@phdthesis{Bergner2003, author = {Bergner, Andreas G. N.}, title = {Lake-level fluctuations and Late Quaternary climate change in the Central Kenya Rift}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001428}, school = {Universit{\"a}t Potsdam}, year = {2003}, abstract = {Diese Arbeit besch{\"a}ftigt sich mit der Rekonstruktion von Klima in historischen Zeiten im tropischen Ostafrika. Nach einer {\"U}bersicht {\"u}ber die heutigen klimatischen Bedingungen der Tropen und den Besonderheiten des ostafrikanischen Klimas, werden die M{\"o}glichkeiten der Klimarekonstruktion anhand von Seesedimenten diskutiert. Es zeigt sich, dass die hoch gelegenen Seen des Zentralen Keniarifts, als Teil des Ostafrikanischen Grabensystems, besonders geeignete Klimaarchive darstellen, da sie sensibel auf klimatische Ver{\"a}nderungen reagieren. Ver{\"a}nderungen der Seechemie, wie sie in den Sedimenten aufgezeichnet werden, eignen sich um die nat{\"u}rlichen Schwankungen in der Quart{\"a}ren Klimageschichte Ostafrikas nachzuzeichnen. Basierend auf der guten 40Ar/39Ar- und 14C-Datierbarkeit der Seesedimente wird eine Chronologie der pal{\"a}o{\"o}kologischen Bedingungen anhand von Diatomeenvergesellschaftungen restauriert. Dabei zeigen sich f{\"u}r die Seen Nakuru, Elmenteita und Naivasha kurzfristige Transgression/ Regressions-Zyklen im Intervall von ca. 11.000 Jahren w{\"a}hrend des letzten (ca. 12.000 bis 6.000 J.v.H.) und vorletzten Interglazials (ca. 140.000 bis 60.000 J.v.H.). Zus{\"a}tzlich kann ein allgemeiner, langfristiger Trend der Seeentwicklung von großen Frischwasserseen hin zu st{\"a}rker salinen Gew{\"a}ssern innerhalb der letzen 1 Mio. Jahre festgestellt werden. Mittels Transferfunktionen und einem hydro-klimatischen Modellansatz k{\"o}nnen die restaurierten limnologischen Bedingungen als klimatische Schwankungen des Einzugsgebietes interpretiert werden. Wenngleich auch der zus{\"a}tzliche Einfluss von tektonischen Ver{\"a}nderungen auf das Seeeinzugsgebiet und das Gewicht ver{\"a}nderter Grundwasserstr{\"o}me abgewogen werden, zeigt sich, dass allein geringf{\"u}gig erh{\"o}hte Niederschlagswerte von ca. 30±10 \% zu dramatischen Seespiegelanstiegen im Zentralen Keniarift f{\"u}hren. Aufgrund der etablierten hydrrologisch-klimatischen Wechselwirkungen werden R{\"u}ckschl{\"u}sse auf die nat{\"u}rliche Variabilit{\"a}t des ostafrikanischen Klimas gezogen. Zudem wird die Sensitivit{\"a}t der Keniarift-Seen in Bezug auf die St{\"a}rke der {\"a}quatorialen Insolation und hinsichtilch variabler Oberfl{\"a}chenwassertemperaturen des Indischen Ozeans bewertet.}, language = {en} } @phdthesis{Clodong2004, author = {Clodong, S{\´e}bastien}, title = {Recurrent outbreaks in ecology : chaotic dynamics in complex networks}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001626}, school = {Universit{\"a}t Potsdam}, year = {2004}, abstract = {Gegenstand der Dissertation ist die Untersuchung von wiederkehrenden Ausbr{\"u}chen (wie z.B. Epidemien) in der Natur. Dies gelang anhand von Modellen, die die Dynamik von Phytoplankton und die Ausbreitung von Krankheiten zwischen St{\"a}dten beschreiben. Diese beide Systeme bilden hervorragende Beispiele f{\"u}r solche Ph{\"a}nomene. Die Frage, ob die in der Zeit wiederkehrenden Ausbr{\"u}che ein Ausdruck chaotischer Dynamik sein k{\"o}nnen, ist aktuell in der {\"O}kologie und fasziniert Wissenschaftler dieser Disziplin. Wir konnten zeigen, dass sich das Plankton-Modell im Falle von periodischem Antreiben {\"u}ber die N{\"a}hrstoffe in einem chaotischen Regime befindet. Diese Dynamik wurde als die komplexe Wechselwirkung zweier Oszillatoren verstanden. Ebenfalls wurde die Ausbreitung von Epidemien in Netzwerken wechselwirkender St{\"a}dte mit unterschiedlichen Gr{\"o}ssen untersucht. Daf{\"u}r wurde zun{\"a}chst die Kopplung zwischen zwei St{\"a}dten als Verh{\"a}ltnis der Stadtgr{\"o}ssen eingef{\"u}hrt. Es konnte gezeigt werden, dass das System sich in einem globalen zweij{\"a}hrigen Zyklus, der auch in den realen Daten beobachtet wird, befinden kann. Der Effekt von Heterogenit{\"a}t in der Gr{\"o}sseverteilung ist durch gewichtete Kopplung von generischen Modellen (Zelt- und Logistische Abbildung) in Netzwerken im Detail untersucht worden. Eine neue Art von Kopplungsfunktion mit nichtlinearer S{\"a}ttigung wurde eingef{\"u}hrt, um die Stabilit{\"a}t des Systems zu gew{\"a}hrleisten. Diese Kopplung beinhaltet einen Parameter, der es erlaubt, die Netzwerktopologie von globaler Kopplung in gerichtete Netzwerke gleichm{\"a}ssig umzuwandeln. Die Dynamik des Systems wurde anhand von Bifurkationsdiagrammen untersucht. Zum Verst{\"a}ndnis dieser Dynamik wurde eine effektive Theorie, die die beobachteten Bifurkationen sehr gut nachahmt, entwickelt.}, language = {en} } @phdthesis{Kneis2007, author = {Kneis, David}, title = {A water quality model for shallow river-lake systems and its application in river basin management}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-14647}, school = {Universit{\"a}t Potsdam}, year = {2007}, abstract = {This work documents the development and application of a new model for simulating mass transport and turnover in rivers and shallow lakes. The simulation tool called 'TRAM' is intended to complement mesoscale eco-hydrological catchment models in studies on river basin management. TRAM aims at describing the water quality of individual water bodies, using problem- and scale-adequate approaches for representing their hydrological and ecological characteristics. The need for such flexible water quality analysis and prediction tools is expected to further increase during the implementation of the European Water Framework Directive (WFD) as well as in the context of climate change research. The developed simulation tool consists of a transport and a reaction module with the latter being highly flexible with respect to the description of turnover processes in the aquatic environment. Therefore, simulation approaches of different complexity can easily be tested and model formulations can be chosen in consideration of the problem at hand, knowledge of process functioning, and data availability. Consequently, TRAM is suitable for both heavily simplified engineering applications as well as scientific ecosystem studies involving a large number of state variables, interactions, and boundary conditions. TRAM can easily be linked to catchment models off-line and it requires the use of external hydrodynamic simulation software. Parametrization of the model and visualization of simulation results are facilitated by the use of geographical information systems as well as specific pre- and post-processors. TRAM has been developed within the research project 'Management Options for the Havel River Basin' funded by the German Ministry of Education and Research. The project focused on the analysis of different options for reducing the nutrient load of surface waters. It was intended to support the implementation of the WFD in the lowland catchment of the Havel River located in North-East Germany. Within the above-mentioned study TRAM was applied with two goals in mind. In a first step, the model was used for identifying the magnitude as well as spatial and temporal patterns of nitrogen retention and sediment phosphorus release in a 100~km stretch of the highly eutrophic Lower Havel River. From the system analysis, strongly simplified conceptual approaches for modeling N-retention and P-remobilization in the studied river-lake system were obtained. In a second step, the impact of reduced external nutrient loading on the nitrogen and phosphorus concentrations of the Havel River was simulated (scenario analysis) taking into account internal retention/release. The boundary conditions for the scenario analysis such as runoff and nutrient emissions from river basins were computed by project partners using the catchment models SWIM and ArcEGMO-Urban. Based on the output of TRAM, the considered options of emission control could finally be evaluated using a site-specific assessment scale which is compatible with the requirements of the WFD. Uncertainties in the model predictions were also examined. According to simulation results, the target of the WFD -- with respect to total phosphorus concentrations in the Lower Havel River -- could be achieved in the medium-term, if the full potential for reducing point and non-point emissions was tapped. Furthermore, model results suggest that internal phosphorus loading will ease off noticeably until 2015 due to a declining pool of sedimentary mobile phosphate. Mass balance calculations revealed that the lakes of the Lower Havel River are an important nitrogen sink. This natural retention effect contributes significantly to the efforts aimed at reducing the river's nitrogen load. If a sustainable improvement of the river system's water quality is to be achieved, enhanced measures to further reduce the immissions of both phosphorus and nitrogen are required.}, language = {en} } @book{Voss2008, author = {Voß, Anja}, title = {Untersuchung und Modellierung der Stickstoff- und Phosphorumsatz- und Transportprozesse in mesoskaligen Einzugsgebieten des Tieflandes am Beispiel von Nuthe, Hammerfließ und Stepenitz}, number = {19}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-940793-13-3}, issn = {1434-2375}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-16356}, publisher = {Universit{\"a}t Potsdam}, pages = {XXI, 170}, year = {2008}, abstract = {Ziel dieser Arbeit war es, die Stickstoff- und Phosphorprozesse im nordostdeutschen Tiefland detailliert zu untersuchen und Handlungsoptionen hinsichtlich der Landnutzung zur nachhaltigen Steuerung der Stickstoff- und Phosphoreintr{\"a}ge in die Fließgew{\"a}sser aufzuzeigen. Als Grundvoraussetzung f{\"u}r die Modellierung des N{\"a}hrstoffhaushaltes mussten zun{\"a}chst die hydrologischen Prozesse und die Abfl{\"u}sse f{\"u}r die Einzugsgebiete validiert werden. Daf{\"u}r wurde in dieser Arbeit das {\"o}kohydrologische Modell SWIM verwendet. Die Abflussmodellierung umfasste den Zeitraum 1991 - 2000. Die Ergebnisse dazu zeigen, dass SWIM in der Lage war, die hydrologischen Prozesse in den Untersuchungsgebieten ad{\"a}quat wiederzugeben. Auf der Grundlage der Modellierung des Wasserhaushaltes wurden mit SWIM die Stoffumsatzprozesse f{\"u}r den Zeitraum 1996 - 2000 simuliert. Um dabei besonders das Prozessgeschehen im Tiefland zu ber{\"u}cksichtigen, war die Erweiterung von SWIM um einen Ammonium-Pool mit dessen Umsatzprozessen erforderlich. Außerdem wurde der Prozess der N{\"a}hrstoffversickerung so erg{\"a}nzt, dass neben Nitrat auch Ammonium und Phosphat durch das gesamte Bodenprofil verlagert und {\"u}ber die Abflusskomponenten zum Gebietsauslass transportiert werden k{\"o}nnen. Mit diesen Modellerweiterungen konnten die Stickstoff und Phosphorprozesse in den Untersuchungsgebieten gut abgebildet werden. Mit dem so validierten Modell wurden weitere Anwendungen erm{\"o}glicht. N{\"a}hrstoffsimulationen f{\"u}r den Zeitraum 1981 bis 2000 dienten der Untersuchung des abnehmenden Trends in den N{\"a}hrstoffkonzentrationen der Nuthe. Die Untersuchungsergebnisse lassen deutlich erkennen, dass sich die Konzentrationen nach 1990 haupts{\"a}chlich auf Grund der Reduzierung der Eintr{\"a}ge aus punktf{\"o}rmigen Quellen und Rieselfeldern verringert haben. Weitere Modellrechnungen zur Herkunft der N{\"a}hrstoffe haben ergeben, dass Nitrat {\"u}berwiegend aus diffusen Quellen, Ammonium und Phosphat dagegen aus punktf{\"o}rmigen Quellen stammen. Als besonders sensitiv auf die Modellergebnisse haben sich die Parameter zu Landnutzung und -management und die Durchwurzelungstiefe der Pflanzen herausgestellt. Abschließend wurden verschiedene Landnutzungsszenarien angewendet. Die Ergebnisse zu den Szenariorechnungen zeigen, dass fast alle vorgegebenen Landnutzungsszenarien zu einer Verringerung der Stickstoff- bzw. Phosphoremissionen f{\"u}hrten. Die Anwendung von Szenarien, die alle relevanten Zielvorgaben und Empfehlungen zum Ressourcenschutz ber{\"u}cksichtigen, zeigen die gr{\"o}ßten Ver{\"a}nderungen.}, language = {de} } @phdthesis{Jechow2009, author = {Jechow, Andreas}, title = {Tailoring the emission of stripe-array diode lasers with external cavities to enable nonlinear frequency conversion}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-031-1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-39653}, school = {Universit{\"a}t Potsdam}, pages = {ii, 139}, year = {2009}, abstract = {A huge number of applications require coherent radiation in the visible spectral range. Since diode lasers are very compact and efficient light sources, there exists a great interest to cover these applications with diode laser emission. Despite modern band gap engineering not all wavelengths can be accessed with diode laser radiation. Especially in the visible spectral range between 480 nm and 630 nm no emission from diode lasers is available, yet. Nonlinear frequency conversion of near-infrared radiation is a common way to generate coherent emission in the visible spectral range. However, radiation with extraordinary spatial temporal and spectral quality is required to pump frequency conversion. Broad area (BA) diode lasers are reliable high power light sources in the near-infrared spectral range. They belong to the most efficient coherent light sources with electro-optical efficiencies of more than 70\%. Standard BA lasers are not suitable as pump lasers for frequency conversion because of their poor beam quality and spectral properties. For this purpose, tapered lasers and diode lasers with Bragg gratings are utilized. However, these new diode laser structures demand for additional manufacturing and assembling steps that makes their processing challenging and expensive. An alternative to BA diode lasers is the stripe-array architecture. The emitting area of a stripe-array diode laser is comparable to a BA device and the manufacturing of these arrays requires only one additional process step. Such a stripe-array consists of several narrow striped emitters realized with close proximity. Due to the overlap of the fields of neighboring emitters or the presence of leaky waves, a strong coupling between the emitters exists. As a consequence, the emission of such an array is characterized by a so called supermode. However, for the free running stripe-array mode competition between several supermodes occurs because of the lack of wavelength stabilization. This leads to power fluctuations, spectral instabilities and poor beam quality. Thus, it was necessary to study the emission properties of those stripe-arrays to find new concepts to realize an external synchronization of the emitters. The aim was to achieve stable longitudinal and transversal single mode operation with high output powers giving a brightness sufficient for efficient nonlinear frequency conversion. For this purpose a comprehensive analysis of the stripe-array devices was done here. The physical effects that are the origin of the emission characteristics were investigated theoretically and experimentally. In this context numerical models could be verified and extended. A good agreement between simulation and experiment was observed. One way to stabilize a specific supermode of an array is to operate it in an external cavity. Based on mathematical simulations and experimental work, it was possible to design novel external cavities to select a specific supermode and stabilize all emitters of the array at the same wavelength. This resulted in stable emission with 1 W output power, a narrow bandwidth in the range of 2 MHz and a very good beam quality with M²<1.5. This is a new level of brightness and brilliance compared to other BA and stripe-array diode laser systems. The emission from this external cavity diode laser (ECDL) satisfied the requirements for nonlinear frequency conversion. Furthermore, a huge improvement to existing concepts was made. In the next step newly available periodically poled crystals were used for second harmonic generation (SHG) in single pass setups. With the stripe-array ECDL as pump source, more than 140 mW of coherent radiation at 488 nm could be generated with a very high opto-optical conversion efficiency. The generated blue light had very good transversal and longitudinal properties and could be used to generate biphotons by parametric down-conversion. This was feasible because of the improvement made with the infrared stripe-array diode lasers due to the development of new physical concepts.}, language = {en} } @misc{NikoloskivanDongen2011, author = {Nikoloski, Zoran and van Dongen, Joost T.}, title = {Modeling alternatives for interpreting the change in oxygen-consumption rates during hypoxic conditions}, series = {New phytologist : international journal of plant science}, volume = {190}, journal = {New phytologist : international journal of plant science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0028-646X}, doi = {10.1111/j.1469-8137.2011.03674.x}, pages = {273 -- 276}, year = {2011}, language = {en} } @article{ArvidssonPerezRodriguezMuellerRoeber2011, author = {Arvidsson, Samuel Janne and Perez-Rodriguez, Paulino and M{\"u}ller-R{\"o}ber, Bernd}, title = {A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects}, series = {New phytologist : international journal of plant science}, volume = {191}, journal = {New phytologist : international journal of plant science}, number = {3}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0028-646X}, doi = {10.1111/j.1469-8137.2011.03756.x}, pages = {895 -- 907}, year = {2011}, abstract = {To gain a deeper understanding of the mechanisms behind biomass accumulation, it is important to study plant growth behavior. Manually phenotyping large sets of plants requires important human resources and expertise and is typically not feasible for detection of weak growth phenotypes. Here, we established an automated growth phenotyping pipeline for Arabidopsis thaliana to aid researchers in comparing growth behaviors of different genotypes. The analysis pipeline includes automated image analysis of two-dimensional digital plant images and evaluation of manually annotated information of growth stages. It employs linear mixed-effects models to quantify genotype effects on total rosette area and relative leaf growth rate (RLGR) and ANOVAs to quantify effects on developmental times. Using the system, a single researcher can phenotype up to 7000 plants d(-1). Technical variance is very low (typically < 2\%). We show quantitative results for the growth-impaired starch-excessmutant sex4-3 and the growth-enhancedmutant grf9. We show that recordings of environmental and developmental variables reduce noise levels in the phenotyping datasets significantly and that careful examination of predictor variables (such as d after sowing or germination) is crucial to avoid exaggerations of recorded phenotypes and thus biased conclusions.}, language = {en} } @article{AliHomannKreiseletal.2012, author = {Ali, Mostafa and Homann, Thomas and Kreisel, Janka and Khalil, Mahmoud and Puhlmann, Ralf and Kruse, Hans-Peter and Rawel, Harshadrai Manilal}, title = {Characterization and modeling of the interactions between coffee storage proteins and phenolic compounds}, series = {Journal of agricultural and food chemistry : a publication of the American Chemical Society}, volume = {60}, journal = {Journal of agricultural and food chemistry : a publication of the American Chemical Society}, number = {46}, publisher = {American Chemical Society}, address = {Washington}, issn = {0021-8561}, doi = {10.1021/jf303372a}, pages = {11601 -- 11608}, year = {2012}, abstract = {This study addresses the interactions of coffee storage proteins with coffee-specific phenolic compounds. Protein profiles, of Coffea arabica and Coffea canephora (var robusta) were compared. Major Phenolic compounds were extracted and analyzed with appropriate methods. The polyphenol-protein interactions during protein extraction have been addressed by different analytical setups [reversed-phase high-performance liquid chromatography (RP-HPLC), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS), and Trolox equivalent antioxidant capacity (TEAC) assays], with focus directed toward identification of covalent adduct formation. The results indicate that C. arabica proteins are more susceptible to these interactions and the polyphenol oxidase activity seems to be a crucial factor for the formation of these addition products. A tentative allocation of the modification type and site in the protein has been attempted. Thus, the first available in silico modeling of modified coffee proteins is reported. The extent of these modifications may contribute to the structure and function of "coffee melanoidins" and are discussed in the context of coffee flavor formation.}, language = {en} } @book{BeckerGiese2012, author = {Becker, Basil and Giese, Holger}, title = {Cyber-physical systems with dynamic structure : towards modeling and verification of inductive invariants}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-217-9}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-62437}, publisher = {Universit{\"a}t Potsdam}, pages = {iv, 27}, year = {2012}, abstract = {Cyber-physical systems achieve sophisticated system behavior exploring the tight interconnection of physical coupling present in classical engineering systems and information technology based coupling. A particular challenging case are systems where these cyber-physical systems are formed ad hoc according to the specific local topology, the available networking capabilities, and the goals and constraints of the subsystems captured by the information processing part. In this paper we present a formalism that permits to model the sketched class of cyber-physical systems. The ad hoc formation of tightly coupled subsystems of arbitrary size are specified using a UML-based graph transformation system approach. Differential equations are employed to define the resulting tightly coupled behavior. Together, both form hybrid graph transformation systems where the graph transformation rules define the discrete steps where the topology or modes may change, while the differential equations capture the continuous behavior in between such discrete changes. In addition, we demonstrate that automated analysis techniques known for timed graph transformation systems for inductive invariants can be extended to also cover the hybrid case for an expressive case of hybrid models where the formed tightly coupled subsystems are restricted to smaller local networks.}, language = {en} } @article{BarthelmeTrukenbrodEngbertetal.2013, author = {Barthelme, Simon and Trukenbrod, Hans Arne and Engbert, Ralf and Wichmann, Felix A.}, title = {Modeling fixation locations using spatial point processes}, series = {Journal of vision}, volume = {13}, journal = {Journal of vision}, number = {12}, publisher = {Association for Research in Vision and Opthalmology}, address = {Rockville}, issn = {1534-7362}, doi = {10.1167/13.12.1}, pages = {34}, year = {2013}, abstract = {Whenever eye movements are measured, a central part of the analysis has to do with where subjects fixate and why they fixated where they fixated. To a first approximation, a set of fixations can be viewed as a set of points in space; this implies that fixations are spatial data and that the analysis of fixation locations can be beneficially thought of as a spatial statistics problem. We argue that thinking of fixation locations as arising from point processes is a very fruitful framework for eye-movement data, helping turn qualitative questions into quantitative ones. We provide a tutorial introduction to some of the main ideas of the field of spatial statistics, focusing especially on spatial Poisson processes. We show how point processes help relate image properties to fixation locations. In particular we show how point processes naturally express the idea that image features' predictability for fixations may vary from one image to another. We review other methods of analysis used in the literature, show how they relate to point process theory, and argue that thinking in terms of point processes substantially extends the range of analyses that can be performed and clarify their interpretation.}, language = {en} }