TY - JOUR A1 - Huenemoerder, D. A1 - Gayley, K. A1 - Hamann, Wolf-Rainer A1 - Ignace, R. A1 - Nichols, J. A1 - Oskinova, Lida A1 - Pollock, A. M. T. A1 - Schulz, N. T1 - High Resolution X-Ray Spectra of WR 6 JF - Wolf-Rayet Stars : Proceedings of an International Workshop held in Potsdam, Germany, 1.–5. June 2015 N2 - As WR 6 is a putatively single WN4 star, and is relatively bright (V = 6.9), it is an ideal case for studying the wind mechanisms in these extremely luminous stars. To obtain higher resolution spectra at higher energy (above 1 keV) than previously obtained with the XMM/Newton RGS, we have observed WR 6 with the Chandra High Energy Transmission Grating Spectrometer for 450 ks. We have resolved emission lines of S, Si, Mg, Ne, and Fe, which all show a “fin"-shaped prole, characteristic of a self-absorbed uniformly expanding shell. Steep blue edges gives robust maximal expansion velocities of about 2000 km/s, somewhat larger than the 1700km/s derived from UV lines. The He-like lines all indicate that X-ray emitting plasmas are far from the photosphere – even at the higher energies where opacity is lowest { as was also the case for the longer wavelength lines observed with XMM-Newton/RGS. Abundances determined from X-ray spectral modeling indicate enhancements consistent with nucleosynthesis. The star was also variable in X-rays and in simultaneous optical photometry obtained with Chandra aspect camera, but not coherently with the optically known period of 3.765 days. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-88236 SP - 301 EP - 304 ER - TY - JOUR A1 - Oskinova, Lida T1 - X-ray emission from single WR stars JF - Wolf-Rayet Stars : Proceedings of an International Workshop held in Potsdam, Germany, 1.–5. June 2015 N2 - In this review I briefly summarize our knowledge of the X-ray emission from single WN, WC, and WO stars. These stars have relatively modest X-ray luminosities, typically not exceeding 1L⊙. The analysis of X-ray spectra usually reveals thermal plasma with temperatures reaching a few x10 MK. X-ray variability is detected in some WN stars. At present we don't fully understand how X-ray radiation in produced in WR stars, albeit there are some promising research avenues, such as the presence of CIRs in the winds of some stars. To fully understand WR stars we need to unravel mechanisms of X-ray production in their winds. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-88228 SP - 295 EP - 300 ER - TY - JOUR A1 - Todt, Helge Tobias A1 - Hamann, Wolf-Rainer T1 - Wolf-Rayet central stars of planetary nebulae JF - Wolf-Rayet Stars : Proceedings of an International Workshop held in Potsdam, Germany, 1.–5. June 2015 N2 - A significant number of the central stars of planetary nebulae (CSPNe) are hydrogen-deficient, showing a chemical composition of helium, carbon, and oxygen. Most of them exhibit Wolf-Rayet-like emission line spectra, similar to those of the massive WC Pop I stars, and are therefore classified as of spectral type [WC]. In the last years, CSPNe of other Wolf-Rayet spectral subtypes have been identified, namely PB 8, which is of spectral type [WN/C], and IC 4663 and Abell 48, which are of spectral type [WN]. We review spectral analyses of Wolf-Rayet type central stars of different evolutionary stages and discuss the results in the context of stellar evolution. Especially we consider the question of a common evolutionary channel for [WC] stars. The constraints on the formation of [WN] or [WC/N] subtype stars will also be addressed. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-88147 SP - 253 EP - 258 ER - TY - JOUR A1 - Shenar, Tomer A1 - Hamann, Wolf-Rainer A1 - Todt, Helge Tobias T1 - The impact of rotation on the line profiles of Wolf-Rayet stars JF - Wolf-Rayet Stars : Proceedings of an International Workshop held in Potsdam, Germany, 1.–5. June 2015 N2 - The distribution of angular momentum in massive stars is a critical component of their evolution, yet not much is known on the rotation velocities of Wolf-Rayet stars. There are various indications that rapidly rotating Wolf-Rayet stars should exist. Unfortunately, due to their expanding atmospheres, rotational velocities of Wolf-Rayet stars are very difficult to measure. In this work, we model the effects of rotation on the atmospheres of Wolf-Rayet stars by implementing a 3D integration scheme in the PoWR code. We further investigate whether the peculiar spectra of five Wolf-Rayet stars may imply rapid rotation, infer the corresponding rotation parameters, and discuss the implications of our results. We find that rotation helps to reproduce the unique spectra analyzed here. However, if rotation is indeed involved, the inferred rotational velocities at the stellar surface are large (∼ 200 km/s), and the implied co-rotation radii (∼ 10R∗) suggest the existence of very strong photospheric magnetic fields (∼ 20 kG). Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-88008 SP - 193 EP - 196 ER - TY - JOUR A1 - Sander, A. A1 - Hamann, Wolf-Rainer A1 - Hainich, Rainer A1 - Shenar, Tomer A1 - Todt, Helge Tobias T1 - Hydrodynamic modeling of massive star atmospheres JF - Wolf-Rayet Stars : Proceedings of an International Workshop held in Potsdam, Germany, 1.–5. June 2015 N2 - In the last decades, stellar atmosphere codes have become a key tool in understanding massive stars, including precise calculations of stellar and wind parameters, such as temperature, massloss rate, and terminal wind velocity. Nevertheless, for these models the hydrodynamic equation is not solved in the wind. Motivated by the results of the CAK theory, the models typically use a beta velocity law, which however turns out not to be adequate for stars with very strong winds, and treat the mass-loss rate as a free parameter. In a new branch of the Potsdam Wolf-Rayet model atmosphere (PoWR) code, we solve the hydrodynamic equation consistently throughout the stellar atmosphere. The PoWR code performs the calculation of the radiative force without approximations (e.g. Sobolev). We show the impact of hydrodynamically consistent modelling on OB and WR stars in comparison to conventional models and discuss the obtained velocity fields and their impact on the observed spectral lines. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-87857 SP - 139 EP - 142 ER - TY - JOUR A1 - Kubátová, Brankica A1 - Hamann, Wolf-Rainer A1 - Todt, Helge Tobias A1 - Sander, A. A1 - Steinke, M. A1 - Hainich, Rainer A1 - Shenar, Tomer T1 - Macroclumping in WR 136 JF - Wolf-Rayet Stars : Proceedings of an International Workshop held in Potsdam, Germany, 1.–5. June 2015 N2 - Macroclumping proved to resolve the discordance between different mass-loss rate diagnostics for O-type stars, in particular between Hα and the P v resonance lines. In this paper, we report first results from a corresponding investigation for WR stars. We apply our detailed 3-D Monte Carlo (MC) line formation code to the P v resonance doublet and show, for the Galactic WNL star WR136, that macroclumping is require to bring this line in accordance with the mass-loss rate derived from the emission-line spectrum. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-87823 SP - 125 EP - 128 ER - TY - JOUR A1 - Hainich, Rainer A1 - Rühling, U. A1 - Pasemann, D. A1 - Hamann, Wolf-Rainer T1 - The WN population in the Magellanic Clouds JF - Wolf-Rayet Stars : Proceedings of an International Workshop held in Potsdam, Germany, 1.–5. June 2015 N2 - A detailed and comprehensive study of the Wolf-Rayet stars of the nitrogen sequence (WN stars) in the Small Magellanic Cloud (SMC) and the Large Magellanic Cloud (LMC) is presented. We derived the fundamental stellar and wind parameters for more than 100 massive stars, encompassing almost the whole WN population in the Magellanic Clouds (MCs). The observations are fitted with synthetic spectra, using the PotsdamWolf-Rayet model atmosphere code (PoWR). For this purpose, large grids of line-blanket models for different metallicities have been calculated, covering a wide range of stellar temperatures, mass-loss rates, and hydrogen abundances. Our comprehensive sample facilitates statistical studies of the WN properties in the MCs without selection bias. To investigate the impact of the low LMC metallicity and the even lower SMC metallicity, we compare our new results to previous analyses of the Galactic WN population and the late type WN stars from M31. Based on these studies we derived an empirical relation between the WN mass-loss rates and the metallicity. Current stellar evolution tracks, even when accounting for rotationally induced mixing, partly fail to reproduce the observed ranges of luminosities and initial masses. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-87806 SP - 117 EP - 120 ER - TY - JOUR A1 - Hamann, Wolf-Rainer T1 - Wind models and spectral analyses JF - Wolf-Rayet Stars : Proceedings of an International Workshop held in Potsdam, Germany, 1.–5. June 2015 N2 - The emission-line dominated spectra of Wolf-Rayet stars are formed in expanding layers of their atmosphere, i.e. in their strong stellar wind. Adequate modeling of such spectra has to face a couple of difficulties. Because of the supersonic motion, the radiative transfer is preferably formulated in the co-moving frame. The strong deviations from local thermodynamical equilibrium (LTE) require to solve the equations of statistical equilibrium for the population numbers, accounting for many hundred atomic energy levels and thousands of line transitions. Moreover, millions of lines from iron-group elements must be taken into account for their blanketing effect. Model atmospheres of the described kind can reproduce the observed WR spectra satisfyingly, and have been widely applied for corresponding spectral analyses. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-87748 SP - 91 EP - 96 ER - TY - JOUR A1 - Pulkkinen, Otto A1 - Metzler, Ralf T1 - Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation JF - Scientific reports N2 - 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. Y1 - 2015 U6 - https://doi.org/10.1038/srep17820 SN - 2045-2322 IS - 5 PB - Nature Publishing Group CY - London ER - TY - JOUR 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 JF - Scientific Reports 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. KW - gene regulatory networks KW - biological physics Y1 - 2015 U6 - https://doi.org/10.1038/srep10072 SN - 2045-2322 VL - 5 IS - 10072 PB - Nature Publishing Group CY - London ER - TY - JOUR A1 - Metzler, Ralf A1 - Cherstvy, Andrey G. A1 - Chechkin, Aleksei V. A1 - Bodrova, Anna S. T1 - Ultraslow scaled Brownian motion JF - New journal of physics : the open-access journal for physics N2 - We define and study in detail utraslow scaled Brownian motion (USBM) characterized by a time dependent diffusion coefficient of the form . For unconfined motion the mean squared displacement (MSD) of USBM exhibits an ultraslow, logarithmic growth as function of time, in contrast to the conventional scaled Brownian motion. In a harmonic potential the MSD of USBM does not saturate but asymptotically decays inverse-proportionally to time, reflecting the highly non-stationary character of the process. We show that the process is weakly non-ergodic in the sense that the time averaged MSD does not converge to the regular MSD even at long times, and for unconfined motion combines a linear lag time dependence with a logarithmic term. The weakly non-ergodic behaviour is quantified in terms of the ergodicity breaking parameter. The USBM process is also shown to be ageing: observables of the system depend on the time gap between initiation of the test particle and start of the measurement of its motion. Our analytical results are shown to agree excellently with extensive computer simulations. KW - anomalous diffusion KW - stochastic processes KW - ageing Y1 - 2015 U6 - https://doi.org/10.1088/1367-2630/17/6/063038 SN - 1367-2630 VL - 17 IS - 063038 PB - Dt. Physikalische Ges., IOP CY - Bad Honnef, London ER - TY - JOUR A1 - Goychuk, Igor A1 - Goychuk, Andriy T1 - Stochastic Wilson BT - Cowan models of neuronal network dynamics with memory and delay JF - New journal of physics N2 - We consider a simple Markovian class of the stochastic Wilson–Cowan type models of neuronal network dynamics, which incorporates stochastic delay caused by the existence of a refractory period of neurons. From the point of view of the dynamics of the individual elements, we are dealing with a network of non-Markovian stochastic two-state oscillators with memory, which are coupled globally in a mean-field fashion. This interrelation of a higher-dimensional Markovian and lower-dimensional non-Markovian dynamics is discussed in its relevance to the general problem of the network dynamics of complex elements possessing memory. The simplest model of this class is provided by a three-state Markovian neuron with one refractory state, which causes firing delay with an exponentially decaying memory within the two-state reduced model. This basic model is used to study critical avalanche dynamics (the noise sustained criticality) in a balanced feedforward network consisting of the excitatory and inhibitory neurons. Such avalanches emerge due to the network size dependent noise (mesoscopic noise). Numerical simulations reveal an intermediate power law in the distribution of avalanche sizes with the critical exponent around −1.16. We show that this power law is robust upon a variation of the refractory time over several orders of magnitude. However, the avalanche time distribution is biexponential. It does not reflect any genuine power law dependence. KW - neuronal networks KW - stochastic models KW - memory and delay KW - critical avalanche dynamics Y1 - 2015 U6 - https://doi.org/10.1088/1367-2630/17/4/045029 SN - 1367-2630 VL - 17 IS - 4 PB - Deutsche Physikalische Gesellschaft, Institute of Physics CY - Bad Honnef, London ER - TY - JOUR A1 - Goychuk, Igor A. A1 - Kharchenko, Vasyl O. A1 - Metzler, Ralf T1 - Molecular motors pulling cargos in the viscoelastic cytosol: how power strokes beat subdiffusion JF - Physical Chemistry Chemical Physics N2 - 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. KW - royal soc chemistry KW - thomas graham house KW - science park KW - milton rd KW - cambridge cb4 0wf KW - cambs KW - england Y1 - 2014 SN - 1463-9076 IS - 16 SP - 16524 EP - 16535 PB - the Royal Society of Chemistry CY - Cambridge ER - 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 - Palyulin, Vladimir V. A1 - Ala-Nissila, Tapio A1 - Metzler, Ralf ED - Metzler, Ralf T1 - Polymer translocation: the first two decades and the recent diversification JF - Soft matter 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. 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-opus4-76266 SN - 1744-683X VL - 45 IS - 10 SP - 9016 EP - 9037 PB - the Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Bauer, Maximilian A1 - Godec, Aljaž A1 - Metzler, Ralf T1 - Diffusion of finite-size particles in two-dimensional channels with random wall configurations JF - Physical chemistry, chemical physics : PCCP ; a journal of European chemical societies N2 - 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]. KW - anomalous diffusion KW - fractional dynamics KW - transport KW - nonergodicity KW - coefficient Y1 - 2014 U6 - https://doi.org/10.1039/C3CP55160A SN - 1463-9084 SN - 1463-9076 VL - 16 IS - 13 SP - 6118 EP - 6128 PB - RSC Publications CY - Cambridge ER -