I.A. Vartanyants

Publications (47)73.31 Total impact

• Article: Orientation Determination in Single Particle X-ray Coherent Diffraction Imaging Experiments

  O. M. Yefanov, I. A. Vartanyants
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  ABSTRACT: Single particle diffraction imaging experiments at free-electron lasers (FEL) have a great potential for structure determination of reproducible biological specimens that can not be crystallized. One of the challenges in processing the data from such an experiment is to determine correct orientation of each diffraction pattern from samples randomly injected in the FEL beam. We propose an algorithm (see also O. Yefanov et al., Photon Science - HASYLAB Annual Report 2010) that can solve this problem and can be applied to samples from tens of nanometers to microns in size, measured with sub-nanometer resolution in the presence of noise. This is achieved by the simultaneous analysis of a large number of diffraction patterns corresponding to different orientations of the particles. The algorithms efficiency is demonstrated for two biological samples, an artificial protein structure without any symmetry and a virus with icosahedral symmetry. Both structures are few tens of nanometers in size and consist of more than 100 000 non-hydrogen atoms. More than 10 000 diffraction patterns with Poisson noise were simulated and analyzed for each structure. Our simulations indicate the possibility to achieve resolution of about 3.3 {\AA} at 3 {\AA} wavelength and incoming flux of 10^{12} photons per pulse focused to 100\times 100 nm^2.
  02/2013;
• Article: Hanbury Brown and Twiss interferometry at a free-electron laser

  A. Singer, U. Lorenz, F. Sorgenfrei, N. Gerasimova, J. Gulden, O. M. Yefanov, R. P. Kurta, A. Shabalin, R. Dronyak, R. Treusch, V. Kocharyan, E. Weckert, W. Wurth, I. A. Vartanyants
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  ABSTRACT: We present measurements of second- and higher-order intensity correlation functions (so-called Hanbury Brown and Twiss experiment) performed at the free-electron laser (FEL) FLASH in the non-linear regime of its operation. We demonstrate the high transverse coherence properties of the FEL beam with a degree of transverse coherence of about 80% and degeneracy parameter of the order 10^9 that makes it similar to laser sources. Intensity correlation measurements in spatial and frequency domain gave an estimate of the FEL average pulse duration of 50 fs. Our measurements of the higher-order correlation functions indicate that FEL radiation obeys Gaussian statistics, which is characteristic to chaotic sources.
  01/2013;
• Article: Impact of ultrafast electronic damage in single-particle x-ray imaging experiments.

  U Lorenz, N M Kabachnik, E Weckert, I A Vartanyants
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  ABSTRACT: In single-particle coherent x-ray diffraction imaging experiments, performed at x-ray free-electron lasers (XFELs), samples are exposed to intense x-ray pulses to obtain single-shot diffraction patterns. The high intensity induces electronic dynamics on the femtosecond time scale in the system, which can reduce the contrast of the obtained diffraction patterns and adds an isotropic background. We quantify the degradation of the diffraction pattern from ultrafast electronic damage by performing simulations on a biological sample exposed to x-ray pulses with different parameters. We find that the contrast is substantially reduced and the background is considerably strong only if almost all electrons are removed from their parent atoms. This happens at fluences of at least one order of magnitude larger than provided at currently available XFEL sources.
  Physical Review E 11/2012; 86(5-1):051911. · 2.26 Impact Factor
• Article: Spatial and temporal coherence properties of single free-electron laser pulses.

  A Singer, F Sorgenfrei, A P Mancuso, N Gerasimova, O M Yefanov, J Gulden, T Gorniak, T Senkbeil, A Sakdinawat, Y Liu, D Attwood, S Dziarzhytski, D D Mai, R Treusch, E Weckert, T Salditt, A Rosenhahn, W Wurth, I A Vartanyants
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  ABSTRACT: The experimental characterization of the spatial and temporal coherence properties of the free-electron laser in Hamburg (FLASH) at a wavelength of 8.0 nm is presented. Double pinhole diffraction patterns of single femtosecond pulses focused to a size of about 10×10 μm² were measured. A transverse coherence length of 6.2 ± 0.9 μm in the horizontal and 8.7 ± 1.0 μm in the vertical direction was determined from the most coherent pulses. Using a split and delay unit the coherence time of the pulses produced in the same operation conditions of FLASH was measured to be 1.75 ± 0.01 fs. From our experiment we estimated the degeneracy parameter of the FLASH beam to be on the order of 10¹⁰ to 10¹¹, which exceeds the values of this parameter at any other source in the same energy range by many orders of magnitude.
  Optics Express 07/2012; 20(16):17480-95. · 3.59 Impact Factor
• Article: Dynamics of colloidal crystals studied by pump-probe experiments at FLASH

  R. Dronyak, J. Gulden, O. M. Yefanov, A. Singer, T. Gorniak, T. Senkbeil, J. -M. Meijer, A. Al-Shemmary, J. Hallmann, D. D. Mai, [......], U. Lorenz, A. V. Petukhov, S. Duesterer, R. Treusch, M. N. Strikhanov, E. Weckert, A. P. Mancuso, T. Salditt, A. Rosenhahn, I. A. Vartanyants
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  ABSTRACT: We present a time-resolved infrared (IR) pump and extreme-ultraviolet (XUV) probe diffraction experiment to investigate ultrafast structural dynamics in colloidal crystals with picosecond resolution. The experiment was performed at the FLASH facility at DESY with a fundamental wavelength of 8 nm. In our experiment, the temporal changes of Bragg peaks were analyzed and their frequency components were calculated using Fourier analysis. Periodic modulations in the colloidal crystal were localized at a frequency of about 4-5 GHz. Based on the Lamb theory, theoretical calculations of vibrations of the isotropic elastic polystyrene spheres of 400 nm in size reveal a 5.07 GHz eigenfrequency of the ground (breathing) mode.
  06/2012;
• Article: Three dimensional reconstruction of nanoislands from grazing-incidence small-angle X-ray scattering

  O. M. Yefanov, I. A. Vartanyants
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  ABSTRACT: The combination of grazing-incidence small-angle x-ray scattering (GISAXS) with tomographic methods and phase retrieval is proposed for the reconstruction of the three-dimensional (3D) electron density of nanometer sized objects. In this approach GISAXS data from a small object are collected successively at different azimuthal angular positions. This 3D intensity distribution in reciprocal space is used for the phase retrieval and reconstruction of the 3D electron density. The power of our approach is demonstrated in a series of calculations performed in the frame of kinematical and distorted-wave Born approximation (DWBA) theories for the case of GISAXS scattering on a 200 nm island in the form of truncated pyramid.
  The European Physical Journal Special Topics 04/2012; 167(1):81-86. · 1.56 Impact Factor
• Article: The soft x-ray instrument for materials studies at the linac coherent light source x-ray free-electron laser.

  W F Schlotter, J J Turner, M Rowen, P Heimann, M Holmes, O Krupin, M Messerschmidt, S Moeller, J Krzywinski, R Soufli, [......], B Abbey, K A Nugent, H Sinn, J Lüning, S Schaffert, S Eisebitt, W-S Lee, A Scherz, A R Nilsson, W Wurth
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  ABSTRACT: The soft x-ray materials science instrument is the second operational beamline at the linac coherent light source x-ray free electron laser. The instrument operates with a photon energy range of 480-2000 eV and features a grating monochromator as well as bendable refocusing mirrors. A broad range of experimental stations may be installed to study diverse scientific topics such as: ultrafast chemistry, surface science, highly correlated electron systems, matter under extreme conditions, and laboratory astrophysics. Preliminary commissioning results are presented including the first soft x-ray single-shot energy spectrum from a free electron laser.
  The Review of scientific instruments 04/2012; 83(4):043107. · 1.52 Impact Factor
• Article: Three-dimensional structure of a single colloidal crystal grain studied by coherent x-ray diffraction.

  J Gulden, O M Yefanov, A P Mancuso, R Dronyak, A Singer, V Bernátová, A Burkhardt, O Polozhentsev, A Soldatov, M Sprung, I A Vartanyants
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  ABSTRACT: A coherent x-ray diffraction experiment was performed on an isolated colloidal crystal grain at the coherence beamline P10 at PETRA III. Using azimuthal rotation scans the three-dimensional (3D) scattered intensity from the sample in the far-field was measured. It includes several Bragg peaks as well as the coherent interference around these peaks. The analysis of the scattered intensity reveals the presence of plane defects in a single grain of the colloidal sample. We confirm these findings by model simulations. In these simulations we also analyze the experimental conditions required to phase the 3D diffraction pattern from a single colloidal grain. This approach has the potential to produce a high resolution image of the sample revealing its inner structure, with possible structural defects.
  Optics Express 02/2012; 20(4):4039-49. · 3.59 Impact Factor
• Article: Coherent X‐ray nanodiffraction on single GaAs nanowires

  J. Gulden, S. O. Mariager, A. P. Mancuso, O. M. Yefanov, J. Baltser, P. Krogstrup, J. Patommel, M. Burghammer, R. Feidenhans'l, I. A. Vartanyants
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  ABSTRACT: Coherent X-ray nanodiffraction was applied to investigate single GaAs nanowires. Using the nanofocus hard X-ray setup at ID13 of the ESRF, the diffraction signal from isolated nanowires was measured. The diffraction patterns were recorded for different rotations of the sample. These diffraction patterns were then combined to yield three-dimensional information around a Wurzite [101] Bragg peak.
  Physica Status Solidi (A) Applications and Materials 10/2011; 208(11):2495 - 2498. · 1.46 Impact Factor
• Source

  Available from: Keith Alexander Nugent

  Article: Coherence properties of individual femtosecond pulses of an x-ray free-electron laser.

  I A Vartanyants, A Singer, A P Mancuso, O M Yefanov, A Sakdinawat, Y Liu, E Bang, G J Williams, G Cadenazzi, B Abbey, [......], V Joshi, J Krzywinski, R Soufli, M Fernandez-Perea, S Hau-Riege, A G Peele, Y Feng, O Krupin, S Moeller, W Wurth
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  ABSTRACT: Measurements of the spatial and temporal coherence of single, femtosecond x-ray pulses generated by the first hard x-ray free-electron laser, the Linac Coherent Light Source, are presented. Single-shot measurements were performed at 780 eV x-ray photon energy using apertures containing double pinholes in "diffract-and-destroy" mode. We determined a coherence length of 17  μm in the vertical direction, which is approximately the size of the focused Linac Coherent Light Source beam in the same direction. The analysis of the diffraction patterns produced by the pinholes with the largest separation yields an estimate of the temporal coherence time of 0.55 fs. We find that the total degree of transverse coherence is 56% and that the x-ray pulses are adequately described by two transverse coherent modes in each direction. This leads us to the conclusion that 78% of the total power is contained in the dominant mode.
  Physical Review Letters 09/2011; 107(14):144801. · 7.37 Impact Factor
• Article: X-ray holographic microscopy with zone plates applied to biological samples in the water window using 3rd harmonic radiation from the free-electron laser FLASH.

  T Gorniak, R Heine, A P Mancuso, F Staier, C Christophis, M E Pettitt, A Sakdinawat, R Treusch, N Guerassimova, J Feldhaus, C Gutt, G Grübel, S Eisebitt, A Beyer, A Gölzhäuser, E Weckert, M Grunze, I A Vartanyants, A Rosenhahn
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  ABSTRACT: The imaging of hydrated biological samples - especially in the energy window of 284-540 eV, where water does not obscure the signal of soft organic matter and biologically relevant elements - is of tremendous interest for life sciences. Free-electron lasers can provide highly intense and coherent pulses, which allow single pulse imaging to overcome resolution limits set by radiation damage. One current challenge is to match both the desired energy and the intensity of the light source. We present the first images of dehydrated biological material acquired with 3rd harmonic radiation from FLASH by digital in-line zone plate holography as one step towards the vision of imaging hydrated biological material with photons in the water window. We also demonstrate the first application of ultrathin molecular sheets as suitable substrates for future free-electron laser experiments with biological samples in the form of a rat fibroblast cell and marine biofouling bacteria Cobetia marina.
  Optics Express 06/2011; 19(12):11059-70. · 3.59 Impact Factor
• Article: Coherence properties of hard x-ray synchrotron sources and x-ray free-electron lasers

  I A Vartanyants, A Singer
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  ABSTRACT: A general theoretical approach based on the results of statistical optics is used for the analysis of the transverse coherence properties of third generation hard x-ray synchrotron sources and x-ray free-electron lasers (XFEL). Correlation properties of the wavefields are calculated at different distances from an equivalent Gaussian Schell-model source. This model is used to describe coherence properties of the 5 m undulator source at the synchrotron storage ring PETRA III. In the case of XFEL sources the decomposition of the statistical fields into a sum of independently propagating transverse modes is used for the analysis of the coherence properties of these new sources. A detailed calculation is performed for the parameters of the SASE1 undulator at the European XFEL. It is demonstrated that only a few modes contribute significantly to the total radiation field of that source.
  New Journal of Physics 03/2010; 12(3):035004. · 4.18 Impact Factor
• Article: Coherent diffractive imaging of biological samples at synchrotron and free electron laser facilities.

  A P Mancuso, O M Yefanov, I A Vartanyants
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  ABSTRACT: Coherent X-ray diffractive imaging (CXDI) is a new imaging technique that offers the potential to image non-crystalline materials to sub-nanometer resolutions. Here we review the progress in CXDI of biological samples at both synchrotron and free electron laser (FEL) sources. We outline the experimental design of a CXDI experiment and summarize the iterative phase retrieval techniques that are used to produce images from the measured diffraction patterns. We describe a selection of key experiments performed in bio-imaging with CXDI from synchrotron sources, and we discuss the proof-of-principle experiments performed at FLASH at DESY in Hamburg. Finally, we show through simulation that for realistic parameters of hard X-ray FELs a resolution of a few nanometers may be achieved for individual biological objects imaged with single pulses of FEL radiation. Furthermore, we revise how this resolution may be improved to the sub-nanometer range if we image multiple copies of samples with a reproducible structure.
  Journal of biotechnology 02/2010; 149(4):229-37. · 2.88 Impact Factor
• Source

  Available from: cnrs.fr

  Article: Coherence measurements and coherent diffractive imaging at FLASH

  I A Vartanyants, A P Mancuso, A Singer, O M Yefanov, J Gulden
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  ABSTRACT: We present an overview of recent experiments performed at the free-electron laser (FEL) FLASH at DESY in Hamburg. Experiments were focused on coherence measurements and coherent x-ray diffractive imaging (CXDI) of periodic and non-periodic biological samples. Young's double slit experiment was performed at FLASH to measure its coherence properties at a fundamental wavelength of 13.7 nm. Additionally, a uniformly redundant array (URA) was used to measure coherence properties of the 3 rd harmonic (2.7 nm) of an 8 nm fundamental wavelength at FLASH. Coherent imaging of a two-dimensional (2D) finite crystal structure using a single pulse train of FLASH radiation was demonstrated. We show that the structure is reconstructed to the detector limited resolution of 220 nm, given an adequate signal to noise ratio. We have also employed CXDI in a non-destructive regime to compare images of a biological sample using single, femtosecond pulses of FLASH radiation. We have verified that images reconstructed using CXDI are similar for statistically different FEL pulses. We have also demonstrated Fourier transform holography (FTH) of the same biological sample and present diffraction data measured at the third harmonic of FLASH, reaching into the water window.
  Journal of Physics B: Atomic, Molecular and Optical Physics. 01/2010; 432530(87).
• Source

  Available from: ArXiv

  Article: Analysis of Coherence Properties of 3-rd Generation Synchrotron Sources and Free-Electron Lasers

  I.A. Vartanyants, A Singer
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  ABSTRACT: A general theoretical approach based on the results of statistical optics is used for the analysis of the transverse coherence properties of 3-rd generation synchrotron sources and x-ray free-electron lasers (XFEL). Correlation properties of the wavefields are calculated at different distances from an equivalent Gaussian Schell-model source. This model is used to describe coherence properties of the five meter undulator source at the synchrotron storage ring PETRA III. In the case of XFEL sources the decomposition of the statistical fields into a sum of independently propagating transverse modes is used for the analysis of the coherence properties of these new sources. A detailed calculation is performed for the parameters of the SASE1 undulator at the European XFEL. It is demonstrated that only a few modes contribute significantly to the total radiation field of that source. Comment: 30 pages, 12 figures
  07/2009;
• Article: Coherent diffraction tomography of nanoislands from grazing-incidence small-angle x-ray scattering

  O. M. Yefanov, A. V. Zozulya, I. A. Vartanyants, J. Stangl, C. Mocuta, T. H. Metzger, G. Bauer, T. Boeck, M. Schmidbauer
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  ABSTRACT: The combination of grazing-incidence small-angle x-ray scattering with tomographic and phase retrieval methods is presented for the reconstruction of the three-dimensional (3D) electron density of nanometer sized objects. The measured 3D intensity distribution in reciprocal space is used for the phase retrieval and reconstruction of the shape and electron density of epitaxial SiGe islands with the shape of truncated pyramids with a 200 nm square base. A spatial resolution below 20 nm demonstrated in this work cannot be achieved by traditional tomographic methods.
  Applied Physics Letters 03/2009; 94(12):123104-123104-3. · 3.84 Impact Factor
• Article: Coherent-pulse 2D crystallography using a free-electron laser x-ray source.

  A P Mancuso, A Schropp, B Reime, L-M Stadler, A Singer, J Gulden, S Streit-Nierobisch, C Gutt, G Grübel, J Feldhaus, [......], N Guerassimova, K Honkavaara, V Kocharyan, R Treusch, E Saldin, S Schreiber, E A Schneidmiller, M V Yurkov, E Weckert, I A Vartanyants
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  ABSTRACT: Coherent diffractive imaging for the reconstruction of a two-dimensional (2D) finite crystal structure with a single pulse train of free-electron laser radiation at 7.97 nm wavelength is demonstrated. This measurement shows an advance on traditional coherent imaging techniques by applying it to a periodic structure. It is also significant that this approach paves the way for the imaging of the class of specimens which readily form 2D, but not three-dimensional crystals. We show that the structure is reconstructed to the detected resolution, given an adequate signal-to-noise ratio.
  Physical Review Letters 02/2009; 102(3):035502. · 7.37 Impact Factor
• Article: Transverse-coherence properties of the free-electron-laser FLASH at DESY.

  A Singer, I A Vartanyants, M Kuhlmann, S Duesterer, R Treusch, J Feldhaus
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  ABSTRACT: A general theoretical approach based on the decomposition of statistical fields into a sum of independently propagating transverse modes was used for the analysis of the coherence properties of the new free-electron laser source FLASH operated at 13.7 nm wavelength. The analysis shows that several transverse modes are contributing to the total radiation field of FLASH. The results of theoretical calculations are compared with measurements using Young's double-slit experiment. The coherence lengths in the horizontal and in the vertical directions 20 m downstream from the source are estimated at 300 and 250 microm, respectively.
  Physical Review Letters 01/2009; 101(25):254801. · 7.37 Impact Factor
• Article: Beyond the ensemble average: X-ray microdiffraction analysis of single SiGe islands

  C. Mocuta, J. Stangl, K. Mundboth, T. H. Metzger, G. Bauer, I. A. Vartanyants, M. Schmidbauer, T. Boeck
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  ABSTRACT: X-ray microdiffraction is used to analyze strain and composition profiles in individual micron-sized SiGe islands grown by liquid phase epitaxy on Si(001) substrates. From the variation of the scattered intensity while scanning the sample through a focused x-ray beam of few μm size, an image of the island distribution on the sample is created. Using this image it is possible to identify particular islands and select them for analysis one by one. The Ge and strain distribution within each island is obtained from the intensity distribution in reciprocal space measured for several individual islands. The detailed shape of each measured island is obtained from scanning electron microscopy. Apart from truncated pyramid-shaped islands, we detect and characterize a small number of flat islands and show that they represent an earlier growth stage of the pyramidal shaped ones. This analysis is only possible by combining the local x-ray diffraction with scanning electron microscopy on exactly the same islands.
  Phys. Rev. B. 06/2008; 77(24).
• Article: Crystal truncation planes revealed by three-dimensional reconstruction of reciprocal space

  I. A. Vartanyants, A. V. Zozulya, K. Mundboth, O. M. Yefanov, M.-I. Richard, E. Wintersberger, J. Stangl, A. Diaz, C. Mocuta, T. H. Metzger, G. Bauer, T. Boeck, M. Schmidbauer
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  ABSTRACT: For studying surface properties of nanocrystals, we present an approach based on a combination of the grazing incidence small angle x-ray scattering (GISAXS) technique and tomographic methods. In this approach, GISAXS data from a micro- or nanometer sized object are collected successively at different azimuthal angular positions, which makes it possible to measure the whole three-dimensional (3D) intensity distribution in reciprocal space. As an example, the full 3D reciprocal space intensity originating from the truncated epitaxially grown {111} facetted SiGe pyramids with a square base on (001) Si substrate was measured. This technique enables us to observe and explain crystal truncation planes which originate from scattering on the edges of the nanocrystals.
  Phys. Rev. B. 03/2008; 77(11).