TY - JOUR 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 JF - Physical chemistry, chemical physics : PCCP 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. 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 - https://doi.org/10.1039/C4CP02019G VL - 30 IS - 16 SP - 15811 EP - 15817 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Shin, Jaeoh A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf ED - Metzler, Ralf T1 - Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size JF - Soft Matter N2 - 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. KW - gene-regulation kinetics KW - physiological consequences KW - spatial-organization KW - anomalous diffusion KW - folding kinetics KW - living cells KW - dna coiling KW - in-vitro KW - dynamics KW - mixtures Y1 - 2014 SN - 1744-683X SP - 472 EP - 488 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - GEN A1 - Shin, Jaeoh A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf T1 - Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 185 KW - gene-regulation kinetics KW - physiological consequences KW - spatial-organization KW - anomalous diffusion KW - folding kinetics KW - living cells KW - dna coiling KW - in-vitro KW - dynamics KW - mixtures Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-76961 SP - 472 EP - 488 PB - The Royal Society of Chemistry CY - Cambridge 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 - Levermann, Anders A1 - Winkelmann, Ricarda T1 - A simple equation for the melt elevation feedback of ice sheets T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 529 KW - sea-level rise KW - mass-balance KW - climate-change KW - Greenland KW - model KW - glacier KW - projections KW - dynamics KW - impact KW - 21st-Century Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-409834 SN - 1866-8372 IS - 529 ER - TY - GEN A1 - Fondell, Mattis A1 - Eckert, Sebastian A1 - Jay, Raphael Martin A1 - Weniger, Christian A1 - Quevedo, Wilson A1 - Niskanen, Johannes A1 - Kennedy, Brian A1 - Sorgenfrei, Nomi A1 - Schick, Daniel A1 - Giangrisostomi, Erika A1 - Ovsyannikov, Ruslan A1 - Adamczyk, Katrin A1 - Huse, Nils A1 - Wernet, Philippe A1 - Mitzner, Rolf A1 - Föhlisch, Alexander T1 - Time-resolved soft X-ray absorption spectroscopy in transmission mode on liquids at MHz repetition rates T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 780 KW - l-edge xas KW - electronic-structure KW - molecular-structure KW - spin-state KW - dynamics KW - complexes KW - probe KW - water KW - iron(II) KW - spectra Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-437529 SN - 1866-8372 IS - 780 ER - TY - GEN A1 - Pudell, Jan-Etienne A1 - Maznev, Alexei A1 - Herzog, Marc A1 - Kronseder, M. A1 - Back, Christian A1 - Malinowski, Gregory A1 - von Reppert, Alexander A1 - Bargheer, Matias T1 - Layer specific observation of slow thermal equilibration in ultrathin metallic nanostructures by femtosecond X-ray diffraction T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 797 KW - thin magnetic layers KW - optical-excitation KW - heat-capacity KW - electron KW - gold KW - dynamics Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-426233 SN - 1866-8372 IS - 797 ER - TY - GEN A1 - Schrön, Martin A1 - Köhli, Markus A1 - Scheiffele, Lena A1 - Iwema, Joost A1 - Bogena, Heye R. A1 - Lv, Ling A1 - Martini, Edoardo A1 - Baroni, Gabriele A1 - Rosolem, Rafael A1 - Weimar, Jannis A1 - Mai, Juliane A1 - Cuntz, Matthias A1 - Rebmann, Corinna A1 - Oswald, Sascha A1 - Dietrich, Peter A1 - Schmidt, Ulrich A1 - Zacharias, Steffen T1 - Improving calibration and validation of cosmic-ray neutron sensors in the light of spatial sensitivity T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 636 KW - forested headwater catchment KW - moisture observing system KW - soil-water content KW - parameterization methods KW - scale KW - field KW - dynamics KW - observatories KW - networks Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-419134 IS - 636 SP - 5009 EP - 5030 ER -