Modeling complex gene interacting systems as Boolean networks lead to a significant simplification of computational investigation. This can be achieved by discretization of the expression level to ON or OFF states and classifying the interactions to inhibitory and activating. In this respect, Boolean functions are responsible for the evolution of the binary elements of the Boolean networks. In this thesis, we investigate the mostly used Boolean functions in modeling gene regulatory networks. Moreover, we introduce a new type of function with strong inhibitory namely the veto function. Our computational and analytic studies on the verity of the networks capable of constructing the same State Transition Graph lead to define a new concept namely the “degeneracy” of Boolean functions. We further derive analytically the sensitivity of the Boolean functions to perturbations. It turns out that the veto function forms the most robust dynamics. Furthermore, we verify the applicability of veto function to model the yeast cell cycle networks. In particular, we show that in an intracellular signal transduction network [Helikar et al, PNAS (2008)], the functions with veto are over-represented by a factor exceeding the over-representation of threshold functions and canalyzing functions in the same system. The statistics of the connections of the functional networks are studied in detail. Finally, we look at a different scale of biological phenomena using a binary model. We propose a simple correlation-based model to describe the pattern formation of Fly eye. Specifically, we model two different procedures of Fly eye formation, and provide a generic approach for Fly eye simulation.

Im Mittelpunkt dieser Arbeit steht die Untersuchung der kollektiven Dynamik des binaeren Systems Rb-Sb im fluessigen Zustand. Die dynamische Struktur wurde fuer zwei Zusammensetzungen durch inelastische Neutronenstreuung bestimmt. Die daraus ermittelten Dispersionsrelationen geben Aufschluss ueber die kollektiven Anregungen im System. Um kuenftig noch bessere Experimente durchfuehren zu koennen, wurden die Parameter eines neues Neutronen Brillouin Spektrometers mittels Monte-Carlo Simulation optimiert. / In the first part of this report the collective atomic dynamics of liquid Rb-Sb is discussed. The dynamic structure factors were measured by inelastic neutron scattering. The resulting dispersion relations show how the dynamics of this system alters with the change in the interatomic potential. To improve the experimental part the setup of a new neutron Brillouin spectrometer was optimized by a Monte-Carlo simulation. These results are presented in the second part.

The atomic dynamics in liquids is still a challenging subject. The objective of this thesis was to study how the dynamics depends on the TYPE of the atomic interaction. Dynamic properties extracted from inelastic neutron scattering experiments on three binary systems clearly show a discontinous behaviour in the transition from a pure metallic to an ionic and partly covalent bonding regime. Further, results of Monte-Carlo simulations of a new type of spectrometer, a Neutron-Brillouin-Spectrometer, that is currently under construction, are presented. / In dieser Arbeit wurde der Einfluss der Art der zwischenatomaren Wechselwirkung auf die atomare Dynamik in Fluessigkeiten untersucht. Dafuer wurden geeignete binaere Systeme ausgewaehlt und deren Dichtefluktuationen mittels unelastischer Neutronenstreuung gemessen. Neben den teilweise bekannten strukturellen Veraenderungen, die beim Uebergang von rein metallischen zu ionischen und teilweise kovalenten Bindungen auftreten, konnten vor allem die Auswirkungen wechselnder Bindungsverhaeltnisse auf eine Reihe dynamischer Eigenschaften nachgewiesen werden. Besonders hervorzuheben sind dabei der Nachweis eines Hochfrequenzbandes im Frequenzspektrum des fluessigen RbSb sowie in den fluessigen Na-Sn Legierungen die Aufspaltung der aus der longitudinalen Stromkorrelationsfunktion abgeleiteten Dispersion in zwei Baender, die die verschiedenartige Dynamik der unterschiedlich schweren Komponenten widerspiegeln. Desweiteren werden in dieser Arbeit Ergebnisse umfangreicher Monte-Carlo Simulationen fuer ein im Bau befindliches neuartiges Neutronen-Brillouin-Spektrometer vorgestellt.

Kerstin Zimmermann, Wien, betrachtete verschiedene Klassifikationen zur Beschreibung von Technologien. Hierbei geht es auch um Eingruppierungen von neuen Technolo­giefeldern mit einem besonderen Augenmerk auf IKT. Die OECD-Klassifikation misst nur die F&E Intensität am Gesamtumsatz. NACE Code und ISIC beziehen sich auf Produktion, Handel und Dienstleistungen. Im cross-sektoralen Bereich gilt es aber, sinnvolle Indikatoren für die Anwendung einer generischen Technologie zu finden, der allerdings neuere Meßmethoden zur Seite gestellt werden müssen. Entspre­chende Parameter stellte sie vor.

Einen Überblick erlaubt das Inhaltsverzeichnis. Das Buch enthält ergänzende handschriftliche Bemerkungen von Herrn Professor Dresig.:* Vorwort, Inhaltsverzeichnis, Einleitung * Kapitel 1 Kinematik zwangläufiger Mechanismen * Kapitel 2 Kinetik zwangläufiger Mechanismen * Kapitel 3 Dynamischer Ausgleich * Kapitel 4.1-2 Schwingungsmodelle mit einem Freiheitsgrad * Kapitel 4.3 Lösung der Bewegungsgleichung bei konstanten Koeffizienten * Kapitel 4.4 Lösung der Bewegungsgleichung bei veränderlichen Koeffizienten * Kapitel 4.5-6 Bedingungen der kinetischen Stabilität bei Parametererregung * Kapitel 5.1-2 Schwingungsmodelle mit mehreren Freiheitsgraden * Kapitel 5.3 Lösung linearisierter Gleichungen * Kapitel 5.4 Antriebe mit verzweigter Struktur * Kapitel 5.5 Nichtlineare Schwingungen von Mechanismen * Literaturverzeichnis, Kurzzeichen, Sachverzeichnis

Der Vortrag zeigt die einzelnen notwendigen Schritte auf, die zur Lösung des Resonanzproblems an der Vorderradaufhängung eines E-Rollstuhls der Firma MEYRA-ORTOPEDIA notwendig waren. Alle Lösungsschritte wurden mit Creo Elements/Pro und seinen Modulen Mechanism Design Option (MDO) und Advanced Mechanica erarbeitet.

The concept of magnetic frustration is a fundamental topic in modern solid-state physics having direct consequences in systems with rich magnetic phases hosting emergent excitations, such as the magnetic monopoles in the spin-ice compounds. One important ingredient of frustration is the lattice that constrains the magnetic spins on it to a site anisotropy and inter-site coupling. Therefore, strong magnetoelastic interactions between the magnetic system and the lattice are expected and investigated in this thesis in detail. At first, I investigate the dependence of the relative length change of single crystals of the classical spin ices \dto{} and \hto{} on the magnetic field and temperature by capacitive dilatometry. In terms of the magnetostriction and thermal expansion \dto{} and \hto{} show qualitatively similar behavior, that seems to be independent of the Kramer or non-Kramers character of the rare-earth ion. The magnitude of the magnetostrictive effect deep in the spin-ice phase at \SI{0.3}{\kelvin} is $\deltaL{} = \SI{2e-5}{}$ and $\SI{2e-4}{}$ for \dto{} and \hto{}, respectively. In numerical simulations using a manifold model, the experimental results could be qualitatively reproduced by a combination of exchange and crystal-field striction. A second highlight of the dilatometric measurements of the spin-ice compounds is the observation of the lattice dynamics. The relaxation processes are rather slow, the longest relaxation times were observed at lowest temperatures and in the field range with magnetostrictive hysteresis, \ie{}, below \SI{0.9}{\tesla} for \dto{} and below \SI{1.5}{\tesla} for \hto{}. I find that the region of longest relaxation coincides well with the kagome-ice phase of the magnetic phase diagrams; the laxation time is of the order of \SI{5000}{\second} ($> \SI{80}{\minute}$). With increasing temperatures the time scale of the relaxation reduces to minutes at around \SI{0.7}{\kelvin} corresponding to the spin-freezing temperature obtained from ac-susceptibility measurements. In the second study I investigate the variation of the magnetic properties in dependence of the lattice constant. A systematic reduction of the lattice constant of \dgsoxx{} can be achieved by substituting the non-magnetic germanium ion in the cubic pyrochlore oxide with silicon. Characteristic properties of a spin-ice phase could be observed in measurements of magnetization, ac susceptibility, and heat capacity. From the temperature shift of the peaks, observed in the temperature-dependent heat capacity, an increase of the strength of the magnetic exchange interaction by a changed ratio of the competing exchange and dipolar interaction is deduced. The new spin-ice compounds are, thus, closer to the phase boundary between spin-ice phase and antiferromagnetically ordered all-in-all-out phase consistent with a reduction of the energy of monopole excitations.

Quasi two-dimensional turbulent flows, like mesoscale oceanic and large-scale atmospheric flows, create finite-time coherent structures, compact fluid masses that resist mixing for finite-time despite the turbulent nature of the ambient flow. These coherent structures significantly affect the mixing and transport of fluid elements. In return, the transport of passive scalars like heat, humidity, salinity, chemical concentration, nutrients and even algae has a substantial impact on countless geophysical phenomena. Thus, in order to understand these effects reliable methods for coherent structure detection and the identification of their boundaries are necessary. Here, in this thesis, we present two contributions in this regard. First, we present improvements of the transfer operator approach, an established stochastic approach for the detection of almost-invariant and coherent sets. The approach approximates the transport properties of a complicated flow by a linear transfer operator and aims to partition a given domain in multiple sets such that the inter-set mass transport is minimized. The improvements include the introduction of mixing boundary conditions in stationary and time-dependent flows. By modifying the transfer operator we couple the filaments that surround the coherent and jointly rotating fluid volume such that effectively only two non-communicating sets remain: the coherent eddy core and the ambient flow. This significantly stabilizes the inference of coherent eddy cores and makes the use of popular but error-prone clustering techniques unnecessary. In addition, we discuss the identification of temporally consistent areas of increased coherence. Instead of coherent structures that are defined by advected non-filamenting masses, the concept describes consistent and moving patches of reduced mixing whose mass can change over time. This permits the decoupling of the coherence time scale from the time window under consideration. Both modifications are used to study the transport properties of eight selected Baltic Sea eddies. Secondly, we introduce the MSCS-search, a new algorithm for the inference of finite-time coherent volumes that is solely based upon the concept of convexity. Persistent convexity is a sufficient condition for coherence in two-dimensional flows if coherent structures are understood as non-filamenting volumes. However, convexity has never been considered as condition of coherence, even though some methods use it, for practical reasons, as an explicit constraint. The approach identifies the largest structure inside a given volume that remains star-convex with respect to a given reference trajectory within a given time window. We test the approach thoroughly and our results show that the approach yields good and reliable estimations of coherent structures in all test cases. Moreover, since the results depend explicitly on the considered time window, the results are intuitive and enable the identification and study of filaments. The novel approach is then used to re-evaluate transport processes in the data set of Baltic eddies.:1 Introduction 2 Theoretical Background 2.1 Methods 2.1.1 Okubo-Weiss criterion 2.1.2 Finite-Time Lyapunov Exponents 2.1.3 Lagrangian Descriptors and Lagrangian averaged vorticity deviation 2.2 Models 2.2.1 Euler equation 2.2.2 Stationary Gaussian Blob Model 2.2.3 Periodically Perturbed Gaussian Blob Model 2.2.4 Bickley-Jet 3 Transfer Operator Approach I: State of the Art 3.1 Frobenius-Perron Operator 3.2 Markov-Chains 3.3 Laplacian matrices 3.4 Finding Almost-Invariant Sets 3.5 Finding Coherent Sets 3.5.1 Coherent pairs as tuples 3.5.2 Coherent pairs as triples 3.6 Spectral Clustering 3.7 Critique and Discussion 4 Transfer Operator Approach II: Mixing Boundary Conditions in Stationary Flows 4.1 Overview 4.2 Estimation of Transfer Probability Matrices P 4.3 Mixing Boundary Conditions 4.4 Thresholding 4.5 Results 4.5.1 Robustness with respect to parameters 4.5.2 Comparison and alternatives 4.5.3 Handling of false positives 4.5.4 Periodically perturbed flow 4.6 Closing Remark 5 Transfer operator approach III: Analysis of Oceanic Transport 5.1 Mixing Boundary Conditions: Time-Dependent Flows 5.1.1 Method 5.1.2 Results 5.2 Temporal consistency 5.2.1 Method 5.2.2 Results 5.3 Treatment of Coastal Effects 5.4 Application to Baltic velocity fields 5.4.1 Method 5.4.2 Results 5.5 Closing Remark 6 Prototypes of Coherent Sets: Star-Convex Structures 6.1 Mathematical Considerations 6.2 MSCS-Algorithm 6.3 Extracting star-convex sub-volumes 6.4 Results 6.4.1 Stationary Gaussian blob model 6.4.2 Bickley-Jet 6.4.3 Two dimensional inviscid flow 6.4.4 Real data sets 6.5 Closing Remark 7 Conclusion and Outlook / Es ist bekannt, dass quasi-zweidimensionale turbulente Strömungen, wie etwa Strömungen an der Meeresoberfläche oder großskalige Atmosphärenbewegungen, kohärente Strukturen ausbilden, kompakte Volumina, welche einer Mischung mit dem umgebenden Material für endliche Zeit widerstehen, obwohl die Strömung als solche turbulent ist. Diese Strukturen haben einen signifikanten Einfluss auf den Transport von Fluidelementen. Der Transport von passiven skalaren Größen, wie etwa Wärme, Feuchtigkeit, Salzgehalt, Nährstoffgehalt, jegliche Konzentration che- mischer Stoffe und sogar Algendichte hat wiederum einen Effekt auf unzählige geophysikalische Phänomene. Um diese Phänomene im Detail zu verstehen, sind zuverlässige Methoden für die Detektion von kohärenten Strukturen und die Identifikation ihrer Grenzen notwendig. In der vorliegenden Arbeit präsentieren wir zwei Beiträge zur Lösung dieses Problems. Als erstes präsentieren wir Verbesserungen der Transferoperatormethode. Diese etablierte Methode zur Identifikation von fast-invarianten und kohärenten Mengen approximiert die Transporteigenschaften eines Flusses mithilfe eines linearen Transferoperators, mit dem Ziel, das betrachtete Gebiet in Bereiche zu unterteilen, welche den Materialaustausch zwischen den Bereichen minimieren. Die Verbesserungen beinhalten die Einführung von mischenden Randbedingungen in stationären und nicht-stationären Flüssen. Dabei wird der Transferoperator so modifiziert, dass Filamente, welche die kohärente Struktur umgeben, gekoppelt werden, was zur Folge hat, dass effektiv nur zwei nicht kommunizierende Strukturen übrig bleiben: die kohärente Struktur und das sie umgebende Volumen. Dies führt zu einer signifikant erhöhten Stabilität der Methode ohne auf die sonst üblichen aber fehleranfälligen clustering-Techniken zurückgreifen zu müssen. Des Weiteren diskutieren wir die Identifikation von zeitlich konsistenten Regionen erhöhter Kohärenz. Anstatt von kohärenten Strukturen als bewegliche nicht filamentierende Massen zu sprechen, beschreibt dieses Konzept kohärente Strukturen als konsistente sich bewegende Regionen reduzierten Mischverhaltens deren beteiligte Masse zeitlich veränderlich ist. Dies erlaubt die Entkopplung der Kohärenzzeitskala vom betrachteten Zeitfenster. Im Anschluss verwenden wir beide Modifikationen, um die Transporteigenschaften von acht ausgewählten Ostseewirbeln zu untersuchen. Als zweiten Beitrag stellen wir den MSCS-Algorithmus vor, eine neue Methode zur Identifikation von kohärenten Strukturen, welche einzig und allein auf dem Prinzip von Konvexität basiert. Versteht man kohärente Strukturen als nicht filamentierende Massen, ist persistente Konvexität eine hinreichende Bedingung für Kohärenz. Konvexität wurde bisher noch nie als Grundlage für Kohärenz untersucht, obwohl sie aus praktischen Gründen in einigen Methoden bereits als einschränkende Bedingung verwendet wird. Die Methode identifiziert die größte Struktur innerhalb eines gegebenen Volumens, welches während eines gegebenen Zeitraums stern-konvex bezüglich einer gegebenen Referenztrajektor bleibt. Alle studierten Testszenarien zeigen, dass der Ansatz gute und zuverlässige Ergebnisse liefert. Diese Ergebnisse hängen darüber hinaus direkt von den Eingangsparametern ab, was die Interpretation der Ergebnisse stark erleichtert und zusätzlich die Untersuchung von Filamentbildung erlaubt. Die neue Methode wird verwendet um den kohärenten Transport in den bereits untersuchten Ostseewirbeln zu reevaluieren.:1 Introduction 2 Theoretical Background 2.1 Methods 2.1.1 Okubo-Weiss criterion 2.1.2 Finite-Time Lyapunov Exponents 2.1.3 Lagrangian Descriptors and Lagrangian averaged vorticity deviation 2.2 Models 2.2.1 Euler equation 2.2.2 Stationary Gaussian Blob Model 2.2.3 Periodically Perturbed Gaussian Blob Model 2.2.4 Bickley-Jet 3 Transfer Operator Approach I: State of the Art 3.1 Frobenius-Perron Operator 3.2 Markov-Chains 3.3 Laplacian matrices 3.4 Finding Almost-Invariant Sets 3.5 Finding Coherent Sets 3.5.1 Coherent pairs as tuples 3.5.2 Coherent pairs as triples 3.6 Spectral Clustering 3.7 Critique and Discussion 4 Transfer Operator Approach II: Mixing Boundary Conditions in Stationary Flows 4.1 Overview 4.2 Estimation of Transfer Probability Matrices P 4.3 Mixing Boundary Conditions 4.4 Thresholding 4.5 Results 4.5.1 Robustness with respect to parameters 4.5.2 Comparison and alternatives 4.5.3 Handling of false positives 4.5.4 Periodically perturbed flow 4.6 Closing Remark 5 Transfer operator approach III: Analysis of Oceanic Transport 5.1 Mixing Boundary Conditions: Time-Dependent Flows 5.1.1 Method 5.1.2 Results 5.2 Temporal consistency 5.2.1 Method 5.2.2 Results 5.3 Treatment of Coastal Effects 5.4 Application to Baltic velocity fields 5.4.1 Method 5.4.2 Results 5.5 Closing Remark 6 Prototypes of Coherent Sets: Star-Convex Structures 6.1 Mathematical Considerations 6.2 MSCS-Algorithm 6.3 Extracting star-convex sub-volumes 6.4 Results 6.4.1 Stationary Gaussian blob model 6.4.2 Bickley-Jet 6.4.3 Two dimensional inviscid flow 6.4.4 Real data sets 6.5 Closing Remark 7 Conclusion and Outlook

Endosomes are dynamic vesicular structures which transport cargo molecules internalized into the cell via endocytosis. Endosomal trafficking of cargo involves a large number of individual endosomes that regularly interact with each other via fusion and fission and thus form a dynamic network wherein endocytosed cargo is sorted and transported to various other intracellular compartments. In this study we present a general theoretical framework that takes into account individual endosomes and several key microscopic interaction processes among them. By combining theory with quantitative experiments, we seek to address the fundamental question of how the behaviour of the endosomal network emerges from the interactions among many individual endosomes of different sizes and cargo contents. Our theory is based on distributions of endosomes of various sizes and cargo amount. We compare our theory to experimental time course distributions of LDL, a degradative cargo, in a population of early endosomes. Early endosomes display a broad distribution of cargo with a characteristic power law, which we show is a consequence of stochastic fusion events of cargo carrying early endosomes. A simple model can quantitatively describe time-dependent statistics of LDL distributions in individual early endosomes. From fits of the theory to experimental data we can determine key parameters of endosomal trafficking such as the endosome fusion rate and the fluxes of cargo into and out of the network. Our theory predicts several experimentally confirmed scaling behaviours, which arise as a result of endosome fusion. Our theory provides a link between the dynamics at individual endosome level and average properties of the endosomal network. We show from our theory that some features of the endosomal distributions, which arise from interactions among individual endosomes, are sensitive to alterations in chosen parameters. This provides a direct means to study perturbation experiments wherein the cargo distribution can vary in response to changes of the endocytic system. Our analysis provides a powerful tool for the study of genetic and chemical perturbations that may alter specific systems properties and for extracting various kinetic rates involved in endosomal trafficking from only still images at different points.

We investigate thermalization in finite quantum systems using coherent state-based approaches to solve the time-dependent Schr\'odinger equation. Earlier, a lot of work has been done in the quantum realm, to study thermalization in spin systems, but not for the case of continuous systems. Here, we focus on continuous systems. We study the zero temperature thermalization i.e., we consider the ground states of the bath oscillators (environment). In order to study the quantum dynamics of a system under investigation, we require numerical methods to solve the time-dependent Schr\'odinger equation. We describe different numerical methods like the split-operator fast fourier transform, coupled coherent states, static grid of coherent states, semiclassical Herman-Kluk propagator and the linearized semiclassical initial value representation to study the quantum dynamics. We also give a comprehensive comparison of the most widely used coherent state based methods. Starting from the fully variational coherent states method, after a first approximation, the coupled coherent states method can be derived, whereas an additional approximation leads to the semiclassical Herman-Kluk method. We numerically compare the different methods with another one, based on a static rectangular grid of coherent states, by applying all of them to the revival dynamics in a one-dimensional Morse oscillator, with a special focus on the number of basis states (for the coupled coherent states and Herman-Kluk methods the number of classical trajectories) needed for convergence. We also extend the Husimi (coherent state) based version of linearized semiclassical theories for the calculation of correlation functions to the case of survival probabilities. This is a case that could be dealt with before only by use of the Wigner version of linearized semiclassical theory. Numerical comparisons of the Husimi and the Wigner case with full quantum results as well as with full semiclassical ones is given for the revival dynamics in a Morse oscillator with and without coupling to an additional harmonic degree of freedom. From this, we see the quantum to classical transition of the system dynamics due to the coupling to the environment (bath harmonic oscillator), which then can lead ultimately to our final goal of thermalization for long-time dynamics. In regard to thermalization in quantum systems, we address the following questions--- is it enough to increase the interaction strength between the different degrees of freedom in order to fully develop chaos which is the classical prerequisite for thermalization, or if, in addition, the number of those degrees of freedom has to be increased (possibly all the way to the thermodynamic limit) in order to observe thermalization. We study the ``toppling pencil'' model, i.e., an excited initial state on top of the barrier of a symmetric quartic double well to investigate thermalization. We apply the method of coupled coherent states to study the long-time dynamics of this system. We investigate if the coupling of the central quartic double well to a finite, environmental bath of harmonic oscillators in their ground states will let the central system evolve towards its uncoupled ground state. This amounts to thermalization i.e., a cooling down to the bath ``temperature'' (strictly only defined in the thermodynamic limit) of the central system. It is shown that thermalization can be achieved in finite quantum system with continuous variables using coherent state-based methods to solve the time-dependent Schr\'odinger equation. Also, here we witness thermalization by coupling the system to a bath of only few oscillators (less than ten), which until now has been seen for more than ten to twenty bath oscillators.