This thesis aims to improve the detection from ultra-weak single emitter by enhancing their emission properties with plasmonic nanostructures. We exploit the wet-chemically synthesized single... Show moreThis thesis aims to improve the detection from ultra-weak single emitter by enhancing their emission properties with plasmonic nanostructures. We exploit the wet-chemically synthesized single crystalline gold nanorods (GNRs) as our basic frameworks in the whole studies, simply because of their unique optical properties, such as the intense electromagnetic fields enhancement near the tips, and the narrow, tunable resonance with light. We first explore the lower limit of fluorescence quantum yield for single-molecule detection by enhancing the fluorescence with a single gold nanorod. Later, we develop a method to synthesize end-to-end gold nanorod dimers on glass substrates with the aid of molecular linkers, and then apply these strong plasmon coupling systems to enhance the single-molecule fluorescence under two-photon excitation. Show less
Systems with local constraints is a new finding in recent researches on complex systems. The heterogeneous spatial interactions and the temporal dependencies among those numerous units make it... Show moreSystems with local constraints is a new finding in recent researches on complex systems. The heterogeneous spatial interactions and the temporal dependencies among those numerous units make it difficult to describe by traditional statistical physics.These complex structures also make information storage and transmission in it is impossible to describe by the random variables with finite outcomes in the classical information theory. In this thesis, we use the statistical ensemble with local constraints to describe those complex systems with heterogeneous interactions and dependencies. This description also helps us find the new information-theoretical bounds in the systems with local constraints, even when the temporal dependencies among numerous units break the asymptotic equipartition property in the classical information theory.Furthermore, we find that the breaking of ensemble equivalence generally exists in systems with local constraints even without the presence of phase transition, and this ensemble nonequivalence in the systems with local constraints without phase transition can be the same strong as the one that only appears on the boundary of phase transitions caused by the long-range interactions. We also find that this breaking of ensemble equivalence will affect the limit of information storage and transmission in systems with local constraints.These results in this thesis extend our understanding of complex systems and information theory. Show less
In this thesis we use Josephson and noise scanning tunneling microscopy for the study of conventional, unconventional (iron-based) and disordered superconductors. On the one hand, Josephson... Show moreIn this thesis we use Josephson and noise scanning tunneling microscopy for the study of conventional, unconventional (iron-based) and disordered superconductors. On the one hand, Josephson scanning tunneling microscopy allows us to directly visualize the superfluid density with high spatial resolution. On the other hand, noise scanning tunneling microscopy is employed for measuring the shot noise which detects the charge of the carriers forming a superconducting condensate. Show less
The elementary excitations of magnets are called spin waves, and their corresponding quasi-particles are known as magnons. The rapidly growing field of Magnonics aims at using them as information... Show moreThe elementary excitations of magnets are called spin waves, and their corresponding quasi-particles are known as magnons. The rapidly growing field of Magnonics aims at using them as information carriers in a new generation of electronic devices, (almost) free of electric currents. Encoding information in the amplitude and/or phase of these coherent waves could lead to a drastic decrease in dissipated power, typically related to the motion of electrons ("Joule" or "Ohmic" heating).This dissertation describes the development and use of a new technique to study spin waves. This technique uses the electronic spins associated with nitrogen-vacancy (NV) centers as magnetic field sensors. An NV center is a light-emitting defect in the crystal lattice of diamond. Remarkably, the brightness of its emission depends on its spin state, sensitive to magnetic fields. This way, magnetic information can be investigated optically. Show less
This thesis is dedicated to the exploration of the primordial dark ages: unknown physics during the earliest stages of the Universe’s expansion that have not yet been directly probed by... Show moreThis thesis is dedicated to the exploration of the primordial dark ages: unknown physics during the earliest stages of the Universe’s expansion that have not yet been directly probed by observations. Cosmic inflation is a burst of exponential expansion of space after the “Big Bang”. The energy that drives inflation must be transferred to elementary particles and radiation. This process is called reheating. The unknown expansion history of the universe during the reheating era connects the cosmic microwave background (CMB) observations to inflationary physics. CMB is a relic radiation that provides us a snapshot of the primordial universe. Both the inflationary and reheating eras generate signatures to be seen via upcoming gravitational waves and CMB polarization experiments. In this thesis we show analytically a scaling behaviour that allows for an easy estimate of the reheating efficiency for one broad family of multi-field models of inflation that is called α-attractors. We show the influence of the asymmetry around the minimum of potential on the reheating efficiency. Moreover, we study the predictions for chiral gravitational waves production by a spectator gauge field sector in scalar single-field inflation. Finally, we present a new class of inflationary models that is called “shift-symmetric orbital inflation”. Show less
In unconventional high temperature superconductors, supercurrent vortices are known to spoil the Landau levels. In this thesis the emergence of Landau levels is studied in different types of... Show moreIn unconventional high temperature superconductors, supercurrent vortices are known to spoil the Landau levels. In this thesis the emergence of Landau levels is studied in different types of superconductors: Weyl superconductors, and the Fu-Kane heterostructure. It is shown that in those materials the zeroth Landau level can withstand the scattering off vortices. Show less
Synthetic microswimmers take an important place within the interdisciplinary field of active soft matter. Many efforts are being made to develop, understand and ultimately control them, because of... Show moreSynthetic microswimmers take an important place within the interdisciplinary field of active soft matter. Many efforts are being made to develop, understand and ultimately control them, because of their great potential for fundamental studies and applications. A widely employed type is that of catalytically propelled microswimmers, such as platinum-half-coated colloids which achieve self-propulsion in aqueous hydrogen peroxide environments via a catalytic reaction taking place on the platinum. Surprisingly, although these swimmers are typically found self-propelling parallel to walls, the origins for this near-wall behavior and the influence of the walls are still largely unexplored. In this thesis, we examine the behavior of catalytic microswimmers near walls. We find that the physical property of slip of the nearby wall significantly impacts their speed. We develop a new diffusion-based analysis method, and uncover that swimmers tend to fixed heights above planar walls. Using obstacles of different shapes 3D-printed on the planar wall, we found cooperative swimmer behaviors along one-dimensional environments. Overall, our findings provide new insights into the still-debated propulsion mechanism of catalytic microswimmers, and may also aid in predicting and controlling swimmer motions in future applications, where synthetic swimmers will be needed to perform tasks inside complex environments. Show less
We have studied the impact of particle shape anisotropy, multivalent interactions and flexibility on systems of micron-sized colloidal particles. In short, we have characterized the diffusive... Show moreWe have studied the impact of particle shape anisotropy, multivalent interactions and flexibility on systems of micron-sized colloidal particles. In short, we have characterized the diffusive properties of anisotropic dumbbell particles near surfaces. Furthermore, by using experiments and simulations, we have uncovered marked flexibility-induces effects in the Brownian motion of reconfigurable colloidal structures. Our work demonstrates the rich dynamics and possibilities for applications of shape-changing colloidal systems. We hope our findings further the study of the diffusivity of flexible objects found in complex mixtures relevant in, for example, the cosmetic, pharmaceutical and food industries, as well as in biological and drug-delivery systems. For example, our results may have implications for understanding both the diffusive behavior and the most likely conformations of macromolecular systems such as polymers, single-stranded DNA and other chain-like molecules. Show less
Errors are everywhere, and mechanical failures are especially common: buckled grain silos and cracked support columns are, justly, seen as an issue to be avoided. But flaws can also be used to... Show moreErrors are everywhere, and mechanical failures are especially common: buckled grain silos and cracked support columns are, justly, seen as an issue to be avoided. But flaws can also be used to design materials with unique functionalities. In the work presented here, we use two types of imperfections to create functional structures. First, we design materials that are locally stiff or soft, depending on how they are actuated, using topological imperfections: mistakes in their underlying architecture. Second, we create structures that shape-morph, because their individual elements fail, buckle, and snap- features that should be avoided otherwise. Show less
The human body consists of hundreds, perhaps thousands of different types of cells, each with different morphologies and functions, despite having the same genome. This diversity is created by gene... Show moreThe human body consists of hundreds, perhaps thousands of different types of cells, each with different morphologies and functions, despite having the same genome. This diversity is created by gene regulation, a set of mechanisms that determine, which genes are used to make proteins and which genes are kept silent. During embryonic development, gene are turned on and off in a tightly orchestrated manner, to make sure that the right cell type is created at the right time and place.In this thesis we report several studies pertaining to gene regulation in embryonic development. Each of the four chapters will cover a different layer of the gene regulation toolbox: gene inactivation by DNA methylation, transcriptional regulation in the developing kidney, regulation of protein turnover and translational regulation through micro-RNAs. Together, these studies provide a refined understanding of the crucial role of gene regulation for embryonic development. Show less
This dissertation is an experimental study of laser-generated, atmospheric pressure, transient toroidal helium plasmas.The formation mechanism of these toroidal plasmas is identified and an... Show moreThis dissertation is an experimental study of laser-generated, atmospheric pressure, transient toroidal helium plasmas.The formation mechanism of these toroidal plasmas is identified and an estimate of their main plasma parameters is obtained. Furthermore, preliminary experiments are presented, aimed at heating these plasmas by absorption of microwave radiation, in order to counteract their transient nature.Through a tomographic reconstruction, cross-sectional images of the toroidal plasma are obtained, visualising the fluid flow responsible for the generation of the toroidal structure. The origin of the flow is traced back to the structure of the plasma kernel. The shocks generated by this kernel interact akin to a Mach reflection and generate a low pressure region whose replenishment transforms the plasma into a toroid. Schlieren imaging, complemented with a novel scanning-probe technique, and thermodynamic modelling, as well as deliberately breaking the flow symmetry, confirm the formation mechanism. A high-power, sub-microsecond rise time, pulsed magnetron source has been designed for the microwave heating experiments. Its detailed design and the effect of the microwave pulse on the plasma are discussed.This work is part of a larger study on self-organising knotted magnetic structures in plasma, which may find their application in nuclear fusion and astrophysical research. Show less
Single-molecule spectroscopy has become a powerful method for using organic fluorescent molecules in numerous applications. Along with sensing applications in biology and solid-state physics or a... Show moreSingle-molecule spectroscopy has become a powerful method for using organic fluorescent molecules in numerous applications. Along with sensing applications in biology and solid-state physics or a variety of applications in quantum information technology, molecules offer interesting possibilities for fundamental research. One of the very interesting areas is the study of charge transport and electric field sensing at the nanoscale. Developing molecular nanosensors for electric fields can not only help to fundamentally explore the motion of charges in conductors and semiconductors but can also lead to very sensitive and accurate instruments for quasi-static charge tracing or even single-electron charge detection. Such research could eventually lead to the construction of precise electric field sensors that can act as an interface between the quantum state of an electron and the outside word. We developed fluorescence molecular systems and electronic circuits with the aim of electric-field sensing and optical detection of one single electron. Show less
Geometric phases lead to a nontrivial interference result when an electron's different quantum mechanical paths choices encircle a magnetic coil in an Aharonov-Bohm experiment. They are also... Show moreGeometric phases lead to a nontrivial interference result when an electron's different quantum mechanical paths choices encircle a magnetic coil in an Aharonov-Bohm experiment. They are also responsible for the daily precession of a Foucault pendulum in Paris. A dynamical shape change induces a geometric phase, which, for instance, cats use to rotate when falling and swimmers use to swim forward.A modern application of such geometric phases has led to the notion of topological phases, which are described by a global property of the system. These phases are very different from the classical phases of matter, which are characterized by a local order parameter. A topological phase transition is therefore a fundamentally different process compared to a classical one as in a liquid-gas transition, because the former requires a change of a global topological index of the system. Topological phases can, for example, lead to the presence of traveling electronic modes which are robust against being backscattered by obstacles at the boundary of an insulator.This thesis describes some applications of geometric and topological phases in soft-matter systems. Show less
In this thesis we investigated the ability of two-photon multifocal microscopy for single-molecule microscopy in live cells and organisms. Two-photon excitation combined with multifocal scanning... Show moreIn this thesis we investigated the ability of two-photon multifocal microscopy for single-molecule microscopy in live cells and organisms. Two-photon excitation combined with multifocal scanning has the potential to achieve, high (temporal) resolution imaging at a low background. Splitting the laser beam into multiple beamlets reduced laser power to all but eliminate photobleaching. The low background combined with the fast scan speeds and absence of photobleaching allowed us to measure single-particles and single-molecules in live zebrafish embryo's for long time periods. To the best of our knowledge, it is the first time that single-molecule molecules have been observed in a wide-field two-photon microscope. Show less
This thesis presents the results of a study on the interfaces of insulating oxides with and without the insertion of a magnetic layer. Such interfaces can host a two-dimensional electron liquid,... Show moreThis thesis presents the results of a study on the interfaces of insulating oxides with and without the insertion of a magnetic layer. Such interfaces can host a two-dimensional electron liquid, making the interface conducting, with a wealth of phenomena to study. In order to create such interfaces, layers of oxides such as lanthanum aluminate, lanthanum titanate, and rare earth titanates were grown on the surface of crystalline strontium titanate. The growth method was pulsed laser deposition, in which short laser pulses ablate a target of the required material. The transport properties of these systems were studied by applying an external voltage to the back surface of the insulating substrate. Such a gate voltage allows us to vary the amount of charge carriers at the interface. In this way we could investigate magnetic effects occurring in the charge transport and their connection to the superconducting properties of oxide interfaces. The work resulted in a deeper of understanding of the so-called anomalous Hall effect, the magnetoresistance behavior, the origin of a resistance minimum in the back-gate experiments, and magnetoresistance hysteresis in the superconducting state in the various systems which were studied. Show less
The genetic information of all living organisms is contained in their DNA. Cells modify the degree of DNA compaction by epigenetics, which largely determines what genes are read out and which genes... Show moreThe genetic information of all living organisms is contained in their DNA. Cells modify the degree of DNA compaction by epigenetics, which largely determines what genes are read out and which genes are transcriptionally silent. Despite decades of research into this mechanism, there is no consensus on how cells realize the various degrees of DNA compaction in vivo. Eukaryotes, such as humans, compact their DNA into higher-order structures called compact chromatin fibers. We characterize these fibers through a combination of single-molecule force spectroscopy techniques like magnetic tweezers, and rigid base pair Monte Carlo simulations. We show that, for instance, the length and sequence of the linker DNA, the DNA between adjacent nucleosomes, control the mechanical properties of chromatin fibers. Our measurements suggest the formation of more than one higher-order fiber structure. A deeper understanding of the chromatin fiber and its compaction mechanism is important because the dysfunction of such regulation results in various medical conditions such as the epigenetic disorder type 1 diabetes, fragile X syndrome, or various cancers. Show less
The theoretical explanation of cosmic acceleration is nowadays one of the biggest puzzles in cosmology. Within the standard cosmological model (LCDM) the expansion is sourced by the vacuum energy... Show moreThe theoretical explanation of cosmic acceleration is nowadays one of the biggest puzzles in cosmology. Within the standard cosmological model (LCDM) the expansion is sourced by the vacuum energy associatedto the Cosmological Constant L. Despite its simplicity, the Cosmological Constant presents various unresolved problems from both the theoretical and the observational side.However, even if we dismiss these puzzles, the study of theoretical alternatives to LCDM is still of primary importance. In fact, the wealth and quality of cosmological data that we are expecting for thenext decade will allow us to test gravity on cosmological scales with unprecedented accuracy. This will give us the chance to investigate many of our theoretical ideas and to assess the strength of the standard model of cosmology on the largest scales.In this thesis we present different approaches that we can adopt to study modifications of gravity by means of cosmology. Show less
This thesis contributes to studying primordial cosmology theories and their detectability in future observations. The first part of the thesis studies a class of inflation models with curved field... Show moreThis thesis contributes to studying primordial cosmology theories and their detectability in future observations. The first part of the thesis studies a class of inflation models with curved field spaces, which are typically motivated in high energy physics theories. The second part of the thesis focuses on one particularly important cosmological observable -- primordial non-Gaussianity, whose phenomenology may reveal new physics effects in the very early Universe. Show less
This thesis focuses on amyloid proteins, a class of proteins that convert into amyloid fibrils. Such proteins are of high interest because they are related to many of the neurodegenerative diseases... Show moreThis thesis focuses on amyloid proteins, a class of proteins that convert into amyloid fibrils. Such proteins are of high interest because they are related to many of the neurodegenerative diseases. In the brains of patients with neurodegenerative diseases, plaques of β-sheet amyloid aggregates are found, but the mechanism of their formation and their role vis-à-vis the disease are unknown. Aggregation is difficult to study because amyloids are intrinsically disordered proteins that lack an ordered structure in solution. Here we apply electron paramagnetic resonance (EPR) as a new technique to better understand the properties of amyloid oligomers and their formation. Show less
Mechanical interactions between cells and their environment play an important role in many biological processes. These interactions are often anisotropic in nature, but most mathematical models in... Show moreMechanical interactions between cells and their environment play an important role in many biological processes. These interactions are often anisotropic in nature, but most mathematical models in the field of cell mechanics describe cells as isotropic entities. In this thesis we theoretically study the role of anisotropic forces in cell mechanics, and compare our predictions to experimental data. Show less
