@article{LiuCherstvyMetzler2017, author = {Liu, Lin and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Facilitated Diffusion of Transcription Factor Proteins with Anomalous Bulk Diffusion}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {121}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.6b12413}, pages = {1284 -- 1289}, year = {2017}, abstract = {What are the physical laws of the diffusive search of proteins for their specific binding sites on DNA in the presence of the macromolecular crowding in cells? We performed extensive computer simulations to elucidate the protein target search on DNA. The novel feature is the viscoelastic non-Brownian protein bulk diffusion recently observed experimentally. We examine the influence of the protein-DNA binding affinity and the anomalous diffusion exponent on the target search time. In all cases an optimal search time is found. The relative contribution of intermittent three-dimensional bulk diffusion and one-dimensional sliding of proteins along the DNA is quantified. Our results are discussed in the light of recent single molecule tracking experiments, aiming at a better understanding of the influence of anomalous kinetics of proteins on the facilitated diffusion mechanism.}, language = {en} } @article{SmirnovOsipovPikovskij2017, author = {Smirnov, Lev A. and Osipov, Grigory V. and Pikovskij, Arkadij}, title = {Chimera patterns in the Kuramoto-Battogtokh model}, series = {Journal of physics : A, Mathematical and theoretical}, volume = {50}, journal = {Journal of physics : A, Mathematical and theoretical}, number = {8}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1751-8113}, doi = {10.1088/1751-8121/aa55f1}, pages = {10}, year = {2017}, abstract = {Kuramoto and Battogtokh (2002 Nonlinear Phenom. Complex Syst. 5 380) discovered chimera states represented by stable coexisting synchrony and asynchrony domains in a lattice of coupled oscillators. After a reformulation in terms of a local order parameter, the problem can be reduced to partial differential equations. We find uniformly rotating, spatially periodic chimera patterns as solutions of a reversible ordinary differential equation, and demonstrate a plethora of such states. In the limit of neutral coupling they reduce to analytical solutions in the form of one-and two-point chimera patterns as well as localized chimera solitons. Patterns at weakly attracting coupling are characterized by virtue of a perturbative approach. Stability analysis reveals that only the simplest chimeras with one synchronous region are stable.}, language = {en} } @article{AbeysekaraArchambaultArcheretal.2017, author = {Abeysekara, A. U. and Archambault, S. and Archer, A. and Benbow, Wystan and Bird, Ralph and Buchovecky, M. and Buckley, J. H. and Bugaev, V. and Byrum, K. and Cerruti, M. and Chen, X. and Ciupik, L. and Cui, W. and Dickinson, H. J. and Eisch, J. D. and Errando, M. and Falcone, A. and Feng, Q. and Finley, J. P. and Fleischhack, H. and Fortson, L. and Furniss, A. and Gillanders, G. H. and Griffin, S. and Grube, J. and Hutten, M. and Hakansson, N. and Hanna, D. and Holder, J. and Humensky, T. B. and Johnson, C. A. and Kaaret, P. and Kar, P. and Kertzman, M. and Kieda, D. and Krause, M. and Krennrich, F. and Kumar, S. and Lang, M. J. and Maier, G. and McArthur, S. and McCann, A. and Meagher, K. and Moriarty, P. and Mukherjee, R. and Nguyen, T. and Nieto, D. and Ong, R. A. and Otte, A. N. and Park, N. and Pelassa, V. and Pohl, Martin and Popkow, A. and Pueschel, Elisa and Quinn, J. and Ragan, K. and Reynolds, P. T. and Richards, G. T. and Roache, E. and Rulten, C. and Santander, M. and Sembroski, G. H. and Shahinyan, K. and Staszak, D. and Telezhinsky, Igor O. and Tucci, J. V. and Tyler, J. and Wakely, S. P. and Weiner, O. M. and Weinstein, A. and Wilhelm, Alina and Williams, D. A. and Fegan, S. and Giebels, B. and Horan, D. and Berdyugin, A. and Kuan, J. and Lindfors, E. and Nilsson, K. and Oksanen, A. and Prokoph, H. and Reinthal, R. and Takalo, L. and Zefi, F.}, title = {A Luminous and Isolated Gamma-Ray Flare from the Blazar B2 1215+30}, series = {The astrophysical journal : an international review of spectroscopy and astronomical physics}, volume = {836}, journal = {The astrophysical journal : an international review of spectroscopy and astronomical physics}, number = {2}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, organization = {VERITAS Collaboration;Fermi-LAT Collaboration}, issn = {0004-637X}, doi = {10.3847/1538-4357/836/2/205}, pages = {6}, year = {2017}, abstract = {B2 1215+30 is a BL-Lac-type blazar that was first detected at TeV energies by the MAGIC atmospheric Cherenkov telescopes and subsequently confirmed by the Very Energetic Radiation Imaging Telescope Array System (VERITAS) observatory with data collected between 2009 and 2012. In 2014 February 08, VERITAS detected a large-amplitude flare from B2. 1215+30 during routine monitoring observations of the blazar 1ES. 1218+304, located in the same field of view. The TeV flux reached 2.4 times the Crab Nebula flux with a variability timescale of <3.6 hr. Multiwavelength observations with Fermi-LAT, Swift, and the Tuorla Observatory revealed a correlated high GeV flux state and no significant optical counterpart to the flare, with a spectral energy distribution where the gamma-ray luminosity exceeds the synchrotron luminosity. When interpreted in the framework of a onezone leptonic model, the observed emission implies a high degree of beaming, with Doppler factor delta > 10, and an electron population with spectral index p < 2.3.}, language = {en} } @article{GodecMetzler2017, author = {Godec, Aljaž and Metzler, Ralf}, title = {First passage time statistics for two-channel diffusion}, series = {Journal of physics : A, Mathematical and theoretical}, volume = {50}, journal = {Journal of physics : A, Mathematical and theoretical}, number = {8}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1751-8113}, doi = {10.1088/1751-8121/aa5204}, pages = {17}, year = {2017}, abstract = {We present rigorous results for the mean first passage time and first passage time statistics for two-channel Markov additive diffusion in a 3-dimensional spherical domain. Inspired by biophysical examples we assume that the particle can only recognise the target in one of the modes, which is shown to effect a non-trivial first passage behaviour. We also address the scenario of intermittent immobilisation. In both cases we prove that despite the perfectly non-recurrent motion of two-channel Markov additive diffusion in 3 dimensions the first passage statistics at long times do not display Poisson-like behaviour if none of the phases has a vanishing diffusion coefficient. This stands in stark contrast to the standard (one-channel) Markov diffusion counterpart. We also discuss the relevance of our results in the context of cellular signalling.}, language = {en} } @article{GorobtsovMercurioBrenneretal.2017, author = {Gorobtsov, O. Yu. and Mercurio, G. and Brenner, G. and Lorenz, Ulf and Gerasimova, N. and Kurta, R. P. and Hieke, F. and Skopintsev, P. and Zaluzhnyy, I. and Lazarev, S. and Dzhigaev, D. and Rose, M. and Singer, A. and Wurth, W. and Vartanyants, I. A.}, title = {Statistical properties of a free-electron laser revealed by Hanbury Brown-Twiss interferometry}, series = {Physical review : A, Atomic, molecular, and optical physics}, volume = {95}, journal = {Physical review : A, Atomic, molecular, and optical physics}, number = {2}, publisher = {American Physical Society}, address = {College Park}, issn = {2469-9926}, doi = {10.1103/PhysRevA.95.023843}, pages = {16}, year = {2017}, abstract = {We present a comprehensive experimental analysis of statistical properties of the self-amplified spontaneous emission free-electron laser (FEL) FLASH by means of Hanbury Brown and Twiss interferometry. The experiments were performed at FEL wavelengths of 5.5, 13.4, and 20.8 nm. We determined the second-order intensity correlation function for all wavelengths and different operation conditions of FLASH. In all experiments a high degree of spatial coherence (above 50\%) was obtained. Our analysis performed in spatial and spectral domains provided us with the independent measurements of an average pulse duration of the FEL that were below 60 fs. To explain the complicated behavior of the second-order intensity correlation function we developed an advanced theoretical model that includes the presence of multiple beams and external positional jitter of the FEL pulses. By this analysis we determined that in one of the experiments external positional jitter was about 25\% of the beam size. We envision that methods developed in our study will be used widely for analysis and diagnostics of FEL radiation.}, language = {en} } @article{PetereitPikovskij2017, author = {Petereit, Johannes and Pikovskij, Arkadij}, title = {Chaos synchronization by nonlinear coupling}, series = {Communications in nonlinear science \& numerical simulation}, volume = {44}, journal = {Communications in nonlinear science \& numerical simulation}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1007-5704}, doi = {10.1016/j.cnsns.2016.09.002}, pages = {344 -- 351}, year = {2017}, abstract = {We study synchronization properties of three nonlinearly coupled chaotic maps. Coupling is introduced in such a way, that it cannot be reduced to pairwise terms, but includes combined action of all interacting units. For two models of nonlinear coupling we characterize the transition to complete synchrony, as well as partially synchronized states. Relation to hypernetworks of chaotic units is also discussed.}, language = {en} } @article{RamachandranDasTejetal.2017, author = {Ramachandran, Varsha and Das, S. R. and Tej, A. and Vig, S. and Ghosh, S. K. and Ojha, D. K.}, title = {Radio and infrared study of the star-forming region IRAS 20286+4105}, series = {Monthly notices of the Royal Astronomical Society}, volume = {465}, journal = {Monthly notices of the Royal Astronomical Society}, number = {4}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0035-8711}, doi = {10.1093/mnras/stw2906}, pages = {4753 -- 4771}, year = {2017}, abstract = {In this paper, we present a multi wavelength investigation of the star-forming complex IRAS 20286+4105, located in the Cygnus X region. Near-infrared K-band data are used to revisit the cluster/stellar group identified in previous studies. Radio continuum observations at 610 and 1280 MHz show the presence of a H II region possibly powered by a star of spectral type B0-B0.5. The cometary morphology of the ionized region is explained by invoking the bowshock model, where the likely association with a nearby supernova remnant is also explored. A compact radio knot with a non-thermal spectral index is detected towards the centre of the cloud. Mid-infrared data from the Spitzer Legacy Survey of the Cygnus X region show the presence of six Class I young stellar objects inside the cloud. Thermal dust emission in this complex is modelled using Herschel far-infrared data to generate dust temperature and column density maps. Herschel images also show the presence of two clumps in this region, the masses of which are estimated to be similar to 175 and 30 M-circle dot. The mass-radius relation and the surface density of the clumps mean that they do not qualify as massive star-forming sites. An overall picture of a runaway star ionizing the cloud and a triggered population of intermediatemass, Class I sources located towards the cloud centre emerges from this multiwavelength study. Variation in the dust emissivity spectral index is shown to exist in this region and is seen to have an inverse relation with the dust temperature.}, language = {en} } @article{ZachariasChenWagner2017, author = {Zacharias, Michael and Chen, Xuhui and Wagner, Stefan}, title = {Attenuation of TeV gamma-rays by the starlight photon field of the host galaxy}, series = {Monthly notices of the Royal Astronomical Society}, volume = {465}, journal = {Monthly notices of the Royal Astronomical Society}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0035-8711}, doi = {10.1093/mnras/stw3032}, pages = {3767 -- 3774}, year = {2017}, abstract = {The absorption of TeV gamma-ray photons produced in relativistic jets by surrounding soft photon fields is a long-standing problem of jet physics. In some cases, the most likely emission site close to the central black hole is ruled out because of the high opacity caused by strong optical and infrared photon sources, such as the broad-line region. Mostly neglected for jet modelling is the absorption of gamma-rays in the starlight photon field of the host galaxy. Analysing the absorption for arbitrary locations and observation angles of the gamma-ray emission site within the host galaxy, we find that the distance to the galaxy centre, the observation angle, and the distribution of starlight in the galaxy are crucial for the amount of absorption. We derive the absorption value for a sample of 20 TeV-detected blazars with a redshift z(r) < 0.2. The absorption value of the gamma-ray emission located in the galaxy centre may be as high as 20 per cent, with an average value of 6 per cent. This is important in order to determine the intrinsic blazar parameters. We see no significant trends in our sample between the degree of absorption and host properties, such as starlight emissivity, galactic size, half-light radius, and redshift. While the uncertainty of the spectral properties of the extragalactic background light exceeds the effect of absorption by stellar light from the host galaxy in distant objects, the latter is a dominant effect in nearby sources. It may also be revealed in a differential comparison of sources with similar redshifts.}, language = {en} } @article{FandrichBullerMemczaketal.2017, author = {Fandrich, Artur and Buller, Jens and Memczak, Henry and Stoecklein, W. and Hinrichs, K. and Wischerhoff, E. and Schulz, B. and Laschewsky, Andr{\´e} and Lisdat, Fred}, title = {Responsive Polymer-Electrode Interface-Study of its Thermo- and pH-Sensitivity and the Influence of Peptide Coupling}, series = {Electrochimica acta : the journal of the International Society of Electrochemistry (ISE)}, volume = {229}, journal = {Electrochimica acta : the journal of the International Society of Electrochemistry (ISE)}, publisher = {Elsevier}, address = {Oxford}, issn = {0013-4686}, doi = {10.1016/j.electacta.2017.01.080}, pages = {325 -- 333}, year = {2017}, abstract = {This study introduces a thermally responsive, polymer-based electrode system. The key component is a surface-attached, temperature-responsive poly(oligoethylene glycol) methacrylate (poly(OEGMA)) type polymer bearing photoreactive benzophenone and carboxy groups containing side chains. The responsive behavior of the polymer in aqueous media has been investigated by turbidimetry measurements. Polymer films are formed on gold substrates by means of the photoreactive 2(dicyclohexylphosphino)benzophenone (DPBP) through photocrosslinking. The electrochemical behavior of the resulting polymer-substrate interface has been investigated in buffered [Fe(CN)6](3-)/[Fe (CN)6](4-)solutions at room temperature and under temperature variation by cyclic voltammetry (CV). The CV experiments show that with increasing temperature structural changes of the polymer layer occur, which alter the output of the electrochemical measurement. Repeated heating/cooling cycles analyzed by CV measurements and pH changes analyzed by quartz crystal microbalance with dissipation monitoring (QCM-D) reveal the reversible nature of the restructuring process. The immobilized films are further modified by covalent coupling of two small biomolecules - a hydrophobic peptide and a more hydrophilic one. These attached components influence the hydrophobicity of the layer in a different way the resulting change of the temperature-caused behavior has been studied by CV indicating a different state of the polymer after coupling of the hydrophobic peptide.}, language = {en} } @article{SchoellerHubrigFossatietal.2017, author = {Sch{\"o}ller, Markus and Hubrig, Swetlana and Fossati, L. and Carroll, Thorsten Anthony and Briquet, Maryline and Oskinova, Lida and J{\"a}rvinen, S. and Ilyin, Ilya and Castro, N. and Morel, T. and Langer, N. and Przybilla, N. and Nieva, M. -F. and Kholtygin, A. F. and Sana, H. and Herrero, A. and Barba, R. H. and de Koter, A.}, title = {B fields in OB stars (BOB)}, series = {Astronomy and astrophysics : an international weekly journal}, volume = {599}, journal = {Astronomy and astrophysics : an international weekly journal}, publisher = {EDP Sciences}, address = {Les Ulis}, organization = {BOB Collaboration}, issn = {1432-0746}, doi = {10.1051/0004-6361/201628905}, pages = {11}, year = {2017}, abstract = {Aims. The B fields in OB stars (BOB) Collaboration is based on an ESO Large Programme to study the occurrence rate, properties, and ultimately the origin of magnetic fields in massive stars. Methods. In the framework of this program, we carried out low-resolution spectropolarimetric observations of a large sample of massive stars using FORS2 installed at the ESO VLT 8m telescope. Results. We determined the magnetic field values with two completely independent reduction and analysis pipelines. Our in-depth study of the magnetic field measurements shows that differences between our two pipelines are usually well within 3 sigma errors. From the 32 observations of 28 OB stars, we were able to monitor the magnetic fields in CPD -57 degrees 3509 and HD164492C, confirm the magnetic field in HD54879, and detect a magnetic field in CPD -62 degrees 2124. We obtain a magnetic field detection rate of 6 +/- 3\% for the full sample of 69 OB stars observed with FORS 2 within the BOB program. For the preselected objects with a nu sin i below 60 km s(-1), we obtain a magnetic field detection rate of 5 +/- 5\%. We also discuss X-ray properties and multiplicity of the objects in our FORS2 sample with respect to the magnetic field detections.}, language = {en} }