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Sample records for anomalous small-angle x-ray

  1. Use of anomalous small angle x-ray scattering to investigate microstructural features in complex alloys

    SciTech Connect

    Weertman, J.R.

    1988-08-01

    This report covers the last 5 months of the second year of this grant and the first 8 months of the third year. The research thrust of this grant has been directed into two areas. The principal effort has been spent in an investigation of the use of anomalous small angle x-ray scattering (ASAXS) to observe changes in the microstructure of a relatively complex alloy produced by high temperature deformation or aging. The second effort involves a study of the high temperature behavior of several ferritic steels. During this past year we have been examining the effect of environment (air vs vacuum) on the high temperature strength of Fe9Cr1Mo modified by the addition of small amounts of V and Nb.

  2. Anomalous small-angle x-ray scattering of a femtosecond irradiated germano silicate fibre preform.

    SciTech Connect

    Hindle, F.; Fertein, E.; Seifert, S.; Przygodski, C.S.; Bocquet, R.; Douay, M.; Bychkov, E.; Experimental Facilities Division; LPCA, CNRS; PhLAM; Univ. des Sciences et Tech. de Lille

    2005-01-01

    RADIATION is shown to induce significant mesoscopic structure. The scattering intensity for irradiated glasses is close to two orders of magnitude greater than that of unexposed material. Anomalous small-angle X-ray scattering (ASAXS) around the germanium K-edge for the silica and germanium doped silica regions of a fiber preform is used to demonstrate that identical structures are induced in both glass materials, with germanium displaying a capacity to isomorphically replace silicon in the case of the germanium doped silica. Analysis of measured scattering indicates that photo-inscribed features are produced at two distinct scales with typical radii of R {approx} 20 Angstroms and R{sub min} {approx} 200 Angstroms.

  3. Application of X-ray absorption spectroscopy and anomalous small angle scattering to RNA polymerase

    NASA Astrophysics Data System (ADS)

    Powers, L.; Wu, F. Y.-H.; Phillips, J. C.; Huang, W.-J.; Sinclair, R. B.

    1990-05-01

    X-ray absorption spectroscopy is ideally suited for the investigation of the electronic structure and the local environment (≤ ˜ 5 Å) of specific atoms in biomolecules. While the edge region provides information about the valence state of the absorbing atom, the chemical identity of neighboring atoms, and the coordination geometry, the EXAFS region contains information about the number and average distance of neighboring atoms and their relative disorder. The development of sensitive detection methods has allowed studies using near-physiological concentrations (as low as ˜ 100 μM). With careful choice of model compounds, judicious use of fitting procedures, and consideration of the results of biochemical and other spectroscopic results, this data has provided pivotal information about the structures of these active sites which store energy in their conformation changes or ligand exchanges. Although the application of anomalous small angle scattering to biomolecules has occurred more recently, it clearly provides a method of determining distances between active sites that are outside the range of X-ray absorption spectroscopy. The wavelength dependence of the X-ray scattering power varies rapidly near the edge of the absorbing atom in both amplitude and phase. This behavior selectively alters the contribution of the absorbing atom to the scattering pattern. The structure-function relationship of the intermediate states provide the key to understanding the mechanisms of these complex molecules. It is this precise structural information about the active sites that is not obtainable by other spectroscopic techniques. Combination of these techniques offers a unique approach to the determination of the organization of active sites in biomolecules, especially metalloenzymes. Application of these methods to the substrate and template binding sites of RNA polymerase which contain zinc atoms demonstrates the versatility of this approach.

  4. Use of anomalous small angle x-ray scattering to investigate microstructural features in complex alloys

    SciTech Connect

    Weertman, J.R.

    1990-08-01

    The research thrust has been directed into two areas. The principal effort has been spent in an investigation of the use of anomalous small angle x-ray scattering (ASAXS) to observe changes in the microstructure of a relatively complex alloy produced by high temperature deformation or aging. A second effort involves a study of the high temperature behavior of several ferritic steels. In particular, we are investigating the precursors and earliest stages of fatigue crack initiation, especially how initiation is affected by hold times and by environment. We have been studying carbides in two ferritic steel alloys. The first is Fe9CrlMo modified by the addition of small amounts of the strong carbide formers, V and Nb. This alloy, which has been studied at ORNL and in the course of this grant, is used in power-generating equipment. The second alloy is AF1410 (primarily Fel4Col0Ni), an ultra high-strength, high toughness steel. 8 figs.,

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

    SciTech Connect

    Rice, Marybeth

    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-FexGe100-x) system with particular emphasis on the semiconductor-rich regime. Brief excursions are made into the amorphous tungsten-germanium (a-WxGe100-x) and the amorphous molybdenum-germanium (a-MoxGe100-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-FexGe100-x system and a superconducting transition in the a-MoxGe100-x system. A long standing question, particularly in the a-FexGe100-x and the a-MoxGe100-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-FexGe100-x, a-WxGe100-x, and a-MoxGe100-x systems in the semiconductor-metal transition region. Furthermore, ASAXS shows that germanium

  6. 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.

  7. Copper and copper oxide nanoparticles in a cellulose support studied using anomalous small-angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Vainio, U.; Pirkkalainen, K.; Kisko, K.; Goerigk, G.; Kotelnikova, N. E.; Serimaa, R.

    2007-04-01

    Microcrystalline cellulose is a porous natural material which can be used both as a support for nanoparticles and as a reducer of metal ions. Cellulose supported nanoparticles can act as catalysts in many reactions. Cu, CuO, and Cu2O particles were prepared in microcrystalline cellulose by adding a solution of copper salt to the insoluble cellulose matrix and by reducing the copper ions with several reducers. The porous nanocomposites were studied using anomalous small angle X-ray scattering (ASAXS), X-ray absorption spectroscopy, and X-ray diffraction. Reduction of Cu2+ with cellulose in ammonium hydrate medium yielded crystalline CuO nanoparticles and the crystallite size was about 6-20 nm irrespective of the copper concentration. The size distribution of the CuO particles was determined with ASAXS measurements and coincided with the crystallite sizes. Using sodium borohydrate or hydrazine sulfate as a reducer both metallic Cu and Cu2O nanoparticles were obtained and the crystallite size and the oxidation state depended on the amount of reducer.

  8. 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.

  9. Trends in anomalous small-angle X-ray scattering in grazing incidence for supported nanoalloyed and core-shell metallic nanoparticles

    NASA Astrophysics Data System (ADS)

    Andreazza, P.; Khelfane, H.; Lyon, O.; Andreazza-Vignolle, C.; Ramos, A. Y.; Samah, M.

    2012-06-01

    As atomic structure and morphology of particles are directly correlated to their functional properties, experimental methods probing local and average features of particles at the nanoscale elicit a growing interest. Anomalous small-angle X-ray scattering (ASAXS) is a very attractive technique to investigate the size, shape and spatial distribution of nanoobjects embedded in a homogeneous matrix or in porous media. The anomalous variation of the scattering factor close to an absorption edge enables element specific investigations. In the case of supported nano-objects, the use of grazing incidence is necessary to limit the probed depth. The combination of grazing incidence with the anomalous technique provides a powerful new method, anomalous grazing incidence small-angle X-ray scattering (AGISAXS), to disentangle complex chemical patterns in supported multi-component nano-structures. Nevertheless, a proper data analysis requires accurate quantitative measurements associated to an adapted theoretical framework. This paper presents anomalous methods applied to nanoalloys phase separation in the 1-10 nm size range, and focuses on the application of AGISAXS in bimetallic systems: nanocomposite films and core-shell supported nanoparticles.

  10. Small Angle X-Ray Scattering Detector

    SciTech Connect

    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., qmax/qmin approx=lO0.

  11. Anomalous Small Angle X-Ray Scattering Simulations: Proof of Concept for Distance Measurements for Nanoparticle-Labelled Biomacromolecules in Solution

    PubMed Central

    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

  12. 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.

  13. Use of anomalous small angle x-ray scattering to investigate microstructural features in complex alloys. Technical progress report, July 1, 1987--July 31, 1988

    SciTech Connect

    Weertman, J.R.

    1988-08-01

    This report covers the last 5 months of the second year of this grant and the first 8 months of the third year. The research thrust of this grant has been directed into two areas. The principal effort has been spent in an investigation of the use of anomalous small angle x-ray scattering (ASAXS) to observe changes in the microstructure of a relatively complex alloy produced by high temperature deformation or aging. The second effort involves a study of the high temperature behavior of several ferritic steels. During this past year we have been examining the effect of environment (air vs vacuum) on the high temperature strength of Fe9Cr1Mo modified by the addition of small amounts of V and Nb.

  14. Absolute Intra-Molecular Distance Measurements with Ångström-Resolution using Anomalous Small-Angle X-ray Scattering

    DOE PAGES

    Zettl, Thomas; Mathew, Rebecca S.; Seifert, Sönke; ...

    2016-05-31

    Accurate determination of molecular distances is fundamental to understanding the structure, dynamics, and conformational ensembles of biological macromolecules. Here we present a method to determine the full,distance,distribution between small (~7 Å) gold labels attached to macromolecules with very high-precision(≤1 Å) and on an absolute distance scale. Our method uses anomalous small-angle X-ray scattering close to a gold absorption edge to separate the gold-gold interference pattern from other scattering contributions. Results for 10-30 bp DNA constructs achieve excellent signal-to-noise and are in good agreement with previous results obtained by single-energy,SAXS measurements without requiring the preparation and measurement of single labeled andmore » unlabeled samples. Finally, the use of small gold labels in combination with ASAXS read out provides an attractive approach to determining molecular distance distributions that will be applicable to a broad range of macromolecular systems.« less

  15. Absolute Intra-Molecular Distance Measurements with Ångström-Resolution using Anomalous Small-Angle X-ray Scattering

    SciTech Connect

    Zettl, Thomas; Mathew, Rebecca S.; Seifert, Sönke; Doniach, Sebastian; Harbury, Pehr A.B.; Lipfert, Jan

    2016-05-31

    Accurate determination of molecular distances is fundamental to understanding the structure, dynamics, and conformational ensembles of biological macromolecules. Here we present a method to determine the full,distance,distribution between small (~7 Å) gold labels attached to macromolecules with very high-precision(≤1 Å) and on an absolute distance scale. Our method uses anomalous small-angle X-ray scattering close to a gold absorption edge to separate the gold-gold interference pattern from other scattering contributions. Results for 10-30 bp DNA constructs achieve excellent signal-to-noise and are in good agreement with previous results obtained by single-energy,SAXS measurements without requiring the preparation and measurement of single labeled and unlabeled samples. Finally, the use of small gold labels in combination with ASAXS read out provides an attractive approach to determining molecular distance distributions that will be applicable to a broad range of macromolecular systems.

  16. 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).

  17. 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.

  18. 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.

  19. Probing the extent of the Sr{sup 2+} ion condensation to anionic polyacrylate coils: A quantitative anomalous small-angle x-ray scattering study

    SciTech Connect

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

    2007-10-21

    The shrinking process of anionic sodium polyacrylate (NaPA) chains in aqueous solution induced by Sr{sup 2+} 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 Sr{sup 2+} counterions, was used to analyze the extent of Sr{sup 2+} condensation onto the polyacrylate coils. A series of four samples with different ratios [Sr{sup 2+}]/[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{sup 17} and 2.01x10{sup 17} cm{sup -3} corresponding to an amount of Sr cations in the collapsed phase between 9% and 23% of the total Sr{sup 2+} cations in solution. If compared to the concentration of polyacrylate expressed in moles of monomers [NaPA], a degree of site binding of r=[Sr{sup 2+}]/[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.

  20. Pt Catalyst Degradation in Aqueous and Fuel Cell Environments studied via In-Operando Anomalous Small-Angle X-ray Scattering

    SciTech Connect

    Gilbert, James A.; Kariuki, Nancy N.; Wang, Xiaoping; Kropf, A. Jeremy; Yu, Kang; Groom, Daniel J.; Ferreira, Paulo J.; Morgan, Dane; Myers, Deborah J.

    2015-08-10

    The evolution of Pt nanoparticle cathode electrocatalyst size distribution in a polymer electrolyte membrane fuel cell (PEMFC) was followed during accelerated stress tests using in-operando anomalous small-angle X-ray scattering (ASAXS). This evolution was compared to that observed in an aqueous electrolyte environment using stagnant electrolyte, flowing electrolyte, and flowing electrolyte at elevated temperature to reveal the different degradation trends in the PEMFC and aqueous environments and to determine the relevance of aqueous measurements to the stability of Pt nanoparticle catalyst in the fuel cell environment. The observed changes in the particle size distributions (PSDs) were analyzed to elucidate the extent and mechanisms of particle growth and corresponding mass and active surface area losses in the different environments. These losses indicate a Pt nanoparticle surface area loss mechanism 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. Based on the geometric surface area loss, mass loss, and mean particle size increase trends, the aqueous environment best reflecting the fuel cell environment was found to be one in which the electrolyte is flowing rather than stagnant. Pt nanoparticle surface area loss resulting from potential cycling can be inhibited by reducing the number of particles smaller than a critical particle diameter (CPD), which was found to be similar to 3.5 to similar to 4 nm, with the CPD dependent on both the cycling protocol (square wave vs triangle wave) and the catalyst environment (fuel cell, aqueous stagnant, aqueous flowing electrolyte, or elevated temperature flowing electrolyte)

  1. 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.

  2. 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.

  3. 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.

  4. Windows for small-angle X-ray scattering cryostats.

    PubMed

    Lurio, Laurence; Mulders, Norbert; Paetkau, Mark; Jemian, Pete R; Narayanan, Suresh; Sandy, Alec

    2007-11-01

    To determine the suitability of commonly used windows for small-angle X-ray scattering, a range of materials, including Kapton, (aluminized) Mylar, beryllium, high-purity aluminium foil, mica and silicon nitride have been studied. At small wavevector transfers, Q, in the range 2 x 10(-3) to 0.2 nm(-1), the scattering from Kapton, mica and beryllium is reasonably well described by power laws in Q with exponents of -3.25, -3.6 and -3.9, respectively. There are large variations in the scattering from mica, but a freshly cleaved natural mica window was by far the weakest scatterer. For applications where radiation in the infrared or visible range should be blocked, aluminized Mylar is the most suitable material. Both Mylar and Kapton can be used to make very simple demountable superfluid-tight windows using indium O-ring seals.

  5. Small-Angle X-ray Scattering (SAXS) Instrument Performance and Validation Using Silver Nanoparticles

    DTIC Science & Technology

    2016-12-01

    Using Silver Nanoparticles by Frederick L Beyer Approved for public release; distribution is unlimited. NOTICES...Small-Angle X-ray Scattering (SAXS) Instrument Performance and Validation Using Silver Nanoparticles by Frederick L Beyer Weapons and Materials...2016 4. TITLE AND SUBTITLE Small-Angle X-ray Scattering (SAXS) Instrument Performance and Validation Using Silver Nanoparticles 5a. CONTRACT

  6. Small Angle X ray Scattering (SAXS) Instrument Performance and Validation Using Silver Nanoparticles

    DTIC Science & Technology

    2016-12-01

    Using Silver Nanoparticles by Frederick L Beyer Approved for public release; distribution is unlimited. NOTICES...Small-Angle X-ray Scattering (SAXS) Instrument Performance and Validation Using Silver Nanoparticles by Frederick L Beyer Weapons and Materials...2016 4. TITLE AND SUBTITLE Small-Angle X-ray Scattering (SAXS) Instrument Performance and Validation Using Silver Nanoparticles 5a. CONTRACT

  7. Small Angle X-ray Scattering for Nanoparticle Research

    SciTech Connect

    Lee, Byeongdu; Senesi-Good, Andrew J.; Li, Tao

    2016-09-28

    X-ray scattering is a structural characterization tool that has impacted diverse fields of study. It is unique in its ability to examine materials in real time and under realistic sample environments, enabling researchers to understand morphology at nanometer and ångström length scales using complementary small and wide angle X-ray scattering (SAXS, WAXS), respectively. Herein, we focus on the use of SAXS to examine nanoscale particulate systems. We provide a theoretical foundation for X-ray scattering, considering both form factor and structure factor, as well as the use of correlation functions, which may be used to determine a particle’s size, size distribution, shape, and organization into hierarchal structures. The theory is expanded upon with contemporary use cases. Both transmission and reflection (grazing incidence) geometries are addressed, as well the combination of SAXS with other X-ray and non-X ray characterization tools. We conclude with an examination of several key areas of research where X-rays scattering has played a pivotal role, including in situ nanoparticle synthesis, nanoparticle assembly, and in operando studies of catalysts and energy storage materials. Throughout this review we highlight the unique capabilities of X-ray scattering for structural characterization of materials in their native environment.

  8. Small Angle X-ray Scattering for Nanoparticle Research

    SciTech Connect

    Li, Tao; Senesi, Andrew J.; Lee, Byeongdu

    2016-04-07

    X-ray scattering is a structural characterization tool that has impacted diverse fields of study. It is unique in its ability to examine materials in real time and under realistic sample environments, enabling researchers to understand morphology at nanometer and ångström length scales using complementary small and wide angle X-ray scattering (SAXS, WAXS), respectively. Herein, we focus on the use of SAXS to examine nanoscale particulate systems. We provide a theoretical foundation for X-ray scattering, considering both form factor and structure factor, as well as the use of correlation functions, which may be used to determine a particle’s size, size distribution, shape, and organization into hierarchal structures. The theory is expanded upon with contemporary use cases. Both transmission and reflection (grazing incidence) geometries are addressed, as well the combination of SAXS with other X-ray and non-X ray characterization tools. Furthermore, we conclude with an examination of several key areas of research where X-rays scattering has played a pivotal role, including in situ nanoparticle synthesis, nanoparticle assembly, and in operando studies of catalysts and energy storage materials. Throughout this review we highlight the unique capabilities of X-ray scattering for structural characterization of materials in their native environment.

  9. Small Angle X-ray Scattering for Nanoparticle Research

    DOE PAGES

    Li, Tao; Senesi, Andrew J.; Lee, Byeongdu

    2016-04-07

    X-ray scattering is a structural characterization tool that has impacted diverse fields of study. It is unique in its ability to examine materials in real time and under realistic sample environments, enabling researchers to understand morphology at nanometer and ångström length scales using complementary small and wide angle X-ray scattering (SAXS, WAXS), respectively. Herein, we focus on the use of SAXS to examine nanoscale particulate systems. We provide a theoretical foundation for X-ray scattering, considering both form factor and structure factor, as well as the use of correlation functions, which may be used to determine a particle’s size, size distribution,more » shape, and organization into hierarchal structures. The theory is expanded upon with contemporary use cases. Both transmission and reflection (grazing incidence) geometries are addressed, as well the combination of SAXS with other X-ray and non-X ray characterization tools. Furthermore, we conclude with an examination of several key areas of research where X-rays scattering has played a pivotal role, including in situ nanoparticle synthesis, nanoparticle assembly, and in operando studies of catalysts and energy storage materials. Throughout this review we highlight the unique capabilities of X-ray scattering for structural characterization of materials in their native environment.« less

  10. Small Angle X-ray Scattering for Nanoparticle Research.

    PubMed

    Li, Tao; Senesi, Andrew J; Lee, Byeongdu

    2016-09-28

    X-ray scattering is a structural characterization tool that has impacted diverse fields of study. It is unique in its ability to examine materials in real time and under realistic sample environments, enabling researchers to understand morphology at nanometer and angstrom length scales using complementary small and wide angle X-ray scattering (SAXS, WAXS), respectively. Herein, we focus on the use of SAXS to examine nanoscale particulate systems. We provide a theoretical foundation for X-ray scattering, considering both form factor and structure factor, as well as the use of correlation functions, which may be used to determine a particle's size, size distribution, shape, and organization into hierarchical structures. The theory is expanded upon with contemporary use cases. Both transmission and reflection (grazing incidence) geometries are addressed, as well as the combination of SAXS with other X-ray and non-X-ray characterization tools. We conclude with an examination of several key areas of research where X-ray scattering has played a pivotal role, including in situ nanoparticle synthesis, nanoparticle assembly, and operando studies of catalysts and energy storage materials. Throughout this review we highlight the unique capabilities of X-ray scattering for structural characterization of materials in their native environment.

  11. Ultra Low-{kappa} Metrology Using X-Ray Reflectivity And Small-Angle X-Ray Scattering Techniques

    SciTech Connect

    Plantier, L.; Gonchond, J.-P.; Pernot, F.; Peled, A.; Yokhin, B.; Wyon, C.; Royer, J.-C.

    2007-09-26

    The automated metrology tool, combining X-ray reflectivity XRR and small-angle X-ray scattering SAXS has been demonstrated as a capable equipment to assess standard porous Ultra low-{kappa} (ULK) metrology. Therefore those techniques have enabled characterizations of several ULK used in sub-65 nm nodes integration. Standard ULK material for 65 nm node technology has been monitored through the whole C065 integration steps using those combined techniques.

  12. A preliminary study of breast cancer diagnosis using laboratory based small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Round, A. R.; Wilkinson, S. J.; Hall, C. J.; Rogers, K. D.; Glatter, O.; Wess, T.; Ellis, I. O.

    2005-09-01

    Breast tissue collected from tumour samples and normal tissue from bi-lateral mastectomy procedures were examined using small angle x-ray scattering. Previous work has indicated that breast tissue disease diagnosis could be performed using small angle x-ray scattering (SAXS) from a synchrotron radiation source. The technique would be more useful to health services if it could be made to work using a conventional x-ray source. Consistent and reliable differences in x-ray scatter distributions were observed between samples from normal and tumour tissue samples using the laboratory based 'SAXSess' system. Albeit from a small number of samples, a sensitivity of 100% was obtained. This result encourages us to pursue the implementation of SAXS as a laboratory based diagnosis technique.

  13. Quantitative characterization of the contrast mechanisms of ultra-small angle x-ray scattering imaging.

    SciTech Connect

    Zhang, F.; Long, G. G.; Levine, L.E.; Ilavsky, J.; Jemain, P.R.; NIST

    2008-04-01

    A general treatment of X-ray imaging contrast for ultra-small-angle X-ray scattering (USAXS) imaging is presented; this approach makes use of phase propagation and dynamical diffraction theory to account quantitatively for the intensity distribution at the detector plane. Simulated results from a model system of micrometer-sized spherical SiO{sub 2} particles embedded in a polypropylene matrix show good agreement with experimental measurements. Simulations by means of a separate geometrical ray-tracing method also account for the features in the USAXS images and offer a complementary view of small-angle X-ray scattering as a contrast mechanism. The ray-tracing analysis indicates that refraction, in the form of Porod scattering, and, to a much lesser extent, X-ray reflection account for the USAXS imaging contrast.

  14. X-ray small-angle scattering from sputtered CeO{sub 2}/C bilayers

    SciTech Connect

    Haviar, S.; Dubau, M.; Khalakhan, I.; Vorokhta, M.; Matolinova, I.; Matolin, V.; Vales, V.; Endres, J.; Holy, V.; Buljan, M.; Bernstorff, S.

    2013-01-14

    Surface and interface morphology of cerium oxide/carbon bilayers used as thin-film catalysts is studied by grazing-incidence small-angle x-ray scattering, scanning electron microscopy, and atomic-force microscopy, and the dependence of the structural parameters on the thicknesses of the constituting layers is investigated. The applicability of x-ray scattering and its advantages over standard analytical methods are discussed.

  15. 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.

  16. 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.

  17. Small angle X-ray scattering study of coal soot formation

    SciTech Connect

    Winans, R. E.; Parker, J. T.; Seifert, S.; Fletcher, T. H.

    2000-02-14

    The objective of this study is to examine, by small angle X-ray scattering (SAXS), the formation of soot from individual coal particle combustion in a methane flat flame burner. The SAXS instrument at the Basic Energy Sciences Synchrotron Radiation Center (BESSRC) at the Advanced Photon Source (APS) can be used to observe both the formation of spherules and clusters since it can access length scales of 6--6000 {angstrom}. The high X-ray flux enables rapid acquisition of scattering data of various regions of the flame. SAXS data reveal particle size, shape, surface areas, and surface roughness.

  18. 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

  19. 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

    2015-07-10

    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.

  20. 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.

  1. Energy-dispersive small-angle X-ray scattering with cone collimation using X-ray capillary optics

    NASA Astrophysics Data System (ADS)

    Li, Fangzuo; Liu, Zhiguo; Sun, Tianxi

    2016-09-01

    Energy-dispersive small-angle X-ray scattering (ED-SAXS) with an innovative design of cone collimation based on an ellipsoidal single-bounce capillary (ESBC) and a polycapillary parallel X-ray lens (PPXRL) had been explored. Using this new cone collimation system, scattering angle 2θ has a theoretical minimum angle related to the mean half-opening angle of the hollow cone beam of 1.42 mrad, and with the usable X-ray energy ranging from 4 to 30 keV, the resulting observable scattering vector q is down to a minimum value of about 0.003 Å-1 (or a Bragg spacing of about 2100 Å). However, the absorption of lower energies by X-ray capillary optics, sample transmission, and detector response function limits the application range to lower energy. Cone collimation ED-SAXS experiments carried out on pure water, Lupolen, and in situ temperature-dependent measurement of diacetylenic acid/melamine micelle solid were presented at three different scattering angles 2θ of 0.18°, 0.70° and 1.18° to illustrate the new opportunities offered by this technique as well as its limitations. Also, a comparison has been made by replacing the PPXRL with a pinhole, and the result shows that cone collimation ED-SAXS based on ESBC with PPXRL was helpful in improving the signal-to-noise ratio (i.e., reducing the parasitic background scattering) than ESBC with a pinhole. The cone collimation instrument based on X-ray capillary optics could be considered as a promising tool to perform SAXS experiments, especially cone collimation ED-SAXS has potential application for the in situ temperature-dependent studying on the kinetics of phase transitions.

  2. The anomalous X-ray pulsars

    NASA Astrophysics Data System (ADS)

    Chen, Rui; Li, Xiangdong

    2002-03-01

    In the last few years it has been recognized that a group of X-ray pulsars have peculiar properties which set them apart from the majority of accreting pulars in X-ray binaries. They are called the Anomalous X-ray Pulsars (AXP). These objects are characterized by very soft X-ray spectra with low and steady X-ray fluxes, narrow-distributed spin periods, steady spin-down, no optical/infrared counterparts. Some of them may associate with supernova remnants. The nature of AXP remains mysterious. It has been suggested that AXP are accreting neutron stars, or solitary "magnetars", neutron stars with super strong magnetic fields (≍1010-1011T). In this paper we review the recent progress in the studies of AXP, and discuss the possible implications from comparison of AXP with other neutron stars, such as radio pulsars, radio quiet X-ray pulsar candidates and soft γ-ray repeaters.

  3. Small-Angle Scattering of X-Rays from Extragalactic Sources by Dust in Intervening Galaxies

    NASA Astrophysics Data System (ADS)

    Miralda-Escudé, Jordi

    1999-02-01

    Gamma-ray bursts are now known to be a cosmological population of objects, which are often accompanied by X-ray and optical afterglows. The total energy emitted in the afterglow can be similar to the energy radiated in the gamma-ray burst itself. If a galaxy containing a large column density of dust is near the line of sight to a gamma-ray burst, small-angle scattering of the X-rays due to diffraction by the dust grains will give rise to an X-ray echo of the afterglow. A measurement of the angular size of the echo at a certain time after the afterglow is observed yields a combination of the angular diameter distances to the scattering galaxy and the gamma-ray burst that can be used to constrain cosmological models in the same way as a time delay in a gravitational lens. The scattering galaxy will generally cause gravitational lensing as well, and this should modify the shape of the X-ray echo from a circular ring. The main difficulty in detecting this phenomenon is the very low flux expected for the echo. The flux can be increased when the gamma-ray burst is highly magnified by gravitational lensing, or when the deflecting galaxy is at low redshift. X-ray echoes of continuous (but variable) sources, such as quasars, may also be detectable with high-resolution instruments and would allow similar measurements.

  4. Application of small-angle X-ray scattering for differentiation among breast tumors

    PubMed Central

    Changizi, V.; Kheradmand, A. Arab; Oghabian, M. A.

    2008-01-01

    Small-angle X-ray scattering (SAXS) is an X-ray diffraction-based technique where a narrow collimated beam of X-rays is focused onto a sample and the scattered X-rays recorded by a detector. The pattern of the scattered X-rays carries information on the molecular structure of the material. As breast cancer is the most widespread cancer in women and differentiation among its tumors is important, this project compared the results of coherent X-ray scattering measurements obtained from benign and malignant breast tissues. The energy-dispersive method with a setup including X-ray tube, primary collimator, sample holder, secondary collimator and high-purity germanium (HpGe) detector was used. One hundred thirty-one breast-tissue samples, including normal, fibrocystic changes and carcinoma, were studied at the 6° scattering angle. Diffraction profiles (corrected scattered intensity versus momentum transfer) of normal, fibrocystic changes and carcinoma were obtained. These profiles showed a few peak positions for adipose (1.15 ± 0.06 nm−1), mixed normal (1.15 ± 0.06 nm−1 and 1.4 ± 0.04 nm−1), fibrocystic changes (1.46 ± 0.05 nm−1 and 1.74 ± 0.04 nm−1) and carcinoma (1.55 ± 0.04 nm−1, 1.73 ± 0.06 nm−1, 1.85 ± 0.05 nm−1). We were able to differentiate between normal, fibrocystic changes (benign) and carcinoma (malignant) breast tissues by SAXS. However, we were unable to differentiate between different types of carcinoma. PMID:20041048

  5. Quaternary structure built from subunits combining NMR and small-angle x-ray scattering data.

    PubMed Central

    Mattinen, Maija-Liisa; Pääkkönen, Kimmo; Ikonen, Teemu; Craven, Jeremy; Drakenberg, Torbjörn; Serimaa, Ritva; Waltho, Jonathan; Annila, Arto

    2002-01-01

    A new principle in constructing molecular complexes from the known high-resolution domain structures joining data from NMR and small-angle x-ray scattering (SAXS) measurements is described. Structure of calmodulin in complex with trifluoperazine was built from N- and C-terminal domains oriented based on residual dipolar couplings measured by NMR in a dilute liquid crystal, and the overall shape of the complex was derived from SAXS data. The residual dipolar coupling data serves to reduce angular degrees of freedom, and the small-angle scattering data serves to confine the translational degrees of freedom. The complex built by this method was found to be consistent with the known crystal structure. The study demonstrates how approximate tertiary structures of modular proteins or quaternary structures composed of subunits can be assembled from high-resolution structures of domains or subunits using mutually complementary NMR and SAXS data. PMID:12124297

  6. Characterization of porous materials using combined small-angle X-ray and neutron scattering techniques

    SciTech Connect

    Hu, Naiping; Borkar, Neha; Kohls, Doug; Schaefer, Dale W.

    2014-09-24

    A combination of ultra small angle X-ray scattering (USAXS) and ultra small angle neutron scattering (USANS) is used to characterize porous materials. The analysis methods yield quantitative information, including the mean skeletal chord length, mean pore chord length, skeletal density, and composition. A mixed cellulose ester (MCE) membrane with a manufacturer-labeled pore size of 0.1 {mu}m was used as a model to elucidate the specifics of the method. Four approaches describing four specific scenarios (different known parameters and form of the scattering data) are compared. Pore chords determined using all four approaches are in good agreement with the scanning electron microscopy estimates but are larger than the manufacturer's nominal pore size. Our approach also gives the average chord of the skeletal solid (struts) of the membrane, which is also consistent for all four approaches. Combined data from USAXS and USANS gives the skeletal density and the strut composition.

  7. Integrative structural modeling with small angle X-ray scattering profiles

    PubMed Central

    2012-01-01

    Recent technological advances enabled high-throughput collection of Small Angle X-ray Scattering (SAXS) profiles of biological macromolecules. Thus, computational methods for integrating SAXS profiles into structural modeling are needed more than ever. Here, we review specifically the use of SAXS profiles for the structural modeling of proteins, nucleic acids, and their complexes. First, the approaches for computing theoretical SAXS profiles from structures are presented. Second, computational methods for predicting protein structures, dynamics of proteins in solution, and assembly structures are covered. Third, we discuss the use of SAXS profiles in integrative structure modeling approaches that depend simultaneously on several data types. PMID:22800408

  8. 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

  9. 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.

  10. Correlation between fractal dimension and surface characterization by small angle X-ray scattering in marble.

    PubMed

    Salinas-Nolasco, Manlio Favio; Méndez-Vivar, Juan

    2010-03-16

    Among several analysis techniques applied to the study of surface passivation using dicarboxylic acids, small angle X-ray scattering (SAXS) has proved to be relevant in the physicochemical interpretation of the surface association resulting between calcium carbonate and the molecular structure of malonic acid. It is possible to establish chemical affinity principles through bidimensional geometric analysis in terms of the fractal dimension obtained experimentally by SAXS. In this Article, we present results about the adsorption of malonic acid on calcite, using theoretical and mathematical principles of the fractal dimension.

  11. 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)

  12. 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.

  13. Structural Analysis of the Flagellar Component Proteins in Solution by Small Angle X-Ray Scattering.

    PubMed

    Lee, Lawrence K

    2017-01-01

    Small angle X-ray scattering is an increasingly utilized method for characterizing the shape and structural properties of proteins in solution. The technique is amenable to very large protein complexes and to dynamic particles with different conformational states. It is therefore ideally suited to the analysis of some flagellar motor components. Indeed, we recently used the method to analyze the solution structure of the flagellar motor protein FliG, which when combined with high-resolution snapshots of conformational states from crystal structures, led to insights into conformational transitions that are important in mediating the self-assembly of the bacterial flagellar motor. Here, we describe procedures for X-ray scattering data collection of flagellar motor components, data analysis, and interpretation.

  14. A Laboratory Scale Critical-Dimension Small-Angle X-ray Scattering Instrument

    SciTech Connect

    Ho, Derek L.; Wang Chengqing; Lin, Eric K.; Jones, Ronald L.; Wu Wenli

    2007-09-26

    New methods for critical dimension (CD) measurements may be needed to enable the detailed characterization of nanoscale structures produced in the semiconductor industry and for nanotechnology applications. In earlier work, small angle x-ray scattering (SAXS) measurements with synchrotron sources have shown promise in meeting several grand challenges for CD metrology. However, it is not practical to depend upon x-ray synchrotron sources, which are large national facilities with limitations in the number of available instruments. To address this problem, a laboratory scale SAXS instrument for critical dimension measurements on periodic nanoscale patterns has been designed, installed, and tested. The system possesses two configurations, SAXS and ultra-small-angle x-ray scattering (USAXS), with a radiation target of either copper or molybdenum. With these configurations, the instrument is capable of accessing scattering angles that probe length scales ranging from ca. 0.5 nm to 2 {mu}m. In this work, we compare CD-SAXS measurements taken from a synchrotron-based SAXS at the Advanced Photon Source of the Argonne National Laboratory with those from the National Institute of Standards and Technology laboratory-scale SAXS instrument. The results from standard line/space gratings possessing periodic line-space patterns with CDs of tens to hundreds of nanometers show that the laboratory-scale system can quantitatively measure parameters, such as the pitch, line width, height, line-width roughness and sidewall angle. These results show that laboratory-scale measurements are feasible and can be used for research and development purposes or to assist calibration of optical scatterometry and CD-scanning electron microscopy instruments. The primary limitation of the measurement is that the data collection rate is unacceptably slow for production metrology because of the significantly lower x-ray beam fluxes currently available.

  15. Probing the Complex Architecture of Multimodular Carbohydrate-Active Enzymes Using a Combination of Small Angle X-Ray Scattering and X-Ray Crystallography.

    PubMed

    Czjzek, Mirjam; Ficko-Blean, Elizabeth

    2017-01-01

    The various modules in multimodular carbohydrate-active enzymes (CAZymes) may function in catalysis, carbohydrate binding, protein-protein interactions or as linkers. Here, we describe how combining the biophysical techniques of Small Angle X-ray Scattering (SAXS) and macromolecular X-ray crystallography (XRC) provides a powerful tool for examination into questions related to overall structural organization of ultra multimodular CAZymes.

  16. A Microbeam Small-Angle X-ray Scattering Study on Enamel Crystallites in Subsurface Lesion

    NASA Astrophysics Data System (ADS)

    Yagi, N.; Ohta, N.; Matsuo, T.; Tanaka, T.; Terada, Y.; Kamasaka, H.; Kometani, T.

    2010-10-01

    The early caries lesion in bovine tooth enamel was studied by two different X-ray diffraction systems at the SPring-8 third generation synchrotron radiation facility. Both allowed us simultaneous measurement of the small and large angle regions. The beam size was 6μm at BL40XU and 50μm at BL45XU. The small-angle scattering from voids in the hydroxyapatite crystallites and the wide-angle diffraction from the hydroxyapatite crystals were observed simultaneously. At BL40XU an X-ray image intensifier was used for the small-angle and a CMOS flatpanel detector for the large-angle region. At BL45XU, a large-area CCD detector was used to cover both regions. A linear microbeam scan at BL40XU showed a detailed distribution of voids and crystals and made it possible to examine the structural details in the lesion. The two-dimensional scan at BL45XU showed distribution of voids and crystals in a wider region in the enamel. The simultaneous small- and wide-angle measurement with a microbeam is a powerful tool to elucidate the mechanisms of demineralization and remineralization in the early caries lesion.

  17. 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.

  18. Upgrade of small angle x-ray scattering beamline BL-6A at the photon factory

    SciTech Connect

    Takagi, H. Igarashi, N.; Mori, T.; Saijo, S.; Nagatani, Y.; Kosuge, T.; Shimizu, N.; Ohta, H.

    2016-07-27

    BL-6A has been operational since 2011 as a small angle X-ray scattering (SAXS) beamline at the Photon Factory (PF), and beginning in 2013 its old components and systems, which were mainly inside the experimental hutch, have been extensively updated. Both the vacuum-passes located between the sample stage and the detector and the fixed surface plate have been replaced by a new semi-automatic diffractometer. These upgrades allow simultaneous SAXS/WAXS experiments and grazing-incidence small angle X-ray scattering (GISAXS) measurements to be conducted. The hybrid pixel detector PILATUS3 1M is installed for SAXS, and PILATUS 100K is available as a WAXS detector. Additionally, a pinhole equipped with a micro-ion chamber is available to realize a lower-background and higher-resolution of low angles. Moreover, in a simultaneous SAXS/WAXS experiment, we developed a new beam stop with an embedded photodiode. Thus, BL-6A has evolved into a multipurpose beamline capable of dealing with various types of samples and experimental techniques.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    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.

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

    PubMed

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

    2014-12-01

    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.

  1. 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

  2. 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.

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

    DOE PAGES

    Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; ...

    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

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

    PubMed

    Singh, Marsha A; Groves, Michael N

    2009-05-01

    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.

  5. 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.

  6. 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.

  7. NIST Standard Reference Material 3600: Absolute Intensity Calibration Standard for Small-Angle X-ray Scattering.

    PubMed

    Allen, Andrew J; Zhang, Fan; Kline, R Joseph; Guthrie, William F; Ilavsky, Jan

    2017-04-01

    The certification of a new standard reference material for small-angle scattering [NIST Standard Reference Material (SRM) 3600: Absolute Intensity Calibration Standard for Small-Angle X-ray Scattering (SAXS)], based on glassy carbon, is presented. Creation of this SRM relies on the intrinsic primary calibration capabilities of the ultra-small-angle X-ray scattering technique. This article describes how the intensity calibration has been achieved and validated in the certified Q range, Q = 0.008-0.25 Å(-1), together with the purpose, use and availability of the SRM. The intensity calibration afforded by this robust and stable SRM should be applicable universally to all SAXS instruments that employ a transmission measurement geometry, working with a wide range of X-ray energies or wavelengths. The validation of the SRM SAXS intensity calibration using small-angle neutron scattering (SANS) is discussed, together with the prospects for including SANS in a future renewal certification.

  8. Mobile x-ray complex based on ironless pulsed betatrons. X-ray complex conception for small-angle tomography

    NASA Astrophysics Data System (ADS)

    Kozlov, S. G.; Kuropatkin, Yu P.; Nizhegorodtsev, V. I.; Savchenko, K. V.; Selemir, V. D.; Urlin, E. V.; Shamro, O. A.

    2017-05-01

    The conception of creating mobile radiographic complex based on ironless pulsed betatrons is proposed for radiography of dynamic objects having large optical thicknesses. Realization of this conception allows: a) optimizing geometry of the hydrodynamic experiment at the expense of the change of the radiation source and recorder position relatively to the test object, located in the explosion-proof chamber(EPC). Thus, it lets the intensity of the x-ray radiation be increased twice in the recorder plane as compared with available Russian complexes; b) creating an efficient environment protection system at the expense of localization of dangerous explosion products, and a shock wave connected with them; c) significantly decreasing the cost of radiographic complexes, if not building heavy protective casemates and their infrastructure. Instead of them it is possible to use cheap rapidly erected constructions. The mobile radiographic complex is described. Its characteristics, obtained during the testing powering were provided. Thickness of the lead test at 1m from the tantalum target at the limiting energy of the betatron electron beam Elim∼12 MeV( it is determined by the value of a capacitive storage of the pulsed powering system of the electromagnet) was ∼115 mm. Conception of a multibeam complex creation based on ironless pulsed betatrons for small-angle tomography was also considered.

  9. 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.

  10. 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

  11. 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.

  12. Quantitative evaluation of statistical errors in small-angle X-ray scattering measurements.

    PubMed

    Sedlak, Steffen M; Bruetzel, Linda K; Lipfert, Jan

    2017-04-01

    A new model is proposed for the measurement errors incurred in typical small-angle X-ray scattering (SAXS) experiments, which takes into account the setup geometry and physics of the measurement process. The model accurately captures the experimentally determined errors from a large range of synchrotron and in-house anode-based measurements. Its most general formulation gives for the variance of the buffer-subtracted SAXS intensity σ(2)(q) = [I(q) + const.]/(kq), where I(q) is the scattering intensity as a function of the momentum transfer q; k and const. are fitting parameters that are characteristic of the experimental setup. The model gives a concrete procedure for calculating realistic measurement errors for simulated SAXS profiles. In addition, the results provide guidelines for optimizing SAXS measurements, which are in line with established procedures for SAXS experiments, and enable a quantitative evaluation of measurement errors.

  13. Small angle x-ray scattering studies of carbon anodes used in lithium rechargeable batteries.

    SciTech Connect

    Sandi, G.; Carrado, K. A.; Winans, R. E.; Seifert, S.; Johnson, C. S.

    1999-11-16

    In ANL laboratories, disordered carbons with predictable surface area and porosity properties have been prepared using inorganic templates containing well defined pore sizes. The carbons have been tested in electrochemical cells as anodes in lithium secondary batteries. They deliver high specific capacity and display excellent performance in terms of the number of cycles run. In situ small angle X-ray scattering (SAXS) during electrochemical cycling was carried out at the Advanced Photon Source, at ANL. In order to monitor the carbon electrode structural changes upon cycling, an electrochemical cell was specially designed to allow for the application of electrical current and the collection of SAXS data at the same time. Results show that upon cycling the structure of the carbon remains unchanged, which is desirable in reversible systems.

  14. 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.

  15. 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.

  16. Quantitative evaluation of statistical errors in small-angle X-ray scattering measurements

    PubMed Central

    Sedlak, Steffen M.; Bruetzel, Linda K.; Lipfert, Jan

    2017-01-01

    A new model is proposed for the measurement errors incurred in typical small-angle X-ray scattering (SAXS) experiments, which takes into account the setup geometry and physics of the measurement process. The model accurately captures the experimentally determined errors from a large range of synchrotron and in-house anode-based measurements. Its most general formulation gives for the variance of the buffer-subtracted SAXS intensity σ2(q) = [I(q) + const.]/(kq), where I(q) is the scattering intensity as a function of the momentum transfer q; k and const. are fitting parameters that are characteristic of the experimental setup. The model gives a concrete procedure for calculating realistic measurement errors for simulated SAXS profiles. In addition, the results provide guidelines for optimizing SAXS measurements, which are in line with established procedures for SAXS experiments, and enable a quantitative evaluation of measurement errors. PMID:28381982

  17. Titanium sample holder for small-angle x-ray scattering measurements of supercritical aqueous solutions

    NASA Astrophysics Data System (ADS)

    Morita, Takeshi; Kusano, Kouhei; Nishikawa, Keiko; Miyagi, Hiroshi; Shimokawa, Yuji; Matsuo, Hitoshi

    2001-07-01

    A titanium high-temperature sample holder for small-angle x-ray scattering (SAXS) was newly constructed. It is applicable to aqueous solutions in the supercritical state up to 750 K and 50 MPa. The use of high-tension titanium for assemblies and high-purity titanium for gaskets enables us to apply the holder to fluids in extreme conditions such as supercritical water, supercritical aqueous solutions, and other corrosive hydrothermal aqueous solutions. Details are presented for the diamond window sealed by a flange set made of titanium. The seal is superior to the conventional unsupported-area-seal by a screw cap and plug for the titanium high-temperature sample holder. As a test of the instrument, the SAXS experiments for supercritical water were made at the isothermal condition of T=662 K with pressures from 22.8 to 29.3 MPa. The first SAXS measurements for supercritical aqueous solution were also carried out.

  18. Characterization of Nanocomposite filler Morphology using Ultra Small-Angle X-ray Scattering

    SciTech Connect

    Justice, Ryan S.; Schaefer, Dale W.

    2010-10-22

    Loading polymer matrices with nanoscale fillers is widely believed to have the potential to push polymer properties to extreme values. Realization of anticipated properties, however, has proven elusive. Recent nanocomposite research suggests better characterization of the large-scale morphology will provide insight explaining these shortfalls. This work will present ultra-small angle X-ray scattering as a viable tool for elucidating the hierarchical filler morphology that exists within polymer nanocomposites. Scattering analysis tools developed by our group will be applied to scattering data from nanocomposites filled with carbon nanotubes, layered silicates, and colloidal silica. The relationship between imaging data and scattering data will be discussed in the context of filler dispersion. Finally, the impact of large-scale filler morphology on mechanical and electrical properties will be discussed.

  19. Small Angle X-ray Diffraction Study of DNA—Cationic Liposomes Aggregates

    NASA Astrophysics Data System (ADS)

    Pullmannová, Petra; Uhríková, Daniela; Funari, Sergio S.; Lacko, Ivan; Devínsky, Ferdinand; Balgavý, Pavol

    2010-01-01

    The microstructure of DNA—dioleoylphosphatidylethanolamine (DOPE)—propane-1,3-diyl-bis(dodecyldimethylammonium bromide) (C3GS12) aggregates as a function of the C3GS12:DOPE molar ratio and temperature was investigated using small angle X-ray diffraction. At 20° C, we observe a condensed lamellar phase (Lαc) with the lattice parameter d˜6.8-6.2 nm and the DNA—DNA distance dDNA˜5.8-3.2 nm decreasing with increasing content of C3GS12 in the phospholipid bilayer. Increase in temperature induces a phase transition from Lαc phase to condensed inverted hexagonal phase (HIIc). The temperature of the Lαc→HIIc phase transition increases with increasing C3GS12:DOPE molar ratio.

  20. Small angle x-ray scattering and electron microscopy of nanoparticles formed in an electrical arc

    NASA Astrophysics Data System (ADS)

    Carvou, E.; Garrec, J. L. Le; Pérez, J.; Praquin, J.; Djeddi, M.; Mitchell, J. B. A.

    2013-03-01

    Small Angle X-ray Scattering has been used to characterize nanoparticles generated by electrical arcing between metallic (AgSnO2) electrodes. The particles are found to have diameters between 30 and 40 nm and display smooth surfaces suggesting that they are either in liquid form or have solidified from the liquid state. Particles collected around the electrodes were analyzed by Transmission Electron Microscopy and were seen to be much larger than those seen in the SAXS measurement, to be spherical in form and composed of silver metal with irregular tin oxide particles deposited on their surface. Mixed metal nanoparticles can have important practical applications and the use of mixed sintered electrodes may be a direct method for their production.

  1. Small-angle x-ray scattering study of polymer structure: Carbosilane dendrimers in hexane solution

    NASA Astrophysics Data System (ADS)

    Shtykova, E. V.; Feigin, L. A.; Volkov, V. V.; Malakhova, Yu. N.; Streltsov, D. R.; Buzin, A. I.; Chvalun, S. N.; Katarzhanova, E. Yu.; Ignatieva, G. M.; Muzafarov, A. M.

    2016-09-01

    The three-dimensional organization of monodisperse hyper-branched macromolecules of regular structure—carbosilane dendrimers of zero, third, and sixth generations—has been studied by small-angle X-ray scattering (SAXS) in solution. The use of modern methods of SAXS data interpretation, including ab initio modeling, has made it possible to determine the internal architecture of the dendrimers in dependence of the generation number and the number of cyclosiloxane end groups (forming the shell of dendritic macromolecules) and show dendrimers to be spherical. The structural results give grounds to consider carbosilane dendrimers promising objects for forming crystals with subsequent structural analysis and determining their structure with high resolution, as well as for designing new materials to be used in various dendrimer-based technological applications.

  2. 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.

  3. Characterization of Nanocellulose Using Small-Angle Neutron, X-ray, and Dynamic Light Scattering Techniques.

    PubMed

    Mao, Yimin; Liu, Kai; Zhan, Chengbo; Geng, Lihong; Chu, Benjamin; Hsiao, Benjamin S

    2017-02-16

    Nanocellulose extracted from wood pulps using TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl radical)-mediated oxidation and sulfuric acid hydrolysis methods was characterized by small-angle neutron scattering (SANS), small-angle X-ray scattering (SAXS), and dynamic light scattering (DLS) techniques. The dimensions of this nanocellulose (TEMPO-oxidized cellulose nanofiber (TOCN) and sulfuric acid hydrolyzed cellulose nanocrystal (SACN)) revealed by the different scattering methods were compared with those characterized by transmission electron microscopy (TEM). The SANS and SAXS data were analyzed using a parallelepiped-based form factor. The width and thickness of the nanocellulose cross section were ∼8 and ∼2 nm for TOCN and ∼20 and ∼3 nm for SACN, respectively, where the fitting results from SANS and SAXS profiles were consistent with each other. DLS was carried out under both the VV mode with the polarizer and analyzer parallel to each other and the HV mode having them perpendicular to each other. Using rotational and translational diffusion coefficients obtained under the HV mode yielded a nanocellulose length qualitatively consistent with that observed by TEM, whereas the length derived by the translational diffusion coefficient under the VV mode appeared to be overestimated.

  4. Small-angle x-ray scattering investigation of the solution structure of troponin C

    SciTech Connect

    Hubbard, S.R.; Hodgson, K.O.; Doniach, S.

    1988-03-25

    X-ray crystallographic studies of troponin C have revealed a novel protein structure consisting of two globular domains, each containing two Ca/sup 2 +/-binding sites, connected via a nine-turn alpha-helix, three turns of which are fully exposed to solvent. Since the crystals were grown at pH approximately 5, it is of interest to determine whether this structure is applicable to the protein in solution under physiological conditions. We have used small-angle x-ray scattering to examine the solution structure of troponin C at pH 6.8 and the effect of Ca/sup 2 +/ on the structure. The scattering data are consistent with an elongated structure in solution with a radius of gyration of approximately 23.0 A, which is quite comparable to that computed for the crystal structure. The experimental scattering profile and the scattering profile computed from the crystal structure coordinates do, however, exhibit differences at the 40-A level. A weak Ca/sup 2 +/-facilitated dimerization of troponin C was observed. The data rule out large Ca/sup 2 +/-induced structural changes, indicating rather that the molecule with Ca/sup 2 +/ bound is only slightly more compact than the Ca/sup 2 +/-free molecule.

  5. 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

  6. 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.

  7. 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

  8. Synchrotron-based small-angle X-ray scattering of proteins in solution.

    PubMed

    Skou, Soren; Gillilan, Richard E; Ando, Nozomi

    2014-07-01

    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. 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 use 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 nonspecialist. 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. 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 before the experiment.

  9. Global analysis of riboswitches by small-angle X-ray scattering and calorimetry

    PubMed Central

    Zhang, Jinwei; Jones, Christopher P.; Ferré-D’Amaré, Adrian R.

    2014-01-01

    Riboswitches are phylogenetically widespread non-coding mRNA domains that directly bind cellular metabolites and regulate transcription, translation, RNA stability or splicing via alternative RNA structures modulated by ligand binding. The details of ligand recognition by many riboswitches have been elucidated using X-ray crystallography and NMR. However, the global dynamics of riboswitch-ligand interactions and their thermodynamic driving forces are less understood. By compiling the work of many laboratories investigating riboswitches using small-angle X-ray scattering (SAXS) and isothermal titration calorimetry (ITC), we uncover general trends and common themes. There is a pressing need for community-wide consensus experimental conditions to allow results of riboswitch studies to be compared rigorously. Nonetheless, our meta-analysis reveals considerable diversity in the extent to which ligand binding reorganizes global riboswitch structures. It also demonstrates a wide spectrum of enthalpy-entropy compensation regimes across riboswitches that bind a diverse set of ligands, giving rise to a relatively narrow range of physiologically relevant free energies and ligand affinities. From the strongly entropy-driven binding of glycine to the predominantly enthalpy-driven binding of c-di-GMP to their respective riboswitches, these distinct thermodynamic signatures reflect the versatile strategies employed by RNA to adapt to the chemical natures of diverse ligands. Riboswitches have evolved to use a combination of long-range tertiary interactions, conformational selection, and induced fit to work with distinct ligand structure, charge, and solvation properties. PMID:24769285

  10. 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

    2011-06-02

    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.

  11. Quantifying radiation damage in biomolecular small-angle X-ray scattering.

    PubMed

    Hopkins, Jesse B; Thorne, Robert E

    2016-06-01

    Small-angle X-ray scattering (SAXS) is an increasingly popular technique that provides low-resolution structural information about biological macromolecules in solution. Many of the practical limitations of the technique, such as minimum required sample volume, and of experimental design, such as sample flow cells, are necessary because the biological samples are sensitive to damage from the X-rays. Radiation damage typically manifests as aggregation of the sample, which makes the collected data unreliable. However, there has been little systematic investigation of the most effective methods to reduce damage rates, and results from previous damage studies are not easily compared with results from other beamlines. Here a methodology is provided for quantifying radiation damage in SAXS to provide consistent results between different experiments, experimenters and beamlines. These methods are demonstrated on radiation damage data collected from lysozyme, glucose isomerase and xylanase, and it is found that no single metric is sufficient to describe radiation damage in SAXS for all samples. The radius of gyration, molecular weight and integrated SAXS profile intensity constitute a minimal set of parameters that capture all types of observed behavior. Radiation sensitivities derived from these parameters show a large protein dependence, varying by up to six orders of magnitude between the different proteins tested. This work should enable consistent reporting of radiation damage effects, allowing more systematic studies of the most effective minimization strategies.

  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. Small-angle x-ray scattering study on the structure of microcrystalline and nanofibrillated cellulose

    NASA Astrophysics Data System (ADS)

    Leppänen, Kirsi; Pirkkalainen, Kari; Penttilä, Paavo; Sievänen, Jenni; Kotelnikova, Nina; Serimaa, Ritva

    2010-10-01

    The effects of different solvents on the structure of microcrystalline and nanofibrillated cellulose (MCC, NFC) were studied using small-angle x-ray scattering (SAXS). MCC was immersed in water, ethanol, and acetone, and NFC was immersed only in water and ethanol, but studied also in the form of foam-like water-NFC-gel in wet, air-dried and re-wet states. The solvent affected the average chord length, which reveals the typical length scale of the structure of the sample: 2.4 ± 0.1 nm was obtained for MCC-water, 2.5 ± 0.1 nm for re-wet NFC-gel, 1.6 ± 0.1 nm for MCC-ethanol, 1.2 ± 0.1 nm for NFC-ethanol, and 1.3 ± 0.1 nm for MCC-acetone. The specific surface of cellulose increased strongly when MCC and NFC were immersed in the solvents compared to dry cellulose. The specific surface of cellulose was determined to be larger for NFC-water than MCC-water, and slightly larger for dry NFC powder than for dry MCC, which can be explained by the fact that the width of cellulose crystallites perpendicular to the cellulose chain direction was slightly larger in MCC than in NFC on the basis of wide-angle x-ray scattering results.

  14. Small Angle X-Ray Scattering from Lipid-Bound Myelin Basic Protein in Solution

    PubMed Central

    Haas, H.; Oliveira, C. L. P.; Torriani, I. L.; Polverini, E.; Fasano, A.; Carlone, G.; Cavatorta, P.; Riccio, P.

    2004-01-01

    The structure of myelin basic protein (MBP), purified from the myelin sheath in both lipid-free (LF-MBP) and lipid-bound (LB-MBP) forms, was investigated in solution by small angle x-ray scattering. The water-soluble LF-MBP, extracted at pH < 3.0 from defatted brain, is the classical preparation of MBP, commonly regarded as an intrinsically unfolded protein. LB-MBP is a lipoprotein-detergent complex extracted from myelin with its native lipidic environment at pH > 7.0. Under all conditions, the scattering from the two protein forms was different, indicating different molecular shapes. For the LB-MBP, well-defined scattering curves were obtained, suggesting that the protein had a unique, compact (but not globular) structure. Furthermore, these data were compatible with earlier results from molecular modeling calculations on the MBP structure which have been refined by us. In contrast, the LF-MBP data were in accordance with the expected open-coil conformation. The results represent the first direct structural information from x-ray scattering measurements on MBP in its native lipidic environment in solution. PMID:14695288

  15. 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.

  16. 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.

  17. Planar small-angle x-ray scattering imaging of phantoms and biological samples

    NASA Astrophysics Data System (ADS)

    Choi, M.; Badano, A.

    2017-04-01

    Coherent small-angle x-ray scattering (SAXS) provides molecular and nanometer-scale structural information. By capturing SAXS data at multiple locations across a sample, we obtained planar images and observed improved contrast given by the difference in the material scattering cross sections. We use phantoms made with 3D printing techniques, with tissue-mimicking plastic (PMMA), and with a highly scattering reference material (AgBe), which were chosen because of their well characterized scattering cross section to demonstrate and characterize the planar imaging of a laboratory SAXS system. We measure 1.07 and 2.14 nm-1 angular intensity maps for AgBe, 9.5 nm-1 for PMMA, and 12.3 nm-1 for Veroclear. The planar SAXS images show material discrimination based on their cross sectional features. The image signal-to-noise ratio (SNR) of each q image was dependent on exposure time and x-ray flux. We observed a lower SNR (91 ± 48) at q angles where no characteristic peaks for either material exist. To improve the visualization of the acquired data by utilizing all q-binned data, we describe a weighted-sum presentation method with a priori knowledge of relevant cross sections to improve the SNR (10 000 ± 6400) over the SNR from a single q-image at 1.07 nm-1 (1100 ± 620). In addition, we describe planar SAXS imaging of a mouse brain slice showing differentiation of tissue types as compared to a conventional absorption-based x-ray imaging technique.

  18. Self crowding of globular proteins studied by small-angle x-ray scattering.

    PubMed

    Goldenberg, David P; Argyle, Brian

    2014-02-18

    Small-angle x-ray scattering (SAXS) was used to study the behavior of equine metmyoglobin (Mb) and bovine pancreatic trypsin inhibitor (BPTI) at concentrations up to 0.4 and 0.15 g/mL, respectively, in solutions also containing 50% D2O and 1 M urea. For both proteins, significant effects because of interference between x-rays scattered by different molecules (interparticle interference) were observed, indicating nonideal behavior at high concentrations. The experimental data were analyzed by comparison of the observed scattering profiles with those predicted by crystal structures of the proteins and a hard-sphere fluid model used to represent steric exclusion effects. The Mb scattering data were well fit by the hard-sphere model using a sphere radius of 18 Å, only slightly smaller than that estimated from the three-dimensional structure (20 Å). In contrast, the scattering profiles for BPTI in phosphate buffer displayed substantially less pronounced interparticle interference than predicted by the hard-sphere model and the radius estimated from the known structure of the protein (15 Å). Replacing the phosphate buffer with 3-(N-morpolino)propane sulfonic acid (MOPS) led to increased interparticle interference, consistent with a larger effective radius and suggesting that phosphate ions may mediate attractive intermolecular interactions, as observed in some BPTI crystal structures, without the formation of stable oligomers. The scattering data were also used to estimate second virial coefficients for the two proteins: 2.0 ×10(-4) cm(3)mol/g(2) for Mb in phosphate buffer, 1.6 ×10(-4) cm(3)mol/g(2) for BPTI in phosphate buffer and 9.2 ×10(-4) cm(3)mol/g(2) for BPTI in MOPS. The results indicate that the behavior of Mb, which is nearly isoelectric under the conditions used, is well described by the hard-sphere model, but that of BPTI is considerably more complex and is likely influenced by both repulsive and attractive electrostatic interactions. The hard

  19. Self Crowding of Globular Proteins Studied by Small-Angle X-Ray Scattering

    PubMed Central

    Goldenberg, David P.; Argyle, Brian

    2014-01-01

    Small-angle x-ray scattering (SAXS) was used to study the behavior of equine metmyoglobin (Mb) and bovine pancreatic trypsin inhibitor (BPTI) at concentrations up to 0.4 and 0.15 g/mL, respectively, in solutions also containing 50% D2O and 1 M urea. For both proteins, significant effects because of interference between x-rays scattered by different molecules (interparticle interference) were observed, indicating nonideal behavior at high concentrations. The experimental data were analyzed by comparison of the observed scattering profiles with those predicted by crystal structures of the proteins and a hard-sphere fluid model used to represent steric exclusion effects. The Mb scattering data were well fit by the hard-sphere model using a sphere radius of 18 Å, only slightly smaller than that estimated from the three-dimensional structure (20 Å). In contrast, the scattering profiles for BPTI in phosphate buffer displayed substantially less pronounced interparticle interference than predicted by the hard-sphere model and the radius estimated from the known structure of the protein (15 Å). Replacing the phosphate buffer with 3-(N-morpolino)propane sulfonic acid (MOPS) led to increased interparticle interference, consistent with a larger effective radius and suggesting that phosphate ions may mediate attractive intermolecular interactions, as observed in some BPTI crystal structures, without the formation of stable oligomers. The scattering data were also used to estimate second virial coefficients for the two proteins: 2.0 ×10-4 cm3mol/g2 for Mb in phosphate buffer, 1.6 ×10-4 cm3mol/g2 for BPTI in phosphate buffer and 9.2 ×10-4 cm3mol/g2 for BPTI in MOPS. The results indicate that the behavior of Mb, which is nearly isoelectric under the conditions used, is well described by the hard-sphere model, but that of BPTI is considerably more complex and is likely influenced by both repulsive and attractive electrostatic interactions. The hard-sphere model may be

  20. Grazing incidence small-angle X-ray scattering microtomography demonstrated on a self-ordered dried drop of nanoparticles.

    PubMed

    Kuhlmann, Marion; Feldkamp, Jan M; Patommel, Jens; Roth, Stephan V; Timmann, Andreas; Gehrke, Rainer; Müller-Buschbaum, Peter; Schroer, Christian G

    2009-07-07

    We combine grazing-incidence small-angle X-ray scattering (GISAXS) with scanning X-ray microtomography to investigate the nanostructure in a dried gold/polystyrene nanocomposite drop. Local GISAXS structure factors are reconstructed at each position on the surface of this two-dimensionally heterogeneous sample with 30 microm pixel size. Evidence for four types of self-assembled colloidal crystalline structures is provided by the reconstructed data of the drop demonstrating the feasibility of the method.

  1. Nano-Scale Morphology of Melanosomes Revealed by Small-Angle X-Ray Scattering

    PubMed Central

    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

  2. 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.

  3. Recent improvements in small angle x-ray diffraction for the study of muscle physiology

    NASA Astrophysics Data System (ADS)

    Reconditi, Massimo

    2006-10-01

    The molecular mechanism of muscle contraction is one of the most important unresolved problems in biology and biophysics. Notwithstanding the great advances of recent years, it is not yet known in detail how the molecular motor in muscle, the class II myosin, converts the free energy of ATP hydrolysis into work by interacting with its track, the actin filament; neither is it understood how the high efficiency in energy conversion depends on the cooperative action of myosin motors working in parallel along the actin filament. Research in muscle contraction involves the combination of mechanical, biochemical and structural methods in studies that span from tissue to single molecule. Therefore, more than for any other research field, progress in the comprehension of muscle contraction at the molecular level is related to, and in turn contributes to, the advancement of methods in biophysics. This review will focus on the progress achieved by time-resolved small angle x-ray scattering (SAXS) from muscle, an approach made possible by the highly ordered arrangement of both the contractile proteins myosin and actin in the ca 2 µm long structural unit, the sarcomere, that repeats along the whole length of the muscle cell. Among time-resolved structural techniques, SAXS has proved to be the most powerful method of investigation, as it allows the molecular motor to be studied in situ, in intact single muscle cells, where it is possible to combine the structural study with fast mechanical methods that synchronize the action of the molecular motors. The latest development of this technique allows Angstrom-scale measurements of the axial movement of the motors that pull the actin filament towards the centre of the sarcomere, by exploiting the x-ray interference between the two arrays of myosin motors in the two halves of the sarcomere.

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

    PubMed

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

    2011-07-01

    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(13) photons is focused to a ~100-nm spot diameter, provided that the effects of solvent background can be reduced sufficiently.

  5. RECENT IMPROVEMENTS IN SMALL ANGLE X-RAY DIFFRACTION FOR THE STUDY OF MUSCLE PHYSIOLOGY.

    PubMed

    Reconditi, Massimo

    2006-10-01

    The molecular mechanism of muscle contraction is one of the most important unresolved problems in Biology and Biophysics. Notwithstanding the great advances of recent years, it is not yet known in detail how the molecular motor in muscle, the class II myosin, converts the free energy of ATP hydrolysis into work by interacting with its track, the actin filament, neither it is understood how the high efficiency in energy conversion depends on the cooperative action of myosin motors working in parallel along the actin filament. Researches in muscle contraction imply the combination of mechanical, biochemical and structural methods in studies that span from tissue to single molecule. Therefore, more than for any other research field, progresses in the comprehension of muscle contraction at molecular level are related to, and in turn contribute to, the advancement of methods in Biophysics.This review will focus on the progresses achieved by time resolved small angle X-ray scattering (SAXS) from muscle, an approach made possible by the highly ordered arrangement of both the contractile proteins myosin and actin in the ca 2 mum long structural unit the sarcomere that repeats along the whole length of the muscle cell. Among the time resolved structural techniques, SAXS has proved to be the most powerful method of investigation, as it allows the molecular motor to be studied in situ, in intact single muscle cells, where it is possible to combine the structural study with fast mechanical methods that synchronize the action of the molecular motors. The latest development of this technique allows Angstrom-scale measurements of the axial movement of the motors that pull the actin filament toward the centre of the sarcomere, by exploiting the X-ray interference between the two arrays of myosin motors in the two halves of the sarcomere.

  6. 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).

  7. Structure parameters of synaptic vesicles quantified by small-angle x-ray scattering.

    PubMed

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

    2010-04-07

    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 [Ca(2+)] 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.

  8. Joint small-angle X-ray and neutron scattering data analysis of asymmetric lipid vesicles

    PubMed Central

    Eicher, Barbara; Heberle, Frederick A.; Marquardt, Drew; Rechberger, Gerald N.; Katsaras, John

    2017-01-01

    Low- and high-resolution models describing the internal transbilayer structure of asymmetric lipid vesicles have been developed. These models can be used for the joint analysis of small-angle neutron and X-ray scattering data. The models describe the underlying scattering length density/electron density profiles either in terms of slabs or through the so-called scattering density profile, previously applied to symmetric lipid vesicles. Both models yield structural details of asymmetric membranes, such as the individual area per lipid, and the hydrocarbon thickness of the inner and outer bilayer leaflets. The scattering density profile model, however, comes at a cost of increased computational effort but results in greater structural resolution, showing a slightly lower packing of lipids in the outer bilayer leaflet of ∼120 nm diameter palmitoyl­oleoyl phosphatidyl­choline (POPC) vesicles, compared to the inner leaflet. Analysis of asymmetric dipalmitoyl phosphatidylcholine/POPC vesicles did not reveal evidence of transbilayer coupling between the inner and outer leaflets at 323 K, i.e. above the melting transition temperature of the two lipids. PMID:28381971

  9. 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.

  10. 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.

  11. Modeling the Structure of RNA Molecules with Small-Angle X-Ray Scattering Data

    PubMed Central

    Gajda, Michal Jan; Martinez Zapien, Denise; Uchikawa, Emiko; Dock-Bregeon, Anne-Catherine

    2013-01-01

    We propose a novel fragment assembly method for low-resolution modeling of RNA and show how it may be used along with small-angle X-ray solution scattering (SAXS) data to model low-resolution structures of particles having as many as 12 independent secondary structure elements. We assessed this model-building procedure by using both artificial data on a previously proposed benchmark and publicly available data. With the artificial data, SAXS-guided models show better similarity to native structures than ROSETTA decoys. The publicly available data showed that SAXS-guided models can be used to reinterpret RNA structures previously deposited in the Protein Data Bank. Our approach allows for fast and efficient building of de novo models of RNA using approximate secondary structures that can be readily obtained from existing bioinformatic approaches. We also offer a rigorous assessment of the resolving power of SAXS in the case of small RNA structures, along with a small multimetric benchmark of the proposed method. PMID:24223750

  12. Revealing nanocomposite filler structures by swelling and small-angle X-ray scattering.

    PubMed

    Baeza, Guilhem P; Genix, Anne-Caroline; Paupy-Peyronnet, Nathalie; Degrandcourt, Christophe; Couty, Marc; Oberdisse, Julian

    2016-01-01

    Polymer nanocomposites are used widely, mainly for the industrial application of car tyres. The rheological behavior of such nanocomposites depends in a crucial way on the dispersion of the hard filler particles - typically silica nanoparticles embedded in a soft polymer matrix. It is thus important to assess the filler structure, which may be quite difficult for aggregates of nanoparticles of high polydispersity, and with strong interactions at high loading. This has been achieved recently using a coupled TEM/SAXS structural model describing the filler microstructure of simplified industrial nanocomposites with grafted or ungrafted silica of high structural disorder. Here, we present an original method capable of reducing inter-aggregate interactions by swelling of nanocomposites, diluting the filler to low-volume fractions. Note that this is impossible to reach by solid mixing due to the large differences in viscoelasticity between the composite and the pure polymer. By combining matrix crosslinking, swelling in a good monomer solvent, and post-polymerization of these monomers, it is shown that it is possible to separate the filler into small aggregates. The latter have then been characterized by electron microscopy and small-angle X-ray scattering, confirming the conclusions of the above mentioned TEM-SAXS structural model applied directly to the highly loaded cases.

  13. 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.

  14. Conformational Changes and Flexibility of DNA Devices Observed by Small-Angle X-ray Scattering.

    PubMed

    Bruetzel, Linda K; Gerling, Thomas; Sedlak, Steffen M; Walker, Philipp U; Zheng, Wenjun; Dietz, Hendrik; Lipfert, Jan

    2016-08-10

    Self-assembled DNA origami nanostructures enable the creation of precisely defined shapes at the molecular scale. Dynamic DNA devices that are capable of switching between defined conformations could afford completely novel functionalities for diagnostic, therapeutic, or engineering applications. Developing such objects benefits strongly from experimental feedback about conformational changes and 3D structures, ideally in solution, free of potential biases from surface attachment or labeling. Here, we demonstrate that small-angle X-ray scattering (SAXS) can quantitatively resolve the conformational changes of a DNA origami two-state switch device as a function of the ionic strength of the solution. In addition, we show how SAXS data allow for refinement of the predicted idealized three-dimensional structure of the DNA object using a normal mode approach based on an elastic network model. The results reveal deviations from the idealized design geometries that are otherwise difficult to resolve. Our results establish SAXS as a powerful tool to investigate conformational changes and solution structures of DNA origami and we anticipate our methodology to be broadly applicable to increasingly complex DNA and RNA devices.

  15. The cubic phase of phosphatidylethanolamine film by small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Sun, Run Guang; Zhang, Jing

    2004-02-01

    Using small angle x-ray scattering, we have investigated the effects of polyvinylpyrrolidone (PVP) and oleic acid (OA) on the structures of the cubic phase of 1,2-dielaidoyl-sn-glycero-3-phosphoethanolamine (DEPE) films. At lower PVP concentrations, DEPE-PVP mixed films existed in two cubic phases. With increasing PVP concentration in the DEPE-PVP mixed phase, a phase transition from Q229 (Im3m) to Q224 (Pn3m) occurred. The effect of addition of OA to a DEPE-PVP mixed phase was also determined using a certain fixed amount. At 0.5 mol% OA, the presence of low amounts of OA allows the DEPE-PVP-OA system to organize in a cubic Q229 phase. At 1.0 mol% OA, the presence of larger amounts of OA induces formation of coexisting Q229 and Q224 phases. At 1.5 mol% OA, the presence of even larger amounts of OA promotes formation of a cubic Q224 phase in the DEPE-PVP-OA mixture.

  16. Structural evaluation of an amyloid fibril model using small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Dahal, Eshan; Choi, Mina; Alam, Nadia; Bhirde, Ashwinkumar A.; Beaucage, Serge L.; Badano, Aldo

    2017-08-01

    Amyloid fibrils are highly structured protein aggregates associated with a wide range of diseases including Alzheimer’s and Parkinson’s. We report a structural investigation of an amyloid fibril model prepared from a commonly used plasma protein (bovine serum albumin (BSA)) using small-angle x-ray scattering (SAXS) technique. As a reference, the size estimates from SAXS are compared to dynamic light scattering (DLS) data and the presence of amyloid-like fibrils is confirmed using Congo red absorbance assay. Our SAXS results consistently show the structural transformation of BSA from spheroid to rod-like elongated structures during the fibril formation process. We observe the elongation of fibrils over two months with fibril length growing from 35.9  ±  3.0 nm to 51.5  ±  2.1 nm. Structurally metastable fibrils with distinct SAXS profiles have been identified. As proof of concept, we demonstrate the use of such distinct SAXS profiles to detect fibrils in the mixture solutions of two species by estimating their volume fractions. This easily detectable and well-characterized amyloid fibril model from BSA can be readily used as a control or standard reference to further investigate SAXS applications in the detection of structurally diverse amyloid fibrils associated with protein aggregation diseases.

  17. 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.

  18. Scanning of Adsorption Hysteresis In Situ with Small Angle X-Ray Scattering

    PubMed Central

    Mitropoulos, Athanasios Ch.; Favvas, Evangelos P.; Stefanopoulos, Konstantinos L.; Vansant, Etienne F.

    2016-01-01

    Everett’s theorem-6 of the domain theory was examined by conducting adsorption in situ with small angle x-ray scattering (SAXS) supplemented by the contrast matching technique. The study focuses on the spectrum differences of a point to which the system arrives from different scanning paths. It is noted that according to this theorem at a common point the system has similar macroscopic properties. Furthermore it was examined the memory string of the system. We concluded that opposite to theorem-6: a) at a common point the system can reach in a finite (not an infinite) number of ways, b) a correction for the thickness of the adsorbed film prior to capillary condensation is necessary, and c) the scattering curves although at high-Q values coincide, at low-Q values are different indicating different microscopic states. That is, at a common point the system holds different metastable states sustained by hysteresis effects. These metastable states are the ones which highlight the way of a system back to a return point memory (RPM). Entering the hysteresis loop from different RPMs different histories are implanted to the paths toward the common point. Although in general the memory points refer to relaxation phenomena, they also constitute a characteristic feature of capillary condensation. Analogies of the no-passing rule and the adiabaticity assumption in the frame of adsorption hysteresis are discussed. PMID:27741263

  19. Characterization of Athabasca Asphaltenes Separated Physically and Chemically Using Small-Angle X-Ray Scattering

    NASA Astrophysics Data System (ADS)

    Amundarain Hurtado, Jesus Leonardo

    Athabasca asphaltenes were characterized using small-angle X-ray scattering (SAXS) with synchrotron radiation. Two methods were used to separate asphaltenes from Athabasca bitumen. Conventional chemical separation by precipitation with n-pentane, and physical separation realized by passing bitumen through a zirconia membrane with a 20 nm average pore size. The Athabasca permeates and chemically separated samples were dispersed in 1-methylnaphtalene and n-dodecane, with temperature and asphaltene concentration ranges of 50-310 °C and 1-8 wt. %, respectively. Two approaches were also taken in the analysis of the SAXS emissions. A model-independent approach provided radii of gyration and scattering coefficients. A model-dependent fit provided size distributions for asphaltenes aggregates assuming that they are dense and spherical. Physically and chemically separated asphaltenes showed significant differences in nominal size and structure, and their structural properties exhibited different temperature dependencies. The results challenge the merits of using chemically separated asphaltene properties as a basis for asphaltene property prediction in crude oil/bitumen.

  20. 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.

  1. Characterization of coal morphology by small angle x-ray scattering (SAXS)

    SciTech Connect

    Foster, M.; Jensen, K.F.

    1984-01-01

    The objectives of the present small angle x-ray scattering (SAXS) studies are: (1) to measure the specific surface area of the sample; and (2) to infer a pore size distribution. In pursuing these objectives three types of samples are used; a model microporous carbon, Carbosieve-S, three coals, and a porous ..gamma..-alumina. Changes in the porous structure with conversion are clearly evident in scattering data from both the model carbon and anthracite coal. Growth of the micropores in Carbosieve and of both micro- and mesopores in the coal is seen in the increasing intensity at intermediate values of h. Also, the intensity drop-off at high values of h moves in toward the mesopore scattering. The Voronoi and Fully Penetrable Polydisperse Spheres (FPPS) models are better for analyzing SAXS than traditional discrete models since they correspond to interconnected, random porous structures with irregular pore sizes and shapes. The Voronoi model can be used with the model carbon which appears to have a bimodal distribution with pore sizes closely grouped about the modes. However, the FPPS model, which allows for broad distributions, is more widely applicable. The FPPS model closely approximates the scattering from a characterized sample with polydisperse porosity. However, there is a marked difference betwe

  2. 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.

  3. Modeling detergent organization around aquaporin-0 using small-angle X-ray scattering.

    PubMed

    Berthaud, Alice; Manzi, John; Pérez, Javier; Mangenot, Stéphanie

    2012-06-20

    Solubilization of integral membrane proteins in aqueous solutions requires the presence of amphiphilic molecules like detergents. The transmembrane region of the proteins is then surrounded by a corona formed by these molecules, ensuring a hydrophilic outer surface. The presence of this corona has strongly hampered structural studies of solubilized membrane proteins by small-angle X-ray scattering (SAXS), a technique frequently used to monitor conformational changes of soluble proteins. Through the online combination of size exclusion chromatography, SAXS, and refractometry, we have determined a precise geometrical model of the n-dodecyl β-d-maltopyranoside corona surrounding aquaporin-0, the most abundant membrane protein of the eye lens. The SAXS data were well-fitted by a detergent corona shaped in an elliptical toroid around the crystal structure of the protein, similar to the elliptical shape recently reported for nanodiscs (Skar-Gislinge et al. J. Am. Chem. Soc. 2010, 132, 13713-13722). The torus thickness determined from the curve-fitting protocol is in excellent agreement with the thickness of a lipid bilayer, while the number of detergent molecules deduced from the volume of the torus compares well with those obtained on the same sample from refractometry and mass analysis based on SAXS forward scattering. For the first time, the partial specific volume of the detergent surrounding a protein was measured. The present protocol is a crucial step toward future conformational studies of membrane proteins in solution.

  4. Small angle X-ray study of cellulose macromolecules produced by tunicates and bacteria.

    PubMed

    Khandelwal, Mudrika; Windle, Alan H

    2014-07-01

    The organisation of poly-glucan chains into cellulose macromolecular microfibrils has been studied using small angle X-ray scattering (SAXS). Three kinds of cellulose - bacterial cellulose (BC), nata-de-coco (NdC) (food grade bacterial cellulose) and tunicate cellulose (TC) have been investigated. Given the large ambiguity in literature on the microfibril dimensions owing to different methods and data analysis strategies, a method to extract dimensions of cellulose microfibrils using SAXS has been shown, which was found to be consistent across all the samples. The results have been verified with microscopy data. Two populations of microfibrils with different cross-section dimensions were identified. The dimensions of the rectangular cross-sections of BC were found to be 32nm by 16nm and 21nm by 10nm. The dimensions for NdC were calculated to be 25nm×8nm and 14nm×6nm and that for TC were determined to be 25nm×10nm and 15nm×8nm. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Joint small-angle X-ray and neutron scattering data analysis of asymmetric lipid vesicles

    DOE PAGES

    Eicher, Barbara; Heberle, Frederick A.; Marquardt, Drew T.; ...

    2017-02-28

    Low- and high-resolution models describing the internal transbilayer structure of asymmetric lipid vesicles have been developed. These models can be used for the joint analysis of small-angle neutron and X-ray scattering data. The models describe the underlying scattering length density/electron density profiles either in terms of slabs or through the so-called scattering density profile, previously applied to symmetric lipid vesicles. Both models yield structural details of asymmetric membranes, such as the individual area per lipid, and the hydrocarbon thickness of the inner and outer bilayer leaflets. The scattering density profile model, however, comes at a cost of increased computational effortmore » but results in greater structural resolution, showing a slightly lower packing of lipids in the outer bilayer leaflet of ~120 nm diameter palmitoyloleoyl phosphatidylcholine (POPC) vesicles, compared to the inner leaflet. Here, analysis of asymmetric dipalmitoyl phosphatidylcholine/POPC vesicles did not reveal evidence of transbilayer coupling between the inner and outer leaflets at 323 K,i.e.above the melting transition temperature of the two lipids.« less

  6. Collagen Orientation and Crystallite Size in Human Dentin: A Small Angle X-ray Scattering Study

    SciTech Connect

    Pople, John A.

    2001-03-29

    The mechanical properties of dentin are largely determined by the intertubular dentin matrix, which is a complex composite of type I collagen fibers and a carbonate-rich apatite mineral phase. The authors perform a small angle x-ray scattering (SAXS) study on fully mineralized human dentin to quantify this fiber/mineral composite architecture from the nanoscopic through continuum length scales. The SAXS results were consistent with nucleation and growth of the apatite phase within periodic gaps in the collagen fibers. These mineralized fibers were perpendicular to the dentinal tubules and parallel with the mineralization growth front. Within the plane of the mineralization front, the mineralized collagen fibers were isotropic near the pulp, but became mildly anisotropic in the mid-dentin. Analysis of the data also indicated that near the pulp the mineral crystallites were approximately needle-like, and progressed to a more plate-like shape near the dentino-enamel junction. The thickness of these crystallites, {approx} 5 nm, did not vary significantly with position in the tooth. These results were considered within the context of dentinogenesis and maturation.

  7. 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.

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

    SciTech Connect

    Settens, Charles M.

    2015-01-01

    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, H2 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 CDSEM, 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.

  9. 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.

  10. Topological Structure Determination of RNA Using Small-Angle X-Ray Scattering.

    PubMed

    Bhandari, Yuba R; Fan, Lixin; Fang, Xianyang; Zaki, George F; Stahlberg, Eric A; Jiang, Wei; Schwieters, Charles D; Stagno, Jason R; Wang, Yun-Xing

    2017-09-14

    Knowledge of RNA three-dimensional topological structures provides important insight into the relationship between RNA structural components and function. It is often likely that near-complete sets of biochemical and biophysical data containing structural restraints are not available, but one still wants to obtain knowledge about approximate topological folding of RNA. In this regard, general methods for determining such topological structures with minimum readily available restraints are lacking. Naked RNAs are difficult to crystallize and NMR spectroscopy is generally limited to small RNA fragments. By nature, sequence determines structure and all interactions that drive folding are self-contained within sequence. Nevertheless, there is little apparent correlation between primary sequences and three-dimensional folding unless supplemented with experimental or phylogenetic data. Thus, there is an acute need for a robust high-throughput method that can rapidly determine topological structures of RNAs guided by some experimental data. We present here a novel method (RS3D) that can assimilate the RNA secondary structure information, small-angle X-ray scattering data, and any readily available tertiary contact information to determine the topological fold of RNA. Conformations are firstly sampled at glob level where each glob represents a nucleotide. Best-ranked glob models can be further refined against solvent accessibility data, if available, and then converted to explicit all-atom coordinates for refinement against SAXS data using the Xplor-NIH program. RS3D is widely applicable to a variety of RNA folding architectures currently present in the structure database. Furthermore, we demonstrate applicability and feasibility of the program to derive low-resolution topological structures of relatively large multi-domain RNAs. Published by Elsevier Ltd.

  11. 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.

  12. Characterization of zein assemblies by ultra-small-angle X-ray scattering

    DOE PAGES

    Uzun, Suzan; Ilavsky, Jan; Padua, Graciela Wild

    2017-03-23

    Zein, a protein of corn, has an amphiphilic molecule capable of self-assembly into distinctly different structures. In this work, ultra-small-angle X-ray scattering (USAXS) was applied to investigate the formation of self-assembled zein structures in binary solvent systems of ethanol and water. Our study included observing structural changes due to aging. Three hierarchical structures were identified in zein-solvent systems, molecular zein 2D films, believed to be formed by zein rods assembled first into one-dimensional fibers and then into two-dimensional films, and 3D spherical aggregates. Aging did not change the size or shape of primary units, but promoted their self-assembly into intermediatemore » 2D structures and shaped 3D structures into well19 defined spheres. We found that the rheological parameters, consistency index (K) and behavior index (n), storage and loss moduli (G’ and G”) were also measured. K and n, changed markedly with aging, from nearly Newtonian low consistency fresh samples to highly viscous pseudoplastic aged samples. G’ and G” increased with aging for all samples reflecting increased interactions among zein self-assembled structures. Furthermore, viscoelastic parameters indicated that zein dispersions formed gels upon aging. It was observed that USAX reported on molecular scale self-assembly processes, while rheological measurements reported on the macroscale interaction between self-assembled particles. Raman spectra suggested that α-helix to β-sheet transformations prompted zein self-assembly, which influenced the size and morphology of molecular assemblies and ultimately the rheological properties of zein dispersions.« less

  13. 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.

  14. NIST Standard Reference Material 3600: Absolute Intensity Calibration Standard for Small-Angle X-ray Scattering

    PubMed Central

    Zhang, Fan; Kline, R. Joseph; Guthrie, William F.; Ilavsky, Jan

    2017-01-01

    The certification of a new standard reference material for small-angle scattering [NIST Standard Reference Material (SRM) 3600: Absolute Intensity Calibration Standard for Small-Angle X-ray Scattering (SAXS)], based on glassy carbon, is presented. Creation of this SRM relies on the intrinsic primary calibration capabilities of the ultra-small-angle X-ray scattering technique. This article describes how the intensity calibration has been achieved and validated in the certified Q range, Q = 0.008–0.25 Å−1, together with the purpose, use and availability of the SRM. The intensity calibration afforded by this robust and stable SRM should be applicable universally to all SAXS instruments that employ a transmission measurement geometry, working with a wide range of X-ray energies or wavelengths. The validation of the SRM SAXS intensity calibration using small-angle neutron scattering (SANS) is discussed, together with the prospects for including SANS in a future renewal certification. PMID:28381972

  15. NIST Standard Reference Material 3600: Absolute Intensity Calibration Standard for Small-Angle X-ray Scattering

    DOE PAGES

    Allen, Andrew J.; Zhang, Fan; Kline, R. Joseph; ...

    2017-03-07

    The certification of a new standard reference material for small-angle scattering [NIST Standard Reference Material (SRM) 3600: Absolute Intensity Calibration Standard for Small-Angle X-ray Scattering (SAXS)], based on glassy carbon, is presented. Creation of this SRM relies on the intrinsic primary calibration capabilities of the ultra-small-angle X-ray scattering technique. This article describes how the intensity calibration has been achieved and validated in the certified Q range, Q = 0.008–0.25 Å–1, together with the purpose, use and availability of the SRM. The intensity calibration afforded by this robust and stable SRM should be applicable universally to all SAXS instruments that employmore » a transmission measurement geometry, working with a wide range of X-ray energies or wavelengths. As a result, the validation of the SRM SAXS intensity calibration using small-angle neutron scattering (SANS) is discussed, together with the prospects for including SANS in a future renewal certification.« less

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

    PubMed Central

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

    2016-01-01

    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

  17. 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.

  18. Versatile wide angle diffraction setup for simultaneous wide and small angle x-ray scattering measurements with synchrotron radiation

    SciTech Connect

    Rueda, D.R.; Garcia-Gutierrez, M.C.; Nogales, A.; Capitan, M.J.; Ezquerra, T.A.; Labrador, A.; Fraga, E.; Beltran, D.; Juanhuix, J.; Herranz, J.F.; Bordas, J.

    2006-03-15

    Here we present a novel, simple, and versatile experimental setup aimed to perform wide angle x-ray scattering (WAXS) measurements alone or in simultaneous combination with small angle x-ray scattering measurements. The design of the WAXS goniometer allows one to obtain high resolution diffraction patterns in a broad angular range. The setup can incorporate a hot stage in order to evaluate temperature resolved experiments. The performance of the equipment has been verified in the BM16 beam line of the European Synchrotron Radiation Facility with different well known samples such as alumina, isotropic film of high density polyethylene (HDPE), and oriented HPDE fiber.

  19. Small Angle X-Ray Scattering of Carbon and Kevlar Fibers Under Load

    NASA Astrophysics Data System (ADS)

    Effler, Lawrence Joseph, Jr.

    Small angle X-ray scattering (SAXS) was used as the primary tool for investigating the microporous structure of Kevlar and mesophase pitch based carbon fibers. The orientation present in the scattering entities was determined by extending Porod's invariant into a pseudo-invariant for one-dimensional data slices. By comparing the pseudo -invariants at different aximuthal angles the extent of the orientation present in the scattering system was determined. The orientation of the microvoids was found to correlate best with the modulus of the carbon fibers. Distance distribution functions were also determined for the fibers. For the carbon fibers the average size of the voids and the breadth of the distribution was found to increase with both fiber modulus and strength. In addition, the distance distribution curves were able to distinguish between fibers spun under different conditions. These results were found to mirror the enhancement of crystalline orientation and the development of graphitic phases in the fibers. Studies were also conducted to determine the response of the microvoids to an applied tensile load. Both Kevlar and the carbon fibers indicated a loss of outer fiber surface, with the most dramatic loss being seen for Kevlar. Experiments were conducted which compared both as received fibers to those which had been strained to failure. Additional experiments were done with the fibers being strained while in the SAXS camera. For the Kevlar fibers the loss of its skin layer was indicated by less anisotropic scattering patterns of the fractured fibers. The dynamic studies indicated that initially void orientation increases accompanied by the formation of newer, smaller voids. However these trends are reversed as the fiber tow approaches and reaches fracture. The loss of the skin region was confirmed by both laser backscattering and optical microscopy. The response of the microvoid phase of Kevlar to loading is interpreted in light of Morgan's chain end model

  20. 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.

  1. 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.

  2. Thermal degradation of M41S-class mesoporous sieves as revealed by small angle X-ray scattering

    SciTech Connect

    Hunt, J. E.; Xu, L.; Winans, R. E.; Seifert, S.

    2000-02-16

    The authors have studied the temperature stability of M41S class siliceous mesoporous materials loaded with carbonaceous material by temperature programmed small-angle X-ray scattering (TPSAXS) techniques. Results show the thermal structural instability of large pore pure silica sieve material with carbonaceous material (such as coal extracts) occluded within the pores of mesoporous 31 {angstrom} M41S materials. Unfilled pore M41S materials do not show thermal-related structural instability.

  3. 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.

  4. Anomalous x-ray scattering from terbium-labeled parvalbumin in solution.

    PubMed Central

    Miake-Lye, R C; Doniach, S; Hodgson, K O

    1983-01-01

    We have used anomalous small-angle x-ray scattering as a structural probe for solutions of rabbit parvalbumin labeled with terbium. This technique makes use of the large changes in the terbium scattering factor that occur when the x-ray energy is tuned around an L3 absorption edge of this heavy-atom label. These changes in scattering result in changes in the small-angle scattering curve of the labeled protein as a whole, which can then be analyzed to derive structural information concerning the distribution of labels in the protein. Based on a Gaussian model for the protein electron density, the mean distance from the terbiums to the protein center of mass is determined to be 13.2 A and is consistent with crystallographic results. Our results demonstrate the usefulness of terbium as an anomalous scattering label and provide criteria to help establish anomalous scattering as a reliable structural technique for proteins in solution. PMID:6838970

  5. A method for determining transmembrane helix association and orientation in detergent micelles using small angle x-ray scattering.

    PubMed Central

    Bu, Z; Engelman, D M

    1999-01-01

    Solution small angle x-ray scattering can be used to study the association of transmembrane proteins solubilized in detergent micelles. We have used the alpha-helical transmembrane domain of the human erythrocyte glycophorin A (GpA) fused to the carboxyl terminus of monomeric staphylococcal nuclease (SN/GpA) as a model system for study. By matching the average electron density of the detergent micelles to that of the buffer solution, the micelle contribution to the small angle scattering vanishes, and the molecular weight and the radius of gyration of the proteins can be determined. SN/GpA has been found to dimerize in a zwitterionic detergent micelle, N-dodecyl-N,N-(dimethylammonio)butyrate (DDMAB), whose average electron density naturally matches the electron density of an aqueous buffer. The dimerization occurs through the transmembrane domains of GpA. With the aid of the nuclease domain scattering, the orientation of the helices within a dimer can be determined to be parallel by radius of gyration analysis. The association constant of a mutant (G83I) that weakens the GpA dimerization has been determined to be 24 microM in the DDMAB environment. The experimental methods established here could be used to apply solution small angle x-ray scattering to studying the association and interactions of other membrane proteins. PMID:10423450

  6. An upgrade beamline for combined wide, small and ultra small-angle x-ray scattering at the ESRF

    SciTech Connect

    Van Vaerenbergh, Pierre; Léonardon, Joachim; Sztucki, Michael; Boesecke, Peter; Gorini, Jacques; Claustre, Laurent; Sever, Franc; Morse, John; Narayanan, Theyencheri

    2016-07-27

    This contribution presents the main design features of the upgraded beamline ID02 (TRUSAXS). The beamline combines different small-angle X-ray scattering techniques in one unique instrument. The key component of this instrument is an evacuated (5×10{sup −3} mbar) stainless steel detector tube of length 34 m and diameter 2 m. Three different detectors (Rayonix MX170, Pilatus 300 K and FReLoN 4M) are housed inside a motorized wagon which travels along a rail system with very low parasitic lateral movements (± 0.3 mm). This system allows automatically changing the sample-to-detector distance from about 1 m to 31 m and selecting the desired detector. In addition, a wide angle detector (Rayonix LX170) is installed just above the entrance cone of the tube for optional wide-angle X-ray scattering measurements. The beamstop system enables monitoring of the X-ray beam intensity in addition to blocking the primary beam, and automated insertion of selected masks behind the primary beamstop. The focusing optics and collimation system permit to cover a scattering vector (q) range of 0.002 nm{sup −1} ≤ q ≤ 50 nm{sup −1} with one unique setting using 0.1 nm X-ray wavelength for moderate flux (5×10{sup 12} photons/sec). However, for higher flux (6x10{sup 13} photons/sec) or higher resolution (minimum q < 0.001 nm{sup −1}), focusing and collimation, respectively need to be varied. For a sample-to-detector distance of 31 m and 0.1 nm wavelength, two dimensional ultra small-angle X-ray scattering patterns can be recorded down to q≈0.001 nm{sup −1} with far superior quality as compared to one dimensional profiles obtained with a Bonse-Hart instrument.

  7. 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

  8. 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.

  9. Simbol-X Mirror Module Thermal Shields: II-Small Angle X-Ray Scattering Measurements

    SciTech Connect

    Barbera, M.; Ayers, T.; Collura, A.; Nasillo, G.; Pareschi, G.; Tagliaferri, G.

    2009-05-11

    The formation flight configuration of the Simbol-X mission implies that the X-ray mirror module will be open to Space on both ends. In order to reduce the power required to maintain the thermal stability and, therefore, the high angular resolution of the shell optics, a thin foil thermal shield will cover the mirror module. Different options are presently being studied for the foil material of these shields. We report results of an experimental investigation conducted to verify that the scattering of X-rays, by interaction with the thin foil material of the thermal shield, will not significantly affect the performances of the telescope.

  10. Simbol-X Mirror Module Thermal Shields: II-Small Angle X-Ray Scattering Measurements

    NASA Astrophysics Data System (ADS)

    Barbera, M.; Ayers, T.; Collura, A.; Nasillo, G.; Pareschi, G.; Tagliaferri, G.

    2009-05-01

    The formation flight configuration of the Simbol-X mission implies that the X-ray mirror module will be open to Space on both ends. In order to reduce the power required to maintain the thermal stability and, therefore, the high angular resolution of the shell optics, a thin foil thermal shield will cover the mirror module. Different options are presently being studied for the foil material of these shields. We report results of an experimental investigation conducted to verify that the scattering of X-rays, by interaction with the thin foil material of the thermal shield, will not significantly affect the performances of the telescope.

  11. 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.

  12. Silver behenate as a calibration standard of grazing-incidence small-angle X-ray scattering

    SciTech Connect

    Lee, Byeongdu; Lo, Chieh-Tsung; Seifert, Soenke; Winans, Randall E.

    2006-09-12

    Grazing-incidence small-angle X-ray scattering (GISAXS) patterns of a silver behenate composite film, which has a typical layered structure, are described. The peak position of the film in the GISAXS pattern was varied depending on the incident angle, which was well described by taking into account the refraction and the reflection effects. Since the refractive index of samples depends on sample preparation, it is recommended that the measurement of silver behenate as a standard be done in conventional transmission mode to avoid any complexity.

  13. Single-crystal CVD diamonds as small-angle X-ray scattering windows for high-pressure research.

    PubMed

    Wang, Suntao; Meng, Yu-Fei; Ando, Nozomi; Tate, Mark; Krasnicki, Szczesny; Yan, Chih-Shiue; Liang, Qi; Lai, Joseph; Mao, Ho-Kwang; Gruner, Sol M; Hemley, Russell J

    2012-06-01

    Small-angle X-ray scattering (SAXS) was performed on single-crystal chemical vapor deposition (CVD) diamonds with low nitrogen concentrations, which were fabricated by microwave plasma-assisted chemical vapor deposition at high growth rates. High optical quality undoped 500 µm-thick single-crystal CVD diamonds grown without intentional nitrogen addition proved to be excellent as windows on SAXS cells, yielding parasitic scattering no more intense than a 7.5 µm-thick Kapton film. A single-crystal CVD diamond window was successfully used in a high-pressure SAXS cell.

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

    PubMed

    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.

  15. 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.

  16. Processing two-dimensional X-ray diffraction and small-angle scattering data in DAWN 2

    PubMed Central

    Filik, J.; Ashton, A. W.; Chang, P. C. Y.; Chater, P. A.; Day, S. J.; Drakopoulos, M.; Gerring, M. W.; Hart, M. L.; Magdysyuk, O. V.; Michalik, S.; Smith, A.; Tang, C. C.; Terrill, N. J.; Wharmby, M. T.; Wilhelm, H.

    2017-01-01

    A software package for the calibration and processing of powder X-ray diffraction and small-angle X-ray scattering data is presented. It provides a multitude of data processing and visualization tools as well as a command-line scripting interface for on-the-fly processing and the incorporation of complex data treatment tasks. Customizable processing chains permit the execution of many data processing steps to convert a single image or a batch of raw two-dimensional data into meaningful data and one-dimensional diffractograms. The processed data files contain the full data provenance of each process applied to the data. The calibration routines can run automatically even for high energies and also for large detector tilt angles. Some of the functionalities are highlighted by specific use cases. PMID:28656043

  17. 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.

  18. Performance of the micro-PIC gaseous area detector in small-angle X-ray scattering experiments.

    PubMed

    Hattori, Kaori; Tsuchiya, Ken'ichi; Ito, Kazuki; Okada, Yoko; Fujii, Kotaro; Kubo, Hidetoshi; Miuchi, Kentaro; Takata, Masaki; Tanimori, Toru; Uekusa, Hidehiro

    2009-03-01

    The application of a two-dimensional photon-counting detector based on a micro-pixel gas chamber (micro-PIC) to high-resolution small-angle X-ray scattering (SAXS), and its performance, are reported. The micro-PIC is a micro-pattern gaseous detector fabricated by printed circuit board technology. This article describes the performance of the micro-PIC in SAXS experiments at SPring-8. A dynamic range of >10(5) was obtained for X-ray scattering from a polystyrene sphere solution. A maximum counting rate of up to 5 MHz was observed with good linearity and without saturation. For a diffraction pattern of collagen, weak peaks were observed in the high-angle region in one accumulation of photons.

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

    PubMed

    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 RNA molecules, particularly those that have proven difficult to study using other structure-determination 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.

  20. 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.

  1. Processing two-dimensional X-ray diffraction and small-angle scattering data in DAWN 2.

    PubMed

    Filik, J; Ashton, A W; Chang, P C Y; Chater, P A; Day, S J; Drakopoulos, M; Gerring, M W; Hart, M L; Magdysyuk, O V; Michalik, S; Smith, A; Tang, C C; Terrill, N J; Wharmby, M T; Wilhelm, H

    2017-06-01

    A software package for the calibration and processing of powder X-ray diffraction and small-angle X-ray scattering data is presented. It provides a multitude of data processing and visualization tools as well as a command-line scripting interface for on-the-fly processing and the incorporation of complex data treatment tasks. Customizable processing chains permit the execution of many data processing steps to convert a single image or a batch of raw two-dimensional data into meaningful data and one-dimensional diffractograms. The processed data files contain the full data provenance of each process applied to the data. The calibration routines can run automatically even for high energies and also for large detector tilt angles. Some of the functionalities are highlighted by specific use cases.

  2. Magnetic design evolution in perpendicular magnetic recording media as revealed by resonant small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Wang, Tianhan; Mehta, Virat; Ikeda, Yoshihiro; Do, Hoa; Takano, Kentaro; Florez, Sylvia; Terris, Bruce D.; Wu, Benny; Graves, Catherine; Shu, Michael; Rick, Ramon; Scherz, Andreas; Stöhr, Joachim; Hellwig, Olav

    2013-09-01

    We analyze the magnetic design for different generations of perpendicular magnetic recording (PMR) media using resonant soft x-ray small angle x-ray scattering. This technique allows us to simultaneously extract in a single experiment the key structural and magnetic parameters, i.e., lateral structural grain and magnetic cluster sizes as well as their distributions. We find that earlier PMR media generations relied on an initial reduction in the magnetic cluster size down to the grain level of the high anisotropy granular base layer, while very recent media designs introduce more exchange decoupling also within the softer laterally continuous cap layer. We highlight that this recent development allows optimizing magnetic cluster size and magnetic cluster size distribution within the composite media system for maximum achievable area density, while keeping the structural grain size roughly constant.

  3. Nonuniformity in natural rubber as revealed by small-angle neutron scattering, small-angle X-ray scattering, and atomic force microscopy.

    PubMed

    Karino, Takeshi; Ikeda, Yuko; Yasuda, Yoritaka; Kohjiya, Shinzo; Shibayama, Mitsuhiro

    2007-02-01

    The microscopic structures of natural rubber (NR) and deproteinized NR (DPNR) were investigated by means of small-angle neutron scattering (SANS), small-angle X-ray scattering (SAXS), and atomic force microscopy (AFM). They were compared to those of isoprene rubber (IR), which is a synthetic analogue of NR in terms of chemical structure without any non-rubber components like proteins. Comparisons of the structure and mechanical properties of NR, DPNR, and IR lead to the following conclusions. (i) The well-known facts, for example, the outstanding green strength of NR and strain-induced crystallization, are due not much to the presence of proteins but to other components such as the presence of phospholipids and/or the higher stereoregularity of NR. It also became clear the naturally residing proteins accelerate the upturn of stress at low strain. The protein phases work as cross-linking sites and reinforcing fillers in the rubbery matrix. (ii) The microscopic structures of NR were successfully reproduced by SANS intensity functions consisting of squared-Lorentz and Lorentz functions, indicating the presence of inhomogeneities in bulk and thermal concentration fluctuations in swollen state, respectively. On the other hand, IR rubbers were homogeneous in bulk. (iii) The inhomogeneities in NR are assigned to protein aggregates of the order of 200 A or larger. Although these aggregates are larger in size as well as in volume fraction than those of cross-link inhomogeneities introduced by cross-linking, they are removed by deproteinization. (iv) Swelling of both NR and IR networks introduces gel-like concentration fluctuations whose mesh size is of the order of 20 A.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Smith, Randall K.

    2008-07-01

    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 performed by Smith, Edgar, & Shafer 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'' and 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 these data for a dense cloud near the source, as suggested by Xiang et al. Finally, although no model leads to formally acceptable results, the Weingartner & Draine model and nearly all of the composite grain models from Zubko, Dwek, & Arendt give poor fits.

  6. Multiwavelength Anomalous Diffraction at High X-Ray Intensity

    NASA Astrophysics Data System (ADS)

    Son, Sang-Kil; Chapman, Henry N.; Santra, Robin

    2011-11-01

    The multiwavelength anomalous diffraction (MAD) method is used to determine phase information in x-ray crystallography by employing anomalous scattering from heavy atoms. X-ray free-electron lasers (FELs) show promise for revealing the structure of single molecules or nanocrystals, but the phase problem remains largely unsolved. Because of the ultrabrightness of x-ray FEL, samples experience severe electronic radiation damage, especially to heavy atoms, which hinders direct implementation of MAD with x-ray FELs. Here, we propose a generalized version of MAD phasing at high x-ray intensity. We demonstrate the existence of a Karle-Hendrickson-type equation in the high-intensity regime and calculate relevant coefficients with detailed electronic damage dynamics of heavy atoms. The present method offers a potential for ab initio structural determination in femtosecond x-ray nanocrystallography.

  7. Multiwavelength anomalous diffraction at high x-ray intensity.

    PubMed

    Son, Sang-Kil; Chapman, Henry N; Santra, Robin

    2011-11-18

    The multiwavelength anomalous diffraction (MAD) method is used to determine phase information in x-ray crystallography by employing anomalous scattering from heavy atoms. X-ray free-electron lasers (FELs) show promise for revealing the structure of single molecules or nanocrystals, but the phase problem remains largely unsolved. Because of the ultrabrightness of x-ray FEL, samples experience severe electronic radiation damage, especially to heavy atoms, which hinders direct implementation of MAD with x-ray FELs. Here, we propose a generalized version of MAD phasing at high x-ray intensity. We demonstrate the existence of a Karle-Hendrickson-type equation in the high-intensity regime and calculate relevant coefficients with detailed electronic damage dynamics of heavy atoms. The present method offers a potential for ab initio structural determination in femtosecond x-ray nanocrystallography.

  8. Grazing exit small angle X-ray scattering on grain formation in polycrystalline metal films

    SciTech Connect

    Zhang, Wei; Robinson, Ian K.

    2009-09-25

    We recently proposed a new grazing exit geometry for measuring the small-angle scattering from thin film materials, which we call GESAXS, to contrast with the successful grazing incidence version, GISAXS. The technique is particularly useful for probing nanostructured thin film materials, especially when the coherence properties of the beam are employed. Here we demonstrate the application of GESAXS to evaporated metal films, prepared using an in-situ diffraction chamber, to investigate how their structure evolves upon annealing. Contrasting behavior is seen for Au, which preserves a roughly exponential distribution of domain sizes, and Fe for which the size distribution narrows by an Ostwald ripening process.

  9. Ultrafast small-angle x-ray scattering from laser-produced plasmas using an x-ray free electron laser

    NASA Astrophysics Data System (ADS)

    Roedel, Christian; Pelka, Alexander; Kluge, Thomas; Roedel, Melanie; Cowan, Thomas; Kemp, Andreas; Fletcher, Luke; Schumaker, Will; Goede, Sebastian; Galtier, Eric; Lee, Hae Ja; Glenzer, Siegfried; SLAC/Uni JEna Team; HZDR Team; LLNL Team; SLAC Team

    2016-10-01

    Small-angle x-ray scattering (SAXS) using ultrashort x-ray pulses from free electron lasers has the potential to resolve transient phenomena in dense laser-produced plasmas with nanometer spatial and femtosecond temporal resolution. As a proof-of-principle experiment, we demonstrated ultrafast SAXS from a laser-irradiated wire target using the Matter in Extreme Conditions (MEC) instrument at the Linac Coherent Light Source (LCLS). A 5 µm Al wire was irradiated with a high-intensity laser pulse (up to 200 mJ, 50 fs) leading to a rapidly expanding laser plasma. X-ray pulses from the free-electron laser (60 fs, 5.5 keV) probe the laser produced plasma 80 ps after the interaction. The SAXS data reveals that an indentation of the dense plasma is initiated due to plasma expansion. The measurements will be discussed using two-dimensional particle-in-cell simulations of the laser plasma interaction. This work was supported by the Volkswagen Foundation and DOE Office of Science, Fusion Energy Science under FWP 100182.

  10. Real-Time Studies of Gallium Adsorption and Desorption Kinetics by Grazing-Incidence Small-Angle X-ray Scattering and X-ray Fluorescence

    SciTech Connect

    Wang, Y.; Ozcan, A; Ludwig, K; Bhattacharyya, A

    2008-01-01

    Gallium adsorption and desorption on c-plane sapphire has been studied by real-time grazing incidence small-angle x-ray scattering and x-ray fluorescence as a function of substrate temperature (680-740 C) and Ga flux. The x-ray techniques monitor the surface morphology evolution and amount of Ga on the surface. During deposition, nanodroplets of liquid Ga are observed to form on the surface and coarsen. The growth of droplet size during continuous deposition follows dynamical scaling, in agreement with expectations from theory and simulations which include deposition-induced droplet coalescence. However, observation of continued droplet distance scale coarsening during desorption points to the necessity of including further physical processes in the modeling. The desorption rate at different substrate temperatures gives the activation energy of Ga desorption as 2.7 eV, comparable to measured activation energies for desorption from Ga droplets on other substrates and to the Ga heat of vaporization.

  11. Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments.

    PubMed

    Jeffries, Cy M; Graewert, Melissa A; Blanchet, Clément E; Langley, David B; Whitten, Andrew E; Svergun, Dmitri I

    2016-11-01

    Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions from all atoms within the illuminated sample volume, including the solvent and buffer components, as well as the macromolecules of interest. To obtain structural information, it is essential to prepare an exactly matched solvent blank so that background scattering contributions can be accurately subtracted from the sample scattering to obtain the net scattering from the macromolecules in the sample. In addition, sample heterogeneity caused by contaminants, aggregates, mismatched solvents, radiation damage or other factors can severely influence and complicate data analysis, so it is essential that the samples be pure and monodisperse for the duration of the experiment. This protocol outlines the basic physics of SAXS and SANS, and it reveals how the underlying conceptual principles of the techniques ultimately 'translate' into practical laboratory guidance for the production of samples of sufficiently high quality for scattering experiments. The procedure describes how to prepare and characterize protein and nucleic acid samples for both SAXS and SANS using gel electrophoresis, size-exclusion chromatography (SEC) and light scattering. Also included are procedures that are specific to X-rays (in-line SEC-SAXS) and neutrons, specifically preparing samples for contrast matching or variation experiments and deuterium labeling of proteins.

  12. 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.

  13. Time resolved small angle x-ray scattering studies of macromolecular folding

    NASA Astrophysics Data System (ADS)

    Kwok, Lisa; Smith, Heather; Sandy, Alec; Pollack, Lois

    2005-03-01

    Large biological molecules like proteins and RNA, carry out their functions by folding to well-defined three-dimensional structures. We are interested in the physical interactions that direct this self-assembly process. By combining microfabricated rapid mixers with synchrotron x-ray scattering, we have gained insight into the earliest steps of folding of the Tetrahymena ribozyme, a model for large RNAs. Previous work has shown that the first folding step involves electrostatic relaxation of the molecule. We will discuss a recent series of experiments that identify the tertiary contacts that form from within this compact state.

  14. 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.

  15. 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.

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

    DOE PAGES

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

    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

  17. 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

  18. 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.).

  19. A method for sizing sub-micron particles using small angle diffraction of soft x-rays

    SciTech Connect

    Berkeland, D.J.; Underwood, J.H.; Perera, R.C.C.

    1988-10-01

    The purpose of this work is to develop a method of sizing sub-micron particles using small-angle soft x-ray diffraction. Solid poly-styrene spheres of known sizes were used as scattering samples, with C-K..cap alpha.. (44.8/angstrom/) and V-L..cap alpha.. (24.3/angstrom/) radiation from a conventional x-ray source. Two devices were used to diffract the x-rays. One collimates the radiation using a series of pinholes immediately preceding the sample, and directs the unfocussed radiation onto film placed far from the sample. The other utilizes radiation from a single pinhole above the source onto the sample and a spherical multilayer mirror in series, so that the radiation passes twice through the sample and is focused onto film immediately above the pinhole assembly to increase the effective sample area. Using the latter device, two types of diffraction patterns were obtained: a sharp, relatively small pattern from spheres which form a hexagonal lattice structure, and a diffuse, larger pattern from an unordered, or random, array of spheres. Both patterns are presented in this work, along with the calculations, based upon light scattering from an unordered and an ordered array of particles, of the scattering patterns. 9 refs., 32 figs., 2 tabs.

  20. Measuring the distribution of cellulose microfibril angles in primary cell walls by small angle X-ray scattering

    PubMed Central

    2014-01-01

    Background X-ray scattering is a well-established method for measuring cellulose microfibril angles in secondary cell walls. However, little data is available on the much thinner primary cell walls. Here, we show that microfibril orientation distributions can be determined by small angle X-ray scattering (SAXS) even in primary cell walls. The technique offers a number of advantages: samples can be analyzed in the native hydrated state without any preparation which minimizes the risk of artifacts and allows for fast data acquisition. The method provides data averaged over a specimen region, determined by the size of the used X-ray beam and, thus, yields the microfibril orientation distribution within this region. Results Cellulose microfibril orientation distributions were obtained for single cells of the alga Chara corallina, as well as for the multicellular hypocotyl of Arabidopsis thaliana. In both, Chara and Arabidopsis, distributions with a broad scattering around mean microfibril angles of approximately 0° and 90° towards the longitudinal axis of the cells were found. Conclusions With SAXS, the structure of primary cell walls can be analysed in their native state and new insights into the cellulose microfibril orientation of primary cell walls can be gained. The data shows that SAXS can serve as a valuable tool for the analysis of cellulose microfibril orientation in primary cell walls and, in consequence, add to the understanding of its mechanical behaviour and the intriguing mechanisms behind cell growth. PMID:25170343

  1. Thorough small-angle X-ray scattering analysis of the instability of liquid micro-jets in air.

    PubMed

    Marmiroli, Benedetta; Cacho-Nerin, Fernando; Sartori, Barbara; Pérez, Javier; Amenitsch, Heinz

    2014-01-01

    Liquid jets are of interest, both for their industrial relevance and for scientific applications (more important, in particular for X-rays, after the advent of free-electron lasers that require liquid jets as sample carrier). Instability mechanisms have been described theoretically and by numerical simulation, but confirmed by few experimental techniques. In fact, these are mainly based on cameras, which is limited by the imaging resolution, and on light scattering, which is hindered by absorption, reflection, Mie scattering and multiple scattering due to complex air/liquid interfaces during jet break-up. In this communication it is demonstrated that synchrotron small-angle X-ray scattering (SAXS) can give quantitative information on liquid jet dynamics at the nanoscale, by detecting time-dependent morphology and break-up length. Jets ejected from circular tubes of different diameters (100-450 µm) and speeds (0.7-21 m s(-1)) have been explored to cover the Rayleigh and first wind-induced regimes. Various solvents (water, ethanol, 2-propanol) and their mixtures have been examined. The determination of the liquid jet behaviour becomes essential, as it provides background data in subsequent studies of chemical and biological reactions using SAXS or X-ray diffraction based on synchrotron radiation and free-electron lasers.

  2. Microfocus small-angle X-ray scattering at SSRF BL16B1

    NASA Astrophysics Data System (ADS)

    Hua, Wen-Qiang; Wang, Yu-Zhu; Zhou, Ping; Hu, Tao; Li, Xiu-Hong; Bian, Feng-Gang; Wang, Jie

    2017-04-01

    Offering high-brilliance X-ray beams on micrometer length scales, the μSAXS at SSRF BL16B1 has been established with a KB mirror system for studying small sample volumes, or probing microscopic morphologies. The SAXS minimum q value is 0.1 nm-1 with a flux of 1.5 × 1010 photons/s. Two position-resolved scanning experimental methods, STXM and CT, are combined with μSAXS. To improve the significant smearing effect in the horizontal direction, an effective and easy-to-use desmearing procedure for two-dimensional SAXS patterns based on blind deconvolution was developed, and the deblurring results demonstrate the good restoration effect for the defocused image. Finally, a bamboo sample was used in the SAXS-CT experiment to illustrate the performance of the μSAXS method. Supported by National Natural Science Foundation of China (11505278 and 11675253)

  3. Structure of the Lassa virus nucleoprotein revealed by X-ray crystallography, small-angle X-ray scattering, and electron microscopy.

    PubMed

    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

    2011-11-04

    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 m(7)GpppN 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.

  4. Characterization of Nanoclay Orientation in Polymer Nanocomposite Film by Small-angle X-ray Scattering

    SciTech Connect

    P Nawani; C Burger; L Rong; B Chu; B Hsiao; A Tsou; W Weng

    2011-12-31

    The orientation distribution of layer-shaped nanoclays (e.g. organoclays and pristine clays) dispersed in a polymer matrix is an important parameter to control the properties of polymer nanocomposites. In this study, we demonstrate that the use of multi-directional 2-D small-angleX-rayscattering (SAXS) can quantitatively describe the orientation distribution of organoclays (e.g. Cloisite C20A) in melt-pressed nanocompositefilms, containing ethylene-vinyl acetate (EVA) copolymers as polymer matrices. Different weight fractions of organoclays were used to alter the orientation profile of nanocompositefilms, in which the dispersion and morphology of organoclays were also characterized by complementary 2-D and 3-D transmission electron microscopy (TEM). All nanocomposites exhibited mixed intercalation/exfoliation clay morphology, where the intercalated structure possessed partial orientation parallel to the in-plane direction of the film. The higher content of the clay loading showed a higher clay orientation. A simple analytical scheme for SAXS data analysis to determine the orientation parameter (P{sub 2}) was demonstrated, the results of which are in agreement with the gas permeation properties of the nanocompositefilms.

  5. 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.

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

    PubMed Central

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

    2011-01-01

    X-ray Raman scattering (XRS) spectroscopy and small angle x-ray scattering (SAXS) are used to study water in aqueous solutions of NaCl, MgCl2, and AlCl3 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. Mg2+ and Al3+, on the other hand, cause the formation of short and strong hydrogen bonds between the surrounding water molecules. The SAXS data show that Mg2+ and Al3+ 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 Mg2+ and Al3+ 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 Mg2+ and Al3+ is, respectively, ∼61% and ∼71% higher than in bulk water. PMID:21322711

  7. Human breast cancer in vitro: matching histo-pathology with small-angle x-ray scattering and diffraction enhanced x-ray imaging

    NASA Astrophysics Data System (ADS)

    Fernández, Manuel; Keyriläinen, Jani; Serimaa, Ritva; Torkkeli, Mika; Karjalainen-Lindsberg, Marja-Liisa; Leidenius, Marjut; von Smitten, Karl; Tenhunen, Mikko; Fiedler, Stefan; Bravin, Alberto; Weiss, Thomas M.; Suortti, Pekka

    2005-07-01

    Twenty-eight human breast tumour specimens were studied with small-angle x-ray scattering (SAXS), and 10 of those were imaged by the diffraction enhanced x-ray imaging (DEI) technique. The sample diameter was 20 mm and the thickness 1 mm. Two examples of ductal carcinoma are illustrated by histology images, DEI, and maps of the collagen d-spacing and scattered intensity in the Porod regime, which characterize the SAXS patterns from collagen-rich regions of the samples. Histo-pathology reveals the cancer-invaded regions, and the maps of the SAXS parameters show that in these regions the scattering signal differs significantly from scattering by the surrounding tissue, indicating a degradation of the collagen structure in the invaded regions. The DEI images show the borders between collagen and adipose tissue and provide a co-ordinate system for tissue mapping by SAXS. In addition, degradation of the collagen structure in an invaded region is revealed by fading contrast of the DEI refraction image. The 28 samples include fresh, defrosted tissue and formalin-fixed tissue. The d-values with their standard deviations are given. In the fresh samples there is a systematic 0.76% increase of the d-value in the invaded regions, averaged over 11 samples. Only intra-sample comparisons are made for the formalin-fixed samples, and with a long fixation time, the difference in the d-value stabilizes at about 0.7%. The correspondence between the DEI images, the SAXS maps and the histo-pathology suggests that definitive information on tumour growth and malignancy is obtained by combining these x-ray methods.

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

    PubMed

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

    2016-07-29

    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.

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

    PubMed

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

    2012-01-28

    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 ZnBr(2) and NaCl systems from the literature.

  10. Early nucleation events in the polymerization of actin, probed by time-resolved small-angle x-ray scattering

    PubMed Central

    Oda, Toshiro; Aihara, Tomoki; Wakabayashi, Katsuzo

    2016-01-01

    Nucleators generating new F-actin filaments play important roles in cell activities. Detailed information concerning the events involved in nucleation of actin alone in vitro is fundamental to understanding these processes, but such information has been hard to come by. We addressed the early process of salt-induced polymerization of actin using the time-resolved synchrotron small-angle X-ray scattering (SAXS). Actin molecules in low salt solution maintain a monomeric state by an electrostatic repulsive force between molecules. On mixing with salts, the repulsive force was rapidly screened, causing an immediate formation of many of non-polymerizable dimers. SAXS kinetic analysis revealed that tetramerization gives the highest energetic barrier to further polymerization, and the major nucleation is the formation of helical tetramers. Filaments start to grow rapidly with the formation of pentamers. These findings suggest an acceleration mechanism of actin assembly by a variety of nucleators in cells. PMID:27775032

  11. 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.

  12. In situ probing calcium carbonate formation by combining fast controlled precipitation method and small-angle X-ray scattering.

    PubMed

    Chao, Yanjia; Horner, Olivier; Vallée, Philippe; Meneau, Florian; Alos-Ramos, Olga; Hui, Franck; Turmine, Mireille; Perrot, Hubert; Lédion, Jean

    2014-04-01

    The initial stage of calcium carbonate nucleation and growth, found usually in "natural" precipitation conditions, is still not well understood. The calcium carbonate formation for moderate supersaturation level could be achieved by an original method called the fast controlled precipitation (FCP) method. FCP was coupled with SAXS (small-angle X-ray scattering) measurements to get insight into the nucleation and growth mechanisms of calcium carbonate particles in Ca(HCO3)2 aqueous solutions. Two size distributions of particles were observed. The particle size evolutions of these two distributions were obtained by analyzing the SAXS data. A nice agreement was obtained between the total volume fractions of CaCO3 obtained by SAXS analysis and by pH-resistivity curve modeling (from FCP tests).

  13. 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

  14. 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.

  15. Small angle X-ray scattering and 31P NMR studies on the phase behavior of phospholipid bilayered mixed micelles

    NASA Astrophysics Data System (ADS)

    Bolze, Jörg; Fujisawa, Tetsuro; Nagao, Takashi; Norisada, Kazushi; Saitô, Hazime; Naito, Akira

    2000-10-01

    The phase behavior of lipid bilayered micelles (`bicelles') (dimyristoyl-phosphatidylcholine, DMPC/dihexanoyl-phosphatidyl-choline, DHPC 2.6/1) has been studied by small angle X-ray scattering and 31P NMR. Below 3% w/v the bilayers are arranged in tightly packed stacks. At intermediate concentrations single units are observed, whereas at 24% w/v and higher, weak stacking occurs again. The DMPC/DHPC ratio in the bicelles strongly increases at low concentration, which is correlated with an increase in the bicelle size and stacking. The increase of the order parameter in a magnetic field is related to the stack formation. Below 297 K there is no stacking at any concentration and no magnetic alignment.

  16. Temperature dependence of the ripple structure in dimyristoylphosphatidylcholine studied by synchrotron X-ray small-angle diffraction.

    PubMed

    Matuoka, S; Kato, S; Akiyama, M; Amemiya, Y; Hatta, I

    1990-10-05

    The ripple structure of 1,2-dimyristoyl-L-phosphatidylcholine (DMPC) multibilayer containing excess water (60 wt%) was studied by synchrotron X-ray small-angle diffraction. The (0,1) spacing which corresponds to the ripple repeat distance depends on temperature: At 13 degrees C the (0,1) spacing is 14.15 nm, the spacing decreases at higher temperatures and reaches 12.1 nm at 23.5 degrees C, just below the main transition temperature. The spacing is in good agreement between heating process and cooling process except for the supercooling region. The result suggests that the rearrangement of the ripple structure takes place during temperature change successively. The Landau-de Gennes free energy equation explains well the temperature dependence of the ripple repeat distance.

  17. 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.

  18. Molecular shapes from small-angle X-ray scattering: extension of the theory to higher scattering angles.

    PubMed

    Shneerson, V L; Saldin, D K

    2009-03-01

    A low-resolution shape of a molecule in solution may be deduced from measured small-angle X-ray scattering I(q) data by exploiting a Hankel transform relation between the coefficients of a multipole expansion of the scattered amplitude and corresponding coefficients of the electron density. In the past, the radial part of the Hankel transform has been evaluated with the aid of a truncated series expansion of a spherical Bessel function. It is shown that series truncation may be avoided by analytically performing the radial integral over an entire Bessel function. The angular part of the integral involving a spherical harmonic kernel is performed by quadrature. Such a calculation also allows a convenient incorporation of a molecular hydration shell of constant density intermediate between that of the protein and the solvent. Within this framework, we determine the multipole coefficients of the shape function by optimization of the agreement with experimental data by simulated annealing.

  19. Guinier peak analysis for visual and automated inspection of small-angle X-ray scattering data.

    PubMed

    Putnam, Christopher D

    2016-10-01

    The Guinier region in small-angle X-ray scattering (SAXS) defines the radius of gyration, Rg, and the forward scattering intensity, I(0). In Guinier peak analysis (GPA), the plot of qI(q) versus q(2) transforms the Guinier region into a characteristic peak for visual and automated inspection of data. Deviations of the peak position from the theoretical position in dimensionless GPA plots can suggest parameter errors, problematic low-resolution data, some kinds of intermolecular interactions or elongated scatters. To facilitate automated analysis by GPA, the elongation ratio (ER), which is the ratio of the areas in the pair-distribution function P(r) after and before the P(r) maximum, was characterized; symmetric samples have ER values around 1, and samples with ER values greater than 5 tend to be outliers in GPA analysis. Use of GPA+ER can be a helpful addition to SAXS data analysis pipelines.

  20. Investigating the Effect of Adding Drug (Lidocaine) to a Drug Delivery System Using Small-Angle X-Ray Scattering

    NASA Astrophysics Data System (ADS)

    Balogh, Joakim; Pedersen, Jan Skov

    The effect on a model drug delivery system when adding a drug, lidocaine, has been studied. Temperature and concentration dependence of a nonionic microemulsion with part of the oil, 1 and %[vol.]10, substituted with drug has been investigated. A nonionic oil-in-water microemulsion consisting of CH3(CH2)11(OCH2CH2)5OH, (C12E5), decane, water and the drug (lidocaine) that has been used to substitute part of the oil was studied. The microscopic differences have been derived from small-angle X-ray scattering (SAXS) data and the results are compared with light scattering data. Using these results together with the macroscopic differences, as observed in the phase diagram (lowering of phase boundaries), between the systems with and without lidocaine can be explained.

  1. Porosity of microporous zeolites A, X and ZSM-5 studied by small angle X-ray scattering and nitrogen adsorption

    NASA Astrophysics Data System (ADS)

    Du, Xiaoming; Wu, Erdong

    2007-09-01

    Small-angle X-ray scattering (SAXS) using synchrotron radiation and nitrogen adsorption have been applied to characterizations of porosities and microporous structures for the zeolites of NaA, KA, CaA, NaX and ZSM-5. Besides the information on the external morphology of the particles of the zeolites, the complementation of the two techniques has revealed rich and consistent structural and surface information on the molecular scale crystalline pores of these zeolites. Analyses of the data suggest that the determined sizes of the micropores imply the pore spaces occupied by the probe molecules of water in the SAXS and nitrogen in adsorption techniques, respectively. The microporous information of NaA and KA are difficult to obtain from nitrogen adsorption, due to the blocking of nitrogen by their narrow channels, but have been satisfactorily measured by SAXS. The factors causing variations of the measured values of the parameters in different analysis methods have been discussed.

  2. 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.

  3. Insights on the structural dynamics of Leishmania braziliensis Hsp90 molecular chaperone by small angle X-ray scattering.

    PubMed

    Seraphim, Thiago V; Silva, Kelly P; Dores-Silva, Paulo R; Barbosa, Leandro R S; Borges, Júlio C

    2017-04-01

    Heat shock protein of 90kDa (Hsp90) is an essential molecular chaperone involved in a plethora of cellular activities which modulate protein homeostasis. During the Hsp90 mechanochemical cycle, it undergoes large conformational changes, oscillating between open and closed states. Although structural and conformational equilibria of prokaryotic and some eukaryotic Hsp90s are known, some protozoa Hsp90 structures and dynamics are poorly understood. In this study, we report the solution structure and conformational dynamics of Leishmania braziliensis Hsp90 (LbHsp90) investigated by small angle X-ray scattering (SAXS). The results indicate that LbHsp90 coexists in open and closed conformations in solution and that the linkers between domains are not randomly distributed. These findings noted interesting features of the LbHsp90 system, opening doors for further conformational studies of other protozoa chaperones. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Resolving Individual Components in Protein-RNA Complexes Using Small-Angle X-ray Scattering Experiments.

    PubMed

    Rambo, Robert P

    2015-01-01

    Small-angle X-ray scattering (SAXS) of protein-RNA complexes has developed into an efficient and economical approach for determining low-resolution shapes of particles in solution. Here, we demonstrate a mutliphase volumetric modeling approach capable of resolving individual components within a low-resolution shape. Through three case studies, we describe the SAXS data collecting strategies, premodeling analysis, and computational methods required for deconstructing complexes into their respective components. This chapter presents an approach using the programs ScÅtter and MONSA and custom scripts for averaging and aligning of multiple independent modeling runs. The method can image small (7kDa) masses within the context of complex and is capable of visualizing ligand-induced conformational changes. Nevertheless, computational algorithms are not without error, and we describe specific considerations during SAXS data reduction and modeling to mitigate possible false positives.

  5. 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.

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

    PubMed

    de la Venta, J; Bouzas, V; Pucci, A; Laguna-Marco, M A; Haskel, D; te Velthuis, S G E; Hoffmann, A; Lal, J; Bleuel, M; Ruggeri, G; de Julián Fernández, C; García, M A

    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 x 10(-4) was found at the Au L3 edge of thiol capped Au NPs embedded in a polyethylene matrix for which Superconducting Quantum Interference Device (SQUID) magnetometry yielded a saturation magnetization, M(S), of 0.06 emu/g(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.

  7. 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

  8. DARA: a web server for rapid search of structural neighbours using solution small angle X-ray scattering data

    PubMed Central

    Kikhney, Alexey G.; Panjkovich, Alejandro; Sokolova, Anna V.; Svergun, Dmitri I.

    2016-01-01

    Motivation: Small angle X-ray scattering (SAXS) is an established method for studying biological macromolecules in solution, whereby the experimental scattering patterns relate to the quaternary and tertiary structure of the macromolecule. Here we present DARA, a web-server, that queries over 150 000 scattering profiles pre-computed from the high resolution models of macromolecules and biological assemblies in the Protein Data Bank, to rapidly find nearest neighbours of a given experimental or theoretical SAXS pattern. Identification of the best scattering equivalents provides a straightforward and automated way of structural assessment of macromolecules based on a SAXS profile. DARA results are useful e.g. for fold recognition and finding of biologically active oligomers. Availability and implementation: http://dara.embl-hamburg.de/ Contact: svergun@embl-hamburg.de PMID:26504146

  9. Dispersed SiC nanoparticles in Ni observed by ultra-small-angle X-ray scattering

    SciTech Connect

    Xie, R.; Ilavsky, J.; Huang, H. F.; Zhou, X. L.; Yang, C.; Wang, Y. Z.; Xu, H. J.

    2016-11-24

    In this paper, a metal-ceramic composite, nickel reinforced with SiC nanoparticles, was synthesized and characterized for its potential application in next-generation molten salt nuclear reactors. Synchrotron ultra-small-angle X-ray scattering (USAXS) measurements were conducted on the composite. The size distribution and number density of the SiC nanoparticles in the material were obtained through data modelling. Scanning and transmission electron microscopy characterization were performed to substantiate the results of the USAXS measurements. Tensile tests were performed on the samples to measure the change in their yield strength after doping with the nanoparticles. Finally, the average interparticle distance was calculated from the USAXS results and is related to the increased yield strength of the composite.

  10. Dispersed SiC nanoparticles in Ni observed by ultra-small-angle X-ray scattering

    DOE PAGES

    Xie, R.; Ilavsky, J.; Huang, H. F.; ...

    2016-11-24

    In this paper, a metal-ceramic composite, nickel reinforced with SiC nanoparticles, was synthesized and characterized for its potential application in next-generation molten salt nuclear reactors. Synchrotron ultra-small-angle X-ray scattering (USAXS) measurements were conducted on the composite. The size distribution and number density of the SiC nanoparticles in the material were obtained through data modelling. Scanning and transmission electron microscopy characterization were performed to substantiate the results of the USAXS measurements. Tensile tests were performed on the samples to measure the change in their yield strength after doping with the nanoparticles. Finally, the average interparticle distance was calculated from the USAXSmore » results and is related to the increased yield strength of the composite.« less

  11. Domain motion in cytochrome P450 reductase: conformational equilibria revealed by NMR and small-angle x-ray scattering.

    PubMed

    Ellis, Jacqueline; Gutierrez, Aldo; Barsukov, Igor L; Huang, Wei-Cheng; Grossmann, J Günter; Roberts, Gordon C K

    2009-12-25

    NADPH-cytochrome P450 reductase (CPR), a diflavin reductase, plays a key role in the mammalian P450 mono-oxygenase system. In its crystal structure, the two flavins are close together, positioned for interflavin electron transfer but not for electron transfer to cytochrome P450. A number of lines of evidence suggest that domain motion is important in the action of the enzyme. We report NMR and small-angle x-ray scattering experiments addressing directly the question of domain organization in human CPR. Comparison of the (1)H-(15)N heteronuclear single quantum correlation spectrum of CPR with that of the isolated FMN domain permitted identification of residues in the FMN domain whose environment differs in the two situations. These include several residues that are solvent-exposed in the CPR crystal structure, indicating the existence of a second conformation in which the FMN domain is involved in a different interdomain interface. Small-angle x-ray scattering experiments showed that oxidized and NADPH-reduced CPRs have different overall shapes. The scattering curve of the reduced enzyme can be adequately explained by the crystal structure, whereas analysis of the data for the oxidized enzyme indicates that it exists as a mixture of approximately equal amounts of two conformations, one consistent with the crystal structure and one a more extended structure consistent with that inferred from the NMR data. The correlation between the effects of adenosine 2',5'-bisphosphate and NADPH on the scattering curve and their effects on the rate of interflavin electron transfer suggests that this conformational equilibrium is physiologically relevant.

  12. Characterization of pore structure in metal-organic framework by small-angle X-ray scattering.

    PubMed

    Tsao, Cheng-Si; Yu, Ming-Sheng; Chung, Tsui-Yun; Wu, Hsiu-Chu; Wang, Cheng-Yu; Chang, Kuei-Sen; Chen, Hsin-Lung

    2007-12-26

    MOF-5-like crystals were studied by small-angle X-ray scattering (SAXS) to reveal, both quantitatively and qualitatively, their real structural details, including pore surface characteristics, pore shape, size distribution, specific surface area (SSA), spatial distribution, and pore-network structure. A combined SAXS and wide-angle X-ray scattering (WAXS) experiment was conducted to investigate the variation of the pore structure with the MOF-5 crystalline phase produced at different cooling rates. The SSA of the MOF-5 crystals synthesized herein spanned a broad range from approximately 3100 to 800 m2/g. The real pore structures were divided into two regimes. In regime I the material consisted mainly of micropores of radius approximately 8 A as well as mesopores of radius 120 approximately 80 A. The structure in regime II was a fractal network of aggregated mesopores with radius >or=32 A as the monomer, reducing SSA and hydrogen uptake capacity at room temperature. The two regimes can be manipulated by controlling the synthesis parameters. The concurrent evolution of pore structure and crystalline phase during heating for solvent removal was also revealed by the in-situ SAXS/WAXS measurement. The understanding of the impact of the real pore structure on the properties is important to establish a favorable synthetic approach for markedly improving the hydrogen storage capacity of MOF-5.

  13. Preparing Monodisperse Macromolecular Samples for Successful Biological Small-Angle X-ray and Neutron Scattering Experiments

    PubMed Central

    Jeffries, Cy M.; Graewert, Melissa A.; Blanchet, Clément E.; Langley, David B.; Whitten, Andrew E.; Svergun, Dmitri I

    2017-01-01

    Small-angle X-ray and neutron scattering (SAXS and SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions from all atoms within the illuminated sample volume including the solvent and buffer components as well as the macromolecules of interest. In order to obtain structural information, it is essential to prepare an exactly matched solvent blank so that background scattering contributions can be accurately subtracted from the sample scattering to obtain the net scattering from the macromolecules in the sample. In addition, sample heterogeneity caused by contaminants, aggregates, mismatched solvents, radiation damage or other factors can severely influence and complicate data analysis so it is essential that the samples are pure and monodisperse for the duration of the experiment. This Protocol outlines the basic physics of SAXS and SANS and reveals how the underlying conceptual principles of the techniques ultimately ‘translate’ into practical laboratory guidance for the production of samples of sufficiently high quality for scattering experiments. The procedure describes how to prepare and characterize protein and nucleic acid samples for both SAXS and SANS using gel electrophoresis, size exclusion chromatography and light scattering. Also included are procedures specific to X-rays (in-line size exclusion chromatography SAXS) and neutrons, specifically preparing samples for contrast matching/variation experiments and deuterium labeling of proteins. PMID:27711050

  14. Structural transformations during gelatinization of starches in limited water: combined wide- and small-angle X-ray scattering study.

    PubMed

    Vermeylen, Rudi; Derycke, Veerle; Delcour, Jan A; Goderis, Bart; Reynaers, Harry; Koch, Michel H J

    2006-04-01

    Rice flour (18-25% moisture) and potato starch (20% moisture) were heated with continuous recording of the X-ray scattering during gelatinization. Rice flours displayed A-type crystallinity, which gradually decreased during gelatinization. The development of the characteristic 9 nm small-angle X-ray scattering (SAXS) peak during heating at sub-gelatinization temperatures indicated the gradual evolution into a stacked lamellar system. At higher temperatures, the crystalline and lamellar order was progressively lost. For potato starch (B-type crystallinity), no 9 nm SAXS peak was observed at ambient temperatures. Following the development of lamellar structures at sub-gelatinization temperatures, B-type crystallinity and lamellar order was lost during gelatinization. On cooling of partially gelatinized potato starch, A-type crystallinity steadily increased, but no formation of stacked lamellar structures was observed. Results were interpreted in terms of a high-temperature B- to A-type recrystallization, in which the lateral movement of double helices was accompanied by a shift along their helical axis. The latter is responsible for the inherent frustration of the lamellar stacks.

  15. Measurement of carbon condensates using small-angle x-ray scattering during detonation of high explosives

    NASA Astrophysics Data System (ADS)

    Willey, T. M.; Bagge-Hansen, M.; Lauderbach, L.; Hodgin, R.; Hansen, D.; May, C.; van Buuren, T.; Dattelbaum, D. M.; Gustavsen, R. L.; Watkins, E. B.; Firestone, M. A.; Jensen, B. J.; Graber, T.; Bastea, S.; Fried, L.

    2017-01-01

    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) endstation has been developed for use at The Dynamic Compression Sector to observe carbon condensation during detonation. The endstation and beamline demonstrate unprecedented fidelity; SAXS profiles can be acquired from single x-ray pulses, which in 24-bunch mode are about 80 ps in duration and arrive every 153.4 ns. This paper presents both the current temporal capabilities of this beamline, and the ability to distinguish different carbon condensate morphologies as they form behind detonation fronts. To demonstrate temporal capabilities, three shots acquired during detonation of hexanitrostilbene (HNS) are interleaved to show the evolution of the SAXS in about 50 ns steps. To show fidelity of the SAXS, the scattering from carbon condensates at several hundred nanoseconds varies with explosive: scattering from HNS is consistent with a complex morphology that we assert is associated with sp2 carbon., while Comp B scattering is consistent with soots containing three-dimensional diamond nanoparticles.

  16. 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.

  17. Intrinsic flexibility of West Nile virus protease in solution characterized using small-angle X-ray scattering.

    PubMed

    Garces, Andrea P; Watowich, Stanley J

    2013-10-01

    West Nile virus (WNV) is a mosquito-borne flavivirus with a rapidly expanding global distribution. Infection can cause severe neurological disease and fatality in humans. Efforts are ongoing to develop antiviral drugs that inhibit the WNV protease, a viral enzyme required for polyprotein processing. Unfortunately, little is known about the solution structure of recombinant WNV protease (NS2B-NS3pro) used for antiviral drug discovery and development, although X-ray crystal structures and nuclear magnetic resonance (NMR) studies have provided valuable insights into the interactions between NS2B-NS3pro and peptide-based inhibitors. We completed small-angle X-ray scattering and Fourier transform infrared spectroscopy experiments to determine the solution structure and dynamics of WNV NS2B-NS3pro in the absence of a bound substrate or inhibitor. Importantly, these solution studies suggested that all or most of the NS2B cofactor was highly flexible and formed an ensemble of structures, in contrast to the NS2B tertiary structures observed in crystallographic and NMR studies. The secondary structure of NS2B-NS3pro in solution had high β-content, similar to the secondary structure observed in crystallographic studies. This work provided evidence of the intrinsic flexibility and conformational heterogeneity of the NS2B chain of the WNV protease in the absence of substratelike ligands, which should be considered during antiviral drug discovery and development efforts.

  18. Combined small angle X-ray solution scattering with atomic force microscopy for characterizing radiation damage on biological macromolecules.

    PubMed

    Costa, Luca; Andriatis, Alexander; Brennich, Martha; Teulon, Jean-Marie; Chen, Shu-Wen W; Pellequer, Jean-Luc; Round, Adam

    2016-10-27

    Synchrotron radiation facilities are pillars of modern structural biology. Small-Angle X-ray scattering performed at synchrotron sources is often used to characterize the shape of biological macromolecules. A major challenge with high-energy X-ray beam on such macromolecules is the perturbation of sample due to radiation damage. By employing atomic force microscopy, another common technique to determine the shape of biological macromolecules when deposited on flat substrates, we present a protocol to evaluate and characterize consequences of radiation damage. It requires the acquisition of images of irradiated samples at the single molecule level in a timely manner while using minimal amounts of protein. The protocol has been tested on two different molecular systems: a large globular tetremeric enzyme (β-Amylase) and a rod-shape plant virus (tobacco mosaic virus). Radiation damage on the globular enzyme leads to an apparent increase in molecular sizes whereas the effect on the long virus is a breakage into smaller pieces resulting in a decrease of the average long-axis radius. These results show that radiation damage can appear in different forms and strongly support the need to check the effect of radiation damage at synchrotron sources using the presented protocol.

  19. The measurement capabilities of cross-sectional profile of Nanoimprint template pattern using small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Yamanaka, Eiji; Taniguchi, Rikiya; Itoh, Masamitsu; Omote, Kazuhiko; Ito, Yoshiyasu; Ogata, Kiyoshi; Hayashi, Naoya

    2016-05-01

    Nanoimprint lithography (NIL) is one of the most potential candidates for the next generation lithography for semiconductor. It will achieve the lithography with high resolution and low cost. High resolution of NIL will be determined by a high definition template. Nanoimprint lithography will faithfully transfer the pattern of NIL template to the wafer. Cross-sectional profile of the template pattern will greatly affect the resist profile on the wafer. Therefore, the management of the cross-sectional profile is essential. Grazing incidence small angle x-ray scattering (GI-SAXS) technique has been proposed as one of the method for measuring cross-sectional profile of periodic nanostructure pattern. Incident x-rays are irradiated to the sample surface with very low glancing angle. It is close to the critical angle of the total reflection of the x-ray. The scattered x-rays from the surface structure are detected on a two-dimensional detector. The observed intensity is discrete in the horizontal (2θ) direction. It is due to the periodicity of the structure, and diffraction is observed only when the diffraction condition is satisfied. In the vertical (β) direction, the diffraction intensity pattern shows interference fringes reflected to height and shape of the structure. Features of the measurement using x-ray are that the optical constant for the materials are well known, and it is possible to calculate a specific diffraction intensity pattern based on a certain model of the cross-sectional profile. The surface structure is estimated by to collate the calculated diffraction intensity pattern that sequentially while changing the model parameters with the measured diffraction intensity pattern. Furthermore, GI-SAXS technique can be measured an object in a non-destructive. It suggests the potential to be an effective tool for product quality assurance. We have developed a cross-sectional profile measurement of quartz template pattern using GI-SAXS technique. In this

  20. Operando Grazing Incidence Small-Angle X-ray Scattering/X-ray Diffraction of Model Ordered Mesoporous Lithium-Ion Battery Anodes

    DOE PAGES

    Bhaway, Sarang M.; Qiang, Zhe; Xia, Yanfeng; ...

    2017-02-07

    Emergent lithium-ion (Li+) batteries commonly rely on nanostructuring of the active electrode materials to decrease the Li+ ion diffusion path length and to accommodate the strains associated with the insertion and de-insertion of Li+, but in many cases these nanostructures evolve during electrochemical charging–discharging. This change in the nanostructure can adversely impact performance, and challenges remain regarding how to control these changes from the perspective of morphological design. In order to address these questions, operando grazing-incidence small-angle X-ray scattering and X-ray diffraction (GISAXS/GIXD) were used to assess the structural evolution of a family of model ordered mesoporous NiCo2O4 anode filmsmore » during battery operation. The pore dimensions were systematically varied and appear to impact the stability of the ordered nanostructure during the cycling. For the anodes with small mesopores (≈9 nm), the ordered nanostructure collapses during the first two charge–discharge cycles, as determined from GISAXS. This collapse is accompanied by irreversible Li-ion insertion within the oxide framework, determined from GIXD and irreversible capacity loss. Anodes with larger ordered mesopores (17–28 nm) mostly maintained their nanostructure through the first two cycles with reversible Li-ion insertion. During the second cycle, there was a small additional deformation of the mesostructure. Furthermore, this preservation of the ordered structure lead to significant improvement in capacity retention during these first two cycles; but, a gradual loss in the ordered nanostructure from continuing deformation of the ordered structure during additional charge–discharge cycles leads to capacity decay in battery performance. We translate these multiscale operando measurements provide insight into how changes at the atomic scale (lithium insertion and de-insertion) to the nanostructure during battery operation. Moreover, small changes in the

  1. Operando Grazing Incidence Small-Angle X-ray Scattering/X-ray Diffraction of Model Ordered Mesoporous Lithium-Ion Battery Anodes.

    PubMed

    Bhaway, Sarang M; Qiang, Zhe; Xia, Yanfeng; Xia, Xuhui; Lee, Byeongdu; Yager, Kevin G; Zhang, Lihua; Kisslinger, Kim; Chen, Yu-Ming; Liu, Kewei; Zhu, Yu; Vogt, Bryan D

    2017-02-28

    Emergent lithium-ion (Li(+)) batteries commonly rely on nanostructuring of the active electrode materials to decrease the Li(+) ion diffusion path length and to accommodate the strains associated with the insertion and de-insertion of Li(+), but in many cases these nanostructures evolve during electrochemical charging-discharging. This change in the nanostructure can adversely impact performance, and challenges remain regarding how to control these changes from the perspective of morphological design. In order to address these questions, operando grazing-incidence small-angle X-ray scattering and X-ray diffraction (GISAXS/GIXD) were used to assess the structural evolution of a family of model ordered mesoporous NiCo2O4 anode films during battery operation. The pore dimensions were systematically varied and appear to impact the stability of the ordered nanostructure during the cycling. For the anodes with small mesopores (≈9 nm), the ordered nanostructure collapses during the first two charge-discharge cycles, as determined from GISAXS. This collapse is accompanied by irreversible Li-ion insertion within the oxide framework, determined from GIXD and irreversible capacity loss. Conversely, anodes with larger ordered mesopores (17-28 nm) mostly maintained their nanostructure through the first two cycles with reversible Li-ion insertion. During the second cycle, there was a small additional deformation of the mesostructure. This preservation of the ordered structure lead to significant improvement in capacity retention during these first two cycles; however, a gradual loss in the ordered nanostructure from continuing deformation of the ordered structure during additional charge-discharge cycles leads to capacity decay in battery performance. These multiscale operando measurements provide insight into how changes at the atomic scale (lithium insertion and de-insertion) are translated to the nanostructure during battery operation. Moreover, small changes in the

  2. 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

    2015-09-09

    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.

  3. Microstructural characterization of dental zinc phosphate cements using combined small angle neutron scattering and microfocus X-ray computed tomography.

    PubMed

    Viani, Alberto; Sotiriadis, Konstantinos; Kumpová, Ivana; Mancini, Lucia; Appavou, Marie-Sousai

    2017-04-01

    To characterize the microstructure of two zinc phosphate cement formulations in order to investigate the role of liquid/solid ratio and composition of powder component, on the developed porosity and, consequently, on compressive strength. X-ray powder diffraction with the Rietveld method was used to study the phase composition of zinc oxide powder and cements. Powder component and cement microstructure were investigated with scanning electron microscopy. Small angle neutron scattering (SANS) and microfocus X-ray computed tomography (XmCT) were together employed to characterize porosity and microstructure of dental cements. Compressive strength tests were performed to evaluate their mechanical performance. The beneficial effects obtained by the addition of Al, Mg and B to modulate powder reactivity were mitigated by the crystallization of a Zn aluminate phase not involved in the cement setting reaction. Both cements showed spherical pores with a bimodal distribution at the micro/nano-scale. Pores, containing a low density gel-like phase, developed through segregation of liquid during setting. Increasing liquid/solid ratio from 0.378 to 0.571, increased both SANS and XmCT-derived specific surface area (by 56% and 22%, respectively), porosity (XmCT-derived porosity increased from 3.8% to 5.2%), the relative fraction of large pores ≥50μm, decreased compressive strength from 50±3MPa to 39±3MPa, and favored microstructural and compositional inhomogeneities. Explain aspects of powder design affecting the setting reaction and, in turn, cement performance, to help in optimizing cement formulation. The mechanism behind development of porosity and specific surface area explains mechanical performance, and processes such as erosion and fluoride release/uptake. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. Microstructural characterization of dental zinc phosphate cements using combined small angle neutron scattering and microfocus X-ray computed tomography.

    PubMed

    Viani, Alberto; Sotiriadis, Konstantinos; Kumpová, Ivana; Mancini, Lucia; Appavou, Marie-Sousai

    2017-02-17

    To characterize the microstructure of two zinc phosphate cement formulations in order to investigate the role of liquid/solid ratio and composition of powder component, on the developed porosity and, consequently, on compressive strength. X-ray powder diffraction with the Rietveld method was used to study the phase composition of zinc oxide powder and cements. Powder component and cement microstructure were investigated with scanning electron microscopy. Small angle neutron scattering (SANS) and microfocus X-ray computed tomography (XmCT) were together employed to characterize porosity and microstructure of dental cements. Compressive strength tests were performed to evaluate their mechanical performance. The beneficial effects obtained by the addition of Al, Mg and B to modulate powder reactivity were mitigated by the crystallization of a Zn aluminate phase not involved in the cement setting reaction. Both cements showed spherical pores with a bimodal distribution at the micro/nano-scale. Pores, containing a low density gel-like phase, developed through segregation of liquid during setting. Increasing liquid/solid ratio from 0.378 to 0.571, increased both SANS and XmCT-derived specific surface area (by 56% and 22%, respectively), porosity (XmCT-derived porosity increased from 3.8% to 5.2%), the relative fraction of large pores ≥50μm, decreased compressive strength from 50±3MPa to 39±3MPa, and favored microstructural and compositional inhomogeneities. Explain aspects of powder design affecting the setting reaction and, in turn, cement performance, to help in optimizing cement formulation. The mechanism behind development of porosity and specific surface area explains mechanical performance, and processes such as erosion and fluoride release/uptake. Copyright © 2017 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

  5. Coupling High Throughput Microfluidics and Small-Angle X-ray Scattering to Study Protein Crystallization from Solution.

    PubMed

    Pham, Nhat; Radajewski, Dimitri; Round, Adam; Brennich, Martha; Pernot, Petra; Biscans, Béatrice; Bonneté, Françoise; Teychené, Sébastien

    2017-02-21

    In this work, we propose the combination of small-angle X-ray scattering (SAXS) and high throughput, droplet based microfluidics as a powerful tool to investigate macromolecular interactions, directly related to protein solubility. For this purpose, a robust and low cost microfluidic platform was fabricated for achieving the mixing of proteins, crystallization reagents, and buffer in nanoliter volumes and the subsequent generation of nanodroplets by means of a two phase flow. The protein samples are compartmentalized inside droplets, each one acting as an isolated microreactor. Hence their physicochemical conditions (concentration, pH, etc.) can be finely tuned without cross-contamination, allowing the screening of a huge number of saturation conditions with a small amount of biological material. The droplet flow is synchronized with synchrotron radiation SAXS measurements to probe protein interactions while minimizing radiation damage. To this end, the experimental setup was tested with rasburicase (known to be very sensitive to denaturation), proving the structural stability of the protein in the droplets and the absence of radiation damage. Subsequently weak interaction variations as a function of protein saturation was studied for the model protein lysozime. The second virial coefficients (A2) were determined from the X-ray structure factors extrapolated to the origin. A2 obtained values were found to be in good agreement with data previously reported in literature but using only a few milligrams of protein. The experimental results presented here highlight the interest and convenience of using this methodology as a promising and potential candidate for studying protein interactions for the construction of phase diagrams.

  6. Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering

    PubMed Central

    Wang, Yun-Xing; Zuo, Xiaobing; Wang, Jinbu; Yu, Ping; Butcher, Samuel E.

    2013-01-01

    Among the greatest advances in biology today are the discoveries of various roles played by RNA in biological processes. However, despite significant advances in RNA structure determination using X-ray crystallography [1] and solution NMR [2–4], the number of bona fide RNA structures is very limited, in comparison with the growing number of known functional RNAs. This is because of great difficulty in growing crystals or/and obtaining phase information, and severe size constraints on structure determination by solution NMR spectroscopy. Clearly, there is an acute need for new methodologies for RNA structure determination. The prevailing approach for structure determination of RNA in solution is a “bottom-up” approach that was basically transplanted from the approach used for determining protein structures, despite vast differences in both structural features and chemical compositions between these two types of biomacromolecules. In this chapter, we describe a new method, which has been reported recently, for rapid global structure determination of RNAs using solution-based NMR spectroscopy and small-angle X-ray scattering. The method treats duplexes as major building blocks of RNA structures. By determining the global orientations of the duplexes and the overall shape, the global structure of an RNA can be constructed and further regularized using Xplor-NIH. The utility of the method was demonstrated in global structure determination of two RNAs, a 71-nt and 102-nt RNAs with an estimated backbone RMSD ~3.0 Å. The global structure opens door to high-resolution structure determination in solution. PMID:20554045

  7. Small-angle X-ray scattering for imaging of surface layers on intact bacteria in the native environment.

    PubMed

    Sekot, Gerhard; Schuster, David; Messner, Paul; Pum, Dietmar; Peterlik, Herwig; Schäffer, Christina

    2013-05-01

    Crystalline cell surface layers (S-layers) represent a natural two-dimensional (2D) protein self-assembly system with nanometer-scale periodicity that decorate many prokaryotic cells. Here, we analyze the S-layer on intact bacterial cells of the Gram-positive organism Geobacillus stearothermophilus ATCC 12980 and the Gram-negative organism Aquaspirillum serpens MW5 by small-angle X-ray scattering (SAXS) and relate it to the structure obtained by transmission electron microscopy (TEM) after platinum/carbon shadowing. By measuring the scattering pattern of X rays obtained from a suspension of bacterial cells, integral information on structural elements such as the thickness and lattice parameters of the S-layers on intact, hydrated cells can be obtained nondestructively. In contrast, TEM of whole mounts is used to analyze the S-layer lattice type and parameters as well as the physical structure in a nonaqueous environment and local information on the structure is delivered. Application of SAXS to S-layer research on intact bacteria is a challenging task, as the scattering volume of the generally thin (3- to 30-nm) bacterial S-layers is low in comparison to the scattering volume of the bacterium itself. For enhancement of the scattering contrast of the S-layer in SAXS measurement, either silicification (treatment with tetraethyl orthosilicate) is used, or the difference between SAXS signals from an S-layer-deficient mutant and the corresponding S-layer-carrying bacterium is used for determination of the scattering signal. The good agreement of the SAXS and TEM data shows that S-layers on the bacterial cell surface are remarkably stable.

  8. Crystallization of a layered silicate clay as monitored by small- angle x-ray scattering and NMR.

    SciTech Connect

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

    2000-10-01

    The 48-h hydrothermal crystallization of a magnesium silicate clay called hectorite has been investigated in detail. Tetraethylammonium (TEA) ions are used to aid crystallization and become incorporated as the exchange cations within the interlayers. Data from small-angle X-ray scattering (SAXS) using aliquots ex situ are consistent with results obtained previously by X-ray powder diffraction (XRD), thermal gravimetric analysis (TGA), atomic force microscopy (AFM), and IR. All these techniques see clay crystallites beginning to form within the first few hours of reaction. {sup 29}Si NMR displays a visible clay silicate peak after just 1 h. Solid-state {sup 13}C NMR shows evidence of TEA-clay formation in as little as 30 min and also that 80% of the final TEA loading is accomplished in the first 10-12 h. Up to 36 h more is needed to incorporate the remaining 20% of TEA, indicating that a slower event is dominating at the later stages of crystallization. Data from {sup 13}C NMR and SAXS are compared to and are consistent with data from earlier AFM experiments. All present a scenario where initial nucleation and crystallization end after about 14 h, after which this occurs to a lesser extent and primarily agglomeration of particles is taking place. The SAXS data show this in progressively increasing power law values, indicating more 'open' structures that condense into more dense structures with time. In addition, the first in situ study of clay crystallization of any kind was performed by in situ SAXS. A possible clay crystallization mechanism is proposed.

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

    PubMed

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

    2012-04-01

    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.

  10. 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.

  11. 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

  12. Guanidine hydrochloride denaturation of dopamine-induced α-synuclein oligomers: a small-angle X-ray scattering study.

    PubMed

    Pham, Chi L L; Kirby, Nigel; Wood, Kathleen; Ryan, Timothy; Roberts, Blaine; Sokolova, Anna; Barnham, Kevin J; Masters, Colin L; Knott, Robert B; Cappai, Roberto; Curtain, Cyril C; Rekas, Agata

    2014-01-01

    Alpha-synuclein (α-syn) forms the amyloid-containing Lewy bodies found in the brain in Parkinson's disease. The neurotransmitter dopamine (DA) reacts with α-syn to form SDS-resistant soluble, non-amyloid, and melanin-containing oligomers. Their toxicity is debated, as is the nature of their structure and their relation to amyloid-forming conformers of α-syn. The small-angle X-ray scattering technique in combination with modeling by the ensemble optimization method showed that the un-reacted native protein populated three broad classes of conformer, while reaction with DA gave a restricted ensemble range suggesting that the rigid melanin molecule played an important part in their structure. We found that 6 M guanidine hydrochloride did not dissociate α-syn DA-reacted dimers and trimers, suggesting covalent linkages. The pathological significance of covalent association is that if they are non-toxic, the oligomers would act as a sink for toxic excess DA and α-syn; if toxic, their stability could enhance their toxicity. We argue it is essential, therefore, to resolve the question of whether they are toxic or not.

  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. Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering

    PubMed Central

    Bernadó, Pau; Pérez, Yolanda; Blobel, Jascha; Fernández-Recio, Juan; Svergun, Dmitri I; Pons, Miquel

    2009-01-01

    Signal transducer and activator of transcription (STAT) proteins play a crucial role in the activation of gene transcription in response to extracellular stimuli. The regulation and activity of these proteins require a complex rearrangement of the domains. According to the established models, based on crystallographic data, STATs convert from a basal antiparallel inactive dimer into a parallel active one following phosphorylation. The simultaneous analysis of small-angle X-ray scattering data measured at different concentrations of unphosphorylated human STAT5a core domain unambiguously identifies the simultaneous presence of a monomer and a dimer. The dimer is the minor species but could be structurally characterized by SAXS in the presence of the monomer using appropriate computational tools and shown to correspond to the antiparallel assembly. The equilibrium is governed by a moderate dissociation constant of Kd ∼ 90 μM. Integration of these results with previous knowledge of the N-terminal domain structure and dissociation constants allows the modeling of the full-length protein. A complex network of intermolecular interactions of low or medium affinity is suggested. These contacts can be eventually formed or broken to trigger the dramatic modifications in the dimeric arrangement needed for STAT regulation and activity. PMID:19309697

  15. 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.

  16. The Structure of Urease Activation Complexes Examined by Flexibility Analysis, Mutagenesis, and Small-Angle X-Ray Scattering

    PubMed Central

    Quiroz-Valenzuela, 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)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)3, and (UreABC-UreDF)3 confirm that UreD and UreF bind near UreB at the periphery of the (UreAC)3 structure. This study supports an activation model in which a domain-shifted UreB conformation in (UreABC-UreDF)3 allows CO2 and nickel ions to gain access to the nascent active site. PMID:18823937

  17. 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

  18. First Structural Glimpse of CCN3 and CCN5 Multifunctional Signaling Regulators Elucidated by Small Angle X-ray Scattering*

    PubMed Central

    Holbourn, Kenneth P.; Malfois, Marc; Acharya, K. Ravi

    2011-01-01

    The CCN (cyr61, ctgf, nov) proteins (CCN1–6) are an important family of matricellular regulatory factors involved in internal and external cell signaling. They are central to essential biological processes such as adhesion, proliferation, angiogenesis, tumorigenesis, wound healing, and modulation of the extracellular matrix. They possess a highly conserved modular structure with four distinct modules that interact with a wide range of regulatory proteins and ligands. However, at the structural level, little is known although their biological function(s) seems to require cooperation between individual modules. Here we present for the first time structural determinants of two of the CCN family members, CCN3 and CCN5 (expressed in Escherichia coli), using small angle x-ray scattering. The results provide a description of the overall molecular shape and possible general three-dimensional modular arrangement for CCN proteins. These data unequivocally provide insight of the nature of CCN protein(s) in solution and thus important insight into their structure-function relationships. PMID:21543320

  19. Measurements of droplet size in shear-driven atomization using ultra-small angle x-ray scattering

    DOE PAGES

    Kastengren, A.; Ilavsky, J.; Viera, Juan Pablo; ...

    2017-03-16

    Measurements of droplet size in optically-thick, non-evaporating, shear-driven sprays have been made using ultra-small angle x-ray scattering (USAXS). The sprays are produced by orifice-type nozzles coupled to diesel injectors, with measurements conducted from 1 – 24 mm from the orifice, spanning from the optically-dense near-nozzle region to more dilute regions where optical diagnostics are feasible. The influence of nozzle diameter, liquid injection pressure, and ambient density were examined. The USAXS measurements reveal few if any nanoscale droplets, in conflict with a popular computational model of diesel spray breakup. The average droplet diameter rapidly decreases with downstream distance from the nozzlemore » until a plateau value is reached, after which only small changes are seen in droplet diameter. This plateau droplet size is consistent with the droplets being small enough to be stable with respect to further breakup. As a result, liquid injection pressure and nozzle diameter have the biggest impact on droplet size, while ambient density has a smaller effect.« less

  20. Kinetics of copper growth on graphene revealed by time-resolved small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Hodas, M.; Siffalovic, P.; Jergel, M.; Pelletta, M.; Halahovets, Y.; Vegso, K.; Kotlar, M.; Majkova, E.

    2017-01-01

    Metal growth on graphene has many applications. Transition metals are known to favor three-dimensional (3D) cluster growth on graphene. Copper is of particular interest for cost-effective surface-supported catalysis applications and as a contact material in electronics. This paper presents an in situ real-time study of Cu growth kinetics on graphene covering all stages preceding formation of a continuous film performed by laboratory-based grazing-incidence small-angle x-ray scattering (GISAXS) technique. In particular, nucleation and 3D cluster growth, coalescence, and percolation stages were identified. The cluster nucleation saturates after reaching a density of 1012c m-2 at ≈1 monolayer thickness. A Kratky plot and a paracrystal model with cumulative structural disorder were necessary to evaluate properly cluster growth and coalescence, respectively. The power law scaling constants 0.27 ±0.05 and 0.81 ±0.02 of the temporal evolution of Cu cluster size suggest the growth of isolated clusters and dynamic cluster coalescence keeping the cluster shape, respectively. Coalescence and percolation thresholds occur at Cu thicknesses of 2 ±0.4 and 8.8 ±0.7 nm , respectively. This paper demonstrates the potential of laboratory-based in situ GISAXS as a vital diagnostic tool for tailoring a large variety of Cu nanostructures on graphene based on an in situ Cu growth monitoring which is applicable in a broad range of deposition times.

  1. 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

  2. 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.

  3. A potential for overestimating the absolute magnitudes of second virial coefficients by small-angle X-ray scattering.

    PubMed

    Scott, David J; Patel, Trushar R; Winzor, Donald J

    2013-04-15

    Theoretical consideration is given to the effect of cosolutes (including buffer and electrolyte components) on the determination of second virial coefficients for proteins by small-angle X-ray scattering (SAXS)-a factor overlooked in current analyses in terms of expressions for a two-component system. A potential deficiency of existing practices is illustrated by reassessment of published results on the effect of polyethylene glycol concentration on the second virial coefficient for urate oxidase. This error reflects the substitution of I(0,c3,0), the scattering intensity in the limit of zero scattering angle and solute concentration, for I(0,0,0), the corresponding parameter in the limit of zero cosolute concentration (c3) as well. Published static light scattering results on the dependence of the apparent molecular weight of ovalbumin on buffer concentration are extrapolated to zero concentration to obtain the true value (M2) and thereby establish the feasibility of obtaining the analogous SAXS parameter, I(0,0,0), experimentally.

  4. 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

  5. Fluid adsorption in ordered mesoporous solids determined by in situ small-angle X-ray scattering.

    PubMed

    Findenegg, Gerhard H; Jähnert, Susanne; Müter, Dirk; Prass, Johannes; Paris, Oskar

    2010-07-14

    The adsorption of two organic fluids (n-pentane and perfluoropentane) in a periodic mesoporous silica material (SBA-15) is investigated by in situ small-angle X-ray scattering (SAXS) using synchrotron radiation. Structural changes are monitored as the ordered and disordered pores in the silica matrix are gradually filled with the fluids. The experiments yield integrated peak intensities from up to ten Bragg reflections from the 2D hexagonal pore lattice, and additionally diffuse scattering contributions arising from disordered (mostly intrawall) porosity. The analysis of the scattering data is based on a separation of these two contributions. Bragg scattering is described by adopting a form factor model for ordered pores of cylindrical symmetry which accounts for the filling of the microporous corona, the formation of a fluid film at the pore walls, and condensation of the fluid in the core. The filling fraction of the disordered intrawall pores is extracted from the diffuse scattering intensity and its dependence on the fluid pressure is analyzed on the basis of a three-phase model. The data analysis introduced here provides an important generalisation of a formalism presented recently (J. Phys. Chem. C, 2009, 13, 15201), which was applicable to contrast-matching fluids only. In this way, the adsorption behaviour of fluids into ordered and disordered pores in periodic mesoporous materials can be analyzed quantitatively irrespective of the fluid density.

  6. 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

  7. Methods for analysis of size-exclusion chromatography-small-angle X-ray scattering and reconstruction of protein scattering.

    PubMed

    Malaby, Andrew W; Chakravarthy, Srinivas; Irving, Thomas C; Kathuria, Sagar V; Bilsel, Osman; Lambright, David G

    2015-08-01

    Size-exclusion chromatography in line with small-angle X-ray scattering (SEC-SAXS) has emerged as an important method for investigation of heterogeneous and self-associating systems, but presents specific challenges for data processing including buffer subtraction and analysis of overlapping peaks. This paper presents novel methods based on singular value decomposition (SVD) and Guinier-optimized linear combination (LC) to facilitate analysis of SEC-SAXS data sets and high-quality reconstruction of protein scattering directly from peak regions. It is shown that Guinier-optimized buffer subtraction can reduce common subtraction artifacts and that Guinier-optimized linear combination of significant SVD basis components improves signal-to-noise and allows reconstruction of protein scattering, even in the absence of matching buffer regions. In test cases with conventional SAXS data sets for cytochrome c and SEC-SAXS data sets for the small GTPase Arf6 and the Arf GTPase exchange factors Grp1 and cytohesin-1, SVD-LC consistently provided higher quality reconstruction of protein scattering than either direct or Guinier-optimized buffer subtraction. These methods have been implemented in the context of a Python-extensible Mac OS X application known as Data Evaluation and Likelihood Analysis (DELA), which provides convenient tools for data-set selection, beam intensity normalization, SVD, and other relevant processing and analytical procedures, as well as automated Python scripts for common SAXS analyses and Guinier-optimized reconstruction of protein scattering.

  8. 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.

  9. 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.

  10. An analysis of FtsZ assembly using small angle X-ray scattering and electron microscopy.

    PubMed

    Kuchibhatla, Anuradha; Abdul Rasheed, A S; Narayanan, Janaky; Bellare, Jayesh; Panda, Dulal

    2009-04-09

    Small angle X-ray scattering (SAXS) was used for the first time to study the self-assembly of the bacterial cell division protein, FtsZ, with three different additives: calcium chloride, monosodium glutamate and DEAE-dextran hydrochloride in solution. The SAXS data were analyzed assuming a model form factor and also by a model-independent analysis using the pair distance distribution function. Transmission electron microscopy (TEM) was used for direct observation of the FtsZ filaments. By sectioning and negative staining with glow discharged grids, very high bundling as well as low bundling polymers were observed under different assembly conditions. FtsZ polymers formed different structures in the presence of different additives and these additives were found to increase the bundling of FtsZ protofilaments by different mechanisms. The combined use of SAXS and TEM provided us a significant insight of the assembly of FtsZ and microstructures of the assembled FtsZ polymers.

  11. 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

  12. 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.

  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. A small angle X-ray scattering study of the structure and development of looseness in bovine hides and leather.

    PubMed

    Wells, Hannah C; Holmes, Geoff; Jeng, U-Ser; Wu, Wei-Ru; Kirby, Nigel; Hawley, Adrian; Mudie, Stephen; Haverkamp, Richard G

    2017-03-01

    Some bovine hides produce poor quality leather, termed loose leather. The structural characteristics of hides and the intermediate processed stages that lead to loose leather are not well understood. In the present study, synchrotron-based small angle X-ray scattering (SAXS) is used to investigate collagen fibril orientation at the different stages of processing (i.e. from hide through to leather) that result in both tight and loose leathers. Tight leather of a relatively isotropic texture has a lower orientation index (OI) than loose leather of a more pronounced stratified texture; conversely, tight pickled hide and wet blue have a higher OI than loose pickled hide and wet blue. There is a greater increase in OI on processing from pickled hide to dry crust (leather) for loose material. This is largely the result of a greater increase in hide thickness prior to pickling for loose hide than tight hide, followed by a greater decrease at the dry crust stage. The collagen fibrils in loose leather and wet blue more readily orient under stress than do those in tight leather. Loose leather has a more pronounced layered structure than tight leather, although this difference is not apparent from SAXS measurements of hide prior to the dry crust stage; it develops during processing. The greater swelling of the loose hide during processing disrupts the structure and leads to a more layered collagen arrangement on shrinking at the final dry crust stage. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  15. Rupture and regeneration of colloidal crystals as studied by two-dimensional ultra-small-angle X-ray scattering.

    PubMed

    Konishi, Toshiki; Ise, Norio

    2006-11-21

    The structure of colloidal crystals of silica particles in water was studied by using the two-dimensional (2D) ultra-small-angle X-ray scattering (USAXS) technique. By violent shaking of the dispersion, large (body-centered cubic, bcc) crystals were broken into microcrystals while the lattice structure and lattice constant were preserved. The 2D-USAXS profiles revealed that the [111] direction of bcc microcrystals was parallel to the capillary axis and their orientational distribution with respect to the capillary axis was random. While a prepeak was observed in the one-dimensional USAXS measurements, no such peak was detected by the 2D-USAXS technique. The prepeak was concluded to be due to {110} being rotated by 54.7 degrees (the angle between [001] and [111]) from the capillary axis. The diffraction from the plane was out of the horizontal plane and was observed at a lower angle as a prepeak by detector scanning in the horizontal direction.

  16. Small-angle X-ray scattering as a useful supplementary technique to determine molecular masses of polyelectrolytes in solution.

    PubMed

    Plazzotta, Beatrice; Diget, Jakob Stensgaard; Zhu, Kaizheng; Nyström, Bo; Pedersen, Jan Skov

    2016-10-01

    Determination of molecular masses of charged polymers is often nontrivial and most methods have their drawbacks. For polyelectrolytes, a new possibility for the determination of number-average molecular masses is represented by small-angle X-ray scattering (SAXS) which allows fast determinations with a 10% accuracy. This is done by relating the mass to the position of a characteristic peak feature which arises in SAXS due to the local ordering caused by charge-repulsions between polyelectrolytes. Advantages of the technique are the simplicity of data analysis, the independency from polymer architecture, and the low sample and time consumption. The method was tested on polyelectrolytes of various structures and chemical compositions, and the results were compared with those obtained from more conventional techniques, such as asymmetric flow field-flow fractionation, gel permeation chromatography, and classical SAXS data analysis, showing that the accuracy of the suggested method is similar to that of the other techniques. © 2016 The Authors. Journal of Polymer Science Part B: Polymer Physics Published by Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 1913-1917.

  17. Ultra-small-angle X-ray scattering characterization of diesel/gasoline soot: sizes and particle-packing conditions

    NASA Astrophysics Data System (ADS)

    Kameya, Yuki; Lee, Kyeong O.

    2013-10-01

    Regulations on particulate emissions from internal combustion engines tend to become more stringent, accordingly the importance of particulate filters in the after-treatment system has been increasing. In this work, the applicability of ultra-small-angle X-ray scattering (USAXS) to diesel soot cake and gasoline soot was investigated. Gasoline-direct-injection engine soot was collected at different fuel injection timings. The unified fits method was applied to analyze the resultant scattering curves. The validity of analysis was supported by comparing with carbon black and taking the sample images using a transmission electron microscope, which revealed that the primary particle size ranged from 20 to 55 nm. In addition, the effects of particle-packing conditions on the USAXS measurement were demonstrated by using samples suspended in acetone. Then, the investigation was extended to characterization of diesel soot cake deposited on a diesel particulate filter (DPF). Diesel soot was trapped on a small piece of DPF at different deposition conditions which were specified using the Peclet number. The dependence of scattering curve on soot-deposition conditions was demonstrated. To support the interpretation of the USAXS results, soot cake samples were observed using a scanning electron microscope and the influence of particle-packing conditions on scattering curve was discussed.

  18. 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.

  19. Investigation of a catalyst ink dispersion using both ultra-small-angle X-ray scattering and cryogenic TEM.

    PubMed

    Xu, Fan; Zhang, HangYu; Ilavsky, Jan; Stanciu, Lia; Ho, Derek; Justice, Matthew J; Petrache, Horia I; Xie, Jian

    2010-12-21

    The dispersion of Nafion ionomer particles and Pt/C catalyst aggregates in liquid media was studied using both ultra-small-angle X-ray scattering (USAXS) and cryogenic TEM. A systematic approach was taken to study first the dispersion of each component (i.e., ionomer particles and Pt/C aggregates), then the combination of the components, and last the catalyst ink. Multiple-level curve fitting was used to extract the particle size, size distribution, and geometry of the Pt/C aggregates and the Nafion particles in liquid media from the scattering data. The results suggest that the particle size, size distribution, and geometry are not uniform throughout the systems but rather vary significantly. It was found that the interaction of each component (i.e., the Nafion ionomer particles and the Pt/C aggregates) occurs in the dispersion. Cryogenic TEM was used to observe the size and geometry of the particles in liquid directly and to validate the scattering results. The TEM results showed excellent agreement.

  20. Small Angle X-Ray Scattering and Quasi-Elastic Light Scattering Studies of Polymer Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Ao, Xiaolei

    In order to understand the structural properties of semiflexible polymer liquid crystals, small angle X -ray scattering data from the synthetic polypeptide poly -gamma-benzyl glutamate (PBG) in the nematic phase are presented. The important features of the data are discussed in terms of the current understanding of the nature of nematic ordering in main chain polymer systems. This includes analysis of the angular distribution function for the polymer segments, long wavelength fluctuations dictated by elastic phenomena, the effects of finite chain lengths, and the effects due to the short range interactions and packing of the chains. The rigid rod-like biological macromolecule, tobacco mosaic virus (TMV), in the nematic and the smectic A phases is studied by quasi-elastic light scattering in order to understand the hydrodynamic properties of rigid rod-like lyotropic liquid crystals. A nonlocal behavior of the elasticity in the nematic phase is observed and discussed in terms of a recent developed nonlocal theory. The relative diffusion and undulation modes in the smectic A phase are observed. The results are compared with theory.

  1. Nano-Structural Investigation on Cellulose Highly Dissolved in Ionic Liquid: A Small Angle X-ray Scattering Study.

    PubMed

    Endo, Takatsugu; Hosomi, Shota; Fujii, Shunsuke; Ninomiya, Kazuaki; Takahashi, Kenji

    2017-01-21

    We investigated nano-structural changes of cellulose dissolved in 1-ethyl-3-methylimidazolium acetate-an ionic liquid (IL)-using a small angle X-ray scattering (SAXS) technique over the entire concentration range (0-100 mol %). Fibril structures of cellulose disappeared at 40 mol % of cellulose, which is a significantly higher concentration than the maximum concentration of dissolution (24-28 mol %) previously determined in this IL. This behavior is explained by the presence of the anion bridging, whereby an anion prefers to interact with multiple OH groups of different cellulose molecules at high concentrations, discovered in our recent work. Furthermore, we observed the emergence of two aggregated nano-structures in the concentration range of 30-80 mol %. The diameter of one structure was 12-20 nm, dependent on concentration, which is ascribed to cellulose chain entanglement. In contrast, the other with 4.1 nm diameter exhibited concentration independence and is reminiscent of a cellulose microfibril, reflecting the occurrence of nanofibrillation. These results contribute to an understanding of the dissolution mechanism of cellulose in ILs. Finally, we unexpectedly proposed a novel cellulose/IL composite: the cellulose/IL mixtures of 30-50 mol % that possess liquid crystallinity are sufficiently hard to be moldable.

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

    SciTech Connect

    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 (1 nm to 1 {mu}m). 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.

  3. Counterion distribution surrounding spherical nucleic acid-Au nanoparticle conjugates probed by small-angle x-ray scattering.

    PubMed

    Kewalramani, Sumit; Zwanikken, Jos W; Macfarlane, Robert J; Leung, Cheuk-Yui; Olvera de la Cruz, Monica; Mirkin, Chad A; Bedzyk, Michael J

    2013-12-23

    The radial distribution of monovalent cations surrounding spherical nucleic acid-Au nanoparticle conjugates (SNA-AuNPs) is determined by in situ small-angle x-ray scattering (SAXS) and classical density functional theory (DFT) calculations. Small differences in SAXS intensity profiles from SNA-AuNPs dispersed in a series of solutions containing different monovalent ions (Na(+), K(+), Rb(+), or Cs(+)) are measured. Using the "heavy ion replacement" SAXS (HIRSAXS) approach, we extract the cation-distribution-dependent contribution to the SAXS intensity and show that it agrees with DFT predictions. The experiment-theory comparisons reveal the radial distribution of cations as well as the conformation of the DNA in the SNA shell. The analysis shows an enhancement to the average cation concentration in the SNA shell that can be up to 15-fold, depending on the bulk solution ionic concentration. The study demonstrates the feasibility of HIRSAXS in probing the distribution of monovalent cations surrounding nanoparticles with an electron dense core (e.g., metals).

  4. Small-angle x-ray scattering analysis of polymer-protected platinum, rhodium, and platinum/rhodium colloidal dispersions

    NASA Astrophysics Data System (ADS)

    Hashimoto, Takeji; Saijo, Kenji; Harada, Masafumi; Toshima, Naoki

    1998-10-01

    Formations of poly(N-vinyl-2-pyrrolidone)(PVP)-metal ion (Pt, Rh or Pt/Rh(1/1)) complexes in H2O/C2H5OH ("polymer-metal ion complexes") before alcohol-reduction and PVP-Pt, Rh, or Pt/Rh(1/1) metal cluster ("polymer-metal cluster") after alcohol-reduction were studied by small-angle x-ray scattering (SAXS). SAXS intensity of the solution containing polymer-metal ion complexes is higher than that of the reference polymer solution without metal ions, suggesting that concentration fluctuations of polymer segments are enhanced due to the formation of polymer-metal ion complexes. Spatial distributions of metal clusters in colloidal dispersions are different from each other among the cases of Pt, Rh, and Pt/Rh(1/1) colloidal dispersions. The superstructure (greater than 10.0 nm in diameter), whose average sizes highly depend on the metal element employed, are formed. These superstructures are composed of several fundamental clusters with a diameter of ˜2.0-4.0 nm. Colloidal dispersions of Rh form a percolation network of clusters with an average period of ˜6.0 nm inside the higher-order organization of its superstructure. Experimental results concerning the physical aging show the high stability of colloidal dispersions of metal clusters protected by water-soluble PVP.

  5. 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.

  6. 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.

  7. 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

  8. Small-scale screening method for low-viscosity antibody solutions using small-angle X-ray scattering.

    PubMed

    Fukuda, Masakazu; Watanabe, Atsushi; Hayasaka, Akira; Muraoka, Masaru; Hori, Yuji; Yamazaki, Tadao; Imaeda, Yoshimi; Koga, Akiko

    2017-03-01

    In this study, we investigated the concentration range in which self-association starts to form in humanized IgG monoclonal antibody (mAb) solutions. Furthermore, on the basis of the results, we developed a practical method of screening for low-viscosity antibody solutions by using small-angle X-ray scattering (SAXS) measurements utilizing small quantities of samples. With lower-viscosity mAb3, self-association was not detected in the range of 1-80mg/mL. With higher-viscosity mAb1, on the other hand, self-association was detected in the range of 10-20mg/mL and was clearly enhanced by a decrease in temperature. The viscosities of mAb solutions at 160, 180, and 200mg/mL at 25°C quantitatively correlated very well with the particle size parameters obtained by SAXS measurements of mAb solutions at 15mg/mL at 5°C. The quantity of mAb sample required for the SAXS measurements was only 0.15mg, which is about one-hundredth of that required for actual viscosity measurements at a high concentration, and such quantities could be available even at an early stage of development. In conclusion, the SAXS analysis method proposed in this study is a valuable tool for the development of concentrated mAb therapeutics with high manufacturability and high usability for subcutaneous injection.

  9. Dynamical process of skyrmion-helical magnetic transformation of the chiral-lattice magnet FeGe probed by small-angle resonant soft x-ray scattering

    NASA Astrophysics Data System (ADS)

    Yamasaki, Y.; Morikawa, D.; Honda, T.; Nakao, H.; Murakami, Y.; Kanazawa, N.; Kawasaki, M.; Arima, T.; Tokura, Y.

    2015-12-01

    Small-angle soft x-ray scattering in resonance with Fe L absorption edge has been investigated for helical magnetic order and magnetic skyrmion crystal (SkX) in B20-type cubic FeGe. Transformation of magnetic structures among helical, conical, SkX, and field-polarized spin-collinear forms is observed with the application of a magnetic field parallel to the incident soft x-ray. The resonant soft x-ray scattering with high q -resolution revealed a transient dynamics of SkX, such as rotation of SkX and variation of the SkX lattice constant, upon the change of magnetic field.

  10. 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.

  11. Small-angle X-ray scattering study of conditions for the formation of growth units of protein crystals in lysozyme solutions

    NASA Astrophysics Data System (ADS)

    Dyakova, Yu. A.; Ilina, K. B.; Konarev, P. V.; Kryukova, A. E.; Marchenkova, M. A.; Blagov, A. E.; Volkov, V. V.; Pisarevsky, Yu. V.; Kovalchuk, M. V.

    2017-05-01

    The structural composition of lysozyme solutions favorable for the formation of the tetragonal form of protein crystals was studied by synchrotron-based small-angle X-ray scattering depending on the protein concentration and the temperature. Along with lysozyme monomers, dimers and octamers are found in crystallization solutions; the octamer content increases with an increase in the protein concentration.

  12. 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.

  13. ``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

  14. Studies of structural dynamics in polymer blends using rheology and small-angle x-ray scattering techniques

    NASA Astrophysics Data System (ADS)

    Brinker, Kristin Leigh

    Structural dynamics in three polymer blend systems, differing largely with respect to morphology, have been investigated. The first system, composed of two immiscible homopolymers, exhibits a microstructure of micron-sized droplets dispersed in a matrix phase. We have examined small-angle x-ray scattering (SAXS) as a new approach for conducting in situ studies of flow-induced structural changes in these types of blends. This approach relies on Porod scattering, which is related to the interfacial properties in two-phase systems. Indeed, we have successfully performed in situ SAXS measurements of an immiscible blend in response to applied shear, allowing for the observation of deformation and relaxation of interface with time. The second blend system, a bicontinuous microemulsion (BmuE), consists of two cocontinuous domains of immiscible homopolymers compatibilized by diblock copolymer at the interface. The equilibrium dynamics were characterized via x-ray photon correlation spectroscopy. These measurements were used to test rheological predictions for bicontinuous microemulsions by Patzold and Dawson. Although the predictions describe the shape of the relaxation spectrum fairly well, the theory fails to predict absolute values of the rheological properties. These results highlight a need for the development of more sophisticated theory to describe the dynamics of bicontinuous microemulsions. The shear-induced dynamics of the BmE microstructure were interrogated using rheology, in situ SAXS, and optical microscopy. Optical microscopy revealed micron-sized phase-separated structures coexisting with the nano-scale BmuE phase at equilibrium. Direct comparison of this multi-phase system to a previously documented BmuE system by Bates, Lodge, and coworkers strongly indicates that the microemulsion morphology dominates the rheology and scattering behavior at linear to moderately non-linear shear conditions, whereas the phase-separated structures govern the response under

  15. Small-angle X-ray scattering from salt-free solutions of star-branched polyelectrolytes

    NASA Astrophysics Data System (ADS)

    Heinrich, M.; Rawiso, M.; Zilliox, J. G.; Lesieur, P.; Simon, J. P.

    2001-02-01

    The dispersion state of sodium-sulphonated polystyrene (ensuremathNaPSS) star-branched polyelectrolytes was investigated in salt-free aqueous solutions, by use of the small-angle X-ray scattering technique. With respect to polystyrene (PS) star-branched polymers of identical functionality, the ordering phenomenon occurring in the neighborhood of the overlap concentration c^* is reinforced and observed in a larger range of concentrations. Moreover, the degree of order is no longer maximum at c^* and is improved as the concentration decreases. The dispersion state is then mainly controlled by the electrostatic interaction. A crystalline order should therefore be achieved with stars of lower functionality, provided the electrostatic interaction is added to the osmotic repulsion. On the other hand, unusual scattering patterns are measured for aqueous solutions of ensuremathNaPSS star polyelectrolytes. Indeed, a diffuse scattering is revealed at high angles, in addition to the regular diffraction rings related to preferred interstar distances. It is similar to the broad scattering peak produced by semidilute solutions of ensuremathNaPSS linear polyelectrolytes and associated to the electrostatic correlation hole within the isotropic model. In the dilute regime (c< c^*), it is just an intramolecular characteristic and represents the electrostatic repulsion between arms belonging to the same star. In the semidilute regime (c> c^*), it also reflects the electrostatic repulsion between arms of distinct stars. So, as the concentration increases, it is mainly caused by the interpenetration of ensuremathNaPSS stars. Such an observation is in agreement with the composite structure earlier proposed by Daoud and Cotton for star semidilute solutions. For c> c^*, ensuremathNaPSS star aqueous solutions can therefore be pictured as effective stars immersed in a matrix formed by the overlap of the arm ends. With respect to the dilute regime, the effective stars are smaller; the higher

  16. 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.

  17. Solution structure of monomeric and trimeric photosystem I of Thermosynechococcus elongatus investigated by small-angle X-ray scattering.

    PubMed

    Golub, Maksym; Hejazi, Mahdi; Kölsch, Adrian; Lokstein, Heiko; Wieland, D C Florian; Zouni, Athina; Pieper, Jörg

    2017-03-03

    The structure of monomeric and trimeric photosystem I (PS I) of Thermosynechococcus elongatus BP1 (T. elongatus) was investigated by small-angle X-ray scattering (SAXS). The scattering data reveal that the protein-detergent complexes possess radii of gyration of 58 and 78 Å in the cases of monomeric and trimeric PS I, respectively. The results also show that the samples are monodisperse, virtually free of aggregation, and contain empty detergent micelles. The shape of the protein-detergent complexes can be well approximated by elliptical cylinders with a height of 78 Å. Monomeric PS I in buffer solution exhibits minor and major radii of the elliptical cylinder of about 50 and 85 Å, respectively. In the case of trimeric PS I, both radii are equal to about 110 Å. The latter model can be shown to accommodate three elliptical cylinders equal to those describing monomeric PS I. A structure reconstitution also reveals that the protein-detergent complexes are larger than their respective crystal structures. The reconstituted structures are larger by about 20 Å mainly in the region of the hydrophobic surfaces of the monomeric and trimeric PS I complexes. This seeming contradiction can be resolved by the addition of a detergent belt constituted by a monolayer of dodecyl-β-D-maltoside molecules. Assuming a closest possible packing, a number of roughly 1024 and 1472 detergent molecules can be determined for monomeric and trimeric PS I, respectively. Taking the monolayer of detergent molecules into account, the solution structure can be almost perfectly modeled by the crystal structures of monomeric and trimeric PS I.

  18. Small-angle X-ray scattering and rheological characterization of alginate gels. 3. Alginic acid gels.

    PubMed

    Draget, Kurt Ingar; Stokke, Bjørn T; Yuguchi, Yoshiaki; Urakawa, Hiroshi; Kajiwara, Kanji

    2003-01-01

    Alginic acid gels were studied by small-angle X-ray scattering and rheology to elucidate the influence of alginate chemical composition and molecular weight on the gel elasticity and molecular structure. The alginic acid gels were prepared by homogeneous pH reduction throughout the sample. Three alginates with different chemical composition and sequence, and two to three different molecular weights of each sample were examined. Three alginate samples with fractions of guluronic acid residues of 0.39 (LoG), 0.50 (InG), and 0.68 (HiG), covering the range of commercially available alginates, were employed. The excess scattering intensity I of the alginic acid gels was about 1 order of magnitude larger and exhibited a stronger curvature toward low q compared to ionically cross-linked alginate. The I(q) were decomposed into two components by assuming that the alginic acid gel is composed of aggregated multiple junctions and single chains. Time-resolved experiments showed a large increase in the average size of aggregates and their weight fraction within the first 2 h after onset of gelling, which also coincides with the most pronounced rheological changes. At equilibrium, little or no effect of molecular weight was observed, whereas at comparable molecular weights, an increased scattering intensity with increasing content of guluronic acid residues was recorded, probably because of a larger apparent molecular mass of domains. The results suggest a quasi-ordered junction zone is formed in the initial stage, followed by subsequent assembling of such zones, forming domains in the order of 50 A. The average length of the initial junction zones, being governed by the relative fraction of stabilizing G-blocks and destabilizing alternating (MG) blocks, determines the density of the final random aggregates. Hence, high-G alginates give alginic acid gels of a higher aggregate density compared to domains composed of loosely packed shorter junction zones in InG or LoG system.

  19. 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.

  20. 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.

  1. Structural stability of soybean lipoxygenase-1 in solution as probed by small angle X-ray scattering.

    PubMed

    Dainese, Enrico; Sabatucci, Annalaura; van Zadelhoff, Guus; Angelucci, Clotilde Beatrice; Vachette, Patrice; Veldink, Gerrit A; Agrò, Alessandro Finazzi; Maccarrone, Mauro

    2005-05-27

    Soybean lipoxygenase-1 (LOX-1) is used widely as a model for studying the structural and functional properties of the homologous family of lipoxygenases. The crystallographic structure revealed that LOX-1 is organized in a beta-sheet N-terminal domain and a larger, mostly helical, C-terminal domain. Here, we describe the overall structural characterization of native unliganded LOX-1 in solution, using small angle X-ray scattering (SAXS). We show that the scattering pattern of the unliganded enzyme in solution does not display any significant difference compared with that calculated from the crystal structure, and that models of the overall shape of the protein calculated ab initio from the SAXS pattern provide a close envelope to the crystal structure. These data, demonstrating that LOX-1 has a compact structure also in solution, rule out any major motional flexibility of the LOX-1 molecule in aqueous solutions. In addition we show that eicosatetraynoic acid, an irreversible inhibitor of lipoxygenase used to mimic the effect of substrate binding, does not alter the overall conformation of LOX-1 nor its ability to bind to membranes. In contrast, the addition of glycerol (to 5%, v/v) causes an increase in the binding of the enzyme to membranes without altering its catalytic efficiency towards linoleic acid nor its SAXS pattern, suggesting that the global conformation of the enzyme is unaffected. Therefore, the compact structure determined in the crystal appears to be essentially preserved in these various solution conditions. During the preparation of this article, a paper by M. Hammel and co-workers showed instead a sharp difference between crystal and solution conformations of rabbit 15-LOX-1. The possible cause of this difference might be the presence of oligomers in the rabbit lipoxygenase preparations.

  2. 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.

  3. 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.

  4. A review of multi-domain and flexible molecular chaperones studies by small-angle X-ray scattering.

    PubMed

    Borges, Júlio C; Seraphim, Thiago V; Dores-Silva, Paulo R; Barbosa, Leandro R S

    2016-06-01

    Intrinsic flexibility is closely related to protein function, and a plethora of important regulatory proteins have been found to be flexible, multi-domain or even intrinsically disordered. On the one hand, understanding such systems depends on how these proteins behave in solution. On the other, small-angle X-ray scattering (SAXS) is a technique that fulfills the requirements to study protein structure and dynamics relatively quickly with few experimental limitations. Molecular chaperones from Hsp70 and Hsp90 families are multi-domain proteins containing flexible and/or disordered regions that play central roles in cellular proteostasis. Here, we review the structure and function of these proteins by SAXS. Our general approach includes the use of SAXS data to determine size and shape parameters, as well as protein shape reconstruction and their validation by using accessory biophysical tools. Some remarkable examples are presented that exemplify the potential of the SAXS technique. Protein structure can be determined in solution even at limiting protein concentrations (for example, human mortalin, a mitochondrial Hsp70 chaperone). The protein organization, flexibility and function (for example, the J-protein co-chaperones), oligomeric status, domain organization, and flexibility (for the Hsp90 chaperone and the Hip and Hep1 co-chaperones) may also be determined. Lastly, the shape, structural conservation, and protein dynamics (for the Hsp90 chaperone and both p23 and Aha1 co-chaperones) may be studied by SAXS. We believe this review will enhance the application of the SAXS technique to the study of the molecular chaperones.

  5. 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

  6. Dynamics of intermediate filament assembly followed in micro-flow by small angle X-ray scattering.

    PubMed

    Brennich, Martha Elisabeth; Nolting, Jens-Friedrich; Dammann, Christian; Nöding, Bernd; Bauch, Susanne; Herrmann, Harald; Pfohl, Thomas; Köster, Sarah

    2011-02-21

    The assembly of intermediate filaments (IFs) is a complex process that can be recapitulated through a series of distinct steps in vitro. The combination of microfluidics and small angle X-ray scattering (SAXS) provides a powerful tool to investigate the kinetics of this process on the relevant timescales. Microfluidic mixers based on the principle of hydrodynamic focusing allow for precise control of the mixing of proteins and smaller reagents like ions. Here, we present a multi-layer device that prevents proteins from adsorbing to the channel walls by engulfing the protein jet with a fluid layer of buffer. To ensure compatibility with SAXS, the device is fabricated from UV-curable adhesive (NOA 81). To demonstrate the successful prevention of contact between the protein jet and the channel walls we measure the distribution of a fluorescent dye in the device by confocal microscopy at various flow speeds and compare the results to finite element method (FEM) simulations. The prevention of contact enables the investigation of the assembly of IFs in flow by gradually increasing the salt concentration in the protein jet. The diffusion of salt into the jet can be determined by FEM simulations. SAXS data are collected at different positions in the jet, corresponding to different salt concentrations, and they reveal distinct differences between the earliest assembly states. We find that the mean square radius of gyration perpendicular to the filament axis increases from 13 nm(2) to 58 nm(2) upon assembly. Thereby we provide dynamic structural data of a complex assembly process that was amenable up to now only by microscopic techniques.

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

    PubMed Central

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

    2014-01-01

    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. PMID:27877646

  8. 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.

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

    DOE PAGES

    Bagge-Hansen, M.; Lauderbach, L.; Hodgin, R.; ...

    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

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

    PubMed

    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.

  11. 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

    2016-04-07

    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.

  12. 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.

  13. Effects of phosphonium-based ionic liquids on phospholipid membranes studied by small-angle X-ray scattering.

    PubMed

    Kontro, Inkeri; Svedström, Kirsi; Duša, Filip; Ahvenainen, Patrik; Ruokonen, Suvi-Katriina; Witos, Joanna; Wiedmer, Susanne K

    2016-12-01

    The effects of ionic liquids on model phospholipid membranes were studied by small-angle X-ray scattering, dynamic light scattering (DLS) and zeta potential measurements. Multilamellar 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine liposomes and large unilamellar vesicles composed of l-α-phosphatidylcholine (eggPC) and l-α-phosphatidylglycerol (eggPG) (80:20mol%) or eggPC, eggPG, and cholesterol (60:20:20mol%) were used as biomimicking membrane models. The effects of the phosphonium-based ionic liquids: tributylmethylphosphonium acetate, trioctylmethylphosphonium acetate, tributyl(tetradecyl)-phosphonium acetate, and tributyl(tetradecyl)-phosphonium chloride, were compared to those of 1-ethyl-3-methyl-imidazolium acetate. With multilamellar vesicles, the ionic liquids that did not disrupt liposomes decreased the lamellar spacing as a function of concentration. The magnitude of the effect depended on concentration for all studied ionic liquids. Using large unilamellar vesicles, first a slight decrease in the vesicle size, then aggregation of vesicles was observed by DLS for increasing ionic liquid concentrations. At concentrations just below those that caused aggregation of liposomes, large unilamellar vesicles were coated by ionic liquid cations, evidenced by a change in their zeta potential. The ability of phosphonium-based ionic liquids to affect liposomes is related to the length of the hydrocarbon chains in the cation. Generally, the ability of ionic liquids to disrupt liposomes goes hand in hand with inducing disorder in the phospholipid membrane. However, trioctylmethylphosphonium acetate selectively extracted and induced a well-ordered lamellar structure in phospholipids from disrupted cholesterol-containing large unilamellar vesicles. This kind of effect was not seen with any other combination of ionic liquids and liposomes.

  14. Structural studies of a double-stranded RNA from trypanosome RNA editing by small-angle X-ray scattering.

    PubMed

    Criswell, Angela; Mooers, Blaine H M

    2015-01-01

    We used small-angle X-ray scattering (SAXS) to evaluate the solution structure of a double-stranded RNA with 32 base pairs. We wanted to compare the solution structure to the crystal structure to assess the impact of the crystal lattice on the overall conformation of the RNA. The RNA was designed to self-anneal and form a head-to-head fusion of two identical mRNA/oligo(U) tail domains (the U-helix) from a trypanosome RNA editing substrate formed by the annealing of a guide RNA to a pre-edited mRNA. This substrate is from the U insertion/deletion RNA editing system of trypanosomes. Each strand in the fusion RNA had 16 purines from the pre-mRNA followed by 16 uracils (Us) from the U-tail at the 3' end of the guide RNA. The strands were designed to form a double helix with blunt ends, but each strand had the potential to form hairpins and single-stranded RNA helices. Hairpins could form by the 3' oligouridylate tract folding back to hybridize with the 5' oligopurine tract and forming an intervening loop. Single-stranded helices could form by the stacking of bases in the polypurine tract. Some of the 16 Us 3' to the polypurine tract may have been unstacked and in random coils. Our SAXS studies showed that the RNA formed a mix of single-stranded structures in the absence of MgCl2. In the presence of MgCl2 at concentrations similar to those in the crystal, the solution structure was consistent with the double-stranded, blunt-ended structure, in agreement with the crystal structure. Here we describe the preparation of RNA samples, data collection with an in-house SAXS instrument designed for biological samples, and the processing and modeling of the scattering data.

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

    2007-07-01

    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 1nm, 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.

  17. 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.

  18. 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

  19. Small-Angle X-Ray Scattering of the Cholesterol Incorporation into Human ApoA1-POPC Discoidal Particles

    PubMed Central

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

    2015-01-01

    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

  20. Small angle X-ray scattering analysis of Cu(2+)-induced oligomers of the Alzheimer's amyloid β peptide.

    PubMed

    Ryan, Timothy M; Kirby, Nigel; Mertens, Haydyn D T; Roberts, Blaine; Barnham, Kevin J; Cappai, Roberto; Pham, Chi Le Lan; Masters, Colin L; Curtain, Cyril C

    2015-03-01

    Research into causes of Alzheimer's disease and its treatment has produced a tantalising array of hypotheses about the role of transition metal dyshomeostasis, many of them on the interaction of these metals with the neurotoxic amyloid-β peptide (Aβ). Here, we have used small angle X-ray scattering (SAXS) to study the effect of the molar ratio, Cu(2+)/Aβ, on the early three-dimensional structures of the Aβ1-40 and Cu(2+)/Aβ1-42 peptides in solution. We found that at molar ratios of 0.5 copper to peptide Aβ1-40 aggregated, while Aβ1-42 adopted a relatively monodisperse cylindrical shape, and at a ratio of 1.5 copper to peptide Aβ1-40 adopted a monodisperse cylindrical shape, while Aβ1-42 adopted the shape of an ellipsoid of rotation. We also found, via in-line rapid mixing SAXS analysis, that both peptides in the absence of copper were monodisperse at very short timeframes (<2 s). Kratky plots of these scattering profiles indicated that immediately after mixing both were intrinsically disordered. Ensemble optimisation modelling reflected this, indicating a wide range of structural conformers. These data reflect the ensembles from which the Cu(2+)-promoted oligomers were derived. Our results are discussed in the light of other studies that have shown that the Cu(2+)/Aβ has a marked effect on fibril and oligomer formation by this peptide, with a higher ratio favouring the formation of cytotoxic non-amyloid oligomers. Our results are relatively consistent with previous two-dimensional studies of the conformations of these Cu(2+)-induced entities, made on a much longer time-scale than SAXS, by transmission electron microscopy and atomic force microscopy, which showed that a range of oligomeric species are formed. We propose that SAXS carried out on a modern synchrotron beamline enables studies on initial events in disordered protein folding on physiologically-relevant time-scales, and will likely provide great insight into the initiating processes of the A

  1. 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

  2. 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

  3. Internal structures of thermosensitive hybrid microgels investigated by means of small-angle X-ray scattering.

    PubMed

    Suzuki, Daisuke; Nagase, Yasuhisa; Kureha, Takuma; Sato, Takaaki

    2014-02-27

    Internal structures of thermosensitive microgels and their hybrid counterparts that contain Au nanoparticles are investigated by means of small-angle X-ray scattering (SAXS). Thermosensitive cationic microgels were synthesized by aqueous free radical precipitation polymerization from N-isopropylacrylamide and 3-(methacrylamino) propyltrimethylammonium chloride used as monomers. Using the microgels as templates, Au nanoparticles were synthesized in situ, using the cationic sites in the microgel to nucleate particle growth. To obtain different types of the hybrid microgels, Au nanoparticles were synthesized in the presence of the microgels by changing the reduction conditions of the precursor ions, such as temperature and species of reducing reagent. The hybrid microgels were characterized mainly by TEM and SAXS. For SAXS investigation, the hybrid microgels were analyzed in the wide q-range of 0.07 nm(-1) < q < 20 nm(-1), where q is the magnitude of the scattering vector. A quantitative description of the scattering intensities, I(q), for the nonhybrid microgels requires a sum of five components having different physical origins. An upturn increase of the forward intensity originates from the interface of microgels, obeying the Porod law, I(q) ∝ q(-4). An additional Guinier term found in q < 0.2 nm(-1) seems to arise from solidlike density fluctuation due to the inhomogeneities of chemical cross-links. The power-law behavior manifested in the low- to intermediate-q range is directly linked with the fractal nature of the swollen (coil) polymer networks and well described by the Ornstein-Zernike equation. Two interference peaks centered at q ≈ 5 nm (-1) and q ≈ 15 nm(-1) are likely to reflect inter- and intrachain correlations of pNIPAm, respectively, which are formally fitted by pseudo-Voigt equations. As for the hybrid microgels, a pronounced new contribution from the Au nanoparticles emerges, which calls for an additional scattering component describing

  4. [Heat-induced structural transition of alpha-crystallin in the eye lens tissue observed by small-angle X-ray scattering].

    PubMed

    Krivandin, A V

    2009-01-01

    Heat-induced structural transitions of crystallins in the eye lens tissue have been studied by small-angle X-ray scattering. It was shown that a short-time (approximately 1 min) incubation of the bovine eye lens tissue at a temperature of about 60 degrees C leads to a pronounced shift of the small-angle X-ray diffraction maximum due to the short-range order of alpha-crystallin oligomers. This shift indicates an increase in the molecular mass of alpha-crystallin oligomers. The results are evidence that, in the native surrounding and at the native concentration of alpha-crystallin, heat-induced transition of alpha-crystallin quaternary structure takes place. Earlier, this transition of alpha-crystallin has been observed only in solutions and gels of this protein. The results confirm the identity of alpha-crystallin properties in vitro and in vivo.

  5. Use of small-angle X-ray scattering to resolve intracellular structure changes of Escherichia coli cells induced by antibiotic treatment1

    PubMed Central

    von Gundlach, A. R.; Garamus, V. M.; Willey, T. M.; Ilavsky, J.; Hilpert, K.; Rosenhahn, A.

    2016-01-01

    The application of small-angle X-ray scattering (SAXS) to whole Escherichia coli cells is challenging owing to the variety of internal constituents. To resolve their contributions, the outer shape was captured by ultra-small-angle X-ray scattering and combined with the internal structure resolved by SAXS. Building on these data, a model for the major structural components of E. coli was developed. It was possible to deduce information on the occupied volume, occurrence and average size of the most important intracellular constituents: ribosomes, DNA and proteins. E. coli was studied after treatment with three different antibiotic agents (chloramphenicol, tetracycline and rifampicin) and the impact on the intracellular constituents was monitored. PMID:27980516

  6. Small Angle X-ray Scattering Studies of Poly(arylethinylene): Molecular Conformation in Solution and Orientational Ordering in Rod-coil Ionomer Blends

    SciTech Connect

    Pople, John A

    2001-03-29

    Poly(pyridyl/phenyl-ethinylene) polymers of tuned rigidity/flexibility were synthesized and their molecular conformation in solution determined by small angle x-ray scattering. These polymers were used as molecularly dispersed reinforcing components in ionomer blends with partially sulfonated polystyrene. Homogeneous ionomer blends were formed by acid-base interactions between the two blend components. Small angle x-ray scattering revealed that in the case of rodlike or semiflexible poly(pyridyl/phenyl-ethinylenes) an elongation induced orientational ordering is obtained. However blend samples prepared with flexible poly(pyridyl/phenyl-ethinylene) polymers do not show any observable orientation. The orientation parameter varied systematically with the rigidity/flexibility of the reinforcing component, as did the Young modulus determined from stress strain measurements.

  7. Hard X-ray Characteristics of Anomalous X-ray Pulsars: Results from RXTE and INTEGRAL

    NASA Astrophysics Data System (ADS)

    den Hartog, Peter R.

    Until recently anomalous X-ray pulsars (AXPs) were known as soft X-ray emitters. This has changed drastically since the discovery of hard X-ray emission (>10 keV) from several AXPs by INTEGRAL (Molkov et al. 2004, Revnivtsev et al. 2004 and den Hartog et al. 2004). Kuiper et al. (2004) discovered pulsed emission in the same energy range using RXTE (PCA and HEXTE) data. Currently four AXPs (1RXS J170849.0-400910, 1E 1841-045, 4U 0142+614 and 1E 2259+586) have been detected, some of them showing emission up to 200 keV. The spectra exhibit extremely hard power laws with photon indices < 1.0 and with apparent luminosities 2-3 orders of magnitude above the rotational energy loss. The origin of this behaviour is not yet understood. An overview containing the current observational status in the temporal and the spectral domains as well as future prospects of AXPs at high energies is presented.

  8. In-situ small-angle x-ray scattering study of nanoparticles in the plasma plume induced by pulsed laser irradiation of metallic targets

    SciTech Connect

    Lavisse, L.; Jouvard, J.-M.; Girault, M.; Potin, V.; Andrzejewski, H.; Marco de Lucas, M. C.; Bourgeois, S.; Le Garrec, J.-L.; Carles, S.; Mitchell, J. B. A.; Hallo, L.; Perez, J.; Decloux, J.

    2012-04-16

    Small angle x-ray scattering was used to probe in-situ the formation of nanoparticles in the plasma plume generated by pulsed laser irradiation of a titanium metal surface under atmospheric conditions. The size and morphology of the nanoparticles were characterized as function of laser irradiance. Two families of nanoparticles were identified with sizes on the order of 10 and 70 nm, respectively. These results were confirmed by ex-situ transmission electron microscopy experiments.

  9. 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

  10. 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.

  11. Measurements of Anomalous Dispersion Made with X-Ray Interferometers

    NASA Astrophysics Data System (ADS)

    Hart, M.; Siddons, D. P.

    1981-05-01

    Absolute measurements of the anomalous dispersion constants f' for zirconium, niobium and molybdenum made with a computer controlled X-ray interferometer have achieved a precision that permits systematic comparison with the available theories. Measurements were made at about 80 wavelengths within ±3 keV of the elements' K-absorption edge. After modification, to minimize computational errors, the theory of Cromer and Liberman is in satisfactory agreement with the results obtained so far, but small systematic differences between theory and experiment are apparent. Further work on a wide variety of elements and over a wide wavelength band is in progress.

  12. Precision Timing of Two Anomalous X-Ray Pulsars.

    PubMed

    Kaspi; Chakrabarty; Steinberger

    1999-11-01

    We report on long-term X-ray timing of two anomalous X-ray pulsars, 1RXS J170849.0-400910 and 1E 2259+586, using the Rossi X-Ray Timing Explorer. In monthly observations made over 1.4 and 2.6 yr for the two pulsars, respectively, we have obtained phase-coherent timing solutions which imply that these objects have been rotating with great stability throughout the course of our observations. For 1RXS J170849.0-400910, we find a rotation frequency of 0.0909169331(5) Hz and frequency derivative -15.687&parl0;4&parr0;x10-14 Hz s-1 for epoch MJD 51215.931. For 1E 2259+586, we find a rotation frequency of 0.1432880613(2) Hz and frequency derivative -1.0026&parl0;7&parr0;x10-14 Hz s-1 for epoch MJD 51195.583. The rms phase residuals from these simple models are only approximately 0.01 cycles for both sources. We show that the frequency derivative for 1E 2259+586 is inconsistent with that inferred from incoherent frequency observations made over the last 20 yr. Our observations are consistent with the magnetar hypothesis and make binary accretion scenarios appear unlikely.

  13. Diffusion and nucleation in multilayer growth of PTCDI-C8 studied with in situ X-ray growth oscillations and real-time small angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Zykov, Anton; Bommel, Sebastian; Wolf, Christopher; Pithan, Linus; Weber, Christopher; Beyer, Paul; Santoro, Gonzalo; Rabe, Jürgen P.; Kowarik, Stefan

    2017-02-01

    We study nucleation and multilayer growth of the perylene derivative PTCDI-C8 and find a persistent layer-by-layer growth, transformation of island shapes, and an enhancement of molecular diffusivity in upper monolayers (MLs). These findings result from the evaluation of the ML-dependent island densities, obtained by in situ real-time grazing incidence small angle X-ray scattering measurements and simultaneous X-ray growth oscillations. Complementary ex situ atomic force microscopy snapshots of different growth stages agree quantitatively with both X-ray techniques. The rate and temperature-dependent island density is analyzed using different mean-field nucleation models. Both a diffusion limited aggregation and an attachment limited aggregation model yield in the first two MLs the same critical nucleus size i, similar surface diffusion attempt frequencies in the 1019-1020 s-1 range, and a decrease of the diffusion barrier Ed in the 2nd ML by 140 meV.

  14. Small-angle X-ray scattering and differential scanning calorimetry studies on reversibly modified human-serum low density lipoproteins.

    PubMed

    Mateu, L; Kirchhausen, T; Camejo, G

    1978-04-18

    Small-angle x-ray scattering diagrams of human serum low density lipoprotein (LDL) were recorded at several temperatures in solutions of different freezing points. It was found that modifications of the x-ray patterns observed on cooling the lipoprotein samples below 0 degrees C are due to reversible alterations of the LDL surface structure induced by the freezing process (independent of temperature). With both intact and partially dehydrated LDL, differential scanning calorimetry (DSC) carried out in the body temperature range revealed a heat absorption characteristic of the transition from a liquid crystal to an isotropic liquid phase of cholesteryl esters within the lipoproteins (Deckelbaum, R. J., Shipley, R. J., Small, P. M., Lees, R. S., & George, P. K. (1975) Science 190, 392). However, small-angle x-ray scattering diagrams recorded with the same LDL sample before and after the partial removal of water were found to be very different: the scattering curve for intact LDL showed a strong band centered at (36 A)-1 which disappeared upon drying and reappeared upon restoring the water. Our results suggest that the presence of this signal strongly depends on the molecular structure of the lipoprotein surface.

  15. 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.

  16. Small-angle X-ray scattering of apolipoprotein A-IV reveals the importance of its termini for structural stability.

    PubMed

    Deng, Xiaodi; Morris, Jamie; Chaton, Catherine; Schröder, Gunnar F; Davidson, W Sean; Thompson, Thomas B

    2013-02-15

    ApoA-IV is an amphipathic protein that can emulsify lipids and has been linked to protective roles against cardiovascular disease and obesity. We previously reported an x-ray crystal structure of apoA-IV that was truncated at its N and C termini. Here, we have extended this work by demonstrating that self-associated states of apoA-IV are stable and can be structurally studied using small-angle x-ray scattering. Both the full-length monomeric and dimeric forms of apoA-IV were examined, with the dimer showing an elongated rod core with two nodes at opposing ends. The monomer is roughly half the length of the dimer with a single node. Small-angle x-ray scattering visualization of several deletion mutants revealed that removal of both termini can have substantial conformational effects throughout the molecule. Additionally, the F334A point mutation, which we previously showed increases apoA-IV lipid binding, also exhibited large conformational effects on the entire dimer. Merging this study's low-resolution structural information with the crystal structure provides insight on the conformation of apoA-IV as a monomer and as a dimer and further defines that a clasp mechanism may control lipid binding and, ultimately, protein function.

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

    PubMed Central

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

    2011-01-01

    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. PMID:21454648

  18. 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

  19. 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.

  20. Molecular weight-gyration radius relation of globular proteins: a comparison of light scattering, small-angle X-ray scattering and structure-based data.

    PubMed

    Smilgies, Detlef-M; Folta-Stogniew, Ewa

    2015-10-01

    The molecular weight-gyration radius relation for a number of globular proteins based on experimental light scattering data is compared with small-angle X-ray scattering data recently published by Mylonas & Svergun [J. Appl. Cryst. (2007 ▸), 40, s245-s249]. In addition, other recent experimental data and theoretical calculations are reviewed. It is found that the MW-Rg relation for the globular proteins is well represented by a power law with an exponent of 0.37 (2).

  1. Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

    DOE PAGES

    Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; ...

    2014-10-29

    We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

  2. 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.

  3. Size distribution of gold nanoparticles covered with thiol-terminated cyanobiphenyl-type liquid crystal molecules studied with small-angle X-ray scattering and TEM

    NASA Astrophysics Data System (ADS)

    Hino, Kazuyuki; Shingai, Rie; Morita, Takeshi; Toku, Kiyohisa; Hirano, Takahiro; Yoshikawa, Hideyuki; Nakano, Hirofumi; Nishi, Nobuyuki

    2008-07-01

    We have generated gold nanoparticles bound to the octyl group of 4'-octyloxy-4-cyanobiphenyl through thiolation of the terminal group. Two methods were employed for the generation. The first ligand exchange method produced the particles with a mono-dispersed size distribution, while the second method of photochemical reduction led to a bimodal particle size distribution. Small-angle X-ray scattering signals have shown that in the latter method the size of a seed particle formed in a precursor complex suspension remains almost unchanged, and hindered collisions among the particles can induce their heterogeneous coalescence in response to photoirradiation.

  4. Small angle X-ray scattering of wheat seed-storage proteins: alpha-, gamma- and omega-gliadins and the high molecular weight (HMW) subunits of glutenin.

    PubMed

    Thomson, N H; Miles, M J; Popineau, Y; Harries, J; Shewry, P; Tatham, A S

    1999-03-19

    Small angle X-ray scattering in solution was performed on seed-storage proteins from wheat. Three different groups of gliadins (alpha-, gamma- and omega-) and a high molecular weight (HMW) subunit of glutenin (1Bx20) were studied to determine molecular size parameters. All the gliadins could be modelled as prolate ellipsoids with extended conformations. The HMW subunit existed as a highly extended rod-like particle in solution with a length of about 69 nm and a diameter of about 6.4 nm. Specific aggregation effects were observed which may reflect mechanisms of self-assembly that contribute to the unique viscoelastic properties of wheat dough.

  5. Advanced small-angle X-ray synchrotron radiation scattering study of hemocyanin oligomers using a high-performance two-dimensional detector

    NASA Astrophysics Data System (ADS)

    La Monaca, Andrea; Barteri, Mario; Borghi, Elena; Beltramini, Mariano; Salvato, Benedetto; Congiu-Castellano, Agostina; Shantilal Shah, Jitendra

    1991-09-01

    Structural parameters of lyophilized hemocyanin oligomers from Octopus vulgaris have been obtained by continuous small-angle X-ray scattering experiments using a high-performance area detector realized at Frascati Laboratories on an Adone wiggler beam line. The new apparatus allowed fast collection of two-dimensional diffraction patterns and showed in real-time graphic display both the presence of different scattering units with superparticles of very high molecular weight and the anisotropic effects. The results of the experiments on lyophilized half-met hemocyanin derivative have stressed the fundamental presence of the 19S fraction.

  6. Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; Ho, Chian-Sing; Khadka, Nawal; Katsaras, John

    2014-10-29

    We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

  7. Small-angle X-ray scattering studies of peptide-lipid interactions using the mouse paneth cell α-defensin cryptdin-4.

    PubMed

    Mishra, Abhijit; Tai, Kenneth P; Schmidt, Nathan W; Ouellette, André J; Wong, Gerard C L

    2011-01-01

    In the presence of specialized proteins or peptides, a biological membrane can spontaneously restructure itself to allow communication between the intracellular and the extracellular sides. Examples of these proteins include cell-penetrating peptides and antimicrobial peptides (AMPs), which interact with cell membranes in complex ways. We briefly review cell-penetrating peptides and AMPs, and describe in detail how recombinant AMPs are made and their activity evaluated, using α-defensins as a specific example. We also review X-ray scattering methods used in studying peptide-membrane interactions, focusing on the procedures for small-angle X-ray scattering experiments on peptide-membrane interactions at realistic solution conditions, using both laboratory and synchrotron sources.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. A point-focusing small angle x-ray scattering camera using a doubly curved monochromator of a W/Si multilayer

    NASA Astrophysics Data System (ADS)

    Sasanuma, Yuji; Law, Robert V.; Kobayashi, Yuji

    1996-03-01

    A point-focusing small angle x-ray scattering (SAXS) camera using a doubly curved monochromator of a W/Si multilayer has been designed, constructed, and tested. The two radii of curvature of the monochromator are 20 400 and 7.6 mm. The reflectivity of its first-order Bragg reflection for CuKα radiation was calculated to be 0.82, being comparable to that (0.81) of its total reflection. By only 10 s x-ray exposure, scattering from a high-density polyethylene film was detected on an imaging plate (IP). A rotating-anode x-ray generator operated at 40 kV and 30 mA was used. Diffraction from rat-tail collagen has shown that the optical arrangement gives the Bragg spacing up to, at least, 30 nm for CuKα radiation. Combined with IPs, the camera may permit us to carry out time-resolved SAXS measurements for phase behaviors of liquid crystals, lipids, polymer alloys, etc., on conventional x-ray generators available in laboratories.

  14. [Small-angle x-ray and sedimentation studies on alpha-haemocyanin H. pomatia (halve molecules) in glycerol and sucrose solutions (author's transl)].

    PubMed

    Berger, J; Pilz, I; Witters, R; Lontie, R

    1976-01-01

    The alpha-haemocyanin molecules of Helix pomatia were decomposed into halves and studied in solution by small-angle X-ray scattering. The following parameters of the molecule could be obtained: radius of gyration, volume, molecular weight, overall shape and dimensions of the molecule. With small-angle X-ray scattering fluctuations of the electron density within the protein cause parasitic scattering at larger angles. According to Stuhrmann and Kirste it is possible to eliminate it mathematically by varying the electron density of the buffer. For this purpose different quantities of glycerol respectively saccharose were added to the solvent to study the scattering of alpha-haemocyanin halves in solvents of varied electron density. The change of the isopotential specific volume of haemocyanin and the strong increase of the statistical errors of its scattering by decreasing of the excess scattering of solution over solvent per unit volume did not allow an application of the method of Stuhrmann and Kirste. The data obtained for alpha-haemocanin halves in different solvents are given. Besides also the sedimentation of the alpha-haemocyanin halves were studied in solutions containing varied amounts of glycerol and saccharose. An attempt was made to calculate the change of the partial specific volume of haemocyanin by adding glycerol or saccharose.

  15. 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

    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

    2014-10-01

    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.

  16. Dimyristoylphosphatidylcholine/C16:0-ceramide binary liposomes studied by differential scanning calorimetry and wide- and small-angle x-ray scattering.

    PubMed Central

    Holopainen, J M; Lemmich, J; Richter, F; Mouritsen, O G; Rapp, G; Kinnunen, P K

    2000-01-01

    Ceramide has recently been established as a central messenger in the signaling cascades controlling cell behavior. Physicochemical studies have revealed a strong tendency of this lipid toward phase separation in mixtures with phosphatidylcholines. The thermal phase behavior and structure of fully hydrated binary membranes composed of dimyristoylphosphatidylcholine (DMPC) and N-palmitoyl-ceramide (C16:0-ceramide, up to a mole fraction X(cer) = 0.35) were resolved in further detail by high-sensitivity differential scanning calorimetry (DSC) and x-ray diffraction. Both methods reveal very strong hysteresis in the thermal phase behavior of ceramide-containing membranes. A partial phase diagram was constructed based on results from a combination of these two methods. DSC heating scans show that with increased X(cer) the pretransition temperature T(p) first increases, whereafter at X(cer) > 0.06 it can no longer be resolved. The main transition enthalpy DeltaH remains practically unaltered while its width increases significantly, and the upper phase boundary temperature of the mixture shifts to approximately 63 degrees C at X(cer) = 0.30. Upon cooling, profound phase separation is evident, and for all of the studied compositions there is an endotherm in the region close to the T(m) for DMPC. At X(cer) >/= 0.03 a second endotherm is evident at higher temperatures, starting at 32.1 degrees C and reaching 54.6 degrees C at X(cer) = 0.30. X-ray small-angle reflection heating scans reveal a lamellar phase within the temperature range of 15-60 degrees C, regardless of composition. The pretransition is observed up to X(cer) < 0.18, together with an increase in T(p). In the gel phase the lamellar repeat distance d increases from approximately 61 A at X(cer) = 0. 03, to 67 A at X(cer) = 0.35. In the fluid phase increasing X(cer) from 0.06 to 0.35 augments d from 61 A to 64 A. An L(beta')/L(alpha) (ripple/fluid) phase coexistence region is observed at high temperatures (from 31 to

  17. Time resolved small angle X-ray scattering experiments performed on detonating explosives at the advanced photon source: Calculation of the time and distance between the detonation front and the x-ray beam

    NASA Astrophysics Data System (ADS)

    Gustavsen, R. L.; Dattelbaum, D. M.; Watkins, E. B.; Firestone, M. A.; Podlesak, D. W.; Jensen, B. J.; Ringstrand, B. S.; Huber, R. C.; Mang, J. T.; Johnson, C. E.; Velizhanin, K. A.; Willey, T. M.; Hansen, D. W.; May, C. M.; Hodgin, R. L.; Bagge-Hansen, M.; van Buuren, A. W.; Lauderbach, L. M.; Jones, A. C.; Graber, T. J.; Sinclair, N.; Seifert, S.; Gog, T.

    2017-03-01

    Time resolved Small Angle X-ray Scattering (SAXS) experiments on detonating explosives have been conducted at Argonne National Laboratory's Advanced Photon Source Dynamic Compression Sector. The purpose of the experiments is to measure the SAXS patterns at tens of ns to a few μs behind the detonation front. Corresponding positions behind the detonation front are of order 0.1-10 mm. From the scattering patterns, properties of the explosive products relative to the time behind the detonation front can be inferred. This report describes how the time and distance from the x-ray probe location to the detonation front is calculated, as well as the uncertainties and sources of uncertainty associated with the calculated times and distances.

  18. Time resolved small angle X-ray scattering experiments performed on detonating explosives at the advanced photon source: Calculation of the time and distance between the detonation front and the x-ray beam

    DOE PAGES

    Gustavsen, Richard L.; Dattelbaum, Dana Mcgraw; Watkins, Erik Benjamin; ...

    2017-03-10

    Time resolved Small Angle X-ray Scattering (SAXS) experiments on detonating explosives have been conducted at Argonne National Laboratory's Advanced Photon Source Dynamic Compression Sector. The purpose of the experiments is to measure the SAXS patterns at tens of ns to a few μs behind the detonation front. Corresponding positions behind the detonation front are of order 0.1–10 mm. From the scattering patterns, properties of the explosive products relative to the time behind the detonation front can be inferred. Lastly, this report describes how the time and distance from the x-ray probe location to the detonation front is calculated, as wellmore » as the uncertainties and sources of uncertainty associated with the calculated times and distances.« less

  19. Small-Angle X-Ray Scattering of Reduced Ribonuclease A: Effects of Solution Conditions And Comparisons With a Computational Model of Unfolded Proteins

    SciTech Connect

    Wang, Y.; Trewhella, J.; Goldenberg, D.P.

    2009-05-26

    The disulfide-reduced form of bovine ribonuclease A, with the Cys thiols irreversibly blocked, was characterized by small-angle x-ray scattering. To help resolve the conflicting results and interpretations from previous studies of this model unfolded protein, we measured scattering profiles using a range of solution conditions and compared them with the profiles predicted by a computational model for a random-coil polypeptide. Analysis of the simulated and experimental profiles reveals that scattering intensities at intermediate angles, corresponding to interatomic distances in the range of 5--20 {angstrom}, are particularly sensitive to changes in solvation and can be used to assess the internal scaling behavior of the polypeptide chain, expressed as a mass fractal dimension, D{sub m}. This region of the scattering curve is also much less sensitive to experimental artifacts than is the very small angle regime (the Guinier region) that has been more typically used to characterize unfolded proteins. The experimental small-angle x-ray scattering profiles closely matched those predicted by the computational model assuming relatively small solvation energies. The scaling behavior of the polypeptide approaches that of a well-solvated polymer under conditions where it has a large net charge and at high urea concentrations. At lower urea concentrations and neutral pH, the behavior of the chain approaches that expected for {theta}-conditions, where the effects of slightly unfavorable interactions with solvent balance those of excluded volume, leading to scaling behavior comparable to that of an idealized random walk chain. Though detectable, the shift toward more compact conformations at lower urea concentrations does not correspond to a transition to a globule state and is associated with little or no reduction in conformational entropy. This type of collapse, therefore, is unlikely to greatly reduce the conformational search for the native state.

  20. Structural characterization of the phospholipid stabilizer layer at the solid-liquid interface of dispersed triglyceride nanocrystals with small-angle x-ray and neutron scattering

    NASA Astrophysics Data System (ADS)

    Schmiele, Martin; Schindler, Torben; Unruh, Tobias; Busch, Sebastian; Morhenn, Humphrey; Westermann, Martin; Steiniger, Frank; Radulescu, Aurel; Lindner, Peter; Schweins, Ralf; Boesecke, Peter

    2013-06-01

    Dispersions of crystalline nanoparticles with at least one sufficiently large unit cell dimension can give rise to Bragg reflections in the small-angle scattering range. If the nanocrystals possess only a small number of unit cells along these particular crystallographic directions, the corresponding Bragg reflections will be broadened. In a previous study of phospholipid stabilized dispersions of β-tripalmitin platelets [Unruh, J. Appl. Crystallogr.JACGAR0021-889810.1107/S0021889807044378 40, 1008 (2007)], the x-ray powder pattern simulation analysis (XPPSA) was developed. The XPPSA method facilitates the interpretation of the rather complicated small-angle x-ray scattering (SAXS) curves of such dispersions of nanocrystals. The XPPSA method yields the distribution function of the platelet thicknesses and facilitates a structural characterization of the phospholipid stabilizer layer at the solid-liquid interface between the nanocrystals and the dispersion medium from the shape of the broadened 001 Bragg reflection. In this contribution an improved and extended version of the XPPSA method is presented. The SAXS and small-angle neutron scattering patterns of dilute phospholipid stabilized tripalmitin dispersions can be reproduced on the basis of a consistent simulation model for the particles and their phospholipid stabilizer layer on an absolute scale. The results indicate a surprisingly flat arrangement of the phospholipid molecules in the stabilizer layer with a total thickness of only 12 Å. The stabilizer layer can be modeled by an inner shell for the fatty acid chains and an outer shell including the head groups and additional water. The experiments support a dense packing of the phospholipid molecules on the nanocrystal surfaces rather than isolated phospholipid domains.

  1. Protein denaturation: a small-angle X-ray scattering study of the ensemble of unfolded states of cytochrome c.

    PubMed

    Segel, D J; Fink, A L; Hodgson, K O; Doniach, S

    1998-09-08

    Solution X-ray scattering was used to study the equilibrium unfolding of cytochrome c as a function of guanidine hydrochloride concentration at neutral pH. The radius of gyration (Rg) shows a cooperative transition with increasing denaturant with a similar Cm to that observed with circular dichroism. However, the lack of an isoscattering point in the X-ray scattering patterns suggests the equilibrium unfolding is not simply a two-state process. Singular value decomposition (SVD) analysis was applied to the scattering patterns to determine the number of distinct scattering species. SVD analysis reveals the existence of three components, suggesting that at least three equilibrium states of the protein exist. A model was employed to determine the thermodynamic parameters and the scattering profiles of the three equilibrium states. These scattering profiles show that one state is native (N). The other two states (U1, U2) are unfolded, with U2 being fully unfolded and U1 having some residual structure. Using the thermodynamic parameters to calculate fractional populations, U1 is maximally populated at intermediate denaturant concentrations while U2 is maximally populated at high denaturant concentrations. It is likely that there is a multiplicity of denatured states with U1 and U2 representing an average of the denatured states populated at intermediate and high denaturant concentrations, respectively.

  2. 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.

  3. 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.

  4. Grazing-incidence small-angle X-ray scattering in a twofold rough-interface medium: a new theoretical approach using the q-eigenwave formalism.

    PubMed

    Chukhovskii, F N; Roshchin, B S

    2015-11-01

    Based on the rigorous Green function formalism to describe the grazing-incidence small-angle X-ray scattering (GISAXS) problem, a system of two linked integral equations is derived with respect to amplitudes of the reflected and transmitted plane q-eigenwaves (eigenstate functions) propagating through two homogeneous media separated from each other by a rough surface interface. To build up the coupled solutions of these basic equations beyond the perturbation theory constraint 2kσθ0 < 1, a simple iteration procedure is proposed as opposed to the self-consistent wave approach [Chukhovskii (2011). Acta Cryst. A67, 200-209; Chukhovski (2012). Acta Cryst. A68, 505-512]. Using the first-order iteration, analytical expressions for the averaged specular and non-specular scattering intensity distributions have been obtained. These expressions are further analysed in terms of the GISAXS parameters {k, θ, θ0} and surface finish ones {σ, l, h}, where θ and θ0 are the scattering and incidence angles of the X-rays, respectively, σ is the root-mean-square roughness, l is the correlation length, h is the fractal surface model index, k = 2π/λ, and λ is the X-ray wavelength. A direct way to determine the surface finish parameters from the experimental specular and diffuse scattering indicatrix scan data is discussed for an example of GISAXS measurements from rough surfaces of α-quartz and CdTe samples.

  5. Density minimum of confined water at low temperatures: a combined study by small-angle scattering of X-rays and neutrons.

    PubMed

    Erko, M; Wallacher, D; Hoell, A; Hauss, T; Zizak, I; Paris, O

    2012-03-21

    A simple explanation is given for the low-temperature density minimum of water confined within cylindrical pores of ordered nanoporous materials of different pore size. The experimental evidence is based on combined data from in-situ small-angle scattering of X-rays (SAXS) and neutrons (SANS), corroborated by additional wide-angle X-ray scattering (WAXS). The combined scattering data cannot be described by a homogeneous density distribution of water within the pores, as was originally suggested from SANS data alone. A two-step density model reveals a wall layer covering approximately two layers of water molecules with higher density than the residual core water in the central part of the pores. The temperature-induced changes of the scattering signal from both X-rays and neutrons are consistent with a minimum of the average water density. We show that the temperature at which this minimum occurs depends monotonically on the pore size. Therefore we attribute this minimum to a liquid-solid transition of water influenced by confinement. For water confined in the smallest pores of only 2 nm in diameter, the density minimum is explained in terms of a structural transition of the surface water layer closest to the hydrophilic pore walls.

  6. Dynamic investigation of gold nanocrystal assembly using in situ grazing-incidence small angle x-ray scattering.

    SciTech Connect

    Dunphy, D.; Fan, H.; Li, X.; Wang, J.; Brinker, C. J.; X-Ray Science Division; Univ. of New Mexico; SNL

    2008-01-01

    Here we investigate the dynamic self-assembly pathway of ordered gold nanocrystal arrays during the self-assembly of gold nanocrystal micelles, with and without the presence of colloidal silica precursors, using grazing-incidence X-ray scattering performed at a synchrotron source. With silica precursors present, a lattice with rhombohedral symmetry is formed from the partial collapse of a face-centered cubic structure. In the absence of silica, a transient body-centered orthorhombic phase appears, which rapidly collapses into a glassy nanocrystal film. The appearance of face-centered and body-centered structures is consistent with a phase diagram for charged colloidal particles with assembly modulated via Coulomb screening.

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

    SciTech Connect

    Williams, S.P.; Langmore, J.P. )

    1991-03-01

    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 {plus minus} 0.5, 12.1 {plus minus} 0.4, and 15.9 {plus minus} 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 {plus minus} 0.5, 8.3 {plus minus} 0.6, and 11.8 {plus minus} 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.

  8. 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.

  9. Growth Kinetics of Polyelectrolyte Complexes Formed from Oppositely-Charged Homopolymers Studied by Time-Resolved Ultra-Small-Angle X-ray Scattering.

    PubMed

    Takahashi, Rintaro; Narayanan, Theyencheri; Sato, Takahiro

    2017-02-16

    We have monitored the kinetic process of polyelectrolyte complex formation between sodium polyacrylate (SPA) and polyallylamine hydrochrolide (PAH) in aqueous NaCl solution by time-resolved ultra-small-angle X-ray scattering (TR-USAXS) combined with rapid mixing. SPA and PAH with different NaCl concentrations from 0 to 1 M were rapidly mixed in equimolar concentration of the monomer units using a stopped-flow apparatus with a dead time of about 2.5 ms. Within the dead time, percolated aggregate-like structures were observed suggesting that the initially formed small charge neutral aggregates further assembled to form higher order agglomerates. The early stage time evolution of the molar mass of the global structure in the presence of NaCl was found to be comparable to the Brownian-coagulation rate.

  10. 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.

  11. Comprehension of direct extraction of hydrophilic antioxidants using vegetable oils by polar paradox theory and small angle X-ray scattering analysis.

    PubMed

    Li, Ying; Fabiano-Tixier, Anne Sylvie; Ruiz, Karine; Rossignol Castera, Anne; Bauduin, Pierre; Diat, Olivier; Chemat, Farid

    2015-04-15

    Since the polar paradox theory rationalised the fact that polar antioxidants are more effective in nonpolar media, extractions of phenolic compounds in vegetable oils were inspired and achieved in this study for obtaining oils enriched in phenolic compounds. Moreover, the influence of surfactants on the extractability of phenolic compounds was experimentally studied first, followed by the small angle X-ray scattering analysis for the oil structural observation before and after extraction so as to better understand the dissolving mechanism underpinning the extraction. The results showed a significant difference on the extraction yield of phenolic compounds among oils, which was mainly dependent on their composition instead of the unsaturation of fatty acids. Appropriate surfactant additions could significantly improve extraction yield for refined sunflower oils, which 1% w/w addition of glyceryl oleate was determined as the optimal. Besides, 5% w/w addition of lecithin performed the best in oil enrichments compared with mono- and di-glycerides.

  12. On-line determination by small angle X-ray scattering of the shape of hen egg white lysozyme immediately following elution from a hydrophobic interaction chromatography column.

    PubMed

    Kulsing, Chadin; Komaromy, Andras Z; Boysen, Reinhard I; Hearn, Milton T W

    2016-10-21

    This study documents the use of an integrated approach, involving on-line hydrophobic interaction chromatography interfaced with Small Angle X-ray Scattering (HIC-SAXS) measurements, to monitor the conformational status of proteins immediately upon elution from a chromatographic column operated at different temperatures. Moreover, this approach provides an additional avenue to interrogate the changes in protein shape that may occur across the eluted chromatographic peak. To this end, radii of gyration were extrapolated from the Guinier approximation with the HIC-SAXS data, whilst pair distribution functions and bead model simulations were generated by using the indirect transform program GNOM and ab initio reconstruction with GASBOR to provide further insight into protein conformational changes that occur during hydrophobic interaction chromatography.

  13. 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.

  14. Characterization of white poplar and eucalyptus after ionic liquid pretreatment as a function of biomass loading using X-ray diffraction and small angle neutron scattering.

    PubMed

    Yuan, Xueming; Duan, Yonghao; He, Lilin; Singh, Seema; Simmons, Blake; Cheng, Gang

    2017-05-01

    A systematic study was performed to understand interactions among biomass loading during ionic liquid (IL) pretreatment, biomass type and biomass structures. White poplar and eucalyptus samples were pretreated using 1-ethyl-3-methylimidazolium acetate (EmimOAc) at 110°C for 3h at biomass loadings of 5, 10, 15, 20 and 25wt%. All of the samples were chemically characterized and tested for enzymatic hydrolysis. Physical structures including biomass crystallinity and porosity were measured by X-ray diffraction (XRD) and small angle neutron scattering (SANS), respectively. SANS detected pores of radii ranging from ∼25 to 625Å, enabling assessment of contributions of pores with different sizes to increased porosity after pretreatment. Contrasting dependences of sugar conversion on white poplar and eucalyptus as a function of biomass loading were observed and cellulose crystalline structure was found to play an important role. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Microfluidic Platform for the Continuous Production and Characterization of Multilamellar Vesicles: A Synchrotron Small-Angle X-ray Scattering (SAXS) Study.

    PubMed

    Ghazal, Aghiad; Gontsarik, Mark; Kutter, Jörg P; Lafleur, Josiane P; Ahmadvand, Davoud; Labrador, Ana; Salentinig, Stefan; Yaghmur, Anan

    2017-01-05

    A microfluidic platform combined with synchrotron small-angle X-ray scattering (SAXS) was used for monitoring the continuous production of multilamellar vesicles (MLVs). Their production was fast and started to evolve within less than 0.43 s of contact between the lipids and the aqueous phase. To obtain nanoparticles with a narrow size distribution, it was important to use a modified hydrodynamic flow focusing (HFF) microfluidic device with narrower microchannels than those normally used for SAXS experiments. Monodispersed MLVs as small as 160 nm in size, with a polydispersity index (PDI) of approximately 0.15 were achieved. The nanoparticles produced were smaller and had a narrower size distribution than those obtained via conventional bulk mixing methods. This microfluidic platform therefore has a great potential for the continuous production of monodispersed NPs.

  16. 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.

  17. Mapping the structural order of laser-induced periodic surface structures in thin polymer films by microfocus beam grazing incidence small-angle X-ray scattering.

    PubMed

    Martín-Fabiani, Ignacio; Rebollar, Esther; García-Gutiérrez, Mari Cruz; Rueda, Daniel R; Castillejo, Marta; Ezquerra, Tiberio A

    2015-02-11

    In this work we present an accurate mapping of the structural order of laser-induced periodic surface structures (LIPSS) in spin-coated thin polymer films, via a microfocus beam grazing incidence small-angle X-ray scattering (μGISAXS) scan, GISAXS modeling, and atomic force microscopy imaging all along the scanned area. This combined study has allowed the evaluation of the effects on LIPSS formation due to nonhomogeneous spatial distribution of the laser pulse energy, mapping with micrometric resolution the evolution of the period and degree of structural order of LIPSS across the laser beam diameter in a direction perpendicular to the polarization vector. The experiments presented go one step further toward controlling nanostructure formation in LIPSS through a deep understanding of the parameters that influence this process.

  18. 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.

  19. 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.

  20. 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

    2015-10-07

    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.

  1. 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.

  2. Application of the small-angle X-ray scattering technique for the study of two-step equilibrium enzyme-substrate interactions.

    PubMed

    Tuzikov, F V; Zinoviev, V V; Vavilin, V I; Malygin, E G

    1996-02-01

    The small-angle x-ray scattering (SAXS) technique is used for the investigation of two-stage equilibrium macromolecular interactions of the enzyme-substrate type in solution. Experimental procedures and methods of analyzing the data obtained from SAXS have been elaborated. The algorithm for the data analysis allows one to determine the stoichiometric, equilibrium, and structural parameters of the enzyme-substrate complexes obtained. The thermodynamic characteristics for the formation of complexes of double-stranded oligonucleotide with Eco dam methyltransferase (MTase) have been determined and demonstrate a high cooperativity of MTase binding when the ternary complex containing the dimeric enzyme is formed. The structural parameters (Rg, Rc, semiaxes) have been determined for free enzyme and polynucleotides and of enzyme-substrate complexes, indicating structural rearrangements of the enzyme in the interaction with substrates.

  3. Analysis of liquid crystalline nanoparticles by small angle X-ray diffraction: evaluation of drug and pharmaceutical additives influence on the internal structure.

    PubMed

    Rossetti, Fábia Cristina; Fantini, Márcia C A; Carollo, Aline Regina H; Tedesco, Antônio Cláudio; Bentley, Maria Vitória Lopes Badra

    2011-07-01

    The goal of this work was to study the liquid crystalline structure of a nanodispersion delivery system intended to be used in photodynamic therapy after loading with photosensitizers (PSs) and additives such as preservatives and thickening polymers. Polarized light microscopy and light scattering were performed on a standard nanodispersion in order to determine the anisotropy of the liquid crystalline structure and the mean diameter of the nanoparticles, respectively. Small angle X-ray diffraction (SAXRD) was used to verify the influence of drug loading and additives on the liquid crystalline structure of the nanodispersions. The samples, before and after the addition of PSs and additives, were stable over 90 days, as verified by dynamic light scattering. SAXRD revealed that despite the alteration observed in some of the samples analyzed in the presence of photosensitizing drugs and additives, the hexagonal phase still remained in the crystalline phase. Copyright © 2011 Wiley-Liss, Inc. and the American Pharmacists Association

  4. 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.

  5. 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.

  6. 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.

  7. Symmetric faceting of a sapphire vicinal surface revealed by grazing incidence small-angle X-ray scattering 3D mapping

    NASA Astrophysics Data System (ADS)

    Matringe, C.; Fakih, A.; Thune, E.; Babonneau, D.; Arnaud, S.; Blanc, N.; Boudet, N.; Guinebretière, R.

    2017-07-01

    A one dimensional periodic vicinal surface of sapphire was obtained through a self-ordering process after high-temperature thermal treatment. The morphology of the surface is described as an assembly of prisms exhibiting a rectangular base and a triangular profile orthogonal to the mean surface. Careful measurements of the whole 3D reciprocal map around the origin of the reciprocal space were performed through grazing incidence small-angle X-ray scattering experiments combined with a strict orientation procedure with respect to specific crystallographic directions of the sapphire crystal. We were thus able to determine accurately the actual shape of the prisms, which exhibit an isosceles triangular profile. Such a profile symmetric with respect to a plane normal to the mean sapphire vicinal surface has never been reported.

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

    PubMed

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

    2011-04-14

    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 PbSeO(3) nanorods.

  9. 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.

  10. Quantitative determination of the lateral density and intermolecular correlation between proteins anchored on the membrane surfaces using grazing incidence small-angle X-ray scattering and grazing incidence X-ray fluorescence.

    PubMed

    Abuillan, Wasim; Vorobiev, Alexei; Hartel, Andreas; Jones, Nicola G; Engstler, Markus; Tanaka, Motomu

    2012-11-28

    As a physical model of the surface of cells coated with densely packed, non-crystalline proteins coupled to lipid anchors, we functionalized the surface of phospholipid membranes by coupling of neutravidin to biotinylated lipid anchors. After the characterization of fine structures perpendicular to the plane of membrane using specular X-ray reflectivity, the same membrane was characterized by grazing incidence small angle X-ray scattering (GISAXS). Within the framework of distorted wave Born approximation and two-dimensional Percus-Yevick function, we can analyze the form and structure factors of the non-crystalline, membrane-anchored proteins for the first time. As a new experimental technique to quantify the surface density of proteins on the membrane surface, we utilized grazing incidence X-ray fluorescence (GIXF). Here, the mean intermolecular distance between proteins from the sulfur peak intensities can be calculated by applying Abelé's matrix formalism. The characteristic correlation distance between non-crystalline neutravidin obtained by the GISAXS analysis agrees well with the intermolecular distance calculated by GIXF, suggesting a large potential of the combination of GISAXS and GIXF in probing the lateral density and correlation of non-crystalline proteins displayed on the membrane surface.

  11. Quantitative determination of the lateral density and intermolecular correlation between proteins anchored on the membrane surfaces using grazing incidence small-angle X-ray scattering and grazing incidence X-ray fluorescence

    NASA Astrophysics Data System (ADS)

    Abuillan, Wasim; Vorobiev, Alexei; Hartel, Andreas; Jones, Nicola G.; Engstler, Markus; Tanaka, Motomu

    2012-11-01

    As a physical model of the surface of cells coated with densely packed, non-crystalline proteins coupled to lipid anchors, we functionalized the surface of phospholipid membranes by coupling of neutravidin to biotinylated lipid anchors. After the characterization of fine structures perpendicular to the plane of membrane using specular X-ray reflectivity, the same membrane was characterized by grazing incidence small angle X-ray scattering (GISAXS). Within the framework of distorted wave Born approximation and two-dimensional Percus-Yevick function, we can analyze the form and structure factors of the non-crystalline, membrane-anchored proteins for the first time. As a new experimental technique to quantify the surface density of proteins on the membrane surface, we utilized grazing incidence X-ray fluorescence (GIXF). Here, the mean intermolecular distance between proteins from the sulfur peak intensities can be calculated by applying Abelé's matrix formalism. The characteristic correlation distance between non-crystalline neutravidin obtained by the GISAXS analysis agrees well with the intermolecular distance calculated by GIXF, suggesting a large potential of the combination of GISAXS and GIXF in probing the lateral density and correlation of non-crystalline proteins displayed on the membrane surface.

  12. 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.

  13. Scattering Density Profile Model of POPG Bilayers as Determined by Molecular Dynamics Simulations and Small-Angle Neutron and X-ray Scattering Experiments

    SciTech Connect

    Kucerka, Norbert; Holland, B; Gray, C.G; Tomberli, B; Katsaras, John

    2012-01-01

    We combine molecular dynamics (MD) simulations and experiment, both small-angle neutron (SANS) and small-angle X-ray scattering (SAXS), to determine the precise structure of bilayers composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG), a lipid commonly encountered in bacterial membranes. Experiment and simulation are used to develop a one-dimensional scattering density profile (SDP) model suitable for the analysis of experimental data. The joint refinement of such data (i.e., SANS and SAXS) results in the area per lipid that is then used in the fixed-area simulations. In the final step, the direct comparison of simulated-to-experimental data gives rise to the detailed structure of POPG bilayers. From these studies we conclude that POPG s molecular area is 66.0 +/- 1.3 ^2, its overall bilayer thickness is 36.7 +/- 0.7 , and its hydrocarbon region thickness is 27.9 ( 0.6 , assuming a simulated value of 1203 ^3 for the total lipid volume.

  14. Small-angle X-ray and light scattering analysis of multi-layered Curdlan gels prepared by a diffusion method.

    PubMed

    Maki, Yasuyuki; Furusawa, Kazuya; Dobashi, Toshiaki; Sugimoto, Yasunobu; Wakabayashi, Katsuzo

    2017-01-02

    Curdlan, a microbial polysaccharide, forms a multi-layered gel consisting of four layers with different turbidity when its alkaline solution is dialyzed against aqueous solutions containing Ca(2+) (diffusion-set gel). The present study clarified the microstructure of each layer of the diffusion-set Curdlan gel by small-angle X-ray scattering (SAXS) and small-angle light scattering (SALS). The SAXS data showed that Curdlan chains assume a helical ordered conformation in the gel and that the gel consists of the fibrils formed by the association of Curdlan chains and the aggregates of fibrils. The SAXS results also indicated that the gelation is induced by the formation of a network of Ca(2+)-cross-linked fibrils in the outer region of the gel, whereas by the network formation of the aggregation of fibrils in the neutralization process in the inner region of the gel. A structural anisotropy of the gel was investigated by analysis of two-dimensional SAXS images, showing that the fibril is oriented circumferentially in the outer region of the cylindrical gel, whereas it is oriented randomly in the inner region of the gel. The SALS data showed that a characteristic length of an inhomogeneous structure in the turbid layers is of the order of micrometers. The observed spatial variation of the microscopic structure is caused by the difference in the paths of pH and [Ca(2+)] traced in the gelation process. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Assessment of firing conditions in old fired-clay bricks: The contribution of X-ray powder diffraction with the Rietveld method and small angle neutron scattering

    SciTech Connect

    Viani, Alberto; Sotiriadis, Konstantinos; Len, Adél; Šašek, Petr; Ševčík, Radek

    2016-06-15

    Full characterization of fired-clay bricks is crucial for the improvement of process variables in manufacturing and, in case of old bricks, for restoration/replacement purposes. To this aim, five bricks produced in a plant in Czech Republic in the past have been investigated with a combination of analytical techniques in order to derive information on the firing process. An additional old brick from another brickyard was also used to study the influence of different raw materials on sample microstructure. The potential of X-ray diffraction with the Rietveld method and small angle neutron scattering technique has been exploited to describe the phase transformations taking place during firing and characterize the brick microstructure. Unit-cell parameter of spinel and amount of hematite are proposed as indicators of the maximum firing temperature, although for the latter, limited to bricks produced from the same raw material. The fractal quality of the surface area of pores obtained from small angle neutron scattering is also suggested as a method to distinguish between bricks produced from different raw clays. - Highlights: • Rietveld method helps in describing microstructure and physical properties of bricks. • XRPD derived cell parameter of spinel is proposed as an indicator of firing temperature. • SANS effectively describes brick micro and nanostructure, including closed porosity. • Fractal quality of pore surface is proposed as ‘fingerprint’ of brick manufacturing.

  16. Microstructural changes of globules in calcium-silicate-hydrate gels with and without additives determined by small-angle neutron and X-ray scattering.

    PubMed

    Chiang, Wei-Shan; Fratini, Emiliano; Ridi, Francesca; Lim, Sung-Hwan; Yeh, Yi-Qi; Baglioni, Piero; Choi, Sung-Min; Jeng, U-Ser; Chen, Sow-Hsin

    2013-05-15

    The microstructure of calcium-silicate-hydrate (C-S-H) gel, a major hydrated phase of Ordinary Portland Cement, with and without polycarboxylic ether (PCE) additives is investigated by combined analyses of small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) data. The results show that these comb-shaped polymers tend to increase the size of the disk-like globules but have little influence on the thickness of the water and calcium silicate layers within the globules. As a result, the fractal packing of the globules becomes more open in the range of a few hundred nanometers, in the sense that the mass fractal dimension diminishes, since the PCE adsorption on the globules increases the repulsive force between and polydispersity of the C-S-H units. Moreover, scanning electron microscope (SEM) study of the synthesized C-S-H gels in the micrometer range shows that the PCEs depress the formation of fibrils while enhancing the foil-like morphology.

  17. 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.

  18. Micellar Surfactant Association in the Presence of a Glucoside-based Amphiphile Detected via High-Throughput Small Angle X-ray Scattering

    SciTech Connect

    Stanic, Vesna; Broadbent, Charlotte; DiMasi, Elaine; Galleguillos, Ramiro; Woodward, Valerie

    2016-11-14

    The interactions of mixtures of anionic and amphoteric surfactants with sugar amphiphiles were studied via high throughput small angle x-ray scattering (SAXS). The sugar amphiphile was composed of Caprate, Caprylate, and Oleate mixed ester of methyl glucoside, MeGCCO. Optimal surfactant interactions are sought which have desirable physical properties, which must be identified in a cost effective manner that can access the large phase space of possible molecular combinations. X-ray scattering patterns obtained via high throughput SAXS can probe a combinatorial sample space and reveal the incorporation of MeGCCO into the micelles and the molecular associations between surfactant molecules. Such data make it possible to efficiently assess the effects of the new amphiphiles in the formulation. A specific finding of this study is that formulations containing comparatively monodisperse and homogeneous surfactant mixtures can be reliably tuned by addition of NaCl, which swells the surfactant micelles with a monotonic dependence on salt concentration. In contrast, the presence of multiple different surfactants destroys clear correlations with NaCl concentration, even in otherwise similar series of formulations.

  19. Small-angle x-ray scattering study of phase separation in amorphous alloys during heating with use of synchrotron radiation

    SciTech Connect

    Yavari, A.R.; Osamura, K.; Okuda, H.; Amemia, Y.

    1988-05-01

    Some recent reports suggest that amorphous Pd/sub 46/Ni/sub 36/P/sub 18/ and Cu/sub 50/Zr/sub 50/ alloys phase separate during heating at temperatures 50--200 K below their crystallization temperatures. We have therefore obtained improved small-angle x-ray scattering (SAXS) measurements during heating of these alloys using a new experimental setup. The experimental improvements included in-the-beam heating using the very-high-intensity x-ray radiation available at the Synchrotron Radiation Laboratory, K.E.K., the use of Joule self-heating of the samples, which is made possible by the high resistivity of the amorphous phase and the use of regularly shaped, constant thickness amorphous tapes obtained by planar flow casting. No evidence of phase separation during heating prior to crystallization was obtained in glassy Pd/sub 46/Ni/sub 36/P/sub 18/ and Cu/sub 50/Zr/sub 50/ alloys.

  20. 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

  1. Gelatinization of starch in excess water: beyond the melting of lamellar crystallites. A combined wide- and small-angle X-ray scattering study.

    PubMed

    Vermeylen, Rudi; Derycke, Veerle; Delcour, Jan A; Goderis, Bart; Reynaers, Harry; Koch, Michel H J

    2006-09-01

    The gelatinization of waxy rice, regular rice, and potato starch suspensions (66% w/w moisture) was investigated by real-time small-angle X-ray scattering (SAXS) and wide-angle X-ray diffraction (WAXD) during heating and by fast ramp differential scanning calorimetry (DSC). The high-angle tail of the SAXS patterns suggested the transition from surface to mass fractal structures in the DSC gelatinization range. Amylose plays a major role in determining the dimensions of the self-similar structures that develop during this process as the characteristic power-law scattering behavior extends to lower scattering angles for regular than for waxy starches. Crystallinity of A-type starches is lost in the temperature region roughly corresponding to the DSC gelatinization range. At the end of the gelatinization endotherm, the B-type potato starch showed residual crystallinity (WAXD), while SAXS-patterns exhibited features of remaining lamellar stacks. Results indicate that the melting of amylopectin crystallites during gelatinization is accompanied by the (exothermic) formation of amorphous networks.

  2. Atomic layer deposition-based tuning of the pore size in mesoporous thin films studied by in situ grazing incidence small angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Dendooven, Jolien; Devloo-Casier, Kilian; Ide, Matthias; GrandfieldPresent Address: Department Of Materials Science; Engineering, Mcmaster University, Hamilton, Ontario, Canada., Kathryn; Kurttepeli, Mert; Ludwig, Karl F.; Bals, Sara; van der Voort, Pascal; Detavernier, Christophe

    2014-11-01

    Atomic layer deposition (ALD) enables the conformal coating of porous materials, making the technique suitable for pore size tuning at the atomic level, e.g., for applications in catalysis, gas separation and sensing. It is, however, not straightforward to obtain information about the conformality of ALD coatings deposited in pores with diameters in the low mesoporous regime (<10 nm). In this work, it is demonstrated that in situ synchrotron based grazing incidence small angle X-ray scattering (GISAXS) can provide valuable information on the change in density and internal surface area during ALD of TiO2 in a porous titania film with small mesopores (3-8 nm). The results are shown to be in good agreement with in situ X-ray fluorescence data representing the evolution of the amount of Ti atoms deposited in the porous film. Analysis of both datasets indicates that the minimum pore diameter that can be achieved by ALD is determined by the size of the Ti-precursor molecule.

  3. Atomic layer deposition-based tuning of the pore size in mesoporous thin films studied by in situ grazing incidence small angle X-ray scattering.

    PubMed

    Dendooven, Jolien; Devloo-Casier, Kilian; Ide, Matthias; Grandfield, Kathryn; Kurttepeli, Mert; Ludwig, Karl F; Bals, Sara; Van Der Voort, Pascal; Detavernier, Christophe

    2014-12-21

    Atomic layer deposition (ALD) enables the conformal coating of porous materials, making the technique suitable for pore size tuning at the atomic level, e.g., for applications in catalysis, gas separation and sensing. It is, however, not straightforward to obtain information about the conformality of ALD coatings deposited in pores with diameters in the low mesoporous regime (<10 nm). In this work, it is demonstrated that in situ synchrotron based grazing incidence small angle X-ray scattering (GISAXS) can provide valuable information on the change in density and internal surface area during ALD of TiO(2) in a porous titania film with small mesopores (3-8 nm). The results are shown to be in good agreement with in situ X-ray fluorescence data representing the evolution of the amount of Ti atoms deposited in the porous film. Analysis of both datasets indicates that the minimum pore diameter that can be achieved by ALD is determined by the size of the Ti-precursor molecule.

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

    PubMed Central

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

    2014-01-01

    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. PMID:25382272

  6. 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.

  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. 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.

  9. A Mo-anode-based in-house source for small-angle X-ray scattering measurements of biological macromolecules

    SciTech Connect

    Bruetzel, Linda K.; Fischer, Stefan; Salditt, Annalena; Sedlak, Steffen M.; Nickel, Bert; Lipfert, Jan

    2016-02-15

    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{sup 6} photons/s at a beam size of 1.2 × 1.2 mm{sup 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{sup −1} down to 0.009 Å{sup −1} in SAXS configuration and of 0.26 Å{sup −1} up to 5.7 Å{sup −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{sup −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.

  10. Model-based Approaches for the Determination of Lipid Bilayer Structure from Small-Angle Neutron and X-ray Scattering Data

    SciTech Connect

    Heberle, Frederick A; Pan, Jianjun; Standaert, Robert F; Drazba, Paul; Kucerka, Norbert; Katsaras, John

    2012-01-01

    Some of our recent work has resulted in the detailed structures of fully hydrated, fluid phase phosphatidylcholine (PC) and phosphatidylglycerol (PG) bilayers. These structures were obtained from the joint refinement of small-angle neutron and X-ray data using the scattering density profile (SDP) models developed by Ku erka et al. (Ku erka et al. 2012; Ku erka et al. 2008). In this review, we first discuss models for the standalone analysis of neutron or X-ray scattering data from bilayers, and assess the strengths and weaknesses inherent in these models. In particular, it is recognized that standalone data do not contain enough information to fully resolve the structure of inherently disordered fluid bilayers, and therefore may not provide a robust determination of bilayer structural parameters, including the much sought after area per lipid. We then discuss the development of matter density-based models (including the SDP model) that allow for the joint refinement of different contrast neutron and X-ray data sets, as well as the implementation of local volume conservation in the unit cell (i.e., ideal packing). Such models provide natural definitions of bilayer thicknesses (most importantly the hydrophobic and Luzzati thicknesses) in terms of Gibbs dividing surfaces, and thus allow for the robust determination of lipid areas through equivalent slab relationships between bilayer thickness and lipid volume. In the final section of this review, we discuss some of the significant findings/features pertaining to structures of PC and PG bilayers as determined from SDP model analyses.

  11. Asymmetry of the GroEL-GroES complex under physiological conditions as revealed by small-angle x-ray scattering.

    PubMed

    Inobe, Tomonao; Takahashi, Kazunobu; Maki, Kosuke; Enoki, Sawako; Kamagata, Kiyoto; Kadooka, Akio; Arai, Munehito; Kuwajima, Kunihiro

    2008-02-15

    Despite the well-known functional importance of GroEL-GroES complex formation during the chaperonin cycle, the stoichiometry of the complex has not been clarified. The complex can occur either as an asymmetric 1:1 GroEL-GroES complex or as a symmetric 1:2 GroEL-GroES complex, although it remains uncertain which type is predominant under physiological conditions. To resolve this question, we studied the structure of the GroEL-GroES complex under physiological conditions by small-angle x-ray scattering, which is a powerful technique to directly observe the structure of the protein complex in solution. We evaluated molecular structural parameters, the radius of gyration and the maximum dimension of the complex, from the x-ray scattering patterns under various nucleotide conditions (3 mM ADP, 3 mM ATP gamma S, and 3 mM ATP in 10 mM MgCl(2) and 100 mM KCl) at three different temperatures (10 degrees C, 25 degrees C, and 37 degrees C). We then compared the experimentally observed scattering patterns with those calculated from the known x-ray crystallographic structures of the GroEL-GroES complex. The results clearly demonstrated that the asymmetric complex must be the major species stably present in solution under physiological conditions. On the other hand, in the presence of ATP (3 mM) and beryllium fluoride (10 mM NaF and 300 microM BeCl(2)), we observed the formation of a stable symmetric complex, suggesting the existence of a transiently formed symmetric complex during the chaperonin cycle.

  12. 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.

  13. 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.

  14. A study of the effect of formalin preservation on normal and cancerous breast tissues using small angle X-ray scattering (SAXS)

    NASA Astrophysics Data System (ADS)

    Changizi, V.; Wilkinson, S.; Hall, C. J.; Grossmann, G.

    2006-09-01

    Small angle X-ray scattering (SAXS) has the ability to provide information on a molecular and supra-molecular scale from biological tissue specimens. It has been postulated that this information will be useful in providing histopathological diagnoses for certain diseases of the breast. In this category, we include cancer, a major health problem for a number of populations around the world. So far studies in our group have been made using flash-frozen tissue samples. This limits the range and ease of use of the technique. If we were able to obtain the same information from preserved tissues then a more extensive use of SAXS diagnosis would be possible. Here we report on the first investigations into this possibility. In the research reported in this paper, 84 human breast biopsies including cancer and normal tissues were obtained from human patients. Small angle scatter data were collected at station 2.1 of the SRS at the Daresbury Laboratory, UK using a beam size of 0.25 mm 2 at the sample and a wavelength of 1.54 Å. The sample to detector distance was 2000 mm. The results verify that there is a quantifiable difference between the scatter curves from flash-frozen cancer and normal breast tissue in the range of scatter vector Q between 0.4 and 0.7 nm -1. After preserving the tissues in formalin, the difference between the normal and cancerous tissues is less marked. The preservation of the tissue in formalin can essentially mask the effects that disease would have on the tissue supra-molecular structure rendering the preserved specimens of less useful for this histopathology technique.

  15. Analysis of InGaN nanodots grown by droplet heteroepitaxy using grazing incidence small-angle X-ray scattering and electron microscopy

    NASA Astrophysics Data System (ADS)

    Woodward, J. M.; Nikiforov, A. Yu.; Ludwig, K. F.; Moustakas, T. D.

    2017-08-01

    We present a detailed structural investigation of self-assembled indium gallium nitride nanodots grown on c-plane aluminum nitride templates by the droplet heteroepitaxy technique in a plasma-assisted molecular beam epitaxy reactor. Various growth parameters, including the total coverage of the metal species, relative and total metal effusion fluxes, and nitridation temperature were investigated. Analyses of in situ reflection high-energy electron diffraction patterns and comparison with simulations showed that the resulting crystal structure was a mixture of wurtzite and twinned zinc blende phases, with the zinc blende phase increasingly dominant for lower metal coverages and lower nitridation temperatures, and the wurtzite phase increasingly dominant for higher nitridation temperature. Studies by field emission scanning electron microscopy and atomic force microscopy revealed that the nanodots exhibit trimodal size distributions, with the dot morphologies of the intermediate size mode often resembling aggregations of distinct clusters. Nanodots grown at higher nitridation temperatures had larger inter-dot spacings, with hexagonal in-plane ordering observable at a sufficiently high temperature. Using grazing incidence small angle X-ray scattering, we determined the nanodots to be approximately truncated cone shaped, and extracted the mean radius, height, and inter-dot distance for each distribution. Microstructural investigations of the nanodots by cross-sectional transmission electron microscopy indicated that the majority of the dots were formed in dislocation-free regions, and confirmed that the intermediate size dots were approximately truncated cone shaped and consisted of both zinc blende and wurtzite regions. Mapping of the elemental distributions by energy dispersive X-ray spectroscopy in scanning transmission electron microscopy mode indicated highly nonuniform indium distributions within both small and intermediate size dots which are potentially

  16. The filament forming reactions of vimentin tetramers studied in a serial-inlet microflow device by small angle x-ray scattering

    PubMed Central

    Saldanha, Oliva; Brennich, Martha E.; Burghammer, Manfred; Herrmann, Harald; Köster, Sarah

    2016-01-01

    The structural organization of metazoan cells and their shape are established through the coordinated interaction of a composite network consisting of three individual filament systems, collectively termed the cytoskeleton. Specifically, microtubules and actin filaments, which assemble from monomeric globular proteins, provide polar structures that serve motor proteins as tracks. In contrast, intermediate filaments (IFs) assemble from highly charged, extended coiled coils in a hierarchical assembly mechanism of lateral and longitudinal interaction steps into non-polar structures. IF proteins are expressed in a distinctly tissue-specific way and thereby serve to generate the precise plasticity of the respective cells and tissues. Accordingly, in the cell, numerous parameters such as pH and salt concentration are adjusted such that the generation of functional networks is ensured. Here, we transfer the problem for the mesenchymal IF protein vimentin to an in vitro setting and combine small angle x-ray scattering with microfluidics and finite element method simulations. Our approach is adapted to resolve the early assembly steps, which take place in the sub-second to second range. In particular, we reveal the influence of ion species and concentrations on the assembly. By tuning the flow rates and thus concentration profiles, we find a minimal critical salt concentration for the initiation of the assembly. Furthermore, our analysis of the surface sensitive Porod regime in the x-ray data reveals that the formation of first assembly intermediates, so-called unit length filaments, is not a one-step reaction but consists of distinct consecutive lateral association steps followed by radial compaction as well as smoothening of the surface of the full-width filament. PMID:27042250

  17. Probing the MgATP-Bound Conformation of the Nitrogenase Fe Protein By Solution Small-Angle X-Ray Scattering

    SciTech Connect

    Sarma, R.; Mulder, D.W.; Brecht, E.; Szilagyi, R.K.; Seefeldt, L.C.; Tsuruta, H.; Peters, J.W.; /Montana State U. /SLAC, SSRL /Utah State U.

    2009-04-30

    The MgATP-bound conformation of the Fe protein of nitrogenase from Azotobacter vinelandii has been examined in solution by small-angle X-ray scattering (SAXS) and compared to existing crystallographically characterized Fe protein conformations. The results of the analysis of the crystal structure of an Fe protein variant with a Switch II single-amino acid deletion recently suggested that the MgATP-bound state of the Fe protein may exist in a conformation that involves a large-scale reorientation of the dimer subunits, resulting in an overall elongated structure relative to the more compact structure of the MgADP-bound state. It was hypothesized that the Fe protein variant may be a conformational mimic of the MgATP-bound state of the native Fe protein largely on the basis of the observation that the spectroscopic properties of the [4Fe-4S] cluster of the variant mimicked in part the spectroscopic signatures of the native nitrogenase Fe protein in the MgATP-bound state. In this work, SAXS studies reveal that the large-scale conformational differences between the native Fe protein and the variant observed by X-ray crystallography are also observed in solution. In addition, comparison of the SAXS curves of the Fe protein nucleotide-bound states to the nucleotide-free states indicates that the conformation of the MgATP-bound state in solution does not resemble the structure of the variant as initially proposed, but rather, at the resolution of this experiment, it resembles the structure of the nucleotide-free state. These results provide insights into the Fe protein conformations that define the role of MgATP in nitrogenase catalysis.

  18. 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

  19. 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

  20. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data

    SciTech Connect

    Bunkóczi, Gábor; McCoy, Airlie J.; Echols, Nathaniel; Grosse-Kunstleve, Ralf W.; Adams, Paul D.; Holton, James M.; Read, Randy J.; Terwilliger, Thomas C.

    2014-12-22

    We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases.

  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.

  2. Morphological Changes During Secondary Crystallization and Melting in Poly(ether ether ketone) as Studied by Small Angle X-Ray Scattering

    NASA Astrophysics Data System (ADS)

    Verma, Ravi; Marand, Herve; Hsiao, Benjamin

    1996-03-01

    Poly(aryl ether ether ketone) [PEEK] is a semicrystalline polymer which exhibits the double endothermic melting behavior. Most authors are of the opinion that the origin of the low endotherm lies in the melting of thinner crystals, although some argue in favor of a melting-recrystallization model. It is now established that the low endotherm develops linearly with logarithm of crystallization time. However, all morphological studies conducted to date on the origin of the low endotherm have been limited to short times. As a result, the exact morphological changes associated with the low endotherm are not fully understood. We have monitored the morphological changes during long time melt crystallization and subsequent melting in PEEK. Morphological changes were monitored via real time small angle X-ray scattering [SAXS] using synchrotron radiations. Our novel analysis of the SAXS data indicates that the development of the low endotherm is accompanied by the formation of! secondary lamellar stacks compris ed of thinner lamellae (average thickness 70 A vs 120 A for primary lamallae). Further, our analysis suggests that during melting, the low endotherm is accompanied by the melting of these secondary lamellar stacks.

  3. The new NCPSS BL19U2 beamline at the SSRF for small-angle X-ray scattering from biological macromolecules in solution1

    PubMed Central

    Li, Na; Li, Xiuhong; Wang, Yuzhu; Liu, Guangfeng; Zhou, Ping; Wu, Hongjin; Hong, Chunxia; Bian, Fenggang; Zhang, Rongguang

    2016-01-01

    The beamline BL19U2 is located in the Shanghai Synchrotron Radiation Facility (SSRF) and is its first beamline dedicated to biological material small-angle X-ray scattering (BioSAXS). The electrons come from an undulator which can provide high brilliance for the BL19U2 end stations. A double flat silicon crystal (111) monochromator is used in BL19U2, with a tunable monochromatic photon energy ranging from 7 to 15 keV. To meet the rapidly growing demands of crystallographers, biochemists and structural biologists, the BioSAXS beamline allows manual and automatic sample loading/unloading. A Pilatus 1M detector (Dectris) is employed for data collection, characterized by a high dynamic range and a short readout time. The highly automated data processing pipeline SASFLOW was integrated into BL19U2, with help from the BioSAXS group of the European Molecular Biology Laboratory (EMBL, Hamburg), which provides a user-friendly interface for data processing. The BL19U2 beamline was officially opened to users in March 2015. To date, feedback from users has been positive and the number of experimental proposals at BL19U2 is increasing. A description of the new BioSAXS beamline and the setup characteristics is given, together with examples of data obtained. PMID:27738413

  4. 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.

  5. 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.

  6. Morphological transformations in the magnetite biomineralizing protein Mms6 in iron solutions: A small-angle x-ray scattering study

    DOE PAGES

    Zhang, Honghu; Liu, Xunpei; Feng, Shuren; ...

    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

  7. 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; Ankner, John Francis; Liang, Liyuan

    2010-01-01

    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 electron shuttling, generated by the bacteria s metabolism, to extracellular acceptors that include solid metal oxides such as hematite ( -Fe2O3). To investigate the mechanism by which OmcA interacts with hematite, we purified OmcA and characterized its solution structure by small angle X-ray scattering (SAXS) and its interaction with hematite by neutron reflectometry (NR). SAXS results showed that OmcA is a monomer that adopts a flat ellipsoidal shape with a dimension of 3.4 9.0 6.5 nm3. Changes in redox state affect OmcA conformation. In addition, OmcA interacts with small organic ligands known to act as electron shuttle molecules, such as flavin mononucleotide (FMN), resulting in the formation of high molecular weight assemblies. A model system, developed using NR to study the interaction of OmcA with hematite, shows that OmcA forms a well-defined monomolecular layer on hematite surfaces. This allows OmcA to preferentially interact with hematite in a conformation that maximizes its contact area with the mineral surface. Overall, these results provide experimental and quantitative evidence for OmcA reduction of solid metal oxides involving both direct and indirect mechanisms.

  8. Characterization of oxidized tannins: comparison of depolymerization methods, asymmetric flow field-flow fractionation and small-angle X-ray scattering.

    PubMed

    Vernhet, Aude; Dubascoux, Stéphane; Cabane, Bernard; Fulcrand, Hélène; Dubreucq, Eric; Poncet-Legrand, Céline

    2011-09-01

    Condensed tannins are a major class of plant polyphenols. They play an important part in the colour and taste of foods and beverages. Due to their chemical reactivity, tannins are not stable once extracted from plants. A number of chemical reactions can take place, leading to structural changes of the native structures to give so-called derived tannins and pigments. This paper compares results obtained on native and oxidized tannins with different techniques: depolymerization followed by high-performance liquid chromatography analysis, small-angle X-ray scattering (SAXS) and asymmetric flow field-flow fractionation (AF4). Upon oxidation, new macromolecules were formed. Thioglycolysis experiments showed no evidence of molecular weight increase, but thioglycolysis yields drastically decreased. When oxidation was performed at high concentration (e.g., 10 g L(-1)), the weight average degree of polymerization determined from SAXS increased, whereas it remained stable when oxidation was done at low concentration (0.1 g L(-1)), indicating that the reaction was intramolecular, yet the conformations were different. Differences in terms of solubility were observed; ethanol being a better solvent than water. We also separated soluble and non-water-soluble species of a much oxidized fraction. Thioglycolysis showed no big differences between the two fractions, whereas SAXS and AF4 showed that insoluble macromolecules have a weight average molecular weight ten times higher than the soluble ones.

  9. 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.

  10. 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

    2015-07-07

    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.

  11. 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.

  12. A study of degradation of historic parchment using small-angle X-ray scattering, synchrotron-IR and multivariate data analysis.

    PubMed

    Možir, Alenka; Gonzalez, Lee; Kralj Cigić, Irena; Wess, Tim J; Rabin, Ira; Hahn, Oliver; Strlič, Matija

    2012-02-01

    Parchment has been in use for thousands of years and has been used as the writing or drawing support for many important historic works. A variety of analytical techniques is currently used for routine assessment of the degree of denaturation of historic parchment; however, because parchment has a heterogeneous nature, analytical methods with high spatial resolution are desirable. In this work, the use of small-angle X-ray scattering (SAXS) and synchrotron-IR (SR-IR) was examined in conjunction with multivariate data analysis to study degradation of an extended set of historic parchment samples, and particularly to investigate the effect of lipids and the presence of iron gall ink on the degradation processes. In the data analysis, shrinkage temperature, lipid content, sample age, presence of ink and accelerated degradation were included. The analysis of loading factors in partial least-squares regression and principal component analyses based on SAXS, SR-IR and other analytical and descriptive data reveals the effect of lipid removal on diffraction patterns, and lipids are found to cause the degradation process in parchment to accelerate. The effect of iron gall ink is also evident, although the mechanism of ageing is different to that of natural ageing in the absence of ink. In addition, a historic parchment score from ca. 1750 is examined, demonstrating the significant effect of iron gall ink, and lipids and inorganic soiling on its increased degradation.

  13. The location of coenzyme Q10 in phospholipid membranes made of POPE: a small-angle synchrotron X-ray diffraction study.

    PubMed

    Wollstein, Christoph; Winterhalter, Mathias; Funari, Sérgio S

    2015-07-01

    The location of coenzyme Q10 (Q10) inside the inner mitochondrial membrane is a topic of research aiming at a deeper understanding of the function of the mitochondrial respiratory chain. We investigated the location of Q10 inside model membranes made of 1-palmitoyl-2-oleoyl-phosphatidylethanolamine by means of small-angle synchrotron X-ray diffraction. Q10, which stands for ubiquinone-10 (UQ) or ubihydroquinone-10 (UH), did not remarkably influence the main phase transition temperature, but significantly decreased the lamellar-inverse hexagonal phase transition temperature (T(h)). The effect of UH on T(h) was stronger than the effect of UQ and the effect of liquid Q10 on T(h) was stronger than the effect of crystalline Q10. In the presence of Q10, the lattice parameters of the lamellar phases remained unchanged, whereas the H II lattice parameter was clearly influenced: While UQ had an increasing effect, UH had a decreasing effect. Furthermore, Q10 prevented the formation of cubic phases. The results give new evidence that the headgroup of Q10 is distant from the center of the membrane, which might be important for the function of the mitochondrial respiratory chain.

  14. Structure of Immune Stimulating Complex Matrices and Immune Stimulating Complexes in Suspension Determined by Small-Angle X-Ray Scattering

    PubMed Central

    Pedersen, Jan Skov; Oliveira, Cristiano L.P.; Hübschmann, Henriette Baun; Arleth, Lise; Manniche, Søren; Kirkby, Nicolai; Nielsen, Hanne Mørck

    2012-01-01

    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

  15. Small-angle X-ray scattering study of the ATP modulation of the structural features of the nucleotide binding domains of the CFTR in solution.

    PubMed

    Galeno, Lauretta; Galfrè, Elena; Moran, Oscar

    2011-07-01

    Nucleotide binding domains (NBD1 and NBD2) of the cystic fibrosis transmembrane conductance (CFTR), the defective protein in cystic fibrosis, are responsible for controlling the gating of the chloride channel and are the putative binding site for several candidate drugs in the disease treatment. We studied the structural properties of recombinant NBD1, NBD2, and an equimolar NBD1/NBD2 mixture in solution by small-angle X-ray scattering. We demonstrated that NBD1 or NBD2 alone have an overall structure similar to that observed for crystals. Application of 2 mM ATP induces a dimerization of NBD1 but does not modify the NBD2 monomeric conformation. An equimolar mixture of NBD1/NBD2 in solution shows a dimeric conformation, and the application of ATP to the solution causes a conformational change in the NBD1/NBD2 complex into a tight heterodimer. We hypothesize that a similar conformation change occurs in situ and that transition is part of the gating mechanism. To our knowledge, this is the first direct observation of a conformational change of the NBD1/NBD2 interaction by ATP. This information may be useful to understand the physiopathology of cystic fibrosis.

  16. Characterization of the shape and line-edge roughness of polymer gratings with grazing incidence small-angle X-ray scattering and atomic force microscopy

    SciTech Connect

    Suh, Hyo Seon; Chen, Xuanxuan; Rincon-Delgadillo, Paulina A.; Jiang, Zhang; Strzalka, Joseph; Wang, Jin; Chen, Wei; Gronheid, Roel; de Pablo, Juan J.; Ferrier, Nicola; Doxastakis, Manolis; Nealey, Paul F.

    2016-04-22

    Grazing-incidence small-angle X-ray scattering (GISAXS) is increasingly used for the metrology of substrate-supported nanoscale features and nanostructured films. In the case of line gratings, where long objects are arranged with a nanoscale periodicity perpendicular to the beam, a series of characteristic spots of high-intensity (grating truncation rods, GTRs) are recorded on a two-dimensional detector. The intensity of the GTRs is modulated by the three-dimensional shape and arrangement of the lines. Previous studies aimed to extract an average cross-sectional profile of the gratings, attributing intensity loss at GTRs to sample imperfections. Such imperfections are just as important as the average shape when employing soft polymer gratings which display significant line-edge roughness. Herein are reported a series of GISAXS measurements of polymer line gratings over a range of incident angles. Both an average shape and fluctuations contributing to the intensity in between the GTRs are extracted. Lastly, the results are critically compared with atomic force microscopy (AFM) measurements, and it is found that the two methods are in good agreement if appropriate corrections for scattering from the substrate (GISAXS) and contributions from the probe shape (AFM) are accounted for.

  17. 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

  18. 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}.

  19. 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.

  20. Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures

    SciTech Connect

    Tong, Dudu; Yang, Sichun; Lu, Lanyuan

    2016-06-20

    Structure modellingviasmall-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures. This EDM method is compared with and tested against other CG SAXS computing methods, and the resulting CG SAXS profiles from EDM agree better with all-atom theoretical SAXS data. By including the protein hydration shell represented by explicit CG water molecules and the correction of protein excluded volume, the developed CG form factors also reproduce the selected experimental SAXS profiles with very small deviations. Taken together, these EDM-derived CG form factors present an accurate and efficient computational approach for SAXS computing, especially when higher molecular details (represented by theqrange of the SAXS data) become necessary for effective structure modelling.

  1. 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

  2. Characterization of nanostructured zirconia prepared by hydrolysis and reverse micelle synthesis by small-angle neutron and X-ray scattering

    SciTech Connect

    Thiyagarajan, P.; Li, X.; Littrell, K.; Seifert, S.; Csencsits, R.; Loong, C.

    1999-12-07

    Low temperature techniques such as hydrolysis and reverse micelle syntheses provide the opportunity to determine the relationship between the structural properties and preparation conditions of zirconia powders as well as to tailor their physicochemical properties. The authors have performed small-angle neutron and synchrotron X-ray scattering (SANS and SAXS) experiments to study the nucleation and organization of zirconia nanoparticles via different preparation routes. First, the formation of reverse micelles in individual and mixed solutions of (ZrOCl{sub 2}+D{sub 2}O)/AOT/C{sub 6}D{sub 5}CD{sub 3}, and (NH{sub 4}OH+H{sub 2}O)/AOT/C{sub 6}D{sub 5}CD{sub 3} systems at water/AOT molar ratio of 20 was characterized. Second, the aggregation of zirconia gels obtained from the reaction of the reverse micelle solutions after heat treatments was studied. Third, the nanostructure of zirconia powders prepared by the reverse micelle method is compared with the corresponding powders prepared by hydrolysis after different heat treatments.

  3. Using three-dimensional 3D grazing-incidence small-angle X-ray scattering (GISAXS) analysis to probe pore deformation in mesoporous silica films.

    PubMed

    Panduro, Elvia Anabela Chavez; Granlund, Håvard; Sztucki, Michael; Konovalov, Oleg; Breiby, Dag W; Gibaud, Alain

    2014-02-26

    In the past decade, remarkable progress has been made in studying nanoscale objects deposited on surfaces by grazing-incidence small-angle X-ray scattering (GISAXS). However, unravelling the structural properties of mesostructured thin films containing highly organized internal three-dimensional (3D) structures remains a challenging issue, because of the lack of efficient algorithms that allow prediction of the GISAXS intensity patterns. Previous attempts to calculate intensities have mostly been limited to cases of two-dimensional (2D) assemblies of nanoparticles at surfaces, or have been adapted to specific 3D cases. Here, we demonstrate that highly organized 3D mesoscale structures (for example, porous networks) can be modeled by the combined use of established crystallography formalism and the Distorted Wave Born Approximation (DWBA). Taking advantage of the near-zero intensity of symmetry-allowed Bragg reflections, the casual extinction or existence of certain reflections related to the anisotropy of the form factor of the pores can be used as a highly sensitive method to extract structural information. We employ this generic method to probe the slightly compressed anisotropic shape and orientation of pores in a mesoporous silica thin film having P63/mmc symmetry.

  4. Tracking Structural Changes in Lipid-based Multicomponent Food Materials due to Oil Migration by Microfocus Small-Angle X-ray Scattering.

    PubMed

    Reinke, Svenja K; Roth, Stephan V; Santoro, Gonzalo; Vieira, Josélio; Heinrich, Stefan; Palzer, Stefan

    2015-05-13

    One of the major problems in the confectionery industry is chocolate fat blooming, that is, the formation of white defects on the chocolate surface due to fat crystals. Nevertheless, the mechanism responsible for the formation of chocolate fat blooming is not fully understood yet. Chocolate blooming is often related to the migration of lipids to the surface followed by subsequent recrystallization. Here, the migration pathway of oil into a cocoa butter matrix with different dispersed particles was investigated by employing microfocus small-angle X-ray scattering and contact angle measurements. Our results showed that the chocolate powders get wet by the oil during the migration process and that the oil is migrating into the pores within seconds. Subsequently, cocoa butter is dissolved by the oil, and thus, its characteristic crystalline structure is lost. The chemical process provoked by the dissolution is also reflected by microscopical changes of the surface morphology of chocolate model samples after several hours from the addition of oil to the sample. Finally, the surface morphology was investigated before and after oil droplet exposure and compared to that of water exposure, whereby water seems to physically migrate through the particles, namely cocoa powder, sucrose, and milk powder, which dissolve in the presence of water.

  5. The new NCPSS BL19U2 beamline at the SSRF for small-angle X-ray scattering from biological macromolecules in solution.

    PubMed

    Li, Na; Li, Xiuhong; Wang, Yuzhu; Liu, Guangfeng; Zhou, Ping; Wu, Hongjin; Hong, Chunxia; Bian, Fenggang; Zhang, Rongguang

    2016-10-01

    The beamline BL19U2 is located in the Shanghai Synchrotron Radiation Facility (SSRF) and is its first beamline dedicated to biological material small-angle X-ray scattering (BioSAXS). The electrons come from an undulator which can provide high brilliance for the BL19U2 end stations. A double flat silicon crystal (111) monochromator is used in BL19U2, with a tunable monochromatic photon energy ranging from 7 to 15 keV. To meet the rapidly growing demands of crystallographers, biochemists and structural biologists, the BioSAXS beamline allows manual and automatic sample loading/unloading. A Pilatus 1M detector (Dectris) is employed for data collection, characterized by a high dynamic range and a short readout time. The highly automated data processing pipeline SASFLOW was integrated into BL19U2, with help from the BioSAXS group of the European Molecular Biology Laboratory (EMBL, Hamburg), which provides a user-friendly interface for data processing. The BL19U2 beamline was officially opened to users in March 2015. To date, feedback from users has been positive and the number of experimental proposals at BL19U2 is increasing. A description of the new BioSAXS beamline and the setup characteristics is given, together with examples of data obtained.

  6. 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

  7. Measuring the molecular dimensions of wine tannins: comparison of small-angle X-ray scattering, gel-permeation chromatography and mean degree of polymerization.

    PubMed

    McRae, Jacqui M; Kirby, Nigel; Mertens, Haydyn D T; Kassara, Stella; Smith, Paul A

    2014-07-23

    The molecular size of wine tannins can influence astringency, and yet it has been unclear as to whether the standard methods for determining average tannin molecular weight (MW), including gel-permeation chromatography (GPC) and depolymerization reactions, are actually related to the size of the tannin in wine-like conditions. Small-angle X-ray scattering (SAXS) was therefore used to determine the molecular sizes and corresponding MWs of wine tannin samples from 3 and 7 year old Cabernet Sauvignon wine in a variety of wine-like matrixes: 5-15% and 100% ethanol; 0-200 mM NaCl and pH 3.0-4.0, and compared to those measured using the standard methods. The SAXS results indicated that the tannin samples from the older wine were larger than those of the younger wine and that wine composition did not greatly impact on tannin molecular size. The average tannin MWs as determined by GPC correlated strongly with the SAXS results, suggesting that this method does give a good indication of tannin molecular size in wine-like conditions. The MW as determined from the depolymerization reactions did not correlate as strongly with the SAXS results. To our knowledge, SAXS measurements have not previously been attempted for wine tannins.

  8. 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.

  9. The structure of DNA-DOPC aggregates formed in presence of calcium and magnesium ions: a small-angle synchrotron X-ray diffraction study.

    PubMed

    Uhríková, Daniela; Hanulová, Mária; Funari, Sérgio S; Khusainova, Raylja S; Sersen, Frantisek; Balgavý, Pavol

    2005-07-15

    The structure of aggregates formed due to DNA interaction with dioleoylphosphatidylcholine (DOPC) vesicles in presence of Ca(2+) and Mg(2+) cations was investigated using synchrotron small-angle X-ray diffraction. For DOPC/DNA=1:1 mol/base and in the range of concentration of the cation(2+) 0-76.5 mM, the diffractograms show the coexistence of two lamellar phases: L(x) phase with repeat distance d(Lx) approximately 8.26-7.39 nm identified as a phase where the DNA strands are intercalated in water layers between adjacent lipid bilayers, and L(DOPC) phase with repeat distance d(DOPC) approximately 6.45-5.65 nm identified as a phase of partially dehydrated DOPC bilayers without any divalent cations and DNA strands. The coexistence of these phases was investigated as a function of DOPC/DNA molar ratio, length of DNA fragments and temperature. If the amount of lipid increases, the fraction of partially dehydrated L(DOPC) phase is limited, depends on the portion of DNA in the sample and also on the length of DNA fragments. Thermal behaviour of DOPC+DNA+Ca(2+) aggregates was investigated in the range 20-80 degrees C. The transversal thermal expansivities of both phases were evaluated.

  10. Characterization of the shape and line-edge roughness of polymer gratings with grazing incidence small-angle X-ray scattering and atomic force microscopy

    DOE PAGES

    Suh, Hyo Seon; Chen, Xuanxuan; Rincon-Delgadillo, Paulina A.; ...

    2016-04-22

    Grazing-incidence small-angle X-ray scattering (GISAXS) is increasingly used for the metrology of substrate-supported nanoscale features and nanostructured films. In the case of line gratings, where long objects are arranged with a nanoscale periodicity perpendicular to the beam, a series of characteristic spots of high-intensity (grating truncation rods, GTRs) are recorded on a two-dimensional detector. The intensity of the GTRs is modulated by the three-dimensional shape and arrangement of the lines. Previous studies aimed to extract an average cross-sectional profile of the gratings, attributing intensity loss at GTRs to sample imperfections. Such imperfections are just as important as the average shapemore » when employing soft polymer gratings which display significant line-edge roughness. Herein are reported a series of GISAXS measurements of polymer line gratings over a range of incident angles. Both an average shape and fluctuations contributing to the intensity in between the GTRs are extracted. Lastly, the results are critically compared with atomic force microscopy (AFM) measurements, and it is found that the two methods are in good agreement if appropriate corrections for scattering from the substrate (GISAXS) and contributions from the probe shape (AFM) are accounted for.« less

  11. Insights into Surface Interactions between Metal Organic Frameworks and Gases during Transient Adsorption and Diffusion by In-Situ Small Angle X-ray Scattering

    PubMed Central

    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

  12. Core-Shell-Corona Silica Hybrid Nanoparticles Templated by Spherical Polyelectrolyte Brushes: A Study by Small Angle X-ray Scattering.

    PubMed

    Han, Haoya; Li, Li; Wang, Weihua; Tian, Yuchuan; Wang, Yunwei; Wang, Junyou; von Klitzing, Regine; Guo, Xuhong

    2017-09-06

    Core-shell-corona silica/polymer hybrid nanoparticles with narrow size distribution were prepared in the template of spherical polyelectrolyte brushes (SPB) which consist of a solid polystyrene (PS) core densely grafted with linear poly(acrylic acid) (PAA) chains. The microstructure of obtained hybrid nanoparticles was studied by small-angle X-ray scattering (SAXS) and in combination with dynamic light scattering (DLS) and transmission electron microscopy (TEM). The generation of silica shell within the brush is confirmed by the significant increase of the electron density in the shell, and the silica shell showed a unique inner-loose-outer-dense structure, whose thickness is pH sensitive but is insensitive to ionic strength as revealed by fitting SAXS data. After dissolving the PS core, hollow silica nanoparticles were obtained and determined by SAXS, which should be ideal carriers for pH-triggered drug delivery. SAXS is confirmed to be a powerful method to characterize the core-shell-corona silica/polymer hybrid and hollow silica nanoparticles.

  13. 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 PAGES

    Ishige, Ryohei; Williams, Gregory A.; Higaki, Yuji; ...

    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

  14. 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.

  15. 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

  16. Structure of dimeric and tetrameric complexes of the BAR domain protein PICK1 determined by small-angle X-ray scattering

    PubMed Central

    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.

    2015-01-01

    Summary PICK1 is a neuronal scaffolding protein containing a PDZ domain and an autoinhibited 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 suggest 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 where oligomerization governs auto-inhibition of BAR domain function. PMID:26073603

  17. 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.

  18. Structure and dynamics of water in nonionic reverse micelles: A combined time-resolved infrared and small angle x-ray scattering study

    NASA Astrophysics Data System (ADS)

    van der Loop, Tibert H.; Panman, Matthijs R.; Lotze, Stephan; Zhang, Jing; Vad, Thomas; Bakker, Huib J.; Sager, Wiebke F. C.; Woutersen, Sander

    2012-07-01

    We study the structure and reorientation dynamics of nanometer-sized water droplets inside nonionic reverse micelles (water/Igepal-CO-520/cyclohexane) with time-resolved mid-infrared pump-probe spectroscopy and small angle x-ray scattering. In the time-resolved experiments, we probe the vibrational and orientational dynamics of the O-D bonds of dilute HDO:H2O mixtures in Igepal reverse micelles as a function of temperature and micelle size. We find that even small micelles contain a large fraction of water that reorients at the same rate as water in the bulk, which indicates that the polyethylene oxide chains of the surfactant do not penetrate into the water volume. We also observe that the confinement affects the reorientation dynamics of only the first hydration layer. From the temperature dependent surface-water dynamics, we estimate an activation enthalpy for reorientation of 45 ± 9 kJ mol-1 (11 ± 2 kcal mol-1), which is close to the activation energy of the reorientation of water molecules in ice.

  19. Structure and dynamics of water in nonionic reverse micelles: a combined time-resolved infrared and small angle x-ray scattering study.

    PubMed

    van der Loop, Tibert H; Panman, Matthijs R; Lotze, Stephan; Zhang, Jing; Vad, Thomas; Bakker, Huib J; Sager, Wiebke F C; Woutersen, Sander

    2012-07-28

    We study the structure and reorientation dynamics of nanometer-sized water droplets inside nonionic reverse micelles (water/Igepal-CO-520/cyclohexane) with time-resolved mid-infrared pump-probe spectroscopy and small angle x-ray scattering. In the time-resolved experiments, we probe the vibrational and orientational dynamics of the O-D bonds of dilute HDO:H(2)O mixtures in Igepal reverse micelles as a function of temperature and micelle size. We find that even small micelles contain a large fraction of water that reorients at the same rate as water in the bulk, which indicates that the polyethylene oxide chains of the surfactant do not penetrate into the water volume. We also observe that the confinement affects the reorientation dynamics of only the first hydration layer. From the temperature dependent surface-water dynamics, we estimate an activation enthalpy for reorientation of 45 ± 9 kJ mol(-1) (11 ± 2 kcal mol(-1)), which is close to the activation energy of the reorientation of water molecules in ice.

  20. Lyotropic model membrane structures of hydrated DPPC: DSC and small-angle X-ray scattering studies of phase transitions in the presence of membranotropic agents

    NASA Astrophysics Data System (ADS)

    Bulavin, L. A.; Soloviov, D. V.; Gordeliy, V. I.; Svechnikova, O. S.; Krasnikova, A. O.; Kasian, N. A.; Vashchenko, O. V.; Lisetski, L. N.

    2015-06-01

    Multibilayer structures of hydrated phospholipids, often considered as model biological membranes, are, from the physical viewpoint, lyotropic liquid crystalline systems undergoing temperature-induced mesomorphic phase transitions. Effects of silver nitrate and urocanic acid on lyotropic phase states of hydrated L-α-dipalmitoylphosphatidylcholine (DPPC) have been studied by small-angle X-ray scattering and differential scanning calorimetry (DSC). Both methods show increase of the main phase-transition temperature (Tm) of hydrated DPPC upon introduction of AgNO3 or urocanic acid, decrease of pre-transition temperature (Tp) in the presence of urocanic acid and its increase in the presence of AgNO3. Thus, urocanic acid widened the ripple-phase temperature region. Silver nitrate caused the appearance of an additional high-temperature peak on DSC thermograms, evidencing phase separation in the system. Both agents caused minor effects on DPPC lipid bilayer repeat distance (D) in gel phase, but resulted in noticeable increase of D in the liquid crystal phase with temperature as compared to undoped DPPC structures.

  1. Quantitative Correlation between Viscosity of Concentrated MAb Solutions and Particle Size Parameters Obtained from Small-Angle X-ray Scattering.

    PubMed

    Fukuda, Masakazu; Moriyama, Chifumi; Yamazaki, Tadao; Imaeda, Yoshimi; Koga, Akiko

    2015-12-01

    To investigate the relationship between viscosity of concentrated MAb solutions and particle size parameters obtained from small-angle X-ray scattering (SAXS). The viscosity of three MAb solutions (MAb1, MAb2, and MAb3; 40-200 mg/mL) was measured by electromagnetically spinning viscometer. The protein interactions of MAb solutions (at 60 mg/mL) was evaluated by SAXS. The phase behavior of 60 mg/mL MAb solutions in a low-salt buffer was observed after 1 week storage at 25°C. The MAb1 solutions exhibited the highest viscosity among the three MAbs in the buffer containing 50 mM NaCl. Viscosity of MAb1 solutions decreased with increasing temperature, increasing salt concentration, and addition of amino acids. Viscosity of MAb1 solutions was lowest in the buffer containing histidine, arginine, and aspartic acid. Particle size parameters obtained from SAXS measurements correlated very well with the viscosity of MAb solutions at 200 mg/mL. MAb1 exhibited liquid-liquid phase separation at a low salt concentration. Simultaneous addition of basic and acidic amino acids effectively suppressed intermolecular attractive interactions and decreased viscosity of MAb1 solutions. SAXS can be performed using a small volume of samples; therefore, the particle size parameters obtained from SAXS at intermediate protein concentration could be used to screen for low viscosity antibodies in the early development stage.

  2. In situ monitoring of laser-induced periodic surface structures formation on polymer films by grazing incidence small-angle X-ray scattering.

    PubMed

    Rebollar, Esther; Rueda, Daniel R; Martín-Fabiani, Ignacio; Rodríguez-Rodríguez, Álvaro; García-Gutiérrez, Mari-Cruz; Portale, Giuseppe; Castillejo, Marta; Ezquerra, Tiberio A

    2015-04-07

    The formation of laser-induced periodic surface structures (LIPSS) on model spin-coated polymer films has been followed in situ by grazing incidence small-angle X-ray scattering (GISAXS) using synchrotron radiation. The samples were irradiated at different repetition rates ranging from 1 up to 10 Hz by using the fourth harmonic of a Nd:YAG laser (266 nm) with pulses of 8 ns. Simultaneously, GISAXS patterns were acquired during laser irradiation. The variation of both the GISAXS signal with the number of pulses and the LIPSS period with laser irradiation time is revealing key kinetic aspects of the nanostructure formation process. By considering LIPSS as one-dimensional paracrystalline lattice and using a correlation found between the paracrystalline disorder parameter, g, and the number of reflections observed in the GISAXS patterns, the variation of the structural order of LIPSS can be assessed. The role of the laser repetition rate in the nanostructure formation has been clarified. For high pulse repetition rates (i.e., 10 Hz), LIPSS evolve in time to reach the expected period matching the wavelength of the irradiating laser. For lower pulse repetition rates LIPSS formation is less effective, and the period of the ripples never reaches the wavelength value. Results support and provide information on the existence of a feedback mechanism for LIPSS formation in polymer films.

  3. Extracting magnetic cluster size and its distributions in advanced perpendicular recording media with shrinking grain size using small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Mehta, Virat; Wang, Tianhan; Ikeda, Yoshihiro; Takano, Ken; Terris, Bruce D.; Wu, Benny; Graves, Catherine; Dürr, Hermann A.; Scherz, Andreas; Stöhr, Jo; Hellwig, Olav

    2015-05-01

    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 L3 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.

  4. Characterization of the shape and line-edge roughness of polymer gratings with grazing incidence small-angle X-ray scattering and atomic force microscopy

    SciTech Connect

    Suh, Hyo Seon; Chen, Xuanxuan; Rincon-Delgadillo, Paulina A.; Jiang, Zhang; Strzalka, Joseph; Wang, Jin; Chen, Wei; Gronheid, Roel; de Pablo, Juan J.; Ferrier, Nicola; Doxastakis, Manolis; Nealey, Paul F.

    2016-04-22

    Grazing-incidence small-angle X-ray scattering (GISAXS) is increasingly used for the metrology of substrate-supported nanoscale features and nanostructured films. In the case of line gratings, where long objects are arranged with a nanoscale periodicity perpendicular to the beam, a series of characteristic spots of high-intensity (grating truncation rods, GTRs) are recorded on a two-dimensional detector. The intensity of the GTRs is modulated by the three-dimensional shape and arrangement of the lines. Previous studies aimed to extract an average cross-sectional profile of the gratings, attributing intensity loss at GTRs to sample imperfections. Such imperfections are just as important as the average shape when employing soft polymer gratings which display significant line-edge roughness. Herein are reported a series of GISAXS measurements of polymer line gratings over a range of incident angles. Both an average shape and fluctuations contributing to the intensity in between the GTRs are extracted. Lastly, the results are critically compared with atomic force microscopy (AFM) measurements, and it is found that the two methods are in good agreement if appropriate corrections for scattering from the substrate (GISAXS) and contributions from the probe shape (AFM) are accounted for.

  5. Small angle X-ray scattering study of meso-tetrakis (4-sulfonatophenyl) porphyrin in aqueous solution: a self-aggregation model.

    PubMed

    Gandini, S C M; Gelamo, E L; Itri, R; Tabak, M

    2003-08-01

    The aggregate morphology of meso-tetrakis(4-sulfonatophenyl) porphyrin (TPPS(4)) in aqueous solution is investigated by using small angle x-ray scattering (SAXS) technique. Measurements were performed at pH 4.0 and 9.0 to monitor the pH influence on the structural parameters of the aggregates. Radii of gyration were obtained from distance distribution functions p(r) analysis. The experimental data of TPPS(4) at pH 4.0 showed well-defined oscillations characteristic of large aggregates in contrast to the SAXS curve of 5 mM TPPS(4) at pH 9.0, where both a significant decrease in the intensity and the disappearance of the oscillation peaks suggest the dissociation of the aggregate. A 340-A long "hollow" cylinder with shell thickness of 20 A, compatible to the porphyrin molecule dimension, represents well the scattering curve of the aggregates at pH 4.0. According to the fitting parameters, 26 porphyrin molecules self-associate into a ringlike configuration in the plane of the cylinder cross-section. The total number of porphyrin molecules in the whole aggregate was also estimated as approximately 3000. The model compatible to SAXS data of a hollow cylinder with J-aggregation in the cross-section and H-aggregation (columnar stacking) between the cylinder layers is consistent with optical absorption spectroscopic data both in the literature and obtained in this work.

  6. Real time evolution of liquid crystalline nanostructure during the digestion of formulation lipids using synchrotron small-angle X-ray scattering.

    PubMed

    Warren, Dallas B; Anby, Mette U; Hawley, Adrian; Boyd, Ben J

    2011-08-02

    The role of the digestion of lipids in facilitating absorption of poorly water-soluble compounds, such as vitamins, is not only an important nutritional issue but is increasingly being recognized as an important determinant in the effectiveness of lipid-based drug formulations. It has been known for some time that lipids often form complex liquid crystalline structures during digestion and that this may impact drug solubilization and absorption. However, until recently we have been unable to detect and characterize those structures in real time and have been limited in establishing the interplay between composition, digestion, and nanostructure. Here, we establish the use of an in vitro lipid digestion model used in conjunction with synchrotron small-angle X-ray scattering by first confirming its validity using known, nondigestible liquid crystalline systems, and then extend the model to study the real time evolution of nanostructure during the digestion of common formulation lipids. The formation of liquid crystalline structures from unstructured liquid formulations is discovered, and the kinetics of formation and dependence on composition is investigated.

  7. 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.

  8. 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

    2011-02-02

    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.

  9. 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.

  10. Precise small-angle X-ray scattering evaluation of the pore structures in track-etched membranes: Comparison with other convenient evaluation methods

    NASA Astrophysics Data System (ADS)

    Miyazaki, Tsukasa; Takenaka, Mikihito

    2017-03-01

    Poly(ethylene terephthalate) (PET)-based track-etched membranes (TMs) with pore sizes ranging from few nanometers to approximately 1 μm are used in various applications in the biological field, and their pore structures are determined by small-angle X-ray scattering (SAXS). These TMs with the nanometer-sized cylindrical pores aligned parallel to the film thickness direction are produced by chemical etching of the track in the PET films irradiated by heavy ions with the sodium hydroxide aqueous solution. It is well known that SAXS allows us to precisely and statistically estimate the pore size and the pore size distribution in the TMs by using the form factor of a cylinder with the extremely long pore length relative to the pore diameter. The results obtained were compared with those estimated with scanning electron microscopy and gas permeability measurements. The result showed that the gas permeability measurement is convenient to evaluate the pore size of TMs within a wide length scale, and the SEM observation is also suited to estimate the pore size, although SEM observation is usually limited above approximately 30 nm.

  11. Steroid hormones partition to distinct sites in a model membrane bilayer: direct demonstration by small-angle X-ray diffraction.

    PubMed

    Golden, G A; Rubin, R T; Mason, R P

    1998-01-19

    The classical, genomic mechanisms of steroid hormone action cannot account for their rapid cellular effects. Membrane-bound steroid receptors have been partially characterized, but many rapid steroid effects occur in the absence of steroid-protein binding. Although it has been proposed that these effects could be due to steroid-induced biophysical alterations of the cell membrane, only indirect supporting evidence for this hypothesis has been forthcoming. In the present study, the ability of cortisol and estradiol (E2), natural steroids of different lipophilicity, to induce alterations in a model membrane (lecithin) bilayer was examined directly by small-angle X-ray diffraction under physiologic-like conditions. Within minutes, both steroids partitioned to distinct sites in the membrane. With increasing membrane cholesterol content, cortisol was displaced toward the polar headgroup region of the phospholipid bilayer, whereas E2 was displaced in the opposite direction, toward the nonpolar hydrocarbon core. Membrane-based partition coefficients (Kp[mem]) for both steroids (>100:1) were highest at those cholesterol concentrations that displaced the steroids toward the headgroup region (high cholesterol for cortisol; low for E2). Both steroids, when located in the headgroup region, increased overall bilayer width by 3-4 A, a change that could modulate the structure and function of integral membrane proteins independent from steroid effects on the genome.

  12. 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.

  13. Small-angle X-ray Solution Scattering Study of the Multi-aminoacyl-tRNA Synthetase Complex Reveals an Elongated and Multi-armed particle*

    PubMed Central

    Dias, José; Renault, Louis; Pérez, Javier; Mirande, Marc

    2013-01-01

    In animal cells, nine aminoacyl-tRNA synthetases are associated with the three auxiliary proteins p18, p38, and p43 to form a stable and conserved large multi-aminoacyl-tRNA synthetase complex (MARS), whose molecular mass has been proposed to be between 1.0 and 1.5 MDa. The complex acts as a molecular hub for coordinating protein synthesis and diverse regulatory signal pathways. Electron microscopy studies defined its low resolution molecular envelope as an overall rather compact, asymmetric triangular shape. Here, we have analyzed the composition and homogeneity of the native mammalian MARS isolated from rabbit liver and characterized its overall internal structure, size, and shape at low resolution by hydrodynamic methods and small-angle x-ray scattering in solution. Our data reveal that the MARS exhibits a much more elongated and multi-armed shape than expected from previous reports. The hydrodynamic and structural features of the MARS are large compared with other supramolecular assemblies involved in translation, including ribosome. The large dimensions and non-compact structural organization of MARS favor a large protein surface accessibility for all its components. This may be essential to allow structural rearrangements between the catalytic and cis-acting tRNA binding domains of the synthetases required for binding the bulky tRNA substrates. This non-compact architecture may also contribute to the spatiotemporal controlled release of some of its components, which participate in non-canonical functions after dissociation from the complex. PMID:23836901

  14. 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

  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. 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.

  17. The role played by salts in the formation of SBA-15, an in situ small-angle X-ray scattering/diffraction study.

    PubMed

    Teixeira, C V; Amenitsch, H; Linton, P; Lindén, M; Alfredsson, V

    2011-06-07

    The influence of salts (NaCl, NaBr, and NaI) on the formation of mesoporous silica SBA-15 was studied in situ by small-angle X-ray scattering and diffraction. Pluronic P104 was used as structure director. The micellar properties and the dynamics of formation were clearly dependent on the presence of salt. It was also shown that the kinetics of mesophase formation, the initial value of the cell parameters, and the extent of long-range order were all influenced by salt additions. The observations are explained to primarily originate from the influence of the anions on the ethylene oxide part of the polymer, i.e., the corona region of the Pluronic micelles. Two effects are identified: a general ion effect causing dehydration of the ethylene oxide part and consequently inducing micellar growth, and a specific ion effect that counterbalances this. The study provides the basis for understanding the means by which addition of simple Na-salts influence the formation of mesoscopically ordered silicas synthesized using nonionic surfactants as structure directors, hence advancing the knowledge base toward a more rational design of mesoporous materials.

  18. 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.

  19. 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.

  20. Small-angle x-ray scattering studies of microvoids in amorphous-silicon-based semiconductors. Annual subcontract report, February 1, 1992--January 31, 1993

    SciTech Connect

    Williamson, D L; Jones, S J; Chen, Y

    1994-05-01

    Our general objectives are to provide new details of the microstructure for the size scale from about 1 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 new and emerging deposition technologies and thereby help determine the role of microvoids and other density fluctuations in controlling the opto-electronic properties. More specifically, the objectives are to determine whether the presence of microstructure as detected by small-angle x-ray scattering (SAXS) (1) limits the photovoltaic properties of device-quality a-Si:H, (2) plays a role in determining the photo-stability of a-Si:H, and (3) is responsible for degradation of the photovoltaic properties due to alloying with Ge, C and other constituents. The approach involves collaboration with several groups that can supply relevant systematic sets of samples and the associated opto-electronic data to help address these issues. Since the SAXS technique has not been a standard characterization technique for thin-film materials, and was recently set up at CSM with support by NREL, the project involves considerable development of the method with regard to standardizing the procedures, minimizing substrate influences and implementing improved data reduction and modeling methodology. Precise, highly reproducible, and accurate results are being sought in order to allow useful, reliable, and sensitive comparisons of materials deposited under different conditions, by different methods, and by different systems that represent the same nominal method.

  1. Anisotropic x-ray anomalous diffraction and forbidden reflections

    SciTech Connect

    Carra, P.; Thole, B.T. )

    1994-10-01

    In this paper the authors present a general analysis of resonant elastic scattering of x rays. The approach exploits crystal symmetry, scattering geometry, and polarization. Extinction rules, their breaking, and the observation of forbidden reflections are discussed. As an application, a detailed description of the experiment performed by Finkelstein, Shen, and Shastri at the iron [ital K] edge in [alpha] Fe[sub 2]O[sub 3] (hematite) is reported.

  2. Scanning microbeam small-angle X-ray diffraction study of interfacial heterogeneous crystallization of fat crystals in oil-in-water emulsion droplets.

    PubMed

    Arima, S; Ueno, S; Ogawa, A; Sato, K

    2009-09-01

    We performed scanning microbeam small-angle X-ray diffraction (micro-SAXD) experiments, differential scanning calorimetry (DSC) analysis, and optical microscopic observation of palm mid fraction (PMF) crystals in oil-in-water emulsion droplets. The scanning micro-SAXD experiment was performed by irradiating a synchrotron radiation X-ray microbeam having an area of 5 x 5 microm(2) onto different positions on a 50 microm diameter emulsion droplet after the crystallization of PMF by chilling the emulsion at 5 degrees C. The micro-SAXD patterns were recorded with a two-dimensional (2D) detector, which enabled spatial analysis of polymorphic structures and the orientation of lamella planes of PMF crystals at different positions inside the emulsion droplet. Particular attention was paid to compare the crystallization of PMF in two types of emulsion droplets, hydrophilic polyoxyethylene sorbitan mono-oleate (Tween 80) alone (Tween 80 emulsion) and Tween 80 and hydrophobic sucrose palmitic acid oligoester (P-170) (Tween 80+P-170 emulsion). The DSC study revealed that the PMF crystallization temperature in the Tween 80+P-170 emulsion droplets increased by 3 degrees C compared to that of the Tween 80 emulsion because of the effects of the P-170 additive in promoting PMF crystallization. The micro-SAXD studies revealed the following results. (1) The lamella planes of PMF crystals near the outer edges of the droplet in the Tween 80+P-170 emulsion were mostly parallel to an oil-water interface, whereas the lamella planes of PMF crystals were not always aligned with the oil-water interface in the Tween 80 emulsion droplet. (2) The degree of orientation of the lamellar planes of PMF crystals, which was evaluated from the values of full width at half-maximum of 2D micro-SAXD patterns with respect to azimuthal angle extension, was remarkably higher in the Tween 80+P-170 emulsion than in the Tween 80 emulsion. (3) Polymorphic transformation of PMF from alpha to beta' in the Tween 80

  3. Annealing Behavior of Atomic Layer Deposited HfO2 Films Studied by Synchrotron X-ray Reflectivity and Grazing Incidence Small Angle Scattering

    SciTech Connect

    Green, M.; Allen, A; Jordan-Sweet, J; Ilavsky, J

    2009-01-01

    New results are presented for the annealing behavior of ultrathin complementary-metal-oxide-semiconductor (CMOS) gate dielectric HfO{sub 2} films grown by atomic layer deposition (ALD). A series of ALD HfO{sub 2} dielectric films has been studied by a combination of x-ray reflectivity (XRR) and grazing-incidence small-angle x-ray scattering (GISAXS) measurements. By using these techniques together, we have shown that the surface, interfaces, and internal structure of thin ALD films can be characterized with unprecedented sensitivity. Changes in film thickness, film roughness, or diffuseness of the film/substrate interface as measured by XRR are correlated with the corresponding changes in the internal film nanostructure, as measured by GISAXS. Although the films are dense, an internal film structure is shown to exist, attributed primarily to {approx} 2 nm 'missing island' porosity features close to the substrate; these are most likely associated with coalescence defects as a result of initial ALD growth, as they are not observed in the upper regions of the film. Some 8-9 nm heterogeneities are also present, which may indicate a widespread modulation in the film density pervading the entire film volume, and which likely also give rise to surface roughness. Comparison of the data between different scattering geometries and among a carefully designed sequence of samples has enabled important insights to be derived for the annealing behavior of the ALD HfO{sub 2} films. The main effects of single, brief, high temperature excursions to above 900C are to anneal out some of the fine voids and reduce the mean roughness and interfacial diffuseness of the film. These changes are indicative of densification. However, depending on the film thickness, the annealing behavior at temperatures between 650 and 800C is quite different for single excursion and cyclic anneals. Particularly for thin, just-coalesced films, XRR indicates marked increases in the film thickness and in the

  4. 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.

  5. Structure of Carbon Nanotube Porins in Lipid Bilayers: An in Situ Small-Angle X-ray Scattering (SAXS) Study [Atomic-level structure of carbon nanotube porins in lipid bilayers: an in-situ small-angle x-ray scattering (SAXS) study

    DOE PAGES

    Tran, Ich C.; Tunuguntla, Ramya H.; Kim, Kyunghoon; ...

    2016-06-20

    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. Furthermore, 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.more » These 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.« less

  6. Structure of Carbon Nanotube Porins in Lipid Bilayers: An in Situ Small-Angle X-ray Scattering (SAXS) Study [Atomic-level structure of carbon nanotube porins in lipid bilayers: an in-situ small-angle x-ray scattering (SAXS) study

    SciTech Connect

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

    2016-06-20

    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. Furthermore, 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. These 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.

  7. Alpha-synuclein oligomers and fibrils originate in two distinct conformer pools: a small angle X-ray scattering and ensemble optimisation modelling study.

    PubMed

    Curtain, Cyril C; Kirby, Nigel M; Mertens, Haydyn D T; Barnham, Kevin J; Knott, Robert B; Masters, Colin L; Cappai, Roberto; Rekas, Agata; Kenche, Vijaya B; Ryan, Timothy

    2015-01-01

    The 140 residue intrinsically disordered protein α-synuclein (α-syn) self-associates to form fibrils that are the major constituent of the Lewy body intracellular protein inclusions, and neurotoxic oligomers. Both of these macromolecular structures are associated with a number of neurodegenerative diseases, including Parkinson's disease and dementia with Lewy bodies. Using ensemble optimisation modelling (EOM) and small angle X-ray scattering (SAXS) on a size-exclusion column equipped beamline, we studied how the distribution of structural conformers in α-syn may be influenced by the presence of the familial early-onset mutations A30P, E45K and A53T, by substituting the four methionine residues with alanines and by reaction with copper (Cu2+) or an anti-fibril organic platinum (Pt) complex. We found that the WT had two major conformer groups, representing ensembles of compact and extended structures. The population of the extended group was increased in the more rapidly fibril-forming E45K and A53T mutants, while the compact group was enlarged in the oligomer-forming A30P mutant. Addition of Cu2+ resulted in the formation of an ensemble of compact conformers, while the anti-fibril agent and alanine substitution substantially reduced the population of extended conformers. Since our observations with the mutants suggest that fibrils may be drawn from the extended conformer ensemble, we propose that the compact and extended ensembles represent the beginning of oligomer and fibril formation pathways respectively, both of which have been reported to lead to a toxic gain of function. Manipulating these pathways and monitoring the results by EOM and SAXS may be useful in the development of anti-Parkinson's disease therapies.

  8. A New Insight into Growth Mechanism and Kinetics of Mesoporous Silica Nanoparticles by in Situ Small Angle X-ray Scattering.

    PubMed

    Yi, Zhifeng; Dumée, Ludovic F; Garvey, Christopher J; Feng, Chunfang; She, Fenghua; Rookes, James E; Mudie, Stephen; Cahill, David M; Kong, Lingxue

    2015-08-04

    The growth mechanism and kinetics of mesoporous silica nanoparticles (MSNs) were investigated for the first time by using a synchrotron time-resolved small-angle X-ray scattering (SAXS) analysis. The synchrotron SAXS offers unsurpassed time resolution and the ability to detect structural changes of nanometer sized objects, which are beneficial for the understanding of the growth mechanism of small MSNs (∼20 nm). The Porod invariant was used to quantify the conversion of tetraethyl orthosilicate (TEOS) in silica during MSN formation, and the growth kinetics were investigated at different solution pH and temperature through calculating the scattering invariant as a function of reaction time. The growth of MSNs was found to be accelerated at high temperature and high pH, resulting in a higher rate of silica formation. Modeling SAXS data of micelles, where a well-defined electrostatic interaction is assumed, determines the size and shape of hexadecyltrimethylammonium bromide (CTAB) micelles before and after the addition of TEOS. The results suggested that the micelle size increases and the micelle shape changes from ellipsoid to spherical, which might be attributed to the solubilization of TEOS in the hydrophobic core of CTAB micelles. A new "swelling-shrinking" mechanism is proposed. The mechanism provides new insights into understanding MSN growth for the formation of functional mesoporous materials exhibiting controlled morphologies. The SAXS analyses were correlated to the structure of CTAB micelles and chemical reaction of TEOS. This study has provided critical information to an understanding of the growth kinetics and mechanism of MSNs.

  9. 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.

  10. 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

    2011-07-05

    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

  11. 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, A.; Shi, L.; Droubay, T.; Ankner, J. F.; Liang, L.

    2010-06-15

    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. Finally, 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.

  12. Characterization of the decaheme c-type cytochrome OmcA in solution and on hematite surfaces by small angle x-ray scattering and neutron reflectometry.

    PubMed

    Johs, A; Shi, L; Droubay, T; Ankner, J F; Liang, L

    2010-06-16

    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 (alpha-Fe(2)O(3)). 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 65 A(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 approximately 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. (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  13. A new small-angle X-ray scattering set-up on the crystallography beamline I711 at MAX-lab.

    PubMed

    Knaapila, M; Svensson, C; Barauskas, J; Zackrisson, M; Nielsen, S S; Toft, K N; Vestergaard, B; Arleth, L; Olsson, U; Pedersen, J S; Cerenius, Y

    2009-07-01

    A small-angle X-ray scattering (SAXS) set-up has recently been developed at beamline I711 at the MAX II storage ring in Lund (Sweden). An overview of the required modifications is presented here together with a number of application examples. The accessible q range in a SAXS experiment is 0.009-0.3 A(-1) for the standard set-up but depends on the sample-to-detector distance, detector offset, beamstop size and wavelength. The SAXS camera has been designed to have a low background and has three collinear slit sets for collimating the incident beam. The standard beam size is about 0.37 mm x 0.37 mm (full width at half-maximum) at the sample position, with a flux of 4 x 10(10) photons s(-1) and lambda = 1.1 A. The vacuum is of the order of 0.05 mbar in the unbroken beam path from the first slits until the exit window in front of the detector. A large sample chamber with a number of lead-throughs allows different sample environments to be mounted. This station is used for measurements on weakly scattering proteins in solutions and also for colloids, polymers and other nanoscale structures. A special application supported by the beamline is the effort to establish a micro-fluidic sample environment for structural analysis of samples that are only available in limited quantities. Overall, this work demonstrates how a cost-effective SAXS station can be constructed on a multipurpose beamline.

  14. Condition for the appearance of the metastable P beta' phase in fully hydrated phosphatidylcholines as studied by small-angle x-ray diffraction.

    PubMed

    Matuoka, S; Yao, H; Kato, S; Hatta, I

    1993-05-01

    In the ripple phase of fully hydrated multilamellar vesicles of dipalmitoylphosphatidylcholine (DPPC), two kinds of small-angle x-ray diffraction profiles are observed on cooling through the main transition. One is a seemingly normal profile similar to that observed on heating and the other is the superposition of the diffraction profiles for the primary (normal) and the secondary ripple structures. We found that the profile obtained depended on the cooling rate. Increasing the cooling rate from 0.1 degrees C/min to 1 degrees C/min caused the peaks originating from the secondary ripple structure to diminish. After a cooling scan at 43 degrees C/min, the profile became similar to that of the normal ripple structure, although a trace of the secondary ripple structure remains. The results are interpreted in terms of the rise and fall of three-dimensional correlated domains composed of both primary and secondary ripple structures. At slow cooling rates, correlated domains of both kinds of ripple structures develop. As the cooling rate is increased, the domain of the primary ripple structure remains correlated, while that of the secondary ripple structure becomes less correlated. In addition, the multipeak profile appears even at rapid cooling rates, if the final low temperature lies just below the Tm for the main transition. This results suggests that formation of the correlated domains of the secondary ripple structure requires a certain time interval during which the DPPC vesicles experience the temperature just below the main transition. The secondary ripple structure takes place in phosphatidylcholines having more than 15 carbons in each hydrocarbon chain upon cooling through the main transition.

  15. 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.

  16. Small-angle X-ray scattering and rheological characterization of alginate gels. 2. Time-resolved studies on ionotropic gels

    NASA Astrophysics Data System (ADS)

    Yuguchi, Y.; Urakawa, H.; Kajiwara, K.; Draget, K. I.; Stokke, B. T.

    2000-10-01

    Gelation was observed by time-resolved small-angle X-ray scattering and rheology on 10 mg/ml Ca-alginate gels prepared by in situ release of Ca 2+ from CaEGTA or CaCO 3 with total Ca 2+ concentration in the range 10-20 mM. This was carried out for alginates having a fraction of α- L-GulA (G) of FG=0.39 and 0.68, respectively, obtained by the selection of alginates isolated from two different brown algae, Ascophyllum nodosum and Laminaria hyperborea stipe. Correlation between the rheological data and SAXS data shows that a large fraction of the lateral association precedes the formation of a continuous network through the sample cell. Following the initial association of chain segments in junction zones, the analysis using two-component broken rod model indicates the formation of larger bundles, and that the relative weight of these bundles increases with increasing time. The molecular model for the bundles is proposed by associating 2-16 units (G-blocks) composed of 14 (1→4) linked residues of α- L-GulA in parallel according to the available crystallographic data. The storage modulus increases as the bundles composed of associated alginate chains grow during the gel formation. The gel elasticity is mainly sustained by single chains in the alginate sample with a low fraction of α- L-GulA. The alginates with a high fraction of α- L-GulA associate into thicker bundles which join to form a network. Here the gel elasticity seems to be due to the flexible joints between bundles, since the fraction of single chains is extremely low.

  17. 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.

  18. Microfibrillar structure of PGG-glucan in aqueous solution as triple-helix aggregates by small angle x-ray scattering.

    PubMed

    Gawronski, M; Park, J T; Magee, A S; Conrad, H

    1999-11-01

    The conformation of polysaccharide PGG-Glucan, isolated from yeast cell walls, in aqueous solution was investigated by small angle x-ray scattering (SAXS) and multidetector gel permeation chromatography coupled with postcolumn delivery (GPC/PCD) techniques in comparison with scleroglucan. It was shown that both polysaccharides exhibit a rigid rod-like conformation in aqueous solution by SAXS experiments. The mass per unit length (M/L) and radius (R) of rod cross section of PGG-Glucan were measured to be 6300 daltons/nm and 1.89 nm, while those of scleroglucan are 2300 and 0.83, respectively. Utilizing a GPC/light scattering technique, the average aggregation number of PGG-Glucan is 9, while that of scleroglucan is around 3. From the comparison of the M/L and R of the respective rod cross sections as well as their aggregation number data, it is concluded that PGG-Glucan is composed of triple helices, which tend to aggregate as triplets in solution, whereas scleroglucan is composed of a single triple helix. The aggregation number distribution of PGG-Glucan was found to range from 1 to about 25 determined by GPC/PCD. From the observation of a Debye-Scherrer ring type of peak in the macroscopic scattering cross section of PGG-Glucan by SAXS, the existence of a small amount of ordered clusters of PGG-Glucan can be deduced. The "lattice parameter" of these ordered fasces-like clusters is consistent with the radius of the individual triple-helical rods forming a microfibrillar superstructure. These results indicate that higher aggregated forms of PGG-Glucan containing up to 8 triple helices behave as ordered fasces-like clusters. We conclude that PGG-Glucan is triple-helix aggregates formed by rigid rods stacking together side by side. We propose a molecular structural model for PGG-Glucan conformations.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Investigation of the effect of sugar stereochemistry on biologically relevant lyotropic phases from branched-chain synthetic glycolipids by small-angle X-ray scattering.

    PubMed

    Zahid, N Idayu; Conn, Charlotte E; Brooks, Nicholas J; Ahmad, Noraini; Seddon, John M; Hashim, Rauzah

    2013-12-23

    Synthetic branched-chain glycolipids are suitable as model systems in understanding biological cell membranes, particularly because certain natural lipids possess chain branching. Herein, four branched-chain glycopyranosides, namely, 2-hexyl-decyl-α-D-glucopyranoside (α-Glc-OC10C6), 2-hexyl-decyl-β-D-glucopyranoside (β-Glc-OC10C6), 2-hexyl-decyl-α-D-galactopyranoside (α-Gal-OC10C6), and 2-hexyl-decyl-β-D-galactopyranoside (β-Gal-OC10C6), with a total alkyl chain length of 16 carbon atoms have been synthesized, and their phase behavior has been studied. The partial binary phase diagrams of these nonionic surfactants in water were investigated by optical polarizing microscopy (OPM) and small-angle X-ray scattering (SAXS). The introduction of chain branching in the hydrocarbon chain region is shown to result in the formation of inverse structures such as inverse hexagonal and inverse bicontinuous cubic phases. A comparison of the four compounds showed that they exhibited different polymorphism, especially in the thermotropic state, as a result of contributions from anomeric and epimeric effects according to their ste