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The potential increase in frequency and magnitude of extreme floods is currently discussed in terms of global warming and the intensification of the hydrological cycle. The profound knowledge of past natural variability of floods is of utmost importance in order to assess flood risk for the future. Since instrumental flood series cover only the last ~150 years, other approaches to reconstruct historical and pre-historical flood events are needed. Annually laminated (varved) lake sediments are meaningful natural geoarchives because they provide continuous records of environmental changes > 10000 years down to a seasonal resolution. Since lake basins additionally act as natural sediment traps, the riverine sediment supply, which is preserved as detrital event layers in the lake sediments, can be used as a proxy for extreme discharge events. Within my thesis I examined a ~ 8.50 m long sedimentary record from the pre-Alpine Lake Mondsee (Northeast European Alps), which covered the last 7000 years. This sediment record consists of calcite varves and intercalated detrital layers, which range in thickness from 0.05 to 32 mm. Detrital layer deposition was analysed by a combined method of microfacies analysis via thin sections, Scanning Electron Microscopy (SEM), μX-ray fluorescence (μXRF) scanning and magnetic susceptibility. This approach allows characterizing individual detrital event layers and assigning a corresponding input mechanism and catchment. Based on varve counting and controlled by 14C age dates, the main goals of this thesis are (i) to identify seasonal runoff processes, which lead to significant sediment supply from the catchment into the lake basin and (ii) to investigate flood frequency under changing climate boundary conditions. This thesis follows a line of different time slices, presenting an integrative approach linking instrumental and historical flood data from Lake Mondsee in order to evaluate the flood record inferred from Lake Mondsee sediments. The investigation of eleven short cores covering the last 100 years reveals the abundance of 12 detrital layers. Therein, two types of detrital layers are distinguished by grain size, geochemical composition and distribution pattern within the lake basin. Detrital layers, which are enriched in siliciclastic and dolomitic material, reveal sediment supply from the Flysch sediments and Northern Calcareous Alps into the lake basin. These layers are thicker in the northern lake basin (0.1-3.9 mm) and thinner in the southern lake basin (0.05-1.6 mm). Detrital layers, which are enriched in dolomitic components forming graded detrital layers (turbidites), indicate the provenance from the Northern Calcareous Alps. These layers are generally thicker (0.65-32 mm) and are solely recorded within the southern lake basin. In comparison with instrumental data, thicker graded layers result from local debris flow events in summer, whereas thin layers are deposited during regional flood events in spring/summer. Extreme summer floods as reported from flood layer deposition are principally caused by cyclonic activity from the Mediterranean Sea, e.g. July 1954, July 1997 and August 2002. During the last two millennia, Lake Mondsee sediments reveal two significant flood intervals with decadal-scale flood episodes, during the Dark Ages Cold Period (DACP) and the transition from the Medieval Climate Anomaly (MCA) into the Little Ice Age (LIA) suggesting a linkage of transition to climate cooling and summer flood recurrences in the Northeastern Alps. In contrast, intermediate or decreased flood episodes appeared during the MWP and the LIA. This indicates a non-straightforward relationship between temperature and flood recurrence, suggesting higher cyclonic activity during climate transition in the Northeast Alps. The 7000-year flood chronology reveals 47 debris flows and 269 floods, with increased flood activity shifting around 3500 and 1500 varve yr BP (varve yr BP = varve years before present, before present = AD 1950). This significant increase in flood activity shows a coincidence with millennial-scale climate cooling that is reported from main Alpine glacier advances and lower tree lines in the European Alps since about 3300 cal. yr BP (calibrated years before present). Despite relatively low flood occurrence prior to 1500 varve yr BP, floods at Lake Mondsee could have also influenced human life in early Neolithic lake dwellings (5750-4750 cal. yr BP). While the first lake dwellings were constructed on wetlands, the later lake dwellings were built on piles in the water suggesting an early flood risk adaptation of humans and/or a general change of the Late Neolithic Culture of lake-dwellers because of socio-economic reasons. However, a direct relationship between the final abandonment of the lake dwellings and higher flood frequencies is not evidenced.
In the context of cosmological structure formation sheets, filaments and eventually halos form due to gravitational instabilities. It is noteworthy, that at all times, the majority of the baryons in the universe does not reside in the dense halos but in the filaments and the sheets of the intergalactic medium. While at higher redshifts of z > 2, these baryons can be detected via the absorption of light (originating from more distant sources) by neutral hydrogen at temperatures of T ~ 10^4 K (the Lyman-alpha forest), at lower redshifts only about 20 % can be found in this state. The remain (about 50 to 70 % of the total baryons mass) is unaccounted for by observational means. Numerical simulations predict that these missing baryons could reside in the filaments and sheets of the cosmic web at high temperatures of T = 10^4.5 - 10^7 K, but only at low to intermediate densities, and constitutes the warm-hot intergalactic medium (WHIM). The high temperatures of the WHIM are caused by the formation of shocks and the subsequent shock-heating of the gas. This results in a high degree of ionization and renders the reliable detection of the WHIM a challenging task. Recent high-resolution hydrodynamical simulations indicate that, at redshifts of z ~ 2, filaments are able to provide very massive galaxies with a significant amount of cool gas at temperatures of T ~ 10^4 K. This could have an important impact on the star-formation in those galaxies. It is therefore of principle importance to investigate the particular hydro- and thermodynamical conditions of these large filament structures. Density and temperature profiles, and velocity fields, are expected to leave their special imprint on spectroscopic observations. A potential multiphase structure may act as tracer in observational studies of the WHIM. In the context of cold streams, it is important to explore the processes, which regulate the amount of gas transported by the streams. This includes the time evolution of filaments, as well as possible quenching mechanisms. In this context, the halo mass range in which cold stream accretion occurs is of particular interest. In order to address these questions, we perform particular hydrodynamical simulations of very high resolution, and investigate the formation and evolution of prototype structures representing the typical filaments and sheets of the WHIM. We start with a comprehensive study of the one-dimensional collapse of a sinusoidal density perturbation (pancake formation) and examine the influence of radiative cooling, heating due to an UV background, thermal conduction, and the effect of small-scale perturbations given by the cosmological power spectrum. We use a set of simulations, parametrized by the wave length of the initial perturbation L. For L ~ 2 Mpc/h the collapse leads to shock-confined structures. As a result of radiative cooling and of heating due to an UV background, a relatively cold and dense core forms. With increasing L the core becomes denser and more concentrated. Thermal conduction enhances this trend and may lead to an evaporation of the core at very large L ~ 30 Mpc/h. When extending our simulations into three dimensions, instead of a pancake structure, we obtain a configuration consisting of well-defined sheets, filaments, and a gaseous halo. For L > 4 Mpc/h filaments form, which are fully confined by an accretion shock. As with the one-dimensional pancakes, they exhibit an isothermal core. Thus, our results confirm a multiphase structure, which may generate particular spectral tracers. We find that, after its formation, the core becomes shielded against further infall of gas onto the filament, and its mass content decreases with time. In the vicinity of the halo, the filament's core can be attributed to the cold streams found in other studies. We show, that the basic structure of these cold streams exists from the very beginning of the collapse process. Further on, the cross section of the streams is constricted by the outwards moving accretion shock of the halo. Thermal conduction leads to a complete evaporation of the cold stream for L > 6 Mpc/h. This corresponds to halos with a total mass higher than M_halo = 10^13 M_sun, and predicts that in more massive halos star-formation can not be sustained by cold streams. Far away from the gaseous halo, the temperature gradients in the filament are not sufficiently strong for thermal conduction to be effective.
The field of machine learning studies algorithms that infer predictive models from data. Predictive models are applicable for many practical tasks such as spam filtering, face and handwritten digit recognition, and personalized product recommendation. In general, they are used to predict a target label for a given data instance. In order to make an informed decision about the deployment of a predictive model, it is crucial to know the model’s approximate performance. To evaluate performance, a set of labeled test instances is required that is drawn from the distribution the model will be exposed to at application time. In many practical scenarios, unlabeled test instances are readily available, but the process of labeling them can be a time- and cost-intensive task and may involve a human expert. This thesis addresses the problem of evaluating a given predictive model accurately with minimal labeling effort. We study an active model evaluation process that selects certain instances of the data according to an instrumental sampling distribution and queries their labels. We derive sampling distributions that minimize estimation error with respect to different performance measures such as error rate, mean squared error, and F-measures. An analysis of the distribution that governs the estimator leads to confidence intervals, which indicate how precise the error estimation is. Labeling costs may vary across different instances depending on certain characteristics of the data. For instance, documents differ in their length, comprehensibility, and technical requirements; these attributes affect the time a human labeler needs to judge relevance or to assign topics. To address this, the sampling distribution is extended to incorporate instance-specific costs. We empirically study conditions under which the active evaluation processes are more accurate than a standard estimate that draws equally many instances from the test distribution. We also address the problem of comparing the risks of two predictive models. The standard approach would be to draw instances according to the test distribution, label the selected instances, and apply statistical tests to identify significant differences. Drawing instances according to an instrumental distribution affects the power of a statistical test. We derive a sampling procedure that maximizes test power when used to select instances, and thereby minimizes the likelihood of choosing the inferior model. Furthermore, we investigate the task of comparing several alternative models; the objective of an evaluation could be to rank the models according to the risk that they incur or to identify the model with lowest risk. An experimental study shows that the active procedure leads to higher test power than the standard test in many application domains. Finally, we study the problem of evaluating the performance of ranking functions, which are used for example for web search. In practice, ranking performance is estimated by applying a given ranking model to a representative set of test queries and manually assessing the relevance of all retrieved items for each query. We apply the concepts of active evaluation and active comparison to ranking functions and derive optimal sampling distributions for the commonly used performance measures Discounted Cumulative Gain and Expected Reciprocal Rank. Experiments on web search engine data illustrate significant reductions in labeling costs.
One of the major problems for the implementation of water resources planning and management in arid and semi-arid environments is the scarcity of hydrological data and, consequently, research studies. In this thesis, the hydrology of dryland river systems was analyzed and a semi-distributed hydrological model and a forecasting approach were developed for flow transmission processes in river-systems with a focus on semi-arid conditions. Three different sources of hydrological data (streamflow series, groundwater level series and multi-temporal satellite data) were combined in order to analyze the channel transmission losses of a large reach of the Jaguaribe River in NE Brazil. A perceptual model of this reach was derived suggesting that the application of models, which were developed for sub-humid and temperate regions, may be more suitable for this reach than classical models, which were developed for arid and semi-arid regions. Summarily, it was shown that this river reach is hydraulically connected with groundwater and shifts from being a losing river at the dry and beginning of rainy seasons to become a losing/gaining (mostly losing) river at the middle and end of rainy seasons. A new semi-distributed channel transmission losses model was developed, which was based primarily on the capability of simulation in very different dryland environments and flexible model structures for testing hypotheses on the dominant hydrological processes of rivers. This model was successfully tested in a large reach of the Jaguaribe River in NE Brazil and a small stream in the Walnut Gulch Experimental Watershed in the SW USA. Hypotheses on the dominant processes of the channel transmission losses (different model structures) in the Jaguaribe river were evaluated, showing that both lateral (stream-)aquifer water fluxes and ground-water flow in the underlying alluvium parallel to the river course are necessary to predict streamflow and channel transmission losses, the former process being more relevant than the latter. This procedure not only reduced model structure uncertainties, but also reported modelling failures rejecting model structure hypotheses, namely streamflow without river-aquifer interaction and stream-aquifer flow without groundwater flow parallel to the river course. The application of the model to different dryland environments enabled learning about the model itself from differences in channel reach responses. For example, the parameters related to the unsaturated part of the model, which were active for the small reach in the USA, presented a much greater variation in the sensitivity coefficients than those which drove the saturated part of the model, which were active for the large reach in Brazil. Moreover, a nonparametric approach, which dealt with both deterministic evolution and inherent fluctuations in river discharge data, was developed based on a qualitative dynamical system-based criterion, which involved a learning process about the structure of the time series, instead of a fitting procedure only. This approach, which was based only on the discharge time series itself, was applied to a headwater catchment in Germany, in which runoff are induced by either convective rainfall during the summer or snow melt in the spring. The application showed the following important features: • the differences between runoff measurements were more suitable than the actual runoff measurements when using regression models; • the catchment runoff system shifted from being a possible dynamical system contaminated with noise to a linear random process when the interval time of the discharge time series increased; • and runoff underestimation can be expected for rising limbs and overestimation for falling limbs. This nonparametric approach was compared with a distributed hydrological model designed for real-time flood forecasting, with both presenting similar results on average. Finally, a benchmark for hydrological research using semi-distributed modelling was proposed, based on the aforementioned analysis, modelling and forecasting of flow transmission processes. The aim of this benchmark was not to describe a blue-print for hydrological modelling design, but rather to propose a scientific method to improve hydrological knowledge using semi-distributed hydrological modelling. Following the application of the proposed benchmark to a case study, the actual state of its hydrological knowledge and its predictive uncertainty can be determined, primarily through rejected hypotheses on the dominant hydrological processes and differences in catchment/variables responses.
Estimation of the self-similarity exponent has attracted growing interest in recent decades and became a research subject in various fields and disciplines. Real-world data exhibiting self-similar behavior and/or parametrized by self-similarity exponent (in particular Hurst exponent) have been collected in different fields ranging from finance and human sciencies to hydrologic and traffic networks. Such rich classes of possible applications obligates researchers to investigate qualitatively new methods for estimation of the self-similarity exponent as well as identification of long-range dependencies (or long memory). In this thesis I present the Bayesian estimation of the Hurst exponent. In contrast to previous methods, the Bayesian approach allows the possibility to calculate the point estimator and confidence intervals at the same time, bringing significant advantages in data-analysis as discussed in this thesis. Moreover, it is also applicable to short data and unevenly sampled data, thus broadening the range of systems where the estimation of the Hurst exponent is possible. Taking into account that one of the substantial classes of great interest in modeling is the class of Gaussian self-similar processes, this thesis considers the realizations of the processes of fractional Brownian motion and fractional Gaussian noise. Additionally, applications to real-world data, such as the data of water level of the Nile River and fixational eye movements are also discussed.
In this thesis, different aspects within the research field of protein spectro- and electro-chemistry on nanostructured materials are addressed. On the one hand, this work is related to the investigation of nanostructured transparent and conductive metal oxides as platform for the immobilization of electroactive enzymes. On the other hand the second part of this work is related to the immobilization of sulfite oxidase on gold nanoparticles modified electrode. Finally direct and mediated spectroelectrochemistry protein with high structure complexity such as the xanthine dehydrogenase from Rhodobacter capsulatus and its high homologues the mouse aldehyde oxidase homolog 1. Stable immobilization and reversible electrochemistry of cytochrome c in a transparent and conductive tin-doped and tin-rich indium oxide film with a well-defined mesoporosity is reported. The transparency and good conductivity, in combination with the large surface area of these materials, allow the incorporation of a high amount of electroactive biomolecules (between 250 and 2500 pmol cm-2) and their electrochemical and spectroscopic investigation. Both, the electrochemical behavior and the immobilization of proteins are influenced by the geometric parameters of the porous material, such as the structure and pore shape, the surface chemistry, as well as the protein size and charge. UV-Vis and resonance Raman spectroscopy, in combination with direct protein voltammetry, are employed for the characterization of cytochrome c immobilized in the mesoporous indium tin oxide and reveal no perturbation of the structural integrity of the redox protein. A long term protein immobilization is reached using these unmodified mesoporous indium oxide based materials, i.e. more than two weeks even at high ionic strength. The potential of this modified material as an amperometric biosensor for the detection of superoxide anions is demonstrated. A sensitivity of about 100 A M-1 m-2, in a linear measuring range of the superoxide concentration between 0.13 and 0.67 μM, is estimated. In addition an electrochemical switchable protein-based optical device is designed with the core part composed of cytochrome c immobilized on a mesoporous indium tin oxide film. A color developing redox sensitive dye is used as switchable component of the system. The cytochrome c-catalyzed oxidation of the dye by hydrogen peroxide is spectroscopically investigated. When the dye is co-immobilized with the protein, its redox state is easily controlled by application of an electrical potential at the supporting material. This enables to electrochemical reset the system to the initial state and repetitive signal generation. The case of negative charged proteins, which does not have a good interaction with the negative charged indium oxide based films, is also explored. The modification of an indium tin oxide film with a positive charged polymer and the employment of a antimony doped tin oxide film were investigated in this work in order to overcome the repulsion induced by similar charges of the protein and electrode. Human sulfite oxidase and its separated heme-containing domain are able to direct exchange electrons with the supporting material. A study of a new approach for sulfite biosensing, based on enhanced direct electron transfer of a human sulfite oxidase immobilized on a gold nanoparticles modified electrode is reported. The spherical gold nanoparticles were prepared via a novel method by reduction of HAuCl4 with branched poly(ethyleneimine) in an ionic liquid resulting in particles of about 10 nm in hydrodynamic diameter. These nanoparticles were covalently attached to a mercaptoundecanoic acid modified Au-electrode and act as platform where human sulfite oxidase is adsorbed. An enhanced interfacial electron transfer and electrocatalysis is therefore achieved. UV-Vis and resonance Raman spectroscopy, in combination with direct protein voltammetry, were employed for the characterization of the system and reveal no perturbation of the structural integrity of the redox protein. The proposed biosensor exhibited a quick steady-state current response, within 2 s and a linear detection range between 0.5 and 5.4 μM with high sensitivity (1.85 nA μM-1). The investigated system provides remarkable advantages, since it works at low applied potential and at very high ionic strength. Therefore these properties could make the proposed system useful in the development of bioelectronic devices and its application in real samples. Finally protein with high structure complexity such as the xanthine dehydrogenase from Rhodobacter capsulatus and the mouse aldehyde oxidase homolog 1 were spectroelectrochemically studied. It could be demonstrated that different cofactors present in the protein structure, like the FAD and the molybdenum cofactor, are able to directly exchange electrons with an electrode and are displayed as a single peak in a square wave voltammogram. Protein mutants bearing a serine substituted to the cysteines, bounding to the most exposed iron sulfur cluster additionally showed direct electron transfer which can be attributable to this cluster. On the other hand a mediated spectroelectrochemical titration of the protein bound FAD cofactor was performed in presence of transparent iron and cobalt complex mediators. The results showed the formation of the stable semiquinone and the fully reduced flavin. Two formal potentials for each single electron exchange step were then determined.
Bioinformatics studies of biological systems across multiple levels of molecular organization
(2012)
Carbohydrate recognition is a ubiquitous principle underlying many fundamental biological processes like fertilization, embryogenesis and viral infections. But how carbohydrate specificity and affinity induce a molecular event is not well understood. One of these examples is bacteriophage P22 that binds and infects three distinct Salmonella enterica (S.) hosts. It recognizes and depolymerizes repetitive carbohydrate structures of O antigen in its host´s outer membrane lipopolysaccharide molecule. This is mediated by tailspikes, mainly β helical appendages on phage P22 short non contractile tail apparatus (podovirus). The O antigen of all three Salmonella enterica hosts is built from tetrasaccharide repeating units consisting of an identical main chain with a distinguished 3,6 dideoxyhexose substituent that is crucial for P22 tailspike recognition: tyvelose in S. Enteritidis, abequose in S. Typhimurium and paratose in S. Paratyphi. In the first study the complexes of P22 tailspike with its host’s O antigen octasaccharide were characterized. S. Paratyphi octasaccharide binds less tightly (ΔΔG≈7 kJ/mol) to the tailspike than the other two hosts. Crystal structure analysis of P22 tailspike co crystallized with S. Paratyphi octasaccharides revealed different interactions than those observed before in tailspike complexes with S. Enteritidis and S. Typhimurium octasaccharides. These different interactions occur due to a structural rearrangement in the S. Paratyphi octasaccharide. It results in an unfavorable glycosidic bond Φ/Ψ angle combination that also had occurred when the S. Paratyphi octasaccharide conformation was analyzed in an aprotic environment. Contributions of individual protein surface contacts to binding affinity were analyzed showing that conserved structural waters mediate specific recognition of all three different Salmonella host O antigens. Although different O antigen structures possess distinct binding behavior on the tailspike surface, all are recognized and infected by phage P22. Hence, in a second study, binding measurements revealed that multivalent O antigen was able to bind with high avidity to P22 tailspike. Dissociation rates of the polymer were three times slower than for an octasaccharide fragment pointing towards high affinity for O antigen polysaccharide. Furthermore, when phage P22 was incubated with lipopolysaccharide aggregates before plating on S. Typhimurium cells, P22 infectivity became significantly reduced. Therefore, in a third study, the function of carbohydrate recognition on the infection process was characterized. It was shown that large S. Typhimurium lipopolysaccharide aggregates triggered DNA release from the phage capsid in vitro. This provides evidence that phage P22 does not use a second receptor on the Salmonella surface for infection. P22 tailspike binding and cleavage activity modulate DNA egress from the phage capsid. DNA release occurred more slowly when the phage possessed mutant tailspikes with less hydrolytic activity and was not induced if lipopolysaccharides contained tailspike shortened O antigen polymer. Furthermore, the onset of DNA release was delayed by tailspikes with reduced binding affinity. The results suggest a model for P22 infection induced by carbohydrate recognition: tailspikes position the phage on Salmonella enterica and their hydrolytic activity forces a central structural protein of the phage assembly, the plug protein, onto the host´s membrane surface. Upon membrane contact, a conformational change has to occur in the assembly to eject DNA and pilot proteins from the phage to establish infection. Earlier studies had investigated DNA ejection in vitro solely for viruses with long non contractile tails (siphovirus) recognizing protein receptors. Podovirus P22 in this work was therefore the first example for a short tailed phage with an LPS recognition organelle that can trigger DNA ejection in vitro. However, O antigen binding and cleaving tailspikes are widely distributed in the phage biosphere, for example in siphovirus 9NA. Crystal structure analysis of 9NA tailspike revealed a complete similar fold to P22 tailspike although they only share 36 % sequence identity. Moreover, 9NA tailspike possesses similar enzyme activity towards S. Typhimurium O antigen within conserved amino acids. These are responsible for a DNA ejection process from siphovirus 9NA triggered by lipopolysaccharide aggregates. 9NA expelled its DNA 30 times faster than podovirus P22 although the associated conformational change is controlled with a similar high activation barrier. The difference in DNA ejection velocity mirrors different tail morphologies and their efficiency to translate a carbohydrate recognition signal into action.
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.
Taking advantage of ATRP and using functionalized initiators, different functionalities were introduced in both α and ω chain-ends of synthetic polymers. These functionalized polymers could then go through modular synthetic pathways such as click cycloaddition (copper-catalyzed or copper-free) or amidation to couple synthetic polymers to other synthetic polymers, biomolecules or silica monoliths. Using this general strategy and designing these co/polymers so that they are thermoresponsive, yet bioinert and biocompatible with adjustable cloud point values (as it is the case in the present thesis), the whole generated system becomes "smart" and potentially applicable in different branches. The applications which were considered in the present thesis were in polymer post-functionalization (in situ functionalization of micellar aggregates with low and high molecular weight molecules), hydrophilic/hydrophobic tuning, chromatography and bioconjugation (enzyme thermoprecipitation and recovery, improvement of enzyme activity). Different α-functionalized co/polymers containing cholesterol moiety, aldehyde, t-Boc protected amine, TMS-protected alkyne and NHS-activated ester were designed and synthesized in this work.
This work investigates diffusion in nonlinear Hamiltonian systems. The diffusion, more precisely subdiffusion, in such systems is induced by the intrinsic chaotic behavior of trajectories and thus is called chaotic diffusion''. Its properties are studied on the example of one- or two-dimensional lattices of harmonic or nonlinear oscillators with nearest neighbor couplings. The fundamental observation is the spreading of energy for localized initial conditions. Methods of quantifying this spreading behavior are presented, including a new quantity called excitation time. This new quantity allows for a more precise analysis of the spreading than traditional methods. Furthermore, the nonlinear diffusion equation is introduced as a phenomenologic description of the spreading process and a number of predictions on the density dependence of the spreading are drawn from this equation. Two mathematical techniques for analyzing nonlinear Hamiltonian systems are introduced. The first one is based on a scaling analysis of the Hamiltonian equations and the results are related to similar scaling properties of the NDE. From this relation, exact spreading predictions are deduced. Secondly, the microscopic dynamics at the edge of spreading states are thoroughly analyzed, which again suggests a scaling behavior that can be related to the NDE. Such a microscopic treatment of chaotically spreading states in nonlinear Hamiltonian systems has not been done before and the results present a new technique of connecting microscopic dynamics with macroscopic descriptions like the nonlinear diffusion equation. All theoretical results are supported by heavy numerical simulations, partly obtained on one of Europe's fastest supercomputers located in Bologna, Italy. In the end, the highly interesting case of harmonic oscillators with random frequencies and nonlinear coupling is studied, which resembles to some extent the famous Discrete Anderson Nonlinear Schroedinger Equation. For this model, a deviation from the widely believed power-law spreading is observed in numerical experiments. Some ideas on a theoretical explanation for this deviation are presented, but a conclusive theory could not be found due to the complicated phase space structure in this case. Nevertheless, it is hoped that the techniques and results presented in this work will help to eventually understand this controversely discussed case as well.
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.
Agriculture is one of the most important human activities providing food and more agricultural goods for seven billion people around the world and is of special importance in sub-Saharan Africa. The majority of people depends on the agricultural sector for their livelihoods and will suffer from negative climate change impacts on agriculture until the middle and end of the 21st century, even more if weak governments, economic crises or violent conflicts endanger the countries’ food security. The impact of temperature increases and changing precipitation patterns on agricultural vegetation motivated this thesis in the first place. Analyzing the potentials of reducing negative climate change impacts by adapting crop management to changing climate is a second objective of the thesis. As a precondition for simulating climate change impacts on agricultural crops with a global crop model first the timing of sowing in the tropics was improved and validated as this is an important factor determining the length and timing of the crops´ development phases, the occurrence of water stress and final crop yield. Crop yields are projected to decline in most regions which is evident from the results of this thesis, but the uncertainties that exist in climate projections and in the efficiency of adaptation options because of political, economical or institutional obstacles have to be considered. The effect of temperature increases and changing precipitation patterns on crop yields can be analyzed separately and varies in space across the continent. Southern Africa is clearly the region most susceptible to climate change, especially to precipitation changes. The Sahel north of 13° N and parts of Eastern Africa with short growing seasons below 120 days and limited wet season precipitation of less than 500 mm are also vulnerable to precipitation changes while in most other part of East and Central Africa, in contrast, the effect of temperature increase on crops overbalances the precipitation effect and is most pronounced in a band stretching from Angola to Ethiopia in the 2060s. The results of this thesis confirm the findings from previous studies on the magnitude of climate change impact on crops in sub-Saharan Africa but beyond that helps to understand the drivers of these changes and the potential of certain management strategies for adaptation in more detail. Crop yield changes depend on the initial growing conditions, on the magnitude of climate change, and on the crop, cropping system and adaptive capacity of African farmers which is only now evident from this comprehensive study for sub-Saharan Africa. Furthermore this study improves the representation of tropical cropping systems in a global crop model and considers the major food crops cultivated in sub-Saharan Africa and climate change impacts throughout the continent.
Design and development of novel three color-FRET systems in synthetic peptides and oligonucleotides
(2012)
In this work, the synthesis of biopolymer-based hydrogel networks with defined architecture is presented. In order to obtain materials with defined properties, the chemoselective copper-catalyzed azide-alkyne cycloaddition (or Click Chemistry) was used for the synthesis of gelatin-based hydrogels. Alkyne-functionalized gelatin was reacted with four different diazide crosslinkers above its sol-gel transition to suppress the formation of triple helices. By variation of the crosslinking density and the crosslinker flexibility, the swelling (Q: 150-470 vol.-%;) and the Young’s and shear moduli (E: 50 kPa - 635 kPa, G’: 0.1 kPa - 16 kPa) could be tuned in the kPa range. In order to understand the network structure, a method based on the labelling of free functional groups within the hydrogel was developed. Gelatin-based hydrogels were incubated with alkyne-functionalized fluorescein to detect the free azide groups, resulting from the formation of dangling chains. Gelatin hydrogels were also incubated with azido-functionalized fluorescein to check the presence of alkyne groups available for the attachment of bioactive molecules. By using confocal laser scanning microscopy and fluorescence spectroscopy, the amount of crosslinking, grafting and free alkyne groups could be determined. Dangling chains were observed in samples prepared by using an excess of crosslinker and also when using equimolar amounts of alkyne:azide. In the latter case the amount of dangling chains was affected by the crosslinker structure. Specifically, 0.1% of dangling chains were found using 4,4’-diazido-2,2’-stilbene-disulfonic acid as cosslinker, 0.06% with 1,8-diazidooctane, 0.05% with 1,12-diazidododecane and 0.022 % with PEG-diazide. This observation could be explained considering the structure of the crosslinkers. During network formation, the movements of the gelatin chains are restricted due to the formation of covalent netpoints. A further crosslinking will be possible only in the case of crosslinker that are flexible and long enough to reach another chain. The method used to obtain defined gelatin-based hydrogels enabled also the synthesis of hyaluronic acid-based hydrogels with tailorable properties. Alkyne-functionalized hyaluronic acid was crosslinked with three different linkers having two terminal azide functionalities. By variation of the crosslinking density and crosslinker type, hydrogels with elastic moduli in the range of 0.5-3 kPa have been prepared. The variation of the crosslinking density and crosslinker type had furthermore an influence also on the hydrolytic and enzymatic degradation of gelatin-based hydrogels. Hydrogels with a low crosslinker amount experienced a faster decrease in mass loss and elastic modulus compared to hydrogels with higher crosslinker content. Moreover, the structure of the crosslinker had a strong influence on the enzymatic degradation. Hydrogels containing a crosslinker with a rigid structure were much more resistant to enzymatic degradation than hydrogels containing a flexible crosslinker. During hydrolytic degradation, the hydrogel became softer while maintaining the same outer dimensions. These observations are in agreement with a bulk degradation mechanism, while the decrease in size of the hydrogels during enzymatic degradation suggested a surface erosion mechanism. Because of the use of small amount of crosslinker (0.002 mol.% 0.02 mol.%) the networks synthesized can still be defined as biopolymer-based hydrogels. However, they contain a small percentage of synthetic residues. Alternatively, a possible method to obtain biopolymer-based telechelics, which could be used as crosslinkers, was investigated. Gelatin-based fragments with defined molecular weight were obtained by controlled degradation of gelatin with hydroxylamine, due to its specific action on asparaginyl-glycine bonds. The reaction of gelatin with hydroxylamine resulted in fragments with molecular weights of 15, 25, 37, and 50 kDa (determined by SDS-PAGE) independently of the reaction time and conditions. Each of these fragments could be potentially used for the synthesis of hydrogels in which all components are biopolymer-based materials.
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.
The microscopic origin of ultrafast demagnetization, i.e. the quenching of the magnetization of a ferromagnetic metal on a sub-picosecond timescale after laser excitation, is still only incompletely understood, despite a large body of experimental and theoretical work performed since the discovery of the effect more than 15 years ago. Time- and element-resolved x-ray magnetic circular dichroism measurements can provide insight into the microscopic processes behind ultrafast demagnetization as well as its dependence on materials properties. Using the BESSY II Femtoslicing facility, a storage ring based source of 100 fs short soft x-ray pulses, ultrafast magnetization dynamics of ferromagnetic NiFe and GdTb alloys as well as a Au/Ni layered structure were investigated in laser pump – x-ray probe experiments. After laser excitation, the constituents of Ni50Fe50 and Ni80Fe20 exhibit distinctly different time constants of demagnetization, leading to decoupled dynamics, despite the strong exchange interaction that couples the Ni and Fe sublattices under equilibrium conditions. Furthermore, the time constants of demagnetization for Ni and Fe are different in Ni50Fe50 and Ni80Fe20, and also different from the values for the respective pure elements. These variations are explained by taking the magnetic moments of the Ni and Fe sublattices, which are changed from the pure element values due to alloying, as well as the strength of the intersublattice exchange interaction into account. GdTb exhibits demagnetization in two steps, typical for rare earths. The time constant of the second, slower magnetization decay was previously linked to the strength of spin-lattice coupling in pure Gd and Tb, with the stronger, direct spin-lattice coupling in Tb leading to a faster demagnetization. In GdTb, the demagnetization of Gd follows Tb on all timescales. This is due to the opening of an additional channel for the dissipation of spin angular momentum to the lattice, since Gd magnetic moments in the alloy are coupled via indirect exchange interaction to neighboring Tb magnetic moments, which are in turn strongly coupled to the lattice. Time-resolved measurements of the ultrafast demagnetization of a Ni layer buried under a Au cap layer, thick enough to absorb nearly all of the incident pump laser light, showed a somewhat slower but still sub-picosecond demagnetization of the buried Ni layer in Au/Ni compared to a Ni reference sample. Supported by simulations, I conclude that demagnetization can thus be induced by transport of hot electrons excited in the Au layer into the Ni layer, without the need for direct interaction between photons and spins.
Engineering hyaluronic acid / poly-L-lysine films as a platform for controlling cell behaviour
(2012)
Immune genes of the major histocompatibility complex (MHC) constitute a central component of the adaptive immune system and play an essential role in parasite resistance and associated life-history strategies. In addition to pathogen-mediated selection also sexual selection mechanisms have been identified as the main drivers of the typically-observed high levels of polymorphism in functionally important parts of the MHC. The recognition of the individual MHC constitution is presumed to be mediated through olfactory cues. Indeed, MHC genes are in physical linkage with olfactory receptor genes and alter the individual body odour. Moreover, they are expressed on sperm and trophoplast cells. Thus, MHC-mediated sexual selection processes might not only act in direct mate choice decisions, but also through cryptic processes during reproduction. Bats (Chiroptera) represent the second largest mammalian order and have been identified as important vectors of newly emerging infectious diseases affecting humans and wildlife. In addition, they are interesting study subjects in evolutionary ecology in the context of olfactory communication, mate choice and associated fitness benefits. Thus, it is surprising that Chiroptera belong to the least studied mammalian taxa in terms of their MHC evolution. In my doctoral thesis I aimed to gain insights in the evolution and diversity pattern of functional MHC genes in some of the major New World bat families by establishing species-specific primers through genome-walking into unknown flanking parts of familiar sites. Further, I took a free-ranging population of the lesser bulldog bat (Noctilio albiventris) in Panama as an example to understand the functional importance of the individual MHC constitution in parasite resistance and reproduction as well as the possible underlying selective forces shaping the observed diversity. My studies indicated that the typical MHC characteristics observed in other mammalian orders, like evidence for balancing and positive selection as well as recombination and gene conversion events, are also present in bats shaping their MHC diversity. I found a wide range of copy number variation of expressed DRB loci in the investigated species. In Saccopteryx bilineata, a species with a highly developed olfactory communication system, I found an exceptionally high number of MHC loci duplications generating high levels of variability at the individual level, which has never been described for any other mammalian species so far. My studies included for the first time phylogenetic relationships of MHC genes in bats and I found signs for a family-specific independent mode of evolution of duplicated genes, regardless whether the highly variable exon 2 (coding for the antigen binding region of the molecule) or more conserved exons (3, 4; encoding protein stabilizing parts) were considered indicating a monophyletic origin of duplicated loci within families. This result questions the general assumed pattern of MHC evolution in mammals where duplicated genes of different families usually cluster together suggesting that duplication occurred before speciation took place, which implies a trans-species mode of evolution. However, I found a trans-species mode of evolution within genera (Noctilio, Myotis) based on exon 2 signified by an intermingled clustering of DRB alleles. The gained knowledge on MHC sequence evolution in major New World bat families will facilitate future MHC investigations in this order. In the N. albiventris study population, the single expressed MHC class II DRB gene showed high sequence polymorphism, moderate allelic variability and high levels of population-wide heterozygosity. Whereas demographic processes had minor relevance in shaping the diversity pattern, I found clear evidence for parasite-mediated selection. This was evident by historical positive Darwinian selection maintaining diversity in the functionally important antigen binding sites, and by specific MHC alleles which were associated with low and high ectoparasite burden according to predictions of the ‘frequency dependent selection hypothesis’. Parasite resistance has been suggested to play an important role in mediating costly life history trade-offs leading to e.g. MHC- mediated benefits in sexual selection. The ‘good genes model’ predicts that males with a genetically well-adapted immune system in defending harmful parasites have the ability to allocate more resources to reproductive effort. I found support for this prediction since non-reproductive adult N. albiventris males carried more often an allele associated with high parasite loads, which differentiated them genetically from reproductively active males as well as from subadults, indicating a reduced transmission of this allele in subsequent generations. In addition, they suffered from increased ectoparasite burden which presumably reduced resources to invest in reproduction. Another sign for sexual selection was the observation of gender-specific difference in heterozygosity, with females showing lower levels of heterozygosity than males. This signifies that the sexes differ in their selection pressures, presumably through MHC-mediated molecular processes during reproduction resulting in a male specific heterozygosity advantage. My data make clear that parasite-mediated selection and sexual selection are interactive and operate together to form diversity at the MHC. Furthermore, my thesis is one of the rare studies contributing to fill the gap between MHC-mediated effects on co-evolutionary processes in parasite-host-interactions and on aspects of life-history evolution.