Science.gov

Sample records for anomalous small-angle x-ray

  1. Radiation embrittlement studies using anomalous small-angle x-ray scattering

    SciTech Connect

    Alexander, D. E.; Kestel, B. J.; Seifert, S.; Jemian, P. R.; Odette, G. R.; Klingensmith, D.; Gragg, D.

    1999-12-06

    Anomalous small angle x-ray scattering (ASAXS) was performed on an Fe-O.9 wt.% Cu-1.0 wt.% Mn alloy subjected to annealing or electron irradiation. ASAXS takes advantage of natural variations in the atomic scattering factor which exist at energies very near an element's x-ray absorption edge. By performing systematic SAXS experiments at energies near these absorption edges of the constituent alloy elements it is possible to vary the contrast of scattering centers containing the elements and in doing so quantify scatterer composition. The results of such an analysis for the samples in this work indicate the presence of Cu-rich, Cu{sub 85}Mn{sub 15} precipitates in the alloy. By applying the maximum entropy technique to the scattering data, it was possible to extract size distributions of scattering centers fog the different treatments. The results demonstrate the ability to detect and characterize small (11 {angstrom} radius) scatterers at quite low irradiation damage levels (5x10{sup {minus} 4} displacements per atom).

  2. Anomalous small angle x-ray scattering studies of amorphous metal-germanium alloys

    SciTech Connect

    Rice, M.

    1993-12-01

    This dissertation addresses the issue of composition modulation in sputtered amorphous metal-germanium thin films with the aim of understanding the intermediate range structure of these films as a function of composition. The investigative tool used in this work is anomalous small-angle X-ray scattering (ASAXS). The primary focus of this investigation is the amorphous iron-germanium (a-Fe{sub x}Ge{sub 100-x}) system with particular emphasis on the semiconductor-rich regime. Brief excursions are made into the amorphous tungsten-germanium (a-W{sub x}Ge{sub 100-x}) and the amorphous molybdenum-germanium (a-Mo{sub x}Ge{sub 100-x}) systems. All three systems exhibit an amorphous structure over a broad composition range extending from pure amorphous germanium to approximately 70 atomic percent metal when prepared as sputtered films. Across this composition range the structures change from the open, covalently bonded, tetrahedral network of pure a-Ge to densely packed metals. The structural changes are accompanied by a semiconductor-metal transition in all three systems as well as a ferromagnetic transition in the a-Fe{sub x}Ge{sub 100-x} system and a superconducting transition in the a-Mo{sub x}Ge{sub 100-x} system. A long standing question, particularly in the a-Fe{sub x}Ge{sub 100-x} and the a-Mo{sub x}Ge{sub 100-x} systems, has been whether the structural changes (and therefore the accompanying electrical and magnetic transitions) are accomplished by homogeneous alloy formation or phase separation. The application of ASAXS to this problem proves unambiguously that fine scale composition modulations, as distinct from the simple density fluctuations that arise from cracks and voids, are present in the a-Fe{sub x}Ge{sub 100-x}, a-W{sub x}Ge{sub 100-x}, and a-Mo{sub x}Ge{sub 100-x} systems in the semiconductor-metal transition region. Furthermore, ASAXS shows that germanium is distributed uniformly throughout each sample in the x<25 regime of all three systems.

  3. Anomalous grazing incidence small-angle x-ray scattering studies of platinum nanoparticles formed by cluster deposition.

    PubMed

    Lee, Byeongdu; Seifert, Sönke; Riley, Stephen J; Tikhonov, George; Tomczyk, Nancy A; Vajda, Stefan; Winans, Randall E

    2005-08-15

    The size evolution of platinum nanoparticles formed on a SiO2/Si(111) substrate as a function of the level of surface coverage with deposited clusters has been investigated. The anisotropic shapes of sub-nanometer-size nanoparticles are changed to isotropic on the amorphous substrate as their sizes increased. Using anomalous grazing incidence small-angle x-ray scattering (AGISAXS), the scattering from nanoparticles on the surface of a substrate is well separated from that of surface roughness and fluorescence. We show that AGISAXS is a very effective method to subtract the background and can provide unbiased information about particle sizes of less than 1 nm. PMID:16229604

  4. Anomalous small-angle X-ray scattering of nanoporous two-phase atomistic models for amorphous silicon–germanium alloys

    SciTech Connect

    Chehaidar, A.

    2015-09-15

    The present work deals with a detailed analysis of the anomalous small-angle X-ray scattering in amorphous silicon–germanium alloy using the simulation technique. We envisage the nanoporous two-phase alloy model consisting in a mixture of Ge-rich and Ge-poor domains and voids at the nanoscale. By substituting Ge atoms for Si atoms in nanoporous amorphous silicon network, compositionally heterogeneous alloys are generated with various composition-contrasts between the two phases. After relaxing the as-generated structure, we compute its radial distribution function, and then we deduce by the Fourier transform technique its anomalous X-ray scattering pattern. Using a smoothing procedure, the computed X-ray scattering patterns are corrected for the termination errors due to the finite size of the model, allowing so a rigorous quantitative analysis of the anomalous small-angle scattering. Our simulation shows that, as expected, the anomalous small-angle X-ray scattering technique is a tool of choice for characterizing compositional heterogeneities coexisting with structural inhomogeneities in an amorphous alloy. Furthermore, the sizes of the compositional nanoheterogeneities, as measured by anomalous small-angle X-ray scattering technique, are X-ray energy independent. A quantitative analysis of the separated reduced anomalous small-angle X-ray scattering, as defined in this work, provided a good estimate of their size.

  5. New method for analyzing the periodic structure of multilayer by differential anomalous small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Kato, K.; Matsubara, E.; Saito, M.; Kosaka, T.; Waseda, Y.; Inomata, K.

    1995-03-01

    A new method has been proposed for analyzing the periodic structure of a multilayered sample by the differential anomalous small-angle X-ray scattering method in the reflection geometry. The scattering peaks due to the periodically layered structure in the small angle region are often observed with a large background intensity. These peak intensities strongly depend upon the anomalous dispersion terms of the constituent element near its absorption edge. Thus, by taking a difference of these peak intensities observed at two energies near the edge, the scattering intensity attributed to various causes can be accurately eliminated except the periodically layered structure. Namely, only the intrinsic peak intensities are precisely determined by this method. Furthermore, this method is the most effective for analyzing the periodic structures of multilayers composed of the next neighboring elements in the periodic table. The experimental details and the usefulness of the present new method have been presented by obtaining the concentration profile of a Cu/Co multilayer using the peak intensity variation arising from the anomalous dispersion terms of Cu and Co near their K absorption edges.

  6. Anomalous small angle x-ray scattering studies of heavy metal ion solvation behavior in clay minerals

    SciTech Connect

    Carrado, K.A.; Thiyagarajan, P.; Winans, R.E.; Song, Kang

    1997-09-01

    The authors have exploited anomalous small angle x-ray scattering (ASAXS) to monitor the solvation behavior of Cu(II), Er(III) and Yb(III) ions within the interlayers of the natural aluminosilicate clay mineral montmorillonite. The ASAXS technique can reveal the distribution of specific metallic species within a heterogeneous and disordered matrix. The variations of signal intensity as a function of absorption energy were monitored for all of the metal-clays as a function of hydration. Two different hydration levels were probed: as prepared at ambient conditions, or so-called {open_quotes}dry{close_quotes} powders, and {open_quotes}wet{close_quotes} pastes. ASAXS intensities should increase with absorption energy if the metal ion is associated with the interlayer solvent (water in this case), and decrease if the metal ion is associated with the solid matrix. The results show that: (1) Cu(II) is solvated within the interlayers of the wet sample, as expected, and (2) Er(III) and Yb(III) decrease in ASAXS intensity with increased hydration. This latter result was not expected and there is speculation that these ions have associated as hydrolyzed products with the clay surface. The basic principles underlying SAXS and ASAXS will also be presented in this paper.

  7. The distribution of Sr2+ counterions around polyacrylate chains analyzed by anomalous small-angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Goerigk, G.; Schweins, R.; Huber, K.; Ballauff, M.

    2004-05-01

    The distribution of Sr counterions around negatively charged sodium polyacrylate chains (NaPA) in aqueous solution was studied by anomalous small-angle X-ray scattering. Different ratios of the concentrations of SrCl2/[NaPA] reveal dramatic changes in the scattering curves. At the lower ratio the scattering curves indicate a coil-like behavior, while at the higher ratio the scattering curves are contracted to smaller q-values, caused by the collapse of the NaPA coil. The form factor of the scattering contribution of the counterions was separated and analyzed. For the scattering curves of the collapsed chains, this analysis agrees with the model of a pearl necklace, consisting of collapsed sphere-like subdomains which are connected by stretched chain segments. An averaged radius of the pearls of 19 nm and a distance between neighbouring pearls close to 60 nm could be established for the collapsed state of the NaPA chains.

  8. In-Situ Anomalous Small-Angle X-ray Scattering Studies of Polymer Electrolyte Membrane Fuel Cell Catalyst Degradation

    NASA Astrophysics Data System (ADS)

    Gilbert, James Andrew

    Polymer electrolyte membrane fuel cells (PEMFCs) are a promising high efficiency energy conversion technology, but their cost effective implementation, especially for automotive power, has been hindered by degradation of the electrochemically-active surface area (ECA) of the Pt nanoparticle electrocatalysts. While numerous studies using ex-situ post-mortem techniques have provided insight into the effect of operating conditions on ECA loss, the governing mechanisms and underlying processes are not fully understood. Toward the goal of elucidating the electrocatalyst degradation mechanisms, we have followed particle size distribution (PSD) growth evolutions of Pt and Pt-alloy nanoparticle catalysts during potential cycling in an aqueous acidic environment (with and without flow of electrolyte) and in a fuel cell environment using in-situ anomalous small-angle X-ray scattering (ASAXS). The results of this thesis show a surface area loss mechanism of Pt nanoparticles supported on carbon to be predominantly controlled by Pt dissolution, the particle size dependence of Pt dissolution, the loss of dissolved Pt into the membrane and electrolyte, and, to a lesser extent, the re-deposition of dissolved Pt onto larger particles. The relative extent of these loss mechanisms are shown to be dependent on the environment, the temperature, and the potential cycling conditions. Correlation of ASAXS-determined particle growth with both calculated and voltammetrically-determined oxide coverages demonstrates that the oxide coverage is playing a key role in the dissolution process and in the corresponding growth of the mean Pt nanoparticle size and loss of ECA. This understanding potentially reduces the complex changes in PSDs and ECA resulting from various voltage profiles to the response to a single variable, oxide coverage. A better understanding of the degradation mechanisms of Pt and Pt-alloy nanoparticle distributions could lead to more stable electrocatalysts while

  9. In situ anomalous small-angle X-ray scattering studies of platinum nanoparticle fuel cell electrocatalyst degradation.

    PubMed

    Gilbert, James A; Kariuki, Nancy N; Subbaraman, Ram; Kropf, A Jeremy; Smith, Matt C; Holby, Edward F; Morgan, Dane; Myers, Deborah J

    2012-09-12

    Polymer electrolyte fuel cells (PEFCs) are a promising high-efficiency energy conversion technology, but their cost-effective implementation, especially for automotive power, has been hindered by degradation of the electrochemically active surface area (ECA) of the Pt nanoparticle electrocatalysts. While numerous studies using ex situ post-mortem techniques have provided insight into the effect of operating conditions on ECA loss, the governing mechanisms and underlying processes are not fully understood. Toward the goal of elucidating the electrocatalyst degradation mechanisms, we have followed Pt nanoparticle growth during potential cycling of the electrocatalyst in an aqueous acidic environment using in situ anomalous small-angle X-ray scattering (ASAXS). ASAXS patterns were analyzed to obtain particle size distributions (PSDs) of the Pt nanoparticle electrocatalysts at periodic intervals during the potential cycling. Oxide coverages reached under the applied potential cycling protocols were both calculated and determined experimentally. Changes in the PSD, mean diameter, and geometric surface area identify the mechanism behind Pt nanoparticle coarsening in an aqueous environment. Over the first 80 potential cycles, the dominant Pt surface area loss mechanism when cycling to 1.0-1.1 V was found to be preferential dissolution or loss of the smallest particles with varying extents of reprecipitation of the dissolved species onto existing particles, resulting in particle growth, depending on potential profile. Correlation of ASAXS-determined particle growth with both calculated and voltammetrically determined oxide coverages demonstrates that the oxide coverage is playing a key role in the dissolution process and in the corresponding growth of the mean Pt nanoparticle size and loss of ECA. This understanding potentially reduces the complex changes in PSD and ECA resulting from various voltage profiles to a response dependent on oxide coverage. PMID:22857132

  10. Anomalous small angle x-ray scattering simulations: proof of concept for distance measurements for nanoparticle-labelled biomacromolecules in solution.

    PubMed

    Pinfield, Valerie J; Scott, David J

    2014-01-01

    Anomalous small angle X-ray scattering can in principle be used to determine distances between metal label species on biological molecules. Previous experimental studies in the past were unable to distinguish the label-label scattering contribution from that of the molecule, because of the use of atomic labels; these labels contribute only a small proportion of the total scattering signal. However, with the development of nanocrystal labels (of 50-100 atoms) there is the possibility for a renewed attempt at applying anomalous small angle X-ray scattering for distance measurement. This is because the contribution to the scattered signal is necessarily considerably stronger than for atomic labels. Here we demonstrate through simulations, the feasibility of the technique to determine the end-to-end distances of labelled nucleic acid molecules as well as other internal distances mimicking a labelled DNA binding protein if the labels are dissimilar metal nanocrystals. Of crucial importance is the ratio of mass of the nanocrystals to that of the labelled macromolecule, as well as the level of statistical errors in the scattering intensity measurements. The mathematics behind the distance determination process is presented, along with a fitting routine than incorporates maximum entropy regularisation. PMID:24759797

  11. Small Angle X-Ray Scattering Detector

    DOEpatents

    Hessler, Jan P.

    2004-06-15

    A detector for time-resolved small-angle x-ray scattering includes a nearly constant diameter, evacuated linear tube having an end plate detector with a first fluorescent screen and concentric rings of first fiber optic bundles for low angle scattering detection and an annular detector having a second fluorescent screen and second fiber optic bundles concentrically disposed about the tube for higher angle scattering detection. With the scattering source, i.e., the specimen under investigation, located outside of the evacuated tube on the tube's longitudinal axis, scattered x-rays are detected by the fiber optic bundles, to each of which is coupled a respective photodetector, to provide a measurement resolution, i.e., dq/q, where q is the momentum transferred from an incident x-ray to an x-ray scattering specimen, of 2% over two (2) orders of magnitude in reciprocal space, i.e., q.sub.max /q.sub.min.congruent.100.

  12. X-Ray Small Angle Scattering

    PubMed Central

    Pape, E. H.

    1974-01-01

    The direct determination of the electron density distributions of multilayered specimens with a small number of unit cells from X-ray small angle scattering experiments via the Q-function method of Hosemann and Bagchi includes the deconvolution of the so-called Qo-function, the generalized Patterson function of one unit cell. In this paper a new and direct deconvolution method on the basis of Fourier series is presented which is suitable for one-dimensional centrosymmetrical (or antisymmetrical) density distributions. A FORTRAN-program has been written which has an execution time of ca. 20 s on an UNIVAC 1106-computer. The procedure has been successfully tested on some convolution functions generated by membrane-type electron density distributions. PMID:4830467

  13. In-situ study of precipitates in Al–Zn–Mg–Cu alloys using anomalous small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Chun-Ming, Yang; Feng-Gang, Bian; Bai-Qing, Xiong; Dong-Mei, Liu; Yi-Wen, Li; Wen-Qiang, Hua; Jie, Wang

    2016-06-01

    In the present work, the precipitate compositions and precipitate amounts of these elements (including the size distribution, volume fraction, and inter-precipitate distance) on the Cu-containing 7000 series aluminum alloys (7150 and 7085 Al alloys), are investigated by anomalous small-angle x-ray scattering (ASAXS) at various energies. The scattering intensity of 7150 alloy with T6 aging treatment decreases as the incident x-ray energy approaches the Zn absorption edge from the lower energy side, while scattering intensity does not show a noticeable energy dependence near the Cu absorption edge. Similar results are observed in the 7085 alloy in an aging process (120 °C) by employing in-situ ASAXS measurements, indicating that the precipitate compositions should include Zn element and should not be strongly related to Cu element at the early stage after 10 min. In the aging process, the precipitate particles with an initial average size of ∼ 8 Å increase with aging time at an energy of 9.60 keV, while the increase with a slower rate is observed at an energy of 9.65 keV as near the Zn absorption edge. Project supported by the National Natural Science Foundation of China (Grant Nos. 11005143, 11405259, and 51274046) and the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry of China (Grant No. [2014]1685).

  14. Anomalous small angle x-ray scattering study of layered silicate clays containing Ni(II) and Er(III)

    SciTech Connect

    Thiyagarajan, P.; Carrado, K.A.; Wasserman, S.R.; Song, K.; Winans, R.E.

    1995-12-01

    These studies concern the synthesis of heterogeneous catalysts and the incorporation of heavy metals in trapping media. The Ni(II) containing clays were synthesized at 200{degree}C whereas those containing Er(III) were ion-exchanged natural clays. For the first system, ASAXS data were measured at 5 different energies near the K{alpha} edge of Ni at three different reaction times: unreacted, 4 hrs, and 15 hrs, when the crystallization is essentially complete. The data for the unreacted sample showed no correlations for a lamellar particle, while that reacted for 4 hrs indicated the evolution of lamella, and the crystallized sample (15 hrs) exhibits much larger lamellar correlations. Systematic variations are seen in the data for the 4 hr and 15 hr samples that are due to the anomalous scattering from the ordered Ni atoms in the layered silicates. The erbium study provides the first scattering measurements of heavy metal ion salvation and migration in clays, which has implications for both catalysis and environmental issues. Systematic energy-dependent variations in the signals near the L{sub III} edge of Er are observed for the hydrated sample, but not for the ``dry,`` as-prepared sample.

  15. Probing the extent of the Sr2+ ion condensation to anionic polyacrylate coils: a quantitative anomalous small-angle x-ray scattering study.

    PubMed

    Goerigk, G; Huber, K; Schweins, R

    2007-10-21

    The shrinking process of anionic sodium polyacrylate (NaPA) chains in aqueous solution induced by Sr2+ counterions was analyzed by anomalous small-angle x-ray scattering. Scattering experiments were performed close to the precipitation threshold of strontium polyacrylate. The pure-resonant scattering contribution, which is related to the structural distribution of the Sr2+ counterions, was used to analyze the extent of Sr2+ condensation onto the polyacrylate coils. A series of four samples with different ratios [Sr2+][NaPA] (between 0.451 and 0.464) has been investigated. From the quantitative analysis of the resonant invariant, the amount of Sr cations localized in the collapsed phase was calculated with concentrations v between 0.94x10(17) and 2.01x10(17) cm(-3) corresponding to an amount of Sr cations in the collapsed phase between 9% and 23% of the total Sr2+ cations in solution. If compared to the concentration of polyacrylate expressed in moles of monomers [NaPA], a degree of site binding of r=[Sr2+][NaPA] between 0.05 and 0.11 was estimated. These values clearly differ from r=0.25, which was established from former light scattering experiments, indicating that the counterion condensation starts before the phase border is reached and increases rather sharply at the border. PMID:17949215

  16. Probing the extent of the Sr2+ ion condensation to anionic polyacrylate coils: A quantitative anomalous small-angle x-ray scattering study

    NASA Astrophysics Data System (ADS)

    Goerigk, G.; Huber, K.; Schweins, R.

    2007-10-01

    The shrinking process of anionic sodium polyacrylate (NaPA) chains in aqueous solution induced by Sr2+ counterions was analyzed by anomalous small-angle x-ray scattering. Scattering experiments were performed close to the precipitation threshold of strontium polyacrylate. The pure-resonant scattering contribution, which is related to the structural distribution of the Sr2+ counterions, was used to analyze the extent of Sr2+ condensation onto the polyacrylate coils. A series of four samples with different ratios [Sr2+]/[NaPA] (between 0.451 and 0.464) has been investigated. From the quantitative analysis of the resonant invariant, the amount of Sr cations localized in the collapsed phase was calculated with concentrations v¯ between 0.94×1017 and 2.01×1017cm-3 corresponding to an amount of Sr cations in the collapsed phase between 9% and 23% of the total Sr2+ cations in solution. If compared to the concentration of polyacrylate expressed in moles of monomers [NaPA], a degree of site binding of r =[Sr2+]/[NaPA] between 0.05 and 0.11 was estimated. These values clearly differ from r =0.25, which was established from former light scattering experiments, indicating that the counterion condensation starts before the phase border is reached and increases rather sharply at the border.

  17. Anomalous and resonance small angle scattering: Revision

    SciTech Connect

    Epperson, J.E.; Thiyagarajan, P.

    1987-11-01

    Significant changes in the small angle scattered intensity can be induced by making measurements with radiation close to an absorption edge of an appropriate atomic species contained in the sample. These changes can be related quantitatively to the real and imaginary anomalous dispersion terms for the scattering factor (x-rays) or scattering length (neutrons). The physics inherent in these anomalous dispersion terms is first discussed before considering how they enter the relevant scattering theory. Two major areas of anomalous scattering research have emerged; macromolecules in solution and unmixing of metallic alloys. Research in each area is reviewed, illustrating both the feasibility and potential of these techniques. All the experimental results reported to date have been obtained with x-rays. However, it is pointed out that the formalism is the same for the analogue experiment with neutrons, and a number of suitable isotopes exist which exhibit resonance in an accessible range of energy. Potential applications of resonance small angle neutron scatterings are discussed. 54 refs., 8 figs., 1 tab.

  18. Anomalous and resonance small angle scattering

    SciTech Connect

    Epperson, J.E.; Thiyagarajan, P.

    1987-11-01

    Significant changes in the small angle scattered intensity can be induced by making measurements with radiation close to an absorption edge of an appropriate atomic species contained in the sample. These changes can be related quantitatively to the real and imaginary anomalous dispersion terms for the scattering factor (x-rays) or scattering length (neutrons). The physics inherent in these anomalous dispersion terms is first discussed before considering how they enter the relevant scattering theory. Two major areas of anomalous scattering research have emerged; macromolecules in solution and unmixing of metallic alloys. Research in each area is reviewed, illustrating both the feasibility and potential of these techniques. All the experimental results reported to date have been obtained with x-rays. However, it is pointed out that the formalism is the same or the analogue experiment with neutrons, and a number of suitable isotopes exist which exhibit resonance in an accessible range of energy. Potential applications of resonance small-angle neutron scatterings are discussed. 8 figs.

  19. Small angle x-ray scattering with edge-illumination.

    PubMed

    Modregger, Peter; Cremona, Tiziana P; Benarafa, Charaf; Schittny, Johannes C; Olivo, Alessandro; Endrizzi, Marco

    2016-01-01

    Sensitivity to sub-pixel sample features has been demonstrated as a valuable capability of phase contrast x-ray imaging. Here, we report on a method to obtain angular-resolved small angle x-ray scattering distributions with edge-illumination- based imaging utilizing incoherent illumination from an x-ray tube. Our approach provides both the three established image modalities (absorption, differential phase and scatter strength), plus a number of additional contrasts related to unresolved sample features. The complementarity of these contrasts is experimentally validated by using different materials in powder form. As a significant application example we show that the extended complementary contrasts could allow the diagnosis of pulmonary emphysema in a murine model. In support of this, we demonstrate that the properties of the retrieved scattering distributions are consistent with the expectation of increased feature sizes related to pulmonary emphysema. Combined with the simplicity of implementation of edge-illumination, these findings suggest a high potential for exploiting extended sub-pixel contrasts in the diagnosis of lung diseases and beyond. PMID:27491917

  20. Small angle x-ray scattering with edge-illumination

    NASA Astrophysics Data System (ADS)

    Modregger, Peter; Cremona, Tiziana P.; Benarafa, Charaf; Schittny, Johannes C.; Olivo, Alessandro; Endrizzi, Marco

    2016-08-01

    Sensitivity to sub-pixel sample features has been demonstrated as a valuable capability of phase contrast x-ray imaging. Here, we report on a method to obtain angular-resolved small angle x-ray scattering distributions with edge-illumination- based imaging utilizing incoherent illumination from an x-ray tube. Our approach provides both the three established image modalities (absorption, differential phase and scatter strength), plus a number of additional contrasts related to unresolved sample features. The complementarity of these contrasts is experimentally validated by using different materials in powder form. As a significant application example we show that the extended complementary contrasts could allow the diagnosis of pulmonary emphysema in a murine model. In support of this, we demonstrate that the properties of the retrieved scattering distributions are consistent with the expectation of increased feature sizes related to pulmonary emphysema. Combined with the simplicity of implementation of edge-illumination, these findings suggest a high potential for exploiting extended sub-pixel contrasts in the diagnosis of lung diseases and beyond.

  1. Small angle x-ray scattering with edge-illumination

    PubMed Central

    Modregger, Peter; Cremona, Tiziana P.; Benarafa, Charaf; Schittny, Johannes C.; Olivo, Alessandro; Endrizzi, Marco

    2016-01-01

    Sensitivity to sub-pixel sample features has been demonstrated as a valuable capability of phase contrast x-ray imaging. Here, we report on a method to obtain angular-resolved small angle x-ray scattering distributions with edge-illumination- based imaging utilizing incoherent illumination from an x-ray tube. Our approach provides both the three established image modalities (absorption, differential phase and scatter strength), plus a number of additional contrasts related to unresolved sample features. The complementarity of these contrasts is experimentally validated by using different materials in powder form. As a significant application example we show that the extended complementary contrasts could allow the diagnosis of pulmonary emphysema in a murine model. In support of this, we demonstrate that the properties of the retrieved scattering distributions are consistent with the expectation of increased feature sizes related to pulmonary emphysema. Combined with the simplicity of implementation of edge-illumination, these findings suggest a high potential for exploiting extended sub-pixel contrasts in the diagnosis of lung diseases and beyond. PMID:27491917

  2. Dietary iron-loaded rat liver haemosiderin and ferritin: in situ measurement of iron core nanoparticle size and cluster structure using anomalous small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Bovell, Eliza; Buckley, Craig E.; Chua-anusorn, Wanida; Cookson, David; Kirby, Nigel; Saunders, Martin; St. Pierre, Timothy G.

    2009-03-01

    The morphology, particle size distribution and cluster structure of the hydrated iron(III) oxyhydroxide particles associated with haemosiderin and ferritin in dietary iron-loaded rat liver tissue have been investigated using transmission electron microscopy (TEM) and anomalous small-angle x-ray scattering (ASAXS). Rat liver tissue was removed from a series of female Porton rats which had been fed an iron-rich diet until sacrifice at various ages from 2-24 months. Hepatic iron concentrations ranged from 1 to 65 mg Fe g-1 dry tissue. TEM studies showed both dispersed and clustered iron-containing nanoparticles. The dispersed particles were found to have mean sizes (±standard deviation) of 54 ± 8 Å for the iron-loaded animals and 55 ± 7 Å for the controls. Superposition of particles in TEM images prevented direct measurement of nanoparticulate size in the clusters. The ASAXS data were modelled to provide a quantitative estimate of both the size and spacing of iron oxyhydroxide particles in the bulk samples. The modelling yielded close-packed particles with sizes of 60 to 78 Å which when corrected for anomalous scattering suggests sizes from 54 to 70 Å. Particle size distributions are of particular importance since they determine the surface iron to core iron ratios, which in turn are expected to be related to the molar toxicity of iron deposits in cells.

  3. Mapping the local nanostructure inside a specimen by tomographic small-angle x-ray scattering

    SciTech Connect

    Schroer, C.G.; Kuhlmann, M.; Roth, S.V.; Gehrke, R.; Stribeck, N.; Almendarez-Camarillo, A.; Lengeler, B.

    2006-04-17

    Small-angle x-ray scattering is combined with scanning microtomography to reconstruct the small-angle diffraction pattern in the direction of the tomographic rotation axis at each location on a virtual section through a specimen. These data yield information about the local nanoscale structure of the sample. With rotational symmetry present in the diffraction patterns, e.g., for isotropic or fiber-textured scatterers, the full reciprocal space information in the small-angle scattering regime can be reconstructed at each location inside the specimen. The method is illustrated investigating a polymer rod made by injection molding.

  4. X-ray small angle scattering. A new deconvolution method for evaluating electron density distributions from small angle scattering diagrams.

    PubMed

    Pape, E H

    1974-04-01

    The direct determination of the electron density distributions of multilayered specimens with a small number of unit cells from X-ray small angle scattering experiments via the Q-function method of Hosemann and Bagchi includes the deconvolution of the so-called Q(o)-function, the generalized Patterson function of one unit cell. In this paper a new and direct deconvolution method on the basis of Fourier series is presented which is suitable for one-dimensional centrosymmetrical (or antisymmetrical) density distributions. A FORTRAN-program has been written which has an execution time of ca. 20 s on an UNIVAC 1106-computer. The procedure has been successfully tested on some convolution functions generated by membrane-type electron density distributions. PMID:4830467

  5. Small angle x-ray scattering with a beryllium compound refractive lens as focusing optic

    SciTech Connect

    Timmann, Andreas; Doehrmann, Ralph; Schubert, Tom; Schulte-Schrepping, Horst; Hahn, Ulrich; Kuhlmann, Marion; Gehrke, Rainer; Roth, Stephan Volkher; Schropp, Andreas; Schroer, Christian; Lengeler, Bruno

    2009-04-15

    At BW4 at HASYLAB a beryllium compound refractive lens (Be-CRL) is used for the focusing in small-angle x-ray scattering experiments. Using it provides the advantages of higher long-term stability and a much easier alignment compared to a setup with focusing mirrors. In our investigations presented here, we show the advantages of using a Be-CRL in small-angle and also ultra small-angle x-ray scattering. We investigated the beam characteristics at the sample position with respect to spot size and photon flux. The spot size is comparable to that of a setup with focusing mirrors but with a gain in flux and better long-term stability. It is also shown that plane mirrors are still necessary to suppress higher order energies passing the monochromator.

  6. Counterion Distribution Around Protein-SNAs probed by Small-angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Krishnamoorthy, Kurinji; Bedzyk, Michael; Kewalramani, Sumit; Moreau, Liane; Mirkin, Chad

    Protein-DNA conjugates couple the advanced cell transfection capabilities of spherical DNA architecture and the biocompatible enzymatic activity of a protein core to potentially create therapeutic agents with dual functionality. An understanding of their stabilizing ionic environment is crucial to better understand and predict their properties. Here, we use Small-angle X-ray scattering techniques to decipher the structure of the counterion cloud surrounding these DNA coated nanoparticles. Through the use of anomalous scattering techniques we have mapped the local concentrations of Rb+ ions in the region around the Protein-DNA constructs. These results are further corroborated with simulations using a geometric model for the excess charge density as function of radial distance from the protein core. Further, we investigate the influence of solution ionic strength on the structure of the DNA corona and demonstrate a reduction in the extension of the DNA corona with increasing concentration of NaCl in solution for the case of both single and double stranded DNA shells. Our work reveals the distribution of counterions in the vicinity of Protein-DNA conjugates and decouples the effect of solution ionic strength on the thickness of the DNA layer.

  7. X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

    SciTech Connect

    Yennawar, Hemant; Møller, Magda; Gillilan, Richard; Yennawar, Neela

    2011-05-01

    The X-ray crystal structure and a small-angle X-ray scattering solution structure of sheep liver sorbitol dehydrogenase have been determined. The details of the interactions that enable the tetramer scaffold to be the functional biological unit have been analyzed. The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer that superposes well with that seen in hSDH (despite belonging to a different space group) and obeying the 222 crystal symmetry is seen in slSDH. An acetate molecule is bound in the active site, coordinating to the active-site zinc through a water molecule. Glycerol, a substrate of slSDH, also occupies the substrate-binding pocket together with the acetate designed by nature to fit large polyol substrates. The substrate-binding pocket is seen to be in close proximity to the tetramer interface, which explains the need for the structural integrity of the tetramer for enzyme activity. Small-angle X-ray scattering was also used to identify the quaternary structure of the tetramer of slSDH in solution.

  8. Sample environments and techniques combined with small angle X-ray scattering.

    PubMed

    Bras, W; Ryan, A J

    1998-03-31

    The number of synchrotron radiation-based Small Angle X-ray Scattering beamlines has increased considerably over the last decade. With the high X-ray flux and collimation of these beamlines it not only has become possible to perform time-resolved experiments on time scales down to the millisecond/frame range, but also it allows experimenters to utilise new sample environments and use simultaneous several experimental techniques on one sample. An overview of recent developments in this field is given. PMID:9611762

  9. BIOISIS: Biological Macromolecules by Small Angle X-ray Scattering (SAXS)

    DOE Data Explorer

    Tainer, John [Scripps Research Institute; Hura, Greg [LBNL; Rambo, Robert P. [LBNL

    BIOISIS is an open access database dedicated to the study of biological macromolecules by small angle X-ray scattering (SAXS). BIOISIS aims to become the complete source for the deposition, distribution and maintenance of small angle X-ray scattering data and technologies. The database is designed around the concept of an ôexperimentö and relates a specific experiment to a set of genes, organisms, computational models and experimental data. As of May 2012, BIOSIS contains 7,118 genes covering four different organisms. Forty-two modeled structures are available. Clicking on a structures reveals scattering curves, experimental conditions, and experimental values. The data are collected at Beamline 12.3.1 of the Advanced Light Source (ALS).[Copied with editing from http://www.bioisis.net/about

  10. Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept.

    PubMed

    Allec, Nicholas; Choi, Mina; Yesupriya, Nikhil; Szychowski, Brian; White, Michael R; Kann, Maricel G; Garcin, Elsa D; Daniel, Marie-Christine; Badano, Aldo

    2015-01-01

    Characterizing biomolecular interactions is crucial to the understanding of biological processes. Existing characterization methods have low spatial resolution, poor specificity, and some lack the capability for deep tissue imaging. We describe a novel technique that relies on small-angle X-ray scattering signatures from high-contrast molecular probes that correlate with the presence of biomolecular interactions. We describe a proof-of-concept study that uses a model system consisting of mixtures of monomer solutions of gold nanoparticles (GNPs) as the non-interacting species and solutions of GNP dimers linked with an organic molecule (dimethyl suberimidate) as the interacting species. We report estimates of the interaction fraction obtained with the proposed small-angle X-ray scattering characterization method exhibiting strong correlation with the known relative concentration of interacting and non-interacting species. PMID:26160052

  11. X-ray small angle scattering of the human transferrin protein aggregates. A fractal study.

    PubMed Central

    Castellano, A C; Barteri, M; Bianconi, A; Borghi, E; Cassiano, L; Castagnola, M; Della Longa, S

    1993-01-01

    X-ray small angle scattering experiments, using a pin hole SAXS camera with Synchrotron radiation source, have been performed to study the conformational changes of lyophilized samples of Apo-, Mono-, and Diferric- human transferrin. We report the experimental evidence that the analysis of the scattered intensity through the fractal theory may give information on the particle size and its variation upon iron binding. PMID:8457675

  12. Brain tumor imaging using small-angle x-ray scattering tomography

    NASA Astrophysics Data System (ADS)

    Jensen, Torben H.; Bech, Martin; Bunk, Oliver; Thomsen, Maria; Menzel, Andreas; Bouchet, Audrey; Le Duc, Géraldine; Feidenhans'l, Robert; Pfeiffer, Franz

    2011-03-01

    We demonstrate high-resolution small-angle x-ray scattering computed tomography (SAXS-CT) of soft matter and soft tissue samples. Complete SAXS patterns over extended ranges of momentum transfer are reconstructed spatially resolved from volumes inside an extended sample. Several SAXS standard samples are used to quantitatively validate the method and demonstrate its performance. Further results on biomedical tissue samples (rat brains) are presented that demonstrate the advantages of the method compared to existing biomedical x-ray imaging approaches. Functional areas of the brains as well as tumor morphology are imaged. By providing insights into the structural organization at the nano-level, SAXS-CT complements and extends results obtainable with standard methods such as x-ray absorption tomography and histology.

  13. Time-resolved studies of dynamic biomolecules using small angle X-ray scattering.

    PubMed

    Kirby, Nigel M; Cowieson, Nathan P

    2014-10-01

    Small angle X-ray scattering (SAXS) of biomacromolecules in solution has become a prominent technique in structural biology. Whilst the majority of current use is for static measurements, the field is also advancing for measurements where the sample at the beam position changes with time, using high throughput systems, chromatography, high speed mixing and pump-probe techniques in particular. Time resolved work is greatly aided by increasingly sophisticated software for acquiring and analysing data, together with developments in X-ray sources, beamline optics and detectors. The exploitation of spatial coherence is under development, with X-ray free electron lasers aiming to provide major advances in single molecule structure reconstruction and time resolution. Here we provide an overview of current developments advancing time resolved solution SAXS. PMID:25108308

  14. Small angle X-ray and neutron scattering on cadmium sulfide nanoparticles in silicate glass

    NASA Astrophysics Data System (ADS)

    Kuznetsova, Yu. V.; Rempel, A. A.; Meyer, M.; Pipich, V.; Gerth, S.; Magerl, A.

    2016-08-01

    Small angle X-ray and neutron scattering on Cd and S doped glass annealed at 600 °C shows after the first 12 h nucleation and growth of spherical CdS nanoparticles with a radius of up to 34±4 Å. After the nucleation is completed after 24 h, further growth in this amorphous environment is governed by oriented particle attachment mechanism as found for a liquid medium. Towards 48 h the particle shape has changed into spheroidal with short and long axis of 40±2 Å and 120±2 Å, respectively.

  15. Characterising density fluctuations in liquid yttria aluminates with small angle x-ray scattering

    SciTech Connect

    Greaves, G. Neville; Wilding, Martin C.; Vu Van, Quang; Majerus, Odile; Hennet, Louis

    2009-01-29

    Small angle x-ray scattering (SAXS) has been measured in the wavevector range 0.01

  16. Small-angle X-ray scattering probe of intermolecular interaction in red blood cells

    NASA Astrophysics Data System (ADS)

    Liu, Guan-Fen; Wang, We-Jia; Xu, Jia-Hua; Dong, Yu-Hui

    2015-03-01

    With high concentrations of hemoglobin (Hb) in red blood cells, self-interactions among these molecules could increase the propensities of their polymerization and aggregation. In the present work, high concentration Hb in solution and red blood cells were analyzed by small-angle X-ray scattering. Calculation of the effective structure factor indicates that the interaction of Hb molecules is the same when they are crowded together in both the cell and physiological saline. The Hb molecules stay individual without the formation of aggregates and clusters in cells. Supported by National Basic Research Program of China (2009CB918600) and National Natural Science Foundation of China (10979005)

  17. Measurement of protein size in concentrated solutions by small angle X-ray scattering.

    PubMed

    Liu, Jun; Li, Zhihong; Wei, Yanru; Wang, Wenjia; Wang, Bing; Liang, Hongli; Gao, Yuxi

    2016-08-01

    By simulations on the distance distribution function (DDF) derived from small angle X-ray scattering (SAXS) theoretical data of a dense monodisperse system, we found a quantitative mathematical correlation between the apparent size of a spherically symmetric (or nearly spherically symmetric) homogenous particle and the concentration of the solution. SAXS experiments on protein solutions of human hemoglobin and horse myoglobin validated the correlation. This gives a new method to determine, from the SAXS DDF, the size of spherically symmetric (or nearly spherically symmetric) particles of a dense monodisperse system, specifically for protein solutions with interference effects. PMID:27241796

  18. Small-angle X-ray scattering analysis of stearic acid modified lipase.

    PubMed

    Maruyama, T; Nakajima, M; Ichikawa, S; Sano, Y; Nabetani, H; Furusaki, S; Seki, M

    2001-04-01

    Stearic acid modified lipase (from Rhizopus japonicus) exhibited remarkable interesterification activity in n-hexane, but crude native lipase did not. The structure of the fatty acid modified lipase had not been analyzed until now. We analyzed the modified lipase by small-angle X-ray scattering (SAXS) measurements in order to clarify the structure. SAXS measurements showed that the modified lipase consisted of a lipid lamellar structure and implied that the lipase was incorporated into the lamellar structure of stearic acid. The long spacings in the lamellar structures of the modified lipase and stearic acid were measured. PMID:11388447

  19. Ion track annealing in quartz investigated by small angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Schauries, D.; Afra, B.; Rodriguez, M. D.; Trautmann, C.; Hawley, A.; Kluth, P.

    2015-12-01

    We report on the reduction of cross-section and length of amorphous ion tracks embedded within crystalline quartz during thermal annealing. The ion tracks were created via Au ion irradiation with an energy of 2.2 GeV. The use of synchrotron-based small angle X-ray scattering (SAXS) allowed characterization of the latent tracks, without the need for chemical etching. Temperatures between 900 and 1000 °C were required to see a notable change in track size. The shrinkage in cross-section and length was found to be comparable for tracks aligned perpendicular and parallel to the c-axis.

  20. Small-angle scattering studies of meso-scopic structures with synchrotron X-rays

    NASA Astrophysics Data System (ADS)

    Dore, J. C.; North, A. N.; Rigden, J. S.

    1995-03-01

    The use of small-angle X-ray scattering techniques for the study of spatial inhomogeneities over the range 20 Å to 2 μm is reviewed. The basic formalism for scattering by an inhomogeneous medium is developed with particular reference to liquid suspensions, porous solids and solid aggregates. The instrumentation available on the Synchrotron Radiation Source at the Daresbury Laboratory is briefly presented and the use of the Bonse-Hart method for studies at ultra-low scattering angles described. The extraction of structural information for a range of natural and synthetic materials is presented with particular reference to microemulsions, porous silicas, clays and composites. The complementarity of X-ray and neutron techniques is critically reviewed and prospects for future developments, particularly for the study of anisotropic systems, are discussed.

  1. Probing ballistic microdrop coalescence by stroboscopic small-angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Graceffa, R.; Burghammer, M.; Davies, R. J.; Riekel, C.

    2012-12-01

    The coalescence of ballistic microdrops has been explored by stroboscopic synchrotron radiation microbeam small-angle X-ray scattering (μSAXS). About 80 μm diameter microdrops generated by a drop-on-demand inkjet system travelled at ˜1.7 m/s through a ˜1 μm X-ray beam. Microdrops of cytochrome C and acetate buffer solutions were merged in order to study the pH driven conformational change. μSAXS patterns were accumulated on a pixel detector, which was activated for a few μsec during the transit time of each microdrop through the microbeam. Local probing of the merging microdrops reveals the internal protein solution flow.

  2. Pinhole-type two-dimensional ultra-small-angle X-ray scattering on the micrometer scale.

    PubMed

    Kishimoto, Hiroyuki; Shinohara, Yuya; Suzuki, Yoshio; Takeuchi, Akihisa; Yagi, Naoto; Amemiya, Yoshiyuki

    2014-01-01

    A pinhole-type two-dimensional ultra-small-angle X-ray scattering set-up at a so-called medium-length beamline at SPring-8 is reported. A long sample-to-detector distance, 160.5 m, can be used at this beamline and a small-angle resolution of 0.25 µm(-1) was thereby achieved at an X-ray energy of 8 keV. PMID:24365910

  3. Pinhole-type two-dimensional ultra-small-angle X-ray scattering on the micrometer scale

    PubMed Central

    Kishimoto, Hiroyuki; Shinohara, Yuya; Suzuki, Yoshio; Takeuchi, Akihisa; Yagi, Naoto; Amemiya, Yoshiyuki

    2014-01-01

    A pinhole-type two-dimensional ultra-small-angle X-ray scattering set-up at a so-called medium-length beamline at SPring-8 is reported. A long sample-to-detector distance, 160.5 m, can be used at this beamline and a small-angle resolution of 0.25 µm−1 was thereby achieved at an X-ray energy of 8 keV. PMID:24365910

  4. A small-angle x-ray scattering system with a vertical layout

    SciTech Connect

    Wang, Zhen; Chen, Xiaowei; Meng, Lingpu; Cui, Kunpeng; Wu, Lihui; Li, Liangbin

    2014-12-15

    A small-angle x-ray scattering (SAXS) system with a vertical layout (V-SAXS) has been designed and constructed for in situ detection on nanostructures, which is well suitable for in situ study on self-assembly of nanoparticles at liquid interface and polymer processing. A steel-tower frame on a reinforced basement is built as the supporting skeleton for scattering beam path and detector platform, ensuring the system a high working stability and a high operating accuracy. A micro-focus x-ray source combining parabolic three-dimensional multi-layer mirror and scatteringless collimation system provides a highly parallel beam, which allows us to detect the very small angle range. With a sample-to-detector distance of 7 m, the largest measurable length scale is 420 nm in real space. With a large sample zone, it is possible to install different experimental setups such as film stretching machine, which makes the system perfect to follow the microstructures evolution of materials during processing. The capability of the V-SAXS on in situ study is tested with a drying experiment of a free latex droplet, which confirms our initial design.

  5. Time-resolved small-angle x-ray-scattering study of ordering kinetics in diblock styrene-butadiene

    NASA Astrophysics Data System (ADS)

    Singh, M. A.; Harkless, C. R.; Nagler, S. E.; Shannon, R. F., Jr.; Ghosh, S. S.

    1993-04-01

    A detailed study of the kinetics of phase transformations of the diblock copolymer, styrene-butadiene, is reported. The technique of in situ time-resolved small-angle x-ray scattering with the use of synchrotron radiation has been used to study the first-order phase transitions of microphase separation and microdomain ordering. These transitions occur following a rapid, thermal quench from the homogeneous, disordered state to temperatures below the transition point. The isothermal ordering process is discussed in the context of classical theories of nucleation and growth. Anomalous temporal oscillations in the ordered-volume fraction are observed following quenches to temperatures just below the ordering transition. These results are reported and qualitatively discussed.

  6. Time-resolved small-angle x-ray-scattering study of ordering kinetics in diblock styrene-butadiene

    SciTech Connect

    Singh, M.A. ); Harkless, C.R. ); Nagler, S.E. ); Shannon, R.F. Jr.; Ghosh, S.S. )

    1993-04-01

    A detailed study of the kinetics of phase transformations of the diblock copolymer, styrene-butadiene, is reported. The technique of [ital in] [ital situ] time-resolved small-angle x-ray scattering with the use of synchrotron radiation has been used to study the first-order phase transitions of microphase separation and microdomain ordering. These transitions occur following a rapid, thermal quench from the homogeneous, disordered state to temperatures below the transition point. The isothermal ordering process is discussed in the context of classical theories of nucleation and growth. Anomalous temporal oscillations in the ordered-volume fraction are observed following quenches to temperatures just below the ordering transition. These results are reported and qualitatively discussed.

  7. Depth profiling of polymer films with grazing-incidence small-angle X-ray scattering

    PubMed Central

    Singh, Marsha A.; Groves, Michael N.

    2009-01-01

    A model-free method of reconstructing depth-specific lateral scattering from incident-angle-resolved grazing-incidence small-angle X-ray scattering (GISAXS) data is proposed. The information on the material which is available through variation of the X-ray penetration depth with incident angle is accessed through reference to the reflected branch of the GISAXS process. Reconstruction of the scattering from lateral density fluctuations is achieved by solving the resulting Fredholm integral equation with minimal a priori information about the experimental system. Results from simulated data generated for hypothetical multilayer polymer systems with constant absorption coefficient are used to verify that the method can be applied to cases with large X-ray penetration depths, as typically seen with polymer materials. Experimental tests on a spin-coated thick film of a blend of diblock copolymers demonstrate that the approach is capable of reconstruction of the scattering from a multilayer structure with the identification of lateral scattering profiles as a function of sample depth. PMID:19349663

  8. The accurate assessment of small-angle X-ray scattering data

    SciTech Connect

    Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; Matsui, Tsutomu; Weiss, Thomas M.; Martel, Anne; Snell, Edward H.

    2015-01-01

    A set of quantitative techniques is suggested for assessing SAXS data quality. These are applied in the form of a script, SAXStats, to a test set of 27 proteins, showing that these techniques are more sensitive than manual assessment of data quality. Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.

  9. The accurate assessment of small-angle X-ray scattering data

    DOE PAGESBeta

    Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; Matsui, Tsutomu; Weiss, Thomas M.; Martel, Anne; Snell, Edward H.

    2015-01-23

    Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targetsmore » for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.« less

  10. The accurate assessment of small-angle X-ray scattering data

    SciTech Connect

    Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; Matsui, Tsutomu; Weiss, Thomas M.; Martel, Anne; Snell, Edward H.

    2015-01-23

    Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.

  11. Synchrotron Small-Angle X-ray Scattering Study of Cross-Linked Polymeric Micelles.

    PubMed

    Kim, Hyun-Chul; Jin, Kyeong Sik; Lee, Se Guen; Kim, Eunjoo; Lee, Sung Jun; Jeong, Sang Won; Lee, Seung Woo; Kim, Kwang-Woo

    2016-06-01

    Polymeric micelles of methoxypoly(ethylene glycol)-b-poly(lactide) containing lysine units (mPEG-PLA-Lys4) were cross-linked by reacting of lysine moieties with a bifunctional bis(N-hydroxy-succinimide ester). The micelles were characterized in aqueous solution using dynamic light scattering, transmission electron microscopy, and synchrotron small-angle X-ray scattering. The mPEG-PLA-Lys4 was synthesized through the ring-opening polymerization of N6-carbobenzyloxy-L-lysine N-carboxyanhydride with amine-terminated mPEG-PLA and subsequent deprotection. The polymeric micelles showed enhanced micelle stability after cross-linking, which was confirmed by adding sodium dodecyl sulfate as a destabilizing agent. The average diameters measured via dynamic light scattering were 19.1 nm and 29.2 nm for non-cross-linked polymeric micelles (NCPMs) and cross-linked polymeric micelles (CPMs), respectively. The transmission electron microscopy images showed that the size of the polymeric micelles increased slightly due to cross-linking, which was in good agreement with the DLS measurements. The overall structures and internal structural changes of NCPMs and CPMs in aqueous solution were studied in detail using synchrotron X-ray scattering method. According to the structural parameters of X-ray scattering analysis, CPMs with a more densely packed core structure were formed by reacting bifunctional cross-linking agents with lysine amino groups located in the innermost core of the polymeric micelles. PMID:27427731

  12. The accurate assessment of small-angle X-ray scattering data

    PubMed Central

    Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; Matsui, Tsutomu; Weiss, Thomas M.; Martel, Anne; Snell, Edward H.

    2015-01-01

    Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality. PMID:25615859

  13. In situ microfluidic dialysis for biological small-angle X-ray scattering

    PubMed Central

    Skou, Magda; Skou, Søren; Jensen, Thomas G.; Vestergaard, Bente; Gillilan, Richard E.

    2014-01-01

    Owing to the demand for low sample consumption and automated sample changing capabilities at synchrotron small-angle X-ray (solution) scattering (SAXS) beamlines, X-ray microfluidics is receiving continuously increasing attention. Here, a remote-controlled microfluidic device is presented for simultaneous SAXS and ultraviolet absorption measurements during protein dialysis, integrated directly on a SAXS beamline. Microfluidic dialysis can be used for monitoring structural changes in response to buffer exchange or, as demonstrated, protein concentration. By collecting X-ray data during the concentration procedure, the risk of inducing protein aggregation due to excessive concentration and storage is eliminated, resulting in reduced sample consumption and improved data quality. The proof of concept demonstrates the effect of halted or continuous flow in the microfluidic device. No sample aggregation was induced by the concentration process at the levels achieved in these experiments. Simulations of fluid dynamics and transport properties within the device strongly suggest that aggregates, and possibly even higher-order oligomers, are preferentially retained by the device, resulting in incidental sample purification. Hence, this versatile microfluidic device enables investigation of experimentally induced structural changes under dynamically controllable sample conditions. PMID:25242913

  14. Small angle x-ray scattering study of the porosity in coals

    NASA Astrophysics Data System (ADS)

    Schmidt, P. W.; Kalliat, M.; Kwak, C. Y.

    1981-02-01

    Small-angle scattering curves have bee obtained for some Pennsylvania State University PSOC coal samples and for several other coals. The x-ray scattering data provide information about the porosity in the coals and suggest that there are three classes of pores, which have average dimensions of the order of 1000 A˚, 30 A˚, and less than 5 A˚, corresponding to the macropores, transition pores and micropores discussed by Dubinin. The principal factor determining the form of the scattering curves has been found to be the rank of the coal. In coals of all ranks, the specific surface associated with the macropores is about 1 to 10 m2/gm. The micropores are most highly developed in high-rank coals. Comparison of the x-ray and adsorption results suggests that x-ray scattering and nitrogen adsorption detect only the specific surface of the macropores and transition pores, while carbon dioxide adsorption measures the total porosity from the micropores. Scattering data have also been recorded for a series of coals which had been tested for their suitability for conversion to liquid fuels. All the coals which were well-suited for producing liquid fuels were found to have a well-developed transition pore structure, while coals which were not especially good for coal liquefaction processes had almost no transition pores.

  15. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

    SciTech Connect

    Hura, Greg L.; Menon, Angeli L.; Hammel, Michal; Rambo, Robert P.; Poole II, Farris L.; Tsutakawa, Susan E.; Jenney Jr, Francis E.; Classen, Scott; Frankel, Kenneth A.; Hopkins, Robert C.; Yang, Sungjae; Scott, Joseph W.; Dillard, Bret D.; Adams, Michael W. W.; Tainer, John A.

    2009-07-20

    We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

  16. Time resolved small angle x-ray scattering reactivity studies on coals, asphaltenes, and polymers.

    SciTech Connect

    Seifert, S.; Thiyagarajan, P.; Winans, R. E.

    1999-07-02

    The objective of this study is to examine changes in the structures of coals, asphaltenes, and polymers in situ with small angle X-ray scattering (SAXS) during thermal treatments. We have built a SAXS instrument at the Basic Energy Sciences Synchrotrons Radiation Center at the Advanced Photon Source that allows us to obtain scattering data on very small samples and in the millisecond time domain. The Argonne Premium Coal samples, petroleum derived asphaltenes, and polymers with functionality to model fossil fuels were used in this study. The information that can be derived from these experiments includes: changes in fractal dimensionality, surface topology, and size and type of porosity. The information is correlated with other methods on the same samples.

  17. Small-Angle X-Ray Scattering From RNA, Proteins, And Protein Complexes

    SciTech Connect

    Lipfert, Jan; Doniach, Sebastian; /Stanford U., Phys. Dept. /Stanford U., Appl. Phys. Dept. /SLAC, SSRL

    2007-09-18

    Small-angle X-ray scattering (SAXS) is increasingly used to characterize the structure and interactions of biological macromolecules and their complexes in solution. Although still a low-resolution technique, the advent of high-flux synchrotron sources and the development of algorithms for the reconstruction of 3-D electron density maps from 1-D scattering profiles have made possible the generation of useful low-resolution molecular models from SAXS data. Furthermore, SAXS is well suited for the study of unfolded or partially folded conformational ensembles as a function of time or solution conditions. Here, we review recently developed algorithms for 3-D structure modeling and applications to protein complexes. Furthermore, we discuss the emerging use of SAXS as a tool to study membrane protein-detergent complexes. SAXS is proving useful to study the folding of functional RNA molecules, and finally we discuss uses of SAXS to study ensembles of denatured proteins.

  18. Tackiness of pressure-sensitive adhesives: An ultra-small-angle X-ray scattering investigation

    NASA Astrophysics Data System (ADS)

    Müller-Buschbaum, P.; Ittner, T.; Petry, W.

    2004-05-01

    The debonding of a model pressure-sensitive adhesive (PSA) poly-n-buthylacrylate is investigated by a combination of the mechanical tack test, optical microscopy and in situ ultra-small-angle X-ray scattering. From the mechanical test, macroscopic values such as force-distance curves are determined. The force-distance curve exhibits the typical non-linear behavior. With microscopy the macroscopic cavitation structure is observed. Scattering addresses the structure of the PSA on a microscopic level for the first time. As a new feature, a sub-structure of the usual optically resolvable macroscopic fibrils between the PSA surface and the probe punch is detected. The sub-structure exists over a large distance between the PSA and the probe surface and remains constant in diameter. This behavior of the sub-structure as well as the dependence of the force plateau on the film thickness are compared with theoretical predictions.

  19. Small Angle X-ray and Neutron Scattering in the Study of Polymers and Supramolecular Systems

    NASA Astrophysics Data System (ADS)

    Zeng, X. B.; Liu, F.; Xie, F.; Ungar, G.; Tschierske, C.; MacDonald, J. E.

    2008-03-01

    Some recent work carried out in our research group on complex structures found in polymers and supramolecular systems, using Small Angle X-ray and Neutron Scattering (SAXS and SANS) methods, are reviewed. These include, Combined SAXS and SANS study of superlattice structures in pure and mixed model polymers; Real-time SANS study of transient phases during polymer crystallization; Columnar phases with polygonal cross-sections in T-shaped polyphilic compounds;Complex 3-d phases formed by packing spherical objects (e.g. micelles self-assembled from tree-like molecules), including the recently discovered liquid quasi-crystals which possess 12-fold rotational symmetry. Examples of powder, fibre or surface oriented, and single-domain diffractions will be given. Reconstruction of electron density maps as well as computer modelling are also applied to help solving various complex structures.

  20. Small angle x ray scattering studies of aggregation in supercritical fluid solutions

    NASA Astrophysics Data System (ADS)

    Fulton, J. L.; Pfund, D. M.

    1994-10-01

    Small-angle x ray scattering (SAXS) can be used to derive structural information on molecular aggregates having sizes from 2 to 200 nm. Not only is the technique useful for probing fluid structure in pure and simple binary supercritical fluid systems, but the technique is also well suited to investigate a range of much more complex multi-molecular aggregates that form when surfactants are added to supercritical fluids. The authors describe the experimental apparatus that was constructed for these studies and the experimental approach used to collect the scattering data. They present scattering results for pure fluids and for fluids containing various types of microemulsion phases, including reverse micelle and normal micelle phases. These results demonstrate that SAXS is a powerful technique for probing various types of molecular aggregation in supercritical fluid solutions.

  1. π-conjugation and conformation in a semiconducting polymer: small angle x-ray scattering study

    NASA Astrophysics Data System (ADS)

    Choudhury, Paramita Kar; Bagchi, Debjani; Menon, Reghu

    2009-05-01

    Small angle x-ray scattering (SAXS) in a poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) solution has shown the important role of π-electron conjugation in controlling the chain conformation and assembly. By increasing the extent of conjugation from 30 to 100%, the persistence length (lp) increases from 20 to 66 Å. Moreover, a pronounced second peak in the pair distribution function has been observed in a fully conjugated chain, at larger length scales. This feature indicates that the chain segments tend to self-assemble as the conjugation along the chain increases. Xylene enhances the rigidity of the PPV backbone to yield extended structures, while tetrahydrofuran solvates the side groups to form compact coils in which the lp is much shorter.

  2. Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering

    PubMed Central

    Lipfert, Jan; Herschlag, Daniel; Doniach, Sebastian

    2015-01-01

    Summary Riboswitches are functional RNA molecules that control gene expression through conformational changes in response to small-molecule ligand binding. In addition, riboswitch 3D structure, like that of other RNA molecules, is dependent on cation–RNA interactions as the RNA backbone is highly negatively charged. Here, we show how small-angle X-ray scattering (SAXS) can be used to probe RNA conformations as a function of ligand and ion concentration. In a recent study of a glycine-binding tandem aptamer from Vibrio cholerae, we have used SAXS data and thermodynamic modeling to investigate how Mg2+-dependent folding and glycine binding are energetically coupled. In addition, we have employed ab initio shape reconstruction algorithms to obtain low-resolution models of the riboswitch structure from SAXS data under different solution conditions. PMID:19381558

  3. Small Angle X-ray Scattering in Structural Investigation of Selected Biological Systems

    SciTech Connect

    Kozak, Maciej

    2007-11-26

    Small angle X-ray scattering method (SAXS) is a technique complementary to the protein crystallography, allowing determination of the structural parameters such as the radius of gyration or the maximum size characterizing the macromolecules, and providing information on the conformational changes taking place in solution. The use of SAXS method enables a comparison of the protein crystal structure with the data collected in solution. Recent development of the measurement techniques (mainly those based on synchrotron radiation) and calculation methods has permitted introduction of advanced techniques also in the field of structural analysis of biomolecules (e.g. for determination of the shape of the protein molecule in solution). The paper presents a few selected methods of structural analysis of biological systems based on the SAXS data and illustrates their performance on the example of xylanase from Trichoderma longibrachiatum and a model phospholipid system.

  4. Three dimensional reconstruction of nanoislands from grazing-incidence small-angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Yefanov, O. M.; Vartanyants, I. A.

    2009-02-01

    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.

  5. The crystallization of hectorite clays as monitored by small angle X-ray scattering and NMR

    SciTech Connect

    Carrado, K. A.; Xu, L.; Seifert, S.; Gregory, D.; Song, K.; Botto, R. E.

    1999-12-13

    The authors have probed the 48-hr crystallization of a magnesium silicate clay called hectorite. Small angle X-ray scattering (SAXS) at the Advanced Photon Source using aliquots ex situ has revealed that data is consistent with ex situ XRD, TGA, AFM, and IR data in that all these techniques see clay crystallite beginning to form in the first few hours of reaction. Tetraethylammonium (TEA) ions are used to aid crystallization and become incorporated as the exchange cations within the interlayers. {sup 13}C NMR shows that 80% of the final TEA loading is accomplished in the first 10 hrs. {sup 29}Si NMR displays a visible clay silicate peak after just 1 hr. In addition, the first in situ study of clay crystallization of any kind was performed by in situ SAXS. Results are consistent with the ex situ data as well as showing the sensitivity of SAXS to sol gel reactions occurring on the order of minutes.

  6. Sample holder for small-angle x-ray scattering static and flow cell measurements

    SciTech Connect

    Lipfert, Jan; Millett, Ian S.; Seifert, Soenke; Doniach, Sebastian

    2006-04-15

    We present the design of a sample holder for small-angle x-ray scattering (SAXS) that can be used for both static and flow cell measurements, allowing to switch between these two types of measurement without having to realign the detector and camera geometry. The device makes possible high signal-to-noise experiments with sample volumes as small as 16 {mu}l and can be thermocontrolled using a standard circulating water bath. The setup has been used successfully for a range of biological SAXS measurements, including peptides, detergent micelles, membrane proteins, and nucleic acids. As a performance test, we present scattering data for horse heart cytochrome c, collected at the BESSRC CAT beam line 12-ID of the Advanced Photon Source. The design drawings are provided in the supplementary material.

  7. Small angle X-ray scattering studies of aggregation in supercritical fluid solutions

    SciTech Connect

    Fulton, J.L.; Pfund, D.M.

    1994-10-01

    Small-angle X-ray scattering (SAXS) can be used to derive structural information on molecular aggregates having sizes from 2 to 200 nm. Not only is the technique useful for probing fluid structure in pure and simple binary supercritical fluid systems, but the technique is also well suited to investigate a range of much more complex multi-molecular aggregates that form when surfactants are added to supercritical fluids. The authors describe the experimental apparatus that was constructed for these studies and the experimental approach used to collect the scattering data. They present scattering results for pure fluids and for fluids containing various types of microemulsion phases, including reverse micelle and normal micelle phases. These results demonstrate that SAXS is a powerful technique for probing various types of molecular aggregation in supercritical fluid solutions.

  8. Small-angle neutron and X-ray scattering reveal conformational changes in rhodopsin activation

    NASA Astrophysics Data System (ADS)

    Shrestha, Utsab R.; Bhowmik, Debsindhu; Perera, Suchitrhanga M. C. D.; Chawla, Udeep; Struts, Andrey V.; Graziono, Vito; Pingali, Sai Venkatesh; Heller, William T.; Qian, Shuo; Brown, Michael F.; Chu, Xiang-Qiang

    2015-03-01

    Understanding G-protein-coupled receptor (GPCR) activation plays a crucial role in the development of novel improved molecular drugs. During photo-activation, the retinal chromophore of the visual GPCR rhodopsin isomerizes from 11-cis to all-trans conformation, yielding an equilibrium between inactive Meta-I and active Meta-II states. The principal goals of this work are to address whether the activation of rhodopsin leads to a single state or a conformational ensemble, and how protein organizational structure changes with detergent environment in solution. We use both small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS) techniques to answer the above questions. For the first time we observe the change in protein conformational ensemble upon photo-activation by SANS with contrast variation, which enables the separate study of the protein structure within the detergent assembly. In addition, SAXS study of protein structure within detergent assembly suggests that the detergent molecules form a belt of monolayer (micelle) around protein with different geometrical shapes to keep the protein in folded state.

  9. Polarized Resonant Critical Dimension Small Angle X-Ray Scattering for the Characterization of Polymer Patterns

    NASA Astrophysics Data System (ADS)

    Liman, Christopher; Sunday, Daniel; Ro, Hyun Wook; Richter, Lee; Hannon, Adam; Kline, R. Joseph

    Critical dimension small angle X-ray scattering (CDSAXS) is a recently developed technique that enables the characterization of the three-dimensional shape of periodic patterns, such as directed self-assembled (DSA) block copolymer (BCP) lamellae thin films. Information about the polymer patterns is extracted by fitting simulated scattering patterns to the experimental ones using an inverse iterative algorithm. Conducting CDSAXS at resonant energies near the carbon or nitrogen edge can enhance the strength of the scattering, but also causes the scattering to be influenced by any anisotropic orientation of the polymer chains. In this work, to assess the degree to which the scattering may be influenced by orientation, we simulate polarized resonant CDSAXS patterns for BCP lamellae with varying degrees of orientation, as well as orientation as a function of location within the lamellae, for different polarizations of the incident X-rays. Also, to assess the influence of a higher degree of orientation, we use capillary force lithography to pattern nanogratings of two semiconducting homopolymers which are known to orient strongly. We characterize these nanogratings, which have similar length scales to DSA BCP lamellae, with polarized resonant CDSAXS and spectroscopic ellipsometry. Finally, we fit simulated CDSAXS and ellipsometric data to the experimental data to obtain information about the shape and the orientation of the nanogratings.

  10. Synchrotron-based small-angle X-ray scattering (SAXS) of proteins in solution

    PubMed Central

    Skou, Soren; Gillilan, Richard E

    2015-01-01

    Summary With recent advances in data analysis algorithms, X-ray detectors, and synchrotron sources, small-angle X-ray scattering (SAXS) has become much more accessible to the structural biology community than ever before. Although limited to ~10 Å resolution, SAXS can provide a wealth of structural information on biomolecules in solution and is compatible with a wide range of experimental conditions. SAXS is thus an attractive alternative when crystallography is not possible. Moreover, advanced usage of SAXS can provide unique insight into biomolecular behavior that can only be observed in solution, such as large conformational changes and transient protein-protein interactions. Unlike crystal diffraction data, however, solution scattering data are subtle in appearance, highly sensitive to sample quality and experimental errors, and easily misinterpreted. In addition, synchrotron beamlines that are dedicated to SAXS are often unfamiliar to the non-specialist. Here, we present a series of procedures that can be used for SAXS data collection and basic cross-checks designed to detect and avoid aggregation, concentration effects, radiation damage, buffer mismatch, and other common problems. The protein, human serum albumin (HSA), serves as a convenient and easily replicated example of just how subtle these problems can sometimes be, but also of how proper technique can yield pristine data even in problematic cases. Because typical data collection times at a synchrotron are only one to several days, we recommend that the sample purity, homogeneity, and solubility be extensively optimized prior to the experiment. PMID:24967622

  11. Alzheimer's disease imaging biomarkers using small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Choi, Mina; Alam, Nadia; Dahal, Eshan; Ghammraoui, Bahaa; Badano, Aldo

    2016-03-01

    There is a need for novel imaging techniques for the earlier detection of Alzheimer's disease (AD). Two hallmarks of AD are amyloid beta (Aβ) plaques and tau tangles that are formed in the brain. Well-characterized x-ray cross sections of Aβ and tau proteins in a variety of structural states could potentially be used as AD biomarkers for small-angle x-ray scattering (SAXS) imaging without the need for injectable probes or contrast agents. First, however, the protein structures must be controlled and measured to determine accurate biomarkers for SAXS imaging. Here we report SAXS measurements of Aβ42 and tau352 in a 50% dimethyl sulfoxide (DMSO) solution in which these proteins are believed to remain monomeric because of the stabilizing interaction of DMSO solution. Our SAXS analysis showed the aggregation of both proteins. In particular, we found that the aggregation of Aβ42 slowly progresses with time in comparison to tau352 that aggregates at a faster rate and reaches a steady-state. Furthermore, the measured signals were compared to the theoretical SAXS profiles of Aβ42 monomer, Aβ42 fibril, and tau352 that were computed from their respective protein data bank structures. We have begun the work to systematically control the structural states of these proteins in vitro using various solvent conditions. Our future work is to utilize the distinct SAXS profiles of various structural states of Aβ and tau to build a library of signals of interest for SAXS imaging in brain tissue.

  12. Density of hydrophobically confined deeply cooled water investigated by small angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Liu, Kao-Hsiang; Zhang, Yang; Jeng, U.-Ser; Mou, Chung-Yuan

    2015-09-01

    Water's behavior near hydrophobic surfaces has attracted great attention due to chemical and geological applications. Here, we report small angle X-ray scattering (SAXS) studies of water confined in the hydrophobic nanoporous carbon material, CMK-1-14, from ambient to deeply cooled temperatures. By monitoring the scattering intensity of the first Bragg peak, which is directly related to the scattering length density contrast between the carbon matrix and the confined water, the average density of the hydrophobically confined water was determined from 300 K to 150 K at ambient pressure. Furthermore, differential scanning calorimetry and X-ray diffraction measurements showed that the majority of such hydrophobically confined water did not crystallize in the investigated temperature range. By exploiting the fast speed of SAXS measurements and the continuous temperature ramping, the average density profile and the deduced thermal expansion coefficient (αp) were obtained. We found that the well-known density maximum of water at 277 K downshifted to 260 K, and the density minimum which has been observed in hydrophilic confinement disappeared. In addition, the previously measured large density decreasing of 18% at low temperature was recalibrated to a more reasonable 10% instead. Consequently, the recalculated αp peak was found to be quite similar to that of the water confined in hydrophilic MCM-41-S-15 suggesting an intrinsic property of water, which does not sensitively depend on the confinement surface.

  13. Improving small-angle X-ray scattering data for structural analyses of the RNA world

    PubMed Central

    Rambo, Robert P.; Tainer, John A.

    2010-01-01

    Defining the shape, conformation, or assembly state of an RNA in solution often requires multiple investigative tools ranging from nucleotide analog interference mapping to X-ray crystallography. A key addition to this toolbox is small-angle X-ray scattering (SAXS). SAXS provides direct structural information regarding the size, shape, and flexibility of the particle in solution and has proven powerful for analyses of RNA structures with minimal requirements for sample concentration and volumes. In principle, SAXS can provide reliable data on small and large RNA molecules. In practice, SAXS investigations of RNA samples can show inconsistencies that suggest limitations in the SAXS experimental analyses or problems with the samples. Here, we show through investigations on the SAM-I riboswitch, the Group I intron P4-P6 domain, 30S ribosomal subunit from Sulfolobus solfataricus (30S), brome mosaic virus tRNA-like structure (BMV TLS), Thermotoga maritima asd lysine riboswitch, the recombinant tRNAval, and yeast tRNAphe that many problems with SAXS experiments on RNA samples derive from heterogeneity of the folded RNA. Furthermore, we propose and test a general approach to reducing these sample limitations for accurate SAXS analyses of RNA. Together our method and results show that SAXS with synchrotron radiation has great potential to provide accurate RNA shapes, conformations, and assembly states in solution that inform RNA biological functions in fundamental ways. PMID:20106957

  14. Application of small angle X-ray scattering synchrotron technology for measuring ovine meat quality.

    PubMed

    Hoban, J M; Hopkins, D L; Kirby, N; Collins, D; Dunshea, F R; Kerr, M G; Bailes, K; Cottrell, J J; Holman, B W B; Brown, W; Ponnampalam, E N

    2016-07-01

    A small angle X-ray scattering (SAXS) synchrotron was used to evaluate 100 ovine m. longissimus lumborum, representing lamb (n=50) and sheep (n=50). The diffraction of X-rays gives information on muscle myofibril structure and fat content. The linear relationships between SAXS measures with measures such as, shear force, intramuscular fat content (IMF) and collagen content/solubility, were investigated. A relationship was found between the d-spacing of the actin/myosin fibril spacing (SAX1 and SAX2) and the cross sectional area of the rhombohedral unit cell (Cell area) and shear force after 1 and 5day ageing. There was a positive relationship between IMF and a SAXS Fat area measure. There was a muscle site effect on SAX1, SAX2 and Cell area, with the cranial site having a larger distance between myofibrils. The potential of SAXS as a powerful research tool to determine not only the structural components of ovine tenderness, but also the fat content related to IMF is evident. PMID:26971308

  15. Insight into asphaltene nanoaggregate structure inferred by small angle neutron and X-ray scattering.

    PubMed

    Eyssautier, Joëlle; Levitz, Pierre; Espinat, Didier; Jestin, Jacques; Gummel, Jérémie; Grillo, Isabelle; Barré, Loïc

    2011-06-01

    Complementary neutron and X-ray small angle scattering results give prominent information on the asphaltene nanostructure. Precise SANS and SAXS measurements on a large q-scale were performed on the same dilute asphaltene-toluene solution, and absolute intensity scaling was carried out. Direct comparison of neutron and X-ray spectra enables description of a fractal organization made from the aggregation of small entities of 16 kDa, exhibiting an internal fine structure. Neutron contrast variation experiments enhance the description of this nanoaggregate in terms of core-shell disk organization, giving insight into core and shell dimensions and chemical compositions. The nanoaggregates are best described by a disk of total radius 32 Å with 30% polydispersity and a height of 6.7 Å. Composition and density calculations show that the core is a dense and aromatic structure, contrary to the shell, which is highly aliphatic. These results show a good agreement with the general view of the Yen model (Yen, T. F.; et al. Anal. Chem.1961, 33, 1587-1594) and as for the modified Yen model (Mullins, O. C. Energy Fuels2010, 24, 2179-2207), provide characteristic dimensions of the asphaltene nanoaggregate in good solvent. PMID:21553910

  16. Morphological and structural characterization of PHBV/organoclay nanocomposites by small angle X-ray scattering.

    PubMed

    Carli, Larissa N; Bianchi, Otávio; Machado, Giovanna; Crespo, Janaina S; Mauler, Raquel S

    2013-03-01

    In this work, the morphological and structural behaviors of poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV) nanocomposites were investigated using small angle X-ray scattering (SAXS), wide angle X-ray diffraction (WAXD) and transmission electron microscopy (TEM). The nanocomposites with 1, 3 and 5 wt.% of organically modified montmorillonite Cloisite® 30B (OMMT) were prepared by melt processing in a twin screw extruder using two different processing conditions (low and high shear intensity). The lamellar long period of the polymer was lower for the nanocomposites, with high polydispersity values. However, the crystalline thickness increased with the clay content and was independent of the processing conditions. This behavior resulted in a high linear crystallinity of the nanocomposites with 3 and 5 wt.% OMMT. The disruption factor (β) was in agreement with the WAXD and TEM findings, indicating a good dispersion of the nanoparticles in the PHBV matrix with 3 wt.% of OMMT during the high shear intensity of melt processing. PMID:25427508

  17. Density of hydrophobically confined deeply cooled water investigated by small angle X-ray scattering

    SciTech Connect

    Liu, Kao-Hsiang; Zhang, Yang; Jeng, U-Ser; Mou, Chung-Yuan

    2015-09-07

    The behavior of water near hydrophobic surfaces has attracted great attention due to chemical and geological applications. Here, we report small angle X-ray scattering (SAXS) studies of water confined in the hydrophobic nanoporous carbon material, CMK-1-14, from ambient to deeply cooled temperatures. Moreover, by monitoring the scattering intensity of the first Bragg peak, which is directly related to the scattering length density contrast between the carbon matrix and the confined water, the average density of the hydrophobically confined water was determined from 300 K to 150 K at ambient pressure. Furthermore, differential scanning calorimetry and X-ray diffraction measurements showed that the majority of such hydrophobically confined water did not crystallize in the investigated temperature range. By exploiting the fast speed of SAXS measurements and the continuous temperature ramping, the average density profile and the deduced thermal expansion coefficient (alpha(p)) were obtained. We found that the well-known density maximum of water at 277 K downshifted to 260 K, and the density minimum which has been observed in hydrophilic confinement disappeared. Additionally, the previously measured large density decreasing of 18% at low temperature was recalibrated to a more reasonable 10% instead. Consequently, the recalculated ap peak was found to be quite similar to that of the water confined in hydrophilic MCM-41-S-15 suggesting an intrinsic property of water, which does not sensitively depend on the confinement surface.

  18. Density of hydrophobically confined deeply cooled water investigated by small angle X-ray scattering

    DOE PAGESBeta

    Liu, Kao-Hsiang; Zhang, Yang; Jeng, U-Ser; Mou, Chung-Yuan

    2015-09-07

    The behavior of water near hydrophobic surfaces has attracted great attention due to chemical and geological applications. Here, we report small angle X-ray scattering (SAXS) studies of water confined in the hydrophobic nanoporous carbon material, CMK-1-14, from ambient to deeply cooled temperatures. Moreover, by monitoring the scattering intensity of the first Bragg peak, which is directly related to the scattering length density contrast between the carbon matrix and the confined water, the average density of the hydrophobically confined water was determined from 300 K to 150 K at ambient pressure. Furthermore, differential scanning calorimetry and X-ray diffraction measurements showed thatmore » the majority of such hydrophobically confined water did not crystallize in the investigated temperature range. By exploiting the fast speed of SAXS measurements and the continuous temperature ramping, the average density profile and the deduced thermal expansion coefficient (alpha(p)) were obtained. We found that the well-known density maximum of water at 277 K downshifted to 260 K, and the density minimum which has been observed in hydrophilic confinement disappeared. Additionally, the previously measured large density decreasing of 18% at low temperature was recalibrated to a more reasonable 10% instead. Consequently, the recalculated ap peak was found to be quite similar to that of the water confined in hydrophilic MCM-41-S-15 suggesting an intrinsic property of water, which does not sensitively depend on the confinement surface.« less

  19. Modeling RNA topological structures using small angle X-ray scattering.

    PubMed

    Bhandari, Yuba R; Jiang, Wei; Stahlberg, Eric A; Stagno, Jason R; Wang, Yun-Xing

    2016-07-01

    Detailed understanding of the structure and function relationship of RNA requires knowledge about RNA three-dimensional (3D) topological folding. However, there are very few unique RNA entries in structure databases. This is due to challenges in determining 3D structures of RNA using conventional methods, such as X-ray crystallography and NMR spectroscopy, despite significant advances in both of these technologies. Computational methods have come a long way in accurately predicting the 3D structures of small (<50nt) RNAs to within a few angstroms compared to their native folds. However, lack of an apparent correlation between an RNA primary sequence and its 3D fold ultimately limits the success of purely computational approaches. In this context, small angle X-ray scattering (SAXS) serves as a valuable tool by providing global shape information of RNA. In this article, we review the progress in determining RNA 3D topological structures, including a new method that combines secondary structural information and SAXS data to sample conformations generated through hierarchical moves of commonly observed RNA motifs. PMID:27090001

  20. Colloidal crystallite suspensions studied by high pressure small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Schroer, M. A.; Westermeier, F.; Lehmkühler, F.; Conrad, H.; Schavkan, A.; Zozulya, A. V.; Fischer, B.; Roseker, W.; Sprung, M.; Gutt, C.; Grübel, G.

    2016-02-01

    We report on high pressure small angle x-ray scattering on suspensions of colloidal crystallites in water. The crystallites made out of charge-stabilized poly-acrylate particles exhibit a complex pressure dependence which is based on the specific pressure properties of the suspending medium water. The dominant effect is a compression of the crystallites caused by the compression of the water. In addition, we find indications that also the electrostatic properties of the system, i.e. the particle charge and the dissociation of ions, might play a role for the pressure dependence of the samples. The data further suggest that crystallites in a metastable state induced by shear-induced melting can relax to a similar structural state upon the application of pressure and dilution with water. X-ray cross correlation analysis of the two-dimensional scattering patterns indicates a pressure-dependent increase of the orientational order of the crystallites correlated with growth of these in the suspension. This study underlines the potential of pressure as a very relevant parameter to understand colloidal crystallite systems in aqueous suspension.

  1. Density of hydrophobically confined deeply cooled water investigated by small angle X-ray scattering

    SciTech Connect

    Liu, Kao-Hsiang; Zhang, Yang; Jeng, U-Ser; Mou, Chung-Yuan

    2015-09-07

    Water’s behavior near hydrophobic surfaces has attracted great attention due to chemical and geological applications. Here, we report small angle X-ray scattering (SAXS) studies of water confined in the hydrophobic nanoporous carbon material, CMK-1-14, from ambient to deeply cooled temperatures. By monitoring the scattering intensity of the first Bragg peak, which is directly related to the scattering length density contrast between the carbon matrix and the confined water, the average density of the hydrophobically confined water was determined from 300 K to 150 K at ambient pressure. Furthermore, differential scanning calorimetry and X-ray diffraction measurements showed that the majority of such hydrophobically confined water did not crystallize in the investigated temperature range. By exploiting the fast speed of SAXS measurements and the continuous temperature ramping, the average density profile and the deduced thermal expansion coefficient (α{sub p}) were obtained. We found that the well-known density maximum of water at 277 K downshifted to 260 K, and the density minimum which has been observed in hydrophilic confinement disappeared. In addition, the previously measured large density decreasing of 18% at low temperature was recalibrated to a more reasonable 10% instead. Consequently, the recalculated α{sub p} peak was found to be quite similar to that of the water confined in hydrophilic MCM-41-S-15 suggesting an intrinsic property of water, which does not sensitively depend on the confinement surface.

  2. Small-angle x-ray scattering studies of the manganese stabilizing subunit in photosystem II.

    SciTech Connect

    Svensson, B.; Tiede, D. M.; Barry, B. A.; Univ. of Minnesota

    2002-08-29

    Small-angle X-ray scattering studies (SAXS) were used to determine the size, shape, and oligomeric composition of the manganese stabilizing protein (MSP) of photosystem II. This extrinsic protein subunit plays an important role in photosynthetic oxygen evolution. As its name implies, MSP stabilizes the tetranuclear Mn cluster of the water oxidation complex. Removal of MSP lowers activity and decreases the stability of active-site manganese. Reconstitution of MSP reverses these effects. In this study, MSP was extracted from spinach PSII membranes using CaCl{sub 2} or urea. Through the use of MALDI-TOF mass spectrometry, the molecular weight of MSP was determined to be 26.53 kDa. X-ray scattering results show that both samples display a monodisperse scattering pattern; this pattern is consistent with a homogeneous protein solution. The CaCl{sub 2} extracted and urea extracted MSP samples have radii of gyration of 25.9 {+-} 0.4 and 27.0 {+-} 0.01 {angstrom}, respectively. MSP is shown to be monomeric in solution. This was determined using a cytochrome c standard and the scattering intensity, extrapolated to zero scattering angle, which is proportional to the molecular weight. This SAXS study suggests that, in solution, MSP is a monomeric, elongated prolate ellipsoid with dimensions, 112 x 23 x 23 {angstrom}{sup 3} and an axial ratio of 4.8.

  3. Density of hydrophobically confined deeply cooled water investigated by small angle X-ray scattering.

    PubMed

    Liu, Kao-Hsiang; Zhang, Yang; Jeng, U-Ser; Mou, Chung-Yuan

    2015-09-01

    Water's behavior near hydrophobic surfaces has attracted great attention due to chemical and geological applications. Here, we report small angle X-ray scattering (SAXS) studies of water confined in the hydrophobic nanoporous carbon material, CMK-1-14, from ambient to deeply cooled temperatures. By monitoring the scattering intensity of the first Bragg peak, which is directly related to the scattering length density contrast between the carbon matrix and the confined water, the average density of the hydrophobically confined water was determined from 300 K to 150 K at ambient pressure. Furthermore, differential scanning calorimetry and X-ray diffraction measurements showed that the majority of such hydrophobically confined water did not crystallize in the investigated temperature range. By exploiting the fast speed of SAXS measurements and the continuous temperature ramping, the average density profile and the deduced thermal expansion coefficient (αp) were obtained. We found that the well-known density maximum of water at 277 K downshifted to 260 K, and the density minimum which has been observed in hydrophilic confinement disappeared. In addition, the previously measured large density decreasing of 18% at low temperature was recalibrated to a more reasonable 10% instead. Consequently, the recalculated αp peak was found to be quite similar to that of the water confined in hydrophilic MCM-41-S-15 suggesting an intrinsic property of water, which does not sensitively depend on the confinement surface. PMID:26342380

  4. Signal, noise, and resolution in correlated fluctuations from snapshot small-angle x-ray scattering

    SciTech Connect

    Kirian, Richard A.; Schmidt, Kevin E.; Wang Xiaoyu; Doak, R. Bruce; Spence, John C. H.

    2011-07-15

    It has been suggested that the three-dimensional structure of one particle may be reconstructed using the scattering from many identical, randomly oriented copies ab initio, without modeling or a priori information. This may be possible if these particles are frozen in either space or time, so that the conventional two-dimensional small-angle x-ray scattering (SAXS) distribution contains fluctuations and is no longer isotropic. We consider the magnitude of the correlated fluctuation SAXS (CFSAXS) signal for typical x-ray free-electron laser (XFEL) beam conditions and compare this against the errors derived with the inclusion of Poisson photon counting statistics. The resulting signal-to-noise ratio (SNR) is found to rapidly approach a limit independent of the number of particles contributing to each diffraction pattern, so that the addition of more particles to a ''single-particle-per-shot'' experiment may be of little value, apart from reducing solvent background. When the scattering power is significantly less than one photon per particle per Shannon pixel, the SNR grows in proportion to incident flux. We provide simulations for protein molecules in support of these analytical results, and discuss the effects of solvent background scatter. We consider the SNR dependence on resolution and particle size, and discuss the application of the method to glasses and liquids, and the implications of more powerful XFELs, smaller focused beams, and higher pulse repetition rates for this approach. We find that an accurate CFSAXS measurement may be acquired to subnanometer resolution for protein molecules if a 9-keV beam containing 10{sup 13} photons is focused to a {approx}100-nm spot diameter, provided that the effects of solvent background can be reduced sufficiently.

  5. Nano-scale morphology of melanosomes revealed by small-angle X-ray scattering.

    PubMed

    Gorniak, Thomas; Haraszti, Tamas; Garamus, Vasyl M; Buck, Andreas R; Senkbeil, Tobias; Priebe, Marius; Hedberg-Buenz, Adam; Koehn, Demelza; Salditt, Tim; Grunze, Michael; Anderson, Michael G; Rosenhahn, Axel

    2014-01-01

    Melanosomes are highly specialized organelles that produce and store the pigment melanin, thereby fulfilling essential functions within their host organism. Besides having obvious cosmetic consequences--determining the color of skin, hair and the iris--they contribute to photochemical protection from ultraviolet radiation, as well as to vision (by defining how much light enters the eye). Though melanosomes can be beneficial for health, abnormalities in their structure can lead to adverse effects. Knowledge of their ultrastructure will be crucial to gaining insight into the mechanisms that ultimately lead to melanosome-related diseases. However, due to their small size and electron-dense content, physiologically intact melanosomes are recalcitrant to study by common imaging techniques such as light and transmission electron microscopy. In contrast, X-ray-based methodologies offer both high spatial resolution and powerful penetrating capabilities, and thus are well suited to study the ultrastructure of electron-dense organelles in their natural, hydrated form. Here, we report on the application of small-angle X-ray scattering--a method effective in determining the three-dimensional structures of biomolecules--to whole, hydrated murine melanosomes. The use of complementary information from the scattering signal of a large ensemble of suspended organelles and from single, vitrified specimens revealed a melanosomal sub-structure whose surface and bulk properties differ in two commonly used inbred strains of laboratory mice. Whereas melanosomes in C57BL/6J mice have a well-defined surface and are densely packed with 40-nm units, their counterparts in DBA/2J mice feature a rough surface, are more granular and consist of 60-nm building blocks. The fact that these strains have different coat colors and distinct susceptibilities to pigment-related eye disease suggest that these differences in size and packing are of biological significance. PMID:24621581

  6. Metastable ripple phase of fully hydrated dipalmitoylphosphatidylcholine as studied by small angle x-ray scattering

    PubMed Central

    Yao, Haruhiko; Matuoka, Sinzi; Tenchov, Boris; Hatta, Ichiro

    1991-01-01

    Fully hydrated dipalmitoylphosphatidylcholine (DPPC) undergoes liquid crystalline to metastable Pβ, phase transition in cooling. A small angle x-ray scattering study has been performed for obtaining further evidence about the structure of this phase. From a high-resolution observation of x-ray diffraction profiles, a distinct multipeak pattern has become obvious. Among them the (01) reflection in the secondary ripple structure is identified clearly. There are peaks assigned straightforwardly to (10) and (20) reflections in the primary ripple structure and peaks assigned to (10) and (20) reflections in the secondary ripple structure. Therefore the multipeak pattern is due to superposition of the reflections cause by the primary and secondary ripple structures. The lattice parameters are estimated as follows: for the primary ripple structure a = 7.09 nm, b = 13.64 nm, and γ = 95°, and for the secondary ripple structure a = 8.2 nm, b = 26.6 nm, and γ = 90°. The lattice parameters thus obtained for the secondary ripple structure are not conclusive, however. The hydrocarbon chains in the primary ripple structure have been reported as being tilted against the bilayer plane and, on the other hand, the hydrocarbon chains in the secondary ripple structure are likely to be perpendicular to the bilayer plane. This fact seems to be related to a sequential mechanism of phase transitions. On heating from the Lβ, phase where the hydrocarbon chains are tilted the primary ripple structure having tilted hydrocarbon chains takes place and on cooling from the Lα phase where the hydrocarbon chains are not tilted the secondary ripple structure with untilted chains tends to be stabilized. It appears that the truly metastable ripple phase is expressed by the second ripple structure although in the course of the actual cooling transition both the secondary and primary ripple structures form and coexist. PMID:19431787

  7. A triple axis double crystal multiple reflection camera for ultra small angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Lambard, Jacques; Lesieur, Pierre; Zemb, Thomas

    1992-06-01

    To extend the domain of small angle X-ray scattering requires multiple reflection crystals to collimate the beam. A double crystal, triple axis X-ray camera using multiple reflection channel cut crystals is described. Procedures for measuring the desmeared scattering cross-section on absolute scale are described as well as the measurement from several typical samples : fibrils of collagen, 0.3 μm diameter silica spheres, 0.16 μm diameter interacting latex spheres, porous lignite coal, liquid crystals in a surfactant-water system, colloidal crystal of 0.32 μm diameter silica spheres. L'extension du domaine de diffusion des rayons-X vers les petits angles demande l'emploi de cristaux à réflexions multiples pour collimater le faisceau. Nous décrivons une caméra à rayons-X à trois axes où les réflexions multiples sont réalisées dans deux cristaux à gorge. Nous donnons ensuite les procédures de déconvolution pour obtenir la section efficace de diffusion en échelle absolue, ainsi que les résultats des mesures effectuées avec plusieurs échantillons typiques : fibres de collagène, sphères de silice de 0,3 μm de diamètre, sphères de latex de 0,16 μm de diamètre en interaction, charbon lignite poreux, cristaux liquides formés dans un système eau-tensioactif, solution colloïdale de sphères de silice de 0,32 μm de diamètre.

  8. Docking and small angle X-ray scattering studies of purine nucleoside phosphorylase.

    PubMed

    Filgueira de Azevedo, Walter; dos Santos, Giovanni César; dos Santos, Denis Marangoni; Olivieri, Johnny Rizzieri; Canduri, Fernanda; Silva, Rafael Guimarães; Basso, Luiz Augusto; Renard, Gaby; da Fonseca, Isabel Osório; Mendes, Maria Anita; Palma, Mário Sérgio; Santos, Diógenes Santiago

    2003-10-01

    Docking simulations have been used to assess protein complexes with some success. Small angle X-ray scattering (SAXS) is a well-established technique to investigate protein spatial configuration. This work describes the integration of geometric docking with SAXS to investigate the quaternary structure of recombinant human purine nucleoside phosphorylase (PNP). This enzyme catalyzes the reversible phosphorolysis of N-ribosidic bonds of purine nucleosides and deoxynucleosides. A genetic deficiency due to mutations in the gene encoding for PNP causes gradual decrease in T-cell immunity. Inappropriate activation of T-cells has been implicated in several clinically relevant human conditions such as transplant rejection, rheumatoid arthritis, lupus, and T-cell lymphomas. PNP is therefore a target for inhibitor development aiming at T-cell immune response modulation and has been submitted to extensive structure-based drug design. The present analysis confirms the trimeric structure observed in the crystal. The potential application of the present procedure to other systems is discussed. PMID:13679062

  9. Structural modeling of proteins by integrating small-angle x-ray scattering data

    NASA Astrophysics Data System (ADS)

    Zhang, Yong-Hui; Peng, Jun-Hui; Zhang, Zhi-Yong

    2015-12-01

    Elucidating the structure of large biomolecules such as multi-domain proteins or protein complexes is challenging due to their high flexibility in solution. Recently, an “integrative structural biology” approach has been proposed, which aims to determine the protein structure and characterize protein flexibility by combining complementary high- and low-resolution experimental data using computer simulations. Small-angle x-ray scattering (SAXS) is an efficient technique that can yield low-resolution structural information, including protein size and shape. Here, we review computational methods that integrate SAXS with other experimental datasets for structural modeling. Finally, we provide a case study of determination of the structure of a protein complex formed between the tandem SH3 domains in c-Cb1-associated protein and the proline-rich loop in human vinculin. Project supported by the National Key Basic Research Program of China (Grant Nos. 2013CB910203 and 2011CB911104), the National Natural Science Foundation of China (Grant No. 31270760), the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDB08030102), and the Specialized Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20113402120013).

  10. Six-dimensional real and reciprocal space small-angle X-ray scattering tomography

    NASA Astrophysics Data System (ADS)

    Schaff, Florian; Bech, Martin; Zaslansky, Paul; Jud, Christoph; Liebi, Marianne; Guizar-Sicairos, Manuel; Pfeiffer, Franz

    2015-11-01

    When used in combination with raster scanning, small-angle X-ray scattering (SAXS) has proven to be a valuable imaging technique of the nanoscale, for example of bone, teeth and brain matter. Although two-dimensional projection imaging has been used to characterize various materials successfully, its three-dimensional extension, SAXS computed tomography, poses substantial challenges, which have yet to be overcome. Previous work using SAXS computed tomography was unable to preserve oriented SAXS signals during reconstruction. Here we present a solution to this problem and obtain a complete SAXS computed tomography, which preserves oriented scattering information. By introducing virtual tomography axes, we take advantage of the two-dimensional SAXS information recorded on an area detector and use it to reconstruct the full three-dimensional scattering distribution in reciprocal space for each voxel of the three-dimensional object in real space. The presented method could be of interest for a combined six-dimensional real and reciprocal space characterization of mesoscopic materials with hierarchically structured features with length scales ranging from a few nanometres to a few millimetres—for example, biomaterials such as bone or teeth, or functional materials such as fuel-cell or battery components.

  11. Structure Parameters of Synaptic Vesicles Quantified by Small-Angle X-Ray Scattering

    PubMed Central

    Castorph, Simon; Riedel, Dietmar; Arleth, Lise; Sztucki, Michael; Jahn, Reinhard; Holt, Matthew; Salditt, Tim

    2010-01-01

    Synaptic vesicles (SVs) are small, membrane-bound organelles that are found in the synaptic terminal of neurons, and which are crucial in neurotransmission. After a rise in internal [Ca2+] during neuronal stimulation, SVs fuse with the plasma membrane releasing their neurotransmitter content, which then signals neighboring neurons. SVs are subsequently recycled and refilled with neurotransmitter for further rounds of release. Recently, tremendous progress has been made in elucidating the molecular composition of SVs, as well as putative protein-protein interactions. However, what is lacking is an empirical description of SV structure at the supramolecular level—which is necessary to enable us to fully understand the processes of membrane fusion, retrieval, and recycling. Using small-angle x-ray scattering, we have directly investigated the size and structure of purified SVs. From this information, we deduced detailed size and density parameters for the protein layers responsible for SV function, as well as information about the lipid bilayer. To achieve a convincing model fit, a laterally anisotropic structure for the protein shell is needed, as a rotationally symmetric density profile does not explain the data. Not only does our model confirm many of the preexisting ideas concerning SV structure, but also for the first time, to our knowledge, it indicates structural refinements, such as the presence of protein microdomains. PMID:20371319

  12. Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis.

    PubMed

    Panjkovich, Alejandro; Svergun, Dmitri I

    2016-02-17

    Structural flexibility and conformational rearrangements are often related to important functions of biological macromolecules, but the experimental characterization of such transitions with high-resolution techniques is challenging. At a lower resolution, small angle X-ray scattering (SAXS) can be used to obtain information on biomolecular shapes and transitions in solution. Here, we present SREFLEX, a hybrid modeling approach that uses normal mode analysis (NMA) to explore the conformational space of high-resolution models and refine the structure guided by the agreement with the experimental SAXS data. The method starts from a given conformation of the protein (which does not agree with the SAXS data). The structure is partitioned into pseudo-domains either using structural classification databases or automatically from the protein dynamics as predicted by the NMA. The algorithm proceeds hierarchically employing NMA to first probe large rearrangements and progresses into smaller and more localized movements. At the large rearrangements stage the pseudo-domains stay as rigid bodies allowing one to avoid structural disruptions inherent to the earlier NMA-based algorithms. To validate the approach, we compiled a representative benchmark set of 88 conformational states known experimentally at high resolution. The performance of the algorithm is demonstrated in the simulated data on the benchmark set and also in a number of experimental examples. SREFLEX is included into the ATSAS program package freely available to the academic users, both for download and in the on-line mode. PMID:26611321

  13. Small-angle x-ray scattering to discern microstructure of semicrystalline polyanhydrides for drug delivery.

    SciTech Connect

    Kipper, M. J.; Seifert, S.; Thiyagarajan, P.; Narasimhan, B.; Iowa State Univ.

    2005-01-01

    Polyanhydride copolymers based on 1,6-bis(p-carboxyphenoxy)hexane (CPH) and sebacic acid (SA) are bioerodible, semicrystalline polymers that have been used for drug delivery. In addition to their semicrystallinity, these materials also exhibit microphase separation in the amorphous phase. This complex phase behavior, combined with the disparity in the erosion rates of the two different chemical moieties, leads to a complex erosion kinetics that can be used to tailor drug release kinetics. Thus, accurate design of drug delivery devices requires a detailed description of the microphase separation. Here, we employ in situ synchrotron small-angle X-ray scattering (SAXS) to explore the microstructure of these materials. First, we examine the crystallization kinetics of the homopolymers and CPH-SA copolymers. Next, we perform experiments on poly(CPH)/poly(SA) homopolymer blends in the miscible melt in order to discern the segment-segment interaction parameter, {chi}{sub CPH-SA}. This parameter predicts the enthalpy of mixing poly(CPH) and poly(SA) at the monomer level and can be used to predict the phase behavior of the blend. It also offers insights into the thermodynamics that drive the microphase separation in the copolymers. The homopolymer phase diagram has an upper-critical solution temperature and compares well with cloud point data obtained from optical microscopy and predictions of the interaction parameter from molecular simulation.

  14. The small angle x-ray scattering of globular proteins in solution during heat denaturation

    NASA Astrophysics Data System (ADS)

    Banuelos, Jose; Urquidi, Jacob

    2008-10-01

    The ability of proteins to change their conformation in response to changes in their environment has consequences in biological processes like metabolism, chemical regulation in cells, and is believed to play a role in the onset of several neurodegenerative diseases. Factors such as a change in temperature, pressure, and the introduction of ions into the aqueous environment of a protein can give rise to the folding/unfolding of a protein. As a protein unfolds, the ratio of nonpolar to polar groups exposed to water changes, affecting a protein's thermodynamic properties. Using small angle x-ray scattering (SAXS), we are currently studying the intermediate protein conformations that arise during the folding/unfolding process as a function of temperature for five globular proteins. Trends in the observed intermediate structures of these globular proteins, along with correlations with data on protein thermodynamics may help elucidate shared characteristics between all proteins in the folding/unfolding process. Experimental design considerations will be discussed and preliminary results for some of these systems will be presented.

  15. Structural Studies of Bleached Melanin by Synchrotron Small-angle X-ray Scattering¶

    SciTech Connect

    Littrell, Kenneth C.; Gallas, James M.; Zajac, Gerry W.; Thiyagarajan, Pappannan

    2003-01-01

    Small-angle X-ray scattering was used to measure the effects of chemical bleaching on the size and morphology of tyrosine-derived synthetic melanin dispersed in aqueous media. The average size as measured by the radius of gyration of the melanin particles in solution, at neutral to mildly basic pH, decreases from 16.5 to 12.5 angstroms with increased bleaching. The melanin particles exhibit scattering characteristic of sheet-like structures with a thickness of approximately 11 angstroms at all but the highest levels of bleaching. The scattering data are well described by the form factor for scattering from a pancake-like circular cylinder. These data are consistent with the hypothesis that unbleached melanin, at neutral to mildly basic pH, is a planar aggregate of 6- to 10-nm-sized melanin protomolecules, hydrogen bonded through their quinone and phenolic perimeters. The observed decrease in melanin particle size with increased bleaching is interpreted as evidence for deaggregation, most probably the result of oxidative disruption of hydrogen bonds and an increase in the number of charged, carboxylic acid groups, whereby the melanin aggregates disassociate into units composed of decreasing numbers of protomolecules.

  16. Characterization of Physically and Chemically Separated Athabasca Asphaltenes Using Small-Angle X-ray Scattering

    SciTech Connect

    Amundaraín Hurtado, Jesús Leonardo; Chodakowski, Martin; Long, Bingwen; Shaw, John M.

    2012-02-07

    Athabasca asphaltenes were characterized using small-angle X-ray scattering (SAXS). Two methods were used to separate asphaltenes from the Athabasca bitumen: namely, chemical separation by precipitation with n-pentane and physical separation by nanofiltration using a zirconia membrane with a 20 nm average pore size. The permeate and chemically separated samples were diluted in 1-methylnaphtalene and n-dodecane prior to SAXS measurements. The temperature and asphaltene concentration ranges were 50-310 C and 1-10.4 wt %, respectively. Model-independent analysis of SAXS data provided the radius of gyration and the scattering coefficients. Model-dependent fits provided size distributions for asphaltenes assuming that they are dense and spherical. Model-independent analysis for physically and chemically separated asphaltenes showed significant differences in nominal size and structure, and the temperature dependence of structural properties. The results challenge the merits of using chemically separated asphaltene properties as a basis for asphaltene property prediction in hydrocarbon resources. While the residuals for model-dependent fits are small, the results are inconsistent with the structural parameters obtained from model-independent analysis.

  17. Elastic deformations in hexagonal phases studied by small-angle X-ray diffraction and simulations.

    PubMed

    Perutková, Šárka; Daniel, Matej; Rappolt, Michael; Pabst, Georg; Dolinar, Gregor; Kralj-Iglič, Veronika; Iglič, Aleš

    2011-02-28

    In this study we present experimental and theoretical results which concern the deviations from circularity of the pivotal plane in the inverse hexagonal phases (H(II)) of phospholipid self-assemblies. Due to packing constraints, the cross-section of the polar/apolar interface deviates from a circle, which we studied in minute detail by analysing small-angle X-ray diffraction data of dioleoyl-phosphatidylethanolamine (DOPE) and stearoyl-oleoyl-phosphatidylethanolamine (SOPE), respectively. On this structural basis, Monte Carlo (MC) simulated annealing variations of the free energy were carried out, both on the formation of the H(II)-phase and on the particular shape of the cross-section in the H(II)-phase. The equilibrium of the H(II)-phase pivotal plane contour and the corresponding values of the mean intrinsic curvature, H(m), and the hydrocarbon chain stiffness, τ, were determined from MC calculations. The results of these calculations were tested by solving the corresponding system of non-linear differential equations derived using variational calculus. Here our main aim is to predict the range of possible values of H(m) and τ. Comparing the measured structural data with predictions from MC calculations including lipid anisotropy, and accounting for the elastic deformations of the pivotal plane allowed us to determine a relationship between the bending deformation and stretching of hydrocarbon chains. PMID:21063616

  18. Six-dimensional real and reciprocal space small-angle X-ray scattering tomography.

    PubMed

    Schaff, Florian; Bech, Martin; Zaslansky, Paul; Jud, Christoph; Liebi, Marianne; Guizar-Sicairos, Manuel; Pfeiffer, Franz

    2015-11-19

    When used in combination with raster scanning, small-angle X-ray scattering (SAXS) has proven to be a valuable imaging technique of the nanoscale, for example of bone, teeth and brain matter. Although two-dimensional projection imaging has been used to characterize various materials successfully, its three-dimensional extension, SAXS computed tomography, poses substantial challenges, which have yet to be overcome. Previous work using SAXS computed tomography was unable to preserve oriented SAXS signals during reconstruction. Here we present a solution to this problem and obtain a complete SAXS computed tomography, which preserves oriented scattering information. By introducing virtual tomography axes, we take advantage of the two-dimensional SAXS information recorded on an area detector and use it to reconstruct the full three-dimensional scattering distribution in reciprocal space for each voxel of the three-dimensional object in real space. The presented method could be of interest for a combined six-dimensional real and reciprocal space characterization of mesoscopic materials with hierarchically structured features with length scales ranging from a few nanometres to a few millimetres--for example, biomaterials such as bone or teeth, or functional materials such as fuel-cell or battery components. PMID:26581292

  19. BCL::SAXS: GPU Accelerated Debye Method for computation of Small Angle X Ray Scattering Profiles

    PubMed Central

    Putnam, Daniel K.; Weiner, Brian E.; Woetzel, Nils; Lowe, Edward W.; Meiler, Jens

    2016-01-01

    Small angle X-ray scattering (SAXS) is an experimental technique used for structural characterization of macromolecules in solution. Here, we introduce BCL::SAXS – an algorithm designed to replicate SAXS profiles from rigid protein models at different levels of detail. We first show our derivation of BCL::SAXS and compare our results with the experimental scattering profile of Hen Egg White Lysozyme. Using this protein we show how to generate SAXS profiles representing: 1) complete models, 2) models with approximated side chain coordinates, and 3) models with approximated side chain and loop region coordinates. We evaluated the ability of SAXS profiles to identify a correct protein topology from a non-redundant benchmark set of proteins. We find that complete SAXS profiles can be used to identify the correct protein by receiver operating characteristic (ROC) analysis with an area under the curve (AUC) > 99%. We show how our approximation of loop coordinates between secondary structure elements improves protein recognition by SAXS for protein models without loop regions and side chains. Agreement with SAXS data is a necessary but not sufficient condition for structure determination. We conclude that experimental SAXS data can be used as a filter to exclude protein models with large structural differences from the native. PMID:26018949

  20. Dynamic Conformations of Nucleosome Arrays in Solution from Small-Angle X-ray Scattering

    NASA Astrophysics Data System (ADS)

    Howell, Steven C.

    Chromatin conformation and dynamics remains unsolved despite the critical role of the chromatin in fundamental genetic functions such as transcription, replication, and repair. At the molecular level, chromatin can be viewed as a linear array of nucleosomes, each consisting of 147 base pairs (bp) of double-stranded DNA (dsDNA) wrapped around a protein core and connected by 10 to 90 bp of linker dsDNA. Using small-angle X-ray scattering (SAXS), we investigated how the conformations of model nucleosome arrays in solution are modulated by ionic condition as well as the effect of linker histone proteins. To facilitate ensemble modeling of these SAXS measurements, we developed a simulation method that treats coarse-grained DNA as a Markov chain, then explores possible DNA conformations using Metropolis Monte Carlo (MC) sampling. This algorithm extends the functionality of SASSIE, a program used to model intrinsically disordered biological molecules, adding to the previous methods for simulating protein, carbohydrates, and single-stranded DNA. Our SAXS measurements of various nucleosome arrays together with the MC generated models provide valuable solution structure information identifying specific differences from the structure of crystallized arrays.

  1. Studies of protein structure in solution and protein folding using synchrotron small-angle x-ray scattering

    SciTech Connect

    Chen, Lingling

    1996-04-01

    Synchrotron small angle x-ray scattering (SAXS) has been applied to the structural study of several biological systems, including the nitrogenase complex, the heat shock cognate protein (hsc70), and lysozyme folding. The structural information revealed from the SAXS experiments is complementary to information obtained by other physical and biochemical methods, and adds to our knowledge and understanding of these systems.

  2. Small-Angle X-ray Study of the Three-Dimensional Collagen/Mineral Superstructure in Intramuscular Fish Bone

    SciTech Connect

    Zhou,H.; Burger, C.; Sics, I.; Hsiao, B.; Chu, B.; Graham, L.; Glimcher, M.

    2007-01-01

    Synchrotron small-angle X-ray scattering (SAXS) was conducted on native intramuscular shad/herring bone samples. Two-dimensional SAXS patterns were quantitatively analyzed with special consideration for preferred orientation effects, leading to new insights into the three-dimensional superstructure of mineralized collagen fibrils in shad/herring bone.

  3. Shear Induced Alignment of Multi-Walled Carbon Nanotube Dispersions via Small Angle X-Ray Scattering

    NASA Astrophysics Data System (ADS)

    Pujari, Saswati; Burghardt, Wesley R.; Rahatekar, Sameer S.; Windle, Alan H.; Koziol, Krzysztof K.

    2008-07-01

    We report small-angle x-ray scattering studies of shear-induced alignment of multi-walled carbon nanotube (MWCNT) dispersions. Uncured epoxy was used as a viscous, Newtonian suspending medium, and samples were prepared from `aligned' MWCNTs using methods previously reported (Rahatekar et al. J Rheol 40:599, 2006); here we emphasize measurements on rather dilute dispersions. Flow-induced alignment was studied in both the flow-gradient (1-2) plane, and the flow-vorticity (1-3) plane using, respectively, annular cone and plate and rotating disk x-ray shear cells. Small-angle x-ray scattering patterns were rendered anisotropic under application of shear flow. Measurements in the 1-2 plane indicate that the average MWCNT orientation direction is intermediate between the flow and gradient directions. Transient measurements of structure evolution enabled by high flux synchrotron radiation allowed study of time-dependent behavior following flow reversal and flow cessation.

  4. Size And Shape of Detergent Micelles Determined By Small-Angle X-Ray Scattering

    SciTech Connect

    Lipfert, Jan; Columbus, Linda; Chu, Vincent B.; Lesley, Scott A.; Doniach, Sebastian; /Stanford U., Phys. Dept. /Stanford U., Appl. Phys. Dept. /SLAC, SSRL /Pasteur Inst., Paris /Scripps Res. Inst. /Novartis Res. Found.

    2009-04-29

    We present a systematic analysis of the aggregation number and shape of micelles formed by nine detergents commonly used in the study of membrane proteins. Small-angle X-ray scattering measurements are reported for glucosides with 8 and 9 alkyl carbons (OG/NG), maltosides and phosphocholines with 10 and 12 alkyl carbons (DM/DDM and FC-10/FC-12), 1,2-dihexanoyl-sn-glycero-phosphocholine (DHPC), 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG), and 3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonate (CHAPS). The SAXS intensities are well described by two-component ellipsoid models, with a dense outer shell corresponding to the detergent head groups and a less electron dense hydrophobic core. These models provide an intermediate resolution view of micelle size and shape. In addition, we show that Guinier analysis of the forward scattering intensity can be used to obtain an independent and model-free measurement of the micelle aggregation number and radius of gyration. This approach has the advantage of being easily generalizable to protein-detergent complexes, where simple geometric models are inapplicable. Furthermore, we have discovered that the position of the second maximum in the scattering intensity provides a direct measurement of the characteristic head group-head group spacing across the micelle core. Our results for the micellar aggregation numbers and dimensions agree favorably with literature values as far as they are available. We de novo determine the shape of FC-10, FC-12, DM, LPPG, and CHAPS micelles and the aggregation numbers of FC-10 and OG to be ca. 50 and 250, respectively. Combined, these data provide a comprehensive view of the determinants of micelle formation and serve as a starting point to correlate detergent properties with detergent-protein interactions.

  5. An Assessment of Critical Dimension Small Angle X-ray Scattering Metrology for Advanced Semiconductor Manufacturing

    NASA Astrophysics Data System (ADS)

    Settens, Charles M.

    Simultaneous migration of planar transistors to FinFET architectures, the introduction of a plurality of materials to ensure suitable electrical characteristics, and the establishment of reliable multiple patterning lithography schemes to pattern sub-10 nm feature sizes imposes formidable challenges to current in-line dimensional metrologies. Because the shape of a FinFET channel cross-section immediately influences the electrical characteristics, the evaluation of 3D device structures requires measurement of parameters beyond traditional critical dimension (CD), including their sidewall angles, top corner rounding and footing, roughness, recesses and undercuts at single nanometer dimensions; thus, metrologies require sub-nm and approaching atomic level measurement uncertainty. Synchrotron critical dimension small angle X-ray scattering (CD-SAXS) has unique capabilities to non-destructively monitor the cross-section shape of surface structures with single nanometer uncertainty and can perform overlay metrology to sub-nm uncertainty. In this dissertation, we perform a systematic experimental investigation using CD-SAXS metrology on a hierarchy of semiconductor 3D device architectures including, high-aspect-ratio contact holes, H 2 annealed Si fins, and a series of grating type samples at multiple points along a FinFET fabrication process increasing in structural intricacy and ending with fully fabricated FinFET. Comparative studies between CD-SAXS metrology and other relevant semiconductor dimensional metrologies, particularly CD-SEM, CD-AFM and TEM are used to determine physical limits of CD-SAXS approach for advanced semiconductor samples. CD-SAXS experimental tradeoffs, advice for model-dependent analysis and thoughts on the compatibility with a semiconductor manufacturing environment are discussed.

  6. Structural characterization of the human cerebral myelin sheath by small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    DeFelici, M.; Felici, R.; Ferrero, C.; Tartari, A.; Gambaccini, M.; Finet, S.

    2008-10-01

    Myelin is a multi-lamellar membrane surrounding neuronal axons and increasing their conduction velocity. When investigated by small-angle x-ray scattering (SAXS), the lamellar quasi-periodical arrangement of the myelin sheath gives rise to distinct peaks, which allow the determination of its molecular organization and the dimensions of its substructures. In this study we report on the myelin sheath structural determination carried out on a set of human brain tissue samples coming from surgical biopsies of two patients: a man around 60 and a woman nearly 90 years old. The samples were extracted either from white or grey cerebral matter and did not undergo any manipulation or chemical-physical treatment, which could possibly have altered their structure, except dipping them into a formalin solution for their conservation. Analysis of the scattered intensity from white matter of intact human cerebral tissue allowed the evaluation not only of the myelin sheath periodicity but also of its electronic charge density profile. In particular, the thicknesses of the cytoplasm and extracellular regions were established, as well as those of the hydrophilic polar heads and hydrophobic tails of the lipid bilayer. SAXS patterns were measured at several locations on each sample in order to establish the statistical variations of the structural parameters within a single sample and among different samples. This work demonstrates that a detailed structural analysis of the myelin sheath can also be carried out in randomly oriented samples of intact human white matter, which is of importance for studying the aetiology and evolution of the central nervous system pathologies inducing myelin degeneration.

  7. Anomalous nonlinear X-ray Compton scattering

    NASA Astrophysics Data System (ADS)

    Fuchs, Matthias; Trigo, Mariano; Chen, Jian; Ghimire, Shambhu; Shwartz, Sharon; Kozina, Michael; Jiang, Mason; Henighan, Thomas; Bray, Crystal; Ndabashimiye, Georges; Bucksbaum, Philip H.; Feng, Yiping; Herrmann, Sven; Carini, Gabriella A.; Pines, Jack; Hart, Philip; Kenney, Christopher; Guillet, Serge; Boutet, Sébastien; Williams, Garth J.; Messerschmidt, Marc; Seibert, M. Marvin; Moeller, Stefan; Hastings, Jerome B.; Reis, David A.

    2015-11-01

    X-ray scattering is typically used as a weak linear atomic-scale probe of matter. At high intensities, such as produced at free-electron lasers, nonlinearities can become important, and the probe may no longer be considered weak. Here we report the observation of one of the most fundamental nonlinear X-ray-matter interactions: the concerted nonlinear Compton scattering of two identical hard X-ray photons producing a single higher-energy photon. The X-ray intensity reached 4 × 1020 W cm-2, corresponding to an electric field well above the atomic unit of strength and within almost four orders of magnitude of the quantum-electrodynamic critical field. We measure a signal from solid beryllium that scales quadratically in intensity, consistent with simultaneous non-resonant two-photon scattering from nearly-free electrons. The high-energy photons show an anomalously large redshift that is incompatible with a free-electron approximation for the ground-state electron distribution, suggesting an enhanced nonlinearity for scattering at large momentum transfer.

  8. Ultra small angle x-ray scattering in complex mixtures of triacylglycerols

    NASA Astrophysics Data System (ADS)

    Peyronel, Fernanda; Quinn, Bonnie; Marangoni, Alejandro G.; Pink, David A.

    2014-11-01

    Ultra-small angle x-ray scattering (USAXS) has been used to elucidate, in situ, the aggregation structure of unsheared model edible oils. Each system comprised one or two solid lipids and a combination of liquid lipids. The 3D nano- to micro-structures of each system were characterized. The length scale investigated, using the Bonse-Hart camera at beamline ID-15D at the Advanced Photon Source, ANL, ranged from 300 Å-10 µm. Using the Unified Fit model, level-1 analysis showed that the scatterers were 2D objects with either a smooth, a rough, or a diffuse surface. These 2D objects had an average radius of gyration Rg1 between 200-1500 Å. Level-2 analysis displayed a slope between -1 and -2. Use of the Guinier-Porod model gave s ≈ 1 thus showing that it was cylinders (TAGwoods) aggregating with fractal dimension 1 ≤ D2 ≤ 2. D2 = 1 is consistent with 1D structures formed from TAGwoods, while D2 = 2 implies that the TAGwoods had formed structures characteristic of diffusion or reaction limited cluster-cluster aggregation (DLCA/RLCA). These aggregates exhibited radii of gyration, Rg2, between 2500 and 6500 Å. Level-3 analyses showed diffuse surfaces, for most of the systems. These interpretations are in accord with theoretical models which studied crystalline nano-platelets (CNPs) coated with nano-scale layers arising from phase separation at the CNP surfaces. These layers could be due to either liquid-liquid phase separation with the CNPs coated, uniformly or non-uniformly, by a diffuse layer of TAGs, or solid-liquid phase separation with the CNPs coated by a rough layer of crystallites. A fundamental understanding of the self-organizing structures arising in these systems helps advance the characterization of fat crystal networks from nanometres to micrometres. This research can be used to design novel fat structures that use healthier fats via nano- and meso-scale structural engineering.

  9. Multi-speckle X-ray photon correlation spectroscopy in the ultra-small-angle X-ray scattering range.

    PubMed

    Möller, Johannes; Chushkin, Yuriy; Prevost, Sylvain; Narayanan, Theyencheri

    2016-07-01

    Multi-speckle X-ray photon correlation spectroscopy (XPCS) measurements in the ultra-small-angle range are performed using a long pinhole collimation instrument in combination with two-dimensional photon-counting and high-sensitivity imaging detectors. The feasibility of the presented setup to measure dynamics on different time and length scales pertinent to colloidal systems is shown. This setup offers new research opportunities, such as for example in the investigation of non-equilibrium dynamics in optically opaque, complex systems over length scales from tens of nanometres to several micrometres. In addition, due to the short duration of the X-ray exposure involved in the ultra-small-angle range, possible radiation-induced effects are alleviated. Furthermore, the performance of two different detectors, a photon-counting Pilatus 300K and an integrating FReLoN CCD, are compared, and their applicability for accurate XPCS measurements is demonstrated. PMID:27359141

  10. Grazing-incidence small-angle X-ray scattering: application to the study of quantum dot lattices

    SciTech Connect

    Buljan, Maja Radić, Nikola; Bernstorff, Sigrid; Dražić, Goran; Bogdanović-Radović, Iva; Holý, Václav

    2012-01-01

    The modelling of grazing-incidence small-angle X-ray scattering (GISAXS) from three-dimensional quantum dot lattices is described. The ordering of quantum dots in three-dimensional quantum dot lattices is investigated by grazing-incidence small-angle X-ray scattering (GISAXS). Theoretical models describing GISAXS intensity distributions for three general classes of lattices of quantum dots are proposed. The classes differ in the type of disorder of the positions of the quantum dots. The models enable full structure determination, including lattice type, lattice parameters, the type and degree of disorder in the quantum dot positions and the distributions of the quantum dot sizes. Applications of the developed models are demonstrated using experimentally measured data from several types of quantum dot lattices formed by a self-assembly process.

  11. Small angle X-ray scattering and transmission electron microscopy study of the Lactobacillus brevis S-layer protein

    NASA Astrophysics Data System (ADS)

    Jääskeläinen, Pentti; Engelhardt, Peter; Hynönen, Ulla; Torkkeli, Mika; Palva, Airi; Serimaa, Ritva

    2010-10-01

    The structure of self-assembly domain containing recombinant truncation mutants of Lactobacillus brevis surface layer protein SlpA in aqueous solution was studied using small-angle X-ray scattering and transmission electron microscopy. The proteins were found out to interact with each other forming stable globular oligomers of about 10 monomers. The maximum diameter of the oligomers varied between 75 Å and 435 Å.

  12. Quantitative Analysis of the Orientation of Mineral in Bone from Small-Angle X-Ray Scattering Patterns

    NASA Astrophysics Data System (ADS)

    Matsushima, Norio; Akiyama, Morio; Terayama, Yoshio

    1982-01-01

    The small-angle X-ray scattering data from a rabbit femur is quantitatively evaluated with respect to the mineral distribution in bone. The results show the existence of a needle-like mineral with a length of at least 300 A and a preferred orientation of the needle axes parallel to the long axis of the bone. The angular distribution of the needle axes gives a value of 30° for the mean inclination.

  13. Method to study sample object size limit of small-angle x-ray scattering computed tomography

    NASA Astrophysics Data System (ADS)

    Choi, Mina; Ghammraoui, Bahaa; Badal, Andreu; Badano, Aldo

    2016-03-01

    Small-angle x-ray scattering (SAXS) imaging is an emerging medical tool that can be used for in vivo detailed tissue characterization and has the potential to provide added contrast to conventional x-ray projection and CT imaging. We used a publicly available MC-GPU code to simulate x-ray trajectories in a SAXS-CT geometry for a target material embedded in a water background material with varying sample sizes (1, 3, 5, and 10 mm). Our target materials were water solution of gold nanoparticle (GNP) spheres with a radius of 6 nm and a water solution with dissolved serum albumin (BSA) proteins due to their well-characterized scatter profiles at small angles and highly scattering properties. The background material was water. Our objective is to study how the reconstructed scatter profile degrades at larger target imaging depths and increasing sample sizes. We have found that scatter profiles of the GNP in water can still be reconstructed at depths up to 5 mm embedded at the center of a 10 mm sample. Scatter profiles of BSA in water were also reconstructed at depths up to 5 mm in a 10 mm sample but with noticeable signal degradation as compared to the GNP sample. This work presents a method to study the sample size limits for future SAXS-CT imaging systems.

  14. Small-Angle X-ray Scattering Study of Intramuscular Fish Bone: Collagen Fibril Superstructure Determined from Equidistant Meridional Reflections

    SciTech Connect

    Burger,C.; Zhou, H.; Sics, I.; Hsiao, B.; Chu, B.; Graham, L.; Glimcher, M.

    2008-01-01

    New insights into the bone collagen fibril superstructure have been obtained by novel small-angle X-ray scattering analysis. The analysis was carried out on the small-angle equidistant meridional reflections resulting from the periodic structure of collagen fibrils in their axial direction. Conventional two-dimensional analysis is difficult because of the large discrepancy of longitudinal and lateral length scales for individual fibrils, as well as their preferred orientation. The new approach represents an unapproximated analysis of the equidistant meridional reflections, which takes the exact separation of preferred orientation and fibril size effects into account. The analytical results (e.g. axial period, fibril diameter etc.) agree well with the parameters obtained from transmission electron microscopy.

  15. Ultra-Small-Angle X-ray Scattering – X-ray Photon Correlation Spectroscopy Studies of Incipient Structural Changes in Amorphous Calcium Phosphate Based Dental Composites

    PubMed Central

    Zhang, F.; Allen, A.J.; Levine, L.E.; Espinal, L.; Antonucci, J.M.; Skrtic, D.; O’Donnell, J.N.R.; Ilavsky, J.

    2012-01-01

    The local structural changes in amorphous calcium phosphate (ACP) based dental composites were studied under isothermal conditions using both static, bulk measurement techniques and a recently developed methodology based on combined ultra-small angle X-ray scattering – X-ray photon correlation spectroscopy (USAXS-XPCS), which permits a dynamic approach. While results from conventional bulk measurements do not show clear signs of structural change, USAXS-XPCS results reveal unambiguous evidence for local structural variations on a similar time scale to that of water loss in the ACP fillers. A thermal-expansion based simulation indicates that thermal behavior alone does not account for the observed dynamics. Together, these results suggest that changes in the water content of ACP affect the composite morphology due to changes in ACP structure that occur without an amorphous-to-crystalline conversion. It is also noted that biomedical materials research could benefit greatly from USAXS-XPCS, a dynamic approach. PMID:22374649

  16. Combined small-angle x-ray scattering/extended x-ray absorption fine structure study of coated Co nanoclusters in bis(2-ethylhexyl)sulfosuccinate

    NASA Astrophysics Data System (ADS)

    Longo, A.; Giordano, F.; Giannici, F.; Martorana, A.; Portale, G.; Ruggirello, A.; Turco Liveri, V.

    2009-06-01

    Chemically stable cobalt nanostructures have been prepared with Co(II) reduction in the confined space of cobalt bis(2-ethylhexyl)sulfosuccinate, Co(AOT)2, reverse micelles dispersed in n-heptane. The reaction was carried out by adding a solution of sodium borohydride in ethanol (1% weight) to a 0.2M micellar solution of Co(AOT)2 in n-heptane at a reductant to Co(II) molar ratio of 4. This procedure involves the rapid formation of surfactant-coated Co nanoparticles followed by their slow separation as nanostructures embedded in a sodium bis(2-ethylhexyl)sulfosuccinate matrix. The resulting composites, characterized by extended x-ray absorption fine structure and small-angle x-ray scattering, showed the presence of subnanometer sized cobalt nanoparticles aggregated together to form elongated structures coated by the surfactant molecules.

  17. Analysis of small-angle X-ray scattering data in the presence of significant instrumental smearing

    PubMed Central

    Bergenholtz, Johan; Ulama, Jeanette; Zackrisson Oskolkova, Malin

    2016-01-01

    A laboratory-scale small-angle X-ray scattering instrument with pinhole collimation has been used to assess smearing effects due to instrumental resolution. A new, numerically efficient method to smear ideal model intensities is developed and presented. It allows for directly using measured profiles of isotropic but otherwise arbitrary beams in smearing calculations. Samples of low-polydispersity polymer spheres have been used to show that scattering data can in this way be quantitatively modeled even when there is substantial distortion due to instrumental resolution. PMID:26937235

  18. [Prediction of Protein Conformational Mobility and Evaluation of Its Reliability Using Small-Angle X-ray Scattering].

    PubMed

    Knyazev, S N; Kalyakin, V Y; Deryabin, I N; Fedorov, B A; Smirnov, A V; Stepanov, E O; Porozov, Yu B

    2015-01-01

    The "coarse-grained" model of protein conformational mobility is presented. We compared the trajectories of conformational motions predicted for five proteins using this model with the motion obtained by the method of the "nearest neighbor", based on small-angle X-ray scattering data. It is shown that for all studied proteins the sequence of conformations calculated on the basis of "coarse-grained" model and on the basis of the "nearest neighbor", coincides well, although there are exceptions. Some separate consideration should be given to each protein to discern the causes of these exceptions. PMID:26841499

  19. Analysis of biostructural changes, dynamics, and interactions - Small-angle X-ray scattering to the rescue.

    PubMed

    Vestergaard, Bente

    2016-07-15

    Solution small angle X-ray scattering from biological macromolecules (BioSAXS) plays an increasingly important role in biostructural research. The analysis of complex protein mixtures, dynamic equilibriums, intrinsic disorder and evolving structural processes is facilitated by SAXS data, either in stand-alone applications, or with SAXS taking a prominent role in hybrid biostructural analysis. This is not the least due to the significant advances in both hardware and software that have taken place in particular at the large-scale facilities. Here, recent developments and the future potential of BioSAXS are reviewed, exemplified by numerous examples of elegant applications to challenging systems. PMID:26945933

  20. Measuring helium bubble diameter distributions in tungsten with grazing incidence small angle x-ray scattering (GISAXS)

    NASA Astrophysics Data System (ADS)

    Thompson, M.; Kluth, P.; Doerner, R. P.; Kirby, N.; Riley, D.; Corr, C. S.

    2016-02-01

    Grazing incidence small angle x-ray scattering was performed on tungsten samples exposed to helium plasma in the MAGPIE and Pisces-A linear plasma devices to measure the size distributions of resulting helium nano-bubbles. Nano-bubbles were fitted assuming spheroidal particles and an exponential diameter distribution. These particles had mean diameters between 0.36 and 0.62 nm. Pisces-A exposed samples showed more complex patterns, which may suggest the formation of faceted nano-bubbles or nano-scale surface structures.

  1. A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins.

    PubMed

    Kikhney, Alexey G; Svergun, Dmitri I

    2015-09-14

    Small-angle X-ray scattering (SAXS) is a biophysical method to study the overall shape and structural transitions of biological macromolecules in solution. SAXS provides low resolution information on the shape, conformation and assembly state of proteins, nucleic acids and various macromolecular complexes. The technique also offers powerful means for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs). Here, the basic principles of SAXS are presented, and profits and pitfalls of the characterization of multidomain flexible proteins and IDPs using SAXS are discussed from the practical point of view. Examples of the synergistic use of SAXS with high resolution methods like X-ray crystallography and nuclear magnetic resonance (NMR), as well as other experimental and in silico techniques to characterize completely, or partially unstructured proteins, are presented. PMID:26320411

  2. Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures

    SciTech Connect

    Fang, Xianyang; Stagno, Jason R.; Bhandari, Yuba R.; Zuo, Xiaobing; Wang, Yun-Xing

    2015-02-01

    Whereas the structures of small to medium-sized well folded RNA molecules often can be determined by either X-ray crystallography or NMR spectroscopy, obtaining structural information for large RNAs using experimental, computational, or combined approaches remains a major interest and challenge. RNA is very sensitive to small-angle X-ray scattering (SAXS) due to high electron density along phosphate-sugar backbones, whose scattering contribution dominates SAXS intensity. For this reason, SAXS is particularly useful in obtaining global RNA structural information that outlines backbone topologies and, therefore, molecular envelopes. Such information is extremely valuable in bridging the gap between the secondary structures and three-dimensional topological structures of RNAmolecules, particularly those that have proven difficult to study using other structuredetermination methods. Here we review published results of RNA topological structures derived from SAXS data or in combination with other experimental data, as well as details on RNA sample preparation for SAXS experiments.

  3. Grazing incidence small angle X-ray scattering study of silver nanoparticles in ion-exchanged glasses

    NASA Astrophysics Data System (ADS)

    Cheng, Weidong; Wu, Zhaojun; Gu, Xiaohua; Xing, Xueqing; Mo, Guang; Wu, Zhonghua

    2015-05-01

    The size and distribution of silver nanoparticles in ion-exchanged silicate glass induced by thermal treatments in air at different temperatures were investigated by means of grazing incidence small angle X-ray scattering technique, X-ray diffraction and optical absorption spectra. Silver-sodium ion exchange of soda-lime silicate glasses was done at 350 °C for 240 min, then the samples were treated by thermal annealing in air at different temperatures 400, 500 and 550 °C, respectively, for 1 h. After the annealing treatment above 400 °C for 1 h, smaller Ag nanoparticles occurred, together with bigger ones. Both dissolution of smaller Ag nanoparticles and diffusion of larger ones are discussed in these stages of annealing in this contribution.

  4. Probing helium nano-bubble formation in tungsten with grazing incidence small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Thompson, M.; Kluth, P.; Doerner, R. P.; Kirby, N.; Corr, C.

    2015-04-01

    Helium nano-bubble formation in plasma facing materials has emerged as a major concern for the next-step fusion experiment ITER, where helium plasmas will be used during the tokamak's start-up phase. Here, we demonstrate that grazing incidence small-angle x-ray scattering is a powerful technique for the analysis of helium nano-bubble formation in tungsten. We measured helium bubbles with sizes between 1.5-2.5 nm in tungsten exposed to helium plasma at 700 °C, where a smaller number of larger bubbles were also observed. Depth distributions can be estimated by taking successive measurements across a range of x-ray incidence angles. Compared with traditional approaches in the field, such as transmission electron microscopy, this technique provides information across a much larger volume with high statistical precision, whilst also being non-destructive.

  5. X-Ray Dust Scattering At Small Angles: The Complete Halo Around GX13+1

    NASA Technical Reports Server (NTRS)

    Smith, Randall K.

    2007-01-01

    The exquisite angular resolution available with Chandra should allow precision measurements of faint diffuse emission surrounding bright sources, such as the X-ray scattering halos created by interstellar dust. However, the ACIS CCDs suffer from pileup when observing bright sources, and this creates difficulties when trying to extract the scattered halo near the source. The initial study of the X-ray halo around GX13+1 using only the ACIS-I detector done by Smith, Edgar & Shafer (2002) suffered from a lack of sensitivity within 50" of the source, limiting what conclusions could be drawn. To address this problem, observations of GX13+1 were obtained with the Chandra HRC-I and simultaneously with the RXTE PCA. Combined with the existing ACIS-I data, this allowed measurements of the X-ray halo between 2-1000". After considering a range of dust models, each assumed to be smoothly distributed with or without a dense cloud along the line of sight, the results show that there is no evidence in this data for a dense cloud near the source, as suggested by Xiang et al. (2005). In addition, although no model leads to formally acceptable results, the Weingartner & Draine (2001) and all but one of the composite grain models from Zubko, Dwek & Arendt (2004) give particularly poor fits.

  6. Application of Small-Angle Neutron and X-ray Scattering in Determining Lipid Bilayer Structure

    NASA Astrophysics Data System (ADS)

    Pan, Jianjun; Heberle, Frederick A.; Kucerka, Norbert; Tristram-Nagle, Stephanie; Szymanski, Michelle; Koepfinger, Mary; Katsaras, John

    2012-02-01

    Accurately determining lipid structure in biologically relevant fluid bilayers is not straightforward. We have recently developed a hybrid experimental/computational technique (i.e., the scattering density profile, or SDP model), which exploits the fact that neutron and X-ray scattering are sensitive to different bilayer thicknesses - the large difference in neutron scattering length density (SLD) between proteated lipid and deuterated water defines the overall bilayer thickness, while X-ray scattering resolves the headgroup-headgroup distance due to the large scattering contrast between the electron-rich phosphate groups and the hydrocarbon/aqueous medium. A key step in the SDP analysis is the use of MD simulations to parse the lipid molecule into fragments whose volume probability distributions follow simple analytical functional forms. Given the appropriate atomic scattering lengths, these volume probabilities can simultaneously predict both the neutron and X-ray SLD profiles, and hence the scattering form factors. Structural results for commonly used phosphatidylcholine and phosphatidylglycerol lipids will be given.

  7. Mineral crystal alignment in mineralized fracture callus determined by 3D small-angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Liu, Yifei; Manjubala, Inderchand; Roschger, Paul; Schell, Hanna; Duda, Georg N.; Fratzl, Peter

    2010-10-01

    Callus tissue formed during bone fracture healing is a mixture of different tissue types as revealed by histological analysis. But the structural characteristics of mineral crystals within the healing callus are not well known. Since two-dimensional (2D) scanning small-angle X-ray scattering (sSAXS) patterns showed that the size and orientation of callus crystals vary both spatially and temporally [1] and 2D electron microscopic analysis implies an anisotropic property of the callus morphology, the mineral crystals within the callus are also expected to vary in size and orientation in 3D. Three-dimensional small-angle X-ray scattering (3D SAXS), which combines 2D SAXS patterns collected at different angles of sample tilting, has been previously applied to investigate bone minerals in horse radius [2] and oim/oim mouse femur/tibia [3]. We implement a similar 3D SAXS method but with a different way of data analysis to gather information on the mineral alignment in fracture callus. With the proposed accurate yet fast assessment of 3D SAXS information, it was shown that the plate shaped mineral particles in the healing callus were aligned in groups with their predominant orientations occurring as a fiber texture.

  8. Investigation of the structure of unilamellar dimyristoylphosphatidylcholine vesicles in aqueous sucrose solutions by small-angle neutron and X-ray scattering

    SciTech Connect

    Kiselev, M. A. Zemlyanaya, E. V.; Zhabitskaya, E. I.; Aksenov, V. L.

    2015-01-15

    The structure of a polydispersed population of unilamellar dimyristoylphosphatidylcholine (DMPC) vesicles in sucrose solutions has been investigated by small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS). Calculations within the model of separated form factors (SFF) show that the structure of the vesicle system depends strongly on the sucrose concentration.

  9. Imaging method based on attenuation, refraction and ultra-small-angle-scattering of x-rays

    DOEpatents

    Wernick, Miles N.; Chapman, Leroy Dean; Oltulu, Oral; Zhong, Zhong

    2005-09-20

    A method for detecting an image of an object by measuring the intensity at a plurality of positions of a transmitted beam of x-ray radiation emitted from the object as a function of angle within the transmitted beam. The intensity measurements of the transmitted beam are obtained by a crystal analyzer positioned at a plurality of angular positions. The plurality of intensity measurements are used to determine the angular intensity spectrum of the transmitted beam. One or more parameters, such as an attenuation property, a refraction property and a scatter property, can be obtained from the angular intensity spectrum and used to display an image of the object.

  10. Structural Significance of Lipid Diversity as Studied by Small Angle Neutron and X-ray Scattering.

    PubMed

    Kučerka, Norbert; Heberle, Frederick A; Pan, Jianjun; Katsaras, John

    2015-01-01

    We review recent developments in the rapidly growing field of membrane biophysics, with a focus on the structural properties of single lipid bilayers determined by different scattering techniques, namely neutron and X-ray scattering. The need for accurate lipid structural properties is emphasized by the sometimes conflicting results found in the literature, even in the case of the most studied lipid bilayers. Increasingly, accurate and detailed structural models require more experimental data, such as those from contrast varied neutron scattering and X-ray scattering experiments that are jointly refined with molecular dynamics simulations. This experimental and computational approach produces robust bilayer structural parameters that enable insights, for example, into the interplay between collective membrane properties and its components (e.g., hydrocarbon chain length and unsaturation, and lipid headgroup composition). From model studies such as these, one is better able to appreciate how a real biological membrane can be tuned by balancing the contributions from the lipid's different moieties (e.g., acyl chains, headgroups, backbones, etc.). PMID:26402708

  11. Structural Significance of Lipid Diversity as Studied by Small Angle Neutron and X-ray Scattering

    PubMed Central

    Kučerka, Norbert; Heberle, Frederick A.; Pan, Jianjun; Katsaras, John

    2015-01-01

    We review recent developments in the rapidly growing field of membrane biophysics, with a focus on the structural properties of single lipid bilayers determined by different scattering techniques, namely neutron and X-ray scattering. The need for accurate lipid structural properties is emphasized by the sometimes conflicting results found in the literature, even in the case of the most studied lipid bilayers. Increasingly, accurate and detailed structural models require more experimental data, such as those from contrast varied neutron scattering and X-ray scattering experiments that are jointly refined with molecular dynamics simulations. This experimental and computational approach produces robust bilayer structural parameters that enable insights, for example, into the interplay between collective membrane properties and its components (e.g., hydrocarbon chain length and unsaturation, and lipid headgroup composition). From model studies such as these, one is better able to appreciate how a real biological membrane can be tuned by balancing the contributions from the lipid’s different moieties (e.g., acyl chains, headgroups, backbones, etc.). PMID:26402708

  12. Structural Significance of Lipid Diversity as Studied by Small Angle Neutron and X-ray Scattering

    DOE PAGESBeta

    Kučerka, Norbert; Heberle, Frederick A.; Pan, Jianjun; Katsaras, John

    2015-09-21

    In this paper, we review recent developments in the rapidly growing field of membrane biophysics, with a focus on the structural properties of single lipid bilayers determined by different scattering techniques, namely neutron and X-ray scattering. The need for accurate lipid structural properties is emphasized by the sometimes conflicting results found in the literature, even in the case of the most studied lipid bilayers. Increasingly, accurate and detailed structural models require more experimental data, such as those from contrast varied neutron scattering and X-ray scattering experiments that are jointly refined with molecular dynamics simulations. This experimental and computational approach producesmore » robust bilayer structural parameters that enable insights, for example, into the interplay between collective membrane properties and its components (e.g., hydrocarbon chain length and unsaturation, and lipid headgroup composition). Finally, from model studies such as these, one is better able to appreciate how a real biological membrane can be tuned by balancing the contributions from the lipid’s different moieties (e.g., acyl chains, headgroups, backbones, etc.).« less

  13. Structural Significance of Lipid Diversity as Studied by Small Angle Neutron and X-ray Scattering

    SciTech Connect

    Kučerka, Norbert; Heberle, Frederick A.; Pan, Jianjun; Katsaras, John

    2015-09-21

    In this paper, we review recent developments in the rapidly growing field of membrane biophysics, with a focus on the structural properties of single lipid bilayers determined by different scattering techniques, namely neutron and X-ray scattering. The need for accurate lipid structural properties is emphasized by the sometimes conflicting results found in the literature, even in the case of the most studied lipid bilayers. Increasingly, accurate and detailed structural models require more experimental data, such as those from contrast varied neutron scattering and X-ray scattering experiments that are jointly refined with molecular dynamics simulations. This experimental and computational approach produces robust bilayer structural parameters that enable insights, for example, into the interplay between collective membrane properties and its components (e.g., hydrocarbon chain length and unsaturation, and lipid headgroup composition). Finally, from model studies such as these, one is better able to appreciate how a real biological membrane can be tuned by balancing the contributions from the lipid’s different moieties (e.g., acyl chains, headgroups, backbones, etc.).

  14. Facilitating model reconstruction for single-particle scattering using small-angle X-ray scattering methods1

    PubMed Central

    Ma, Shufen; Liu, Haiguang

    2016-01-01

    X-ray free-electron lasers generate intense femtosecond X-ray pulses, so that high-resolution structure determination becomes feasible from noncrystalline samples, such as single particles or single molecules. At the moment, the orientation of sample particles cannot be precisely controlled, and consequently the unknown orientation needs to be recovered using computational algorithms. This delays the model reconstruction until all the scattering patterns have been re-oriented, which often entails a long elapse of time and until the completion of the experiment. The scattering patterns from single particles or multiple particles can be summed to form a virtual powder diffraction pattern, and the low-resolution region, corresponding to the small-angle X-ray scattering (SAXS) regime, can be analysed using existing SAXS methods. This work presents a pipeline that converts single-particle data sets into SAXS data, from which real-time model reconstruction is achieved using the model retrieval approach implemented in the software package SASTBX [Liu, Hexemer & Zwart (2012). J. Appl. Cryst.45, 587–593]. To illustrate the applications, two case studies are presented with real experimental data sets collected at the Linac Coherent Light Source. PMID:27047310

  15. Measurement of illite particle thickness using a direct Fourier transform of small-angle X-ray scattering data

    USGS Publications Warehouse

    Shang, C.; Rice, J.A.; Eberl, D.D.; Lin, S.-J.

    2003-01-01

    It has been suggested that interstratified illite-smectite (I-S) minerals are composed of aggregates of fundamental particles. Many attempts have been made to measure the thickness of such fundamental particles, but each of the methods used suffers from its own limitations and uncertainties. Small-angle X-ray scattering (SAXS) can be used to measure the thickness of particles that scatter X-rays coherently. We used SAXS to study suspensions of Na-rectorite and other illites with varying proportions of smectite. The scattering intensity (I) was recorded as a function of the scattering vector, q = (4 ??/??) sin(??/2), where ?? is the X-ray wavelength and ?? is the scattering angle. The experimental data were treated with a direct Fourier transform to obtain the pair distance distribution function (PDDF) that was then used to determine the thickness of illite particles. The Guinier and Porod extrapolation were used to obtain the scattering intensity beyond the experimental q, and the effects of such extrapolations on the PDDF were examined. The thickness of independent rectorite particles (used as a reference mineral) is 18.3 A??. The SAXS results are compared with those obtained by X-ray diffraction peak broadening methods. It was found that the power-law exponent (??) obtained by fitting the data in the region of q = 0.1 -0.6 nm-1 to the power law (I = Ioq-??) is a linear function of illite particle thickness. Therefore, illite particle thickness could be predicted by the linear relationship as long as the thickness is within the limit where ?? <4.0.

  16. Structure of the Lassa Virus Nucleoprotein Revealed by X-ray Crystallography, Small-angle X-ray Scattering, and Electron Microscopy*

    PubMed Central

    Brunotte, Linda; Kerber, Romy; Shang, Weifeng; Hauer, Florian; Hass, Meike; Gabriel, Martin; Lelke, Michaela; Busch, Carola; Stark, Holger; Svergun, Dmitri I.; Betzel, Christian; Perbandt, Markus; Günther, Stephan

    2011-01-01

    The nucleoprotein (NP) of Lassa virus (LASV) strain AV was expressed in a recombinant baculovirus system. The crystal structure of full-length NP was solved at a resolution of 2.45 Å. The overall fold corresponds to that of NP of LASV strain Josiah (Qi, X., Lan, S., Wang, W., Schelde, L. M., Dong, H., Wallat, G. D., Ly, H., Liang, Y., and Dong, C. (2010) Nature 468, 779–783) with a root mean square deviation of 0.67 Å for all atoms (6.3% difference in primary sequence). As the packing in the crystal offers two different trimer architectures for the biological assembly, the quaternary structure of NP in solution was determined by small-angle x-ray scattering and EM. After classification and averaging of >6000 EM raw images, trimeric centrosymmetric structures were obtained, which correspond in size and shape to one trimer in the crystal structure formed around a crystallographic 3-fold rotation axis (symmetric trimer). The symmetric trimer is also a good model for the small-angle x-ray scattering data and could be well embedded into the ab initio model. The N-terminal domain of NP contains a deep nucleotide-binding cavity that has been proposed to bind cellular cap structures for priming viral mRNA synthesis. All residues implicated in m7GpppN binding were exchanged, and the transcription/replication phenotype of the NP mutant was tested using a LASV replicon system. None of the mutants showed a specific defect in mRNA expression; most were globally defective in RNA synthesis. In conclusion, we describe the full-length crystal structure and the quaternary structure in solution of LASV NP. The nucleotide-binding pocket of NP could not be assigned a specific role in viral mRNA synthesis. PMID:21917929

  17. Influence of monovalent ions on density fluctuations in hydrothermal aqueous solutions by small angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Da Silva-Cadoux, Cécile; Hazemann, Jean-Louis; Testemale, Denis; Proux, Olivier; Rochas, Cyrille

    2012-01-01

    Synchrotron small angle X-ray scattering measurements on water and alkaline bromine aqueous solutions (XBr, with X = Li, Rb, or Cs) were carried out from ambient to supercritical conditions. The temperature was increased from 300 to 750 K along several isobars between 24 and 35 MPa. The correlation length and the structure factor were extracted from the data following the Ornstein-Zernike formalism. We obtained experimental evidence of the shift of the critical point and isochore and their dependence on the ions concentration (0.33 mol/kg and 1.0 mol/kg). We also observed that the size of the density fluctuations and the structure factor increase with the presence of the ions and that this effect is positively correlated with the atomic number of the cation. These behaviors were compared with ZnBr2 and NaCl systems from the literature.

  18. Measurement of latent tracks in amorphous SiO 2 using small angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Kluth, P.; Schnohr, C. S.; Sprouster, D. J.; Byrne, A. P.; Cookson, D. J.; Ridgway, M. C.

    2008-06-01

    In this paper we present preliminary yet promising results on the measurement of latent ion tracks in amorphous, 2 μm thick SiO2 layers using small angle X-ray scattering (SAXS). The tracks were generated by ion irradiation with 89 MeV Au ions to fluences between 3 × 1010 and 3 × 1012 ions/cm2. Transmission SAXS measurements show distinct scattering from the irradiated SiO2 as compared to the unirradiated material. Analysis of the SAXS spectra using a cylindrical model suggests a core-shell like density distribution in the ion tracks with a lower density core and a higher density shell as compared to unirradiated material. The total track radius of ∼48 Å is in very good agreement with previous experiments and calculations based on an inelastic thermal spike model.

  19. Use of Ultra Small Angle X-Ray Scattering to Measure Grain Size of Styrene-Butadiene Block Copolymers

    NASA Astrophysics Data System (ADS)

    Cohen, Robert E.; Myers, Randall T.; Bellare, Anuj

    1998-03-01

    Simultaneous determination of the lamellar morphological length scale and the grain size of several commercial heterogeneous styrene - butadiene block copolymers was accomplished through the use of ultra small angle x-ray scattering measurements. NIST's X23A3 ultra SAXS beamline at the Brookhaven National Laboratory provided a range of scattering vector q from 0.0004 to 0.1 ÅThe grain dimension was determined by analysis of both the Bragg peaks and the Porod region coupled with the invarient assosciated with the scattering intensities at very low values of q. Grain size was controlled in a given block copolymer by the choice of evaporation solvent and temperature as well as annealing time and temperature. Conventional 2-dimensional SAXS and transmission electron microscopy corroborated the ultra SAXS analysis.

  20. Grazing-incidence small-angle X-ray scattering from alkaline phosphatase immobilized in atmospheric plasmapolymer coatings

    NASA Astrophysics Data System (ADS)

    Ortore, M. G.; Sinibaldi, R.; Heyse, P.; Paulussen, S.; Bernstorff, S.; Sels, B.; Mariani, P.; Rustichelli, F.; Spinozzi, F.

    2008-06-01

    Grazing-incidence small-angle X-ray scattering (GISAXS) has been used to study proteins embedded in thin polymer films obtained by a new cold, atmospheric-pressure plasma technique. In order to test the efficiency of the technology, four samples of alkaline phosphatase incorporated in organic polymer coatings in different plasma conditions have been investigated. Data have been analysed in the framework of the distorted-wave Born approximation (DWBA), by using a new method for the simultaneous fitting of the two-dimensional diffuse scattering from each sample. As a result, protein film concentration and aggregation state as well as a set of parameters describing the polymer coatings have been obtained.

  1. Grazing-incidence small-angle X-ray scattering: application to the study of quantum dot lattices

    PubMed Central

    Buljan, Maja; Radić, Nikola; Bernstorff, Sigrid; Dražić, Goran; Bogdanović-Radović, Iva; Holý, Václav

    2012-01-01

    The ordering of quantum dots in three-dimensional quantum dot lattices is investigated by grazing-incidence small-angle X-ray scattering (GISAXS). Theoretical models describing GISAXS intensity distributions for three general classes of lattices of quantum dots are proposed. The classes differ in the type of disorder of the positions of the quantum dots. The models enable full structure determination, including lattice type, lattice parameters, the type and degree of disorder in the quantum dot positions and the distributions of the quantum dot sizes. Applications of the developed models are demonstrated using experimentally measured data from several types of quantum dot lattices formed by a self-assembly process. PMID:22186289

  2. A small-angle X-ray scattering study of alpha-synuclein from human red blood cells

    PubMed Central

    Araki, Katsuya; Yagi, Naoto; Nakatani, Rie; Sekiguchi, Hiroshi; So, Masatomo; Yagi, Hisashi; Ohta, Noboru; Nagai, Yoshitaka; Goto, Yuji; Mochizuki, Hideki

    2016-01-01

    α-synuclein (α-syn) is the main component of Lewy bodies, which are neuropathological hallmarks of patients with Parkinson’s disease. As it has been controversial whether human α-syn from erythrocytes exists as a tetramer under physiological conditions, we tried solving this issue by the small-angle X-ray solution scattering method. Under two different conditions (high ionic strength with a Tris buffer and low ionic strength with an ammonium acetate buffer), no evidence was found for the presence of tetramer. When comparing erythrocyte and recombinant α-syn molecules, we found no significant difference of the molecular weight and the secondary structure although the buffer conditions strongly affect the radius of gyration of the protein. The results indicate that, even though a stable tetramer may not be formed, conformation of α-syn depends much on its environment, which may be the reason for its tendency to aggregate in cells. PMID:27469540

  3. X-ray magnetic circular dichroism and small angle neutron scattering study of thiol capped gold nanoparticles.

    SciTech Connect

    de la Venta, J.; Bouzas, V.; Pucci, A.; Laguna-Marco, M. A.; Haskel, D.; Pinel, E. F.; te Velthuis, S. G. E.; Hoffmann, A.; Lal, J.; Bleuel, M.; Ruggeri, G.; de Julian, C.; Garcia, M. A.; Univ. Complutense de Madrid; Inst. de Magnetismo Aplicado UCM; Univ. Pisa; Univ. di Padova

    2009-11-01

    X-ray magnetic circular dichroism (XMCD) and Small Angle Neutron Scattering (SANS) measurements were performed on thiol capped Au nanoparticles (NPs) embedded into polyethylene. An XMCD signal of 0.8 {center_dot} 10{sup -4} was found at the Au L{sub 3} edge of thiol capped Au NPs embedded in a polyethylene matrix for which Superconducting Quantum Interference Device (SQUID) magnetometry yielded a saturation magnetization, M{sub s}, of 0.06 emu/g{sub Au}. SANS measurements showed that the 3.2 nm average-diameter nanoparticles are 28% polydispersed, but no detectable SANS magnetic signal was found with the resolution and sensitivity accessible with the neutron experiment. A comparison with previous experiments carried out on Au NPs and multilayers, yield to different values between XMCD signals and magnetization measured by SQUID magnetometer. We discuss the origin of those differences.

  4. Quantitative analysis of nanoripple and nanoparticle patterns by grazing incidence small-angle x-ray scattering 3D mapping

    NASA Astrophysics Data System (ADS)

    Babonneau, D.; Camelio, S.; Vandenhecke, E.; Rousselet, S.; Garel, M.; Pailloux, F.; Boesecke, P.

    2012-06-01

    3D reciprocal space mapping in the grazing incidence small-angle x-ray scattering geometry was used to obtain accurate morphological characteristics of nanoripple patterns prepared by broad beam-ion sputtering of Al2O3 and Si3N4 amorphous thin films as well as 2D arrays of Ag nanoparticles obtained by glancing angle deposition on Al2O3 nanorippled buffer layers. Experiments and theoretical simulations based on the distorted-wave Born approximation make it possible to determine the average 3D shape of the ripples and nanoparticles together with crucial information on their in-plane organization. In the case of nanoparticle arrays, the approach was also used to quantify the growth conformity of an additional capping layer, which proceeds by replication of the buried ripple pattern.

  5. Modular structure of the full-length DNA gyrase B subunit revealed by small-angle X-ray scattering.

    PubMed

    Costenaro, Lionel; Grossmann, J Günter; Ebel, Christine; Maxwell, Anthony

    2007-03-01

    DNA gyrase, the only topoisomerase able to introduce negative supercoils into DNA, is essential for bacterial transcription and replication; absent from humans, it is a successful target for antibacterials. From biophysical experiments in solution, we report a structural model at approximately 12-15 A resolution of the full-length B subunit (GyrB). Analytical ultracentrifugation shows that GyrB is mainly a nonglobular monomer. Ab initio modeling of small-angle X-ray scattering data for GyrB consistently yields a "tadpole"-like envelope. It allows us to propose an organization of GyrB into three domains-ATPase, Toprim, and Tail-based on their crystallographic and modeled structures. Our study reveals the modular organization of GyrB and points out its potential flexibility, needed during the gyrase catalytic cycle. It provides important insights into the supercoiling mechanism by gyrase and suggests new lines of research. PMID:17355868

  6. Structure of Carbon Nanotube Porins in Lipid Bilayers: An in Situ Small-Angle X-ray Scattering (SAXS) Study.

    PubMed

    Tran, Ich C; Tunuguntla, Ramya H; Kim, Kyunghoon; Lee, Jonathan R I; Willey, Trevor M; Weiss, Thomas M; Noy, Aleksandr; van Buuren, Tony

    2016-07-13

    Carbon nanotube porins (CNTPs), small segments of carbon nanotubes capable of forming defined pores in lipid membranes, are important future components for bionanoelectronic devices as they could provide a robust analog of biological membrane channels. In order to control the incorporation of these CNT channels into lipid bilayers, it is important to understand the structure of the CNTPs before and after insertion into the lipid bilayer as well as the impact of such insertion on the bilayer structure. Here we employed a noninvasive in situ probe, small-angle X-ray scattering, to study the integration of CNT porins into dioleoylphosphatidylcholine bilayers. Our results show that CNTPs in solution are stabilized by a monolayer of lipid molecules wrapped around their outer surface. We also demonstrate that insertion of CNTPs into the lipid bilayer results in decreased bilayer thickness with the magnitude of this effect increasing with the concentration of CNTPs. PMID:27322135

  7. Characterizing the Morphologies of Mechanically Manipulated Multiwall Carbon Nanotube Films by Small-Angle X-ray Scattering

    SciTech Connect

    Wang,B.; Bennett, R.; Verploegen, E.; Hart, A.; Cohen, R.

    2007-01-01

    We used small-angle X-ray scattering (SAXS) to quantitatively characterize the morphological characteristics of pristine and mechanically manipulated multiwall carbon nanotube (MWCNT) films. We determined that CNT diameters measured near the edges of a film were smaller compared to those measured in the interior. Uniaxially compressed MWCNT films exhibited a buckling deformation that was observable both in scanning electron microscopy (SEM) and SAXS. CNT films were also converted into cellular foams of CNTs through capillarity-induced densification. By examining spatially- and time-resolved SAXS data for the cellular foams, we identified low angle features in the scattering curves that correspond to the average spacing between CNTs, demonstrating that SAXS is a useful method for monitoring the packing density of CNTs in a film. For all of the morphologies that were examined (aligned, disordered, compressed, and densified), SAXS data showed good correspondence with SEM images.

  8. Intermediate states of globular proteins during temperature-induced folding and unfolding studied using small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Banuelos, Jose; Urquidi, Jacob

    2009-03-01

    The ability of proteins to change their conformation in response to changes in their environment has consequences in biological processes like metabolism, chemical regulation in cells, and is believed to play a role in the onset of several neurodegenerative diseases. Factors such as concentration, degree of crowding from other entities, and solvent medium affect how a protein folds. As a protein unfolds, the ratio of nonpolar to polar groups exposed to water changes, affecting a protein's thermodynamic properties. Using small angle x-ray scattering (SAXS), we are currently studying the intermediate protein conformations that arise during the folding/unfolding process as a function of temperature for a series of globular proteins. The temporal stability of these ensembles is also under investigation. Trends in the scattering profiles, along with correlations with protein thermodynamics, may help elucidate shared characteristics between all proteins in their folding behavior.

  9. Conformational landscape of cytochrome c folding studied by microsecond-resolved small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Akiyama, Shuji; Takahashi, Satoshi; Kimura, Tetsunari; Ishimori, Koichiro; Morishima, Isao; Nishikawa, Yukihiro; Fujisawa, Tetsuro

    2002-02-01

    To investigate protein folding dynamics in terms of compactness, we developed a continuous-flow mixing device to make small-angle x-ray scattering measurements with the time resolution of 160 μs and characterized the radius of gyration (Rg) of two folding intermediates of cytochrome c (cyt c). The early intermediate possesses 20 Å of Rg, which is smaller by 4 Å than that of the acid-unfolded state. The Rg of the later intermediate is ≈18 Å, which is close to that of the molten globule state. Considering the α-helix content (fH) of the intermediates, we clarified the folding pathway of cyt c on the conformational landscape defined by Rg and fH. Cyt c folding proceeds with a collapse around a specific region of the protein followed by a cooperative acquisition of secondary structures and compactness.

  10. Characterization of protein flexibility using small-angle x-ray scattering and amplified collective motion simulations.

    PubMed

    Wen, Bin; Peng, Junhui; Zuo, Xiaobing; Gong, Qingguo; Zhang, Zhiyong

    2014-08-19

    Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations. PMID:25140431

  11. Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations

    PubMed Central

    Wen, Bin; Peng, Junhui; Zuo, Xiaobing; Gong, Qingguo; Zhang, Zhiyong

    2014-01-01

    Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations. PMID:25140431

  12. Pressure-induced structural phase transition of dense droplet microemulsions studied by small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Seto, Hideki; Nagao, Michihiro; Kawabata, Youhei; Takeda, Takayoshi

    2001-11-01

    A small-angle x-ray scattering (SAXS) study of dense water-in-oil droplet microemulsions composed of water, decane, and AOT [sodium bis(2-ethylhexyl) sulfosuccinate] was performed in order to clarify phase behavior with applied pressure and the corresponding structural phase transitions. SAXS spectra were collected for pressures between ambient pressure (0.1 MPa) and 80 MPa and droplet volume fraction, φ, from 0.40 to 0.70. With increasing φ, the mean radius of droplets decreased slightly and polydispersity increased. With increasing pressure, the droplet structure transformed to a two-phase system with coexistence of lamellar and droplet structures, independent of the droplet volume fraction. These results suggest that, with increasing pressure, the increasing inter-droplet attractive force controls the pressure variation of the structure.

  13. Structural investigations of E. Coli dihydrolipoamide dehydrogenase in solution: Small-angle X-ray scattering and molecular docking

    NASA Astrophysics Data System (ADS)

    Dadinova, L. A.; Rodina, E. V.; Vorobyeva, N. N.; Kurilova, S. A.; Nazarova, T. I.; Shtykova, E. V.

    2016-05-01

    Dihydrolipoamide dehydrogenase from Escherichia coli (LpD) is a bacterial enzyme that is involved in the central metabolism and shared in common between the pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes. In the crystal structure, E. coli LpD is known to exist as a dimer. The present work is focused on analyzing the solution structure of LpD by small-angle X-ray scattering, molecular docking, and analytical ultracentrifugation. It was shown that in solution LpD exists as an equilibrium mixture of a dimer and a tetramer. The presence of oligomeric forms is determined by the multifunctionality of LpD in the cell, in particular, the required stoichiometry in the complexes.

  14. Monitoring intermediate filament assembly by small-angle x-ray scattering reveals the molecular architecture of assembly intermediates

    PubMed Central

    Sokolova, Anna V.; Kreplak, Laurent; Wedig, Tatjana; Mücke, Norbert; Svergun, Dmitri I.; Herrmann, Harald; Aebi, Ueli; Strelkov, Sergei V.

    2006-01-01

    Intermediate filaments (IFs), along with microtubules, microfilaments, and associated cross-bridging proteins, constitute the cytoskeleton of metazoan cells. While crystallographic data on the dimer representing the elementary IF “building block” have recently become available, little structural detail is known about both the mature IF architecture and its assembly pathway. Here, we have applied solution small-angle x-ray scattering to investigate the in vitro assembly of a 53-kDa human IF protein vimentin at pH 8.4 by systematically varying the ionic strength conditions, and complemented these experiments by electron microscopy and analytical ultracentrifugation. While a vimentin solution in 5 mM Tris·HCl (pH 8.4) contains predominantly tetramers, addition of 20 mM NaCl induces further lateral assembly evidenced by the shift of the sedimentation coeficient and yields a distinct octameric intermediate. Four octamers eventually associate into unit-length filaments (ULFs) that anneal longitudinally. Based on the small-angle x-ray scattering experiments supplemented by crystallographic data and additional structural constraints, 3D molecular models of the vimentin tetramer, octamer, and ULF were constructed. Within each of the three oligomers, the adjacent dimers are aligned exclusively in an approximately half-staggered antiparallel A11 mode with a distance of 3.2–3.4 nm between their axes. The ULF appears to be a dynamic and a relatively loosely packed structure with a roughly even mass distribution over its cross-section. PMID:17050693

  15. Extensive small-angle X-ray scattering studies of blood coagulation factor VIIa reveal interdomain flexibility.

    PubMed

    Mosbaek, Charlotte Rode; Nolan, David; Persson, Egon; Svergun, Dmitri I; Bukrinsky, Jens Thostrup; Vestergaard, Bente

    2010-11-16

    Blood coagulation factor VIIa (FVIIa) is used in the treatment of replacement therapy resistant hemophilia patients, and FVIIa is normally activated upon complex formation with tissue factor (TF), potentially in context with structural rearrangements. The solution behavior of uncomplexed FVIIa is important for understanding the mechanism of activation and for the stability and activity of the pharmaceutical product. However, crystal structures of FVIIa in complex with TF and of truncated free FVIIa reveal different overall conformations while previous small-angle scattering studies suggest FVIIa always to be fully extended in solution. Here, small-angle X-ray scattering analysis of multiple forms of FVIIa and TF under several experimental conditions elaborate extensively on the understanding of the solution behavior of FVIIa. We reveal significant FVIIa domain flexibility in solution, whereas TF has a well-defined conformation. Unspecific formation of dimers of FVIIa is also observed and varies with experimental conditions. In particular, active site-inhibited FVIIa displays a distinct solution behavior different from that of uninhibited FVIIa, which may reflect structural rearrangements causing resistance to activation, thereby emphasizing the connection between the distribution of different conformations of FVII and the mechanism of activation. PMID:20873866

  16. The structure of water in the hydration shell of cations from x-ray Raman and small angle x-ray scattering measurements.

    PubMed

    Waluyo, Iradwikanari; Huang, Congcong; Nordlund, Dennis; Bergmann, Uwe; Weiss, Thomas M; Pettersson, Lars G M; Nilsson, Anders

    2011-02-14

    X-ray Raman scattering (XRS) spectroscopy and small angle x-ray scattering (SAXS) are used to study water in aqueous solutions of NaCl, MgCl(2), and AlCl(3) with the particular aim to provide information about the structure of the hydration shells of the cations. The XRS spectra show that Na(+) weakens the hydrogen bonds of water molecules in its vicinity, similar to the effect of increased temperature and pressure. Mg(2+) and Al(3+), on the other hand, cause the formation of short and strong hydrogen bonds between the surrounding water molecules. The SAXS data show that Mg(2+) and Al(3+) form tightly bound hydration shells that give a large density contrast in the scattering data. From the form factors extracted from the SAXS data, we found that Mg(2+) and Al(3+) have, respectively, an equivalent of one and one and a half stable hydration shells that appear as a density contrast. In addition, we estimated that the density of water in the hydration shells of Mg(2+) and Al(3+) is, respectively, ∼61% and ∼71% higher than in bulk water. PMID:21322711

  17. The structure of water in the hydration shell of cations from x-ray Raman and small angle x-ray scattering measurements

    SciTech Connect

    Waluyo, Iradwikanari; Huang Congcong; Nordlund, Dennis; Weiss, Thomas M.; Bergmann, Uwe; Pettersson, Lars G. M.; Nilsson, Anders

    2011-02-14

    X-ray Raman scattering (XRS) spectroscopy and small angle x-ray scattering (SAXS) are used to study water in aqueous solutions of NaCl, MgCl{sub 2}, and AlCl{sub 3} with the particular aim to provide information about the structure of the hydration shells of the cations. The XRS spectra show that Na{sup +} weakens the hydrogen bonds of water molecules in its vicinity, similar to the effect of increased temperature and pressure. Mg{sup 2+} and Al{sup 3+}, on the other hand, cause the formation of short and strong hydrogen bonds between the surrounding water molecules. The SAXS data show that Mg{sup 2+} and Al{sup 3+} form tightly bound hydration shells that give a large density contrast in the scattering data. From the form factors extracted from the SAXS data, we found that Mg{sup 2+} and Al{sup 3+} have, respectively, an equivalent of one and one and a half stable hydration shells that appear as a density contrast. In addition, we estimated that the density of water in the hydration shells of Mg{sup 2+} and Al{sup 3+} is, respectively, {approx}61% and {approx}71% higher than in bulk water.

  18. Shape and Interhelical Spacing of DNA Origami Nanostructures Studied by Small-Angle X-ray Scattering.

    PubMed

    Fischer, Stefan; Hartl, Caroline; Frank, Kilian; Rädler, Joachim O; Liedl, Tim; Nickel, Bert

    2016-07-13

    Scaffolded DNA origami nanostructures enable the self-assembly of arbitrarily shaped objects with unprecedented accuracy. Yet, varying physiological conditions are prone to induce slight structural changes in the nanoscale architecture. Here, we report on high precision measurements of overall shape and interhelical distance of three prototypic DNA origami structures in solution using synchrotron small-angle X-ray scattering. Sheet-, brick-, and cylinder-shaped DNA constructs were assembled and the shape factors determined with angstrom resolution from fits to the scattering profiles. With decreasing MgCl2 concentration electrostatic swelling of both shape cross section and interhelical DNA spacing of the DNA origami structures is observed. The structures tolerate up to 10% interhelical expansion before they disintegrate. In contrast, with increasing temperature, the cylinder-shaped structures show no thermal expansion in a wide temperature window before they abruptly melt above 50 °C. Details on molecular structure of DNA origami can also be obtained using in-house X-ray scattering equipment and, hence, allow for routine folding and stability testing of DNA-based agents that are designed to operate under varying salt conditions. PMID:27184452

  19. In-situ small-angle X-ray scattering study of the precipitation behavior in a Fe-25 at.%Co-9 at.%Mo alloy

    SciTech Connect

    Zickler, Gerald A. Eidenberger, Elisabeth; Leitner, Harald; Stergar, Erich; Clemens, Helmut; Staron, Peter; Lippmann, Thomas; Schreyer, Andreas

    2008-12-15

    Fe-Co-Mo alloys show extraordinary mechanical properties which make them potential candidates for various high-performance applications. In the present study, for the first time, the precipitation behavior in a Fe-25 at.%Co-9 at.%Mo alloy was studied by small-angle X-ray scattering using high-energy synchrotron radiation. The specimens were isothermally aged in an in-situ furnace. The small-angle X-ray scattering patterns showed scaling behavior and were evaluated by employing a model function from the literature. This approach provides information about the characteristic length scale and the volume fraction of the precipitates in the alloy.

  20. Strontium and bone nanostructure in normal and ovariectomized rats investigated by scanning small-angle X-ray scattering.

    PubMed

    Bünger, Mathias H; Oxlund, Hans; Hansen, Toke K; Sørensen, Søren; Bibby, Bo M; Thomsen, Jesper S; Langdahl, Bente L; Besenbacher, Flemming; Pedersen, Jan S; Birkedal, Henrik

    2010-04-01

    The effect of SrCl(2) treatment on bone nanostructure in a rat ovariectomy model was studied using scanning small-angle X-ray scattering (sSAXS). Twelve 6-month-old female Wistar rats were used. Six animals were ovariectomized (+ovx) and six were left intact after sham surgery (-ovx). Six animals, three +ovx and three -ovx, were treated with 4 mmol SrCl(2) (aq)/kg/day (+Sr), whereas the remaining six received placebo (-Sr) for 140 days. Rats were labeled with flourochromes at days 7, 126, and 136. Femoral cross sections were studied using fluorescence microscopy, scanning electron microscopy including energy-dispersive X-ray analysis, and sSAXS. The SAXS data comprised about 5,500 measurements and provided information about mineral crystal thickness and orientation in new and old bone. The newly formed bone contained higher levels of Sr(2+) in +Sr than in -Sr animals, indicating that the Sr(2+) was incorporated into the new bone. Mineral plates were significantly thicker in old bone, 2.62 nm (95% CI 2.58-2.66), than in new bone, 2.41 nm (95% CI 2.36-2.46). Surprisingly, mineral plates in new bone were significantly thicker (2.52 [95% CI 2.47-2.57] nm vs. 2.41 [95% CI 2.36-2.46] nm, P = 0.017) in +ovx rats than in -ovx rats. However, no significant effect of SrCl(2) on mineral plate thicknesses in new bone was observed. The statistical model yielded estimates of the difference in bone mineral plate thickness induced by Sr. The estimated effect of Sr was -0.09 (95% CI -0.21 to 0.03) and 0.02 (95% CI -0.10 to 0.14) nm for new bone in -ovx and +ovx rats, respectively. PMID:20221590

  1. Critical dimension small angle X-ray scattering measurements of FinFET and 3D memory structures

    NASA Astrophysics Data System (ADS)

    Settens, Charles; Bunday, Benjamin; Thiel, Brad; Kline, R. Joseph; Sunday, Daniel; Wang, Chengqing; Wu, Wen-li; Matyi, Richard

    2013-04-01

    We have demonstrated that transmission critical dimension small angle X-ray scattering (CD-SAXS) provides high accuracy and precision CD measurements on advanced 3D microelectronic architectures. The competitive advantage of CD-SAXS over current 3D metrology methods such as optical scatterometry is that CD-SAXS is able to decouple and fit cross-section parameters without any significant parameter cross-correlations. As the industry aggressively scales beyond the 22 nm node, CD-SAXS can be used to quantitatively measure nanoscale deviations in the average crosssections of FinFETs and high-aspect ratio (HAR) memory devices. Fitting the average cross-section of 18:1 isolated HAR contact holes with an effective trapezoid model yielded an average pitch of 796.9 +/- 0.4 nm, top diameter of 70.3 +/- 0.9 nm, height of 1088 +/- 4 nm, and sidewall angle below 0.1°. Simulations of dense 40:1 HAR contact holes and FinFET fin-gate crossbar structures have been analyzed using CD-SAXS to inquire the theoretical precision of the technique to measure important process parameters such as fin CD, height, and sidewall angle; BOX etch recess, thickness of hafnium oxide and titanium nitride layers; gate CD, height, and sidewall angle; and hafnium oxide and titanium nitride etch recess. The simulations of HAR and FinFET structures mimic the characteristics of experimental data collected at a synchrotron x-ray source. Using the CD-SAXS simulator, we estimate the measurement capabilities for smaller similar structures expected at future nodes to predict the applicability of this technique to fulfill important CD metrology needs.

  2. High-throughput biological small-angle X-ray scattering with a robotically loaded capillary cell

    PubMed Central

    Nielsen, S. S.; Møller, M.; Gillilan, R. E.

    2012-01-01

    With the rise in popularity of biological small-angle X-ray scattering (BioSAXS) measurements, synchrotron beamlines are confronted with an ever-increasing number of samples from a wide range of solution conditions. To meet these demands, an increasing number of beamlines worldwide have begun to provide automated liquid-handling systems for sample loading. This article presents an automated sample-loading system for BioSAXS beamlines, which combines single-channel disposable-tip pipetting with a vacuum-enclosed temperature-controlled capillary flow cell. The design incorporates an easily changeable capillary to reduce the incidence of X-ray window fouling and cross contamination. Both the robot-control and the data-processing systems are written in Python. The data-processing code, RAW, has been enhanced with several new features to form a user-friendly BioSAXS pipeline for the robot. The flow cell also supports efficient manual loading and sample recovery. An effective rinse protocol for the sample cell is developed and tested. Fluid dynamics within the sample capillary reveals a vortex ring pattern of circulation that redistributes radiation-damaged material. Radiation damage is most severe in the boundary layer near the capillary surface. At typical flow speeds, capillaries below 2 mm in diameter are beginning to enter the Stokes (creeping flow) regime in which mixing due to oscillation is limited. Analysis within this regime shows that single-pass exposure and multiple-pass exposure of a sample plug are functionally the same with regard to exposed volume when plug motion reversal is slow. The robot was tested on three different beamlines at the Cornell High-Energy Synchrotron Source, with a variety of detectors and beam characteristics, and it has been used successfully in several published studies as well as in two introductory short courses on basic BioSAXS methods. PMID:22509071

  3. Characterization of nanofibers formed by self-assembly of {beta}-peptide oligomers using small angle x-ray scattering

    SciTech Connect

    Pizzey, Claire L.; Abbott, Nicholas L.; Pomerantz, William C.; Sung, Bong-June; Gellman, Samuel H.; Yethiraj, Arun; Yuwono, Virany M.; Hartgerink, Jeffery D.

    2008-09-07

    Helical oligomers of {beta}-peptides represent a particularly promising type of building block for directed assembly of organic nanostructures because the helical secondary structure can be designed to be very stable and because control of the {beta}-amino acid sequence can lead to precise patterning of chemical functional groups over the helix surfaces. In this paper, we report the use of small angle x-ray scattering measurements (SAXS) to characterize nanostructures formed by the directed assembly of {beta}-peptide A with sequence H{sub 2}N-{beta}{sup 3}hTyr-{beta}{sup 3}hLys-{beta}{sup 3}hPhe-ACHC-{beta}{sup 3}hPhe-ACHC-{beta}{sup 3}hPhe-{beta}{sup 3}hLys-ACHC-ACHC-{beta}{sup 3}hPhe-{beta}{sup 3}hLys-CONH{sub 2}. Whereas prior cryo-TEM studies have revealed the presence of nanofibers in aqueous solutions of {beta}-peptide A, SAXS measurements from the nanofibers were not well-fit by a form factor model describing solid nanofibers. An improved fit to the scattering data at high q was obtained by using a form factor model describing a cylinder with a hollow center and radial polydispersity. When combined with a structure factor calculated from the polymer reference interaction site model (PRISM) theory, the scattered intensity of x-rays measured over the entire q range was well described by the model. Analysis of our SAXS data suggests a model in which individual {beta}-peptides assemble to form long cylindrical nanofibers with a hollow core radius of 15 A (polydispersity of 21%) and a shell thickness of 20 A. This model is supported by negative stain transmission electron microscopy.

  4. Size Determination of a Liposomal Drug by Small-Angle X-ray Scattering Using Continuous Contrast Variation.

    PubMed

    Garcia-Diez, Raul; Gollwitzer, Christian; Krumrey, Michael; Varga, Zoltan

    2016-01-26

    The continuously growing complexity of nanodrugs urges for complementary characterization techniques which can elude the current limitations. In this paper, the applicability of continuous contrast variation in small-angle X-ray scattering (SAXS) for the accurate size determination of a complex nanocarrier is demonstrated on the example of PEGylated liposomal doxorubicin (Caelyx). The mean size and average electron density of Caelyx was determined by SAXS using a gradient of aqueous iodixanol (Optiprep), an iso-osmolar suspending medium. The study is focused on the isoscattering point position and the analysis of the Guinier region of the scattering curves recorded at different solvent densities. An average diameter of (69 ± 5) nm and electron density of (346.2 ± 1.2) nm(-3) were determined for the liposomal formulation of doxorubicin. The response of the liposomal nanocarrier to increasing solvent osmolality and the structure of the liposome-encapsulated doxorubicin after the osmotic shrinkage of the liposome are evaluated with sucrose contrast variation in SAXS and wide-angle X-ray scattering (WAXS). In the case of using sucrose as contrast agent, a clear osmolality threshold at 670 mOsm kg(-1) was observed, above which the liposomal drug carriers start to shrink, though preserving the intraliposomal doxorubicin structure. The average size obtained by this technique is smaller than the value measured by dynamic light scattering (DLS), though this difference is expected due to the hydrodynamic size of the PEG moieties attached to the liposomal surface, which are not probed with solvent contrast variation in SAXS. The advantages and drawbacks of the proposed technique are discussed in comparison to DLS, the most frequently used sizing method in nanomedicine. PMID:26673729

  5. Gold Nanoparticle Internal Structure and Symmetry Probed by Unified Small-Angle X-ray Scattering and X-ray Diffraction Coupled with Molecular Dynamics Analysis.

    PubMed

    Fleury, Blaise; Cortes-Huerto, Robinson; Taché, Olivier; Testard, Fabienne; Menguy, Nicolas; Spalla, Olivier

    2015-09-01

    Shape and size are known to determine a nanoparticle's properties. Hardly ever studied in synthesis, the internal crystal structure (i.e., particle defects, crystallinity, and symmetry) is just as critical as shape and size since it directly impacts catalytic efficiency, plasmon resonance, and orients anisotropic growth of metallic nanoparticles. Hence, its control cannot be ignored any longer in today's research and applications in nanotechnology. This study implemented an unprecedented reliable measurement combining these three structural aspects. The unified small-angle X-ray scattering and diffraction measurement (SAXS/XRD) was coupled with molecular dynamics to allow simultaneous determination of nanoparticles' shape, size, and crystallinity at the atomic scale. Symmetry distribution (icosahedra-Ih, decahedra-Dh, and truncated octahedra-TOh) of 2-6 nm colloidal gold nanoparticles synthesized in organic solvents was quantified. Nanoparticle number density showed the predominance of Ih, followed by Dh, and little, if any, TOh. This result contradicts some theoretical predictions and highlights the strong effect of the synthesis environment on structure stability. We foresee that this unified SAXS/XRD analysis, yielding both statistical and quantitative counts of nanoparticles' symmetry distribution, will provide new insights into nanoparticle formation, growth, and assembly. PMID:26263393

  6. Small-angle scattering computed tomography (SAS-CT) using a Talbot-Lau interferometer and a rotating anode x-ray tube: theory and experiments

    PubMed Central

    Chen, Guang-Hong; Bevins, Nicholas; Zambelli, Joseph; Qi, Zhihua

    2013-01-01

    X-ray differential phase contrast imaging methods, including projection imaging and the corresponding computed tomography (CT), have been implemented using a Talbot interferometer and either a synchrotron beam line or a low brilliance x-ray source generated by a stationary-anode x-ray tube. From small-angle scattering events which occur as an x-ray propagates through a medium, a signal intensity loss can be recorded and analyzed for an understanding of the micro-structures in an image object. This has been demonstrated using a Talbot-Lau interferometer and a stationary-anode x-ray tube. In this paper, theoretical principles and an experimental implementation of the corresponding CT imaging method are presented. First, a line integral is derived from analyzing the cross section of the small-angle scattering events. This method is referred to as small-angle scattering computed tomography (SAS-CT). Next, a Talbot-Lau interferometer and a rotating-anode x-ray tube were used to implement SAS-CT. A physical phantom and human breast tissue sample were used to demonstrate the reconstructed SAS-CT image volumes. PMID:20588425

  7. Poisson's ratio of collagen fibrils measured by small angle X-ray scattering of strained bovine pericardium

    SciTech Connect

    Wells, Hannah C.; Sizeland, Katie H.; Kayed, Hanan R.; Haverkamp, Richard G.; Kirby, Nigel; Hawley, Adrian; Mudie, Stephen T.

    2015-01-28

    Type I collagen is the main structural component of skin, tendons, and skin products, such as leather. Understanding the mechanical performance of collagen fibrils is important for understanding the mechanical performance of the tissues that they make up, while the mechanical properties of bulk tissue are well characterized, less is known about the mechanical behavior of individual collagen fibrils. In this study, bovine pericardium is subjected to strain while small angle X-ray scattering (SAXS) patterns are recorded using synchrotron radiation. The change in d-spacing, which is a measure of fibril extension, and the change in fibril diameter are determined from SAXS. The tissue is strained 0.25 (25%) with a corresponding strain in the collagen fibrils of 0.045 observed. The ratio of collagen fibril width contraction to length extension, or the Poisson's ratio, is 2.1 ± 0.7 for a tissue strain from 0 to 0.25. This Poisson's ratio indicates that the volume of individual collagen fibrils decreases with increasing strain, which is quite unlike most engineering materials. This high Poisson's ratio of individual fibrils may contribute to high Poisson's ratio observed for tissues, contributing to some of the remarkable properties of collagen-based materials.

  8. Temperature Assisted in-Situ Small Angle X-ray Scattering Analysis of Ph-POSS/PC Polymer Nanocomposite

    PubMed Central

    Yadav, Ramdayal; Naebe, Minoo; Wang, Xungai; Kandasubramanian, Balasubramanian

    2016-01-01

    Inorganic/organic nanofillers have been extensively exploited to impart thermal stability to polymer nanocomposite via various strategies that can endure structural changes when exposed a wide range of thermal environment during their application. In this abstraction, we have utilized temperature assisted in-situ small angle X-ray scattering (SAXS) to examine the structural orientation distribution of inorganic/organic nanofiller octa phenyl substituted polyhedral oligomeric silsesquioxane (Ph-POSS) in Polycarbonate (PC) matrix from ambient temperature to 180 °C. A constant interval of 30 °C with the heating rate of 3 °C/min was utilized to guise the temperature below and above the glass transition temperature of PC followed by thermal gravimetric, HRTEM, FESEM and hydrophobic analysis at ambient temperature. The HRTEM images of Ph-POSS nano unit demonstrated hyperrectangular structure, while FESEM image of the developed nano composite rendered separated phase containing flocculated and overlapped stacking of POSS units in the PC matrix. The phase separation in polymer nanocomposite was further substantiated by thermodynamic interaction parameter (χ) and mixing energy (Emix) gleaned via Accelrys Materials studio. The SAXS spectra has demonstrated duplex peak at higher scattering vector region, postulated as a primary and secondary segregated POSS domain and followed by abundance of secondary peak with temperature augmentation. PMID:27436152

  9. Small Angle X-ray and Neutron Scattering: Powerful Tools for Studying the Structure of Drug-Loaded Liposomes

    PubMed Central

    Di Cola, Emanuela; Grillo, Isabelle; Ristori, Sandra

    2016-01-01

    Nanovectors, such as liposomes, micelles and lipid nanoparticles, are recognized as efficient platforms for delivering therapeutic agents, especially those with low solubility in water. Besides being safe and non-toxic, drug carriers with improved performance should meet the requirements of (i) appropriate size and shape and (ii) cargo upload/release with unmodified properties. Structural issues are of primary importance to control the mechanism of action of loaded vectors. Overall properties, such as mean diameter and surface charge, can be obtained using bench instruments (Dynamic Light Scattering and Zeta potential). However, techniques with higher space and time resolution are needed for in-depth structural characterization. Small-angle X-ray (SAXS) and neutron (SANS) scattering techniques provide information at the nanoscale and have therefore been largely used to investigate nanovectors loaded with drugs or other biologically relevant molecules. Here we revise recent applications of these complementary scattering techniques in the field of drug delivery in pharmaceutics and medicine with a focus to liposomal carriers. In particular, we highlight those aspects that can be more commonly accessed by the interested users. PMID:27043614

  10. Small angle X-ray scattering studies of CTNNBL1 dimerization and CTNNBL1/CDC5L complex

    PubMed Central

    Ahn, Jae-Woo; Sik Jin, Kyeong; Francis Son, Hyeoncheol; Ho Chang, Jeong; Kim, Kyung-Jin

    2015-01-01

    The hPrp19/CDC5L complex is a non-snRNP spliceosome complex that plays a key role in the spliceosome activation during pre-mRNA splicing, and CTNNBL1 and CDC5L are essential components of the complex. In this study, to investigate the oligomeric state of CTNNBL1 in solution, we performed small angle X-ray scattering experiments in various concentrations of NaCl. We observed that CTNNBL1 existed as a dimer in physiological NaCl concentrations. Site-directed mutagenesis experiment of CTNNBL1 confirmed that N-terminal capping region and the first four ARM repeats are important for dimerization of the protein. We also found that the positively-charged NLS3-containing region (residues 197–235) of CDC5L bound to the negatively-charged patch of CTNNBL1 and that the CTNNBL1/CDC5L complex formed a heterotetramer consisting of one CTNNBL1 dimer and one CDC5L dimer. Moreover, reconstruction of 3D models of CTNNBL1/CDC5L complexes containing CTNNBL1 and three different truncated forms of CDC5L showed that the CDC5L141–196 region and the CDC5L236–377 region were positioned at the top of the N-terminal capping region and at the bottom of ARM VII of CTNNBL1, respectively. PMID:26381213

  11. Thermal quenching sample chamber for grazing incidence small angle x-ray scattering studies of polymer films.

    PubMed

    Singh, M A; Groves, M N; Müller, M S; Stahlbrand, I J; Smilgies, D-M

    2007-11-01

    The second generation of a sample chamber designed for in situ measurement of temperature- and time-dependent polymer film nanostructure using the method of grazing incidence small angle x-ray scattering is presented. An increased operating temperature limit (from 260 to 400 degrees C) with precise control (+/-0.1 degrees C) at fixed temperatures as well as a fourfold increase in maximum instantaneous cooling rate (up to 73 degrees C/s) relative to the first generation chamber [M. N. Groves et al, J. Appl. Crystallogr. 39, 120 (2006)] are reported. Thermal quenches from 220 to 90 degrees C are shown to be reproducible to within +/-1 degrees C of the final temperature. Experimental tests on spin-coated films of symmetric diblock styrene-butadiene copolymer demonstrate the ability to resolve the kinetics of orientation of lamellar domains parallel to the silicon substrate, distinct from the initial formation of randomly oriented lamellar domains immediately following the thermal quench. PMID:18052491

  12. Thermal quenching sample chamber for grazing incidence small angle x-ray scattering studies of polymer films

    NASA Astrophysics Data System (ADS)

    Singh, M. A.; Groves, M. N.; Müller, M. S.; Stahlbrand, I. J.; Smilgies, D.-M.

    2007-11-01

    The second generation of a sample chamber designed for in situ measurement of temperature- and time-dependent polymer film nanostructure using the method of grazing incidence small angle x-ray scattering is presented. An increased operating temperature limit (from 260to400°C) with precise control (±0.1°C) at fixed temperatures as well as a fourfold increase in maximum instantaneous cooling rate (up to 73°C/s) relative to the first generation chamber [M. N. Groves et al, J. Appl. Crystallogr. 39, 120 (2006)] are reported. Thermal quenches from 220to90°C are shown to be reproducible to within ±1°C of the final temperature. Experimental tests on spin-coated films of symmetric diblock styrene-butadiene copolymer demonstrate the ability to resolve the kinetics of orientation of lamellar domains parallel to the silicon substrate, distinct from the initial formation of randomly oriented lamellar domains immediately following the thermal quench.

  13. Aluminum Nitride Grown by Atomic Layer Epitaxy Characterized with Real-Time Grazing Incidence Small Angle X-ray Scattering

    NASA Astrophysics Data System (ADS)

    Anderson, Virginia; Nepal, Neeraj; Johnson, Scooter; Robinson, Zachary; Demasi, Alexander; Hite, Jennifer; Ludwig, Karl; Eddy, Charles

    Aluminum nitride, gallium nitride, and indium nitride are being considered for many applications, and are currently being used commercially for LEDs. These III-nitride films are conventionally deposited by metalorganic chemical vapor deposition and molecular beam epitaxy. Research into depositing III-nitrides with atomic layer epitaxy (ALE) is underway as it is a fabrication friendly technique for thin films at lower temperatures. AlN deposited with ALE at 500°C have been shown to have good crystallinity, but relatively high carbon and oxygen impurities, and understanding the film deposition mechanism is an ongoing project. Grazing incidence small angle x-ray scattering (GISAXS) is sensitive to surface features, making it useful for real time monitoring of deposition processes. AlN was monitored by GISAXS while being deposited with ALE using trimethylaluminum and hydrogen/nitrogen plasma at the Brookhaven National Synchrotron Light Source and the Cornell High Energy Synchrotron Source. The GISAXS of AlN ALE at nominally 400°C, 450°C, and 500°C was compared to ex situ characterization with XPS and AFM.

  14. Morphology of Photopolymerized End-linked Poly(ethylene glycol) Hydrogels by Small Angle X-ray Scattering

    PubMed Central

    Waters, Dale J.; Engberg, Kristin; Parke-Houben, Rachel; Hartmann, Laura; Ta, Christopher N.; Toney, Michael F.; Frank, Curtis W.

    2010-01-01

    Due to the biocompatibility of poly(ethylene glycol) (PEG), PEG-based hydrogels have attracted considerable interest for use as biomaterials in tissue engineering applications. In this work, we show that PEG-based hydrogels prepared by photopolymerization of PEG macromonomers functionalized with either acrylate or acrylamide end-groups generate networks with crosslink junctions of high functionality. Although the crosslink functionality is not well controlled, the resultant networks are sufficiently well ordered to generate a distinct correlation peak in the small angle x-ray scattering (SAXS) related to the distance between crosslink junctions within the PEG network. The crosslink spacing is a useful probe of the PEG chain conformation within the hydrogel and ranges from approximately 6 to 16 nm, dependent upon both the volume fraction of polymer and the molecular weight of the PEG macromonomers. The presence of a peak in the scattering of photopolymerized PEG networks is also correlated with an enhanced compressive modulus in comparison to PEG networks reported in the literature with much lower crosslink functionality that exhibit no scattering peak. This comparison demonstrates that the method used to link together PEG macromonomers has a critical impact on both the nanoscale structure and the macroscopic properties of the resultant hydrogel network. PMID:21403767

  15. Local structure of Ca(2+) induced hydrogels of alginate-oligoguluronate blends determined by small-angle-X-ray scattering.

    PubMed

    Yuguchi, Yoshiaki; Hasegawa, Ami; Padoł, Anna Maria; Draget, Kurt Ingar; Stokke, Bjørn Torger

    2016-11-01

    Short oligoguluronates, oligoG's, are reported to affect the ionotropic gelation of alginates both with respect to altered gelation kinetics and elastic properties of the resulting gels. The local structure of Ca(2+) induced changes in oligoguluronates and blends of oligoguluronates and alginates was determined by small angle X-ray scattering (SAXS). Calcium was introduced in the aqueous polysaccharide solutions by in situ release of Ca(2+) from Ca-EGTA. The scattering profiles of the Ca(2+)-induced structures in the alginate-oligoG blends were accounted for by a two-component broken rod-like model, also with an additional term representing structural inhomogeneity by a Debye-Bueche term. Adding oligoG to the alginate yields an increase in the largest cross-sectional radius in the region of fractional Ca(2+) saturation of α-l-GulA units from 0.5 to 1. The time-lapse characterization during the Ca-induced changes in the alginate-oligoG blends shows that oligoG delays the emergence of the more extensive laterally aggregated junction zones. PMID:27516301

  16. Monitoring simultaneously the growth of nanoparticles and aggregates by in situ ultra-small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Kammler, Hendrik K.; Beaucage, Gregory; Kohls, Douglas J.; Agashe, Nikhil; Ilavsky, Jan

    2005-03-01

    Ultra-small-angle x-ray scattering can provide information about primary particles and aggregates from a single scattering experiment. This technique is applied in situ to flame aerosol reactors for monitoring simultaneously the primary particle and aggregate growth dynamics of oxide nanoparticles in a flame. This was enabled through the use of a third generation synchrotron source (Advanced Photon Source, Argonne IL, USA) using specialized scattering instrumentation at the UNICAT facility which is capable of simultaneously measuring nanoscales to microscales (1nmto1μm). More specifically, the evolution of primary-particle diameter, mass-fractal dimension, geometric standard deviation, silica volume fraction, number concentration, radius of gyration of the aggregate, and number of primary particles per aggregate are measured along the flame axis for two different premixed flames. All these particle characteristics were derived from a single and nonintrusive measurement technique. Flame temperature profiles were measured in the presence of particles by in situ Fourier transform infrared spectroscopy and thermophoretic sampling was used to visualize particle growth with height above the burner as well as in the radial direction.

  17. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

    PubMed Central

    Boldon, Lauren; Laliberte, Fallon; Liu, Li

    2015-01-01

    In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques. PMID:25721341

  18. Early aggregation preceding the nucleation of insulin amyloid fibrils as monitored by small angle X-ray scattering

    PubMed Central

    Chatani, Eri; Inoue, Rintaro; Imamura, Hiroshi; Sugiyama, Masaaki; Kato, Minoru; Yamamoto, Masahide; Nishida, Koji; Kanaya, Toshiji

    2015-01-01

    The nucleation event of amyloid fibrils is one of the most crucial processes that dictate the timing and rate of the pathology of diseases; however, information regarding how protein molecules associate to produce fibril nuclei is currently limited. In order to explore this issue in more detail, we performed time-resolved small angle X-ray scattering (SAXS) measurements on insulin fibrillation, in combination with additional multidirectional analyses of thioflavin T fluorescence, FTIR spectroscopy, light scattering, and light transmittance, during the fibrillation process of bovine insulin. SAXS monitoring revealed that insulin molecules associated into rod-like prefibrillar aggregates in the very early stage of the reaction. After the formation of these early aggregates, they appeared to further coalesce mutually to form larger clusters, and the SAXS profiles subsequently showed the further time evolution of conformational development towards mature amyloid fibrils. Distinct types of structural units in terms of shape in a nano-scale order, cross-β content, and thioflavin T fluorescence intensity were observed in a manner that was dependent on the fibrillation pathways. These results suggest the presence of diverse substructures that characterize various fibrillation pathways, and eventually, manifest polymorphisms in mature amyloid fibrils. PMID:26503463

  19. Structure of diglycerol monomyristate reverse micelles in styrene: a small-angle X-ray scattering (SAXS) study.

    PubMed

    Shrestha, Lok Kumar; Shrestha, Rekha Goswami; Aramaki, Kenji; Ariga, Katsuhiko

    2011-08-01

    Structure of diglycerol monomyristate (designated as C14G2) nonionic surfactant reverse micelles in aromatic solvent styrene has been investigated as a function of surfactant concentration, temperature, and water addition by using small-angle X-ray scattering (SAXS) technique. Structure of micelles in real-space so called pair-distance distribution function, p(r), was obtained by the generalized indirect fourier transformation (GIFT) evaluation of SAXS data. It was found that C14G2 spontaneously self-assembles into spheroid reverse micelles with maximum diameter approximately 3.0 nm when added into styrene under ambient condition. The micellar shape and size remained essentially the same despite a wide variation in surfactant concentration (5 to 30%) but an opposite trend was observed with the rise of temperature; size decreased by approximately 25% with increase in temperature from 25 to 75 degrees C. Addition of traces water favored micellar growth and eventually ellipsoid prolate type micelles were formed, whose scenario is understood in terms of decrease in the critical packing parameter (cpp); water hydrates the surfactant's headgroup and decreases cpp. At a particular concentration of water, increasing temperature decreased the micellar size due to dehydration of headgroup. It is interesting to note that size of 1.57% water incorporated micelle is approximately 2.5 times bigger than the empty micelles. PMID:22103110

  20. Distribution of Sulfur in Carbon/Sulfur Nanocomposites Analyzed by Small-Angle X-ray Scattering.

    PubMed

    Petzold, Albrecht; Juhl, Anika; Scholz, Jonas; Ufer, Boris; Goerigk, Günter; Fröba, Michael; Ballauff, Matthias; Mascotto, Simone

    2016-03-22

    The analysis of sulfur distribution in porous carbon/sulfur nanocomposites using small-angle X-ray scattering (SAXS) is presented. Ordered porous CMK-8 carbon was used as the host matrix and gradually filled with sulfur (20-50 wt %) via melt impregnation. Owing to the almost complete match between the electron densities of carbon and sulfur, the porous nanocomposites present in essence a two-phase system and the filling of the host material can be precisely followed by this method. The absolute scattering intensities normalized per unit of mass were corrected accounting for the scattering contribution of the turbostratic microstructure of carbon and amorphous sulfur. The analysis using the Porod parameter and the chord-length distribution (CLD) approach determined the specific surface areas and filling mechanism of the nanocomposite materials, respectively. Thus, SAXS provides comprehensive characterization of the sulfur distribution in porous carbon and valuable information for a deeper understanding of cathode materials of lithium-sulfur batteries. PMID:26915534

  1. Small angle X-ray scattering coupled with in situ electromechanical probing of nanoparticle-based resistive strain gauges.

    PubMed

    Decorde, Nicolas; Sangeetha, Neralagatta M; Viallet, Benoit; Viau, Guillaume; Grisolia, Jérémie; Coati, Alessandro; Vlad, Alina; Garreau, Yves; Ressier, Laurence

    2014-12-21

    A comprehensive study on the electromechanical behavior of nanoparticle-based resistive strain gauges in action through normal and grazing incidence small angle X-ray scattering (SAXS/GISAXS) investigations is presented. The strain gauges were fabricated from arrays of colloidal gold nanoparticle (NP) wires assembled on flexible polyethylene terephthalate and polyimide substrates by convective self-assembly. Microstructural changes (mean interparticle distance variations) within these NP wires under uniaxial stretching estimated by SAXS/GISAXS are correlated to their macroscopic electrical resistance variations. SAXS measurements suggest a linear longitudinal extension and transversal contraction of the NP wires with applied strain (0 to ∼ 13%). The slope of this longitudinal variation is less than unity, implying a partial strain transfer from the substrate to the NP wires. The simultaneously measured electrical resistance of the strain gauges shows an exponential variation within the elastic domain of the substrate deformation, consistent with electron tunnelling through the interparticle gaps. A slower variation observed within the plastic domain suggests the formation of new electronic conduction pathways. Implications of transversal contraction of the NP wires on the directional sensitivities of strain gauges are evaluated by simulating electronic conduction in models mimicking a realistic NP arrangement. A loss of directionality of the NP-based strain gauges due to transversal current flow within the NP wires is deduced. PMID:25371292

  2. Subsecond Morphological Changes in Nafion during Water Uptake Detected by Small-Angle X-ray Scattering

    SciTech Connect

    Kusoglu, Ahmet; Modestino, Miguel A.; Hexemer, Alexander; Segalman, Rachel A.; Weber, Adam Z.

    2011-11-09

    The ability of the Nafion membrane to absorb water rapidly and create a network of hydrated interconnected water domains provides this material with an unmatched ability to conduct ions through a chemically and mechanically robust membrane. The morphology and composition of these hydrated membranes significantly affects their transport properties and performance. This research demonstrates that differences in interfacial interactions between the membranes exposed to vapor or liquid water can cause significant changes in kinetics of water uptake. In situ small-angle X-ray scattering (SAXS) experiments captured the rapid swelling of the membrane in liquid water with a nanostructure rearrangement on the order of seconds. For membranes in contact with water vapor, morphological changes are four orders-of-magnitude slower than in liquid water, suggesting that interfacial resistance limits the penetration of water into the membrane. Furthermore, upon water absorption from liquid water, a structural rearrangement from a distribution of spherical and cylindrical domains to exclusively cylindrical-like domains is suggested. These differences in water-uptake kinetics and morphology provide a new perspective into Schroeder's paradox, which dictates a different water content for vapor- and liquid-equilibrated ionomers at unit activity. Lastly, the findings of this work provide critical insights into the fast kinetics of water absorption of the Nafion membrane, which can aid in the design of energy conversion devices that operate under frequent changes in environmental conditions.

  3. Small-angle neutron and X-ray scattering from amphiphilic stimuli-responsive diamond-type bicontinuous cubic phase.

    PubMed

    Angelov, Borislav; Angelova, Angelina; Garamus, Vasil M; Lebas, Geneviève; Lesieur, Sylviane; Ollivon, Michel; Funari, Sérgio S; Willumeit, Regine; Couvreur, Patrick

    2007-11-01

    The structural evolution of a diamond-type bicontinuous lipid cubic phase upon application of thermal and chemical (hydration agent) stimuli is investigated by means of small-angle neutron (SANS) and X-ray scattering (SAXS). The soft-matter cubic architecture responds by dramatic swelling (DLarge cubic structure) upon incorporation of a hydration-enhancing guest component (octyl glucoside) at low and ambient temperatures, the aqueous channel diameter increasing twice to approximately 7 nm. DLarge appears to be built up from an assembly of cubosomic domains, which may coexist with an amphiphilic lamellae domain at low temperatures. The chemical stimulus concentration can be selected as to tune the hydration of the nanochannels in the DLarge phase and its transformation into a DNormal phase at temperatures above the body temperature. Two-dimensional SANS images recorded upon heating scan reveal growth of spontaneously oriented domains of single-crystal cubic nature. Phase separation and squeezing out the guest-hydrating agent from the higher-curvature regions of the amphiphilic bilayer suggest a possible mechanism for the established transformations. The order-order structural transition, cubic DLarge-cubic DNormal, is found to be reversible upon cooling. The obtained results put forward a structure-based concept for release of encapsulated guest molecules from stimuli-responsive and self-regulated cubosomic nanocarriers. PMID:17929809

  4. Early aggregation preceding the nucleation of insulin amyloid fibrils as monitored by small angle X-ray scattering.

    PubMed

    Chatani, Eri; Inoue, Rintaro; Imamura, Hiroshi; Sugiyama, Masaaki; Kato, Minoru; Yamamoto, Masahide; Nishida, Koji; Kanaya, Toshiji

    2015-01-01

    The nucleation event of amyloid fibrils is one of the most crucial processes that dictate the timing and rate of the pathology of diseases; however, information regarding how protein molecules associate to produce fibril nuclei is currently limited. In order to explore this issue in more detail, we performed time-resolved small angle X-ray scattering (SAXS) measurements on insulin fibrillation, in combination with additional multidirectional analyses of thioflavin T fluorescence, FTIR spectroscopy, light scattering, and light transmittance, during the fibrillation process of bovine insulin. SAXS monitoring revealed that insulin molecules associated into rod-like prefibrillar aggregates in the very early stage of the reaction. After the formation of these early aggregates, they appeared to further coalesce mutually to form larger clusters, and the SAXS profiles subsequently showed the further time evolution of conformational development towards mature amyloid fibrils. Distinct types of structural units in terms of shape in a nano-scale order, cross-β content, and thioflavin T fluorescence intensity were observed in a manner that was dependent on the fibrillation pathways. These results suggest the presence of diverse substructures that characterize various fibrillation pathways, and eventually, manifest polymorphisms in mature amyloid fibrils. PMID:26503463

  5. Probing Anisotropic Structure Changes in Proteins with Picosecond Time-Resolved Small Angle X-ray Scattering

    PubMed Central

    Cho, Hyun Sun; Schotte, Friedrich; Dashdorj, Naranbaatar; Kyndt, John; Anfinrud, Philip A.

    2014-01-01

    We have exploited the principle of photoselection and the method of time-resolved Small Angle X-ray Scattering (SAXS) to investigate protein size and shape changes following photoactivation of photoactive yellow protein (PYP) in solution with ~150 ps time resolution. This study partially overcomes the orientational average intrinsic to solution scattering methods, and provides structural information at a higher level of detail. Photoactivation of the p-coumaric acid (pCA) chromophore in PYP produces a highly-contorted, short-lived, red shifted intermediate (pR0), and triggers prompt, protein compaction of approximately 0.3% along the direction defined by the electronic transition dipole moment of the chromophore. Contraction along this dimension is accompanied by expansion along the orthogonal directions, with the net protein volume change being approximately -0.25%. More than half the strain arising from formation of pR0 is relieved by the pR0 to pR1 structure transition (1.8 ± 0.2 ns), with the persistent strain presumably contributing to the driving force needed to generate the spectroscopically blue-shifted pB signaling state. The results reported here are consistent with the near-atomic resolution structural dynamics reported in a recent time-resolved Laue crystallography study of PYP crystals, and suggest that the early-time structural dynamics in the crystalline state carry over to proteins in solution. PMID:24125473

  6. Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis

    SciTech Connect

    Baird, Nathan J.; Ferré-D'Amaré, Adrian R.

    2010-05-25

    Riboswitches are structured mRNA elements that regulate gene expression upon binding specific cellular metabolites. It is thought that the highly conserved metabolite-binding domains of riboswitches undergo conformational change upon binding their cognate ligands. To investigate the generality of such a mechanism, we employed small-angle X-ray scattering (SAXS). We probed the nature of the global metabolite-induced response of the metabolite-binding domains of four different riboswitches that bind, respectively, thiamine pyrophosphate (TPP), flavin mononucleotide (FMN), lysine, and S-adenosyl methionine (SAM). We find that each RNA is unique in its global structural response to metabolite. Whereas some RNAs exhibit distinct free and bound conformations, others are globally insensitive to the presence of metabolite. Thus, a global conformational change of the metabolite-binding domain is not a requirement for riboswitch function. It is possible that the range of behaviors observed by SAXS, rather than being a biophysical idiosyncrasy, reflects adaptation of riboswitches to the regulatory requirements of their individual genomic context.

  7. Colloidal Nanoparticle Interaction Transition during Solvent Evaporation Investigated by in-Situ Small-Angle X-ray Scattering.

    PubMed

    Bahadur, J; Sen, D; Mazumder, S; Santoro, G; Yu, S; Roth, S V; Melnichenko, Y B

    2015-04-28

    In-situ scanning small-angle X-ray scattering (SAXS) experiments have been performed to probe the drying of a single suspended droplet of silica colloids. It has been demonstrated that the formation of a nanoparticle shell during drying can be confirmed just by measuring the temporal evolution of the spatial transmission profile across the drying droplet. The shrinkage of the droplet stops once the shell is formed. The temporal dependence of the shell thickness and droplet radius has been estimated by quantitative analysis of the functionality of the transmission profiles. It is revealed that the position of the correlation peak originating from interactions between silica nanoparticles evolves linearly during the initial stage of drying and exhibits sigmoidal growth behavior in later stages. The interaction between colloidal particles in different drying stages has been investigated. We provide experimental confirmation of the transition from repulsive interaction to a capillary-driven short-range attraction during shell formation. The present work demonstrates that in-situ scanning SAXS on a suspended droplet is an invaluable technique for monitoring the dynamic self-organization of colloids as it probes the drying of complex fluids without the interference of a substrate. PMID:25839830

  8. Characterizing dispersion and fragmentation of fractal, pyrogenic silica nanoagglomerates by small-angle X-ray scattering.

    PubMed

    Wengeler, R; Wolf, F; Dingenouts, N; Nirschl, H

    2007-04-10

    Typical characterization of nanoparticle dispersion and compounding processes by dynamic light scattering (DLS) and TEM lack quantitative information on fractal structure, aggregation number, and specific surface area. In this work a synchrotron ultra-small-angle X-ray scattering (USAXS) investigation on diffusion flame and 'Aerosil' silica powders, as well as on their desagglomeration by high-pressure liquid dispersion (200-1400 bar) is presented. Primary particle size, polydispersity, and specific surface area are measured for powders, stirred-in dispersions, and after high-pressure processing with identical results, showing the in-situ applicability of USAXS. These parameters, as well as the hard aggregate mass fractal dimension, with typically Df = 2.15 representing reaction-limited cluster aggregation, are determined by synthesis process conditions. They are unchanged even at the highest hydrodynamic stresses; thus, neither comminution nor agglomerate restructuring nor re-agglomeration occurs. Fragmentation reflects in decreasing radii of gyration, which are compared to mobility equivalent radii from DLS in agreement with theory. PMID:17371058

  9. Asymmetric grazing incidence small angle x-ray scattering and anisotropic domain wall motion in obliquely grown nanocrystalline Co films.

    PubMed

    Quirós, C; Peverini, L; Díaz, J; Alija, A; Blanco, C; Vélez, M; Robach, O; Ziegler, E; Alameda, J M

    2014-08-22

    Strong asymmetries have been observed in grazing incidence small angle x-ray scattering (GISAXS) in situ patterns obtained from 30 nm-thick nanocrystalline Co films prepared by oblique sputtering (15°-75° off-sample normal). These asymmetries have been qualitatively simulated by a simple model consisting of an ensemble of 8 nm-wide inclined Co nanocolumns. It is found that narrow inclined features appear in the diffuse background resembling those characteristic of faceted systems, which can be used to obtain straightforward non-destructive estimations of buried nanocolumnar grains inclination, even for oblique angles below 45°, when the stronger and broader asymmetric features of the pattern are not yet fully formed. Furthermore, using magneto-optical microscopy, a marked change in the magnetic domain's nucleation and growth process has been observed in the sample prepared at 75°, with the stronger GISAXS asymmetries. Easy axis magnetization reversal starts by a random and homogeneous nucleation of small (∼μm) elongated domains aligned with the nanocolumn's long axis and proceeds through the preferred propagation of head-to-head domain walls (DWs) along the applied field direction. This peculiar magnetic behavior indicates that the strongly anisotropic nanostructuring created by the oblique growth process is equivalent, from a magnetic point of view, to an array of self-assembled buried nanowires. These results show how GISAXS and magneto-optical microscopy can be combined as a powerful tool for correlating the morphology and magnetism of thin nanostructured systems. PMID:25074483

  10. Small angle x-ray diffraction through living muscle links the lattice structure to macroscopic material properties

    NASA Astrophysics Data System (ADS)

    Tune, Travis; Irving, Tom; Sponberg, Simon

    Muscle is a unique hierarchical material composed of millions of molecular motors arranged on filaments in a regular lattice structure. The macroscopic, material behavior of muscle can be characterized by its workloop, a periodically activated force-length curve. Muscle is capable of operating as a spring, motor, brake, or strut, defined by its workloop. We are interested in the multiscale physics of muscle that drive its ``energetic versatility'' - the ability of muscle to alter its function. Here we introduce a system of two muscles from the cockroach whose workloops are not explained by our current understanding of the determinants of workloop function (the classic force-length, force-velocity, and twitch response). Differences in material behavior may arise from structural differences in the muscle's active lattice. Using the BIOCat beam at the Advanced Photon Source at Argonne NL, we tested for differences in the two muscles' lattice structure. Small-angle x-ray scattering (SAXS) revealed a difference of 4-8

  11. Small Angle X-ray and Neutron Scattering: Powerful Tools for Studying the Structure of Drug-Loaded Liposomes.

    PubMed

    Di Cola, Emanuela; Grillo, Isabelle; Ristori, Sandra

    2016-01-01

    Nanovectors, such as liposomes, micelles and lipid nanoparticles, are recognized as efficient platforms for delivering therapeutic agents, especially those with low solubility in water. Besides being safe and non-toxic, drug carriers with improved performance should meet the requirements of (i) appropriate size and shape and (ii) cargo upload/release with unmodified properties. Structural issues are of primary importance to control the mechanism of action of loaded vectors. Overall properties, such as mean diameter and surface charge, can be obtained using bench instruments (Dynamic Light Scattering and Zeta potential). However, techniques with higher space and time resolution are needed for in-depth structural characterization. Small-angle X-ray (SAXS) and neutron (SANS) scattering techniques provide information at the nanoscale and have therefore been largely used to investigate nanovectors loaded with drugs or other biologically relevant molecules. Here we revise recent applications of these complementary scattering techniques in the field of drug delivery in pharmaceutics and medicine with a focus to liposomal carriers. In particular, we highlight those aspects that can be more commonly accessed by the interested users. PMID:27043614

  12. Poisson's ratio of collagen fibrils measured by small angle X-ray scattering of strained bovine pericardium

    NASA Astrophysics Data System (ADS)

    Wells, Hannah C.; Sizeland, Katie H.; Kayed, Hanan R.; Kirby, Nigel; Hawley, Adrian; Mudie, Stephen T.; Haverkamp, Richard G.

    2015-01-01

    Type I collagen is the main structural component of skin, tendons, and skin products, such as leather. Understanding the mechanical performance of collagen fibrils is important for understanding the mechanical performance of the tissues that they make up, while the mechanical properties of bulk tissue are well characterized, less is known about the mechanical behavior of individual collagen fibrils. In this study, bovine pericardium is subjected to strain while small angle X-ray scattering (SAXS) patterns are recorded using synchrotron radiation. The change in d-spacing, which is a measure of fibril extension, and the change in fibril diameter are determined from SAXS. The tissue is strained 0.25 (25%) with a corresponding strain in the collagen fibrils of 0.045 observed. The ratio of collagen fibril width contraction to length extension, or the Poisson's ratio, is 2.1 ± 0.7 for a tissue strain from 0 to 0.25. This Poisson's ratio indicates that the volume of individual collagen fibrils decreases with increasing strain, which is quite unlike most engineering materials. This high Poisson's ratio of individual fibrils may contribute to high Poisson's ratio observed for tissues, contributing to some of the remarkable properties of collagen-based materials.

  13. Mass-fractal growth in niobia/silsesquioxane mixtures: a small-angle X-ray scattering study

    PubMed Central

    Besselink, Rogier; ten Elshof, Johan E.

    2014-01-01

    The nucleation and growth of niobium pentaethoxide (NPE)-derived clusters in ethanol, through acid-catalyzed hydrolysis/condensation in the presence and absence of the silsesquioxane 1,2-bis(triethoxysilyl)ethane (BTESE), was monitored at 298–333 K by small-angle X-ray scattering. The data were analyzed with a newly derived model for polydisperse mass-fractal-like structures. At 298–313 K in the absence of BTESE the data indicated the development of relatively monodisperse NPE-derived structures with self-preserving polydispersity during growth. The growth exponent was consistent with irreversible diffusion-limited cluster agglomeration. At 333 K the growth exponent was characteristic for fast-gelling reaction-limited cluster agglomeration. The reaction yielded substantially higher degrees of polydispersity. In the presence of BTESE the growth exponents were substantially smaller. The smaller growth exponent in this case is not consistent with irreversible Smoluchowski-type agglomeration. Instead, reversible Lifshitz–Slyozov-type agglomeration seems to be more consistent with the experimental data. PMID:25294980

  14. Measurement of Carbon Condensates Using Small-Angle X-ray Scattering During Detonation of High Explosives

    NASA Astrophysics Data System (ADS)

    Willey, Trevor; Bagge-Hansen, M.; Lauderbach, L.; Hodgin, R.; Bastea, S.; Fried, L.; Jones, A.; Hansen, D.; Benterou, J.; May, C.; van Buuren, T.; Graber, T.; Jensen, B.; Ilavsky, J.

    2015-06-01

    The lack of experimental validation for processes occurring at sub-micron length scales on time scales ranging from nanoseconds to microseconds hinders detonation model development. Particularly, quantification of late-time energy release requires measurement of carbon condensation kinetics behind detonation fronts. A new small-angle x-ray scattering (SAXS) end station has been developed for use at The Dynamic Compression Sector to observe carbon condensation during detonation. We started with hexanitrostilbene (HNS) due to its stability, ease of initiation, vacuum compatibility, and oxygen deficiency. The endstation and beamline demonstrate unprecedented fidelity; the first SAXS data contains a clear Guinier knee and power law slope, giving information about the size and morphology of the resultant carbon nanoparticles. HNS detonation produces particles with an Rg of 2.7 nm in less than 400 ns, and this size is constant over the next several microseconds. This result with HNS differs dramatically compared with previous pioneering work on RDX/TNT and TATB, where observations indicate significant particle growth (>50%) continues over several microseconds. The power-law slope is consistent with sp2 carbon. We have also begun to measure, and will present preliminary results on carbon condensates from Comp B, DNTF, and other explosives.

  15. Temperature Assisted in-Situ Small Angle X-ray Scattering Analysis of Ph-POSS/PC Polymer Nanocomposite

    NASA Astrophysics Data System (ADS)

    Yadav, Ramdayal; Naebe, Minoo; Wang, Xungai; Kandasubramanian, Balasubramanian

    2016-07-01

    Inorganic/organic nanofillers have been extensively exploited to impart thermal stability to polymer nanocomposite via various strategies that can endure structural changes when exposed a wide range of thermal environment during their application. In this abstraction, we have utilized temperature assisted in-situ small angle X-ray scattering (SAXS) to examine the structural orientation distribution of inorganic/organic nanofiller octa phenyl substituted polyhedral oligomeric silsesquioxane (Ph-POSS) in Polycarbonate (PC) matrix from ambient temperature to 180 °C. A constant interval of 30 °C with the heating rate of 3 °C/min was utilized to guise the temperature below and above the glass transition temperature of PC followed by thermal gravimetric, HRTEM, FESEM and hydrophobic analysis at ambient temperature. The HRTEM images of Ph-POSS nano unit demonstrated hyperrectangular structure, while FESEM image of the developed nano composite rendered separated phase containing flocculated and overlapped stacking of POSS units in the PC matrix. The phase separation in polymer nanocomposite was further substantiated by thermodynamic interaction parameter (χ) and mixing energy (Emix) gleaned via Accelrys Materials studio. The SAXS spectra has demonstrated duplex peak at higher scattering vector region, postulated as a primary and secondary segregated POSS domain and followed by abundance of secondary peak with temperature augmentation.

  16. In situ small-angle X-ray scattering analysis of palladium nanoparticle growth on tobacco mosaic virus nanotemplates.

    PubMed

    Manocchi, Amy K; Seifert, Soenke; Lee, Byeongdu; Yi, Hyunmin

    2011-06-01

    We present an examination of palladium (Pd) nanoparticle growth on genetically modified tobacco mosaic virus (TMV1cys) nanotemplates via in situ small-angle X-ray scattering (SAXS). Specifically, we examine the role of the TMV1cys templates in Pd nanoparticle formation through the electroless reduction of Pd precursor by a chemical reducing agent as compared to identical conditions in the absence of the TMV1cys templates. We show that in the presence of TMV1cys, the viral nanotemplates provide preferential growth sites for Pd nanoparticle formation, as no measurable Pd particle growth was observed in the bulk solution. In situ SAXS confirmed that particle formation was due to the rapid adsorption of Pd atoms onto the TMV1cys templates at the very early stage of mixing, rather than adsorption of particles formed in the bulk solution. Importantly, Pd nanoparticles were significantly smaller and more uniform as compared to particle formation in the absence of TMV1cys. The Pd nanoparticle coating density was tunable based on Pd precursor concentration. Finally, we show that Pd particle growth on the TMV1cys templates was highly rapid, and complete within 33 s for most samples, in contrast to slower Pd particle growth in the absence of TMV templates. We envision that the results presented here will be valuable in furthering the fundamental understanding of the role of viral nanotemplates in particle formation, as well as of their utility in a wide range of applications. PMID:21520923

  17. Temperature Assisted in-Situ Small Angle X-ray Scattering Analysis of Ph-POSS/PC Polymer Nanocomposite.

    PubMed

    Yadav, Ramdayal; Naebe, Minoo; Wang, Xungai; Kandasubramanian, Balasubramanian

    2016-01-01

    Inorganic/organic nanofillers have been extensively exploited to impart thermal stability to polymer nanocomposite via various strategies that can endure structural changes when exposed a wide range of thermal environment during their application. In this abstraction, we have utilized temperature assisted in-situ small angle X-ray scattering (SAXS) to examine the structural orientation distribution of inorganic/organic nanofiller octa phenyl substituted polyhedral oligomeric silsesquioxane (Ph-POSS) in Polycarbonate (PC) matrix from ambient temperature to 180 °C. A constant interval of 30 °C with the heating rate of 3 °C/min was utilized to guise the temperature below and above the glass transition temperature of PC followed by thermal gravimetric, HRTEM, FESEM and hydrophobic analysis at ambient temperature. The HRTEM images of Ph-POSS nano unit demonstrated hyperrectangular structure, while FESEM image of the developed nano composite rendered separated phase containing flocculated and overlapped stacking of POSS units in the PC matrix. The phase separation in polymer nanocomposite was further substantiated by thermodynamic interaction parameter (χ) and mixing energy (Emix) gleaned via Accelrys Materials studio. The SAXS spectra has demonstrated duplex peak at higher scattering vector region, postulated as a primary and secondary segregated POSS domain and followed by abundance of secondary peak with temperature augmentation. PMID:27436152

  18. The Structure of Urease Activiation Complexes Examined by Flexibility Analysis, Mutagenesis, and Small-angle X-ray Scattering Approaches

    SciTech Connect

    Quiroz, Soledad; Sukuru, Sai Chetan K.; Hausinger, Robert P.; Kuhn, Leslie A.; Heller, William T

    2008-01-01

    Conformational changes of Klebsiella aerogenes urease apoprotein (UreABC){sub 3} induced upon binding of the UreD and UreF accessory proteins were examined by a combination of flexibility analysis, mutagenesis, and small-angle X-ray scattering (SAXS). ProFlex analysis of urease provided evidence that the major domain of UreB can move in a hinge-like motion to account for prior chemical cross-linking results. Rigidification of the UreB hinge region, accomplished through a G11P mutation, reduced the extent of urease activation, in part by decreasing the nickel content of the mutant enzyme, and by sequestering a portion of the urease apoprotein in a novel activation complex that includes all of the accessory proteins. SAXS analyses of urease, (UreABC-UreD){sub 3}, and (UreABC-UreDF){sub 3} confirm that UreD and UreF bind near UreB at the periphery of the (UreAC){sub 3} structure. This study supports an activation model in which a domain-shifted UreB conformation in (UreABC-UreDF){sub 3} allows CO{sub 2} and nickel ions to gain access to the nascent active site.

  19. Investigation of the solid surface structural inhomogeneities by the 'combined' small-angle X-ray scattering and Hg porosimetry methods

    NASA Astrophysics Data System (ADS)

    Skatkov, L. I.; Cheremskoy, P. G.; Gomozov, V. P.; Bayrachny, B. I.

    1996-08-01

    The surface inhomogeneities, i.e. submicropores of porous solids, were investigated by combination of the small-angle X-ray scattering (SAXS) [1-4] and Hg porosimetry methods [5,6]. An optimal approximation of the submicropore shapes and correlation between the shape and the radius of the pores was obtained. The fractal nature of the investigated structure was shown.

  20. Quantum size effect as evidenced by small-angle X-ray scattering of In{sub 2}O{sub 3} nanoparticles

    SciTech Connect

    Souza, E. C. C.; Rey, J. F. Q.; Muccillo, E. N. S.

    2009-01-29

    Indium oxide nanoparticles were synthesized by a surfactant-free room-temperature soft chemistry route. The medium particle size of the thermally treated gel was evaluated by X-ray diffraction experiments, nitrogen adsorption measurements, transmission electron microscopy observations and small-angle X-ray scattering using synchrotron radiation. The main results show the single-crystalline nature of the prepared nanoparticles with 8 nm in diameter. The photoluminescence emission spectrum at room-temperature shows a broad peak with onset at, approximately, 315 nm as a result of quantum size effect produced by a small population of nanoparticles with average size of about 2.8 nm as revealed by small-angle X-ray scattering.

  1. Lattice strain and damage evolution of 9-12/%Cr ferritic/martensitic steel during in situ tensile test by x-ray diffraction and small angle scattering.

    SciTech Connect

    Pan, X.; Wu, X.; Mo, K.; Chen, X,; Almer, J. D.; Ilavsky, J.; Haeffner, D. R.; Stubbins, J. F.; X-Ray Science Division; Univ. of Illinois

    2010-01-01

    In situ X-ray diffraction and small angle scattering measurements during tensile tests were performed on 9-12% Cr ferritic/martensitic steels. The lattice strains in both particle and matrix phases, along two principal directions, were directly measured. The load transfer between particle and matrix was calculated based on matrix/particle elastic mismatch, matrix plasticity and interface decohesion. In addition, the void or damage evolution during the test was measured using small angle X-ray scattering. By combining stress and void evolution during deformation, the critical interfacial strength for void nucleation was determined, and compared with pre-existing void nucleation criteria. These comparisons show that models overestimate the measured critical strength, and require a larger particle size than measured to match the X-ray observations.

  2. Monomeric Form of Peptidylarginine Deiminase Type I Revealed by X-ray Crystallography and Small-Angle X-ray Scattering.

    PubMed

    Saijo, Shinya; Nagai, Anna; Kinjo, Saya; Mashimo, Ryutaro; Akimoto, Megumi; Kizawa, Kenji; Yabe-Wada, Toshiki; Shimizu, Nobutaka; Takahara, Hidenari; Unno, Masaki

    2016-07-31

    Peptidylarginine deiminase (PAD; EC 3.5.3.15) is a post-translational modification enzyme that catalyzes the conversion of arginine in protein molecules to a citrulline residue in a Ca(2+)-dependent manner. In this study, we determined the structure of an active form of human PAD1 crystallized in the presence of Ca(2+) at 3.2-Å resolution. Although human PAD2 and PAD4 isozymes were previously reported to form a head-to-tail homodimer, it is still unknown whether this quaternary structure is common to other PAD isozymes. The asymmetric unit of the crystal contained two PAD1 molecules; however, the head-to-tail dimeric form was not found. Small-angle X-ray scattering analyses revealed PAD1 to be a monomer in solution, while PAD3 was dimerized with a structure similar to PAD2 and PAD4. PAD1 was apparently different from the crystal structures of PAD2 and PAD4, with an elongated N-terminal loop that appears to prevent the formation of the homodimer. Of interest, the N-terminal loop occupied the substrate binding site of the adjacent PAD1 molecules in the crystal. Deimination of S100A3 peptides in vitro implied that PAD isozymes recognize the quaternary structure of S100A3. The substrate-accessible monomeric structure brought about by the extension of its N terminus may partly account for the highest tolerant substrate recognition of PAD1. This is the first ever report on the molecular structure of PAD1 demonstrating the unique monomeric form of the PAD isozyme. PMID:27393304

  3. Conformation of human IgG subclasses in solution. Small-angle X-ray scattering and hydrodynamic studies.

    PubMed

    Kilár, F; Simon, I; Lakatos, S; Vonderviszt, F; Medgyesi, G A; Závodszky, P

    1985-02-15

    The structure of six human myeloma proteins: IgG1(Bal), IgG2(Klu), IgG3(Bak), IgG3(Het), IgG4(Kov) and IgG4(Pol), was studied in solution using small-angle X-ray scattering and hydrodynamic methods. For IgG1(Bal) and IgG3(Het) the experimental data, including radius of gyration (Rg degree), radii of gyration of the cross-section (Rq1, Rq2), intrinsic viscosity [eta], sedimentation coefficient (S degree 20,w) and molecular mass, were interpreted in terms of structural models based on the Fab and Fc conformations, observed in crystal, by varying the relative positions of the Fab and Fc parts, i.e. their relative angles and distances. The values Rg degree = (6.00 +/- 0.05) nm, S degree 20,w = (6.81 +/- 0.10) S and [eta] = 0.0062 +/- 0.0005 cm3/mg obtained for IgG1(Bal) are compatible with a planar model in which the angle between the Fab arms is about 120 degrees. For IgG3(Het) the following data were obtained: Rg degree = (4.90 +/- 0.05) nm, S degree 20,w = (6.32 +/- 0.01) S and [eta] = (0.0065 +/- 0.0005) cm3/mg. The apparent contradiction between the higher molecular mass and lower Rg degree and S degree 20,w values for IgG3(Het) in comparison to IgG1(Bal) can be resolved by proposing a 'non-planar' (tetrahedral) molecular shape, in which the long hinge peptide is in a folded conformation and the two Fab and Fc parts are in a closely packed arrangement. In this model the angle between the two Fab arms is about 90 degrees, in the average position. The X-ray scattering and hydrodynamic behaviour of the IgG2 and IgG4 types of antibodies appeared to be similar to IgG1(Bal). The parameters of the two IgG3 proteins are similar while they are different to the others. PMID:3971974

  4. ``Ordered'' structure in dilute solutions of sodium polystyrenesulfonates as studied by small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Ise, Norio; Okubo, Tsuneo; Kunugi, Shigeru; Matsuoka, Hideki; Yamamoto, K.; Ishii, Yasuo

    1984-10-01

    The small angle x-ray scattering measurements were performed for aqueous solutions of sodium polystyrenesulfonates having relatively narrow molecular weight distributions. As was observed for other synthetic macroions, polynucleotide and proteins, a single, broad peak was observed. The scattering vector at the peak position (Sm) was shifted toward larger values with increasing polymer concentration and toward lower values with increasing salt concentration, which confirmed earlier observations with polyacrylate and poly-L-lysine. The molecular weight dependence of the scattering behavior, which was earlier observed, was confirmed to be true for samples with Mw of 74 000, 18 000, and 4600. The mixture of two fractions with different Mw's gave a scattering curve which was again different from the composite curve obtained with the parent curves before mixing. A similar situation was observed for the mixture of polystyrenesulfonate and polyacrylate. Thus, it was concluded that the observed single peak indicates the presence of an intermolecular ordering, not an intramolecular ordering. The intermacroion distance (2Dexp) was thus calculated by using the Bragg equation. 2Dexp decreased with increasing polymer concentration and increased (not decreased) with increasing concentration of added salt and Mw. The 2Dexp values thus obtained were smaller beyond the experimental error than 2D0, a theoretical distance calculated from the concentration by assuming the uniform distribution of the macroions throughout the solution and the 2D0/2Dexp value amounted to 3.5 for high molecular weight samples. This fact indicates the presence of an intermacroion attractive interaction. When two fractions with different Mw's were compared at a given number concentration of macroions, the 2Dexp value for the sample of a larger Mw was smaller than that for the fraction of a smaller Mw. This implies that the attraction must be intensified, though unexpectedly, with increasing valency of the

  5. Small angle X-ray scattering coupled with in situ electromechanical probing of nanoparticle-based resistive strain gauges

    NASA Astrophysics Data System (ADS)

    Decorde, Nicolas; Sangeetha, Neralagatta M.; Viallet, Benoit; Viau, Guillaume; Grisolia, Jérémie; Coati, Alessandro; Vlad, Alina; Garreau, Yves; Ressier, Laurence

    2014-11-01

    A comprehensive study on the electromechanical behavior of nanoparticle-based resistive strain gauges in action through normal and grazing incidence small angle X-ray scattering (SAXS/GISAXS) investigations is presented. The strain gauges were fabricated from arrays of colloidal gold nanoparticle (NP) wires assembled on flexible polyethylene terephthalate and polyimide substrates by convective self-assembly. Microstructural changes (mean interparticle distance variations) within these NP wires under uniaxial stretching estimated by SAXS/GISAXS are correlated to their macroscopic electrical resistance variations. SAXS measurements suggest a linear longitudinal extension and transversal contraction of the NP wires with applied strain (0 to ~13%). The slope of this longitudinal variation is less than unity, implying a partial strain transfer from the substrate to the NP wires. The simultaneously measured electrical resistance of the strain gauges shows an exponential variation within the elastic domain of the substrate deformation, consistent with electron tunnelling through the interparticle gaps. A slower variation observed within the plastic domain suggests the formation of new electronic conduction pathways. Implications of transversal contraction of the NP wires on the directional sensitivities of strain gauges are evaluated by simulating electronic conduction in models mimicking a realistic NP arrangement. A loss of directionality of the NP-based strain gauges due to transversal current flow within the NP wires is deduced.A comprehensive study on the electromechanical behavior of nanoparticle-based resistive strain gauges in action through normal and grazing incidence small angle X-ray scattering (SAXS/GISAXS) investigations is presented. The strain gauges were fabricated from arrays of colloidal gold nanoparticle (NP) wires assembled on flexible polyethylene terephthalate and polyimide substrates by convective self-assembly. Microstructural changes (mean

  6. Prion Protein—Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering

    PubMed Central

    Carter, Lester; Kim, Seung Joong; Schneidman-Duhovny, Dina; Stöhr, Jan; Poncet-Montange, Guillaume; Weiss, Thomas M.; Tsuruta, Hiro; Prusiner, Stanley B.; Sali, Andrej

    2015-01-01

    Aberrant self-assembly, induced by structural misfolding of the prion proteins, leads to a number of neurodegenerative disorders. In particular, misfolding of the mostly α-helical cellular prion protein (PrPC) into a β-sheet-rich disease-causing isoform (PrPSc) is the key molecular event in the formation of PrPSc aggregates. The molecular mechanisms underlying the PrPC-to-PrPSc conversion and subsequent aggregation remain to be elucidated. However, in persistently prion-infected cell-culture models, it was shown that treatment with monoclonal antibodies against defined regions of the prion protein (PrP) led to the clearing of PrPSc in cultured cells. To gain more insight into this process, we characterized PrP-antibody complexes in solution using a fast protein liquid chromatography coupled with small-angle x-ray scattering (FPLC-SAXS) procedure. High-quality SAXS data were collected for full-length recombinant mouse PrP [denoted recPrP(23–230)] and N-terminally truncated recPrP(89–230), as well as their complexes with each of two Fab fragments (HuM-P and HuM-R1), which recognize N- and C-terminal epitopes of PrP, respectively. In-line measurements by fast protein liquid chromatography coupled with SAXS minimized data artifacts caused by a non-monodispersed sample, allowing structural analysis of PrP alone and in complex with Fab antibodies. The resulting structural models suggest two mechanisms for how these Fabs may prevent the conversion of PrPC into PrPSc. PMID:26287631

  7. Microphase Separation and Shear Alignment of Gradient Copolymers: Melt Rheology and Small-Angle X-Ray Scattering Analysis

    SciTech Connect

    Mok, Michelle M.; Pujari, Saswati; Burghardt, Wesley R.; Dettmer, Christine M.; Nguyen, SonBinh T.; Ellison, Christopher J.; Torkelson, John M.

    2008-10-24

    The degree of microphase or nanophase segregation in gradient copolymers with compositions varying across the whole copolymer backbone is studied via low-amplitude oscillatory shear (LAOS) measurements and small-angle X-ray scattering (SAXS). Studies are done as a function of comonomer segregation strength, molecular weight (MW), gradient architecture and temperature. Controlled radical polymerization is used to synthesize strongly segregating styrene/4-acetoxystyrene (S/AS) and the more weakly segregating S/n-butyl acrylate (S/nBA) gradient copolymers. Results are compared to those from S/AS and S/nBA random and block copolymers. The higher MW S/AS gradient copolymer exhibits LAOS behavior similar to the highly microphase segregated S/AS block copolymer, while the lower MW S/AS gradient copolymer exhibits complex, nonterminal behavior indicative of a lower degree of microphase segregation. The S/nBA gradient copolymers demonstrate more liquidlike behavior, with the lower MW sample exhibiting near-Newtonian behavior, indicative of a weakly segregating structure, while the higher MW, steeper gradient sample shows behavior ranging from solidlike to more liquidlike with increasing temperature. With the exception of the lower MW S/nBA case, the gradient copolymers exhibit temperature-dependent LAOS behavior over a wide temperature range, reflecting their temperature-dependent nanodomain composition amplitudes. The S/AS samples have SAXS results consistent with the degree of microphase segregation observed via rheology. Shear alignment studies are done on the higher MW S/AS gradient copolymer, which is the most highly microphase segregated gradient copolymer. Rheology and SAXS provide evidence of shear alignment, despite the gradual variation in composition profile across the nanodomains of such gradient copolymers. A short review of the nomenclature and behavior of linear copolymer architectures is also provided.

  8. Tertiary and quaternary structural differences between two genetic variants of bovine casein by small-angle X-ray scattering

    SciTech Connect

    Pessen, H.; Kumosinski, T.F.; Farrell, H.M. Jr.; Brumberger, H. )

    1991-01-01

    The casein complexes of bovine milk consist of four major protein fractions, alpha s1, alpha s2, beta, and kappa. Colloidal particles of casein (termed micelles) contain inorganic calcium and phosphate; they are very roughly spherical with an average radius of 650 A. Removal of Ca2+ leads to the formation of smaller protein aggregates with an average radius of 94 A. Two genetic variants, A and B, of the predominant fraction, alpha s1-casein, result in milks with markedly different physical properties, such as solubility and heat stability. To investigate the molecular basis for these differences, small-angle X-ray scattering was performed on the respective colloidal micelles and submicelles. Scattering curves for submicelles of both variants showed multiple Gaussian character; data for the B variant were previously interpreted in terms of two concentric regions of different electron density, i.e., a compact core and a relatively loose shell. For the submicelle of A, there was a third Gaussian, reflecting a negative contribution due to interparticle interference. Molecular parameters for submicelles of both A and B are in agreement with hydrodynamic data in the literature. Data for the micelles, for which scattering yields cross-sectional information, were fitted by a sum of three Gaussians for both variants; for these, the corresponding two lower radii of gyration represent the two concentric regions of the submicelles, while the third reflects the average packing of submicelles within the micellar cross section. Most of the molecular parameters obtained showed small but consistent differences between A and B, but for submicelles within the micelle several differences were particularly notable: A has a greater molecular weight for the compact region of the constituent submicelle (82,000 vs 60,000) and a much greater submicellar packing number.

  9. EXPRESSION, PURIFICATION, AND SMALL ANGLE X-RAY SCATTERING OF DNA REPLICATION AND REPAIR PROTEINS FROM THE HYPERTHERMOPHILE SULFOLOBUS SOLFATARICUS

    SciTech Connect

    Patterson, S.M.; Hatherill, J.R.; Hammel, M.; Hura, G.L.; Tainer, J.A.; Yannone, S.M.

    2008-01-01

    Vital molecular processes such as DNA replication, transcription, translation, and maintenance occur through transient protein interactions. Elucidating the mechanisms by which these protein complexes and interactions function could lead to treatments for diseases related to DNA damage and cell division control. In the recent decades since its introduction as a third domain, Archaea have shown to be simpler models for complicated eukaryotic processes such as DNA replication, repair, transcription, and translation. Sulfolobus solfataricus is one such model organism. A hyperthermophile with an optimal growth temperature of 80°C, Sulfolobus protein-protein complexes and transient protein interactions should be more stable at moderate temperatures, providing a means to isolate and study their structure and function. Here we provide the initial steps towards characterizing three DNA-related Sulfolobus proteins with small angle X-ray scattering (SAXS): Sso0257, a cell division control and origin recognition complex homolog, Sso0768, the small subunit of the replication factor C, and Sso3167, a Mut-T like protein. SAXS analysis was performed at multiple concentrations for both short and long exposure times. The Sso0257 sample was determined to be either a mixture of monomeric and dimeric states or a population of dynamic monomers in various conformational states in solution, consistent with a fl exible winged helix domain. Sso0768 was found to be a complex mixture of multimeric states in solution. Finally, molecular envelope reconstruction from SAXS data for Sso3167 revealed a novel structural component which may function as a disordered to ordered region in the presence of its substrates and/or protein partners.

  10. Mass fractal characteristics of silica sonogels as determined by small-angle x-ray scattering and nitrogen adsorption

    SciTech Connect

    Donatti, D.A.; Vollet, D.R.; Ibanez Ruiz, A.; Mesquita, A.; Silva, T.F.P.

    2005-01-01

    A sample series of silica sonogels was prepared using different water-tetraethoxysilane molar ratio (r{sub w}) in the gelation step of the process in order to obtain aerogels with different bulk densities after the supercritical drying. The samples were analyzed by means of small-angle x-ray-scattering (SAXS) and nitrogen-adsorption techniques. Wet sonogels exhibit mass fractal structure with fractal dimension D increasing from {approx}2.1 to {approx}2.4 and mass-fractal correlation length {xi} diminishing from {approx}13 nm to {approx}2 nm, as r{sub w} is changed in the nominal range from 66 to 6. The process of obtaining aerogels from sonogels and heat treatment at 500 deg. C, in general, increases the mass-fractal dimension D, diminishes the characteristic length {xi} of the fractal structure, and shortens the fractal range at the micropore side for the formation of a secondary structured particle, apparently evolved from the original wet structure at a high resolution level. The overall mass-fractal dimension D of aerogels was evaluated as {approx}2.4 and {approx}2.5, as determined from SAXS and from pore-size distribution by nitrogen adsorption, respectively. The fine structure of the 'secondary particle' developed in the obtaining of aerogels could be described as a surface-mass fractal, with the correlated surface and mass-fractal dimensions decreasing from {approx}2.4 to {approx}2.0 and from {approx}2.7 to {approx}2.5, respectively, as the aerogel bulk density increases from 0.25 (r{sub w}=66) up to 0.91 g/cm{sup 3} (r{sub w}=6)

  11. Measurement of carbon condensates using small-angle x-ray scattering during detonation of the high explosive hexanitrostilbene

    SciTech Connect

    Bagge-Hansen, M.; Lauderbach, L.; Hodgin, R.; Bastea, S.; Fried, L.; Jones, A.; Buuren, T. van; Hansen, D.; Benterou, J.; May, C.; Willey, T. M.; Graber, T.; Jensen, B. J.; Ilavsky, J.

    2015-06-28

    The dynamics of carbon condensation in detonating high explosives remains controversial. Detonation model validation requires data for processes occurring at nanometer length scales on time scales ranging from nanoseconds to microseconds. A new detonation endstation has been commissioned to acquire and provide time-resolved small-angle x-ray scattering (SAXS) from detonating explosives. Hexanitrostilbene (HNS) was selected as the first to investigate due to its ease of initiation using exploding foils and flyers, vacuum compatibility, high thermal stability, and stoichiometric carbon abundance that produces high carbon condensate yields. The SAXS data during detonation, collected with 300 ns time resolution, provide unprecedented signal fidelity over a broad q-range. This fidelity permits the first analysis of both the Guinier and Porod/power-law regions of the scattering profile during detonation, which contains information about the size and morphology of the resultant carbon condensate nanoparticles. To bolster confidence in these data, the scattering angle and intensity were additionally cross-referenced with a separate, highly calibrated SAXS beamline. The data show that HNS produces carbon particles with a radius of gyration of 2.7 nm in less than 400 ns after the detonation front has passed, and this size and morphology are constant over the next several microseconds. These data directly contradict previous pioneering work on RDX/TNT mixtures and TATB, where observations indicate significant particle growth (50% or more) continues over several microseconds. The power-law slope is about −3, which is consistent with a complex disordered, irregular, or folded sp{sup 2} sub-arrangement within a relatively monodisperse structure possessing radius of gyration of 2.7 nm after the detonation of HNS.

  12. Studying nanostructure gradients in injection-molded polypropylene/montmorillonite composites by microbeam small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Stribeck, Norbert; Schneider, Konrad; Zeinolebadi, Ahmad; Li, Xuke; Sanporean, Catalina-Gabriela; Vuluga, Zina; Iancu, Stela; Duldner, Monica; Santoro, Gonzalo; Roth, Stephan V.

    2014-02-01

    The core-shell structure in oriented cylindrical rods of polypropylene (PP) and nanoclay composites (NCs) from PP and montmorillonite (MMT) is studied by microbeam small-angle x-ray scattering (SAXS). The structure of neat PP is almost homogeneous across the rod showing regular semicrystalline stacks. In the NCs the discrete SAXS of arranged crystalline PP domains is limited to a skin zone of 300 μm thickness. Even there only frozen-in primary lamellae are detected. The core of the NCs is dominated by diffuse scattering from crystalline domains placed at random. The SAXS of the MMT flakes exhibits a complex skin-core gradient. Both the direction of the symmetry axis and the apparent perfection of flake-orientation are varying. Thus there is no local fiber symmetry, and the structure gradient cannot be reconstructed from a scan across the full rod. To overcome the problem the rods are machined. Scans across the residual webs are performed. For the first time webs have been carved out in two principal directions. Comparison of the corresponding two sets of SAXS patterns demonstrates the complexity of the MMT orientation. Close to the surface (< 1 mm) the flakes cling to the wall. The variation of the orientation distribution widths indicates the presence of both MMT flakes and grains. The grains have not been oriented in the flowing melt. An empirical equation is presented which describes the variation from skin to core of one component of the inclination angle of flake-shaped phyllosilicate filler particles.

  13. Measurement of carbon condensates using small-angle x-ray scattering during detonation of the high explosive hexanitrostilbene

    DOE PAGESBeta

    Bagge-Hansen, M.; Lauderbach, L.; Hodgin, R.; Bastea, S.; Fried, L.; Jones, A.; van Buuren, T.; Hansen, D.; Benterou, J.; May, C.; et al

    2015-06-24

    In this study, the dynamics of carbon condensation in detonating high explosives remains controversial. Detonation model validation requires data for processes occurring at nanometer length scales on time scales ranging from nanoseconds to microseconds. A new detonation end station has been commissioned to acquire and provide time-resolved small-angle x-ray scattering (SAXS) from detonating explosives. Hexanitrostilbene (HNS) was selected as the first to investigate due to its ease of initiation using exploding foils and flyers, vacuum compatibility, high thermal stability, and stoichiometric carbon abundance that produces high carbon condensate yields. The SAXS data during detonation, collected with 300 ns time resolution,more » provide unprecedented signal fidelity over a broad q-range. This fidelity permits the first analysis of both the Guinier and Porod/power-law regions of the scattering profile during detonation, which contains information about the size and morphology of the resultant carbon condensate nanoparticles. To bolster confidence in these data, the scattering angle and intensity were additionally cross-referenced with a separate, highly calibrated SAXS beamline. The data show that HNS produces carbon particles with a radius of gyration of 2.7 nm in less than 400 ns after the detonation front has passed, and this size and morphology are constant over the next several microseconds. These data directly contradict previous pioneering work on RDX/TNT mixtures and TATB, where observations indicate significant particle growth (50% or more) continues over several microseconds. The power-law slope is about -3, which is consistent with a complex disordered, irregular, or folded sp2 sub-arrangement within a relatively monodisperse structure possessing radius of gyration of 2.7 nm after the detonation of HNS.« less

  14. Structural properties of archaeal lipid bilayers: small-angle X-ray scattering and molecular dynamics simulation study.

    PubMed

    Polak, Andraž; Tarek, Mounir; Tomšič, Matija; Valant, Janez; Ulrih, Nataša Poklar; Jamnik, Andrej; Kramar, Peter; Miklavčič, Damijan

    2014-07-22

    Aeropyrum pernix is an aerobic hyperthermophilic archaeon that grows in harsh environmental conditions and as such possesses unique structural and metabolic features. Its membrane interfaces with the extreme environment and is the first line of defense from external factors. Therefore, lipids composing this membrane have special moieties that increase its stability. The membrane of A. pernix is composed predominantly of two polar lipids 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-1'(2'-O-α-D-glucosyl)-myo-inositol (AGI) and 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-myo-inositol (AI). Both have methyl branches in their lipid tails and ether linkages and carbohydrates in their headgroup. These moieties significantly affect the structure and dynamics of the bilayer. To provide a molecular level insight into these characteristics, we used here Molecular Dynamics (MD) simulations of lipid bilayers of composition similar to those of the archaeal membranes. First, we show that the electron density profiles along the normal to the bilayers derived from the simulations are in good agreement with the profiles obtained by the small-angle X-ray scattering (SAXS) technique, which provides confidence in the force fields used. Analyses of the simulation data show that the archaeal lipid bilayers are less hydrated than conventional phosphatidylcholine (PC) lipids and that their structure is not affected by the salt present in the surrounding solution. Furthermore, the lateral pressure in their hydrophobic core, due to the presence of the branched tails, is much higher than that at PC-based lipid bilayers. Both the methyl branched tails and the special headgroup moieties contribute to slow drastically the lateral diffusion of the lipids. Furthermore, we found that the lipid head groups associate via hydrogen bonding, which affects their reorientational dynamics. All together, our data provide links between the microscopic properties of these membranes and their overall

  15. LabDisk for SAXS: a centrifugal microfluidic sample preparation platform for small-angle X-ray scattering.

    PubMed

    Schwemmer, Frank; Blanchet, Clement E; Spilotros, Alessandro; Kosse, Dominique; Zehnle, Steffen; Mertens, Haydyn D T; Graewert, Melissa A; Rössle, Manfred; Paust, Nils; Svergun, Dmitri I; von Stetten, Felix; Zengerle, Roland; Mark, Daniel

    2016-03-23

    We present a centrifugal microfluidic LabDisk for protein structure analysis via small-angle X-ray scattering (SAXS) on synchrotron beamlines. One LabDisk prepares 120 different measurement conditions, grouped into six dilution matrices. Each dilution matrix: (1) features automatic generation of 20 different measurement conditions from three input liquids and (2) requires only 2.5 μl of protein solution, which corresponds to a tenfold reduction in sample volume in comparison to the state of the art. Total hands on time for preparation of 120 different measurement conditions is less than 5 min. Read-out is performed on disk within the synchrotron beamline P12 at EMBL Hamburg (PETRA III, DESY). We demonstrate: (1) aliquoting of 40 nl aliquots for five different liquids typically used in SAXS and (2) confirm fluidic performance of aliquoting, merging, mixing and read-out from SAXS experiments (2.7-4.4% CV of protein concentration). We apply the LabDisk for SAXS for basic analysis methods, such as measurement of the radius of gyration, and advanced analysis methods, such as the ab initio calculation of 3D models. The suitability of the LabDisk for SAXS for protein structure analysis under different environmental conditions is demonstrated for glucose isomerase under varying protein and NaCl concentrations. We show that the apparent radius of gyration of the negatively charged glucose isomerase decreases with increasing protein concentration at low salt concentration. At high salt concentration the radius of gyration (Rg) does not change with protein concentrations. Such experiments can be performed by a non-expert, since the LabDisk for SAXS does not require attachment of tubings or pumps and can be filled with regular pipettes. The new platform has the potential to introduce routine high-throughput SAXS screening of protein structures with minimal input volumes to the regular operation of synchrotron beamlines. PMID:26931639

  16. Measurement of carbon condensates using small-angle x-ray scattering during detonation of the high explosive hexanitrostilbene

    SciTech Connect

    Bagge-Hansen, M.; Lauderbach, L.; Hodgin, R.; Bastea, S.; Fried, L.; Jones, A.; van Buuren, T.; Hansen, D.; Benterou, J.; May, C.; Graber, T.; Jensen, B. J.; Ilavsky, J.; Willey, T. M.

    2015-06-24

    In this study, the dynamics of carbon condensation in detonating high explosives remains controversial. Detonation model validation requires data for processes occurring at nanometer length scales on time scales ranging from nanoseconds to microseconds. A new detonation end station has been commissioned to acquire and provide time-resolved small-angle x-ray scattering (SAXS) from detonating explosives. Hexanitrostilbene (HNS) was selected as the first to investigate due to its ease of initiation using exploding foils and flyers, vacuum compatibility, high thermal stability, and stoichiometric carbon abundance that produces high carbon condensate yields. The SAXS data during detonation, collected with 300 ns time resolution, provide unprecedented signal fidelity over a broad q-range. This fidelity permits the first analysis of both the Guinier and Porod/power-law regions of the scattering profile during detonation, which contains information about the size and morphology of the resultant carbon condensate nanoparticles. To bolster confidence in these data, the scattering angle and intensity were additionally cross-referenced with a separate, highly calibrated SAXS beamline. The data show that HNS produces carbon particles with a radius of gyration of 2.7 nm in less than 400 ns after the detonation front has passed, and this size and morphology are constant over the next several microseconds. These data directly contradict previous pioneering work on RDX/TNT mixtures and TATB, where observations indicate significant particle growth (50% or more) continues over several microseconds. The power-law slope is about -3, which is consistent with a complex disordered, irregular, or folded sp2 sub-arrangement within a relatively monodisperse structure possessing radius of gyration of 2.7 nm after the detonation of HNS.

  17. Measurement of carbon condensation using small-angle x-ray scattering during detonation of the high explosive hexanitrostilbene

    SciTech Connect

    Bagge-Hansen, M.; Lauderbach, L. M.; Hodgin, R.; Bastea, S.; Fried, L.; Jones, A.; van Buuren, T.; Hansen, D.; Benterou, J.; May, C.; Graber, T.; Jensen, B. J.; Ilavsky, J.; Willey, T. M.

    2015-06-24

    The dynamics of carboncondensation in detonating high explosives remains controversial. Detonation model validation requires data for processes occurring at nanometer length scales on time scales ranging from nanoseconds to microseconds. A new detonation endstation has been commissioned to acquire and provide time-resolved small-angle x-ray scattering (SAXS) from detonating explosives. Hexanitrostilbene (HNS) was selected as the first to investigate due to its ease of initiation using exploding foils and flyers, vacuum compatibility, high thermal stability, and stoichiometric carbon abundance that produces high carbon condensate yields. The SAXS data during detonation, collected with 300 ns time resolution, provide unprecedented signal fidelity over a broad q-range. This fidelity permits the first analysis of both the Guinier and Porod/power-law regions of the scattering profile during detonation, which contains information about the size and morphology of the resultant carbon condensate nanoparticles. To bolster confidence in these data, the scattering angle and intensity were additionally cross-referenced with a separate, highly calibrated SAXS beamline. The data show that HNS produces carbon particles with a radius of gyration of 2.7 nm in less than 400 ns after the detonation front has passed, and this size and morphology are constant over the next several microseconds. These data directly contradict previous pioneering work on RDX/TNT mixtures and TATB, where observations indicate significant particle growth (50% or more) continues over several microseconds. As a result, the power-law slope is about –3, which is consistent with a complex disordered, irregular, or folded sp2 sub-arrangement within a relatively monodisperse structure possessing radius of gyration of 2.7 nm after the detonation of HNS.

  18. Measurement of carbon condensates using small-angle x-ray scattering during detonation of the high explosive hexanitrostilbene

    NASA Astrophysics Data System (ADS)

    Bagge-Hansen, M.; Lauderbach, L.; Hodgin, R.; Bastea, S.; Fried, L.; Jones, A.; van Buuren, T.; Hansen, D.; Benterou, J.; May, C.; Graber, T.; Jensen, B. J.; Ilavsky, J.; Willey, T. M.

    2015-06-01

    The dynamics of carbon condensation in detonating high explosives remains controversial. Detonation model validation requires data for processes occurring at nanometer length scales on time scales ranging from nanoseconds to microseconds. A new detonation endstation has been commissioned to acquire and provide time-resolved small-angle x-ray scattering (SAXS) from detonating explosives. Hexanitrostilbene (HNS) was selected as the first to investigate due to its ease of initiation using exploding foils and flyers, vacuum compatibility, high thermal stability, and stoichiometric carbon abundance that produces high carbon condensate yields. The SAXS data during detonation, collected with 300 ns time resolution, provide unprecedented signal fidelity over a broad q-range. This fidelity permits the first analysis of both the Guinier and Porod/power-law regions of the scattering profile during detonation, which contains information about the size and morphology of the resultant carbon condensate nanoparticles. To bolster confidence in these data, the scattering angle and intensity were additionally cross-referenced with a separate, highly calibrated SAXS beamline. The data show that HNS produces carbon particles with a radius of gyration of 2.7 nm in less than 400 ns after the detonation front has passed, and this size and morphology are constant over the next several microseconds. These data directly contradict previous pioneering work on RDX/TNT mixtures and TATB, where observations indicate significant particle growth (50% or more) continues over several microseconds. The power-law slope is about -3, which is consistent with a complex disordered, irregular, or folded sp2 sub-arrangement within a relatively monodisperse structure possessing radius of gyration of 2.7 nm after the detonation of HNS.

  19. Integration of Small Angle X-Ray Scattering Data Into Structural Modeling of Proteins And Their Assemblies

    SciTech Connect

    Forster, F.; Webb, B.; Krukenberg, K.A.; Tsuruta, H.; Agard, D.A.; Sali, A.

    2009-05-18

    A major challenge in structural biology is to determine the configuration of domains and proteins in multidomain proteins and assemblies, respectively. All available data should be considered to maximize the accuracy and precision of these models. Small-angle X-ray scattering (SAXS) efficiently provides low-resolution experimental data about the shapes of proteins and their assemblies. Thus, we integrated SAXS profiles into our software for modeling proteins and their assemblies by satisfaction of spatial restraints. Specifically, we modeled the quaternary structures of multidomain proteins with structurally defined rigid domains as well as quaternary structures of binary complexes of structurally defined rigid proteins. In addition to SAXS profiles and the component structures, we used stereochemical restraints and an atomic distance-dependent statistical potential. The scoring function is optimized by a biased Monte Carlo protocol, including quasi-Newton and simulated annealing schemes. The final prediction corresponds to the best scoring solution in the largest cluster of many independently calculated solutions. To quantify how well the quaternary structures are determined based on their SAXS profiles, we used a benchmark of 12 simulated examples as well as an experimental SAXS profile of the homotetramer D-xylose isomerase. Optimization of the SAXS-dependent scoring function generally results in accurate models if sufficiently precise approximations for the constituent rigid bodies are available; otherwise, the best scoring models can have significant errors. Thus, SAXS profiles can play a useful role in the structural characterization of proteins and assemblies if they are combined with additional data and used judiciously. Our integration of a SAXS profile into modeling by satisfaction of spatial restraints will facilitate further integration of different kinds of data for structure determination of proteins and their assemblies.

  20. In situ characterization of Grade 92 steel during tensile deformation using concurrent high energy X-ray diffraction and small angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Wang, Leyun; Li, Meimei; Almer, Jonathan

    2013-09-01

    The tensile deformation in Grade 92 steel was studied in situ using simultaneous high energy X-ray diffraction (HE-XRD), radiography, and small angle X-ray scattering (SAXS) at room temperature (RT), 400, and 650 °C. Temperature-dependent elastic properties, i.e. Young's modulus and Poisson's ratio, were measured for α-Fe matrix, M23C6 and Nb(C,N) phases in various crystallographic orientation. Significant differences in the evolution of lattice strain, peak broadening/sharpening, and void development in the α-Fe matrix, M23C6 and Nb(C,N) precipitates revealed markedly different deformation and damage mechanisms at low and high temperature in the alloy. The strengthening effect of each type of precipitates measured by lattice strain agrees with the dislocation pile-up model at room temperature, while a different dislocation behavior was observed at 650 °C. Void volume fraction as a function of strain measured by SAXS can be described by a classic void nucleation and growth model at room temperature but not at 650 °C, implying a different damage process at high temperature. The ultimate tensile strength is ordered as RT > 400 °C > 650 °C; strain to failure is ordered as 650 °C > RT > 400 °C. For the 650 °C test, there was a long softening stage between the UTS and specimen necking. M23C6 and Nb(C,N) precipitates were identified in the Fe matrix. At RT and 400 °C, apparent load transfer from the matrix to the precipitates took place after the matrix's early yielding. Measured von Mises stresses in the precipitates can be quantitatively explained using the established models of precipitate strengthening. Increase of dislocation density with deformation caused peak broadening in both matrix and precipitates. At 650 °C, load transfer was much less, and peak broadening was also largely subdued at 650 °C. Anisotropy of lattice strains was observed both in the matrix and precipitates. The elastic modulus of Fe (2 0 0) is lower than Fe (2 1 1) and Fe (2 2 0

  1. Ultra-small-angle X-ray scattering study of second- phase particles in heat-treated Zircaloy-4

    SciTech Connect

    Srirangam, Prakash; Idrees, Yasir; Ilavsky, Jan; Daymond, Mark R.

    2015-01-01

    The ultra-small-angle X-ray scattering (USAXS) technique has been used to investigate and to quantify the morphology and size distribution of secondphase particles in Zircaloy-4 under various heat-treatment conditions. The alloy samples were solutionized in the phase field at 1293 K for 15 min and then cooled at different rates, including water quenching, air cooling and furnace cooling. The water-quenched samples were subsequently subjected to a thermal aging treatment at 873 K for different aging times (30, 60, 120 and 300 min). The USAXS results show that water quenching and air cooling from the phase field produces a narrow size distribution of fine-size precipitates with an average diameter of 300–800 A ° , while furnace cooling resulted in coarsening of the particles, with a broad size distribution having an average precipitate size of 600–1200 A ° . Further, the furnace-cooled sample shows a higher volume fraction of particles than the water-quenched or air-cooled sample. The USAXS results on the quenched then aged samples show that aging at 873 K for 10 min resulted in very fine size precipitates with an average diameter of 200–350 A ° . A rapid precipitation with the highest number density of second-phase particles amongst all the heat-treated samples (4.3 1020 m3) was observed in the sample aged for 10 min at 873 K. Particles of larger size and with a broad size distribution were observed in the sample aged at 873 K for 300 min. A bimodal type of particle size distribution was observed in all the heat-treated samples. Important parameters in the characterization of second-phase particles, such as the average size, size distribution, volume fraction and number density, were evaluated and quantified. These parameters are discussed for both heat-treated and aged specimens. Transmission and scanning transmission electron microscopy characterization were carried out on all heat-treated samples, to assist in interpretation and to substantiate the

  2. Small-angle X-ray scattering of the cholesterol incorporation into human ApoA1-POPC discoidal particles.

    PubMed

    Midtgaard, Søren Roi; Pedersen, Martin Cramer; Arleth, Lise

    2015-07-21

    Structural and functional aspects of high-density lipoproteins have been studied for over half a century. Due to the plasticity of this highly complex system, new aspects continue to be discovered. Here, we present a structural study of the human Apolipoprotein A1 (ApoA1) and investigate the role of its N-terminal domain, the so-called globular domain of ApoA1, in discoidal complexes with phospholipids and increasing amounts of cholesterol. Using a combination of solution-based small-angle x-ray scattering (SAXS) and molecular constrained data modeling, we show that the ApoA1-1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-based particles are disk shaped with an elliptical cross section and composed by a central lipid bilayer surrounded by two stabilizing ApoA1 proteins. This structure is very similar to the particles formed in the so-called nanodisc system, which is based on N-terminal truncated ApoA1 protein. Although it is commonly agreed that the nanodisc is plain disk shaped, several more advanced structures have been proposed for the full-length ApoA1 in combination with POPC and cholesterol. This prompted us to make a detailed comparative study of the ApoA1 and nanodisc systems upon cholesterol uptake. Based on the presented SAXS analysis it is found that the N-terminal domains of ApoA1-POPC-cholesterol particles are not globular but instead an integrated part of the protein belt stabilizing the particles. Upon incorporation of increasing amounts of cholesterol, the presence of the N-terminal domain allows the bilayer thickness to increase while maintaining an overall flat bilayer structure. This is contrasted by the energetically more strained and less favorable lens shape required to fit the SAXS data from the N-terminal truncated nanodisc system upon cholesterol incorporation. This suggests that the N-terminal domain of ApoA1 actively participates in the stabilization of the ApoA1-POPC-cholesterol discoidal particle and allows for a more optimal

  3. Small Angle X-ray Scattering Study of Palladium Nanoparticle Growth on Genetically Engineered Tobacco Mosaic Virus Nanotemplates

    NASA Astrophysics Data System (ADS)

    Manocchi, Amy K.

    Transition metal nanoparticles possess valuable specific size dependent properties that arise at the nanoscale, and differ significantly from their bulk properties. However, the fabrication of these nanoparticles is often difficult to predict and control due to harsh reaction conditions and effects of capping agents or surfactants. Therefore, there is a critical need for facile routes toward controllable nanoparticle fabrication. Biological supramolecules, such as viruses, offer attractive templates for nanoparticle synthesis, due to their precise size and shape. In addition, simple genetic modifications can be employed to confer additional functionality with a high number of precisely spaced functional groups. In this work we exploit the specificity of genetically modified Tobacco Mosaic Virus (TMV1cys) for readily controllable palladium (Pd) nanoparticle synthesis via simple electroless deposition. TMV1cys, engineered to display one cysteine residue on the surface of each of over 2000 identical coat proteins, provides high density precisely spaced thiol groups for the preferential nucleation and growth of Pd nanoparticles. Small-Angle X-ray Scattering (SAXS) was employed to provide a statistically meaningful route to the investigation of Pd nanoparticle size ranges formed on the viral-nanotemplates. Specifically, we examine the size range and thermal stability of Pd nanoparticles formed on surface assembled TMV1cys. Further, we investigate the growth of Pd nanoparticles on TMV1cys in solution using in situ SAXS to better understand and predict nanoparticle growth on these nanotemplates. Lastly, we compare TMV1cys templated particle growth to Pd nanoparticle growth in the absence of TMV1cys to elucidate the role of TMV in particle formation. We show that Pd nanoparticles form preferentially on surface assembled TMV1cys in high density in a broad particle size range (4-18nm). Further, we show that Pd nanoparticles are significantly smaller and more uniform when

  4. Small angle X-ray scattering as a high-throughput method to classify antimicrobial modes of action.

    PubMed

    von Gundlach, A R; Garamus, V M; Gorniak, T; Davies, H A; Reischl, M; Mikut, R; Hilpert, K; Rosenhahn, A

    2016-05-01

    Multi-drug resistant bacteria are currently undermining our health care system worldwide. While novel antimicrobial drugs, such as antimicrobial peptides, are urgently needed, identification of new modes of action is money and time consuming, and in addition current approaches are not available in a high throughput manner. Here we explore how small angle X-ray scattering (SAXS) as high throughput method can contribute to classify the mode of action for novel antimicrobials and therefore supports fast decision making in drug development. Using data bases for natural occurring antimicrobial peptides or predicting novel artificial peptides, many candidates can be discovered that will kill a selected target bacterium. However, in order to narrow down the selection it is important to know if these peptides follow all the same mode of action. In addition, the mode of action should be different from conventional antibiotics, in consequence peptide candidates can be developed further into drugs against multi-drug resistant bacteria. Here we used one short antimicrobial peptide with unknown mode of action and compared the ultrastructural changes of Escherichia coli cells after treatment with the peptide to cells treated with classic antibiotics. The key finding is that SAXS as a structure sensitive tool provides a rapid feedback on drug induced ultrastructural alterations in whole E. coli cells. We could demonstrate that ultrastructural changes depend on the used antibiotics and their specific mode of action. This is demonstrated using several well characterized antimicrobial compounds and the analysis of resulting SAXS curves by principal component analysis. To understand the result of the PCA analysis, the data is correlated with TEM images. In contrast to real space imaging techniques, SAXS allows to obtain nanoscale information averaged over approximately one million cells. The measurement takes only seconds, while conventional tests to identify a mode of action require

  5. Synchrotron Small-Angle X-Ray Scattering Investigation on Integral Membrane Protein Light-Harvesting Complex LH2 from Photosynthetic Bacterium Rhodopseudomonas Acidophila

    NASA Astrophysics Data System (ADS)

    Du, Lu-Chao; Weng, Yu-Xiang; Hong, Xin-Guo; Xian, Ding-Chang; Kobayashi, Katsumi

    2006-07-01

    Structures of membrane protein in solution are different from that in crystal phase. We present the primary results of small angle x-ray scattering (SAXS) resolved topological structures of a light harvesting antenna membrane protein complex LH2 from photosynthetic bacteria Rhodopseudomonas acidophila in detergent solution for the first time. Our results show that the elliptical shape of the LH2 complex in solution clearly deviates from its circular structure in crystal phase determined by x-ray diffraction. This result provides an insight into the structure and function interplay in LH2.

  6. Small-angle x-ray scattering measurement of a mist of ethanol nanodroplets: an approach to understanding ultrasonic separation of ethanol-water mixtures.

    PubMed

    Yano, Yohko F; Matsuura, Kazuo; Fukazu, Tetsuo; Abe, Fusatsugu; Wakisaka, Akihiro; Kobara, Hitomi; Kaneko, Kazuyuki; Kumagai, Atsushi; Katsuya, Yoshio; Tanaka, Masahiko

    2007-07-21

    Small-angle x-ray scattering measurements using a brilliant x-ray source revealed nanometer sized liquid droplets in a mist formed by ultrasonic atomization. Ultrasonic atomization of ethanol-water mixtures produced a combination of water-rich droplets of micrometer order and ethanol-rich droplets as small as 1 nm, which is 10(-3) times smaller than the predicted size. These sizes were also obtained for mists generated from the pure liquids. These results will help to clarify the mechanism of "ultrasonic ethanol separation," which has the potential to become an alternative to distillation. PMID:17655423

  7. Study of the gel films of Acetobacter Xylinum cellulose and its modified samples by {sup 1}H NMR cryoporometry and small-angle X-ray scattering

    SciTech Connect

    Babushkina, T. A.; Klimova, T. P.; Shtykova, E. V.; Dembo, K. A.; Volkov, V. V.; Khripunov, A. K.; Klechkovskaya, V. V.

    2010-03-15

    Gel films of Acetobacter Xylinum cellulose and its modified samples have been investigated by 1H nuclear magnetic resonance (NMR) cryoporometry and small-angle X-ray scattering. The joint use of these two methods made it possible to characterize the sizes of aqueous pores in gel films and estimate the sizes of structural inhomogeneities before and after the sorption of polyvinylpyrrolidone and Se{sub 0} nanoparticles (stabilized by polyvinylpyrrolidone) into the films. According to small-angle X-ray scattering data, the sizes of inhomogeneities in a gel film change only slightly upon the sorption of polyvinylpyrrolidone and nanoparticles. The impregnated material is sorbed into water-filled cavities that are present in the gel film. {sup 1}H NMR cryoporometry allowed us to reveal the details of changes in the sizes of small aqueous pores during modifications.

  8. Study of the gel films of Acetobacter Xylinum cellulose and its modified samples by 1H NMR cryoporometry and small-angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Babushkina, T. A.; Klimova, T. P.; Shtykova, É. V.; Dembo, K. A.; Volkov, V. V.; Khripunov, A. K.; Klechkovskaya, V. V.

    2010-03-01

    Gel films of Acetobacter Xylinum cellulose and its modified samples have been investigated by 1H nuclear magnetic resonance (NMR) cryoporometry and small-angle X-ray scattering. The joint use of these two methods made it possible to characterize the sizes of aqueous pores in gel films and estimate the sizes of structural inhomogeneities before and after the sorption of polyvinylpyrrolidone and Se0 nanoparticles (stabilized by polyvinylpyrrolidone) into the films. According to small-angle X-ray scattering data, the sizes of inhomogeneities in a gel film change only slightly upon the sorption of polyvinylpyrrolidone and nanoparticles. The impregnated material is sorbed into water-filled cavities that are present in the gel film. 1H NMR cryoporometry allowed us to reveal the details of changes in the sizes of small aqueous pores during modifications.

  9. EXTINCTION AND DISTANCE TO ANOMALOUS X-RAY PULSARS FROM X-RAY SCATTERING HALOS

    SciTech Connect

    Rivera-Ingraham, A.; Van Kerkwijk, M. H. E-mail: mhvk@astro.utoronto.c

    2010-02-10

    We analyze the X-ray scattering halos around three Galactic Anomalous X-ray Pulsars in order to constrain the distance and the optical extinction of each source. We obtain surface brightness distributions from EPIC-pn data obtained with XMM-Newton, compare the profiles of different sources, and fit them with a model based on the standard theory of X-ray scattering by dust grains, both for a uniform distribution of dust along the line of sight, and for dust distributions constrained by previous measurements. Somewhat surprisingly, we find that for all three sources, the uniform distribution reproduces the observed surface brightness as well as or better than the distributions that are informed by previous constraints. Nevertheless, the inferred total dust columns are robust, and serve to confirm that previous measurements based on interstellar edges in high-resolution X-ray spectra and on modeling of broadband X-ray spectra were reliable. Specifically, we find A{sub V} {approx_equal} 4, 6, and 8 mag for 4U 0142+61, 1E 1048.1 - 5937, and 1RXS J170849.0 - 400910, respectively. For 1E 1048.1 - 5937, this is well in excess of the extinction expected toward an H I bubble along the line of sight, thus casting further doubt on the suggested association with the source.

  10. Microstructure of amorphous-silicon-based solar cell materials by small-angle x-ray scattering. Annual subcontract report, 6 April 1994--5 April 1995

    SciTech Connect

    Williamson, D.L.

    1995-08-01

    The general objective of this research is to provide detailed microstructural information on the amorphous-silicon-based, thin-film materials under development for improved multijunction solar cells. The experimental technique used is small-angle x-ray scattering (SAXS) providing microstructural data on microvoid fractions, sizes, shapes, and their preferred orientations. Other microstructural features such as alloy segregation, hydrogen-rich clusters and alloy short-range order are probed.

  11. Further application of size-exclusion chromatography combined with small-angle X-ray scattering optics for characterization of biological macromolecules.

    PubMed

    Watanabe, Yasushi; Inoko, Yoji

    2011-02-01

    Size-exclusion chromatography (gel filtration chromatography or gel permeation chromatography) in conjunction with online synchrotron radiation solution small-angle X-ray scattering optics, absorbance, and/or refractive index detectors was further assessed by application of biological macromolecules, such as the hollow sphere protein complex, apoferritin, and a linear polysaccharide, pullulan. The net X-ray scattering patterns of the eluted 24-mer molecule of apoferritin showed the specific character for the hollow spherical shape. The chromatographic (time-resolved) X-ray scattering data of the linear polysaccharide pullulan revealed the flexible chain structure during the chromatographic separation in an aqueous solution. These further applications demonstrated that the present measurement technique will be useful for not only the determination of the radius of gyration value of less than about 10 nm and molecular weight below several hundred thousand but also for the structural characterization of the various macromolecules during the chromatography. PMID:20811739

  12. Global small-angle X-ray scattering data analysis for multilamellar vesicles: the evolution of the scattering density profile model

    PubMed Central

    Heftberger, Peter; Kollmitzer, Benjamin; Heberle, Frederick A.; Pan, Jianjun; Rappolt, Michael; Amenitsch, Heinz; Kučerka, Norbert; Katsaras, John; Pabst, Georg

    2014-01-01

    The highly successful scattering density profile (SDP) model, used to jointly analyze small-angle X-ray and neutron scattering data from unilamellar vesicles, has been adapted for use with data from fully hydrated, liquid crystalline multilamellar vesicles (MLVs). Using a genetic algorithm, this new method is capable of providing high-resolution structural information, as well as determining bilayer elastic bending fluctuations from standalone X-ray data. Structural parameters such as bilayer thickness and area per lipid were determined for a series of saturated and unsaturated lipids, as well as binary mixtures with cholesterol. The results are in good agreement with previously reported SDP data, which used both neutron and X-ray data. The inclusion of deuterated and non-deuterated MLV neutron data in the analysis improved the lipid backbone information but did not improve, within experimental error, the structural data regarding bilayer thickness and area per lipid. PMID:24587787

  13. Anomalous X-ray diffraction with soft X-ray synchrotron radiation.

    PubMed

    Carpentier, P; Berthet-Colominas, C; Capitan, M; Chesne, M L; Fanchon, E; Lequien, S; Stuhrmann, H; Thiaudière, D; Vicat, J; Zielinski, P; Kahn, R

    2000-07-01

    Anomalous diffraction with soft X-ray synchrotron radiation opens new possibilities in protein crystallography and materials science. Low-Z elements like silicon, phosphorus, sulfur and chlorine become accessible as new labels in structural studies. Some of the heavy elements like uranium exhibit an unusually strong dispersion at their M(V) absorption edge (lambdaMV = 3.497 A, E(MV) = 3545 eV) and so does thorium. Two different test experiments are reported here showing the feasibility of anomalous X-ray diffraction at long wavelengths with a protein containing uranium and with a salt containing chlorine atoms. With 110 electrons the anomalous scattering amplitude of uranium exceeds by a factor of 4 the resonance scattering of other strong anomalous scatterers like that of the lanthanides at their L(III) edge. The resulting exceptional phasing power of uranium is most attractive in protein crystallography using the multi-wavelength anomalous diffraction (MAD) method. The anomalous dispersion of an uranium derivative of asparaginyl-tRNA synthetase (hexagonal unit cell; a = 123.4 A, c = 124.4 A) has been measured for the first time at 4 wavelengths near the M(V) edge using the beamline ID1 of ESRF (Grenoble, France). The present set up allowed to measure only 30% of the possible reflections at a resolution of 4 A, mainly because of the low sensitivity of the CCD detector. In the second experiment, the dispersion of the intensity of 5 X-ray diffraction peaks from pentakismethylammonium undecachlorodibismuthate (PMACB, orthorhombic unit cell; a = 13.003 A, b = 14.038 A, c = 15.450 A) has been measured at 30 wavelengths near the K absorption edge of chlorine (lambdaK = 4.397 A, EK= 2819.6 eV). All reflections within the resolution range from 6.4 A to 3.4 A expected in the 20 degree scan were observed. The chemical state varies between different chlorine atoms of PMACB, and so does the dispersion of different Bragg peaks near the K-edge of chlorine. The results reflect

  14. Architecture of a Full-length Retroviral Integrase Monomer and Dimer, Revealed by Small Angle X-ray Scattering and Chemical Cross-linking

    SciTech Connect

    Bojja, Ravi S.; Andrake, Mark D.; Weigand, Steven; Merkel, George; Yarychkivska, Olya; Henderson, Adam; Kummerling, Marissa; Skalka, Anna Marie

    2012-02-07

    We determined the size and shape of full-length avian sarcoma virus (ASV) integrase (IN) monomers and dimers in solution using small angle x-ray scattering. The low resolution data obtained establish constraints for the relative arrangements of the three component domains in both forms. Domain organization within the small angle x-ray envelopes was determined by combining available atomic resolution data for individual domains with results from cross-linking coupled with mass spectrometry. The full-length dimer architecture so revealed is unequivocally different from that proposed from x-ray crystallographic analyses of two-domain fragments, in which interactions between the catalytic core domains play a prominent role. Core-core interactions are detected only in cross-linked IN tetramers and are required for concerted integration. The solution dimer is stabilized by C-terminal domain (CTD-CTD) interactions and by interactions of the N-terminal domain in one subunit with the core and CTD in the second subunit. These results suggest a pathway for formation of functional IN-DNA complexes that has not previously been considered and possible strategies for preventing such assembly.

  15. Beyond simple small-angle X-ray scattering: developments in online complementary techniques and sample environments.

    PubMed

    Bras, Wim; Koizumi, Satoshi; Terrill, Nicholas J

    2014-11-01

    Small- and wide-angle X-ray scattering (SAXS, WAXS) are standard tools in materials research. The simultaneous measurement of SAXS and WAXS data in time-resolved studies has gained popularity due to the complementary information obtained. Furthermore, the combination of these data with non X-ray based techniques, via either simultaneous or independent measurements, has advanced understanding of the driving forces that lead to the structures and morphologies of materials, which in turn give rise to their properties. The simultaneous measurement of different data regimes and types, using either X-rays or neutrons, and the desire to control parameters that initiate and control structural changes have led to greater demands on sample environments. Examples of developments in technique combinations and sample environment design are discussed, together with a brief speculation about promising future developments. PMID:25485128

  16. Beyond simple small-angle X-ray scattering: developments in online complementary techniques and sample environments

    PubMed Central

    Bras, Wim; Koizumi, Satoshi; Terrill, Nicholas J

    2014-01-01

    Small- and wide-angle X-ray scattering (SAXS, WAXS) are standard tools in materials research. The simultaneous measurement of SAXS and WAXS data in time-resolved studies has gained popularity due to the complementary information obtained. Furthermore, the combination of these data with non X-ray based techniques, via either simultaneous or independent measurements, has advanced understanding of the driving forces that lead to the structures and morphologies of materials, which in turn give rise to their properties. The simultaneous measurement of different data regimes and types, using either X-rays or neutrons, and the desire to control parameters that initiate and control structural changes have led to greater demands on sample environments. Examples of developments in technique combinations and sample environment design are discussed, together with a brief speculation about promising future developments. PMID:25485128

  17. Period clustering of anomalous X-ray pulsars

    NASA Astrophysics Data System (ADS)

    Bisnovatyi-Kogan, G. S.; Ikhsanov, N. R.

    2015-06-01

    The question of why the observed periods of anomalous X-ray pulsars (AXPs) and soft gamma-ray repeaters (SGRs) cluster in the range 2-12 s is discussed. The possibility that AXPs and SGRs are the descendants of high-mass X-ray binaries that have disintegrated in core-collapse supernova explosions is investigated. The spin periods of neutron stars in high-mass X-ray binaries evolve towards the equilibrium period, which is a few seconds, on average. After the explosion of its massive companion, the neutron star becomes embedded in a dense gaseous envelope, and accretion from this envelope leads to the formation of a residual magnetically levitating disk. It is shown that the expected mass of the disk in this case is 10-7-10-8 M⊙, which is sufficient to support accretion at the rate 1014-1015 g/s over a few thousand years. During this period, the star manifests itself as an isolated X-ray pulsar with a number of parameters similar to those of AXPs and SGRs. The periods of such pulsars can cluster if the lifetime of the residual disk does not exceed the spin-down timescale of the neutron star.

  18. GENFIT: software for the analysis of small-angle X-ray and neutron scattering data of macro­molecules in solution

    PubMed Central

    Spinozzi, Francesco; Ferrero, Claudio; Ortore, Maria Grazia; De Maria Antolinos, Alejandro; Mariani, Paolo

    2014-01-01

    Many research topics in the fields of condensed matter and the life sciences are based on small-angle X-ray and neutron scattering techniques. With the current rapid progress in source brilliance and detector technology, high data fluxes of ever-increasing quality are produced. In order to exploit such a huge quantity of data and richness of information, wider and more sophisticated approaches to data analysis are needed. Presented here is GENFIT, a new software tool able to fit small-angle scattering data of randomly oriented macromolecular or nanosized systems according to a wide list of models, including form and structure factors. Batches of curves can be analysed simultaneously in terms of common fitting parameters or by expressing the model parameters via physical or phenomenological link functions. The models can also be combined, enabling the user to describe complex heterogeneous systems. PMID:24904247

  19. Linear, position-sensitive x-ray detector used for real-time calculations of small-angle scattering parameters with submillisecond resolution

    SciTech Connect

    Borso, C.S.

    1984-01-01

    The advent of high-intensity X-ray synchrotron sources has made possible the measurement of fluctuations in small-angle scattering parameters from typical specimens on a submillisecond time scale in real-time. The fundamental design of any fast detector system optimized for such measurements will incorporate some type of solid state detector array capable of rapid encoding algorithms. A prototype with a self-scanning photodiode array has been designed and tested at beamline 1 to 4 at the Stanford Synchrotron Radiation Laboratory (SSRL), and the results indicate that the device will operate at speeds yielding submillisecond temporal resolution in real-time.

  20. Salt Dependence of the Radius of Gyration and Flexibility of Single-stranded DNA in Solution probed by Small-angle X-ray Scattering

    SciTech Connect

    Sim, Adelene Y.L.; Lipfert, Jan; Herschlag, Daniel; Doniach, Sebastian

    2012-07-06

    Short single-stranded nucleic acids are ubiquitous in biological processes and understanding their physical properties provides insights to nucleic acid folding and dynamics. We used small angle x-ray scattering to study 8-100 residue homopolymeric single-stranded DNAs in solution, without external forces or labeling probes. Poly-T's structural ensemble changes with increasing ionic strength in a manner consistent with a polyelectrolyte persistence length theory that accounts for molecular flexibility. For any number of residues, poly-A is consistently more elongated than poly-T, likely due to the tendency of A residues to form stronger base-stacking interactions than T residues.

  1. Structural variability of tRNA: small-angle x-ray scattering of the yeast tRNAphe-Escherichia coli tRNAGlu2 complex.

    PubMed Central

    Nilsson, L; Rigler, R; Laggner, P

    1982-01-01

    The structure of the complex formed in solution between yeast tRNAPhe and Escherichia coli tRNAGlu2 has been studied by small-angle x-ray scattering. The complex has a radius of gyration of 4.0 nm and an electron-pair distance distribution that is incompatible with a model composed to two tRNAs joined at their complementary anticodons and exhibiting the L shape seen in the crystal. Instead a model in which the two tRNAs, still bound via the anticodons, assume a conformation with the acceptor arms folded toward the anticodon arms agrees with the observed scattering curves. PMID:6764532

  2. Multiaxial deformation of polyethylene and polyethylene/clay nanocomposites: In situ synchrotron small angle and wide angle X-ray scattering study

    SciTech Connect

    Gurun, Bilge; Bucknall, David G.; Thio, Yonathan S.; Teoh, Chin Ching; Harkin-Jones, Eileen

    2013-01-10

    A unique in situ multiaxial deformation device has been designed and built specifically for simultaneous synchrotron small angle X-ray scattering (SAXS) and wide angle X-ray scattering (WAXS) measurements. SAXS and WAXS patterns of high-density polyethylene (HDPE) and HDPE/clay nanocomposites were measured in real time during in situ multiaxial deformation at room temperature and at 55 C. It was observed that the morphological evolution of polyethylene is affected by the existence of clay platelets as well as the deformation temperature and strain rate. Martensitic transformation of orthorhombic into monoclinic crystal phases was observed under strain in HDPE, which is delayed and hindered in the presence of clay nanoplatelets. From the SAXS measurements, it was observed that the thickness of the interlamellar amorphous region increased with increasing strain, which is due to elongation of the amorphous chains. The increase in amorphous layer thickness is slightly higher for the nanocomposites compared to the neat polymer.

  3. Gas gain operations with single photon resolution using an integrating ionization chamber in small-angle X-ray scattering experiments

    NASA Astrophysics Data System (ADS)

    Menk, R. H.; Sarvestani, A.; Besch, H. J.; Walenta, A. H.; Amenitsch, H.; Bernstorff, S.

    2000-01-01

    In this work a combination of an ionization chamber with one-dimensional spatial resolution and a MicroCAT structure will be presented. Initially, MicroCAT was thought of as a shielding grid (Frisch-grid) but later was used as an active electron amplification device that enables single X-ray photon resolution measurements at low fluxes even with integrating readout electronics. Moreover, the adjustable gas gain that continuously covers the entire range from pure ionization chamber mode up to high gas gains (30 000 and more) provides stable operation yielding a huge dynamic range of about 10 8 and more. First measurements on biological samples using small angle X-ray scattering techniques with synchrotron radiation will be presented.

  4. Detection of short range order in SiO2 thin-films by grazing-incidence wide and small-angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Nagata, Kohki; Ogura, Atsushi; Hirosawa, Ichiro; Suwa, Tomoyuki; Teramoto, Akinobu; Ohmi, Tadahiro

    2016-04-01

    The effects of the fabrication process conditions on the microstructure of silicon dioxide thin films of <10 nm thickness are presented. The microstructure was investigated using grazing-incidence wide and small-angle X-ray scattering methods with synchrotron radiation. The combination of a high brilliance light source and grazing incident configuration enabled the observation of very weak diffuse X-ray scattering from SiO2 thin films. The results revealed different microstructures, which were dependent on oxidizing species or temperature. The micro-level properties differed from bulk properties reported in the previous literature. It was indicated that these differences originate from inner stress. The detailed structure in an amorphous thin film was not revealed owing to detection difficulties.

  5. Small angle X-ray scattering study of the effect of pressure on the aggregation of asphaltene fractions in petroleum fluids under near-critical solvent conditions

    SciTech Connect

    Carnahan, N.F.; Quintero, L. ); Pfund, D.M.; Fulton, J.L.; Smith, R.D. ); Capel, M. ); Leontaritis, K. )

    1993-08-01

    Small angle X-ray scattering was used to determine the effect of pressure on the extent of asphaltene aggregation for a system under near-critical conditions. A mixture containing 60 vol% Crude Oil A in n-pentane was studied at 110[degree]C, at pressures ranging from 25 to 400 bar. As the pressure of the near-critical solution is isothermally decreased, these results indicate (1) an increase in the extent of asphaltene aggregation and/or; (2) increased attractive interactions among aggregates. Information derived from different regions of the X-ray scattering curve indicate increasing aggregation with decreasing pressure. From these experimental results, together with theoretical interpretation, we infer that as the pressure is reduced, increased aggregation of asphaltenes results which may contribute to formation damage in hydrocarbon reservoirs, and to fouling in hydrotreatment and cracking catalysts. 71 refs., 10 figs., 2 tabs.

  6. Small-Angle X-Ray Scattering on the ChemMatCARS Beamline at the Advanced Photon Source: A Study of Shear-Induced Crystallisation in Polypropylene

    SciTech Connect

    Sutton, D.; Hanley, T.; Knott, R.; Cookson, D.

    2008-09-08

    The first ever time-resolved small-angle X-ray scattering (SAXS) data from the undulator 15-ID-D beamline (ChemMatCARS) are presented. A 1.3 {angstrom} (9.54 keV) X-ray beam was selected to study the structure development in a polypropylene sample during shear-induced crystallization. A Linkam CSS450 shear cell provided the temperature and shear control. The polypropylene was first melted and then quenched to the crystallization temperature, where a step shear was applied. The SAXS data were collected using a Bruker 6000 CCD detector, which provided images of excellent resolution. The SAXS images (with 180{sup o} rotational symmetry) indicated that the polypropylene crystallizes with a high degree of anisotropy, and the lamellae are oriented perpendicular to the flow direction.

  7. Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small angle X-ray scattering

    PubMed Central

    Rambo, Robert P.; Tainer, John A.

    2010-01-01

    Summary Small-Angle X-ray Scattering (SAXS) is changing how we perceive biological structures, because it reveals dynamic macromolecular conformations and assemblies in solution. SAXS information captures thermodynamic ensembles, enhances static structures detailed by high-resolution methods, uncovers commonalities among diverse macromolecules, and helps define biological mechanisms. SAXS-based experiments on RNA riboswitches and ribozymes and on DNA-protein complexes including DNA-PK and p53 discover flexibilities that better define structure-function relationships. Furthermore, SAXS results suggest conformational variation is a general functional feature of macromolecules. Thus, accurate structural analyses will require a comprehensive approach that assesses both flexibility, as seen by SAXS, and detail, as determined by X-ray crystallography and NMR. Here, we review recent SAXS computational tools, technologies, and applications to nucleic acids and related structures. PMID:20097063

  8. A high-speed one-dimensional detector for time-resolved small-angle x-ray scattering : design and characterization.

    SciTech Connect

    De Lurgio, P. M.; Drake, G. R.; Krepps, A. S.; Jennings, G.; Weizeorick, J. T.; Molitsky, M. J.; Naday, I.; Hessler, J. P.

    2010-06-01

    A high-speed one-dimensional detector for time-resolved small-angle x-ray scattering has been designed and built for experiments at the Advanced Photon Source of Argonne National Laboratory. This detector is made from a 500-{mu}m thick by 150-mm diameter ultra-high-purity n-type silicon wafer. The electrodes, which are a series of concentric rings that are deposited in the wafer, integrate the scattered x-rays over the azimuthal angle and, thereby, produce a one-dimensional detector. This design yields 128 rings, which allows parallel processing of the signal from each ring. The readout electronics consist of transimpedance front-end amplifiers, one for each ring, followed by active pulse-shaping filters. The amplifier signals are digitized using 12-bit analog-to-digital converters, one per ring, which operate at 20 MHz. The frame rate of the system is 271 kHz. Up to 2{sup 20} - 1 scattering profiles may be stored on a random access memory chip and transferred to a data file at a rate of 16 x 10{sup 3} profiles/sec. For X-ray energies between 3.5 and 13.2 keV the efficiency exceeds 80%. The resolving time of the electronics is 300 ns, which is sufficient to isolate electronically a single pulse of scattered x-rays when the synchrotron is operated in a hybrid or asymmetric fill pattern. Therefore, laser-pump/x-ray-probe experiments can be performed without a mechanical shutter. Examples of time-resolved speckle and the kinetics of the formation of sodium chloride particles are presented. This detector is capable of acquiring small-angle x-ray scattering profiles over multiple time scales, which are needed to characterize many chemical, physical, and biological processes. In addition, this detector may be tested and calibrated before experimental runs, without access to an intense beam of x-rays, with alpha particles from a radioactive source such as {sup 241}Am.

  9. A high-speed one-dimensional detector for time-resolved small-angle x-ray scattering: design, construction, and characterization.

    SciTech Connect

    De Lurgio, P. M.; Drake, G. R.; Kreps, A. S.; Jennings, G.; Weizeorick, J. T.; Molitsky, M. J.; Naday, I.; Hessler, J. P.

    2010-06-01

    A high-speed one-dimensional detector for time-resolved small-angle x-ray scattering has been designed and built for experiments at the Advanced Photon Source of Argonne National Laboratory. This detector is made from a 500-{micro}m thick by 150-mm diameter ultra-high-purity n-type silicon wafer. The electrodes, which are a series of concentric rings that are deposited in the wafer, integrate the scattered x-rays over the azimuthal angle and, thereby, produce a one-dimensional detector. This design yields 128 rings, which allows parallel processing of the signal from each ring. The readout electronics consist of transimpedance front-end amplifiers, one for each ring, followed by active pulse-shaping filters. The amplifier signals are digitized using 12-bit analog-to-digital converters, one per ring, which operate at 20 MHz. The frame rate of the system is 271 kHz. Up to 2{sup 20} - 1 scattering profiles may be stored on a random access memory chip and transferred to a data file at a rate of 16 x 10{sup 3} profiles/sec. For X-ray energies between 3.5 and 13.2 keV the efficiency exceeds 80%. The resolving time of the electronics is 300 ns, which is sufficient to isolate electronically a single pulse of scattered x-rays when the synchrotron is operated in a hybrid or asymmetric fill pattern. Therefore, laser-pump/x-ray-probe experiments can be performed without a mechanical shutter. Examples of time-resolved speckle and the kinetics of the formation of sodium chloride particles are presented. This detector is capable of acquiring small-angle x-ray scattering profiles over multiple time scales, which are needed to characterize many chemical, physical, and biological processes. In addition, this detector may be tested and calibrated before experimental runs, without access to an intense beam of x-rays, with alpha particles from a radioactive source such as {sup 241}Am.

  10. A high-speed one-dimensional detector for time-resolved small -angle X-ray scattering : design and characterization.

    SciTech Connect

    De Lurgio, P. M.; Drake, G. R.; Kreps, A. S.; Jennings, G.; Weizeorick, J. T.; Molitsky, M. J.; Naday, I.; Hessler, J. P.; Illinois Inst. of Tech.; Aviex L.L.C.

    2010-06-01

    A high-speed one-dimensional detector for time-resolved small-angle x-ray scattering has been designed and built for experiments at the Advanced Photon Source of Argonne National Laboratory. This detector is made from a 500-?m thick by 150-mm diameter ultra-high-purity n-type silicon wafer. The electrodes, which are a series of concentric rings that are deposited in the wafer, integrate the scattered x-rays over the azimuthal angle and, thereby, produce a one-dimensional detector. This design yields 128 rings, which allows parallel processing of the signal from each ring. The readout electronics consist of transimpedance front-end amplifiers, one for each ring, followed by active pulse-shaping filters. The amplifier signals are digitized using 12-bit analog-to-digital converters, one per ring, which operate at 20 MHz. The frame rate of the system is 271 kHz. Up to 220 - 1 scattering profiles may be stored on a random access memory chip and transferred to a data file at a rate of 16 x 103 profiles/sec. For X-ray energies between 3.5 and 13.2 keV the efficiency exceeds 80%. The resolving time of the electronics is 300 ns, which is sufficient to isolate electronically a single pulse of scattered x-rays when the synchrotron is operated in a hybrid or asymmetric fill pattern. Therefore, laser-pump/x-ray-probe experiments can be performed without a mechanical shutter. Examples of time-resolved speckle and the kinetics of the formation of sodium chloride particles are presented. This detector is capable of acquiring small-angle x-ray scattering profiles over multiple time scales, which are needed to characterize many chemical, physical, and biological processes. In addition, this detector may be tested and calibrated before experimental runs, without access to an intense beam of x-rays, with alpha particles from a radioactive source such as 241Am.

  11. Structural characterization of the N-terminal part of the MERS-CoV nucleocapsid by X-ray diffraction and small-angle X-ray scattering.

    PubMed

    Papageorgiou, Nicolas; Lichière, Julie; Baklouti, Amal; Ferron, François; Sévajol, Marion; Canard, Bruno; Coutard, Bruno

    2016-02-01

    The N protein of coronaviruses is a multifunctional protein that is organized into several domains. The N-terminal part is composed of an intrinsically disordered region (IDR) followed by a structured domain called the N-terminal domain (NTD). In this study, the structure determination of the N-terminal region of the MERS-CoV N protein via X-ray diffraction measurements is reported at a resolution of 2.4 Å. Since the first 30 amino acids were not resolved by X-ray diffraction, the structural study was completed by a SAXS experiment to propose a structural model including the IDR. This model presents the N-terminal region of the MERS-CoV as a monomer that displays structural features in common with other coronavirus NTDs. PMID:26894667

  12. A customizable software for fast reduction and analysis of large X-ray scattering data sets: applications of the new DPDAK package to small-angle X-ray scattering and grazing-incidence small-angle X-ray scattering

    PubMed Central

    Benecke, Gunthard; Wagermaier, Wolfgang; Li, Chenghao; Schwartzkopf, Matthias; Flucke, Gero; Hoerth, Rebecca; Zizak, Ivo; Burghammer, Manfred; Metwalli, Ezzeldin; Müller-Buschbaum, Peter; Trebbin, Martin; Förster, Stephan; Paris, Oskar; Roth, Stephan V.; Fratzl, Peter

    2014-01-01

    X-ray scattering experiments at synchrotron sources are characterized by large and constantly increasing amounts of data. The great number of files generated during a synchrotron experiment is often a limiting factor in the analysis of the data, since appropriate software is rarely available to perform fast and tailored data processing. Furthermore, it is often necessary to perform online data reduction and analysis during the experiment in order to interactively optimize experimental design. This article presents an open-source software package developed to process large amounts of data from synchrotron scattering experiments. These data reduction processes involve calibration and correction of raw data, one- or two-dimensional integration, as well as fitting and further analysis of the data, including the extraction of certain parameters. The software, DPDAK (directly programmable data analysis kit), is based on a plug-in structure and allows individual extension in accordance with the requirements of the user. The article demonstrates the use of DPDAK for on- and offline analysis of scanning small-angle X-ray scattering (SAXS) data on biological samples and microfluidic systems, as well as for a comprehensive analysis of grazing-incidence SAXS data. In addition to a comparison with existing software packages, the structure of DPDAK and the possibilities and limitations are discussed. PMID:25294982

  13. Microfluidic Platforms for on-chip Formulation and Small-Angle x-ray Analysis of the Phase Behavior of Lipid/Water Mixtures

    SciTech Connect

    Khvostichenko, Daria S.; Perry, Sarah L.; Kondrashkina, Elena; Guha, Sudipto; Brister, Keith; Kenis, Paul J.A.

    2012-03-27

    We present a microfluidic platform for on-chip formulation and X-ray analysis of lipidic mesophases formed upon mixing lipids and water. The platform is designed to study the effect of detergents on the phase behavior of lipid/water mixtures. The platform allows automated preparation of multiple samples of different composition from stock solutions and subsequent on-chip small-angle X-ray diffraction (SAXS) data collection. To ensure X-ray transparency of the platform we used thin layers of cyclic olefin copolymer (COC) and PDMS. The viability of the platform is demonstrated by mapping out a section of the phase diagram for lipid monoolein mixed with solutions of detergent {beta}-octylglucoside. The platform reported here is a viable alternative to the traditional method of establishing phase diagrams for lipid/solution mixtures. Compared to the conventional approach, a significantly smaller amount of sample is required for mapping phase diagrams of lipidic mesophases and samples of various compositions are prepared automatically. In ongoing work we are using these chips to rapidly determine the phase behavior of a range of lipids to establish their suitability for membrane protein crystallization, especially with respect to their sensitivity to detergent concentration.

  14. Small-angle and wide-angle X-ray scattering study on the bilayer structure of synthetic and bovine heart cardiolipins

    NASA Astrophysics Data System (ADS)

    Takahashi, Hiroshi; Hayakawa, Tomohiro; Ito, Kazuki; Takata, Masaki; Kobayashi, Toshihide

    2010-10-01

    Cardiolipin (CL) is a membrane phospholipid containing four fatty acid chains. CL plays an important role in energy transformation in mitochondria. The disorder of CL biosynthesis is involved in a genetic disease, Barth syndrome. Alteration of fatty acid composition of CLs has been found in Barth syndrome patients, i.e., the decrease of unsaturated fatty acid chains. In this study, we investigated how the degree of saturation alters the structure of CL bilayers by using X-ray scattering. Bovine heart CL and two synthetic CLs were compared. Fatty acid compositions of these three CLs have different saturation. Small-angle X-ray scattering data showed that the decrease of the number of double bonds in the unsaturated fatty acid chains causes to thicken the CL bilayers. In addition, wide-angle X-ray scattering data suggested that the decrease reduces the degree of disorder of the hydrophobic region in a liquid crystalline phase. These results may be related to the dysfunction of mitochondria in Barth syndrome.

  15. Ultrahigh vacuum/high-pressure flow reactor for surface x-ray diffraction and grazing incidence small angle x-ray scattering studies close to conditions for industrial catalysis

    SciTech Connect

    Rijn, R. van; Ackermann, M. D.; Balmes, O.; Dufrane, T.; Gonzalez, H.; Isern, H.; Petit, L.; Sole, V. A.; Wermeille, D.; Felici, R.; Geluk, A.; Kuyper, E. de; Frenken, J. W. M.

    2010-01-15

    A versatile instrument for the in situ study of catalyst surfaces by surface x-ray diffraction and grazing incidence small angle x-ray scattering in a 13 ml flow reactor combined with reaction product analysis by mass spectrometry has been developed. The instrument bridges the so-called ''pressure gap'' and ''materials gap'' at the same time, within one experimental setup. It allows for the preparation and study of catalytically active single crystal surfaces and is also equipped with an evaporator for the deposition of thin, pure metal films, necessary for the formation of small metal particles on oxide supports. Reactions can be studied in flow mode and batch mode in a pressure range of 100-1200 mbar and temperatures up to 950 K. The setup provides a unique combination of sample preparation, characterization, and in situ experiments where the structure and reactivity of both single crystals and supported nanoparticles can be simultaneously determined.

  16. In Operando Monitoring of the Pore Dynamics in Ordered Mesoporous Electrode Materials by Small Angle X-ray Scattering.

    PubMed

    Park, Gwi Ok; Yoon, Jeongbae; Park, Eunjun; Park, Su Bin; Kim, Hyunchul; Kim, Kyoung Ho; Jin, Xing; Shin, Tae Joo; Kim, Hansu; Yoon, Won-Sub; Kim, Ji Man

    2015-05-26

    To monitor dynamic volume changes of electrode materials during electrochemical lithium storage and removal process is of utmost importance for developing high performance lithium storage materials. We herein report an in operando probing of mesoscopic structural changes in ordered mesoporous electrode materials during cycling with synchrotron-based small angel X-ray scattering (SAXS) technique. In operando SAXS studies combined with electrochemical and other physical characterizations straightforwardly show how porous electrode materials underwent volume changes during the whole process of charge and discharge, with respect to their own reaction mechanism with lithium. This comprehensive information on the pore dynamics as well as volume changes of the electrode materials will not only be critical in further understanding of lithium ion storage reaction mechanism of materials, but also enable the innovative design of high performance nanostructured materials for next generation batteries. PMID:25869353

  17. Small angle x-ray scattering of chromatin. Radius and mass per unit length depend on linker length.

    PubMed Central

    Williams, S P; Langmore, J P

    1991-01-01

    Analyses of low angle x-ray scattering from chromatin, isolated by identical procedures but from different species, indicate that fiber diameter and number of nucleosomes per unit length increase with the amount of nucleosome linker DNA. Experiments were conducted at physiological ionic strength to obtain parameters reflecting the structure most likely present in living cells. Guinier analyses were performed on scattering from solutions of soluble chromatin from Necturus maculosus erythrocytes (linker length 48 bp), chicken erythrocytes (linker length 64 bp), and Thyone briareus sperm (linker length 87 bp). The results were extrapolated to infinite dilution to eliminate interparticle contributions to the scattering. Cross-sectional radii of gyration were found to be 10.9 +/- 0.5, 12.1 +/- 0.4, and 15.9 +/- 0.5 nm for Necturus, chicken, and Thyone chromatin, respectively, which are consistent with fiber diameters of 30.8, 34.2, and 45.0 nm. Mass per unit lengths were found to be 6.9 +/- 0.5, 8.3 +/- 0.6, and 11.8 +/- 1.4 nucleosomes per 10 nm for Necturus, chicken, and Thyone chromatin, respectively. The geometrical consequences of the experimental mass per unit lengths and radii of gyration are consistent with a conserved interaction among nucleosomes. Cross-linking agents were found to have little effect on fiber external geometry, but significant effect on internal structure. The absolute values of fiber diameter and mass per unit length, and their dependencies upon linker length agree with the predictions of the double-helical crossed-linker model. A compilation of all published x-ray scattering data from the last decade indicates that the relationship between chromatin structure and linker length is consistent with data obtained by other investigators. Images FIGURE 1 PMID:2049522

  18. Interaction between lamellar (vesicles) and nonlamellar lipid liquid-crystalline nanoparticles as studied by time-resolved small-angle X-ray diffraction.

    PubMed

    Vandoolaeghe, Pauline; Barauskas, Justas; Johnsson, Markus; Tiberg, Fredrïk; Nylander, Tommy

    2009-04-01

    The kinetics of structure change when dispersions of two different types of lipid-based liquid-crystalline phases, one lamellar and one reversed, are mixed has been investigated using synchrotron small-angle X-ray diffraction and ellipsometry. The systems studied were (i) cubic-phase nanoparticles (CPNPs) based on glycerol monooleate (GMO) stabilized with a nonionic block copolymer, Pluronic F-127; (ii) CPNPs based on phytantriol (PtOH) stabilized with D-alpha-Tocopheryl polyethylene glycol 1000 succinate (Vitamin E TPGS); and (iii) hexagonal-phase nanoparticles (HPNPs) based on a lipid mixture of diglycerol monooleate/glycerol dioleate, stabilized by Pluronic F-127. Time-resolved small-angle X-ray diffraction was used to track structural changes within nonlamellar nanoparticles when they interact with uni- and multilamellar vesicles of dioleoylphosphatidylcholine and dipalmitoylphatidylcholine. The results are very dependent on the type of nanoparticles under investigation. For GMO-based CPNPs, a strong interaction is observed on mixing with vesicular dispersions that leads to large changes in unit size dimensions as well as a later transition from cubic to lamellar structure. These results are in good agreement with previous studies on the interaction of GMO-based CPNPs with planar bilayers using neutron reflectivity, where the diffraction peak shifted with time upon mixing. The structural changes are much less prominent for the PtOH-based CPNPs and the HPNPs upon mixing with phospholipid vesicles. These results are correlated with those from measurement studying interactions between the liquid-crystalline nanoparticles and supported phospholipid bilayers by ellipsometry. Also, here the GMO-based CPNPs show more pronounced and rapid adsorption and interaction with the supported bilayer surface than do the other types of nonlamellar nanoparticles. The interaction also depends on the bilayer properties, where significantly slower lipid mixing is observed for a

  19. Anomalous X-ray Diffraction Studies for Photovoltaic Applications

    SciTech Connect

    Not Available

    2011-06-22

    Anomalous X-ray Diffraction (AXRD) has become a useful technique in characterizing bulk and nanomaterials as it provides specific information about the crystal structure of materials. In this project we present the results of AXRD applied to materials for photovoltaic applications: ZnO loaded with Ga and ZnCo{sub 2}O{sub 4} spinel. The X-ray diffraction data collected for various energies were plotted in Origin software. The peaks were fitted using different functions including Pseudo Voigt, Gaussian, and Lorentzian. This fitting provided the integrated intensity data (peaks area values), which when plotted as a function of X-ray energies determined the material structure. For the first analyzed sample, Ga was not incorporated into the ZnO crystal structure. For the ZnCo{sub 2}O{sub 4} spinel Co was found in one or both tetrahedral and octahedral sites. The use of anomalous X-ray diffraction (AXRD) provides element and site specific information for the crystal structure of a material. This technique lets us correlate the structure to the electronic properties of the materials as it allows us to probe precise locations of cations in the spinel structure. What makes it possible is that in AXRD the diffraction pattern is measured at a number of energies near an X-ray absorption edge of an element of interest. The atomic scattering strength of an element varies near its absorption edge and hence the total intensity of the diffraction peak changes by changing the X-ray energy. Thus AXRD provides element specific structural information. This method can be applied to both crystalline and liquid materials. One of the advantages of AXRD in crystallography experiments is its sensitivity to neighboring elements in the periodic tables. This method is also sensitive to specific crystallographic phases and to a specific site in a phase. The main use of AXRD in this study is for transparent conductors (TCs) analysis. TCs are considered to be important materials because of their

  20. Small-Angle X-ray Scattering Demonstrates Similar Nanostructure in Cortical Bone from Young Adult Animals of Different Species.

    PubMed

    Kaspersen, Jørn Døvling; Turunen, Mikael Juhani; Mathavan, Neashan; Lages, Sebastian; Pedersen, Jan Skov; Olsson, Ulf; Isaksson, Hanna

    2016-07-01

    Despite the vast amount of studies focusing on bone nanostructure that have been performed for several decades, doubts regarding the detailed structure of the constituting hydroxyapatite crystal still exist. Different experimental techniques report somewhat different sizes and locations, possibly due to different requirements for the sample preparation. In this study, small- and wide-angle X-ray scattering is used to investigate the nanostructure of femur samples from young adult ovine, bovine, porcine, and murine cortical bone, including three different orthogonal directions relative to the long axis of the bone. The radially averaged scattering from all samples reveals a remarkable similarity in the entire q range, which indicates that the nanostructure is essentially the same in all species. Small differences in the data from different directions confirm that the crystals are elongated in the [001] direction and that this direction is parallel to the long axis of the bone. A model consisting of thin plates is successfully employed to describe the scattering and extract the plate thicknesses, which are found to be in the range of 20-40 Å for most samples but 40-60 Å for the cow samples. It is demonstrated that the mineral plates have a large degree of polydispersity in plate thickness. Additionally, and equally importantly, the scattering data and the model are critically evaluated in terms of model uncertainties and overall information content. PMID:26914607

  1. A new look at anomalous X-ray Pulsars

    NASA Astrophysics Data System (ADS)

    Bisnovatyi-Kogan, G. S.; Ikhsanov, N. R.

    2014-04-01

    We explore the possibility of explaining Anomalous X-ray Pulsars (AXPs) and Soft Gammaray Repeaters (SGRs) in a scenario with fall-back magnetic accretion onto a young isolated neutron star. The X-ray emission of the pulsar in this case originates due to the accretion of matter onto the surface of the neutron star from a magnetic slab surrounding its magnetosphere. The spin-down rate of the neutron star expected in this picture is close to the observed value. We show that such neutron stars are relatively young and are going through the transition from the propeller state to the accretor state. The pulsar's activity in gamma-rays is connected with its relative youth, and is enabled by energy stored in a non-equilibrium layer located in the crust of the low-mass neutron star. This energy can be released due to the mixing of matter in the neutron star crust with super heavy nuclei approaching its surface and becoming unstable. The fission of nuclei in the low-density region initiates chain reactions leading to a nuclear explosion. Outbursts are probably triggered by instability developing in the region where the matter accreted by the neutron star accumulates in the magnetic polar regions.

  2. Unraveling the Nanostructure and Chain Conformation of Peptide-polymer Conjugates in Solution using Small-angle X-ray Scattering

    NASA Astrophysics Data System (ADS)

    Lund, Reidar; Xu, Ting; Dong, He

    For therapeutics, polymer functionalization, often by poly(ethylene glycol), PEG (``PEGylation''), is an effective method to improve the solubility, increase the life time and protect the proteins from the immune system[1]. However it is essential that the proteins maintain their structural integrity in solution- thus the role of the polymer and their interactions with proteins needs to be understood. In this work we show how small-angle X-ray scattering (SAXS) can be used as a powerful technique to characterize the structural components of peptide-polymer conjugates in solution [2, 3]. We specifically show that by applying detailed modelling very detailed structural features can be revealed, including the PEG chain conformation. In the presentation we will provide an overview of the methodology, specifically addressing peptides that form either alpha-helical bundles [2, 3] or beta-sheet structures [4, 5] and relate their structure in solution to their crystal structure.

  3. Study of Small Angle X-Ray Scattering Features of Acid- and Alkali-Treated Silk Fibre (Mulberry) Using Correlation Functions

    NASA Astrophysics Data System (ADS)

    Misra, Tripurari; Panda, Pramoda; Patel, Tnkadhar; Bisoyi, Dillip K.; Panda, Dillip K.

    1993-10-01

    Silk fibres at room temperature after treatment with solutions of HCl (pH=2) and NaOH (pH=10) have been investigated using the SAXS (small angle X-ray scattering) technique. The theories developed by Vonk (1973) and Ruland (1971) for nonideal two-phase structure characterised by continuous variation of electron density at the phase boundary have been applied to calculate various macromolecular parameters such as the width of transition layer, the average periodicity transverse to the layer, the specific inner surface, the length of coherence, the transversal lengths in matter and void, the range of inhomogeneity, the volume fractions of matter and void, the volume fraction of the transition layer and the characteristic number.

  4. Structural evolution of perpendicular lamellae in diblock copolymer thin films during solvent vapor treatment investigated by grazing-incidence small-angle X-ray scattering.

    PubMed

    Zhang, Jianqi; Posselt, Dorthe; Sepe, Alessandro; Shen, Xuhu; Perlich, Jan; Smilgies, Detlef-M; Papadakis, Christine M

    2013-08-01

    The structural evolution in poly(styrene-b-butadiene) (P(S-b-B)) diblock copolymer thin films during solvent vapor treatment is investigated in situ using time-resolved grazing-incidence small-angle X-ray scattering (GISAXS). Using incident angles above and below the polymer critical angle, structural changes near the film surface and in the entire film are distinguished. The swelling of the film is one-dimensional along the normal of the substrate. During swelling, the initially perpendicular lamellae tilt within the film to be able to shrink. In contrast, at the film surface, the lamellae stay perpendicular, and eventually vanish at the expense of a thin PB wetting layer. During the subsequent drying, the perpendicular lamellae reappear at the surface, and finally, PS blocks protrude. By modeling, the time-dependent height of the protrusions can be quantitatively extracted. PMID:23843127

  5. Note: Comparison of grazing incidence small angle x-ray scattering of a titania sponge structure at the beamlines BW4 (DORIS III) and P03 (PETRA III)

    SciTech Connect

    Rawolle, M.; Koerstgens, V.; Ruderer, M. A.; Metwalli, E.; Guo, S.; Mueller-Buschbaum, P.; Herzog, G.; Benecke, G.; Schwartzkopf, M.; Buffet, A.; Perlich, J.; Roth, S. V.

    2012-10-15

    Grazing incidence small angle x-ray scattering (GISAXS) is a powerful technique for morphology investigation of nanostructured thin films. GISAXS measurements at the newly installed P03 beamline at the storage ring PETRA III in Hamburg, Germany, are compared to the GISAXS data from the beamline BW4 at the storage ring DORIS III, which had been used extensively for GISAXS investigations in the past. As an example, a titania thin film sponge structure is investigated. Compared to BW4, at beamline P03 the resolution of larger structures is slightly improved and a higher incident flux leads to a factor of 750 in scattered intensity. Therefore, the acquisition time in GISAXS geometry is reduced significantly at beamline P03.

  6. Study of the Crystalline Morphology Evolution of PET and PET/PC Blends by Time-resolved Synchrotron Small Angle X-ray Scattering (SAXS) and DSC

    SciTech Connect

    Barbosa, Irineu; Larocca, Nelson M.; Hage, Elias; Plivelic, Tomas S.; Torriani, Iris L.; Mantovani, Gerson L.

    2009-01-29

    Isothermal melt crystallization of poly(ethylene terephthalate)(PET) and PET/PC (polycarbonate) blend, with and without a transesterification catalyst, was studied by time-resolved small-angle X-ray scattering (SAXS) and differential scanning calorimetry (DSC) in order to achieve the variation of the morphological parameters throughout the whole crystallization time. For neat PET, the catalyst promotes a decrease of the crystal lamellar thickness but for the blend no variations were observed. The effect of incorporation of catalyst in crystallization kinetics was very distinct in PET pure and the blend: in the former the catalyst leads to an increase of this kinetics while for the latter it was observed a decreasing.

  7. Nanostructure characterization of Co-Pd-Si-O soft magnetic nanogranular film using small-angle X-ray and neutronscattering

    NASA Astrophysics Data System (ADS)

    Oba, Yojiro; Ohnuma, Masato; Ohnuma, Shigehiro; Furusaka, Michihiro; Koppoju, Suresh; Takeda, Shin

    2013-05-01

    The nanostructure of a Co-Pd-Si-O nanogranular film was investigated with the combined use of small-angle x-ray (SAXS) and neutron scattering (SANS). Using a new, compact type of SANS instrument, the SANS profiles of individual particles with a diameter of about 2-4 nm were successfully observed. The structures of magnetic regions were found to be the same as the chemical structures of the particles, and a sharp interface was observed between the matrix and the particles. The SAXS to SANS ratio clearly indicates that the particles are a CoPd alloy and the matrix is not pure SiO2. In fact, the matrix is composed of a meaningful amountof Co.

  8. In situ study of the state of lysozyme molecules at the very early stage of the crystallization process by small-angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Marchenkova, M. A.; Volkov, V. V.; Blagov, A. E.; Dyakova, Yu. A.; Ilina, K. B.; Tereschenko, E. Yu.; Timofeev, V. I.; Pisarevsky, Yu. V.; Kovalchuk, M. V.

    2016-01-01

    The molecular state of hen egg white lysozyme in solution has been studied by small-angle X-ray scattering (SAXS) combined with molecular simulation. The addition of a precipitant is shown to change the state of the protein molecules in solution. The SAXS data were processed using the constructed models of different oligomers. Under the crystallization conditions, lysozyme is shown to be present in solution as monomers (96.0%), dimers (1.9%), and octamers (2.1%), whereas tetramers and hexamers are not found. The modeled structure of the octamer is not consistent with the commonly accepted unit cell containing eight lysozyme molecules. Meanwhile, the modeled octamers are well-fitted to the crystal structure and can serve as building blocks in the course of crystal growth.

  9. In situ synchrotron study of liquid phase separation process in Al-10 wt.% Bi immiscible alloys by radiography and small angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Lu, W. Q.; Zhang, S. G.; Li, J. G.

    2016-03-01

    Liquid phase separation process of immiscible alloys has been repeatedly tuned to create special structure for developing materials with unique properties. However, the fundamental understanding of the liquid phase separation process is still under debate due to the characteristics of immiscible alloys in opacity and high temperature environment of alloy melt. Here, the liquid phase separation process in solidifying Al-Bi immiscible alloys was investigated by synchrotron radiography and small angle X-ray scattering. We provide the first direct evidence of surface segregation prior to liquid decomposition and present that the time dependence on the number of Bi droplets follows Logistic curve. The liquid decomposition results from a nucleation and growth process rather than spinodal decomposition mechanism because of the positive deviation from Porod's law. We also found that the nanometer-sized Bi-rich droplets in Al matrix melt present mass fractal characteristics.

  10. Structural Resolution of the Complex between a Fungal Polygalacturonase and a Plant Polygalacturonase-Inhibiting Protein by Small-Angle X-Ray Scattering1[W

    PubMed Central

    Benedetti, Manuel; Leggio, Claudia; Federici, Luca; De Lorenzo, Giulia; Pavel, Nicolae Viorel; Cervone, Felice

    2011-01-01

    We report here the low-resolution structure of the complex formed by the endo-polygalacturonase from Fusarium phyllophilum and one of the polygalacturonase-inhibiting protein from Phaseolus vulgaris after chemical cross-linking as determined by small-angle x-ray scattering analysis. The inhibitor engages its concave surface of the leucine-rich repeat domain with the enzyme. Both sides of the enzyme active site cleft interact with the inhibitor, accounting for the competitive mechanism of inhibition observed. The structure is in agreement with previous site-directed mutagenesis data and has been further validated with structure-guided mutations and subsequent assay of the inhibitory activity. The structure of the complex may help the design of inhibitors with improved or new recognition capabilities to be used for crop protection. PMID:21859985

  11. Melting and Sintering of a Body-Centered Cubic Superlattice of PbSe Nanocrystals Followed by Small Angle X-ray Scattering

    PubMed Central

    Goodfellow, Brian W.; Patel, Reken N.; Panthani, Matthew G.; Smilgies, Detlef-M.; Korgel, Brian A.

    2011-01-01

    The structural evolution of a body-centered cubic (bcc) superlattice of 6.6 nm diameter organic ligand-coated PbSe nanocrystals was studied in situ by small angle X-ray scattering (SAXS) as it was heated in air from room temperature to 350°C. As it was heated above room temperature, the superlattice contracted slightly, but maintained bcc structure up to 110°C. Once the temperature rose above 110°C, the superlattice began to disorder, by first losing long-range translational order and then local positional order. At temperatures exceeding 168°C, the nanocrystals sintered and oxidized, transforming into PbSeO3 nanorods. PMID:21566701

  12. In-Situ Small-Angle X-Ray Scattering Study of Simple Shear Oriented Poly(ethylene Terephthalate) during Heating

    NASA Astrophysics Data System (ADS)

    Wang, Zhigang; Xia, Zhiyong; Hsiao, Benjamin; Sue, Hj; Han, Charles

    2002-03-01

    An equal channel angular extrusion (ECAE) process was used to prepare poly(ethylene terephthalate) samples with segmental lamellar orientations. In-situ small-angle X-ray scattering measurements were carried out to follow the structure changes during heating of sections of equal-channel-angular-extruded PET samples before and after the transition line. The total scattering power, fractions of anisotropic and isotropic scattering, orientation factors and long periods along the flow directions were obtained. The changes in these parameters revealed the processes of lamellar relaxation, recrystallization and melting during heating in specimens of different orientation and morphology. Acknowledgements. The financial support of this work is provided by a grant from NIST and NSF (DMR 0098104). The Advanced Polymers Beamline is supported by DOE (DE-FG02-99ER 45760).

  13. Transformation from Multilamellar to Unilamellar Vesicles by Addition of a Cationic Lipid to PEGylated Liposomes Explored with Synchrotron Small Angle X-ray Scattering

    NASA Astrophysics Data System (ADS)

    Sakuragi, Mina; Koiwai, Kazunori; Nakamura, Kouji; Masunaga, Hiroyasu; Ogawa, Hiroki; Sakurai, Kazuo

    2011-01-01

    PEGylated liposomes composed of a benzamidine derivative (TRX), hydrogenated soybean phosphatidylcholine (HSPC), and N-(monomethoxy-polyethyleneglycolcarbamyl) distearoyl phosphatidylethanolamine (PEG-PE) were examined in terms of how the addition of TRX affects their structures with small angle x-ray scattering (SAXS) as well as transmission electron microscopy (TEM). TEM images showed the presence of unilamella vesicles for both with and without TRX, though a small amount of multilamella vesicles were observed in absence of TRX. We analyzed SAXS profiles at contained TRX composition combined with contrast variation technique by adding PEG solution and unilamella vesicle model could be reproduced. Subsequently, we analyzed SAXS profiles at no TRX composition. The mixture model of unilamella and multilamella vesicle was reconstructed and we estimated about 10 % multilamella vesicles from a fitting parameter.

  14. Effect of compressed CO2 on the size and stability of reverse micelles: Small-angle x-ray scattering and phase behavior study

    NASA Astrophysics Data System (ADS)

    Zhang, Jianling; Han, Buxing; Liu, Juncheng; Zhang, Xiaogang; Yang, Guanying; He, Jun; Liu, Zhimin; Jiang, Tao; Wang, Jun; Dong, Baozhong

    2003-02-01

    Synchrotron radiation small-angle x-ray scattering (SAXS) and phase behavior investigations were combined to study the effect of compressed CO2 on the stability and structure of sodium bis(2-ethylhexyl)sulfosuccinate (AOT) reverse micelles in isooctane at different temperatures, CO2 pressures, AOT concentrations, and the molar ratios of water to surfactant w ([H2O]/[AOT]). SAXS measurements indicate that the size of the reverse micelles depends markedly on the pressure of CO2 and w. Increasing pressure of CO2 results in reduction of the micellar size. The effect of CO2 pressure on the size and structure of the reverse micelles is nearly independent of the concentration of the surfactant. The results of SAXS also give the information about the stability of the reverse micelles, which agrees with that obtained from the phase behavior investigation.

  15. Effects of detergents on the oligomeric structures of hemolytic lectin CEL-III as determined by small-angle X-ray scattering.

    PubMed

    Goda, Shuichiro; Sadakata, Hitoshi; Unno, Hideaki; Hatakeyama, Tomomitsu

    2013-01-01

    Hemolytic lectin CEL-III isolated from the sea cucumber Cucumaria echinata forms transmembrane pores by self-oligomerization in target cell membranes. It also formed soluble oligomers in aqueous solution upon binding with specific carbohydrates under conditions of high pH and a high salt concentration. The size of the soluble CEL-III oligomers decreased when treated with detergents such as Triton X-100 and SDS. Small-angle X-ray scattering measurements suggested that the dissociated unit of the oligomer was a tightly associated CEL-III heptamer. Without detergents in solution, these heptamers further assembled into larger 21mer oligomers, comprising three heptamers held together by relatively weak hydrophobic interactions. PMID:23470749

  16. Effect of additives on distributions of lamellar structures in sheared polymer: a study of synchrotron small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Zhu, Peng-Wei; Edward, Graham; Nichols, Lance

    2009-12-01

    The effects of additives on the distributions of lamellar morphology and orientation in sheared isotactic polypropylene were investigated using the small beam of synchrotron small-angle x-ray scattering. The Cu-phthalocyanine can template the lamellar orientation even under low shear rates, whereas the ultramarine blue cannot. The surface contact is suggested to play a role in stabilizing the formation of oriented nuclei which subsequently direct the growth of oriented lamellae. The additives have no notable effects on the long spacing in the shear region. However, at high shear rates, they decrease the thickness of crystalline lamellae or increase the thickness of amorphous lamellae. Since the additives increase the degree of volume crystalline in the shear region, the number of crystalline lamellae should be increased. The results are helpful in designing and selecting suitable additives for controlling lamellar morphology and orientation.

  17. Crystal Structures and Small-angle X-ray Scattering Analysis of UDP-galactopyranose Mutase from the Pathogenic Fungus Aspergillus fumigatus

    SciTech Connect

    Dhatwalia, Richa; Singh, Harkewal; Oppenheimer, Michelle; Karr, Dale B.; Nix, Jay C.; Sobrado, Pablo; Tanner, John J.

    2015-10-15

    UDP-galactopyranose mutase (UGM) is a flavoenzyme that catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, which is a central reaction in galactofuranose biosynthesis. Galactofuranose has never been found in humans but is an essential building block of the cell wall and extracellular matrix of many bacteria, fungi, and protozoa. The importance of UGM for the viability of many pathogens and its absence in humans make UGM a potential drug target. Here we report the first crystal structures and small-angle x-ray scattering data for UGM from the fungus Aspergillus fumigatus, the causative agent of aspergillosis. The structures reveal that Aspergillus UGM has several extra secondary and tertiary structural elements that are not found in bacterial UGMs yet are important for substrate recognition and oligomerization. Small-angle x-ray scattering data show that Aspergillus UGM forms a tetramer in solution, which is unprecedented for UGMs. The binding of UDP or the substrate induces profound conformational changes in the enzyme. Two loops on opposite sides of the active site move toward each other by over 10 {angstrom} to cover the substrate and create a closed active site. The degree of substrate-induced conformational change exceeds that of bacterial UGMs and is a direct consequence of the unique quaternary structure of Aspergillus UGM. Galactopyranose binds at the re face of the FAD isoalloxazine with the anomeric carbon atom poised for nucleophilic attack by the FAD N5 atom. The structural data provide new insight into substrate recognition and the catalytic mechanism and thus will aid inhibitor design.

  18. The role of counterions on the elasticity of highly charged lamellar phases: A small-angle x-ray and neutron-scattering determination

    NASA Astrophysics Data System (ADS)

    Brotons, Guillaume; Dubois, Monique; Belloni, Luc; Grillo, Isabelle; Narayanan, Theyencheri; Zemb, Thomas

    2005-07-01

    The structure and fluctuations of the swollen Lα lamellar phase of highly charged surfactant didodecyldimethylammonium halide fluid bilayers (DDA+X-) are studied using high-resolution small-angle x-ray scattering and medium-resolution, high-contrast small-angle neutron-scattering. The Caillé parameter η, as a function of the swelling (Lα periodicity d), was determined from the full q-range fits of the measured scattering profiles for three different counterions (X-=Cl-, Br-, and NO3-). This parameter quantifies the amplitude of the membrane fluctuations within the Landau-de Gennes smectic-A linear elasticity theory. The different anions used gave strong specific effects at the maximum swelling of the Lα phase, while at lower swellings a two-phase coexistence of swollen and collapsed lamellae (d ˜30 and ˜80Å) was observed for bromide and nitrate ions. Over the intermediate dilution range for all three counterions, a single Lα phase can be continuously swollen with pure water which is governed by an equation of state (i.e., osmotic pressure versus period) and thermally excited fluctuation amplitudes that can be well described by the same Poisson-Boltzmann calculation. The membranes were found to be slightly stiffer than predicted by purely electrostatic repulsions, and this is tentatively attributed to an extra bending rigidity contribution from the surfactant chains.

  19. Domain Movements upon Activation of Phenylalanine Hydroxylase Characterized by Crystallography and Chromatography-Coupled Small-Angle X-ray Scattering.

    PubMed

    Meisburger, Steve P; Taylor, Alexander B; Khan, Crystal A; Zhang, Shengnan; Fitzpatrick, Paul F; Ando, Nozomi

    2016-05-25

    Mammalian phenylalanine hydroxylase (PheH) is an allosteric enzyme that catalyzes the first step in the catabolism of the amino acid phenylalanine. Following allosteric activation by high phenylalanine levels, the enzyme catalyzes the pterin-dependent conversion of phenylalanine to tyrosine. Inability to control elevated phenylalanine levels in the blood leads to increased risk of mental disabilities commonly associated with the inherited metabolic disorder, phenylketonuria. Although extensively studied, structural changes associated with allosteric activation in mammalian PheH have been elusive. Here, we examine the complex allosteric mechanisms of rat PheH using X-ray crystallography, isothermal titration calorimetry (ITC), and small-angle X-ray scattering (SAXS). We describe crystal structures of the preactivated state of the PheH tetramer depicting the regulatory domains docked against the catalytic domains and preventing substrate binding. Using SAXS, we further describe the domain movements involved in allosteric activation of PheH in solution and present the first demonstration of chromatography-coupled SAXS with Evolving Factor Analysis (EFA), a powerful method for separating scattering components in a model-independent way. Together, these results support a model for allostery in PheH in which phenylalanine stabilizes the dimerization of the regulatory domains and exposes the active site for substrate binding and other structural changes needed for activity. PMID:27145334

  20. Small angle x-ray scattering of a supercritical electrolyte solution: the effect of density fluctuations on the hydration of ions.

    PubMed

    Testemale, Denis; Coulet, Marie Vanessa; Hazemann, Jean Louis; Simon, Jean Paul; Bley, Françoise; Geaymond, Olivier; Argoud, Roger

    2005-05-15

    Synchrotron small angle x-ray scattering measurements on water and zinc bromide ZnBr2 aqueous solutions were carried out from ambient to supercritical conditions. For both systems several isobars (between 285 and 600 bars) were followed beyond the critical isochore. The data were analyzed through an Ornstein-Zernike formalism in terms of correlation length and null angle structure factor. The results for pure water are in agreement with previously published values. Solutions of different electrolyte concentrations were studied. In each case, the values of the correlation length and null angle structure factor are larger than those of pure water. This effect is more pronounced for higher concentrations and/or for pressure closer to the critical point of pure water. This is in agreement with the shift of the critical point determined in the literature for NaCl solutions. Comparing these results to previous x-ray absorption measurements carried out on identical samples we propose the following two step sequence for ionic hydration up to supercritical conditions: (1) from ambient to about 300 degrees C, an increase of ion pairing and formation of multi-ionic complexes which can be correlated to the decrease of the dielectric constant; (2) an enhancement of the local solvation shell of ions due to the onset of the thermal density fluctuations at high temperature, leading to a screening effect between ions and inhibiting the ion pairing processes. PMID:16161595

  1. Small angle x-ray scattering of a supercritical electrolyte solution: The effect of density fluctuations on the hydration of ions

    NASA Astrophysics Data System (ADS)

    Testemale, Denis; Coulet, Marie Vanessa; Hazemann, Jean Louis; Simon, Jean Paul; Bley, Françoise; Geaymond, Olivier; Argoud, Roger

    2005-05-01

    Synchrotron small angle x-ray scattering measurements on water and zinc bromide ZnBr2 aqueous solutions were carried out from ambient to supercritical conditions. For both systems several isobars (between 285 and 600bars) were followed beyond the critical isochore. The data were analyzed through an Ornstein-Zernike formalism in terms of correlation length and null angle structure factor. The results for pure water are in agreement with previously published values. Solutions of different electrolyte concentrations were studied. In each case, the values of the correlation length and null angle structure factor are larger than those of pure water. This effect is more pronounced for higher concentrations and/or for pressure closer to the critical point of pure water. This is in agreement with the shift of the critical point determined in the literature for NaCl solutions. Comparing these results to previous x-ray absorption measurements carried out on identical samples we propose the following two step sequence for ionic hydration up to supercritical conditions: (1) from ambient to about 300°C, an increase of ion pairing and formation of multi-ionic complexes which can be correlated to the decrease of the dielectric constant; (2) an enhancement of the local solvation shell of ions due to the onset of the thermal density fluctuations at high temperature, leading to a screening effect between ions and inhibiting the ion pairing processes.

  2. Characterization of Lipid-Templated Silica and Hybrid Thin Film Mesophases by Grazing Incidence Small-Angle X-ray Scattering

    PubMed Central

    Dunphy, Darren R.; Alam, Todd M.; Tate, Michael P.; Hillhouse, Hugh W.; Smarsly, Bernd; Collord, Andrew D.; Carnes, Eric; Baca, Helen K.; Köhn, Ralf; Sprung, Michael; Wang, Jin; Brinker, C. Jeffrey

    2009-01-01

    The nanostructure of silica and hybrid thin film mesophases templated by phospholipids via an evaporation-induced self-assembly (EISA) process was investigated by grazing-incidence small-angle X-ray scattering (GISAXS). Diacyl phosphatidylcholines with two tails of 6 or 8 carbons were found to template 2D hexagonal mesophases, with the removal of lipid from these lipid/silica films by thermal or UV/O3 processing resulting in a complete collapse of the pore volume. Monoacyl phosphatidylcholines with single tails of 10–14 carbons formed 3D micellular mesophases; the lipid was found to be extractable from these 3D materials, yielding a porous material. In contrast to pure lipid/silica thin film mesophases, films formed from the hybrid bridged silsesquioxane precursor bis(triethoxysilyl)ethane exhibited greater stability toward (both diacyl and monoacyl) lipid removal. Ellipsometric, FTIR, and NMR studies show that the presence of phospholipid suppresses siloxane network formation, while actually promoting condensation reactions in the hybrid material. 1D X-ray scattering and FTIR data were found to be consistent with strong interactions between lipid headgroups and the silica framework. PMID:19496546

  3. Element-selective investigation of domain structure in CoPd and FePd alloys using small-angle soft X-ray scattering

    NASA Astrophysics Data System (ADS)

    Weier, C.; Adam, R.; Frömter, R.; Bach, J.; Winkler, G.; Kobs, A.; Oepen, H. P.; Grychtol, P.; Kapteyn, H. C.; Murnane, M. M.; Schneider, C. M.

    2014-03-01

    Recent optical pump-probe experiments on magnetic multilayers and alloys identified perpendicular spin superdiffusion as one of possible mechanisms responsible for femtosecond magnetization dynamics. On the other hand, no strong evidence for the ultrafast lateral spin transport has been reported, so far. To address this question, we studied magnetic domain structure of CoPd and FePd thin films using small-angle scattering of soft X-rays. By tuning the synchrotron-generated X-rays to the absorption edges of Fe or Co we recorded Fourier images of the magnetic domain structure corresponding to a chosen element. Applying in - situ magnetic fields resulted in pronounced rearrangement of domain structure that was clearly observed in scattering images. Our analysis of both the stand-alone, as well as magnetically coupled CoPd/FePd layers provides insight into the formation of domains under small magnetic field perturbations and pave the way to better understanding of transient changes expected in magneto-dynamic measurements.

  4. An Optimized Table-Top Small-Angle X-ray Scattering Set-up for the Nanoscale Structural Analysis of Soft Matter

    NASA Astrophysics Data System (ADS)

    Sibillano, T.; de Caro, L.; Altamura, D.; Siliqi, D.; Ramella, M.; Boccafoschi, F.; Ciasca, G.; Campi, G.; Tirinato, L.; di Fabrizio, E.; Giannini, C.

    2014-11-01

    The paper shows how a table top superbright microfocus laboratory X-ray source and an innovative restoring-data algorithm, used in combination, allow to analyze the super molecular structure of soft matter by means of Small Angle X-ray Scattering ex-situ experiments. The proposed theoretical approach is aimed to restore diffraction features from SAXS profiles collected from low scattering biomaterials or soft tissues, and therefore to deal with extremely noisy diffraction SAXS profiles/maps. As biological test cases we inspected: i) residues of exosomes' drops from healthy epithelial colon cell line and colorectal cancer cells; ii) collagen/human elastin artificial scaffolds developed for vascular tissue engineering applications; iii) apoferritin protein in solution. Our results show how this combination can provide morphological/structural nanoscale information to characterize new artificial biomaterials and/or to get insight into the transition between healthy and pathological tissues during the progression of a disease, or to morphologically characterize nanoscale proteins, based on SAXS data collected in a room-sized laboratory.

  5. Small angle X-ray scattering analysis of the effect of cold compaction of Al/MoO3 thermite composites.

    PubMed

    Hammons, Joshua A; Wang, Wei; Ilavsky, Jan; Pantoya, Michelle L; Weeks, Brandon L; Vaughn, Mark W

    2008-01-01

    Nanothermites composed of aluminum and molybdenum trioxide (MoO(3)) have a high energy density and are attractive energetic materials. To enhance the surface contact between the spherical Al nanoparticles and the sheet-like MoO(3) particles, the mixture can be cold-pressed into a pelleted composite. However, it was found that the burn rate of the pellets decreased as the density of the pellets increased, contrary to expectation. Ultra-small angle X-ray scattering (USAXS) data and scanning electron microscopy (SEM) were used to elucidate the internal structure of the Al nanoparticles, and nanoparticle aggregate in the composite. Results from both SEM imaging and USAXS analysis indicate that as the density of the pellet increased, a fraction of the Al nanoparticles are compressed into sintered aggregates. The sintered Al nanoparticles lost contrast after forming the larger aggregates and no longer scattered X-rays as individual particles. The sintered aggregates hinder the burn rate, since the Al nanoparticles that make them up can no longer diffuse freely as individual particles during combustion. Results suggest a qualitative relationship for the probability that nanoparticles will sinter, based on the particle sizes and the initial structure of their respective agglomerates, as characterized by the mass fractal dimension. PMID:18075699

  6. A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements.

    PubMed

    Wang, Jinbu; Zuo, Xiaobing; Yu, Ping; Xu, Huan; Starich, Mary R; Tiede, David M; Shapiro, Bruce A; Schwieters, Charles D; Wang, Yun-Xing

    2009-10-30

    We report a "top-down" method that uses mainly duplexes' global orientations and overall molecular dimension and shape restraints, which were extracted from experimental NMR and small-angle X-ray scattering data, respectively, to determine global architectures of RNA molecules consisting of mostly A-form-like duplexes. The method is implemented in the G2G (from global measurement to global structure) toolkit of programs. We demonstrate the efficiency and accuracy of the method by determining the global structure of a 71-nt RNA using experimental data. The backbone root-mean-square deviation of the ensemble of the calculated global structures relative to the X-ray crystal structure is 3.0+/-0.3 A using the experimental data and is only 2.5+/-0.2 A for the three duplexes that were orientation restrained during the calculation. The global structure simplifies interpretation of multidimensional nuclear Overhauser spectra for high-resolution structure determination. The potential general application of the method for RNA structure determination is discussed. PMID:19666030

  7. Line Edge Roughness and Cross Sectional Characterization of Sub-50 nm Structures Using Critical Dimension Small Angle X-ray Scattering

    SciTech Connect

    Wang Chengqing; Jones, Ronald L.; Lin, Eric K.; Wu Wenli; Ho, Derek L.; Villarrubia, John S.; Choi, Kwang-Woo; Clarke, James S.; Roberts, Jeanette; Bristol, Robert; Bunday, Benjamin

    2007-09-26

    The need to characterize line edge and line width roughness in patterns with sub-50 nm critical dimensions challenges existing platforms based on electron microscopy and optical scatterometry. The development of x-ray based metrology platforms provides a potential route to characterize a variety of parameters related to line edge roughness by analyzing the diffracted intensity from a periodic array of test patterns. In this study, data from a series of photoresist line/space patterns featuring programmed line width roughness are measured by critical dimension small angle x-ray scattering (CD-SAXS). For samples with designed periodic roughness, CD-SAXS provides the wavelength and amplitude of the periodic roughness through satellite diffraction peaks. For real world applications, the rate of decay of intensity, termed an effective 'Debye-Waller' factor in CD-SAXS, provides an overall measure of the defects of the patterns. CD-SAXS data are compared to values obtained from critical dimension scanning electron microscopy (CD-SEM). Correlations between the techniques exist, however significant differences are observed for the current samples. A tapered cross sectional profile provides a likely explanation for the observed differences between CD-SEM and CD-SAXS measurements.

  8. Small-angle X-ray scattering and crystallographic studies of arcelin-1: an insecticidal lectin-like glycoprotein from Phaseolus vulgaris L.

    PubMed

    Mourey, L; Pédelacq, J D; Fabre, C; Causse, H; Rougé, P; Samama, J P

    1997-12-01

    Arcelin-1 and alpha-amylase inhibitor are two lectin-like glycoproteins expressed in the seeds of the kidney bean (Phaseolus vulgaris). They display insecticidal activities and protect the seeds from predation by larvae of various bruchids through different biological actions. Solution-state investigations by small-angle X-ray scattering (SAXS) show the dimeric structure of arcelin-1, a requirement for its hemagglutinating properties. Anions were found to have specific properties in their effectiveness to disrupt protein aggregates, affect solubility, and improve crystallizability. The SAXS results were used to improve crystallization conditions, and single crystals diffracting beyond 1.9 A resolution were obtained. X-ray diffraction data analysis shows that noncrystallographic symmetry-related arcelin-1 molecules form a lectin-like dimer and reveals the presence of a solvent-exposed anion binding site on the protein, at a crystal-packing interface. The solution state properties of arcelin-1 and crystal twinning may be explained by the anion specificity of this binding site. PMID:9408941

  9. Coagulation of Na-montmorillonite by inorganic cations at neutral pH. A combined transmission X-ray microscopy, small angle and wide angle X-ray scattering study.

    PubMed

    Michot, Laurent J; Bihannic, Isabelle; Thomas, Fabien; Lartiges, Bruno S; Waldvogel, Yves; Caillet, Céline; Thieme, Juergen; Funari, Sérgio S; Levitz, Pierre

    2013-03-12

    The coagulation of sodium montmorillonite by inorganic salts (NaNO3, Ca(NO3)2 and La(NO3)3) was studied by combining classical turbidity measurements with wide-angle-X-ray scattering (WAXS), small-angle-X-ray scattering (SAXS), and transmission X-ray microscopy (TXM). Using size-selected samples, such a combination, associated with an original quantitative treatment of TXM images, provides a true multiscale investigation of the formed structures in a spatial range extending from a few ångstroms to a few micrometers. We then show that, at neutral pH and starting with fully Na-exchanged samples, coagulation proceeds via the formation of stacks of particles with a slight mismatch between layers. These stacks arrange themselves into larger porous anisotropic particles, the porosity of which depends on the valence of the cation used for coagulation experiments. Face-face coagulation is clearly dominant under those conditions, and no evidence for significant face-edge coagulation was found. These structures appear to arrange as larger clusters, the organization of which should control the mechanical properties of the flocs. PMID:23421550

  10. A Mo-anode-based in-house source for small-angle X-ray scattering measurements of biological macromolecules

    NASA Astrophysics Data System (ADS)

    Bruetzel, Linda K.; Fischer, Stefan; Salditt, Annalena; Sedlak, Steffen M.; Nickel, Bert; Lipfert, Jan

    2016-02-01

    We demonstrate the use of a molybdenum-anode-based in-house small-angle X-ray scattering (SAXS) setup to study biological macromolecules in solution. Our system consists of a microfocus X-ray tube delivering a highly collimated flux of 2.5 × 106 photons/s at a beam size of 1.2 × 1.2 mm2 at the collimation path exit and a maximum beam divergence of 0.16 mrad. The resulting observable scattering vectors q are in the range of 0.38 Å-1 down to 0.009 Å-1 in SAXS configuration and of 0.26 Å-1 up to 5.7 Å-1 in wide-angle X-ray scattering (WAXS) mode. To determine the capabilities of the instrument, we collected SAXS data on weakly scattering biological macromolecules including proteins and a nucleic acid sample with molecular weights varying from ˜12 to 69 kDa and concentrations of 1.5-24 mg/ml. The measured scattering data display a high signal-to-noise ratio up to q-values of ˜0.2 Å-1 allowing for an accurate structural characterization of the samples. Moreover, the in-house source data are of sufficient quality to perform ab initio 3D structure reconstructions that are in excellent agreement with the available crystallographic structures. In addition, measurements for the detergent decyl-maltoside show that the setup can be used to determine the size, shape, and interactions (as characterized by the second virial coefficient) of detergent micelles. This demonstrates that the use of a Mo-anode based in-house source is sufficient to determine basic geometric parameters and 3D shapes of biomolecules and presents a viable alternative to valuable beam time at third generation synchrotron sources.

  11. A Mo-anode-based in-house source for small-angle X-ray scattering measurements of biological macromolecules.

    PubMed

    Bruetzel, Linda K; Fischer, Stefan; Salditt, Annalena; Sedlak, Steffen M; Nickel, Bert; Lipfert, Jan

    2016-02-01

    We demonstrate the use of a molybdenum-anode-based in-house small-angle X-ray scattering (SAXS) setup to study biological macromolecules in solution. Our system consists of a microfocus X-ray tube delivering a highly collimated flux of 2.5 × 10(6) photons/s at a beam size of 1.2 × 1.2 mm(2) at the collimation path exit and a maximum beam divergence of 0.16 mrad. The resulting observable scattering vectors q are in the range of 0.38 Å(-1) down to 0.009 Å(-1) in SAXS configuration and of 0.26 Å(-1) up to 5.7 Å(-1) in wide-angle X-ray scattering (WAXS) mode. To determine the capabilities of the instrument, we collected SAXS data on weakly scattering biological macromolecules including proteins and a nucleic acid sample with molecular weights varying from ∼12 to 69 kDa and concentrations of 1.5-24 mg/ml. The measured scattering data display a high signal-to-noise ratio up to q-values of ∼0.2 Å(-1) allowing for an accurate structural characterization of the samples. Moreover, the in-house source data are of sufficient quality to perform ab initio 3D structure reconstructions that are in excellent agreement with the available crystallographic structures. In addition, measurements for the detergent decyl-maltoside show that the setup can be used to determine the size, shape, and interactions (as characterized by the second virial coefficient) of detergent micelles. This demonstrates that the use of a Mo-anode based in-house source is sufficient to determine basic geometric parameters and 3D shapes of biomolecules and presents a viable alternative to valuable beam time at third generation synchrotron sources. PMID:26931887

  12. Difference in hydration structures between F-actin and myosin subfragment-1 detected by small-angle X-ray and neutron scattering

    PubMed Central

    Matsuo, Tatsuhito; Arata, Toshiaki; Oda, Toshiro; Fujiwara, Satoru

    2013-01-01

    Hydration structures around F-actin and myosin subfragment-1 (S1), which play central roles as counterparts in muscle contraction, were investigated by small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS). The radius of gyration of chymotryptic S1 was evaluated to be 41.3±1.1 Å for SAXS, 40.1±3.0 Å for SANS in H2O, and 37.8±0.8 Å for SANS in D2O, respectively. The values of the cross-sectional radius of gyration of F-actin were 25.4±0.03 Å for SAXS, 23.4±2.4 Å for SANS in H2O, and 22.6 ± 0.6 Å for SANS in D2O, respectively. These differences arise from different contributions of the hydration shell to the scattering curves. Analysis by model calculations showed that the hydration shell of S1 has the average density 10–15% higher than bulk water, being the typical hydration shell. On the other hand, the hydration shell of F-actin has the average density more than 19% higher than bulk water, indicating that F-actin has a denser, unusual hydration structure. The results indicate a difference in the hydration structures around F-actin and S1. The unusual hydration structure around F-actin may have the structural property of so-called “hyper-mobile water” around F-actin. PMID:27493547

  13. Small angle x-ray scattering: Instrument development and studies of protein aggregation, cellulose hydrolysis, and the production of nanoporous metals using surfactact templates

    NASA Astrophysics Data System (ADS)

    Banuelos, Jose Leobardo

    Small angle x-ray scattering (SAXS) was used to obtain structural insights into protein aggregation, the enzymatic hydrolysis of cellulose, and the structural evolution of surfactant-templated nanoporous palladium and platinum systems during their synthesis. SAXS is bulk technique that allows probing the nanometer-scale morphology, interactions, density, and distribution of a variety of nonperiodic systems in the solid, liquid, or gaseous state. A 10-meter Small Angle Scattering camera, originally at ORNL, was assembled. During its re-commissioning, several upgrades were made including new data acquisition software built using National Instrument's Labview development environment, as well as portability to use analysis tools in wide use in scattering community. The Multiple Energy Diffractometer Using Small, medium and wide Angles (MEDUSA) was designed and built, its development will be discussed. The ability of proteins to change their conformation in response to changes in pressure, temperature, the presence of other molecular species, and ionic concentration in the solvents they are found, is a remarkable phenomenon that allows living cells to function properly. When proteins irreversibly unfold or mis-fold and aggregate this gives rise to severely debilitating diseases such as Alzheimer's and prion diseases. Protein aggregation was measured using SAXS on aqueous solutions of bovine serum albumin, myoglobin, and cellulase enzymes. Understanding how cellulose can be broken down into fermentable sugars is an important step in the development of strategies for producing alternative energy from biomass. The enzymatic hydrolysis of cellulose was studied using both small angle neutron scattering and SAXS. One result from these investigations was finding supporting evidence that nanopores within the cellulose fibril matrix allow biologically active enzymes access to digest parts of the fibers. The production of mesoporous materials for hydrogen storage applications was

  14. Studies of protein-protein and protein-water interactions by small angle x-ray scattering, terahertz spectroscopy, ASMOS, and computer simulation

    NASA Astrophysics Data System (ADS)

    Kim, Seung Joong

    The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 microm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

  15. MgATP-induced conformational changes in the iron protein from Azotobacter vinelandii, as studied by small-angle x-ray scattering.

    PubMed

    Chen, L; Gavini, N; Tsuruta, H; Eliezer, D; Burgess, B K; Doniach, S; Hodgson, K O

    1994-02-01

    Small angle x-ray scattering experiments have been carried out on the purified iron proteins of nitrogenase from wild-type Azotobacter vinelandii and from a Nif- mutant strain, A. vinelandii UW91 (which has an A157S mutation). This study was designed to investigate the influence of MgATP and MgADP binding on the protein structure in solution. For the wild-type protein, the binding of MgATP induces a significant conformational change that is observed as a decrease of about 2.0 A in the radius of gyration. In contrast, the binding of MgADP to the wild-type iron protein does not detectably affect the radius of gyration. In the absence of nucleotides, the radius of gyration for the UW91 mutant is indistinguishable from that of the wild-type. However, unlike for the wild-type protein, the radius of gyration of the UW91 iron protein is unaffected by the addition of MgATP. We have previously shown that the UW91 iron protein has a normal [4Fe-4S] cluster and MgATP binding ability but that it is completely blocked for electron transfer and MgATP hydrolysis (Gavini, N., and Burgess, B. K. (1992) J. Biol. Chem. 267, 21179-21186). These x-ray scattering measurements suggest that a conformation different from that of the native state is therefore required for the iron protein to perform electron transfer to the MoFe protein. These results also support the hypothesis that Ala-157 is crucial for the iron protein to establish the electron-transfer-favored conformation induced by MgATP binding. PMID:8106367

  16. The Structure of Human Apolipoprotein A-IV as Revealed by Stable Isotope-assisted Cross-linking, Molecular Dynamics, and Small Angle X-ray Scattering*

    PubMed Central

    Walker, Ryan G.; Deng, Xiaodi; Melchior, John T.; Morris, Jamie; Tso, Patrick; Jones, Martin K.; Segrest, Jere P.; Thompson, Thomas B.; Davidson, W. Sean

    2014-01-01

    Apolipoprotein (apo)A-IV plays important roles in dietary lipid and glucose metabolism, and knowledge of its structure is required to fully understand the molecular basis of these functions. However, typical of the entire class of exchangeable apolipoproteins, its dynamic nature and affinity for lipid has posed challenges to traditional high resolution structural approaches. We previously reported an x-ray crystal structure of a dimeric truncation mutant of apoA-IV, which showed a unique helix-swapping molecular interface. Unfortunately, the structures of the N and C termini that are important for lipid binding were not visualized. To build a more complete model, we used chemical cross-linking to derive distance constraints across the full-length protein. The approach was enhanced with stable isotope labeling to overcome ambiguities in determining molecular span of the cross-links given the remarkable similarities in the monomeric and dimeric apoA-IV structures. Using 51 distance constraints, we created a starting model for full-length monomeric apoA-IV and then subjected it to two modeling approaches: (i) molecular dynamics simulations and (ii) fitting to small angle x-ray scattering data. This resulted in the most detailed models yet for lipid-free monomeric or dimeric apoA-IV. Importantly, these models were of sufficient detail to direct the experimental identification of new functional residues that participate in a “clasp” mechanism to modulate apoA-IV lipid affinity. The isotope-assisted cross-linking approach should prove useful for further study of this family of apolipoproteins in both the lipid-free and -bound states. PMID:24425874

  17. Small-angle X-ray Scattering Studies of the Oligomeric State and Quaternary Structure of the Trifunctional Proline Utilization A (PutA) Flavoprotein from Escherichia coli*

    PubMed Central

    Singh, Ranjan K.; Larson, John D.; Zhu, Weidong; Rambo, Robert P.; Hura, Greg L.; Becker, Donald F.; Tanner, John J.

    2011-01-01

    The trifunctional flavoprotein proline utilization A (PutA) links metabolism and gene regulation in Gram-negative bacteria by catalyzing the two-step oxidation of proline to glutamate and repressing transcription of the proline utilization regulon. Small-angle x-ray scattering (SAXS) and domain deletion analysis were used to obtain solution structural information for the 1320-residue PutA from Escherichia coli. Shape reconstructions show that PutA is a symmetric V-shaped dimer having dimensions of 205 × 85 × 55 Å. The particle consists of two large lobes connected by a 30-Å diameter cylinder. Domain deletion analysis shows that the N-terminal DNA-binding domain mediates dimerization. Rigid body modeling was performed using the crystal structure of the DNA-binding domain and a hybrid x-ray/homology model of residues 87–1113. The calculations suggest that the DNA-binding domain is located in the connecting cylinder, whereas residues 87–1113, which contain the two catalytic active sites, reside in the large lobes. The SAXS data and amino acid sequence analysis suggest that the Δ1-pyrroline-5-carboxylate dehydrogenase domains lack the conventional oligomerization flap, which is unprecedented for the aldehyde dehydrogenase superfamily. The data also provide insight into the function of the 200-residue C-terminal domain. It is proposed that this domain serves as a lid that covers the internal substrate channeling cavity, thus preventing escape of the catalytic intermediate into the bulk medium. Finally, the SAXS model is consistent with a cloaking mechanism of gene regulation whereby interaction of PutA with the membrane hides the DNA-binding surface from the put regulon thereby activating transcription. PMID:22013066

  18. Effects of the environmental factors on the casein micelle structure studied by cryo transmission electron microscopy and small-angle x-ray scattering/ultrasmall-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Marchin, Stéphane; Putaux, Jean-Luc; Pignon, Frédéric; Léonil, Joëlle

    2007-01-01

    Casein micelles are colloidal protein-calcium-transport complexes whose structure has not been unequivocally elucidated. This study used small-angle x-ray scattering (SAXS) and ultrasmall angle x-ray scattering (USAXS) as well as cryo transmission electron microscopy (cryo-TEM) to provide fine structural details on their structure. Cryo-TEM observations of native casein micelles fractionated by differential centrifugation showed that colloidal calcium phosphate appeared as nanoclusters with a diameter of about 2.5nm. They were uniformly distributed in a homogeneous tangled web of caseins and were primarily responsible for the intensity distribution in the SAXS profiles at the highest q vectors corresponding to the internal structure of the casein micelles. A specific demineralization of casein micelles by decreasing the pH from 6.7 to 5.2 resulted in a reduced granular aspect of the micelles observed by cryo-TEM and the existence of a characteristic point of inflection in SAXS profiles. This supports the hypothesis that the smaller substructures detected by SAXS are colloidal calcium phosphate nanoclusters rather than putative submicelles.

  19. In Situ Synchrotron X-Ray Diffraction and Small Angle X-Ray Scattering Studies on Rapidly Heated and Cooled Ti-Al and Al-Cu-Mg Alloys Using Laser-Based Heating

    NASA Astrophysics Data System (ADS)

    Kenel, C.; Schloth, P.; Van Petegem, S.; Fife, J. L.; Grolimund, D.; Menzel, A.; Van Swygenhoven, H.; Leinenbach, C.

    2016-03-01

    Beam-based additive manufacturing (AM) typically involves high cooling rates in a range of 103-104 K/s. Therefore, new techniques are required to understand the non-equilibrium evolution of materials at appropriate time scales. Most technical alloys have not been optimized for such rapid solidification, and microstructural, phase, and elemental solubility behavior can be very different. In this work, the combination of complementary in situ synchrotron micro-x-ray diffraction (microXRD) and small angle x-ray scattering (SAXS) studies with laser-based heating and rapid cooling is presented as an approach to study alloy behavior under processing conditions similar to AM techniques. In rapidly solidified Ti-48Al, the full solidification and phase transformation sequences are observed using microXRD with high temporal resolution. The high cooling rates are achieved by fast heat extraction. Further, the temperature- and cooling rate-dependent precipitation of sub-nanometer clusters in an Al-Cu-Mg alloy can be studied by SAXS. The sensitivity of SAXS on the length scales of the newly formed phases allows their size and fraction to be determined. These techniques are unique tools to help provide a deeper understanding of underlying alloy behavior and its influence on resulting microstructures and properties after AM. Their availability to materials scientists is crucial for both in-depth investigations of novel alloys and also future production of high-quality parts using AM.

  20. Structural analysis of the yeast exosome Rrp6p–Rrp47p complex by small-angle X-ray scattering

    SciTech Connect

    Dedic, Emil; Seweryn, Paulina; Jonstrup, Anette Thyssen; Flygaard, Rasmus Koch; Fedosova, Natalya U.; Hoffmann, Søren Vrønning; Boesen, Thomas; Brodersen, Ditlev Egeskov

    2014-07-18

    Highlights: • We show that S. cerevisiae Rrp6p and Rrp47p stabilise each other in vitro. • We determine molecular envelopes of the Rrp6p–Rrp47p complex by SAXS. • Rrp47p binds at the top of the Rrp6p exonuclease domain. • Rrp47p modulates the activity of Rrp6p on a variety of RNA substrates. • Rrp47p does not affect RNA affinity by Rrp6p. - Abstract: The RNase D-type 3′–5′ exonuclease Rrp6p from Saccharomyces cerevisiae is a nuclear-specific cofactor of the RNA exosome and associates in vivo with Rrp47p (Lrp1p). Here, we show using biochemistry and small-angle X-ray scattering (SAXS) that Rrp6p and Rrp47p associate into a stable, heterodimeric complex with an elongated shape consistent with binding of Rrp47p to the nuclease domain and opposite of the HRDC domain of Rrp6p. Rrp47p reduces the exonucleolytic activity of Rrp6p on both single-stranded and structured RNA substrates without significantly altering the affinity towards RNA or the ability of Rrp6p to degrade RNA secondary structure.

  1. Small-angle x-ray scattering studies of microvoids in amorphous silicon-based semiconductors. Annual subcontract report, 1 February 1992--31 January 1993

    SciTech Connect

    Williamson, D.L.; Jones, S.J.; Chen, Y.

    1994-06-01

    This report describes work to provide now details of the microstructure for the size scale from about 1 nm to 30 nm in high-quality a-Si:H and related alloys prepared by current state-of-the-art deposition methods as well as by now and emerging deposition technologies to help determine the role of microvoids and other density fluctuations in controlling the opto-electronic properties. The objectives are to determine whether the presence of microstructure as detected by small-angle X-ray scattering (SAXS) (1) limits the photovoltaic (PV) properties of device-quality a-Si:H; (2) plays a role in determine the photostability of a-Si:H; and (3) is responsible for degradation of the PV properties due to alloying with Ge, C, and other constituents. We collaborated with several groups that can supply relevant systematic sets of samples and the associated opto-electronic data to help address these issues. The project also included developing a method to standardize the procedures, minimize substrate influences, and implement improved data reduction and modeling methodology.

  2. Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: From protein structure to nanodisk assemblies

    SciTech Connect

    Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B.; Peterlik, Herwig; Jungbauer, Alois; Tscheliessnig, Rupert

    2010-11-07

    Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.

  3. In situ ultra-small-angle X-ray scattering study under uniaxial stretching of colloidal crystals prepared by silica nanoparticles bearing hydrogen-bonding polymer grafts.

    PubMed

    Ishige, Ryohei; Williams, Gregory A; Higaki, Yuji; Ohta, Noboru; Sato, Masugu; Takahara, Atsushi; Guan, Zhibin

    2016-05-01

    A molded film of single-component polymer-grafted nanoparticles (SPNP), consisting of a spherical silica core and densely grafted polymer chains bearing hydrogen-bonding side groups capable of physical crosslinking, was investigated by in situ ultra-small-angle X-ray scattering (USAXS) measurement during a uniaxial stretching process. Static USAXS revealed that the molded SPNP formed a highly oriented twinned face-centered cubic (f.c.c.) lattice structure with the [11-1] plane aligned nearly parallel to the film surface in the initial state. Structural analysis of in situ USAXS using a model of uniaxial deformation induced by rearrangement of the nanoparticles revealed that the f.c.c. lattice was distorted in the stretching direction in proportion to the macroscopic strain until the strain reached 35%, and subsequently changed into other f.c.c. lattices with different orientations. The lattice distortion and structural transition behavior corresponded well to the elastic and plastic deformation regimes, respectively, observed in the stress-strain curve. The attractive interaction of the hydrogen bond is considered to form only at the top surface of the shell and then plays an effective role in cross-linking between nanoparticles. The rearrangement mechanism of the nanoparticles is well accounted for by a strong repulsive interaction between the densely grafted polymer shells of neighboring particles. PMID:27158507

  4. Protein crowding in solution, frozen and freeze-dried states: small-angle neutron and X-ray scattering study of lysozyme/sorbitol/water systems

    NASA Astrophysics Data System (ADS)

    Krueger, Susan; Khodadadi, Sheila; Clark, Nicholas; McAuley, Arnold; Cristiglio, Viviana; Theyencheri, Narayanan; Curtis, Joseph; Shalaev, Evgenyi

    2015-03-01

    For effective preservation, proteins are often stored as frozen solutions or in glassy states using a freeze-drying process. However, aggregation is often observed after freeze-thaw or reconstitution of freeze-dried powder and the stability of the protein is no longer assured. In this study, small-angle neutron and X-ray scattering (SANS and SAXS) have been used to investigate changes in protein-protein interaction distances of a model protein/cryoprotectant system of lysozyme/sorbitol/water, under representative pharmaceutical processing conditions. The results demonstrate the utility of SAXS and SANS methods to monitor protein crowding at different stages of freezing and drying. The SANS measurements of solution samples showed at least one protein interaction peak corresponding to an interaction distance of ~ 90 Å. In the frozen state, two protein interaction peaks were observed by SANS with corresponding interaction distances at 40 Å as well as 90 Å. On the other hand, both SAXS and SANS data for freeze-dried samples showed three peaks, suggesting interaction distances ranging from ~ 15 Å to 170 Å. Possible interpretations of these interaction peaks will be discussed, as well as the role of sorbitol as a cryoprotectant during the freezing and drying process.

  5. Unravelling the shape and structural assembly of the photosynthetic GAPDH-CP12-PRK complex from Arabidopsis thaliana by small-angle X-ray scattering analysis.

    PubMed

    Del Giudice, Alessandra; Pavel, Nicolae Viorel; Galantini, Luciano; Falini, Giuseppe; Trost, Paolo; Fermani, Simona; Sparla, Francesca

    2015-12-01

    Oxygenic photosynthetic organisms produce sugars through the Calvin-Benson cycle, a metabolism that is tightly linked to the light reactions of photosynthesis and is regulated by different mechanisms, including the formation of protein complexes. Two enzymes of the cycle, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK), form a supramolecular complex with the regulatory protein CP12 with the formula (GAPDH-CP122-PRK)2, in which both enzyme activities are transiently inhibited during the night. Small-angle X-ray scattering analysis performed on both the GAPDH-CP12-PRK complex and its components, GAPDH-CP12 and PRK, from Arabidopsis thaliana showed that (i) PRK has an elongated, bent and screwed shape, (ii) the oxidized N-terminal region of CP12 that is not embedded in the GAPDH-CP12 complex prefers a compact conformation and (iii) the interaction of PRK with the N-terminal region of CP12 favours the approach of two GAPDH tetramers. The interaction between the GAPDH tetramers may contribute to the overall stabilization of the GAPDH-CP12-PRK complex, the structure of which is presented here for the first time. PMID:26627646

  6. Morphological transformations in the magnetite biomineralizing protein Mms6 in iron solutions: A small-angle x-ray scattering study

    SciTech Connect

    Zhang, Honghu; Liu, Xunpei; Feng, Shuren; Wang, Wenjie; Schmidt-Rohr, Klaus; Akinc, Mufit; Nilsen-Hamilton, Marit; Vaknin, David; Mallapragada, Surya

    2015-02-10

    In this study, magnetotactic bacteria that produce magnetic nanocrystals of uniform size and well-defined morphologies have inspired the use of biomineralization protein Mms6 to promote formation of uniform magnetic nanocrystals in vitro. Small angle X-ray scattering (SAXS) studies in physiological solutions reveal that Mms6 forms compact globular three-dimensional (3D) micelles (approximately 10 nm in diameter) that are, to a large extent, independent of concentration. In the presence of iron ions in the solutions, the general micellar morphology is preserved, however, with associations among micelles that are induced by iron ions. Compared with Mms6, the m2Mms6 mutant (with the sequence of hydroxyl/carboxyl containing residues in the C-terminal domain shuffled) exhibits subtle morphological changes in the presence of iron ions in solutions. The analysis of the SAXS data is consistent with a hierarchical core–corona micellar structure similar to that found in amphiphilic polymers. The addition of ferric and ferrous iron ions to the protein solution induces morphological changes in the micellar structure by transforming the 3D micelles into objects of reduced dimensionality of 2, with fractal-like characteristics (including Gaussian-chain-like) or, alternatively, platelet-like structures.

  7. Morphological transformations in the magnetite biomineralizing protein Mms6 in iron solutions: A small-angle x-ray scattering study

    DOE PAGESBeta

    Zhang, Honghu; Liu, Xunpei; Feng, Shuren; Wang, Wenjie; Schmidt-Rohr, Klaus; Akinc, Mufit; Nilsen-Hamilton, Marit; Vaknin, David; Mallapragada, Surya

    2015-02-10

    In this study, magnetotactic bacteria that produce magnetic nanocrystals of uniform size and well-defined morphologies have inspired the use of biomineralization protein Mms6 to promote formation of uniform magnetic nanocrystals in vitro. Small angle X-ray scattering (SAXS) studies in physiological solutions reveal that Mms6 forms compact globular three-dimensional (3D) micelles (approximately 10 nm in diameter) that are, to a large extent, independent of concentration. In the presence of iron ions in the solutions, the general micellar morphology is preserved, however, with associations among micelles that are induced by iron ions. Compared with Mms6, the m2Mms6 mutant (with the sequence ofmore » hydroxyl/carboxyl containing residues in the C-terminal domain shuffled) exhibits subtle morphological changes in the presence of iron ions in solutions. The analysis of the SAXS data is consistent with a hierarchical core–corona micellar structure similar to that found in amphiphilic polymers. The addition of ferric and ferrous iron ions to the protein solution induces morphological changes in the micellar structure by transforming the 3D micelles into objects of reduced dimensionality of 2, with fractal-like characteristics (including Gaussian-chain-like) or, alternatively, platelet-like structures.« less

  8. Convective assembly of 2D lattices of virus-like particles visualized by in-situ grazing-incidence small-angle X-ray scattering.

    PubMed

    Ashley, Carlee E; Dunphy, Darren R; Jiang, Zhang; Carnes, Eric C; Yuan, Zhen; Petsev, Dimiter N; Atanassov, Plamen B; Velev, Orlin D; Sprung, Michael; Wang, Jin; Peabody, David S; Brinker, C Jeffrey

    2011-04-18

    The rapid assembly of icosohedral virus-like particles (VLPs) into highly ordered (domain size > 600 nm), oriented 2D superlattices directly onto a solid substrate using convective coating is demonstrated. In-situ grazing-incidence small-angle X-ray scattering (GISAXS) is used to follow the self-assembly process in real time to characterize the mechanism of superlattice formation, with the ultimate goal of tailoring film deposition conditions to optimize long-range order. From water, GISAXS data are consistent with a transport-limited assembly process where convective flow directs assembly of VLPs into a lattice oriented with respect to the water drying line. Addition of a nonvolatile solvent (glycerol) modified this assembly pathway, resulting in non-oriented superlattices with improved long-range order. Modification of electrostatic conditions (solution ionic strength, substrate charge) also alters assembly behavior; however, a comparison of in-situ assembly data between VLPs derived from the bacteriophages MS2 and Qβ show that this assembly process is not fully described by a simple Derjaguin-Landau-Verwey-Overbeek model alone. PMID:21425464

  9. Small angle X-ray scattering data and structure factor fitting for the study of the quaternary structure of the spermidine N-acetyltransferase SpeG

    PubMed Central

    Weigand, Steven; Filippova, Ekaterina V.; Kiryukhina, Olga; Anderson, Wayne F.

    2015-01-01

    Here we describe the treatment of the small-angle X-ray Scattering (SAXS) data used during SpeG quaternary structure study as part of the research article “Substrate induced allosteric change in the quaternary structure of the spermidine N-acetyltransferase SpeG” published in Journal of Molecular Biology [1]. These data were collected on two separate area detectors as separate dilution series of the SpeG and the SpeG with spermine samples along with data from their companion buffers. The data were radially integrated, corrected for incident beam variation, and scaled to absolute units. After subtraction of volume-fraction scaled buffer scattering and division by the SpeG concentration, multiple scattering curves free of an inter-molecular structure factor were derived from the dilution series. Rather than extrapolating to infinite dilution, the structure factor contribution was estimated by fitting to the full set of data provided by dividing the scattering curves of a dilution series by the curve from the most dilute sample in that series. PMID:26793756

  10. Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source

    PubMed Central

    Classen, Scott; Hura, Greg L.; Holton, James M.; Rambo, Robert P.; Rodic, Ivan; McGuire, Patrick J.; Dyer, Kevin; Hammel, Michal; Meigs, George; Frankel, Kenneth A.; Tainer, John A.

    2013-01-01

    The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world’s mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B4C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources. PMID:23396808

  11. Structure of Dimeric and Tetrameric Complexes of the BAR Domain Protein PICK1 Determined by Small-Angle X-Ray Scattering.

    PubMed

    Karlsen, Morten L; Thorsen, Thor S; Johner, Niklaus; Ammendrup-Johnsen, Ina; Erlendsson, Simon; Tian, Xinsheng; Simonsen, Jens B; Høiberg-Nielsen, Rasmus; Christensen, Nikolaj M; Khelashvili, George; Streicher, Werner; Teilum, Kaare; Vestergaard, Bente; Weinstein, Harel; Gether, Ulrik; Arleth, Lise; Madsen, Kenneth L

    2015-07-01

    PICK1 is a neuronal scaffolding protein containing a PDZ domain and an auto-inhibited BAR domain. BAR domains are membrane-sculpting protein modules generating membrane curvature and promoting membrane fission. Previous data suggest that BAR domains are organized in lattice-like arrangements when stabilizing membranes but little is known about structural organization of BAR domains in solution. Through a small-angle X-ray scattering (SAXS) analysis, we determine the structure of dimeric and tetrameric complexes of PICK1 in solution. SAXS and biochemical data reveal a strong propensity of PICK1 to form higher-order structures, and SAXS analysis suggests an offset, parallel mode of BAR-BAR oligomerization. Furthermore, unlike accessory domains in other BAR domain proteins, the positioning of the PDZ domains is flexible, enabling PICK1 to perform long-range, dynamic scaffolding of membrane-associated proteins. Together with functional data, these structural findings are compatible with a model in which oligomerization governs auto-inhibition of BAR domain function. PMID:26073603

  12. Novel in situ setup to study the formation of nanoparticles in the gas phase by small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Shyjumon, I.; Rappolt, M.; Sartori, B.; Amenitsch, H.; Laggner, P.

    2008-04-01

    An in-house built aerosol generator setup for in situ gas phase studies of aerosol and nanoparticles is described. The aerosol generator with an ultrasonic ceramic disk mist maker provides high enough particle concentrations for structural gas phase analysis by synchrotron small angle x-ray scattering (for water ˜4×108droplets/s with a droplet size of ˜2.5μm). The working principle was proved by scattering of gold nanoparticles. For evaporation induced self-assembly studies of nanostructured particles, an additional thermal treatment chamber was included in the setup. The first on-line gas phase data with our setup for mesostructured silica particles are presented for different thermal treatments. Scanning electron microscope imaging revealed the average particle size to be ˜1μm. Furthermore, to quantify their internal nanostructure, diffraction experiments of deposited silica aerosols were carried out and the corresponding electron density map indicates a silica wall thickness of about 1nm.

  13. Polymer-induced transient networks in water-in-oil microemulsions studied by small-angle x-ray and dynamic light scattering

    NASA Astrophysics Data System (ADS)

    Blochowicz, T.; Gögelein, C.; Spehr, T.; Müller, M.; Stühn, B.

    2007-10-01

    We study water-in-oil microemulsions, in particular dispersions of water droplets coated with a monolayer of the anionic surfactant AOT in a continuous phase of n -decane. Upon addition of the amphiphilic triblock copolymer PEO(polyethylenoxide)-PI(polyisoprene)-PEO, a transient network is formed. At constant droplet size we vary the polymer concentration and there is clear evidence for an increasing crosslinking of the droplets from structural investigations with small-angle x-ray scattering. The dynamics of concentration fluctuations consisting of the translational diffusion of the droplets and the relaxation of the network are monitored with photon correlation spectroscopy. We mainly focus on the variation of the dynamic behavior as a function of the number of polymer molecules per droplet and the droplet volume fraction, which may be taken as a measure for the interdroplet distance. With increasing polymer content the dynamics of the system slows down and three different relaxation processes may be distinguished. We discuss the origin of the different relaxation modes. In particular, it turns out that the intermediate relaxation mode may be suppressed by index matching the oil matrix and the PI block and that it is effectively slowed down by an additional loading of the emulsion droplets with polyethylene glycol of increasing molecular weight.

  14. The occludin and ZO-1 complex, defined by small angle X-ray scattering and NMR, has implications for modulating tight junction permeability.

    PubMed

    Tash, Brian R; Bewley, Maria C; Russo, Mariano; Keil, Jason M; Griffin, Kathleen A; Sundstrom, Jeffrey M; Antonetti, David A; Tian, Fang; Flanagan, John M

    2012-07-01

    Tight junctions (TJs) are dynamic cellular structures that are critical for compartmentalizing environments within tissues and regulating transport of small molecules, ions, and fluids. Phosphorylation-dependent binding of the transmembrane protein occludin to the structural organizing protein ZO-1 contributes to the regulation of barrier properties; however, the details of their interaction are controversial. Using small angle X-ray scattering (SAXS), NMR chemical shift perturbation, cross-saturation, in vitro binding, and site-directed mutagenesis experiments. we define the interface between the ZO-1 PDZ3-SH3-U5-GuK (PSG) and occludin coiled-coil (CC) domains. The interface is comprised of basic residues in PSG and an acidic region in CC. Complex formation is blocked by a peptide (REESEEYM) that corresponds to CC residues 468-475 and includes a previously uncharacterized phosphosite, with the phosphorylated version having a larger effect. Furthermore, mutation of E470 and E472 reduces cell border localization of occludin. Together, these results localize the interaction to an acidic region in CC and a predominantly basic helix V within the ZO-1 GuK domain. This model has important implications for the phosphorylation-dependent regulation of the occludin:ZO-1 complex. PMID:22711802

  15. Amorphous supramolecular structure of carboxymethyl cellulose in aqueous solution at different pH values as determined by rheology, small angle X-ray and light scattering.

    PubMed

    Dogsa, Iztok; Tomšič, Matija; Orehek, Janez; Benigar, Elizabeta; Jamnik, Andrej; Stopar, David

    2014-10-13

    Carboxymethyl cellulose (CMC) is one of the most widely used thickening agents in industry. The combination of small-angle X-ray scattering (SAXS), static and dynamic light scattering, as well as viscosity measurements and microscopy at different pH values was utilized to explore the physicochemical properties of CMC on a scale ranging from individual macromolecules to supramolecular assemblies. The supramolecular structure of CMC was represented as a set of characteristic sample subspaces based on SAXS data utilizing the string-of-beads model. The results indicate that at pH 7.0 individual CMC molecules are approximately uniformly distributed in a supramolecular structure owing to strong intra- and intermolecular repulsive interactions. The structure of CMC is most expanded at the value of pKa, where it has the largest radius of gyration, persistence length, and size of heterogeneous regions. Below pKa the majority of the CMC sample volume belongs to the low density subspaces. Most of CMC molecules, however, reside in a few high density subspaces. Dynamically, supramolecular structure of CMC is composed of fast diffusive relaxation processes embedded in a background of non-diffusive slow relaxation process at high pH and mostly slow relaxation processes at low pH. The rheological properties of CMC at different pH values were directly related to the CMC supramolecular structure in the aqueous environment. PMID:25037380

  16. Structure of Fucoidan from Brown Seaweed Turbinaria ornata as Studied by Electrospray Ionization Mass Spectrometry (ESIMS) and Small Angle X-ray Scattering (SAXS) Techniques

    PubMed Central

    Thanh, Thuy Thi Thu; Tran, Van Thi Thanh; Yuguchi, Yoshiaki; Bui, Ly Minh; Nguyen, Tai Tien

    2013-01-01

    The purpose of this study is to elucidate both the chemical and conformational structure of an unfractionated fucoidan extracted from brown seaweed Turbinaria ornata collected at Nha-trang bay, Vietnam. Electrospray ionization mass spectrometry (ESI-MS) was used for determining the chemical structure and small angle X-ray scattering (SAXS) provided conformational of the structure at the molecular level. The results showed that the fucoidan has a sulfate content of 25.6% and is mainly composed of fucose and galactose residues (Fuc:Gal ≈ 3:1). ESIMS analysis suggested that the fucoidan has a backbone of 3-linked α-l-Fucp residues with branches, →4)-Galp(1→ at C-4 of the fucan chain. Sulfate groups are attached mostly at C-2 and sometimes at C-4 of both fucose and galactose residues. A molecular model of the fucoidan was built based on obtained chemical structure and scattering curves estimated from molecular model and observed SAXS measurement were fitted. The results indicated that fucoidan under study has a rod-like bulky chain conformation. PMID:23857110

  17. Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: From protein structure to nanodisk assemblies

    NASA Astrophysics Data System (ADS)

    Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B.; Peterlik, Herwig; Jungbauer, Alois; Tscheliessnig, Rupert

    2010-11-01

    Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.

  18. Salts employed in hydrophobic interaction chromatography can change protein structure - insights from protein-ligand interaction thermodynamics, circular dichroism spectroscopy and small angle X-ray scattering.

    PubMed

    Komaromy, Andras Z; Kulsing, Chadin; Boysen, Reinhard I; Hearn, Milton T W

    2015-03-01

    Key requirements of protein purification by hydrophobic interaction chromatography (HIC) are preservation of the tertiary/quaternary structure, maintenance of biological function, and separation of the correctly folded protein from its unfolded forms or aggregates. This study examines the relationship between the HIC retention behavior of hen egg white lysozyme (HEWL) in high concentrations of several kosmotropic salts and its conformation, assessed by circular dichroism (CD) spectroscopy. Further, the physicochemical properties of HEWL in the presence of high concentrations of ammonium sulfate, sodium chloride and magnesium chloride were investigated by small angle X-ray scattering (SAXS) at different temperatures. Radii of gyration were extrapolated from Guinier approximations and the indirect transform program GNOM with protein-protein interaction and contrast variation taken into account. A bead model simulation provided information on protein structural changes using ab initio reconstruction with GASBOR. These results correlated to the secondary structure content obtained from CD spectroscopy of HEWL. These changes in SAXS and CD data were consistent with heat capacity ΔCp -values obtained from van't Hoff plot analyses of the retention data. Collectively, these insights enable informed decisions to be made on the choice of chromatographic conditions, leading to improved separation selectivity and opportunities for innovative column-assisted protein refolding methods. PMID:25690783

  19. In situ ultra-small-angle X-ray scattering study under uniaxial stretching of colloidal crystals prepared by silica nanoparticles bearing hydrogen-bonding polymer grafts

    PubMed Central

    Ishige, Ryohei; Williams, Gregory A.; Higaki, Yuji; Ohta, Noboru; Sato, Masugu; Takahara, Atsushi; Guan, Zhibin

    2016-01-01

    A molded film of single-component polymer-grafted nanoparticles (SPNP), consisting of a spherical silica core and densely grafted polymer chains bearing hydrogen-bonding side groups capable of physical crosslinking, was investigated by in situ ultra-small-angle X-ray scattering (USAXS) measurement during a uniaxial stretching process. Static USAXS revealed that the molded SPNP formed a highly oriented twinned face-centered cubic (f.c.c.) lattice structure with the [11−1] plane aligned nearly parallel to the film surface in the initial state. Structural analysis of in situ USAXS using a model of uniaxial deformation induced by rearrangement of the nanoparticles revealed that the f.c.c. lattice was distorted in the stretching direction in proportion to the macroscopic strain until the strain reached 35%, and subsequently changed into other f.c.c. lattices with different orientations. The lattice distortion and structural transition behavior corresponded well to the elastic and plastic deformation regimes, respectively, observed in the stress–strain curve. The attractive interaction of the hydrogen bond is considered to form only at the top surface of the shell and then plays an effective role in cross-linking between nanoparticles. The rearrangement mechanism of the nanoparticles is well accounted for by a strong repulsive interaction between the densely grafted polymer shells of neighboring particles. PMID:27158507

  20. Small angle X-ray scattering data and structure factor fitting for the study of the quaternary structure of the spermidine N-acetyltransferase SpeG.

    PubMed

    Weigand, Steven; Filippova, Ekaterina V; Kiryukhina, Olga; Anderson, Wayne F

    2016-03-01

    Here we describe the treatment of the small-angle X-ray Scattering (SAXS) data used during SpeG quaternary structure study as part of the research article "Substrate induced allosteric change in the quaternary structure of the spermidine N-acetyltransferase SpeG" published in Journal of Molecular Biology [1]. These data were collected on two separate area detectors as separate dilution series of the SpeG and the SpeG with spermine samples along with data from their companion buffers. The data were radially integrated, corrected for incident beam variation, and scaled to absolute units. After subtraction of volume-fraction scaled buffer scattering and division by the SpeG concentration, multiple scattering curves free of an inter-molecular structure factor were derived from the dilution series. Rather than extrapolating to infinite dilution, the structure factor contribution was estimated by fitting to the full set of data provided by dividing the scattering curves of a dilution series by the curve from the most dilute sample in that series. PMID:26793756

  1. Small-angle X-ray scattering of BAMLET at pH 12: a complex of α-lactalbumin and oleic acid.

    PubMed

    Rath, Emma M; Duff, Anthony P; Håkansson, Anders P; Knott, Robert B; Church, W Bret

    2014-07-01

    BAMLET (Bovine Alpha-lactalbumin Made LEthal to Tumors) is a member of the family of the HAMLET-like complexes, a novel class of protein-based anti-cancer complexes that incorporate oleic acid and deliver it to cancer cells. Small angle X-ray scattering (SAXS) was performed on the complex at pH 12, examining the high pH structure as a function of oleic acid added. The SAXS data for BAMLET species prepared with a range of oleic acid concentrations indicate extended, irregular, partially unfolded protein conformations that vary with the oleic acid concentration. Increases in oleic acid concentration correlate with increasing radius of gyration without an increase in maximum particle dimension, indicating decreasing protein density. The models for the highest oleic acid content BAMLET indicate an unusual coiled elongated structure that contrasts with apo-α-lactalbumin at pH 12, which is an elongated globular molecule, suggesting that oleic acid inhibits the folding or collapse of the protein component of BAMLET to the globular form. Circular dichroism of BAMLET and apo-α-lactalbumin was performed and the results suggest that α-lactalbumin and BAMLET unfold in a continuum of increasing degree of unfolded states. Taken together, these results support a model in which BAMLET retains oleic acid by non-specific association in the core of partially unfolded protein, and represent a new type of lipoprotein structure. PMID:24408789

  2. Structure of immune stimulating complex matrices and immune stimulating complexes in suspension determined by small-angle x-ray scattering.

    PubMed

    Pedersen, Jan Skov; Oliveira, Cristiano L P; Hübschmann, Henriette Baun; Arleth, Lise; Manniche, Søren; Kirkby, Nicolai; Nielsen, Hanne Mørck

    2012-05-16

    Immune stimulating complex (ISCOM) particles consisting of a mixture of Quil-A, cholesterol, and phospholipids were structurally characterized by small-angle x-ray scattering (SAXS). The ISCOM particles are perforated vesicles of very well-defined structures. We developed and implemented a novel (to our knowledge) modeling method based on Monte Carlo simulation integrations to describe the SAXS data. This approach is similar to the traditional modeling of SAXS data, in which a structure is assumed, the scattering intensity is calculated, and structural parameters are optimized by weighted least-squares methods when the model scattering intensity is fitted to the experimental data. SAXS data from plain ISCOM matrix particles in aqueous suspension, as well as those from complete ISCOMs (i.e., with an antigen (tetanus toxoid) incorporated) can be modeled as a polydisperse distribution of perforated bilayer vesicles with icosahedral, football, or tennis ball structures. The dominating structure is the tennis ball structure, with an outer diameter of 40 nm and with 20 holes 5-6 nm in diameter. The lipid bilayer membrane is 4.6 nm thick, with a low-electron-density, 2.0-nm-thick hydrocarbon core. Surprisingly, in the ISCOMs, the tetanus toxoid is located just below the membrane inside the particles. PMID:22677391

  3. Solution Structures of 2 : 1 And 1 : 1 DNA Polymerase - DNA Complexes Probed By Ultracentrifugation And Small-Angle X-Ray Scattering

    SciTech Connect

    Tang, K.H.; Niebuhr, M.; Aulabaugh, A.; Tsai, M.D.; /Ohio State U. /SLAC, SSRL

    2009-04-30

    We report small-angle X-ray scattering (SAXS) and sedimentation velocity (SV) studies on the enzyme-DNA complexes of rat DNA polymerase {beta} (Pol {beta}) and African swine fever virus DNA polymerase X (ASFV Pol X) with one-nucleotide gapped DNA. The results indicated formation of a 2 : 1 Pol {beta}-DNA complex, whereas only 1 : 1 Pol X-DNA complex was observed. Three-dimensional structural models for the 2 : 1 Pol {beta}-DNA and 1 : 1 Pol X-DNA complexes were generated from the SAXS experimental data to correlate with the functions of the DNA polymerases. The former indicates interactions of the 8 kDa 5{prime}-dRP lyase domain of the second Pol {beta} molecule with the active site of the 1 : 1 Pol {beta}-DNA complex, while the latter demonstrates how ASFV Pol X binds DNA in the absence of DNA-binding motif(s). As ASFV Pol X has no 5{prime}-dRP lyase domain, it is reasonable not to form a 2 : 1 complex. Based on the enhanced activities of the 2 : 1 complex and the observation that the 8 kDa domain is not in an optimal configuration for the 5{prime}-dRP lyase reaction in the crystal structures of the closed ternary enzyme-DNA-dNTP complexes, we propose that the asymmetric 2 : 1 Pol {beta}-DNA complex enhances the function of Pol {beta}.

  4. Solution structures of 2 : 1 and 1 : 1 DNA polymerase-DNA complexes probed by ultracentrifugation and small-angle X-ray scattering

    SciTech Connect

    Tang, Kuo-Hsiang; Niebuhr, Marc; Aulabaugh, Ann; Tsai, Ming-Daw

    2008-03-25

    We report small-angle X-ray scattering (SAXS) and sedimentation velocity (SV) studies on the enzyme-DNA complexes of rat DNA polymerase β (Pol β) and African swine fever virus DNA polymerase X (ASFV Pol X) with one-nucleotide gapped DNA. The results indicated formation of a 2 : 1 Pol β-DNA complex, whereas only 1 : 1 Pol X-DNA complex was observed. Three-dimensional structural models for the 2 : 1 Pol β-DNA and 1 : 1 Pol X-DNA complexes were generated from the SAXS experimental data to correlate with the functions of the DNA polymerases. The former indicates interactions of the 8 kDa 5'-dRP lyase domain of the second Pol β molecule with the active site of the 1 : 1 Pol β-DNA complex, while the latter demonstrates how ASFV Pol X binds DNA in the absence of DNA-binding motif(s). As ASFV Pol X has no 5'-dRP lyase domain, it is reasonable not to form a 2 : 1 complex. Based on the enhanced activities of the 2 : 1 complex and the observation that the 8 kDa domain is not in an optimal configuration for the 5'-dRP lyase reaction in the crystal structures of the closed ternary enzyme-DNA-dNTP complexes, we propose that the asymmetric 2 : 1 Pol β-DNA complex enhances the function of Pol β.

  5. Extracting magnetic cluster size and its distributions in advanced perpendicular recording media with shrinking grain size using small angle x-ray scattering

    SciTech Connect

    Mehta, Virat; Ikeda, Yoshihiro; Takano, Ken; Terris, Bruce D.; Hellwig, Olav; Wang, Tianhan; Wu, Benny; Graves, Catherine; Dürr, Hermann A.; Scherz, Andreas; Stöhr, Jo

    2015-05-18

    We analyze the magnetic cluster size (MCS) and magnetic cluster size distribution (MCSD) in a variety of perpendicular magnetic recording (PMR) media designs using resonant small angle x-ray scattering at the Co L{sub 3} absorption edge. The different PMR media flavors considered here vary in grain size between 7.5 and 9.5 nm as well as in lateral inter-granular exchange strength, which is controlled via the segregant amount. While for high inter-granular exchange, the MCS increases rapidly for grain sizes below 8.5 nm, we show that for increased amount of segregant with less exchange the MCS remains relatively small, even for grain sizes of 7.5 and 8 nm. However, the MCSD still increases sharply when shrinking grains from 8 to 7.5 nm. We show evidence that recording performance such as signal-to-noise-ratio on the spin stand correlates well with the product of magnetic cluster size and magnetic cluster size distribution.

  6. Long-living intermediates during a lamellar to a diamond-cubic lipid phase transition: a small-angle X-ray scattering investigation.

    PubMed

    Angelov, Borislav; Angelova, Angelina; Vainio, Ulla; Garamus, Vasil M; Lesieur, Sylviane; Willumeit, Regine; Couvreur, Patrick

    2009-04-01

    To generate nanostructured vehicles with tunable internal organization, the structural phase behavior of a self-assembled amphiphilic mixture involving poly(ethylene glycol) monooleate (MO-PEG) and glycerol monooleate (MO) is studied in excess aqueous medium by time-resolved small-angle X-ray scattering (SAXS) in the temperature range from 1 to 68 degrees C. The SAXS data indicate miscibility of the two components in lamellar and nonlamellar soft-matter nanostructures. The functionalization of the MO assemblies by a MO-PEG amphiphile, which has a flexible large hydrophilic moiety, appears to hinder the epitaxial growth of a double diamond (D) cubic lattice from the lamellar (L) bilayer structure during the thermal phase transition. The incorporated MO-PEG additive is found to facilitate the formation of structural intermediates. They exhibit greater characteristic spacings and large diffusive scattering in broad temperature and time intervals. Their features are compared with those of swollen long-living intermediates in MO/octylglucoside assemblies. A conclusion can be drawn that long-living intermediate states can be equilibrium stabilized in two- or multicomponent amphiphilic systems. Their role as cubic phase precursors is to smooth the structural distortions arising from curvature mismatch between flat and curved regions. The considered MO-PEG functionalized assemblies may be useful for preparation of sterically stabilized liquid-crystalline nanovehicles for confinement of therapeutic biomolecules. PMID:19708151

  7. Insights into open/closed conformations of the catalytically active human guanylate kinase as investigated by small-angle X-ray scattering.

    PubMed

    Jain, Rohit; Khan, Nazimuddin; Menzel, Andreas; Rajkovic, Ivan; Konrad, Manfred; Techert, Simone

    2016-01-01

    Bio-catalysis is the outcome of a subtle interplay between internal motions in enzymes and chemical kinetics. Small-angle X-ray scattering (SAXS) investigation of an enzyme's internal motions during catalysis offers an integral view of the protein's structural plasticity, dynamics, and function, which is useful for understanding allosteric effects and developing novel medicines. Guanylate kinase (GMPK) is an essential enzyme involved in the guanine nucleotide metabolism of unicellular and multicellular organisms. It is also required for the intracellular activation of numerous antiviral and anticancer purine nucleoside analog prodrugs. Catalytically active recombinant human GMPK (hGMPK) was purified for the first time and changes in the size and shape of open/closed hGMPK were tracked by SAXS. The binding of substrates (GMP + AMPPNP or Ap5G or GMP + ADP) resulted in the compaction of size and shape of hGMPK. The structural changes between open and completely closed hGMPK conformation were confirmed by observing differences in the hGMPK secondary structures with circular dichroism spectroscopy. PMID:26446352

  8. Molecular Assembly of Wheat Gliadins into Nanostructures: A Small-Angle X-ray Scattering Study of Gliadins in Distilled Water over a Wide Concentration Range.

    PubMed

    Sato, Nobuhiro; Matsumiya, Aoi; Higashino, Yuki; Funaki, Satoshi; Kitao, Yuki; Oba, Yojiro; Inoue, Rintaro; Arisaka, Fumio; Sugiyama, Masaaki; Urade, Reiko

    2015-10-01

    Gliadin, one of the major proteins together with glutenin composing gluten, affects the physical properties of wheat flour dough. In this study, nanoscale structures of hydrated gliadins extracted into distilled water were investigated primarily by small-angle X-ray scattering (SAXS) over a wide range of concentrations. Gliadins are soluble in distilled water below 10 wt %. Guinier analyses of SAXS profiles indicate that gliadins are present as monomers together with small amounts of dimers and oligomers in a very dilute solution. The SAXS profiles also indicate that interparticle interference appears above 0.5 wt % because of electrostatic repulsion among gliadin assemblies. Above 15 wt %, gliadins form gel-like hydrated solids. At greater concentrations, a steep upturn appears in the low-q region owing to the formation of large aggregates, and a broad shoulder appears in the middle-q region showing density fluctuation inside. This study demonstrates that SAXS can effectively disclose the nanostructure of hydrated gliadin assemblies. PMID:26365302

  9. Small-angle x-ray scattering studies of microvoids in amorphous-silicon-based semiconductors. Final subcontract report, 1 February 1991--31 January 1994

    SciTech Connect

    Williamson, D.L.; Jone, S.J.; Chen, Y.

    1994-07-01

    This report describes work performed to provide new details of the microstructure for the size scale from about 1 nm to 30 nm in high-quality hydrogenated amorphous-silicon and related alloys prepared by current state-of-the-art deposition methods as well as by new and emerging deposition technologies. The purpose of this work is to help determine the role of microvoids and other density fluctuations in controlling the opto-electronic and photovoltaic properties. The approach involved collaboration with several groups that supplied relevant systematic sets of samples and the associated opto-electronic/photovoltaic data to help address particular issues. The small-angle X-ray scattering (SAXS) technique, as developed during this project, was able to provide microstructural information with a high degree of sensitivity not available from other methods. It is particularly sensitive to microvoids or H-rich microdomains and to the presence of oriented microstructures. The latter is readily associated with columnar-type growth and can even be observed in premature stages not detectable by transmission electron microscopy. Flotation density measurements provided important complementary data. Systematic correlations demonstrated that material with more SAXS-detected microstructure has to-electronic and photovoltaic properties and increased degradation under light soaking. New results related to alloy randomness emerged from our ability to measure the difffuse scattering component of the SAXS.

  10. Microstructure evolution during the isostructural decomposition of TiAlN—A combined in-situ small angle x-ray scattering and phase field study

    NASA Astrophysics Data System (ADS)

    Knutsson, A.; Ullbrand, J.; Rogström, L.; Norrby, N.; Johnson, L. J. S.; Hultman, L.; Almer, J.; Johansson Jöesaar, M. P.; Jansson, B.; Odén, M.

    2013-06-01

    This paper describes details of the spinodal decomposition and coarsening in metastable cubic Ti0.33Al0.67N and Ti0.50Al0.50N coatings during isothermal annealing, studied by in-situ small angle x-ray scattering, in combination with phase field simulations. We show that the isostructural decomposition occurs in two stages. During the initial stage, spinodal decomposition, of the Ti0.50Al0.50N alloy, the phase separation proceeds with a constant compositional wavelength of ˜2.8 nm of the AlN- and TiN-rich domains. The time for spinodal decomposition depends on annealing temperature as well as alloy composition. After the spinodal decomposition, the coherent cubic AlN- and TiN-rich domains coarsen. The coarsening rate is kinetically limited by diffusion, which allowed us to estimate the diffusivity and activation energy of the metals to 1.4 × 10-6 m2 s-1 and 3.14 eV at-1, respectively.

  11. Effective interaction of charged platelets in aqueous solution: Investigations of colloid laponite suspensions by static light scattering and small-angle x-ray scattering

    SciTech Connect

    Li Li; Rosenfeldt, S.; Ballauff, M.; Harnau, L.

    2005-11-01

    We study dilute aqueous solutions of charged disklike mineral particles (laponite) by a combination of static light scattering (SLS) and small-angle x-ray scattering (SAXS). Laponite solutions are known to form gels above a certain critical concentration that must be described as nonequilibrium states. Here we focus on the investigation by SLS and SAXS at concentrations below gelation (c<0.016 g/L) and at low concentrations of added salt (0.001M and 0.005M). Thus, we have obtained the scattering function of single Laponite platelets as well as the structure factor describing their interaction at finite concentration. A detailed analysis of the combined sets of data proves that the solutions are in a well-defined equilibrium state. Moreover, this analysis demonstrates the internal consistency and accuracy of the scattering functions obtained at finite concentrations. We find that laponite particles interact through an effective pair potential that is attractive on short range but repulsive on longer range. This finding demonstrates that Laponite solutions exhibit only a limited stability at the concentration of added salt used herein. Raising the ionic strength to 0.005M already leads to slow flocculation as is evidenced from the enhanced scattering intensity at smallest scattering angles. All data strongly suggest that the gelation occurring at higher concentration is related to aggregation.

  12. Novel in situ setup to study the formation of nanoparticles in the gas phase by small angle x-ray scattering

    SciTech Connect

    Shyjumon, I.; Rappolt, M.; Sartori, B.; Amenitsch, H.; Laggner, P.

    2008-04-15

    An in-house built aerosol generator setup for in situ gas phase studies of aerosol and nanoparticles is described. The aerosol generator with an ultrasonic ceramic disk mist maker provides high enough particle concentrations for structural gas phase analysis by synchrotron small angle x-ray scattering (for water {approx}4x10{sup 8} droplets/s with a droplet size of {approx}2.5 {mu}m). The working principle was proved by scattering of gold nanoparticles. For evaporation induced self-assembly studies of nanostructured particles, an additional thermal treatment chamber was included in the setup. The first on-line gas phase data with our setup for mesostructured silica particles are presented for different thermal treatments. Scanning electron microscope imaging revealed the average particle size to be {approx}1 {mu}m. Furthermore, to quantify their internal nanostructure, diffraction experiments of deposited silica aerosols were carried out and the corresponding electron density map indicates a silica wall thickness of about 1 nm.

  13. Novel in situ setup to study the formation of nanoparticles in the gas phase by small angle x-ray scattering.

    PubMed

    Shyjumon, I; Rappolt, M; Sartori, B; Amenitsch, H; Laggner, P

    2008-04-01

    An in-house built aerosol generator setup for in situ gas phase studies of aerosol and nanoparticles is described. The aerosol generator with an ultrasonic ceramic disk mist maker provides high enough particle concentrations for structural gas phase analysis by synchrotron small angle x-ray scattering (for water approximately 4 x 10(8) droplets/s with a droplet size of approximately 2.5 microm). The working principle was proved by scattering of gold nanoparticles. For evaporation induced self-assembly studies of nanostructured particles, an additional thermal treatment chamber was included in the setup. The first on-line gas phase data with our setup for mesostructured silica particles are presented for different thermal treatments. Scanning electron microscope imaging revealed the average particle size to be approximately 1 microm. Furthermore, to quantify their internal nanostructure, diffraction experiments of deposited silica aerosols were carried out and the corresponding electron density map indicates a silica wall thickness of about 1 nm. PMID:18447533

  14. Conformational Activation of Poly(ADP-ribose) Polymerase-1 upon DNA Binding Revealed by Small-Angle X-ray Scattering

    PubMed Central

    2015-01-01

    Poly(ADP-ribose) polymerase-1 (PARP-1) is a nuclear protein that plays key roles in several fundamental cellular processes. PARP-1 catalyzes the polymerization of nicotinamide adenine dinucleotide on itself and other acceptor proteins, forming long branched poly(ADP-ribose) polymers. The catalytic activity of PARP-1 is stimulated upon binding to damaged DNA, but how this signal is transmitted from the N-terminal DNA binding domain to the C-terminal catalytic domain in the context of the full-length enzyme is unknown. In this paper, small-angle X-ray scattering experiments and molecular dynamics simulations were used to gain insight into the conformational changes that occur during the catalytic activation of PARP-1 by an 8-mer DNA ligand. The data are consistent with a model in which binding of the DNA ligand establishes interdomain interactions between the DNA binding and catalytic domains, which induces an allosteric change in the active site that promotes catalysis. Moreover, the PARP-1–8-mer complex is seen to adopt a conformation that is poised to recruit DNA repair factors to the site of DNA damage. This study provides the first structural information about the DNA-induced conformational activation of full-length PARP-1. PMID:24588584

  15. Small angle X-ray scattering study of poly(N-isopropyl acrylamide) based cryogels near the volume-phase transition temperature

    NASA Astrophysics Data System (ADS)

    Chalal, Mohand; Ehrburger-Dolle, Françoise; Morfin, Isabelle; Aguilar de Armas, Maria-Rosa; López, Maria-Luisa; Bley, Françoise

    2010-10-01

    The structural modifications induced by changes in temperature are investigated by Small-Angle X-ray Scattering (SAXS) over a broad range of q-values (3.5×10-2 - 12 nm-1) in cryogels based on N-isopropylacrylamide (NIPA) and/or 2-Hydroxyethyl methacrylate-L-Lactide-Dextran (HEMA-LLA-D) macromer. Various copolymeric cryogels of these two monomers are prepared by cryopolymerization yielding macroporous gels (cryogels). For the plain pNIPA cryogel, the SAXS curves obtained at each temperature are well fitted by a sum of four equations describing respectively the scattering resulting from the gel surface (power law), from the solid-like (Guinier equation) and liquid-like (Ornstein-Zernike equation) heterogeneities and from the chain-chain correlation yielding a broad peak (pseudo-Voigt equation) in the high-q domain. The temperature dependence of the parameters obtained from the fit is analyzed and discussed. It is shown that the existence of an isoscattering (or isosbestic) point observed in pNIPA gels and in some copolymers is related to features observed by Differential Scanning Calorimetry and swelling ratio measurements.

  16. Core–Shell Structure of Monodisperse Poly(ethylene glycol)-Grafted Iron Oxide Nanoparticles Studied by Small-Angle X-ray Scattering

    PubMed Central

    2015-01-01

    The promising applications of core–shell nanoparticles in the biological and medical field have been well investigated in recent years. One remaining challenge is the characterization of the structure of the hydrated polymer shell. Here we use small-angle X-ray scattering (SAXS) to investigate iron oxide core–poly(ethylene glycol) brush shell nanoparticles with extremely high polymer grafting density. It is shown that the shell density profile can be described by a scaling model that takes into account the locally very high grafting density near the core. A good fit to a constant density region followed by a star-polymer-like, monotonously decaying density profile is shown, which could help explain the unique colloidal properties of such densely grafted core–shell nanoparticles. SAXS experiments probing the thermally induced dehydration of the shell and the response to dilution confirmed that the observed features are associated with the brush and not attributed to structure factors from particle aggregates. We thereby demonstrate that the structure of monodisperse core–shell nanoparticles with dense solvated shells can be well studied with SAXS and that different density models can be distinguished from each other. PMID:26321792

  17. Insights into Surface Interactions between Metal Organic Frameworks and Gases during Transient Adsorption and Diffusion by In-Situ Small Angle X-ray Scattering.

    PubMed

    Dumée, Ludovic F; He, Li; Hodgson, Peter; Kong, Lingxue

    2016-01-01

    The fabrication of molecular gas sieving materials with specific affinities for a single gas species and able to store large quantities of materials at a low or atmospheric pressure is desperately required to reduce the adverse effects of coal and oil usage in carbon capture. Fundamental understanding of the dynamic adsorption of gas, the diffusion mechanisms across thin film membranes, and the impact of interfaces play a vital role in developing these materials. In this work, single gas permeation tests across micro-porous membrane materials, based on metal organic framework crystals grown on the surface of carbon nanotubes (ZiF-8@CNT), were performed for the first time in-situ at the Australian Synchrotron on the small angle X-ray scattering beamline in order to reveal molecular sieving mechanisms and gas adsorption within the material. The results show that specific chemi-sorption of CO₂ across the ZiF-8 crystal lattices affected the morphology and unit cell parameters, while the sieving of other noble or noble like gases across the ZiF-8@CNT membranes was found to largely follow Knudsen diffusion. This work demonstrates for the first time a novel and effective technique to assess molecular diffusion at the nano-scale across sub-nano-porous materials by probing molecular flexibility across crystal lattice and single cell units. PMID:27598211

  18. In situ ultra-small-angle X-ray scattering study under uniaxial stretching of colloidal crystals prepared by silica nanoparticles bearing hydrogen-bonding polymer grafts

    DOE PAGESBeta

    Ishige, Ryohei; Williams, Gregory A.; Higaki, Yuji; Ohta, Noboru; Sato, Masugu; Takahara, Atsushi; Guan, Zhibin

    2016-04-19

    A molded film of single-component polymer-grafted nanoparticles (SPNP), consisting of a spherical silica core and densely grafted polymer chains bearing hydrogen-bonding side groups capable of physical crosslinking, was investigated byin situultra-small-angle X-ray scattering (USAXS) measurement during a uniaxial stretching process. Static USAXS revealed that the molded SPNP formed a highly oriented twinned face-centered cubic (f.c.c.) lattice structure with the [11-1] plane aligned nearly parallel to the film surface in the initial state. Structural analysis ofin situUSAXS using a model of uniaxial deformation induced by rearrangement of the nanoparticles revealed that the f.c.c. lattice was distorted in the stretching direction inmore » proportion to the macroscopic strain until the strain reached 35%, and subsequently changed into other f.c.c. lattices with different orientations. The lattice distortion and structural transition behavior corresponded well to the elastic and plastic deformation regimes, respectively, observed in the stress–strain curve. The attractive interaction of the hydrogen bond is considered to form only at the top surface of the shell and then plays an effective role in cross-linking between nanoparticles. The rearrangement mechanism of the nanoparticles is well accounted for by a strong repulsive interaction between the densely grafted polymer shells of neighboring particles.« less

  19. Location of cholesterol in liposomes by using small-angle X-ray scattering (SAXS) data and the generalized indirect Fourier transformation (GIFT) method.

    PubMed

    Aburai, Kenichi; Ogura, Taku; Hyodo, Ryo; Sakai, Hideki; Abe, Masahiko; Glatter, Otto

    2013-01-01

    We investigated the location of cholesterol (Chol) in liposomes and its interaction with phospholipids using small-angle x-ray scattering (SAXS) data and applying the generalized indirect Fourier transformation (GIFT) method. The GIFT method has been applied to lamellar liquid crystal systems and it gives quantitative data on bilayer thickness, electron density profile, and membrane flexibility (Caillé parameter). When the GIFT method is applied to the SAXS data of dipalmitoylphosphatidylcholine (DPPC) alone (Chol [-]) or a DPPC/Chol = 7/3 mixed system (Chol [+], molar ratio), change in the bilayer thickness was insignificant in both systems. However, the electron density for the Chol (+) system was higher than that for the Chol (-) system at the location of hydrophilic groups of phospholipids, and whereas Caillé parameter value increased with temperature for the Chol (-) system, no significant change with temperature was observed in the Caillé parameter for the Chol (+) system. These results indicated that Chol is located in the vicinity of the hydrophilic group of the phospholipids and constricts the packing of the acyl chain of phospholipids in the bilayer. PMID:24200939

  20. Time-resolved small-angle X-ray scattering studies of polymer-silica nanocomposite particles: initial formation and subsequent silica redistribution.

    PubMed

    Balmer, Jennifer A; Mykhaylyk, Oleksandr O; Armes, Steven P; Fairclough, J Patrick A; Ryan, Anthony J; Gummel, Jeremie; Murray, Martin W; Murray, Kenneth A; Williams, Neal S J

    2011-02-01

    Small angle X-ray scattering (SAXS) is a powerful characterization technique for the analysis of polymer-silica nanocomposite particles due to their relatively narrow particle size distributions and high electron density contrast between the polymer core and the silica shell. Time-resolved SAXS is used to follow the kinetics of both nanocomposite particle formation (via silica nanoparticle adsorption onto sterically stabilized poly(2-vinylpyridine) (P2VP) latex in dilute aqueous solution) and also the spontaneous redistribution of silica that occurs when such P2VP-silica nanocomposite particles are challenged by the addition of sterically stabilized P2VP latex. Silica adsorption is complete within a few seconds at 20 °C and the rate of adsorption strongly dependent on the extent of silica surface coverage. Similar very short time scales for silica redistribution are consistent with facile silica exchange occurring as a result of rapid interparticle collisions due to Brownian motion; this interpretation is consistent with a zeroth-order Smoluchowski-type calculation. PMID:21171624

  1. ON THE X-RAY OUTBURSTS OF TRANSIENT ANOMALOUS X-RAY PULSARS AND SOFT GAMMA-RAY REPEATERS

    SciTech Connect

    Cal Latin-Small-Letter-Dotless-I skan, Sirin; Ertan, Uenal

    2012-10-20

    We show that the X-ray outburst light curves of four transient anomalous X-ray pulsars (AXPs) and soft gamma-ray repeaters (SGRs), namely, XTE J1810-197, SGR 0501+4516, SGR 1627-41, and CXOU J164710.2-455216, can be produced by the fallback disk model that was also applied to the outburst light curves of persistent AXPs and SGRs in our earlier work. The model solves the diffusion equation for the relaxation of a disk that has been pushed back by a soft gamma-ray burst. The sets of main disk parameters used for these transient sources are very similar to each other and to those employed in our earlier models of persistent AXPs and SGRs. There is a characteristic difference between the X-ray outburst light curves of transient and persistent sources. This can be explained by the differences in the disk surface density profiles of the transient and persistent sources in quiescence indicated by their quiescent X-ray luminosities. Our results imply that a viscous disk instability operating at a critical temperature in the range of {approx}1300-2800 K is a common property of all fallback disks around AXPs and SGRs. The effect of the instability is more pronounced and starts earlier for the sources with lower quiescent luminosities, which leads to the observable differences in the X-ray enhancement light curves of transient and persistent sources. A single active disk model with the same basic disk parameters can account for the enhancement phases of both transient and persistent AXPs and SGRs. We also present a detailed parameter study to show the effects of disk parameters on the evolution of the X-ray luminosity of AXPs and SGRs in the X-ray enhancement phases.

  2. In-situ small angle x-ray scattering studies of continuous nano-particle synthesis in premixed and diffusion flames

    NASA Astrophysics Data System (ADS)

    Agashe, Nikhil

    Flame technology has proven to be an extremely effective method to synthesize nano-particles of ceramic oxides. The single-step chemistry, the ability to control shape and size and to produce millions of tons of nano-powders per annum with relative ease have made it popular with industry. Although this process primarily focused on oxides of silicon and titanium, it has now been adopted for manufacture of several other oxides of bismuth, vanadium, aluminum, iron, germanium and zirconium. There has been extraordinary progress in the application of flame burner to synthesize new oxides having wide range of particle size, polydispersity, composition and aggregation. But the fundamentals behind the mechanisms for particle formation and growth are still not well understood. Due to the extremely fast rates of reaction, high temperatures and low concentrations associated with this process, it is difficult to accurately observe the formation of nuclei and their growth to form aggregated nano-particles. Entire particle growth from inception to aggregation takes place in a few milliseconds! Light scattering and thermophoretic sampling have been used extensively to study such flames. But light scattering suffers from the brightness of the flame and the limitation on the range of size-scale it can probe. It can only detect aggregates, and information about primary particles needs to be obtained by thermophoretic sampling. However thermophoretic sampling is an intrusive technique and sample collection in the flame involves disturbance of flow dynamics of the gases and the particles in the flame. It is necessary to find a single non-intrusive technique that can give complete information for the flame and handle the fast rates of growth. In-situ small angle x-ray scattering (iSAXS), which utilizes high energy x-rays from synchrotron sources fits such a role perfectly. iSAXS of particles in the flame provides full information from nano-scale to micron-scale and about the evolution

  3. Preparation and characterization of nonpolar fluorinated carbosilane dendrimers by APcI mass spectrometry and small-angle X-ray scattering

    SciTech Connect

    Omotowa, B.A.; Keefer, K.D.; Kirchmeier, R.L.; Shreeve, J.M.

    1999-12-08

    The following highly fluorinated nonpolar dendrimers were obtained in high yields from multiple hydrosilylation reactions between core hydride terminated carbosilane dendrimers and allyl-1,1-dihydrotrifluoroethyl ether or allyl-1,1-dihydroheptadecafluorononyl ether through divergent synthetic routes: Si[CH{sub 2}CH{sub 2}SiMe{sub 2}(CH{sub 2}CH{sub 2}CH{sub 2}OCH{sub 2}CF{sub 3})]{sub 4} (7), Si{l{underscore}brace}CH{sub 2}CH{sub 2}SiMe[CH{sub 2}{l{underscore}brace}CH{sub 2}SiMe(CH{sub 2}CH{sub 2}CH{sub 2}OCH{sub 2}CF{sub 3}){sub 2}]{sub 2}{r{underscore}brace}{sub 4} (8), Si[CH{sub 2}CH{sub 2}Si(CH{sub 2}CH{sub 2}CH{sub 2}OCH{sub 2}C{sub 8}F{sub 17}){sub 3}]{sub 4} (9), Si[CH{sub 2}CH{sub 2}SiMe{sub 2}(CH{sub 2}CH{sub 2}OCH{sub 2}C{sub 8}F{sub 17})]{sub 4} (10), and Si{l{underscore}brace}CH{sub 2}CH{sub 2}Si[CH{sub 2}CH{sub 2}Si(CH{sub 2}CH{sub 2}OCH{sub 2}C{sub 8}F{sub 17}){sub 3}]{sub 3}{r{underscore}brace}{sub 4} (11). These compounds were characterized by elemental and spectroscopic analyses. Valuable mass spectral data were obtained by using atmospheric pressure chemical ionization (APcI). The fluorinated dendrimer molecule and the nonfluorinated core scatter X-ray light differently and present unique slopes on the Guinier Plot of data from small-angle X-ray light scattering (SAXS) in hexafluorobenzene. Glass transition temperatures (T{sub g}) and thermogravimetric analyses (TGA) of the dendrimers were determined.

  4. Characterization of the Decaheme c-Type Cytochrome OmcA in Solution and on Hematite Surfaces by Small Angle X-Ray Scattering and Neutron Reflectometry

    PubMed Central

    Johs, A.; Shi, L.; Droubay, T.; Ankner, J.F.; Liang, L.

    2010-01-01

    Abstract The outer membrane protein OmcA is an 85 kDa decaheme c-type cytochrome located on the surface of the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1. It is assumed to mediate shuttling of electrons to extracellular acceptors that include solid metal oxides such as hematite (α-Fe2O3). No information is yet available concerning OmcA structure in physiologically relevant conditions such as aqueous environments. We purified OmcA and characterized its solution structure by small angle x-ray scattering (SAXS), and its interaction at the hematite-water interface by neutron reflectometry. SAXS showed that OmcA is a monomer that adopts a flat ellipsoidal shape with an overall dimension of 34 × 90 × 65 Å3. To our knowledge, we obtained the first direct evidence that OmcA undergoes a redox state-dependent conformational change in solution whereby reduction decreases the overall length of OmcA by ∼7 Å (the maximum dimension was 96 Å for oxidized OmcA, and 89 Å for NADH and dithionite-reduced OmcA). OmcA was also found to physically interact with electron shuttle molecules such as flavin mononucleotide, resulting in the formation of high-molecular-weight assemblies. Neutron reflectometry showed that OmcA forms a well-defined monomolecular layer on hematite surfaces, where it assumes an orientation that maximizes its contact area with the mineral surface. These novel insights into the molecular structure of OmcA in solution, and its interaction with insoluble hematite and small organic ligands, demonstrate the fundamental structural bases underlying OmcA's role in mediating redox processes. PMID:20550916

  5. Characterization of the Decaheme c-Type Cytochrome OmcA in Solution and on Hematite Surfaces by Small Angle X-Ray Scattering and Neutron Reflectometry

    SciTech Connect

    Johs, Alexander; Shi, Liang; Droubay, Timothy C.; Ankner, John F.; Liang, L.

    2010-06-01

    The outer membrane protein OmcA is an 85 kDa decaheme c-type cytochrome located on the surface of the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1. It is assumed to mediate shuttling of electrons to extracellular acceptors that include solid metal oxides such as hematite (a-Fe2O3). No information is yet available concerning OmcA structure in physiologically relevant conditions such as aqueous environments. We purified OmcA and characterized its solution structure by small angle x-ray scattering (SAXS), and its interaction at the hematite-water interface by neutron reflectometry. SAXS showed that OmcA is a monomer that adopts a flat ellipsoidal shape with an overall dimension of 34 x 90 x 65A˚ 3. To our knowledge, we obtained the first direct evidence that OmcA undergoes a redox state-dependent conformational change in solution whereby reduction decreases the overall length of OmcA by ~7 A˚ (the maximum dimension was 96 A˚ for oxidized OmcA, and 89 A˚ for NADH and dithionite-reduced OmcA). OmcA was also found to physically interact with electron shuttle molecules such as flavin mononucleotide, resulting in the formation of high-molecular-weight assemblies. Neutron reflectometry showed that OmcA forms a well-defined monomolecular layer on hematite surfaces, where it assumes an orientation that maximizes its contact area with the mineral surface. These novel insights into the molecular structure of OmcA in solution, and its interaction with insoluble hematite and small organic ligands, demonstrate the fundamental structural bases underlying OmcA’s role in mediating redox processes.

  6. Investigation on the structure of water/AOT/IPM/alcohols reverse micelles by conductivity, dynamic light scattering, and small angle X-ray scattering.

    PubMed

    Zhang, Xiaoguang; Chen, Yingjun; Liu, Jiexiang; Zhao, Chuanzhuang; Zhang, Haijiao

    2012-03-29

    We have systematically investigated the effect of alcohols (ethanol, propanol, butanol, and pentanol) on the structure of the water/AOT/IPM system using conductivity, dynamic light scattering (DLS), and small-angle X-ray scattering (SAXS) techniques. The results show that no percolation phenomenon is observed in the water/AOT/IPM system, whereas the addition of ethanol (propanol and butanol) induces apparently percolation. The threshold water content (W(p)) depends closely on the alcohol type and concentration. The effect of alcohols on the conductance behavior is discussed from the physical properties of alcohols, the interfacial flexibility, and the attractive interactions between droplets. The hydrodynamic diameter of droplets (d(H)) obtained from DLS increases markedly with the increase in water content (W(0)); however, it decreases gradually with increasing alcohol chain length and concentration. SAXS measurements display distinctly the shoulder, the low hump peaks, and the heavy tail phenomenon in the pair distance distribution function p(r) profile, which rely strongly on the alcohol species and its concentration. The gyration radius (R(g)) increases with increasing W(0), and decreases with the increase of alcohol chain length and concentration. Schematic diagram of the conductance mechanism of water/AOT/IPM/alcohol systems is primarily depicted. Three different phases of the discrete droplets, the oligomers, and the isolated ellipsoidal droplets existed in the different W(0) ranges correspond to three different stages in the conductivity-W(0) curve. Coupling the structure characteristics of reverse micelles obtained from DLS and SAXS techniques with conductivity could be greatly helpful to deeply understand the percolation mechanism of water/AOT/IPM/alcohols systems. PMID:22380931

  7. {beta}-connectin studies by small-angle x-ray scattering and single-molecule force spectroscopy by atomic force microscopy

    SciTech Connect

    Marchetti, S.; Carla, M.; Gambi, C. M. C.; Sbrana, F.; Vassalli, M.; Toscano, A.; Pacini, A.; Fratini, E.; Tiribilli, B.

    2011-05-15

    The three-dimensional structure and the mechanical properties of a {beta}-connectin fragment from human cardiac muscle, belonging to the I band, from I{sub 27} to I{sub 34}, were investigated by small-angle x-ray scattering (SAXS) and single-molecule force spectroscopy (SMFS). This molecule presents an entropic elasticity behavior, associated to globular domain unfolding, that has been widely studied in the last 10 years. In addition, atomic force microscopy based SMFS experiments suggest that this molecule has an additional elastic regime, for low forces, probably associated to tertiary structure remodeling. From a structural point of view, this behavior is a mark of the fact that the eight domains in the I{sub 27}-I{sub 34} fragment are not independent and they organize in solution, assuming a well-defined three-dimensional structure. This hypothesis has been confirmed by SAXS scattering, both on a diluted and a concentrated sample. Two different models were used to fit the SAXS curves: one assuming a globular shape and one corresponding to an elongated conformation, both coupled with a Coulomb repulsion potential to take into account the protein-protein interaction. Due to the predominance of the structure factor, the effective shape of the protein in solution could not be clearly disclosed. By performing SMFS by atomic force microscopy, mechanical unfolding properties were investigated. Typical sawtooth profiles were obtained and the rupture force of each unfolding domain was estimated. By fitting a wormlike chain model to each peak of the sawtooth profile, the entropic elasticity of octamer was described.

  8. Determination of the quaternary structural states of bovine casein by small-angle X-ray scattering: submicellar and micellar forms

    SciTech Connect

    Kumosinski, T.F.; Pessen, H.; Farrell, H.M. Jr.; Brumberger, H.

    1988-11-01

    Whole casein occurs in milk as a spherical colloidal complex of protein and salts called the casein micelle, with approximate average radii of 650 A as determined by electron microscopy. Removal of Ca2+ is thought to result in dissociation into smaller noncolloidal protein complexes called submicelles. Hydrodynamic and light scattering studies on whole casein submicelles suggest that they are predominantly spherical particles with a hydrophobic core. To investigate whether the integrity of a hydrophobically stabilized submicellar structure is preserved in the electrostatically stabilized colloidal micellar structure, small-angle X-ray scattering (SAXS) experiments were undertaken on whole casein from bovine milk under submicellar and micellar conditions. All SAXS results showed multiple Gaussian character and could be analyzed best by nonlinear regression in place of the customary Guinier plot. Analysis of the SAXS data for submicellar casein showed two Gaussian components which could be interpreted in terms of a particle with two concentric regions of different electron density, designated as a compact core and a loose shell, respectively. The submicelle was found to have an average molecular weight of 285,000 +/- 14,600 and a mass fraction of higher electron density core, k, of 0.212 +/- 0.028. The radius of gyration of the core, RC, was 37.98 +/- 0.01 A with an electron density difference, delta rho C, of 0.0148 +/- 0.0014 e-/A3, while the loose region had values of RL = 88.2 +/- 0.8 A with delta rho L = 0.0091 +/- 0.0003 e-/A3. Calculated distance distribution functions and normalized scattering curves also were consistent with an overall spherical particle with a concentric spherical inner core of higher electron density. (Abstract Truncated)

  9. Structure of poly(propyl ether imine) dendrimer from fully atomistic molecular dynamics simulation and by small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Jana, Chandan; Jayamurugan, G.; Ganapathy, Rajesh; Maiti, Prabal K.; Jayaraman, N.; Sood, A. K.

    2006-05-01

    We study the structure of carboxylic acid terminated neutral poly(propyl ether imine) (PETIM) dendrimer from generations 1-6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a function of generation the structural properties such as radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, and end-group distribution functions. The sizes obtained from the MD simulations have been validated by small angle x-ray scattering experiment on dendrimer of generations 2-4 (G2-G4). A good agreement between the experimental and theoretical value of radius of gyration has been observed. We find a linear increase in radius of gyration with the generation. In contrast, Rg scales as ˜Nx with the number of monomers. We find two distinct exponents depending on the generations, x =0.47 for G1-G3 and x =0.28 for G3-G6, which reveal their nonspace filling nature. In comparison with the amine terminated poly(amidoamine) (PAMAM) dendrimer, we find that Rg of Gth generation PETIM dendrimer is nearly equal to that of (G +1)th generation of PAMAM dendrimer as observed by Maiti et al. [Macromolecules 38, 979 (2005)]. We find substantial back folding of the outer subgenerations into the interior of the dendrimer. Due to their highly flexible nature of the repeating branch units, the shape of the PETIM dendrimer deviates significantly from the spherical shape and the molecules become more and more spherical as the generation increases. The interior of the dendrimer is quite open with internal cavities available for accommodating guest molecules, suggesting the use of PETIM dendrimer for guest-host applications. We also give a quantitative measure of the number of water molecules present inside the dendrimer.

  10. 3D Structure of Sulfolobus solfataricus Carboxypeptidase Developed by Molecular Modeling is Confirmed by Site-Directed Mutagenesis and Small Angle X-Ray Scattering

    PubMed Central

    Occhipinti, Emanuela; Martelli, Pier Luigi; Spinozzi, Francesco; Corsi, Federica; Formantici, Cristina; Molteni, Laura; Amenitsch, Heintz; Mariani, Paolo; Tortora, Paolo; Casadio, Rita

    2003-01-01

    Sulfolobus solfataricus carboxypeptidase (CPSso) is a thermostable zinc-metalloenzyme with a Mr of 43,000. Taking into account the experimentally determined zinc content of one ion per subunit, we developed two alternative 3D models, starting from the available structures of Thermoactinomyces vulgaris carboxypeptidase (Model A) and Pseudomonas carboxypeptidase G2 (Model B). The former enzyme is monomeric and has one metal ion in the active site, while the latter is dimeric and has two bound zinc ions. The two models were computed by exploiting the structural alignment of the one zinc- with the two zinc-containing active sites of the two templates, and with a threading procedure. Both computed structures resembled the respective template, with only one bound zinc with tetrahedric coordination in the active site. With these models, two different quaternary structures can be modeled: one using Model A with a hexameric symmetry, the other from Model B with a tetrameric symmetry. Mutagenesis experiments directed toward the residues putatively involved in metal chelation in either of the models disproved Model A and supported Model B, in which the metal-binding site comprises His108, Asp109, and His168. We also identified Glu142 as the acidic residue interacting with the water molecule occupying the fourth chelation site. Furthermore, the overall fold and the oligomeric structure of the molecule was validated by small angle x-ray scattering (SAXS). An ab initio original approach was used to reconstruct the shape of the CPSso in solution from the experimental curves. The results clearly support a tetrameric structure. The Monte Carlo method was then used to compare the crystallographic coordinates of the possible quaternary structures for CPSso with the SAXS profiles. The fitting procedure showed that only the model built using the Pseudomonas carboxypeptidase G2 structure as a template fitted the experimental data. PMID:12885660

  11. Structure and optical function of amorphous photonic nanostructures from avian feather barbs: a comparative small angle X-ray scattering (SAXS) analysis of 230 bird species

    PubMed Central

    Saranathan, Vinodkumar; Forster, Jason D.; Noh, Heeso; Liew, Seng-Fatt; Mochrie, Simon G. J.; Cao, Hui; Dufresne, Eric R.; Prum, Richard O.

    2012-01-01

    Non-iridescent structural colours of feathers are a diverse and an important part of the phenotype of many birds. These colours are generally produced by three-dimensional, amorphous (or quasi-ordered) spongy β-keratin and air nanostructures found in the medullary cells of feather barbs. Two main classes of three-dimensional barb nanostructures are known, characterized by a tortuous network of air channels or a close packing of spheroidal air cavities. Using synchrotron small angle X-ray scattering (SAXS) and optical spectrophotometry, we characterized the nanostructure and optical function of 297 distinctly coloured feathers from 230 species belonging to 163 genera in 51 avian families. The SAXS data provided quantitative diagnoses of the channel- and sphere-type nanostructures, and confirmed the presence of a predominant, isotropic length scale of variation in refractive index that produces strong reinforcement of a narrow band of scattered wavelengths. The SAXS structural data identified a new class of rudimentary or weakly nanostructured feathers responsible for slate-grey, and blue-grey structural colours. SAXS structural data provided good predictions of the single-scattering peak of the optical reflectance of the feathers. The SAXS structural measurements of channel- and sphere-type nanostructures are also similar to experimental scattering data from synthetic soft matter systems that self-assemble by phase separation. These results further support the hypothesis that colour-producing protein and air nanostructures in feather barbs are probably self-assembled by arrested phase separation of polymerizing β-keratin from the cytoplasm of medullary cells. Such avian amorphous photonic nanostructures with isotropic optical properties may provide biomimetic inspiration for photonic technology. PMID:22572026

  12. β-connectin studies by small-angle x-ray scattering and single-molecule force spectroscopy by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Marchetti, S.; Sbrana, F.; Toscano, A.; Fratini, E.; Carlà, M.; Vassalli, M.; Tiribilli, B.; Pacini, A.; Gambi, C. M. C.

    2011-05-01

    The three-dimensional structure and the mechanical properties of a β-connectin fragment from human cardiac muscle, belonging to the I band, from I27 to I34, were investigated by small-angle x-ray scattering (SAXS) and single-molecule force spectroscopy (SMFS). This molecule presents an entropic elasticity behavior, associated to globular domain unfolding, that has been widely studied in the last 10 years. In addition, atomic force microscopy based SMFS experiments suggest that this molecule has an additional elastic regime, for low forces, probably associated to tertiary structure remodeling. From a structural point of view, this behavior is a mark of the fact that the eight domains in the I27-I34 fragment are not independent and they organize in solution, assuming a well-defined three-dimensional structure. This hypothesis has been confirmed by SAXS scattering, both on a diluted and a concentrated sample. Two different models were used to fit the SAXS curves: one assuming a globular shape and one corresponding to an elongated conformation, both coupled with a Coulomb repulsion potential to take into account the protein-protein interaction. Due to the predominance of the structure factor, the effective shape of the protein in solution could not be clearly disclosed. By performing SMFS by atomic force microscopy, mechanical unfolding properties were investigated. Typical sawtooth profiles were obtained and the rupture force of each unfolding domain was estimated. By fitting a wormlike chain model to each peak of the sawtooth profile, the entropic elasticity of octamer was described.

  13. Small-angle X-ray scattering study of Zr{sub 4}(Fe,Cr) precipitate in beta-quenched zircaloy-4

    SciTech Connect

    Tsao, C.S.; Yu, M.S.; Lin, T.L.; Lee, C.H.; Lee, H.Y.

    1995-04-01

    Zircaloy-4 through beta quenching treatment has been extensively used as cladding and core structure material in water-cooled nuclear reactors, due to its high nodular corrosion resistance and mechanical strength. Research shows that corrosion resistance is highly related to the sites and size distribution of the second phase precipitate particles after quenching. The nodular corrosion resistance decreases as particle size increases, while uniform corrosion resistance increases. The existence of a large amount of quenched-in vacancies enhances the nucleation and growth of precipitates during the quench process. The microstructure of zircaloy-4 transforms from beta phase (bcc) to Widmanstaetten alpha phase (hcp) with a lathe structure by martensitic transformation. The main intermetallic precipitates, Zr{sub 4}(Fe,Cr), with a fcc phase mostly precipitated at the lathe boundaries, having sizes from 4 to 35 nm. These particles can be considered as a polydispersive system. SAXS (Small-Angle X-ray Scattering) technique, which is used in this study, is a powerful tool to determine the size distribution of fine particles. The IFT (Indirect Fourier Transformation) method is used in this study to analyze the measured scattering intensity distribution which comes from the scattering of all particles (below 50 nm) within the specimen. This work attempts to more accurately reconstruct or determine the size distribution of the second phase particles in beta-quenched zircaloy-4 without prior assumption of the shape of size distribution. The results can be used in future work to explore the mechanism of growth kinetics of Zr{sub 4}(Fe,Cr) precipitate.

  14. In-Situ Monitoring of the Microstructure of TATB-based Explosive Formulations During Temperature Cycling using Ultra-small Angle X-ray Scattering

    SciTech Connect

    Willey, T M; Hoffman, D M; van Buuren, T; Lauderbach, L; Ilavsky, J; Gee, R H; Maiti, A; Overturf, G; Fried, L

    2008-02-06

    TATB (1,3,5 triamino-2,4,6-trinitrobenzene), an extremely insensitive explosive, is used both in plastic-bonded explosives (PBXs) and as an ultra-fine pressed powder (UFTATB). With both PBXs and UFTATB, an irreversible expansion occurs with temperature cycling known as ratchet growth. In TATB-based explosives using Kel-F 800 as binder (LX-17 and PBX-9502), additional voids, sizes hundreds of nanometers to a few microns account for much of the volume expansion caused by temperature cycling. These voids are in the predicted size regime for hot-spot formation during ignition and detonation, and thus an experimental measure of these voids is important feedback for hot-spot theory and for determining the relationship between void size distributions and detonation properties. Also, understanding the mechanism of ratchet growth allows future choice of explosive/binder mixtures to minimize these types of changes to explosives, further extending PBX shelf life. This paper presents the void size distributions of LX-17, UFTATB, and PBXs using commercially available Cytop M, Cytop A, and Hyflon AD60 binders during temperature cycling between -55 C and 70 C. These void size distributions are derived from ultra-small angle x-ray scattering (USAXS), a technique sensitive to structures from about 10 nm to about 2 mm. Structures with these sizes do not appreciably change in UFTATB, indicating voids or cracks larger than a few microns appear in UFTATB during temperature cycling. Compared to Kel-F 800 binders, Cytop M and Cytop A show relatively small increases in void volume from 0.9% to 1.3% and 0.6% to 1.1%, respectively, while Hyflon fails to prevent irreversible volume expansion (1.2% to 4.6%). Computational mesoscale models of ratchet growth and binder wetting and adhesion properties point to mechanisms of ratchet growth, and are discussed in combination with the experimental results.

  15. Ternary systems of nonionic surfactant Brij 35, water and various simple alcohols: Structural investigations by small-angle X-ray scattering and dynamic light scattering.

    PubMed

    Tomsic, Matija; Bester-Rogac, Marija; Jamnik, Andrej; Kunz, Werner; Touraud, Didier; Bergmann, Alexander; Glatter, Otto

    2006-02-01

    Structural properties of ternary systems composed of nonionic surfactant dodecyl-poly(ethylene oxide-23) ether (C12E23, commercial name: Brij 35), water and various alcohols from ethanol to 1-decanol have been investigated using small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) techniques. All measurements were performed at the temperature 25 degrees C. SAXS experimental data were put on absolute scale using water as a secondary standard. The data of water-rich mixtures at low to moderate surfactant concentrations were evaluated using the generalized indirect Fourier transformation method (GIFT), which is based on the simultaneous determination of the intra- and inter-particle scattering contributions. In this way, the size and the shape of interacting scattering particles in real space could be deduced. The systems with a relatively low surfactant concentration (5 mass%) were studied most extensively. In these cases, the water-rich regions of the phase diagrams could be investigated into more detail, since in the alcohol-rich regions problems with the GIFT evaluation of the SAXS data were encountered. The presented results demonstrate the level of structural details that can be obtained on the basis of scattering methods and point out the specific stages of data evaluation and interpretation where one must be extremely precautious. As such they reveal the inner structuration of the complex ternary systems of our present interest. In parallel, they also indicate that the longer chain alcohols actually behave as real oil phases in the studied systems, as one might expect, and also confirm the well-known properties of different short to medium chain alcohols that act as co-solvents and/or co-surfactants in microemulsion systems depending on their chain length. PMID:16085085

  16. Structures of the troponin core domain containing the cardiomyopathy-causing mutants studied by small-angle X-ray scattering

    PubMed Central

    Matsuo, Tatsuhito; Takeda, Soichi; Oda, Toshiro; Fujiwara, Satoru

    2015-01-01

    Troponin (Tn), consisting of three subunits, TnC, TnI, and TnT, is a protein in the thin filaments in muscle, and, together with another thin-filament protein tropomyosin (Tm), plays a major role in regulation of muscle contraction. Various mutations of Tn cause familial hypertrophic cardiomyopathy. These mutations are directly related to aberrations in this regulatory mechanism. Here we focus on the mutations E244D and K247R of TnT, which reside in the middle of the pathway of the Ca2+-binding signal from TnC to Tm. These mutations induce an increase in the maximum tension of cardiac muscle without changes in Ca2+-sensitivity. As a first step toward elucidating the molecular mechanism underlying this functional aberration, we carried out small-angle X-ray scattering experiments on the Tn core domain containing the wild type subunits and those containing the mutant TnT in the absence and presence of Ca2+. Changes in the overall shape induced by the mutations were detected for the first time by the changes in the radius of gyration and the maximum dimension between the wild type and the mutants. Analysis of the scattering curves by model calculations shows that TnC adopts a dumbbell structure regardless of the mutations, and that the mutations change the distributions of the conformational ensembles so that the flexible N- and C-terminal regions of TnT become close to the center of the whole moelcule. This suggests, since these regions are related to the Tn-Tm interactions, that alteration of the Tn-Tm interactions induced by the mutations causes the functional aberration. PMID:27493864

  17. Solution-Based Structural Analysis of the Decaheme Cytochrome, MtrA, by Small-Angle X-ray Scattering and Analytical Ultracentrifugation

    PubMed Central

    2011-01-01

    The potential exploitation of metal-reducing bacteria as a means for environmental cleanup or alternative fuel is an exciting prospect; however, the cellular processes that would allow for these applications need to be better understood. MtrA is a periplasmic decaheme c-type cytochrome from Shewanella oneidensis involved in the reduction of extracellular iron oxides and therefore is a critical element in Shewanella ability to engage in extracellular charge transfer. As a relatively small 333-residue protein, the heme content is surprisingly high. MtrA is believed to obtain electrons from the inner membrane-bound quinol oxidoreductase, CymA, and shuttle them across the outer membrane to MtrC, another decaheme cytochrome that directly interacts with insoluble metal oxides. How MtrA is able to perform this task is a question of interest. Here through the use of two solution-based techniques, small-angle X-ray scattering (SAXS) and analytical ultracentrifugation (AUC), we present the first structural analysis of MtrA. Our results establish that between 0.5 and 4 mg/mL, MtrA exists as a monomeric protein that is shaped like an extended molecular “wire” with a maximum protein dimension (Dmax) of 104 Å and a rod-like aspect ratio of 2.2 to 2.5. This study contributes to a greater understanding of how MtrA fulfills its role in the redox processes that must occur before electrons reach the outside of the cell. PMID:21838277

  18. Characterization of polymer-silica nanocomposite particles with core-shell morphologies using Monte Carlo simulations and small angle X-ray scattering.

    PubMed

    Balmer, Jennifer A; Mykhaylyk, Oleksandr O; Schmid, Andreas; Armes, Steven P; Fairclough, J Patrick A; Ryan, Anthony J

    2011-07-01

    A two-population model based on standard small-angle X-ray scattering (SAXS) equations is verified for the analysis of core-shell structures comprising spherical colloidal particles with particulate shells. First, Monte Carlo simulations of core-shell structures are performed to demonstrate the applicability of the model. Three possible shell packings are considered: ordered silica shells due to either charge-dependent repulsive or size-dependent Lennard-Jones interactions or randomly arranged silica particles. In most cases, the two-population model produces an excellent fit to calculated SAXS patterns for the simulated core-shell structures, together with a good correlation between the fitting parameters and structural parameters used for the simulation. The limits of application are discussed, and then, this two-population model is applied to the analysis of well-defined core-shell vinyl polymer/silica nanocomposite particles, where the shell comprises a monolayer of spherical silica nanoparticles. Comprehensive SAXS analysis of a series of poly(styrene-co-n-butyl acrylate)/silica colloidal nanocomposite particles (prepared by the in situ emulsion copolymerization of styrene and n-butyl acrylate in the presence of a glycerol-functionalized silica sol) allows the overall core-shell particle diameter, the copolymer latex core diameter and polydispersity, the mean silica shell thickness, the mean silica diameter and polydispersity, the volume fractions of the two components, the silica packing density, and the silica shell structure to be obtained. These experimental SAXS results are consistent with electron microscopy, dynamic light scattering, thermogravimetry, helium pycnometry, and BET surface area studies. The high electron density contrast between the (co)polymer and the silica components, together with the relatively low polydispersity of these core-shell nanocomposite particles, makes SAXS ideally suited for the characterization of this system. Moreover

  19. Characterisation of an intrinsically disordered protein complex of Swi5-Sfr1 by ion mobility mass spectrometry and small-angle X-ray scattering.

    PubMed

    Saikusa, Kazumi; Kuwabara, Naoyuki; Kokabu, Yuichi; Inoue, Yu; Sato, Mamoru; Iwasaki, Hiroshi; Shimizu, Toshiyuki; Ikeguchi, Mitsunori; Akashi, Satoko

    2013-03-01

    It is now recognized that intrinsically disordered proteins (IDPs) play important roles as hubs in intracellular networks, and their structural characterisation is of significance. However, due to their highly dynamic features, it is challenging to investigate the structures of IDPs solely by conventional methods. In the present study, we demonstrate a novel method to characterise protein complexes using electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) in combination with small-angle X-ray scattering (SAXS). This method enables structural characterisation even of proteins that have difficulties in crystallisation. With this method, we have characterised the Schizosaccharomyces pombe Swi5-Sfr1 complex, which is expected to have a long disordered region at the N-terminal portion of Sfr1. ESI-IM-MS analysis of the Swi5-Sfr1 complex revealed that its experimental collision cross-section (CCS) had a wide distribution, and the CCS values of the most dominant ions were ∼56% of the theoretically calculated value based on the SAXS low-resolution model, suggesting a significant size reduction in the gas phase. The present study demonstrates that the newly developed method for calculation of the theoretical CCSs of the SAXS low-resolution models of proteins allows accurate evaluation of the experimental CCS values of IDPs provided by ESI-IM-MS by comparing with the low-resolution solution structures. Furthermore, it was revealed that the combination of ESI-IM-MS and SAXS is a promising method for structural characterisation of protein complexes that are unable to crystallise. PMID:23324799

  20. Edible oil structures at low and intermediate concentrations. II. Ultra-small angle X-ray scattering of in situ tristearin solids in triolein

    NASA Astrophysics Data System (ADS)

    Peyronel, Fernanda; Ilavsky, Jan; Mazzanti, Gianfranco; Marangoni, Alejandro G.; Pink, David A.

    2013-12-01

    Ultra-small angle X-ray scattering has been used for the first time to elucidate, in situ, the aggregation structure of a model edible oil system. The three-dimensional nano- to micro-structure of tristearin solid particles in triolein solvent was investigated using 5, 10, 15, and 20% solids. Three different sample preparation procedures were investigated: two slow cooling rates of 0.5°/min, case 1 (22 days of storage at room temperature) and case 2 (no storage), and one fast cooling of 30°/min, case 3 (no storage). The length scale investigated, by using the Bonse-Hart camera at beamline ID-15D at the Advanced Photon Source, Argonne National Laboratory, covered the range from 300 Å to 10 μm. The unified fit and the Guinier-Porod models in the Irena software were used to fit the data. The former was used to fit 3 structural levels. Level 1 structures showed that the primary scatterers were essentially 2-dimensional objects for the three cases. The scatterers possessed lateral dimensions between 1000 and 4300 Å. This is consistent with the sizes of crystalline nanoplatelets present which were observed using cryo-TEM. Level 2 structures were aggregates possessing radii of gyration, Rg2 between 1800 Å and 12000 Å and fractal dimensions of either D2=1 for case 3 or 1.8≤D2≤2.1 for case 1 and case 2. D2 = 1 is consistent with unaggregated 1-dimensional objects. 1.8 ≤ D2 ≤ 2.1 is consistent with these 1-dimensional objects (below) forming structures characteristic of diffusion or reaction limited cluster-cluster aggregation. Level 3 structures showed that the spatial distribution of the level 2 structures was uniform, on the average, for case 1, with fractal dimension D3≈3 while for case 2 and case 3 the fractal dimension was D3≈2.2, which suggested that the large-scale distribution had not come to equilibrium. The Guinier-Porod model showed that the structures giving rise to the aggregates with a fractal dimension given by D2 in the unified fit level 2

  1. Microstructure investigation on micropore formation in microporous silica materials prepared via a catalytic sol-gel process by small angle X-ray scattering.

    PubMed

    Shimizu, Wataru; Hokka, Junsuke; Sato, Takaaki; Usami, Hisanao; Murakami, Yasushi

    2011-08-01

    The so-called sol-gel technique has been shown to be a template-free, efficient way to create functional porous silica materials having uniform micropores. This appears to be closely linked with a postulation that the formation of weakly branched polymer-like aggregates in a precursor solution is a key to the uniform micropore generation. However, how such a polymer-like structure can precisely be controlled, and further, how the generated low-fractal dimension solution structure is imprinted on the solid silica materials still remain elusive. Here we present fabrication of microporous silica from tetramethyl orthosilicate (TMOS) using a recently developed catalytic sol-gel process based on a nonionic hydroxyacetone (HA) catalyst. Small angle X-ray scattering (SAXS), nitrogen adsorption porosimetry, and transmission electron microscope (TEM) allowed us to observe the whole structural evolution, ranging from polymer-like aggregates in the precursor solution to agglomeration with heat treatment and microporous morphology of silica powders after drying and hydrolysis. Using the HA catalyst with short chain monohydric alcohols (methanol or ethanol) in the precursor solution, polymer-like aggregates having microscopic correlation length (or mesh-size) < 2 nm and low fractal dimensions ∼2, which is identical to that of an ideal coil polymer, can selectively be synthesized, yielding the uniform micropores with diameters <2 nm in the solid materials. In contrast, the absence of HA or substitution of 1-propanol led to considerably different scattering behavior reflecting the particle-like aggregate formation in the precursor solution, which resulted in the formation of mesopores (diameter >2 nm) in the solid product due to apertures between the particle-like aggregates. The data demonstrate that the extremely fine porous silica architecture comes essentially from a gaussian polymer-like nature of the silica aggregates in the precursor having the microscopic mesh-size and

  2. Phase Separation in Binary Mixtures of Bipolar and Monopolar Lipid Dispersions Revealed by 2H NMR Spectroscopy, Small Angle X-Ray Scattering, and Molecular Theory

    PubMed Central

    Brownholland, David P.; Longo, Gabriel S.; Struts, Andrey V.; Justice, Matthew J.; Szleifer, Igal; Petrache, Horia I.; Brown, Michael F.; Thompson, David H.

    2009-01-01

    Abstract Binary mixtures of C20BAS and POPC membranes were studied by solid-state 2H NMR spectroscopy and small angle x-ray scattering (SAXS) over a wide range of concentrations and at different temperatures. Three specifically deuterated C20BAS derivatives—[1′,1′,20′,20′-2H4]C20BAS, [2′,2′,19′,19′-2H4]C20BAS, and [10′,11′-2H2]C20BAS—combined with protiated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), as well as membranes containing POPC-d31 and fully protiated bolalipid, were used in NMR experiments to obtain structural information for the mixtures. The 2H NMR spectra of [10′,11′-2H2]C20BAS/POPC membrane dispersions reveal that the bolalipid is predominantly in the transmembrane conformation at high bolalipid concentrations (100, 90, and 70 mol %). At ≤50 mol % C20BAS, smaller quadrupolar couplings appear in the spectra, indicating the presence of U-shaped conformers. The proportion of U-shaped bolalipids increases as the amount of POPC in the membrane increases; however, the transmembrane component remains the dominant bolalipid conformation in the membrane even at 45°C and 10 mol % C20BAS, where it accounts for ∼50% of the bolalipid population. The large fraction of C20BAS transmembrane conformers, regardless of the C20BAS/POPC ratio, together with the findings from molecular mean-field theory calculations, suggests the coexistence of phase-separated bolalipid-rich domains and POPC-rich domains. A single lamellar repeat distance was observed in SAXS experiments corresponding to the average repeat spacing expected for C20BAS- and POPC-rich domains. These observations are consistent with the presence of microphase-separated domains in the mixed membrane samples that arise from POPC-C20BAS hydrophobic mismatch. PMID:19917223

  3. X-ray polaroids based on the total external reflection in anomalous-dispersion regions

    NASA Astrophysics Data System (ADS)

    Machavariani, V. Sh

    1996-12-01

    A new method of development of x-ray polaroids is suggested. The idea is based on the effect of total external reflection from an anisotropic crystal in the anomalous-dispersion region. The polarization coefficient for hexagonal BN crystal near the boron K absorption edge is calculated for different glancing angles and thicknesses of sample. It is shown that the method treated provides a simple way of constructing an effective x-ray polaroid.

  4. Edible oil structures at low and intermediate concentrations. II. Ultra-small angle X-ray scattering of in situ tristearin solids in triolein

    SciTech Connect

    Peyronel, Fernanda; Marangoni, Alejandro G.; Ilavsky, Jan; Mazzanti, Gianfranco; Pink, David A.

    2013-12-21

    Ultra-small angle X-ray scattering has been used for the first time to elucidate, in situ, the aggregation structure of a model edible oil system. The three-dimensional nano- to micro-structure of tristearin solid particles in triolein solvent was investigated using 5, 10, 15, and 20% solids. Three different sample preparation procedures were investigated: two slow cooling rates of 0.5°/min, case 1 (22 days of storage at room temperature) and case 2 (no storage), and one fast cooling of 30°/min, case 3 (no storage). The length scale investigated, by using the Bonse-Hart camera at beamline ID-15D at the Advanced Photon Source, Argonne National Laboratory, covered the range from 300 Å to 10 μm. The unified fit and the Guinier-Porod models in the Irena software were used to fit the data. The former was used to fit 3 structural levels. Level 1 structures showed that the primary scatterers were essentially 2-dimensional objects for the three cases. The scatterers possessed lateral dimensions between 1000 and 4300 Å. This is consistent with the sizes of crystalline nanoplatelets present which were observed using cryo-TEM. Level 2 structures were aggregates possessing radii of gyration, R{sub g2} between 1800 Å and 12000 Å and fractal dimensions of either D{sub 2}=1 for case 3 or 1.8≤D{sub 2}≤2.1 for case 1 and case 2. D{sub 2} = 1 is consistent with unaggregated 1-dimensional objects. 1.8 ≤ D{sub 2} ≤ 2.1 is consistent with these 1-dimensional objects (below) forming structures characteristic of diffusion or reaction limited cluster-cluster aggregation. Level 3 structures showed that the spatial distribution of the level 2 structures was uniform, on the average, for case 1, with fractal dimension D{sub 3}≈3 while for case 2 and case 3 the fractal dimension was D{sub 3}≈2.2, which suggested that the large-scale distribution had not come to equilibrium. The Guinier-Porod model showed that the structures giving rise to the aggregates

  5. Probing bismuth ferrite nanoparticles by hard x-ray photoemission: Anomalous occurrence of metallic bismuth

    SciTech Connect

    Chaturvedi, Smita; Rajendra, Ranguwar; Ballav, Nirmalya; Kulkarni, Sulabha; Sarkar, Indranil; Shirolkar, Mandar M.; Jeng, U-Ser; Yeh, Yi-Qi

    2014-09-08

    We have investigated bismuth ferrite nanoparticles (∼75 nm and ∼155 nm) synthesized by a chemical method, using soft X-ray (1253.6 eV) and hard X-ray (3500, 5500, and 7500 eV) photoelectron spectroscopy. This provided an evidence for the variation of chemical state of bismuth in crystalline, phase pure nanoparticles. X-ray photoelectron spectroscopy analysis using Mg Kα (1253.6 eV) source showed that iron and bismuth were present in both Fe{sup 3+} and Bi{sup 3+} valence states as expected for bismuth ferrite. However, hard X-ray photoelectron spectroscopy analysis of the bismuth ferrite nanoparticles using variable photon energies unexpectedly showed the presence of Bi{sup 0} valence state below the surface region, indicating that bismuth ferrite nanoparticles are chemically inhomogeneous in the radial direction. Consistently, small-angle X-ray scattering reveals a core-shell structure for these radial inhomogeneous nanoparticles.

  6. Structure of low-density nanoporous dielectrics revealed by low-vacuum electron microscopy and small-angle x-ray scattering

    SciTech Connect

    Kucheyev, S O; Toth, M; Baumann, T F; Hamza, A V; Ilavsky, J; Knowles, W R; Thiel, B L; Tileli, V; van Buuren, T; Wang, Y M; Willey, T M

    2006-06-05

    We use low-vacuum scanning electron microscopy to image directly the ligament and pore size and shape distributions of representative aerogels over a wide range of length scales ({approx} 10{sup 0}-10{sup 5} nm). The images are used for unambiguous, real-space interpretation of small-angle scattering data for these complex nanoporous systems.

  7. Can Charge Exchange Explain Anomalous Soft X-Ray Emission in the Cygnus Loop?

    NASA Astrophysics Data System (ADS)

    Cumbee, R. S.; Henley, D. B.; Stancil, P. C.; Shelton, R. L.; Nolte, J. L.; Wu, Y.; Schultz, D. R.

    2014-06-01

    Recent X-ray studies have shown that supernova shock models are unable to satisfactorily explain X-ray emission in the rim of the Cygnus Loop. In an attempt to account for this "anomalously" enhanced X-ray flux, we fit the region with a model including theoretical charge exchange (CX) data along with shock and background X-ray models. The model includes the CX collisions of O8 +, O7 +, N7 +, N6 +, C6 +, and C5 + with H with an energy of 1 keV u-1 (438 km s-1). The observations reveal a strong emission feature near 0.7 keV that cannot fully be accounted for by a shock model, nor the current CX data. Inclusion of CX, specifically O7 + + H, does provide for a statistically significant improvement over a pure shock model.

  8. Anomalous x-ray scattering studies of short-, intermediate- and extended-range order in glasses

    SciTech Connect

    Price, D.L.; Saboungi, M.L.; Armand, P.; Cox, D.E.

    1998-08-01

    The authors present the formalism of anomalous x-ray scattering as applied to partial structure analysis of disordered materials, and give an example of how the technique has been applied, together with that of neutron diffraction, to investigate short-, intermediate- and extended-range order in vitreous germania and rubidium germanate.

  9. Nanostructure of a-Si:H and related alloys by small-angle scattering of neutrons and X-rays: Annual technical progress report: May 22, 1998 -- May 21, 1999

    SciTech Connect

    Williamson, D. L.

    1999-12-21

    This report describes work being performed to provide details of the microstructure in high-quality hydrogenated amorphous silicon and related alloys on the nanometer scale. The materials under study are being prepared by state-of-the-art deposition methods, as well as by new and emerging deposition techniques. The purpose is to establish the role of nanostructural features in controlling opto-electronic and photovoltaic properties. The approach centers around the use of the uncommon technique of small-angle scattering of both X-rays (SAXS) and neutrons (SANS). SAXS has already been established as highly sensitive to microvoids and columnar-like microstructure. A major goal of this research is to establish the sensitivity of SANS to the hydrogen nanostructure. Conventional X-ray diffraction techniques are being used to examine medium-range order and microcrystallinity, particularly near the boundary between amorphous and microcrystalline material.

  10. Period Clustering of the Anomalous X-Ray Pulsars and Magnetic Field Decay in Magnetars.

    PubMed

    Colpi; Geppert; Page

    2000-01-20

    We confront theoretical models for the rotational, magnetic, and thermal evolution of an ultramagnetized neutron star, or magnetar, with available data on the anomalous X-ray pulsars (AXPs). We argue that, if the AXPs are interpreted as magnetars, their clustering of spin periods between 6 and 12 s (observed at present in this class of objects), their period derivatives, their thermal X-ray luminosities, and the association of two of them with young supernova remnants can only be understood globally if the magnetic field in magnetars decays significantly on a timescale of the order of 104 yr. PMID:10615029

  11. Structural evolution of regenerated silk fibroin under shear: Combined wide- and small-angle x-ray scattering experiments using synchrotron radiation

    SciTech Connect

    Rossle, Manfred; Panine, Pierre; Urban, Volker S; Riekel, Christine

    2004-04-01

    The structural evolution of regenerated Bombyx mori silk fibroin during shearing with a Couette cell has been studied in situ by synchrotron radiation small- and wide-angle x-ray scattering techniques. An elongation of fibroin molecules was observed with increasing shear rate, followed by an aggregation phase. The aggregates were found to be amorphous with {beta}-conformation according to infrared spectroscopy. Scanning x-ray microdiffraction with a 5 {micro}m beam on aggregated material, which had solidified in air, showed silk II reflections and a material with equatorial reflections close to the silk I structure reflections, but with strong differences in reflection intensities. This silk I type material shows up to two low-angle peaks suggesting the presence of water molecules that might be intercalated between hydrogen-bonded sheets.

  12. Synchrotron X-ray Imaging via Ultra-small-angle Scattering: Principles of Quantitative Analysis and Application in Studyingbone Integration to Synthetic Grafting Materials

    SciTech Connect

    Morelhao, S.; Coelho, P; Honnicke, M

    2010-01-01

    Optimized experimental conditions for extracting accurate information at subpixel length scales from analyzer-based X-ray imaging were obtained and applied to investigate bone regeneration by means of synthetic {beta}-TCP grafting materials in a rat calvaria model. The results showed a 30% growth in the particulate size due to bone ongrowth/ingrowth within the critical size defect over a 1-month healing period.

  13. Searching for plasmas with anomalous dispersion in the soft X-ray regime

    SciTech Connect

    Nilsen, J; Johnson, W R; Cheng, K T

    2007-08-24

    Over the last decade the electron density of plasmas has been measured using X-ray laser interferometers in the 14 to 47 nm wavelength regime. With the same formula used in decades of experiments with optical interferometers, the data analysis assumes the index of refraction is due only to the free electrons, which makes the index less than one. Over the last several years, interferometer experiments in C, Al, Ag, and Sn plasmas have observed plasmas with index of refraction greater than one at 14 or 47 nm and demonstrated unequivocally that the usual formula for calculating the index of refraction is not always valid as the contribution from bound electrons can dominate the free electrons in certain cases. In this paper we search for other materials with strong anomalous dispersion that could be used in X-ray laser interferometer experiments to help understand this phenomena. An average atom code is used to calculate the plasma properties. This paper discusses the calculations of anomalous dispersion in Ne and Na plasmas near 47 nm and Xe plasmas near 14 nm. With the advent of the FLASH X-ray free electron laser in Germany and the LCLS X-FEL coming online at Stanford in 2 years the average atom code will be an invaluable tool to explore plasmas at higher X-ray energy to identify potential experiments for the future. During the next decade X-ray free electron lasers and other X-ray sources will be used to probe a wider variety of plasmas at higher densities and shorter wavelengths so understanding the index of refraction in plasmas will be even more essential.

  14. TINY HICCUPS TO TITANIC EXPLOSIONS: Tackling Transients in Anomalous X-ray Pulsars

    NASA Astrophysics Data System (ADS)

    Kaspi, Victoria

    2011-09-01

    The past decade has seen major progress in neutron star astrophysics, with the discovery of magnetars in general, and the recognition that the Anomalous X-ray Pulsars (AXPs) fall in this class. AXPs have recently revealed surprising and dramatic variability behavior, which theorists have begun to show are highly constraining of physical models of magnetars, including their crusts, atmospheres, coronae and magnetospheres. In this proposal, we request Chandra/ACIS-S Target-of-Opportunity observations of one major Anomalous X-ray Pulsar (AXP) outburst in AO13, in order to study in detail the evolution of the spectrum, pulsed fraction and pulse profile, for quantitative confrontation with recently developed models for the structure and electrodynamics of magnetars.

  15. TINY HICCUPS TO TITANIC EXPLOSIONS: Tackling Transients in Anomalous X-ray Pulsars

    NASA Astrophysics Data System (ADS)

    Kaspi, Victoria

    2010-09-01

    The past decade has seen major progress in neutron star astrophysics, with the discovery of magnetars in general, and the recognition that the Anomalous X-ray Pulsars (AXPs) fall in this class. AXPs have recently revealed surprising and dramatic variability behavior, which theorists have begun to show are highly constraining of physical models of magnetars, including their crusts, atmospheres, coronae and magnetospheres. In this proposal, we request Chandra/ACIS-S Target-of-Opportunity observations of one major Anomalous X-ray Pulsar (AXP) outburst in AO12, in order to study in detail the evolution of the spectrum, pulsed fraction and pulse profile, for quantitative confrontation with recently developed models for the structure and electrodynamics of magnetars.

  16. Nanometer-scale characterization of laser-driven plasmas, compression, shocks and phase transitions, by coherent small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Kluge, Thomas

    2015-11-01

    Combining ultra-intense short-pulse and high-energy long-pulse lasers, with brilliant coherent hard X-ray FELs, such as the Helmholtz International Beamline for Extreme Fields (HIBEF) under construction at the HED Instrument of European XFEL, or MEC at LCLS, holds the promise to revolutionize our understanding of many High Energy Density Physics phenomena. Examples include the relativistic electron generation, transport, and bulk plasma response, and ionization dynamics and heating in relativistic laser-matter interactions, or the dynamics of laser-driven shocks, quasi-isentropic compression, and the kinetics of phase transitions at high pressure. A particularly promising new technique is the use of coherent X-ray diffraction to characterize electron density correlations, and by resonant scattering to characterize the distribution of specific charge-state ions, either on the ultrafast time scale of the laser interaction, or associated with hydrodynamic motion. As well one can image slight density changes arising from phase transitions inside of shock-compressed high pressure matter. The feasibility of coherent diffraction techniques in laser-driven matter will be discussed. including recent results from demonstration experiments at MEC. Among other things, very sharp density changes from laser-driven compression are observed, having an effective step width of 10 nm or smaller. This compares to a resolution of several hundred nm achievedpreviously with phase contrast imaging. and on behalf of HIBEF User Consortium, for the Helmholtz International Beamline for Extreme Fields at the European XFEL.

  17. Alkyl Chain Length and Temperature Effects on Structural Properties of Pyrrolidinium-Based Ionic Liquids: A Combined Atomistic Simulation and Small-Angle X-ray Scattering Study

    SciTech Connect

    Li, Song; Bañuelos, José Leobardo; Guo, Jianchang; Anovitz, Lawrence; Rother, Gernot; Shaw, Robert W.; Hillesheim, Patrick C.; Dai, Sheng; Baker, Gary A.; Cummings, Peter T.

    2011-12-21

    Molecular dynamics (MD) simulations of 1-alkyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([CnMPy][Tf₂N], n = 3, 4, 6, 8, 10) were conducted using an all-atom model. Radial distribution functions (RDF) were computed and structure functions were generated to compare with new X-ray scattering experimental results, reported herein. The scattering peaks in the structure functions generally shift to lower Q values with increased temperature for all the liquids in this series. However, the first sharp diffraction peak (FSDP) in the longer alkyl chain liquids displays a marked shift to higher Q values with increasing temperature. Alkyl chain-dependent ordering of the polar groups and increased tail aggregation with increasing alkyl chain length were observed in the partial pair correlation functions and the structure functions. The reasons for the observed alkyl chain-dependent phenomena and temperature effects were explored.

  18. Alkyl Chain Length and Temperature Effects on Structural Properties of Pyrrolidinium-Based Ionic Liquids: A Combined Atomistic Simulation and Small-Angle X-ray Scattering Study.

    SciTech Connect

    Li, Song; Banuelos, Jose Leo; Guo, Jianchang; Anovitz, Lawrence {Larry} M; Rother, Gernot; Shaw, Robert W; Hillesheim, Patrick C; Dai, Sheng; Baker, Gary A; Cummings, Peter T

    2011-01-01

    Molecular dynamics (MD) simulations of 1-alkyl-1-methylpyrrolidinium 12 bis(trifluoromethanesulfonyl)imide ([CnMPy][Tf2N], n = 3, 4, 6, 8, 10) were conducted 13 using an all-atom model. Radial distribution functions (RDF) were computed and structure 14 functions were generated to compare with new X-ray scattering experimental results, 15 reported herein. The scattering peaks in the structure functions generally shift to lower Q 16 values with increased temperature for all the liquids in this series. However, the first sharp 17 diffraction peak (FSDP) in the longer alkyl chain liquids displays a marked shift to higher Q 18 values with increasing temperature. Alkyl chain-dependent ordering of the polar groups and 19 increased tail aggregation with increasing alkyl chain length were observed in the partial pair 20 correlation functions and the structure functions. The reasons for the observed alkyl chain- 21 dependent phenomena and temperature effects were explored.

  19. Two new sealed sample cells for small angle x-ray scattering from macromolecules in solution and complex fluids using synchrotron radiation

    SciTech Connect

    Cavalcanti, L.P.; Torriani, I.L.; Plivelic, T.S.; Oliveira, C.L.P.; Kellermann, G.; Neuenschwander, R.

    2004-11-01

    Two different vacuum tight sample cells for in situ temperature dependent small angle scattering from liquids are presented in this article. In the first one, the sample fills a 1 mm thickness gap sealed on both sides by two thin parallel mica windows (volume 300 {mu}l). In the second one, the liquid is injected into a 1 mm cylindrical capillary tube (volume 130 {mu}l). The cells are lodged into temperature controlled chambers directly connected to the beamline vacuum path. Several important improvements with respect to similar instrumentation previously reported are: (1) versatile application of the mica cell, that can be used for all types of samples (gels, liquid crystals, and dispersions in organic solvents) and (2) the design of the chamber for the capillary cell allows registration of wider angle data and a convenient replacement of the capillary tube after each experiment. Signal to background ratio and data reproducibility were tested using protein solutions. We give a brief report of scattering experiments performed with different protein samples and two-dimensional data collection.

  20. Structural characterization of Green River oil-shale at high-pressure using pair distribution function analysis and small angle x-ray scattering.

    SciTech Connect

    Locke, D. R.; Chupas, P. J.; Chapman, K. W.; Pugmire, R. J.; Winans, R. E.; Univ. of Utah

    2008-01-01

    The compression behavior of a silicate-rich oil shale from the Green River formation in the pressure range 0.0-2.4 GPa was studied using in situ high pressure X-ray pair distribution function (PDF) measurements for the sample contained within a Paris-Edinburgh cell. The real-space local structural information in the PDF, G(r), was used to evaluate the compressibility of the oil shale. Specifically, the pressure-induced reduction in the medium- to long-range atom distances (6-20 {angstrom}) yielded an average sample compressibility corresponding to a bulk modulus of ca. 61-67 GPa. A structural model consisting of a three phase mixture of the principal crystalline oil shale components (quartz, albite and Illite) provided a good fit to the ambient pressure PDF data (R 30.7%). Indeed the features in the PDF beyond 6 {angstrom}, were similarly well fit by a single phase model of the highest symmetry, highly crystalline quartz component.

  1. A small angle x-ray scattering study of the droplet-cylinder transition in oil-rich sodium bis(2-ethylhexyl) sulfosuccinate microemulsions

    NASA Astrophysics Data System (ADS)

    Svergun, D. I.; Konarev, P. V.; Volkov, V. V.; Koch, M. H. J.; Sager, W. F. C.; Smeets, J.; Blokhuis, E. M.

    2000-07-01

    A method for nonlinear fitting of x-ray scattering data from polydisperse mixtures was developed. It was applied to the analysis of the structural changes in the droplet phase of oil-rich water-in-oil (w/o) sodium bis(2-ethylhexyl) sulfosuccinate (AOT) microemulsions with increasing temperature or upon addition of salt. Data were collected at different temperatures (15 to 60 °C) and salt concentrations (up to 0.6% NaCl) within the one-phase region of the L2 phase (w/o microemulsion) for different droplet sizes (water/AOT molar ratio wo=25 to 56) and concentrations (droplet weight fraction cw=2% to 20%). This allowed us to distinguish between contributions from individual scattering particles, e.g., droplets and cylinders to the total scattering intensity. The complete data set containing over 500 scattering curves could be interpreted by fitting the scattering of weighted sums of AOT covered water droplets, long cylinders, and inverse AOT micelles containing bound water only, to the experimental scattering curves. The polydispersity of the droplets and cylinders is described by Schulz distributions and the interactions between the droplets are calculated using a sticky hard-sphere potential in the Percus-Yevick approximation. The volume fractions of the components, their average sizes and polydispersity, and the stickiness of the water/AOT droplets are determined by a nonlinear fit to the experimental data.

  2. CAN CHARGE EXCHANGE EXPLAIN ANOMALOUS SOFT X-RAY EMISSION IN THE CYGNUS LOOP?

    SciTech Connect

    Cumbee, R. S.; Henley, D. B.; Stancil, P. C.; Shelton, R. L.; Nolte, J. L.; Wu, Y.; Schultz, D. R.

    2014-06-01

    Recent X-ray studies have shown that supernova shock models are unable to satisfactorily explain X-ray emission in the rim of the Cygnus Loop. In an attempt to account for this ''anomalously'' enhanced X-ray flux, we fit the region with a model including theoretical charge exchange (CX) data along with shock and background X-ray models. The model includes the CX collisions of O{sup 8} {sup +}, O{sup 7} {sup +}, N{sup 7} {sup +}, N{sup 6} {sup +}, C{sup 6} {sup +}, and C{sup 5} {sup +} with H with an energy of 1 keV u{sup –1} (438 km s{sup –1}). The observations reveal a strong emission feature near 0.7 keV that cannot fully be accounted for by a shock model, nor the current CX data. Inclusion of CX, specifically O{sup 7} {sup +} + H, does provide for a statistically significant improvement over a pure shock model.

  3. Outburst of the 2 s Anomalous X-ray Pulsar 1E 1547.0-5408

    NASA Technical Reports Server (NTRS)

    Halpern, J. P.; Gotthelf, E. V.; Camilo, F.; Reynolds, J.; Ransom, S. M.

    2008-01-01

    Following our discovery of radio pulsations from the newly recognized anomalous X-ray pulsar (AXP) 1E 1547.0-5408, we initiated X-ray monitoring with the Swift X-ray telescope and obtained a single target-of-opportunity observation with the Newton X-ray Multi-Mirror Mission (XMM-Newton). In comparison with its historic minimum flux of 3 x 10(exp -l3)ergs/sq cm/s, the source was found to be in a record high state, f(sub x)(1-8 keV) = 5 x 10(exp -12)ergs/sq cm/s, or L(sub x) = 1.7 x 10(exp 35)(d/9 kpc )(sup 2)ergs/s, and declining by 25% in 1 month. Extrapolating the decay, we bound the total energy in this outburst to 1042 ergs < E < ergs. The spectra (fitted with a Comptonized blackbody) show that an increase in the temperature and area of a hot region, to 0.5 keV and -16% of the surface area of the neutron star, respectively, are primarily responsible for its increase in luminosity. The energy, spectrum, and timescale of decay are consistent with a deep crustal heating event, similar to an interpretation of the X-ray turn-on of the transient AXP XTE J18 10- 197. Simultaneous with the 4.6 hr ATdA4-Newton observation, we observed at 6.4 GHz with the Parkes telescope, measuring the phase relationship of the radio and X-ray pulse. The X-ray pulsed fraction of 1E 1547.0-5408 is only approx. 7 %, while its radio pulse is relatively broad for such a slow pulsar, which may indicate a nearly aligned rotator. As also inferred from the transient behavior of XTE J18 10-197, the only other AXP known to emit in the radio, the magnetic field rearrangement responsible for this X-ray outburst of 1E 1547.0-5408 is probably the cause of its radio turn-on.

  4. Determination of the size and phase composition of silver nanoparticles in a gel film of bacterial cellulose by small-angle X-ray scattering, electron diffraction, and electron microscopy

    SciTech Connect

    Volkov, V. V.; Klechkovskaya, V. V. Shtykova, E. V.; Dembo, K. A.; Arkharova, N. A.; Ivakin, G. I.; Smyslov, R. Yu.

    2009-03-15

    The nanoscale structural features in a composite (gel film of Acetobacter Xylinum cellulose with adsorbed silver nanoparticles, stabilized by N-polyvinylpyrrolidone) have been investigated by small-angle X-ray scattering. The size distributions of inhomogeneities in the porous structure of the cellulose matrix and the size distributions of silver nanoparticles in the composite have been determined. It is shown that the sizes of synthesized nanoparticles correlate with the sizes of inhomogeneities in the gel film. Particles of larger size (with radii up to 100 nm) have also been found. Electron microscopy of thin cross sections of a dried composite layer showed that large particles are located on the cellulose layer surface. Electron diffraction revealed a crystal structure of silver nanoparticles in the composite.

  5. Synchrotron Small Angle X-Ray Scattering Quantitatively Detects Angstrom Level Changes in the Average Radius of Taxol-Stabilized Microtubules Decorated with the Microtubule-Associated-Protein Tau

    NASA Astrophysics Data System (ADS)

    Choi, Myung Chul; Raviv, Uri; Li, Youli; Miller, Herbert P.; Needleman, Daniel J.; Kim, Mahn Won; Wilson, Leslie; Feinstein, Stuart C.; Safinya, Cyrus R.

    2011-01-01

    With the emerging proteomics era the scientific community is beginning the daunting task of understanding the structures and functions of a large number of self-assembling proteins. Here, our study was concerned with the effect of the microtubule-associated-protein (MAP) tau on the assembled structure of taxol-stabilized microtubules. Significantly, the synchrotron small angle x-ray scattering (SAXS) technique is able to quantitatively detect angstrom level changes in the average diameter of the microtubules modeled as a simple hollow nanotube with a fixed wall thickness. We show that the electrostatic binding of MAP tau isoforms to taxol-stabilized MTs leads to a controlled increase in the average radius of microtubules with increasing coverage of tau on the MT surface. The increase in the average diameter results from an increase in the distribution of protofilament numbers in MTs upon binding of MAP tau.

  6. Determination of the size and phase composition of silver nanoparticles in a gel film of bacterial cellulose by small-angle X-ray scattering, electron diffraction, and electron microscopy

    NASA Astrophysics Data System (ADS)

    Volkov, V. V.; Klechkovskaya, V. V.; Shtykova, E. V.; Dembo, K. A.; Arkharova, N. A.; Ivakin, G. I.; Smyslov, R. Yu.

    2009-03-01

    The nanoscale structural features in a composite (gel film of Acetobacter Xylinum cellulose with adsorbed silver nanoparticles, stabilized by N-polyvinylpyrrolidone) have been investigated by small-angle X-ray scattering. The size distributions of inhomogeneities in the porous structure of the cellulose matrix and the size distributions of silver nanoparticles in the composite have been determined. It is shown that the sizes of synthesized nanoparticles correlate with the sizes of inhomogeneities in the gel film. Particles of larger size (with radii up to 100 nm) have also been found. Electron microscopy of thin cross sections of a dried composite layer showed that large particles are located on the cellulose layer surface. Electron diffraction revealed a crystal structure of silver nanoparticles in the composite.

  7. Resonant X-ray diffraction in incommensurately modulated crystals. Symmetry consideration of anisotropic anomalous scattering.

    PubMed

    Ovchinnikova; Dmitrienko

    1999-01-01

    Symmetry restrictions on the intensities and polarization properties of main reflections and their satellites are found for incommensurately modulated crystals in the case of anisotropic anomalous X-ray diffraction near absorption edges. It is shown that the modulation becomes a source of additional anisotropy for each resonant scatterer and induces a modulated behaviour of the susceptibility tensor. The four-dimensional approach is used to calculate the set of possible reflections. It is found that additional ('forbidden') reflections may appear both in the system of main reflections and in the system of satellites. The anisotropy also results in complex azimuthal and polarization properties of each reflection. The displacive modulation is discussed in detail. The ATS reflections corresponding to the resonant X-ray diffraction near the K-edge of iron in pyrrhotite-5.5C are considered. PMID:10927227

  8. Anomalous X-ray Pulsars and Soft Gamma Repeaters as Magnetars: The RXTE Legacy

    NASA Astrophysics Data System (ADS)

    Kaspi, Victoria M.

    2012-01-01

    Prior to the launch of RXTE, the hypothesis by Thompson and Duncan that there exists a class of ultra-highly magnetized young neutron stars whose emission is powered by the decay of their magnetic field -- the so-called `magnetar' model -- was beautiful, yet unproven. The magnetar model was motivated the existence of Soft Gamma Repeaters (SGRs), which had been observed to exhibit dramatic X-ray and soft gamma ray bursts and in one case, 8-s pulsations in the tail of a major flare. Meanwhile, there was recognized another puzzling group of seemingly very different objects, the 'Anomalous X-ray Pulsars' (AXPs), so-called due to their bright, several-second X-ray pulsations, steady spin down, low spin-down power and absence of any binary companion from which mass could be accreted. AXPs had also been suggested to be magnetars by Thompson and Duncan, though this too was unproven. Today, thanks to multiple landmark RXTE results, these two groups of object have been united into a single source class, which is now nearly universally identified with magnetars. Specifically, the discovery from SGRs of regular X-ray pulsations and steady spin-down (as had been observed in AXPs), as well as the discovery of bright X-ray bursts from AXPs (as had been observed in SGRs) has demonstrated unambiguously the common nature of AXPs and SGRs, as was predicted uniquely in the magnetar model. Moreover, RXTE discoveries of several observational links between AXPs, SGRs and rotation-powered pulsars, specifically the detection of spin-up glitches in AXPs, as well as the observation of a temporary metamorphosis of one rotation-powered pulsar into a magnetar-like source, hint at a broader unification of the magnetars with the general radio pulsar population, with the observational differences attributable to a combination of age and magnetic field.

  9. Probing the surface microstructure of layer-by-layer self-assembly chitosan/poly(l-glutamic acid) multilayers: A grazing-incidence small-angle X-ray scattering study.

    PubMed

    Zhao, Nie; Yang, Chunming; Wang, Yuzhu; Zhao, Binyu; Bian, Fenggang; Li, Xiuhong; Wang, Jie

    2016-01-01

    This study characterized the surface structure of layer-by-layer self-assembly chitosan/poly(L-glutamic acid) multilayers through grazing-incidence small-angle X-ray scattering (GISAXS), X-ray reflectivity (XRR), and atomic force microscopy (AFM). A weakly long-period ordered structure along the in-plane direction was firstly observed in the polyelectrolyte multilayer by the GISAXS technique. This structure can be attributed to the specific domains on the film surface. In the domain, nanodroplets that were formed by polyelectrolyte molecules were orderly arranged along the free surface of the films. This ordered structure gradually disappeared with the increasing bilayer number because of the complex merging behavior of nanodroplets into large islands. Furthermore, resonant diffuse scattering became evident in the GISAXS patterns as the number of bilayers in the polyelectrolyte multilayer was increased. Notably, the lateral cutoff length of resonant diffuse scattering for these polyelectrolyte films was comparable with the long-period value of the ordered nanodroplets in the polyelectrolyte multilayer. Therefore, the nanodroplets could be considered as a basic transmission unit for structure propagation from the inner interface to the film surface. It suggests that the surface structure with length scale larger than the size of nanodroplets was partially complicated from the interface structure near the substrate, but surface structure smaller than the cutoff length was mainly depended on the conformation of nanodroplets. PMID:26478320

  10. Determination of the polarization state of x rays with the help of anomalous transmission

    SciTech Connect

    Schulze, K. S. Uschmann, I.; Förster, E.; Marx, B.; Paulus, G. G.; Stöhlker, T.

    2014-04-14

    Besides intensity and direction, the polarization of an electromagnetic wave provides characteristic information on the crossed medium. Here, we present two methods for the determination of the polarization state of x rays by polarizers based on anomalous transmission (Borrmann effect). Using a polarizer-analyzer setup, we have measured a polarization purity of less than 1.5 × 10{sup −5}, three orders of magnitude better than obtained in earlier work. Using the analyzer crystal in multiple-beam case with slightly detuned azimuth, we show how the first three Stokes parameters can be determined with a single angular scan. Thus, polarization analyzers based on anomalous transmission make it possible to detect changes of the polarization in a range from degrees down to arcseconds.

  11. Optical pulsations from the anomalous X-ray pulsar 4U0142+61.

    PubMed

    Kern, B; Martin, C

    2002-05-30

    Anomalous X-ray pulsars (AXPs) differ from ordinary radio pulsars in that their X-ray luminosity is orders of magnitude greater than their rate of rotational energy loss, and so they require an additional energy source. One possibility is that AXPs are highly magnetized neuron stars or 'magnetars' having surface magnetic fields greater than 10(14) G. This would make them similar to the soft gamma-ray repeaters (SGRs), but alternative models that do not require extreme magnetic fields also exist. An optical counterpart to the AXP 4U0142+61 was recently discovered, consistent with emission from a magnetar, but also from a magnetized hot white dwarf, or an accreting isolated neutron star. Here we report the detection of optical pulsations from 4U0142+61. The pulsed fraction of optical light (27 per cent) is five to ten times greater than that of soft X-rays, from which we conclude that 4U0142+61 is a magnetar. Although this establishes a direct relationship between AXPs and the soft gamma-ray repeaters, the evolutionary connection between AXPs, SGRs and radio pulsars remains controversial. PMID:12037561

  12. Long-term evolution of anomalous X-ray pulsars and soft gamma repeaters

    NASA Astrophysics Data System (ADS)

    Benli, O.; Ertan, Ü.

    2016-04-01

    We have investigated the long-term evolution of individual anomalous X-ray pulsars (AXPs) and soft gamma repeaters (SGRs) with relatively well constrained X-ray luminosity and rotational properties. In the frame of the fallback disc model, we have obtained the ranges of disc mass and dipole field strength that can produce the observed source properties. We have compared our results with those obtained earlier for dim isolated neutron stars (XDINs). Our results show that (1) the X-ray luminosity, period and period derivative of the individual AXP/SGR sources can be produced self-consistently in the fallback disc model with very similar basic disc parameters to those used earlier in the same model to explain the long-term evolution of XDINs, (2) except two sources, AXP/SGRs are evolving in the accretion phase; these two exceptional sources, like XDINs, completed their accretion phase in the past and are now evolving in the final propeller phase and still slowing down with the disc torques, (3) the dipole field strengths (at the poles) of XDINs are in the 1011-1012 G range, while AXP/SGRs have relatively strong dipole fields between 1 and 6 × 1012 G, and (4) the source properties can be obtained with large ranges of disc masses which do not allow a clear test of correlation between disc masses and the magnetic dipole fields for the whole AXP/SGRs and XDIN population.

  13. Discovery of Radio Emission From Transient Anomalous X-Ray Pulsar XTE J1810-197

    SciTech Connect

    Halpern, J P; Gotthelf, E V; Becker, R H; Helfand, D J; White, R L

    2005-10-25

    We report the first detection of radio emission from any anomalous X-ray pulsar (AXP). Data from the Very Large Array (VLA) MAGPIS survey with angular resolution 6'' reveals a point-source of flux density 4.5 {+-} 0.5 mJy at 1.4 GHz at the precise location of the 5.54 s pulsar XTE J1810-197. This is greater than upper limits from all other AXPs and from quiescent states of soft gamma-ray repeaters (SGRs). The detection was made in 2004 January, 1 year after the discovery of XTE J1810-197 during its only known outburst. Additional VLA observations both before and after the outburst yield only upper limits that are comparable to or larger than the single detection, neither supporting nor ruling out a decaying radio afterglow related to the X-ray turn-on. Another hypothesis is that, unlike the other AXPs and SGRs, XTE J1810-197 may power a radio synchrotron nebula by the interaction of its particle wind with a moderately dense environment that was not evacuated by previous activity from this least luminous, in X-rays, of the known magnetars.

  14. The roles of the RIIβ linker and N-terminal cyclic nucleotide-binding domain in determining the unique structures of the type IIβ protein kinase A: a small angle x-ray and neutron scattering study.

    PubMed

    Blumenthal, Donald K; Copps, Jeffrey; Smith-Nguyen, Eric V; Zhang, Ping; Heller, William T; Taylor, Susan S

    2014-10-10

    Protein kinase A (PKA) is ubiquitously expressed and is responsible for regulating many important cellular functions in response to changes in intracellular cAMP concentrations. The PKA holoenzyme is a tetramer (R2:C2), with a regulatory subunit homodimer (R2) that binds and inhibits two catalytic (C) subunits; binding of cAMP to the regulatory subunit homodimer causes activation of the catalytic subunits. Four different R subunit isoforms exist in mammalian cells, and these confer different structural features, subcellular localization, and biochemical properties upon the PKA holoenzymes they form. The holoenzyme containing RIIβ is structurally unique in that the type IIβ holoenzyme is much more compact than the free RIIβ homodimer. We have used small angle x-ray scattering and small angle neutron scattering to study the solution structure and subunit organization of a holoenzyme containing an RIIβ C-terminal deletion mutant (RIIβ(1-280)), which is missing the C-terminal cAMP-binding domain to better understand the structural organization of the type IIβ holoenzyme and the RIIβ domains that contribute to stabilizing the holoenzyme conformation. Our results demonstrate that compaction of the type IIβ holoenzyme does not require the C-terminal cAMP-binding domain but rather involves large structural rearrangements within the linker and N-terminal cyclic nucleotide-binding domain of the RIIβ homodimer. The structural rearrangements are significantly greater than seen previously with RIIα and are likely to be important in mediating short range and long range interdomain and intersubunit interactions that uniquely regulate the activity of the type IIβ isoform of PKA. PMID:25112875

  15. The roles of RIIbeta linker and N-terminal cyclic nucleotide-binding domain in determining the unique structures of Type IIbeta Protein Kinase A. A small angle X-ray and neutron scattering study

    DOE PAGESBeta

    Blumenthal, Donald K.; Copps, Jeffrey; Smith-Nguyen, Eric V.; Zhang, Ping; Heller, William T.; Taylor, Susan S.

    2014-08-11

    Protein kinase A (PKA) is ubiquitously expressed and is responsible for regulating many important cellular functions in response to changes in intracellular cAMP concentrations. Moreover, the PKA holoenzyme is a tetramer (R2:C2), with a regulatory subunit homodimer (R2) that binds and inhibits two catalytic (C) subunits; binding of cAMP to the regulatory subunit homodimer causes activation of the catalytic subunits. Four different R subunit isoforms exist in mammalian cells, and these confer different structural features, subcellular localization, and biochemical properties upon the PKA holoenzymes they form. The holoenzyme containing RIIβ is structurally unique in that the type IIβ holoenzyme ismore » much more compact than the free RIIβ homodimer. We have used small angle x-ray scattering and small angle neutron scattering to study the solution structure and subunit organization of a holoenzyme containing an RIIβ C-terminal deletion mutant (RIIβ(1–280)), which is missing the C-terminal cAMP-binding domain to better understand the structural organization of the type IIβ holoenzyme and the RIIβ domains that contribute to stabilizing the holoenzyme conformation. These results demonstrate that compaction of the type IIβ holoenzyme does not require the C-terminal cAMP-binding domain but rather involves large structural rearrangements within the linker and N-terminal cyclic nucleotide-binding domain of the RIIβ homodimer. The structural rearrangements are significantly greater than seen previously with RIIα and are likely to be important in mediating short range and long range interdomain and intersubunit interactions that uniquely regulate the activity of the type IIβ isoform of PKA.« less

  16. The roles of RIIbeta linker and N-terminal cyclic nucleotide-binding domain in determining the unique structures of Type IIbeta Protein Kinase A. A small angle X-ray and neutron scattering study

    SciTech Connect

    Blumenthal, Donald K.; Copps, Jeffrey; Smith-Nguyen, Eric V.; Zhang, Ping; Heller, William T.; Taylor, Susan S.

    2014-08-11

    Protein kinase A (PKA) is ubiquitously expressed and is responsible for regulating many important cellular functions in response to changes in intracellular cAMP concentrations. Moreover, the PKA holoenzyme is a tetramer (R2:C2), with a regulatory subunit homodimer (R2) that binds and inhibits two catalytic (C) subunits; binding of cAMP to the regulatory subunit homodimer causes activation of the catalytic subunits. Four different R subunit isoforms exist in mammalian cells, and these confer different structural features, subcellular localization, and biochemical properties upon the PKA holoenzymes they form. The holoenzyme containing RIIβ is structurally unique in that the type IIβ holoenzyme is much more compact than the free RIIβ homodimer. We have used small angle x-ray scattering and small angle neutron scattering to study the solution structure and subunit organization of a holoenzyme containing an RIIβ C-terminal deletion mutant (RIIβ(1–280)), which is missing the C-terminal cAMP-binding domain to better understand the structural organization of the type IIβ holoenzyme and the RIIβ domains that contribute to stabilizing the holoenzyme conformation. These results demonstrate that compaction of the type IIβ holoenzyme does not require the C-terminal cAMP-binding domain but rather involves large structural rearrangements within the linker and N-terminal cyclic nucleotide-binding domain of the RIIβ homodimer. The structural rearrangements are significantly greater than seen previously with RIIα and are likely to be important in mediating short range and long range interdomain and intersubunit interactions that uniquely regulate the activity of the type IIβ isoform of PKA.

  17. In situ small-angle x-ray and nuclear resonant scattering study of the evolution of structural and magnetic properties of an Fe thin film on MgO (001)

    NASA Astrophysics Data System (ADS)

    Sharma, Gagan; Gupta, Ajay; Gupta, Mukul; Schlage, Kai; Wille, H.-C.

    2015-12-01

    Growth of magnetron sputtered Fe films on clean single crystalline MgO (001) substrate has been studied using in situ grazing incidence small angle x-ray scattering (GISAXS) and grazing incidence nuclear resonant scattering (GINRS) measurements. While GISAXS provides information about morphological changes, GINRS provides information about structural and magnetic properties, thus making it possible to correlate the evolution of magnetic properties with that of morphology and structure of the film. The film exhibits a Volmer-Weber type growth, with percolation transition occurring around 2 nm film thickness. Presence of a finite quadrupole splitting, as seen in GINRS measurements, suggests a significant distortion from cubic symmetry up to a film thickness of 3.5 nm, which can be attributed to hybridization between Fe 3 d and O 2 p orbitals at the interface as well as in-plane tensile strain induced as a result of coalescence of islands. Initially Fe islands exhibit superparamagnetic relaxation, while finite magnetic moment appears upon formation of macroscopic percolation islands. The film exhibits a weak perpendicular magnetic anisotropy (PMA), which vanishes concurrently with disappearance of structural distortion, suggesting that the observed PMA at least partly originates from inherent strain in the film. No presence of any known oxide of Fe was detected at the interface. More precise information about topological and magnetic structure of the interfaces between Fe and MgO layers is obtained using combined x-ray reflectivity and nuclear resonance reflectivity measurements on a 57Fe/MgO multilayer. Measurements show that about two monolayers of Fe at the interface have a reduced hyperfine field, providing evidence for hybridization with O atoms, as predicted by theory.

  18. Site Determination of Sr in Sr3YB3O9 Crystals by Anomalous X-ray Scattering

    NASA Astrophysics Data System (ADS)

    Simura, R.; Sugiyama, K.

    2014-04-01

    The distribution of Sr in Sr3YB3O9 crystals was determined by anomalous X-ray scattering. The Sr3YB3O9 sample was grown by the floating-zone method in dry air. The Sr3YB3O9 crystal has three cation sites (3a, 3b, and 18f). The results of single-crystal structural analysis using anomalous X-ray scattering at the Sr K-edge suggested that Sr is distributed at the 3a site as well as it is at the chemically disordered 18f site.

  19. Kinetics of Hexagonal-Body-Centered Cubic Transition in a Triblock Copolymer in a Selective Solvent: Time-Resolved Small-Angle X-ray Scattering Measurements and Model Calculations

    SciTech Connect

    Li,M.; Liu, Y.; Nie, H.; Bansil, R.; Steinhart, M.

    2007-01-01

    Time-resolved small-angle X-ray scattering (SAXS) was used to examine the kinetics of the transition from hexagonal (hex) cylinders to body-centered cubic (bcc) spheres at various temperatures in poly(styrene-b-ethylene-co-butylene-b-styrene) (SEBS) in mineral oil, a selective solvent for the middle ethylene-co-butylene (EB) block. Temperature-ramp SAXS and rheology measurements show the hex to bcc order-order transition (OOT) at 127 C and order-disorder transition (ODT) at 180 C. We also observed the metastability limit of hex in bcc with a spinodal temperature, Ts 150 C. The OOT exhibits three stages and occurs via a nucleation and growth mechanism when the final temperature Tf < Ts. Spinodal decomposition in a continuous ordering system was seen when Ts < Tf < TODT. We observed that hex cylinders transform to disordered spheres via a transient bcc state. We develop a geometrical model of coupled anisotropic fluctuations and calculate the scattering which shows very good agreement with the SAXS data. The splitting of the primary peak into two peaks when the cylinder spacing and modulation wavelength are incommensurate predicted by the model is confirmed by analysis of the SAXS data.

  20. Stabilization of asphaltenes in aliphatic solvents using alkylbenzene-derived amphiphiles. 2. Study of the asphaltene-amphiphile interactions and structures using Fourier transform infrared spectroscopy and small-angle X-ray scattering techniques

    SciTech Connect

    Chang, C.L.; Fogler, H.S. )

    1994-06-01

    In the preceding paper in this issue, the influence of the chemical structure of a series of alkylbenzene-derived amphiphiles on the stabilization of asphaltenes was described. In this paper, we present the results of using Fourier transform infrared (FTIR) spectroscopy and small-angle X-ray scattering (SAXS) techniques to study the interaction between asphaltenes and two alkylbenzene-derived amphiphiles, p-alkylphenol and p-alkylbenzenesulfonic acid. FTIR spectroscopy was used to characterize and quantify the acid-base interactions between asphaltenes and amphiphiles. It was found that asphaltenes could hydrogen-bond to p-dodecylphenol amphiphiles. The hydrogen-bonding capacity of asphaltenes was estimated to be 1.6-2.0 mmol/g of asphaltene. On the other hand, the FTIR spectroscopic study indicated that asphaltenes had a complicated acid-base interaction with p-dodecylbenzenesulfonic acid (DBSA) amphiphiles with a stoichiometry of about 1.8 mmol of DBSA/g of asphaltene. The UV/vis spectroscopic study suggested that asphaltenes and DBSA could associate into large electronic conjugated complexes. Physical evidence of the association between asphaltenes and amphiphiles was obtained by SAXS measurements. 27 refs., 10 figs.

  1. Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics.

    PubMed

    Anami, Yasuaki; Shimizu, Nobutaka; Ekimoto, Toru; Egawa, Daichi; Itoh, Toshimasa; Ikeguchi, Mitsunori; Yamamoto, Keiko

    2016-09-01

    Vitamin D receptor (VDR) controls the expression of numerous genes through the conformational change caused by binding 1α,25-dihydroxyvitamin D3. Helix 12 in the ligand-binding domain (LBD) is key to regulating VDR activation. The structures of apo VDR-LBD and the VDR-LBD/antagonist complex are unclear. Here, we reveal their unprecedented structures in solution using a hybrid method combining small-angle X-ray scattering and molecular dynamics simulations. In apo rat VDR-LBD, helix 12 is partially unraveled, and it is positioned around the canonical active position and fluctuates. Helix 11 greatly bends toward the outside at Q396, creating a kink. In the rat VDR-LBD/antagonist complex, helix 12 does not generate the activation function 2 surface, and loop 11-12 is remarkably flexible compared to that in the apo rat VDR-LBD. On the basis of these structural insights, we propose a "folding-door model" to describe the mechanism of agonism/antagonism of VDR-LBD. PMID:27535484

  2. Detection of Ligand- and Solvent-Induced Shape Alterations of Cell-Growth-Regulatory Human Lectin Galectin-1 in Solution by Small Angle Neutron and X-Ray Scattering

    PubMed Central

    He, Lizhong; André, Sabine; Siebert, Hans-Christian; Helmholz, Heike; Niemeyer, Bernd; Gabius, Hans-Joachim

    2003-01-01

    The bioactivity of galectin-1 in cell growth regulation and adhesion prompted us to answer the questions whether ligand presence and a shift to an aprotic solvent typical for bioaffinity chromatography might alter the shape of the homodimeric human lectin in solution. We used small angle neutron and synchrotron x-ray scattering studies for this purpose. Upon ligand accommodation, the radius of gyration of human galectin-1 decreased from 19.1 ± 0.1 Å in the absence of ligand to 18.2 ± 0.1 Å. In the aprotic solvent dimethyl sulfoxide, which did not impair binding capacity, galectin-1 formed dimers of a dimer, yielding tetramers with a cylindrical shape. Intriguingly, no dissociation into subunits occurred. In parallel, NMR monitoring was performed. The spectral resolution was in accord with these data. In contrast to the properties of the human protein, a nonhomologous agglutinin from mistletoe sharing galactose specificity was subject to a reduction in the radius of gyration from ∼62 Å in water to 48.7 Å in dimethyl sulfoxide. Evidently, the solvent caused opposite responses in the two tested galactoside-binding lectins with different folding patterns. We have hereby proven that ligand presence and an aprotic solvent significantly affect the shape of galectin-1 in solution. PMID:12829506

  3. Small-angle X-ray scattering analysis reveals the ATP-bound monomeric state of the ATPase domain from the homodimeric MutL endonuclease, a GHKL phosphotransferase superfamily protein.

    PubMed

    Iino, Hitoshi; Hikima, Takaaki; Nishida, Yuya; Yamamoto, Masaki; Kuramitsu, Seiki; Fukui, Kenji

    2015-05-01

    DNA mismatch repair is an excision system that removes mismatched bases chiefly generated by replication errors. In this system, MutL endonucleases direct the excision reaction to the error-containing strand of the duplex by specifically incising the newly synthesized strand. Both bacterial homodimeric and eukaryotic heterodimeric MutL proteins belong to the GHKL ATPase/kinase superfamily that comprises the N-terminal ATPase and C-terminal dimerization regions. Generally, the GHKL proteins show large ATPase cycle-dependent conformational changes, including dimerization-coupled ATP binding of the N-terminal domain. Interestingly, the ATPase domain of human PMS2, a subunit of the MutL heterodimer, binds ATP without dimerization. The monomeric ATP-bound state of the domain has been thought to be characteristic of heterodimeric GHKL proteins. In this study, we characterized the ATP-bound state of the ATPase domain from the Aquifex aeolicus MutL endonuclease, which is a homodimeric GHKL protein unlike the eukaryotic MutL. Gel filtration, dynamic light scattering, and small-angle X-ray scattering analyses clearly showed that the domain binds ATP in a monomeric form despite its homodimeric nature. This indicates that the uncoupling of dimerization and ATP binding is a common feature among bacterial and eukaryotic MutL endonucleases, which we suggest is closely related to the molecular mechanisms underlying mismatch repair. PMID:25809295

  4. Small-angle X-ray analysis of the effect of grain size on the thermal damage of octahydro-1, 3, 5, 7-tetranitro-1, 3, 5, 7 tetrazocine-based plastic-bounded expolsives

    NASA Astrophysics Data System (ADS)

    Yan, Guan-Yun; Tian, Qiang; Liu, Jia-Hui; Chen, Bo; Sun, Guang-Ai; Huang, Ming; Li, Xiu-Hong

    2014-07-01

    The microstructure evolution of plastic-bonded explosives (PBXs) after thermal stimulus plays a key role in PBX performance. In this paper, the nanoscale pores of thermal-treated octahydro-1,3,5,7-tetranitro-1,3,5,7 tetrazocine (HMX)-based PBXs with different HMX particle sizes [approximately 40 (FHP) and 100 μm (LHP)] were measured using small-angle X-ray scattering (SAXS). No obvious pore variations were found in the LHP samples heated at 160 °C for 6 h, whereas the amount of pores of FHP decreased when subjected to 160 °C for 6 h. At 180 °C, the average pore radii of FHP and LHP decreased from approximately 45 nm to 25 nm, and the total pore volume increased distinctively because of phase transformation. The LHP sample reached a high level of pore content after being held at 180 °C for 1 h, whereas FHP required 3 h. Both FHP and LHP had relatively high pore volumes when subjected to 200 °C for 1 and 3 h.

  5. Effects of blending poly(D,L-lactide) with poly(ethylene glycol) on the higher-oder crystalline structures of poly(ethylene glycol) as revealed by small-angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Tien, N. D.; Hoa, T. P.; Kimura, G.; Yamashiro, Y.; Fujiwara, H.; Mochizuki, M.; Sasaki, S.; Sakurai, S.

    2011-01-01

    Effects of blending poly(lactic acid) (PLA) with poly(ethylene glycol) (PEG) on higher-order crystalline structures of PEG were examined using small-angle X-ray scattering (SAXS). For this purpose, the fact that two polymers are both crystalline makes situtation much complicated. To simplify, non-crystalline PLA is suitable. Thus, we used poly(D,L-lactic acid) (DLPLA), which is random copolymer comprising D- and L-lactic acid moieties. Multiple scattering peaks arising from the regular crystalline lamellar structure were observed for the PEG homopolymer and the blends. Surprisingly, the structure is much more regular for the blend DLPLA/PEG at composition of 20/80 wt.% than for the PEG homopolymer. Also for this blend sample as well as for a PEG homopolymer, very peculiar SAXS profiles were observed just 1°C below Tm of PEG. This is found to be a particle scattering of plate-like objects, which has never been reported for polymer blends or crystalline polymers. Futhermore, it was found that there was strong hysteresis of the higher-order structure formation.

  6. Small-Angle X-ray Scattering Screening Complements Conventional Biophysical Analysis: Comparative Structural and Biophysical Analysis of Monoclonal Antibodies IgG1, IgG2, and IgG4

    PubMed Central

    Tian, Xinsheng; Langkilde, Annette E; Thorolfsson, Matthias; Rasmussen, Hanne B; Vestergaard, Bente

    2014-01-01

    A crucial step in the development of therapeutic monoclonal antibodies is the selection of robust pharmaceutical candidates and screening of efficacious protein formulations to increase the resistance toward physicochemical degradation and aggregation during processing and storage. Here, we introduce small-angle X-ray scattering (SAXS) to characterize antibody solution behavior, which strongly complements conventional biophysical analysis. First, we apply a variety of conventional biophysical techniques for the evaluation of structural, conformational, and colloidal stability and report a systematic comparison between designed humanized IgG1, IgG2, and IgG4 with identical variable regions. Then, the high information content of SAXS data enables sensitive detection of structural differences between three IgG subclasses at neutral pH and rapid formation of dimers of IgG2 and IgG4 at low pH. We reveal subclass-specific variation in intermolecular repulsion already at low and medium protein concentrations, which explains the observed improved stability of IgG1 with respect to aggregation. We show how excipients dramatically influence such repulsive effects, hence demonstrating the potential application of extensive SAXS screening in antibody selection, eventual engineering, and formulation development. PMID:24700358

  7. In Situ Lipolysis and Synchrotron Small-Angle X-ray Scattering for the Direct Determination of the Precipitation and Solid-State Form of a Poorly Water-Soluble Drug During Digestion of a Lipid-Based Formulation.

    PubMed

    Khan, Jamal; Hawley, Adrian; Rades, Thomas; Boyd, Ben J

    2016-09-01

    In situ lipolysis and synchrotron small-angle X-ray scattering (SAXS) were used to directly detect and elucidate the solid-state form of precipitated fenofibrate from the digestion of a model lipid-based formulation (LBF). This method was developed in light of recent findings that indicate variability in solid-state form upon the precipitation of some drugs during the digestion of LBFs, addressing the need to establish a real-time technique that enables solid-state analysis during in vitro digestion. In addition, an ex situ method was also used to analyse the pellet phase formed during an in vitro lipolysis experiment at various time points for the presence of crystalline drug. Fenofibrate was shown to precipitate in its thermodynamically stable crystalline form upon digestion of the medium-chain LBF, and an increase in scattering intensity over time corresponded well to an increase in concentration of precipitated fenofibrate quantified from the pellet phase using high-performance liquid chromatography. Crossed polarized light microscopy served as a secondary technique confirming the crystallinity of the precipitated fenofibrate. Future application of in situ lipolysis and SAXS may focus on drugs, and experimental conditions, which are anticipated to produce altered solid-state forms upon the precipitation of drug (i.e., polymorphs, amorphous forms, and salts). PMID:26359590

  8. Structural dynamics and ssDNA binding activity of the three N-terminal domains of the large subunit of Replication Protein A from small angle X-ray scattering

    SciTech Connect

    Pretto, Dalyir I.; Tsutakawa, Susan; Brosey, Chris A.; Castillo, Amalchi; Chagot, Marie-Eve; Smith, Jarrod A.; Tainer, John A.; Chazin, Walter J.

    2010-03-11

    Replication Protein A (RPA) is the primary eukaryotic ssDNA binding protein utilized in diverse DNA transactions in the cell. RPA is a heterotrimeric protein with seven globular domains connected by flexible linkers, which enable substantial inter-domain motion that is essential to its function. Small angle X-ray scattering (SAXS) experiments on two multi-domain constructs from the N-terminus of the large subunit (RPA70) were used to examine the structural dynamics of these domains and their response to the binding of ssDNA. The SAXS data combined with molecular dynamics simulations reveal substantial interdomain flexibility for both RPA70AB (the tandem high affinity ssDNA binding domains A and B connected by a 10-residue linker) and RPA70NAB (RPA70AB extended by a 70-residue linker to the RPA70N protein interaction domain). Binding of ssDNA to RPA70NAB reduces the interdomain flexibility between the A and B domains, but has no effect on RPA70N. These studies provide the first direct measurements of changes in orientation of these three RPA domains upon binding ssDNA. The results support a model in which RPA70N remains structurally independent of RPA70AB in the DNA bound state and therefore freely available to serve as a protein recruitment module.

  9. Nucleation and crystal growth in a suspension of charged colloidal silica spheres with bi-modal size distribution studied by time-resolved ultra-small-angle X-ray scattering.

    PubMed

    Hornfeck, Wolfgang; Menke, Dirk; Forthaus, Martin; Subatzus, Sebastian; Franke, Markus; Schöpe, Hans-Joachim; Palberg, Thomas; Perlich, Jan; Herlach, Dieter

    2014-12-01

    A suspension of charged colloidal silica spheres exhibiting a bi-modal size distribution of particles, thereby mimicking a binary mixture, was studied using time-resolved ultra-small-angle synchrotron X-ray scattering (USAXS). The sample, consisting of particles of diameters d(A) = (104.7 ± 9.0) nm and d(B) = (88.1 ± 7.8) nm (d(A)/d(B) ≈ 1.2), and with an estimated composition A(0.6(1))B(0.4(1)), was studied with respect to its phase behaviour in dependance of particle number density and interaction, of which the latter was modulated by varying amounts of added base (NaOH). Moreover, its short-range order in the fluid state and its eventual solidification into a long-range ordered colloidal crystal were observed in situ, allowing the measurement of the associated kinetics of nucleation and crystal growth. Key parameters of the nucleation kinetics such as crystallinity, crystallite number density, and nucleation rate density were extracted from the time-resolved scattering curves. By this means an estimate on the interfacial energy for the interface between the icosahedral short-range ordered fluid and a body-centered cubic colloidal crystal was obtained, comparable to previously determined values for single-component colloidal systems. PMID:25481168

  10. Polar atomic displacements in multiferroics observed via anomalous x-ray diffraction

    NASA Astrophysics Data System (ADS)

    Azimonte, C.; Granado, E.; Terashita, H.; Park, S.; Cheong, S.-W.

    2010-01-01

    The minute polar atomic displacements in multiferroics are shown to be within the reach of crystallography. A nonconventional methodology with anomalous x-ray diffraction is employed to investigate such displacements in DyMn2O5 with giant magnetoelectric coupling and two distinct Mn3+ and Mn4+ sites. Intensity differences of a selected Bragg reflection were measured as the direction of electric polarization is switched by a poling field. A significant differential effect, which is strongly enhanced at energies near and above the MnK edge, was observed near and below the ferroelectric transition temperature, Tc˜40K . The direct participation of ionic displacements in the ferroelectric polarization, particularly the Mn3+ sublattice, is demonstrated, dismissing a purely electronic mechanism for the multiferroicity.

  11. Anomalous high-pressure behavior of amorphous selenium from synchrotron x-ray diffraction and microtomography

    PubMed Central

    Liu, Haozhe; Wang, Luhong; Xiao, Xianghui; De Carlo, Francesco; Feng, Ji; Mao, Ho-kwang; Hemley, Russell J.

    2008-01-01

    The high-pressure behavior of amorphous selenium has been investigated with time-resolved diamond anvil cell synchrotron x-ray diffraction and computed microtomography techniques. A two-step dynamic crystallization process is observed in which the monoclinic phase crystallized from the amorphous selenium and gradually converted to the trigonal phase, thereby explaining previously observed anomalous changes in electrical conductivity of the material under pressure. The crystallization of this elemental system involves local topological fluctuations and results in an unusual pressure-induced volume expansion. The metastability of the phases involved in the transition accounts for this phenomenon. The results demonstrate the use of pressure to control and directly monitor the relative densities and energetics of phases to create new phases from highly metastable states. The microtomographic technique developed here represents a method for determination of the equations of state of amorphous materials at extreme pressures and temperatures. PMID:18768800

  12. On the Extended Emission of the Anomalous X-ray Pulsar IE 1547.0-5408

    NASA Technical Reports Server (NTRS)

    Olausen, S. A.; Kaspi, V. M.; Ng, C. -Y.; Zhu, W. W.; Gavriil, F. P.; Woods, P. M.

    2012-01-01

    We present an analysis of the extended emission around the anomalous X-ray pulsar IE 1547.0-5408 using four XMM-Newton observations taken with the source in varying states of outburst as well as in quiescence. We find that the extended emission flux is highly variable and strongly correlated with the flux of the magnetar. Based on this result, as well as on spectral and energetic considerations, we conclude that the extended emission is dominated by a dust-scattering halo and not a pulsar wind nebula (P-VVN), as has been previously argued. We obtain an upper limit on the 2-10 keV flux of a possible PWN of 4.7 x 10(exp -14) erg/s/sq cm, three times less than the previously claimed value, implying an efficiency for conversion of spin-down energy into nebular luminosity of <9 x 10(exp -4) .

  13. Anomalous elastic scattering of x-ray photon by an atom with an open shell

    NASA Astrophysics Data System (ADS)

    Hopersky, A. N.; Petrov, I. D.; Nadolinsky, A. M.; Yavna, V. A.; Koneev, R. V.

    2004-08-01

    In the non-relativistic approximation for the wavefunctions of the one-electron states and in the dipole approximation for the scattering amplitude the effect of relaxation of atomic shells in the field of core vacancies, multiplet splitting, Auger and radiative vacancy decays and virtual processes of one-photon double excitation/ionization from the atomic ground state on the differential cross section of anomalous elastic scattering of the linearly polarized x-ray photon by the copper atom near its 1s-shell ionization threshold are studied. The results of calculations are found to be in agreement with the high-precision synchrotron radiation experiment by Arp et al (1993 J. Phys. B: At. Mol. Opt. Phys. 26 4381).

  14. THE DUST-SCATTERING X-RAY RINGS OF THE ANOMALOUS X-RAY PULSAR 1E 1547.0-5408

    SciTech Connect

    Tiengo, A.; Vianello, G.; Esposito, P.; Mereghetti, S.; Giuliani, A.; Israel, G. L.; Stella, L.; Bernardini, F.; Zane, S.; Rea, N.; Goetz, D.; Gehrels, N.

    2010-02-10

    On 2009 January 22 numerous strong bursts were detected from the anomalous X-ray pulsar 1E 1547.0-5408. Swift/XRT and XMM-Newton/EPIC observations carried out in the following two weeks led to the discovery of three X-ray rings centered on this source. The ring radii increased with time following the expansion law expected for a short impulse of X-rays scattered by three dust clouds. Assuming different models for the dust composition and grain size distribution, we fit the intensity decay of each ring as a function of time at different energies, obtaining tight constraints on the distance of the X-ray source. Although the distance strongly depends on the adopted dust model, we find that some models are incompatible with our X-ray data, restricting to 4-8 kpc the range of possible distances for 1E 1547.0-5408. The best-fitting dust model provides a source distance of 3.91 +- 0.07 kpc, which is compatible with the proposed association with the supernova remnant G327.24-0.13, and implies distances of 2.2 kpc, 2.6 kpc and 3.4 kpc for the dust clouds, in good agreement with the dust distribution inferred by CO line observations toward 1E 1547.0-5408. However, dust distances in agreement with CO data are also obtained for a set of similarly well-fitting models that imply a source distance of {approx}5 kpc. A distance of {approx}4-5 kpc is also favored by the fact that these dust models are already known to provide good fits to the dust-scattering halos of bright X-ray binaries. Assuming N{sub H} = 10{sup 22} cm{sup -2} in the dust cloud responsible for the brightest ring and a bremsstrahlung spectrum with kT = 100 keV, we estimate that the burst producing the X-ray ring released an energy of 10{sup 44}-10{sup 45} erg in the 1-100 keV band, suggesting that this burst was the brightest flare without any long-lasting pulsating tail ever detected from a magnetar.

  15. Application of focused-beam flat-sample method to synchrotron powder X-ray diffraction with anomalous scattering effect

    NASA Astrophysics Data System (ADS)

    Tanaka, M.; Katsuya, Y.; Matsushita, Y.

    2013-03-01

    The focused-beam flat-sample method (FFM), which is a method for high-resolution and rapid synchrotron X-ray powder diffraction measurements by combination of beam focusing optics, a flat shape sample and an area detector, was applied for diffraction experiments with anomalous scattering effect. The advantages of FFM for anomalous diffraction were absorption correction without approximation, rapid data collection by an area detector and good signal-to-noise ratio data by focusing optics. In the X-ray diffraction experiments of CoFe2O4 and Fe3O4 (By FFM) using X-rays near the Fe K absorption edge, the anomalous scattering effect between Fe/Co or Fe2+/Fe3+ can be clearly detected, due to the change of diffraction intensity. The change of observed diffraction intensity as the incident X-ray energy was consistent with the calculation. The FFM is expected to be a method for anomalous powder diffraction.

  16. AN ACCRETION MODEL FOR THE ANOMALOUS X-RAY PULSAR 4U 0142+61

    SciTech Connect

    Truemper, J. E.; Dennerl, K.; Kylafis, N. D.; Zezas, A.; Ertan, Ue.

    2013-02-10

    We propose that the quiescent emission of anomalous X-ray pulsars/soft gamma-ray repeaters (AXPs/SGRs) is powered by accretion from a fallback disk, requiring magnetic dipole fields in the range 10{sup 12}-10{sup 13} G, and that the luminous hard tails of their X-ray spectra are produced by bulk-motion Comptonization in the radiative shock near the bottom of the accretion column. This radiation escapes as a fan beam, which is partly absorbed by the polar cap photosphere, heating it up to relatively high temperatures. The scattered component and the thermal emission from the polar cap form a polar beam. We test our model on the well-studied AXP 4U 0142+61, whose energy-dependent pulse profiles show double peaks, which we ascribe to the fan and polar beams. The temperature of the photosphere (kT {approx} 0.4 keV) is explained by the heating effect. The scattered part forms a hard component in the polar beam. We suggest that the observed high temperatures of the polar caps of AXPs/SGRs, compared with other young neutron stars, are due to the heating by the fan beam. Using beaming functions for the fan beam and the polar beam and taking gravitational bending into account, we fit the energy-dependent pulse profiles and obtain the inclination angle and the angle between the spin axis and the magnetic dipole axis, as well as the height of the radiative shock above the stellar surface. We do not explain the high-luminosity bursts, which may be produced by the classical magnetar mechanism operating in super-strong multipole fields.

  17. The Crystal Structure and Small-Angle X-Ray Analysis of CsdL/TcdA Reveal a New tRNA Binding Motif in the MoeB/E1 Superfamily

    PubMed Central

    López-Estepa, Miguel; Ardá, Ana; Savko, Martin; Round, Adam; Shepard, William E.; Bruix, Marta; Coll, Miquel; Fernández, Francisco J.; Jiménez-Barbero, Jesús; Vega, M. Cristina

    2015-01-01

    Cyclic N6-threonylcarbamoyladenosine (‘cyclic t6A’, ct6A) is a non-thiolated hypermodification found in transfer RNAs (tRNAs) in bacteria, protists, fungi and plants. In bacteria and yeast cells ct6A has been shown to enhance translation fidelity and efficiency of ANN codons by improving the faithful discrimination of aminoacylated tRNAs by the ribosome. To further the understanding of ct6A biology we have determined the high-resolution crystal structures of CsdL/TcdA in complex with AMP and ATP, an E1-like activating enzyme from Escherichia coli, which catalyzes the ATP-dependent dehydration of t6A to form ct6A. CsdL/TcdA is a dimer whose structural integrity and dimer interface depend critically on strongly bound K+ and Na+ cations. By using biochemical assays and small-angle X-ray scattering we show that CsdL/TcdA can associate with tRNA with a 1:1 stoichiometry and with the proper position and orientation for the cyclization of t6A. Furthermore, we show by nuclear magnetic resonance that CsdL/TcdA engages in transient interactions with CsdA and CsdE, which, in the latter case, involve catalytically important residues. These short-lived interactions may underpin the precise channeling of sulfur atoms from cysteine to CsdL/TcdA as previously characterized. In summary, the combination of structural, biophysical and biochemical methods applied to CsdL/TcdA has afforded a more thorough understanding of how the structure of this E1-like enzyme has been fine tuned to accomplish ct6A synthesis on tRNAs while providing support for the notion that CsdA and CsdE are able to functionally interact with CsdL/TcdA. PMID:25897750

  18. Structural effects of insulin-loading into HII mesophases monitored by electron paramagnetic resonance (EPR), small angle X-ray spectroscopy (SAXS), and attenuated total reflection Fourier transform spectroscopy (ATR-FTIR).

    PubMed

    Mishraki, Tehila; Ottaviani, Maria Francesca; Shames, Alexander I; Aserin, Abraham; Garti, Nissim

    2011-06-30

    Insulin entrapment within a monoolein-based reverse hexagonal (H(II)) mesophase was investigated under temperature-dependent conditions at acidic (pH 3) and basic (pH 8) conditions. Studying the structure of the host H(II) system and the interactions of insulin under temperature-dependent conditions has great impact on the enhancement of its thermal stabilization and controlled release for the purposes of transdermal delivery. Small angle X-ray spectroscopy (SAXS) measurements show that pH variation and/or insulin entrapment preserve the hexagonal structure and do not influence the lattice parameter. Attenuated total reflection Fourier transform spectroscopy (ATR-FTIR) spectra indicate that, although insulin interacts with hydroxyl groups of GMO in the interface region, it is not affected by pH variations. Hence different microenvironments within the H(II) mesophase were monitored by a computer-aided electron paramagnetic resonance (EPR) analysis using 5-doxylstearic acid (5-DSA) as a pH-dependent probe. The microviscosity, micropolarity, order of systems, and distribution of the probes in different microenvironments were influenced by three factors: temperature, pH, and insulin solubilization. When the temperature is increased, microviscosity and order parameters decreased at both pH 3 and 8, presenting different decrease trends. It was found that, at pH 3, the protein perturbs the lipid structure while "pushing aside" the un-ionized 5-DSA probe to fit into the narrow water cylinders. At the interface region (pH 8), the probe was distributed in two differently structured environments that significantly modifies by increasing temperature. Insulin loading within the H(II) mesophase decreased the order and microviscosity of both the microenvironments and increased their micropolarity. Finally, the EPR analysis also provides information about the unfolding/denaturation of insulin within the channel at high temperatures. PMID:21591776

  19. Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6′)-Ie-APH(2′′)-Ia revealed by crystallographic and small-angle X-ray scattering analysis

    PubMed Central

    Smith, Clyde A.; Toth, Marta; Weiss, Thomas M.; Frase, Hilary; Vakulenko, Sergei B.

    2014-01-01

    Broad-spectrum resistance to aminoglycoside antibiotics in clinically important Gram-positive staphylococcal and entero­coccal pathogens is primarily conferred by the bifunctional enzyme AAC(6′)-Ie-APH(2′′)-Ia. This enzyme possesses an N-terminal coenzyme A-dependent acetyltransferase domain [AAC(6′)-Ie] and a C-terminal GTP-dependent phosphotransferase domain [APH(2′′)-Ia], and together they produce resistance to almost all known aminoglycosides in clinical use. Despite considerable effort over the last two or more decades, structural details of AAC(6′)-Ie-APH(2′′)-Ia have remained elusive. In a recent breakthrough, the structure of the isolated C-terminal APH(2′′)-Ia enzyme was determined as the binary Mg2GDP complex. Here, the high-resolution structure of the N-terminal AAC(6′)-Ie enzyme is reported as a ternary kanamycin/coenzyme A abortive complex. The structure of the full-length bifunctional enzyme has subsequently been elucidated based upon small-angle X-ray scattering data using the two crystallographic models. The AAC(6′)-Ie enzyme is joined to APH(2′′)-Ia by a short, predominantly rigid linker at the N-terminal end of a long α-helix. This α-helix is in turn intrinsically associated with the N-terminus of APH(2′′)-Ia. This structural arrangement supports earlier observations that the presence of the intact α-helix is essential to the activity of both functionalities of the full-length AAC(6′)-Ie-APH(2′′)-Ia enzyme. PMID:25286858

  20. Soft gamma-ray repeaters and anomalous X-ray pulsars as highly magnetized white dwarfs

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Banibrata; Rao, A. R.

    2016-05-01

    We explore the possibility that soft gamma-ray repeaters (SGRs) and anomalous X-ray pulsars (AXPs) are powered by highly magnetized white dwarfs (B-WDs). We take a sample of SGRs and AXPs and provide the possible parameter space in mass, radius, and surface magnetic field based on their observed properties (period and its derivative) and the assumption that these sources obey the mass-radius relation derived for the B-WDs. The radius and magnetic field of B-WDs are adequate to explain energies in SGRs/AXPs as the rotationally powered energy. In addition, B-WDs also adequately explain the perplexing radio transient GCRT J1745-3009 as a white dwarf pulsar. Note that the radius and magnetic fields of B-WDs are neither extreme (unlike of highly magnetized neutron stars) nor ordinary (unlike of magnetized white dwarfs, yet following the Chandrasekhar's mass-radius relation (C-WDs)). In order to explain SGRs/AXPs, while the highly magnetized neutron stars require an extra, observationally not well established yet, source of energy, the C-WDs predict large ultra-violet luminosity which is observationally constrained from a strict upper limit. Finally, we provide a set of basic differences between the magnetar and B-WD hypotheses for SGRs/AXPs.

  1. Detailed Physical Modeling Reveals the Magnetar Nature of a Transient Anomalous X-ray Pulsar

    NASA Technical Reports Server (NTRS)

    Guever, T.; Oezel, F.; Goegues, E.; Kouveliotou, C.

    2007-01-01

    Anomalous X-ray Pulsars (AXPs) belong to a class of neutron stars believed to harbor the strongest magnetic fields in the universe, as indicated by their energetic bursts and their rapid spindowns. However, a direct measurement of their surface field strengths has not been made to date. It is also not known whether AXP outbursts result from changes in the neutron star magnetic field or crust properties. Here we report the first, spectroscopic measurement of the surface magnetic field strength of an AXP, XTE J1810-197, and solidify its magnetar nature. The field strength obtained from detailed spectral analysis and modeling is remarkably close to the value inferred from the rate of spindown of this source and remains nearly constant during numerous observations spanning over two orders of magnitude in source flux. The surface temperature, on the other hand, declines steadily and dramatically following the 2003 outburst of this source. Our findings demonstrate that heating occurs in the upper neutron star crust during an outburst and sheds light on the transient behaviour of AXPs.

  2. The Magnetar Nature and the Outburst Mechanism of a Transient Anomalous X-ray Pulsar

    NASA Technical Reports Server (NTRS)

    Guver, Tolga; Ozel, Feryal; Gogus, Ersin; Kouveliotou, Chryssa

    2007-01-01

    Anomalous X-ray Pulsars (AXPs) belong to a class of neutron stars believed to harbor the strongest magnetic fields in the universe, as indicated by their energetic bursts and their rapid spindowns. However, a direct measurement of their surface field strengths has not been made to date. It is also not known whether AXP outbursts result from changes in the neutron star magnetic field or crust properties. Here we report the first, spectroscopic measurement of the surface magnetic field strength of an AXP, XTE J1810-197, and solidify its magnetar nature. The field strength obtained from detailed spectral analysis and modeling is remarkably close to the value inferred from the rate of spindown of this source and remains nearly constant during numerous observations spanning over two orders of magnitude in source flux. The surface temperature, on the other hand, declines steadily and dramatically following the 2003 outburst of this source. Our findings demonstrate that heating occurs in the upper neutron star crust during an outburst and sheds light on the transient behaviour of AXPs.

  3. Anomalous elastic scattering of x-ray photons by a neon-like ion

    NASA Astrophysics Data System (ADS)

    Hopersky, A. N.; Nadolinsky, A. M.; Dzuba, D. V.; Yavna, V. A.

    2005-05-01

    In the non-relativistic approximation for the wavefunctions of the one-electron states and in the dipole approximation for the scattering amplitude, the effect of radial monopole rearrangement of electron shells within the field of a vacancy and of the processes of one-photon double excitation/ionization on the absolute values and the shapes of the differential cross sections of anomalous non-zero-angle elastic scattering of linearly polarized x-ray photons by the Ne atom and by the neon-like Si4+ and Ar8+ ions in the vicinity of K- and KL23-ionization thresholds is studied. The results of calculations for the Ne atom were found to be in agreement with the high-precision synchrotron radiation experiments by Coreno et al (1999 Phys. Rev. A 59 2494; K-ionization threshold) and by Avaldi et al (1996 J. Phys. B: At. Mol. Opt. Phys. 29 L737; KL23-ionization threshold). The results of calculations for the Si4+ and Ar8+ ions are predictions.

  4. Resonant anomalous x-ray reflectivity as a probe of ion adsorption at solid-liquid interfaces.

    SciTech Connect

    Fenter, P.; Park, C.; Nagy, K. L.; Sturchio, N. C.; Chemistry; Univ. of Illinois at Chicago

    2007-05-23

    We discuss new opportunities to understand processes at the solid-liquid interface using resonant anomalous X-ray reflectivity (RAXR). This approach is illustrated by determination of element-specific density profiles at mica surfaces in aqueous electrolyte solutions containing Rb{sup +} and Sr{sup 2+}. The total interfacial electron density profile is determined by specular reflectivity (i.e., reflected intensity vs. momentum transfer, q, at an energy, E, far from any characteristic absorption edge). RAXR spectra (i.e., intensity vs. E at fixed q) reveal element-specific ion distributions. Key differences in the interaction of Rb{sup +} and Sr{sup 2+} with mica are observed using resonant anomalous X-ray reflectivity: Rb{sup +} adsorbs in a partially hydrated state, but Sr{sup 2+} adsorbs in both fully and partially hydrated states.

  5. Imaging X-Ray, Optical, and Infrared Observations of the Transient Anomalous X-Ray Pulsar XTE J1810-197

    NASA Astrophysics Data System (ADS)

    Gotthelf, E. V.; Halpern, J. P.; Buxton, M.; Bailyn, C.

    2004-04-01

    We report X-ray imaging, timing, and spectral studies of XTE J1810-197, a 5.54 s pulsar discovered by Ibrahim and coworkers in recent Rossi X-Ray Timing Explorer (RXTE) observations. In a set of short exposures with the High Resolution Camera on board the Chandra X-Ray Observatory, we detect a strongly modulated signal (55%+/-4% pulsed fraction) with the expected period located at (J2000) 18h09m51s08, -19deg43'51.7", with a uncertainty radius of 0.6" (90% confidence level). Spectra obtained with XMM-Newton are well fitted by a two-component model that typically describes anomalous X-ray pulsars (AXPs), an absorbed blackbody plus power law with parameters kT=0.67+/-0.01 keV, Γ=3.7+/-0.2, NH=(1.05+/-0.05)×1022 cm-2, and FX(0.5-10keV)=3.98×10-11 ergs cm-2 s-1. Alternatively, a two-temperature blackbody fit is just as acceptable. The location of CXOU J180951.0-194351 is consistent with a point source seen in archival Einstein, ROSAT, and ASCA images, when its flux was nearly 2 orders of magnitude fainter, and from which no pulsations are found. The spectrum changed dramatically between the ``quiescent'' and ``active'' states; the former can be modeled as a softer blackbody. Using XMM-Newton timing data, we place an upper limit of 0.03 lt-s on any orbital motion in the period range 10 minutes-8 hr. Optical and infrared images obtained on the SMARTS 1.3 m telescope at the Cerro Tololo Inter-American Observatory (CTIO) show no object in the Chandra error circle to limits V=22.5, I=21.3, J=18.9, and K=17.5. Together, these results argue that CXOU J180951.0-194351 is an isolated neutron star, one most similar to the transient AXP AX J1844.8-0256. Continuing study of XTE J1810-197 in various states of luminosity is important for understanding and possibly unifying a growing class of isolated, young neutron stars that are not powered by rotation.

  6. 16 yr of RXTE monitoring of five anomalous X-ray pulsars

    SciTech Connect

    Dib, Rim; Kaspi, Victoria M. E-mail: vkaspi@physics.mcgill.ca

    2014-03-20

    We present a summary of the long-term evolution of various properties of the five non-transient anomalous X-ray pulsars (AXPs) 1E 1841–045, RXS J170849.0–400910, 1E 2259+586, 4U 0142+61, and 1E 1048.1–5937, regularly monitored with RXTE from 1996 to 2012. We focus on three properties of these sources: the evolution of the timing, pulsed flux, and pulse profile. We report several new timing anomalies and radiative events, including a putative anti-glitch seen in 1E 2259+586 in 2009, and a second epoch of very large spin-down rate fluctuations in 1E 1048.1–5937 following a large flux outburst. We compile the properties of the 11 glitches and 4 glitch candidates observed from these 5 AXPs between 1996 and 2012. Overall, these monitoring observations reveal several apparent patterns in the behavior of this sample of AXPs: large radiative changes in AXPs (including long-lived flux enhancements, short bursts, and pulse profile changes) are rare, occurring typically only every few years per source; large radiative changes are almost always accompanied by some form of timing anomaly, usually a spin-up glitch; only 20%-30% of timing anomalies are accompanied by any form of radiative change. We find that AXP radiative behavior at the times of radiatively loud glitches is sufficiently similar to suggest common physical origins. The similarity in glitch properties when comparing radiatively loud and radiatively silent glitches in AXPs suggests a common physical origin in the stellar interior. Finally, the overall similarity of AXP and radio pulsar glitches suggests a common physical origin for both phenomena.

  7. Suzaku Observation of the Anomalous X-Ray Pulsar 1E 1841-045

    NASA Astrophysics Data System (ADS)

    Morii, Mikio; Kitamoto, Shunji; Shibazaki, Noriaki; Kawai, Nobuyuki; Arimoto, Makoto; Ueno, Masaru; Kohmura, Takayoshi; Terada, Yukikatsu; Yamauchi, Shigeo; Takahashi, Hiromitsu

    2010-10-01

    We report on the results of a Suzaku observation of the anomalous X-ray pulsar (AXP) 1E 1841-045 at the center of the supernova remnant Kes 73. We confirmed that the energy-dependent spectral models obtained by previous separate observations were also satisfied over a wide energy range from 0.4 to ˜70 keV, simultaneously. Here, the models below ˜10 keV were a combination of blackbody (BB) and power-law (PL) functions, or of two BBs with different temperatures at 0.6-7.0 keV (Morii et al. 2003, PASJ, 55, L45), and that above ˜20 keV was a PL function (Kuiper et al. 2004, ApJ, 613, 1173). The combination BB + PL + PL was found to best represent the phase-averaged spectrum. Phase-resolved spectroscopy indicated the existence of two emission regions, one with a thermal and the other with a non-thermal nature. The combination BB + BB + PL was also found to represent the phase-averaged spectrum well. However, we found that this model is physically unacceptable due to an excessively large area of the emission region of the blackbody. Nonetheless, we found that the temperatures and radii of the two blackbody components showed moderate correlations in the phase-resolved spectra. The fact that the same correlations have been observed between the phase-averaged spectra of various magnetars (Nakagawa et al. 2009, PASJ, 61, 109) suggests that a self-similar function can approximate the intrinsic energy spectra of magnetars below ˜10keV.

  8. Emerging applications of small angle solution scattering in structural biology

    PubMed Central

    Chaudhuri, Barnali N

    2015-01-01

    Small angle solution X-ray and neutron scattering recently resurfaced as powerful tools to address an array of biological problems including folding, intrinsic disorder, conformational transitions, macromolecular crowding, and self or hetero-assembling of biomacromolecules. In addition, small angle solution scattering complements crystallography, nuclear magnetic resonance spectroscopy, and other structural methods to aid in the structure determinations of multidomain or multicomponent proteins or nucleoprotein assemblies. Neutron scattering with hydrogen/deuterium contrast variation, or X-ray scattering with sucrose contrast variation to a certain extent, is a convenient tool for characterizing the organizations of two-component systems such as a nucleoprotein or a lipid-protein assembly. Time-resolved small and wide-angle solution scattering to study biological processes in real time, and the use of localized heavy-atom labeling and anomalous solution scattering for applications as FRET-like molecular rulers, are amongst promising newer developments. Despite the challenges in data analysis and interpretation, these X-ray/neutron solution scattering based approaches hold great promise for understanding a wide variety of complex processes prevalent in the biological milieu. PMID:25516491

  9. Structural characterization of the pressure-denatured state and unfolding/refolding kinetics of staphylococcal nuclease by synchrotron small-angle X-ray scattering and Fourier-transform infrared spectroscopy.

    PubMed

    Panick, G; Malessa, R; Winter, R; Rapp, G; Frye, K J; Royer, C A

    1998-01-16

    The pressure-induced unfolding of wild-type staphylococcal nuclease (Snase WT) was studied using synchrotron X-ray small-angle scattering (SAXS) and Fourier-transform infrared (FT-IR) spectroscopy, which monitor changes in the tertiary and secondary structural properties of the protein upon pressurization. The experimental results reveal that application of high-pressure up to 3 kbar leads to an approximate twofold increase of the radius of gyration Rg of the native protein (Rg approximately 17 A) and a large broadening of the pair-distance-distribution function, indicating a transition from a globular to an ellipsoidal or extended chain structure. Analysis of the FT-IR amide I' spectral components reveals that the pressure-induced denaturation process sets in at 1.5 kbar at 25 degrees C and is accompanied by an increase in disordered and turn structures while the content of beta-sheets and alpha-helices drastically decreases. The pressure-induced denatured state above 3 kbar retains nonetheless some degree of beta-like secondary structure and the molecule cannot be described as a fully extended random coil. Temperature-induced denaturation involves a further unfolding of the protein molecule which is indicated by a larger Rg value and significantly lower fractional intensities of IR-bands associated with secondary-structure elements. In addition, we have carried out pressure-jump kinetics studies of the secondary-structural evolution and the degree of compactness in the folding/unfolding reactions of Snase. The effect of pressure on the kinetics arises from a larger positive activation volume for folding than for unfolding, and leads to a significant slowing down of the folding rate with increasing pressure. Moreover, the system becomes two-state under pressure. These properties make it ideal for probing multiple order parameters in order to compare the kinetics of changes in secondary structure by pressure-jump FT-IR and chain collapse by pressure-jump SAXS

  10. Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data

    PubMed Central

    Nass, Karol; Meinhart, Anton; Barends, Thomas R. M.; Foucar, Lutz; Gorel, Alexander; Aquila, Andrew; Botha, Sabine; Doak, R. Bruce; Koglin, Jason; Liang, Mengning; Shoeman, Robert L.; Williams, Garth; Boutet, Sebastien; Schlichting, Ilme

    2016-01-01

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL data de novo is complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exceedingly strong anomalous or isomorphous difference signals, have been reported. Here, it is shown that SFX data from thaumatin microcrystals can be successfully phased using only the weak anomalous scattering from the endogenous S atoms. Moreover, a step-by-step investigation is presented of the particular problems of SAD phasing of SFX data, analysing data from a derivative with a strong anomalous signal as well as the weak signal from endogenous S atoms. PMID:27158504

  11. Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data

    DOE PAGESBeta

    Nass, Karol; Meinhart, Anton; Barends, Thomas R. M.; Foucar, Lutz; Gorel, Alexander; Aquila, Andrew; Botha, Sabine; Doak, R. Bruce; Koglin, Jason; Liang, Mengning; et al

    2016-03-09

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL data de novo is complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exceedingly strong anomalous or isomorphous difference signals, have been reported. Here, it is shown that SFX data from thaumatin microcrystals can be successfully phased using only the weak anomalous scattering from the endogenous S atoms. Furthermore, a step-by-step investigation is presented of the particular problems of SAD phasing of SFX data, analysingmore » data from a derivative with a strong anomalous signal as well as the weak signal from endogenous S atoms.« less

  12. ON THE EVOLUTION OF ANOMALOUS X-RAY PULSARS AND SOFT GAMMA-RAY REPEATERS WITH FALL BACK DISKS

    SciTech Connect

    Ertan, Ue.; Alpar, M. A.; Eksi, K. Y.; Erkut, M. H.

    2009-09-10

    We show that the period clustering of anomalous X-ray pulsars (AXPs) and soft gamma-ray repeaters (SGRs), their X-ray luminosities, ages, and statistics can be explained with fall back disks with large initial specific angular momentum. The disk evolution models are developed by comparison to self-similar analytical models. The initial disk mass and angular momentum set the viscous timescale. An efficient torque, with (1 - {omega}{sup 2}{sub *}) dependence on the fastness parameter {omega}{sub *}, leads to period clustering in the observed AXP-SGR period range under a wide range of initial conditions. The timescale t{sub 0} for the early evolution of the fall back disk, and the final stages of fall back disk evolution, when the disk becomes passive, are the crucial determinants of the evolution. The disk becomes passive at temperatures around 100 K, which provides a natural cutoff for the X-ray luminosity and defines the end of evolution in the observable AXP and SGR phase. This low value for the minimum temperature for active disk turbulence indicates that the fall back disks are active up to a large radius, {approx}>10{sup 12} cm. We find that transient AXPs and SGRs are likely to be older than their persistent cousins. A fall back disk with mass transfer rates corresponding to the low quiescent X-ray luminosities of the transient sources in early evolutionary phases would have a relatively lower initial mass, such that the mass-flow rate in the disk is not sufficient for the inner disk to penetrate into the light cylinder of the young neutron star, making mass accretion onto the neutron star impossible. The transient AXP phase therefore must start later. The model results imply that the transient AXP/SGRs, although older, are likely to be similar in number to persistent sources. This is because the X-ray luminosities of AXPs and SGRs are found to decrease faster at the end of their evolution, and the X-ray luminosities of transient AXP and SGRs in quiescence lie

  13. Polarity characterization by anomalous x-ray dispersion of ZnO films and GaN lateral polar structures

    SciTech Connect

    Shelton, Christopher T.; Sachet, Edward; Paisley, Elizabeth A.; Hoffmann, Marc P.; Rajan, Joseph; Collazo, Ramón; Sitar, Zlatko; Maria, Jon-Paul

    2014-01-28

    We demonstrate the use of anomalous x-ray scattering of constituent cations at their absorption edge, in a conventional Bragg-Brentano diffractometer, to measure absolutely and quantitatively the polar orientation and polarity fraction of unipolar and mixed polar wurtzitic crystals. In one set of experiments, the gradual transition between c+ and c− polarity of epitaxial ZnO films on sapphire as a function of MgO buffer layer thickness is monitored quantitatively, while in a second experiment, we map the polarity of a lateral polar homojunction in GaN. The dispersion measurements are compared with piezoforce microscopy images, and we demonstrate how x-ray dispersion and scanning probe methods can provide complementary information that can discriminate between polarity fractions at a material surface and polarity fractions averaged over the film bulk.

  14. InGaN Selfassembled Quantum Dots Investigated By X-Ray Diffraction-Anomalous-Fine Structure Technique

    SciTech Connect

    Piskorska, E.; Siebert, M.; Schmidt, T.; Falta, J.; Yamaguchi, T.; Hommel, D.; Renevier, H.

    2007-04-10

    Local chemical composition of InGaN quantum dots grown by molecular-beam epitaxy on GaN virtual substrates was investigated by x-ray diffraction anomalous fine-structure method. Using this approach, we found that the In content increases from 20% at the dot base to 40-50% at the top. From the detailed numerical analysis of the data we were able to reconstruct the local neighborhood of Ga atoms in different positions in the dots, as well as the local elastic relaxation state.

  15. Quantitative comparison of the void distribution in a. beta. '-phase Ni-Al-In alloy using x-ray small-angle scattering and transmission-electron microscopy. [Ni-51. 2 at. % Al-2. 6 at. % In

    SciTech Connect

    Epperson, J.E.; Loomis, B.A.; Lin, J.S.

    1981-11-01

    Small-angle scattering is a rather mature discipline which can yield valuable information on the size, amount, and distribution of inhomogeneities encountered in materials-science research. Methods have been publisheed which permit one to extend the standard analysis of data from a small-angle-scattering experiment to include determination of the distribution of particle sizes. This extended analysis has been carried out for voids in a ..beta..'-phase Ni-Al-In alloy, and, in order to assess the reliability of the procedure, the identical void distribution as been characterized by transmission-electron microscopy. A quantitative comparison is made of the results from thses two independent experiments, and the general performance of the Brill-Schmidt method for particle-size determinations is discussed. 6 figures, 1 table.

  16. Observation of parametric X-ray radiation in an anomalous diffraction region

    NASA Astrophysics Data System (ADS)

    Alexeyev, V. I.; Eliseyev, A. N.; Irribarra, E.; Kishin, I. A.; Kubankin, A. S.; Nazhmudinov, R. M.

    2016-08-01

    A new possibility to expand the energy region of diffraction processes based on the interaction of relativistic charged particles with crystalline structures is presented. Diffracted photons related to parametric X-ray radiation produced by relativistic electrons are detected below the low energy threshold for the X-ray diffraction mechanism in crystalline structures for the first time. The measurements were performed during the interaction of 7 MeV electrons with a textured polycrystalline tungsten foil and a highly oriented pyrolytic graphite crystal. The experiment results are in good agreement with a developed model based on the PXR kinematical theory. The developed experimental approach can be applied to separate the contributions of real and virtual photons to the total diffracted radiation generated during the interaction of relativistic charged particles with crystalline targets.

  17. A scenario of the formation of isolated X-ray pulsars with anomalously long period

    NASA Astrophysics Data System (ADS)

    Ikhsanov, N. R.; Kim, V. Yu.; Beskrovnaya, N. G.

    2015-01-01

    A scenario of the formation of isolated X-ray pulsars is discussed with an application to one of the best studied objects of this class 1E 161348-5055. This moderately luminous, 1033-1035 erg s-1, pulsar with a relatively soft spectrum, kT ˜ 0.6-0.8 keV, is associated with an isolated neutron star, which is located near the center of the young (˜2000 yr) compact supernova remnant RCW 103 and rotates steadily ( Hz s-1) with the period of 6.7 h. We show that in the current epoch the neutron star is in the accretor state. The parameters of the source emission can be explained in terms of the magnetic-levitation accretion scenario in which the star with the surface magnetic field of 1012 G accretes material onto its surface from a non-Keplerian magnetic fossil disk at the rate 1014 g s-1. A neutron star could evolve to this state in a High-Mass X-ray Binary (HMXB), which had disintegrated during the supernova explosion powered by the core-collapse of its massive component. The life-time of an isolated X-ray pulsar formed this way can be as long as a few thousand years.

  18. Axino dark matter in light of an anomalous X-ray line

    SciTech Connect

    Liew, Seng Pei

    2014-05-01

    Axino as the superpartner of axion that solves the strong CP problem can be a good candidate of dark matter. Inspired by the 3.5 keV X-ray line signal found to be originated from galaxy clusters and Andromeda galaxy, we study axino models with R-parity violations, and point out that axino dark matter with trilinear R-parity violations is an attractive scenario that reproduces the X-ray line. The Peccei-Quinn scale is required to be f{sub a} ∼ O(10{sup 9}–10{sup 11}) GeV for trilinear R-parity violating couplings λ ∼ O(10{sup −3}–10{sup −1}) in order to explain the line signal. Moreover, the right-handed stau is predicted to be light, i.e. ∼ O(100) GeV, and thus can be looked for at the LHC. Cosmological aspects of the model are also discussed in this study.

  19. Rb+ adsorption at the quartz(101)-aqueous interface: comparison of resonant anomalous x-ray reflectivity with ab initio calculations

    DOE PAGESBeta

    Bellucci, Francesco; Lee, Sang Soo; Kubicki, James D.; Bandura, Andrei V.; Zhang, Zhan; Wesolowski, David J.; Fenter, Paul

    2015-01-29

    We study adsorption of Rb+ to the quartz(101)–aqueous interface at room temperature with specular X-ray reflectivity, resonant anomalous X-ray reflectivity, and density functional theory. The interfacial water structures observed in deionized water and 10 mM RbCl solution at pH 9.8 were similar, having a first water layer at height of 1.7 ± 0.1 Å above the quartz surface and a second layer at 4.8 ± 0.1 Å and 3.9 ± 0.8 Å for the water and RbCl solutions, respectively. The adsorbed Rb+ distribution is broad and consists of presumed inner-sphere (IS) and outer-sphere (OS) complexes at heights of 1.8 ±more » 0.1 and 6.4 ± 1.0 Å, respectively. Projector-augmented planewave density functional theory (DFT) calculations of potential configurations for neutral and negatively charged quartz(101) surfaces at pH 7 and 12, respectively, reveal a water structure in agreement with experimental results. These DFT calculations also show differences in adsorbed speciation of Rb+ between these two conditions. At pH 7, the lowest energy structure shows that Rb+ adsorbs dominantly as an IS complex, whereas at pH 12 IS and OS complexes have equivalent energies. The DFT results at pH 12 are generally consistent with the two site Rb distribution observed from the X-ray data at pH 9.8, albeit with some differences that are discussed. In conclusion, surface charge estimated on the basis of the measured total Rb+ coverage was -0.11 C/m2, in good agreement with the range of the surface charge magnitudes reported in the literature.« less

  20. Unique Properties of Thermally Tailored Copper: Magnetically Active Regions and Anomalous X-ray Fluorescence Emissions

    PubMed Central

    2009-01-01

    When high-purity copper (≥99.98%wt) is melted, held in its liquid state for a few hours with iterative thermal cycling, then allowed to resolidify, the ingot surface is found to have many small regions that are magnetically active. X-ray fluorescence analysis of these regions exhibit remarkably intense lines from “sensitized elements” (SE), including in part or fully the contiguous series V, Cr, Mn, Fe, and Co. The XRF emissions from SE are far more intense than expected from known impurity levels. Comparison with blanks and standards show that the thermal “tailoring” also introduces strongly enhanced SE emissions in samples taken from the interior of the copper ingots. For some magnetic regions, the location as well as the SE emissions, although persistent, vary irregularly with time. Also, for some regions extraordinarily intense “sensitized iron” (SFe) emissions occur, accompanied by drastic attenuation of Cu emissions. PMID:20037657

  1. Small Angle Neutron Scattering

    SciTech Connect

    Urban, Volker S

    2012-01-01

    Small Angle Neutron Scattering (SANS) probes structural details at the nanometer scale in a non-destructive way. This article gives an introduction to scientists who have no prior small-angle scattering knowledge, but who seek a technique that allows elucidating structural information in challenging situations that thwart approaches by other methods. SANS is applicable to a wide variety of materials including metals and alloys, ceramics, concrete, glasses, polymers, composites and biological materials. Isotope and magnetic interactions provide unique methods for labeling and contrast variation to highlight specific structural features of interest. In situ studies of a material s responses to temperature, pressure, shear, magnetic and electric fields, etc., are feasible as a result of the high penetrating power of neutrons. SANS provides statistical information on significant structural features averaged over the probed sample volume, and one can use SANS to quantify with high precision the structural details that are observed, for example, in electron microscopy. Neutron scattering is non-destructive; there is no need to cut specimens into thin sections, and neutrons penetrate deeply, providing information on the bulk material, free from surface effects. The basic principles of a SANS experiment are fairly simple, but the measurement, analysis and interpretation of small angle scattering data involves theoretical concepts that are unique to the technique and that are not widely known. This article includes a concise description of the basics, as well as practical know-how that is essential for a successful SANS experiment.

  2. A WHITE DWARF MERGER AS PROGENITOR OF THE ANOMALOUS X-RAY PULSAR 4U 0142+61?

    SciTech Connect

    Rueda, J. A.; Boshkayev, K.; Izzo, L.; Ruffini, R.; Loren-Aguilar, P.; Kuelebi, B.; Aznar-Siguan, G.; Garcia-Berro, E. E-mail: enrique.garcia-berro@upc.edu

    2013-08-01

    It has been recently proposed that massive, fast-rotating, highly magnetized white dwarfs could describe the observational properties of some of soft gamma-ray repeaters and anomalous X-ray pulsars (AXPs). Moreover, it has also been shown that high-field magnetic white dwarfs can be the outcome of white dwarf binary mergers. The products of these mergers consist of a hot central white dwarf surrounded by a rapidly rotating disk. Here we show that the merger of a double degenerate system can explain the characteristics of the peculiar AXP 4U 0142+61. This scenario accounts for the observed infrared excess. We also show that the observed properties of 4U 0142+6 are consistent with an approximately 1.2 M{sub Sun} white dwarf, remnant of the coalescence of an original system made of two white dwarfs of masses 0.6 M{sub Sun} and 1.0 M{sub Sun }. Finally, we infer a post-merging age {tau}{sub WD} Almost-Equal-To 64 kyr and a magnetic field B Almost-Equal-To 2 Multiplication-Sign 10{sup 8} G. Evidence for such a magnetic field may come from the possible detection of the electron cyclotron absorption feature observed between the B and V bands at Almost-Equal-To 10{sup 15} Hz in the spectrum of 4U 0142+61.

  3. Anomalously strong two-electron one-photon X-ray decay transitions in CO caused by avoided crossing.

    PubMed

    Couto, Rafael C; Guarise, Marco; Nicolaou, Alessandro; Jaouen, Nicolas; Chiuzbăian, Gheorghe S; Lüning, Jan; Ekholm, Victor; Rubensson, Jan-Erik; Såthe, Conny; Hennies, Franz; Kimberg, Victor; Guimarães, Freddy F; Agren, Hans; Gel'mukhanov, Faris; Journel, Loïc; Simon, Marc

    2016-01-01

    The unique opportunity to study and control electron-nuclear quantum dynamics in coupled potentials offered by the resonant inelastic X-ray scattering (RIXS) technique is utilized to unravel an anomalously strong two-electron one-photon transition from core-excited to Rydberg final states in the CO molecule. High-resolution RIXS measurements of CO in the energy region of 12-14 eV are presented and analyzed by means of quantum simulations using the wave packet propagation formalism and ab initio calculations of potential energy curves and transition dipole moments. The very good overall agreement between the experimental results and the theoretical predictions allows an in-depth interpretation of the salient spectral features in terms of Coulomb mixing of "dark" with "bright" final states leading to an effective two-electron one-photon transition. The present work illustrates that the improved spectral resolution of RIXS spectra achievable today may call for more advanced theories than what has been used in the past. PMID:26860458

  4. Anomalously strong two-electron one-photon X-ray decay transitions in CO caused by avoided crossing

    PubMed Central

    Couto, Rafael C.; Guarise, Marco; Nicolaou, Alessandro; Jaouen, Nicolas; Chiuzbăian, Gheorghe S.; Lüning, Jan; Ekholm, Victor; Rubensson, Jan-Erik; Såthe, Conny; Hennies, Franz; Kimberg, Victor; Guimarães, Freddy F.; Agren, Hans; Gel’mukhanov, Faris; Journel, Loïc; Simon, Marc

    2016-01-01

    The unique opportunity to study and control electron-nuclear quantum dynamics in coupled potentials offered by the resonant inelastic X-ray scattering (RIXS) technique is utilized to unravel an anomalously strong two-electron one-photon transition from core-excited to Rydberg final states in the CO molecule. High-resolution RIXS measurements of CO in the energy region of 12–14 eV are presented and analyzed by means of quantum simulations using the wave packet propagation formalism and ab initio calculations of potential energy curves and transition dipole moments. The very good overall agreement between the experimental results and the theoretical predictions allows an in-depth interpretation of the salient spectral features in terms of Coulomb mixing of “dark” with “bright” final states leading to an effective two-electron one-photon transition. The present work illustrates that the improved spectral resolution of RIXS spectra achievable today may call for more advanced theories than what has been used in the past. PMID:26860458

  5. Influence of growth temperature on interdiffusion in uncapped SiGe-islands on Si(001) determined by anomalous x-ray diffraction and reciprocal space mapping

    SciTech Connect

    Schuelli, T.U.; Stoffel, M.; Schmidt, O.G.; Hesse, A.; Stangl, J.; Lechner, R.T.; Wintersberger, E.; Bauer, G.; Sztucki, M.; Metzger, T.H.

    2005-01-15

    The influence of growth temperature in the regime of dome formation in Stranski-Krastanow growth is studied systematically on a series of Ge on Si(001) samples. A combination of complementary x-ray scattering methods is applied, in order to resolve the island size, their strain state, and the composition distribution. The composition is determined using anomalous x-ray diffraction at high momentum transfer in combination with atomic force microscopy and from x-ray reciprocal space mapping. For growth temperatures between 620 and 840 deg. C, the maximum Ge content of the as-grown islands decreases from about 70 to about 22%. The results are corroborated by a selective etching study of the Ge islands.

  6. Many-electron effects in anomalous elastic scattering of linearly polarized x-ray photons by Xe near the K-edge

    NASA Astrophysics Data System (ADS)

    Hopersky, A. N.; Yavna, V. A.; Popov, V. A.

    1997-11-01

    Within the non-relativistic approximation the effect of radial monopole rearrangement of electron shells within the field of a vacancy and of the processes of one-photon double excitation - ionization on the differential cross section of anomalous non-zero-angle elastic scattering of linearly polarized x-ray photons by the Xe atom in the region of its 1s-shell ionization threshold is studied. Theoretical results for the anomalous dispersion region of scattering demonstrate a strong dependence of the cross section value on the approximation used.

  7. Long-term timing and glitch characteristics of anomalous X-ray pulsar 1RXS J170849.0–400910

    SciTech Connect

    Muş, Sinem Şaşmaz; Göğüş, Ersin

    2013-12-01

    We present the results of our detailed timing studies of an anomalous X-ray pulsar, 1RXS J170849.0–400910, using Rossi X-ray Timing Explorer (RXTE) observations spanning over ∼6 yr from 2005 until the end of the RXTE mission. We constructed the long-term spin characteristics of the source and investigated the time and energy dependence of the pulse profile and pulsed count rates. We find that the pulse profile and pulsed count rates in the 2-10 keV band do not show any significant variations in ∼6 yr. 1RXS J170849.0–400910 has been the most frequently glitching anomalous X-ray pulsar: three spin-up glitches and three candidate glitches were observed prior to 2005. Our extensive search for glitches later in the timeline resulted in no unambiguous glitches, though we identified two glitch candidates (with Δν/ν ∼ 10{sup –6}) in two data gaps: a strong candidate around MJD 55532 and another one around MJD 54819, which is slightly less robust. We discuss our results in the context of pulsar glitch models and expectancy of glitches within the vortex unpinning model.

  8. The 2006-2007 Active Phase Of Anomalous X-Ray Pulsar 4U 0142+61: Radiative and Timing Changes, Bursts, and Burst Spectral Features

    NASA Technical Reports Server (NTRS)

    Gavril, Fotis P.; Dib, Rim; Kaspi, Victoria M.

    2009-01-01

    After at least 6 years of quiescence, Anomalous X-ray Pulsar (AXP) 4U 0142+61 entered an active phase in 2006 March that lasted several months and included six X-ray bursts as well as many changes in the persistent X-ray emission. The bursts, the first seen from this AXP in >11 years of Rossi X-ray Timing Explorer monitoring, all occurred in the interval between 2006 April 6 and 2007 February 7. The burst durations ranged from 8-3x10(exp 3)s. The first five burst spectra are well modeled by blackbodies, with temperatures kT approx. 2 - 6 keV. However, the sixth burst had a complicated spectrum that is well characterized by a blackbody plus three emission features whose amplitude varied throughout the burst. The most prominent feature was at 14.0 keV. Upon entry into the active phase the pulsar showed a significant change in pulse morphology and a likely timing glitch. The glitch had a total frequency jump of (1.9+/-0.4)x10(exp -7) Hz, which recovered with a decay time of 17+/-2 days by more than the initial jump, implying a net spin-down of the pulsar. We discuss these events in the context of the magnetar model.

  9. Small angle neutron scattering

    NASA Astrophysics Data System (ADS)

    Cousin, Fabrice

    2015-10-01

    Small Angle Neutron Scattering (SANS) is a technique that enables to probe the 3-D structure of materials on a typical size range lying from ˜ 1 nm up to ˜ a few 100 nm, the obtained information being statistically averaged on a sample whose volume is ˜ 1 cm3. This very rich technique enables to make a full structural characterization of a given object of nanometric dimensions (radius of gyration, shape, volume or mass, fractal dimension, specific area…) through the determination of the form factor as well as the determination of the way objects are organized within in a continuous media, and therefore to describe interactions between them, through the determination of the structure factor. The specific properties of neutrons (possibility of tuning the scattering intensity by using the isotopic substitution, sensitivity to magnetism, negligible absorption, low energy of the incident neutrons) make it particularly interesting in the fields of soft matter, biophysics, magnetic materials and metallurgy. In particular, the contrast variation methods allow to extract some informations that cannot be obtained by any other experimental techniques. This course is divided in two parts. The first one is devoted to the description of the principle of SANS: basics (formalism, coherent scattering/incoherent scattering, notion of elementary scatterer), form factor analysis (I(q→0), Guinier regime, intermediate regime, Porod regime, polydisperse system), structure factor analysis (2nd Virial coefficient, integral equations, characterization of aggregates), and contrast variation methods (how to create contrast in an homogeneous system, matching in ternary systems, extrapolation to zero concentration, Zero Averaged Contrast). It is illustrated by some representative examples. The second one describes the experimental aspects of SANS to guide user in its future experiments: description of SANS spectrometer, resolution of the spectrometer, optimization of spectrometer

  10. Anomalous resistivity effect on multiple ion beam emission and hard x-ray generation in a Mather type plasma focus device

    SciTech Connect

    Behbahani, R. A.; Aghamir, F. M.

    2011-10-15

    Multi ion beam and hard x-ray emissions were detected in a high inductance (more than 100 nH) Mather type plasma focus (PF) device at different filling gas pressures and charging voltages. The signal analysis was performed through the current trace, as it is the fundamental signal from which all of the phenomena in a PF device can be extracted. Two different fitting processes were carried out according to Lee's computational (snow-plow) model. In the first process, only plasma dynamics and classical (Spitzer) resistances were considered as energy consumer parameters for plasma. This led to an unsuccessful fitting and did not answer the energy transfer mechanism into plasma. A second fitting process was considered through the addition of anomalous resistance, which provided the best fit. Anomalous resistance was the source of long decrease in current trace, and multi dips and multi peaks of high voltage probe. Multi-peak features were interpreted considering the second fitting process along with the mechanisms for ion beam production and hard x-ray emission. To show the important role of the anomalous resistance, the duration of the current drop was discussed.

  11. Anomalous elastic scattering of linearly polarized X-ray radiation by multicharged atomic ions in the range of the ionization threshold of the 1 s-shell

    NASA Astrophysics Data System (ADS)

    Hopersky, A. N.; Novikov, S. A.; Chuvenkov, V. V.

    2002-04-01

    The absolute values and shape of differential cross-section of the process of the anomalous elastic scattering for non-zero angle are investigated within non-relativistic approximation for linearly polarized X-ray radiation scattered by multicharged atomic ions Ne 6+ in the range of the ionization threshold of 1 s-shell. The many-particle effects of radial rearrangement of electron shells in the field of an inner 1 s-vacancy and the effect of vacancy stabilization are taken into account. The results of the work are predictions.

  12. X-ray microdiffraction of biominerals.

    PubMed

    Tamura, Nobumichi; Gilbert, Pupa U P A

    2013-01-01

    Biominerals have complex and heterogeneous architectures, hence diffraction experiments with spatial resolutions between 500 nm and 10 μm are extremely useful to characterize them. X-ray beams in this size range are now routinely produced at many synchrotrons. This chapter provides a review of the different hard X-ray diffraction and scattering techniques, used in conjunction with efficient, state-of-the-art X-ray focusing optics. These include monochromatic X-ray microdiffraction, polychromatic (Laue) X-ray microdiffraction, and microbeam small-angle X-ray scattering. We present some of the most relevant discoveries made in the field of biomineralization using these approaches. PMID:24188780

  13. Site-specific Incorporation of 3-Iodo-L-tyrosine into Proteins and Single-wavelength Anomalous Dispersion Phasing with Soft X-ray in Protein Crystallography

    NASA Astrophysics Data System (ADS)

    Murayama, Kazutaka; Sakamoto, Kensaku

    Iodine is a good anomalous scatter for radiations from in-house X-ray generators (Cu/CrKα). Non-natural amino acid, 3-iodo-L-tyrosine, is able to be site-specifically incorporated into proteins with amber suppresser tRNA and mutated TyrRS from M. jannaschii in the E. coli expression system. To determine the crystal structure of acetyl transferase from T. thermophilus, iodotyrosine-containing proteins were prepared and crystallized. Structure determination was successfully conducted with the protein variant with iodotyrosine at position 111. Anomalous signals from iodotyrosine with Cu/CrKα radiations were both sufficient to calculate clear electron density map. In the crystal structure, iodotyrosine did not significantly disturb the native structure.

  14. Quantification of Site-Specific Cation Exchange in Metal-Organic Frameworks Using Multi-Wavelength Anomalous X-ray Dispersion

    SciTech Connect

    Brozek, Carl K.; Cozzolino, Anthony F.; Teat, Simon J.; Chen, Yu-Sheng; Dinc,; #259; Mircea,

    2013-09-23

    We employed multiwavelength anomalous X-ray dispersion to determine the relative cation occupation at two crystallographically distinct metal sites in Fe2+-, Cu2+-, and Zn2+-exchanged versions of the microporous metal–organic framework (MOF) known as MnMnBTT (BTT = 1,3,5-benzenetristetrazolate). By exploiting the dispersive differences between Mn, Fe, Cu, and Zn, the extent and location of cation exchange were determined from single crystal X-ray diffraction data sets collected near the K edges of Mn2+ and of the substituting metal, and at a wavelength remote from either edge as a reference. Comparing the anomalous dispersion between these measurements indicated that the extent of Mn2+ replacement depends on the identity of the substituting metal. We contrasted two unique methods to analyze this data with a conventional approach and evaluated their limitations with emphasis on the general application of this method to other heterometallic MOFs, where site-specific metal identification is fundamental to tuning catalytic and physical properties.

  15. The 2006-2007 Active Phase of Anomalous X-Ray Pulsar 4U 0142+61: Radiative and Timing Changes, Bursts,and Burst Spectral Features

    NASA Technical Reports Server (NTRS)

    Gavriil, Fotis P.; Dib, Rim; Kaspi, Victoria M.

    2011-01-01

    After at least 6 years of quiescence, Anomalous X-ray Pulsar (AXP) 4U 0142+61 entered an active phase in 2006 March that lasted several months and included six X-ray bursts as well as many changes in the persistent X-ray emission. The bursts, the first seen from this AXP in > 11 years of Rossi X-ray Timing Explorer monitoring, all occurred in the interval between 2006 April 6 and 2007 February 7. The burst durations ranged from 0.4 - 1.8 x 10(exp 3) s. The first five burst spectra are well modeled by blackbodies, with temperatures kT approx 2 - 9 keV. However, the sixth burst had a complicated spectrum that is well characterized by a blackbody plus two emission features whose amplitude varied throughout the burst. The most prominent feature was at 14.0 keV. Upon entry into the active phase the pulsar showed a significant change in pulse morphology and a likely timing glitch. The glitch had a total frequency jump of (1.9+/-0.4) x 10(exp -7) Hz, which recovered with a decay time of 17+/-2 days by more than the initial jump, implying a net spin-down of the pulsar. Within the framework of the magnetar model, the net spin-down of the star could be explained by regions of the superfluid that rotate. slower than the rest. The bursts, flux enhancements, and pulse morphology changes can be explained as arising from crustal deformations due to stresses imposed by the highly twisted internal magnetic field. However, unlike other AXP outbursts, we cannot account for a major twist being implanted in the magnetosphere.

  16. X-ray nanotomography

    NASA Astrophysics Data System (ADS)

    Sasov, Alexander

    2004-10-01

    A compact laboratory x-ray "nano-CT" scanner has been created for 3D non-invasive imaging with 150-200 nanometers 3D spatial resolution, using advanced x-ray technologies and specific physical phenomena for signal detection. This spatial resolution in volume terms is 3 orders better than can be achieved in synchrotron tomography, 5 orders better then in existing laboratory micro-CT instruments and 10-12 orders better in comparison to clinical CT. The instrument employs an x-ray source with a 300-400nm x-ray spot size and uses small-angle scattering to attain a detail detectability of 150-200nm. An object manipulator allows positioning and rotation with an accuracy of 150nm. The x-ray detector is based on an intensified CCD with single-photon sensitivity. A typical acquisition cycle for 3D reconstruction of the full object volume takes from 10 to 60 minutes, with the collection of several hundred angular views. Subsequent volumetric reconstruction produces results as a set of cross sections with isotropic voxel size down to 140 x 140 x 140nm, or as a 3D-model, which can be virtually manipulated and measured. This unique spatial resolution in non-invasive investigations gives previously unattainable 3D images in several application areas, such as composite materials, paper and wood microstructure, biomedical applications and others.

  17. Synchrotron X-ray Diffraction Investigation of the Anomalous Behavior of Ice During Freezing of Aqueous Systems

    SciTech Connect

    Varshney, Dushyant B.; Elliott, James A.; Gatlin, Larry A.; Kumar, Satyendra; Suryanarayanan, Raj; Shalaev, Evgenyi Y.

    2009-06-01

    Simple aqueous systems, i.e., phosphate-glycine buffers and pure water, were studied at subambient temperatures by X-ray difractometry using a high-intensity synchrotron radiation source at the Advanced Photon Source of Argonne National Laboratory. Complex X-ray diffraction (XRD) patterns, with two or more poorly resolved peaks in place of each of the four diagnostic peaks of hexagonal ice, 100, 002, 101, and 102, referred as 'splitting', were observed in the majority of cases. The splitting of up to 0.05 {angstrom} (d-spacing) was detected for 100, 002, and 101 peaks, whereas 102 peak was less affected. Deformation of the lattice of hexagonal ice, probably due to local stress created on the ice/ice or ice/container interface during water-to-ice transformation, is proposed as a possible mechanism for the observed splitting of XRD peaks. Using molecular modeling, it was estimated that the observed shifts in the peak positions are equivalent to applying a hydrostatic pressure of 2-3 kbars. The splitting can be used to quantify stresses during freezing, which could improve our understanding of the role of water-to-ice transformation on the destabilization of proteins and other biological systems.

  18. Crowding and Anomalous Capacitance at an Electrode–Ionic Liquid Interface Observed Using Operando X-ray Scattering

    PubMed Central

    2016-01-01

    Room temperature ionic liquids are widely recognized as novel electrolytes with properties very different from those of aqueous solutions, and thus with many potential applications, but observing how they actually behave at electrolytic interfaces has proved to be challenging. We have studied the voltage-dependent structure of [TDTHP]+[NTF2]− near its interface with an electrode, using in situ synchrotron X-ray reflectivity. An anion-rich layer develops at the interface above a threshold voltage of +1.75 V, and the layer thickness increases rapidly with voltage, reaching ∼6 nm (much larger that the anion dimensions) at +2.64 V. These results provide direct confirmation of the theoretical prediction of “crowding” of ions near the interface. The interfacial layer is not purely anionic but a mixture of up to ∼80% anions and the rest cations. The static differential capacitance calculated from X-ray measurements shows an increase at higher voltages, consistent with a recent zero-frequency capacitance measurement but inconsistent with ac capacitance measurements. PMID:27163044

  19. Crowding and Anomalous Capacitance at an Electrode-Ionic Liquid Interface Observed Using Operando X-ray Scattering.

    PubMed

    Chu, Miaoqi; Miller, Mitchell; Dutta, Pulak

    2016-03-23

    Room temperature ionic liquids are widely recognized as novel electrolytes with properties very different from those of aqueous solutions, and thus with many potential applications, but observing how they actually behave at electrolytic interfaces has proved to be challenging. We have studied the voltage-dependent structure of [TDTHP](+)[NTF2](-) near its interface with an electrode, using in situ synchrotron X-ray reflectivity. An anion-rich layer develops at the interface above a threshold voltage of +1.75 V, and the layer thickness increases rapidly with voltage, reaching ∼6 nm (much larger that the anion dimensions) at +2.64 V. These results provide direct confirmation of the theoretical prediction of "crowding" of ions near the interface. The interfacial layer is not purely anionic but a mixture of up to ∼80% anions and the rest cations. The static differential capacitance calculated from X-ray measurements shows an increase at higher voltages, consistent with a recent zero-frequency capacitance measurement but inconsistent with ac capacitance measurements. PMID:27163044

  20. X-ray study of the anomalous thermal hystereses of the modulation wavevectors in Cs2HgCl4

    NASA Astrophysics Data System (ADS)

    Bagautdinov, Bagautdin; Shaw, Zachery; Orlov, Andrii; Aliev, Marat A.

    2016-05-01

    A rich sequence of structural modulations in Cs2HgCl4 as a function of temperature was studied by means of X-ray diffraction. Accurate satellite-position measurements on the cooling and heating paths of the crystal revealed abnormal thermal hystereses for incommensurate phases and coexistences of neighboring commensurate phases. A well-defined X-ray picture of the a-axis modulated phases in the range of 221-184 K were observed on the heating path, while the c-axis modulated phases existing below 184 K were definitely detected on the cooling path. The proper conditions for a precise phase diagram of Cs2HgCl4 can be correlated with relatively defect-free transformations of a-axis modulations at heating and of c-axis modulations at cooling. The peculiarity of Cs2HgCl4 to switch modulation direction among the a- and c-axes at 184 K allows us deliberately accumulate and thus control a majority of mobile defects on the mutually perpendicular (100) or (001) planes by possessing crystal within temperature domain of a- or c-axes modulations, respectively.

  1. Rb+ adsorption at the quartz(101)-aqueous interface: comparison of resonant anomalous x-ray reflectivity with ab initio calculations

    SciTech Connect

    Bellucci, Francesco; Lee, Sang Soo; Kubicki, James D.; Bandura, Andrei V.; Zhang, Zhan; Wesolowski, David J.; Fenter, Paul

    2015-01-29

    We study adsorption of Rb+ to the quartz(101)–aqueous interface at room temperature with specular X-ray reflectivity, resonant anomalous X-ray reflectivity, and density functional theory. The interfacial water structures observed in deionized water and 10 mM RbCl solution at pH 9.8 were similar, having a first water layer at height of 1.7 ± 0.1 Å above the quartz surface and a second layer at 4.8 ± 0.1 Å and 3.9 ± 0.8 Å for the water and RbCl solutions, respectively. The adsorbed Rb+ distribution is broad and consists of presumed inner-sphere (IS) and outer-sphere (OS) complexes at heights of 1.8 ± 0.1 and 6.4 ± 1.0 Å, respectively. Projector-augmented planewave density functional theory (DFT) calculations of potential configurations for neutral and negatively charged quartz(101) surfaces at pH 7 and 12, respectively, reveal a water structure in agreement with experimental results. These DFT calculations also show differences in adsorbed speciation of Rb+ between these two conditions. At pH 7, the lowest energy structure shows that Rb+ adsorbs dominantly as an IS complex, whereas at pH 12 IS and OS complexes have equivalent energies. The DFT results at pH 12 are generally consistent with the two site Rb distribution observed from the X-ray data at pH 9.8, albeit with some differences that are discussed. In conclusion, surface charge estimated on the basis of the measured total Rb+ coverage was -0.11 C/m2, in good agreement with the range of the surface charge magnitudes reported in the literature.

  2. Chain Packing in the Inverted Hexagonal Phase of Phospholipids: A Study by X-ray Anomalous Diffraction on Bromine-Labeled Chains

    SciTech Connect

    Pan,D.; Wang, W.; Liu, W.; Yang, L.; Huang, H.

    2006-01-01

    Although lipid phases are routinely studied by X-ray diffraction, construction of their unit cell structures from the diffraction data is difficult except for the lamellar phases. This is due to the well-known phase problem of X-ray diffraction. Here we successfully applied the multiwavelength anomalous dispersion (MAD) method to solve the phase problem for an inverted hexagonal phase of a phospholipid with brominated chains. Although the principle of the MAD method for all systems is the same, we found that for lipid structures it is necessary to use a procedure of analysis significantly different from that used for protein crystals. The inverted hexagonal phase has been used to study the chain packing in a hydrophobic interstice where three monolayers meet. Hydrophobic interstices are of great interest, because they occur in the intermediate states of membrane fusion. It is generally believed that chain packing in such a region is energy costly. Consequently, it has been speculated that the inverted lipid tube is likely to deviate from a circular shape, and the chain density distribution might be nonuniform. The bromine distribution obtained from the MAD analysis provides the information for the chain packing in the hexagonal unit cell. The intensity of the bromine distribution is undulated around the unit cell. The analysis shows that the lipid chains pack the hexagonal unit cell at constant volume per chain, with no detectable effect from a high-energy interstitial region.

  3. 10 Years of RXTE Monitoring of the Anomalous X-Ray Pulsar 4U 0142+61: Long-Term Variability

    NASA Astrophysics Data System (ADS)

    Dib, Rim; Kaspi, Victoria M.; Gavriil, Fotis P.

    2007-09-01

    We report on 10 years of monitoring of the 8.7 s anomalous X-ray pulsar 4U 0142+61 using the Rossi X-Ray Timing Explorer (RXTE). This pulsar exhibited stable rotation from 2000 March until 2006 February; the rms phase residual for a spin-down model, which includes ν, ν˙, and ν̈, is 2.3%. We report a possible phase-coherent timing solution valid over a 10 yr span extending back to 1996 March. A glitch may have occurred between 1998 and 2000, but is not required by the existing timing data. The pulse profile has been evolving since 2000. In particular, the dip of emission between its two peaks got shallower between 2002 and 2006, as if the profile were evolving back to its pre-2000 morphology, following an earlier event, which possibly also included the glitch suggested by the timing data. These profile variations are seen in the 2-4 keV band, but not in 6-8 keV. We also detect a slow increase in the pulsed flux between 2002 May and 2004 December, such that it has risen by 36%+/-3% over 2.6 yr in the 2-10 keV band. The pulsed flux variability and the narrowband pulse profile changes present interesting challenges to aspects of the magnetar model.

  4. Structural and chemical ordering of Heusler CoxMnyGez epitaxial films on Ge (111). Quantitative study using traditional and anomalous x-ray diffraction techniques

    DOE PAGESBeta

    Collins, B. A.; Chu, Y.; He, L.; Haskel, D.; Tsui, F.

    2015-12-14

    We found that epitaxial films of CoxMnyGez grown on Ge (111) substrates by molecular-beam-epitaxy techniques have been investigated as a continuous function of composition using combinatorial synchrotron x-ray diffraction (XRD) and x-ray fluorescence (XRF) spectroscopy techniques. A high-resolution ternary epitaxial phase diagram is obtained, revealing a small number of structural phases stabilized over large compositional regions. Ordering of the constituent elements in the compositional region near the full Heusler alloy Co2MnGe has been examined in detail using both traditional XRD and a new multiple-edge anomalous diffraction (MEAD) technique. Multiple-edge anomalous diffraction involves analyzing the energy dependence of multiple reflections acrossmore » each constituent absorption edge in order to detect and quantify the elemental distribution of occupation in specific lattice sites. Results of this paper show that structural and chemical ordering are very sensitive to the Co : Mn atomic ratio, such that the ordering is the highest at an atomic ratio of 2 but significantly reduced even a few percent off this ratio. The in-plane lattice is nearly coherent with that of the Ge substrate, while the approximately 2% lattice mismatch is accommodated by the out-of-plane tetragonal strain. Furthermore, the quantitative MEAD analysis reveals no detectable amount (<0.5%) of Co-Mn site swapping, but instead high levels (26%) of Mn-Ge site swapping. Increasing Ge concentration above the Heusler stoichiometry (Co 0.5 Mn 0.25 Ge 0.25 ) is shown to correlate with increased lattice vacancies, antisites, and stacking faults, but reduced lattice relaxation. The highest degree of chemical ordering is observed off the Heusler stoichiometry with a Ge enrichment of 5 at.%.« less

  5. Using X-ray absorption spectra to monitor specific radiation damage to anomalously scattering atoms in macromolecular crystallography.

    PubMed

    Oliéric, V; Ennifar, E; Meents, A; Fleurant, M; Besnard, C; Pattison, P; Schiltz, M; Schulze-Briese, C; Dumas, P

    2007-07-01

    Radiation damage in macromolecular crystals is not suppressed even at 90 K. This is particularly true for covalent bonds involving an anomalous scatterer (such as bromine) at the 'peak wavelength'. It is shown that a series of absorption spectra recorded on a brominated RNA faithfully monitor the extent of cleavage. The continuous spectral changes during irradiation preserve an 'isosbestic point', each spectrum being a linear combination of 'zero' and 'infinite' dose spectra. This easily yields a good estimate of the partial occupancy of bromine at any intermediate dose. The considerable effect on the near-edge features in the spectra of the crystal orientation versus the beam polarization has also been examined and found to be in good agreement with a previous study. Any significant influence of the (C-Br bond/beam polarization) angle on the cleavage kinetics of bromine was also searched for, but was not detected. These results will be useful for standard SAD/MAD experiments and for the emerging 'radiation-damage-induced phasing' method exploiting both the anomalous signal of an anomalous scatterer and the 'isomorphous' signal resulting from its cleavage. PMID:17582167

  6. A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations

    PubMed Central

    Blachowicz, Lydia; Roux, Benoît

    2013-01-01

    OmpF, a multiionic porin from Escherichia coli, is a useful protypical model system for addressing general questions about electrostatic interactions in the confinement of an aqueous molecular pore. Here, favorable anion locations in the OmpF pore were mapped by anomalous X-ray scattering of Br− ions from four different crystal structures and compared with Mg2+ sites and Rb+ sites from a previous anomalous diffraction study to provide a complete picture of cation and anion transfer paths along the OmpF channel. By comparing structures with various crystallization conditions, we find that anions bind in discrete clusters along the entire length of the OmpF pore, whereas cations find conserved binding sites with the extracellular, surface-exposed loops. Results from molecular dynamics simulations are consistent with the experimental data and help highlight the critical residues that preferentially contact either cations or anions during permeation. Analysis of these results provides new insights into the molecular mechanisms that determine ion selectivity in OmpF porin. PMID:24106986

  7. RXTE Monitoring of the Anomalous X-ray Pulsar 1E 1048.1-5937: Long-Term Variability and the 2007 March Event

    NASA Technical Reports Server (NTRS)

    Dib, Rim; Kaspi, Victoria M.; Gavriil, Fotis P.

    2009-01-01

    After three years of no unusual activity, Anomalous X-ray Pulsar 1E 1048.1-5937 reactivated in 2007 March. We report on the detection of a large glitch (deltav/v = 1.63(2) x 10(exp -5)) on 2007 March 26 (MJD 54185.9), contemporaneous with the onset of a pulsed-flux flare, the third flare observed from this source in 10 years of monitoring with the Rossi X-ray Timing Explorer. Additionally, we report on a detailed study of the evolution of the timing properties, the pulsed flux, and the pulse profile of this source as measured by RXTE from 1996 July to 2008 January. In our timing study, we attempted phase coherent timing of all available observations. We show that in 2001, a timing anomaly of uncertain nature occurred near the rise of the first pulsed flux flare; we show that a likely glitch (deltav/v = 2.91(9) x 10(exp -6)) occurred in 2002, near the rise of the second flare, and we present a detailed description of the variations in the spin-down. In our pulsed flux study, we compare the decays of the three flares and discuss changes in the hardness ratio. In our pulse profile study, we show that the profile exhibited large variations near the peak of the first two flares, and several small short-term profile variations during the most recent flare. Finally, we report on the discovery of a small burst 27 days after the peak of the last flare, the fourth burst discovered from this source. We discuss the relationships between the observed properties in the framework of the magnetar model.

  8. An Alternative Formation Theory of Beat. (II) Revelations of Recursion Formulas of the Reflected X-rays and the Anomalous Transmission and Absorption by the Binomial Theorem

    NASA Astrophysics Data System (ADS)

    Nakajima, Tetsuo

    2008-11-01

    The recursion formulas for the photon paths in the Borrmann triangle, which satisfy a new modified Pascal triangle can be derived from the binomial theorem by regarding the permutation of the stochastic variables of the diffracted and transmitted X-ray photons. The Borrmann triangle for the n-multiple X-ray reflections expanded by the n-degree binomial distribution consists of the two sub-triangles given by the ( n-1)-degree binomial distribution of the diffracted and transmitted photons. The former sub-triangle shows perfectly flawless symmetry but the latter one shows inevitable asymmetry. A reasonable understanding of both the high intense and very weak photon flows in the Borrmann triangle, which are popularly known as the anomalous transmission and absorption, respectively, are derived from the binomial theorem. Incident photons irradiated at a point O that forms the vertex of the Borrmann triangle propagate through the bypasses parallel to only the complementary half of the integral whole median with the high probabilities from the binomial theorem and emanate them from a short width slit of overline{O'O''} on the base of the high intense photon flow Borrmann triangle ▵ OO' O″, which can be defined by the standard deviation of the normal distribution. The parallel paths to the whole median also pass the very weak photon flows from the high power exponent of d multinomials through the triangle ▵ OO' O″. Both the above contrastive photon flows could coexist in ▵ OO' O″ based upon the complementary rivalry duality from the binomial theorem of ( d+ t) n =1, including the very weak photon flows from the high power exponent of t multinomials near both sides of the Borrmann triangle.

  9. Chest x-ray

    MedlinePlus

    ... Images Aortic rupture, chest x-ray Lung cancer, frontal chest x-ray Adenocarcinoma - chest x-ray Coal ... cancer - chest x-ray Lung nodule, right middle lobe - chest x-ray Lung mass, right upper lung - ...

  10. Structural analysis of Fe–Mn–O nanoparticles in glass ceramics by small angle scattering

    SciTech Connect

    Raghuwanshi, Vikram Singh; Harizanova, Ruzha; Tatchev, Dragomir; Hoell, Armin; Rüssel, Christian

    2015-02-15

    Magnetic nanocrystals containing Fe and Mn were obtained by annealing of silicate glasses with the composition 13.6Na{sub 2}O–62.9SiO{sub 2}–8.5MnO–15.0Fe{sub 2}O{sub 3−x} (mol%) at 580 °C for different periods of time. Here, we present Small Angle Neutron Scattering using Polarized neutrons (SANSPOL) and Anomalous Small Angle X-ray Scattering (ASAXS) investigation on these glass ceramic samples. Analysis of scattering data from both methods reveals the formation of spherical core–shell type of nanoparticles with mean sizes between 10 nm and 100 nm. ASAXS investigation shows the particles have higher concentration of iron atoms and the shell like region surrounding the particles is enriched in SiO{sub 2}. SANSPOL investigation shows the particles are found to be magnetic and are surrounded by a non-magnetic shell-like region. - Graphical abstract: Magnetic spherical core–shell nanoparticles in glass ceramics: SANSPOL and ASAXS investigations. - Highlights: • Formation and growth mechanisms of magnetic nanoparticles in silicate glass. • SANSPOL and ASAXS methods employed to evaluate quantitative information. • Analyses showed formation of nanoparticles with spherical core–shell structures. • Core of the particle is magnetic and surrounded by weak magnetic shell like region.

  11. Phase sensitive small angle neutron scattering

    NASA Astrophysics Data System (ADS)

    Brok, Erik; Majkrzak, Charles F.; Krycka, Kathryn

    It is a well-known problem that information about the scattered wave is lost in scattering experiments because the measured quantity is the modulus squared of the complex wave function. This ''phase problem'' leads to ambiguity in determining the physical properties of the scattering sample. Small angle neutron scattering (SANS) is a useful technique for determining the structure of biomolecules, in particular proteins that cannot be crystallized and studied with x-ray crystallography. However, because the biomolecules are usually suspended in a liquid the observed scattering is an average of all possible orientations, making it difficult to obtain three dimensional structural information. In a proposed method polarized SANS and magnetic nanoparticle references attached to the sample molecules is used to obtain phase sensitive structural information and simultaneously circumvent the problem of orientational averaging (Majkrzak et al. J. Appl. Cryst. 47, 2014) If realized and perfected the technique is very promising for unambiguous determination of the three dimensional structure of biomolecules. We demonstrate the principles of our method and show the first experimental data obtained on a simple test system consisting of core shell magnetic nanoparticles.

  12. Charge ordering in NaV_2O_5: INS of the spin dynamics and X-ray anomalous scattering studies.

    NASA Astrophysics Data System (ADS)

    Grenier, Beatrice

    2002-03-01

    At room temperature, NaV_2O5 is well described by a quarter-filled two-leg ladder system, with only one type of vanadium site V^4.5+, spins 1/2 being delocalized on the V-O-V rungs. Interestingly, NaV_2O5 undergoes a phase transition at T_c~= 34 K associated to 1/ a lattice distorsion leading to a large unit cell (2a.2b.4c), 2/ the opening of a finite energy gap to the lowest triplet state, 3/ a charge ordering with two types of vanadium sites, V^4.5+δ and V^4.5-δ. But the 3D configuration of the charge ordering is still under debate. The aim of this paper is the determination of the electronic re-distribution occuring below Tc using two complementary techniques. Inelastic neutron scattering results are first presented.^1 Spin excitations have been studied along the two directions (Q_a,1/2,0) and (Q_a,1,0). Two branches with distinct energy gaps are identified, with a weak dispersion along Qa (δ J ~= 1 meV along the ladder rungs), reflecting the low dimensionality of the magnetic interactions (Jb ~= 60 meV along the ladder legs). From the dispersion and the analysis of the structure factors, the 2D charge distribution is deduced in the (a,b) planes: the experimental data agree well with a zig-zag charge distribution on the ladder rungs and lead to a charge transfer amounting δ = 0.3. An X-ray anomalous scattering study, performed on the K-edge of the vanadium atom, is then discussed.^2 A large number of Bragg reflections from both phases has been measured as a function of the incident photon energy. The data confirm the zig-zag picture issued from INS, with a smaller charge transfer, and the 3D charge order arrangement is found to be rather complex. It suggests stacking faults separating regions corresponding to four possible patterns. In the light of these X-ray results, our neutron data are further analyzed. ^1B. Grenier et al., Phys. Rev. Lett. 86 (2001) 5966. ^2S. Grenier et al., cond-mat/0109091.

  13. Kinoform optics applied to x-ray photon correlation spectroscopy.

    SciTech Connect

    Sandy, A. R.; Narayanan, S.; Sprung, M.; Su, J.-D.; Evans-Lutterodt, K.; Isakovic, A. F.; Stein, A.; BNL

    2010-01-01

    Moderate-demagnification higher-order silicon kinoform focusing lenses have been fabricated to facilitate small-angle X-ray photon correlation spectroscopy (XPCS) experiments. The geometric properties of such lenses, their focusing performance and their applicability for XPCS measurements are described. It is concluded that one-dimensional vertical X-ray focusing via silicon kinoform lenses significantly increases the usable coherent flux from third-generation storage-ring light sources for small-angle XPCS experiments.

  14. Time-lapse anomalous X-ray diffraction shows how Fe(2+) substrate ions move through ferritin protein nanocages to oxidoreductase sites.

    PubMed

    Pozzi, Cecilia; Di Pisa, Flavio; Lalli, Daniela; Rosa, Camilla; Theil, Elizabeth; Turano, Paola; Mangani, Stefano

    2015-04-01

    Ferritin superfamily protein cages reversibly synthesize internal biominerals, Fe2O3·H2O. Fe(2+) and O2 (or H2O2) substrates bind at oxidoreductase sites in the cage, initiating biomineral synthesis to concentrate iron and prevent potentially toxic reactions products from Fe(2+)and O2 or H2O2 chemistry. By freezing ferritin crystals of Rana catesbeiana ferritin M (RcMf) at different time intervals after exposure to a ferrous salt, a series of high-resolution anomalous X-ray diffraction data sets were obtained that led to crystal structures that allowed the direct observation of ferrous ions entering, moving along and binding at enzyme sites in the protein cages. The ensemble of crystal structures from both aerobic and anaerobic conditions provides snapshots of the iron substrate bound at different cage locations that vary with time. The observed differential occupation of the two iron sites in the enzyme oxidoreductase centre (with Glu23 and Glu58, and with Glu58, His61 and Glu103 as ligands, respectively) and other iron-binding sites (with Glu53, His54, Glu57, Glu136 and Asp140 as ligands) reflects the approach of the Fe(2+) substrate and its progression before the enzymatic cycle 2Fe(2+) + O2 → Fe(3+)-O-O-Fe(3+) → Fe(3+)-O(H)-Fe(3+) and turnover. The crystal structures also revealed different Fe(2+) coordination compounds bound to the ion channels located at the threefold and fourfold symmetry axes of the cage. PMID:25849404

  15. Time-lapse anomalous X-ray diffraction shows how Fe2+ substrate ions move through ferritin protein nanocages to oxidoreductase sites

    PubMed Central

    Pozzi, Cecilia; Di Pisa, Flavio; Lalli, Daniela; Rosa, Camilla; Theil, Elizabeth; Turano, Paola; Mangani, Stefano

    2015-01-01

    Ferritin superfamily protein cages reversibly synthesize internal biominerals, Fe2O3·H2O. Fe2+ and O2 (or H2O2) substrates bind at oxidoreductase sites in the cage, initiating biomineral synthesis to concentrate iron and prevent potentially toxic reactions products from Fe2+and O2 or H2O2 chemistry. By freezing ferritin crystals of Rana catesbeiana ferritin M (RcMf) at different time intervals after exposure to a ferrous salt, a series of high-resolution anomalous X-ray diffraction data sets were obtained that led to crystal structures that allowed the direct observation of ferrous ions entering, moving along and binding at enzyme sites in the protein cages. The ensemble of crystal structures from both aerobic and anaerobic conditions provides snapshots of the iron substrate bound at different cage locations that vary with time. The observed differential occupation of the two iron sites in the enzyme oxidoreductase centre (with Glu23 and Glu58, and with Glu58, His61 and Glu103 as ligands, respectively) and other iron-binding sites (with Glu53, His54, Glu57, Glu136 and Asp140 as ligands) reflects the approach of the Fe2+ substrate and its progression before the enzymatic cycle 2Fe2+ + O2 → Fe3+—O—O—Fe3+ → Fe3+—O(H)—Fe3+ and turnover. The crystal structures also revealed different Fe2+ coordination compounds bound to the ion channels located at the threefold and fourfold symmetry axes of the cage. PMID:25849404

  16. Determination of transition metal ion distribution in cubic spinel Co{sub 1.5}Fe{sub 1.5}O{sub 4} using anomalous x-ray diffraction

    SciTech Connect

    Singh, M. N.; Sinha, A. K. Ghosh, Haranath

    2015-08-15

    We report anomalous x-ray diffraction studies on Co ferrite with composition Co{sub 1.5}Fe{sub 1.5}O{sub 4} to obtain the distribution of transition metal ions in tetrahedral and octahedral sites. We synthesize spinel oxide (Co{sub 1.5}Fe{sub 1.5}O{sub 4}) through co-precipitation and subsequent annealing route. The imaginary part (absorption) of the energy dependent anomalous form factor is measured and the real part is calculated theoretically through Kramers–Krönig transformation to analyze anomalous x-ray diffraction peak intensities. Fe and Co K-edge x-ray absorption near edge structure (XANES) spectra are used to estimate charge states of transition metals. Our analysis, within experimental errors, suggests 44% of the tetrahedral sites contain Co in +2 oxidation state and the rest 56% sites contain Fe in +2 and +3 oxidation states. Similarly, 47% of the octahedral sites contain Fe in +3 oxidation states, whereas, the rest of the sites contain Co in +2 and +3 oxidation states. While a distinct pre-edge feature in the Fe K-edge XANES is observed, Co pre-edge remains featureless. Implications of these results to magnetism are briefly discussed.

  17. Small angle neutron scattering (SANS) and small angle x-ray scattering (SAXS) analysis of polyaniline salts and blends

    SciTech Connect

    Hopkins, A.R.; Rasmussen, P.G.; Basheer, R.A.; Annis, B.K.; Wignall, G.D.

    1996-06-01

    Doped polyaniline emeraldine salts (PANI-ES) exhibit good environmental stability with a high level of conductivity (1 to 300 S/cm). However, they suffer from the fact that they have poor mechanical properties and must be blended with an insulating host polymer to be useful in industrial applications. Polyaniline blends are a new type of conducting material that typically show very low onsets of conductivity unlike that of metal filled blends. This is primarily due to the unique cellular geometry of the PANI-ES that is formed within the insulating host polymer. The formation of this immiscible polymer network may be due in part to structural and conformational differences in the blend components.

  18. SASBDB, a repository for biological small-angle scattering data

    PubMed Central

    Valentini, Erica; Kikhney, Alexey G.; Previtali, Gianpietro; Jeffries, Cy M.; Svergun, Dmitri I.

    2015-01-01

    Small-angle X-ray and neutron scattering (SAXS and SANS) are fundamental tools used to study the global shapes of proteins, nucleic acids, macromolecular complexes and assemblies in solution. Due to recent advances in instrumentation and computational methods, the quantity of experimental scattering data and subsequent publications is increasing dramatically. The need for a global repository allowing investigators to locate and access experimental scattering data and associated models was recently emphasized by the wwPDB small-angle scattering task force (SAStf). The small-angle scattering biological data bank (SASBDB) www.sasbdb.org has been designed in accordance with the plans of the SAStf as part of a future federated system of databases for biological SAXS and SANS. SASBDB is a comprehensive repository of freely accessible and fully searchable SAS experimental data and models that are deposited together with the relevant experimental conditions, sample details and instrument characteristics. At present the quality of deposited experimental data and the accuracy of models are manually curated, with future plans to integrate automated systems as the database expands. PMID:25352555

  19. Spectral softening in the X-RAY afterglow of GRB 130925A as predicted by the dust scattering model

    SciTech Connect

    Zhao, Yi-Nan; Shao, Lang

    2014-07-01

    Gamma-ray bursts (GRBs) usually occur in a dense star-forming region with a massive circumburst medium. The small-angle scattering of intense prompt X-ray emission off the surrounding dust grains will have observable consequences and sometimes can dominate the X-ray afterglow. In most of the previous studies, only the Rayleigh-Gans (RG) approximation is employed for describing the scattering process, which works accurately for the typical size of grains (with radius of a ≤ 0.1 μm) in the diffuse interstellar medium. When the size of the grains may significantly increase, as in a more dense region where GRBs would occur, the RG approximation may not be valid enough for modeling detailed observational data. In order to study the temporal and spectral properties of the scattered X-ray emission more accurately with potentially larger dust grains, we provide a practical approach using the series expansions of anomalous diffraction (AD) approximation based on the complicated Mie theory. We apply our calculations to understand the puzzling X-ray afterglow of recently observed GRB 130925A that showed a significant spectral softening. We find that the X-ray scattering scenarios with either AD or RG approximation adopted could well reproduce both the temporal and spectral profile simultaneously. Given the plateau present in the early X-ray light curve, a typical distribution of smaller grains as in the interstellar medium would be suggested for GRB 130925A.

  20. Spectral Softening in the X-Ray Afterglow of GRB 130925A as Predicted by the Dust Scattering Model

    NASA Astrophysics Data System (ADS)

    Zhao, Yi-Nan; Shao, Lang

    2014-07-01

    Gamma-ray bursts (GRBs) usually occur in a dense star-forming region with a massive circumburst medium. The small-angle scattering of intense prompt X-ray emission off the surrounding dust grains will have observable consequences and sometimes can dominate the X-ray afterglow. In most of the previous studies, only the Rayleigh-Gans (RG) approximation is employed for describing the scattering process, which works accurately for the typical size of grains (with radius of a <= 0.1 μm) in the diffuse interstellar medium. When the size of the grains may significantly increase, as in a more dense region where GRBs would occur, the RG approximation may not be valid enough for modeling detailed observational data. In order to study the temporal and spectral properties of the scattered X-ray emission more accurately with potentially larger dust grains, we provide a practical approach using the series expansions of anomalous diffraction (AD) approximation based on the complicated Mie theory. We apply our calculations to understand the puzzling X-ray afterglow of recently observed GRB 130925A that showed a significant spectral softening. We find that the X-ray scattering scenarios with either AD or RG approximation adopted could well reproduce both the temporal and spectral profile simultaneously. Given the plateau present in the early X-ray light curve, a typical distribution of smaller grains as in the interstellar medium would be suggested for GRB 130925A.

  1. X-Rays

    MedlinePlus

    X-rays are a type of radiation called electromagnetic waves. X-ray imaging creates pictures of the inside of ... different amounts of radiation. Calcium in bones absorbs x-rays the most, so bones look white. Fat ...

  2. Cosmic x ray physics

    NASA Technical Reports Server (NTRS)

    Mccammon, Dan; Cox, D. P.; Kraushaar, W. L.; Sanders, W. T.

    1990-01-01

    The annual progress report on Cosmic X Ray Physics is presented. Topics studied include: the soft x ray background, proportional counter and filter calibrations, the new sounding rocket payload: X Ray Calorimeter, and theoretical studies.

  3. Cosmic x ray physics

    NASA Technical Reports Server (NTRS)

    Mccammon, Dan; Cox, D. P.; Kraushaar, W. L.; Sanders, W. T.

    1991-01-01

    The annual progress report on Cosmic X Ray Physics for the period 1 Jan. to 31 Dec. 1990 is presented. Topics studied include: soft x ray background, new sounding rocket payload: x ray calorimeter, and theoretical studies.

  4. Joint x-ray

    MedlinePlus

    X-ray - joint; Arthrography; Arthrogram ... x-ray technologist will help you position the joint to be x-rayed on the table. Once in place, pictures are taken. The joint may be moved into other positions for more ...

  5. Three Biomedical Beamlines at NSLS-II for Macromolecular Crystallography and Small-Angle Scattering

    NASA Astrophysics Data System (ADS)

    Schneider, D. K.; Berman, L. E.; Chubar, O.; Hendrickson, W. A.; Hulbert, S. L.; Lucas, M.; Sweet, R. M.; Yang, L.

    2013-03-01

    We report on the status of the development of three beamlines for the National Synchrotron Light Source-II (NSLS-II), two for macromolecular crystallography (MX), and one for wide- and small-angle x-ray scattering (SAXS). Funded by the National Institutes of Health, this suite of Advanced Beamlines for Biological Investigations with X-rays (ABBIX) is scheduled to begin operation by 2015. The two MX beamlines share a sector with identical canted in-vacuum undulators (IVU21). The microfocusing FMX beamline on the inboard branch employs a two-stage horizontal source demagnification scheme, will cover an energy range of 5 - 23 keV, and at 12.7 keV will focus a flux of up to 1013 ph/s into a spot of 1 μm width. The companion AMX beamline on the short outboard branch of the sector is tunable in the range of 5 - 18 keV and has a native focus of 4 μm (h) × 2 μm (v). This robust beamline will be highly automated, have high throughput capabilities, and with larger beams and low divergence will be well suited for structure determinations on large complexes. The high brightness SAXS beamline, LIX, will provide multiple dynamic and static experimental systems to support scientific programs in solution scattering, membrane structure determination, and tissue imaging. It will occupy a different sector, equipped with a single in-vacuum undulator (IVU23). It can produce beams as small as 1 μm across, and with a broad energy range of 2.1 - 18 keV it will support anomalous SAXS.

  6. Chest x-ray

    MedlinePlus

    Chest radiography; Serial chest x-ray; X-ray - chest ... You stand in front of the x-ray machine. You will be told to hold your breath when the x-ray is taken. Two images are usually taken. You will ...

  7. The study of pinch regimes based on radiation-enhanced compression and anomalous resistivity phenomena and their effects on hard x-ray emission in a Mather type dense plasma focus device (SABALAN2)

    NASA Astrophysics Data System (ADS)

    Piriaei, D.; Mahabadi, T. D.; Javadi, S.; Ghoranneviss, M.; Saw, S. H.; Lee, S.

    2015-12-01

    In this study, by using argon and nitrogen as the filling gases in a Mather type dense plasma focus device at different values of pressure and charging voltage, two different kinds of pinch regimes were observed for each of the gases. The physics of the pinch regimes could be explained by using the two versions of the Lee's computational model which predicted each of the scenarios and clarified their differences between the two gases according to the radiation-enhanced compression and, additionally, predicted the pinch regimes through the anomalous resistivity effect during the pinch time. This was accomplished through the fitting process (simulation) on the current signal. Moreover, the characteristic amplitude and time scales of the anomalous resistances were obtained. The correlations between the features of the plasma current dip and the emitted hard x-ray pulses were observed. The starting time, intensity, duration, and the multiple or single feature of the emitted hard x-ray strongly correlated to the same respective features of the current dip.

  8. The study of pinch regimes based on radiation-enhanced compression and anomalous resistivity phenomena and their effects on hard x-ray emission in a Mather type dense plasma focus device (SABALAN2)

    SciTech Connect

    Piriaei, D.; Javadi, S.; Ghoranneviss, M.; Mahabadi, T. D.; Saw, S. H.; Lee, S.

    2015-12-15

    In this study, by using argon and nitrogen as the filling gases in a Mather type dense plasma focus device at different values of pressure and charging voltage, two different kinds of pinch regimes were observed for each of the gases. The physics of the pinch regimes could be explained by using the two versions of the Lee's computational model which predicted each of the scenarios and clarified their differences between the two gases according to the radiation-enhanced compression and, additionally, predicted the pinch regimes through the anomalous resistivity effect during the pinch time. This was accomplished through the fitting process (simulation) on the current signal. Moreover, the characteristic amplitude and time scales of the anomalous resistances were obtained. The correlations between the features of the plasma current dip and the emitted hard x-ray pulses were observed. The starting time, intensity, duration, and the multiple or single feature of the emitted hard x-ray strongly correlated to the same respective features of the current dip.

  9. Chandra ACIS-S imaging spectroscopy of anomalously faint X-ray emission from Comet 103P/Hartley 2 during the EPOXI encounter

    NASA Astrophysics Data System (ADS)

    Lisse, C. M.; Christian, D. J.; Wolk, S. J.; Dennerl, K.; Bodewits, D.; Combi, M. R.; Lepri, S. T.; Zurbuchen, T. H.; Li, J. Y.; Dello-Russo, N.; Belton, M. J. S.; Knight, M. M.

    2013-02-01

    We present results from the Chandra X-ray Observatory's characterization of the X-ray emission from Comet 103P/Hartley 2, in support of NASA's Deep Impact Extended close flyby of the comet on 04 November 2010. The comet was observed 4 times for a total on target time of ˜60 ks between the 17th of October and 16th of November 2010, with two of the visits occurring during the EPOXI close approach on 04 November and 05 November 2010. X-ray emission from 103P was qualitatively similar to that observed for collisionally thin Comets 2P/Encke (Lisse, C.M. et al. [2005]. Astrophys. J. 635, 1329-1347) and 9P/Tempel 1 (Lisse, C.M. et al. [2007]. Icarus 190, 391-405). Emission morphology offset sunward but asymmetrical from the nucleus and emission lines produced by charge exchange between highly stripped C, N, and O solar wind minor ions and coma neutral gas species were found. The comet was very under-luminous in the X-ray at all times, representing the 3rd faintest comet ever detected (LX = 1.1 ± 0.3 × 1014 erg s-1). The coma was collisionally thin to the solar wind at all times, allowing solar wind ions to flow into the inner coma and interact with the densest neutral coma gas. Localization of the X-ray emission in the regions of the major rotating gas jets was observed, consistent with the major source of cometary neutral gas species being icy coma dust particles. Variable spectral features due to changing solar wind flux densities and charge states were also seen. Modeling of the Chandra observations from the first three visits using observed gas production rates and ACE solar wind ion fluxes with a charge exchange mechanism for the emission is consistent with the temporal and spectral behavior expected for a slow, hot wind typical of low latitude emission from the solar corona interacting with the comet's neutral coma. The X-ray emission during the 4th visit on 16 November 2010 is similar to the unusual behavior seen for Comet 17P/Holmes in 2007 (Christian, D.J. et

  10. X-ray Haloes and Scattering by Interstellar Grains

    NASA Technical Reports Server (NTRS)

    Dwek, Eliahu

    2003-01-01

    The presence of dust in the general interstellar medium is inferred f r o m the general extinction of starlight, the diffuse infrared emission, and the elemental abundance constraints. X-ray haloes around X-ray sources, produced by small angle scattering from intervening interstellar dust particles provide a new probe into the nature of interstellar dust. In this talk I will review the physics of X-ray scattering by dust particles, and present an analysis of dust properties around select X-ray sources.

  11. X-ray Haloes and Scattering by Interstellar Grains

    NASA Technical Reports Server (NTRS)

    Dwek, Eliahu

    2003-01-01

    The presence of dust in the general interstellar medium is inferred from the general extinction of starlight, the diffuse infrared emission, and the elemental abundance constraints. X-ray haloes around X-ray sources, produced by small angle scattering from intervening interstellar dust particles provide a new probe into the nature of interstellar dust. In this talk I will review the physics of X-ray scattering by dust particles, and present an analysis of dust properties around select X-ray sources.

  12. Crystals for astronomical X-ray spectroscopy

    NASA Technical Reports Server (NTRS)

    Burek, A.

    1976-01-01

    Crystal spectrometric properties and the factors that affect their measurement are discussed. Theoretical and experimental results on KAP are summarized and theoretical results based on the dynamical theory of X-ray diffraction are given for the acid phthalates as well as for the commonly used planes of ADP, PET and EDDT. Anomalous dispersion is found to be important for understanding the details of crystal Bragg reflection properties at long X-ray wavelengths and some important effects are pointed out. The theory of anomalous dispersion is applied to explain the anomalous reflectivity exhibited by KAP at 23.3 A.

  13. Irena : tool suite for modeling and analysis of small-angle scattering.

    SciTech Connect

    Ilavsky, J.; Jemian, P.

    2009-04-01

    Irena, a tool suite for analysis of both X-ray and neutron small-angle scattering (SAS) data within the commercial Igor Pro application, brings together a comprehensive suite of tools useful for investigations in materials science, physics, chemistry, polymer science and other fields. In addition to Guinier and Porod fits, the suite combines a variety of advanced SAS data evaluation tools for the modeling of size distribution in the dilute limit using maximum entropy and other methods, dilute limit small-angle scattering from multiple non-interacting populations of scatterers, the pair-distance distribution function, a unified fit, the Debye-Bueche model, the reflectivity (X-ray and neutron) using Parratt's formalism, and small-angle diffraction. There are also a number of support tools, such as a data import/export tool supporting a broad sampling of common data formats, a data modification tool, a presentation-quality graphics tool optimized for small-angle scattering data, and a neutron and X-ray scattering contrast calculator. These tools are brought together into one suite with consistent interfaces and functionality. The suite allows robust automated note recording and saving of parameters during export.

  14. RXTE Observations of Anomalous X-Ray Pulsar 1E 1547.0-5408 during and after its 2008 and 2009 Outbursts

    NASA Astrophysics Data System (ADS)

    Dib, Rim; Kaspi, Victoria M.; Scholz, Paul; Gavriil, Fotis P.

    2012-03-01

    We present the results of Rossi X-ray Timing Explorer and Swift monitoring observations of the magnetar 1E 1547.0-5408 following the pulsar's radiative outbursts in 2008 October and 2009 January. We report on a study of the evolution of the timing properties and the pulsed flux from 2008 October 4 through 2009 December 26. In our timing study, a phase-coherent analysis shows that for the first 29 days following the 2008 outburst, there was a very fast increase in the magnitude of the rotational frequency derivative \\dot{\

  15. LETTER TO THE EDITOR: Anomalous elastic scattering of an x-ray photon by a molybdenum atom near the K-edge

    NASA Astrophysics Data System (ADS)

    Hopersky, A. N.; Yavna, V. A.; Novikov, S. A.; Chuvenkov, V. V.

    2000-06-01

    The differential cross section and dispersional correction for the real part of the elastic scattering amplitude of an x-ray photon by a molybdenum atom in the energy range of the ionization threshold of the 1s-shell is calculated in the non-relativistic approximation. The effect of the rearrangement of electron shells of the atomic residues in the field of the virtual 1s-vacancy is taken into account. The processes of one-photon multiple excitation/ionization of the ground state is also considered. Good agreement with the results of existing experiments is obtained.

  16. Analysis of PKR Structure by Small-Angle Scattering

    SciTech Connect

    VanOudenhove, Jennifer; Anderson, Eric; Krueger, Susan; Cole, James L.

    2009-04-27

    Protein kinase R (PKR) is a key component of the interferon antiviral defense pathway. Upon binding double-stranded RNA, PKR undergoes autophosphorylation reactions that activate the kinase. PKR contains an N-terminal double-stranded RNA binding domain, which consists of two tandem double-stranded RNA binding motifs, and a C-terminal kinase domain. We have used small-angle X-ray scattering and small-angle neutron scattering to define the conformation of latent PKR in solution. Guinier analysis indicates a radius of gyration of about 35 {angstrom}. The p(r) distance distribution function exhibits a peak near 30 {angstrom}, with a broad shoulder extending to longer distances. Good fits to the scattering data require models that incorporate multiple compact and extended conformations of the two interdomain linker regions. Thus, PKR belongs to the growing family of proteins that contain intrinsically unstructured regions. We propose that the flexible linkers may allow PKR to productively dimerize upon interaction with RNA activators that have diverse structures.

  17. Experimental methods in the study of neutron scattering at small angles

    SciTech Connect

    Dragolici, Cristian A.

    2014-11-24

    Small angle scattering (SAS) is the collective name given to the techniques of small angle neutron (SANS) and X-ray (SAXS) scattering. They offer the possibility to analyze particles without disturbing their natural environment. In each of these techniques radiation is elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample. Accordingly, a large number of methods and experimental patterns have been developed to ease the investigation of condensed matter by use of these techniques. Some of them are the discussed in this paper.

  18. Experimental methods in the study of neutron scattering at small angles

    NASA Astrophysics Data System (ADS)

    Dragolici, Cristian A.

    2014-11-01

    Small angle scattering (SAS) is the collective name given to the techniques of small angle neutron (SANS) and X-ray (SAXS) scattering. They offer the possibility to analyze particles without disturbing their natural environment. In each of these techniques radiation is elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample. Accordingly, a large number of methods and experimental patterns have been developed to ease the investigation of condensed matter by use of these techniques. Some of them are the discussed in this paper.

  19. Dental x-rays

    MedlinePlus

    X-ray - teeth; Radiograph - dental; Bitewings; Periapical film; Panoramic film ... dentist's office. There are many types of dental x-rays. Some are: Bitewing Periapical Palatal (also called occlusal) ...

  20. X-ray (image)

    MedlinePlus

    X-rays are a form of ionizing radiation that can penetrate the body to form an image on ... will be shades of gray depending on density. X-rays can provide information about obstructions, tumors, and other ...