TY  - JOUR
A1  - Schmah, Tanya
A1  - Marwan, Norbert
A1  - Thomsen, Jesper Skovhus
A1  - Saparin, Peter
T1  - Long range node-strut analysis of trabecular bone microarchitecture
JF  - Medical physics : the international journal of medical physics research and practice
N2  - Purpose: We present a new morphometric measure of trabecular bone microarchitecture, called mean node strength (NdStr), which is part of a newly developed approach called long range nodestrut analysis. Our general aim is to describe and quantify the apparent "latticelike" microarchitecture of the trabecular bone network.
 Methods: Similar in some ways to the topological node-strut analysis introduced by Garrahan et al. [J. Microsc. 142, 341-349 (1986)], our method is distinguished by an emphasis on long-range trabecular connectivity. Thus, while the topological classification of a pixel (after skeletonization) as a node, strut, or terminus, can be determined from the 3 x 3 neighborhood of that pixel, our method, which does not involve skeletonization, takes into account a much larger neighborhood. In addition, rather than giving a discrete classification of each pixel as a node, strut, or terminus, our method produces a continuous variable, node strength. The node strength is averaged over a region of interest to produce the mean node strength of the region.
 Results: We have applied our long range node-strut analysis to a set of 26 high-resolution peripheral quantitative computed tomography (pQCT) axial images of human proximal tibiae acquired 17 mm below the tibial plateau. We found that NdStr has a strong positive correlation with trabecular volumetric bone mineral density (BMD). After an exponential transformation, we obtain a Pearson's correlation coefficient of r - 0.97. Qualitative comparison of images with similar BMD but with very different NdStr values suggests that the latter measure has successfully quantified the prevalence of the "latticelike" microarchitecture apparent in the image. Moreover, we found a strong correlation (r - 0.62) between NdStr and the conventional node-terminus ratio (Nd/Tm) of Garrahan et al. The Nd/Tm ratios were computed using traditional histomorphometry performed on bone biopsies obtained at the same location as the pQCT scans.
 Conclusions: The newly introduced morphometric measure allows a quantitative assessment of the long-range connectivity of trabecular bone. One advantage of this method is that it is based on pQCT images that can be obtained noninvasively from patients, i.e., without having to obtain a bone biopsy from the patient.
KW  - trabecular bone
KW  - osteoporosis
KW  - structure analysis
KW  - histomorphometry
KW  - pQCT
Y1  - 2011
U6  - https://doi.org/10.1118/1.3622600
SN  - 0094-2405
VL  - 38
IS  - 9
SP  - 5003
EP  - 5011
PB  - American Association of Physicists in Medicine
CY  - Melville
ER  - 
TY  - JOUR
A1  - Carminati, Andrea
A1  - Schneider, Christoph L.
A1  - Moradi, Ahmad B.
A1  - Zarebanadkouki, Mohsen
A1  - Vetterlein, Doris
A1  - Vogel, Hans-Jörg
A1  - Hildebrandt, Anke
A1  - Weller, Ulrich
A1  - Schüler, Lennart
A1  - Oswald, Sascha
T1  - How the rhizosphere may favor water availability to roots
JF  - Vadose zone journal
N2  - Recent studies have shown that rhizosphere hydraulic properties may differ from those of the bulk soil. Specifically, mucilage at the root-soil interface may increase the rhizosphere water holding capacity and hydraulic conductivity during drying. The goal of this study was to point out the implications of such altered rhizosphere hydraulic properties for soil-plant water relations. We addressed this problem through modeling based on a steady-rate approach. We calculated the water flow toward a single root assuming that the rhizosphere and bulk soil were two concentric cylinders having different hydraulic properties. Based on our previous experimental results, we assumed that the rhizosphere had higher water holding capacity and unsaturated conductivity than the bulk soil. The results showed that the water potential gradients in the rhizosphere were much smaller than in the bulk soil. The consequence is that the rhizosphere attenuated and delayed the drop in water potential in the vicinity of the root surface when the soil dried. This led to increased water availability to plants, as well as to higher effective conductivity under unsaturated conditions. The reasons were two: (i) thanks to the high unsaturated conductivity of the rhizosphere, the radius of water uptake was extended from the root to the rhizosphere surface; and (ii) thanks to the high soil water capacity of the rhizosphere, the water depletion in the bulk soil was compensated by water depletion in the rhizosphere. We conclude that under the assumed conditions, the rhizosphere works as an optimal hydraulic conductor and as a reservoir of water that can be taken up when water in the bulk soil becomes limiting.
Y1  - 2011
U6  - https://doi.org/10.2136/vzj2010.0113
SN  - 1539-1663
VL  - 10
IS  - 3
SP  - 988
EP  - 998
PB  - Soil Science Society of America
CY  - Madison
ER  - 
TY  - JOUR
A1  - Krahé, Barbara
A1  - Tomaszewska, Paulina
T1  - Sexual scripts and the acceptance of sexual aggression in Polish adolescents
JF  - European journal of developmental psychology
N2  - A study with 199 Polish adolescents explored the prominence of risk factors of sexual aggression as part of the sexual scripts for consensual sexual encounters and as predictors of the acceptance of sexual aggression. Distinguishing between general scripts, attributed to the age group as a whole, and individual scripts, reflecting personal standards, sexual scripts were linked to the normative endorsement of the risk factors and to the acceptance of sexual aggression. Individual scripts contained fewer risk factors of sexual aggression than general scripts. The more prominently the risk elements featured in the individual (but not in the general) scripts, the more they were seen as acceptable. For boys, risk scores in individual scripts were correlated with sexual behaviour and linked to the acceptance of sexual aggression via their normative endorsement. The distinction between individual and general scripts as guidelines for behaviour is discussed in terms of its significance for the understanding of sexual aggression.
KW  - Sexual scripts
KW  - Sexuality
KW  - Sexual aggression
KW  - Adolescence
KW  - Poland
Y1  - 2011
U6  - https://doi.org/10.1080/17405629.2011.611034
SN  - 1740-5629
VL  - 8
IS  - 6
SP  - 697
EP  - 712
PB  - Wiley
CY  - Hove
ER  - 
TY  - GEN
A1  - Guerrero, Martín A.
A1  - Chu, You-Hua
A1  - Hamann, Wolf-Rainer
A1  - Oskinova, Lida
A1  - Schönberner, Detlef
A1  - Todt, Helge Tobias
A1  - Steffen, Matthias
A1  - Ruiz, Nieves
A1  - Gruendl, Robert A.
A1  - Blair, William P.
T1  - Ablation and wind mass-loading in the born-again planetary nebula A 30
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - We present XMM-Newton and Chandra observations of the born-again planetary nebula A 30. These X-ray observations reveal a bright unresolved source at the position of the central star whose X-ray luminosity exceeds by far the model expectations for photospheric emission and for shocks within the stellar wind. We suggest that a “born-again hot bubble” may be responsible for this X-ray emission. Diffuse X-ray emission associated with the petal-like features and one of the H-poor knots seen in the optical is also found. The weakened emission of carbon lines in the spectrum of the diffuse emission can be interpreted as the dilution of stellar wind by mass-loading or as the detection of material ejected during a very late thermal pulse.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 563 
KW  - planetary nebulae: individual (A 30)
KW  - X-rays: ISM
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412341
SN  - 1866-8372
IS  - 563
ER  - 
TY  - JOUR
A1  - Streich, Rita
A1  - Becken, Michael
A1  - Ritter, Oliver
T1  - 2.5D controlled-source EM modeling with general 3D source geometries
JF  - Geophysics
N2  - Most 2.5D controlled-source electromagnetic (CSEM) modeling algorithms presented to date explicitly consider only sources that are point dipoles oriented parallel or perpendicular to the direction of constant conductivity. This makes simulations of complex source geometries expensive, requiring separate evaluations of many point dipole fields, and thus limits the practical applicability of such schemes for simulating and interpreting field data. We present a novel 2.5D CSEM modeling scheme that overcomes this limitation and permits efficient simulations of sources with general shape and orientation by evaluating fields for the entire source at once. We accommodate general sources by using a secondary field approach, in which primary fields are computed for the general source and a 1D background conductivity model. To carry out the required Fourier transforms between space and wavenumber domain using the same fast cosine and sine transform filters as in conventional algorithms, we split the primary and secondary fields into their symmetric and antisymmetric parts. For complex 3D source geometries, this approach is significantly more efficient than previous 2.5D algorithms. Our finite-difference algorithm also includes novel approaches for divergence correction at low frequencies and EM field interpolation across conductivity discontinuities. We describe the modeling scheme and demonstrate its accuracy and efficiency by comparisons of 2.5D-simulated data with 1D and 3D results.
Y1  - 2011
U6  - https://doi.org/10.1190/GEO2011-0111.1
SN  - 0016-8033
VL  - 76
IS  - 6
SP  - F387
EP  - F393
PB  - Society of Exploration Geophysicists
CY  - Tulsa
ER  - 
TY  - JOUR
A1  - Stankiewicz, Jacek
A1  - Munoz, G.
A1  - Ritter, Oliver
A1  - Bedrosian, Paul A.
A1  - Ryberg, Trond
A1  - Weckmann, Ute
A1  - Weber, Michael H.
T1  - Shallow lithological structure across the Dead Sea Transform derived from geophysical experiments
JF  - Geochemistry, geophysics, geosystems
N2  - In the framework of the DEad SEa Rift Transect (DESERT) project a 150 km magnetotelluric profile consisting of 154 sites was carried out across the Dead Sea Transform. The resistivity model presented shows conductive structures in the western section of the study area terminating abruptly at the Arava Fault. For a more detailed analysis we performed a joint interpretation of the resistivity model with a P wave velocity model from a partially coincident seismic experiment. The technique used is a statistical correlation of resistivity and velocity values in parameter space. Regions of high probability of a coexisting pair of values for the two parameters are mapped back into the spatial domain, illustrating the geographical location of lithological classes. In this study, four regions of enhanced probability have been identified, and are remapped as four lithological classes. This technique confirms the Arava Fault marks the boundary of a highly conductive lithological class down to a depth of similar to 3 km. That the fault acts as an impermeable barrier to fluid flow is unusual for large fault zone, which often exhibit a fault zone characterized by high conductivity and low seismic velocity. At greater depths it is possible to resolve the Precambrian basement into two classes characterized by vastly different resistivity values but similar seismic velocities. The boundary between these classes is approximately coincident with the Al Quweira Fault, with higher resistivities observed east of the fault. This is interpreted as evidence for the original deformation along the DST originally taking place at the Al Quweira Fault, before being shifted to the Arava Fault.
KW  - magnetotellurics
KW  - seismic tomography
Y1  - 2011
U6  - https://doi.org/10.1029/2011GC003678
SN  - 1525-2027
VL  - 12
IS  - 3-4
PB  - American Geophysical Union
CY  - Washington
ER  - 
TY  - JOUR
A1  - Becken, Michael
A1  - Ritter, Oliver
A1  - Bedrosian, Paul A.
A1  - Weckmann, Ute
T1  - Correlation between deep fluids, tremor and creep along the central San Andreas fault
JF  - Nature : the international weekly journal of science
N2  - The seismicity pattern along the San Andreas fault near Parkfield and Cholame, California, varies distinctly over a length of only fifty kilometres. Within the brittle crust, the presence of frictionally weak minerals, fault-weakening high fluid pressures and chemical weakening are considered possible causes of an anomalously weak fault northwest of Parkfield(1-4). Non-volcanic tremor from lower-crustal and upper-mantle depths(5-7) is most pronounced about thirty kilometres southeast of Parkfield and is thought to be associated with high pore-fluid pressures at depth(8). Here we present geophysical evidence of fluids migrating into the creeping section of the San Andreas fault that seem to originate in the region of the uppermost mantle that also stimulates tremor, and evidence that along-strike variations in tremor activity and amplitude are related to strength variations in the lower crust and upper mantle. Interconnected fluids can explain a deep zone of anomalously low electrical resistivity that has been imaged by magnetotelluric data southwest of the Parkfield-Cholame segment. Near Cholame, where fluids seem to be trapped below a high-resistivity cap, tremor concentrates adjacent to the inferred fluids within a mechanically strong zone of high resistivity. By contrast, sub-vertical zones of low resistivity breach the entire crust near the drill hole of the San Andreas Fault Observatory at Depth, northwest of Parkfield, and imply pathways for deep fluids into the eastern fault block, coincident with a mechanically weak crust and the lower tremor amplitudes in the lower crust. Fluid influx to the fault system is consistent with hypotheses of fault-weakening high fluid pressures in the brittle crust.
Y1  - 2011
U6  - https://doi.org/10.1038/nature10609
SN  - 0028-0836
VL  - 480
IS  - 7375
SP  - 87
EP  - U248
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Aliu, E.
A1  - Aune, T.
A1  - Beilicke, M.
A1  - Benbow, W.
A1  - Boettcher, Markus
A1  - Bouvier, A.
A1  - Bradbury, S. M.
A1  - Buckley, J. H.
A1  - Bugaev, V.
A1  - Cannon, A.
A1  - Cesarini, A.
A1  - Ciupik, L.
A1  - Connolly, M. P.
A1  - Cui, W.
A1  - Decerprit, G.
A1  - Dickherber, R.
A1  - Duke, C.
A1  - Errando, M.
A1  - Falcone, A.
A1  - Feng, Q.
A1  - Finnegan, G.
A1  - Fortson, L.
A1  - Furniss, A.
A1  - Galante, N.
A1  - Gall, D.
A1  - Gillanders, G. H.
A1  - Godambe, S.
A1  - Griffin, S.
A1  - Grube, J.
A1  - Gyuk, G.
A1  - Hanna, D.
A1  - Hivick, B.
A1  - Holder, J.
A1  - Huan, H.
A1  - Hughes, G.
A1  - Hui, C. M.
A1  - Humensky, T. B.
A1  - Kaaret, P.
A1  - Karlsson, N.
A1  - Kertzman, M.
A1  - Kieda, D.
A1  - Krawczynski, H.
A1  - Krennrich, F.
A1  - Maier, G.
A1  - Majumdar, P.
A1  - McArthur, S.
A1  - McCann, A.
A1  - Moriarty, P.
A1  - Mukherjee, R.
A1  - Nelson, T.
A1  - Ong, R. A.
A1  - Orr, M.
A1  - Otte, A. N.
A1  - Park, N.
A1  - Perkins, J. S.
A1  - Pichel, A.
A1  - Pohl, Martin
A1  - Prokoph, H.
A1  - Quinn, J.
A1  - Ragan, K.
A1  - Reyes, L. C.
A1  - Reynolds, P. T.
A1  - Roache, E.
A1  - Rose, H. J.
A1  - Ruppel, J.
A1  - Saxon, D. B.
A1  - Sembroski, G. H.
A1  - Skole, C.
A1  - Smith, A. W.
A1  - Staszak, D.
A1  - Tesic, G.
A1  - Theiling, M.
A1  - Thibadeau, S.
A1  - Tsurusaki, K.
A1  - Tyler, J.
A1  - Varlotta, A.
A1  - Vassiliev, V. V.
A1  - Wakely, S. P.
A1  - Weekes, T. C.
A1  - Weinstein, A.
A1  - Williams, D. A.
A1  - Zitzer, B.
A1  - Ciprini, S.
A1  - Fumagalli, M.
A1  - Kaplan, K.
A1  - Paneque, D.
A1  - Prochaska, J. X.
T1  - Multiwavelenght observations of the previously unidentified blzar RX J0648.7+1516
JF  - The astrophysical journal : an international review of spectroscopy and astronomical physics
N2  - We report on the VERITAS discovery of very high energy (VHE) gamma-ray emission above 200 GeV from the high-frequency-peaked BL Lac (HBL) object RX J0648.7+1516 (GB J0648+1516), associated with 1FGL J0648.8+1516. The photon spectrum above 200 GeV is fitted by a power law dN/dE = F-0(E/E-0)(-Gamma) with a photon index Gamma of 4.4 +/- 0.8(stat) +/- 0.3(syst) and a flux normalization F-0 of (2.3 +/- 0.5(stat) +/- 1.2(sys)) x 10(-11) TeV-1 cm(-2) s(-1) with E-0 = 300 GeV. No VHE variability is detected during VERITAS observations of RX J0648.7+1516 between 2010 March 4 and April 15. Following the VHE discovery, the optical identification and spectroscopic redshift were obtained using the Shane 3 m Telescope at the Lick Observatory, showing the unidentified object to be a BL Lac type with a redshift of z = 0.179. Broadband multiwavelength observations contemporaneous with the VERITAS exposure period can be used to subclassify the blazar as an HBL object, including data from the MDM observatory, Swift-UVOT, and X-Ray Telescope, and continuous monitoring at photon energies above 1 GeV from the Fermi Large Area Telescope (LAT). We find that in the absence of undetected, high-energy rapid variability, the one-zone synchrotron self-Compton (SSC) model overproduces the high-energy gamma-ray emission measured by the Fermi-LAT over 2.3 years. The spectral energy distribution can be parameterized satisfactorily with an external-Compton or lepto-hadronic model, which have two and six additional free parameters, respectively, compared to the one-zone SSC model.
KW  - BL Lacertae objects: individual (RX J0648.7+1516, 1FGL J0648.8+1516, VER J0648+152)
KW  - gamma rays: galaxies
Y1  - 2011
U6  - https://doi.org/10.1088/0004-637X/742/2/127
SN  - 0004-637X
VL  - 742
IS  - 2
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  - 
TY  - JOUR
A1  - Acciari, V. A.
A1  - Aliu, E.
A1  - Araya, M.
A1  - Arlen, T.
A1  - Aune, T.
A1  - Beilicke, M.
A1  - Benbow, W.
A1  - Bradbury, S. M.
A1  - Buckley, J. H.
A1  - Bugaev, V.
A1  - Byrum, K.
A1  - Cannon, A.
A1  - Cesarini, A.
A1  - Ciupik, L.
A1  - Collins-Hughes, E.
A1  - Cui, W.
A1  - Dickherber, R.
A1  - Duke, C.
A1  - Falcone, A.
A1  - Finley, J. P.
A1  - Fortson, L.
A1  - Furniss, A.
A1  - Galante, N.
A1  - Gall, D.
A1  - Godambe, S.
A1  - Griffin, S.
A1  - Guenette, R.
A1  - Gyuk, G.
A1  - Hanna, D.
A1  - Holder, J.
A1  - Hughes, G.
A1  - Hui, C. M.
A1  - Humensky, T. B.
A1  - Imran, A.
A1  - Kaaret, P.
A1  - Kertzman, M.
A1  - Krawczynski, H.
A1  - Krennrich, F.
A1  - Madhavan, A. S.
A1  - Maier, G.
A1  - Majumdar, P.
A1  - McArthur, S.
A1  - Moriarty, P.
A1  - Ong, R. A.
A1  - Otte, A. N.
A1  - Pandel, D.
A1  - Park, N.
A1  - Perkins, J. S.
A1  - Pohl, Martin
A1  - Prokoph, H.
A1  - Quinn, J.
A1  - Ragan, K.
A1  - Reyes, L. C.
A1  - Reynolds, P. T.
A1  - Roache, E.
A1  - Rose, H. J.
A1  - Saxon, D. B.
A1  - Sembroski, G. H.
A1  - Sentuerk, G. D.
A1  - Smith, A. W.
A1  - Tesic, G.
A1  - Theiling, M.
A1  - Thibadeau, S.
A1  - Varlotta, A.
A1  - Vincent, S.
A1  - Vivier, M.
A1  - Wakely, S. P.
A1  - Ward, J. E.
A1  - Weekes, T. C.
A1  - Weinstein, A.
A1  - Weisgarber, T.
A1  - Weng, S.
A1  - Williams, D. A.
A1  - Wood, M.
A1  - Zitzer, B.
T1  - Gamma-ray observations of the Be/Pulsar binary 1A 0535+262 during a Giant X-Ray outburst
JF  - The astrophysical journal : an international review of spectroscopy and astronomical physics
N2  - Giant X-ray outbursts, with luminosities of about 10(37) erg s(-1), are observed roughly every five years from the nearby Be/pulsar binary 1A 0535+262. In this article, we present observations of the source with VERITAS at very high energies (VHEs; E > 100 GeV) triggered by the X-ray outburst in 2009 December. The observations started shortly after the onset of the outburst and provided comprehensive coverage of the episode, as well as the 111 day binary orbit. No VHE emission is evident at any time. We also examined data from the contemporaneous observations of 1A 0535+262 with the Fermi/Large Area Telescope at high-energy photons (E > 0.1 GeV) and failed to detect the source at GeV energies. The X-ray continua measured with the Swift/X-Ray Telescope and the RXTE/PCA can be well described by the combination of blackbody and Comptonized emission from thermal electrons. Therefore, the gamma-ray and X-ray observations suggest the absence of a significant population of non-thermal particles in the system. This distinguishes 1A 0535+262 from those Be X-ray binaries (such as PSR B1259-63 and LS I +61 degrees 303) that have been detected at GeV-TeV energies. We discuss the implications of the results on theoretical models.
KW  - acceleration of particles
KW  - binaries: general
KW  - gamma rays: general
KW  - stars: individual (1A 0535+262)
Y1  - 2011
U6  - https://doi.org/10.1088/0004-637X/733/2/96
SN  - 0004-637X
VL  - 733
IS  - 2
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  - 
TY  - JOUR
A1  - Acciari, V. A.
A1  - Aliu, E.
A1  - Arlen, T.
A1  - Aune, T.
A1  - Beilicke, M.
A1  - Benbow, W.
A1  - Bradbury, S. M.
A1  - Buckley, J. H.
A1  - Bugaev, V.
A1  - Byrum, K.
A1  - Cannon, A.
A1  - Cesarini, A.
A1  - Christiansen, J. L.
A1  - Ciupik, L.
A1  - Collins-Hughes, E.
A1  - Connolly, M. P.
A1  - Cui, W.
A1  - Duke, C.
A1  - Errando, M.
A1  - Falcone, A.
A1  - Finley, J. P.
A1  - Finnegan, G.
A1  - Fortson, L.
A1  - Furniss, A.
A1  - Galante, N.
A1  - Gall, D.
A1  - Godambe, S.
A1  - Griffin, S.
A1  - Grube, J.
A1  - Guenette, R.
A1  - Gyuk, G.
A1  - Hanna, D.
A1  - Holder, J.
A1  - Hughes, G.
A1  - Hui, C. M.
A1  - Humensky, T. B.
A1  - Jackson, D. J.
A1  - Kaaret, P.
A1  - Karlsson, N.
A1  - Kertzman, M.
A1  - Kieda, D.
A1  - Krawczynski, H.
A1  - Krennrich, F.
A1  - Lang, M. J.
A1  - Madhavan, A. S.
A1  - Maier, G.
A1  - McArthur, S.
A1  - McCann, A.
A1  - Moriarty, P.
A1  - Newbold, M. D.
A1  - Ong, R. A.
A1  - Orr, M.
A1  - Otte, A. N.
A1  - Park, N.
A1  - Perkins, J. S.
A1  - Pohl, Martin
A1  - Prokoph, H.
A1  - Quinn, J.
A1  - Ragan, K.
A1  - Reyes, L. C.
A1  - Reynolds, P. T.
A1  - Roache, E.
A1  - Rose, H. J.
A1  - Ruppel, J.
A1  - Saxon, D. B.
A1  - Schroedter, M.
A1  - Sembroski, G. H.
A1  - Sentuerk, G. D.
A1  - Smith, A. W.
A1  - Staszak, D.
A1  - Swordy, S. P.
A1  - Tesic, G.
A1  - Theiling, M.
A1  - Thibadeau, S.
A1  - Tsurusaki, K.
A1  - Varlotta, A.
A1  - Vassiliev, V. V.
A1  - Vincent, S.
A1  - Vivier, M.
A1  - Wakely, S. P.
A1  - Ward, J. E.
A1  - Weekes, T. C.
A1  - Weinstein, A.
A1  - Weisgarber, T.
A1  - Williams, D. A.
A1  - Wood, M.
T1  - Veritas observations of gamma-ray bursts detected by swift
JF  - The astrophysical journal : an international review of spectroscopy and astronomical physics
N2  - We present the results of 16 Swift-triggered Gamma-ray burst (GRB) follow-up observations taken with the Very Energetic Radiation Imaging Telescope Array System (VERITAS) telescope array from 2007 January to 2009 June. The median energy threshold and response time of these observations were 260 GeV and 320 s, respectively. Observations had an average duration of 90 minutes. Each burst is analyzed independently in two modes: over the whole duration of the observations and again over a shorter timescale determined by the maximum VERITAS sensitivity to a burst with a t(-1.5) time profile. This temporal model is characteristic of GRB afterglows with high-energy, long-lived emission that have been detected by the Large Area Telescope on board the Fermi satellite. No significant very high energy (VHE) gamma-ray emission was detected and upper limits above the VERITAS threshold energy are calculated. The VERITAS upper limits are corrected for gamma-ray extinction by the extragalactic background light and interpreted in the context of the keV emission detected by Swift. For some bursts the VHE emission must have less power than the keV emission, placing constraints on inverse Compton models of VHE emission.
KW  - astroparticle physics
KW  - gamma-ray burst: general
Y1  - 2011
U6  - https://doi.org/10.1088/0004-637X/743/1/62
SN  - 0004-637X
VL  - 743
IS  - 1
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  - 
TY  - GEN
A1  - Federici, S.
A1  - Pohl, Martin
A1  - Ruppel, J.
A1  - Telezhinsky, Igor O.
A1  - Hofmann, Werner
A1  - Martinez, M.
A1  - Knapp, J.
T1  - Design concepts for the Cherenkov Telescope Array CTA
BT  - an advanced facility for ground-based high-energy gamma-ray astronomy
T2  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - Ground-based gamma-ray astronomy has had a major breakthrough with the impressive results obtained using systems of imaging atmospheric Cherenkov telescopes. Ground-based gamma-ray astronomy has a huge potential in astrophysics, particle physics and cosmology. CTA is an international initiative to build the next generation instrument, with a factor of 5-10 improvement in sensitivity in the 100 GeV-10 TeV range and the extension to energies well below 100 GeV and above 100 TeV. CTA will consist of two arrays (one in the north, one in the south) for full sky coverage and will be operated as open observatory. The design of CTA is based on currently available technology. This document reports on the status and presents the major design concepts of CTA.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1325 
KW  - ground based gamma ray astronomy
KW  - next generation Cherenkov telescopes
KW  - design concepts
Y1  - 2011
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-430149
SN  - 1866-8372
VL  - 32
IS  - 1325
ER  - 
TY  - JOUR
A1  - Acciari, V. A.
A1  - Aliu, E.
A1  - Arlen, T.
A1  - Aune, T.
A1  - Beilicke, M.
A1  - Benbow, W.
A1  - Bradbury, S. M.
A1  - Buckley, J. H.
A1  - Bugaev, V.
A1  - Byrum, K.
A1  - Cannon, A.
A1  - Cesarini, A.
A1  - Ciupik, L.
A1  - Collins-Hughes, E.
A1  - Cui, W.
A1  - Dickherber, R.
A1  - Duke, C.
A1  - Errando, M.
A1  - Finley, J. P.
A1  - Finnegan, G.
A1  - Fortson, L.
A1  - Furniss, A.
A1  - Galante, N.
A1  - Gall, D.
A1  - Gillanders, G. H.
A1  - Godambe, S.
A1  - Griffin, S.
A1  - Grube, J.
A1  - Guenette, R.
A1  - Gyuk, G.
A1  - Hanna, D.
A1  - Holder, J.
A1  - Hughes, J. P.
A1  - Hui, C. M.
A1  - Humensky, T. B.
A1  - Kaaret, P.
A1  - Karlsson, N.
A1  - Kertzman, M.
A1  - Kieda, D.
A1  - Krawczynski, H.
A1  - Krennrich, F.
A1  - Lang, M. J.
A1  - LeBohec, S.
A1  - Madhavan, A. S.
A1  - Maier, G.
A1  - Majumdar, P.
A1  - McArthur, S.
A1  - McCann, A.
A1  - Moriarty, P.
A1  - Mukherjee, R.
A1  - Ong, R. A.
A1  - Orr, M.
A1  - Otte, A. N.
A1  - Pandel, D.
A1  - Park, N. H.
A1  - Perkins, J. S.
A1  - Pohl, Martin
A1  - Quinn, J.
A1  - Ragan, K.
A1  - Reyes, L. C.
A1  - Reynolds, P. T.
A1  - Roache, E.
A1  - Rose, H. J.
A1  - Saxon, D. B.
A1  - Schroedter, M.
A1  - Sembroski, G. H.
A1  - Senturk, G. Demet
A1  - Slane, P.
A1  - Smith, A. W.
A1  - Tesic, G.
A1  - Theiling, M.
A1  - Thibadeau, S.
A1  - Tsurusaki, K.
A1  - Varlotta, A.
A1  - Vassiliev, V. V.
A1  - Vincent, S.
A1  - Vivier, M.
A1  - Wakely, S. P.
A1  - Ward, J. E.
A1  - Weekes, T. C.
A1  - Weinstein, A.
A1  - Weisgarber, T.
A1  - Williams, D. A.
A1  - Wood, M.
A1  - Zitzer, B.
T1  - Discovery of OF TeV Gamma-Ray emission from tycho's supernova remnant
JF  - The astrophysical journal : an international review of spectroscopy and astronomical physics ; Part 2, Letters
N2  - We report the discovery of TeV gamma-ray emission from the Type Ia supernova remnant (SNR) G120.1+1.4, known as Tycho's SNR. Observations performed in the period 2008-2010 with the VERITAS ground-based gamma-ray observatory reveal weak emission coming from the direction of the remnant, compatible with a point source located at 00(h)25(m)27(s).0, +64 degrees 10'50 '' (J2000). The TeV photon spectrum measured by VERITAS can be described with a power law dN/dE = C(E/3.42 TeV)(-Gamma) with Gamma = 1.95 +/- 0.51(stat) +/- 0.30(sys) and C = (1.55 +/- 0.43(stat) +/- 0.47(sys)) x 10(-14) cm(-2) s(-1) TeV-1. The integral flux above 1 TeV corresponds to similar to 0.9% of the steady Crab Nebula emission above the same energy, making it one of the weakest sources yet detected in TeV gamma rays. We present both leptonic and hadronic models that can describe the data. The lowest magnetic field allowed in these models is similar to 80 mu G, which may be interpreted as evidence for magnetic field amplification.
KW  - gamma rays: general
KW  - ISM: individual objects (G120.1+01.4, Tycho=VER J0025+641)
Y1  - 2011
U6  - https://doi.org/10.1088/2041-8205/730/2/L20
SN  - 2041-8205
VL  - 730
IS  - 2
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  - 
TY  - JOUR
A1  - Aliu, E.
A1  - Arlen, T.
A1  - Aune, T.
A1  - Beilicke, M.
A1  - Benbow, W.
A1  - Boettcher, Markus
A1  - Bouvier, A.
A1  - Bradbury, S. M.
A1  - Buckley, J. H.
A1  - Bugaev, V.
A1  - Cannon, A.
A1  - Cesarini, A.
A1  - Ciupik, L.
A1  - Collins-Hughes, E.
A1  - Connolly, M. P.
A1  - Cui, W.
A1  - Dickherber, R.
A1  - Errando, M.
A1  - Falcone, A.
A1  - Finley, J. P.
A1  - Fortson, L.
A1  - Furniss, A.
A1  - Galante, N.
A1  - Gall, D.
A1  - Gillanders, G. H.
A1  - Godambe, S.
A1  - Griffin, S.
A1  - Grube, J.
A1  - Gyuk, G.
A1  - Hanna, D.
A1  - Holder, J.
A1  - Huan, H.
A1  - Hughes, G.
A1  - Hui, C. M.
A1  - Humensky, T. B.
A1  - Kaaret, P.
A1  - Karlsson, N.
A1  - Kertzman, M.
A1  - Kieda, D.
A1  - Krawczynski, H.
A1  - Krennrich, F.
A1  - Madhavan, A. S.
A1  - Maier, G.
A1  - Majumdar, P.
A1  - McArthur, S.
A1  - McCann, A.
A1  - Moriarty, P.
A1  - Mukherjee, R.
A1  - Ong, R. A.
A1  - Orr, M.
A1  - Otte, A. N.
A1  - Park, N.
A1  - Perkins, J. S.
A1  - Pichel, A.
A1  - Pohl, Martin
A1  - Prokoph, H.
A1  - Quinn, J.
A1  - Ragan, K.
A1  - Reyes, L. C.
A1  - Reynolds, P. T.
A1  - Roache, E.
A1  - Rose, H. J.
A1  - Ruppel, J.
A1  - Saxon, D. B.
A1  - Schroedter, M.
A1  - Sembroski, G. H.
A1  - Skole, C.
A1  - Smith, A. W.
A1  - Staszak, D.
A1  - Tesic, G.
A1  - Theiling, M.
A1  - Thibadeau, S.
A1  - Tsurusaki, K.
A1  - Tyler, J.
A1  - Varlotta, A.
A1  - Vincent, S.
A1  - Vivier, M.
A1  - Wakely, S. P.
A1  - Ward, J. E.
A1  - Weinstein, A.
A1  - Weisgarber, T.
A1  - Williams, D. A.
T1  - Veritas observations of unusual extragalactic transient swift J164449.3+573451
JF  - The astrophysical journal : an international review of spectroscopy and astronomical physics ; Part 2, Letters
N2  - We report on very high energy (>100 GeV) gamma-ray observations of Swift J164449.3+573451, an unusual transient object first detected by the Swift Observatory and later detected by multiple radio, optical, and X-ray observatories. A total exposure of 28 hr was obtained on Swift J164449.3+573451 with the Very Energetic Radiation Imaging Telescope Array System ( VERITAS) during 2011 March 28-April 15. We do not detect the source and place a differential upper limit on the emission at 500 GeV during these observations of 1.4 x 10(-12) erg cm(-2) s(-1) (99% confidence level). We also present time-resolved upper limits and use a flux limit averaged over the X-ray flaring period to constrain various emission scenarios that can accommodate both the radio-through-X-ray emission detected from the source and the lack of detection by VERITAS.
KW  - accretion, accretion disks
KW  - galaxies: active
KW  - gamma rays: galaxies
KW  - radiation mechanisms: non-thermal
Y1  - 2011
U6  - https://doi.org/10.1088/2041-8205/738/2/L30
SN  - 2041-8205
VL  - 738
IS  - 2
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  - 
TY  - JOUR
A1  - Aliu, E.
A1  - Arlen, T.
A1  - Aune, T.
A1  - Beilicke, M.
A1  - Benbow, W.
A1  - Bouvier, A.
A1  - Bradbury, S. M.
A1  - Buckley, J. H.
A1  - Bugaev, V.
A1  - Byrum, K.
A1  - Cannon, A.
A1  - Cesarini, A.
A1  - Christiansen, J. L.
A1  - Ciupik, L.
A1  - Collins-Hughes, E.
A1  - Connolly, M. P.
A1  - Cui, W.
A1  - Dickherber, R.
A1  - Duke, C.
A1  - Errando, M.
A1  - Falcone, A.
A1  - Finley, J. P.
A1  - Finnegan, G.
A1  - Fortson, L.
A1  - Furniss, A.
A1  - Galante, N.
A1  - Gall, D.
A1  - Gibbs, K.
A1  - Gillanders, G. H.
A1  - Godambe, S.
A1  - Griffin, S.
A1  - Grube, J.
A1  - Guenette, R.
A1  - Gyuk, G.
A1  - Hanna, D.
A1  - Holder, J.
A1  - Huan, H.
A1  - Hughes, G.
A1  - Hui, C. M.
A1  - Humensky, T. B.
A1  - Imran, A.
A1  - Kaaret, P.
A1  - Karlsson, N.
A1  - Kertzman, M.
A1  - Kieda, D.
A1  - Krawczynski, H.
A1  - Krennrich, F.
A1  - Lang, M. J.
A1  - Lyutikov, M.
A1  - Madhavan, A. S.
A1  - Maier, G.
A1  - Majumdar, P.
A1  - McArthur, S.
A1  - McCann, A.
A1  - McCutcheon, M.
A1  - Moriarty, P.
A1  - Mukherjee, R.
A1  - Nunez, P.
A1  - Ong, R. A.
A1  - Orr, M.
A1  - Otte, A. N.
A1  - Park, N.
A1  - Perkins, J. S.
A1  - Pizlo, F.
A1  - Pohl, Martin
A1  - Prokoph, H.
A1  - Quinn, J.
A1  - Ragan, K.
A1  - Reyes, L. C.
A1  - Reynolds, P. T.
A1  - Roache, E.
A1  - Rose, H. J.
A1  - Ruppel, J.
A1  - Saxon, D. B.
A1  - Schroedter, M.
A1  - Sembroski, G. H.
A1  - Sentuerk, G. D.
A1  - Smith, A. W.
A1  - Staszak, D.
A1  - Tesic, G.
A1  - Theiling, M.
A1  - Thibadeau, S.
A1  - Tsurusaki, K.
A1  - Tyler, J.
A1  - Varlotta, A.
A1  - Vassiliev, V. V.
A1  - Vincent, S.
A1  - Vivier, M.
A1  - Wakely, S. P.
A1  - Ward, J. E.
A1  - Weekes, T. C.
A1  - Weinstein, A.
A1  - Weisgarber, T.
A1  - Williams, D. A.
A1  - Zitzer, B.
T1  - Detection of pulsed Gamma Rays Above 100 GeV from the Crab Pulsar
JF  - Science
N2  - We report the detection of pulsed gamma rays from the Crab pulsar at energies above 100 giga-electron volts (GeV) with the Very Energetic Radiation Imaging Telescope Array System (VERITAS) array of atmospheric Cherenkov telescopes. The detection cannot be explained on the basis of current pulsar models. The photon spectrum of pulsed emission between 100 mega-electron volts and 400 GeV is described by a broken power law that is statistically preferred over a power law with an exponential cutoff. It is unlikely that the observation can be explained by invoking curvature radiation as the origin of the observed gamma rays above 100 GeV. Our findings require that these gamma rays be produced more than 10 stellar radii from the neutron star.
Y1  - 2011
U6  - https://doi.org/10.1126/science.1208192
SN  - 0036-8075
VL  - 334
IS  - 6052
SP  - 69
EP  - 72
PB  - American Assoc. for the Advancement of Science
CY  - Washington
ER  - 
TY  - JOUR
A1  - Ackermann, Margit
A1  - Ajello, M.
A1  - Allafort, A. J.
A1  - Baldini, L.
A1  - Ballet, J.
A1  - Barbiellini, G.
A1  - Bastieri, D.
A1  - Belfiore, A.
A1  - Bellazzini, R.
A1  - Berenji, B.
A1  - Blandford, R. D.
A1  - Bloom, E. D.
A1  - Bonamente, E.
A1  - Borgland, A. W.
A1  - Bottacini, E.
A1  - Brigida, M.
A1  - Bruel, P.
A1  - Buehler, R.
A1  - Buson, S.
A1  - Caliandro, G. A.
A1  - Cameron, R. A.
A1  - Caraveo, P. A.
A1  - Casandjian, J. M.
A1  - Cecchi, C.
A1  - Chekhtman, A.
A1  - Cheung, C. C.
A1  - Chiang, J.
A1  - Ciprini, S.
A1  - Claus, R.
A1  - Cohen-Tanugi, J.
A1  - de Angelis, A.
A1  - de Palma, F.
A1  - Dermer, C. D.
A1  - do Couto e Silva, E.
A1  - Drell, P. S.
A1  - Dumora, D.
A1  - Favuzzi, C.
A1  - Fegan, S. J.
A1  - Focke, W. B.
A1  - Fortin, P.
A1  - Fukazawa, Y.
A1  - Fusco, P.
A1  - Gargano, F.
A1  - Germani, S.
A1  - Giglietto, N.
A1  - Giordano, F.
A1  - Giroletti, M.
A1  - Glanzman, T.
A1  - Godfrey, G.
A1  - Grenier, I. A.
A1  - Guillemot, L.
A1  - Guiriec, S.
A1  - Hadasch, D.
A1  - Hanabata, Y.
A1  - Harding, A. K.
A1  - Hayashida, M.
A1  - Hayashi, K.
A1  - Hays, E.
A1  - Johannesson, G.
A1  - Johnson, A. S.
A1  - Kamae, T.
A1  - Katagiri, H.
A1  - Kataoka, J.
A1  - Kerr, M.
A1  - Knoedlseder, J.
A1  - Kuss, M.
A1  - Lande, J.
A1  - Latronico, L.
A1  - Lee, S. -H.
A1  - Longo, F.
A1  - Loparco, F.
A1  - Lott, B.
A1  - Lovellette, M. N.
A1  - Lubrano, P.
A1  - Martin, P.
A1  - Mazziotta, Mario Nicola
A1  - McEnery, J. E.
A1  - Mehault, J.
A1  - Michelson, P. F.
A1  - Mitthumsiri, W.
A1  - Mizuno, T.
A1  - Monte, C.
A1  - Monzani, M. E.
A1  - Morselli, A.
A1  - Moskalenko, I. V.
A1  - Murgia, S.
A1  - Naumann-Godo, M.
A1  - Nolan, P. L.
A1  - Norris, J. P.
A1  - Nuss, E.
A1  - Ohsugi, T.
A1  - Okumura, A.
A1  - Orlando, E.
A1  - Ormes, J. F.
A1  - Ozaki, M.
A1  - Paneque, D.
A1  - Parent, D.
A1  - Pesce-Rollins, M.
A1  - Pierbattista, M.
A1  - Piron, F.
A1  - Pohl, Martin
A1  - Prokhorov, D.
A1  - Raino, S.
A1  - Rando, R.
A1  - Razzano, M.
A1  - Reposeur, T.
A1  - Ritz, S.
A1  - Parkinson, P. M. Saz
A1  - Sgro, C.
A1  - Siskind, E. J.
A1  - Smith, P. D.
A1  - Spinelli, P.
A1  - Strong, A. W.
A1  - Takahashi, H.
A1  - Tanaka, T.
A1  - Thayer, J. G.
A1  - Thayer, J. B.
A1  - Thompson, D. J.
A1  - Tibaldo, L.
A1  - Torres, D. F.
A1  - Tosti, G.
A1  - Tramacere, A.
A1  - Troja, E.
A1  - Uchiyama, Y.
A1  - Vandenbroucke, J.
A1  - Vasileiou, V.
A1  - Vianello, G.
A1  - Vitale, V.
A1  - Waite, A. P.
A1  - Wang, P.
A1  - Winer, B. L.
A1  - Wood, K. S.
A1  - Yang, Z.
A1  - Zimmer, S.
A1  - Bontemps, S.
T1  - A cocoon of freshly accelerated cosmic rays detected by fermi in the cygnus superbubble
JF  - Science
N2  - The origin of Galactic cosmic rays is a century-long puzzle. Indirect evidence points to their acceleration by supernova shockwaves, but we know little of their escape from the shock and their evolution through the turbulent medium surrounding massive stars. Gamma rays can probe their spreading through the ambient gas and radiation fields. The Fermi Large Area Telescope (LAT) has observed the star-forming region of Cygnus X. The 1- to 100-gigaelectronvolt images reveal a 50-parsec-wide cocoon of freshly accelerated cosmic rays that flood the cavities carved by the stellar winds and ionization fronts from young stellar clusters. It provides an example to study the youth of cosmic rays in a superbubble environment before they merge into the older Galactic population.
Y1  - 2011
U6  - https://doi.org/10.1126/science.1210311
SN  - 0036-8075
VL  - 334
IS  - 6059
SP  - 1103
EP  - 1107
PB  - American Assoc. for the Advancement of Science
CY  - Washington
ER  - 
TY  - JOUR
A1  - Donges, Jonathan
A1  - Donner, Reik Volker
A1  - Trauth, Martin H.
A1  - Marwan, Norbert
A1  - Schellnhuber, Hans Joachim
A1  - Kurths, Jürgen
T1  - Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution
JF  - Proceedings of the National Academy of Sciences of the United States of America
N2  - Potential paleoclimatic driving mechanisms acting on human evolution present an open problem of cross-disciplinary scientific interest. The analysis of paleoclimate archives encoding the environmental variability in East Africa during the past 5 Ma has triggered an ongoing debate about possible candidate processes and evolutionary mechanisms. In this work, we apply a nonlinear statistical technique, recurrence network analysis, to three distinct marine records of terrigenous dust flux. Our method enables us to identify three epochs with transitions between qualitatively different types of environmental variability in North and East Africa during the (i) Middle Pliocene (3.35-3.15 Ma B. P.), (ii) Early Pleistocene (2.25-1.6 Ma B. P.), and (iii) Middle Pleistocene (1.1-0.7 Ma B. P.). A deeper examination of these transition periods reveals potential climatic drivers, including (i) large-scale changes in ocean currents due to a spatial shift of the Indonesian throughflow in combination with an intensification of Northern Hemisphere glaciation, (ii) a global reorganization of the atmospheric Walker circulation induced in the tropical Pacific and Indian Ocean, and (iii) shifts in the dominating temporal variability pattern of glacial activity during the Middle Pleistocene, respectively. A reexamination of the available fossil record demonstrates statistically significant coincidences between the detected transition periods and major steps in hominin evolution. This result suggests that the observed shifts between more regular and more erratic environmental variability may have acted as a trigger for rapid change in the development of humankind in Africa.
KW  - African climate
KW  - Plio-Pleistocene
KW  - climate-driven evolution
KW  - dynamical transitions
KW  - nonlinear time series analysis
Y1  - 2011
U6  - https://doi.org/10.1073/pnas.1117052108
SN  - 0027-8424
VL  - 108
IS  - 51
SP  - 20422
EP  - 20427
PB  - National Acad. of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Delahaye, T.
A1  - Fiasson, A.
A1  - Pohl, Martin
A1  - Salati, P.
T1  - The GeV-TeV Galactic gamma-ray diffuse emission I. Uncertainties in the predictions of the hadronic component
JF  - Astronomy and astrophysics : an international weekly journal
N2  - Context. The Galactic gamma-ray diffuse emission is currently observed in the GeV-TeV energy range with unprecedented accuracy by the Fermi satellite. Understanding this component is crucial because it provides a background to many different signals, such as extragalactic sources or annihilating dark matter. It is timely to reinvestigate how it is calculated and to assess the various uncertainties that are likely to affect the accuracy of the predictions.
 Aims. The Galactic gamma-ray diffuse emission is mostly produced above a few GeV by the interactions of cosmic ray primaries impinging on the interstellar material. The theoretical error on that component is derived by exploring various potential sources of uncertainty. Particular attention is paid to cosmic ray propagation. Nuclear cross sections, the proton and helium fluxes at the Earth's position, the Galactic radial profile of supernova remnants, and the hydrogen distribution can also severely affect the signal.
 Methods. The propagation of cosmic ray species throughout the Galaxy is described in the framework of a semi-analytic two-zone diffusion/convection model. The gamma-ray flux is reliably and quickly determined. This allows conversion of the constraints set by the boron-to-carbon data into a theoretical uncertainty on the diffuse emission. New deconvolutions of the HI and CO sky maps are also used to get the hydrogen distribution within the Galaxy.
 Results. The thickness of the cosmic ray diffusive halo is found to have a significant effect on the Galactic gamma-ray diffuse emission, while the interplay between diffusion and convection has little influence on the signal. The uncertainties related to nuclear cross sections and to the primary cosmic ray fluxes at the Earth are significant. The radial distribution of supernova remnants along the Galactic plane turns out to be a key ingredient. As expected, the predictions are extremely sensitive to the spatial distribution of hydrogen within the Milky Way.
 Conclusions. Most of the sources of uncertainty are likely to be reduced in the near future. The stress should be put (i) on better determination of the thickness of the cosmic ray diffusive halo; and (ii) on refined observations of the radial profile of supernova remnants.
KW  - gamma rays: diffuse background
KW  - cosmic rays
KW  - methods: analytical
KW  - gamma rays: ISM
Y1  - 2011
U6  - https://doi.org/10.1051/0004-6361/201116647
SN  - 0004-6361
VL  - 531
IS  - 4
PB  - EDP Sciences
CY  - Les Ulis
ER  - 
TY  - JOUR
A1  - Flad, Heinz-Jürgen
A1  - Harutyunyan, Gohar
A1  - Schneider, Reinhold
A1  - Schulze, Bert-Wolfgang
T1  - Explicit Green operators for quantum mechanical Hamiltonians
BT  - I. The hydrogen atom
JF  - Manuscripta mathematica
N2  - We study a new approach to determine the asymptotic behaviour of quantum many-particle systems near coalescence points of particles which interact via singular Coulomb potentials. This problem is of fundamental interest in electronic structure theory in order to establish accurate and efficient models for numerical simulations. Within our approach, coalescence points of particles are treated as embedded geometric singularities in the configuration space of electrons. Based on a general singular pseudo-differential calculus, we provide a recursive scheme for the calculation of the parametrix and corresponding Green operator of a nonrelativistic Hamiltonian. In our singular calculus, the Green operator encodes all the asymptotic information of the eigenfunctions. Explicit calculations and an asymptotic representation for the Green operator of the hydrogen atom and isoelectronic ions are presented.
Y1  - 2011
U6  - https://doi.org/10.1007/s00229-011-0429-x
SN  - 0025-2611
VL  - 135
IS  - 3-4
SP  - 497
EP  - 519
PB  - Springer
CY  - New York
ER  - 
TY  - JOUR
A1  - Blakesley, James C.
A1  - Schubert, Marcel
A1  - Steyrleuthner, Robert
A1  - Chen, Zhihua
A1  - Facchetti, Antonio
A1  - Neher, Dieter
T1  - Time-of-flight measurements and vertical transport in a high electron-mobility polymer
JF  - Applied physics letters
N2  - We investigate charge transport in a high-electron mobility polymer, poly(N, N-bis 2-octyldodecyl-naphthalene-1,4,5,8-bis dicarboximide-2,6-diyl-alt-5,5-2,2-bithiophene) [P(NDI2OD-T2), Polyera ActivInk (TM) N2200]. Time-of-flight measurements reveal electron mobilities approaching those measured in field-effect transistors, the highest ever recorded in a conjugated polymer using this technique. The modest temperature dependence and weak dispersion of the transients indicate low energetic disorder in this material. Steady-state electron-only current measurements reveal a barrier to injection of about 300 meV. We propose that this barrier is located within the P(NDI2OD-T2) film and arises from molecular orientation effects.
Y1  - 2011
U6  - https://doi.org/10.1063/1.3657827
SN  - 0003-6951
VL  - 99
IS  - 18
PB  - American Institute of Physics
CY  - Melville
ER  - 
TY  - JOUR
A1  - Turner, Sarah T.
A1  - Pingel, Patrick
A1  - Steyrleuthner, Robert
A1  - Crossland, Edward J. W.
A1  - Ludwigs, Sabine
A1  - Neher, Dieter
T1  - Quantitative analysis of bulk heterojunction films using linear absorption spectroscopy and solar cell performance
JF  - Advanced functional materials
N2  - A fundamental understanding of the relationship between the bulk morphology and device performance is required for the further development of bulk heterojunction organic solar cells. Here, non-optimized (chloroform cast) and nearly optimized (solvent-annealed o-dichlorobenzene cast) P3HT:PCBM blend films treated over a range of annealing temperatures are studied via optical and photovoltaic device measurements. Parameters related to the P3HT aggregate morphology in the blend are obtained through a recently established analytical model developed by F. C. Spano for the absorption of weakly interacting H-aggregates. Thermally induced changes are related to the glass transition range of the blend. In the chloroform prepared devices, the improvement in device efficiency upon annealing within the glass transition range can be attributed to the growth of P3HT aggregates, an overall increase in the percentage of chain crystallinity, and a concurrent increase in the hole mobilities. Films treated above the glass transition range show an increase in efficiency and fill factor not only associated with the change in chain crystallinity, but also with a decrease in the energetic disorder. On the other hand, the properties of the P3HT phase in the solvent-annealed o-dichlorobenzene cast blends are almost indistinguishable from those of the corresponding pristine P3HT layer and are only weakly affected by thermal annealing. Apparently, slow drying of the blend allows the P3HT chains to crystallize into large domains with low degrees of intra- and interchain disorder. This morphology appears to be most favorable for the efficient generation and extraction of charges.
KW  - Organic electronics
KW  - morphology
KW  - solar cells
KW  - mobility
KW  - absorption spectroscopy
Y1  - 2011
U6  - https://doi.org/10.1002/adfm.201101583
SN  - 1616-301X
VL  - 21
IS  - 24
SP  - 4640
EP  - 4652
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Di Giacomo, Domenico
A1  - Bindi, Dino
A1  - Parolai, Stefano
A1  - Oth, Adrien
T1  - Residual analysis of teleseismic P-wave energy magnitude estimates: inter- and intrastation variability
JF  - Geophysical journal international
N2  - P>Computing the magnitude of an earthquake requires correcting for the propagation effects from the source to the receivers. This is often accomplished by performing numerical simulations using a suitable Earth model. In this work, the energy magnitude M(e) is considered and its determination is performed using theoretical spectral amplitude decay functions over teleseismic distances based on the global Earth model AK135Q. Since the high frequency part (above the corner frequency) of the source spectrum has to be considered in computing M(e), the influence of propagation and site effects may not be negligible and they could bias the single station M(e) estimations. Therefore, in this study we assess the inter- and intrastation distributions of errors by considering the M(e) residuals computed for a large data set of earthquakes recorded at teleseismic distances by seismic stations deployed worldwide. To separate the inter- and intrastation contribution of errors, we apply a maximum likelihood approach to the M(e) residuals. We show that the interstation errors (describing a sort of site effect for a station) are within +/- 0.2 magnitude units for most stations and their spatial distribution reflects the expected lateral variation affecting the velocity and attenuation of the Earth's structure in the uppermost layers, not accounted for by the 1-D AK135Q model. The variance of the intrastation error distribution (describing the record-to-record component of variability) is larger than the interstation one (0.240 against 0.159), and the spatial distribution of the errors is not random but shows specific patterns depending on the source-to-station paths. The set of coefficients empirically determined may be used in the future to account for the heterogeneities of the real Earth not considered in the theoretical calculations of the spectral amplitude decay functions used to correct the recorded data for propagation effects.
KW  - Time series analysis
KW  - Earthquake source observations
KW  - Body waves
KW  - Site effects
KW  - Wave propagation
Y1  - 2011
U6  - https://doi.org/10.1111/j.1365-246X.2011.05019.x
SN  - 0956-540X
VL  - 185
IS  - 3
SP  - 1444
EP  - 1454
PB  - Wiley-Blackwell
CY  - Malden
ER  - 
TY  - JOUR
A1  - Rivera Villarreyes, C. A.
A1  - Baroni, Gabriele
A1  - Oswald, Sascha
T1  - Integral quantification of seasonal soil moisture changes in farmland by cosmic-ray neutrons
JF  - Hydrology and earth system sciences : HESS
N2  - Soil moisture at the plot or hill-slope scale is an important link between local vadose zone hydrology and catchment hydrology. However, so far only a few methods are on the way to close this gap between point measurements and remote sensing. One new measurement methodology that could determine integral soil moisture at this scale is the aboveground sensing of cosmic-ray neutrons, more precisely of ground albedo neutrons. The present study performed ground albedo neutron sensing (GANS) at an agricultural field in northern Germany. To test the method it was accompanied by other soil moisture measurements for a summer period with corn crops growing on the field and a later autumn-winter period without crops and a longer period of snow cover. Additionally, meteorological data and aboveground crop biomass were included in the evaluation. Hourly values of ground albedo neutron sensing showed a high statistical variability. Six-hourly values corresponded well with classical soil moisture measurements, after calibration based on one reference dry period and three wet periods of a few days each. Crop biomass seemed to influence the measurements only to minor degree, opposed to snow cover which has a more substantial impact on the measurements. The latter could be quantitatively related to a newly introduced field neutron ratio estimated from neutron counting rates of two energy ranges. Overall, our study outlines a procedure to apply the ground albedo neutron sensing method based on devices now commercially available, without the need for accompanying numerical simulations and suited for longer monitoring periods after initial calibration.
Y1  - 2011
U6  - https://doi.org/10.5194/hess-15-3843-2011
SN  - 1027-5606
VL  - 15
IS  - 12
SP  - 3843
EP  - 3859
PB  - Copernicus
CY  - Göttingen
ER  - 
TY  - JOUR
A1  - Balcke, Gerd U.
A1  - Hahn, M.
A1  - Oswald, Sascha
T1  - Nitrogen as an indicator of mass transfer during in-situ gas sparging
JF  - Journal of contaminant hydrology
N2  - Aiming at the stimulation of intrinsic microbial activity, pulses of pure oxygen or pressurized air were recurrently injected into groundwater polluted with chlorobenzene. To achieve well-controlled conditions and intensive sampling, a large, vertical underground tank was filled with the local unconfined sandy aquifer material. In the course of two individual gas injections, one using pure oxygen and one using pressurized air, the mass transfer of individual gas species between trapped gas phase and groundwater was studied. Field data on the dissolved gas composition in the groundwater were combined with a kinetic model on gas dissolution and transport in porous media. Phase mass transfer of individual gas components caused a temporary enrichment of nitrogen, and to a lower degree of methane, in trapped gas leading to the formation of excess dissolved nitrogen levels downgradient from the dissolving gas phase. By applying a novel gas sampling method for dissolved gases in groundwater it was shown that dissolved nitrogen can be used as a partitioning tracer to indicate complete gas dissolution in porous media.
KW  - Inter-phase mass transfer
KW  - Groundwater
KW  - Remediation
KW  - Gas sparging
KW  - Nitrogen
KW  - Methane
KW  - Kinetics
KW  - Bitterfeld
Y1  - 2011
U6  - https://doi.org/10.1016/j.jconhyd.2011.05.005
SN  - 0169-7722
VL  - 126
IS  - 1-2
SP  - 8
EP  - 18
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - BOOK
A1  - Schedler, Kuno
A1  - Proeller, Isabella
T1  - New Public Management
T3  - UTB ; 2132
N2  - New Public Management hat in den vergangenen Jahren die Ansätze und das Verständnis moderner Verwaltungsführung maßgebend beeinflusst.
Stossrichtungen und Grundanliegen dieses Modells wurden zum Teil in die Führungspraxis übernommen und stellen in vielerlei Hinsicht nach wie vor Entwicklungsziele und Leitlinien für die Steuerung und Führung der öffentlichen Verwaltung dar. NPM soll die öffentliche Verwaltung an geforderte Neuausrichtungen anpassen und effizienter gestalten. Ziele und Gestaltung der öffentlichen Verwaltung unter NPM und die dazu notwendigen Instrumente werden in diesem Lehrbuch umfassend und strukturiert erläutert. Besonderes Augenmerk wird dabei auf die Veränderungslinien und -ansätze für die Verwaltungsführung gelegt.
Y1  - 2011
SN  - 978-3-8252-3638-0
PB  - Haupt Verlag
CY  - Bern
ET  - 5., korrigierte Aufl.
ER  - 
TY  - JOUR
A1  - Hempel, Sabrina
A1  - Koseska, Aneta
A1  - Nikoloski, Zoran
A1  - Kurths, Jürgen
T1  - Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study
JF  - BMC bioinformatics
N2  - Background: Inferring regulatory interactions between genes from transcriptomics time-resolved data, yielding reverse engineered gene regulatory networks, is of paramount importance to systems biology and bioinformatics studies. Accurate methods to address this problem can ultimately provide a deeper insight into the complexity, behavior, and functions of the underlying biological systems. However, the large number of interacting genes coupled with short and often noisy time-resolved read-outs of the system renders the reverse engineering a challenging task. Therefore, the development and assessment of methods which are computationally efficient, robust against noise, applicable to short time series data, and preferably capable of reconstructing the directionality of the regulatory interactions remains a pressing research problem with valuable applications.
 Results: Here we perform the largest systematic analysis of a set of similarity measures and scoring schemes within the scope of the relevance network approach which are commonly used for gene regulatory network reconstruction from time series data. In addition, we define and analyze several novel measures and schemes which are particularly suitable for short transcriptomics time series. We also compare the considered 21 measures and 6 scoring schemes according to their ability to correctly reconstruct such networks from short time series data by calculating summary statistics based on the corresponding specificity and sensitivity. Our results demonstrate that rank and symbol based measures have the highest performance in inferring regulatory interactions. In addition, the proposed scoring scheme by asymmetric weighting has shown to be valuable in reducing the number of false positive interactions. On the other hand, Granger causality as well as information-theoretic measures, frequently used in inference of regulatory networks, show low performance on the short time series analyzed in this study.
 Conclusions: Our study is intended to serve as a guide for choosing a particular combination of similarity measures and scoring schemes suitable for reconstruction of gene regulatory networks from short time series data. We show that further improvement of algorithms for reverse engineering can be obtained if one considers measures that are rooted in the study of symbolic dynamics or ranks, in contrast to the application of common similarity measures which do not consider the temporal character of the employed data. Moreover, we establish that the asymmetric weighting scoring scheme together with symbol based measures (for low noise level) and rank based measures (for high noise level) are the most suitable choices.
Y1  - 2011
U6  - https://doi.org/10.1186/1471-2105-12-292
SN  - 1471-2105
VL  - 12
IS  - 1
PB  - BioMed Central
CY  - London
ER  - 
TY  - JOUR
A1  - Ruprecht, Colin
A1  - Mutwil, Marek
A1  - Saxe, Friederike
A1  - Eder, Michaela
A1  - Nikoloski, Zoran
A1  - Persson, Staffan
T1  - Large-scale co-expression approach to dissect secondary cell wall formation across plant species
JF  - Frontiers in plant science
N2  - Plant cell walls are complex composites largely consisting of carbohydrate-based polymers, and are generally divided into primary and secondary walls based on content and characteristics. Cellulose microfibrils constitute a major component of both primary and secondary cell walls and are synthesized at the plasma membrane by cellulose synthase (CESA) complexes. Several studies in Arabidopsis have demonstrated the power of co-expression analyses to identify new genes associated with secondary wall cellulose biosynthesis. However, across-species comparative co-expression analyses remain largely unexplored. Here, we compared co-expressed gene vicinity networks of primary and secondary wall CESAsin Arabidopsis, barley, rice, poplar, soybean, Medicago, and wheat, and identified gene families that are consistently co-regulated with cellulose biosynthesis. In addition to the expected polysaccharide acting enzymes, we also found many gene families associated with cytoskeleton, signaling, transcriptional regulation, oxidation, and protein degradation. Based on these analyses, we selected and biochemically analyzed T-DNA insertion lines corresponding to approximately twenty genes from gene families that re-occur in the co-expressed gene vicinity networks of secondary wall CESAs across the seven species. We developed a statistical pipeline using principal component analysis and optimal clustering based on silhouette width to analyze sugar profiles. One of the mutants, corresponding to a pinoresinol reductase gene, displayed disturbed xylem morphology and held lower levels of lignin molecules. We propose that this type of large-scale co-expression approach, coupled with statistical analysis of the cell wall contents, will be useful to facilitate rapid knowledge transfer across plant species.
KW  - secondary cell wall
KW  - comparative co-expression analysis
KW  - Arabidopsis
KW  - cellulose
Y1  - 2011
U6  - https://doi.org/10.3389/fpls.2011.00023
SN  - 1664-462X
VL  - 2
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Basler, Georg
A1  - Ebenhoeh, Oliver
A1  - Selbig, Joachim
A1  - Nikoloski, Zoran
T1  - Mass-balanced randomization of metabolic networks
JF  - Bioinformatics
N2  - Motivation: Network-centered studies in systems biology attempt to integrate the topological properties of biological networks with experimental data in order to make predictions and posit hypotheses. For any topology-based prediction, it is necessary to first assess the significance of the analyzed property in a biologically meaningful context. Therefore, devising network null models, carefully tailored to the topological and biochemical constraints imposed on the network, remains an important computational problem.
 Results: We first review the shortcomings of the existing generic sampling scheme-switch randomization-and explain its unsuitability for application to metabolic networks. We then devise a novel polynomial-time algorithm for randomizing metabolic networks under the (bio)chemical constraint of mass balance. The tractability of our method follows from the concept of mass equivalence classes, defined on the representation of compounds in the vector space over chemical elements. We finally demonstrate the uniformity of the proposed method on seven genome-scale metabolic networks, and empirically validate the theoretical findings. The proposed method allows a biologically meaningful estimation of significance for metabolic network properties.
Y1  - 2011
U6  - https://doi.org/10.1093/bioinformatics/btr145
SN  - 1367-4803
VL  - 27
IS  - 10
SP  - 1397
EP  - 1403
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Grimbs, Sergio
A1  - Arnold, Anne
A1  - Koseska, Aneta
A1  - Kurths, Jürgen
A1  - Selbig, Joachim
A1  - Nikoloski, Zoran
T1  - Spatiotemporal dynamics of the Calvin cycle multistationarity and symmetry breaking instabilities
JF  - Biosystems : journal of biological and information processing sciences
N2  - The possibility of controlling the Calvin cycle has paramount implications for increasing the production of biomass. Multistationarity, as a dynamical feature of systems, is the first obvious candidate whose control could find biotechnological applications. Here we set out to resolve the debate on the multistationarity of the Calvin cycle. Unlike the existing simulation-based studies, our approach is based on a sound mathematical framework, chemical reaction network theory and algebraic geometry, which results in provable results for the investigated model of the Calvin cycle in which we embed a hierarchy of realistic kinetic laws. Our theoretical findings demonstrate that there is a possibility for multistationarity resulting from two sources, homogeneous and inhomogeneous instabilities, which partially settle the debate on multistability of the Calvin cycle. In addition, our tractable analytical treatment of the bifurcation parameters can be employed in the design of validation experiments.
KW  - Multistationarity
KW  - Calvin cycle
KW  - Algebraic geometry
KW  - Bifurcation parameters
KW  - Biomass
Y1  - 2011
U6  - https://doi.org/10.1016/j.biosystems.2010.10.015
SN  - 0303-2647
VL  - 103
IS  - 2
SP  - 212
EP  - 223
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Nikoloski, Zoran
A1  - Grimbs, Sergio
A1  - Klie, Sebastian
A1  - Selbig, Joachim
T1  - Complexity of automated gene annotation
JF  - Biosystems : journal of biological and information processing sciences
N2  - Integration of high-throughput data with functional annotation by graph-theoretic methods has been postulated as promising way to unravel the function of unannotated genes. Here, we first review the existing graph-theoretic approaches for automated gene function annotation and classify them into two categories with respect to their relation to two instances of transductive learning on networks - with dynamic costs and with constant costs - depending on whether or not ontological relationship between functional terms is employed. The determined categories allow to characterize the computational complexity of the existing approaches and establish the relation to classical graph-theoretic problems, such as bisection and multiway cut. In addition, our results point out that the ontological form of the structured functional knowledge does not lower the complexity of the transductive learning with dynamic costs - one of the key problems in modern systems biology. The NP-hardness of automated gene annotation renders the development of heuristic or approximation algorithms a priority for additional research.
KW  - Complexity
KW  - Gene function prediction
KW  - External structural measures
KW  - Transductive learning
Y1  - 2011
U6  - https://doi.org/10.1016/j.biosystems.2010.12.003
SN  - 0303-2647
VL  - 104
IS  - 1
SP  - 1
EP  - 8
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Basler, Georg
A1  - Nikoloski, Zoran
T1  - JMassBalance - mass-balanced randomization and analysis of metabolic networks
JF  - Bioinformatics
N2  - Analysis of biological networks requires assessing the statistical significance of network-based predictions by using a realistic null model. However, the existing network null model, switch randomization, is unsuitable for metabolic networks, as it does not include physical constraints and generates unrealistic reactions. We present JMassBalance, a tool for mass-balanced randomization and analysis of metabolic networks. The tool allows efficient generation of large sets of randomized networks under the physical constraint of mass balance. In addition, various structural properties of the original and randomized networks can be calculated, facilitating the identification of the salient properties of metabolic networks with a biologically meaningful null model.
Y1  - 2011
U6  - https://doi.org/10.1093/bioinformatics/btr448
SN  - 1367-4803
VL  - 27
IS  - 19
SP  - 2761
EP  - 2762
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Hempel, Stefan
A1  - Koseska, Aneta
A1  - Kurths, Jürgen
A1  - Nikoloski, Zoran
T1  - Inner composition alignment for inferring directed networks from short time series
JF  - Physical review letters
N2  - Identifying causal links (couplings) is a fundamental problem that facilitates the understanding of emerging structures in complex networks. We propose and analyze inner composition alignment-a novel, permutation-based asymmetric association measure to detect regulatory links from very short time series, currently applied to gene expression. The measure can be used to infer the direction of couplings, detect indirect (superfluous) links, and account for autoregulation. Applications to the gene regulatory network of E. coli are presented.
Y1  - 2011
U6  - https://doi.org/10.1103/PhysRevLett.107.054101
SN  - 0031-9007
VL  - 107
IS  - 5
PB  - American Physical Society
CY  - College Park
ER  - 
TY  - GEN
A1  - Nikoloski, Zoran
A1  - van Dongen, Joost T.
T1  - Modeling alternatives for interpreting the change in oxygen-consumption rates during hypoxic conditions
T2  - New phytologist : international journal of plant science
KW  - hypoxia
KW  - modeling
KW  - regulation
KW  - respiration
KW  - roots
Y1  - 2011
U6  - https://doi.org/10.1111/j.1469-8137.2011.03674.x
SN  - 0028-646X
VL  - 190
IS  - 2
SP  - 273
EP  - 276
PB  - Wiley-Blackwell
CY  - Malden
ER  - 
TY  - JOUR
A1  - Lisec, Jan
A1  - Römisch-Margl, Lilla
A1  - Nikoloski, Zoran
A1  - Piepho, Hans-Peter
A1  - Giavalisco, Patrick
A1  - Selbig, Joachim
A1  - Gierl, Alfons
A1  - Willmitzer, Lothar
T1  - Corn hybrids display lower metabolite variability and complex metabolite inheritance patterns
JF  - The plant journal
N2  - We conducted a comparative analysis of the root metabolome of six parental maize inbred lines and their 14 corresponding hybrids showing fresh weight heterosis. We demonstrated that the metabolic profiles not only exhibit distinct features for each hybrid line compared with its parental lines, but also separate reciprocal hybrids. Reconstructed metabolic networks, based on robust correlations between metabolic profiles, display a higher network density in most hybrids as compared with the corresponding inbred lines. With respect to metabolite level inheritance, additive, dominant and overdominant patterns are observed with no specific overrepresentation. Despite the observed complexity of the inheritance pattern, for the majority of metabolites the variance observed in all 14 hybrids is lower compared with inbred lines. Deviations of metabolite levels from the average levels of the hybrids correlate negatively with biomass, which could be applied for developing predictors of hybrid performance based on characteristics of metabolite patterns.
KW  - heterosis
KW  - Zea mays
KW  - metabolomics
Y1  - 2011
U6  - https://doi.org/10.1111/j.1365-313X.2011.04689.x
SN  - 0960-7412
VL  - 68
IS  - 2
SP  - 326
EP  - 336
PB  - Wiley-Blackwell
CY  - Malden
ER  - 
TY  - JOUR
A1  - Larhlimi, Abdelhalim
A1  - Blachon, Sylvain
A1  - Selbig, Joachim
A1  - Nikoloski, Zoran
T1  - Robustness of metabolic networks a review of existing definitions
JF  - Biosystems : journal of biological and information processing sciences
N2  - Describing the determinants of robustness of biological systems has become one of the central questions in systems biology. Despite the increasing research efforts, it has proven difficult to arrive at a unifying definition for this important concept. We argue that this is due to the multifaceted nature of the concept of robustness and the possibility to formally capture it at different levels of systemic formalisms (e.g, topology and dynamic behavior). Here we provide a comprehensive review of the existing definitions of robustness pertaining to metabolic networks. As kinetic approaches have been excellently reviewed elsewhere, we focus on definitions of robustness proposed within graph-theoretic and constraint-based formalisms.
KW  - Robustness
KW  - Metabolic networks
KW  - Graph theory
KW  - Constraint-based approaches
Y1  - 2011
U6  - https://doi.org/10.1016/j.biosystems.2011.06.002
SN  - 0303-2647
VL  - 106
IS  - 1
SP  - 1
EP  - 8
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Arnold, Anne
A1  - Nikoloski, Zoran
T1  - A quantitative comparison of Calvin-Benson cycle models
JF  - Trends in plant science
N2  - The Calvin-Benson cycle (CBC) provides the precursors for biomass synthesis necessary for plant growth. The dynamic behavior and yield of the CBC depend on the environmental conditions and regulation of the cellular state. Accurate quantitative models hold the promise of identifying the key determinants of the tightly regulated CBC function and their effects on the responses in future climates. We provide an integrative analysis of the largest compendium of existing models for photosynthetic processes. Based on the proposed ranking, our framework facilitates the discovery of best-performing models with regard to metabolomics data and of candidates for metabolic engineering.
Y1  - 2011
U6  - https://doi.org/10.1016/j.tplants.2011.09.004
SN  - 1360-1385
VL  - 16
IS  - 12
SP  - 676
EP  - 683
PB  - Elsevier
CY  - London
ER  - 
TY  - THES
A1  - Kittner, Madeleine
T1  - Folding and aggregation of amyloid peptides
T1  - Faltung und Aggregation von Amyloidpeptiden
N2  - Aggregation of the Amyloid β (Aβ) peptide to amyloid fibrils is associated with the outbreak of Alzheimer’s disease. Early aggregation intermediates in form of soluble oligomers are of special interest as they are believed to be the major toxic components in the process. These oligomers are of disordered and transient nature. Therefore, their detailed molecular structure is difficult to access experimentally and often remains unknown. In the present work extensive, fully atomistic replica exchange molecular dynamics simulations were performed to study the preaggregated, monomer states and early aggregation intermediates (dimers, trimers) of Aβ(25-35) and Aβ(10-35)-NH2 in aqueous solution. The folding and aggregation of Aβ(25-35) were studied at neutral pH and 293 K. Aβ(25-35) monomers mainly adopt β-hairpin conformations characterized by a β-turn formed by residues G29 and A30, and a β-sheet between residues N27–K28 and I31–I32 in equilibrium with coiled conformations. The β-hairpin conformations served as initial configurations to model spontaneous aggregation of Aβ(25-35). As expected, within the Aβ(25-35) dimer and trimer ensembles many different poorly populated conformations appear. Nevertheless, we were able to distinguish between disordered and fibril-like oligomers. Whereas disordered oligomers are rather compact with few intermolecular hydrogen bonds (HBs), fibril-like oligomers are characterized by the formation of large intermolecular β-sheets. In most of the fibril-like dimers and trimers individual peptides are fully extended forming in- or out-of-register antiparallel β-sheets. A small amount of fibril-like trimers contained V-shaped peptides forming parallel β-sheets. The dimensions of extended and V-shaped oligomers correspond well to the diameters of two distinct morphologies found for Aβ(25-35) fibrils. The transition from disordered to fibril-like Aβ(25-35) dimers is unfavorable but driven by energy. The lower energy of fibril-like dimers arises from favorable intermolecular HBs and other electrostatic interactions which compete with a loss in entropy. Approximately 25 % of the entropic cost correspond to configurational entropy. The rest relates to solvent entropy, presumably caused by hydrophobic and electrostatic effects. In contrast to the transition towards fibril-like dimers the first step of aggregation is driven by entropy. Here, we compared structural and thermodynamic properties of the individual monomer, dimer and trimer ensembles to gain qualitative information about the aggregation process. The β-hairpin conformation observed for monomers is successively dissolved in dimer and trimer ensembles while instead intermolecular β-sheets are formed. As expected upon aggregation the configurational entropy decreases. Additionally, the solvent accessible surface area (SASA), especially the hydrophobic SASA, decreases yielding a favorable solvation free energy which overcompensates the loss in configurational entropy. In summary, the hydrophobic effect, possibly combined with electrostatic effects, yields an increase in solvent entropy which is believed to be one major driving force towards aggregation. Spontaneous folding of the Aβ(10-35)-NH2 monomer was modeled using two force fields, GROMOS96 43a1 and OPLS/AA, and compared to primary NMR data collected at pH 5.6 and 283 K taken from the literature. Unexpectedly, the two force fields yielded significantly different main conformations. Comparison between experimental and calculated nuclear Overhauser effect (NOE) distances is not sufficient to distinguish between the different force fields. Additionally, the comparison with scalar coupling constants suggest that the chosen protonation in both simulations corresponds to a pH lower than in the experiment. Based on this analysis we were unable to determine which force field yields a better description of this system. Dimerization of Aβ(10-35)-NH2 was studied at neutral pH and 300 K. Dimer conformations arrange in many distinct, poorly populated and rather complex alignments or interlocking patterns which are rather stabilized by side chain interactions than by specific intermolecular hydrogen bonds. Similar to Aβ(25-35) dimers, transition towards β-sheet-rich, fibril-like Aβ(10-35) dimers is driven by energy competing with a loss in entropy. Here, transition is mediated by favorable peptide-solvent and solvent-solvent interactions mainly arising from electrostatic interactions.
N2  - Die Aggregation des Amyloid β (Aβ) Peptids zu Amyloidfibrillen wird mit dem Ausbruch der Alzheimer Krankheit in Verbindung gebracht. Die toxische Wirkung auf Zellen wird vor allem den zeitigen Intermediaten in Form von löslichen Oligomeren zugeschrieben. Aufgrund deren ungeordneter und flüchtiger Natur kann die molekulare Struktur solcher zeitigen Oligomere oft experimentell nicht aufgelöst werden. In der vorliegenden Arbeit wurden aufwendige atomistische Replica-Exchange-Molekulardynamik-Simulationen durchgeführt, um die molekulare Struktur von Monomeren und Oligomeren der Fragmente Aβ(25-35) und Aβ(10-35)-NH2 in Wasser zu untersuchen. Die Faltung und Aggregation von Aβ(25-35) wurde bei neutralem pH und 293 K untersucht. Monomere dieses Fragments bilden hauptsächlich β-Haarnadelkonformationen im Gleichgewicht mit Knäulstrukturen. Innerhalb der β-Haarnadelkonformationen bilden die Residuen G29 und A30 einen β-turn, während N27–K28 and I31–I32 ein β-Faltblatt bilden. Diese β-Haarnadelkonformationen bildeten den Ausgangspunkt zur Modellierung spontaner Aggregation. Wie zu erwarten, bilden sich eine Vielzahl verschiedener, gering besetzter Dimer- und Trimerkonformationen. Mit Hilfe einer gröberen Einteilung können diese in ungeordnete und fibrillähnliche Oligomere unterteilt werden. Ungeordnete Oligomere bilden kompakte Strukturen, die nur durch wenige intermolekulare Wasserstoffbrückenbindungen (HBB) stabilisiert sind. Typisch für fibrillähnliche Oligomere ist hingegen die Ausbildung großer intermolekularer β-Faltblätter. In vielen dieser Oligomere finden wir antiparallele, in- oder out-of-register β-Faltblätter gebildet durch vollständig ausgestreckte Peptide. Ein kleiner Teil der fibrillähnlichen Trimere bildet parallele, V-förmige β-Faltblätter. Die Ausdehnungen ausgestreckter und V-förmiger Oligomere entspricht in etwa den Durchmessern von zwei verschiedenen, experimentell gefundenen Fibrillmorphologien für Aβ(25-35). Die Umwandlung von ungeordneten zu fibrillähnlichen Aβ(25-35) Dimeren ist energetisch begünstigt, läuft aber nicht freiwillig ab. Fibrillähnliche Dimere haben eine geringere Energie aufgrund günstiger Peptidwechselwirkungen (HBB, Salzbrücken), welche durch den Verlust an Entropie kompensiert wird. Etwa 25 % entsprechen dem Verlust an Konfigurationsentropie. Der restliche Anteil wird einem Verlust an Lösungsmittelentropie aufgrund von hydrophoben und elektrostatischen Effekten zugesprochen. Im Gegensatz zur Umwandlung in fibrillähnliche Dimere, ist die Assoziation von Monomeren oder Oligomeren entropisch begünstigt. Beim Vergleich thermodynamischer Eigenschaften der Monomer-, Dimer- und Trimersysteme zeigt sich im Verlauf der Aggregation, wie erwartet, eine Abnahme der Konfigurationsentropie. Zusätzlich nimmt die dem Lösungsmittel zugängliche Oberfläche (SASA), insbesondere die hydrophobe SASA, ab. In Verbindung damit beobachten wir eine Abnahme der freien Solvatisierungsenergie, welche den Verlust an Konfigurationsentropie kompensiert. Mit anderen Worten, der hydrophobe Effekt in Kombination mit elektrostatischen Wechselwirkungen führt zu einem Ansteigen der Lösungsmittelentropie und begünstigt damit die Aggegation. Die spontane Faltung des Aβ(10-35)-NH2 Monomers wurde für zwei verschiedene Proteinkraftfelder, GROMOS96 43a1 und OPLS/AA, untersucht und mit primären NMR-Daten aus der Literatur, gemessen bei pH 5.6 und 283 K, verglichen. Beide Kraftfelder generieren unterschiedliche Hauptkonformationen. Der Vergleich zwischen experimentellen und berechneten Kern-Overhauser-Effekt (NOE) Abständen ist nicht ausreichend, um zwischen beiden Kraftfeldern zu unterscheiden. Der Vergleich mit Kopplungskonstanten aus Experiment und Simulation zeigt, dass beide Simulationen einem pH-Wert geringer als 5.6 ensprechen. Basierend auf den bisherigen Ergebnissen können wir nicht entscheiden, welches Kraftfeld eine bessere Beschreibung für dieses System liefert. Die Dimerisierung von Aβ(10-35)-NH2 wurde bei neutralem pH und 300 K untersucht. Wir finden eine Vielzahl verschiedener, gering besetzter Dimerstrukturen, welche eher durch Seitenkettenkontakte als durch spezifische HBB stabilisiert sind. Wie bei den Aβ(25-35) Dimeren, ist die Umwandlung zu β-Faltblattreichen, fibrillähnlichen Aβ(10-35) Dimeren energetisch begünstigt, konkurriert aber mit einem Entropieverlust. Die Umwandlung wird in diesem Fall durch elektrostatische Wechselwirkungen zwischen Peptid und Lösungsmittel und innerhalb des Lösungsmittels bestimmt.
KW  - Amyloid beta
KW  - Proteinaggregation
KW  - Alzheimer
KW  - Molekulardynamik-Simulation
KW  - Thermodynamische Stabilität
KW  - amyloid beta
KW  - protein aggregation
KW  - Alzheimer
KW  - molecular dynamics simulation
KW  - thermodynamic stability
Y1  - 2011
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-53570
ER  - 
TY  - JOUR
A1  - Rivnay, Jonathan
A1  - Steyrleuthner, Robert
A1  - Jimison, Leslie H.
A1  - Casadei, Alberto
A1  - Chen, Zhihua
A1  - Toney, Michael F.
A1  - Facchetti, Antonio
A1  - Neher, Dieter
A1  - Salleo, Alberto
T1  - Drastic control of texture in a high performance n-Type polymeric semiconductor and implications for charge transport
JF  - Macromolecules : a publication of the American Chemical Society
N2  - Control of crystallographic texture from mostly face-on to edge-on is observed for the film morphology of the n-type semicrystalline polymer [N,N-9-bis(2-octyldodecyl)naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diy1]alt-5,59-(2,29-bithiophene)}, P(NDI2OD-T2), when annealing the film to the polymer melting point followed by slow cooling to ambient temperature. A variety of X-ray diffraction analyses, including pole figure construction and Fourier transform peak shape deconvolution, are employed to quantify the texture change, relative degree of crystallinity and lattice order. We find that annealing the polymer film to the melt leads to a shift from 77.5% face-on to 94.6% edge-on lamellar texture as well as to a 2-fold increase in crystallinity and a 40% decrease in intracrystallite cumulative disorder. The texture change results in a significant drop in the electron-only diode current density through the film thickness upon melt annealing while little change is observed in the in-plane transport of bottom gated thin film transistors. This suggests that the texture change is prevalent in the film interior and that either the (bottom) surface structure is different from the interior structure or the intracrystalline order and texture play a secondary role in transistor transport for this material.
Y1  - 2011
U6  - https://doi.org/10.1021/ma200864s
SN  - 0024-9297
VL  - 44
IS  - 13
SP  - 5246
EP  - 5255
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Tschöpe, Okka
A1  - Wallschläger, Hans-Dieter
A1  - Burkart, Michael
A1  - Tielbörger, Katja
T1  - Managing open habitats by wild ungulate browsing and grazing a case-study in North-Eastern Germany
JF  - Applied vegetation science : official organ of the International Association for Vegetation Science
N2  - Question: Can wild ungulates efficiently maintain and restore open habitats?
 Location: Brandenburg, NE Germany.
 Methods: The effect of wild ungulate grazing and browsing was studied in three successional stages: (1) Corynephorus canescens-dominated grassland; (2) ruderal tall forb vegetation dominated by Tanacetum vulgare; and (3) Pinus sylvestris-pioneer forest. The study was conducted over 3 yr. In each successional stage, six paired 4 m(2)-monitoring plots of permanently grazed versus ungrazed plots were arranged in three random blocks. Removal of grazing was introduced de novo for the study. In each plot, percentage cover of each plant and lichen species and total cover of woody plants was recorded.
 Results: Wild ungulates considerably affected successional pathways and species composition in open habitats but this influence became evident in alteration of abundances of only a few species. Grazing effects differed considerably between successional stages: species richness was higher in grazed versus ungrazed ruderal and pioneer forest plots, but not in the Corynephorus sites. Herbivory affected woody plant cover only in the Pioneer forest sites. Although the study period was too short to observe drastic changes in species richness and woody plant cover, notable changes in species composition were still detected in all successional stages.
 Conclusion: Wild ungulate browsing is a useful tool to inhibit encroachment of woody vegetation and to conserve a species-rich, open landscape.
KW  - Conservation
KW  - Red deer
KW  - Fallow deer
KW  - Succession
KW  - Species richness
KW  - Woody plant
Y1  - 2011
U6  - https://doi.org/10.1111/j.1654-109X.2010.01119.x
SN  - 1402-2001
VL  - 14
IS  - 2
SP  - 200
EP  - 209
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Donges, Jonathan
A1  - Donner, Reik Volker
A1  - Rehfeld, Kira
A1  - Marwan, Norbert
A1  - Trauth, Martin H.
A1  - Kurths, Jürgen
T1  - Identification of dynamical transitions in marine palaeoclimate records by recurrence network analysis
JF  - Nonlinear processes in geophysics
N2  - The analysis of palaeoclimate time series is usually affected by severe methodological problems, resulting primarily from non-equidistant sampling and uncertain age models. As an alternative to existing methods of time series analysis, in this paper we argue that the statistical properties of recurrence networks - a recently developed approach - are promising candidates for characterising the system's nonlinear dynamics and quantifying structural changes in its reconstructed phase space as time evolves. In a first order approximation, the results of recurrence network analysis are invariant to changes in the age model and are not directly affected by non-equidistant sampling of the data. Specifically, we investigate the behaviour of recurrence network measures for both paradigmatic model systems with non-stationary parameters and four marine records of long-term palaeoclimate variations. We show that the obtained results are qualitatively robust under changes of the relevant parameters of our method, including detrending, size of the running window used for analysis, and embedding delay. We demonstrate that recurrence network analysis is able to detect relevant regime shifts in synthetic data as well as in problematic geoscientific time series. This suggests its application as a general exploratory tool of time series analysis complementing existing methods.
Y1  - 2011
U6  - https://doi.org/10.5194/npg-18-545-2011
SN  - 1023-5809
VL  - 18
IS  - 5
SP  - 545
EP  - 562
PB  - Copernicus
CY  - Göttingen
ER  - 
TY  - JOUR
A1  - Ilnytskyi, Jaroslav M.
A1  - Neher, Dieter
A1  - Saphiannikova, Marina
T1  - Opposite photo-induced deformations in azobenzene-containing polymers with different molecular architecture molecular dynamics study
JF  - The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr
N2  - Photo-induced deformations in azobenzene-containing polymers (azo-polymers) are central to a number of applications, such as optical storage and fabrication of diffractive elements. The microscopic nature of the underlying opto-mechanical coupling is yet not clear. In this study, we address the experimental finding that the scenario of the effects depends on molecular architecture of the used azo-polymer. Typically, opposite deformations in respect to the direction of light polarization are observed for liquid crystalline and amorphous azo-polymers. In this study, we undertake molecular dynamics simulations of two different models that mimic these two types of azo-polymers. We employ hybrid force field modeling and consider only trans-isomers of azobenzene, represented as Gay-Berne sites. The effect of illumination on the orientation of the chromophores is considered on the level of orientational hole burning and emphasis is given to the resulting deformation of the polymer matrix. We reproduce deformations of opposite sign for the two models being considered here and discuss the relevant microscopic mechanisms in both cases.
KW  - amorphous state
KW  - light polarisation
KW  - liquid crystal polymers
KW  - molecular dynamics method
KW  - optical hole burning
KW  - photochemistry
Y1  - 2011
U6  - https://doi.org/10.1063/1.3614499
SN  - 0021-9606
VL  - 135
IS  - 4
PB  - American Institute of Physics
CY  - Melville
ER  - 
TY  - JOUR
A1  - Kniepert, Juliane
A1  - Schubert, Marcel
A1  - Blakesley, James C.
A1  - Neher, Dieter
T1  - Photogeneration and recombination in P3HT/PCBM solar cells probed by time-delayed collection field experiments
JF  - The journal of physical chemistry letters
N2  - Time-delayed collection field (TDCF) experiments are performed on bulk heterojunction solar cells comprised of a blend of poly(3-hexylthiophene) and [6,6]-phenyl C-71 butyric acid methyl ester. TDCF is analogous to a pump-probe experiment using optical excitation and an electrical probe with a resolution of < 100 ns. The number of free charge carriers extracted after a short delay is found to be independent of the electric field during illumination. Also, experiments performed with a variable delay between the optical excitation and the electrical probe do not reveal any evidence for the generation of charge via field-assisted dissociation of bound long-lived polaron pairs. Photocurrent transients are well fitted by computational drift diffusion simulations with only direct generation of free charge carriers. With increasing delay times between pump and probe, two loss mechanisms are identified; first, charge-carriers are swept out of the device by the internal electric field, and second, bimolecular recombination of the remaining carriers takes place with a reduced recombination coefficient.
Y1  - 2011
U6  - https://doi.org/10.1021/jz200155b
SN  - 1948-7185
VL  - 2
IS  - 7
SP  - 700
EP  - 705
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Kuehn, Sergei
A1  - Pingel, Patrick
A1  - Breusing, Markus
A1  - Fischer, Thomas
A1  - Stumpe, Joachim
A1  - Neher, Dieter
A1  - Elsaesser, Thomas
T1  - High-Resolution Near-Field Optical Investigation of Crystalline Domains in Oligomeric PQT-12 Thin Films
JF  - Advanced functional materials
N2  - The structure and morphology on different length scales dictate both the electrical and optical properties of organic semiconductor thin films. Using a combination of spectroscopic methods, including scanning near-field optical microscopy, we study the domain structure and packing quality of highly crystalline thin films of oligomeric PQT-12 with 100 nanometer spatial resolution. The pronounced optical anisotropy of these layers measured by polarized light microscopy facilitates the identification of regions with uniform molecular orientation. We find that a hierarchical order on three different length scales exists in these layers, made up of distinct well-ordered dichroic areas at the ten-micrometer-scale, which are sub-divided into domains with different molecular in-plane orientation. These serve as a template for the formation of smaller needle-like crystallites at the layer surface. A high degree of crystalline order is believed to be the cause of the rather high field-effect mobility of these layers of 10(-3) cm 2 V(-1) s(-1), whereas it is limited by the presence of domain boundaries at macroscopic distances.
Y1  - 2011
U6  - https://doi.org/10.1002/adfm.201001978
SN  - 1616-301X
VL  - 21
IS  - 5
SP  - 860
EP  - 868
PB  - Wiley-Blackwell
CY  - Malden
ER  - 
TY  - JOUR
A1  - Blakesley, James C.
A1  - Neher, Dieter
T1  - Relationship between energetic disorder and open-circuit voltage in bulk heterojunction organic solar cells
JF  - Physical review : B, Condensed matter and materials physics
N2  - We simulate organic bulk heterojunction solar cells. The effects of energetic disorder are incorporated through a Gaussian or exponential model of density of states. Analytical models of open-circuit voltage (V(OC)) are derived from the splitting of quasi-Fermi potentials. Their predictions are backed up by more complex numerical device simulations including effects such as carrier-density-dependent charge-carrier mobilities. It is predicted that the V(OC) depends on: (1) the donor-acceptor energy gap; (2) charge-carrier recombination rates; (3) illumination intensity; (4) the contact work functions (if not in the pinning regime); and (5) the amount of energetic disorder. A large degree of energetic disorder, or a high density of traps, is found to cause significant reductions in V(OC). This can explain why V(OC) is often less than expected in real devices. Energetic disorder also explains the nonideal temperature and intensity dependence of V(OC) and the superbimolecular recombination rates observed in many real bulk heterojunction solar cells.
Y1  - 2011
U6  - https://doi.org/10.1103/PhysRevB.84.075210
SN  - 1098-0121
VL  - 84
IS  - 7
PB  - American Physical Society
CY  - College Park
ER  - 
TY  - JOUR
A1  - Lange, Ilja
A1  - Blakesley, James C.
A1  - Frisch, Johannes
A1  - Vollmer, Antje
A1  - Koch, Norbert
A1  - Neher, Dieter
T1  - Band bending in conjugated polymer layers
JF  - Physical review letters
N2  - We use the Kelvin probe method to study the energy-level alignment of four conjugated polymers deposited on various electrodes. Band bending is observed in all polymers when the substrate work function exceeds critical values. Through modeling, we show that the band bending is explained by charge transfer from the electrodes into a small density of states that extends several hundred meV into the band gap. The energetic spread of these states is correlated with charge-carrier mobilities, suggesting that the same states also govern charge transport in the bulk of these polymers.
Y1  - 2011
U6  - https://doi.org/10.1103/PhysRevLett.106.216402
SN  - 0031-9007
VL  - 106
IS  - 21
PB  - American Physical Society
CY  - College Park
ER  - 
TY  - JOUR
A1  - Hundertmark, Michaela
A1  - Dimova, Rumiana
A1  - Lengefeld, Jan
A1  - Seckler, Robert
A1  - Hincha, Dirk K.
T1  - The intrinsically disordered late embryogenesis abundant protein LEA18 from Arabidopsis thaliana modulates membrane stability through binding and folding
JF  - Biochimica et biophysica acta : Biomembranes
N2  - Intrinsically disordered proteins (IDPs) constitute a substantial part of cellular proteomes. late embryogenesis abundant (LEA) proteins are mostly predicted to be IDPs associated with dehydration tolerance in many plant, animal and bacterial species. Their functions, however, are largely unexplored and also their structure and interactions with potential target molecules have only recently been experimentally investigated in a small number of proteins. Here, we report on the structure and interactions with membranes of the Pfam LEA_1 protein LEA18 from the higher plant Arabidopsis thaliana. This functionally uncharacterized positively charged protein specifically aggregated and destabilized negatively charged liposomes. Isothermal titration calorimetry showed binding of the protein to both charged and uncharged membranes. LEA18 alone was largely unstructured in solution. While uncharged membranes had no influence on the secondary structure of LEA18, the protein partially folded into beta-sheet structure in the presence of negatively charged liposomes. These data suggest that LEA18 does not function as a membrane stabilizing protein, as suggested for other LEA proteins. Instead, a possible function of LEA18 could be the composition-dependent modulation of membrane stability, e.g., during signaling or vesicle-mediated transport.
KW  - Intrinsically disordered protein
KW  - Late embryogenesis abundant protein
KW  - Membrane stability
KW  - Protein-membrane interaction
KW  - Protein folding
Y1  - 2011
U6  - https://doi.org/10.1016/j.bbamem.2010.09.010
SN  - 0005-2736
VL  - 1808
IS  - 1
SP  - 446
EP  - 453
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Popova, Antoaneta V.
A1  - Hundertmark, Michaela
A1  - Seckler, Robert
A1  - Hincha, Dirk K.
T1  - Structural transitions in the intrinsically disordered plant dehydration stress protein LEA7 upon drying are modulated by the presence of membranes
JF  - Biochimica et biophysica acta : Biomembranes
N2  - Dehydration stress-related late embryogenesis abundant (LEA) proteins have been found in plants, invertebrates and bacteria. Most LEA proteins are unstructured in solution, but some fold into amphipathic a-helices during drying. The Pfam LEA_4 (Group 3) protein LEA7 from the higher plant Arabidopsis thaliana was predicted to be 87% alpha-helical, while CD spectroscopy showed it to be largely unstructured in solution and only 35% alpha-helical in the dry state. However, the dry protein contained 15% beta-sheets. FTIR spectroscopy revealed the (beta-sheets to be largely due to aggregation. beta-Sheet content was reduced and alpha-helix content increased when LEA7 was dried in the presence of liposomes with secondary structure apparently influenced by lipid composition. Secondary structure was also affected by the presence of membranes in the fully hydrated state. A temperature-induced increase in the flexibility of the dry protein was also only observed in the presence of membranes. Functional interactions of LEA7 with membranes in the dry state were indicated by its influence on the thermotropic phase transitions of the lipids and interactions with the lipid headgroup phosphates.
KW  - Desiccation
KW  - CD spectroscopy
KW  - FTIR spectroscopy
KW  - LEA protein
KW  - Protein-membrane interactions
KW  - Protein secondary structure
Y1  - 2011
U6  - https://doi.org/10.1016/j.bbamem.2011.03.009
SN  - 0005-2736
VL  - 1808
IS  - 7
SP  - 1879
EP  - 1887
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Eichler, David
A1  - Pohl, Martin
T1  - Can ultrahigh-energy cosmic rays come from Gamma-ray bursts? - cosmic rays below the ankle and galactic gamma-ray bursts
JF  - The astrophysical journal : an international review of spectroscopy and astronomical physics ; Part 2, Letters
N2  - The maximum cosmic-ray energy achievable by acceleration by a relativistic blast wave is derived. It is shown that forward shocks from long gamma-ray bursts (GRBs) in the interstellar medium accelerate protons to large enough energies, and have a sufficient energy budget, to produce the Galactic cosmic-ray component just below the ankle at 4 x 10(18) eV, as per an earlier suggestion. It is further argued that, were extragalactic long GRBs responsible for the component above the ankle as well, the occasional Galactic GRB within the solar circle would contribute more than the observational limits on the outward flux from the solar circle, unless an avoidance scenario, such as intermittency and/or beaming, allows the present-day local flux to be less than 10(-3) of the average. Difficulties with these avoidance scenarios are noted.
KW  - cosmic rays
KW  - galaxies: general
KW  - gamma-ray burst: general
Y1  - 2011
U6  - https://doi.org/10.1088/2041-8205/738/2/L21
SN  - 2041-8205
VL  - 738
IS  - 2
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  - 
TY  - JOUR
A1  - Mizuno, Yosuke
A1  - Pohl, Martin
A1  - Niemiec, Jacek
A1  - Zhang, Bing
A1  - Nishikawa, Ken-Ichi
A1  - Hardee, Philip E.
T1  - Magnetic-field amplification by turbulence in a relativistic shockpropagating through an inhomogeneous medium
JF  - The astrophysical journal : an international review of spectroscopy and astronomical physics
N2  - We perform two-dimensional relativistic magnetohydrodynamic simulations of a mildly relativistic shock propagating through an inhomogeneous medium. We show that the postshock region becomes turbulent owing to preshock density inhomogeneity, and the magnetic field is strongly amplified due to the stretching and folding of field lines in the turbulent velocity field. The amplified magnetic field evolves into a filamentary structure in two-dimensional simulations. The magnetic energy spectrum is flatter than the Kolmogorov spectrum and indicates that a so-called small-scale dynamo is occurring in the postshock region. We also find that the amount of magnetic-field amplification depends on the direction of the mean preshock magnetic field, and the timescale of magnetic-field growth depends on the shock strength.
KW  - gamma-ray burst: general
KW  - magnetohydrodynamics (MHD)
KW  - methods: numerical
KW  - relativistic processes
KW  - shock waves
KW  - turbulence
Y1  - 2011
U6  - https://doi.org/10.1088/0004-637X/726/2/62
SN  - 0004-637X
VL  - 726
IS  - 2
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  - 
TY  - JOUR
A1  - Pohl, Martin
A1  - Eichler, David
T1  - Origin of ultra-high-energy galactic cosmic rays the isotropy problem
JF  - The astrophysical journal : an international review of spectroscopy and astronomical physics
N2  - We study the propagation of ultra-high-energy cosmic rays (UHECRs) in the Galaxy, concentrating on the energy range below the ankle in the spectrum at 4 EeV. A Monte Carlo method, based on analytical solutions to the time-dependent diffusion problem, is used to account for intermittency by placing sources at random locations. Assuming a source population that scales with baryon mass density or star formation (e.g., long GRB), we derive constraints arising from intermittency and the observational limits on the composition and anisotropy. It is shown that the composition and anisotropy at 10(18) eV are difficult to reproduce and require that either (1) the particle mean free path is much smaller than a gyroradius, implying the escape time is very long, (2) the composition is heavier than suggested by recent Auger data, (3) the ultra-high-energy sub-ankle component is mostly extragalactic, or (4) we are living in a rare lull in the UHECR production, and the current UHECR intensity is far below the Galactic time average. We therefore recommend a strong observational focus on determining the UHECR composition around 10(18) eV.
KW  - cosmic rays
KW  - gamma-ray burst: general
Y1  - 2011
U6  - https://doi.org/10.1088/0004-637X/742/2/114
SN  - 0004-637X
VL  - 742
IS  - 2
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  - 
TY  - JOUR
A1  - Abdo, A. A.
A1  - Ackermann, Margit
A1  - Ajello, M.
A1  - Allafort, A. J.
A1  - Baldini, L.
A1  - Ballet, J.
A1  - Barbiellini, G.
A1  - Baring, M. G.
A1  - Bastieri, D.
A1  - Bellazzini, R.
A1  - Berenji, B.
A1  - Blandford, R. D.
A1  - Bloom, E. D.
A1  - Bonamente, E.
A1  - Borgland, A. W.
A1  - Bouvier, A.
A1  - Brandt, T. J.
A1  - Bregeon, Johan
A1  - Brigida, M.
A1  - Bruel, P.
A1  - Buehler, R.
A1  - Buson, S.
A1  - Caliandro, G. A.
A1  - Cameron, R. A.
A1  - Caraveo, P. A.
A1  - Casandjian, J. M.
A1  - Cecchi, C.
A1  - Chaty, S.
A1  - Chekhtman, A.
A1  - Cheung, C. C.
A1  - Chiang, J.
A1  - Cillis, A. N.
A1  - Ciprini, S.
A1  - Claus, R.
A1  - Cohen-Tanugi, J.
A1  - Conrad, Jan
A1  - Corbel, S.
A1  - Cutini, S.
A1  - de Angelis, A.
A1  - de Palma, F.
A1  - Dermer, C. D.
A1  - Digel, S. W.
A1  - do Couto e Silva, E.
A1  - Drell, P. S.
A1  - Drlica-Wagner, A.
A1  - Dubois, R.
A1  - Dumora, D.
A1  - Favuzzi, C.
A1  - Ferrara, E. C.
A1  - Fortin, P.
A1  - Frailis, M.
A1  - Fukazawa, Y.
A1  - Fukui, Y.
A1  - Funk, S.
A1  - Fusco, P.
A1  - Gargano, F.
A1  - Gasparrini, D.
A1  - Gehrels, N.
A1  - Germani, S.
A1  - Giglietto, N.
A1  - Giordano, F.
A1  - Giroletti, M.
A1  - Glanzman, T.
A1  - Godfrey, G.
A1  - Grenier, I. A.
A1  - Grondin, M. -H.
A1  - Guiriec, S.
A1  - Hadasch, D.
A1  - Hanabata, Y.
A1  - Harding, A. K.
A1  - Hayashida, M.
A1  - Hayashi, K.
A1  - Hays, E.
A1  - Horan, D.
A1  - Jackson, M. S.
A1  - Johannesson, G.
A1  - Johnson, A. S.
A1  - Kamae, T.
A1  - Katagiri, H.
A1  - Kataoka, J.
A1  - Kerr, M.
A1  - Knoedlseder, J.
A1  - Kuss, M.
A1  - Lande, J.
A1  - Latronico, L.
A1  - Lee, S. -H.
A1  - Lemoine-Goumard, M.
A1  - Longo, F.
A1  - Loparco, F.
A1  - Lovellette, M. N.
A1  - Lubrano, P.
A1  - Madejski, G. M.
A1  - Makeev, A.
A1  - Mazziotta, Mario Nicola
A1  - McEnery, J. E.
A1  - Michelson, P. F.
A1  - Mignani, R. P.
A1  - Mitthumsiri, W.
A1  - Mizuno, T.
A1  - Moiseev, A. A.
A1  - Monte, C.
A1  - Monzani, M. E.
A1  - Morselli, A.
A1  - Moskalenko, I. V.
A1  - Murgia, S.
A1  - Naumann-Godo, M.
A1  - Nolan, P. L.
A1  - Norris, J. P.
A1  - Nuss, E.
A1  - Ohsugi, T.
A1  - Okumura, A.
A1  - Orlando, E.
A1  - Ormes, J. F.
A1  - Paneque, D.
A1  - Parent, D.
A1  - Pelassa, V.
A1  - Pesce-Rollins, M.
A1  - Pierbattista, M.
A1  - Piron, F.
A1  - Pohl, Martin
A1  - Porter, T. A.
A1  - Raino, S.
A1  - Rando, R.
A1  - Razzano, M.
A1  - Reimer, O.
A1  - Reposeur, T.
A1  - Ritz, S.
A1  - Romani, R. W.
A1  - Roth, M.
A1  - Sadrozinski, H. F. -W.
A1  - Parkinson, P. M. Saz
A1  - Sgro, C.
A1  - Smith, D. A.
A1  - Smith, P. D.
A1  - Spandre, G.
A1  - Spinelli, P.
A1  - Strickman, M. S.
A1  - Tajima, H.
A1  - Takahashi, H.
A1  - Takahashi, T.
A1  - Tanaka, T.
A1  - Thayer, J. G.
A1  - Thayer, J. B.
A1  - Thompson, D. J.
A1  - Tibaldo, L.
A1  - Tibolla, O.
A1  - Torres, D. F.
A1  - Tosti, G.
A1  - Tramacere, A.
A1  - Troja, E.
A1  - Uchiyama, Y.
A1  - Vandenbroucke, J.
A1  - Vasileiou, V.
A1  - Vianello, G.
A1  - Vilchez, N.
A1  - Vitale, V.
A1  - Waite, A. P.
A1  - Wang, P.
A1  - Winer, B. L.
A1  - Wood, K. S.
A1  - Yamamoto, H.
A1  - Yamazaki, R.
A1  - Yang, Z.
A1  - Ziegler, M.
T1  - Observations of the young supernova remnant RX J1713.7-3946 with the fermi large area telescope
JF  - The astrophysical journal : an international review of spectroscopy and astronomical physics
N2  - We present observations of the young supernova remnant (SNR) RX J1713.7-3946 with the Fermi Large Area Telescope (LAT). We clearly detect a source positionally coincident with the SNR. The source is extended with a best-fit extension of 0 degrees.55 +/- 0 degrees.04 matching the size of the non-thermal X-ray and TeV gamma-ray emission from the remnant. The positional coincidence and the matching extended emission allow us to identify the LAT source with SNR RX J1713.7-3946. The spectrum of the source can be described by a very hard power law with a photon index of Gamma = 1.5 +/- 0.1 that coincides in normalization with the steeper H. E. S. S.-detected gamma-ray spectrum at higher energies. The broadband gamma-ray emission is consistent with a leptonic origin as the dominant mechanism for the gamma-ray emission.
KW  - acceleration of particles
KW  - gamma rays: general
KW  - gamma rays: ISM
KW  - ISM: individual objects (RX J1713.7-3946)
KW  - ISM: supernova remnants
KW  - radiation mechanisms: non-thermal
Y1  - 2011
U6  - https://doi.org/10.1088/0004-637X/734/1/28
SN  - 0004-637X
VL  - 734
IS  - 1
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  -