TY - GEN A1 - Prát, Tomáš A1 - Hajny ́, Jakub A1 - Grunewald, Wim A1 - Vasileva, Mina A1 - Molnár, Gergely A1 - Tejos, Ricardo A1 - Schmid, Markus A1 - Sauer, Michael A1 - Friml, Jiří T1 - WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17-and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain-and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1123 KW - apical-basal axis KW - arabidopsis-thaliana KW - root gravitropism KW - DNA-binding KW - gene-expression KW - transport KW - efflux KW - canalization KW - plants KW - phosphorylation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-446331 SN - 1866-8372 IS - 1123 ER - TY - GEN A1 - Francke, Till A1 - Förster, Saskia A1 - Brosinsky, Arlena A1 - Sommerer, Erik A1 - Lopez-Tarazon, Jose Andres A1 - Güntner, Andreas A1 - Batalla Villanueva, Ramon J. A1 - Bronstert, Axel T1 - Water and sediment fluxes in Mediterranean mountainous regions BT - comprehensive dataset for hydro-sedimentological analyses and modelling in a mesoscale catchment (River Isábena, NE Spain) T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - A comprehensive hydro-sedimentological dataset for the Isábena catchment, northeastern (NE) Spain, for the period 2010–2018 is presented to analyse water and sediment fluxes in a Mediterranean mesoscale catchment. The dataset includes rainfall data from 12 rain gauges distributed within the study area complemented by meteorological data of 12 official meteo-stations. It comprises discharge data derived from water stage measurements as well as suspended sediment concentrations (SSCs) at six gauging stations of the River Isábena and its sub-catchments. Soil spectroscopic data from 351 suspended sediment samples and 152 soil samples were collected to characterize sediment source regions and sediment properties via fingerprinting analyses. The Isábena catchment (445 km 2 ) is located in the southern central Pyrenees ranging from 450 m to 2720 m a.s.l.; together with a pronounced topography, this leads to distinct temperature and precipitation gradients. The River Isábena shows marked discharge variations and high sediment yields causing severe siltation problems in the downstream Barasona Reservoir. The main sediment source is badland areas located on Eocene marls that are well connected to the river network. The dataset features a comprehensive set of variables in a high spatial and temporal resolution suitable for the advanced process understanding of water and sediment fluxes, their origin and connectivity and sediment budgeting and for the evaluation and further development of hydro-sedimentological models in Mediterranean mesoscale mountainous catchments. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 547 KW - source siscrimination KW - transport KW - pyrenees KW - connectivity KW - sischarge KW - runoff KW - yield Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-419150 SN - 1866-8372 IS - 547 ER - TY - GEN A1 - Jeon, Jae-Hyung A1 - Chechkin, Aleksei V. A1 - Metzler, Ralf T1 - Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 180 KW - single-particle tracking KW - living cells KW - random-walks KW - subdiffusion KW - dynamics KW - nonergodicity KW - coefficients KW - transport KW - membrane KW - behavior Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-76302 SP - 15811 EP - 15817 ER - TY - GEN A1 - Loritz, Ralf A1 - Hassler, Sibylle K. A1 - Jackisch, Conrad A1 - Allroggen, Niklas A1 - van Schaik, Loes A1 - Wienhöfer, Jan A1 - Zehe, Erwin T1 - Picturing and modeling catchments by representative hillslopes T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - This study explores the suitability of a single hillslope as a parsimonious representation of a catchment in a physically based model. We test this hypothesis by picturing two distinctly different catchments in perceptual models and translating these pictures into parametric setups of 2-D physically based hillslope models. The model parametrizations are based on a comprehensive field data set, expert knowledge and process-based reasoning. Evaluation against streamflow data highlights that both models predicted the annual pattern of streamflow generation as well as the hydrographs acceptably. However, a look beyond performance measures revealed deficiencies in streamflow simulations during the summer season and during individual rainfall-runoff events as well as a mismatch between observed and simulated soil water dynamics. Some of these shortcomings can be related to our perception of the systems and to the chosen hydrological model, while others point to limitations of the representative hillslope concept itself. Nevertheless, our results confirm that representative hillslope models are a suitable tool to assess the importance of different data sources as well as to challenge our perception of the dominant hydrological processes we want to represent therein. Consequently, these models are a promising step forward in the search for the optimal representation of catchments in physically based models. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 635 KW - soil-moisture dynamics KW - hydrologic-response simulation KW - rainfall-runoff response KW - preferential flow KW - subsurface stormflow KW - water-uptake KW - field-scale KW - transport KW - system KW - basin Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-419082 IS - 635 SP - 1225 EP - 1249 ER - TY - GEN A1 - Feldmann, David A1 - Maduar, Salim R. A1 - Santer, Mark A1 - Lomadze, Nino A1 - Vinogradova, Olga I. A1 - Santer, Svetlana T1 - Manipulation of small particles at solid liquid interface BT - light driven diffusioosmosis N2 - The strong adhesion of sub-micron sized particles to surfaces is a nuisance, both for removing contaminating colloids from surfaces and for conscious manipulation of particles to create and test novel micro/nano-scale assemblies. The obvious idea of using detergents to ease these processes suffers from a lack of control: the action of any conventional surface-modifying agent is immediate and global. With photosensitive azobenzene containing surfactants we overcome these limitations. Such photo-soaps contain optical switches (azobenzene molecules), which upon illumination with light of appropriate wavelength undergo reversible trans-cis photo-isomerization resulting in a subsequent change of the physico-chemical molecular properties. In this work we show that when a spatial gradient in the composition of trans- and cis- isomers is created near a solid-liquid interface, a substantial hydrodynamic flow can be initiated, the spatial extent of which can be set, e.g., by the shape of a laser spot. We propose the concept of light induced diffusioosmosis driving the flow, which can remove, gather or pattern a particle assembly at a solid-liquid interface. In other words, in addition to providing a soap we implement selectivity: particles are mobilized and moved at the time of illumination, and only across the illuminated area. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 293 KW - azobenzene KW - brushes KW - films KW - genomic DNA conformation KW - gradients KW - optical manipulation KW - photocontrol KW - photosensitive surfactants KW - tracking KW - transport Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-100338 ER - TY - THES A1 - Schneider, Judith T1 - Dynamical structures and manifold detection in 2D and 3D chaotic flows N2 - In dieser Arbeit werden die dynamischen Strukturen und Mannigfaltigkeiten in geschlossenen chaotischen Systemen untersucht. Das Wissen um diese dynamischen Strukturen (und Mannigfaltigkeiten) ist von Bedeutung, da sie uns einen ersten Überblick über die Dynamik des Systems geben, dass heisst, mit ihrer Hilfe sind wir in der Lage, das System zu charakterisieren und eventuell sogar seine Dynamik vorherzusagen. Die Visualisierung der dynamischen Strukturen, speziell in geschlossenen chaotischen Systemen, ist ein schwieriger und oft langer Prozess. Hier werden wir die sogenannte 'Leaking-Methode' (an Beispielen einfacher mathematischer Modelle wie der Bäcker- oder der Sinus Abbildung) vorstellen, mit deren Hilfe wir die Möglichkeit haben, Teile der Mannigfaltigkeiten des chaotischen Sattels des Systems zu visualisieren. Vergleiche zwischen den gewonnenen Strukturen und Strukturen die durch chemische oder biologische Reaktionen hervorgerufen werden, werden anhand eines kinematischen Modells des Golfstroms durchgeführt. Es wird gezeigt, dass mittels der Leaking-Methode dynamische Strukturen auch in Umweltsystemen sichtbar gemacht werden können. Am Beispiel eines realistischen Modells des Mittelmeeres erweitern wir die Leaking-Methode zur sogenannten 'Exchange-Methode'. Diese erlaubt es den Transport zwischen zwei Regionen zu charakterisieren, die Transport-Routen und Austausch-Bassins sichtbar zu machen und die Austausch-Zeiten zu berechnen. Austausch-Bassins und Zeiten werden für die nördliche und südliche Region des westlichen Mittelmeeres präsentiert. Weiterhin werden Mischungseigenschaften im Erdmantel charakterisiert und die geometrischen Eigenschaften von Mannigfaltigkeiten in einem 3dimensionalen mathematischen Modell (ABC-Abbildung) untersucht. N2 - In this thesis, dynamical structures and manifolds in closed chaotic flows will be investigated. The knowledge about the dynamical structures (and manifolds) of a system is of importance, since they provide us first information about the dynamics of the system - means, with their help we are able to characterize the flow and maybe even to forecast it`s dynamics. The visualization of such structures in closed chaotic flows is a difficult and often long-lasting process. Here, the so-called 'Leaking-method' will be introduced, in examples of simple mathematical maps as the baker- or sine-map, with which we are able to visualize subsets of the manifolds of the system`s chaotic saddle. Comparisons between the visualized manifolds and structures traced out by chemical or biological reactions superimposed on the same flow will be done in the example of a kinematic model of the Gulf Stream. It will be shown that with the help of the leaking method dynamical structures can be also visualized in environmental systems. In the example of a realistic model of the Mediterranean Sea, the leaking method will be extended to the 'exchange-method'. The exchange method allows us to characterize transport between two regions, to visualize transport routes and their exchange sets and to calculate the exchange times. Exchange times and sets will be shown and calculated for a northern and southern region in the western basin of the Mediterranean Sea. Furthermore, mixing properties in the Earth mantle will be characterized and geometrical properties of manifolds in a 3dimensional mathematical model (ABC map) will be investigated. T2 - Dynamical structures and manifold detection in 2D and 3D chaotic flows KW - Chaos KW - Transport KW - Mannigfaltigkeiten KW - Umweltsysteme KW - 2D Systeme KW - 3D Systeme KW - chaos KW - transport KW - manifold detection KW - environmental systems KW - 2d systems KW - 3d systems Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-0001696 ER - TY - GEN A1 - Bauer, Maximilian A1 - Godec, Aljaž A1 - Metzler, Ralf T1 - Diffusion of finite-size particles in two-dimensional channels with random wall configurations N2 - Diffusion of chemicals or tracer molecules through complex systems containing irregularly shaped channels is important in many applications. Most theoretical studies based on the famed Fick–Jacobs equation focus on the idealised case of infinitely small particles and reflecting boundaries. In this study we use numerical simulations to consider the transport of finite-size particles through asymmetrical two-dimensional channels. Additionally, we examine transient binding of the molecules to the channel walls by applying sticky boundary conditions. We consider an ensemble of particles diffusing in independent channels, which are characterised by common structural parameters. We compare our results for the long-time effective diffusion coefficient with a recent theoretical formula obtained by Dagdug and Pineda [J. Chem. Phys., 2012, 137, 024107]. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 177 KW - anomalous diffusion KW - fractional dynamics KW - transport KW - nonergodicity KW - coefficient Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-76199 ER - TY - THES A1 - Beeg, Janina T1 - Cooperative behavior of motor proteins T1 - Transportverhalten kollektiv arbeitender Motorproteine N2 - The cytoskeletal motor protein kinesin-1 (conventional kinesin) is the fast carrier for intracellular cargo transport along microtubules. So far most studies aimed at investigating the transport properties of individual motor molecules. However, the transport in cells usually involves the collective work of more than one motor. In the present work, we have studied the movement of beads as artificial loads/organelles pulled by several kinesin-1 motors in vitro. For a wide range of motor coverage of the beads and different bead (cargo) sizes the transport parameters walking distance or run length, velocity and force generation are measured. The results indicate that the transport parameters are influenced by the number of motors carrying the bead. While the transport velocity slightly decreases, an increase in the run length was measured and higher forces are determined, when more motors are involved. The effective number of motors pulling a bead is estimated by measuring the change in the hydrodynamic diameter of kinesin-coated beads using dynamic light scattering. The geometrical constraints imposed by the transport system have been taken into account. Thus, results for beads of different size and motor-surface coverage could be compared. In addition, run length-distributions obtained for the smallest bead size were matched to theoretically calculated distributions. The latter yielded an average number of pulling motors, which is in agreement with the effective motor numbers determined experimentally. N2 - Kinesin-1 (konventionelles Kinesin) ist ein Motorprotein des Zytoskeletts, das für den schnellen intrazellulären Lastentransport auf Mikrotubuli verantwortlich ist. Das Hauptinteresse vieler Studien lag bisher auf der Erforschung der Transporteigenschaften von Einzelmotormolekülen. Der Transport in der Zelle erfordert aber gewöhnlich kollektive Arbeit von mehreren Motoren. In dieser Arbeit wurde die Bewegung von Kugeln als Modell für Zellorganellen, die von Kinesin-1 Molekülen gezogen werden, in Anhängigkeit von der Motorendichte auf der Kugeloberfläche und unterschiedlichen Kugeldurchmessern in vitro untersuchten. Die Transportparameter Weglänge, Geschwindigkeit und die erzeugte Kraft wurden gemessen. Die Ergebnisse zeigen, dass die Transportgeschwindigkeit leicht abnimmt, wohingegen die Weglänge und die erzeugten Kräfte mit steigender Molekülkonzentration zunehmen. Die tatsächliche Anzahl der Motoren, die aktiv am Transport der Kugeln beteiligt sind, wurde bestimmt, indem die Änderung des hydrodynamischen Durchmessers der mit Kinesin bedeckten Kugeln mittels dynamischer Lichtstreuung gemessen wurde. Außerdem wurden sterische Effekte des verwendeten Transportsystems in die Berechnung einbezogen. Damit werden Ergebnisse vergleichbar, die für unterschiedliche Kugeldurchmesser und Motorkonzentrationen ermittelt wurden. Zusätzlich wurden die Verteilungen der Weglängen für die kleinste Kugelgröße mit theoretisch ermittelten Verteilungen verglichen. Letzteres ergab durchschnittliche Anzahlen der aktiv am Transport beteiligten Motormoleküle, die mit den experimentell bestimmten Ergebnissen übereinstimmen. KW - Transport KW - Weglänge KW - Geschwindigkeit KW - erzeugte Kraft KW - Kinesin KW - transport KW - run length KW - velocity KW - generated force KW - kinesin Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-15712 ER - TY - GEN A1 - Kuik, Friderike A1 - Lauer, Axel A1 - Churkina, Galina A1 - Denier Van der Gon, Hugo Anne Cornelis A1 - Fenner, Daniel A1 - Mar, Kathleen A. A1 - Butler, Tim M. T1 - Air quality modelling in the Berlin–Brandenburg region using WRF-Chem v3.7.1 BT - sensitivity to resolution of model grid and input data T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Air pollution is the number one environmental cause of premature deaths in Europe. Despite extensive regulations, air pollution remains a challenge, especially in urban areas. For studying summertime air quality in the Berlin-Brandenburg region of Germany, the Weather Research and Forecasting Model with Chemistry (WRF-Chem) is set up and evaluated against meteorological and air quality observations from monitoring stations as well as from a field campaign conducted in 2014. The objective is to assess which resolution and level of detail in the input data is needed for simulating urban background air pollutant concentrations and their spatial distribution in the Berlin-Brandenburg area. The model setup includes three nested domains with horizontal resolutions of 15, 3 and 1 km and anthropogenic emissions from the TNO-MACC III inventory. We use RADM2 chemistry and the MADE/SORGAM aerosol scheme. Three sensitivity simulations are conducted updating input parameters to the single-layer urban canopy model based on structural data for Berlin, specifying land use classes on a sub-grid scale (mosaic option) and downscaling the original emissions to a resolution of ca. 1 km x 1 km for Berlin based on proxy data including traffic density and population density. The results show that the model simulates meteorology well, though urban 2m temperature and urban wind speeds are biased high and nighttime mixing layer height is biased low in the base run with the settings described above. We show that the simulation of urban meteorology can be improved when specifying the input parameters to the urban model, and to a lesser extent when using the mosaic option. On average, ozone is simulated reasonably well, but maximum daily 8 h mean concentrations are underestimated, which is consistent with the results from previous modelling studies using the RADM2 chemical mechanism. Particulate matter is underestimated, which is partly due to an underestimation of secondary organic aerosols. NOx (NO + NO2) concentrations are simulated reasonably well on average, but nighttime concentrations are overestimated due to the model's underestimation of the mixing layer height, and urban daytime concentrations are underestimated. The daytime underestimation is improved when using downscaled, and thus locally higher emissions, suggesting that part of this bias is due to deficiencies in the emission input data and their resolution. The results further demonstrate that a horizontal resolution of 3 km improves the results and spatial representativeness of the model compared to a horizontal resolution of 15 km. With the input data (land use classes, emissions) at the level of detail of the base run of this study, we find that a horizontal resolution of 1 km does not improve the results compared to a resolution of 3 km. However, our results suggest that a 1 km horizontal model resolution could enable a detailed simulation of local pollution patterns in the Berlin-Brandenburg region if the urban land use classes, together with the respective input parameters to the urban canopy model, are specified with a higher level of detail and if urban emissions of higher spatial resolution are used. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 531 KW - urban canopy model KW - aqmeii phase-2 KW - Mexico-City KW - Heat-Island KW - ozone KW - performance KW - transport KW - chemistry KW - meteorology KW - simulation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-410131 SN - 1866-8372 IS - 531 ER - TY - GEN A1 - Campforts, Benjamin A1 - Schwanghart, Wolfgang A1 - Govers, Gerard T1 - Accurate simulation of transient landscape evolution by eliminating numerical diffusion BT - the TTLEM 1.0 model T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Landscape evolution models (LEMs) allow the study of earth surface responses to changing climatic and tectonic forcings. While much effort has been devoted to the development of LEMs that simulate a wide range of processes, the numerical accuracy of these models has received less attention. Most LEMs use first-order accurate numerical methods that suffer from substantial numerical diffusion. Numerical diffusion particularly affects the solution of the advection equation and thus the simulation of retreating landforms such as cliffs and river knickpoints. This has potential consequences for the integrated response of the simulated landscape. Here we test a higher-order flux-limiting finite volume method that is total variation diminishing (TVD-FVM) to solve the partial differential equations of river incision and tectonic displacement. We show that using the TVD-FVM to simulate river incision significantly influences the evolution of simulated landscapes and the spatial and temporal variability of catchment-wide erosion rates. Furthermore, a two-dimensional TVD-FVM accurately simulates the evolution of landscapes affected by lateral tectonic displacement, a process whose simulation was hitherto largely limited to LEMs with flexible spatial discretization. We implement the scheme in TTLEM (TopoToolbox Landscape Evolution Model), a spatially explicit, raster-based LEM for the study of fluvially eroding landscapes in TopoToolbox 2. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 664 KW - stream power law KW - river incision model KW - transport KW - topography KW - hillslopes KW - equation KW - implicit KW - erosion KW - ranges Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-418784 SN - 1866-8372 IS - 664 ER -