@misc{PratHajnýGrunewaldetal.2018, author = {Pr{\´a}t, Tom{\´a}š and Hajny', Jakub and Grunewald, Wim and Vasileva, Mina and Moln{\´a}r, Gergely and Tejos, Ricardo and Schmid, Markus and Sauer, Michael and Friml, Jiř{\´i}}, title = {WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1123}, issn = {1866-8372}, doi = {10.25932/publishup-44633}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-446331}, pages = {20}, year = {2018}, abstract = {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.}, language = {en} } @misc{FranckeFoersterBrosinskyetal.2018, author = {Francke, Till and F{\"o}rster, Saskia and Brosinsky, Arlena and Sommerer, Erik and Lopez-Tarazon, Jose Andres and G{\"u}ntner, Andreas and Batalla Villanueva, Ramon J. and Bronstert, Axel}, title = {Water and sediment fluxes in Mediterranean mountainous regions}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {547}, issn = {1866-8372}, doi = {10.25932/publishup-41915}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-419150}, pages = {13}, year = {2018}, abstract = {A comprehensive hydro-sedimentological dataset for the Is{\´a}bena 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 Is{\´a}bena 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 Is{\´a}bena 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 Is{\´a}bena 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.}, 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} } @misc{LoritzHasslerJackischetal.2017, author = {Loritz, Ralf and Hassler, Sibylle K. and Jackisch, Conrad and Allroggen, Niklas and van Schaik, Loes and Wienh{\"o}fer, Jan and Zehe, Erwin}, title = {Picturing and modeling catchments by representative hillslopes}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {635}, doi = {10.25932/publishup-41908}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-419082}, pages = {1225 -- 1249}, year = {2017}, abstract = {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.}, language = {en} } @misc{FeldmannMaduarSanteretal.2016, author = {Feldmann, David and Maduar, Salim R. and Santer, Mark and Lomadze, Nino and Vinogradova, Olga I. and Santer, Svetlana}, title = {Manipulation of small particles at solid liquid interface}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-100338}, pages = {10}, year = {2016}, abstract = {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.}, language = {en} } @misc{BauerGodecMetzler2014, author = {Bauer, Maximilian and Godec, Aljaž and Metzler, Ralf}, title = {Diffusion of finite-size particles in two-dimensional channels with random wall configurations}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76199}, year = {2014}, abstract = {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].}, language = {en} } @misc{KuikLauerChurkinaetal.2016, author = {Kuik, Friderike and Lauer, Axel and Churkina, Galina and Denier Van der Gon, Hugo Anne Cornelis and Fenner, Daniel and Mar, Kathleen A. and Butler, Tim M.}, title = {Air quality modelling in the Berlin-Brandenburg region using WRF-Chem v3.7.1}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {531}, issn = {1866-8372}, doi = {10.25932/publishup-41013}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-410131}, pages = {25}, year = {2016}, abstract = {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.}, language = {en} } @misc{CampfortsSchwanghartGovers2017, author = {Campforts, Benjamin and Schwanghart, Wolfgang and Govers, Gerard}, title = {Accurate simulation of transient landscape evolution by eliminating numerical diffusion}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {664}, issn = {1866-8372}, doi = {10.25932/publishup-41878}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-418784}, pages = {20}, year = {2017}, abstract = {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.}, language = {en} } @misc{HoffmannSchulzHankeAlbaetal.2017, author = {Hoffmann, Mathias and Schulz-Hanke, Maximilian and Alba, Juana Garcia and Jurisch, Nicole and Hagemann, Ulrike and Sachs, Torsten and Sommer, Michael and Augustin, J{\"u}rgen}, title = {A simple calculation algorithm to separate high-resolution CH4 flux measurements into ebullition- and diffusion-derived components}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {604}, issn = {1866-8372}, doi = {10.25932/publishup-41665}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-416659}, pages = {109 -- 118}, year = {2017}, abstract = {Processes driving the production, transformation and transport of methane (CH4) in wetland ecosystems are highly complex. We present a simple calculation algorithm to separate open-water CH4 fluxes measured with automatic chambers into diffusion- and ebullition-derived components. This helps to reveal underlying dynamics, to identify potential environmental drivers and, thus, to calculate reliable CH4 emission estimates. The flux separation is based on identification of ebullition-related sudden concentration changes during single measurements. Therefore, a variable ebullition filter is applied, using the lower and upper quartile and the interquartile range (IQR). Automation of data processing is achieved by using an established R script, adjusted for the purpose of CH4 flux calculation. The algorithm was validated by performing a laboratory experiment and tested using flux measurement data (July to September 2013) from a former fen grassland site, which converted into a shallow lake as a result of rewetting. Ebullition and diffusion contributed equally (46 and 55 \%) to total CH4 emissions, which is comparable to ratios given in the literature. Moreover, the separation algorithm revealed a concealed shift in the diurnal trend of diffusive fluxes throughout the measurement period. The water temperature gradient was identified as one of the major drivers of diffusive CH4 emissions, whereas no significant driver was found in the case of erratic CH4 ebullition events.}, language = {en} } @misc{NordBoudevillainBerneetal.2017, author = {Nord, Guillaume and Boudevillain, Brice and Berne, Alexis and Branger, Flora and Braud, Isabelle and Dramais, Guillaume and G{\´e}rard, Simon and Le Coz, J{\´e}r{\^o}me and Lego{\^u}t, C{\´e}dric and Molini{\´e}, Gilles and Van Baelen, Joel and Vandervaere, Jean-Pierre and Andrieu, Julien and Aubert, Coralie and Calianno, Martin and Delrieu, Guy and Grazioli, Jacopo and Hachani, Sahar and Horner, Ivan and Huza, Jessica and Le Boursicaud, Rapha{\"e}l and Raupach, Timothy H. and Teuling, Adriaan J. and Uber, Magdalena and Vincendon, B{\´e}atrice and Wijbrans, Annette}, title = {A high space-time resolution dataset linking meteorological forcing and hydro-sedimentary response in a mesoscale Mediterranean catchment (Auzon) of the Ard{\`e}che region, France}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {671}, issn = {1866-8372}, doi = {10.25932/publishup-41912}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-419127}, pages = {29}, year = {2017}, abstract = {A comprehensive hydrometeorological dataset is presented spanning the period 1 January 201131 December 2014 to improve the understanding of the hydrological processes leading to flash floods and the relation between rainfall, runoff, erosion and sediment transport in a mesoscale catchment (Auzon, 116 km(2)) of the Mediterranean region. Badlands are present in the Auzon catchment and well connected to high-gradient channels of bedrock rivers which promotes the transfer of suspended solids downstream. The number of observed variables, the various sensors involved (both in situ and remote) and the space-time resolution (similar to km(2), similar to min) of this comprehensive dataset make it a unique contribution to research communities focused on hydrometeorology, surface hydrology and erosion. Given that rainfall is highly variable in space and time in this region, the observation system enables assessment of the hydrological response to rainfall fields. Indeed, (i) rainfall data are provided by rain gauges (both a research network of 21 rain gauges with a 5 min time step and an operational network of 10 rain gauges with a 5 min or 1 h time step), S-band Doppler dual-polarization radars (1 km(2), 5 min resolution), disdrometers (16 sensors working at 30 s or 1 min time step) and Micro Rain Radars (5 sensors, 100m height resolution). Additionally, during the special observation period (SOP-1) of the HyMeX (Hydrological Cycle in the Mediterranean Experiment) project, two X-band radars provided precipitation measurements at very fine spatial and temporal scales (1 ha, 5 min). (ii) Other meteorological data are taken from the operational surface weather observation stations of Meteo-France (including 2m air temperature, atmospheric pressure, 2 m relative humidity, 10m wind speed and direction, global radiation) at the hourly time resolution (six stations in the region of interest). (iii) The monitoring of surface hydrology and suspended sediment is multi-scale and based on nested catchments. Three hydrometric stations estimate water discharge at a 2-10 min time resolution. Two of these stations also measure additional physico-chemical variables (turbidity, temperature, conductivity) and water samples are collected automatically during floods, allowing further geochemical characterization of water and suspended solids. Two experimental plots monitor overland flow and erosion at 1 min time resolution on a hillslope with vineyard. A network of 11 sensors installed in the intermittent hydrographic network continuously measures water level and water temperature in headwater subcatchments (from 0.17 to 116 km(2)) at a time resolution of 2-5 min. A network of soil moisture sensors enables the continuous measurement of soil volumetric water content at 20 min time resolution at 9 sites. Additionally, concomitant observations (soil moisture measurements and stream gauging) were performed during floods between 2012 and 2014. Finally, this dataset is considered appropriate for understanding the rainfall variability in time and space at fine scales, improving areal rainfall estimations and progressing in distributed hydrological and erosion modelling.}, language = {en} }