@article{StangeHintscheSachseetal.2017, author = {Stange, Maike and Hintsche, Marius and Sachse, Kirsten and Gerhardt, Matthias and Valleriani, Angelo and Beta, Carsten}, title = {Analyzing the spatial positioning of nuclei in polynuclear giant cells}, series = {Journal of Physics D: Applied Physics}, volume = {50}, journal = {Journal of Physics D: Applied Physics}, number = {46}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0022-3727}, doi = {10.1088/1361-6463/aa8da0}, pages = {8}, year = {2017}, abstract = {How cells establish and maintain a well-defined size is a fundamental question of cell biology. Here we investigated to what extent the microtubule cytoskeleton can set a predefined cell size, independent of an enclosing cell membrane. We used electropulse-induced cell fusion to form giant multinuclear cells of the social amoeba Dictyostelium discoideum. Based on dual-color confocal imaging of cells that expressed fluorescent markers for the cell nucleus and the microtubules, we determined the subcellular distributions of nuclei and centrosomes in the giant cells. Our two- and three-dimensional imaging results showed that the positions of nuclei in giant cells do not fall onto a regular lattice. However, a comparison with model predictions for random positioning showed that the subcellular arrangement of nuclei maintains a low but still detectable degree of ordering. This can be explained by the steric requirements of the microtubule cytoskeleton, as confirmed by the effect of a microtubule degrading drug.}, language = {en} } @article{ElNagarSarhanAbouserieetal.2017, author = {El-Nagar, Gumaa A. and Sarhan, Radwan Mohamed and Abouserie, Ahed and Maticiuc, Natalia and Bargheer, Matias and Lauermann, Iver and Roth, Christina}, title = {Efficient 3D-Silver Flower-like Microstructures for Non-Enzymatic Hydrogen Peroxide (H2O2) Amperometric Detection}, series = {Scientific reports}, volume = {7}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-017-11965-9}, pages = {8}, year = {2017}, language = {en} } @article{Goychuk2017, author = {Goychuk, Igor}, title = {Fractional Bhatnagar-Gross-Krook kinetic equation}, series = {The European physical journal : B, Condensed matter and complex systems}, volume = {90}, journal = {The European physical journal : B, Condensed matter and complex systems}, publisher = {Springer}, address = {New York}, issn = {1434-6028}, doi = {10.1140/epjb/e2017-80297-x}, pages = {13}, year = {2017}, abstract = {The linear Boltzmann equation approach is generalized to describe fractional superdiffusive transport of the Levy walk type in external force fields. The time distribution between scattering events is assumed to have a finite mean value and infinite variance. It is completely characterized by the two scattering rates, one fractional and a normal one, which defines also the mean scattering rate. We formulate a general fractional linear Boltzmann equation approach and exemplify it with a particularly simple case of the Bohm and Gross scattering integral leading to a fractional generalization of the Bhatnagar, Gross and Krook kinetic equation. Here, at each scattering event the particle velocity is completely randomized and takes a value from equilibrium Maxwell distribution at a given fixed temperature. We show that the retardation effects are indispensable even in the limit of infinite mean scattering rate and argue that this novel fractional kinetic equation provides a viable alternative to the fractional Kramers-Fokker-Planck (KFP) equation by Barkai and Silbey and its generalization by Friedrich et al. based on the picture of divergent mean time between scattering events. The case of divergent mean time is also discussed at length and compared with the earlier results obtained within the fractional KFP. Also a phenomenological fractional BGK equation without retardation effects is proposed in the limit of infinite scattering rates. It cannot be, however, rigorously derived from a scattering model, being rather clever postulated. It this respect, this retardationless equation is similar to the fractional KFP by Barkai and Silbey. However, it corresponds to the opposite, much more physical limit and, therefore, also presents a viable alternative.}, language = {en} } @article{ZhelavskayaShpritsSpasojevic2017, author = {Zhelavskaya, Irina S. and Shprits, Yuri Y. and Spasojevic, Maria}, title = {Empirical Modeling of the Plasmasphere Dynamics Using Neural Networks}, series = {Journal of geophysical research : Space physics}, volume = {122}, journal = {Journal of geophysical research : Space physics}, publisher = {American Geophysical Union}, address = {Washington}, issn = {2169-9380}, doi = {10.1002/2017JA024406}, pages = {11227 -- 11244}, year = {2017}, abstract = {We present the PINE (Plasma density in the Inner magnetosphere Neural network\&\#8208;based Empirical) model \&\#8208; a new empirical model for reconstructing the global dynamics of the cold plasma density distribution based only on solar wind data and geomagnetic indices. Utilizing the density database obtained using the NURD (Neural\&\#8208;network\&\#8208;based Upper hybrid Resonance Determination) algorithm for the period of 1 October 2012 to 1 July 2016, in conjunction with solar wind data and geomagnetic indices, we develop a neural network model that is capable of globally reconstructing the dynamics of the cold plasma density distribution for 2\&\#8804;L\&\#8804;6 and all local times. We validate and test the model by measuring its performance on independent data sets withheld from the training set and by comparing the model\&\#8208;predicted global evolution with global images of He+ distribution in the Earth's plasmasphere from the IMAGE Extreme UltraViolet (EUV) instrument. We identify the parameters that best quantify the plasmasphere dynamics by training and comparing multiple neural networks with different combinations of input parameters (geomagnetic indices, solar wind data, and different durations of their time history). The optimal model is based on the 96\&\#8201;h time history of Kp, AE, SYM\&\#8208;H, and F10.7 indices. The model successfully reproduces erosion of the plasmasphere on the nightside and plume formation and evolution. We demonstrate results of both local and global plasma density reconstruction. This study illustrates how global dynamics can be reconstructed from local in situ observations by using machine learning techniques.}, language = {en} } @article{DelleSideNassisiPennettaetal.2017, author = {Delle Side, Domenico and Nassisi, Vincenzo and Pennetta, Cecilia and Alifano, Pietro and Di Salvo, Marco and Tala, Adelfia and Chechkin, Aleksei V. and Seno, Flavio and Trovato, Antonio}, title = {Bacterial bioluminescence onset and quenching: a dynamical model for a quorum sensing-mediated property}, series = {Royal Society Open Science}, volume = {4}, journal = {Royal Society Open Science}, publisher = {Royal Society}, address = {London}, issn = {2054-5703}, doi = {10.1098/rsos.171586}, pages = {12}, year = {2017}, abstract = {We present an effective dynamical model for the onset of bacterial bioluminescence, one of the most studied quorum sensing-mediated traits. Our model is built upon simple equations that describe the growth of the bacterial colony, the production and accumulation of autoinducer signal molecules, their sensing within bacterial cells, and the ensuing quorum activation mechanism that triggers bioluminescent emission. The model is directly tested to quantitatively reproduce the experimental distributions of photon emission times, previously measured for bacterial colonies of Vibrio jasicida, a luminescent bacterium belonging to the Harveyi clade, growing in a highly drying environment. A distinctive and novel feature of the proposed model is bioluminescence 'quenching' after a given time elapsed from activation. Using an advanced fitting procedure based on the simulated annealing algorithm, we are able to infer from the experimental observations the biochemical parameters used in the model. Such parameters are in good agreement with the literature data. As a further result, we find that, at least in our experimental conditions, light emission in bioluminescent bacteria appears to originate from a subtle balance between colony growth and quorum activation due to autoinducers diffusion, with the two phenomena occurring on the same time scale. This finding is consistent with a negative feedback mechanism previously reported for Vibrio harveyi.}, language = {en} } @article{ColladoFregosoHoodShoaeeetal.2017, author = {Collado-Fregoso, Elisa and Hood, Samantha N. and Shoaee, Safa and Schr{\"o}der, Bob C. and McCulloch, Iain and Kassal, Ivan and Neher, Dieter and Durrant, James R.}, title = {Intercalated vs Nonintercalated Morphologies in Donor-Acceptor Bulk Heterojunction Solar Cells: PBTTT:Fullerene Charge Generation and Recombination Revisited}, series = {The journal of physical chemistry letters}, volume = {8}, journal = {The journal of physical chemistry letters}, publisher = {American Chemical Society}, address = {Washington}, issn = {1948-7185}, doi = {10.1021/acs.jpclett.7b01571}, pages = {4061 -- 4068}, year = {2017}, abstract = {In this Letter, we study the role of the donor:acceptor interface nanostructure upon charge separation and recombination in organic photovoltaic devices and blend films, using mixtures of PBTTT and two different fullerene derivatives (PC70BM and ICTA) as models for intercalated and nonintercalated morphologies, respectively. Thermodynamic simulations show that while the completely intercalated system exhibits a large free-energy barrier for charge separation, this barrier is significantly lower in the nonintercalated system and almost vanishes when energetic disorder is included in the model. Despite these differences, both femtosecond-resolved transient absorption spectroscopy (TAS) and time-delayed collection field (TDCF) exhibit extensive first-order losses in both systems, suggesting that geminate pairs are the primary product of photoexcitation. In contrast, the system that comprises a combination of fully intercalated polymer:fullerene areas and fullerene-aggregated domains (1:4 PBTTT:PC70BM) is the only one that shows slow, second-order recombination of free charges, resulting in devices with an overall higher short-circuit current and fill factor. This study therefore provides a novel consideration of the role of the interfacial nanostructure and the nature of bound charges and their impact upon charge generation and recombination.}, language = {en} } @article{JavanainenMartinezSearaMetzleretal.2017, author = {Javanainen, Matti and Martinez-Seara, Hector and Metzler, Ralf and Vattulainen, Ilpo}, title = {Diffusion of Integral Membrane Proteins in Protein-Rich Membranes}, series = {The journal of physical chemistry letters}, volume = {8}, journal = {The journal of physical chemistry letters}, publisher = {American Chemical Society}, address = {Washington}, issn = {1948-7185}, doi = {10.1021/acs.jpclett.7b01758}, pages = {4308 -- 4313}, year = {2017}, abstract = {The lateral diffusion of embedded proteins along lipid membranes in protein-poor conditions has been successfully described in terms of the Saffman-Delbruck (SD) model, which predicts that the protein diffusion coefficient D is weakly dependent on its radius R as D proportional to ln(1/R). However, instead of being protein-poor, native cell membranes are extremely crowded with proteins. On the basis of extensive molecular simulations, we here demonstrate that protein crowding of the membrane at physiological levels leads to deviations from the SD relation and to the emergence of a stronger Stokes-like dependence D proportional to 1/R. We propose that this 1/R law mainly arises due to geometrical factors: smaller proteins are able to avoid confinement effects much better than their larger counterparts. The results highlight that the lateral dynamics in the crowded setting found in native membranes is radically different from protein-poor conditions and plays a significant role in formation of functional multiprotein complexes.}, language = {en} } @article{PalyulinMantsevichKlagesetal.2017, author = {Palyulin, Vladimir V. and Mantsevich, Vladimir N. and Klages, Rainer and Metzler, Ralf and Chechkin, Aleksei V.}, title = {Comparison of pure and combined search strategies for single and multiple targets}, series = {The European physical journal : B, Condensed matter and complex systems}, volume = {90}, journal = {The European physical journal : B, Condensed matter and complex systems}, publisher = {Springer}, address = {New York}, issn = {1434-6028}, doi = {10.1140/epjb/e2017-80372-4}, pages = {20 -- 37}, year = {2017}, abstract = {We address the generic problem of random search for a point-like target on a line. Using the measures of search reliability and efficiency to quantify the random search quality, we compare Brownian search with Levy search based on long-tailed jump length distributions. We then compare these results with a search process combined of two different long-tailed jump length distributions. Moreover, we study the case of multiple targets located by a Levy searcher.}, language = {en} } @article{CaetanodeCarvalhoMetzleretal.2017, author = {Caetano, Daniel L. Z. and de Carvalho, Sidney J. and Metzler, Ralf and Cherstvy, Andrey G.}, title = {Critical adsorption of periodic and random polyampholytes onto charged surfaces}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {19}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c7cp04040g}, pages = {23397 -- 23413}, year = {2017}, abstract = {How different are the properties of critical adsorption of polyampholytes and polyelectrolytes onto charged surfaces? How important are the details of polyampholyte charge distribution on the onset of critical adsorption transition? What are the scaling relations governing the dependence of critical surface charge density on salt concentration in the surrounding solution? Here, we employ Metropolis Monte Carlo simulations and uncover the scaling relations for critical adsorption for quenched periodic and random charge distributions along the polyampholyte chains. We also evaluate and discuss the dependence of the adsorbed layer width on solution salinity and details of the charge distribution. We contrast our findings to the known results for polyelectrolyte adsorption onto oppositely charged surfaces, in particular, their dependence on electrolyte concentration.}, language = {en} } @article{MuenchKipfstuhlFreitagetal.2017, author = {Muench, Thomas and Kipfstuhl, Sepp and Freitag, Johannes and Meyer, Hanno and Laepple, Thomas}, title = {Constraints on post-depositional isotope modifications in East Antarctic firn from analysing temporal changes of isotope profiles}, series = {The Cryosphere : TC ; an interactive open access journal of the European Geosciences Union}, volume = {11}, journal = {The Cryosphere : TC ; an interactive open access journal of the European Geosciences Union}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1994-0416}, doi = {10.5194/tc-11-2175-2017}, pages = {2175 -- 2188}, year = {2017}, abstract = {The isotopic composition of water in ice sheets is extensively used to infer past climate changes. In low-accumulation regions their interpretation is, however, challenged by poorly constrained effects that may influence the initial isotope signal during and after deposition of the snow. This is reflected in snow-pit isotope data from Kohnen Station, Antarctica, which exhibit a seasonal cycle but also strong interannual variations that contradict local temperature observations. These inconsistencies persist even after averaging many profiles and are thus not explained by local stratigraphic noise. Previous studies have suggested that post-depositional processes may significantly influence the isotopic composition of East Antarctic firn. Here, we investigate the importance of post-depositional processes within the open-porous firn (greater than or similar to 10 cm depth) at Kohnen Station by separating spatial from temporal variability. To this end, we analyse 22 isotope profiles obtained from two snow trenches and examine the temporal isotope modifications by comparing the new data with published trench data extracted 2 years earlier. The initial isotope profiles undergo changes over time due to downward advection, firn diffusion and densification in magnitudes consistent with independent estimates. Beyond that, we find further modifications of the original isotope record to be unlikely or small in magnitude (<< 1 parts per thousand RMSD). These results show that the discrepancy between local temperatures and isotopes most likely originates from spatially coherent processes prior to or during deposition, such as precipitation intermittency or systematic isotope modifications acting on drifting or loose surface snow.}, language = {en} }