@article{DzhigaevShabalinStankevicetal.2016, author = {Dzhigaev, D. and Shabalin, A. and Stankevic, T. and Lorenz, Ulf and Kurta, R. P. and Seiboth, F. and Wallentin, J. and Singer, A. and Lazarev, S. and Yefanov, O. M. and Borgstrom, M. and Strikhanov, M. N. and Samuelson, L. and Falkenberg, G. and Schroer, C. G. and Mikkelsen, A. and Vartanyants, I. A.}, title = {Bragg coherent x-ray diffractive imaging of a single indium phosphide nanowire}, series = {Journal of optics}, volume = {18}, journal = {Journal of optics}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {2040-8978}, doi = {10.1088/2040-8978/18/6/064007}, pages = {10}, year = {2016}, abstract = {Three-dimensional (3D) Bragg coherent x-ray diffractive imaging (CXDI) with a nanofocused beam was applied to quantitatively map the internal strain field of a single indium phosphide nanowire. The quantitative values of the strain were obtained by pre-characterization of the beam profile with transmission ptychography on a test sample. Our measurements revealed the 3D strain distribution in a region of 150 nm below the catalyst Au particle. We observed a slight gradient of the strain in the range of +/- 0.6\% along the [111] growth direction of the nanowire. We also determined the spatial resolution in our measurements to be about 10 nm in the direction perpendicular to the facets of the nanowire. The CXDI measurements were compared with the finite element method simulations and show a good agreement with our experimental results. The proposed approach can become an effective tool for in operando studies of the nanowires.}, language = {en} } @article{MarciszJasseyKosakyanetal.2020, author = {Marcisz, Katarzyna and Jassey, Vincent E. J. and Kosakyan, Anush and Krashevska, Valentyna and Lahr, Daniel J. G. and Lara, Enrique and Lamentowicz, Lukasz and Lamentowicz, Mariusz and Macumber, Andrew and Mazei, Yuri and Mitchell, Edward A. D. and Nasser, Nawaf A. and Patterson, R. Timothy and Roe, Helen M. and Singer, David and Tsyganov, Andrey N. and Fournier, Bertrand}, title = {Testate amoeba functional traits and their use in paleoecology}, series = {Frontiers in Ecology and Evolution}, volume = {8}, journal = {Frontiers in Ecology and Evolution}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-701X}, doi = {10.3389/fevo.2020.575966}, pages = {28}, year = {2020}, abstract = {This review provides a synthesis of current knowledge on the morphological and functional traits of testate amoebae, a polyphyletic group of protists commonly used as proxies of past hydrological changes in paleoecological investigations from peatland, lake sediment and soil archives. A trait-based approach to understanding testate amoebae ecology and paleoecology has gained in popularity in recent years, with research showing that morphological characteristics provide complementary information to the commonly used environmental inferences based on testate amoeba (morpho-)species data. We provide a broad overview of testate amoeba morphological and functional traits and trait-environment relationships in the context of ecology, evolution, genetics, biogeography, and paleoecology. As examples we report upon previous ecological and paleoecological studies that used trait-based approaches, and describe key testate amoebae traits that can be used to improve the interpretation of environmental studies. We also highlight knowledge gaps and speculate on potential future directions for the application of trait-based approaches in testate amoeba research.}, language = {en} } @article{GorobtsovMercurioBrenneretal.2017, author = {Gorobtsov, O. Yu. and Mercurio, G. and Brenner, G. and Lorenz, Ulf and Gerasimova, N. and Kurta, R. P. and Hieke, F. and Skopintsev, P. and Zaluzhnyy, I. and Lazarev, S. and Dzhigaev, D. and Rose, M. and Singer, A. and Wurth, W. and Vartanyants, I. A.}, title = {Statistical properties of a free-electron laser revealed by Hanbury Brown-Twiss interferometry}, series = {Physical review : A, Atomic, molecular, and optical physics}, volume = {95}, journal = {Physical review : A, Atomic, molecular, and optical physics}, number = {2}, publisher = {American Physical Society}, address = {College Park}, issn = {2469-9926}, doi = {10.1103/PhysRevA.95.023843}, pages = {16}, year = {2017}, abstract = {We present a comprehensive experimental analysis of statistical properties of the self-amplified spontaneous emission free-electron laser (FEL) FLASH by means of Hanbury Brown and Twiss interferometry. The experiments were performed at FEL wavelengths of 5.5, 13.4, and 20.8 nm. We determined the second-order intensity correlation function for all wavelengths and different operation conditions of FLASH. In all experiments a high degree of spatial coherence (above 50\%) was obtained. Our analysis performed in spatial and spectral domains provided us with the independent measurements of an average pulse duration of the FEL that were below 60 fs. To explain the complicated behavior of the second-order intensity correlation function we developed an advanced theoretical model that includes the presence of multiple beams and external positional jitter of the FEL pulses. By this analysis we determined that in one of the experiments external positional jitter was about 25\% of the beam size. We envision that methods developed in our study will be used widely for analysis and diagnostics of FEL radiation.}, language = {en} } @article{SulyanovaShabalinZozulyaetal.2015, author = {Sulyanova, Elena A. and Shabalin, Anatoly and Zozulya, Alexey V. and Meijer, Janne-Mieke and Dzhigaev, Dmitry and Gorobtsov, Oleg and Kurta, Ruslan P. and Lazarev, Sergey and Lorenz, Ulf and Singer, Andrej and Yefanov, Oleksandr and Zaluzhnyy, Ivan and Besedin, Ilya and Sprung, Michael and Petukhov, Andrei V. and Vartanyants, Ivan A.}, title = {Structural Evolution of Colloidal Crystal Films in the Process of Melting Revealed by Bragg Peak Analysis}, series = {Langmuir}, volume = {31}, journal = {Langmuir}, number = {19}, publisher = {American Chemical Society}, address = {Washington}, issn = {0743-7463}, doi = {10.1021/la504652z}, pages = {5274 -- 5283}, year = {2015}, abstract = {In situ X-ray diffraction studies of structural evolution of colloidal crystal films formed by polystyrene spherical particles upon incremental heating are reported. The Bragg peak parameters, such as peak position, integrated intensity, and radial and azimuthal widths were analyzed as a function of temperature. A quantitative study of colloidal crystal lattice distortions and mosaic spread as a function of temperature was carried out using Williamson-Hall plots based on mosaic block model. The temperature dependence of the diameter of polystyrene particles was obtained from the analysis of Bragg peaks, and the form factor contribution extracted from the diffraction patterns. Four stages of structural evolution in a colloidal crystal upon heating were identified. Based on this analysis, a model of the heating and melting process in the colloidal crystal film is suggested.}, language = {en} } @article{LiemohnMcColloughJordanovaetal.2018, author = {Liemohn, Michael W. and McCollough, James P. and Jordanova, Vania K. and Ngwira, Chigomezyo M. and Morley, Steven K. and Cid, Consuelo and Tobiska, W. Kent and Wintoft, Peter and Ganushkina, Natalia Yu and Welling, Daniel T. and Bingham, Suzy and Balikhin, Michael A. and Opgenoorth, Hermann J. and Engel, Miles A. and Weigel, Robert S. and Singer, Howard J. and Buresova, Dalia and Bruinsma, Sean and Zhelavskaya, Irina and Shprits, Yuri Y. and Vasile, Ruggero}, title = {Model Evaluation Guidelines for Geomagnetic Index Predictions}, series = {Space Weather: The International Journal of Research and Applications}, volume = {16}, journal = {Space Weather: The International Journal of Research and Applications}, number = {12}, publisher = {American Geophysical Union}, address = {Washington}, issn = {1542-7390}, doi = {10.1029/2018SW002067}, pages = {2079 -- 2102}, year = {2018}, abstract = {Geomagnetic indices are convenient quantities that distill the complicated physics of some region or aspect of near-Earth space into a single parameter. Most of the best-known indices are calculated from ground-based magnetometer data sets, such as Dst, SYM-H, Kp, AE, AL, and PC. Many models have been created that predict the values of these indices, often using solar wind measurements upstream from Earth as the input variables to the calculation. This document reviews the current state of models that predict geomagnetic indices and the methods used to assess their ability to reproduce the target index time series. These existing methods are synthesized into a baseline collection of metrics for benchmarking a new or updated geomagnetic index prediction model. These methods fall into two categories: (1) fit performance metrics such as root-mean-square error and mean absolute error that are applied to a time series comparison of model output and observations and (2) event detection performance metrics such as Heidke Skill Score and probability of detection that are derived from a contingency table that compares model and observation values exceeding (or not) a threshold value. A few examples of codes being used with this set of metrics are presented, and other aspects of metrics assessment best practices, limitations, and uncertainties are discussed, including several caveats to consider when using geomagnetic indices. Plain Language Summary One aspect of space weather is a magnetic signature across the surface of the Earth. The creation of this signal involves nonlinear interactions of electromagnetic forces on charged particles and can therefore be difficult to predict. The perturbations that space storms and other activity causes in some observation sets, however, are fairly regular in their pattern. Some of these measurements have been compiled together into a single value, a geomagnetic index. Several such indices exist, providing a global estimate of the activity in different parts of geospace. Models have been developed to predict the time series of these indices, and various statistical methods are used to assess their performance at reproducing the original index. Existing studies of geomagnetic indices, however, use different approaches to quantify the performance of the model. This document defines a standardized set of statistical analyses as a baseline set of comparison tools that are recommended to assess geomagnetic index prediction models. It also discusses best practices, limitations, uncertainties, and caveats to consider when conducting a model assessment.}, language = {en} }