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
Protein-protein interactions are essential for various biological processes including cell metabolism, muscle contraction, and signal transduction. The dissertation describes a study of the... Show moreProtein-protein interactions are essential for various biological processes including cell metabolism, muscle contraction, and signal transduction. The dissertation describes a study of the interaction between the proteins cytochrome c and cytochrome c peroxidase by electron paramagnetic resonance spectroscopy (EPR). A spin label containing an unpaired electron was placed at the surface of one of the proteins. The combination of spin labelling and EPR provided novel information on the structure and dynamics of the proteins. Show less
Geometric frustration occurs when local order cannot propagate through space. A common example is the surface of a soccer ball, which cannot be tiled with hexaganons only. Geometric frustration can... Show moreGeometric frustration occurs when local order cannot propagate through space. A common example is the surface of a soccer ball, which cannot be tiled with hexaganons only. Geometric frustration can also be present in materials. In fact, geometry can act as an instrument to design the mechanical, optical or physical properties of fluids and solids. The first two parts of this thesis discuss frustrated liquid crystals confined to droplets of various shapes and sizes. The droplet shape determines the orientation of the liquid crystal molecules and in turn its response to light. In the final part we study the fracture mechanics of curved elastic plates. By tuning the curvature of the plate, the critical length at which the crack starts growing can be controlled. Finally, we find that the path that the crack takes depends on the curvature. Show less
Life’s building block is a cell. Different cell types are differentiated by specific functional properties. A white blood cell, for instance, can get rid of bacteria and many muscle cells contract... Show moreLife’s building block is a cell. Different cell types are differentiated by specific functional properties. A white blood cell, for instance, can get rid of bacteria and many muscle cells contract together for proper muscle function. Deformation and force exertion play important roles in these processes. Bacteria have to be physically engulfed by the white blood cell, and the muscle cell has to contract in the right way. In this research we measured how much force cells exert and simultaneously visualized specific proteins. A newly developed technique enabled the visualization of the nanometer-structure of cellular adhesions. We also examined the relationship between cellular shape and orientation of an intracellular network of protein (actin). We discovered that the signal of yet another protein (p130Cas) alters the mechanical behavior of the cell when the stiffness outside the cell changes. Finally, we also examined the structure of other proteins (tubulin and H2B) during cell division. In all these processes we measured how much force a cell exerts on its environment. The results provide important insights in the mechanical component of cellular function and their role in life Show less
This work discusses the flow of granular materials (e.g. sand). Even though a single particle is a simple object, the collective behavior of billions of particles can be very complex. In a... Show moreThis work discusses the flow of granular materials (e.g. sand). Even though a single particle is a simple object, the collective behavior of billions of particles can be very complex. In a surprisingly large amount of cases, it is not exactly known how a granular material behaves, and this while these kinds of materials are omnipresent in everyday life, industry, and nature Similar to materials such as water, which can occur as ice, liquid water and vapor, sand can also exist in different phases of matter. If you for instance walk on the beach, sand behaves like a solid, but if you pour it out of your shoes afterwards, it flows like a liquid. This thesis is dedicated to experiments where we investigate what happens when you try to "liquefy" sand by weakly vibrating it. We use an experimental setup which enables us to study how much stress is required to make sand flow, depending on the desired flow rate and the amount of vibrations. These experiments reveal several physical principles that turn out to be important towards understanding the unique behavior of these kinds of materials Show less
In this thesis, we perform fundamental spectroscopic studies of organic fluorescent chromophores (dyes) for temperatures from 1-10 Kelvins. We use confocal and wide-field fluorescence microscopy... Show moreIn this thesis, we perform fundamental spectroscopic studies of organic fluorescent chromophores (dyes) for temperatures from 1-10 Kelvins. We use confocal and wide-field fluorescence microscopy techniques. We analyzed the spectroscopic properties of well-known dyes, such as perylene, terrylene and dibenzoterrylene embedded in different solids. By doing this systematically, we correlate the presence of methyl groups in the host-crystal (Chapter 2) with the strong spectral diffusion of the resonant line, which lead to spectral broadening and frequency instabilities of the guest DBT. In contrast, the absence or substitution of methyl groups by chloride showed any of these effects. We found that the fluorescent properties of perylene in ortho-dichlorobenzene and terrylene in para-dichlorobenzene solids were those expected for the single quantum system. No reports of lifetime-limited excitation lines for perylene were ever reported till now. Even further, we report the coupling of an acoustic wave created by a macroscopic object to the optical response of a single molecule. The shot-noise limited sensitivity from the response of the single molecule to the displacement of the fork's prongs was found to be in the sub-nanometer regime. Perylene in o-DCB will be used to perform the single molecule all-optical transistor proposed in the introduction. Show less
Since the discovery of the right-handed helical structure of DNA, 61 years have passed. The DNA molecule, which encodes genetic information, is also found twisted into coils. This extra twist of... Show moreSince the discovery of the right-handed helical structure of DNA, 61 years have passed. The DNA molecule, which encodes genetic information, is also found twisted into coils. This extra twist of the helical structure, called supercoiling, plays important roles in both DNA compaction and gene regulation. The DNA in eukaryotic cells is packaged into chromatin. Using single-molecule force spectroscopy, I resolved force/torque induced structural changes of DNA and chromatin fibers. I showed that the structural changes of chromatin fibers can be described by four conformations. I showed for the first time the folding and unfolding of a chromatin fiber under torsion. Th e anisotropic response of chromatin fibers to supercoiling reflects its leftŸ-handed chirality. These findings give a detailed structural insight of a supercoiled chromatin fiber, yielding a better understanding of the response of chromatin during transcription Show less
Cosmological inflation is the most successful theory that explains the homogeneity and flatness of the early universe. It also provides a quantum origin for the primordial perturbations that we... Show moreCosmological inflation is the most successful theory that explains the homogeneity and flatness of the early universe. It also provides a quantum origin for the primordial perturbations that we observe in the Cosmic Microwave Background Radiation (CMB). The simplest models make use of a single scalar field, which produces the exponential expansion of the early universe. In this thesis the effects of additional heavy fields is studied from several points of view. On the one hand, possible signatures due to the presence of such fields are searched for in the current CMB data, and a new formalism is developed, allowing the analytical study of features arising from the presence of these fields. On the other hand, in the context of supergravity theories, the presence of additional heavy fields is ubiquitous, and their stability is needed in order to not spoil the basic predictions of single-field inflation. The viability of inflation in the presence of an additional heavy supersymmetric sector is studied, and several stability constraints are derived. The conclusion is that CMB data might be already sensitive enough to the presence of additional heavy fields, and that the landscape of supergravity scenarios which stabilize these fields is very constrained Show less
This thesis is devoted to applications of string theoretic methods of holography to strongly coupled phases of quantum field theories. In chapter 2 we consider a finite-density system of quarks,... Show moreThis thesis is devoted to applications of string theoretic methods of holography to strongly coupled phases of quantum field theories. In chapter 2 we consider a finite-density system of quarks, realized holographically by a probe brane in Anti-de Sitter space, with a non-trivial gauge field background on its world-volume. We reproduce the holographic zero-sound in the longitudinal channel of the current-current correlation function. We generalize this result to the case of a non-vanishing background magnetic field. This field leads to a gap in the zero-sound mode, which scales proportionally to the magnitude of the field when it is small. In chapter 3 we study the classical dynamics of the tachyon field in an AdS background described by the tachyon-Dirac-Born-Infeld action. By considering a black hole in AdS space and switching on a non-vanishing background gauge field we obtained a holographic model of conformal symmetry breaking in a strongly coupled system at finite temperature and charge density. In chapter 4 we provide the exact string theoretic description of a quantum field theory at finite temperature and charge density Show less
A time integrated search for cosmic neutrinos is discussed in this thesis using four years of data collected by the ANTARES experiment. No statistically significant signal was found, therefore... Show moreA time integrated search for cosmic neutrinos is discussed in this thesis using four years of data collected by the ANTARES experiment. No statistically significant signal was found, therefore upper limits on the neutrino flux were derived. Limits for specific models of RX J1713.7-3946, Vela X and Crab Nebula which include information on the source morphology and spectrum, are also given. Show less
In this PhD thesis we investigated the feasibility to build a spin-flip laser, a spintronic device recently proposed by Kadigrobov that can emit radiation within the so-called terahertz gap. In the... Show moreIn this PhD thesis we investigated the feasibility to build a spin-flip laser, a spintronic device recently proposed by Kadigrobov that can emit radiation within the so-called terahertz gap. In the first part of this thesis, we describe point contact spectroscopy experiments which were meant as a first step to the final observation of radiation coming from the spin-flip laser. The ferromagnet used in our spin-flip laser is SmCo5, a hard ferromagnet with a very large coercive field. The next chapter of the thesis describes the sputter growth of thin films of Sm-Co. We found that one of the main problems of building a spin-flip laser is the issue of spin current injection and the relaxation of the spin current in an adjacent layer. In the last chapters of the thesis, we use the ferromagnetic resonance technique to study how the spin currents behave at the interface of a ferromagnet and a normal metal with large spin-orbit coupling, such as Pt or Pd or a normal metal with weak spin-orbit coupling, such as Cu. Show less
This thesis involves excitonic physics in bilayers of strongly correlated electron materials. The fermionic bilayer extended Hubbard model is studied by means of mean field theory and Determinant... Show moreThis thesis involves excitonic physics in bilayers of strongly correlated electron materials. The fermionic bilayer extended Hubbard model is studied by means of mean field theory and Determinant Quantum Monte Carlo simulations. A bosonic low-energy effective theory is developed, called the exciton t-J model. The phase diagram and the elementary excitations of this model are investigated. Surprisingly, the excitons are predicted to exhibit Ising confinement physics in the antiferromagnetic phase. In the exciton superfluid phase the magnetic triplon modes borrow kinetic energy from the excitons. Show less
When soft, repulsive particles, like foam bubbles or emulsion droplets, are sheared, they show interesting scaling behaviour. We develop a simple scaling model that captures the rheological... Show moreWhen soft, repulsive particles, like foam bubbles or emulsion droplets, are sheared, they show interesting scaling behaviour. We develop a simple scaling model that captures the rheological behavior starting from three assumptions that explicitly depend on the microscopic interactions. This model starts from three ingredients: energy conservation, the concept of an effective steady state strain in our flowing system and a constitutive elasticity equation linking the effective strain to the shear stress. Our model allows for non-linear microscopic particle interactions and it predicts that the global rheological behaviour depends on the details of the microscopic interactions between the particles - in contrast to standard critical scaling theory. We test our model in computer simulations of soft, massless particles under steady shear and find that the numerics are broadly consistent with our model. jamming, rheology, foam, critical scaling Show less
Topological superconductivity is a novel phenomenon, that has recently been predicted to exist in quantum wires. The first signatures of this new superconducting state have recently been reported.... Show moreTopological superconductivity is a novel phenomenon, that has recently been predicted to exist in quantum wires. The first signatures of this new superconducting state have recently been reported. The difference with usual superconductors is the appearance of conducting edge states. It is of interest to investigate how all the well-known effects of superconductivity, including Andreev reflection and Josephson effect, are modified by these edge states, and also to discover new effects that appear only in topological superconductors. This investigation is the main topic of the thesis. Show less
Imaging subsurface structures with nanometer resolution has been a long-standing desire in science and industry. To obtain subsurface information one usually applies ultrasound, like e.g. in... Show moreImaging subsurface structures with nanometer resolution has been a long-standing desire in science and industry. To obtain subsurface information one usually applies ultrasound, like e.g. in echocardiography. Implementing ultrasound in an Atomic Force Microscope, a setup that is capable of imaging surfaces with atomic resolution, gives access to additional information. In particular, it is possible to image subsurface structures with nanometer resolution. However, it is not known why the subsurface structures become visible when applying ultrasound during the imaging with an Atomic Force Microscope. Based on a special excitation scheme, which makes use of two ultrasound excitations (one through the sample and one through the cantilever), Heterodyne Force Microscopy seems to be the most promising candidate for imaging deeply buried objects or structures with nanometer resolution. This thesis focuses on the poorly understood elements in Heterodyne Force Microscopy. We studied the ultrasound propagation in the sample, the dynamics of an ultrasonically excited cantilever near a sample that is also vibrating at a slightly diff erent frequency, and the generation of the heterodyne signal. The insight we gained in these matters allowed us to determine the contrast mechanism in a very well-de fined model sample, which contains gold nanoparticles buried in a soft polymer matrix. We show that the contrast in this system is determined by “friction at shaking nanoparticles”. Show less
We study the dynamics of single molecules and individual gold nanorods in glycerol at variable temperatures. We demonstrate temperature-cycle microscopy on FRET-labeled polyproline and double... Show moreWe study the dynamics of single molecules and individual gold nanorods in glycerol at variable temperatures. We demonstrate temperature-cycle microscopy on FRET-labeled polyproline and double-stranded DNA molecules to access micro-second dynamics of single molecules, and reveal the influences of dye-dye interaction at short interdye distances on the observed FRET values. We use neutron-scattering techniques to examine the origin of solid-like structures suggested in previous reports and the influence of the thermal history. We find that crystal nucleation takes place in glycerol at temperatures very close to the glass transition temperature. This observation suggests that the thermal history of the glycerol sample needs to be controlled for studying dynamical heterogeneity in supercooled liquids. For the first time, we demonstrate gold nanorods as local viscosity reporter to study heterogeneity in supercooled liquids. Following rotational dynamics of individual gold nanorods in glycerol upon cooling below 226K, we start to observe deviations of local viscosity from the bulk viscosity of glycerol. Our observation suggests heterogeneity on relatively large length scale exists at surprisingly high temperatures. In the end, we demonstrate gold nanorods for enhancing fluorescence from single molecules and for fluorescence correlation spectroscopy at micromolar concentrations with single-molecule sensitivity. Show less
In this thesis, we study energy transport and fluctuations in simple models of fragile matter : a unique state of matter that has a vanishingly small window of linear response since one or both of... Show moreIn this thesis, we study energy transport and fluctuations in simple models of fragile matter : a unique state of matter that has a vanishingly small window of linear response since one or both of its elastic moduli (shear and bulk) are nearly zero. As a consequence, even the tiniest perturbations travel as nonlinear waves. In addition, most models of fragile matter have an amorphous structure. It is the interaction of the non-linear waves with the underlying disorder and the resulting fluctuations, that constitutes the unifying theme explored in this thesis. There are at least two seemingly distinct sources of fragility: a local source stemming from the strongly non-linear interaction potential between particles so that one can not expand around a potential minimum to define a spring constant, and a second, global source, whereby the collective response of the sample can be considered weakly linear. As a model of the first kind, we consider a two dimensional packing of soft frictionless elastic disks that are just touching their nearest neighbours. The interaction potential between elastic disks is given by the nonlinear Hertz law that has no harmonic part. Consequently, for a packing in this state, the bulk modulus is vanishingly small and the smallest compressions imparted at the edges leads to nonlinear solitary like waves. As a model of the second kind, we consider a two dimensional random network of harmonic springs where each node has on average around four nearest neighbours. Here, despite the contact interaction being harmonic, the network has a vanishingly small shear modulus. Consequently, even the tiniest shear strains elicit non-linear waves. There are many important similarities and differences between the nature of non-linear waves and the role played by disorder in the two models described above, which we are gradually beginning to understand. Show less
Magnetic resonance force microscopy (MRFM) is a powerful technique to detect a small number of spins that relies on force detection by an ultrasoft magnetically tipped cantilever and selective... Show moreMagnetic resonance force microscopy (MRFM) is a powerful technique to detect a small number of spins that relies on force detection by an ultrasoft magnetically tipped cantilever and selective magnetic resonance manipulation of the spins. MRFM would greatly benefit from ultralow temperature operation, because of lower thermomechanical noise and increased thermal spin polarization. Here we demonstrate MRFM operation at temperatures as low as 30 mK, thanks to a recently developed superconducting quantum interference device (SQUID)-based cantilever detection technique, which avoids cantilever overheating. In our experiment, we detect dangling bond paramagnetic centres on a silicon surface down to millikelvin temperatures. Fluctuations of such defects are supposedly linked to 1/f magnetic noise and decoherence in SQUIDs, as well as in several superconducting and single spin qubits. We find evidence that spin diffusion has a key role in the low-temperature spin dynamics Show less
