Journal of Applied Crystallography
http://journals.iucr.org/j/issues/2016/06/00/isscontsbdy.html
Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.enCopyright (c) 2016 International Union of Crystallography2016-10-19International Union of CrystallographyInternational Union of Crystallographyhttp://journals.iucr.orgurn:issn:1600-5767Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.text/htmlJournal of Applied Crystallography, Volume 49, Part 6, 2016textweekly62002-02-01T00:00+00:006492016-10-19Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallography1858urn:issn:1600-5767med@iucr.orgOctober 20162016-10-19Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
http://journals.iucr.org/j/issues/2016/06/00/isscontsbdy.html
Still imageAtomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)
http://scripts.iucr.org/cgi-bin/paper?zg5003
The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.Copyright (c) 2016 Stephen J. Perkins et al.urn:issn:1600-5767Perkins, S.J.Wright, D.W.Zhang, H.Brookes, E.H.Chen, J.Irving, T.C.Krueger, S.Barlow, D.J.Edler, K.J.Scott, D.J.Terrill, N.J.King, S.M.Butler, P.D.Curtis, J.E.2016-10-14doi:10.1107/S160057671601517XInternational Union of CrystallographyThe CCP-SAS project is currently developing software for the atomistic and coarse-grained molecular modelling of X-ray and neutron small-angle scattering data. Its computational framework is described, alongside applications in biology and soft matter.ENmolecular dynamics (MD)molecular modellingscattering curve fitssmall-angle-neutron scattering (SANS)small-angle-X-ray scattering (SAXS)The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.text/htmlAtomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)text6492016-10-14Copyright (c) 2016 Stephen J. Perkins et al.Journal of Applied Crystallographyresearch papers00A multi-slice simulation algorithm for grazing-incidence small-angle X-ray scattering
http://scripts.iucr.org/cgi-bin/paper?rg5113
Grazing-incidence small-angle X-ray scattering (GISAXS) is an important technique in the characterization of samples at the nanometre scale. A key aspect of GISAXS data analysis is the accurate simulation of samples to match the measurement. The distorted-wave Born approximation (DWBA) is a widely used model for the simulation of GISAXS patterns. For certain classes of sample such as nanostructures embedded in thin films, where the electric field intensity variation is significant relative to the size of the structures, a multi-slice DWBA theory is more accurate than the conventional DWBA method. However, simulating complex structures in the multi-slice setting is challenging and the algorithms typically used are designed on a case-by-case basis depending on the structure to be simulated. In this paper, an accurate algorithm for GISAXS simulations based on the multi-slice DWBA theory is presented. In particular, fundamental properties of the Fourier transform have been utilized to develop an algorithm that accurately computes the average refractive index profile as a function of depth and the Fourier transform of the portion of the sample within a given slice, which are key quantities required for the multi-slice DWBA simulation. The results from this method are compared with the traditionally used approximations, demonstrating that the proposed algorithm can produce more accurate results. Furthermore, this algorithm is general with respect to the sample structure, and does not require any sample-specific approximations to perform the simulations.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Venkatakrishnan, S.V.Donatelli, J.Kumar, D.Sarje, A.Sinha, S.K.Li, X.S.Hexemer, A.2016-10-14doi:10.1107/S1600576716013273International Union of CrystallographyThis paper presents an accurate numerical algorithm for simulating grazing-incidence small-angle X-ray scattering patterns of nanostructures using the multi-slice distorted-wave Born approximation. The method overcomes the typical challenge of requiring the users to manually specify a way to approximate their samples by utilizing properties of Fourier transforms to automate the computation.ENgrazing-incidence small-angle X-ray scatteringGISAXSdistorted-wave Born approximationmulti-slice algorithmGrazing-incidence small-angle X-ray scattering (GISAXS) is an important technique in the characterization of samples at the nanometre scale. A key aspect of GISAXS data analysis is the accurate simulation of samples to match the measurement. The distorted-wave Born approximation (DWBA) is a widely used model for the simulation of GISAXS patterns. For certain classes of sample such as nanostructures embedded in thin films, where the electric field intensity variation is significant relative to the size of the structures, a multi-slice DWBA theory is more accurate than the conventional DWBA method. However, simulating complex structures in the multi-slice setting is challenging and the algorithms typically used are designed on a case-by-case basis depending on the structure to be simulated. In this paper, an accurate algorithm for GISAXS simulations based on the multi-slice DWBA theory is presented. In particular, fundamental properties of the Fourier transform have been utilized to develop an algorithm that accurately computes the average refractive index profile as a function of depth and the Fourier transform of the portion of the sample within a given slice, which are key quantities required for the multi-slice DWBA simulation. The results from this method are compared with the traditionally used approximations, demonstrating that the proposed algorithm can produce more accurate results. Furthermore, this algorithm is general with respect to the sample structure, and does not require any sample-specific approximations to perform the simulations.text/htmlA multi-slice simulation algorithm for grazing-incidence small-angle X-ray scatteringtext6492016-10-14Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Towards high-flux X-ray beam compressing channel-cut monochromators
http://scripts.iucr.org/cgi-bin/paper?rg5105
The issue of a high-flux X-ray beam compressing channel-cut monochromator for applications in X-ray metrology is addressed. A Ge(111) compressor with compression ratio 20.3 was designed on the principle of a combination of symmetric and highly asymmetric diffractions. A pilot application of the single-point diamond technology (SPDT) to finish active surfaces of X-ray optics was tested, providing 50% flux enhancement as compared to a Ge(220) counterpart prepared by traditional surface treatment. This is much more than the theoretical 22% forecast and shows the potential of SPDT for preparation of high-flux X-ray compressors with a high compression ratio, where highly asymmetric diffraction with a very low exit angle is inevitable. The implications for efficient collection of X-rays from microfocus X-ray sources are discussed. A comparison of Ge compressors with Ge parallel channel-cut monochromators combined with a 50 µm slit shows the several times higher flux of the former, making them applicable in X-ray diffraction experiments at medium resolution. Furthermore, the Ge(111) compressor was tested as a collimator in high-resolution grazing-incidence small-angle X-ray scattering (GISAXS) measurements of surface gratings, providing experimental resolution close to 400 nm. This is ∼100 nm smaller than that achieved with the Ge(220) compressor but still approximately twice that of commercial SAXS/GISAXS laboratory setups.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Végsö, K.Jergel, M.Šiffalovič, P.Majková, E.Korytár, D.Zápražný, Z.Mikulík, P.Vagovič, P.2016-10-14doi:10.1107/S1600576716013376International Union of CrystallographyA high-flux Ge(111) X-ray beam compressing channel-cut monochromator with high compression ratio based on a strongly asymmetric diffraction was designed and successfully realized by a pilot application of the single-point diamond technology. Comparative testing demonstrates the potential of the new design and related technology, with direct implications for high-throughput X-ray laboratory setups, in particular those with microfocus X-ray sources.ENX-ray beam compressing channel-cut monochromatorssingle-point diamond technologyX-ray diffractionsmall-angle X-ray scatteringgrazing-incidence small-angle X-ray scatteringSAXS/GISAXSThe issue of a high-flux X-ray beam compressing channel-cut monochromator for applications in X-ray metrology is addressed. A Ge(111) compressor with compression ratio 20.3 was designed on the principle of a combination of symmetric and highly asymmetric diffractions. A pilot application of the single-point diamond technology (SPDT) to finish active surfaces of X-ray optics was tested, providing 50% flux enhancement as compared to a Ge(220) counterpart prepared by traditional surface treatment. This is much more than the theoretical 22% forecast and shows the potential of SPDT for preparation of high-flux X-ray compressors with a high compression ratio, where highly asymmetric diffraction with a very low exit angle is inevitable. The implications for efficient collection of X-rays from microfocus X-ray sources are discussed. A comparison of Ge compressors with Ge parallel channel-cut monochromators combined with a 50 µm slit shows the several times higher flux of the former, making them applicable in X-ray diffraction experiments at medium resolution. Furthermore, the Ge(111) compressor was tested as a collimator in high-resolution grazing-incidence small-angle X-ray scattering (GISAXS) measurements of surface gratings, providing experimental resolution close to 400 nm. This is ∼100 nm smaller than that achieved with the Ge(220) compressor but still approximately twice that of commercial SAXS/GISAXS laboratory setups.text/htmlTowards high-flux X-ray beam compressing channel-cut monochromatorstext6492016-10-14Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00First-principles study of structural and surface properties of (001) and (010) surfaces of hydroxylapatite and carbonated hydroxylapatite
http://scripts.iucr.org/cgi-bin/paper?po5081
Since it was first discovered that the main component of the mineral phase of bone, dentine and enamel is made from non-stoichiometric hydroxylapatite [Ca10(PO4)6(OH)2; OHAp], many successful efforts have been made to characterize its structure physico-chemically and to use it as a biomaterial for tissue repair and reconstruction. For the latter, it has been suggested that the biomimetic features of OHAp can be improved by vacancies and ionic substitutions, as typically found in natural bone tissues. In the present work, this line of thought has been followed, and the structural and electrostatic potential features of the (001) and (010) surfaces of OHAp and defective type A, type B and type AB carbonated hydroxylapatite (COHAp) have been studied using ab initio quantum mechanics at the DFT/B3LYP level. The results are in good agreement with previous experimental and preliminary theoretical work. They provide a deep analysis of the modulation of OHAp features caused by carbonate substitutions, and extend the current knowledge of the structural and surface properties of apatites.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Ulian, G.Moro, D.Valdrè, G.2016-10-14doi:10.1107/S160057671601390XInternational Union of CrystallographyThe (001) and (010) surfaces of hydroxylapatite are key to understanding and modulating the mineral–organic interactions in bone tissues. The present work provides the structural and electrostatic properties of both stoichiometric and carbonated hydroxylapatite surfaces obtained with an ab initio quantum mechanics approach.ENcarbonated hydroxylapatitesurfacesdensity functional theoryelectrostatic potentialhydroxylapatiteSince it was first discovered that the main component of the mineral phase of bone, dentine and enamel is made from non-stoichiometric hydroxylapatite [Ca10(PO4)6(OH)2; OHAp], many successful efforts have been made to characterize its structure physico-chemically and to use it as a biomaterial for tissue repair and reconstruction. For the latter, it has been suggested that the biomimetic features of OHAp can be improved by vacancies and ionic substitutions, as typically found in natural bone tissues. In the present work, this line of thought has been followed, and the structural and electrostatic potential features of the (001) and (010) surfaces of OHAp and defective type A, type B and type AB carbonated hydroxylapatite (COHAp) have been studied using ab initio quantum mechanics at the DFT/B3LYP level. The results are in good agreement with previous experimental and preliminary theoretical work. They provide a deep analysis of the modulation of OHAp features caused by carbonate substitutions, and extend the current knowledge of the structural and surface properties of apatites.text/htmlFirst-principles study of structural and surface properties of (001) and (010) surfaces of hydroxylapatite and carbonated hydroxylapatitetext6492016-10-14Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances
http://scripts.iucr.org/cgi-bin/paper?fs5126
Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debye formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. This algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Zhang, Y.Inouye, H.Crowley, M.Yu, L.Kaeli, D.Makowski, L.2016-10-14doi:10.1107/S1600576716013297International Union of CrystallographyA diffraction pattern simulation of cellulose fibrils is presented, using a modification of the Debye formula in cylindrical coordinates. Pair distances are labelled by atom type and quantized using a two-dimensional histogram, which greatly decreases the computation time and maintains a smaller R factor.ENdiffraction pattern simulationcellulose fibrilspair-distance quantizationbiomass fuelsalgorithmsIntensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debye formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. This algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.text/htmlDiffraction pattern simulation of cellulose fibrils using distributed and quantized pair distancestext6492016-10-14Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographyshort communications00