@phdthesis{Schmallowsky2009, author = {Schmallowsky, Antje}, title = {Visualisierung dynamischer Raumph{\"a}nomene in Geoinformationssystemen}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41262}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Die visuelle Kommunikation ist eine effiziente Methode, um dynamische Ph{\"a}nomene zu beschreiben. Informationsobjekte pr{\"a}zise wahrzunehmen, einen schnellen Zugriff auf strukturierte und relevante Informationen zu erm{\"o}glichen, erfordert konsistente und nach dem formalen Minimalprinzip konzipierte Analyse- und Darstellungsmethoden. Dynamische Raumph{\"a}nomene in Geoinformationssystemen k{\"o}nnen durch den Mangel an konzeptionellen Optimierungsanpassungen aufgrund ihrer statischen Systemstruktur nur bedingt die Informationen von Raum und Zeit modellieren. Die Forschung in dieser Arbeit ist daher auf drei interdisziplin{\"a}re Ans{\"a}tze fokussiert. Der erste Ansatz stellt eine echtzeitnahe Datenerfassung dar, die in Geodatenbanken zeitorientiert verwaltet wird. Der zweite Ansatz betrachtet Analyse- und Simulationsmethoden, die das dynamische Verhalten analysieren und prognostizieren. Der dritte Ansatz konzipiert Visualisierungsmethoden, die insbesondere dynamische Prozesse abbilden. Die Symbolisierung der Prozesse passt sich bedarfsweise in Abh{\"a}ngigkeit des Prozessverlaufes und der Interaktion zwischen Datenbanken und Simulationsmodellen den verschiedenen Entwicklungsphasen an. Dynamische Aspekte k{\"o}nnen so mit Hilfe bew{\"a}hrter Funktionen aus der GI-Science zeitnah mit modularen Werkzeugen entwickelt und visualisiert werden. Die Analyse-, Verschneidungs- und Datenverwaltungsfunktionen sollen hierbei als Nutzungs- und Auswertungspotential alternativ zu Methoden statischer Karten dienen. Bedeutend f{\"u}r die zeitliche Komponente ist das Verkn{\"u}pfen neuer Technologien, z. B. die Simulation und Animation, basierend auf einer strukturierten Zeitdatenbank in Verbindung mit statistischen Verfahren. Methodisch werden Modellans{\"a}tze und Visualisierungstechniken entwickelt, die auf den Bereich Verkehr transferiert werden. Verkehrsdynamische Ph{\"a}nomene, die nicht zusammenh{\"a}ngend und umfassend darstellbar sind, werden modular in einer serviceorientierten Architektur separiert, um sie in verschiedenen Ebenen r{\"a}umlich und zeitlich visuell zu pr{\"a}sentieren. Entwicklungen der Vergangenheit und Prognosen der Zukunft werden {\"u}ber verschiedene Berechnungsmethoden modelliert und visuell analysiert. Die Verkn{\"u}pfung einer Mikrosimulation (Abbildung einzelner Fahrzeuge) mit einer netzgesteuerten Makrosimulation (Abbildung eines gesamten Straßennetzes) erm{\"o}glicht eine maßstabsunabh{\"a}ngige Simulation und Visualisierung des Mobilit{\"a}tsverhaltens ohne zeitaufwendige Bewertungsmodellberechnungen. Zuk{\"u}nftig wird die visuelle Analyse raum-zeitlicher Ver{\"a}nderungen f{\"u}r planerische Entscheidungen ein effizientes Mittel sein, um Informationen {\"u}bergreifend verf{\"u}gbar, klar strukturiert und zweckorientiert zur Verf{\"u}gung zu stellen. Der Mehrwert durch visuelle Geoanalysen, die modular in einem System integriert sind, ist das flexible Auswerten von Messdaten nach zeitlichen und r{\"a}umlichen Merkmalen.}, language = {de} } @article{ZhangCaoXuetal.2022, author = {Zhang, Naimeng and Cao, Xianyong and Xu, Qinghai and Huang, Xiaozhong and Herzschuh, Ulrike and Shen, Zhongwei and Peng, Wei and Liu, Sisi and Wu, Duo and Wang, Jian and Xia, Huan and Zhang, Dongju and Chen, Fahu}, title = {Vegetation change and human-environment interactions in the Qinghai Lake Basin, northeastern Tibetan Plateau, since the last deglaciation}, series = {Catena}, volume = {210}, journal = {Catena}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0341-8162}, doi = {10.1016/j.catena.2021.105892}, pages = {14}, year = {2022}, abstract = {The nature of the interaction between prehistoric humans and their environment, especially the vegetation, has long been of interest. The Qinghai Lake Basin in North China is well-suited to exploring the interactions between prehistoric humans and vegetation in the Tibetan Plateau, because of the comparatively dense distribution of archaeological sites and the ecologically fragile environment. Previous pollen studies of Qinghai Lake have enabled a detailed reconstruction of the regional vegetation, but they have provided relatively little information on vegetation change within the Qinghai Lake watershed. To address the issue we conducted a pollen-based vegetation reconstruction for an archaeological site (YWY), located on the southern shore of Qinghai Lake. We used high temporal-resolution pollen records from the YWY site and from Qinghai Lake, spanning the interval since the last deglaciation (15.3 kyr BP to the present) to quantitatively reconstruct changes in the local and regional vegetation using Landscape Reconstruction Algorithm models. The results show that, since the late glacial, spruce forest grew at high altitudes in the surrounding mountains, while the lakeshore environment was occupied mainly by shrub-steppe. From the lateglacial to the middle Holocene, coniferous woodland began to expand downslope and reached the YWY site at 7.1 kyr BP. The living environment of the local small groups of Paleolithic-Epipaleolithic humans (during 15.3-13.1 kyr BP and 9-6.4 kyr BP) changed from shrub-steppe to coniferous forest-steppe. The pollen record shows no evidence of pronounced changes in the vegetation community corresponding to human activity. However, based on a comparison of the local and regional vegetation reconstructions, low values of biodiversity and a significant increase in two indicators of vegetation degradation, Chenopodiaceae and Rosaceae, suggest that prehistoric hunters-gatherers likely disturbed the local vegetation during 9.0-6.4 kyr BP. Our findings are a preliminary attempt to study human-environment interactions at Paleolithic-Epipaleolithic sites in the region, and they contribute to ongoing environmental archaeology research in the Tibetan Plateau.}, language = {en} } @phdthesis{Koc2018, author = {Ko{\c{c}}, Azize}, title = {Ultrafast x-ray studies on the non-equilibrium of the magnetic and phononic system in heavy rare-earths}, doi = {10.25932/publishup-42328}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-423282}, school = {Universit{\"a}t Potsdam}, pages = {ii, 117}, year = {2018}, abstract = {In this dissertation the lattice and the magnetic recovery dynamics of the two heavy rare-earth metals Dy and Gd after femtosecond photoexcitation are described. For the investigations, thin films of Dy and Gd were measured at low temperatures in the antiferromagnetic phase of Dy and close to room temperature in the ferromagnetic phase of Gd. Two different optical pump-x-ray probe techniques were employed: Ultrafast x-ray diffraction with hard x-rays (UXRD) yields the structural response of heavy rare-earth metals and resonant soft (elastic) x-ray diffraction (RSXD), which allows measuring directly changes in the helical antiferromagnetic order of Dy. The combination of both techniques enables to study the complex interaction between the magnetic and the phononic subsystems.}, language = {en} } @phdthesis{Schroeder2016, author = {Schr{\"o}der, Henning}, title = {Ultrafast electron dynamics in Fe(CO)5 and Cr(CO)6}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-94589}, school = {Universit{\"a}t Potsdam}, pages = {v, 87}, year = {2016}, abstract = {In this thesis, the two prototype catalysts Fe(CO)₅ and Cr(CO)₆ are investigated with time-resolved photoelectron spectroscopy at a high harmonic setup. In both of these metal carbonyls, a UV photon can induce the dissociation of one or more ligands of the complex. The mechanism of the dissociation has been debated over the last decades. The electronic dynamics of the first dissociation occur on the femtosecond timescale. For the experiment, an existing high harmonic setup was moved to a new location, was extended, and characterized. The modified setup can induce dynamics in gas phase samples with photon energies of 1.55eV, 3.10eV, and 4.65eV. The valence electronic structure of the samples can be probed with photon energies between 20eV and 40eV. The temporal resolution is 111fs to 262fs, depending on the combination of the two photon energies. The electronically excited intermediates of the two complexes, as well as of the reaction product Fe(CO)₄, could be observed with photoelectron spectroscopy in the gas phase for the first time. However, photoelectron spectroscopy gives access only to the final ionic states. Corresponding calculations to simulate these spectra are still in development. The peak energies and their evolution in time with respect to the initiation pump pulse have been determined, these peaks have been assigned based on literature data. The spectra of the two complexes show clear differences. The dynamics have been interpreted with the assumption that the motion of peaks in the spectra relates to the movement of the wave packet in the multidimensional energy landscape. The results largely confirm existing models for the reaction pathways. In both metal carbonyls, this pathway involves a direct excitation of the wave packet to a metal-to-ligand charge transfer state and the subsequent crossing to a dissociative ligand field state. The coupling of the electronic dynamics to the nuclear dynamics could explain the slower dissociation in Fe(CO)₅ as compared to Cr(CO)₆.}, language = {en} } @misc{LaraNitzeGrosseetal.2018, author = {Lara, Mark J. and Nitze, Ingmar and Große, Guido and McGuire, David}, title = {Tundra landform and vegetation productivity trend maps for the Arctic Coastal Plain of northern Alaska}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1035}, issn = {1866-8372}, doi = {10.25932/publishup-45987}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459875}, pages = {12}, year = {2018}, abstract = {Arctic tundra landscapes are composed of a complex mosaic of patterned ground features, varying in soil moisture, vegetation composition, and surface hydrology over small spatial scales (10-100 m). The importance of microtopography and associated geomorphic landforms in influencing ecosystem structure and function is well founded, however, spatial data products describing local to regional scale distribution of patterned ground or polygonal tundra geomorphology are largely unavailable. Thus, our understanding of local impacts on regional scale processes (e.g., carbon dynamics) may be limited. We produced two key spatiotemporal datasets spanning the Arctic Coastal Plain of northern Alaska (similar to 60,000 km(2)) to evaluate climate-geomorphological controls on arctic tundra productivity change, using (1) a novel 30m classification of polygonal tundra geomorphology and (2) decadal-trends in surface greenness using the Landsat archive (1999-2014). These datasets can be easily integrated and adapted in an array of local to regional applications such as (1) upscaling plot-level measurements (e.g., carbon/energy fluxes), (2) mapping of soils, vegetation, or permafrost, and/or (3) initializing ecosystem biogeochemistry, hydrology, and/or habitat modeling.}, language = {en} } @misc{HodgkinsRichardsonDommainetal.2018, author = {Hodgkins, Suzanne B. and Richardson, Curtis J. and Dommain, Ren{\´e} and Wang, Hongjun and Glaser, Paul H. and Verbeke, Brittany and Winkler, B. Rose and Cobb, Alexander R. and Rich, Virginia I. and Missilmani, Malak and Flanagan, Neal and Ho, Mengchi and Hoyt, Alison M. and Harvey, Charles F. and Vining, S. Rose and Hough, Moira A. and Moore, Tim R. and Richard, Pierre J. H. and De La Cruz, Florentino B. and Toufaily, Joumana and Hamdan, Rasha and Cooper, William T. and Chanton, Jeffrey P.}, title = {Tropical peatland carbon storage linked to global latitudinal trends in peat recalcitrance}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1125}, issn = {1866-8372}, doi = {10.25932/publishup-45965}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459658}, pages = {15}, year = {2018}, abstract = {Peatlands represent large terrestrial carbon banks. Given that most peat accumulates in boreal regions, where low temperatures and water saturation preserve organic matter, the existence of peat in (sub)tropical regions remains enigmatic. Here we examined peat and plant chemistry across a latitudinal transect from the Arctic to the tropics. Near-surface low-latitude peat has lower carbohydrate and greater aromatic content than near-surface high-latitude peat, creating a reduced oxidation state and resulting recalcitrance. This recalcitrance allows peat to persist in the (sub)tropics despite warm temperatures. Because we observed similar declines in carbohydrate content with depth in high-latitude peat, our data explain recent field-scale deep peat warming experiments in which catotelm (deeper) peat remained stable despite temperature increases up to 9 degrees C. We suggest that high-latitude deep peat reservoirs may be stabilized in the face of climate change by their ultimately lower carbohydrate and higher aromatic composition, similar to tropical peats.}, language = {en} } @phdthesis{Grimbs2009, author = {Grimbs, Sergio}, title = {Towards structure and dynamics of metabolic networks}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-32397}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {This work presents mathematical and computational approaches to cover various aspects of metabolic network modelling, especially regarding the limited availability of detailed kinetic knowledge on reaction rates. It is shown that precise mathematical formulations of problems are needed i) to find appropriate and, if possible, efficient algorithms to solve them, and ii) to determine the quality of the found approximate solutions. Furthermore, some means are introduced to gain insights on dynamic properties of metabolic networks either directly from the network structure or by additionally incorporating steady-state information. Finally, an approach to identify key reactions in a metabolic networks is introduced, which helps to develop simple yet useful kinetic models. The rise of novel techniques renders genome sequencing increasingly fast and cheap. In the near future, this will allow to analyze biological networks not only for species but also for individuals. Hence, automatic reconstruction of metabolic networks provides itself as a means for evaluating this huge amount of experimental data. A mathematical formulation as an optimization problem is presented, taking into account existing knowledge and experimental data as well as the probabilistic predictions of various bioinformatical methods. The reconstructed networks are optimized for having large connected components of high accuracy, hence avoiding fragmentation into small isolated subnetworks. The usefulness of this formalism is exemplified on the reconstruction of the sucrose biosynthesis pathway in Chlamydomonas reinhardtii. The problem is shown to be computationally demanding and therefore necessitates efficient approximation algorithms. The problem of minimal nutrient requirements for genome-scale metabolic networks is analyzed. Given a metabolic network and a set of target metabolites, the inverse scope problem has as it objective determining a minimal set of metabolites that have to be provided in order to produce the target metabolites. These target metabolites might stem from experimental measurements and therefore are known to be produced by the metabolic network under study, or are given as the desired end-products of a biotechological application. The inverse scope problem is shown to be computationally hard to solve. However, I assume that the complexity strongly depends on the number of directed cycles within the metabolic network. This might guide the development of efficient approximation algorithms. Assuming mass-action kinetics, chemical reaction network theory (CRNT) allows for eliciting conclusions about multistability directly from the structure of metabolic networks. Although CRNT is based on mass-action kinetics originally, it is shown how to incorporate further reaction schemes by emulating molecular enzyme mechanisms. CRNT is used to compare several models of the Calvin cycle, which differ in size and level of abstraction. Definite results are obtained for small models, but the available set of theorems and algorithms provided by CRNT can not be applied to larger models due to the computational limitations of the currently available implementations of the provided algorithms. Given the stoichiometry of a metabolic network together with steady-state fluxes and concentrations, structural kinetic modelling allows to analyze the dynamic behavior of the metabolic network, even if the explicit rate equations are not known. In particular, this sampling approach is used to study the stabilizing effects of allosteric regulation in a model of human erythrocytes. Furthermore, the reactions of that model can be ranked according to their impact on stability of the steady state. The most important reactions in that respect are identified as hexokinase, phosphofructokinase and pyruvate kinase, which are known to be highly regulated and almost irreversible. Kinetic modelling approaches using standard rate equations are compared and evaluated against reference models for erythrocytes and hepatocytes. The results from this simplified kinetic models can simulate acceptably the temporal behavior for small changes around a given steady state, but fail to capture important characteristics for larger changes. The aforementioned approach to rank reactions according to their influence on stability is used to identify a small number of key reactions. These reactions are modelled in detail, including knowledge about allosteric regulation, while all other reactions were still described by simplified reaction rates. These so-called hybrid models can capture the characteristics of the reference models significantly better than the simplified models alone. The resulting hybrid models might serve as a good starting point for kinetic modelling of genome-scale metabolic networks, as they provide reasonable results in the absence of experimental data, regarding, for instance, allosteric regulations, for a vast majority of enzymatic reactions.}, language = {en} } @misc{FondellEckertJayetal.2017, author = {Fondell, Mattis and Eckert, Sebastian and Jay, Raphael Martin and Weniger, Christian and Quevedo, Wilson and Niskanen, Johannes and Kennedy, Brian and Sorgenfrei, Nomi and Schick, Daniel and Giangrisostomi, Erika and Ovsyannikov, Ruslan and Adamczyk, Katrin and Huse, Nils and Wernet, Philippe and Mitzner, Rolf and F{\"o}hlisch, Alexander}, title = {Time-resolved soft X-ray absorption spectroscopy in transmission mode on liquids at MHz repetition rates}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {780}, issn = {1866-8372}, doi = {10.25932/publishup-43752}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437529}, pages = {12}, year = {2017}, abstract = {We present a setup combining a liquid flatjet sample delivery and a MHz laser system for time-resolved soft X-ray absorption measurements of liquid samples at the high brilliance undulator beamline UE52-SGM at Bessy II yielding unprecedented statistics in this spectral range. We demonstrate that the efficient detection of transient absorption changes in transmission mode enables the identification of photoexcited species in dilute samples. With iron(II)-trisbipyridine in aqueous solution as a benchmark system, we present absorption measurements at various edges in the soft X-ray regime. In combination with the wavelength tunability of the laser system, the set-up opens up opportunities to study the photochemistry of many systems at low concentrations, relevant to materials sciences, chemistry, and biology.}, language = {en} } @misc{EppKruseKathetal.2018, author = {Epp, Laura Saskia and Kruse, Stefan and Kath, Nadja J. and Stoof-Leichsenring, Kathleen Rosemarie and Tiedemann, Ralph and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike}, title = {Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1052}, issn = {1866-8372}, doi = {10.25932/publishup-46835}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-468352}, pages = {11}, year = {2018}, abstract = {Changes in species' distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species' range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.}, language = {en} } @misc{Metzler2020, author = {Metzler, Ralf}, title = {Superstatistics and non-Gaussian diffusion}, series = {The European physical journal special topics}, volume = {229}, journal = {The European physical journal special topics}, number = {5}, publisher = {Springer}, address = {Heidelberg}, issn = {1951-6355}, doi = {10.1140/epjst/e2020-900210-x}, pages = {711 -- 728}, year = {2020}, abstract = {Brownian motion and viscoelastic anomalous diffusion in homogeneous environments are intrinsically Gaussian processes. In a growing number of systems, however, non-Gaussian displacement distributions of these processes are being reported. The physical cause of the non-Gaussianity is typically seen in different forms of disorder. These include, for instance, imperfect "ensembles" of tracer particles, the presence of local variations of the tracer mobility in heteroegenous environments, or cases in which the speed or persistence of moving nematodes or cells are distributed. From a theoretical point of view stochastic descriptions based on distributed ("superstatistical") transport coefficients as well as time-dependent generalisations based on stochastic transport parameters with built-in finite correlation time are invoked. After a brief review of the history of Brownian motion and the famed Gaussian displacement distribution, we here provide a brief introduction to the phenomenon of non-Gaussianity and the stochastic modelling in terms of superstatistical and diffusing-diffusivity approaches.}, language = {en} } @article{KumarHesseRaoetal.2020, author = {Kumar, Rohini and Hesse, Fabienne and Rao, P. Srinivasa and Musolff, Andreas and Jawitz, James and Sarrazin, Francois and Samaniego, Luis and Fleckenstein, Jan H. and Rakovec, Oldrich and Thober, S. and Attinger, Sabine}, title = {Strong hydroclimatic controls on vulnerability to subsurface nitrate contamination across Europe}, series = {Nature Communications}, volume = {11}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group UK}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-020-19955-8}, pages = {1 -- 10}, year = {2020}, abstract = {Subsurface contamination due to excessive nutrient surpluses is a persistent and widespread problem in agricultural areas across Europe. The vulnerability of a particular location to pollution from reactive solutes, such as nitrate, is determined by the interplay between hydrologic transport and biogeochemical transformations. Current studies on the controls of subsurface vulnerability do not consider the transient behaviour of transport dynamics in the root zone. Here, using state-of-the-art hydrologic simulations driven by observed hydroclimatic forcing, we demonstrate the strong spatiotemporal heterogeneity of hydrologic transport dynamics and reveal that these dynamics are primarily controlled by the hydroclimatic gradient of the aridity index across Europe. Contrasting the space-time dynamics of transport times with reactive timescales of denitrification in soil indicate that similar to 75\% of the cultivated areas across Europe are potentially vulnerable to nitrate leaching for at least onethird of the year. We find that neglecting the transient nature of transport and reaction timescale results in a great underestimation of the extent of vulnerable regions by almost 50\%. Therefore, future vulnerability and risk assessment studies must account for the transient behaviour of transport and biogeochemical transformation processes.}, language = {en} } @misc{KumarHesseRaoetal.2020, author = {Kumar, Rohini and Hesse, Fabienne and Rao, P. Srinivasa and Musolff, Andreas and Jawitz, James and Sarrazin, Francois and Samaniego, Luis and Fleckenstein, Jan H. and Rakovec, Oldrich and Thober, S. and Attinger, Sabine}, title = {Strong hydroclimatic controls on vulnerability to subsurface nitrate contamination across Europe}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1}, issn = {1866-8372}, doi = {10.25932/publishup-54987}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-549875}, pages = {12}, year = {2020}, abstract = {Subsurface contamination due to excessive nutrient surpluses is a persistent and widespread problem in agricultural areas across Europe. The vulnerability of a particular location to pollution from reactive solutes, such as nitrate, is determined by the interplay between hydrologic transport and biogeochemical transformations. Current studies on the controls of subsurface vulnerability do not consider the transient behaviour of transport dynamics in the root zone. Here, using state-of-the-art hydrologic simulations driven by observed hydroclimatic forcing, we demonstrate the strong spatiotemporal heterogeneity of hydrologic transport dynamics and reveal that these dynamics are primarily controlled by the hydroclimatic gradient of the aridity index across Europe. Contrasting the space-time dynamics of transport times with reactive timescales of denitrification in soil indicate that similar to 75\% of the cultivated areas across Europe are potentially vulnerable to nitrate leaching for at least onethird of the year. We find that neglecting the transient nature of transport and reaction timescale results in a great underestimation of the extent of vulnerable regions by almost 50\%. Therefore, future vulnerability and risk assessment studies must account for the transient behaviour of transport and biogeochemical transformation processes.}, language = {en} } @article{JeonChechkinMetzler2014, author = {Jeon, Jae-Hyung and Chechkin, Aleksei V. and Metzler, Ralf}, title = {Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion}, series = {Physical chemistry, chemical physics : PCCP}, volume = {30}, journal = {Physical chemistry, chemical physics : PCCP}, number = {16}, publisher = {The Royal Society of Chemistry}, address = {Cambridge}, doi = {10.1039/C4CP02019G}, pages = {15811 -- 15817}, year = {2014}, abstract = {Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.}, language = {en} } @misc{JeonChechkinMetzler2014, author = {Jeon, Jae-Hyung and Chechkin, Aleksei V. and Metzler, Ralf}, title = {Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76302}, pages = {15811 -- 15817}, year = {2014}, abstract = {Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.}, language = {en} } @article{AndersSaitHorsley2022, author = {Anders, Janet and Sait, Connor R. J. and Horsley, Simon A. R.}, title = {Quantum Brownian motion for magnets}, series = {New journal of physics : the open-access journal for physics}, volume = {24}, journal = {New journal of physics : the open-access journal for physics}, number = {3}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1367-2630}, doi = {10.1088/1367-2630/ac4ef2}, pages = {21}, year = {2022}, abstract = {Spin precession in magnetic materials is commonly modelled with the classical phenomenological Landau-Lifshitz-Gilbert (LLG) equation. Based on a quantized three-dimensional spin + environment Hamiltonian, we here derive a spin operator equation of motion that describes precession and includes a general form of damping that consistently accounts for memory, coloured noise and quantum statistics. The LLG equation is recovered as its classical, Ohmic approximation. We further introduce resonant Lorentzian system-reservoir couplings that allow a systematic comparison of dynamics between Ohmic and non-Ohmic regimes. Finally, we simulate the full non-Markovian dynamics of a spin in the semi-classical limit. At low temperatures, our numerical results demonstrate a characteristic reduction and flattening of the steady state spin alignment with an external field, caused by the quantum statistics of the environment. The results provide a powerful framework to explore general three-dimensional dissipation in quantum thermodynamics.}, language = {en} } @article{JayVazdaCruzEckertetal.2020, author = {Jay, Raphael M. and Vaz da Cruz, Vinicius and Eckert, Sebastian and Fondell, Mattis and Mitzner, Rolf and F{\"o}hlisch, Alexander}, title = {Probing solute-solvent interactions of transition metal complexes using L-edge absorption spectroscopy}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {124}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, number = {27}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.0c00638}, pages = {5636 -- 5645}, year = {2020}, abstract = {In order to tailor solution-phase chemical reactions involving transition metal complexes, it is critical to understand how their valence electronic charge distributions are affected by the solution environment. Here, solute-solvent interactions of a solvatochromic mixed-ligand iron complex were investigated using X-ray absorption spectroscopy at the transition metal L-2,L-3-edge. Due to the selectivity of the corresponding core excitations to the iron 3d orbitals, the method grants direct access to the valence electronic structure around the iron center and its response to interactions with the solvent environment. A linear increase of the total L-2,L-3-edge absorption cross section as a function of the solvent Lewis acidity is revealed. The effect is caused by relative changes in different metal-ligand-bonding channels, which preserve local charge densities while increasing the density of unoccupied states around the iron center. These conclusions are corroborated by a combination of molecular dynamics and spectrum simulations based on time-dependent density functional theory. The simulations reproduce the spectral trends observed in the X-ray but also optical absorption experiments. Our results underscore the importance of solute-solvent interactions when aiming for an accurate description of the valence electronic structure of solvated transition metal complexes and demonstrate how L-2,L-3-edge absorption spectroscopy can aid in understanding the impact of the solution environment on intramolecular covalency and the electronic charge distribution.}, language = {en} } @article{vanVelzen2020, author = {van Velzen, Ellen}, title = {Predator coexistence through emergent fitness equalization}, series = {Ecology : a publication of the Ecological Society of America}, volume = {101}, journal = {Ecology : a publication of the Ecological Society of America}, number = {5}, publisher = {Wiley}, address = {Hoboken}, issn = {0012-9658}, doi = {10.1002/ecy.2995}, pages = {10}, year = {2020}, abstract = {The competitive exclusion principle is one of the oldest ideas in ecology and states that without additional self-limitation two predators cannot coexist on a single prey. The search for mechanisms allowing coexistence despite this has identified niche differentiation between predators as crucial: without this, coexistence requires the predators to have exactly the same R* values, which is considered impossible. However, this reasoning misses a critical point: predators' R* values are not static properties, but affected by defensive traits of their prey, which in turn can adapt in response to changes in predator densities. Here I show that this feedback between defense and predator dynamics enables stable predator coexistence without ecological niche differentiation. Instead, the mechanism driving coexistence is that prey adaptation causes defense to converge to the value where both predators have equal R* values ("fitness equalization"). This result is highly general, independent of specific model details, and applies to both rapid defense evolution and inducible defenses. It demonstrates the importance of considering long-standing ecological questions from an eco-evolutionary viewpoint, and showcases how the effects of adaptation can cascade through communities, driving diversity on higher trophic levels. These insights offer an important new perspective on coexistence theory.}, language = {en} } @article{Omelʹchenko2020, author = {Omelʹchenko, Oleh E.}, title = {Nonstationary coherence-incoherence patterns in nonlocally coupled heterogeneous phase oscillators}, series = {Chaos : an interdisciplinary journal of nonlinear science}, volume = {30}, journal = {Chaos : an interdisciplinary journal of nonlinear science}, number = {4}, publisher = {American Institute of Physics}, address = {Melville}, issn = {1054-1500}, doi = {10.1063/1.5145259}, pages = {8}, year = {2020}, abstract = {We consider a large ring of nonlocally coupled phase oscillators and show that apart from stationary chimera states, this system also supports nonstationary coherence-incoherence patterns (CIPs). For identical oscillators, these CIPs behave as breathing chimera states and are found in a relatively small parameter region only. It turns out that the stability region of these states enlarges dramatically if a certain amount of spatially uniform heterogeneity (e.g., Lorentzian distribution of natural frequencies) is introduced in the system. In this case, nonstationary CIPs can be studied as stable quasiperiodic solutions of a corresponding mean-field equation, formally describing the infinite system limit. Carrying out direct numerical simulations of the mean-field equation, we find different types of nonstationary CIPs with pulsing and/or alternating chimera-like behavior. Moreover, we reveal a complex bifurcation scenario underlying the transformation of these CIPs into each other. These theoretical predictions are confirmed by numerical simulations of the original coupled oscillator system.}, language = {en} } @misc{AlonsoStangeBeta2018, author = {Alonso, Sergio and Stange, Maike and Beta, Carsten}, title = {Modeling random crawling, membrane deformation and intracellular polarity of motile amoeboid cells}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {1014}, issn = {1866-8372}, doi = {10.25932/publishup-45974}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459745}, pages = {24}, year = {2018}, abstract = {Amoeboid movement is one of the most widespread forms of cell motility that plays a key role in numerous biological contexts. While many aspects of this process are well investigated, the large cell-to-cell variability in the motile characteristics of an otherwise uniform population remains an open question that was largely ignored by previous models. In this article, we present a mathematical model of amoeboid motility that combines noisy bistable kinetics with a dynamic phase field for the cell shape. To capture cell-to-cell variability, we introduce a single parameter for tuning the balance between polarity formation and intracellular noise. We compare numerical simulations of our model to experiments with the social amoeba Dictyostelium discoideum. Despite the simple structure of our model, we found close agreement with the experimental results for the center-of-mass motion as well as for the evolution of the cell shape and the overall intracellular patterns. We thus conjecture that the building blocks of our model capture essential features of amoeboid motility and may serve as a starting point for more detailed descriptions of cell motion in chemical gradients and confined environments.}, language = {en} } @misc{PudellMaznevHerzogetal.2018, author = {Pudell, Jan-Etienne and Maznev, Alexei and Herzog, Marc and Kronseder, M. and Back, Christian and Malinowski, Gregory and von Reppert, Alexander and Bargheer, Matias}, title = {Layer specific observation of slow thermal equilibration in ultrathin metallic nanostructures by femtosecond X-ray diffraction}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {797}, issn = {1866-8372}, doi = {10.25932/publishup-42623}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-426233}, pages = {7}, year = {2018}, abstract = {Ultrafast heat transport in nanoscale metal multilayers is of great interest in the context of optically induced demagnetization, remagnetization and switching. If the penetration depth of light exceeds the bilayer thickness, layer-specific information is unavailable from optical probes. Femtosecond diffraction experiments provide unique experimental access to heat transport over single digit nanometer distances. Here, we investigate the structural response and the energy flow in the ultrathin double-layer system: gold on ferromagnetic nickel. Even though the excitation pulse is incident from the Au side, we observe a very rapid heating of the Ni lattice, whereas the Au lattice initially remains cold. The subsequent heat transfer from Ni to the Au lattice is found to be two orders of magnitude slower than predicted by the conventional heat equation and much slower than electron-phonon coupling times in Au. We present a simplified model calculation highlighting the relevant thermophysical quantities.}, language = {en} } @article{ShinCherstvyMetzler2014, author = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size}, series = {Soft Matter}, journal = {Soft Matter}, editor = {Metzler, Ralf}, publisher = {The Royal Society of Chemistry}, address = {Cambridge}, issn = {1744-683X}, pages = {472 -- 488}, year = {2014}, abstract = {The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping-unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions.}, language = {en} } @misc{ShinCherstvyMetzler2014, author = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size}, publisher = {The Royal Society of Chemistry}, address = {Cambridge}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76961}, pages = {472 -- 488}, year = {2014}, abstract = {The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping-unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions.}, language = {en} } @misc{SchroenKoehliScheiffeleetal.2017, author = {Schr{\"o}n, Martin and K{\"o}hli, Markus and Scheiffele, Lena and Iwema, Joost and Bogena, Heye R. and Lv, Ling and Martini, Edoardo and Baroni, Gabriele and Rosolem, Rafael and Weimar, Jannis and Mai, Juliane and Cuntz, Matthias and Rebmann, Corinna and Oswald, Sascha and Dietrich, Peter and Schmidt, Ulrich and Zacharias, Steffen}, title = {Improving calibration and validation of cosmic-ray neutron sensors in the light of spatial sensitivity}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {636}, doi = {10.25932/publishup-41913}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-419134}, pages = {5009 -- 5030}, year = {2017}, abstract = {In the last few years the method of cosmic-ray neutron sensing (CRNS) has gained popularity among hydrologists, physicists, and land-surface modelers. The sensor provides continuous soil moisture data, averaged over several hectares and tens of decimeters in depth. However, the signal still may contain unidentified features of hydrological processes, and many calibration datasets are often required in order to find reliable relations between neutron intensity and water dynamics. Recent insights into environmental neutrons accurately described the spatial sensitivity of the sensor and thus allowed one to quantify the contribution of individual sample locations to the CRNS signal. Consequently, data points of calibration and validation datasets are suggested to be averaged using a more physically based weighting approach. In this work, a revised sensitivity function is used to calculate weighted averages of point data. The function is different from the simple exponential convention by the extraordinary sensitivity to the first few meters around the probe, and by dependencies on air pressure, air humidity, soil moisture, and vegetation. The approach is extensively tested at six distinct monitoring sites: two sites with multiple calibration datasets and four sites with continuous time series datasets. In all cases, the revised averaging method improved the performance of the CRNS products. The revised approach further helped to reveal hidden hydrological processes which otherwise remained unexplained in the data or were lost in the process of overcalibration. The presented weighting approach increases the overall accuracy of CRNS products and will have an impact on all their applications in agriculture, hydrology, and modeling.}, language = {en} } @phdthesis{Kovacs2022, author = {Kov{\´a}cs, R{\´o}bert}, title = {Human-scale personal fabrication}, doi = {10.25932/publishup-55539}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-555398}, school = {Universit{\"a}t Potsdam}, pages = {139}, year = {2022}, abstract = {The availability of commercial 3D printers and matching 3D design software has allowed a wide range of users to create physical prototypes - as long as these objects are not larger than hand size. However, when attempting to create larger, "human-scale" objects, such as furniture, not only are these machines too small, but also the commonly used 3D design software is not equipped to design with forces in mind — since forces increase disproportionately with scale. In this thesis, we present a series of end-to-end fabrication software systems that support users in creating human-scale objects. They achieve this by providing three main functions that regular "small-scale" 3D printing software does not offer: (1) subdivision of the object into small printable components combined with ready-made objects, (2) editing based on predefined elements sturdy enough for larger scale, i.e., trusses, and (3) functionality for analyzing, detecting, and fixing structural weaknesses. The presented software systems also assist the fabrication process based on either 3D printing or steel welding technology. The presented systems focus on three levels of engineering challenges: (1) fabricating static load-bearing objects, (2) creating mechanisms that involve motion, such as kinematic installations, and finally (3) designing mechanisms with dynamic repetitive movement where power and energy play an important role. We demonstrate and verify the versatility of our systems by building and testing human-scale prototypes, ranging from furniture pieces, pavilions, to animatronic installations and playground equipment. We have also shared our system with schools, fablabs, and fabrication enthusiasts, who have successfully created human-scale objects that can withstand with human-scale forces.}, language = {en} } @article{ScherlerSchwanghart2020, author = {Scherler, Dirk and Schwanghart, Wolfgang}, title = {Drainage divide networks}, series = {Earth surface dynamics}, volume = {8}, journal = {Earth surface dynamics}, number = {2}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {2196-6311}, doi = {10.5194/esurf-8-261-2020}, pages = {261 -- 274}, year = {2020}, abstract = {Drainage divides are organized into tree-like networks that may record information about drainage divide mobility. However, views diverge about how to best assess divide mobility. Here, we apply a new approach of automatically extracting and ordering drainage divide networks from digital elevation models to results from landscape evolution model experiments. We compared landscapes perturbed by strike-slip faulting and spatiotemporal variations in erodibility to a reference model to assess which topographic metrics (hillslope relief, flow distance, and chi) are diagnostic of divide mobility. Results show that divide segments that are a minimum distance of similar to 5 km from river confluences strive to attain constant values of hillslope relief and flow distance to the nearest stream. Disruptions of such patterns can be related to mobile divides that are lower than stable divides, closer to streams, and often asymmetric in shape. In general, we observe that drainage divides high up in the network, i.e., at great distances from river confluences, are more susceptible to disruptions than divides closer to these confluences and are thus more likely to record disturbance for a longer time period. We found that across-divide differences in hillslope relief proved more useful for assessing divide migration than other tested metrics. However, even stable drainage divide networks exhibit across-divide differences in any of the studied topographic metrics. Finally, we propose a new metric to quantify the connectivity of divide junctions.}, language = {en} } @phdthesis{Blessmann2010, author = {Bleßmann, Daniela}, title = {Der Einfluss der Dynamik auf die stratosph{\"a}rische Ozonvariabilit{\"a}t {\"u}ber der Arktis im Fr{\"u}hwinter}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-51394}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {Der fr{\"u}hwinterliche Ozongehalt ist ein Indikator f{\"u}r den Ozongehalt im Sp{\"a}twinter/Fr{\"u}hjahr. Jedoch weist dieser aufgrund von Absinkprozessen, chemisch bedingten Ozonabbau und Wellenaktivit{\"a}t von Jahr zu Jahr starke Schwankungen auf. Die vorliegende Arbeit zeigt, dass diese Variabilit{\"a}t weitestgehend auf dynamische Prozesse w{\"a}hrend der Wirbelbildungsphase des arktischen Polarwirbels zur{\"u}ckgeht. Ferner wird der bisher noch ausstehende Zusammenhang zwischen dem fr{\"u}h- und sp{\"a}twinterlichen Ozongehalt bez{\"u}glich Dynamik und Chemie aufgezeigt. F{\"u}r die Untersuchung des Zusammenhangs zwischen der im Polarwirbel eingeschlossenen Luftmassenzusammensetzung und Ozonmenge wurden Beobachtungsdaten von Satellitenmessinstrumenten und Ozonsonden sowie Modellsimulationen des Lagrangschen Chemie/Transportmodells ATLAS verwandt. Die {\"u}ber die Fl{\"a}che (45-75°N) und Zeit (August-November) gemittelte Vertikalkomponente des Eliassen-Palm-Flussvektors durch die 100hPa-Fl{\"a}che zeigt eine Verbindung zwischen der fr{\"u}hwinterlichen wirbelinneren Luftmassenzusammensetzung und der Wirbelbildungsphase auf. Diese ist jedoch nur f{\"u}r die untere Stratosph{\"a}re g{\"u}ltig, da die Vertikalkomponente die sich innerhalb der Stratosph{\"a}re {\"a}ndernden Wellenausbreitungsbedingungen nicht erfasst. F{\"u}r eine verbesserte H{\"o}hendarstellung des Signals wurde eine neue integrale auf der Wellenamplitude und dem Charney-Drazin-Kriterium basierende Gr{\"o}ße definiert. Diese neue Gr{\"o}ße verbindet die Wellenaktivit{\"a}t w{\"a}hrend der Wirbelbildungsphase sowohl mit der Luftmassenzusammensetzung im Polarwirbel als auch mit der Ozonverteilung {\"u}ber die Breite. Eine verst{\"a}rkte Wellenaktivit{\"a}t f{\"u}hrt zu mehr Luft aus niedrigeren ozonreichen Breiten im Polarwirbel. Aber im Herbst und Fr{\"u}hwinter zerst{\"o}ren chemische Prozesse, die das Ozon ins Gleichgewicht bringen, die interannuale wirbelinnere Ozonvariablit{\"a}t, die durch dynamische Prozesse w{\"a}hrend der arktischen Polarwirbelbildungsphase hervorgerufen wird. Eine Analyse in Hinblick auf den Fortbestand einer dynamisch induzierten Ozonanomalie bis in den Mittwinter erm{\"o}glicht eine Absch{\"a}tzung des Einflusses dieser dynamischen Prozesse auf den arktischen Ozongehalt. Zu diesem Zweck wurden f{\"u}r den Winter 1999-2000 Modelll{\"a}ufe mit dem Lagrangesche Chemie/Transportmodell ATLAS gerechnet, die detaillierte Informationen {\"u}ber den Erhalt der k{\"u}nstlichen Ozonvariabilit{\"a}t hinsichtlich Zeit, H{\"o}he und Breite liefern. Zusammengefasst, besteht die dynamisch induzierte Ozonvariabilit{\"a}t w{\"a}hrend der Wirbelbildungsphase l{\"a}nger im Inneren als im {\"A}ußeren des Polarwirbels und verliert oberhalb von 750K potentieller Temperatur ihre signifikante Wirkung auf die mittwinterliche Ozonvariabilit{\"a}t. In darunterliegenden H{\"o}henbereichen ist der Anteil an der urspr{\"u}nglichen St{\"o}rung groß, bis zu 90\% auf der 450K. Innerhalb dieses H{\"o}henbereiches {\"u}ben die dynamischen Prozesse w{\"a}hrend der Wirbelbildungsphase einen entscheidenden Einfluss auf den Ozongehalt im Mittwinter aus.}, language = {de} } @article{EhrlichGaedke2020, author = {Ehrlich, Elias and Gaedke, Ursula}, title = {Coupled changes in traits and biomasses cascading through a tritrophic plankton food web}, series = {Limnology and oceanography}, volume = {65}, journal = {Limnology and oceanography}, number = {10}, publisher = {Wiley}, address = {Hoboken}, issn = {0024-3590}, doi = {10.1002/lno.11466}, pages = {2502 -- 2514}, year = {2020}, abstract = {Trait-based approaches have broadened our understanding of how the composition of ecological communities responds to environmental drivers. This research has mainly focussed on abiotic factors and competition determining the community trait distribution, while effects of trophic interactions on trait dynamics, if considered at all, have been studied for two trophic levels at maximum. However, natural food webs are typically at least tritrophic. This enables indirect interactions of traits and biomasses among multiple trophic levels leading to underexplored effects on food web dynamics. Here, we demonstrate the occurrence of mutual trait adjustment among three trophic levels in a natural plankton food web (Lake Constance) and in a corresponding mathematical model. We found highly recurrent seasonal biomass and trait dynamics, where herbivorous zooplankton increased its size, and thus its ability to counter phytoplankton defense, before phytoplankton defense actually increased. This is contrary to predictions from bitrophic systems where counter-defense of the consumer is a reaction to prey defense. In contrast, counter-defense of carnivores by size adjustment followed the defense of herbivores as expected. By combining observations and model simulations, we show how the reversed trait dynamics at the two lower trophic levels result from a "trophic biomass-trait cascade" driven by the carnivores. Trait adjustment between two trophic levels can therefore be altered by biomass or trait changes of adjacent trophic levels. Hence, analyses of only pairwise trait adjustment can be misleading in natural food webs, while multitrophic trait-based approaches capture indirect biomass-trait interactions among multiple trophic levels.}, language = {en} } @article{MarschallSkorovZakharovetal.2020, author = {Marschall, Raphael and Skorov, Yuri and Zakharov, Vladimir and Rezac, Ladislav and Gerig, Selina-Barbara and Christou, Chariton and Dadzie, S. Kokou and Migliorini, Alessandra and Rinaldi, Giovanna and Agarwal, Jessica and Vincent, Jean-Baptiste and Kappel, David}, title = {Cometary comae-surface links the physics of gas and dust from the surface to a spacecraft}, series = {Space science reviews}, volume = {216}, journal = {Space science reviews}, number = {8}, publisher = {Springer}, address = {Dordrecht}, issn = {0038-6308}, doi = {10.1007/s11214-020-00744-0}, pages = {53}, year = {2020}, abstract = {A comet is a highly dynamic object, undergoing a permanent state of change. These changes have to be carefully classified and considered according to their intrinsic temporal and spatial scales. The Rosetta mission has, through its contiguous in-situ and remote sensing coverage of comet 67P/Churyumov-Gerasimenko (hereafter 67P) over the time span of August 2014 to September 2016, monitored the emergence, culmination, and winding down of the gas and dust comae. This provided an unprecedented data set and has spurred a large effort to connect in-situ and remote sensing measurements to the surface. In this review, we address our current understanding of cometary activity and the challenges involved when linking comae data to the surface. We give the current state of research by describing what we know about the physical processes involved from the surface to a few tens of kilometres above it with respect to the gas and dust emission from cometary nuclei. Further, we describe how complex multidimensional cometary gas and dust models have developed from the Halley encounter of 1986 to today. This includes the study of inhomogeneous outgassing and determination of the gas and dust production rates. Additionally, the different approaches used and results obtained to link coma data to the surface will be discussed. We discuss forward and inversion models and we describe the limitations of the respective approaches. The current literature suggests that there does not seem to be a single uniform process behind cometary activity. Rather, activity seems to be the consequence of a variety of erosion processes, including the sublimation of both water ice and more volatile material, but possibly also more exotic processes such as fracture and cliff erosion under thermal and mechanical stress, sub-surface heat storage, and a complex interplay of these processes. Seasons and the nucleus shape are key factors for the distribution and temporal evolution of activity and imply that the heliocentric evolution of activity can be highly individual for every comet, and generalisations can be misleading.}, language = {en} } @article{BanerjeeLipowskySanter2020, author = {Banerjee, Pallavi and Lipowsky, Reinhard and Santer, Mark}, title = {Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein}, series = {Journal of Chemical Theory and Computation}, volume = {16}, journal = {Journal of Chemical Theory and Computation}, number = {6}, publisher = {ACS Publications}, address = {Washington DC}, issn = {1549-9626}, doi = {10.1021/acs.jctc.0c00056}, pages = {15}, year = {2020}, abstract = {Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.}, language = {en} } @misc{BanerjeeLipowskySanter2020, author = {Banerjee, Pallavi and Lipowsky, Reinhard and Santer, Mark}, title = {Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {6}, issn = {1866-8372}, doi = {10.25932/publishup-52374}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523742}, pages = {17}, year = {2020}, abstract = {Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.}, language = {en} } @misc{NakamuraClaesGrebeetal.2018, author = {Nakamura, Moritaka and Claes, Andrea R. and Grebe, Tobias and Hermkes, Rebecca and Viotti, Corrado and Ikeda, Yoshihisa and Grebe, Markus}, title = {Auxin and ROP GTPase signaling of polar nuclear migration in root epidermal hair cells}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {992}, issn = {1866-8372}, doi = {10.25932/publishup-44127}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441278}, pages = {378 -- 391}, year = {2018}, abstract = {Polar nuclear migration is crucial during the development of diverse eukaryotes. In plants, root hair growth requires polar nuclear migration into the outgrowing hair. However, knowledge about the dynamics and the regulatory mechanisms underlying nuclear movements in root epidermal cells remains limited. Here, we show that both auxin and Rho-of-Plant (ROP) signaling modulate polar nuclear position at the inner epidermal plasma membrane domain oriented to the cortical cells during cell elongation as well as subsequent polar nuclear movement to the outer domain into the emerging hair bulge in Arabidopsis (Arabidopsis thaliana). Auxin signaling via the nuclear AUXIN RESPONSE FACTOR7 (ARF7)/ARF19 and INDOLE ACETIC ACID7 pathway ensures correct nuclear placement toward the inner membrane domain. Moreover, precise inner nuclear placement relies on SPIKE1 Rho-GEF, SUPERCENTIPEDE1 Rho-GDI, and ACTIN7 (ACT7) function and to a lesser extent on VTI11 vacuolar SNARE activity. Strikingly, the directionality and/or velocity of outer polar nuclear migration into the hair outgrowth along actin strands also are ACT7 dependent, auxin sensitive, and regulated by ROP signaling. Thus, our findings provide a founding framework revealing auxin and ROP signaling of inner polar nuclear position with some contribution by vacuolar morphology and of actin-dependent outer polar nuclear migration in root epidermal hair cells.}, language = {en} } @misc{JingKumarHesseetal.2020, author = {Jing, Miao and Kumar, Rohini and Heße, Falk and Thober, Stephan and Rakovec, Oldrich and Samaniego, Luis and Attinger, Sabine}, title = {Assessing the response of groundwater quantity and travel time distribution to 1.5, 2, and 3 °C global warming in a mesoscale central German basin}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {3}, issn = {1866-8372}, doi = {10.25932/publishup-50934}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-509343}, pages = {18}, year = {2020}, abstract = {Groundwater is the biggest single source of high-quality freshwater worldwide, which is also continuously threatened by the changing climate. In this paper, we investigate the response of the regional groundwater system to climate change under three global warming levels (1.5, 2, and 3 ∘C) in a central German basin (N{\"a}gelstedt). This investigation is conducted by deploying an integrated modeling workflow that consists of a mesoscale hydrologic model (mHM) and a fully distributed groundwater model, OpenGeoSys (OGS). mHM is forced with climate simulations of five general circulation models under three representative concentration pathways. The diffuse recharges estimated by mHM are used as boundary forcings to the OGS groundwater model to compute changes in groundwater levels and travel time distributions. Simulation results indicate that groundwater recharges and levels are expected to increase slightly under future climate scenarios. Meanwhile, the mean travel time is expected to decrease compared to the historical average. However, the ensemble simulations do not all agree on the sign of relative change. Changes in mean travel time exhibit a larger variability than those in groundwater levels. The ensemble simulations do not show a systematic relationship between the projected change (in both groundwater levels and travel times) and the warming level, but they indicate an increased variability in projected changes with adjusting the enhanced warming level from 1.5 to 3 ∘C. Correspondingly, it is highly recommended to restrain the trend of global warming.}, language = {en} } @article{JingKumarHesseetal.2020, author = {Jing, Miao and Kumar, Rohini and Heße, Falk and Thober, Stephan and Rakovec, Oldrich and Samaniego, Luis and Attinger, Sabine}, title = {Assessing the response of groundwater quantity and travel time distribution to 1.5, 2, and 3 °C global warming in a mesoscale central German basin}, series = {Hydrology and Earth System Sciences}, volume = {24}, journal = {Hydrology and Earth System Sciences}, number = {3}, publisher = {Copernicus Publ.}, address = {G{\"o}ttingen}, issn = {1607-7938}, doi = {10.5194/hess-24-1511-2020}, pages = {1511 -- 1526}, year = {2020}, abstract = {Groundwater is the biggest single source of high-quality freshwater worldwide, which is also continuously threatened by the changing climate. In this paper, we investigate the response of the regional groundwater system to climate change under three global warming levels (1.5, 2, and 3 ∘C) in a central German basin (N{\"a}gelstedt). This investigation is conducted by deploying an integrated modeling workflow that consists of a mesoscale hydrologic model (mHM) and a fully distributed groundwater model, OpenGeoSys (OGS). mHM is forced with climate simulations of five general circulation models under three representative concentration pathways. The diffuse recharges estimated by mHM are used as boundary forcings to the OGS groundwater model to compute changes in groundwater levels and travel time distributions. Simulation results indicate that groundwater recharges and levels are expected to increase slightly under future climate scenarios. Meanwhile, the mean travel time is expected to decrease compared to the historical average. However, the ensemble simulations do not all agree on the sign of relative change. Changes in mean travel time exhibit a larger variability than those in groundwater levels. The ensemble simulations do not show a systematic relationship between the projected change (in both groundwater levels and travel times) and the warming level, but they indicate an increased variability in projected changes with adjusting the enhanced warming level from 1.5 to 3 ∘C. Correspondingly, it is highly recommended to restrain the trend of global warming.}, language = {en} } @misc{LevermannWinkelmann2016, author = {Levermann, Anders and Winkelmann, Ricarda}, title = {A simple equation for the melt elevation feedback of ice sheets}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {529}, issn = {1866-8372}, doi = {10.25932/publishup-40983}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-409834}, pages = {9}, year = {2016}, abstract = {In recent decades, the Greenland Ice Sheet has been losing mass and has thereby contributed to global sea-level rise. The rate of ice loss is highly relevant for coastal protection worldwide. The ice loss is likely to increase under future warming. Beyond a critical temperature threshold, a meltdown of the Greenland Ice Sheet is induced by the self-enforcing feedback between its lowering surface elevation and its increasing surface mass loss: the more ice that is lost, the lower the ice surface and the warmer the surface air temperature, which fosters further melting and ice loss. The computation of this rate so far relies on complex numerical models which are the appropriate tools for capturing the complexity of the problem. By contrast we aim here at gaining a conceptual understanding by deriving a purposefully simple equation for the self-enforcing feedback which is then used to estimate the melt time for different levels of warming using three observable characteristics of the ice sheet itself and its surroundings. The analysis is purely conceptual in nature. It is missing important processes like ice dynamics for it to be useful for applications to sea-level rise on centennial timescales, but if the volume loss is dominated by the feedback, the resulting logarithmic equation unifies existing numerical simulations and shows that the melt time depends strongly on the level of warming with a critical slow-down near the threshold: the median time to lose 10\% of the present-day ice volume varies between about 3500 years for a temperature level of 0.5 degrees C above the threshold and 500 years for 5 degrees C. Unless future observations show a significantly higher melting sensitivity than currently observed, a complete meltdown is unlikely within the next 2000 years without significant ice-dynamical contributions.}, language = {en} } @misc{EhlertHolzweberLippitzetal.2016, author = {Ehlert, Christopher and Holzweber, Markus and Lippitz, Andreas and Unger, Wolfgang E. S. and Saalfrank, Peter}, title = {A detailed assignment of NEXAFS resonances of imidazolium based ionic liquids}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-394417}, pages = {8654 -- 8661}, year = {2016}, abstract = {In Near Edge X-Ray Absorption Fine Structure (NEXAFS) spectroscopy X-Ray photons are used to excite tightly bound core electrons to low-lying unoccupied orbitals of the system. This technique offers insight into the electronic structure of the system as well as useful structural information. In this work, we apply NEXAFS to two kinds of imidazolium based ionic liquids ([CnC1im]+[NTf2]- and [C4C1im]+[I]-). A combination of measurements and quantum chemical calculations of C K and N K NEXAFS resonances is presented. The simulations, based on the transition potential density functional theory method (TP-DFT), reproduce all characteristic features observed by the experiment. Furthermore, a detailed assignment of resonance features to excitation centers (carbon or nitrogen atoms) leads to a consistent interpretation of the spectra.}, language = {en} }