@phdthesis{Logačev2014, author = {Logačev, Pavel}, title = {Underspecification and parallel processing in sentence comprehension}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-82047}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {The aim of the present thesis is to answer the question to what degree the processes involved in sentence comprehension are sensitive to task demands. A central phenomenon in this regard is the so-called ambiguity advantage, which is the finding that ambiguous sentences can be easier to process than unambiguous sentences. This finding may appear counterintuitive, because more meanings should be associated with a higher computational effort. Currently, two theories exist that can explain this finding. The Unrestricted Race Model (URM) by van Gompel et al. (2001) assumes that several sentence interpretations are computed in parallel, whenever possible, and that the first interpretation to be computed is assigned to the sentence. Because the duration of each structure-building process varies from trial to trial, the parallelism in structure-building predicts that ambiguous sentences should be processed faster. This is because when two structures are permissible, the chances that some interpretation will be computed quickly are higher than when only one specific structure is permissible. Importantly, the URM is not sensitive to task demands such as the type of comprehension questions being asked. A radically different proposal is the strategic underspecification model by Swets et al. (2008). It assumes that readers do not attempt to resolve ambiguities unless it is absolutely necessary. In other words, they underspecify. According the strategic underspecification hypothesis, all attested replications of the ambiguity advantage are due to the fact that in those experiments, readers were not required to fully understand the sentence. In this thesis, these two models of the parser's actions at choice-points in the sentence are presented and evaluated. First, it is argued that the Swets et al.'s (2008) evidence against the URM and in favor of underspecification is inconclusive. Next, the precise predictions of the URM as well as the underspecification model are refined. Subsequently, a self-paced reading experiment involving the attachment of pre-nominal relative clauses in Turkish is presented, which provides evidence against strategical underspecification. A further experiment is presented which investigated relative clause attachment in German using the speed-accuracy tradeoff (SAT) paradigm. The experiment provides evidence against strategic underspecification and in favor of the URM. Furthermore the results of the experiment are used to argue that human sentence comprehension is fallible, and that theories of parsing should be able to account for that fact. Finally, a third experiment is presented, which provides evidence for the sensitivity to task demands in the treatment of ambiguities. Because this finding is incompatible with the URM, and because the strategic underspecification model has been ruled out, a new model of ambiguity resolution is proposed: the stochastic multiple-channel model of ambiguity resolution (SMCM). It is further shown that the quantitative predictions of the SMCM are in agreement with experimental data. In conclusion, it is argued that the human sentence comprehension system is parallel and fallible, and that it is sensitive to task-demands.}, language = {en} } @phdthesis{Goswami2014, author = {Goswami, Bedartha}, title = {Uncertainties in climate data analysis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-78312}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Scientific inquiry requires that we formulate not only what we know, but also what we do not know and by how much. In climate data analysis, this involves an accurate specification of measured quantities and a consequent analysis that consciously propagates the measurement errors at each step. The dissertation presents a thorough analytical method to quantify errors of measurement inherent in paleoclimate data. An additional focus are the uncertainties in assessing the coupling between different factors that influence the global mean temperature (GMT). Paleoclimate studies critically rely on `proxy variables' that record climatic signals in natural archives. However, such proxy records inherently involve uncertainties in determining the age of the signal. We present a generic Bayesian approach to analytically determine the proxy record along with its associated uncertainty, resulting in a time-ordered sequence of correlated probability distributions rather than a precise time series. We further develop a recurrence based method to detect dynamical events from the proxy probability distributions. The methods are validated with synthetic examples and demonstrated with real-world proxy records. The proxy estimation step reveals the interrelations between proxy variability and uncertainty. The recurrence analysis of the East Asian Summer Monsoon during the last 9000 years confirms the well-known `dry' events at 8200 and 4400 BP, plus an additional significantly dry event at 6900 BP. We also analyze the network of dependencies surrounding GMT. We find an intricate, directed network with multiple links between the different factors at multiple time delays. We further uncover a significant feedback from the GMT to the El Ni{\~n}o Southern Oscillation at quasi-biennial timescales. The analysis highlights the need of a more nuanced formulation of influences between different climatic factors, as well as the limitations in trying to estimate such dependencies.}, language = {en} } @phdthesis{Czesnick2014, author = {Czesnick, Hj{\"o}rdis}, title = {Functional specialization of Arabidopsis poly(A) polymerases in relation to flowering time and stress}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-78015}, school = {Universit{\"a}t Potsdam}, pages = {157}, year = {2014}, abstract = {Polyadenylation is a decisive 3' end processing step during the maturation of pre-mRNAs. The length of the poly(A) tail has an impact on mRNA stability, localization and translatability. Accordingly, many eukaryotic organisms encode several copies of canonical poly(A) polymerases (cPAPs). The disruption of cPAPs in mammals results in lethality. In plants, reduced cPAP activity is non-lethal. Arabidopsis encodes three nuclear cPAPs, PAPS1, PAPS2 and PAPS4, which are constitutively expressed throughout the plant. Recently, the detailed analysis of Arabidopsis paps1 mutants revealed a subset of genes that is preferentially polyadenylated by the cPAP isoform PAPS1 (Vi et al. 2013). Thus, the specialization of cPAPs might allow the regulation of different sets of genes in order to optimally face developmental or environmental challenges. To gain insights into the cPAP-based gene regulation in plants, the phenotypes of Arabidopsis cPAPs mutants under different conditions are characterized in detail in the following work. An involvement of all three cPAPs in flowering time regulation and stress response regulation is shown. While paps1 knockdown mutants flower early, paps4 and paps2 paps4 knockout mutants exhibit a moderate late-flowering phenotype. PAPS1 promotes the expression of the major flowering inhibitor FLC, supposedly by specific polyadenylation of an FLC activator. PAPS2 and PAPS4 exhibit partially overlapping functions and ensure timely flowering by repressing FLC and at least one other unidentified flowering inhibitor. The latter two cPAPs act in a novel regulatory pathway downstream of the autonomous pathway component FCA and act independently from the polyadenylation factors and flowering time regulators CstF64 and FY. Moreover, PAPS1 and PAPS2/PAPS4 are implicated in different stress response pathways in Arabidopsis. Reduced activity of the poly(A) polymerase PAPS1 results in enhanced resistance to osmotic and oxidative stress. Simultaneously, paps1 mutants are cold-sensitive. In contrast, PAPS2/PAPS4 are not involved in the regulation of osmotic or cold stress, but paps2 paps4 loss-of-function mutants exhibit enhanced sensitivity to oxidative stress provoked in the chloroplast. Thus, both PAPS1 and PAPS2/PAPS4 are required to maintain a balanced redox state in plants. PAPS1 seems to fulfil this function in concert with CPSF30, a polyadenylation factor that regulates alternative polyadenylation and tolerance to oxidative stress. The individual paps mutant phenotypes and the cPAP-specific genetic interactions support the model of cPAP-dependent polyadenylation of selected mRNAs. The high similarity of the polyadenylation machineries in yeast, mammals and plants suggests that similar regulatory mechanisms might be present in other organism groups. The cPAP-dependent developmental and physiological pathways identified in this work allow the design of targeted experiments to better understand the ecological and molecular context underlying cPAP-specialization.}, language = {en} } @phdthesis{Pussak2014, author = {Pussak, Marcin}, title = {Seismic characterization of geothermal reservoirs by application of the common-reflection-surface stack method and attribute analysis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-77565}, school = {Universit{\"a}t Potsdam}, pages = {viii, 140}, year = {2014}, abstract = {An important contribution of geosciences to the renewable energy production portfolio is the exploration and utilization of geothermal resources. For the development of a geothermal project at great depths a detailed geological and geophysical exploration program is required in the first phase. With the help of active seismic methods high-resolution images of the geothermal reservoir can be delivered. This allows potential transport routes for fluids to be identified as well as regions with high potential of heat extraction to be mapped, which indicates favorable conditions for geothermal exploitation. The presented work investigates the extent to which an improved characterization of geothermal reservoirs can be achieved with the new methods of seismic data processing. The summations of traces (stacking) is a crucial step in the processing of seismic reflection data. The common-reflection-surface (CRS) stacking method can be applied as an alternative for the conventional normal moveout (NMO) or the dip moveout (DMO) stack. The advantages of the CRS stack beside an automatic determination of stacking operator parameters include an adequate imaging of arbitrarily curved geological boundaries, and a significant increase in signal-to-noise (S/N) ratio by stacking far more traces than used in a conventional stack. A major innovation I have shown in this work is that the quality of signal attributes that characterize the seismic images can be significantly improved by this modified type of stacking in particular. Imporoved attribute analysis facilitates the interpretation of seismic images and plays a significant role in the characterization of reservoirs. Variations of lithological and petro-physical properties are reflected by fluctuations of specific signal attributes (eg. frequency or amplitude characteristics). Its further interpretation can provide quality assessment of the geothermal reservoir with respect to the capacity of fluids within a hydrological system that can be extracted and utilized. The proposed methodological approach is demonstrated on the basis on two case studies. In the first example, I analyzed a series of 2D seismic profile sections through the Alberta sedimentary basin on the eastern edge of the Canadian Rocky Mountains. In the second application, a 3D seismic volume is characterized in the surroundings of a geothermal borehole, located in the central part of the Polish basin. Both sites were investigated with the modified and improved stacking attribute analyses. The results provide recommendations for the planning of future geothermal plants in both study areas.}, language = {en} } @phdthesis{Conrad2014, author = {Conrad, Claudia}, title = {Open cluster groups and complexes}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-77605}, school = {Universit{\"a}t Potsdam}, pages = {xii, 172}, year = {2014}, abstract = {It is generally agreed upon that stars typically form in open clusters and stellar associations, but little is known about the structure of the open cluster system. Do open clusters and stellar associations form isolated or do they prefer to form in groups and complexes? Open cluster groups and complexes could verify star forming regions to be larger than expected, which would explain the chemical homogeneity over large areas in the Galactic disk. They would also define an additional level in the hierarchy of star formation and could be used as tracers for the scales of fragmentation in giant molecular clouds? Furthermore, open cluster groups and complexes could affect Galactic dynamics and should be considered in investigations and simulations on the dynamical processes, such as radial migration, disc heating, differential rotation, kinematic resonances, and spiral structure. In the past decade there were a few studies on open cluster pairs (de La Fuente Marcos \& de La Fuente Marcos 2009a,b,c) and on open cluster groups and complexes (Piskunov et al. 2006). The former only considered spatial proximity for the identification of the pairs, while the latter also required tangential velocities to be similar for the members. In this work I used the full set of 6D phase-space information to draw a more detailed picture on these structures. For this purpose I utilised the most homogeneous cluster catalogue available, namely the Catalogue of Open Cluster Data (COCD; Kharchenko et al. 2005a,b), which contains parameters for 650 open clusters and compact associations, as well as for their uniformly selected members. Additional radial velocity (RV) and metallicity ([M/H]) information on the members were obtained from the RAdial Velocity Experiment (RAVE; Steinmetz et al. 2006; Kordopatis et al. 2013) for 110 and 81 clusters, respectively. The RAVE sample was cleaned considering quality parameters and flags provided by RAVE (Matijevič et al. 2012; Kordopatis et al. 2013). To ensure that only real members were included for the mean values, also the cluster membership, as provided by Kharchenko et al. (2005a,b), was considered for the stars cross-matched in RAVE. 6D phase-space information could be derived for 432 out of the 650 COCD objects and I used an adaption of the Friends-of-Friends algorithm, as used in cosmology, to identify potential groupings. The vast majority of the 19 identified groupings were pairs, but I also found four groups of 4-5 members and one complex with 15 members. For the verification of the identified structures, I compared the results to a randomly selected subsample of the catalogue for the Milky Way global survey of Star Clusters (MWSC; Kharchenko et al. 2013), which became available recently, and was used as reference sample. Furthermore, I implemented Monte-Carlo simulations with randomised samples created from two distinguished input distributions for the spatial and velocity parameters. On the one hand, assuming a uniform distribution in the Galactic disc and, on the other hand, assuming the COCD data distributions to be representative for the whole open cluster population. The results suggested that the majority of identified pairs are rather by chance alignments, but the groups and the complex seemed to be genuine. A comparison of my results to the pairs, groups and complexes proposed in the literature yielded a partial overlap, which was most likely because of selection effects and different parameters considered. This is another verification for the existence of such structures. The characteristics of the found groupings favour that members of an open cluster grouping originate from a common giant molecular cloud and formed in a single, but possibly sequential, star formation event. Moreover, the fact that the young open cluster population showed smaller spatial separations between nearest neighbours than the old cluster population indicated that the lifetime of open cluster groupings is most likely comparable to that of the Galactic open cluster population itself. Still even among the old open clusters I could identify groupings, which suggested that the detected structure could be in some cases more long lived as one might think. In this thesis I could only present a pilot study on structures in the Galactic open cluster population, since the data sample used was highly incomplete. For further investigations a far more complete sample would be required. One step in this direction would be to use data from large current surveys, like SDSS, RAVE, Gaia-ESO and VVV, as well as including results from studies on individual clusters. Later the sample can be completed by data from upcoming missions, like Gaia and 4MOST. Future studies using this more complete open cluster sample will reveal the effect of open cluster groupings on star formation theory and their significance for the kinematics, dynamics and evolution of the Milky Way, and thereby of spiral galaxies.}, language = {en} } @phdthesis{Heise2014, author = {Heise, Arvid}, title = {Data cleansing and integration operators for a parallel data analytics platform}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-77100}, school = {Universit{\"a}t Potsdam}, pages = {ii, 179}, year = {2014}, abstract = {The data quality of real-world datasets need to be constantly monitored and maintained to allow organizations and individuals to reliably use their data. Especially, data integration projects suffer from poor initial data quality and as a consequence consume more effort and money. Commercial products and research prototypes for data cleansing and integration help users to improve the quality of individual and combined datasets. They can be divided into either standalone systems or database management system (DBMS) extensions. On the one hand, standalone systems do not interact well with DBMS and require time-consuming data imports and exports. On the other hand, DBMS extensions are often limited by the underlying system and do not cover the full set of data cleansing and integration tasks. We overcome both limitations by implementing a concise set of five data cleansing and integration operators on the parallel data analytics platform Stratosphere. We define the semantics of the operators, present their parallel implementation, and devise optimization techniques for individual operators and combinations thereof. Users specify declarative queries in our query language METEOR with our new operators to improve the data quality of individual datasets or integrate them to larger datasets. By integrating the data cleansing operators into the higher level language layer of Stratosphere, users can easily combine cleansing operators with operators from other domains, such as information extraction, to complex data flows. Through a generic description of the operators, the Stratosphere optimizer reorders operators even from different domains to find better query plans. As a case study, we reimplemented a part of the large Open Government Data integration project GovWILD with our new operators and show that our queries run significantly faster than the original GovWILD queries, which rely on relational operators. Evaluation reveals that our operators exhibit good scalability on up to 100 cores, so that even larger inputs can be efficiently processed by scaling out to more machines. Finally, our scripts are considerably shorter than the original GovWILD scripts, which results in better maintainability of the scripts.}, language = {en} } @phdthesis{Kirchhecker2014, author = {Kirchhecker, Sarah}, title = {Renewable imidazolium zwitterions as platform molecules for the synthesis of ionic liquids and materials}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-77412}, school = {Universit{\"a}t Potsdam}, pages = {136}, year = {2014}, abstract = {Following the principles of green chemistry, a simple and efficient synthesis of functionalised imidazolium zwitterionic compounds from renewable resources was developed based on a modified one-pot Debus-Radziszewski reaction. The combination of different carbohydrate-derived 1,2-dicarbonyl compounds and amino acids is a simple way to modulate the properties and introduce different functionalities. A representative compound was assessed as an acid catalyst, and converted into acidic ionic liquids by reaction with several strong acids. The reactivity of the double carboxylic functionality was explored by esterification with long and short chain alcohols, as well as functionalised amines, which led to the straightforward formation of surfactant-like molecules or bifunctional esters and amides. One of these di-esters is currently being investigated for the synthesis of poly(ionic liquids). The functionalisation of cellulose with one of the bifunctional esters was investigated and preliminary tests employing it for the functionalisation of filter papers were carried out successfully. The imidazolium zwitterions were converted into ionic liquids via hydrothermal decarboxylation in flow, a benign and scalable technique. This method provides access to imidazolium ionic liquids via a simple and sustainable methodology, whilst completely avoiding contamination with halide salts. Different ionic liquids can be generated depending on the functionality contained in the ImZw precursor. Two alanine-derived ionic liquids were assessed for their physicochemical properties and applications as solvents for the dissolution of cellulose and the Heck coupling.}, language = {en} } @phdthesis{Fronton2014, author = {Fronton, Ludivine}, title = {Modeling approaches to characterize the disposition of monoclonal antibodies}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76537}, school = {Universit{\"a}t Potsdam}, pages = {xxi, 133}, year = {2014}, abstract = {Monoclonal antibodies (mAbs) are engineered immunoglobulins G (IgG) used for more than 20 years as targeted therapy in oncology, infectious diseases and (auto-)immune disorders. Their protein nature greatly influences their pharmacokinetics (PK), presenting typical linear and non-linear behaviors. While it is common to use empirical modeling to analyze clinical PK data of mAbs, there is neither clear consensus nor guidance to, on one hand, select the structure of classical compartment models and on the other hand, interpret mechanistically PK parameters. The mechanistic knowledge present in physiologically-based PK (PBPK) models is likely to support rational classical model selection and thus, a methodology to link empirical and PBPK models is desirable. However, published PBPK models for mAbs are quite diverse in respect to the physiology of distribution spaces and the parameterization of the non-specific elimination involving the neonatal Fc receptor (FcRn) and endogenous IgG (IgGendo). The remarkable discrepancy between the simplicity of biodistribution data and the complexity of published PBPK models translates in parameter identifiability issues. In this thesis, we address this problem with a simplified PBPK model—derived from a hierarchy of more detailed PBPK models and based on simplifications of tissue distribution model. With the novel tissue model, we are breaking new grounds in mechanistic modeling of mAbs disposition: We demonstrate that binding to FcRn is indeed linear and that it is not possible to infer which tissues are involved in the unspecific elimination of wild-type mAbs. We also provide a new approach to predict tissue partition coefficients based on mechanistic insights: We directly link tissue partition coefficients (Ktis) to data-driven and species-independent published antibody biodistribution coefficients (ABCtis) and thus, we ensure the extrapolation from pre-clinical species to human with the simplified PBPK model. We further extend the simplified PBPK model to account for a target, relevant to characterize the non-linear clearance due to mAb-target interaction. With model reduction techniques, we reduce the dimensionality of the simplified PBPK model to design 2-compartment models, thus guiding classical model development with physiological and mechanistic interpretation of the PK parameters. We finally derive a new scaling approach for anatomical and physiological parameters in PBPK models that translates the inter-individual variability into the design of mechanistic covariate models with direct link to classical compartment models, specially useful for PK population analysis during clinical development.}, language = {en} } @phdthesis{Schmitt2014, author = {Schmitt, Clemens Nikolaus Zeno}, title = {The role of protein metal complexes in the mechanics of Mytilus californianus byssal threads}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-74216}, school = {Universit{\"a}t Potsdam}, pages = {VIII, 93}, year = {2014}, abstract = {Protein-metal coordination complexes are well known as active centers in enzymatic catalysis, and to contribute to signal transduction, gas transport, and to hormone function. Additionally, they are now known to contribute as load-bearing cross-links to the mechanical properties of several biological materials, including the jaws of Nereis worms and the byssal threads of marine mussels. The primary aim of this thesis work is to better understand the role of protein-metal cross-links in the mechanical properties of biological materials, using the mussel byssus as a model system. Specifically, the focus is on histidine-metal cross-links as sacrificial bonds in the fibrous core of the byssal thread (Chapter 4) and L-3,4-dihydroxyphenylalanine (DOPA)-metal bonds in the protective thread cuticle (Chapter 5). Byssal threads are protein fibers, which mussels use to attach to various substrates at the seashore. These relatively stiff fibers have the ability to extend up to about 100 \% strain, dissipating large amounts of mechanical energy from crashing waves, for example. Remarkably, following damage from cyclic loading, initial mechanical properties are subsequently recovered by a material-intrinsic self-healing capability. Histidine residues coordinated to transition metal ions in the proteins comprising the fibrous thread core have been suggested as reversible sacrificial bonds that contribute to self-healing; however, this remains to be substantiated in situ. In the first part of this thesis, the role of metal coordination bonds in the thread core was investigated using several spectroscopic methods. In particular, X-ray absorption spectroscopy (XAS) was applied to probe the coordination environment of zinc in Mytilus californianus threads at various stages during stretching and subsequent healing. Analysis of the extended X-ray absorption fine structure (EXAFS) suggests that tensile deformation of threads is correlated with the rupture of Zn-coordination bonds and that self-healing is connected with the reorganization of Zn-coordination bond topologies rather than the mere reformation of Zn-coordination bonds. These findings have interesting implications for the design of self-healing metallopolymers. The byssus cuticle is a protective coating surrounding the fibrous thread core that is both as hard as an epoxy and extensible up to 100 \% strain before cracking. It was shown previously that cuticle stiffness and hardness largely depend on the presence of Fe-DOPA coordination bonds. However, the byssus is known to concentrate a large variety of metals from seawater, some of which are also capable of binding DOPA (e.g. V). Therefore, the question arises whether natural variation of metal composition can affect the mechanical performance of the byssal thread cuticle. To investigate this hypothesis, nanoindentation and confocal Raman spectroscopy were applied to the cuticle of native threads, threads with metals removed (EDTA treated), and threads in which the metal ions in the native tissue were replaced by either Fe or V. Interestingly, replacement of metal ions with either Fe or V leads to the full recovery of native mechanical properties with no statistical difference between each other or the native properties. This likely indicates that a fixed number of metal coordination sites are maintained within the byssal thread cuticle - possibly achieved during thread formation - which may provide an evolutionarily relevant mechanism for maintaining reliable mechanics in an unpredictable environment. While the dynamic exchange of bonds plays a vital role in the mechanical behavior and self-healing in the thread core by allowing them to act as reversible sacrificial bonds, the compatibility of DOPA with other metals allows an inherent adaptability of the thread cuticle to changing circumstances. The requirements to both of these materials can be met by the dynamic nature of the protein-metal cross-links, whereas covalent cross-linking would fail to provide the adaptability of the cuticle and the self-healing of the core. In summary, these studies of the thread core and the thread cuticle serve to underline the important and dynamic roles of protein-metal coordination in the mechanical function of load-bearing protein fibers, such as the mussel byssus.}, language = {en} } @phdthesis{Reiter2014, author = {Reiter, Karsten}, title = {Crustal stress variability across spatial scales - examples from Canada, Northern Switzerland and a South African gold mine}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76762}, school = {Universit{\"a}t Potsdam}, pages = {VIII, 149, XI}, year = {2014}, abstract = {The quantitative descriptions of the state of stress in the Earth's crust, and spatial-temporal stress changes are of great importance in terms of scientific questions as well as applied geotechnical issues. Human activities in the underground (boreholes, tunnels, caverns, reservoir management, etc.) have a large impact on the stress state. It is important to assess, whether these activities may lead to (unpredictable) hazards, such as induced seismicity. Equally important is the understanding of the in situ stress state in the Earth's crust, as it allows the determination of safe well paths, already during well planning. The same goes for the optimal configuration of the injection- and production wells, where stimulation for artificial fluid path ways is necessary. The here presented cumulative dissertation consists of four separate manuscripts, which are already published, submitted or will be submitted for peer review within the next weeks. The main focus is on the investigation of the possible usage of geothermal energy in the province Alberta (Canada). A 3-D geomechanical-numerical model was designed to quantify the contemporary 3-D stress tensor in the upper crust. For the calibration of the regional model, 321 stress orientation data and 2714 stress magnitude data were collected, whereby the size and diversity of the database is unique. A calibration scheme was developed, where the model is calibrated versus the in situ stress data stepwise for each data type and gradually optimized using statistically test methods. The optimum displacement on the model boundaries can be determined by bivariate linear regression, based on only three model runs with varying deformation ratio. The best-fit model is able to predict most of the in situ stress data quite well. Thus, the model can provide the full stress tensor along any chosen virtual well paths. This can be used to optimize the orientation of horizontal wells, which e.g. can be used for reservoir stimulation. The model confirms regional deviations from the average stress orientation trend, such as in the region of the Peace River Arch and the Bow Island Arch. In the context of data compilation for the Alberta stress model, the Canadian database of the World Stress Map (WSM) could be expanded by including 514 new data records. This publication of an update of the Canadian stress map after ~20 years with a specific focus on Alberta shows, that the maximum horizontal stress (SHmax) is oriented southwest to northeast over large areas in Northern America. The SHmax orientation in Alberta is very homogeneous, with an average of about 47°. In order to calculate the average SHmax orientation on a regular grid as well as to estimate the wave-length of stress orientation, an existing algorithm has been improved and is applied to the Canadian data. The newly introduced quasi interquartile range on the circle (QIROC) improves the variance estimation of periodic data, as it is less susceptible to its outliers. Another geomechanical-numerical model was built to estimate the 3D stress tensor in the target area "N{\"o}rdlich L{\"a}gern" in Northern Switzerland. This location, with Opalinus clay as a host rock, is a potential repository site for high-level radioactive waste. The performed modelling aims to investigate the sensitivity of the stress tensor on tectonic shortening, topography, faults and variable rock properties within the Mesozoic sedimentary stack, according to the required stability needed for a suitable radioactive waste disposal site. The majority of the tectonic stresses caused by the far-field shortening from the South are admitted by the competent rock units in the footwall and hanging wall of the argillaceous target horizon, the Upper Malm and Upper Muschelkalk. Thus, the differential stress within the host rock remains relatively low. East-west striking faults release stresses driven by tectonic shortening. The purely gravitational influence by the topography is low; higher SHmax magnitudes below topographical depression and lower values below hills are mainly observed near the surface. A complete calibration of the model is not possible, as no stress magnitude data are available for calibration, yet. The collection of this data will begin in 2015; subsequently they will be used to adjust the geomechanical-numerical model again. The third geomechanical-numerical model investigates the stress variation in an ultra-deep gold mine in South Africa. This reservoir model is spatially one order of magnitude smaller than the previous local model from Northern Switzerland. Here, the primary focus is to investigate the hypothesis that the Mw 1.9 earthquake on 27 December 2007 was induced by stress changes due to the mining process. The Coulomb failure stress change (DeltaCFS) was used to analyse the stress change. It confirmed that the seismic event was induced by static stress transfer due to the mining progress. The rock was brought closer to failure on the derived rupture plane by stress changes of up to 1.5-15MPa, in dependence of the DeltaCFS analysis type. A forward modelling of a generic excavation scheme reveals that with decreasing distance to the dyke the DeltaCFS values increase significantly. Hence, even small changes in the mining progress can have a significant impact on the seismic hazard risk, i.e. the change of the occurrence probability to induce a seismic event of economic concern.}, language = {en} } @phdthesis{Hutter2014, author = {Hutter, Anne}, title = {Unveiling the epoch of reionization by simulations and high-redshift galaxies}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76998}, school = {Universit{\"a}t Potsdam}, pages = {vi, 155}, year = {2014}, abstract = {The Epoch of Reionization marks after recombination the second major change in the ionization state of the universe, going from a neutral to an ionized state. It starts with the appearance of the first stars and galaxies; a fraction of high-energy photons emitted from galaxies permeate into the intergalactic medium (IGM) and gradually ionize the hydrogen, until the IGM is completely ionized at z~6 (Fan et al., 2006). While the progress of reionization is driven by galaxy evolution, it changes the ionization and thermal state of the IGM substantially and affects subsequent structure and galaxy formation by various feedback mechanisms. Understanding this interaction between reionization and galaxy formation is further impeded by a lack of understanding of the high-redshift galactic properties such as the dust distribution and the escape fraction of ionizing photons. Lyman Alpha Emitters (LAEs) represent a sample of high-redshift galaxies that are sensitive to all these galactic properties and the effects of reionization. In this thesis we aim to understand the progress of reionization by performing cosmological simulations, which allows us to investigate the limits of constraining reionization by high-redshift galaxies as LAEs, and examine how galactic properties and the ionization state of the IGM affect the visibility and observed quantities of LAEs and Lyman Break galaxies (LBGs). In the first part of this thesis we focus on performing radiative transfer calculations to simulate reionization. We have developed a mapping-sphere-scheme, which, starting from spherically averaged temperature and density fields, uses our 1D radiative transfer code and computes the effect of each source on the IGM temperature and ionization (HII, HeII, HeIII) profiles, which are subsequently mapped onto a grid. Furthermore we have updated the 3D Monte-Carlo radiative transfer pCRASH, enabling detailed reionization simulations which take individual source characteristics into account. In the second part of this thesis we perform a reionization simulation by post-processing a smoothed-particle hydrodynamical (SPH) simulation (GADGET-2) with 3D radiative transfer (pCRASH), where the ionizing sources are modelled according to the characteristics of the stellar populations in the hydrodynamical simulation. Following the ionization fractions of hydrogen (HI) and helium (HeII, HeIII), and temperature in our simulation, we find that reionization starts at z~11 and ends at z~6, and high density regions near sources are ionized earlier than low density regions far from sources. In the third part of this thesis we couple the cosmological SPH simulation and the radiative transfer simulations with a physically motivated, self-consistent model for LAEs, in order to understand the importance of the ionization state of the IGM, the escape fraction of ionizing photons from galaxies and dust in the interstellar medium (ISM) on the visibility of LAEs. Comparison of our models results with the LAE Lyman Alpha (Lya) and UV luminosity functions at z~6.6 reveals a three-dimensional degeneracy between the ionization state of the IGM, the ionizing photons escape fraction and the ISM dust distribution, which implies that LAEs act not only as tracers of reionization but also of the ionizing photon escape fraction and of the ISM dust distribution. This degeneracy does not even break down when we compare simulated with observed clustering of LAEs at z~6.6. However, our results show that reionization has the largest impact on the amplitude of the LAE angular correlation functions, and its imprints are clearly distinguishable from those of properties on galactic scales. These results show that reionization cannot be constrained tightly by exclusively using LAE observations. Further observational constraints, e.g. tomographies of the redshifted hydrogen 21cm line, are required. In addition we also use our LAE model to probe the question when a galaxy is visible as a LAE or a LBG. Within our model galaxies above a critical stellar mass can produce enough luminosity to be visible as a LBG and/or a LAE. By finding an increasing duty cycle of LBGs with Lya emission as the UV magnitude or stellar mass of the galaxy rises, our model reveals that the brightest (and most massive) LBGs most often show Lya emission. Predicting the Lya equivalent width (Lya EW) distribution and the fraction of LBGs showing Lya emission at z~6.6, we reproduce the observational trend of the Lya EWs with UV magnitude. However, the Lya EWs of the UV brightest LBGs exceed observations and can only be reconciled by accounting for an increased Lya attenuation of massive galaxies, which implies that the observed Lya brightest LAEs do not necessarily coincide with the UV brightest galaxies. We have analysed the dependencies of LAE observables on the properties of the galactic and intergalactic medium and the LAE-LBG connection, and this enhances our understanding of the nature of LAEs.}, language = {en} } @phdthesis{Sen2014, author = {Sen, Ali Tolga}, title = {Inversion of seismic source parameters for weak mining-induced and natural earthquakes}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-71914}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {The purpose of this thesis is to develop an automated inversion scheme to derive point and finite source parameters for weak earthquakes, here intended with the unusual meaning of earthquakes with magnitudes at the limit or below the bottom magnitude threshold of standard source inversion routines. The adopted inversion approaches entirely rely on existing inversion software, the methodological work mostly targeting the development and tuning of optimized inversion flows. The resulting inversion scheme is tested for very different datasets, and thus allows the discussion on the source inversion problem at different scales. In the first application, dealing with mining induced seismicity, the source parameters determination is addressed at a local scale, with source-sensor distance of less than 3 km. In this context, weak seismicity corresponds to event below magnitude MW 2.0, which are rarely target of automated source inversion routines. The second application considers a regional dataset, namely the aftershock sequence of the 2010 Maule earthquake (Chile), using broadband stations at regional distances, below 300 km. In this case, the magnitude range of the target aftershocks range down to MW 4.0. This dataset is here considered as a weak seismicity case, since the analysis of such moderate seismicity is generally investigated only by moment tensor inversion routines, with no attempt to resolve source duration or finite source parameters. In this work, automated multi-step inversion schemes are applied to both datasets with the aim of resolving point source parameters, both using double couple (DC) and full moment tensor (MT) models, source duration and finite source parameters. A major result of the analysis of weaker events is the increased size of resulting moment tensor catalogues, which interpretation may become not trivial. For this reason, a novel focal mechanism clustering approach is used to automatically classify focal mechanisms, allowing the investigation of the most relevant and repetitive rupture features. The inversion of the mining induced seismicity dataset reveals the repetitive occurrence of similar rupture processes, where the source geometry is controlled by the shape of the mined panel. Moreover, moment tensor solutions indicate a significant contribution of tensile processes. Also the second application highlights some characteristic geometrical features of the fault planes, which show a general consistency with the orientation of the slab. The additional inversion for source duration allowed to verify the empirical correlation for moment normalized earthquakes in subduction zones among a decreasing rupture duration with increasing source depth, which was so far only observed for larger events.}, language = {en} } @phdthesis{Jueppner2014, author = {J{\"u}ppner, Jessica}, title = {Characterization of metabolomic dynamics in synchronized Chlamydomonas reinhardtii cell cultures and the impact of TOR inhibition on cell cycle, proliferation and growth}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76923}, school = {Universit{\"a}t Potsdam}, pages = {VI, 153}, year = {2014}, abstract = {The adaptation of cell growth and proliferation to environmental changes is essential for the surviving of biological systems. The evolutionary conserved Ser/Thr protein kinase "Target of Rapamycin" (TOR) has emerged as a major signaling node that integrates the sensing of numerous growth signals to the coordinated regulation of cellular metabolism and growth. Although the TOR signaling pathway has been widely studied in heterotrophic organisms, the research on TOR in photosynthetic eukaryotes has been hampered by the reported land plant resistance to rapamycin. Thus, the finding that Chlamydomonas reinhardtii is sensitive to rapamycin, establish this unicellular green alga as a useful model system to investigate TOR signaling in photosynthetic eukaryotes. The observation that rapamycin does not fully arrest Chlamydomonas growth, which is different from observations made in other organisms, prompted us to investigate the regulatory function of TOR in Chlamydomonas in context of the cell cycle. Therefore, a growth system that allowed synchronously growth under widely unperturbed cultivation in a fermenter system was set up and the synchronized cells were characterized in detail. In a highly resolved kinetic study, the synchronized cells were analyzed for their changes in cytological parameters as cell number and size distribution and their starch content. Furthermore, we applied mass spectrometric analysis for profiling of primary and lipid metabolism. This system was then used to analyze the response dynamics of the Chlamydomonas metabolome and lipidome to TOR-inhibition by rapamycin The results show that TOR inhibition reduces cell growth, delays cell division and daughter cell release and results in a 50\% reduced cell number at the end of the cell cycle. Consistent with the growth phenotype we observed strong changes in carbon and nitrogen partitioning in the direction of rapid conversion into carbon and nitrogen storage through an accumulation of starch, triacylglycerol and arginine. Interestingly, it seems that the conversion of carbon into triacylglycerol occurred faster than into starch after TOR inhibition, which may indicate a more dominant role of TOR in the regulation of TAG biosynthesis than in the regulation of starch. This study clearly shows, for the first time, a complex picture of metabolic and lipidomic dynamically changes during the cell cycle of Chlamydomonas reinhardtii and furthermore reveals a complex regulation and adjustment of metabolite pools and lipid composition in response to TOR inhibition.}, language = {en} } @phdthesis{Meissner2014, author = {Meissner, Sven}, title = {Implications of Microcystin Production in Microcystis aeruginosa PCC 7806}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-75199}, school = {Universit{\"a}t Potsdam}, pages = {VII, 141}, year = {2014}, abstract = {Cyanobacteria produce about 40 percent of the world's primary biomass, but also a variety of often toxic peptides such as microcystin. Mass developments, so called blooms, can pose a real threat to the drinking water supply in many parts of the world. This study aimed at characterizing the biological function of microcystin production in one of the most common bloom-forming cyanobacterium Microcystis aeruginosa. In a first attempt, the effect of elevated light intensity on microcystin production and its binding to cellular proteins was studied. Therefore, conventional microcystin quantification techniques were combined with protein-biochemical methods. RubisCO, the key enzyme for primary carbon fixation was a major microcystin interaction partner. High light exposition strongly stimulated microcystin-protein interactions. Up to 60 percent of the total cellular microcystin was detected bound to proteins, i.e. inaccessible for standard quantification procedures. Underestimation of total microcystin contents when neglecting the protein fraction was also demonstrated in field samples. Finally, an immuno-fluorescence based method was developed to identify microcystin producing cyanobacteria in mixed populations. The high light induced microcystin interaction with proteins suggested an impact of the secondary metabolite on the primary metabolism of Microcystis by e.g. modulating the activity of enzymes. For addressing that question, a comprehensive GC/MS-based approach was conducted to compare the accumulation of metabolites in the wild-type of Microcystis aeruginosa PCC 7806 and the microcystin deficient ΔmcyB mutant. From all 501 detected non-redundant metabolites 85 (17 percent) accumulated significantly different in either of both genotypes upon high light exposition. Accumulation of compatible solutes in the ΔmcyB mutant suggests a role of microcystin in fine-tuning the metabolic flow to prevent stress related to excess light, high oxygen concentration and carbon limitation. Co-analysis of the widely used model cyanobacterium Synechocystis PCC 6803 revealed profound metabolic differences between species of cyanobacteria. Whereas Microcystis channeled more resources towards carbohydrate synthesis, Synechocystis invested more in amino acids. These findings were supported by electron microscopy of high light treated cells and the quantification of storage compounds. While Microcystis accumulated mainly glycogen to about 8.5 percent of its fresh weight within three hours, Synechocystis produced higher amounts of cyanophycin. The results showed that the characterization of species-specific metabolic features should gain more attention with regard to the biotechnological use of cyanobacteria.}, language = {en} } @phdthesis{Schmidt2014, author = {Schmidt, Lukas}, title = {Aerosols and boundary layer structure over Arctic sea ice based on airborne lidar and dropsonde measurements}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-75076}, school = {Universit{\"a}t Potsdam}, pages = {vii, 98, xiii}, year = {2014}, abstract = {The atmosphere over the Arctic Ocean is strongly influenced by the distribution of sea ice and open water. Leads in the sea ice produce strong convective fluxes of sensible and latent heat and release aerosol particles into the atmosphere. They increase the occurrence of clouds and modify the structure and characteristics of the atmospheric boundary layer (ABL) and thereby influence the Arctic climate. In the course of this study aircraft measurements were performed over the western Arctic Ocean as part of the campaign PAMARCMIP 2012 of the Alfred Wegener Institute for Polar and Marine Research (AWI). Backscatter from aerosols and clouds within the lower troposphere and the ABL were measured with the nadir pointing Airborne Mobile Aerosol Lidar (AMALi) and dropsondes were launched to obtain profiles of meteorological variables. Furthermore, in situ measurements of aerosol properties, meteorological variables and turbulence were part of the campaign. The measurements covered a broad range of atmospheric and sea ice conditions. In this thesis, properties of the ABL over Arctic sea ice with a focus on the influence of open leads are studied based on the data from the PAMARCMIP campaign. The height of the ABL is determined by different methods that are applied to dropsonde and AMALi backscatter profiles. ABL heights are compared for different flights representing different conditions of the atmosphere and of sea ice and open water influence. The different criteria for ABL height that are applied show large variation in terms of agreement among each other, depending on the characteristics of the ABL and its history. It is shown that ABL height determination from lidar backscatter by methods commonly used under mid-latitude conditions is applicable to the Arctic ABL only under certain conditions. Aerosol or clouds within the ABL are needed as a tracer for ABL height detection from backscatter. Hence an aerosol source close to the surface is necessary, that is typically found under the present influence of open water and therefore convective conditions. However it is not always possible to distinguish residual layers from the actual ABL. Stable boundary layers are generally difficult to detect. To illustrate the complexity of the Arctic ABL and processes therein, four case studies are analyzed each of which represents a snapshot of the interplay between atmosphere and underlying sea ice or water surface. Influences of leads and open water on the aerosol and clouds within the ABL are identified and discussed. Leads are observed to cause the formation of fog and cloud layers within the ABL by humidity emission. Furthermore they decrease the stability and increase the height of the ABL and consequently facilitate entrainment of air and aerosol layers from the free troposphere.}, language = {en} } @phdthesis{Sarkar2014, author = {Sarkar, Saswati}, title = {Holocene variations in the strength of the Indian Monsoon system}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-74905}, school = {Universit{\"a}t Potsdam}, pages = {ix, 114}, year = {2014}, abstract = {The monsoon is an important component of the Earth's climate system. It played a vital role in the development and sustenance of the largely agro-based economy in India. A better understanding of past variations in the Indian Summer Monsoon (ISM) is necessary to assess its nature under global warming scenarios. Instead, our knowledge of spatiotemporal patterns of past ISM strength, as inferred from proxy records, is limited due to the lack of high-resolution paleo-hydrological records from the core monsoon domain. In this thesis I aim to improve our understanding of Holocene ISM variability from the core 'monsoon zone' (CMZ) in India. To achieve this goal, I tried to understand modern and thereafter reconstruct Holocene monsoonal hydrology, by studying surface sediments and a high-resolution sedimentary record from the saline-alkaline Lonar crater lake, central India. My approach relies on analyzing stable carbon and hydrogen isotope ratios from sedimentary lipid biomarkers to track past hydrological changes. In order to evaluate the relationship of the modern ecosystem and hydrology of the lake I studied the distribution of lipid biomarkers in the modern ecosystem and compared it to lake surface sediments. The major plants from dry deciduous mixed forest type produced a greater amount of leaf wax n-alkanes and a greater fraction of n-C31 and n-C33 alkanes relative to n-C27 and n-C29. Relatively high average chain length (ACL) values (29.6-32.8) for these plants seem common for vegetation from an arid and warm climate. Additionally I found that human influence and subsequent nutrient supply result in increased lake primary productivity, leading to an unusually high concentration of tetrahymanol, a biomarker for salinity and water column stratification, in the nearshore sediments. Due to this inhomogeneous deposition of tetrahymanol in modern sediments, I hypothesize that lake level fluctuation may potentially affect aquatic lipid biomarker distributions in lacustrine sediments, in addition to source changes. I reconstructed centennial-scale hydrological variability associated with changes in the intensity of the ISM based on a record of leaf wax and aquatic biomarkers and their stable carbon (δ13C) and hydrogen (δD) isotopic composition from a 10 m long sediment core from the lake. I identified three main periods of distinct hydrology over the Holocene in central India. The period between 10.1 and 6 cal. ka BP was likely the wettest during the Holocene. Lower ACL index values (29.4 to 28.6) of leaf wax n-alkanes and their negative δ13C values (-34.8 per mille to -27.8 per mille) indicated the dominance of woody C3 vegetation in the catchment, and negative δDwax (average for leaf wax n-alkanes) values (-171 per mille to -147 per mille) argue for a wet period due to an intensified monsoon. After 6 cal. ka BP, a gradual shift to less negative δ13C values (particularly for the grass derived n-C31) and appearance of the triterpene lipid tetrahymanol, generally considered as a marker for salinity and water column stratification, marked the onset of drier conditions. At 5.1 cal. ka BP increasing flux of leaf wax n-alkanes along with the highest flux of tetrahymanol indicated proximity of the lakeshore to the center due to a major lake level decrease. Rapid fluctuations in abundance of both terrestrial and aquatic biomarkers between 4.8 and 4 cal. ka BP indicated an unstable lake ecosystem, culminating in a transition to arid conditions. A pronounced shift to less negative δ13C values, in particular for n-C31 (-25.2 per mille to -22.8 per mille), over this period indicated a change of dominant vegetation to C4 grasses. Along with a 40 per mille increase in leaf wax n-alkane δD values, which likely resulted from less rainfall and/or higher plant evapotranspiration, I interpret this period to reflect the driest conditions in the region during the last 10.1 ka. This transition led to protracted late Holocene arid conditions and the establishment of a permanently saline lake. This is supported by the high abundance of tetrahymanol. A late Holocene peak of cyanobacterial biomarker input at 1.3 cal. ka BP might represent an event of lake eutrophication, possibly due to human impact and the onset of cattle/livestock farming in the catchment. The most intriguing feature of the mid-Holocene driest period was the high amplitude and rapid fluctuations in δDwax values, probably due to a change in the moisture source and/or precipitation seasonality. I hypothesize that orbital induced weakening of the summer solar insolation and associated reorganization of the general atmospheric circulation were responsible for an unstable hydroclimate in the mid-Holocene in the CMZ. My findings shed light onto the sequence of changes during mean state changes of the monsoonal system, once an insolation driven threshold has been passed, and show that small changes in solar insolation can be associated to major environmental changes and large fluctuations in moisture source, a scenario that may be relevant with respect to future changes in the ISM system.}, language = {en} } @phdthesis{Strauss2014, author = {Strauß, Jens}, title = {Organic carbon in ice-rich permafrost}, doi = {10.25932/publishup-7523}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-75236}, school = {Universit{\"a}t Potsdam}, pages = {XIII, 107, 102}, year = {2014}, abstract = {Permafrost, defined as ground that is frozen for at least two consecutive years, is a distinct feature of the terrestrial unglaciated Arctic. It covers approximately one quarter of the land area of the Northern Hemisphere (23,000,000 km²). Arctic landscapes, especially those underlain by permafrost, are threatened by climate warming and may degrade in different ways, including active layer deepening, thermal erosion, and development of rapid thaw features. In Siberian and Alaskan late Pleistocene ice-rich Yedoma permafrost, rapid and deep thaw processes (called thermokarst) can mobilize deep organic carbon (below 3 m depth) by surface subsidence due to loss of ground ice. Increased permafrost thaw could cause a feedback loop of global significance if its stored frozen organic carbon is reintroduced into the active carbon cycle as greenhouse gases, which accelerate warming and inducing more permafrost thaw and carbon release. To assess this concern, the major objective of the thesis was to enhance the understanding of the origin of Yedoma as well as to assess the associated organic carbon pool size and carbon quality (concerning degradability). The key research questions were: - How did Yedoma deposits accumulate? - How much organic carbon is stored in the Yedoma region? - What is the susceptibility of the Yedoma region's carbon for future decomposition? To address these three research questions, an interdisciplinary approach, including detailed field studies and sampling in Siberia and Alaska as well as methods of sedimentology, organic biogeochemistry, remote sensing, statistical analyses, and computational modeling were applied. To provide a panarctic context, this thesis additionally includes results both from a newly compiled northern circumpolar carbon database and from a model assessment of carbon fluxes in a warming Arctic. The Yedoma samples show a homogeneous grain-size composition. All samples were poorly sorted with a multi-modal grain-size distribution, indicating various (re-) transport processes. This contradicts the popular pure loess deposition hypothesis for the origin of Yedoma permafrost. The absence of large-scale grinding processes via glaciers and ice sheets in northeast Siberian lowlands, processes which are necessary to create loess as material source, suggests the polygenetic origin of Yedoma deposits. Based on the largest available data set of the key parameters, including organic carbon content, bulk density, ground ice content, and deposit volume (thickness and coverage) from Siberian and Alaskan study sites, this thesis further shows that deep frozen organic carbon in the Yedoma region consists of two distinct major reservoirs, Yedoma deposits and thermokarst deposits (formed in thaw-lake basins). Yedoma deposits contain ~80 Gt and thermokarst deposits ~130 Gt organic carbon, or a total of ~210 Gt. Depending on the approach used for calculating uncertainty, the range for the total Yedoma region carbon store is ±75 \% and ±20 \% for conservative single and multiple bootstrapping calculations, respectively. Despite the fact that these findings reduce the Yedoma region carbon pool by nearly a factor of two compared to previous estimates, this frozen organic carbon is still capable of inducing a permafrost carbon feedback to climate warming. The complete northern circumpolar permafrost region contains between 1100 and 1500 Gt organic carbon, of which ~60 \% is perennially frozen and decoupled from the short-term carbon cycle. When thawed and reintroduced into the active carbon cycle, the organic matter qualities become relevant. Furthermore, results from investigations into Yedoma and thermokarst organic matter quality studies showed that Yedoma and thermokarst organic matter exhibit no depth-dependent quality trend. This is evidence that after freezing, the ancient organic matter is preserved in a state of constant quality. The applied alkane and fatty-acid-based biomarker proxies including the carbon-preference and the higher-land-plant-fatty-acid indices show a broad range of organic matter quality and thus no significantly different qualities of the organic matter stored in thermokarst deposits compared to Yedoma deposits. This lack of quality differences shows that the organic matter biodegradability depends on different decomposition trajectories and the previous decomposition/incorporation history. Finally, the fate of the organic matter has been assessed by implementing deep carbon pools and thermokarst processes in a permafrost carbon model. Under various warming scenarios for the northern circumpolar permafrost region, model results show a carbon release from permafrost regions of up to ~140 Gt and ~310 Gt by the years 2100 and 2300, respectively. The additional warming caused by the carbon release from newly-thawed permafrost contributes 0.03 to 0.14°C by the year 2100. The model simulations predict that a further increase by the 23rd century will add 0.4°C to global mean surface air temperatures. In conclusion, Yedoma deposit formation during the late Pleistocene was dominated by water-related (alluvial/fluvial/lacustrine) as well as aeolian processes under periglacial conditions. The circumarctic permafrost region, including the Yedoma region, contains a substantial amount of currently frozen organic carbon. The carbon of the Yedoma region is well-preserved and therefore available for decomposition after thaw. A missing quality-depth trend shows that permafrost preserves the quality of ancient organic matter. When the organic matter is mobilized by deep degradation processes, the northern permafrost region may add up to 0.4°C to the global warming by the year 2300.}, language = {en} } @phdthesis{Goldshteyn2014, author = {Goldshteyn, Jewgenij}, title = {Frequency-resolved ultrafast dynamics of phonon polariton wavepackets in the ferroelectric crystals LiNbO₃ and LiTaO₃}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-71623}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {During this work I built a four wave mixing setup for the time-resolved femtosecond spectroscopy of Raman-active lattice modes. This setup enables to study the selective excitation of phonon polaritons. These quasi-particles arise from the coupling of electro-magnetic waves and transverse optical lattice modes, the so-called phonons. The phonon polaritons were investigated in the optically non-linear, ferroelectric crystals LiNbO₃ and LiTaO₃. The direct observation of the frequency shift of the scattered narrow bandwidth probe pulses proofs the role of the Raman interaction during the probe and excitation process of phonon polaritons. I compare this experimental method with the measurement where ultra-short laser pulses are used. The frequency shift remains obscured by the relative broad bandwidth of these laser pulses. In an experiment with narrow bandwidth probe pulses, the Stokes and anti-Stokes intensities are spectrally separated. They are assigned to the corresponding counter-propagating wavepackets of phonon polaritons. Thus, the dynamics of these wavepackets was separately studied. Based on these findings, I develop the mathematical description of the so-called homodyne detection of light for the case of light scattering from counter propagating phonon polaritons. Further, I modified the broad bandwidth of the ultra-short pump pulses using bandpass filters to generate two pump pulses with non-overlapping spectra. This enables the frequency-selective excitation of polariton modes in the sample, which allows me to observe even very weak polariton modes in LiNbO₃ or LiTaO₃ that belong to the higher branches of the dispersion relation of phonon polaritons. The experimentally determined dispersion relation of the phonon polaritons could therefore be extended and compared to theoretical models. In addition, I determined the frequency-dependent damping of phonon polaritons.}, language = {en} } @phdthesis{Mallonn2014, author = {Mallonn, Matthias}, title = {Ground-based transmission spectroscopy of three inflated Hot Jupiter exoplanets}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-74403}, school = {Universit{\"a}t Potsdam}, pages = {ix, 115}, year = {2014}, abstract = {The characterization of exoplanets is a young and rapidly expanding field in astronomy. It includes a method called transmission spectroscopy that searches for planetary spectral fingerprints in the light received from the host star during the event of a transit. This techniques allows for conclusions on the atmospheric composition at the terminator region, the boundary between the day and night side of the planet. Observationally a big challenge, first attempts in the community have been successful in the detection of several absorption features in the optical wavelength range. These are for example a Rayleighscattering slope and absorption by sodium and potassium. However, other objects show a featureless spectrum indicative for a cloud or haze layer of condensates masking the probable atmospheric layers. In this work, we performed transmission spectroscopy by spectrophotometry of three Hot Jupiter exoplanets. When we began the work on this thesis, optical transmission spectra have been available for two exoplanets. Our main goal was to advance the current sample of probed objects to learn by comparative exoplanetology whether certain absorption features are common. We selected the targets HAT-P-12b, HAT-P-19b and HAT-P-32b, for which the detection of atmospheric signatures is feasible with current ground-based instrumentation. In addition, we monitored the host stars of all three objects photometrically to correct for influences of stellar activity if necessary. The obtained measurements of the three objects all favor featureless spectra. A variety of atmospheric compositions can explain the lack of a wavelength dependent absorption. But the broad trend of featureless spectra in planets of a wide range of temperatures, found in this work and in similar studies recently published in the literature, favors an explanation based on the presence of condensates even at very low concentrations in the atmospheres of these close-in gas giants. This result points towards the general conclusion that the capability of transmission spectroscopy to determine the atmospheric composition is limited, at least for measurements at low spectral resolution. In addition, we refined the transit parameters and ephemerides of HAT-P-12b and HATP- 19b. Our monitoring campaigns allowed for the detection of the stellar rotation period of HAT-P-19 and a refined age estimate. For HAT-P-12 and HAT-P-32, we derived upper limits on their potential variability. The calculated upper limits of systematic effects of starspots on the derived transmission spectra were found to be negligible for all three targets. Finally, we discussed the observational challenges in the characterization of exoplanet atmospheres, the importance of correlated noise in the measurements and formulated suggestions on how to improve on the robustness of results in future work.}, language = {en} } @phdthesis{Yeldesbay2014, author = {Yeldesbay, Azamat}, title = {Complex regimes of synchronization}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-73348}, school = {Universit{\"a}t Potsdam}, pages = {ii, 60}, year = {2014}, abstract = {Synchronization is a fundamental phenomenon in nature. It can be considered as a general property of self-sustained oscillators to adjust their rhythm in the presence of an interaction. In this work we investigate complex regimes of synchronization phenomena by means of theoretical analysis, numerical modeling, as well as practical analysis of experimental data. As a subject of our investigation we consider chimera state, where due to spontaneous symmetry-breaking of an initially homogeneous oscillators lattice split the system into two parts with different dynamics. Chimera state as a new synchronization phenomenon was first found in non-locally coupled oscillators system, and has attracted a lot of attention in the last decade. However, the recent studies indicate that this state is also possible in globally coupled systems. In the first part of this work, we show under which conditions the chimera-like state appears in a system of globally coupled identical oscillators with intrinsic delayed feedback. The results of the research explain how initially monostable oscillators became effectivly bistable in the presence of the coupling and create a mean field that sustain the coexistence of synchronized and desynchronized states. Also we discuss other examples, where chimera-like state appears due to frequency dependence of the phase shift in the bistable system. In the second part, we make further investigation of this topic by modeling influence of an external periodic force to an oscillator with intrinsic delayed feedback. We made stability analysis of the synchronized state and constructed Arnold tongues. The results explain formation of the chimera-like state and hysteric behavior of the synchronization area. Also, we consider two sets of parameters of the oscillator with symmetric and asymmetric Arnold tongues, that correspond to mono- and bi-stable regimes of the oscillator. In the third part, we demonstrate the results of the work, which was done in collaboration with our colleagues from Psychology Department of University of Potsdam. The project aimed to study the effect of the cardiac rhythm on human perception of time using synchronization analysis. From our part, we made a statistical analysis of the data obtained from the conducted experiment on free time interval reproduction task. We examined how ones heartbeat influences the time perception and searched for possible phase synchronization between heartbeat cycles and time reproduction responses. The findings support the prediction that cardiac cycles can serve as input signals, and is used for reproduction of time intervals in the range of several seconds.}, language = {en} } @phdthesis{Feld2014, author = {Feld, Christian}, title = {Crustal structure of the Eratosthenes Seamount, Cyprus and S. Turkey from an amphibian wide-angle seismic profile}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-73479}, school = {Universit{\"a}t Potsdam}, pages = {xi, 131}, year = {2014}, abstract = {In March 2010, the project CoCoCo (incipient COntinent-COntinent COllision) recorded a 650 km long amphibian N-S wide-angle seismic profile, extending from the Eratosthenes Seamount (ESM) across Cyprus and southern Turkey to the Anatolian plateau. The aim of the project is to reveal the impact of the transition from subduction to continent-continent collision of the African plate with the Cyprus-Anatolian plate. A visual quality check, frequency analysis and filtering were applied to the seismic data and reveal a good data quality. Subsequent first break picking, finite-differences ray tracing and inversion of the offshore wide-angle data leads to a first-arrival tomographic model. This model reveals (1) P-wave velocities lower than 6.5 km/s in the crust, (2) a variable crustal thickness of about 28 - 37 km and (3) an upper crustal reflection at 5 km depth beneath the ESM. Two land shots on Turkey, also recorded on Cyprus, airgun shots south of Cyprus and geological and previous seismic investigations provide the information to derive a layered velocity model beneath the Anatolian plateau and for the ophiolite complex on Cyprus. The analysis of the reflections provides evidence for a north-dipping plate subducting beneath Cyprus. The main features of this layered velocity model are (1) an upper and lower crust with large lateral changes of the velocity structure and thickness, (2) a Moho depth of about 38 - 45 km beneath the Anatolian plateau, (3) a shallow north-dipping subducting plate below Cyprus with an increasing dip and (4) a typical ophiolite sequence on Cyprus with a total thickness of about 12 km. The offshore-onshore seismic data complete and improve the information about the velocity structure beneath Cyprus and the deeper part of the offshore tomographic model. Thus, the wide-angle seismic data provide detailed insights into the 2-D geometry and velocity structures of the uplifted and overriding Cyprus-Anatolian plate. Subsequent gravity modelling confirms and extends the crustal P-wave velocity model. The deeper part of the subducting plate is constrained by the gravity data and has a dip angle of ~ 28°. Finally, an integrated analysis of the geophysical and geological information allows a comprehensive interpretation of the crustal structure related to the collision process.}, language = {en} } @phdthesis{Schulz2014, author = {Schulz, Anneli}, title = {Search for gamma-ray emission from bow shocks of runaway stars}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-73905}, school = {Universit{\"a}t Potsdam}, pages = {123}, year = {2014}, abstract = {The mystery of the origin of cosmic rays has been tackled for more than hundred years and is still not solved. Cosmic rays are detected with energies spanning more than 10 orders of magnitude and reaching energies up to ~10²¹ eV, far higher than any man-made accelerator can reach. Different theories on the astrophysical objects and processes creating such highly energetic particles have been proposed. A very prominent explanation for a process producing highly energetic particles is shock acceleration. The observation of high-energy gamma rays from supernova remnants, some of them revealing a shell like structure, is clear evidence that particles are accelerated to ultrarelativistic energies in the shocks of these objects. The environments of supernova remnants are complex and challenge detailed modelling of the processes leading to high-energy gamma-ray emission. The study of shock acceleration at bow shocks, created by the supersonic movement of individual stars through the interstellar medium, offers a unique possibility to determine the physical properties of shocks in a less complex environment. The shocked medium is heated by the stellar and the shock excited radiation, leading to thermal infrared emission. 28 bow shocks have been discovered through their infrared emission. Nonthermal radiation in radio and X-ray wavelengths has been detected from two bow shocks, pointing to the existence of relativistic particles in these systems. Theoretical models of the emission processes predict high-energy and very high-energy emission at a flux level in reach of current instruments. This work presents the search for gamma-ray emission from bow shocks of runaway stars in the energy regime from 100MeV to ~100TeV. The search is performed with the large area telescope (LAT) on-board the Fermi satellite and the H.E.S.S. telescopes located in the Khomas Highland in Namibia. The Fermi-LAT was launched in 2008 and is continuously scanning the sky since then. It detects photons with energies from 20MeV to over 300 GeV and has an unprecedented sensitivity. The all-sky coverage allows us to study all 28 bow shocks of runaway stars listed in the E-BOSS catalogue of infrared bow shocks. No significant emission was detected from any of the objects, although predicted by several theoretical models describing the non-thermal emission of bow shocks of runaway stars. The H.E.S.S. experiment is the most sensitive system of imaging atmospheric Cherenkov telescopes. It detects photons from several tens of GeV to ~100TeV. Seven of the bow shocks have been observed with H.E.S.S. and the data analysis is presented in this thesis. The analyses of the very-high energy data did not reveal significant emission from any of the sources either. This work presents the first systematic search for gamma-ray emission from bow shocks of runaway stars. For the first time Fermi-LAT data was specifically analysed to reveal emission from bow shocks of runaway stars. In the TeV regime no searches for emission from theses objects have been published so far, the study presented here is the first in this energy regime. The level of the gamma-ray emission from bow shocks of runaway stars is constrained by the calculated upper limits over six orders in magnitude in energy. The upper limits calculated for the bow shocks of runaway stars in the course of this work, constrain several models. For the best candidate, ζ Ophiuchi, the upper limits in the Fermi-LAT energy range are lower than the predictions by a factor ~5. This challenges the assumptions made in this model and gives valuable input for further modelling approaches. The analyses were performed with the software packages provided by the H.E.S.S. and Fermi collaborations. The development of a unified analysis framework for gamma-ray data, namely GammaLib/ctools, is rapidly progressing within the CTA consortium. Recent implementations and cross-checks with current software frameworks are presented in the Appendix.}, language = {en} } @phdthesis{Lindauer2014, author = {Lindauer, T. Marius}, title = {Algorithm selection, scheduling and configuration of Boolean constraint solvers}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-71260}, school = {Universit{\"a}t Potsdam}, pages = {ii, 130}, year = {2014}, abstract = {Boolean constraint solving technology has made tremendous progress over the last decade, leading to industrial-strength solvers, for example, in the areas of answer set programming (ASP), the constraint satisfaction problem (CSP), propositional satisfiability (SAT) and satisfiability of quantified Boolean formulas (QBF). However, in all these areas, there exist multiple solving strategies that work well on different applications; no strategy dominates all other strategies. Therefore, no individual solver shows robust state-of-the-art performance in all kinds of applications. Additionally, the question arises how to choose a well-performing solving strategy for a given application; this is a challenging question even for solver and domain experts. One way to address this issue is the use of portfolio solvers, that is, a set of different solvers or solver configurations. We present three new automatic portfolio methods: (i) automatic construction of parallel portfolio solvers (ACPP) via algorithm configuration,(ii) solving the \$NP\$-hard problem of finding effective algorithm schedules with Answer Set Programming (aspeed), and (iii) a flexible algorithm selection framework (claspfolio2) allowing for fair comparison of different selection approaches. All three methods show improved performance and robustness in comparison to individual solvers on heterogeneous instance sets from many different applications. Since parallel solvers are important to effectively solve hard problems on parallel computation systems (e.g., multi-core processors), we extend all three approaches to be effectively applicable in parallel settings. We conducted extensive experimental studies different instance sets from ASP, CSP, MAXSAT, Operation Research (OR), SAT and QBF that indicate an improvement in the state-of-the-art solving heterogeneous instance sets. Last but not least, from our experimental studies, we deduce practical advice regarding the question when to apply which of our methods.}, language = {en} } @phdthesis{Loersch2014, author = {Loersch, Christian}, title = {Business start-ups and the effect of coaching programs}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-72605}, school = {Universit{\"a}t Potsdam}, pages = {XII, 282}, year = {2014}, abstract = {Entrepreneurship is known to be a main driver of economic growth. Hence, governments have an interest in supporting and promoting entrepreneurial activities. Start-up subsidies, which have been analyzed extensively, only aim at mitigating the lack of financial capital. However, some entrepreneurs also lack in human, social, and managerial capital. One way to address these shortcomings is by subsidizing coaching programs for entrepreneurs. However, theoretical and empirical evidence about business coaching and programs subsidizing coaching is scarce. This dissertation gives an extensive overview of coaching and is the first empirical study for Germany analyzing the effects of coaching programs on its participants. In the theoretical part of the dissertation the process of a business start-up is described and it is discussed how and in which stage of the company's evolvement coaching can influence entrepreneurial success. The concept of coaching is compared to other non-monetary types of support as training, mentoring, consulting, and counseling. Furthermore, national and international support programs are described. Most programs have either no or small positive effects. However, there is little quantitative evidence in the international literature. In the empirical part of the dissertation the effectiveness of coaching is shown by evaluating two German coaching programs, which support entrepreneurs via publicly subsidized coaching sessions. One of the programs aims at entrepreneurs who have been employed before becoming self-employed, whereas the other program is targeted at former unemployed entrepreneurs. The analysis is based on the evaluation of a quantitative and a qualitative dataset. The qualitative data are gathered by intensive one-on-one interviews with coaches and entrepreneurs. These data give a detailed insight about the coaching topics, duration, process, effectiveness, and the thoughts of coaches and entrepreneurs. The quantitative data include information about 2,936 German-based entrepreneurs. Using propensity score matching, the success of participants of the two coaching programs is compared with adequate groups of non-participants. In contrast to many other studies also personality traits are observed and controlled for in the matching process. The results show that only the program for former unemployed entrepreneurs has small positive effects. Participants have a larger survival probability in self-employment and a larger probability to hire employees than matched non-participants. In contrast, the program for former employed individuals has negative effects. Compared to individuals who did not participate in the coaching program, participants have a lower probability to stay in self-employment, lower earned net income, lower number of employees and lower life satisfaction. There are several reasons for these differing results of the two programs. First, former unemployed individuals have more basic coaching needs than former employed individuals. Coaches can satisfy these basic coaching needs, whereas former employed individuals have more complex business problems, which are not very easy to be solved by a coaching intervention. Second, the analysis reveals that former employed individuals are very successful in general. It is easier to increase the success of former unemployed individuals as they have a lower base level of success than former employed individuals. An effect heterogeneity analysis shows that coaching effectiveness differs by region. Coaching for previously unemployed entrepreneurs is especially useful in regions with bad labor market conditions. In summary, in line with previous literature, it is found that coaching has little effects on the success of entrepreneurs. The previous employment status, the characteristics of the entrepreneur and the regional labor market conditions play a crucial role in the effectiveness of coaching. In conclusion, coaching needs to be well tailored to the individual and applied thoroughly. Therefore, governments should design and provide coaching programs only after due consideration.}, language = {en} } @phdthesis{Munack2014, author = {Munack, Henry}, title = {From phantom blocks to denudational noise}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-72629}, school = {Universit{\"a}t Potsdam}, pages = {xvii, 172}, year = {2014}, abstract = {Knowing the rates and mechanisms of geomorphic process that shape the Earth's surface is crucial to understand landscape evolution. Modern methods for estimating denudation rates enable us to quantitatively express and compare processes of landscape downwearing that can be traced through time and space—from the seemingly intact, though intensely shattered, phantom blocks of the catastrophically fragmented basal facies of giant rockslides up to denudational noise in orogen-wide data sets averaging over several millennia. This great variety of spatiotemporal scales of denudation rates is both boon and bane of geomorphic process rates. Indeed, processes of landscape downwearing can be traced far back in time, helping us to understand the Earth's evolution. Yet, this benefit may turn into a drawback due to scaling issues if these rates are to be compared across different observation timescales. This thesis investigates the mechanisms, patterns and rates of landscape downwearing across the Himalaya-Tibet orogen. Accounting for the spatiotemporal variability of denudation processes, this thesis addresses landscape downwearing on three distinctly different spatial scales, starting off at the local scale of individual hillslopes where considerable amounts of debris are generated from rock instantaneously: Rocksliding in active mountains is a major impetus of landscape downwearing. Study I provides a systematic overview of the internal sedimentology of giant rockslide deposits and thus meets the challenge of distinguishing them from macroscopically and microscopically similar glacial deposits, tectonic fault-zone breccias, and impact breccias. This distinction is important to avoid erroneous or misleading deduction of paleoclimatic or tectonic implications. -> Grain size analysis shows that rockslide-derived micro-breccia closely resemble those from meteorite impact or tectonic faults. -> Frictionite may occur more frequently that previously assumed. -> M{\"o}ssbauer-spectroscopy derived results indicate basal rock melting in the absence of water, involving short-term temperatures of >1500°C. Zooming out, Study II tracks the fate of these sediments, using the example of the upper Indus River, NW India. There we use river sand samples from the Indus and its tributaries to estimate basin-averaged denudation rates along a ~320-km reach across the Tibetan Plateau margin, to answer the question whether incision into the western Tibetan Plateau margin is currently active or not. -> We find an about one-order-of-magnitude upstream decay—from 110 to 10 mm kyr^-1—of cosmogenic Be-10-derived basin-wide denudation rates across the morphological knickpoint that marks the transition from the Transhimalayan ranges to the Tibetan Plateau. This trend is corroborated by independent bulk petrographic and heavy mineral analysis of the same samples. -> From the observation that tributary-derived basin-wide denudation rates do not increase markedly until ~150-200 km downstream of the topographic plateau margin we conclude that incision into the Tibetan Plateau is inactive. -> Comparing our postglacial Be-10-derived denudation rates to long-term (>10^6 yr) estimates from low-temperature thermochronometry, ranging from 100 to 750 mm kyr^-1, points to an order- of-magnitude decay of rates of landscape downwearing towards present. We infer that denudation rates must have been higher in the Quaternary, probably promoted by the interplay of glacial and interglacial stages. Our investigation of regional denudation patterns in the upper Indus finally is an integral part of Study III that synthesizes denudation of the Himalaya-Tibet orogen. In order to identify general and time-invariant predictors for Be-10-derived denudation rates we analyze tectonic, climatic and topographic metrics from an inventory of 297 drainage basins from various parts of the orogen. Aiming to get insight to the full response distributions of denudation rate to tectonic, climatic and topographic candidate predictors, we apply quantile regression instead of ordinary least squares regression, which has been standard analysis tool in previous studies that looked for denudation rate predictors. -> We use principal component analysis to reduce our set of 26 candidate predictors, ending up with just three out of these: Aridity Index, topographic steepness index, and precipitation of the coldest quarter of the year. -> Topographic steepness index proves to perform best during additive quantile regression. Our consequent prediction of denudation rates on the basin scale involves prediction errors that remain between 5 and 10 mm kyr^-1. -> We conclude that while topographic metrics such as river-channel steepness and slope gradient—being representative on timescales that our cosmogenic Be-10-derived denudation rates integrate over—generally appear to be more suited as predictors than climatic and tectonic metrics based on decadal records.}, language = {en} } @phdthesis{Albrecht2014, author = {Albrecht, Steve}, title = {Generation, recombination and extraction of charges in polymer}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-72285}, school = {Universit{\"a}t Potsdam}, pages = {144}, year = {2014}, abstract = {A dramatic efficiency improvement of bulk heterojunction solar cells based on electron-donating conjugated polymers in combination with soluble fullerene derivatives has been achieved over the past years. Certified and reported power conversion efficiencies now reach over 9\% for single junctions and exceed the 10\% benchmark for tandem solar cells. This trend brightens the vision of organic photovoltaics becoming competitive with inorganic solar cells including the realization of low-cost and large-area organic photovoltaics. For the best performing organic materials systems, the yield of charge generation can be very efficient. However, a detailed understanding of the free charge carrier generation mechanisms at the donor acceptor interface and the energy loss associated with it needs to be established. Moreover, organic solar cells are limited by the competition between charge extraction and free charge recombination, accounting for further efficiency losses. A conclusive picture and the development of precise methodologies for investigating the fundamental processes in organic solar cells are crucial for future material design, efficiency optimization, and the implementation of organic solar cells into commercial products. In order to advance the development of organic photovoltaics, my thesis focuses on the comprehensive understanding of charge generation, recombination and extraction in organic bulk heterojunction solar cells summarized in 6 chapters on the cumulative basis of 7 individual publications. The general motivation guiding this work was the realization of an efficient hybrid inorganic/organic tandem solar cell with sub-cells made from amorphous hydrogenated silicon and organic bulk heterojunctions. To realize this project aim, the focus was directed to the low band-gap copolymer PCPDTBT and its derivatives, resulting in the examination of the charge carrier dynamics in PCPDTBT:PC70BM blends in relation to by the blend morphology. The phase separation in this blend can be controlled by the processing additive diiodooctane, enhancing domain purity and size. The quantitative investigation of the free charge formation was realized by utilizing and improving the time delayed collection field technique. Interestingly, a pronounced field dependence of the free carrier generation for all blends is found, with the field dependence being stronger without the additive. Also, the bimolecular recombination coefficient for both blends is rather high and increases with decreasing internal field which we suggest to be caused by a negative field dependence of mobility. The additive speeds up charge extraction which is rationalized by the threefold increase in mobility. By fluorine attachment within the electron deficient subunit of PCPDTBT, a new polymer F-PCPDTBT is designed. This new material is characterized by a stronger tendency to aggregate as compared to non-fluorinated PCPDTBT. Our measurements show that for F-PCPDTBT:PCBM blends the charge carrier generation becomes more efficient and the field-dependence of free charge carrier generation is weakened. The stronger tendency to aggregate induced by the fluorination also leads to increased polymer rich domains, accompanied in a threefold reduction in the non-geminate recombination coefficient at conditions of open circuit. The size of the polymer domains is nicely correlated to the field-dependence of charge generation and the Langevin reduction factor, which highlights the importance of the domain size and domain purity for efficient charge carrier generation. In total, fluorination of PCPDTBT causes the PCE to increase from 3.6 to 6.1\% due to enhanced fill factor, short circuit current and open circuit voltage. Further optimization of the blend ratio, active layer thickness, and polymer molecular weight resulted in 6.6\% efficiency for F-PCPDTBT:PC70BM solar cells. Interestingly, the double fluorinated version 2F-PCPDTBT exhibited poorer FF despite a further reduction of geminate and non-geminate recombination losses. To further analyze this finding, a new technique is developed that measures the effective extraction mobility under charge carrier densities and electrical fields comparable to solar cell operation conditions. This method involves the bias enhanced charge extraction technique. With the knowledge of the carrier density under different electrical field and illumination conditions, a conclusive picture of the changes in charge carrier dynamics leading to differences in the fill factor upon fluorination of PCPDTBT is attained. The more efficient charge generation and reduced recombination with fluorination is counterbalanced by a decreased extraction mobility. Thus, the highest fill factor of 60\% and efficiency of 6.6\% is reached for F-PCPDTBT blends, while 2F-PCPDTBT blends have only moderate fill factors of 54\% caused by the lower effective extraction mobility, limiting the efficiency to 6.5\%. To understand the details of the charge generation mechanism and the related losses, we evaluated the yield and field-dependence of free charge generation using time delayed collection field in combination with sensitive measurements of the external quantum efficiency and absorption coefficients for a variety of blends. Importantly, both the yield and field-dependence of free charge generation is found to be unaffected by excitation energy, including direct charge transfer excitation below the optical band gap. To access the non-detectable absorption at energies of the relaxed charge transfer emission, the absorption was reconstructed from the CT emission, induced via the recombination of thermalized charges in electroluminescence. For a variety of blends, the quantum yield at energies of charge transfer emission was identical to excitations with energies well above the optical band-gap. Thus, the generation proceeds via the split-up of the thermalized charge transfer states in working solar cells. Further measurements were conducted on blends with fine-tuned energy levels and similar blend morphologies by using different fullerene derivatives. A direct correlation between the efficiency of free carrier generation and the energy difference of the relaxed charge transfer state relative to the energy of the charge separated state is found. These findings open up new guidelines for future material design as new high efficiency materials require a minimum energetic offset between charge transfer and the charge separated state while keeping the HOMO level (and LUMO level) difference between donor and acceptor as small as possible.}, language = {en} } @phdthesis{Mauri2014, author = {Mauri, Marco}, title = {A model for sigma factor competition in bacterial cells}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-72098}, school = {Universit{\"a}t Potsdam}, pages = {167}, year = {2014}, abstract = {Bacteria respond to changing environmental conditions by switching the global pattern of expressed genes. In response to specific environmental stresses the cell activates several stress-specific molecules such as sigma factors. They reversibly bind the RNA polymerase to form the so-called holoenzyme and direct it towards the appropriate stress response genes. In exponentially growing E. coli cells, the majority of the transcriptional activity is carried out by the housekeeping sigma factor, while stress responses are often under the control of alternative sigma factors. Different sigma factors compete for binding to a limited pool of RNA polymerase (RNAP) core enzymes, providing a mechanism for cross talk between genes or gene classes via the sharing of expression machinery. To quantitatively analyze the contribution of sigma factor competition to global changes in gene expression, we develop a thermodynamic model that describes binding between sigma factors and core RNAP at equilibrium, transcription, non-specific binding to DNA and the modulation of the availability of the molecular components. Association of housekeeping sigma factor to RNAP is generally favored by its abundance and higher binding affinity to the core. In order to promote transcription by alternative sigma subunits, the bacterial cell modulates the transcriptional efficiency in a reversible manner through several strategies such as anti-sigma factors, 6S RNA and generally any kind of transcriptional regulators (e.g. activators or inhibitors). By shifting the outcome of sigma factor competition for the core, these modulators bias the transcriptional program of the cell. The model is validated by comparison with in vitro competition experiments, with which excellent agreement is found. We observe that transcription is affected via the modulation of the concentrations of the different types of holoenzymes, so saturated promoters are only weakly affected by sigma factor competition. However, in case of overlapping promoters or promoters recognized by two types of sigma factors, we find that even saturated promoters are strongly affected. Active transcription effectively lowers the affinity between the sigma factor driving it and the core RNAP, resulting in complex cross talk effects and raising the question of how their in vitro measure is relevant in the cell. We also estimate that sigma factor competition is not strongly affected by non-specific binding of core RNAPs, sigma factors, and holoenzymes to DNA. Finally, we analyze the role of increased core RNAP availability upon the shut-down of ribosomal RNA transcription during stringent response. We find that passive up-regulation of alternative sigma-dependent transcription is not only possible, but also displays hypersensitivity based on the sigma factor competition. Our theoretical analysis thus provides support for a significant role of passive control during that global switch of the gene expression program and gives new insights into RNAP partitioning in the cell.}, language = {en} } @phdthesis{Widdrat2014, author = {Widdrat, Marc}, title = {Formation and alteration of magnetite nanoparticles}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-72239}, school = {Universit{\"a}t Potsdam}, pages = {113}, year = {2014}, abstract = {Magnetite is an iron oxide, which is ubiquitous in rocks and is usually deposited as small nanoparticulate matter among other rock material. It differs from most other iron oxides because it contains divalent and trivalent iron. Consequently, it has a special crystal structure and unique magnetic properties. These properties are used for paleoclimatic reconstructions where naturally occurring magnetite helps understanding former geological ages. Further on, magnetic properties are used in bio- and nanotechnological applications -synthetic magnetite serves as a contrast agent in MRI, is exploited in biosensing, hyperthermia or is used in storage media. Magnetic properties are strongly size-dependent and achieving size control under preferably mild synthesis conditions is of interest in order to obtain particles with required properties. By using a custom-made setup, it was possible to synthesize stable single domain magnetite nanoparticles with the co-precipitation method. Furthermore, it was shown that magnetite formation is temperature-dependent, resulting in larger particles at higher temperatures. However, mechanistic approaches about the details are incomplete. Formation of magnetite from solution was shown to occur from nanoparticulate matter rather than solvated ions. The theoretical framework of such processes has only started to be described, partly due to the lack of kinetic or thermodynamic data. Synthesis of magnetite nanoparticles at different temperatures was performed and the Arrhenius plot was used determine an activation energy for crystal growth of 28.4 kJ mol-1, which led to the conclusion that nanoparticle diffusion is the rate-determining step. Furthermore, a study of the alteration of magnetite particles of different sizes as a function of their storage conditions is presented. The magnetic properties depend not only on particle size but also depend on the structure of the oxide, because magnetite oxidizes to maghemite under environmental conditions. The dynamics of this process have not been well described. Smaller nanoparticles are shown to oxidize more rapidly than larger ones and the lower the storage temperature, the lower the measured oxidation. In addition, the magnetic properties of the altered particles are not decreased dramatically, thus suggesting that this alteration will not impact the use of such nanoparticles as medical carriers. Finally, the effect of biological additives on magnetite formation was investigated. Magnetotactic bacteria¬¬ are able to synthesize and align magnetite nanoparticles of well-defined size and morphology due to the involvement of special proteins with specific binding properties. Based on this model of morphology control, phage display experiments were performed to determine peptide sequences that preferably bind to (111)-magnetite faces. The aim was to control the shape of magnetite nanoparticles during the formation. Magnetotactic bacteria are also able to control the intracellular redox potential with proteins called magnetochromes. MamP is such a protein and its oxidizing nature was studied in vitro via biomimetic magnetite formation experiments based on ferrous ions. Magnetite and further trivalent oxides were found. This work helps understanding basic mechanisms of magnetite formation and gives insight into non-classical crystal growth. In addition, it is shown that alteration of magnetite nanoparticles is mainly based on oxidation to maghemite and does not significantly influence the magnetic properties. Finally, biomimetic experiments help understanding the role of MamP within the bacteria and furthermore, a first step was performed to achieve morphology control in magnetite formation via co-precipitation.}, language = {en} } @phdthesis{Tinnefeld2014, author = {Tinnefeld, Christian}, title = {Building a columnar database on shared main memory-based storage}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-72063}, school = {Universit{\"a}t Potsdam}, pages = {175}, year = {2014}, abstract = {In the field of disk-based parallel database management systems exists a great variety of solutions based on a shared-storage or a shared-nothing architecture. In contrast, main memory-based parallel database management systems are dominated solely by the shared-nothing approach as it preserves the in-memory performance advantage by processing data locally on each server. We argue that this unilateral development is going to cease due to the combination of the following three trends: a) Nowadays network technology features remote direct memory access (RDMA) and narrows the performance gap between accessing main memory inside a server and of a remote server to and even below a single order of magnitude. b) Modern storage systems scale gracefully, are elastic, and provide high-availability. c) A modern storage system such as Stanford's RAMCloud even keeps all data resident in main memory. Exploiting these characteristics in the context of a main-memory parallel database management system is desirable. The advent of RDMA-enabled network technology makes the creation of a parallel main memory DBMS based on a shared-storage approach feasible. This thesis describes building a columnar database on shared main memory-based storage. The thesis discusses the resulting architecture (Part I), the implications on query processing (Part II), and presents an evaluation of the resulting solution in terms of performance, high-availability, and elasticity (Part III). In our architecture, we use Stanford's RAMCloud as shared-storage, and the self-designed and developed in-memory AnalyticsDB as relational query processor on top. AnalyticsDB encapsulates data access and operator execution via an interface which allows seamless switching between local and remote main memory, while RAMCloud provides not only storage capacity, but also processing power. Combining both aspects allows pushing-down the execution of database operators into the storage system. We describe how the columnar data processed by AnalyticsDB is mapped to RAMCloud's key-value data model and how the performance advantages of columnar data storage can be preserved. The combination of fast network technology and the possibility to execute database operators in the storage system opens the discussion for site selection. We construct a system model that allows the estimation of operator execution costs in terms of network transfer, data processed in memory, and wall time. This can be used for database operators that work on one relation at a time - such as a scan or materialize operation - to discuss the site selection problem (data pull vs. operator push). Since a database query translates to the execution of several database operators, it is possible that the optimal site selection varies per operator. For the execution of a database operator that works on two (or more) relations at a time, such as a join, the system model is enriched by additional factors such as the chosen algorithm (e.g. Grace- vs. Distributed Block Nested Loop Join vs. Cyclo-Join), the data partitioning of the respective relations, and their overlapping as well as the allowed resource allocation. We present an evaluation on a cluster with 60 nodes where all nodes are connected via RDMA-enabled network equipment. We show that query processing performance is about 2.4x slower if everything is done via the data pull operator execution strategy (i.e. RAMCloud is being used only for data access) and about 27\% slower if operator execution is also supported inside RAMCloud (in comparison to operating only on main memory inside a server without any network communication at all). The fast-crash recovery feature of RAMCloud can be leveraged to provide high-availability, e.g. a server crash during query execution only delays the query response for about one second. Our solution is elastic in a way that it can adapt to changing workloads a) within seconds, b) without interruption of the ongoing query processing, and c) without manual intervention.}, language = {en} } @phdthesis{Negri2014, author = {Negri, Michael}, title = {How coaches influence referee decisions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-72247}, school = {Universit{\"a}t Potsdam}, pages = {132}, year = {2014}, abstract = {The work elaborates on the question if coaches in non-professional soccer can influence referee decisions. Modeled from a principal-agent perspective, the managing referee boards can be seen as the principal. They aim at facilitating a fair competition which is in accordance with the existing rules and regulations. In doing so, the referees are assigned as impartial agents on the pitch. The coaches take over a non-legitimate principal-like role trying to influence the referees even though they do not have the formal right to do so. Separate questionnaires were set up for referees and coaches. The coach questionnaire aimed at identifying the extent and the forms of influencing attempts by coaches. The referee questionnaire tried to elaborate on the questions if referees take notice of possible influencing attempts and how they react accordingly. The results were put into relation with official match data in order to identify significant influences on personal sanctions (yellow cards, second yellow cards, red cards) and the match result. It is found that there is a slight effect on the referee's decisions. However, this effect is rather disadvantageous for the influencing coach and there is no evidence for an impact on the match result itself.}, language = {en} } @phdthesis{Sorce2014, author = {Sorce, Jenny}, title = {From Spitzer mid-infrared observations and measurements of peculiar velocities to constrained simulations of the local universe}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72486}, school = {Universit{\"a}t Potsdam}, pages = {xx, 303}, year = {2014}, abstract = {Galaxies are observational probes to study the Large Scale Structure. Their gravitational motions are tracers of the total matter density and therefore of the Large Scale Structure. Besides, studies of structure formation and galaxy evolution rely on numerical cosmological simulations. Still, only one universe observable from a given position, in time and space, is available for comparisons with simulations. The related cosmic variance affects our ability to interpret the results. Simulations constrained by observational data are a perfect remedy to this problem. Achieving such simulations requires the projects Cosmic flows and CLUES. Cosmic flows builds catalogs of accurate distance measurements to map deviations from the expansion. These measures are mainly obtained with the galaxy luminosity-rotation rate correlation. We present the calibration of that relation in the mid-infrared with observational data from Spitzer Space Telescope. Resulting accurate distance estimates will be included in the third catalog of the project. In the meantime, two catalogs up to 30 and 150 Mpc/h have been released. We report improvements and applications of the CLUES' method on these two catalogs. The technique is based on the constrained realization algorithm. The cosmic displacement field is computed with the Zel'dovich approximation. This latter is then reversed to relocate reconstructed three-dimensional constraints to their precursors' positions in the initial field. The size of the second catalog (8000 galaxies within 150 Mpc/h) highlighted the importance of minimizing the observational biases. By carrying out tests on mock catalogs, built from cosmological simulations, a method to minimize observational bias can be derived. Finally, for the first time, cosmological simulations are constrained solely by peculiar velocities. The process is successful as resulting simulations resemble the Local Universe. The major attractors and voids are simulated at positions approaching observational positions by a few megaparsecs, thus reaching the limit imposed by the linear theory.}, language = {en} } @phdthesis{Mayer2014, author = {Mayer, Michael}, title = {Pulsar wind nebulae at high energies}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-71504}, school = {Universit{\"a}t Potsdam}, pages = {142}, year = {2014}, abstract = {Pulsar wind nebulae (PWNe) are the most abundant TeV gamma-ray emitters in the Milky Way. The radiative emission of these objects is powered by fast-rotating pulsars, which donate parts of their rotational energy into winds of relativistic particles. This thesis presents an in-depth study of the detected population of PWNe at high energies. To outline general trends regarding their evolutionary behaviour, a time-dependent model is introduced and compared to the available data. In particular, this work presents two exceptional PWNe which protrude from the rest of the population, namely the Crab Nebula and N 157B. Both objects are driven by pulsars with extremely high rotational energy loss rates. Accordingly, they are often referred to as energetic twins. Modelling the non-thermal multi-wavelength emission of N157B gives access to specific properties of this object, like the magnetic field inside the nebula. Comparing the derived parameters to those of the Crab Nebula reveals large intrinsic differences between the two PWNe. Possible origins of these differences are discussed in context of the resembling pulsars. Compared to the TeV gamma-ray regime, the number of detected PWNe is much smaller in the MeV-GeV gamma-ray range. In the latter range, the Crab Nebula stands out by the recent detection of gamma-ray flares. In general, the measured flux enhancements on short time scales of days to weeks were not expected in the theoretical understanding of PWNe. In this thesis, the variability of the Crab Nebula is analysed using data from the Fermi Large Area Telescope (Fermi-LAT). For the presented analysis, a new gamma-ray reconstruction method is used, providing a higher sensitivity and a lower energy threshold compared to previous analyses. The derived gamma-ray light curve of the Crab Nebula is investigated for flares and periodicity. The detected flares are analysed regarding their energy spectra, and their variety and commonalities are discussed. In addition, a dedicated analysis of the flare which occurred in March 2013 is performed. The derived short-term variability time scale is roughly 6h, implying a small region inside the Crab Nebula to be responsible for the enigmatic flares. The most promising theories explaining the origins of the flux eruptions and gamma-ray variability are discussed in detail. In the technical part of this work, a new analysis framework is presented. The introduced software, called gammalib/ctools, is currently being developed for the future CTA observa- tory. The analysis framework is extensively tested using data from the H. E. S. S. experiment. To conduct proper data analysis in the likelihood framework of gammalib/ctools, a model describing the distribution of background events in H.E.S.S. data is presented. The software provides the infrastructure to combine data from several instruments in one analysis. To study the gamma-ray emitting PWN population, data from Fermi-LAT and H. E. S. S. are combined in the likelihood framework of gammalib/ctools. In particular, the spectral peak, which usually lies in the overlap energy regime between these two instruments, is determined with the presented analysis framework. The derived measurements are compared to the predictions from the time-dependent model. The combined analysis supports the conclusion of a diverse population of gamma-ray emitting PWNe.}, language = {en} } @phdthesis{Sayago2014, author = {Sayago, Jhosnella}, title = {Late Paleozoic basin analysis of the Loppa High and Finnmark Platform in the Norwegian Barents Sea : integration of seismic attributes and seismic sequence stratigraphy}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72576}, school = {Universit{\"a}t Potsdam}, pages = {viii, 109}, year = {2014}, abstract = {The subsurface upper Palaeozoic sedimentary successions of the Loppa High half-graben and the Finnmark platform in the Norwegian Barents Sea (southwest Barents Sea) were investigated using 2D/3D seismic datasets combined with well and core data. These sedimentary successions represent a case of mixed siliciclastic-carbonates depositional systems, which formed during the earliest phase of the Atlantic rifting between Greenland and Norway. During the Carboniferous and Permian the southwest part of the Barents Sea was located along the northern margin of Pangaea, which experienced a northward drift at a speed of ~2-3 mm per year. This gradual shift in the paleolatitudinal position is reflected by changes in regional climatic conditions: from warm-humid in the early Carboniferous, changing to warm-arid in the middle to late Carboniferous and finally to colder conditions in the late Permian. Such changes in paleolatitude and climate have resulted in major changes in the style of sedimentation including variations in the type of carbonate factories. The upper Palaeozoic sedimentary succession is composed of four major depositional units comprising chronologically the Billefjorden Group dominated by siliciclastic deposition in extensional tectonic-controlled wedges, the Gipsdalen Group dominated by warm-water carbonates, stacked buildups and evaporites, the Bjarmeland Group characterized by cool-water carbonates as well as by the presence of buildup networks, and the Tempelfjorden Group characterized by fine-grained sedimentation dominated by biological silica production. In the Loppa High, the integration of a core study with multi-attribute seismic facies classification allowed highlighting the main sedimentary unconformities and mapping the spatial extent of a buried paleokarst terrain. This geological feature is interpreted to have formed during a protracted episode of subaerial exposure occurring between the late Palaeozoic and middle Triassic. Based on seismic sequence stratigraphy analysis the palaeogeography in time and space of the Loppa High basin was furthermore reconstructed and a new and more detailed tectono-sedimentary model for this area was proposed. In the Finnmark platform area, a detailed core analysis of two main exploration wells combined with key 2D seismic sections located along the main depositional profile, allowed the evaluation of depositional scenarios for the two main lithostratigraphic units: the {\O}rn Formation (Gipsdalen Group) and the Isbj{\o}rn Formation (Bjarmeland Group). During the mid-Sakmarian, two major changes were observed between the two formations including (1) the variation in the type of the carbonate factories, which is interpreted to be depth-controlled and (2) the change in platform morphology, which evolved from a distally steepened ramp to a homoclinal ramp. The results of this study may help supporting future reservoirs characterization of the upper Palaeozoic units in the Barents Sea, particularly in the Loppa High half-graben and the Finmmark platform area.}, language = {en} } @phdthesis{Nguyen2014, author = {Nguyen, Van Manh}, title = {Large-scale floodplain sediment dynamics in the Mekong Delta : present state and future prospects}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72512}, school = {Universit{\"a}t Potsdam}, pages = {ix, 95}, year = {2014}, abstract = {The Mekong Delta (MD) sustains the livelihood and food security of millions of people in Vietnam and Cambodia. It is known as the "rice bowl" of South East Asia and has one of the world's most productive fisheries. Sediment dynamics play a major role for the high productivity of agriculture and fishery in the delta. However, the MD is threatened by climate change, sea level rise and unsustainable development activities in the Mekong Basin. But despite its importance and the expected threats, the understanding of the present and future sediment dynamics in the MD is very limited. This is a consequence of its large extent, the intricate system of rivers, channels and floodplains and the scarcity of observations. Thus this thesis aimed at (1) the quantification of suspended sediment dynamics and associated sediment-nutrient deposition in floodplains of the MD, and (2) assessed the impacts of likely future boundary changes on the sediment dynamics in the MD. The applied methodology combines field experiments and numerical simulation to quantify and predict the sediment dynamics in the entire delta in a spatially explicit manner. The experimental part consists of a comprehensive procedure to monitor quantity and spatial variability of sediment and associated nutrient deposition for large and complex river floodplains, including an uncertainty analysis. The measurement campaign applied 450 sediment mat traps in 19 floodplains over the MD for a complete flood season. The data also supports quantification of nutrient deposition in floodplains based on laboratory analysis of nutrient fractions of trapped sedimentation.The main findings are that the distribution of grain size and nutrient fractions of suspended sediment are homogeneous over the Vietnamese floodplains. But the sediment deposition within and between ring dike floodplains shows very high spatial variability due to a high level of human inference. The experimental findings provide the essential data for setting up and calibration of a large-scale sediment transport model for the MD. For the simulation studies a large scale hydrodynamic model was developed in order to quantify large-scale floodplain sediment dynamics. The complex river-channel-floodplain system of the MD is described by a quasi-2D model linking a hydrodynamic and a cohesive sediment transport model. The floodplains are described as quasi-2D presentations linked to rivers and channels modeled in 1D by using control structures. The model setup, based on the experimental findings, ignored erosion and re-suspension processes due to a very high degree of human interference during the flood season. A two-stage calibration with six objective functions was developed in order to calibrate both the hydrodynamic and sediment transport modules. The objective functions include hydraulic and sediment transport parameters in main rivers, channels and floodplains. The model results show, for the first time, the tempo-spatial distribution of sediment and associated nutrient deposition rates in the whole MD. The patterns of sediment transport and deposition are quantified for different sub-systems. The main factors influencing spatial sediment dynamics are the network of rivers, channels and dike-rings, sluice gate operations, magnitude of the floods and tidal influences. The superposition of these factors leads to high spatial variability of the sediment transport and deposition, in particular in the Vietnamese floodplains. Depending on the flood magnitude, annual sediment loads reaching the coast vary from 48\% to 60\% of the sediment load at Kratie, the upper boundary of the MD. Deposited sediment varies from 19\% to 23\% of the annual load at Kratie in Cambodian floodplains, and from 1\% to 6\% in the compartmented and diked floodplains in Vietnam. Annual deposited nutrients (N, P, K), which are associated to the sediment deposition, provide on average more than 50\% of mineral fertilizers typically applied for rice crops in non-flooded ring dike compartments in Vietnam. This large-scale quantification provides a basis for estimating the benefits of the annual Mekong floods for agriculture and fishery, for assessing the impacts of future changes on the delta system, and further studies on coastal deposition/erosion. For the estimation of future prospects a sensitivity-based approach is applied to assess the response of floodplain hydraulics and sediment dynamics to the changes in the delta boundaries including hydropower development, climate change in the Mekong River Basin and effective sea level rise. The developed sediment model is used to simulate the mean sediment transport and sediment deposition in the whole delta system for the baseline (2000-2010) and future (2050-2060) periods. For each driver we derive a plausible range of future changes and discretize it into five levels, resulting in altogether 216 possible factor combinations. Our results thus cover all plausible future pathways of sediment dynamics in the delta based on current knowledge. The uncertainty of the range of the resulting impacts can be decreased in case more information on these drivers becomes available. Our results indicate that the hydropower development dominates the changes in sediment dynamics of the Mekong Delta, while sea level rise has the smallest effect. The floodplains of Vietnamese Mekong Delta are much more sensitive to the changes compared to the other subsystems of the delta. In terms of median changes of the three combined drivers, the inundation extent is predicted to increase slightly, but the overall floodplain sedimentation would be reduced by approximately 40\%, while the sediment load to the Sea would diminish to half of the current rates. These findings provide new and valuable information on the possible impacts of future development on the delta, and indicate the most vulnerable areas. Thus, the presented results are a significant contribution to the ongoing international discussion on the hydropower development in the Mekong basin and its impact on the Mekong delta.}, language = {en} } @phdthesis{Kruegel2014, author = {Kr{\"u}gel, Andr{\´e}}, title = {Eye movement control during reading : factors and principles of computing the word center for saccade planning}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72599}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Reading is a complex cognitive task based on the analyses of visual stimuli. Due to the physiology of the eye, only a small number of letters around the fixation position can be extracted with high visual acuity, while the visibility of words and letters outside this so-called foveal region quickly drops with increasing eccentricity. As a consequence, saccadic eye movements are needed to repeatedly shift the fovea to new words for visual word identification during reading. Moreover, even within a foveated word fixation positions near the word center are superior to other fixation positions for efficient word recognition (O'Regan, 1981; Brysbaert, Vitu, and Schroyens, 1996). Thus, most reading theories assume that readers aim specifically at word centers during reading (for a review see Reichle, Rayner, \& Pollatsek, 2003). However, saccades' landing positions within words during reading are in fact systematically modulated by the distance of the launch site from the word center (McConkie, Kerr, Reddix, \& Zola, 1988). In general, it is largely unknown how readers identify the center of upcoming target words and there is no computational model of the sensorimotor translation of the decision for a target word into spatial word center coordinates. Here we present a series of three studies which aim at advancing the current knowledge about the computation of saccade target coordinates during saccade planning in reading. Based on a large corpus analyses, we firstly identified word skipping as a further factor beyond the launch-site distance with a likewise systematic and surprisingly large effect on within-word landing positions. Most importantly, we found that the end points of saccades after skipped word are shifted two and more letters to the left as compared to one-step saccades (i.e., from word N to word N+1) with equal launch-site distances. Then we present evidence from a single saccade experiment suggesting that the word-skipping effect results from highly automatic low-level perceptual processes, which are essentially based on the localization of blank spaces between words. Finally, in the third part, we present a Bayesian model of the computation of the word center from primary sensory measurements of inter-word spaces. We demonstrate that the model simultaneously accounts for launch-site and saccade-type contingent modulations of within-word landing positions in reading. Our results show that the spatial saccade target during reading is the result of complex estimations of the word center based on incomplete sensory information, which also leads to specific systematic deviations of saccades' landing positions from the word center. Our results have important implications for current reading models and experimental reading research.}, language = {en} } @phdthesis{Steinhaus2014, author = {Steinhaus, Sebastian Peter}, title = {Constructing quantum spacetime}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72558}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Despite remarkable progress made in the past century, which has revolutionized our understanding of the universe, there are numerous open questions left in theoretical physics. Particularly important is the fact that the theories describing the fundamental interactions of nature are incompatible. Einstein's theory of general relative describes gravity as a dynamical spacetime, which is curved by matter and whose curvature determines the motion of matter. On the other hand we have quantum field theory, in form of the standard model of particle physics, where particles interact via the remaining interactions - electromagnetic, weak and strong interaction - on a flat, static spacetime without gravity. A theory of quantum gravity is hoped to cure this incompatibility by heuristically replacing classical spacetime by quantum spacetime'. Several approaches exist attempting to define such a theory with differing underlying premises and ideas, where it is not clear which is to be preferred. Yet a minimal requirement is the compatibility with the classical theory, they attempt to generalize. Interestingly many of these models rely on discrete structures in their definition or postulate discreteness of spacetime to be fundamental. Besides the direct advantages discretisations provide, e.g. permitting numerical simulations, they come with serious caveats requiring thorough investigation: In general discretisations break fundamental diffeomorphism symmetry of gravity and are generically not unique. Both complicates establishing the connection to the classical continuum theory. The main focus of this thesis lies in the investigation of this relation for spin foam models. This is done on different levels of the discretisation / triangulation, ranging from few simplices up to the continuum limit. In the regime of very few simplices we confirm and deepen the connection of spin foam models to discrete gravity. Moreover, we discuss dynamical, e.g. diffeomorphism invariance in the discrete, to fix the ambiguities of the models. In order to satisfy these conditions, the discrete models have to be improved in a renormalisation procedure, which also allows us to study their continuum dynamics. Applied to simplified spin foam models, we uncover a rich, non--trivial fixed point structure, which we summarize in a phase diagram. Inspired by these methods, we propose a method to consistently construct the continuum theory, which comes with a unique vacuum state.}, language = {en} } @phdthesis{GuzmanPerez2014, author = {Guzman-Perez, Valentina}, title = {Effect of benzylglucosinolate on signaling pathways associated with type 2 diabetes prevention}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72351}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Type 2 diabetes (T2D) is a health problem throughout the world. In 2010, there were nearly 230 million individuals with diabetes worldwide and it is estimated that in the economically advanced countries the cases will increase about 50\% in the next twenty years. Insulin resistance is one of major features in T2D, which is also a risk factor for metabolic and cardiovascular complications. Epidemiological and animal studies have shown that the consumption of vegetables and fruits can delay or prevent the development of the disease, although the underlying mechanisms of these effects are still unclear. Brassica species such as broccoli (Brassica oleracea var. italica) and nasturtium (Tropaeolum majus) possess high content of bioactive phytochemicals, e.g. nitrogen sulfur compounds (glucosinolates and isothiocyanates) and polyphenols largely associated with the prevention of cancer. Isothiocyanates (ITCs) display their anti-carcinogenic potential by inducing detoxicating phase II enzymes and increasing glutathione (GSH) levels in tissues. In T2D diabetes an increase in gluconeogenesis and triglyceride synthesis, and a reduction in fatty acid oxidation accompanied by the presence of reactive oxygen species (ROS) are observed; altogether is the result of an inappropriate response to insulin. Forkhead box O (FOXO) transcription factors play a crucial role in the regulation of insulin effects on gene expression and metabolism, and alterations in FOXO function could contribute to metabolic disorders in diabetes. In this study using stably transfected human osteosarcoma cells (U-2 OS) with constitutive expression of FOXO1 protein labeled with GFP (green fluorescent protein) and human hepatoma cells HepG2 cell cultures, the ability of benzylisothiocyanate (BITC) deriving from benzylglucosinolate, extracted from nasturtium to modulate, i) the insulin-signaling pathway, ii) the intracellular localization of FOXO1 and iii) the expression of proteins involved in glucose metabolism, ROS detoxification, cell cycle arrest and DNA repair was evaluated. BITC promoted oxidative stress and in response to that induced FOXO1 translocation from cytoplasm into the nucleus antagonizing the insulin effect. BITC stimulus was able to down-regulate gluconeogenic enzymes, which can be considered as an anti-diabetic effect; to promote antioxidant resistance expressed by the up-regulation in manganese superoxide dismutase (MnSOD) and detoxification enzymes; to modulate autophagy by induction of BECLIN1 and down-regulation of the mammalian target of rapamycin complex 1 (mTORC1) pathway; and to promote cell cycle arrest and DNA damage repair by up-regulation of the cyclin-dependent kinase inhibitor (p21CIP) and Growth Arrest / DNA Damage Repair (GADD45). Except for the nuclear factor (erythroid derived)-like2 (NRF2) and its influence in the detoxification enzymes gene expression, all the observed effects were independent from FOXO1, protein kinase B (AKT/PKB) and NAD-dependent deacetylase sirtuin-1 (SIRT1). The current study provides evidence that besides of the anticarcinogenic potential, isothiocyanates might have a role in T2D prevention. BITC stimulus mimics the fasting state, in which insulin signaling is not triggered and FOXO proteins remain in the nucleus modulating gene expression of their target genes, with the advantage of a down-regulation of gluconeogenesis instead of its increase. These effects suggest that BITC might be considered as a promising substance in the prevention or treatment of T2D, therefore the factors behind of its modulatory effects need further investigation.}, language = {en} } @phdthesis{Burdack2014, author = {Burdack, Doreen}, title = {Water management policies and their impact on irrigated crop production in the Murray-Darling Basin, Australia}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-306-0}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72245}, school = {Universit{\"a}t Potsdam}, pages = {307}, year = {2014}, abstract = {The economic impact analysis contained in this book shows how irrigation farming is particularly susceptible when applying certain water management policies in the Australian Murray-Darling Basin, one of the world largest river basins and Australia's most fertile region. By comparing different pricing and non-pricing water management policies with the help of the Water Integrated Market Model, it is found that the impact of water demand reducing policies is most severe on crops that need to be intensively irrigated and are at the same time less water productive. A combination of increasingly frequent and severe droughts and the application of policies that decrease agricultural water demand, in the same region, will create a situation in which the highly water dependent crops rice and cotton cannot be cultivated at all.}, language = {en} } @phdthesis{Ziese2014, author = {Ziese, Ramona}, title = {Geometric electroelasticity}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72504}, school = {Universit{\"a}t Potsdam}, pages = {vi, 113}, year = {2014}, abstract = {In this work a diffential geometric formulation of the theory of electroelasticity is developed which also includes thermal and magnetic influences. We study the motion of bodies consisting of an elastic material that are deformed by the influence of mechanical forces, heat and an external electromagnetic field. To this end physical balance laws (conservation of mass, balance of momentum, angular momentum and energy) are established. These provide an equation that describes the motion of the body during the deformation. Here the body and the surrounding space are modeled as Riemannian manifolds, and we allow that the body has a lower dimension than the surrounding space. In this way one is not (as usual) restricted to the description of the deformation of three-dimensional bodies in a three-dimensional space, but one can also describe the deformation of membranes and the deformation in a curved space. Moreover, we formulate so-called constitutive relations that encode the properties of the used material. Balance of energy as a scalar law can easily be formulated on a Riemannian manifold. The remaining balance laws are then obtained by demanding that balance of energy is invariant under the action of arbitrary diffeomorphisms on the surrounding space. This generalizes a result by Marsden and Hughes that pertains to bodies that have the same dimension as the surrounding space and does not allow the presence of electromagnetic fields. Usually, in works on electroelasticity the entropy inequality is used to decide which otherwise allowed deformations are physically admissible and which are not. It is alsoemployed to derive restrictions to the possible forms of constitutive relations describing the material. Unfortunately, the opinions on the physically correct statement of the entropy inequality diverge when electromagnetic fields are present. Moreover, it is unclear how to formulate the entropy inequality in the case of a membrane that is subjected to an electromagnetic field. Thus, we show that one can replace the use of the entropy inequality by the demand that for a given process balance of energy is invariant under the action of arbitrary diffeomorphisms on the surrounding space and under linear rescalings of the temperature. On the one hand, this demand also yields the desired restrictions to the form of the constitutive relations. On the other hand, it needs much weaker assumptions than the arguments in physics literature that are employing the entropy inequality. Again, our result generalizes a theorem of Marsden and Hughes. This time, our result is, like theirs, only valid for bodies that have the same dimension as the surrounding space.}, language = {en} } @phdthesis{Balzer2014, author = {Balzer, Arnim}, title = {Crab flare observations with H.E.S.S. phase II}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72545}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {The H.E.S.S. array is a third generation Imaging Atmospheric Cherenkov Telescope (IACT) array. It is located in the Khomas Highland in Namibia, and measures very high energy (VHE) gamma-rays. In Phase I, the array started data taking in 2004 with its four identical 13 m telescopes. Since then, H.E.S.S. has emerged as the most successful IACT experiment to date. Among the almost 150 sources of VHE gamma-ray radiation found so far, even the oldest detection, the Crab Nebula, keeps surprising the scientific community with unexplained phenomena such as the recently discovered very energetic flares of high energy gamma-ray radiation. During its most recent flare, which was detected by the Fermi satellite in March 2013, the Crab Nebula was simultaneously observed with the H.E.S.S. array for six nights. The results of the observations will be discussed in detail during the course of this work. During the nights of the flare, the new 24 m × 32 m H.E.S.S. II telescope was still being commissioned, but participated in the data taking for one night. To be able to reconstruct and analyze the data of the H.E.S.S. Phase II array, the algorithms and software used by the H.E.S.S. Phase I array had to be adapted. The most prominent advanced shower reconstruction technique developed by de Naurois and Rolland, the template-based model analysis, compares real shower images taken by the Cherenkov telescope cameras with shower templates obtained using a semi-analytical model. To find the best fitting image, and, therefore, the relevant parameters that describe the air shower best, a pixel-wise log-likelihood fit is done. The adaptation of this advanced shower reconstruction technique to the heterogeneous H.E.S.S. Phase II array for stereo events (i.e. air showers seen by at least two telescopes of any kind), its performance using MonteCarlo simulations as well as its application to real data will be described.}, language = {en} } @phdthesis{Bamberg2014, author = {Bamberg, Marlene}, title = {Planetary mapping tools applied to floor-fractured craters on Mars}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72104}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Planetary research is often user-based and requires considerable skill, time, and effort. Unfortunately, self-defined boundary conditions, definitions, and rules are often not documented or not easy to comprehend due to the complexity of research. This makes a comparison to other studies, or an extension of the already existing research, complicated. Comparisons are often distorted, because results rely on different, not well defined, or even unknown boundary conditions. The purpose of this research is to develop a standardized analysis method for planetary surfaces, which is adaptable to several research topics. The method provides a consistent quality of results. This also includes achieving reliable and comparable results and reducing the time and effort of conducting such studies. A standardized analysis method is provided by automated analysis tools that focus on statistical parameters. Specific key parameters and boundary conditions are defined for the tool application. The analysis relies on a database in which all key parameters are stored. These databases can be easily updated and adapted to various research questions. This increases the flexibility, reproducibility, and comparability of the research. However, the quality of the database and reliability of definitions directly influence the results. To ensure a high quality of results, the rules and definitions need to be well defined and based on previously conducted case studies. The tools then produce parameters, which are obtained by defined geostatistical techniques (measurements, calculations, classifications). The idea of an automated statistical analysis is tested to proof benefits but also potential problems of this method. In this study, I adapt automated tools for floor-fractured craters (FFCs) on Mars. These impact craters show a variety of surface features, occurring in different Martian environments, and having different fracturing origins. They provide a complex morphological and geological field of application. 433 FFCs are classified by the analysis tools due to their fracturing process. Spatial data, environmental context, and crater interior data are analyzed to distinguish between the processes involved in floor fracturing. Related geologic processes, such as glacial and fluvial activity, are too similar to be separately classified by the automated tools. Glacial and fluvial fracturing processes are merged together for the classification. The automated tools provide probability values for each origin model. To guarantee the quality and reliability of the results, classification tools need to achieve an origin probability above 50 \%. This analysis method shows that 15 \% of the FFCs are fractured by intrusive volcanism, 20 \% by tectonic activity, and 43 \% by water \& ice related processes. In total, 75 \% of the FFCs are classified to an origin type. This can be explained by a combination of origin models, superposition or erosion of key parameters, or an unknown fracturing model. Those features have to be manually analyzed in detail. Another possibility would be the improvement of key parameters and rules for the classification. This research shows that it is possible to conduct an automated statistical analysis of morphologic and geologic features based on analysis tools. Analysis tools provide additional information to the user and are therefore considered assistance systems.}, language = {en} } @phdthesis{Takouna2014, author = {Takouna, Ibrahim}, title = {Energy-efficient and performance-aware virtual machine management for cloud data centers}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72399}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Virtualisierte Cloud Datenzentren stellen nach Bedarf Ressourcen zur Verf{\"u}gu-ng, erm{\"o}glichen agile Ressourcenbereitstellung und beherbergen heterogene Applikationen mit verschiedenen Anforderungen an Ressourcen. Solche Datenzentren verbrauchen enorme Mengen an Energie, was die Erh{\"o}hung der Betriebskosten, der W{\"a}rme innerhalb der Zentren und des Kohlendioxidausstoßes verursacht. Der Anstieg des Energieverbrauches kann durch ein ineffektives Ressourcenmanagement, das die ineffiziente Ressourcenausnutzung verursacht, entstehen. Die vorliegende Dissertation stellt detaillierte Modelle und neue Verfahren f{\"u}r virtualisiertes Ressourcenmanagement in Cloud Datenzentren vor. Die vorgestellten Verfahren ziehen das Service-Level-Agreement (SLA) und die Heterogenit{\"a}t der Auslastung bez{\"u}glich des Bedarfs an Speicherzugriffen und Kommunikationsmustern von Web- und HPC- (High Performance Computing) Applikationen in Betracht. Um die pr{\"a}sentierten Techniken zu evaluieren, verwenden wir Simulationen und echte Protokollierung der Auslastungen von Web- und HPC- Applikationen. Außerdem vergleichen wir unser Techniken und Verfahren mit anderen aktuellen Verfahren durch die Anwendung von verschiedenen Performance Metriken. Die Hauptbeitr{\"a}ge dieser Dissertation sind Folgendes: Ein Proaktives auf robuster Optimierung basierendes Ressourcenbereitstellungsverfahren. Dieses Verfahren erh{\"o}ht die F{\"a}higkeit der Hostes zur Verf{\"u}g-ungsstellung von mehr VMs. Gleichzeitig aber wird der unn{\"o}tige Energieverbrauch minimiert. Zus{\"a}tzlich mindert diese Technik unerw{\"u}nschte {\"A}nde-rungen im Energiezustand des Servers. Die vorgestellte Technik nutzt einen auf Intervall basierenden Vorhersagealgorithmus zur Implementierung einer robusten Optimierung. Dabei werden unsichere Anforderungen in Betracht gezogen. Ein adaptives und auf Intervall basierendes Verfahren zur Vorhersage des Arbeitsaufkommens mit hohen, in k{\"u}rzer Zeit auftretenden Schwankungen. Die Intervall basierende Vorhersage ist implementiert in der Standard Abweichung Variante und in der Median absoluter Abweichung Variante. Die Intervall-{\"A}nderungen basieren auf einem adaptiven Vertrauensfenster um die Schwankungen des Arbeitsaufkommens zu bew{\"a}ltigen. Eine robuste VM Zusammenlegung f{\"u}r ein effizientes Energie und Performance Management. Dies erm{\"o}glicht die gegenseitige Abh{\"a}ngigkeit zwischen der Energie und der Performance zu minimieren. Unser Verfahren reduziert die Anzahl der VM-Migrationen im Vergleich mit den neu vor kurzem vorgestellten Verfahren. Dies tr{\"a}gt auch zur Reduzierung des durch das Netzwerk verursachten Energieverbrauches. Außerdem reduziert dieses Verfahren SLA-Verletzungen und die Anzahl von {\"A}nderungen an Energiezus-t{\"a}nden. Ein generisches Modell f{\"u}r das Netzwerk eines Datenzentrums um die verz{\"o}-gerte Kommunikation und ihre Auswirkung auf die VM Performance und auf die Netzwerkenergie zu simulieren. Außerdem wird ein generisches Modell f{\"u}r ein Memory-Bus des Servers vorgestellt. Dieses Modell beinhaltet auch Modelle f{\"u}r die Latenzzeit und den Energieverbrauch f{\"u}r verschiedene Memory Frequenzen. Dies erlaubt eine Simulation der Memory Verz{\"o}gerung und ihre Auswirkung auf die VM-Performance und auf den Memory Energieverbrauch. Kommunikation bewusste und Energie effiziente Zusammenlegung f{\"u}r parallele Applikationen um die dynamische Entdeckung von Kommunikationsmustern und das Umplanen von VMs zu erm{\"o}glichen. Das Umplanen von VMs benutzt eine auf den entdeckten Kommunikationsmustern basierende Migration. Eine neue Technik zur Entdeckung von dynamischen Mustern ist implementiert. Sie basiert auf der Signal Verarbeitung des Netzwerks von VMs, anstatt die Informationen des virtuellen Umstellung der Hosts oder der Initiierung der VMs zu nutzen. Das Ergebnis zeigt, dass unsere Methode die durchschnittliche Anwendung des Netzwerks reduziert und aufgrund der Reduzierung der aktiven Umstellungen Energie gespart. Außerdem bietet sie eine bessere VM Performance im Vergleich zu der CPU-basierten Platzierung. Memory bewusste VM Zusammenlegung f{\"u}r unabh{\"a}ngige VMs. Sie nutzt die Vielfalt des VMs Memory Zuganges um die Anwendung vom Memory-Bus der Hosts zu balancieren. Die vorgestellte Technik, Memory-Bus Load Balancing (MLB), verteilt die VMs reaktiv neu im Bezug auf ihre Anwendung vom Memory-Bus. Sie nutzt die VM Migration um die Performance des gesamtem Systems zu verbessern. Außerdem sind die dynamische Spannung, die Frequenz Skalierung des Memory und die MLB Methode kombiniert um ein besseres Energiesparen zu leisten.}, language = {en} } @phdthesis{Vu2014, author = {Vu, Dinh Phuong}, title = {Using video study to investigate eighth-grade mathematics classrooms in Vietnam}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72464}, school = {Universit{\"a}t Potsdam}, pages = {273}, year = {2014}, abstract = {The International Project for the Evaluation of Educational Achievement (IEA) was formed in the 1950s (Postlethwaite, 1967). Since that time, the IEA has conducted many studies in the area of mathematics, such as the First International Mathematics Study (FIMS) in 1964, the Second International Mathematics Study (SIMS) in 1980-1982, and a series of studies beginning with the Third International Mathematics and Science Study (TIMSS) which has been conducted every 4 years since 1995. According to Stigler et al. (1999), in the FIMS and the SIMS, U.S. students achieved low scores in comparison with students in other countries (p. 1). The TIMSS 1995 "Videotape Classroom Study" was therefore a complement to the earlier studies conducted to learn "more about the instructional and cultural processes that are associated with achievement" (Stigler et al., 1999, p. 1). The TIMSS Videotape Classroom Study is known today as the TIMSS Video Study. From the findings of the TIMSS 1995 Video Study, Stigler and Hiebert (1999) likened teaching to "mountain ranges poking above the surface of the water," whereby they implied that we might see the mountaintops, but we do not see the hidden parts underneath these mountain ranges (pp. 73-78). By watching the videotaped lessons from Germany, Japan, and the United States again and again, they discovered that "the systems of teaching within each country look similar from lesson to lesson. At least, there are certain recurring features [or patterns] that typify many of the lessons within a country and distinguish the lessons among countries" (pp. 77-78). They also discovered that "teaching is a cultural activity," so the systems of teaching "must be understood in relation to the cultural beliefs and assumptions that surround them" (pp. 85, 88). From this viewpoint, one of the purposes of this dissertation was to study some cultural aspects of mathematics teaching and relate the results to mathematics teaching and learning in Vietnam. Another research purpose was to carry out a video study in Vietnam to find out the characteristics of Vietnamese mathematics teaching and compare these characteristics with those of other countries. In particular, this dissertation carried out the following research tasks: - Studying the characteristics of teaching and learning in different cultures and relating the results to mathematics teaching and learning in Vietnam - Introducing the TIMSS, the TIMSS Video Study and the advantages of using video study in investigating mathematics teaching and learning - Carrying out the video study in Vietnam to identify the image, scripts and patterns, and the lesson signature of eighth-grade mathematics teaching in Vietnam - Comparing some aspects of mathematics teaching in Vietnam and other countries and identifying the similarities and differences across countries - Studying the demands and challenges of innovating mathematics teaching methods in Vietnam - lessons from the video studies Hopefully, this dissertation will be a useful reference material for pre-service teachers at education universities to understand the nature of teaching and develop their teaching career.}, language = {en} } @phdthesis{Lotkowska2014, author = {Lotkowska, Magda Ewa}, title = {Functional analysis of MYB112 transcription factor in the model plant Arabidopsis thaliana}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72131}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Transcription factors (TFs) are ubiquitous gene expression regulators and play essential roles in almost all biological processes. This Ph.D. project is primarily focused on the functional characterisation of MYB112 - a member of the R2R3-MYB TF family from the model plant Arabidopsis thaliana. This gene was selected due to its increased expression during senescence based on previous qRT-PCR expression profiling experiments of 1880 TFs in Arabidopsis leaves at three developmental stages (15 mm leaf, 30 mm leaf and 20\% yellowing leaf). MYB112 promoter GUS fusion lines were generated to further investigate the expression pattern of MYB112. Employing transgenic approaches in combination with metabolomics and transcriptomics we demonstrate that MYB112 exerts a major role in regulation of plant flavonoid metabolism. We report enhanced and impaired anthocyanin accumulation in MYB112 overexpressors and MYB112-deficient mutants, respectively. Expression profiling reveals that MYB112 acts as a positive regulator of the transcription factor PAP1 leading to increased anthocyanin biosynthesis, and as a negative regulator of MYB12 and MYB111, which both control flavonol biosynthesis. We also identify MYB112 early responsive genes using a combination of several approaches. These include gene expression profiling (Affymetrix ATH1 micro-arrays and qRT-PCR) and transactivation assays in leaf mesophyll cell protoplasts. We show that MYB112 binds to an 8-bp DNA fragment containing the core sequence (A/T/G)(A/C)CC(A/T)(A/G/T)(A/C)(T/C). By electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation coupled to qPCR (ChIP-qPCR) we demonstrate that MYB112 binds in vitro and in vivo to MYB7 and MYB32 promoters revealing them as direct downstream target genes. MYB TFs were previously reported to play an important role in controlling flavonoid biosynthesis in plants. Many factors acting upstream of the anthocyanin biosynthesis pathway show enhanced expression levels during nitrogen limitation, or elevated sucrose content. In addition to the mentioned conditions, other environmental parameters including salinity or high light stress may trigger anthocyanin accumulation. In contrast to several other MYB TFs affecting anthocyanin biosynthesis pathway genes, MYB112 expression is not controlled by nitrogen limitation, or carbon excess, but rather is stimulated by salinity and high light stress. Thus, MYB112 constitutes a previously uncharacterised regulatory factor that modifies anthocyanin accumulation under conditions of abiotic stress.}, language = {en} } @phdthesis{Trost2014, author = {Trost, Gerda}, title = {Poly(A) Polymerase 1 (PAPS1) influences organ size and pathogen response in Arabidopsis thaliana}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72345}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Polyadenylation of pre-mRNAs is critical for efficient nuclear export, stability, and translation of the mature mRNAs, and thus for gene expression. The bulk of pre-mRNAs are processed by canonical nuclear poly(A) polymerase (PAPS). Both vertebrate and higher-plant genomes encode more than one isoform of this enzyme, and these are coexpressed in different tissues. However, in neither case is it known whether the isoforms fulfill different functions or polyadenylate distinct subsets of pre-mRNAs. This thesis shows that the three canonical nuclear PAPS isoforms in Arabidopsis are functionally specialized owing to their evolutionarily divergent C-terminal domains. A moderate loss-of-function mutant in PAPS1 leads to increase in floral organ size, whereas leaf size is reduced. A strong loss-of-function mutation causes a male gametophytic defect, whereas a weak allele leads to reduced leaf growth. By contrast, plants lacking both PAPS2 and PAPS4 function are viable with wild-type leaf growth. Polyadenylation of SMALL AUXIN UP RNA (SAUR) mRNAs depends specifically on PAPS1 function. The resulting reduction in SAUR activity in paps1 mutants contributes to their reduced leaf growth, providing a causal link between polyadenylation of specific pre-mRNAs by a particular PAPS isoform and plant growth. Additionally, opposite effects of PAPS1 on leaf and flower growth reflect the different identities of these organs. The overgrowth of paps1 mutant petals is due to increased recruitment of founder cells into early organ primordia whereas the reduced leaf size is due to an ectopic pathogen response. This constitutive immune response leads to increased resistance to the biotrophic oomycete Hyaloperonospora arabidopsidis and reflects activation of the salicylic acid-independent signalling pathway downstream of ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)/PHYTOALEXIN DEFICIENT4 (PAD4). Immune responses are accompanied by intracellular redox changes. Consistent with this, the redox-status of the chloroplast is altered in paps1-1 mutants. The molecular effects of the paps1-1 mutation were analysed using an RNA sequencing approach that distinguishes between long- and short tailed mRNA. The results shown here suggest the existence of an additional layer of regulation in plants and possibly vertebrate gene expression, whereby the relative activities of canonical nuclear PAPS isoforms control de novo synthesized poly(A) tail length and hence expression of specific subsets of mRNAs.}, language = {en} } @phdthesis{Arnold2014, author = {Arnold, Anne}, title = {Modeling photosynthesis and related metabolic processes : from detailed examination to consideration of the metabolic context}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72277}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Mathematical modeling of biological systems is a powerful tool to systematically investigate the functions of biological processes and their relationship with the environment. To obtain accurate and biologically interpretable predictions, a modeling framework has to be devised whose assumptions best approximate the examined scenario and which copes with the trade-off of complexity of the underlying mathematical description: with attention to detail or high coverage. Correspondingly, the system can be examined in detail on a smaller scale or in a simplified manner on a larger scale. In this thesis, the role of photosynthesis and its related biochemical processes in the context of plant metabolism was dissected by employing modeling approaches ranging from kinetic to stoichiometric models. The Calvin-Benson cycle, as primary pathway of carbon fixation in C3 plants, is the initial step for producing starch and sucrose, necessary for plant growth. Based on an integrative analysis for model ranking applied on the largest compendium of (kinetic) models for the Calvin-Benson cycle, those suitable for development of metabolic engineering strategies were identified. Driven by the question why starch rather than sucrose is the predominant transitory carbon storage in higher plants, the metabolic costs for their synthesis were examined. The incorporation of the maintenance costs for the involved enzymes provided a model-based support for the preference of starch as transitory carbon storage, by only exploiting the stoichiometry of synthesis pathways. Many photosynthetic organisms have to cope with processes which compete with carbon fixation, such as photorespiration whose impact on plant metabolism is still controversial. A systematic model-oriented review provided a detailed assessment for the role of this pathway in inhibiting the rate of carbon fixation, bridging carbon and nitrogen metabolism, shaping the C1 metabolism, and influencing redox signal transduction. The demand of understanding photosynthesis in its metabolic context calls for the examination of the related processes of the primary carbon metabolism. To this end, the Arabidopsis core model was assembled via a bottom-up approach. This large-scale model can be used to simulate photoautotrophic biomass production, as an indicator for plant growth, under so-called optimal, carbon-limiting and nitrogen-limiting growth conditions. Finally, the introduced model was employed to investigate the effects of the environment, in particular, nitrogen, carbon and energy sources, on the metabolic behavior. This resulted in a purely stoichiometry-based explanation for the experimental evidence for preferred simultaneous acquisition of nitrogen in both forms, as nitrate and ammonium, for optimal growth in various plant species. The findings presented in this thesis provide new insights into plant system's behavior, further support existing opinions for which mounting experimental evidences arise, and posit novel hypotheses for further directed large-scale experiments.}, language = {en} } @phdthesis{Serrano2014, author = {Serrano, Paloma}, title = {Methanogens from Siberian permafrost as models for life on Mars : response to simulated martian conditions and biosignature characterization}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72299}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Mars is one of the best candidates among planetary bodies for supporting life. The presence of water in the form of ice and atmospheric vapour together with the availability of biogenic elements and energy are indicators of the possibility of hosting life as we know it. The occurrence of permanently frozen ground - permafrost, is a common phenomenon on Mars and it shows multiple morphological analogies with terrestrial permafrost. Despite the extreme inhospitable conditions, highly diverse microbial communities inhabit terrestrial permafrost in large numbers. Among these are methanogenic archaea, which are anaerobic chemotrophic microorganisms that meet many of the metabolic and physiological requirements for survival on the martian subsurface. Moreover, methanogens from Siberian permafrost are extremely resistant against different types of physiological stresses as well as simulated martian thermo-physical and subsurface conditions, making them promising model organisms for potential life on Mars. The main aims of this investigation are to assess the survival of methanogenic archaea under Mars conditions, focusing on methanogens from Siberian permafrost, and to characterize their biosignatures by means of Raman spectroscopy, a powerful technology for microbial identification that will be used in the ExoMars mission. For this purpose, methanogens from Siberian permafrost and non-permafrost habitats were subjected to simulated martian desiccation by exposure to an ultra-low subfreezing temperature (-80ºC) and to Mars regolith (S-MRS and P-MRS) and atmospheric analogues. They were also exposed to different concentrations of perchlorate, a strong oxidant found in martian soils. Moreover, the biosignatures of methanogens were characterized at the single-cell level using confocal Raman microspectroscopy (CRM). The results showed survival and methane production in all methanogenic strains under simulated martian desiccation. After exposure to subfreezing temperatures, Siberian permafrost strains had a faster metabolic recovery, whereas the membranes of non-permafrost methanogens remained intact to a greater extent. The strain Methanosarcina soligelidi SMA-21 from Siberian permafrost showed significantly higher methane production rates than all other strains after the exposure to martian soil and atmospheric analogues, and all strains survived the presence of perchlorate at the concentration on Mars. Furthermore, CRM analyses revealed remarkable differences in the overall chemical composition of permafrost and non-permafrost strains of methanogens, regardless of their phylogenetic relationship. The convergence of the chemical composition in non-sister permafrost strains may be the consequence of adaptations to the environment, and could explain their greater resistance compared to the non-permafrost strains. As part of this study, Raman spectroscopy was evaluated as an analytical technique for remote detection of methanogens embedded in a mineral matrix. This thesis contributes to the understanding of the survival limits of methanogenic archaea under simulated martian conditions to further assess the hypothetical existence of life similar to methanogens on the martian subsurface. In addition, the overall chemical composition of methanogens was characterized for the first time by means of confocal Raman microspectroscopy, with potential implications for astrobiological research.}, language = {en} } @phdthesis{Lorey2014, author = {Lorey, Johannes}, title = {What's in a query : analyzing, predicting, and managing linked data access}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72312}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {The term Linked Data refers to connected information sources comprising structured data about a wide range of topics and for a multitude of applications. In recent years, the conceptional and technical foundations of Linked Data have been formalized and refined. To this end, well-known technologies have been established, such as the Resource Description Framework (RDF) as a Linked Data model or the SPARQL Protocol and RDF Query Language (SPARQL) for retrieving this information. Whereas most research has been conducted in the area of generating and publishing Linked Data, this thesis presents novel approaches for improved management. In particular, we illustrate new methods for analyzing and processing SPARQL queries. Here, we present two algorithms suitable for identifying structural relationships between these queries. Both algorithms are applied to a large number of real-world requests to evaluate the performance of the approaches and the quality of their results. Based on this, we introduce different strategies enabling optimized access of Linked Data sources. We demonstrate how the presented approach facilitates effective utilization of SPARQL endpoints by prefetching results relevant for multiple subsequent requests. Furthermore, we contribute a set of metrics for determining technical characteristics of such knowledge bases. To this end, we devise practical heuristics and validate them through thorough analysis of real-world data sources. We discuss the findings and evaluate their impact on utilizing the endpoints. Moreover, we detail the adoption of a scalable infrastructure for improving Linked Data discovery and consumption. As we outline in an exemplary use case, this platform is eligible both for processing and provisioning the corresponding information.}, language = {en} } @phdthesis{Holler2014, author = {Holler, Markus}, title = {Photon reconstruction for the H.E.S.S. 28 m telescope and analysis of Crab Nebula and galactic centre observations}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72099}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {In the presented thesis, the most advanced photon reconstruction technique of ground-based γ-ray astronomy is adapted to the H.E.S.S. 28 m telescope. The method is based on a semi-analytical model of electromagnetic particle showers in the atmosphere. The properties of cosmic γ-rays are reconstructed by comparing the camera image of the telescope with the Cherenkov emission that is expected from the shower model. To suppress the dominant background from charged cosmic rays, events are selected based on several criteria. The performance of the analysis is evaluated with simulated events. The method is then applied to two sources that are known to emit γ-rays. The first of these is the Crab Nebula, the standard candle of ground-based γ-ray astronomy. The results of this source confirm the expected performance of the reconstruction method, where the much lower energy threshold compared to H.E.S.S. I is of particular importance. A second analysis is performed on the region around the Galactic Centre. The analysis results emphasise the capabilities of the new telescope to measure γ-rays in an energy range that is interesting for both theoretical and experimental astrophysics. The presented analysis features the lowest energy threshold that has ever been reached in ground-based γ-ray astronomy, opening a new window to the precise measurement of the physical properties of time-variable sources at energies of several tens of GeV.}, language = {en} } @phdthesis{Truemper2014, author = {Tr{\"u}mper, Jonas}, title = {Visualization techniques for the analysis of software behavior and related structures}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72145}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Software maintenance encompasses any changes made to a software system after its initial deployment and is thereby one of the key phases in the typical software-engineering lifecycle. In software maintenance, we primarily need to understand structural and behavioral aspects, which are difficult to obtain, e.g., by code reading. Software analysis is therefore a vital tool for maintaining these systems: It provides - the preferably automated - means to extract and evaluate information from their artifacts such as software structure, runtime behavior, and related processes. However, such analysis typically results in massive raw data, so that even experienced engineers face difficulties directly examining, assessing, and understanding these data. Among other things, they require tools with which to explore the data if no clear question can be formulated beforehand. For this, software analysis and visualization provide its users with powerful interactive means. These enable the automation of tasks and, particularly, the acquisition of valuable and actionable insights into the raw data. For instance, one means for exploring runtime behavior is trace visualization. This thesis aims at extending and improving the tool set for visual software analysis by concentrating on several open challenges in the fields of dynamic and static analysis of software systems. This work develops a series of concepts and tools for the exploratory visualization of the respective data to support users in finding and retrieving information on the system artifacts concerned. This is a difficult task, due to the lack of appropriate visualization metaphors; in particular, the visualization of complex runtime behavior poses various questions and challenges of both a technical and conceptual nature. This work focuses on a set of visualization techniques for visually representing control-flow related aspects of software traces from shared-memory software systems: A trace-visualization concept based on icicle plots aids in understanding both single-threaded as well as multi-threaded runtime behavior on the function level. The concept's extensibility further allows the visualization and analysis of specific aspects of multi-threading such as synchronization, the correlation of such traces with data from static software analysis, and a comparison between traces. Moreover, complementary techniques for simultaneously analyzing system structures and the evolution of related attributes are proposed. These aim at facilitating long-term planning of software architecture and supporting management decisions in software projects by extensions to the circular-bundle-view technique: An extension to 3-dimensional space allows for the use of additional variables simultaneously; interaction techniques allow for the modification of structures in a visual manner. The concepts and techniques presented here are generic and, as such, can be applied beyond software analysis for the visualization of similarly structured data. The techniques' practicability is demonstrated by several qualitative studies using subject data from industry-scale software systems. The studies provide initial evidence that the techniques' application yields useful insights into the subject data and its interrelationships in several scenarios.}, language = {en} }