CrO2, a half-metal ferromagnet, has shown great promise for superconducting spintronics applications for nearly two decades. Josephson junctions consisting of superconducting (S) contacts on... Show moreCrO2, a half-metal ferromagnet, has shown great promise for superconducting spintronics applications for nearly two decades. Josephson junctions consisting of superconducting (S) contacts on ferromagnetic (F) structures of CrO2, have been shown to sustain remarkably high supercurrents over hundreds of nanometers. However, advancements in this area have been hindered by the metastable nature of CrO2 at ambient conditions. This results in a poorly controlled S-F interface transparency, which is critical for generation of spin triplets. This thesis explores the potential, challenges and possible solutions to overcome the issues with CrO2 devices. Show less
Detecting nanoscopic objects plays an important role in nanoscience in particular, in the rapidly growing field of nanobiology. The forebear to modern super-resolution microscopy for single... Show moreDetecting nanoscopic objects plays an important role in nanoscience in particular, in the rapidly growing field of nanobiology. The forebear to modern super-resolution microscopy for single molecule investigation, is fluorescence microscopy. Fluorescence as a contrast mechanism, however, brings several restrictions. These include (1) the use of the label itself, which may introduce artifacts to the interpretation, (2) the limited photoemission caused by photobleaching and photoblinking as well as (3) low bandwidth of the emission. Fluorescence-free alternatives are thus highly desirable to overcome these limitations. Optical detection of individual proteins with high bandwidth holds great promise for understanding important biological processes on the nanoscale. In this thesis, we investigate label-free optoplasmonic detection of single proteins and particles in motion. Analysing the data provide information about the hydrodynamic volume of the diffuser and interaction such as binding events. Show less
Self-assembly offers a promising route to create complex structures and materials using simple building blocks. Through, colloidal self-assembly, we can understand the governing principles of the... Show moreSelf-assembly offers a promising route to create complex structures and materials using simple building blocks. Through, colloidal self-assembly, we can understand the governing principles of the self-assembly process and unlock its potential in diverse applications in materials science, photonics and electronics. The research outlined in this thesis contributes to our understanding of self-assembly processes in binary colloidal systems. It also sheds light on how the shape, size, and number ratio of colloidal particles impact the final structure of colloidal molecules in both electrostatic and DNA-functionalized colloidal assembly, as well as flexible colloidal lattices. This work showcases the potential for creating novel flexible materials with tailored properties. The research findings also provide fundamental insights into the governing mechanism of self-assembly and the route to the development of functional materials and devices with controlled properties and behavior. Show less
In this thesis, we examine various systems through the lens of several numerical methods. We delve into questions concerning thermalization in closed unitary systems, lattice gauge theories, and... Show moreIn this thesis, we examine various systems through the lens of several numerical methods. We delve into questions concerning thermalization in closed unitary systems, lattice gauge theories, and the intriguing properties of deep neural network phase spaces. Leveraging modern advancements in both software and hardware, we scrutinize these systems in greater detail, accessing previously unreachable regimes. Show less
The studies in this thesis are focused on the physical effects in the flat band materials. The results contain the discovery of strong enhancement of RKKY spin-spin interactions with specific... Show moreThe studies in this thesis are focused on the physical effects in the flat band materials. The results contain the discovery of strong enhancement of RKKY spin-spin interactions with specific geometric arrangement and dynamical generation of excitonic order parameter with high magnitude. A number of physical properties influenced by flat band are studied: optical conductivity, orbital susceptibility and spectral functions in the case of flat-band lattices stacked into bilayer. Additional chapters contain the studies of the methods to distinguish Majorana zero modes from Andreev levels and Majorana fermions in superconductors. Show less
In the traditional theory of linear elasticity, superposition dictates that the response of a material does not depend on the sequence of the applied mechanical actuations. In this dissertation, we... Show moreIn the traditional theory of linear elasticity, superposition dictates that the response of a material does not depend on the sequence of the applied mechanical actuations. In this dissertation, we design non-linear building blocks to realize a non-Abelian metamaterial whose response is sequence-sensitive. We study the behaviour of such metamaterials through simulations and experiments using existing mathematical and engineering frameworks such as finite state machines and Boolean logic circuits. We discover that the non-Abelian metamaterial possesses information processing and storage capabilities: it behaves like a simple computer. This opens up new avenues to realize mechanical computing and memory devices with a complex emergent response. Show less
Ferritin is a spherical metalloprotein, capable of storing and releasing iron in a controllable way. It is composed of a protein shell of about 12 nm and within its cavity, iron is stored in a... Show moreFerritin is a spherical metalloprotein, capable of storing and releasing iron in a controllable way. It is composed of a protein shell of about 12 nm and within its cavity, iron is stored in a mineral form. The ferritin core resembles an iron-based nanoparticle that is isolated from the environment by the ferritin shell, which makes ferritin an attractive element to be used in the fabrication of bioelectronic devices. Another intriguing aspect of ferritin is its potential relation to neurodegenerative diseases, such as Alzheimer’s and Parkinson’s. The relation is not yet well understood, but the studies indicate that dysfunctional ferritin appears to play an important role. This dissertation aims to characterize ferritin electrically and magnetically. First, the electrical properties of single ferritin are explored to understand the charge transport through ferritin, and additionally, the first ferritin single-electron transistor is obtained. Second, the magnetic properties of multiple ferritin particles are studied by electron paramagnetic resonance, which supplies information about the ferritin core. A model of the electron-spin structure of the ferritin core is proposed and extended to the ferritin signal from post-mortem brain tissues. Show less
This thesis presents insights from our study of various correlated electron systems with a scanning tunneling microscope (STM). In ordinary metals, electron-electron interactions exist, but get... Show moreThis thesis presents insights from our study of various correlated electron systems with a scanning tunneling microscope (STM). In ordinary metals, electron-electron interactions exist, but get substantially screened due to the sheer number of electrons. We therefore describe electrons in ordinary metals as a gaseous state of free, or weakly interacting charged particles. This adequately explains their properties, however, this picture does not work for correlated electron materials. The prominent electron-electron interactions present in these materials enable a wide range of exotic electronic phenomena, some of which are presented in this work. In chapter 2, we present STM results measured on an overdoped copper oxide compound and show that the superconducting state that occurs in these materials cannot be described by conventional BCS theory, contrary to what is commonly believed. In chapter 3, we study twisted bilayer graphene devices, and quantify their local twist angle and strain on the nanoscale. In chapter 4, we describe how to build and characterize the hardware needed to do noise spectroscopy measurements in a conventional, low temperature STM setup. Finally, in chapter 5, we present our noise spectroscopy measurements on Sr2IrO4, and explain how random telegraph noise could lead to the observed noise enhancements. Show less
The interest of this thesis lies in spin transport in normal metals and superconducting half-metallic junctions. Spin transport is strongly related to the spin polarization (P) of materials. Half... Show moreThe interest of this thesis lies in spin transport in normal metals and superconducting half-metallic junctions. Spin transport is strongly related to the spin polarization (P) of materials. Half-metallic ferromagnets, or half metals, with 100% spin polarization, are of interest as spin injector, promising a high efficiency; but also as a superconducting spin transport channel between two superconducting electrodes, in which spin-poalrized triplets are generated and exist over long distance. Show less
A single self-assembled semiconductor quantum dot in a high-finesse optical microcavity - the subject of this thesis - is an interesting quantum-mechanical system for future quantum applications.... Show moreA single self-assembled semiconductor quantum dot in a high-finesse optical microcavity - the subject of this thesis - is an interesting quantum-mechanical system for future quantum applications. For instance, this system allows trapping of an extra electron and thus can serve as a spin quantum memory, or enables high-fidelity and high-rate single-photon production. We investigate several aspects in this thesis:First, the operation and manipulation of the system is achieved using resonant laser spectroscopy. This requires filtering out of the relatively strong excitation laser, which is often done using the cross-polarization technique. This approach, however, is complicated in optical setups by spin-orbit coupling of light at the beamsplitter. We experimentally firstly explore this effect in a cryogenic optical microscope and demonstrate its importance for quantum dot based single photon sources. Next, we develop a unique setup with a cold permanent magnet and firstly realise trapping of a single electron in our particular quantum dot - cavity devices and show spin control. Then we show how true single photons from our device can be used to create novel quantum states of light. First, we investigate theoretically single photon addition to coherent laser light including several experimental imperfections - we find an universal behaviour of the photon correlation function. Finally, we demonstrate entanglement of several consecutive photons by repeatedly using Hong-Ou-Mandel quantum interference of single photons with a photon quantum memory in the form of an optical delay loop. We show that this results in quantum states of light that have Poissonian photon statistics like laser light - therefore we call them artificial coherent states - but also that they are more complicated than ordinary coherent states and contain multi-photon quantum entanglement in the form of linear cluster states, a potential resource for universal quantum computing. Show less
The first direct detection of gravitational waves opened the possibility of mapping the Universe via this new and independent messenger. Indeed, during their propagation, gravitational waves pick... Show moreThe first direct detection of gravitational waves opened the possibility of mapping the Universe via this new and independent messenger. Indeed, during their propagation, gravitational waves pick up information about the spacetime as they are affected by its expansion and by the matter structures along the propagation path. The aim of this Thesis is to investigate which cosmological information is accessible from a gravitational wave detection, with a specific interest in the late time Universe. Show less
It has been a long-standing mystery how complex biological structures emerge from such seemingly uncoordinated building blocks as cells and tissues, in the presence of only minimal environmental... Show moreIt has been a long-standing mystery how complex biological structures emerge from such seemingly uncoordinated building blocks as cells and tissues, in the presence of only minimal environmental guidance. In particular, unifying descriptions independent of microscopic details of a specific organism are rare. In recent years, hydrodynamics has successfully been applied to describe certain types living systems. The thesis is concerned with understanding different aspects of structure formation in active liquids and biological systems. In the first chapter we investigate the coarsening dynamics in the Toner-Tu theory and compare it with an experimental colloidal system. Afterwards, we investigate the effect of chirality in active nematics, with applications to biological tissues. In the last part we derive and study a model to explain geometric deformations due to the presence of activity. The resulting dynamics might be able to explain morphogenetic processes. Show less
Make more fluid: In condensed matter systems, electrons can acquire unusual properties from their interaction with the atomic lattice. In some examples, they can behave as massless particles,... Show moreMake more fluid: In condensed matter systems, electrons can acquire unusual properties from their interaction with the atomic lattice. In some examples, they can behave as massless particles, mimicking the relativistic behavior of photons. This thesis is dedicated to the study of such massless electronic excitations, focusing on systems exhibiting Majorana, Weyl, and Dirac fermions. In this thesis, we show how new states can arise in the presence of a magnetic field, find new signatures of such states, and present new methods that can be used to study them. Show less
Mechanical metamaterials are carefully engineered materials whose properties are controlled by their structure, not by their composition, which allows using metamaterials to study and control... Show moreMechanical metamaterials are carefully engineered materials whose properties are controlled by their structure, not by their composition, which allows using metamaterials to study and control physical effects in detail. Here we develop metamaterials to study the sequential, complex response of frustrated materials that are cyclically driven. In particular, we focus on metamaterials that act as collections of hysteretic, bistable elements called hysterons. We create hysterons in metamaterials by using local frustration at defects and by using a competition between two global, incompatible deformations modes. We show how we can tune these hysterons, both by rational design and by using spatial gradients in the mechanical driving. Then we show that collectively, our samples exhibit complex transition pathways, including those with avalanches, and study the role of hysteron interactions. Finally, we explore how to control the frustration by local defects in so-called monoholar metamaterials. Show less
In this thesis, we have used numerical approaches to study the effects of translational symmetry breaking on strange metallic systems as realised by the holographic duality. This involves solving... Show moreIn this thesis, we have used numerical approaches to study the effects of translational symmetry breaking on strange metallic systems as realised by the holographic duality. This involves solving for large-scale coupled partial differential equations, describing the physics of corrugated black holes in negatively curved space-times.We show that the strong-coupling nature of the physics of these holographic systems produces some unique behaviours, which are suggestively close to experimental observations that have been done in the lab. We speculate that strong-coupling physics is what is at the heart of the mysteries that shroud the strange metal. Show less
In this thesis I describe the results of Pulsed Interleaved Excitation and Fluorescence (Cross) Correlation Spectroscopy (PIE-F(C)CS) combined with single-pair Förster Resonance Energy Transfer ... Show moreIn this thesis I describe the results of Pulsed Interleaved Excitation and Fluorescence (Cross) Correlation Spectroscopy (PIE-F(C)CS) combined with single-pair Förster Resonance Energy Transfer (spFRET) used to study dynamics in single nucleosomes, which depends on subtle differences in the length of DNA ends, DNA sequence, histone variants and specific and non-specific protein interactions. This technique, which can resolve distances between two fluorophores of only a few nanometers, is an excellent technique to monitor changes in nucleosomal compaction, as the nucleosome is only ten nanometers in diameter. In combination with F(C)CS and PIE, spFRET makes it possible to monitor conformational dynamics on a timescale of micro- to milliseconds. Show less
In condensed matter systems electron-electron interactions, negligible in everyday metals, can dramatically alter the electronic behavior of the system. Examples of such altered behavior include... Show moreIn condensed matter systems electron-electron interactions, negligible in everyday metals, can dramatically alter the electronic behavior of the system. Examples of such altered behavior include high-temperature superconductivity and modulation of the electron density. A common feature of this correlation driven behavior is the tendency of the spatial electronic structure to vary on the nanometer scale. In this thesis we explore the nanoscale variation of the electronic structure of various correlated electron systems. We use the wave-like oscillations in the electron density of states to probe fundamental properties of the system providing insights into when various experimental probes disagree with each other. Turning our attention to high-temperature superconductors we find that close to the transition between superconductor and metal a granular superconductor emerges, small nanoscale patches of superconductivity interlaces with a metallic matrix. A careful examination of the wave-like oscillations hints at the presence of spatial ordering of the electrons. Finally we study how the presence of strong interactions can alter the way electrons flow through a material such that concepts usually reserved for everyday fluids become relevant. Show less
Despite being the object of intense study, embryonic development has been difficult to model due to a number of reasons. First, complex tissues can be comprised of many cell types, of which we... Show moreDespite being the object of intense study, embryonic development has been difficult to model due to a number of reasons. First, complex tissues can be comprised of many cell types, of which we probably only know a subset. Therefore, we first focused on the discovery of cell types by single-cell RNA-sequencing (scRNA-seq). Cell types are routinely identified by clustering scRNA-seq data, however, there was no principled way to determine the right number of clusters. To improve cell type classification, we developed phiclust, a clusterability measure for scRNA-seq. Another challenge in a developing tissue is that many signaling processes and morphogenic events occur simultaneously, which makes it hard to isolate the individual contributions. For this purpose, I looked at stem cell derived in vitro systems, in which a small number of specific cell types can be combined deliberately and studied in isolation. My analysis of different model systems shows that cellular communication causes structural and transcriptional changes in the developing cells. Finally, while tissue organization has been characterized extensively, we lack generative models that can relate specific patterns to the underlying gene regulatory mechanisms. Therefore, I later focused on deep learning-based approaches to infer gene regulatory networks from observed spatial patterns. Show less
We find ourselves in an era of transition, not just towards a more computing- and data-driven society but also away from unsustainable fossil fuels as an energy source. This leads to a rapidly... Show moreWe find ourselves in an era of transition, not just towards a more computing- and data-driven society but also away from unsustainable fossil fuels as an energy source. This leads to a rapidly increasing demand for computing power on an ever more tight energy budget. Therefore, it is imperative to investigate novel energy-efficient computing techniques, like superconducting spintronics or neuromorphic computing using correlated electron matter. Naturally, understanding the physics governing these processes at the sub-micrometer (i.e., device) scale is crucial for this development to succeed. This thesis examines the effects of size reduction and geometry on ferromagnetic Josephson junctions and highly correlated electron matter through transport experiments. Specifically, it describes how spin-polarized supercurrents can be generated using spin texture, stabilized by carefully tuning the geometry of planar Josephson junctions, and how the bistability of these spin textures can be employed to create non-volatile superconducting memory elements. Furthermore, it reports a strong size dependence of the current density that drives the Mott-insulating-to-metal transition in Ca2RuO4 and shows how various constricted geometries can be used to localize and examine the properties of superconducting chiral domain walls in Sr2RuO4. Show less
The way organisms develop from the initial single-cellular state to a complex final assembly like the human body, and how the final body is maintained throughout life, is one of the greatest... Show moreThe way organisms develop from the initial single-cellular state to a complex final assembly like the human body, and how the final body is maintained throughout life, is one of the greatest mysteries and it’s understanding one of the biggest scientific challenges. Lately, it came as a surprise that the initial assembly and the later maintenance of integrity is not only determined by intricate biochemical communication networks, but in part by physical forces that cells, their neighbors, and their environment apply in a bidirectional manner. The resulting collectivity of cell behavior determines the development of organisms, and are crucial to the health and disease state of the organism.In this thesis, we developed and utilized concepts from physics to quantitatively understand forces that develop between cells and their environment, and towards neighboring cells, and how the interplay between these forces regulates the arrangement, shape, and topology of tissue. The topics range from the development of novel experimental methods to the combination of experimental observations with theoretical descriptions. Our results contribute to a better understanding of cell and tissue integrity. Show less
