TY - GEN A1 - Barbosa Pfannes, Eva Katharina A1 - Anielski, Alexander A1 - Gerhardt, Matthias A1 - Beta, Carsten T1 - Intracellular photoactivation of caged cGMP induces myosin II and actin responses in motile cells N2 - Cyclic GMP (cGMP) is a ubiquitous second messenger in eukaryotic cells. It is assumed to regulate the association of myosin II with the cytoskeleton of motile cells. When cells of the social amoeba Dictyostelium discoideum are exposed to chemoattractants or to increased osmotic stress, intracellular cGMP levels rise, preceding the accumulation of myosin II in the cell cortex. To directly investigate the impact of intracellular cGMP on cytoskeletal dynamics in a living cell, we released cGMP inside the cell by laser-induced photo-cleavage of a caged precursor. With this approach, we could directly show in a live cell experiment that an increase in intracellular cGMP indeed induces myosin II to accumulate in the cortex. Unexpectedly, we observed for the first time that also the amount of filamentous actin in the cell cortex increases upon a rise in the cGMP concentration, independently of cAMP receptor activation and signaling. We discuss our results in the light of recent work on the cGMP signaling pathway and suggest possible links between cGMP signaling and the actin system. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 239 KW - cyclic-gmp KW - dictyostelium-discoideum KW - ena/vasp proteins KW - osmotic-stress KW - chemotaxis KW - phosphorylation KW - amp KW - cytoskeleton KW - oscillations KW - chemoattractant Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-94984 SP - 1456 EP - 1463 ER - TY - GEN A1 - Gühr, Markus T1 - Ultrafast Soft X-ray Probing of Gas Phase Molecular Dynamics N2 - The molecular ability to selectively and efficiently convert sunlight into other forms of energy like heat, bond change, or charge separation is truly remarkable. The decisive steps in these transformations often happen on a femtosecond timescale and require transitions among different electronic states that violate the Born-Oppenheimer approximation (BOA). Non-BOA transitions pose challenges to both theory and experiment. From a theoretical point of view, excited state dynamics and nonadiabatic transitions both are difficult problems (see Figure 1(a)). However, the theory on non-BOA dynamics has advanced significantly over the last two decades. Full dynamical simulations for molecules of the size of nucleobases have been possible for a couple of years and allow predictions of experimental observables like photoelectron energy or ion yield. The availability of these calculations for isolated molecules has spurred new experimental efforts to develop methods that are sufficiently different from all optical techniques. For determination of transient molecular structure, femtosecond X-ray diffraction and electron diffraction have been implemented on optically excited molecules. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 268 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-97215 ER - TY - GEN A1 - Palyulin, Vladimir V. A1 - Ala-Nissila, Tapio A1 - Metzler, Ralf T1 - Polymer translocation: the first two decades and the recent diversification N2 - Probably no other field of statistical physics at the borderline of soft matter and biological physics has caused such a flurry of papers as polymer translocation since the 1994 landmark paper by Bezrukov, Vodyanoy, and Parsegian and the study of Kasianowicz in 1996. Experiments, simulations, and theoretical approaches are still contributing novel insights to date, while no universal consensus on the statistical understanding of polymer translocation has been reached. We here collect the published results, in particular, the famous–infamous debate on the scaling exponents governing the translocation process. We put these results into perspective and discuss where the field is going. In particular, we argue that the phenomenon of polymer translocation is non-universal and highly sensitive to the exact specifications of the models and experiments used towards its analysis. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 179 KW - solid-state nanopores KW - single-stranded-dna KW - posttranslational protein translocation KW - anomalous diffusion KW - monte-carlo KW - structured polynucleotides KW - dynamics simulation KW - equation approach KW - osmotic-pressure KW - membrane channel Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-76287 SP - 9016 EP - 9037 ER - TY - GEN A1 - Metzler, Ralf A1 - Bauer, Maximilian A1 - Rasmussen, Emil S. A1 - Lomholt, Michael A. T1 - Real sequence effects on the search dynamics of transcription factors on DNA N2 - Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events through the cytoplasm. From simulations and theoretical analysis we study the TF-sliding motion for a large section of the DNA-sequence of a common E. coli strain, based on the two-state TF-model with a fast-sliding search state and a recognition state enabling target detection. For the probability to detect the target before dissociating from DNA the TF-search times self-consistently depend heavily on whether or not an auxiliary operator (an accessible sequence similar to the main operator) is present in the genome section. Importantly, within our model the extent to which the interconversion rates between search and recognition states depend on the underlying nucleotide sequence is varied. A moderate dependence maximises the capability to distinguish between the main operator and similar sequences. Moreover, these auxiliary operators serve as starting points for DNA looping with the main operator, yielding a spectrum of target detection times spanning several orders of magnitude. Auxiliary operators are shown to act as funnels facilitating target detection by TFs. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 189 KW - gene regulatory networks KW - biological physics Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-79411 ER - TY - GEN A1 - Goychuk, Igor T1 - Quantum ergodicity breaking in semi-classical electron transfer dynamics N2 - Can the statistical properties of single-electron transfer events be correctly predicted within a common equilibrium ensemble description? This fundamental in nanoworld question of ergodic behavior is scrutinized within a very basic semi-classical curve-crossing problem. It is shown that in the limit of non-adiabatic electron transfer (weak tunneling) well-described by the Marcus–Levich–Dogonadze(MLD) rate the answer is yes. However, in the limit of the so-called solvent-controlled adiabatic electron transfer, a profound breaking of ergodicity occurs. Namely, a common description based on the ensemble reduced density matrix with an initial equilibrium distribution of the reaction coordinate is not able to reproduce the statistics of single-trajectory events in this seemingly classical regime. For sufficiently large activation barriers, the ensemble survival probability in a state remains nearly exponential with the inverse rate given by the sum of the adiabatic curve crossing (Kramers) time and the inverse MLD rate. In contrast, near to the adiabatic regime, the single-electron survival probability is clearly non-exponential, even though it possesses an exponential tail which agrees well with the ensemble description. Initially, it is well described by a Mittag-Leffler distribution with a fractional rate. Paradoxically, the mean transfer time in this classical on the ensemble level regime is well described by the inverse of the nonadiabatic quantum tunneling rate on a single particle level. An analytical theory is developed which perfectly agrees with stochastic simulations and explains our findings. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 299 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-102264 ER - TY - GEN A1 - Risbey, James S. A1 - Lewandowsky, Stephan A1 - Cowtan, Kevin A1 - Oreskes, Naomi A1 - Rahmstorf, Stefan A1 - Jokimäki, Ari A1 - Foster, Grant T1 - A fluctuation in surface temperature in historical context BT - reassessment and retrospective on the evidence T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - This work reviews the literature on an alleged global warming 'pause' in global mean surface temperature (GMST) to determine how it has been defined, what time intervals are used to characterise it, what data are used to measure it, and what methods used to assess it. We test for 'pauses', both in the normally understood meaning of the term to mean no warming trend, as well as for a 'pause' defined as a substantially slower trend in GMST. The tests are carried out with the historical versions of GMST that existed for each pause-interval tested, and with current versions of each of the GMST datasets. The tests are conducted following the common (but questionable) practice of breaking the linear fit at the start of the trend interval ('broken' trends), and also with trends that are continuous with the data bordering the trend interval. We also compare results when appropriate allowance is made for the selection bias problem. The results show that there is little or no statistical evidence for a lack of trend or slower trend in GMST using either the historical data or the current data. The perception that there was a 'pause' in GMST was bolstered by earlier biases in the data in combination with incomplete statistical testing. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1023 KW - climate variability KW - climate trends KW - temperature fluctuation KW - pause hiatus Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-468041 SN - 1866-8372 VL - 13 IS - 1023 ER - TY - GEN A1 - Mann, Michael E. A1 - Rahmstorf, Stefan A1 - Kornhuber, Kai A1 - Steinman, Byron A. A1 - Miller, Sonya K. A1 - Petri, Stefan A1 - Coumou, Dim T1 - Projected changes in persistent extreme summer weather events BT - the role of quasi-resonant amplification T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Persistent episodes of extreme weather in the Northern Hemisphere summer have been associated with high-amplitude quasi-stationary atmospheric Rossby waves, with zonal wave numbers 6 to 8 resulting from the phenomenon of quasi-resonant amplification (QRA). A fingerprint for the occurrence of QRA can be defined in terms of the zonally averaged surface temperature field. Examining state-of-the-art [Coupled Model Intercomparison Project Phase 5 (CMIP5)] climate model projections, we find that QRA events are likely to increase by similar to 50% this century under business-as-usual carbon emissions, but there is considerable variation among climate models. Some predict a near tripling of QRA events by the end of the century, while others predict a potential decrease. Models with amplified Arctic warming yield the most pronounced increase in QRA events. The projections are strongly dependent on assumptions regarding the nature of changes in radiative forcing associated with anthropogenic aerosols over the next century. One implication of our findings is that a reduction in midlatitude aerosol loading could actually lead to Arctic de-amplification this century, ameliorating potential increases in persistent extreme weather events. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 994 KW - planetary wave resonance KW - northern KW - atmosphere KW - attribution KW - circulation Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-446416 SN - 1866-8372 IS - 994 ER - TY - GEN A1 - Alonso, Sergio A1 - Stange, Maike A1 - Beta, Carsten T1 - Modeling random crawling, membrane deformation and intracellular polarity of motile amoeboid cells T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1014 KW - signaling system KW - eukaryotic chemotaxis KW - Dictyostelium cells KW - actin cytoskeleton KW - excitable networks KW - PIP3 waves KW - migration KW - dynamics KW - oscillations KW - transduction Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-459745 SN - 1866-8372 IS - 1014 ER - TY - GEN A1 - Beta, Carsten A1 - Gov, Nir S. A1 - Yochelis, Arik T1 - Why a Large-Scale Mode Can Be Essential for Understanding Intracellular Actin Waves T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - During the last decade, intracellular actin waves have attracted much attention due to their essential role in various cellular functions, ranging from motility to cytokinesis. Experimental methods have advanced significantly and can capture the dynamics of actin waves over a large range of spatio-temporal scales. However, the corresponding coarse-grained theory mostly avoids the full complexity of this multi-scale phenomenon. In this perspective, we focus on a minimal continuum model of activator–inhibitor type and highlight the qualitative role of mass conservation, which is typically overlooked. Specifically, our interest is to connect between the mathematical mechanisms of pattern formation in the presence of a large-scale mode, due to mass conservation, and distinct behaviors of actin waves. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 967 KW - nonlinear waves KW - actin polymerization KW - bifurcation theory KW - mass conservation KW - spatial localization KW - pattern formation KW - activator–inhibitor models Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-473588 SN - 1866-8372 IS - 967 ER - TY - GEN A1 - Mardoukhi, Yousof A1 - Jeon, Jae-Hyung A1 - Metzler, Ralf T1 - Geometry controlled anomalous diffusion in random fractal geometries BT - looking beyond the infinite cluster T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We investigate the ergodic properties of a random walker performing (anomalous) diffusion on a random fractal geometry. Extensive Monte Carlo simulations of the motion of tracer particles on an ensemble of realisations of percolation clusters are performed for a wide range of percolation densities. Single trajectories of the tracer motion are analysed to quantify the time averaged mean squared displacement (MSD) and to compare this with the ensemble averaged MSD of the particle motion. Other complementary physical observables associated with ergodicity are studied, as well. It turns out that the time averaged MSD of individual realisations exhibits non-vanishing fluctuations even in the limit of very long observation times as the percolation density approaches the critical value. This apparent non-ergodic behaviour concurs with the ergodic behaviour on the ensemble averaged level. We demonstrate how the non-vanishing fluctuations in single particle trajectories are analytically expressed in terms of the fractal dimension and the cluster size distribution of the random geometry, thus being of purely geometrical origin. Moreover, we reveal that the convergence scaling law to ergodicity, which is known to be inversely proportional to the observation time T for ergodic diffusion processes, follows a power-law ∼T−h with h < 1 due to the fractal structure of the accessible space. These results provide useful measures for differentiating the subdiffusion on random fractals from an otherwise closely related process, namely, fractional Brownian motion. Implications of our results on the analysis of single particle tracking experiments are provided. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 980 KW - plasma-membrane KW - mechanisms KW - motion KW - nonergodicity KW - models Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-474864 SN - 1866-8372 IS - 980 SP - 30134 EP - 30147 ER - TY - GEN A1 - Menzel, Ralf A1 - Heuer, Axel A1 - Milonni, Peter W. T1 - Entanglement, complementarity, and vacuum fields in spontaneous parametric down-conversion T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Using two crystals for spontaneous parametric down-conversion in a parallel setup, we observe two-photon interference with high visibility. The high visibility is consistent with complementarity and the absence of which-path information. The observations are explained as the effects of entanglement or equivalently in terms of interfering probability amplitudes and also by the calculation of a second-order field correlation function in the Heisenberg picture. The latter approach brings out explicitly the role of the vacuum fields in the down-conversion at the crystals and in the photon coincidence counting. For comparison, we show that the Hong–Ou–Mandel dip can be explained by the same approach in which the role of the vacuum signal and idler fields, as opposed to entanglement involving vacuum states, is emphasized. We discuss the fundamental limitations of a theory in which these vacuum fields are treated as classical, stochastic fields. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1077 KW - complementarity KW - vacuum fields KW - entanglement KW - Hong-Ou-Mandel effect KW - spontaneous parametric down-conversion Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-473542 SN - 1866-8372 IS - 1077 ER - TY - GEN A1 - Shan, Yuli A1 - Guan, Dabo A1 - Hubacek, Klaus A1 - Zheng, Bo A1 - Davis, Steven J. A1 - Jia, Lichao A1 - Liu, Jianghua A1 - Liu, Zhu A1 - Fromer, Neil A1 - Mi, Zhifu A1 - Meng, Jing A1 - Deng, Xiangzheng A1 - Li, Yuan A1 - Lin, Jintai A1 - Schroeder, Heike A1 - Weisz, Helga A1 - Schellnhuber, Hans Joachim T1 - City-level climate change mitigation in China T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - As national efforts to reduce CO2 emissions intensify, policy-makers need increasingly specific, subnational information about the sources of CO2 and the potential reductions and economic implications of different possible policies. This is particularly true in China, a large and economically diverse country that has rapidly industrialized and urbanized and that has pledged under the Paris Agreement that its emissions will peak by 2030. We present new, city level estimates of CO2 emissions for 182 Chinese cities, decomposed into 17 different fossil fuels, 46 socioeconomic sectors, and 7 industrial processes. We find that more affluent cities have systematically lower emissions per unit of gross domestic product (GDP), supported by imports from less affluent, industrial cities located nearby. In turn, clusters of industrial cities are supported by nearby centers of coal or oil extraction. Whereas policies directly targeting manufacturing and electric power infrastructure would drastically undermine the GDP of industrial cities, consumption based policies might allow emission reductions to be subsidized by those with greater ability to pay. In particular, sector based analysis of each city suggests that technological improvements could be a practical and effective means of reducing emissions while maintaining growth and the current economic structure and energy system. We explore city-level emission reductions under three scenarios of technological progress to show that substantial reductions (up to 31%) are possible by updating a disproportionately small fraction of existing infrastructure. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1096 KW - carbon-dioxide emissions KW - fired power plants KW - co2 emissions KW - energy use KW - cluster analysis KW - uncertainties KW - urbanization KW - methodology KW - combustion KW - inventory Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-471541 SN - 1866-8372 IS - 1096 ER - TY - GEN A1 - Granado, Felipe Le Vot A1 - Abad, Enrique A1 - Metzler, Ralf A1 - Yuste, Santos B. T1 - Continuous time random walk in a velocity field BT - role of domain growth, Galilei-invariant advection-diffusion, and kinetics of particle mixing T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We consider the emerging dynamics of a separable continuous time random walk (CTRW) in the case when the random walker is biased by a velocity field in a uniformly growing domain. Concrete examples for such domains include growing biological cells or lipid vesicles, biofilms and tissues, but also macroscopic systems such as expanding aquifers during rainy periods, or the expanding Universe. The CTRW in this study can be subdiffusive, normal diffusive or superdiffusive, including the particular case of a Lévy flight. We first consider the case when the velocity field is absent. In the subdiffusive case, we reveal an interesting time dependence of the kurtosis of the particle probability density function. In particular, for a suitable parameter choice, we find that the propagator, which is fat tailed at short times, may cross over to a Gaussian-like propagator. We subsequently incorporate the effect of the velocity field and derive a bi-fractional diffusion-advection equation encoding the time evolution of the particle distribution. We apply this equation to study the mixing kinetics of two diffusing pulses, whose peaks move towards each other under the action of velocity fields acting in opposite directions. This deterministic motion of the peaks, together with the diffusive spreading of each pulse, tends to increase particle mixing, thereby counteracting the peak separation induced by the domain growth. As a result of this competition, different regimes of mixing arise. In the case of Lévy flights, apart from the non-mixing regime, one has two different mixing regimes in the long-time limit, depending on the exact parameter choice: in one of these regimes, mixing is mainly driven by diffusive spreading, while in the other mixing is controlled by the velocity fields acting on each pulse. Possible implications for encounter–controlled reactions in real systems are discussed. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1005 KW - diffusion KW - expanding medium KW - continuous time random walk Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-479997 SN - 1866-8372 IS - 1005 SP - 28 ER - TY - GEN A1 - Sposini, Vittoria A1 - Metzler, Ralf A1 - Oshanin, Gleb T1 - Single-trajectory spectral analysis of scaled Brownian motion T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Astandard approach to study time-dependent stochastic processes is the power spectral density (PSD), an ensemble-averaged property defined as the Fourier transform of the autocorrelation function of the process in the asymptotic limit of long observation times, T → ∞. In many experimental situations one is able to garner only relatively few stochastic time series of finite T, such that practically neither an ensemble average nor the asymptotic limit T → ∞ can be achieved. To accommodate for a meaningful analysis of such finite-length data we here develop the framework of single-trajectory spectral analysis for one of the standard models of anomalous diffusion, scaled Brownian motion.Wedemonstrate that the frequency dependence of the single-trajectory PSD is exactly the same as for standard Brownian motion, which may lead one to the erroneous conclusion that the observed motion is normal-diffusive. However, a distinctive feature is shown to be provided by the explicit dependence on the measurement time T, and this ageing phenomenon can be used to deduce the anomalous diffusion exponent.Wealso compare our results to the single-trajectory PSD behaviour of another standard anomalous diffusion process, fractional Brownian motion, and work out the commonalities and differences. Our results represent an important step in establishing singletrajectory PSDs as an alternative (or complement) to analyses based on the time-averaged mean squared displacement. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 753 KW - diffusion KW - anomalous diffusion KW - power spectral analysis KW - single trajectory analysis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436522 SN - 1866-8372 IS - 753 ER - TY - GEN A1 - Kosztolowicz, Tadeusz A1 - Metzler, Ralf A1 - Wąsik, Slawomir A1 - Arabski, Michal T1 - Modelling experimentally measured of ciprofloxacin antibiotic diffusion in Pseudomonas aeruginosa biofilm formed in artificial sputum medium T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We study the experimentally measured ciprofloxacin antibiotic diffusion through a gel-like artificial sputum medium (ASM) mimicking physiological conditions typical for a cystic fibrosis layer, in which regions occupied by Pseudomonas aeruginosa bacteria are present. To quantify the antibiotic diffusion dynamics we employ a phenomenological model using a subdiffusion-absorption equation with a fractional time derivative. This effective equation describes molecular diffusion in a medium structured akin Thompson’s plumpudding model; here the ‘pudding’ background represents the ASM and the ‘plums’ represent the bacterial biofilm. The pudding is a subdiffusion barrier for antibiotic molecules that can affect bacteria found in plums. For the experimental study we use an interferometric method to determine the time evolution of the amount of antibiotic that has diffused through the biofilm. The theoretical model shows that this function is qualitatively different depending on whether or not absorption of the antibiotic in the biofilm occurs. We show that the process can be divided into three successive stages: (1) only antibiotic subdiffusion with constant biofilm parameters, (2) subdiffusion and absorption of antibiotic molecules with variable biofilm transport parameters, (3) subdiffusion and absorption in the medium but the biofilm parameters are constant again. Stage 2 is interpreted as the appearance of an intensive defence build–up of bacteria against the action of the antibiotic, and in the stage 3 it is likely that the bacteria have been inactivated. Times at which stages change are determined from the experimentally obtained temporal evolution of the amount of antibiotic that has diffused through the ASM with bacteria. Our analysis shows good agreement between experimental and theoretical results and is consistent with the biologically expected biofilm response. We show that an experimental method to study the temporal evolution of the amount of a substance that has diffused through a biofilm is useful in studying the processes occurring in a biofilm. We also show that the complicated biological process of antibiotic diffusion in a biofilm can be described by a fractional subdiffusion-absorption equation with subdiffusion and absorption parameters that change over time. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1107 KW - Bacterial biofilms KW - Antibiotics KW - Biofilms KW - Cystic fibrosis KW - Pseudomonas aeruginosa KW - Sputum KW - Biological defense mechanisms Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-490866 SN - 1866-8372 IS - 1107 ER - TY - GEN A1 - Xu, Pengbo A1 - Zhou, Tian A1 - Metzler, Ralf A1 - Deng, Weihua T1 - Stochastic harmonic trapping of a Lévy walk: transport and first-passage dynamics under soft resetting strategies T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We introduce and study a Lévy walk (LW) model of particle spreading with a finite propagation speed combined with soft resets, stochastically occurring periods in which an harmonic external potential is switched on and forces the particle towards a specific position. Soft resets avoid instantaneous relocation of particles that in certain physical settings may be considered unphysical. Moreover, soft resets do not have a specific resetting point but lead the particle towards a resetting point by a restoring Hookean force. Depending on the exact choice for the LW waiting time density and the probability density of the periods when the harmonic potential is switched on, we demonstrate a rich emerging response behaviour including ballistic motion and superdiffusion. When the confinement periods of the soft-reset events are dominant, we observe a particle localisation with an associated non-equilibrium steady state. In this case the stationary particle probability density function turns out to acquire multimodal states. Our derivations are based on Markov chain ideas and LWs with multiple internal states, an approach that may be useful and flexible for the investigation of other generalised random walks with soft and hard resets. The spreading efficiency of soft-rest LWs is characterised by the first-passage time statistic. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1262 KW - diffusion KW - anomalous diffusion KW - stochastic resetting KW - Levy walks Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-560402 SN - 1866-8372 SP - 1 EP - 28 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - GEN A1 - Teichmann, Erik A1 - Lewandowski, Heather J. A1 - Alemani, Micol T1 - Investigating students’ views of experimental physics in German laboratory classes T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - There is a large variety of goals instructors have for laboratory courses, with different courses focusing on different subsets of goals. An often implicit, but crucial, goal is to develop students’ attitudes, views, and expectations about experimental physics to align with practicing experimental physicists. The assessment of laboratory courses upon this one dimension of learning has been intensively studied in U.S. institutions using the Colorado Learning Attitudes about Science Survey for Experimental Physics (E-CLASS). However, there is no such an instrument available to use in Germany, and the influence of laboratory courses on students views about the nature of experimental physics is still unexplored at German-speaking institutions. Motivated by the lack of an assessment tool to investigate this goal in laboratory courses at German-speaking institutions, we present a translated version of the E-CLASS adapted to the context at German-speaking institutions. We call the German version of the E-CLASS, the GE-CLASS. We describe the translation process and the creation of an automated web-based system for instructors to assess their laboratory courses. We also present first results using GE-CLASS obtained at the University of Potsdam. A first comparison between E-CLASS and GE-CLASS results shows clear differences between University of Potsdam and U.S. students’ views and beliefs about experimental physics. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1263 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-560429 SN - 1866-8372 SP - 010135-1 EP - 010135-17 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - GEN A1 - Sarabadani, Jalal A1 - Metzler, Ralf A1 - Ala-Nissila, Tapio T1 - Driven polymer translocation into a channel: Isoflux tension propagation theory and Langevin dynamics simulations T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Isoflux tension propagation (IFTP) theory and Langevin dynamics (LD) simulations are employed to study the dynamics of channel-driven polymer translocation in which a polymer translocates into a narrow channel and the monomers in the channel experience a driving force fc. In the high driving force limit, regardless of the channel width, IFTP theory predicts τ ∝ f βc for the translocation time, where β = −1 is the force scaling exponent. Moreover, LD data show that for a very narrow channel fitting only a single file of monomers, the entropic force due to the subchain inside the channel does not play a significant role in the translocation dynamics and the force exponent β = −1 regardless of the force magnitude. As the channel width increases the number of possible spatial configurations of the subchain inside the channel becomes significant and the resulting entropic force causes the force exponent to drop below unity. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1292 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-574387 SN - 1866-8372 IS - 1292 SP - 033003-1 EP - 033003-14 ER - TY - GEN A1 - Smirnov, Lev A. A1 - Bolotov, Maxim A1 - Bolotov, Dmitri A1 - Osipov, Grigory V. A1 - Pikovsky, Arkady T1 - Finite-density-induced motility and turbulence of chimera solitons T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We consider a one-dimensional oscillatory medium with a coupling through a diffusive linear field. In the limit of fast diffusion this setup reduces to the classical Kuramoto–Battogtokh model. We demonstrate that for a finite diffusion stable chimera solitons, namely localized synchronous domain in an infinite asynchronous environment, are possible. The solitons are stable also for finite density of oscillators, but in this case they sway with a nearly constant speed. This finite-density-induced motility disappears in the continuum limit, as the velocity of the solitons is inverse proportional to the density. A long-wave instability of the homogeneous asynchronous state causes soliton turbulence, which appears as a sequence of soliton mergings and creations. As the instability of the asynchronous state becomes stronger, this turbulence develops into a spatio-temporal intermittency. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1291 KW - chimera KW - soliton KW - finite-size effects Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-574281 SN - 1866-8372 IS - 1291 ER - TY - GEN A1 - Vilk, Ohad A1 - Aghion, Erez A1 - Avgar, Tal A1 - Beta, Carsten A1 - Nagel, Oliver A1 - Sabri, Adal A1 - Sarfati, Raphael A1 - Schwartz, Daniel K. A1 - Weiß, Matthias A1 - Krapf, Diego A1 - Nathan, Ran A1 - Metzler, Ralf A1 - Assaf, Michael T1 - Unravelling the origins of anomalous diffusion BT - from molecules to migrating storks T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Anomalous diffusion or, more generally, anomalous transport, with nonlinear dependence of the mean-squared displacement on the measurement time, is ubiquitous in nature. It has been observed in processes ranging from microscopic movement of molecules to macroscopic, large-scale paths of migrating birds. Using data from multiple empirical systems, spanning 12 orders of magnitude in length and 8 orders of magnitude in time, we employ a method to detect the individual underlying origins of anomalous diffusion and transport in the data. This method decomposes anomalous transport into three primary effects: long-range correlations (“Joseph effect”), fat-tailed probability density of increments (“Noah effect”), and nonstationarity (“Moses effect”). We show that such a decomposition of real-life data allows us to infer nontrivial behavioral predictions and to resolve open questions in the fields of single-particle tracking in living cells and movement ecology. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1303 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-577643 SN - 1866-8372 IS - 1303 ER -