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Proteins are chain molecules built from amino acids. The precise sequence of the 20 different types of amino acids in a protein chain defines into which structure a protein folds, and the three-dimensional structure in turn specifies the biological function of the protein. The reliable folding of proteins is a prerequisite for their robust function. Misfolding can lead to protein aggregates that cause severe diseases, such as Alzheimer's, Parkinson's, or the variant Creutzfeldt-Jakob disease. Small single-domain proteins often fold without experimentally detectable metastable intermediate states. The folding dynamics of these proteins is thought to be governed by a single transition-state barrier between the unfolded and the folded state. The transition state is highly instable and cannot be observed directly. However, mutations in which a single amino acid of the protein is substituted by another one can provide indirect access. The mutations slightly change the transition-state barrier and, thus, the folding and unfolding times of the protein. The central question is how to reconstruct the transition state from the observed changes in folding times. In this habilitation thesis, a novel method to extract structural information on transition states from mutational data is presented. The method is based on (i) the cooperativity of structural elements such as alpha-helices and beta-hairpins, and (ii) on splitting up mutation-induced free-energy changes into components for these elements. By fitting few parameters, the method reveals the degree of structure formation of alpha-helices and beta-hairpins in the transition state. In addition, it is shown in this thesis that the folding routes of small single-domain proteins are dominated by loop-closure dependencies between the structural elements.
Die Arbeit beschreibt die Analyse von Beobachtungen zweier Sonnenflecken in zweidimensionaler Spektro-Polarimetrie. Die Daten wurden mit dem Fabry-Pérot-Interferometer der Universität Göttingen am Vakuum-Turm-Teleskop auf Teneriffa erfasst. Von der aktiven Region NOAA 9516 wurde der volle Stokes-Vektor des polarisierten Lichts in der Absorptionslinie bei 630,249 nm in Einzelaufnahmen beobachtet, und von der aktiven Region NOAA 9036 wurde bei 617,3 nm Wellenlänge eine 90-minütige Zeitserie des zirkular polarisierten Lichts aufgezeichnet. Aus den reduzierten Daten werden Ergebniswerte für Intensität, Geschwindigkeit in Beobachtungsrichtung, magnetische Feldstärke sowie verschiedene weitere Plasmaparameter abgeleitet. Mehrere Ansätze zur Inversion solarer Modellatmosphären werden angewendet und verglichen. Die teilweise erheblichen Fehlereinflüsse werden ausführlich diskutiert. Das Frequenzverhalten der Ergebnisse und Abhängigkeiten nach Ort und Zeit werden mit Hilfe der Fourier- und Wavelet-Transformation weiter analysiert. Als Resultat lässt sich die Existenz eines hochfrequenten Bandes für Geschwindigkeitsoszillationen mit einer zentralen Frequenz von 75 Sekunden (13 mHz) bestätigen. In größeren photosphärischen Höhen von etwa 500 km entstammt die Mehrheit der damit zusammenhängenden Schockwellen den dunklen Anteilen der Granulen, im Unterschied zu anderen Frequenzbereichen. Die 75-Sekunden-Oszillationen werden ebenfalls in der aktiven Region beobachtet, vor allem in der Lichtbrücke. In den identifizierten Bändern oszillatorischer Power der Geschwindigkeit sind in einer dunklen, penumbralen Struktur sowie in der Lichtbrücke ausgeprägte Strukturen erkennbar, die sich mit einer Horizontalgeschwindigkeit von 5-8 km/s in die ruhige Sonne bewegen. Diese zeigen einen deutlichen Anstieg der Power, vor allem im 5-Minuten-Band, und stehen möglicherweise in Zusammenhang mit dem Phänomen der „Evershed-clouds“. Eingeschränkt durch ein sehr geringes Signal-Rausch-Verhältnis und hohe Fehlereinflüsse werden auch Magnetfeldvariationen mit einer Periode von sechs Minuten am Übergang von Umbra zu Penumbra in der Nähe einer Lichtbrücke beobachtet. Um die beschriebenen Resultate zu erzielen, wurden bestehende Visualisierungsverfahren der Frequenzanalyse verbessert oder neu entwickelt, insbesondere für Ergebnisse der Wavelet-Transformation.
This thesis describes two main projects; the first one is the optimization of a hierarchical search strategy to search for unknown pulsars. This project is divided into two parts; the first part (and the main part) is the semi-coherent hierarchical optimization strategy. The second part is a coherent hierarchical optimization strategy which can be used in a project like Einstein@Home. In both strategies we have found that the 3-stages search is the optimum strategy to search for unknown pulsars. For the second project we have developed a computer software for a coherent Multi-IFO (Interferometer Observatory) search. To validate our software, we have worked on simulated data as well as hardware injected signals of pulsars in the fourth LIGO science run (S4). While with the current sensitivity of our detectors we do not expect to detect any true Gravitational Wave signals in our data, we can still set upper limits on the strength of the gravitational waves signals. These upper limits, in fact, tell us how weak a signal strength we would detect. We have also used our software to set upper limits on the signal strength of known isolated pulsars using LIGO fifth science run (S5) data.
The intergalactic medium is kept highly photoionised by the intergalactic UV background radiation field generated by the overall population of quasars and galaxies. In the vicinity of sources of UV photons, such as luminous high-redshift quasars, the UV radiation field is enhanced due to the local source contribution. The higher degree of ionisation is visible as a reduced line density or generally as a decreased level of absorption in the Lyman alpha forest of neutral hydrogen. This so-called proximity effect has been detected with high statistical significance towards luminous quasars. If quasars radiate rather isotropically, background quasar sightlines located near foreground quasars should show a region of decreased Lyman alpha absorption close to the foreground quasar. Despite considerable effort, such a transverse proximity effect has only been detected in a few cases. So far, studies of the transverse proximity effect were mostly limited by the small number of suitable projected pairs or groups of high-redshift quasars. With the aim to substantially increase the number of quasar groups in the vicinity of bright quasars we conduct a targeted survey for faint quasars around 18 well-studied quasars at employing slitless spectroscopy. Among the reduced and calibrated slitless spectra of 29000 objects on a total area of 4.39 square degrees we discover in total 169 previously unknown quasar candidates based on their prominent emission lines. 81 potential z>1.7 quasars are selected for confirmation by slit spectroscopy at the Very Large Telescope (VLT). We are able to confirm 80 of these. 64 of the newly discovered quasars reside at z>1.7. The high success rate of the follow-up observations implies that the majority of the remaining candidates are quasars as well. In 16 of these groups we search for a transverse proximity effect as a systematic underdensity in the HI Lyman alpha absorption. We employ a novel technique to characterise the random absorption fluctuations in the forest in order to estimate the significance of the transverse proximity effect. Neither low-resolution spectra nor high-resolution spectra of background quasars of our groups present evidence for a transverse proximity effect. However, via Monte Carlo simulations the effect should be detectable only at the 1-2sigma level near three of the foreground quasars. Thus, we cannot distinguish between the presence or absence of a weak signature of the transverse proximity effect. The systematic effects of quasar variability, quasar anisotopy and intrinsic overdensities near quasars likely explain the apparent lack of the transverse proximity effect. Even in absence of the systematic effects, we show that a statistically significant detection of the transverse proximity effect requires at least 5 medium-resolution quasar spectra of background quasars near foreground quasars whose UV flux exceeds the UV background by a factor 3. Therefore, statistical studies of the transverse proximity effect require large numbers of suitable pairs. Two sightlines towards the central quasars of our survey fields show intergalactic HeII Lyman alpha absorption. A comparison of the HeII absorption to the corresponding HI absorption yields an estimate of the spectral shape of the intergalactic UV radiation field, typically parameterised by the HeII/HI column density ratio eta. We analyse the fluctuating UV spectral shape on both lines of sight and correlate it with seven foreground quasars. On the line of sight towards Q0302-003 we find a harder radiation field near 4 foreground quasars. In the direct vicinity of the quasars eta is consistent with values of 25-100, whereas at large distances from the quasars eta>200 is required. The second line of sight towards HE2347-4342 probes lower redshifts where eta is directly measurable in the resolved HeII forest. Again we find that the radiation field near the 3 foreground quasars is significantly harder than in general. While eta still shows large fluctuations near the quasars, probably due to radiative transfer, the radiation field is on average harder near the quasars than far away from them. We interpret these discoveries as the first detections of the transverse proximity effect as a local hardness fluctuation in the UV spectral shape. No significant HI proximity effect is predicted for the 7 foreground quasars. In fact, the HI absorption near the quasars is close to or slightly above the average, suggesting that the weak signature of the transverse proximity effect is masked by intrinsic overdensities. However, we show that the UV spectral shape traces the transverse proximity effect even in overdense regions or at large distances. Therefore, the spectral hardness is a sensitive physical measure of the transverse proximity effect that is able to break the density degeneracy affecting the traditional searches.
In biological cells, the long-range intracellular traffic is powered by molecular motors which transport various cargos along microtubule filaments. The microtubules possess an intrinsic direction, having a 'plus' and a 'minus' end. Some molecular motors such as cytoplasmic dynein walk to the minus end, while others such as conventional kinesin walk to the plus end. Cells typically have an isopolar microtubule network. This is most pronounced in neuronal axons or fungal hyphae. In these long and thin tubular protrusions, the microtubules are arranged parallel to the tube axis with the minus ends pointing to the cell body and the plus ends pointing to the tip. In such a tubular compartment, transport by only one motor type leads to 'motor traffic jams'. Kinesin-driven cargos accumulate at the tip, while dynein-driven cargos accumulate near the cell body. We identify the relevant length scales and characterize the jamming behaviour in these tube geometries by using both Monte Carlo simulations and analytical calculations. A possible solution to this jamming problem is to transport cargos with a team of plus and a team of minus motors simultaneously, so that they can travel bidirectionally, as observed in cells. The presumably simplest mechanism for such bidirectional transport is provided by a 'tug-of-war' between the two motor teams which is governed by mechanical motor interactions only. We develop a stochastic tug-of-war model and study it with numerical and analytical calculations. We find a surprisingly complex cooperative motility behaviour. We compare our results to the available experimental data, which we reproduce qualitatively and quantitatively.
In the present dissertation paper an approach which ensures an efficient control of such diverse systems as noisy or chaotic oscillators and neural ensembles is developed. This approach is implemented by a simple linear feedback loop. The dissertation paper consists of two main parts. One part of the work is dedicated to the application of the suggested technique to a population of neurons with a goal to suppress their synchronous collective dynamics. The other part is aimed at investigating linear feedback control of coherence of a noisy or chaotic self-sustained oscillator. First we start with a problem of suppressing synchronization in a large population of interacting neurons. The importance of this task is based on the hypothesis that emergence of pathological brain activity in the case of Parkinson's disease and other neurological disorders is caused by synchrony of many thousands of neurons. The established therapy for the patients with such disorders is a permanent high-frequency electrical stimulation via the depth microelectrodes, called Deep Brain Stimulation (DBS). In spite of efficiency of such stimulation, it has several side effects and mechanisms underlying DBS remain unclear. In the present work an efficient and simple control technique is suggested. It is designed to ensure suppression of synchrony in a neural ensemble by a minimized stimulation that vanishes as soon as the tremor is suppressed. This vanishing-stimulation technique would be a useful tool of experimental neuroscience; on the other hand, control of collective dynamics in a large population of units represents an interesting physical problem. The main idea of suggested approach is related to the classical problem of oscillation theory, namely the interaction between a self-sustained (active) oscillator and a passive load (resonator). It is known that under certain conditions the passive oscillator can suppress the oscillations of an active one. In this thesis a much more complicated case of active medium, which itself consists of thousands of oscillators is considered. Coupling this medium to a specially designed passive oscillator, one can control the collective motion of the ensemble, specifically can enhance or suppress it. Having in mind a possible application in neuroscience, the problem of suppression is concentrated upon. Second, the efficiency of suggested suppression scheme is illustrated by considering more complex case, i.e. when the population of neurons generating the undesired rhythm consists of two non-overlapping subpopulations: the first one is affected by the stimulation, while the collective activity is registered from the second one. Generally speaking, the second population can be by itself both active and passive; both cases are considered here. The possible applications of suggested technique are discussed. Third, the influence of the external linear feedback on coherence of a noisy or chaotic self-sustained oscillator is considered. Coherence is one of the main properties of self-oscillating systems and plays a key role in the construction of clocks, electronic generators, lasers, etc. The coherence of a noisy limit cycle oscillator in the context of phase dynamics is evaluated by the phase diffusion constant, which is in its turn proportional to the width of the spectral peak of oscillations. Many chaotic oscillators can be described within the framework of phase dynamics, and, therefore, their coherence can be also quantified by the way of the phase diffusion constant. The analytical theory for a general linear feedback, considering noisy systems in the linear and Gaussian approximation is developed and validated by numerical results.
The mammalian brain is, with its numerous neural elements and structured complex connectivity, one of the most complex systems in nature. Recently, large-scale corticocortical connectivities, both structural and functional, have received a great deal of research attention, especially using the approach of complex networks. Here, we try to shed some light on the relationship between structural and functional connectivities by studying synchronization dynamics in a realistic anatomical network of cat cortical connectivity. We model the cortical areas by a subnetwork of interacting excitable neurons (multilevel model) and by a neural mass model (population model). With weak couplings, the multilevel model displays biologically plausible dynamics and the synchronization patterns reveal a hierarchical cluster organization in the network structure. We can identify a group of brain areas involved in multifunctional tasks by comparing the dynamical clusters to the topological communities of the network. With strong couplings of multilevel model and by using neural mass model, the dynamics are characterized by well-defined oscillations. The synchronization patterns are mainly determined by the node intensity (total input strengths of a node); the detailed network topology is of secondary importance. The biologically improved multilevel model exhibits similar dynamical patterns in the two regimes. Thus, the study of synchronization in a multilevel complex network model of cortex can provide insights into the relationship between network topology and functional organization of complex brain networks.
Wasserdampf in der Stratosphäre und Troposphäre ist eines der wichtigsten atmosphärischen Treibhausgase. Neben seiner Bedeutung für das Klima hat es großen Einfluss auf die Bildung von polaren stratosphärischen Wolken sowie auf die atmosphärische Chemie. Weltweit erstmalig soll innerhalb eines Forscherverbundes in Deutschland ein leistungsstarkes, mobiles, abtastendes Wasserdampf-DIAL zur dreidimensional hochaufgelösten Messung des atmosphärischen Wasserdampfs entwickelt werden. Mit dem Wasserdampf-DIAL können Wasserdampfkonzentrationen in der Atmosphäre mit hoher zeitlicher und räumlicher Auflösung gemessen werden. Das DIAL basiert auf einem Titan-Saphir-Laser oder einem dazu alternativen OPO-Laser (optisch parametrischer Oszillator). Der für das optische Pumpen dieser Laser nötige Pumplaser wurde im Rahmen dieser Arbeit in der Arbeitsgruppe Nichtlineare Optik des Instituts für Physik der Universität Potsdam entwickelt. Ein hochauflösendes, mobiles DIAL erfordert einen Pumplaser mit großen Pulsenergien, guter Strahlqualität und einer hohen Effizienz. Um diese Ziele zu erreichen, wurde ein MOPA-System (Master Oscillator Power Amplifier) mit Frequenzstabilisierung auf der Basis von doppelbrechungskompensierten, transversal diodengepumpten Laserstäben entwickelt und untersucht. Auf dem Weg dahin wurden unterschiedliche Realisierungsmöglichkeiten des MOPA-Systems geprüft. Im Rahmen dessen wurden die Festkörperlasermaterialien Yb:YAG [1], kerndotierte Nd:YAG-Keramik [2] und herkömmliches Nd:YAG vorgestellt und hinsichtlich ihrer Eignung für dieses MOPA-System untersucht. Nachdem die Entscheidung für Nd:YAG als laseraktives Material gefallen war, konnte darauf aufbauend die Konzeptionierung des Lasersystems auf der Basis von Verstärkungsrechnungen vorgenommen werden. Die entwickelte Verstärkungsrechnung trägt den Tatbeständen von realen Systemen Rechnung, indem radiusabhängige Intensitäten und eine radiale, nicht homogene Inversionsdichte berücksichtigt werden. Die Frequenzstabilisierung des gepulsten Oszillators (Frequenzstabilität von 1 MHz) wurde mittels des Pound-Drever-Hall-Verfahrens vorgenommen. Mit der Heterodynmethode wird die Frequenzstabilität des Oszillators gemessen. Nach Untersuchungen über verschiedene Konfigurationen für lineare und ringförmige Oszillatoren, wurde ein Ringoszillator mit zwei Laserköpfen aufgebaut, in welchen von außen mit einem Laser fester Frequenz eingestrahlt wird. Dieser emittiert bei einer Wiederholrate von 400 Hz eine Pulsenergie von Eout = 21 mJ bei nahezu beugungsbegrenzter Strahlqualität (M2 < 1,2). Die Verstärkung dieser Laserpulse erfolgte zunächst durch eine Vorverstärkerstufe und anschließend durch zwei doppelbrechungskompensierte Hauptverstärker im Doppeldurchgang. Eine gute Strahlqualität (M2 = 1,75) konnte unter anderem erzielt werden, indem der Doppeldurchgang durch die Hauptverstärker mit einem phasenkonjugierenden Spiegel (SF6), auf der Basis der stimulierten Brillouin Streuung, realisiert wurde. Der entwickelte Laser emittiert Pulse mit einer Länge von 25 ns und einer Energie von 250 mJ. Insgesamt wurde ein bisher einmaliges Lasersystem entwickelt. In der Literatur sind die erreichte Frequenzstabilität, Strahlqualität und Leistung in dieser Kombination bisher nicht dokumentiert. In der Zukunft soll durch den Einsatz von kerndotierten, keramischen Lasermaterialien, höheren Pumpleistungen der Hauptverstärker und phasenkonjugierenden Spiegeln aus Quarz die Pulsenergie des Systems weiter erhöht werden. [1] M. Ostermeyer, A. Straesser, “Theoretical investigation of Yb:YAG as laser material for nanosecond pulse emission with large energies in the joule range”, Optics Communications, Vol. 274, pp. 422-428 (2007) [2] A. Sträßer and M. Ostermeyer, “Improving the brightness of side pumped power amplifiers by using core doped ceramic rods”, Optics Express, Vol. 14, pp. 6687- 6693 (2006)
The interaction between neuronal cells can be identified as the computing mechanism of the brain. Neurons are complex cells that do not operate in isolation, but they are organized in a highly connected network structure. There is experimental evidence that groups of neurons dynamically synchronize their activity and process brain functions at all levels of complexity. A fundamental step to prove this hypothesis is to analyze large sets of single neurons recorded in parallel. Techniques to obtain these data are meanwhile available, but advancements are needed in the pre-processing of the large volumes of acquired data and in data analysis techniques. Major issues include extracting the signal of single neurons from the noisy recordings (referred to as spike sorting) and assessing the significance of the synchrony. This dissertation addresses these issues with two complementary strategies, both founded on the manipulation of point processes under rigorous analytical control. On the one hand I modeled the effect of spike sorting errors on correlated spike trains by corrupting them with realistic failures, and studied the corresponding impact on correlation analysis. The results show that correlations between multiple parallel spike trains are severely affected by spike sorting, especially by erroneously missing spikes. When this happens sorting strategies characterized by classifying only good'' spikes (conservative strategies) lead to less accurate results than tolerant'' strategies. On the other hand, I investigated the effectiveness of methods for assessing significance that create surrogate data by displacing spikes around their original position (referred to as dithering). I provide analytical expressions of the probability of coincidence detection after dithering. The effectiveness of spike dithering in creating surrogate data strongly depends on the dithering method and on the method of counting coincidences. Closed-form expressions and bounds are derived for the case where the dither equals the allowed coincidence interval. This work provides new insights into the methodologies of identifying synchrony in large-scale neuronal recordings, and of assessing its significance.
Atmospheric circulation and the surface mass balance in a regional climate model of Antarctica
(2007)
Understanding the Earth's climate system and particularly climate variability presents one of the most difficult and urgent challenges in science. The Antarctic plays a crucial role in the global climate system, since it is the principal region of radiative energy deficit and atmospheric cooling. An assessment of regional climate model HIRHAM is presented. The simulations are generated with the HIRHAM model, which is modified for Antarctic applications. With a horizontal resolution of 55km, the model has been run for the period 1958-1998 creating long-term simulations from initial and boundary conditions provided by the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA40 re-analysis. The model output is compared with observations from observation stations, upper air data, global atmospheric analyses and satellite data. In comparison with the observations, the evaluation shows that the simulations with the HIRHAM model capture both the large and regional scale circulation features with generally small bias in the modeled variables. On the annual time scale the largest errors in the model simulations are the overestimation total cloud cover and the colder near-surface temperature over the interior of the Antarctic plateau. The low-level temperature inversion as well as low-level wind jet is well captured by the model. The decadal scale processes were studied based on trend calculations. The long-term run was divided into two 20 years parts. The 2m temperature, 500 hPa temperature, MSLP, precipitation and net mass balance trends were calculated for both periods and over 1958 - 1998. During the last two decades the strong surface cooling was observed over the Eastern Antarctica, this result is in good agreement with the result of Chapman and Walsh (2005) who calculated the temperature trend based on the observational data. The MSLP trend reveals a big disparity between the first and second parts of the 40 year run. The overall trend shows the strengthening of the circumpolar vortex and continental anticyclone. The net mass balance as well as precipitation show a positive trend over the Antarctic Peninsula region, along Wilkes Land and in Dronning Maud Land. The Antarctic ice sheet grows over the Eastern part of Antarctica with small exceptions in Dronning Maud Land and Wilkes Land and sinks in the Antarctic Peninsula; this result is in good agreement with the satellite-measured altitude presented in Davis (2005) . To better understand the horizontal structure of MSLP, temperature and net mass balance trends the influence of the Southern Annual Mode (SAM) on the Antarctic climate was investigated. The main meteorological parameters during the positive and negative Antarctic Oscillation (AAO) phases were compared to each other. A positive/negative AAO index means strengthening/weakening of the circumpolar vortex, poleward/northward storm tracks and prevailing/weakening westerly winds. For detailed investigation of global teleconnection, two positive and one negative periods of AAO phase were chosen. The differences in MSLP and 2m temperature between positive and negative AAO years during the winter months partly explain the surface cooling during the last decades.
Stellar winds play an important role for the evolution of massive stars and their cosmic environment. Multiple lines of evidence, coming from spectroscopy, polarimetry, variability, stellar ejecta, and hydrodynamic modeling, suggest that stellar winds are non-stationary and inhomogeneous. This is referred to as 'wind clumping'. The urgent need to understand this phenomenon is boosted by its far-reaching implications. Most importantly, all techniques to derive empirical mass-loss rates are more or less corrupted by wind clumping. Consequently, mass-loss rates are extremely uncertain. Within their range of uncertainty, completely different scenarios for the evolution of massive stars are obtained. Settling these questions for Galactic OB, LBV and Wolf-Rayet stars is prerequisite to understanding stellar clusters and galaxies, or predicting the properties of first-generation stars. In order to develop a consistent picture and understanding of clumped stellar winds, an international workshop on 'Clumping in Hot Star Winds' was held in Potsdam, Germany, from 18. - 22. June 2007. About 60 participants, comprising almost all leading experts in the field, gathered for one week of extensive exchange and discussion. The Scientific Organizing Committee (SOC) included John Brown (Glasgow), Joseph Cassinelli (Madison), Paul Crowther (Sheffield), Alex Fullerton (Baltimore), Wolf-Rainer Hamann (Potsdam, chair), Anthony Moffat (Montreal), Stan Owocki (Newark), and Joachim Puls (Munich). These proceedings contain the invited and contributed talks presented at the workshop, and document the extensive discussions.
Electron transfer phenomena in proteins represent one of the most common types of biochemical reactions. They play a central role in energy conversion pathways in living cells, and are crucial components in respiration and photosynthesis. These complex biochemical reaction cascades consist of a series of proteins and protein complexes that couple a charge transfer to different forms of chemical energy. The efficiency and sophisticated optimisation of signal transfer in these natural redox chains has inspired engineering of artificial architectures mimicking essential properties of their natural analogues. Implementation of direct electron transfer (DET) in protein assemblies was a breakthrough in bioelectronics, providing a simple and efficient way for coupling biological recognition events to a signal transducer. DET avoids the use of redox mediators, reducing potential interferences and side reactions, as well as being more compatible with in vivo conditions. However, only a few haem proteins, including the redox protein cytochrome c (cyt.c), and blue copper enzymes show efficient DET on different kinds of electrodes. Previous investigations with cyt.c have mainly focused on heterogeneous electron transfer of monolayers of this protein on gold. An important advance was the fabrication of cyt.c multilayers by electrostatic layer-by-layer self-assembly. The ease of fabrication, the stability, and the controllable permeability of polyelectrolyte multilayers have made them particularly attractive for electroanalytical applications. With cyt.c and sulfonated polyaniline it was for the first time possible that fully electro-active multilayers of the redox protein could be prepared. This approach was extended to design an analytical signal chain based on multilayers of cyt.c and xanthine oxidase (XOD). The system does not need an external mediator but relies on an in situ generation of a mediating radical and thus allows a signal transfer from hypoxanthine via the substrate converting enzyme and cyt.c to the electrode. Another kind of a signal chain is based on assembling proteins in complexes on electrodes in such a way that a direct protein-protein electron transfer becomes feasible. This design does not need a redox mediator in analogy to natural protein communication. For this purpose, cyt.c and the enzyme bilirubin oxidase (BOD, EC 1.3.3.5) are co-immobilized in a self-assembled polyelectrolyte multilayer on gold electrodes. Although these two proteins are not natural reaction partners, the protein architecture facilitates an electron transfer from the electrode via multiple protein layers to molecular oxygen resulting in a significant catalytic reduction current. Finally, we describe a novel strategy for multi-protein layer-by-layer self-assembly combining cyt.c with an enzyme sulfite oxidase (SOx) without use of any additional polymer. Electrostatic interactions between these two proteins with rather separated pI values during the assembly process from a low ionic strength buffer were found sufficient for the layer-by-layer deposition of the both biomolecules. It is anticipated that the concepts described in this work will stimulate further progress in multilayer design of even more complex biomimetic signal cascades taking advantage of direct communication between proteins.
Giacconi et al. (1962) discovered a diffuse cosmic X-ray background with rocket experiments when they searched for lunar X-ray emission. Later satellite missions found a spectral peak in the cosmic X-ray background at ~30 keV. Imaging X-ray satellites such as ROSAT (1990-1999) were able to resolve up to 80% of the background below 2 keV into single point sources, mainly active galaxies. The cosmic X-ray background is the integration of all accreting super-massive (several million solar masses) black holes in the centre of active galaxies over cosmic time. Synthesis models need further populations of X-ray absorbed active galaxy nuclei (AGN) in order to explain the cosmic X-ray background peak at ~30 keV. Current X-ray missions such as XMM-Newton and Chandra offer the possibility of studying these additional populations. This Ph.D. thesis studies the populations that dominate the X-ray sky. For this purpose the 120 ksec XMM-Newton Marano field survey, named for an earlier optical quasar survey in the southern hemisphere, is analysed. Based on the optical follow-up observations the X-ray sources are spectroscopically classified. Optical and X-ray properties of the different X-ray source populations are studied and differences are derived. The amount of absorption in the X-ray spectra of type II AGN, which are considered as a main contributor to the X-ray background at ~30 keV, is determined. In order to extend the sample size of the rare type II AGN, this study also includes objects from another survey, the XMM-Newton Serendipitous Medium Sample. In addition, the dependence of the absorption in type II AGN with redshift and X-ray luminosity is analysed. We detected 328 X-ray sources in the Marano field. 140 sources were spectroscopically classified. We found 89 type I AGN, 36 type II AGN, 6 galaxies, and 9 stars. AGN, galaxies, and stars are clearly distinguishable by their optical and X-ray properties. Type I and II AGN do not separate clearly. They have a significant overlap in all studied properties. In a few cases the X-ray properties are in contradiction to the observed optical properties for type I and type II AGN. For example we find type II AGN that show evidence for optical absorption but are not absorbed in X-rays. Based on the additional use of near infra-red imaging (K-band), we were able to identify several of the rare type II AGN. The X-ray spectra of type II AGN from the XMM-Newton Marano field survey and the XMM-Newton Serendipitous Medium Sample were analysed. Since most of the sources have only ~40 X-ray counts in the XMM-Newton PN-detector, I carefully studied the fit results of simulated X-ray spectra as a function of fit statistic and binning method. The objects revealed only moderate absorption. In particular, I do not find any Compton-thick sources (absorbed by column densities of NH > 1.5 x 10^24 cm^−2). This gives evidence that type II AGN are not the main contributor of the X-ray background around 30 keV. Although bias effects may occur, type II AGN show no noticeable trend of the amount of absorption with redshift or X-ray luminosity.
Im Rahmen der vorliegenden Arbeit ist es erstmals gelungen, mit einem ps-Pumplaser (10 ps) Weißlicht mit einer spektralen Breite von mehr als einer optischen Oktave in einer mikrostrukturierten Faser (MSF) bei einer Pumpwellenlänge von 1064 nm zu generieren. Es ließ sich, abgesehen von nichtkonvertierten Resten der Pumpstrahlung, ein unstrukturiertes und zeitlich stabiles Weißlichtspektrum von 700 nm bis 1650 nm generieren. Die maximale Ausgangsleistung dieser Weißlichtstrahlung betrug 3,1 W. Es konnten sehr gute Einkoppeleffizienzen von maximal 62 % erzielt werden. Die an der Weißlichterzeugung beteiligten dispersiven und nichtlinear optischen Effekte, wie z.B. Selbstphasenmodulation, Vierwellenmischung, Modulationsinstabilitäten oder Solitoneneffekte, werden detailliert theoretisch untersucht und erläutert. Die Arbeit beinhaltet ebenfalls eine umfangreiche Beschreibung der Wirkungsweise und Eigenschaften von mikrostrukturierten Fasern mit einem festen Faserkern. Aufgrund der großen Variationsvielfalt des mikrostrukturierten Fasermantels und der damit verbundenen Wellenleitereigenschaften ergeben sich, insbesondere für die Anwendung in der nichtlinearen Optik, eine Reihe von interessanten Eigenschaften. Es wurden insgesamt vier verschiedene mikrostrukturierte Fasern experimentell untersucht. Für die Interpretation der experimentellen Ergebnisse ist die Pulsausbreitung der ps-Pumppulse in einer dispersiven, nichtlinear optischen Faser anhand der verallgemeinerten nichtlinearen Schrödinger-Gleichung berechnet worden. Durch einen Vergleich der Berechnungen mit den Messdaten ließen sich verstärkte Modulationsinstabilitäten und verschiedene Solitoneneffekte als hauptsächlich für die Weißlichterzeugung bei ps-Anregungspulsen verantwortlich identifizieren. Auf der Basis der durchgeführten Untersuchungen wurde in Kooperation mit der Fa. Jenoptik Laser, Optik, Systeme GmbH eine kompakte und leistungsstarke Weißlichtquelle entwickelt. Diese wurde erfolgreich in einer Kohärenztomographiemessung (Optical Coherence Tomography - OCT) getestet: Es konnte in ex vivo-Untersuchungen gezeigt werden, dass sich mit dieser ps-Weißlichtquelle eine hohe Eindringtiefe von ca. 400 µm in die Netzhaut eines Affen erreichen lässt.
In dieser Arbeit wurde die Variabilität der Atmosphäre in einem neuen gekoppelten Klimamodell (ECHO-GiSP) untersucht, welches eine vereinfachte Stratosphärenchemie (bis 80 km Höhe) enthält. Es wurden 2 Simulationen über 150 Jahre durchgeführt. In einer der Simulationen wurde die atmosphärische Chemie modelliert, hatte aber keinen Einfluß auf die Dynamik des Klimamodelles. In der zweiten Simulation wurde hingegen die Wirkung der Chemie auf die Klimadynamik explizit berücksichtigt, die über die Strahlungsbilanz des Modelles erfolgt. Dies ist die erste Langzeitsimulation mit einem voll gekoppelten globalen Klimamodell mit interaktiver Chemie. Die Simulation mit rückgekoppelter Chemie zeigt eine Abschwächung des atmosphärischen Variabilitätsmusters der Arktischen Oszillation (AO). Zudem kommt es in der Troposphäre zu einer Reduzierung der mittleren Windgeschwindigkeiten der gemäßigten Breiten aufgrund verringerter Temperaturgegensätze zwischen den Tropen und den Polargebieten. Auch in der Stratosphäre ergibt sich eine Abschwächung und Erwärmung des Polarwirbels. Diese Auswirkungen der Kopplung zwischen der atmosphärischen Chemie und der Dynamik des Klimamodelles sind eine wichtige Erkenntnis, da in früheren Klimasimulationen die Variabilität der AO oft zu stark ausgeprägt war. In der Stratosphäre reduziert sich infolge des abgeschwächten Polarwirbels auch die großräumige Zirkulation zwischen den beiden Hemisphären der Erde. In der Troposphäre werden hingegen die allgemeine Zirkulation, und damit auch die subtropischen Strahlströme des Windes verstärkt. Zudem kommt es in den Tropen zu Temperaturänderungen durch stratosphärische Ozonschwankungen in Abhängigkeit von der AO. Allgemein verändert sich die Kopplung zwischen Troposphäre und Stratosphäre, einschließlich des durch die Anregung von langen atmosphärischen Wellen erfolgenden vertikalen Energieübertrages aus der Troposphäre in die Stratosphäre.
In this work, some new results to exploit the recurrence properties of quasiperiodic dynamical systems are presented by means of a two dimensional visualization technique, Recurrence Plots(RPs). Quasiperiodicity is the simplest form of dynamics exhibiting nontrivial recurrences, which are common in many nonlinear systems. The concept of recurrence was introduced to study the restricted three body problem and it is very useful for the characterization of nonlinear systems. I have analyzed in detail the recurrence patterns of systems with quasiperiodic dynamics both analytically and numerically. Based on a theoretical analysis, I have proposed a new procedure to distinguish quasiperiodic dynamics from chaos. This algorithm is particular useful in the analysis of short time series. Furthermore, this approach demonstrates to be efficient in recognizing regular and chaotic trajectories of dynamical systems with mixed phase space. Regarding the application to real situations, I have shown the capability and validity of this method by analyzing time series from fluid experiments.
In der vorliegenden Arbeit werden Methoden der Erdsystemanalyse auf die Untersuchung der Habitabilität terrestrischer Exoplaneten angewandt. Mit Hilfe eines parametrisierten Konvektionsmodells für die Erde wird die thermische Evolution von terrestrischen Planeten berechnet. Bei zunehmender Leuchtkraft des Zentralsterns wird über den globalen Karbonat-Silikat-Kreislauf das planetare Klima stabilisiert. Für eine photosynthetisch-aktive Biosphäre, die in einem bestimmten Temperaturbereich bei hinreichender CO2-Konzentration existieren kann, wird eine Überlebenspanne abgeschätzt. Der Abstandsbereich um einen Stern, in dem eine solche Biosphäre produktiv ist, wird als photosynthetisch-aktive habitable Zone (pHZ) definiert und berechnet. Der Zeitpunkt, zu dem die pHZ in einem extrasolaren Planetensystem endgültig verschwindet, ist die maximale Lebenspanne der Biosphäre. Für Supererden, massereiche terrestrische Planeten, ist sie umso länger, je massereicher der Planet ist und umso kürzer, je mehr er mit Kontinenten bedeckt ist. Für Supererden, die keine ausgeprägten Wasser- oder Landwelten sind, skaliert die maximale Lebenspanne mit der Planetenmasse mit einem Exponenten von 0,14. Um K- und M-Sterne ist die Überlebensspanne einer Biosphäre auf einem Planeten immer durch die maximale Lebensspanne bestimmt und nicht durch das Ende der Hauptreihenentwicklung des Zentralsterns limitiert. Das pHZ-Konzept wird auf das extrasolare Planetensystem Gliese 581 angewandt. Danach könnte die 8-Erdmassen-Supererde Gliese 581d habitabel sein. Basierend auf dem vorgestellten pHZ-Konzept wird erstmals die von Ward und Brownlee 1999 aufgestellte Rare-Earth-Hypothese für die Milchstraße quantifiziert. Diese Hypothese besagt, dass komplexes Leben im Universum vermutlich sehr selten ist, wohingegen primitives Leben weit verbreitet sein könnte. Unterschiedliche Temperatur- und CO2-Toleranzen sowie ein unterschiedlicher Einfluss auf die Verwitterung für komplexe und primitive Lebensformen führt zu unterschiedlichen Grenzen der pHZ und zu einer unterschiedlichen Abschätzung für die Anzahl der Planeten, die mit den entsprechenden Lebensformen besiedelt sein könnten. Dabei ergibt sich, dass komplex besiedelte Planeten heute etwa 100-mal seltener sein müssten als primitiv besiedelte.
The biological function and the technological applications of semiflexible polymers, such as DNA, actin filaments and carbon nanotubes, strongly depend on their rigidity. Semiflexible polymers are characterized by their persistence length, the definition of which is the subject of the first part of this thesis. Attractive interactions, that arise e.g.~in the adsorption, the condensation and the bundling of filaments, can change the conformation of a semiflexible polymer. The conformation depends on the relative magnitude of the material parameters and can be influenced by them in a systematic manner. In particular, the morphologies of semiflexible polymer rings, such as circular nanotubes or DNA, which are adsorbed onto substrates with three types of structures, are studied: (i) A topographical channel, (ii) a chemically modified stripe and (iii) a periodic pattern of topographical steps. The results are compared with the condensation of rings by attractive interactions. Furthermore, the bundling of two individual actin filaments, whose ends are anchored, is analyzed. This system geometry is shown to provide a systematic and quantitative method to extract the magnitude of the attraction between the filaments from experimentally observable conformations of the filaments.
The role played by azobenzene polymers in the modern photonic, electronic and opto-mechanical applications cannot be underestimated. These polymers are successfully used to produce alignment layers for liquid crystalline fluorescent polymers in the display and semiconductor technology, to build waveguides and waveguide couplers, as data storage media and as labels in quality product protection. A very hot topic in modern research are light-driven artificial muscles based on azobenzene elastomers. The incorporation of azobenzene chromophores into polymer systems via covalent bonding or even by blending gives rise to a number of unusual effects under visible (VIS) and ultraviolet light irradiation. The most amazing effect is the inscription of surface relief gratings (SRGs) onto thin azobenzene polymer films. At least seven models have been proposed to explain the origin of the inscribing force but none of them describes satisfactorily the light induced material transport on the molecular level. In most models, to explain the mass transport over micrometer distances during irradiation at room temperature, it is necessary to assume a considerable degree of photoinduced softening, at least comparable with that at the glass transition. Contrary to this assumption, we have gathered a convincing evidence that there is no considerable softening of the azobenzene layers under illumination. Presently we can surely say that light induced softening is a very weak accompanying effect rather than a necessary condition for the formation of SRGs. This means that the inscribing force should be above the yield point of the azobenzene polymer. Hence, an appropriate approach to describe the formation and relaxation of SRGs is a viscoplastic theory. It was used to reproduce pulse-like inscription of SRGs as measured by VIS light scattering. At longer inscription times the VIS scattering pattern exhibits some peculiarities which can be explained by the appearance of a density grating that will be shown to arise due to the final compressibility of the polymer film. As a logical consequence of the aforementioned research, a thermodynamic theory explaining the light-induced deformation of free standing films and the formation of SRGs is proposed. The basic idea of this theory is that under homogeneous illumination an initially isotropic sample should stretch itself along the polarization direction to compensate the entropy decrease produced by the photoinduced reorientation of azobenzene chromophores. Finally, some ideas about further development of this controversial topic will be discussed.
Magnetorotational instability (MRI) is one of the most important and most common instabilities in astrophysics. Today it is widely accepted that it serves as a major source of turbulent viscosity in accretion disks, the most energy efficient objects in the universe. The importance of the MRI for astrophysics has been realized only in recent fifteen years. However, originally it was discovered much earlier, in 1959, in a very different context. Theoretical flow of a conducting liquid confined between differentially rotating cylinders in the presence of an external magnetic field was analyzed. The central conclusion is that the additional magnetic field parallel to the axis of rotation can destabilize otherwise stable flow. Theory of non-magnetized fluid motion between rotating cylinders has much longer history, though. It has been studied already in 1888 and today such setup is usually referred as a Taylor-Couette flow. To prove experimentally the existence of MRI in a magnetized Taylor-Couette flow is a demanding task and different MHD groups around the world try to achieve it. The main problem lies in the fact that laboratory liquid metals which are used in such experiments are characterized by small magnetic Prandtl number. Consequently rotation rates of the cylinders must be extremely large and vast amount of technical problems emerge. One of the most important difficulties is an influence of plates enclosing the cylinders in any experiment. For fast rotation the plates tend to dominate the whole flow and the MRI can not be observed. In this thesis we discuss a special helical configuration of the applied magnetic field which allows the critical rotation rates to be much smaller. If only the axial magnetic field is present, the cylinders must rotate with angular velocities corresponding to Reynolds numbers of order Re ≈ 10^6. With the helical field this number is dramatically reduced to Re ≈ 10^3. The azimuthal component of the magnetic field can be easily generated by letting an electric current through the axis of rotation, In a Taylor-Couette flow the (primary) instability manifests itself as Taylor vortices. The specific geometry of the helical magnetic field leads to a traveling wave solution and the vortices are drifting in a direction determined by rotation and the magnetic field. In an idealized study for infinitely long cylinders this is not a problem. However, if the cylinders have finite length and are bounded vertically by the plates the situation is different. In this dissertation it is shown, with use of numerical methods, that the traveling wave solution also exists for MHD Taylor-Couette flow at finite aspect ratio H/D, H being height of the cylinders, D width of the gap between them. The nonlinear simulations provide amplitudes of fluid velocity which are helpful in designing an experiment. Although the plates disturb the flow, parameters like the drift velocity indicate that the helical MRI operates in this case. The idea of the helical MRI was implemented in a very recent experiment PROMISE. The results provided, for the first time, an evidence that the (helical) MRI indeed exists. Nevertheless, the influence of the vertical endplates was evident and the experiment can be, in principle, improved. Exemplary methods of reduction of the end-effect are here proposed. Near the vertical boundaries develops an Ekman-Hartmann layer. Study of this layer for the MHD Taylor-Couette system as well as its impact on the global flow properties is presented. It is shown that the plates, especially if they are conducting, can disturb the flow far more then previously thought also for relatively slow rotation rates.