@phdthesis{Breitenbach2009,
  author    = {Breitenbach, Sebastian Franz Martin},
  title     = {Changes in monsoonal precipitation and atmospheric circulation during the Holocene reconstructed from stalagmites from Northeastern India},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-37807},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {Recent years witnessed a vast advent of stalagmites as palaeoclimate archives. The multitude of geochemical and physical proxies and a promise of a precise and accurate age model greatly appeal to palaeoclimatologists. Although substantial progress was made in speleothem-based palaeoclimate research and despite high-resolution records from low-latitudinal regions, proving that palaeo-environmental changes can be archived on sub-annual to millennial time scales our comprehension of climate dynamics is still fragmentary. This is in particular true for the summer monsoon system on the Indian subcontinent. The Indian summer monsoon (ISM) is an integral part of the intertropical convergence zone (ITCZ). As this rainfall belt migrates northward during boreal summer, it brings monsoonal rainfall. ISM strength depends however on a variety of factors, including snow cover in Central Asia and oceanic conditions in the Indic and Pacific. Presently, many of the factors influencing the ISM are known, though their exact forcing mechanism and mutual relations remain ambiguous. Attempts to make an accurate prediction of rainfall intensity and frequency and drought recurrence, which is extremely important for South Asian countries, resemble a puzzle game; all interaction need to fall into the right place to obtain a complete picture. My thesis aims to create a faithful picture of climate change in India, covering the last 11,000 ka. NE India represents a key region for the Bay of Bengal (BoB) branch of the ISM, as it is here where the monsoon splits into a northwestward and a northeastward directed arm. The Meghalaya Plateau is the first barrier for northward moving air masses and receives excessive summer rainfall, while the winter season is very dry. The proximity of Meghalaya to the Tibetan Plateau on the one hand and the BoB on the other hand make the study area a key location for investigating the interaction between different forcings that governs the ISM. A basis for the interpretation of palaeoclimate records, and a first important outcome of my thesis is a conceptual model which explains the observed pattern of seasonal changes in stable isotopes (d18O and d2H) in rainfall. I show that although in tropical and subtropical regions the amount effect is commonly called to explain strongly depleted isotope values during enhanced rainfall, alone it cannot account for observed rainwater isotope variability in Meghalaya. Monitoring of rainwater isotopes shows no expected negative correlation between precipitation amount and d18O of rainfall. In turn I find evidence that the runoff from high elevations carries an inherited isotopic signature into the BoB, where during the ISM season the freshwater builds a strongly depleted plume on top of the marine water. The vapor originating from this plume is likely to memorize' and transmit further very negative d18O values. The lack of data does not allow for quantication of this plume effect' on isotopes in rainfall over Meghalaya but I suggest that it varies on seasonal to millennial timescales, depending on the runoff amount and source characteristics. The focal point of my thesis is the extraction of climatic signals archived in stalagmites from NE India. High uranium concentration in the stalagmites ensured excellent age control required for successful high-resolution climate reconstructions. Stable isotope (d18O and d13C) and grey-scale data allow unprecedented insights into millennial to seasonal dynamics of the summer and winter monsoon in NE India. ISM strength (i. e. rainfall amount) is recorded in changes in d18Ostalagmites. The d13C signal, reflecting drip rate changes, renders a powerful proxy for dry season conditions, and shows similarities to temperature-related changes on the Tibetan Plateau. A sub-annual grey-scale profile supports a concept of lower drip rate and slower stalagmite growth during dry conditions. During the Holocene, ISM followed a millennial-scale decrease of insolation, with decadal to centennial failures resulting from atmospheric changes. The period of maximum rainfall and enhanced seasonality corresponds to the Holocene Thermal Optimum observed in Europe. After a phase of rather stable conditions, 4.5 kyr ago, the strengthening ENSO system dominated the ISM. Strong El Nino events weakened the ISM, especially when in concert with positive Indian Ocean dipole events. The strongest droughts of the last 11 kyr are recorded during the past 2 kyr. Using the advantage of a well-dated stalagmite record at hand I tested the application of laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to detect sub-annual to sub-decadal changes in element concentrations in stalagmites. The development of a large ablation cell allows for ablating sample slabs of up to 22 cm total length. Each analyzed element is a potential proxy for different climatic parameters. Combining my previous results with the LAICP- MS-generated data shows that element concentration depends not only on rainfall amount and associated leaching from the soil. Additional factors, like biological activity and hydrogeochemical conditions in the soil and vadose zone can eventually affect the element content in drip water and in stalagmites. I present a theoretical conceptual model for my study site to explain how climatic signals can be transmitted and archived in stalagmite carbonate. Further, I establish a first 1500 year long element record, reconstructing rainfall variability. Additionally, I hypothesize that volcanic eruptions, producing large amounts of sulfuric acid, can influence soil acidity and hence element mobilization.},
  language  = {en}
}
@phdthesis{Kruse2023,
  author    = {Kruse, Marlen},
  title     = {Characterization of biomolecules and their interactions using electrically controllable DNA nanolevers},
  doi       = {10.25932/publishup-57738},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-577384},
  school      = {Universit{\"a}t Potsdam},
  pages     = {100, xxii},
  year      = {2023},
  abstract  = {In this work, binding interactions between biomolecules were analyzed by a technique that is based on electrically controllable DNA nanolevers. The technique was applied to virus-receptor interactions for the first time. As receptors, primarily peptides on DNA nanostructures and antibodies were utilized. The DNA nanostructures were integrated into the measurement technique and enabled the presentation of the peptides in a controllable geometrical order. The number of peptides could be varied to be compatible to the binding sites of the viral surface proteins. Influenza A virus served as a model system, on which the general measurability was demonstrated. Variations of the receptor peptide, the surface ligand density, the measurement temperature and the virus subtypes showed the sensitivity and applicability of the technology. Additionally, the immobilization of virus particles enabled the measurement of differences in oligovalent binding of DNA-peptide nanostructures to the viral proteins in their native environment. When the coronavirus pandemic broke out in 2020, work on binding interactions of a peptide from the hACE2 receptor and the spike protein of the SARS-CoV-2 virus revealed that oligovalent binding can be quantified in the switchSENSE technology. It could also be shown that small changes in the amino acid sequence of the spike protein resulted in complete loss of binding. Interactions of the peptide and inactivated virus material as well as pseudo virus particles could be measured. Additionally, the switchSENSE technology was utilized to rank six antibodies for their binding affinity towards the nucleocapsid protein of SARS-CoV-2 for the development of a rapid antigen test device. The technique was furthermore employed to show binding of a non-enveloped virus (adenovirus) and a virus-like particle (norovirus-like particle) to antibodies. Apart from binding interactions, the use of DNA origami levers with a length of around 50 nm enabled the switching of virus material. This proved that the technology is also able to size objects with a hydrodynamic diameter larger than 14 nm. A theoretical work on diffusion and reaction-limited binding interactions revealed that the technique and the chosen parameters enable the determination of binding rate constants in the reaction-limited regime. Overall, the applicability of the switchSENSE technique to virus-receptor binding interactions could be demonstrated on multiple examples. While there are challenges that remain, the setup enables the determination of affinities between viruses and receptors in their native environment. Especially the possibilities regarding the quantification of oligo- and multivalent binding interactions could be presented.},
  language  = {en}
}
@misc{ElsenbeerLackCassel1995,
  author    = {Elsenbeer, Helmut and Lack, Andreas and Cassel, Keith},
  title     = {Chemical fingerprints of hydrological compartments and flow paths at La Cuenca, western Amazonia},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-16937},
  year      = {1995},
  abstract  = {A forested first-order catchment in western Amazonia was monitored for 2 years to determine the chemical fingerprints of precipitation, throughfall, overland flow, pipe flow, soil water, groundwater, and streamflow. We used five tracers (hydrogen, calcium, magnesium, potassium, and silica) to distinguish "fast" flow paths mainly influenced by the biological subsystem from "slow" flow paths in the geochemical subsystem. The former comprise throughfall, overland flow, and pipe flow and are characterized by a high potassium/silica ratio; the latter are represented by soil water and groundwater, which have a low potassium/silica ratio. Soil water and groundwater differ with respect to calcium and magnesium. The groundwater-controlled streamflow chemistry is strongly modified by contributions from fast flow paths during precipitation events. The high potassium/silica ratio of these flow paths suggests that the storm flow response at La Cuenca is dominated by event water.},
  language  = {en}
}
@phdthesis{Brauer2016,
  author    = {Brauer, Doroth{\´e}e},
  title     = {Chemo-kinematic constraints on Milky Way models from the spectroscopic surveys SEGUE \& RAVE},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-403968},
  school      = {Universit{\"a}t Potsdam},
  pages     = {vii, 197},
  year      = {2016},
  abstract  = {The Milky Way is only one out of billions of galaxies in the universe. However, it is a special galaxy because it allows to explore the main mechanisms involved in its evolution and formation history by unpicking the system star-by-star. Especially, the chemical fingerprints of its stars provide clues and evidence of past events in the Galaxy's lifetime. These information help not only to decipher the current structure and building blocks of the Milky Way, but to learn more about the general formation process of galaxies. In the past decade a multitude of stellar spectroscopic Galactic surveys have scanned millions of stars far beyond the rim of the solar neighbourhood. The obtained spectroscopic information provide unprecedented insights to the chemo-dynamics of the Milky Way. In addition analytic models and numerical simulations of the Milky Way provide necessary descriptions and predictions suited for comparison with observations in order to decode the physical properties that underlie the complex system of the Galaxy. In the thesis various approaches are taken to connect modern theoretical modelling of galaxy formation and evolution with observations from Galactic stellar surveys. With its focus on the chemo-kinematics of the Galactic disk this work aims to determine new observational constraints on the formation of the Milky Way providing also proper comparisons with two different models. These are the population synthesis model TRILEGAL based on analytical distribution functions, which aims to simulate the number and distribution of stars in the Milky Way and its different components, and a hybrid model (MCM) that combines an N-body simulation of a Milky Way like galaxy in the cosmological framework with a semi-analytic chemical evolution model for the Milky Way. The major observational data sets in use come from two surveys, namely the "Radial Velocity Experiment" (RAVE) and the "Sloan Extension for Galactic Understanding and Exploration" (SEGUE). In the first approach the chemo-kinematic properties of the thin and thick disk of the Galaxy as traced by a selection of about 20000 SEGUE G-dwarf stars are directly compared to the predictions by the MCM model. As a necessary condition for this, SEGUE's selection function and its survey volume are evaluated in detail to correct the spectroscopic observations for their survey specific selection biases. Also, based on a Bayesian method spectro-photometric distances with uncertainties below 15\% are computed for the selection of SEGUE G-dwarfs that are studied up to a distance of 3 kpc from the Sun. For the second approach two synthetic versions of the SEGUE survey are generated based on the above models. The obtained synthetic stellar catalogues are then used to create mock samples best resembling the compiled sample of observed SEGUE G-dwarfs. Generally, mock samples are not only ideal to compare predictions from various models. They also allow validation of the models' quality and improvement as with this work could be especially achieved for TRILEGAL. While TRILEGAL reproduces the statistical properties of the thin and thick disk as seen in the observations, the MCM model has shown to be more suitable in reproducing many chemo-kinematic correlations as revealed by the SEGUE stars. However, evidence has been found that the MCM model may be missing a stellar component with the properties of the thick disk that the observations clearly show. While the SEGUE stars do indicate a thin-thick dichotomy of the stellar Galactic disk in agreement with other spectroscopic stellar studies, no sign for a distinct metal-poor disk is seen in the MCM model. Usually stellar spectroscopic surveys are limited to a certain volume around the Sun covering different regions of the Galaxy's disk. This often prevents to obtain a global view on the chemo-dynamics of the Galactic disk. Hence, a suitable combination of stellar samples from independent surveys is not only useful for the verification of results but it also helps to complete the picture of the Milky Way. Therefore, the thesis closes with a comparison of the SEGUE G-dwarfs and a sample of RAVE giants. The comparison reveals that the chemo-kinematic relations agree in disk regions where the samples of both surveys show a similar number of stars. For those parts of the survey volumes where one of the surveys lacks statistics they beautifully complement each other. This demonstrates that the comparison of theoretical models on the one side, and the combined observational data gathered by multiple surveys on the other side, are key ingredients to understand and disentangle the structure and formation history of the Milky Way.},
  language  = {en}
}
@phdthesis{Bierbaum2011,
  author    = {Bierbaum, Veronika},
  title     = {Chemomechanical coupling and motor cycles of the molecular motor myosin V},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-53614},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {In the living cell, the organization of the complex internal structure relies to a large extent on molecular motors. Molecular motors are proteins that are able to convert chemical energy from the hydrolysis of adenosine triphosphate (ATP) into mechanical work. Being about 10 to 100 nanometers in size, the molecules act on a length scale, for which thermal collisions have a considerable impact onto their motion. In this way, they constitute paradigmatic examples of thermodynamic machines out of equilibrium. This study develops a theoretical description for the energy conversion by the molecular motor myosin V, using many different aspects of theoretical physics. Myosin V has been studied extensively in both bulk and single molecule experiments. Its stepping velocity has been characterized as a function of external control parameters such as nucleotide concentration and applied forces. In addition, numerous kinetic rates involved in the enzymatic reaction of the molecule have been determined. For forces that exceed the stall force of the motor, myosin V exhibits a 'ratcheting' behaviour: For loads in the direction of forward stepping, the velocity depends on the concentration of ATP, while for backward loads there is no such influence. Based on the chemical states of the motor, we construct a general network theory that incorporates experimental observations about the stepping behaviour of myosin V. The motor's motion is captured through the network description supplemented by a Markov process to describe the motor dynamics. This approach has the advantage of directly addressing the chemical kinetics of the molecule, and treating the mechanical and chemical processes on equal grounds. We utilize constraints arising from nonequilibrium thermodynamics to determine motor parameters and demonstrate that the motor behaviour is governed by several chemomechanical motor cycles. In addition, we investigate the functional dependence of stepping rates on force by deducing the motor's response to external loads via an appropriate Fokker-Planck equation. For substall forces, the dominant pathway of the motor network is profoundly different from the one for superstall forces, which leads to a stepping behaviour that is in agreement with the experimental observations. The extension of our analysis to Markov processes with absorbing boundaries allows for the calculation of the motor's dwell time distributions. These reveal aspects of the coordination of the motor's heads and contain direct information about the backsteps of the motor. Our theory provides a unified description for the myosin V motor as studied in single motor experiments.},
  language  = {en}
}
@phdthesis{Oey2008,
  author    = {Oey, Melanie},
  title     = {Chloroplasts as bioreactors : high-yield production of active bacteriolytic protein antibiotics},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-28950},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {Plants, more precisely their chloroplasts with their bacterial-like expression machinery inherited from their cyanobacterial ancestors, can potentially offer a cheap expression system for proteinaceous pharmaceuticals. This system would be easily scalable and provides appropriate safety due to chloroplasts maternal inheritance. In this work, it was shown that three phage lytic enzymes (Pal, Cpl-1 and PlyGBS) could be successfully expressed at very high levels and with high stability in tobacco chloroplasts. PlyGBS expression reached an amount of foreign protein accumulation (> 70\% TSP) that has never been obtained before. Although the high expression levels of PlyGBS caused a pale green phenotype with retarded growth, presumably due to exhaustion of plastid protein synthesis capacity, development and seed production were not impaired under greenhouse conditions. Since Pal and Cpl-1 showed toxic effects when expressed in E. coli, a special plastid transformation vector (pTox) was constructed to allow DNA amplification in bacteria. The construction of the pTox transformation vector allowing a recombinase-mediated deletion of an E. coli transcription block in the chloroplast, leading to an increase of foreign protein accumulation to up to 40\% of TSP for Pal and 20\% of TSP for Cpl-1. High dose-dependent bactericidal efficiency was shown for all three plant-derived lytic enzymes using their pathogenic target bacteria S. pyogenes and S. pneumoniae. Confirmation of specificity was obtained for the endotoxic proteins Pal and Cpl-1 by application to E. coli cultures. These results establish tobacco chloroplasts as a new cost-efficient and convenient production platform for phage lytic enzymes and address the greatest obstacle for clinical application. The present study is the first report of lysin production in a non-bacterial system. The properties of chloroplast-produced lysins described in this work, their stability, high accumulation rate and biological activity make them highly attractive candidates for future antibiotics.},
  language  = {en}
}
@inproceedings{IgnaceGayley2007,
  author    = {Ignace, R. and Gayley, K. G.},
  title     = {Circumstellar Magnetic Field Diagnostics from Line Polarization},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-18066},
  year      = {2007},
  language  = {en}
}
@inproceedings{MillsHealey2006,
  author    = {Mills, Gregory J. and Healey, Patrick G. T.},
  title     = {Clarifying spatial descriptions : local and global effects on semantic co-ordination},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-10414},
  year      = {2006},
  abstract  = {A key problem for models of dialogue is to explain the mechanisms involved in generating and responding to clarification requests. We report a 'Maze task' experiment that investigates the effect of 'spoof' clarification requests on the development of semantic co-ordination. The results provide evidence of both local and global semantic co-ordination phenomena that are not captured by existing dialogue co-ordination models.},
  language  = {en}
}
@phdthesis{Holsten2013,
  author    = {Holsten, Anne},
  title     = {Climate change vulnerability assessments in the regional context},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-66836},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Adapting sectors to new conditions under climate change requires an understanding of regional vulnerabilities. Conceptually, vulnerability is defined as a function of sensitivity and exposure, which determine climate impacts, and adaptive capacity of a system. Vulnerability assessments for quantifying these components have become a key tool within the climate change field. However, there is a disagreement on how to make the concept operational in studies from a scientific perspective. This conflict leads to many still unsolved challenges, especially regarding the quantification and aggregation of the components and their suitable level of complexity. This thesis therefore aims at advancing the scientific foundation of such studies by translating the concept of vulnerability into a systematic assessment structure. This includes all components and implies that for each considered impact (e.g. flash floods) a clear sensitive entity is defined (e.g. settlements) and related to a direction of change for a specific climatic stimulus (e.g. increasing impact due to increasing days with heavy precipitation). Regarding the challenging aggregation procedure, two alternative methods allowing a cross-sectoral overview are introduced and their advantages and disadvantages discussed. This assessment structure is subsequently exemplified for municipalities of the German state North Rhine-Westphalia via an indicator-based deductive approach using information from literature. It can be transferred also to other regions. As for many relevant sectors, suitable indicators to express the vulnerability components are lacking, new quantification methods are developed and applied in this thesis, for example for the forestry and health sector. A lack of empirical data on relevant thresholds is evident, for example which climatic changes would cause significant impacts. Consequently, the multi-sectoral study could only provide relative measures for each municipality, in relation to the region. To fill this gap, an exemplary sectoral study was carried out on windthrow impacts in forests to provide an absolute quantification of the present and future impact. This is achieved by formulating an empirical relation between the forest characteristics and damage based on data from a past storm event. The resulting measure indicating the sensitivity is then combined with wind conditions. Multi-sectoral vulnerability assessments require considerable resources, which often hinders the implementation. Thus, in a next step, the potential for reducing the complexity is explored. To predict forest fire occurrence, numerous meteorological indices are available, spanning over a range of complexity. Comparing their performance, the single variable relative humidity outperforms complex indicators for most German states in explaining the monthly fire pattern. This is the case albeit it is itself an input factor in most indices. Thus, this meteorological factor alone is well suited to evaluate forest fire danger in many Germany regions and allows a resource-efficient assessment. Similarly, the complexity of methods is assessed regarding the application of the ecohydrological model SWIM to the German region of Brandenburg. The inter-annual soil moisture levels simulated by this model can only poorly be represented by simpler statistical approach using the same input data. However, on a decadal time horizon, the statistical approach shows a good performance and a strong dominance of the soil characteristic field capacity. This points to a possibility to reduce the input factors for predicting long-term averages, but the results are restricted by a lack of empirical data on soil water for validation. The presented assessments of vulnerability and its components have shown that they are still a challenging scientific undertaking. Following the applied terminology, many problems arise when implementing it for regional studies. Advances in addressing shortcomings of previous studies have been made by constructing a new systematic structure for characterizing and aggregating vulnerability components. For this, multiple approaches were presented, but they have specific advantages and disadvantages, which should also be carefully considered in future studies. There is a potential to simplify some methods, but more systematic assessments on this are needed. Overall, this thesis strengthened the use of vulnerability assessments as a tool to support adaptation by enhancing their scientific basis.},
  language  = {en}
}
@phdthesis{Hoffmann2007,
  author    = {Hoffmann, Toni},
  title     = {Cloning and characterisation of the HMA3 gene and its promoter from Arabidopsis halleri (L.) O'Kane and Al'Shehbaz and Arabidopsis thaliana (L.) Heynhold},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15259},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Being living systems unable to adjust their location to changing environmental conditions, plants display homeostatic networks that have evolved to maintain transition metal levels in a very narrow concentration range in order to avoid either deficiency or toxicity. Hence, plants possess a broad repertoire of mechanisms for the cellular uptake, compartmentation and efflux, as well as for the chelation of transition metal ions. A small number of plants are hypertolerant to one or a few specific transition metals. Some metal tolerant plants are also able to hyperaccumulate metal ions. The Brassicaceae family member Arabidopis halleri ssp. halleri (L.) O´KANE and AL´SHEHBAZ is a hyperaccumulator of zinc (Zn), and it is closely related to the non-hypertolerant and non-hyperaccumulating model plant Arabidopsis thaliana (L.) HEYNHOLD. The close relationship renders A. halleri a promising emerging model plant for the comparative investigation of the molecular mechanisms behind hypertolerance and hyperaccumulation. Among several potential candidate genes that are probably involved in mediating the zinc-hypertolerant and zinc-hyperaccumulating trait is AhHMA3. The AhHMA3 gene is highly similar to AtHMA3 (AGI number: At4g30120) in A. thaliana, and its encoded protein belongs to the P-type IB ATPase family of integral membrane transporter proteins that transport transition metals. In contrast to the low AtHMA3 transcript levels in A. thaliana, the gene was found to be constitutively highly expressed across different Zn treatments in A. halleri, especially in shoots. In this study, the cloning and characterisation of the HMA3 gene and its promoter from Arabidopsis halleri (L.) O´KANE and AL´SHEHBAZ and Arabidopsis thaliana (L.) HEYNHOLD is described. Heterologously expressed AhHMA3 mediated enhanced tolerance to Zn and to a much lesser degree to cadmium (Cd) but not to cobalt (Co) in metal-sensitive mutant strains of budding yeast. It is demonstrated that the genome of A. halleri contains at least four copies of AhHMA3, AhHMA3-1 to AhHMA3-4. A copy-specific real-time RT-PCR indicated that an AhHMA3-1 related gene copy is the source of the constitutively high transcript level in A. halleri and not a gene copy similar to AhHMA3-2 or AhHMA3-4. In accordance with the enhanced AtHMA3mRNA transcript level in A. thaliana roots, an AtHMA3 promoter-GUS gene construct mediated GUS activity predominantly in the vascular tissues of roots and not in shoots. However, the observed AhHMA3-1 and AhHMA3-2 promoter-mediated GUS activity in A. thaliana or A. halleri plants did not reflect the constitutively high expression of AhHMA3 in shoots of A. halleri. It is suggested that other factors e. g. characteristic sequence inserts within the first intron of AhHMA3-1 might enable a constitutively high expression. Moreover, the unknown promoter of the AhHMA3-3 gene copy could be the source of the constitutively high AhHMA3 transcript levels in A. halleri. In that case, the AhHMA3-3 sequence is predicted to be highly homologous to AhHMA3-1. The lack of solid localisation data for the AhHMA3 protein prevents a clear functional assignment. The provided data suggest several possible functions of the AhHMA3 protein: Like AtHMA2 and AtHMA4 it might be localised to the plasma membrane and could contribute to the efficient translocation of Zn from root to shoot and/or to the cell-to-cell distribution of Zn in the shoot. If localised to the vacuolar membrane, then a role in maintaining a low cytoplasmic zinc concentration by vacuolar zinc sequestration is possible. In addition, AhHMA3 might be involved in the delivery of zinc ions to trichomes and mesophyll leaf cells that are major zinc storage sites in A. halleri.},
  language  = {en}
}
@inproceedings{Reimer2007,
  author    = {Reimer, A.},
  title     = {Clumping effects on non-thermal particle spectra in massive star systems},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-18246},
  year      = {2007},
  abstract  = {Observational evidence exists that winds of massive stars are clumped. Many massive star systems are known as non-thermal particle production sites, as indicated by their synchrotron emission in the radio band. As a consequence they are also considered as candidate sites for non-thermal high-energy photon production up to gamma-ray energies. The present work considers the effects of wind clumpiness expected on the emitting relativistic particle spectrum in colliding wind systems, built up from the pool of thermal wind particles through diffusive particle acceleration, and taking into account inverse Compton and synchrotron losses. In comparison to a homogeneous wind, a clumpy wind causes flux variations of the emitting particle spectrum when the clump enters the wind collision region. It is found that the spectral features associated with this variability moves temporally from low to high energy bands with the time shift between any two spectral bands being dependent on clump size, filling factor, and the energy-dependence of particle energy gains and losses.},
  language  = {en}
}
@inproceedings{LiermannHamann2007,
  author    = {Liermann, A. and Hamann, Wolf-Rainer},
  title     = {Clumping in Galactic WN stars : a comparison of mass loss rates from UV/optical \& radio diagnostics},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-17816},
  year      = {2007},
  abstract  = {The mass loss rates and other parameters for a large sample of Galactic WN stars have been revised by Hamann et al. (2006), using the most up-to date Potsdam Wolf-Rayet (PoWR) model atmospheres. For a sub-sample of these stars exist measurements of their radio free-free emission. After harmonizing the adopted distance and terminal wind velocities, we compare the mass loss rates obtained from the two diagnostics. The differences are discussed as a possible consequence of different clumping contrast in the line-forming and radio-emitting regions.},
  language  = {en}
}
@inproceedings{OPUS4-1574,
  title     = {Clumping in hot-star winds : proceedings of an international workshop held in Potsdam, Germany, 18. - 22. June 2007},
  editor    = {Hamann, Wolf-Rainer and Feldmeier, Achim and Oskinova, Lida},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-940793-33-1},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-13981},
  pages     = {254},
  year      = {2007},
  abstract  = {Stellar winds play an important role for the evolution of massive stars and their cosmic environment. Multiple lines of evidence, coming from spectroscopy, polarimetry, variability, stellar ejecta, and hydrodynamic modeling, suggest that stellar winds are non-stationary and inhomogeneous. This is referred to as 'wind clumping'. The urgent need to understand this phenomenon is boosted by its far-reaching implications. Most importantly, all techniques to derive empirical mass-loss rates are more or less corrupted by wind clumping. Consequently, mass-loss rates are extremely uncertain. Within their range of uncertainty, completely different scenarios for the evolution of massive stars are obtained. Settling these questions for Galactic OB, LBV and Wolf-Rayet stars is prerequisite to understanding stellar clusters and galaxies, or predicting the properties of first-generation stars. In order to develop a consistent picture and understanding of clumped stellar winds, an international workshop on 'Clumping in Hot Star Winds' was held in Potsdam, Germany, from 18. - 22. June 2007. About 60 participants, comprising almost all leading experts in the field, gathered for one week of extensive exchange and discussion. The Scientific Organizing Committee (SOC) included John Brown (Glasgow), Joseph Cassinelli (Madison), Paul Crowther (Sheffield), Alex Fullerton (Baltimore), Wolf-Rainer Hamann (Potsdam, chair), Anthony Moffat (Montreal), Stan Owocki (Newark), and Joachim Puls (Munich). These proceedings contain the invited and contributed talks presented at the workshop, and document the extensive discussions.},
  language  = {en}
}
@inproceedings{PulsMarkovaNajarroetal.2007,
  author    = {Puls, Joachim and Markova, N. and Najarro, F. and Hanson, M. M.},
  title     = {Clumping in O-star winds},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-17683},
  year      = {2007},
  abstract  = {We review various diagnostics of clumping in O-star winds, with special emphasis on its radial stratification. Implications and problems are discussed, and promising NIR methods are presented.},
  language  = {en}
}
@inproceedings{BouretLanzHillieretal.2007,
  author    = {Bouret, J.-C. and Lanz, T. and Hillier, D. J. and Foellmi, C.},
  title     = {Clumping in O-type Supergiants},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-17662},
  year      = {2007},
  abstract  = {We have analyzed the spectra of seven Galactic O4 supergiants, with the NLTE wind code CMFGEN. For all stars, we have found that clumped wind models match well lines from different species spanning a wavelength range from FUV to optical, and remain consistent with Hα data. We have achieved an excellent match of the P V λλ1118, 1128 resonance doublet and N IV λ1718, as well as He II λ4686 suggesting that our physical description of clumping is adequate. We find very small volume filling factors and that clumping starts deep in the wind, near the sonic point. The most crucial consequence of our analysis is that the mass loss rates of O stars need to be revised downward significantly, by a factor of 3 and more compared to those obtained from smooth-wind models.},
  language  = {en}
}
@inproceedings{UrbanejaKudritzkiPuls2007,
  author    = {Urbaneja, M. A. and Kudritzki, R.-P. and Puls, Joachim},
  title     = {Clumping in the winds of O-type CSPNs},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-17801},
  year      = {2007},
  abstract  = {Recent studies of massive O-type stars present clear evidences of inhomogeneous and clumped winds. O-type (H-rich) central stars of planetary nebulae (CSPNs) are in some ways the low mass-low luminosity analogous of those massive stars. In this contribution, we present preliminary results of our on-going multi-wavelength (FUV, UV and optical) study of the winds of Galactic CSPNs. Particular emphasis will be given to the clumping factors derived by means of optical lines (Hα and Heii 4686) and "classic" FUV (and UV) lines.},
  language  = {en}
}
@phdthesis{Hoffmann2011,
  author    = {Hoffmann, Anne},
  title     = {Comparative aerosol studies based on multi-wavelength Raman LIDAR at Ny-{\AA}lesund, Spitsbergen},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-52426},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {The Arctic is a particularly sensitive area with respect to climate change due to the high surface albedo of snow and ice and the extreme radiative conditions. Clouds and aerosols as parts of the Arctic atmosphere play an important role in the radiation budget, which is, as yet, poorly quantified and understood. The LIDAR (Light Detection And Ranging) measurements presented in this PhD thesis contribute with continuous altitude resolved aerosol profiles to the understanding of occurrence and characteristics of aerosol layers above Ny-{\AA}lesund, Spitsbergen. The attention was turned to the analysis of periods with high aerosol load. As the Arctic spring troposphere exhibits maximum aerosol optical depths (AODs) each year, March and April of both the years 2007 and 2009 were analyzed. Furthermore, stratospheric aerosol layers of volcanic origin were analyzed for several months, subsequently to the eruptions of the Kasatochi and Sarychev volcanoes in summer 2008 and 2009, respectively. The Koldewey Aerosol Raman LIDAR (KARL) is an instrument for the active remote sensing of atmospheric parameters using pulsed laser radiation. It is operated at the AWIPEV research base and was fundamentally upgraded within the framework of this PhD project. It is now equipped with a new telescope mirror and new detection optics, which facilitate atmospheric profiling from 450m above sea level up to the mid-stratosphere. KARL provides highly resolved profiles of the scattering characteristics of aerosol and cloud particles (backscattering, extinction and depolarization) as well as water vapor profiles within the lower troposphere. Combination of KARL data with data from other instruments on site, namely radiosondes, sun photometer, Micro Pulse LIDAR, and tethersonde system, resulted in a comprehensive data set of scattering phenomena in the Arctic atmosphere. The two spring periods March and April 2007 and 2009 were at first analyzed based on meteorological parameters, like local temperature and relative humidity profiles as well as large scale pressure patterns and air mass origin regions. Here, it was not possible to find a clear correlation between enhanced AOD and air mass origin. However, in a comparison of two cloud free periods in March 2007 and April 2009, large AOD values in 2009 coincided with air mass transport through the central Arctic. This suggests the occurrence of aerosol transformation processes during the aerosol transport to Ny-{\AA}lesund. Measurements on 4 April 2009 revealed maximum AOD values of up to 0.12 and aerosol size distributions changing with altitude. This and other performed case studies suggest the differentiation between three aerosol event types and their origin: Vertically limited aerosol layers in dry air, highly variable hygroscopic boundary layer aerosols and enhanced aerosol load across wide portions of the troposphere. For the spring period 2007, the available KARL data were statistically analyzed using a characterization scheme, which is based on optical characteristics of the scattering particles. The scheme was validated using several case studies. Volcanic eruptions in the northern hemisphere in August 2008 and June 2009 arose the opportunity to analyze volcanic aerosol layers within the stratosphere. The rate of stratospheric AOD change was similar within both years with maximum values above 0.1 about three to five weeks after the respective eruption. In both years, the stratospheric AOD persisted at higher rates than usual until the measurements were stopped in late September due to technical reasons. In 2008, up to three aerosol layers were detected, the layer structure in 2009 was characterized by up to six distinct and thin layers which smeared out to one broad layer after about two months. The lowermost aerosol layer was continuously detected at the tropopause altitude. Three case studies were performed, all revealed rather large indices of refraction of m = (1.53-1.55) - 0.02i, suggesting the presence of an absorbing carbonaceous component. The particle radius, derived with inversion calculations, was also similar in both years with values ranging from 0.16 to 0.19 μm. However, in 2009, a second mode in the size distribution was detected at about 0.5 μm. The long term measurements with the Koldewey Aerosol Raman LIDAR in Ny-{\AA}lesund provide the opportunity to study Arctic aerosols in the troposphere and the stratosphere not only in case studies but on longer time scales. In this PhD thesis, both, tropospheric aerosols in the Arctic spring and stratospheric aerosols following volcanic eruptions have been described qualitatively and quantitatively. Case studies and comparative studies with data of other instruments on site allowed for the analysis of microphysical aerosol characteristics and their temporal evolution.},
  language  = {en}
}
@misc{Donges2009,
  type      = {Master Thesis},
  author    = {Donges, Jonathan},
  title     = {Complex networks in the climate system},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-49775},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {Complex network theory provides an elegant and powerful framework to statistically investigate the topology of local and long range dynamical interrelationships, i.e., teleconnections, in the climate system. Employing a refined methodology relying on linear and nonlinear measures of time series analysis, the intricate correlation structure within a multivariate climatological data set is cast into network form. Within this graph theoretical framework, vertices are identified with grid points taken from the data set representing a region on the the Earth's surface, and edges correspond to strong statistical interrelationships between the dynamics on pairs of grid points. The resulting climate networks are neither perfectly regular nor completely random, but display the intriguing and nontrivial characteristics of complexity commonly found in real world networks such as the internet, citation and acquaintance networks, food webs and cortical networks in the mammalian brain. Among other interesting properties, climate networks exhibit the "small-world" effect and possess a broad degree distribution with dominating super-nodes as well as a pronounced community structure. We have performed an extensive and detailed graph theoretical analysis of climate networks on the global topological scale focussing on the flow and centrality measure betweenness which is locally defined at each vertex, but includes global topological information by relying on the distribution of shortest paths between all pairs of vertices in the network. The betweenness centrality field reveals a rich internal structure in complex climate networks constructed from reanalysis and atmosphere-ocean coupled general circulation model (AOGCM) surface air temperature data. Our novel approach uncovers an elaborately woven meta-network of highly localized channels of strong dynamical information flow, that we relate to global surface ocean currents and dub the backbone of the climate network in analogy to the homonymous data highways of the internet. This finding points to a major role of the oceanic surface circulation in coupling and stabilizing the global temperature field in the long term mean (140 years for the model run and 60 years for reanalysis data). Carefully comparing the backbone structures detected in climate networks constructed using linear Pearson correlation and nonlinear mutual information, we argue that the high sensitivity of betweenness with respect to small changes in network structure may allow to detect the footprints of strongly nonlinear physical interactions in the climate system. The results presented in this thesis are thoroughly founded and substantiated using a hierarchy of statistical significance tests on the level of time series and networks, i.e., by tests based on time series surrogates as well as network surrogates. This is particularly relevant when working with real world data. Specifically, we developed new types of network surrogates to include the additional constraints imposed by the spatial embedding of vertices in a climate network. Our methodology is of potential interest for a broad audience within the physics community and various applied fields, because it is universal in the sense of being valid for any spatially extended dynamical system. It can help to understand the localized flow of dynamical information in any such system by combining multivariate time series analysis, a complex network approach and the information flow measure betweenness centrality. Possible fields of application include fluid dynamics (turbulence), plasma physics and biological physics (population models, neural networks, cell models). Furthermore, the climate network approach is equally relevant for experimental data as well as model simulations and hence introduces a novel perspective on model evaluation and data driven model building. Our work is timely in the context of the current debate on climate change within the scientific community, since it allows to assess from a new perspective the regional vulnerability and stability of the climate system while relying on global and not only on regional knowledge. The methodology developed in this thesis hence has the potential to substantially contribute to the understanding of the local effect of extreme events and tipping points in the earth system within a holistic global framework.},
  language  = {en}
}
@article{Grgurina2013,
  author    = {Grgurina, Nataša},
  title     = {Computational thinking in Dutch secondary education},
  series = {Commentarii informaticae didacticae : (CID)},
  journal   = {Commentarii informaticae didacticae : (CID)},
  number    = {6},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {1868-0844},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-64556},
  pages     = {119 -- 123},
  year      = {2013},
  abstract  = {We shall examine the Pedagogical Content Knowledge (PCK) of Computer Science (CS) teachers concerning students' Computational Thinking (CT) problem solving skills within the context of a CS course in Dutch secondary education and thus obtain an operational definition of CT and ascertain appropriate teaching methodology. Next we shall develop an instrument to assess students' CT and design a curriculum intervention geared toward teaching and improving students' CT problem solving skills and competences. As a result, this research will yield an operational definition of CT, knowledge about CT PCK, a CT assessment instrument and teaching materials and accompanying teacher instructions. It shall contribute to CS teacher education, development of CT education and to education in other (STEM) subjects where CT plays a supporting role, both nationally and internationally.},
  language  = {en}
}
@inproceedings{BandaGallagher2010,
  author    = {Banda, Gourinath and Gallagher, John P.},
  title     = {Constraint-based abstraction of a model checker for infinite state systems},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41516},
  year      = {2010},
  abstract  = {Abstract interpretation-based model checking provides an approach to verifying properties of infinite-state systems. In practice, most previous work on abstract model checking is either restricted to verifying universal properties, or develops special techniques for temporal logics such as modal transition systems or other dual transition systems. By contrast we apply completely standard techniques for constructing abstract interpretations to the abstraction of a CTL semantic function, without restricting the kind of properties that can be verified. Furthermore we show that this leads directly to implementation of abstract model checking algorithms for abstract domains based on constraints, making use of an SMT solver.},
  language  = {en}
}