@phdthesis{Heise2014, author = {Heise, Robert}, title = {Estimation of photosynthetic carbon fluxes in intact plants}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, school = {Universit{\"a}t Potsdam}, pages = {178}, year = {2014}, language = {en} } @phdthesis{Liu2015, author = {Liu, Zengyu}, title = {Going off the rails? Guidance of the cellulose synthase complex by cortical microtubules in Arabidopsis}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, school = {Universit{\"a}t Potsdam}, pages = {III , 90}, year = {2015}, language = {en} } @article{GoychukKharchenkoMetzler2014, author = {Goychuk, Igor A. and Kharchenko, Vasyl O. and Metzler, Ralf}, title = {Molecular motors pulling cargos in the viscoelastic cytosol: how power strokes beat subdiffusion}, series = {Physical Chemistry Chemical Physics}, journal = {Physical Chemistry Chemical Physics}, number = {16}, publisher = {the Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, pages = {16524 -- 16535}, year = {2014}, abstract = {The discovery of anomalous diffusion of larger biopolymers and submicron tracers such as endogenous granules, organelles, or virus capsids in living cells, attributed to the viscoelastic nature of the cytoplasm, provokes the question whether this complex environment equally impacts the active intracellular transport of submicron cargos by molecular motors such as kinesins: does the passive anomalous diffusion of free cargo always imply its anomalously slow active transport by motors, the mean transport distance along microtubule growing sublinearly rather than linearly in time? Here we analyze this question within the widely used two-state Brownian ratchet model of kinesin motors based on the continuous-state diffusion along microtubules driven by a flashing binding potential, where the cargo particle is elastically attached to the motor. Depending on the cargo size, the loading force, the amplitude of the binding potential, the turnover frequency of the molecular motor enzyme, and the linker stiffness we demonstrate that the motor transport may turn out either normal or anomalous, as indeed measured experimentally. We show how a highly efficient normal active transport mediated by motors may emerge despite the passive anomalous diffusion of the cargo, and study the intricate effects of the elastic linker. Under different, well specified conditions the microtubule-based motor transport becomes anomalously slow and thus significantly less efficient.}, language = {en} } @article{JeonChechkinMetzler2014, author = {Jeon, Jae-Hyung and Chechkin, Aleksei V. and Metzler, Ralf}, title = {Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion}, series = {Physical chemistry, chemical physics : PCCP}, volume = {30}, journal = {Physical chemistry, chemical physics : PCCP}, number = {16}, publisher = {The Royal Society of Chemistry}, address = {Cambridge}, doi = {10.1039/C4CP02019G}, pages = {15811 -- 15817}, year = {2014}, abstract = {Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.}, language = {en} } @article{PalyulinAlaNissilaMetzler2014, author = {Palyulin, Vladimir V. and Ala-Nissila, Tapio and Metzler, Ralf}, title = {Polymer translocation: the first two decades and the recent diversification}, series = {Soft matter}, volume = {45}, journal = {Soft matter}, number = {10}, editor = {Metzler, Ralf}, publisher = {the Royal Society of Chemistry}, address = {Cambridge}, issn = {1744-683X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76266}, pages = {9016 -- 9037}, year = {2014}, abstract = {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.}, language = {en} } @article{UnterbergLeffersHuebneretal.2014, author = {Unterberg, Marlies and Leffers, Larissa and H{\"u}bner, Florian and Humpf, Hans-Ulrich and Lepikhov, Konstantin and Walter, J{\"o}rn and Ebert, Franziska and Schwerdtle, Tanja}, title = {Toxicity of arsenite and thio-DMAV after long-term (21 days) incubation of human urothelial cells: cytotoxicity, genotoxicity and epigenetics}, series = {Toxicology Research}, volume = {3}, journal = {Toxicology Research}, number = {6}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {2045-4538}, pages = {456 -- 464}, year = {2014}, abstract = {This study aims to further mechanistically understand toxic modes of action after chronic inorganic arsenic exposure. Therefore long-term incubation studies in cultured cells were carried out, to display chronically attained changes, which cannot be observed in the generally applied in vitro short-term incubation studies. Particularly, the cytotoxic, genotoxic and epigenetic effects of an up to 21 days incubation of human urothelial (UROtsa) cells with pico- to nanomolar concentrations of iAsIII and its metabolite thio-DMAV were compared. After 21 days of incubation, cytotoxic effects were strongly enhanced in the case of iAsIII and might partly be due to glutathione depletion and genotoxic effects on the chromosomal level. These results are in strong contrast to cells exposed to thio-DMAV. Thus, cells seemed to be able to adapt to this arsenical, as indicated among others by an increase in the cellular glutathione level. Most interestingly, picomolar concentrations of both iAsIII and thio-DMAV caused global DNA hypomethylation in UROtsa cells, which was quantified in parallel by 5-medC immunostaining and a newly established, reliable, high resolution mass spectrometry (HRMS)-based test system. This is the first time that epigenetic effects are reported for thio-DMAV; iAsIII induced epigenetic effects occur in at least 8000 fold lower concentrations as reported in vitro before. The fact that both arsenicals cause DNA hypomethylation at really low, exposure-relevant concentrations in human urothelial cells suggests that this epigenetic effect might contribute to inorganic arsenic induced carcinogenicity, which for sure has to be further investigated in future studies.}, language = {en} } @article{BauerGodecMetzler2014, author = {Bauer, Maximilian and Godec, Aljaž and Metzler, Ralf}, title = {Diffusion of finite-size particles in two-dimensional channels with random wall configurations}, series = {Physical chemistry, chemical physics : PCCP ; a journal of European chemical societies}, volume = {16}, journal = {Physical chemistry, chemical physics : PCCP ; a journal of European chemical societies}, number = {13}, publisher = {RSC Publications}, address = {Cambridge}, issn = {1463-9084}, doi = {10.1039/C3CP55160A}, pages = {6118 -- 6128}, 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} } @article{WirthNeumannAntoniettietal.2014, author = {Wirth, Jonas and Neumann, Rainer and Antonietti, Markus and Saalfrank, Peter}, title = {Adsorption and photocatalytic splitting of water on graphitic carbon nitride}, series = {physical chemistry, chemical physics : PCCP}, volume = {2014}, journal = {physical chemistry, chemical physics : PCCP}, number = {16}, issn = {1463-9076}, doi = {10.1039/c4cp02021a}, pages = {15917 -- 15926}, year = {2014}, abstract = {Graphitic carbon nitride, g-C₃N₄, is a promising organic photo-catalyst for a variety of redox reactions. In order to improve its efficiency in a systematic manner, however, a fundamental understanding of the microscopic interaction between catalyst, reactants and products is crucial. Here we present a systematic study of water adsorption on g-C₃N₄ by means of density functional theory and the density functional based tight-binding method as a prerequisite for understanding photocatalytic water splitting. We then analyze this prototypical redox reaction on the basis of a thermodynamic model providing an estimate of the overpotential for both water oxidation and H⁺ reduction. While the latter is found to occur readily upon irradiation with visible light, we derive a prohibitive overpotential of 1.56 eV for the water oxidation half reaction, comparing well with the experimental finding that in contrast to H₂ production O₂ evolution is only possible in the presence of oxidation cocatalysts.}, language = {en} } @article{NicenboimVasishthGatteietal.2015, author = {Nicenboim, Bruno and Vasishth, Shravan and Gattei, Carolina and Sigman, Mariano and Kliegl, Reinhold}, title = {Working memory differences in long-distance dependency resolution}, series = {Frontiers in psychology}, volume = {6}, journal = {Frontiers in psychology}, number = {312}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-1078}, doi = {10.3389/fpsyg.2015.00312}, pages = {16}, year = {2015}, abstract = {There is a wealth of evidence showing that increasing the distance between an argument and its head leads to more processing effort, namely, locality effects; these are usually associated with constraints in working memory (DLT: Gibson, 2000; activation-based model: Lewis and Vasishth, 2005). In SOV languages, however, the opposite effect has been found: antilocality (see discussion in Levy et al., 2013). Antilocality effects can be explained by the expectation-based approach as proposed by Levy (2008) or by the activation-based model of sentence processing as proposed by Lewis and Vasishth (2005). We report an eye-tracking and a self-paced reading study with sentences in Spanish together with measures of individual differences to examine the distinction between expectation- and memory-based accounts, and within memory-based accounts the further distinction between DLT and the activation-based model. The experiments show that (i) antilocality effects as predicted by the expectation account appear only for high-capacity readers; (ii) increasing dependency length by interposing material that modifies the head of the dependency (the verb) produces stronger facilitation than increasing dependency length with material that does not modify the head; this is in agreement with the activation-based model but not with the expectation account; and (iii) a possible outcome of memory load on low-capacity readers is the increase in regressive saccades (locality effects as predicted by memory-based accounts) or, surprisingly, a speedup in the self-paced reading task; the latter consistent with good-enough parsing (Ferreira et al., 2002). In sum, the study suggests that individual differences in working memory capacity play a role in dependency resolution, and that some of the aspects of dependency resolution can be best explained with the activation-based model together with a prediction component.}, language = {en} } @phdthesis{Sachse2014, author = {Sachse, Rita}, title = {Biological membranes in cell-free systems}, pages = {111, XIX}, year = {2014}, language = {en} }