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In dieser Arbeit werden die Effekte der Synchronisation nichtlinearer, akustischer Oszillatoren am Beispiel zweier Orgelpfeifen untersucht. Aus vorhandenen, experimentellen Messdaten werden die typischen Merkmale der Synchronisation extrahiert und dargestellt. Es folgt eine detaillierte Analyse der Übergangsbereiche in das Synchronisationsplateau, der Phänomene während der Synchronisation, als auch das Austreten aus der Synchronisationsregion beider Orgelpfeifen, bei verschiedenen Kopplungsstärken. Die experimentellen Befunde werfen Fragestellungen nach der Kopplungsfunktion auf. Dazu wird die Tonentstehung in einer Orgelpfeife untersucht. Mit Hilfe von numerischen Simulationen der Tonentstehung wird der Frage nachgegangen, welche fluiddynamischen und aero-akustischen Ursachen die Tonentstehung in der Orgelpfeife hat und inwiefern sich die Mechanismen auf das Modell eines selbsterregten akustischen Oszillators abbilden lässt. Mit der Methode des Coarse Graining wird ein Modellansatz formuliert.
Cargo transport by molecular motors is ubiquitous in all eukaryotic cells and is typically driven cooperatively by several molecular motors, which may belong to one or several motor species like kinesin, dynein or myosin. These motor proteins transport cargos such as RNAs, protein complexes or organelles along filaments, from which they unbind after a finite run length. Understanding how these motors interact and how their movements are coordinated and regulated is a central and challenging problem in studies of intracellular transport. In this thesis, we describe a general theoretical framework for the analysis of such transport processes, which enables us to explain the behavior of intracellular cargos based on the transport properties of individual motors and their interactions. Motivated by recent in vitro experiments, we address two different modes of transport: unidirectional transport by two identical motors and cooperative transport by actively walking and passively diffusing motors. The case of cargo transport by two identical motors involves an elastic coupling between the motors that can reduce the motors’ velocity and/or the binding time to the filament. We show that this elastic coupling leads, in general, to four distinct transport regimes. In addition to a weak coupling regime, kinesin and dynein motors are found to exhibit a strong coupling and an enhanced unbinding regime, whereas myosin motors are predicted to attain a reduced velocity regime. All of these regimes, which we derive both by analytical calculations and by general time scale arguments, can be explored experimentally by varying the elastic coupling strength. In addition, using the time scale arguments, we explain why previous studies came to different conclusions about the effect and relevance of motor-motor interference. In this way, our theory provides a general and unifying framework for understanding the dynamical behavior of two elastically coupled molecular motors. The second mode of transport studied in this thesis is cargo transport by actively pulling and passively diffusing motors. Although these passive motors do not participate in active transport, they strongly enhance the overall cargo run length. When an active motor unbinds, the cargo is still tethered to the filament by the passive motors, giving the unbound motor the chance to rebind and continue its active walk. We develop a stochastic description for such cooperative behavior and explicitly derive the enhanced run length for a cargo transported by one actively pulling and one passively diffusing motor. We generalize our description to the case of several pulling and diffusing motors and find an exponential increase of the run length with the number of involved motors.
One of the most exciting predictions of Einstein's theory of gravitation that have not yet been proven experimentally by a direct detection are gravitational waves. These are tiny distortions of the spacetime itself, and a world-wide effort to directly measure them for the first time with a network of large-scale laser interferometers is currently ongoing and expected to provide positive results within this decade. One potential source of measurable gravitational waves is the inspiral and merger of two compact objects, such as binary black holes. Successfully finding their signature in the noise-dominated data of the detectors crucially relies on accurate predictions of what we are looking for. In this thesis, we present a detailed study of how the most complete waveform templates can be constructed by combining the results from (A) analytical expansions within the post-Newtonian framework and (B) numerical simulations of the full relativistic dynamics. We analyze various strategies to construct complete hybrid waveforms that consist of a post-Newtonian inspiral part matched to numerical-relativity data. We elaborate on exsisting approaches for nonspinning systems by extending the accessible parameter space and introducing an alternative scheme based in the Fourier domain. Our methods can now be readily applied to multiple spherical-harmonic modes and precessing systems. In addition to that, we analyze in detail the accuracy of hybrid waveforms with the goal to quantify how numerous sources of error in the approximation techniques affect the application of such templates in real gravitational-wave searches. This is of major importance for the future construction of improved models, but also for the correct interpretation of gravitational-wave observations that are made utilizing any complete waveform family. In particular, we comprehensively discuss how long the numerical-relativity contribution to the signal has to be in order to make the resulting hybrids accurate enough, and for currently feasible simulation lengths we assess the physics one can potentially do with template-based searches.
This thesis contains several theoretical studies on optomechanical systems, i.e. physical devices where mechanical degrees of freedom are coupled with optical cavity modes. This optomechanical interaction, mediated by radiation pressure, can be exploited for cooling and controlling mechanical resonators in a quantum regime. The goal of this thesis is to propose several new ideas for preparing meso- scopic mechanical systems (of the order of 10^15 atoms) into highly non-classical states. In particular we have shown new methods for preparing optomechani-cal pure states, squeezed states and entangled states. At the same time, proce-dures for experimentally detecting these quantum effects have been proposed. In particular, a quantitative measure of non classicality has been defined in terms of the negativity of phase space quasi-distributions. An operational al- gorithm for experimentally estimating the non-classicality of quantum states has been proposed and successfully applied in a quantum optics experiment. The research has been performed with relatively advanced mathematical tools related to differential equations with periodic coefficients, classical and quantum Bochner’s theorems and semidefinite programming. Nevertheless the physics of the problems and the experimental feasibility of the results have been the main priorities.
Theory of mRNA degradation
(2012)
One of the central themes of biology is to understand how individual cells achieve a high fidelity in gene expression. Each cell needs to ensure accurate protein levels for its proper functioning and its capability to proliferate. Therefore, complex regulatory mechanisms have evolved in order to render the expression of each gene dependent on the expression level of (all) other genes. Regulation can occur at different stages within the framework of the central dogma of molecular biology. One very effective and relatively direct mechanism concerns the regulation of the stability of mRNAs. All organisms have evolved diverse and powerful mechanisms to achieve this. In order to better comprehend the regulation in living cells, biochemists have studied specific degradation mechanisms in detail. In addition to that, modern high-throughput techniques allow to obtain quantitative data on a global scale by parallel analysis of the decay patterns of many different mRNAs from different genes. In previous studies, the interpretation of these mRNA decay experiments relied on a simple theoretical description based on an exponential decay. However, this does not account for the complexity of the responsible mechanisms and, as a consequence, the exponential decay is often not in agreement with the experimental decay patterns. We have developed an improved and more general theory of mRNA degradation which provides a general framework of mRNA expression and allows describing specific degradation mechanisms. We have made an attempt to provide detailed models for the regulation in different organisms. In the yeast S. cerevisiae, different degradation pathways are known to compete and furthermore most of them rely on the biochemical modification of mRNA molecules. In bacteria such as E. coli, degradation proceeds primarily endonucleolytically, i.e. it is governed by the initial cleavage within the coding region. In addition, it is often coupled to the level of maturity and the size of the polysome of an mRNA. Both for S. cerevisiae and E. coli, our descriptions lead to a considerable improvement of the interpretation of experimental data. The general outcome is that the degradation of mRNA must be described by an age-dependent degradation rate, which can be interpreted as a consequence of molecular aging of mRNAs. Within our theory, we find adequate ways to address this much debated topic from a theoretical perspective. The improvements of the understanding of mRNA degradation can be readily applied to further comprehend the mRNA expression under different internal or environmental conditions such as after the induction of transcription or stress application. Also, the role of mRNA decay can be assessed in the context of translation and protein synthesis. The ultimate goal in understanding gene regulation mediated by mRNA stability will be to identify the relevance and biological function of different mechanisms. Once more quantitative data will become available, our description allows to elaborate the role of each mechanism by devising a suitable model.
Tensorial spacetime geometries carrying predictive, interpretable and quantizable matter dynamics
(2012)
Which tensor fields G on a smooth manifold M can serve as a spacetime structure? In the first part of this thesis, it is found that only a severely restricted class of tensor fields can provide classical spacetime geometries, namely those that can carry predictive, interpretable and quantizable matter dynamics. The obvious dependence of this characterization of admissible tensorial spacetime geometries on specific matter is not a weakness, but rather presents an insight: it was Maxwell theory that justified Einstein to promote Lorentzian manifolds to the status of a spacetime geometry. Any matter that does not mimick the structure of Maxwell theory, will force us to choose another geometry on which the matter dynamics of interest are predictive, interpretable and quantizable. These three physical conditions on matter impose three corresponding algebraic conditions on the totally symmetric contravariant coefficient tensor field P that determines the principal symbol of the matter field equations in terms of the geometric tensor G: the tensor field P must be hyperbolic, time-orientable and energy-distinguishing. Remarkably, these physically necessary conditions on the geometry are mathematically already sufficient to realize all kinematical constructions familiar from Lorentzian geometry, for precisely the same structural reasons. This we were able to show employing a subtle interplay of convex analysis, the theory of partial differential equations and real algebraic geometry. In the second part of this thesis, we then explore general properties of any hyperbolic, time-orientable and energy-distinguishing tensorial geometry. Physically most important are the construction of freely falling non-rotating laboratories, the appearance of admissible modified dispersion relations to particular observers, and the identification of a mechanism that explains why massive particles that are faster than some massless particles can radiate off energy until they are slower than all massless particles in any hyperbolic, time-orientable and energy-distinguishing geometry. In the third part of the thesis, we explore how tensorial spacetime geometries fare when one wants to quantize particles and fields on them. This study is motivated, in part, in order to provide the tools to calculate the rate at which superluminal particles radiate off energy to become infraluminal, as explained above. Remarkably, it is again the three geometric conditions of hyperbolicity, time-orientability and energy-distinguishability that allow the quantization of general linear electrodynamics on an area metric spacetime and the quantization of massive point particles obeying any admissible dispersion relation. We explore the issue of field equations of all possible derivative order in rather systematic fashion, and prove a practically most useful theorem that determines Dirac algebras allowing the reduction of derivative orders. The final part of the thesis presents the sketch of a truly remarkable result that was obtained building on the work of the present thesis. Particularly based on the subtle duality maps between momenta and velocities in general tensorial spacetimes, it could be shown that gravitational dynamics for hyperbolic, time-orientable and energy distinguishable geometries need not be postulated, but the formidable physical problem of their construction can be reduced to a mere mathematical task: the solution of a system of homogeneous linear partial differential equations. This far-reaching physical result on modified gravity theories is a direct, but difficult to derive, outcome of the findings in the present thesis. Throughout the thesis, the abstract theory is illustrated through instructive examples.
This thesis is focussed on the electronic properties of the new material class named topological insulators. Spin and angle resolved photoelectron spectroscopy have been applied to reveal several unique properties of the surface state of these materials. The first part of this thesis introduces the methodical background of these quite established experimental techniques.
In the following chapter, the theoretical concept of topological insulators is introduced. Starting from the prominent example of the quantum Hall effect, the application of topological invariants to classify material systems is illuminated. It is explained how, in presence of time reversal symmetry, which is broken in the quantum Hall phase, strong spin orbit coupling can drive a system into a topologically non trivial phase. The prediction of the spin quantum Hall effect in two dimensional insulators an the generalization to the three dimensional case of topological insulators is reviewed together with the first experimental realization of a three dimensional topological insulator in the Bi1-xSbx alloys given in the literature.
The experimental part starts with the introduction of the Bi2X3 (X=Se, Te) family of materials. Recent theoretical predictions and experimental findings on the bulk and surface electronic structure of these materials are introduced in close discussion to our own experimental results. Furthermore, it is revealed, that the topological surface state of Bi2Te3 shares its orbital symmetry with the bulk valence band and the observation of a temperature induced shift of the chemical potential is to a high probability unmasked as a doping effect due to residual gas adsorption.
The surface state of Bi2Te3 is found to be highly spin polarized with a polarization value of about 70% in a macroscopic area, while in Bi2Se3 the polarization appears reduced, not exceeding 50%. We, however, argue that the polarization is most likely only extrinsically limited in terms of the finite angular resolution and the lacking detectability of the out of plane component of the electron spin. A further argument is based on the reduced surface quality of the single crystals after cleavage and, for Bi2Se3 a sensitivity of the electronic structure to photon exposure.
We probe the robustness of the topological surface state in Bi2X3 against surface impurities in Chapter 5. This robustness is provided through the protection by the time reversal symmetry. Silver, deposited on the (111) surface of Bi2Se3 leads to a strong electron doping but the surface state is observed up to a deposited Ag mass equivalent to one atomic monolayer. The opposite sign of doping, i.e., hole-like, is observed by exposing oxygen to Bi2Te3. But while the n-type shift of Ag on Bi2Se3 appears to be more or less rigid, O2 is lifting the Dirac point of the topological surface state in Bi2Te3 out of the valence band minimum at $\Gamma$. After increasing the oxygen dose further, it is possible to shift the Dirac point to the Fermi level, while the valence band stays well beyond. The effect is found reversible, by warming up the samples which is interpreted in terms of physisorption of O2.
For magnetic impurities, i.e., Fe, we find a similar behavior as for the case of Ag in both Bi2Se3 and Bi2Te3. However, in that case the robustness is unexpected, since magnetic impurities are capable to break time reversal symmetry which should introduce a gap in the surface state at the Dirac point which in turn removes the protection. We argue, that the fact that the surface state shows no gap must be attributed to a missing magnetization of the Fe overlayer. In Bi2Te3 we are able to observe the surface state for deposited iron mass equivalents in the monolayer regime. Furthermore, we gain control over the sign of doping through the sample temperature during deposition.
Chapter6 is devoted to the lifetime broadening of the photoemission signal from the topological surface states of Bi2Se3 and Bi2Te3. It is revealed that the hexagonal warping of the surface state in Bi2Te3 introduces an anisotropy for electrons traveling along the two distinct high symmetry directions of the surface Brillouin zone, i.e., $\Gamma$K and $\Gamma$M. We show that the phonon coupling strength to the surface electrons in Bi2Te3 is in nice agreement with the theoretical prediction but, nevertheless, higher than one may expect. We argue that the electron-phonon coupling is one of the main contributions to the decay of photoholes but the relatively small size of the Fermi surface limits the number of phonon modes that may scatter off electrons. This effect is manifested in the energy dependence of the imaginary part of the electron self energy of the surface state which shows a decay to higher binding energies in contrast to the monotonic increase proportional to E$^2$ in the Fermi liquid theory due to electron-electron interaction.
Furthermore, the effect of the surface impurities of Chapter 5 on the quasiparticle life- times is investigated. We find that Fe impurities have a much stronger influence on the lifetimes as compared to Ag. Moreover, we find that the influence is stronger independently of the sign of the doping. We argue that this observation suggests a minor contribution of the warping on increased scattering rates in contrast to current belief. This is additionally confirmed by the observation that the scattering rates increase further with increasing silver amount while the doping stays constant and by the fact that clean Bi2Se3 and Bi2Te3 show very similar scattering rates regardless of the much stronger warping in Bi2Te3.
In the last chapter we report on a strong circular dichroism in the angle distribution of the photoemission signal of the surface state of Bi2Te3. We show that the color pattern obtained by calculating the difference between photoemission intensities measured with opposite photon helicity reflects the pattern expected for the spin polarization. However, we find a strong influence on strength and even sign of the effect when varying the photon energy. The sign change is qualitatively confirmed by means of one-step photoemission calculations conducted by our collaborators from the LMU München, while the calculated spin polarization is found to be independent of the excitation energy. Experiment and theory together unambiguously uncover the dichroism in these systems as a final state effect and the question in the title of the chapter has to be negated: Circular dichroism in the angle distribution is not a new spin sensitive technique.
Thermal and quantum fluctuations of the electromagnetic near field of atoms and macroscopic bodies play a key role in quantum electrodynamics (QED), as in the Lamb shift. They lead, e.g., to atomic level shifts, dispersion interactions (Van der Waals-Casimir-Polder interactions), and state broadening (Purcell effect) because the field is subject to boundary conditions. Such effects can be observed with high precision on the mesoscopic scale which can be accessed in micro-electro-mechanical systems (MEMS) and solid-state-based magnetic microtraps for cold atoms (‘atom chips’). A quantum field theory of atoms (molecules) and photons is adapted to nonequilibrium situations. Atoms and photons are described as fully quantized while macroscopic bodies can be included in terms of classical reflection amplitudes, similar to the scattering approach of cavity QED. The formalism is applied to the study of nonequilibrium two-body potentials. We then investigate the impact of the material properties of metals on the electromagnetic surface noise, with applications to atomic trapping in atom-chip setups and quantum computing, and on the magnetic dipole contribution to the Van der Waals-Casimir-Polder potential in and out of thermal equilibrium. In both cases, the particular properties of superconductors are of high interest. Surface-mode contributions, which dominate the near-field fluctuations, are discussed in the context of the (partial) dynamic atomic dressing after a rapid change of a system parameter and in the Casimir interaction between two conducting plates, where nonequilibrium configurations can give rise to repulsion.
We investigate properties of quantum mechanical systems in the light of quantum information theory. We put an emphasize on systems with infinite-dimensional Hilbert spaces, so-called continuous-variable systems'', which are needed to describe quantum optics beyond the single photon regime and other Bosonic quantum systems. We present methods to obtain a description of such systems from a series of measurements in an efficient manner and demonstrate the performance in realistic situations by means of numerical simulations. We consider both unconditional quantum state tomography, which is applicable to arbitrary systems, and tomography of matrix product states. The latter allows for the tomography of many-body systems because the necessary number of measurements scales merely polynomially with the particle number, compared to an exponential scaling in the generic case. We also present a method to realize such a tomography scheme for a system of ultra-cold atoms in optical lattices. Furthermore, we discuss in detail the possibilities and limitations of using continuous-variable systems for measurement-based quantum computing. We will see that the distinction between Gaussian and non-Gaussian quantum states and measurements plays an crucial role. We also provide an algorithm to solve the large and interesting class of naturally occurring Hamiltonians, namely frustration free ones, efficiently and use this insight to obtain a simple approximation method for slightly frustrated systems. To achieve this goals, we make use of, among various other techniques, the well developed theory of matrix product states, tensor networks, semi-definite programming, and matrix analysis.
Actin is one of the most abundant and highly conserved proteins in eukaryotic cells. The globular protein assembles into long filaments, which form a variety of different networks within the cytoskeleton. The dynamic reorganization of these networks - which is pivotal for cell motility, cell adhesion, and cell division - is based on cycles of polymerization (assembly) and depolymerization (disassembly) of actin filaments. Actin binds ATP and within the filament, actin-bound ATP is hydrolyzed into ADP on a time scale of a few minutes. As ADP-actin dissociates faster from the filament ends than ATP-actin, the filament becomes less stable as it grows older. Recent single filament experiments, where abrupt dynamical changes during filament depolymerization have been observed, suggest the opposite behavior, however, namely that the actin filaments become increasingly stable with time. Several mechanisms for this stabilization have been proposed, ranging from structural transitions of the whole filament to surface attachment of the filament ends. The key issue of this thesis is to elucidate the unexpected interruptions of depolymerization by a combination of experimental and theoretical studies. In new depolymerization experiments on single filaments, we confirm that filaments cease to shrink in an abrupt manner and determine the time from the initiation of depolymerization until the occurrence of the first interruption. This duration differs from filament to filament and represents a stochastic variable. We consider various hypothetical mechanisms that may cause the observed interruptions. These mechanisms cannot be distinguished directly, but they give rise to distinct distributions of the time until the first interruption, which we compute by modeling the underlying stochastic processes. A comparison with the measured distribution reveals that the sudden truncation of the shrinkage process neither arises from blocking of the ends nor from a collective transition of the whole filament. Instead, we predict a local transition process occurring at random sites within the filament. The combination of additional experimental findings and our theoretical approach confirms the notion of a local transition mechanism and identifies the transition as the photo-induced formation of an actin dimer within the filaments. Unlabeled actin filaments do not exhibit pauses, which implies that, in vivo, older filaments become destabilized by ATP hydrolysis. This destabilization can be identified with an acceleration of the depolymerization prior to the interruption. In the final part of this thesis, we theoretically analyze this acceleration to infer the mechanism of ATP hydrolysis. We show that the rate of ATP hydrolysis is constant within the filament, corresponding to a random as opposed to a vectorial hydrolysis mechanism.