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
In my thesis I study Majorana fermions from three different perspectives. The first one corresponds to non-interacting Majorana fermions that, however, pose non-trivial topological properties. The... Show moreIn my thesis I study Majorana fermions from three different perspectives. The first one corresponds to non-interacting Majorana fermions that, however, pose non-trivial topological properties. The second one corresponds to strongly interacting Majoranas and the third to relic neutrinos. No one knows for sure if they have Dirac or Majorana nature. Show less
Pericytes, the mural cells of blood microvessels, are important regulators of vascular morphogenesis and function that have been postulated to mechanically control microvascular diameter through as... Show morePericytes, the mural cells of blood microvessels, are important regulators of vascular morphogenesis and function that have been postulated to mechanically control microvascular diameter through as yet unknown mechanisms. Their disfunction has been implicated in several pathologies, including cerebral ischemia, Alzheimer's disease and diabetic retinopathy.To reveal mechanisms used by pericytes for mechanical interactions within microvessels we designed models bringing human induced pluripotent stem cell (hiPSC)-derived pericytes in contact with various micropatterned substrates representing the microvascular basement membrane organization. Our findings shed light on how pericytes can mechanically regulate microvascular morphogenesis and function, and open possibilities for testing therapeutic strategies. Show less
In this PhD thesis, the recombination of different atomic lattices in stacked 2D materials such as twisted bilayer graphene is studied. Using the different possibilities of Low-Energy Electron... Show moreIn this PhD thesis, the recombination of different atomic lattices in stacked 2D materials such as twisted bilayer graphene is studied. Using the different possibilities of Low-Energy Electron Microscopy (LEEM), the domain forming between the two atomic layers with small differences is studied. Superlattices in three such 2D material systems are studied. In twisted bilayer graphene, the small difference is caused by a twist of approximately one degree between the layers. In graphene on SiC, the difference is caused by the lattice mismatch between a buffer layer bound to the substrate and the next graphene layer. For both, we show that domains of different shapes and sizes occur and relate them to strain and lattice mismatch. The third system studied is tantalum disulfide. In this layered material, two different superlattices occur: a superlattice between atomic layers with different atomic arrangements in the layers, so-called polytypes, and the superlattices between the atomic lattice and the Charge Density Waves (CDW). CDWs cause a large temperature dependent resistivity change. The influence of a mixture of different polytypes on the precise CDW states is studied using LEEM spectroscopy and local Low-Energy Electron Diffraction. Show less
This thesis covers several aspects of quantum algorithms for near-term quantum computers and its applications to quantum chemistry and material science. These aspects range from error mitigation... Show moreThis thesis covers several aspects of quantum algorithms for near-term quantum computers and its applications to quantum chemistry and material science. These aspects range from error mitigation and error modeling of a quantum computing device to a measurement scheduling to extract the relevant information of a quantum state for quantum chemistry calculations.It also presents a benchmarking study of classical optimization methods for variational quantum algorithms. Additionally, a small quantum simulation is performed on a cloud-based quantum computer to understand the bottlenecks of such infrastructure. Finally, a method to calculate energy derivatives on a quantum computer, a relevant figure for quantum chemistry calculations. Show less
The ultimate goal of cosmologists is to find a cosmological model able to explain the current observational data. In this sense, the Standard Cosmological model establishes that our universe is... Show moreThe ultimate goal of cosmologists is to find a cosmological model able to explain the current observational data. In this sense, the Standard Cosmological model establishes that our universe is mainly composed of two unknown components: a type of matter that is known to only interact through gravitation, Cold Dark Matter, and a substance responsible for the current accelerated expansion of the universe that can be modelled by a cosmological constant. Still, this model, though successful, fails to answer hot-burning questions in the field. For this reason, theoretical cosmologists focus on developing further modifications of the model to test them against astrophysical data and check whether alternative scenarios can provide a better explanation of the observations.This thesis is dedicated to the Bayesian statistical analyses of extensions of the Standard Cosmological model using several astronomical data sets, and to the forecast of new observables and experiments. The first part focuses on data science and inflation, and it aims to constrain inflationary models using advanced inference techniques. The second part of the thesis is dedicated to the novel concept of cross-correlations of gravitational-wave physics and large scale structure observables. The third part of this thesis is dedicated to the incoming ESA Euclid satellite, and in particular, it focuses on a crucial data science analysis software for the mission: the code “Cosmological Likelihood for Observables in Euclid”, also known as CLOE. Show less
My PhD research is devoted to studies of the conjectural cluster-algebraic symmetry in the theory of topological string, which is the simplest, however already non-trivial sector in the theory of... Show moreMy PhD research is devoted to studies of the conjectural cluster-algebraic symmetry in the theory of topological string, which is the simplest, however already non-trivial sector in the theory of string. The language of cluster algebras is the modern tool which was initially developed for solving problems in linear algebra, and has recently been applied to the theory of integrable systems. In this dissertation we identify the cluster-algebraic nature of new classes of integrable systems of string-theoretic origin. We then show how the partition functions of topological string on the corresponding geometries can be naturally fit into a cluster-algebraic context. Show less
Because thin systems can deform along the thickness with relative ease, the interplay between surface mechanics and geometry plays a fundamental role in sculpting their three-dimensional shape.... Show moreBecause thin systems can deform along the thickness with relative ease, the interplay between surface mechanics and geometry plays a fundamental role in sculpting their three-dimensional shape. Often, deformations arise as a consequence of elastic pre-stress in the material, for example because of the small-scale geometry of the constituents or their local arrangement. In this thesis, we look at the connection between geometry, local and global, and mechanics in thin closed shells and open sheets which we consider as two-dimensional solids that we study using linear elasticity theory. In particular, we investigate the elasticity-driven shape deformations in the context of three soft matter systems: dense single-layered crystals, oil-in-water emulsions, and biological thin assemblies of tubulin. Show less
In the thesis we demonstrated an 85% state transfer efficiency between two mechanical modes coupled to a common optical mode via stimulated Raman adiabatic passage (STIRAP) in the classical regime.... Show moreIn the thesis we demonstrated an 85% state transfer efficiency between two mechanical modes coupled to a common optical mode via stimulated Raman adiabatic passage (STIRAP) in the classical regime. We also showed possibilities to manipulate quantum states of the mechanical modes via STIRAP. Show less
Early time-resolved experiments by Frauenfelder on the ensemble of the kinetic rebinding of CO to myoglobin molecules resulted in a stretched exponential relaxa-tion due to a very large spread of... Show moreEarly time-resolved experiments by Frauenfelder on the ensemble of the kinetic rebinding of CO to myoglobin molecules resulted in a stretched exponential relaxa-tion due to a very large spread of the reaction rates of individual molecules. These results were assigned to the heterogeneity in this system originated from different conformations of different single-molecule proteins and from the widely different re-action rates associated with each of these conformations. The work presented in this thesis contains two lines of research. On the one hand, we investigate the Förster Resonance Energy Transfer (FRET) of dye labeled-carboxymyoglobin (MbCO) in the ensemble to show the feasibility of performing single molecule-FRET experiments to study the kinetic rebinding of CO to myoglobin (Chapter 3,4). On the other hand, we study the Förster theory about a stretched-exponential fluorescence intensity decay under ensemble conditions for a distribution of acceptors in the vicinity of each donor; This non-exponential kinetics arise from a distribution of the exponential steps originated from different single molecules. Using single-molecule microscopy, we study the histograms of the decay rates of single fluorophore molecules (Azaoxa-triangulenium, ADOTA dye) as donor in the presence of acceptors (ATTO575Q dye) both doped in thin polymeric layers as exponential which average out as non-exponential decay in the ensemble (Chapter 5). Show less
This thesis examines silicon pore optics (SPO), a technology that exploits silicon wafers from the semiconductor industry to create extremely high quality X-ray optics, by studying its... Show moreThis thesis examines silicon pore optics (SPO), a technology that exploits silicon wafers from the semiconductor industry to create extremely high quality X-ray optics, by studying its manufacturing process, applications, and prospects. SPO technology has become very mature thanks to the continuous development efforts to prepare for the industrial production of Athena, the largest space-borne X-ray telescope yet to be launched. In effect, SPO is also a versatile technology that can be further developed for a wide range of applications, including radiation therapy. Show less
With the help of quantum mechanics, digital quantum hardware may be able to tackle some of the problems that are too difficult for ordinary computers. But despite these expectations and the ongoing... Show moreWith the help of quantum mechanics, digital quantum hardware may be able to tackle some of the problems that are too difficult for ordinary computers. But despite these expectations and the ongoing effort of the research community, reliable quantum computers are not yet realized in a lab setting. The optimal strategies for early applications of such special hardware are not settled either. The present thesis addresses these issues of implementing and harnessing quantum computers.Firstly, several strategies are introduced to implement and characterize digital quantum hardware using the technique called braiding. Two realizations are considered: the edge modes of topological superconductors and the parafermionic modes in Fractional Quantum Hall materials.Secondly, this work explores applying quantum computers to prepare simulated ground states (lowest-energy configurations) of complex quantum systems. To this end, several new techniques are presented in the context of variational quantum algorithms, simulated cooling, and quantum control theory. Show less
DNA carries various forms of information. Out of these forms of information the most well-known is classical genetic information. Throughout this dissertation we discuss what is often referred to... Show moreDNA carries various forms of information. Out of these forms of information the most well-known is classical genetic information. Throughout this dissertation we discuss what is often referred to as the second layer of information on DNA: DNA mechanics. A sequence consisting of only A’s and T’s will bend differently from a sequence of G’s and C’s. An important consequence of this mechanical layer of information is the positioning of nucleosomes. Nucleosomes consist of 147 base pairs of DNA wrapped around a protein core, like a string around a spool. By either allowing or restricting access to a binding site, a nucleosome may serve as an on/off switch, of which the location is extremely important. A third layer of information on DNA is translation speed. Translation speed refers to the rate at which a protein is created, and it depends on the codons used in a genetic sequence. The research in this thesis investigates how these layers of information are multiplexed. It uses multiple novel approaches, one of them being the use of weighted graphs consisting of all possible DNA sequences to find the very best and very worst nucleosome-attracting sequences. Show less
In this work, we investigate the minute circular dichroism effects of single nanoparticles.To this aim, we apply photothermal imaging with a polarization-modulated heating beam. This new technique,... Show moreIn this work, we investigate the minute circular dichroism effects of single nanoparticles.To this aim, we apply photothermal imaging with a polarization-modulated heating beam. This new technique, which we call photothermal circular dichroism microscopy, probes circular dichroism in an absorption measurement, unlike other techniques which usually probe the extinction. We also investigate in detail how to avoid measurement artefacts such as leakage of linear dichroism and residual intensity modulation.We then study the CD of formally achiral and wet-chemically synthesized chiral nanoparticles. We find that the achiral spherical-like particles, can exhibit considerable circular dichroism, some of them display almost as strong CD as specially designed chiral particles. Furthermore, we find that the control of handedness of the synthesized chiral particles is only limited and that, even from a geometric perspective, the relation between the 3D shape of these particles and their handedness is not straightforward.In the last chapter, we apply our method to magnetic samples which exhibit circular dichroism through their magnetization but not due to their shape. The excellent sensitivity of photothermal microscopy not only allows us to perform magnetic imaging of particles, but we also succeeded in obtaining magnetization curves of single particles and estimating their magnetization. Show less
In this thesis, time-lapse fluorescent microscopy plays a pivotal role in investigating functional materials within living cells as well as the migratory behaviour of neural progenitor cells. The... Show moreIn this thesis, time-lapse fluorescent microscopy plays a pivotal role in investigating functional materials within living cells as well as the migratory behaviour of neural progenitor cells. The first part of the thesis focuses on two different functional nanomaterials (Ag-DNA and polymersomes), whereas the second part explores fluorescent labeling of neural progenitor cells and their cell dynamics within different in vitro systems. Show less
