@article{RevereyJeonBaoetal.2015, author = {Reverey, Julia F. and Jeon, Jae-Hyung and Bao, Han and Leippe, Matthias and Metzler, Ralf and Selhuber-Unkel, Christine}, title = {Superdiffusion dominates intracellular particle motion in the supercrowded cytoplasm of pathogenic Acanthamoeba castellanii}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep11690}, pages = {14}, year = {2015}, abstract = {Acanthamoebae are free-living protists and human pathogens, whose cellular functions and pathogenicity strongly depend on the transport of intracellular vesicles and granules through the cytosol. Using high-speed live cell imaging in combination with single-particle tracking analysis, we show here that the motion of endogenous intracellular particles in the size range from a few hundred nanometers to several micrometers in Acanthamoeba castellanii is strongly superdiffusive and influenced by cell locomotion, cytoskeletal elements, and myosin II. We demonstrate that cell locomotion significantly contributes to intracellular particle motion, but is clearly not the only origin of superdiffusivity. By analyzing the contribution of microtubules, actin, and myosin II motors we show that myosin II is a major driving force of intracellular motion in A. castellanii. The cytoplasm of A. castellanii is supercrowded with intracellular vesicles and granules, such that significant intracellular motion can only be achieved by actively driven motion, while purely thermally driven diffusion is negligible.}, language = {en} } @article{RamirezAlegriaCheneBorissovaetal.2015, author = {Ram{\´i}rez Alegr{\´i}a, S. and Chen{\´e}, A.-N. and Borissova, J. and Kurtev, R. and Navarro, C. and Kuhn, M. and Carballo-Bello, J. A.}, title = {A not so massive cluster hosting a very massive star}, series = {Wolf-Rayet Stars : Proceedings of an International Workshop held in Potsdam, Germany, 1.-5. June 2015}, journal = {Wolf-Rayet Stars : Proceedings of an International Workshop held in Potsdam, Germany, 1.-5. June 2015}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-88477}, pages = {362}, year = {2015}, abstract = {We present the first physical characterization of the young open cluster VVVCL041. We spectroscopically observed the cluster main-sequence stellar population and a very-massive star candidate: WR62-2. CMFGEN modelling to our near-infrared spectra indicates that WR62-2 is a very luminous (10^6.4±0.2 L⊙)and massive (∼ 80M⊙) star.}, language = {en} } @article{RaatzHintscheBahrsetal.2015, author = {Raatz, Michael and Hintsche, Marius and Bahrs, Marco and Theves, Matthias and Beta, Carsten}, title = {Swimming patterns of a polarly flagellated bacterium in environments of increasing complexity}, series = {European physical journal special topics}, volume = {224}, journal = {European physical journal special topics}, number = {7}, publisher = {Springer}, address = {Heidelberg}, issn = {1951-6355}, doi = {10.1140/epjst/e2015-02454-3}, pages = {1185 -- 1198}, year = {2015}, abstract = {The natural habitat of many bacterial swimmers is dominated by interfaces and narrow interstitial spacings where they frequently interact with the fluid boundaries in their vicinity. To quantify these interactions, we investigated the swimming behavior of the soil bacterium Pseudomonas putida in a variety of confined environments. Using microfluidic techniques, we fabricated structured microchannels with different configurations of cylindrical obstacles. In these environments, we analyzed the swimming trajectories for different obstacle densities and arrangements. Although the overall swimming pattern remained similar to movement in the bulk fluid, we observed a change in the turning angle distribution that could be attributed to collisions with the cylindrical obstacles. Furthermore, a comparison of the mean run length of the bacteria to the mean free path of a billiard particle in the same geometry indicated that, inside a densely packed environment, the trajectories of the bacterial swimmers are efficiently guided along the open spacings.}, language = {en} } @article{PulkkinenMetzler2015, author = {Pulkkinen, Otto and Metzler, Ralf}, title = {Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep17820}, pages = {11}, year = {2015}, abstract = {Many chemical reactions in biological cells occur at very low concentrations of constituent molecules. Thus, transcriptional gene-regulation is often controlled by poorly expressed transcription-factors, such as E. coli lac repressor with few tens of copies. Here we study the effects of inherent concentration fluctuations of substrate-molecules on the seminal Michaelis-Menten scheme of biochemical reactions. We present a universal correction to the Michaelis-Menten equation for the reaction-rates. The relevance and validity of this correction for enzymatic reactions and intracellular gene-regulation is demonstrated. Our analytical theory and simulation results confirm that the proposed variance-corrected Michaelis-Menten equation predicts the rate of reactions with remarkable accuracy even in the presence of large non-equilibrium concentration fluctuations. The major advantage of our approach is that it involves only the mean and variance of the substrate-molecule concentration. Our theory is therefore accessible to experiments and not specific to the exact source of the concentration fluctuations.}, language = {en} } @article{PulkkinenMetzler2015, author = {Pulkkinen, Otto and Metzler, Ralf}, title = {Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation}, series = {Scientific reports}, journal = {Scientific reports}, number = {5}, publisher = {Nature Publishing Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep17820}, year = {2015}, abstract = {Many chemical reactions in biological cells occur at very low concentrations of constituent molecules. Thus, transcriptional gene-regulation is often controlled by poorly expressed transcription-factors, such as E.coli lac repressor with few tens of copies. Here we study the effects of inherent concentration fluctuations of substrate-molecules on the seminal Michaelis-Menten scheme of biochemical reactions. We present a universal correction to the Michaelis-Menten equation for the reaction-rates. The relevance and validity of this correction for enzymatic reactions and intracellular gene-regulation is demonstrated. Our analytical theory and simulation results confirm that the proposed variance-corrected Michaelis-Menten equation predicts the rate of reactions with remarkable accuracy even in the presence of large non-equilibrium concentration fluctuations. The major advantage of our approach is that it involves only the mean and variance of the substrate-molecule concentration. Our theory is therefore accessible to experiments and not specific to the exact source of the concentration fluctuations.}, language = {en} } @article{PremontSchwarzSchreckIannuzzietal.2015, author = {Premont-Schwarz, Mirabelle and Schreck, Simon and Iannuzzi, Marcella and Nibbering, Erik T. J. and Odelius, Michael and Wernet, Philippe}, title = {Correlating Infrared and X-ray Absorption Energies for Molecular-Level Insight into Hydrogen Bond Making and Breaking in Solution}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {119}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, number = {25}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.5b02954}, pages = {8115 -- 8124}, year = {2015}, abstract = {While ubiquitous, the making and breaking of hydrogen bonds in solution is notoriously difficult to study due to the associated complex changes of nuclear and electronic structures. With the aim to reduce the according uncertainty in correlating experimental observables and hydrogen-bond configurations, we combine the information from proximate methods to study the N-H center dot center dot center dot O hydrogen bond in solution. We investigate hydrogen-bonding of the N-H group of N-methylaniline with oxygen from liquid DMSO and acetone with infrared spectra in the N-H stretching region and X-ray absorption spectra at the N K-edge. We experimentally observe blue shifts of the infrared stretching band and an X-ray absorption pre-edge peak when going from DMSO to acetone. With ab initio molecular dynamics simulations and calculated spectra, we qualitatively reproduce the experimental observables but we do not reach quantitative agreement with experiment. The infrared spectra support the notion of weakening the N-H center dot center dot center dot O hydrogen bond from DMSO to acetone. However, we fail to theoretically reproduce the measured shift of the X-ray absorption pre-edge peak. We discuss possible shortcomings of the simulation models and spectrum calculations. Common features and distinct differences with the O-H center dot center dot center dot O hydrogen bond are highlighted, and the implications for monitoring hydrogen-bond breaking in solution are discussed.}, language = {en} } @article{PolitiRosenblum2015, author = {Politi, Antonio and Rosenblum, Michael}, title = {Equivalence of phase-oscillator and integrate-and-fire models}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {91}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {4}, publisher = {American Physical Society}, address = {College Park}, issn = {1539-3755}, doi = {10.1103/PhysRevE.91.042916}, pages = {11}, year = {2015}, abstract = {A quantitative comparison of various classes of oscillators (integrate-and-fire, Winfree, and Kuramoto-Daido type) is performed in the weak-coupling limit for a fully connected network of identical units. An almost perfect agreement is found, with only tiny differences among the models. We also show that the regime of self-consistent partial synchronization is rather general and can be observed for arbitrarily small coupling strength in any model class. As a byproduct of our study, we are able to show that an integrate-and-fire model with a generic pulse shape can be always transformed into a similar model with delta pulses and a suitable phase response curve.}, language = {en} } @article{PohlWilhelmTelezhinsky2015, author = {Pohl, Manuela and Wilhelm, Alina and Telezhinsky, Igor O.}, title = {Reacceleration of electrons in supernova remnants}, series = {Astronomy and astrophysics : an international weekly journal}, volume = {574}, journal = {Astronomy and astrophysics : an international weekly journal}, publisher = {EDP Sciences}, address = {Les Ulis}, issn = {0004-6361}, doi = {10.1051/0004-6361/201425027}, pages = {11}, year = {2015}, abstract = {Context. radio spectra of many shell-type supernova remnants show deviations from those expected on theoretical grounds. Aims. In this paper we determine the effect of stochastic reacceleration on the spectra of electrons in the GeV band and at lower energies, and we investigate whether reacceleration can explain the observed variation in radio spectral indices. Methods. We explicitely calculated the momentum diffusion coefficient for 3 types of turbulence expected downstream of the forward shock: fast-mode waves, small-scale non-resonant modes, and large-scale modes arising from turbulent dynamo activity. After noting that low-energy particles are efficiently coupled to the quasi-thermal plasma, a simplified cosmic-ray transport equation can be formulated and is numerically solved. Results. Only fast-mode waves can provide momentum diffusion fast enough to significantly modify the spectra of particles. Using a synchrotron emissivity that accurately reflects a highly turbulent magnetic field, we calculated the radio spectral index and find that soft spectra with index a alpha less than or similar to -0.6 can be maintained over more than 2 decades in radio frequency, even if the electrons experience reacceleration for only one acceleration time. A spectral hardening is possible but considerably more frequency-dependent. The spectral modification imposed by stochastic reacceleration downstream of the forward shock depends only weakly on the initial spectrum provided by, e.g., diffusive shock acceleration at the shock itself.}, language = {en} } @article{PikovskijRosenblum2015, author = {Pikovskij, Arkadij and Rosenblum, Michael}, title = {Dynamics of globally coupled oscillators: Progress and perspectives}, series = {Chaos : an interdisciplinary journal of nonlinear science}, volume = {25}, journal = {Chaos : an interdisciplinary journal of nonlinear science}, number = {9}, publisher = {American Institute of Physics}, address = {Melville}, issn = {1054-1500}, doi = {10.1063/1.4922971}, pages = {11}, year = {2015}, abstract = {In this paper, we discuss recent progress in research of ensembles of mean field coupled oscillators. Without an ambition to present a comprehensive review, we outline most interesting from our viewpoint results and surprises, as well as interrelations between different approaches. (c) 2015 AIP Publishing LLC.}, language = {en} } @article{Pikovskij2015, author = {Pikovskij, Arkadij}, title = {First and second sound in disordered strongly nonlinear lattices: numerical study}, series = {Journal of statistical mechanics: theory and experiment}, journal = {Journal of statistical mechanics: theory and experiment}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1742-5468}, doi = {10.1088/1742-5468/2015/08/P08007}, pages = {10}, year = {2015}, abstract = {We study numerically secondary modes on top of a chaotic state in disordered nonlinear lattices. Two basic models are considered, with or without a local on-site potential. By performing periodic spatial modulation of displacement and kinetic energy, and following the temporal evolution of the corresponding spatial profiles, we reveal different modes which can be interpreted as first and second sound.}, language = {en} }