory of computation. Its goal is to design electronic circuits to realize computations... Show moreThe research contained in this thesis lies at the interface between quantum phyiscs, nanotechnology and the theory of computation. Its goal is to design electronic circuits to realize computations that follow the laws of quantum mechanics, and which would allow to execute some algorithms faster than their classical counterparts - for instance, algorithms to solve chemical problems. In particular, these circuits use Majorana modes, very special states which appear in superconductors and are theoretically predicted to protect information from the environment, so that the computation can be executed without errors. The role of my research was to design electronic circuits able to use this fascinating property. Hence, this work is a bridge between some very abstract mathematical ideas and the very concrete world of electronic circuits, made out of inductors and capacitors. Show less
Low Energy Electron Microscopy (LEEM) is a microscopy technique typically used to study surface processes. The sample is illuminated with a parallel beam of electrons under normal incidence and the... Show moreLow Energy Electron Microscopy (LEEM) is a microscopy technique typically used to study surface processes. The sample is illuminated with a parallel beam of electrons under normal incidence and the reflected electrons are projected onto a pixelated detector, where an image is formed. In the first part of this thesis, we use LEEM to study the behavior of submonolayers of gold on Si(111). After a thorough analysis of the Si-Au system, we describe the behavior of these (sub)monolayers when exposed to alkanethiols. In the second part of this thesis we move away from pure surface physics and introduce two new applications for LEEM. The first of these, Low-Energy Electron Potentiometry (LEEP), can be used to visualize electrical conductance. We show that for layered two-dimensional materials we can obtain a higher resolution in LEEP experiments. Finally, in chapter 6, we present a new method to measure the dispersion relation of unoccupied states in two-dimensional layered materials. Show less
This thesis focuses on the investigation of Majorana zero-modes and their quantum transport properties of topological insulators and topological superconductors in several low-dimensional systems,... Show moreThis thesis focuses on the investigation of Majorana zero-modes and their quantum transport properties of topological insulators and topological superconductors in several low-dimensional systems, i.e. 1D nanowire system (Chapter 2), 2D quantum spin Hall system (Chapter 3, 4) and 0D quantum dot system (Chapter 5, 6). Show less
This thesis consists of two different parts, separating research projects carried out in two different groups. In the first and longest part of this thesis, we attempt to fit the signal for a... Show moreThis thesis consists of two different parts, separating research projects carried out in two different groups. In the first and longest part of this thesis, we attempt to fit the signal for a reduction in the speed of sound of the inflaton. In chapter 1, we shortly introduce the topics discussed in this thesis, namely _CDM cosmology, transient reductions in the speed of sound during inflation, and Bayesian statistical inference. Afterwards, we attempt to fit a particular hypothesis for the speed of sound reduction using Cosmic Microwave Background data (chapter 2) and later adding Large Scale Structure data to the search (chapter 3). Finally, in chapter 4 we present two pieces of code that were elaborated for the research in this thesis, and later released to the community. In the second part, consisting solely of chapter 5, we present a classification of all possible 6-dimensional symmetric toroidal orbifolds over which Heterotic String Theory leads to a supersymmetric model. To do that, we made use of standard crystallographic tools. Show less
This thesis starts with an introduction to the quantum electrodynamical description of the interaction between light and matter. The role of optical cavities is discussed and the basic properties... Show moreThis thesis starts with an introduction to the quantum electrodynamical description of the interaction between light and matter. The role of optical cavities is discussed and the basic properties of rare-earth ions are reviewed. In Chapter 2 a bare ring resonator that is coupled to a waveguide is studied. Transmission spectra are measured, from which optical properties of the ring resonator and the waveguide are characterized. Chapter 3 addresses two technical issues that are essential for the research presented in this thesis: the implantation of rare-earth ions into the ring resonator and the permanent fiber connections to the waveguides. Chapter 4 is devoted to the research on the enhancement of the spontaneous emission rate in an ytterbium-doped ring resonator in the temperature range of 5.5-295 K as a result of the Purcell effect. Chapter 5 presents the results of measurements performed on an ytterbium-doped ring resonator in a dilution refrigerator in the range of 12 mK-4.7 K. In Chapter 6 collective effects of an ensemble of emitters in a cavity are theoretically studied with different initial states and pure dephasing rates by using the quantum Monte Carlo method. Chapter 7 concludes the thesis and presents an outlook for future work. Show less
We investigate the detection mechanism in superconducting single photon detectors via quantum detector tomography. We find that the detection event is caused by diffusion of quasiparticles from the... Show moreWe investigate the detection mechanism in superconducting single photon detectors via quantum detector tomography. We find that the detection event is caused by diffusion of quasiparticles from the absorption spot, combined with entrance of a vortex. Moreover, we investigate the behaviour of superconducting single photon detectors in an external magnetic field. Show less
At the basis of the regulation of the genetic code (DNA) in eukaryotes is its organization into nucleosomes. Nucleosomes modulate DNA accessibility through conformational dynamics like DNA... Show moreAt the basis of the regulation of the genetic code (DNA) in eukaryotes is its organization into nucleosomes. Nucleosomes modulate DNA accessibility through conformational dynamics like DNA breathing - the transient unwrapping of DNA from the nucleosome. Single-pair Fluorescence Resonance Energy Transfer (spFRET) has the ability to resolve such conformational dynamics in individual nucleosomes. This thesis describes the results of spFRET studies on the dynamics of individual nucleosomes, modulated by histone modifications, histone variants, and by neighboring nucleosomes. Performing spFRET experiments on nucleosomes and interpreting their results is however far from trivial. Nucleosomes are susceptible to dissociation when diluted to sub-nM concentrations and in the presence of surfaces. This thesis includes a chapter that describes the challenges encountered during the preparation of nucleosome samples, the detection of spFRET with confocal fluorescence spectroscopy and the analysis of FRET efficiencies, and how we have dealt with them. With the use of spFRET on individual nucleosomes we were able to show that the specific acetylation of H3K56 increases DNA breathing several times, and that nucleosomes containing H2A.Z are more stable than H2A-containing nucleosomes. spFRET on dinucleosomes reveals that both electrostatic interactions between the entering and exiting linker DNA and nucleosome-nucleosome interactions increase unwrapping. Show less
