| 1. |
- Akutsu, M, et al.
(författare)
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Crystal structure of Otubain1
- 2008
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Ingår i: ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES. - 2053-2733. ; 64, s. C276-C276
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 10. |
- Gao, Zirui, et al.
(författare)
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High-speed tensor tomography: iterative reconstruction tensor tomography (IRTT) algorithm
- 2019
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Ingår i: Acta Crystallographica Section A: Foundations and Advances. - 2053-2733. ; 75, s. 223-238
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Tidskriftsartikel (refereegranskat)abstract
- The recent advent of tensor tomography techniques has enabled tomographic investigations of the 3D nanostructure organization of biological and material science samples. These techniques extended the concept of conventional X-ray tomography by reconstructing not only a scalar value such as the attenuation coefficient per voxel, but also a set of parameters that capture the local anisotropy of nanostructures within every voxel of the sample. Tensor tomography data sets are intrinsically large as each pixel of a conventional X-ray projection is substituted by a scattering pattern, and projections have to be recorded at different sample angular orientations with several tilts of the rotation axis with respect to the X-ray propagation direction. Currently available reconstruction approaches for such large data sets are computationally expensive. Here, a novel, fast reconstruction algorithm, named iterative reconstruction tensor tomography (IRTT), is presented to simplify and accelerate tensor tomography reconstructions. IRTT is based on a second-rank tensor model to describe the anisotropy of the nanostructure in every voxel and on an iterative error backpropagation reconstruction algorithm to achieve high convergence speed. The feasibility and accuracy of IRTT are demonstrated by reconstructing the nanostructure anisotropy of three samples: a carbon fiber knot, a human bone trabecula specimen and a fixed mouse brain. Results and reconstruction speed were compared with those obtained by the small-angle scattering tensor tomography (SASTT) reconstruction method introduced by Liebi et al. [Nature (2015), 527, 349–352]. The principal orientation of the nanostructure within each voxel revealed a high level of agreement between the two methods. Yet, for identical data sets and computer hardware used, IRTT was shown to be more than an order of magnitude faster. IRTT was found to yield robust results, it does not require prior knowledge of the sample for initializing parameters, and can be used in cases where simple anisotropy metrics are sufficient, i.e. the tensor approximation adequately captures the level of anisotropy and the dominant orientation within a voxel. In addition, by greatly accelerating the reconstruction, IRTT is particularly suitable for handling large tomographic data sets of samples with internal structure or as a real-time analysis tool during the experiment for online feedback during data acquisition. Alternatively, the IRTT results might be used as an initial guess for models capturing a higher complexity of structural anisotropy such as spherical harmonics based SASTT in Liebi et al. (2015), improving both overall convergence speed and robustness of the reconstruction.
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| 11. |
- Garcia-Bonete, Maria-Jose, 1989, et al.
(författare)
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Bayesian machine learning improves single-wavelength anomalous diffraction phasing
- 2019
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Ingår i: Acta Crystallographica a-Foundation and Advances. - : International Union of Crystallography (IUCr). - 2053-2733. ; 75, s. 851-860
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Tidskriftsartikel (refereegranskat)abstract
- Single-wavelength X-ray anomalous diffraction (SAD) is a frequently employed technique to solve the phase problem in X-ray crystallography. The precision and accuracy of recovered anomalous differences are crucial for determining the correct phases. Continuous rotation (CR) and inverse-beam geometry (IBG) anomalous data collection methods have been performed on tetragonal lysozyme and monoclinic survivin crystals and analysis carried out of how correlated the pairs of Friedel's reflections are after scaling. A multivariate Bayesian model for estimating anomalous differences was tested, which takes into account the correlation between pairs of intensity observations and incorporates the a priori knowledge about the positivity of intensity. The CR and IBG data collection methods resulted in positive correlation between I(+) and I(-) observations, indicating that the anomalous difference dominates between these observations, rather than different levels of radiation damage. An alternative pairing method based on near simultaneously observed Bijvoet's pairs displayed lower correlation and it was unsuccessful for recovering useful anomalous differences when using the multivariate Bayesian model. In contrast, multivariate Bayesian treatment of Friedel's pairs improved the initial phasing of the two tested crystal systems and the two data collection methods.
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| 16. |
- Hemberg, Oscar, et al.
(författare)
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High-brightness liquid-metal-jet x-ray tube
- 2011
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Ingår i: Acta Crystallographica Section A. - : International Union of Crystallography. - 2053-2733. ; 67, s. C257-C257
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 17. |
- Henningsson, Axel, et al.
(författare)
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An efficient system matrix factorization method for scanning diffraction based strain tensor tomography
- 2023
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Ingår i: Acta Crystallographica Section A: Foundations and Advances. - 2053-2733. ; 79:Pt 6, s. 542-549
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Tidskriftsartikel (refereegranskat)abstract
- Diffraction-based tomographic strain tensor reconstruction problems in which a strain tensor field is determined from measurements made in different crystallographic directions are considered in the context of sparse matrix algebra. Previous work has shown that the estimation of the crystal elastic strain field can be cast as a linear regression problem featuring a computationally involved assembly of a system matrix forward operator. This operator models the perturbation in diffraction signal as a function of spatial strain tensor state. The structure of this system matrix is analysed and a block-partitioned factorization is derived that reveals the forward operator as a sum of weighted scalar projection operators. Moreover, the factorization method is generalized for another diffraction model in which strain and orientation are coupled and can be reconstructed jointly. The proposed block-partitioned factorization method provides a bridge to classical absorption tomography and allows exploitation of standard tomographic ray-tracing libraries for implementation of the forward operator and its adjoint. Consequently, RAM-efficient, GPUaccelerated, on-the-fly strain/orientation tensor reconstruction is made possible, paving the way for higher spatial resolution studies of intragranular deformation.
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| 21. |
- Katona, Gergely, 1975, et al.
(författare)
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Estimating the difference between structure-factor amplitudes using multivariate Bayesian inference
- 2016
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Ingår i: Acta Crystallographica a-Foundation and Advances. - 2053-2733. ; 72, s. 406-411
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Tidskriftsartikel (refereegranskat)abstract
- In experimental research referencing two or more measurements to one another is a powerful tool to reduce the effect of systematic errors between different sets of measurements. The interesting quantity is usually derived from two measurements on the same sample under different conditions. While an elaborate experimental design is essential for improving the estimate, the data analysis should also maximally exploit the covariance between the measurements. In X-ray crystallography the difference between structure-factor amplitudes carries important information to solve experimental phasing problems or to determine time-dependent structural changes in pump-probe experiments. Here a multivariate Bayesian method was used to analyse intensity measurement pairs to determine their underlying structure-factor amplitudes and their differences. The posterior distribution of the model parameter was approximated with a Markov chain Monte Carlo algorithm. The described merging method is shown to be especially advantageous when systematic and random errors result in recording negative intensity measurements.
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| 24. |
- Kraft, L, et al.
(författare)
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Crystallographic studies of gluconate kinase
- 2000
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Ingår i: ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES. - 2053-2733. ; 56, s. S239-S239
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 25. |
- Lassalle, L., et al.
(författare)
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Structure of intermediates of the water oxidation reaction in photosystem II
- 2019
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Ingår i: Acta Crystallographica Section A. - : International Union of Crystallography. - 2053-2733. ; A75
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Photosystem II (PSII) catalyzes the light driven oxidation of water into dioxygen, protons and electrons. This reaction takes place at the oxygen evolving complex (OEC) a Mn4CaO5 cluster, through five intermediate S-states (S0 to S4), S1 being the dark-stable state and S3 the highest oxidized semi-stable state before O-O bond formation and O2 evolution. We have been using fs X-ray pulses from an X-ray free electron laser (XFEL) to study the geometric and electronic structure of the OEC over the reaction cycle and recently reported high-resolution (around 2 Å) structures of PSII at room temperature for the four stable states in the S-state cycle as well as for two time points in the S2-S3 transition. Our results reveal important structural changes including the binding of one additional ‘water’, Ox, during the S2→S3 state transition. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 suggests O-O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O2 release. We also explored the extended network of H-bonds between amino acid residues and waters connecting the OEC to the bulk solvent. We observed several significant changes in this network during the S-state cycle. Based on these data we will discuss the dynamics of the catalytic site and its environment over the reaction cycle.
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| 26. |
- Liebi, Marianne, 1984, et al.
(författare)
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Small-angle X-ray scattering tensor tomography: Model of the three-dimensional reciprocal-space map, reconstruction algorithm and angular sampling requirements
- 2018
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Ingår i: Acta Crystallographica Section A: Foundations and Advances. - 2053-2733. ; 74:1, s. 12-24
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Tidskriftsartikel (refereegranskat)abstract
- Small-angle X-ray scattering tensor tomography, which allows reconstruction of the local three-dimensional reciprocal-space map within a three-dimensional sample as introduced by Liebi et al. [Nature (2015), 527, 349-352], is described in more detail with regard to the mathematical framework and the optimization algorithm. For the case of trabecular bone samples from vertebrae it is shown that the model of the three-dimensional reciprocal-space map using spherical harmonics can adequately describe the measured data. The method enables the determination of nanostructure orientation and degree of orientation as demonstrated previously in a single momentum transfer q range. This article presents a reconstruction of the complete reciprocal-space map for the case of bone over extended ranges of q. In addition, it is shown that uniform angular sampling and advanced regularization strategies help to reduce the amount of data required.The mathematical framework and reconstruction algorithm for small-angle scattering tensor tomography are introduced in detail, as well as strategies which help to reduce the amount of data and therewith the measurement time required. Experimental validation is provided for the application to trabecular bone.
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| 28. |
- Lyon, Keenan, et al.
(författare)
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Parameterization of magnetic vector potentials and fields for efficient multislice calculations of elastic electron scattering
- 2021
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Ingår i: Acta Crystallographica Section A. - : International Union Of Crystallography. - 2053-2733. ; 77, s. 509-518
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Tidskriftsartikel (refereegranskat)abstract
- The multislice method, which simulates the propagation of the incident electron wavefunction through a crystal, is a well established method for analysing the multiple scattering effects that an electron beam may undergo. The inclusion of magnetic effects into this method proves crucial towards simulating enhanced magnetic interaction of vortex beams with magnetic materials, calculating magnetic Bragg spots or searching for magnon signatures, to name a few examples. Inclusion of magnetism poses novel challenges to the efficiency of the multislice method for larger systems, especially regarding the consistent computation of magnetic vector potentials A and magnetic fields B over large supercells. This work presents a tabulation of parameterized magnetic (PM) values for the first three rows of transition metal elements computed from atomic density functional theory (DFT) calculations, allowing for the efficient computation of approximate A and B across large crystals using only structural and magnetic moment size and direction information. Ferromagnetic b.c.c. (body-centred cubic) Fe and tetragonal FePt are chosen to showcase the performance of PM values versus directly obtaining A and B from the unit-cell spin density by DFT. The magnetic fields of b.c.c. Fe are well described by the PM approach while for FePt the PM approach is less accurate due to deformations in the spin density. Calculations of the magnetic signal, namely the change due to A and B of the intensity of diffraction patterns, show that the PM approach for both b.c.c. Fe and FePt is able to describe the effects of magnetism in these systems to a good degree of accuracy.
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| 32. |
- Morgan, Andrew J., et al.
(författare)
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Ab initio phasing of the diffraction of crystals with translational disorder
- 2019
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Ingår i: Acta Crystallographica Section A. - : INT UNION CRYSTALLOGRAPHY. - 2053-2733. ; 75, s. 25-40
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Tidskriftsartikel (refereegranskat)abstract
- To date X-ray protein crystallography is the most successful technique available for the determination of high-resolution 3D structures of biological molecules and their complexes. In X-ray protein crystallography the structure of a protein is refined against the set of observed Bragg reflections from a protein crystal. The resolution of the refined protein structure is limited by the highest angle at which Bragg reflections can be observed. In addition, the Bragg reflections alone are typically insufficient (by a factor of two) to determine the structure ab initio, and so prior information is required. Crystals formed from an imperfect packing of the protein molecules may also exhibit continuous diffraction between and beyond these Bragg reflections. When this is due to random displacements of the molecules from each crystal lattice site, the continuous diffraction provides the necessary information to determine the protein structure without prior knowledge, to a resolution that is not limited by the angular extent of the observed Bragg reflections but instead by that of the diffraction as a whole. This article presents an iterative projection algorithm that simultaneously uses the continuous diffraction as well as the Bragg reflections for the determination of protein structures. The viability of this method is demonstrated on simulated crystal diffraction.
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| 35. |
- Nielsen, Leonard, 1992, et al.
(författare)
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Small-angle scattering tensor tomography algorithm for robust reconstruction of complex textures
- 2023
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Ingår i: Acta Crystallographica Section A: Foundations and Advances. - 2053-2733. ; 79:Pt 6, s. 515-526
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Tidskriftsartikel (refereegranskat)abstract
- The development of small-angle scattering tensor tomography has enabled the study of anisotropic nanostructures in a volume-resolved manner. It is of great value to have reconstruction methods that can handle many different nanostructural symmetries. For such a method to be employed by researchers from a wide range of backgrounds, it is crucial that its reliance on prior knowledge about the system is minimized, and that it is robust under various conditions. Here, a method is presented that employs band-limited spherical functions to enable the reconstruction of reciprocal-space maps of a wide variety of nanostructures. This method has been thoroughly tested and compared with existing methods in its ability to retrieve known reciprocal-space maps, as well as its robustness to changes in initial conditions, using both simulations and experimental data. It has also been evaluated for its computational performance. The anchoring of this method in a framework of integral geometry and linear algebra highlights its possibilities and limitations.
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