The Experts below are selected from a list of 20232 Experts worldwide ranked by ideXlab platform
S. C. Abrahams - One of the best experts on this subject based on the ideXlab platform.
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Phase transitions and ferroelectricity in NaSb3F10
Journal of Applied Crystallography, 2008Co-Authors: R. J. Christie, Panos Photinos, S. C. AbrahamsAbstract:Atomic Coordinate analysis allows materials with appropriate but previously unrecognized dielectric properties to be predicted as new ferroelectrics if their crystal structure is known. An earlier such prediction that NaSb3F10 is ferroelectric is confirmed herein without ambiguity. Its spontaneous polarization Ps is found to exhibit reproducible dielectric hysteresis at room temperature, with Ps ≃ 60 µC m−2, under the application of a field of 0.3 MV m−1 or greater. The pyroelectric coefficient 〈p〉 = 17 (5) µC m−2 K−1 at 298 K. NaSb3F10 undergoes a phase transition at TC ≃ 461 K, on correction for thermal hysteresis, with entropy change ΔS = 5.7 (3) J mol−1 K−1. The colorless crystals melt at Tm ≃ 515 K and decompose above ∼600 K. The thermal hysteresis of ∼35 K in TC, on heating and cooling at 5–25 K min−1, is typical of first-order phase transitions. The space group in ferroelectric phase III is P63, and that in phase II is predicted to be P6322, a nonpolar supergroup of P63; the supergroup expected in the prototypic nonferroic phase I is P63/mmc. The space group of phase III is not a direct subgroup of phase I. The dielectric permittivity ∊′ at 1 kHz increases over an order of magnitude between 300 K and a major inflection at TC, continuing to increase steadily thereafter to Tm.
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Structurally ferroelectric SrMgF4.
Acta Crystallographica Section B Structural Science, 2001Co-Authors: S. C. AbrahamsAbstract:The crystal structure of 0.06% Ce-doped SrMgF4, strontium magnesium tetrafluoride, reported by Ishizawa et al. [(2001), Acta Cryst. C57, 784–786] is shown to satisfy the structural criteria for ferroelectricity and to have a predicted Curie temperature Tc ≃ l450 K. The estimated spontaneous polarization Ps ≃ 11 × 10−2 C m−2 is consistent with classification as a two-dimensional ferroelectric in which minor Δx and major Δy, Δz Atomic Coordinate component displacements are required for ferroelectric switching.
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Structurally ferroelectric SrMgF4.
Acta crystallographica. Section B Structural science, 2001Co-Authors: S. C. AbrahamsAbstract:The crystal structure of 0.06% Ce-doped SrMgF4, strontium magnesium tetrafluoride, reported by Ishizawa et al. [(2001), Acta Cryst. C57, 784-786] is shown to satisfy the structural criteria for ferroelectricity and to have a predicted Curie temperature T(c) approximately l450 K. The estimated spontaneous polarization P(s) approximately 11 x 10(-2) C x m(-2) is consistent with classification as a two-dimensional ferroelectric in which minor Delta(x) and major Delta(y), Delta(z) Atomic Coordinate component displacements are required for ferroelectric switching.
M J Saraiva - One of the best experts on this subject based on the ideXlab platform.
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Structure of the Val122Ile variant transthyretin - a cardiomyopathic mutant.
Acta crystallographica. Section D Biological crystallography, 1996Co-Authors: A M Damas, S Ribeiro, V S Lamzin, J A Palha, M J SaraivaAbstract:The Val122Ile mutant transthyretin (TTR Ile122) is an amyloidogenic protein which has been described as the major protein component of amyloid fibrils isolated from patients with familial amyloidotic cardiomyopathy (FAC), a disease characterized by cardiac failure and amyloid deposits in the heart. The reasons for the deposition of TTR are still unknown and it is conceivable that a conformational alteration, resulting from the mutation, is fundamental for amyloid formation. The three-dimensional structure of TTR Ile122 was determined and refined to a crystallographic R factor of 15.8% at 1.9 A resolution. The r.m.s. deviation from ideality in bond distances is 0.019 A and in angle-bonded distances is 0.027 A. The presence of two crystallographically independent monomers in the asymmetric unit allowed additional means of estimation of Atomic Coordinate error. The structure of the mutant is essentially identical to that of the wild-type transthyretin (TTR). The largest deviations occur in surface loops and in the region of the substitution. The protein is a tetramer composed of identical subunits; each monomer has two four-stranded beta-sheets which are extended to eight-stranded beta-sheets when two monomers associate through hydrogen bonds forming a dimer, which is the crystallographic asymmetric unit. The replacement of valine for isoleucine introduces very small alterations in relation to the wild-type protein; nevertheless they seem to confirm a tendency for a less stable tetrameric structure. This would support the idea that the tetrameric structure might be disrupted in amyloid fibrils.
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Structure of the Val122Ile Variant Transthyretin – a Cardiomyopathic Mutant
Acta Crystallographica Section D Biological Crystallography, 1996Co-Authors: A M Damas, S Ribeiro, V S Lamzin, J A Palha, M J SaraivaAbstract:The Val122Ile mutant transthyretin (TTR Ile122) is an amyloidogenic protein which has been described as the major protein component of amyloid fibrils isolated from patients with familial amyloidotic cardiomyopathy (FAC), a disease characterized by cardiac failure and amyloid deposits in the heart. The reasons for the deposition of TTR are still unknown and it is conceivable that a conformational alteration, resulting from the mutation, is fundamental for amyloid formation. The three-dimensional structure of TTR Ile122 was determined and refined to a crystallographic R factor of 15.8% at 1.9 A resolution. The r.m.s. deviation from ideality in bond distances is 0.019 A and in angle-bonded distances is 0.027 A. The presence of two crystallographically independent monomers in the asymmetric unit allowed additional means of estimation of Atomic Coordinate error. The structure of the mutant is essentially identical to that of the wild-type transthyretin (TTR). The largest deviations occur in surface loops and in the region of the substitution. The protein is a tetramer composed of identical subunits; each monomer has two four-stranded β-sheets which are extended to eight-stranded β-sheets when two monomers associate through hydrogen bonds forming a dimer, which is the crystallographic asymmetric unit. The replacement of valine for isoleucine introduces very small alterations in relation to the wild-type protein; nevertheless they seem to confirm a tendency for a less stable tetrameric structure. This would support the idea that the tetrameric structure might be disrupted in amyloid fibrils.
A M Damas - One of the best experts on this subject based on the ideXlab platform.
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Structure of the Val122Ile variant transthyretin - a cardiomyopathic mutant.
Acta crystallographica. Section D Biological crystallography, 1996Co-Authors: A M Damas, S Ribeiro, V S Lamzin, J A Palha, M J SaraivaAbstract:The Val122Ile mutant transthyretin (TTR Ile122) is an amyloidogenic protein which has been described as the major protein component of amyloid fibrils isolated from patients with familial amyloidotic cardiomyopathy (FAC), a disease characterized by cardiac failure and amyloid deposits in the heart. The reasons for the deposition of TTR are still unknown and it is conceivable that a conformational alteration, resulting from the mutation, is fundamental for amyloid formation. The three-dimensional structure of TTR Ile122 was determined and refined to a crystallographic R factor of 15.8% at 1.9 A resolution. The r.m.s. deviation from ideality in bond distances is 0.019 A and in angle-bonded distances is 0.027 A. The presence of two crystallographically independent monomers in the asymmetric unit allowed additional means of estimation of Atomic Coordinate error. The structure of the mutant is essentially identical to that of the wild-type transthyretin (TTR). The largest deviations occur in surface loops and in the region of the substitution. The protein is a tetramer composed of identical subunits; each monomer has two four-stranded beta-sheets which are extended to eight-stranded beta-sheets when two monomers associate through hydrogen bonds forming a dimer, which is the crystallographic asymmetric unit. The replacement of valine for isoleucine introduces very small alterations in relation to the wild-type protein; nevertheless they seem to confirm a tendency for a less stable tetrameric structure. This would support the idea that the tetrameric structure might be disrupted in amyloid fibrils.
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Structure of the Val122Ile Variant Transthyretin – a Cardiomyopathic Mutant
Acta Crystallographica Section D Biological Crystallography, 1996Co-Authors: A M Damas, S Ribeiro, V S Lamzin, J A Palha, M J SaraivaAbstract:The Val122Ile mutant transthyretin (TTR Ile122) is an amyloidogenic protein which has been described as the major protein component of amyloid fibrils isolated from patients with familial amyloidotic cardiomyopathy (FAC), a disease characterized by cardiac failure and amyloid deposits in the heart. The reasons for the deposition of TTR are still unknown and it is conceivable that a conformational alteration, resulting from the mutation, is fundamental for amyloid formation. The three-dimensional structure of TTR Ile122 was determined and refined to a crystallographic R factor of 15.8% at 1.9 A resolution. The r.m.s. deviation from ideality in bond distances is 0.019 A and in angle-bonded distances is 0.027 A. The presence of two crystallographically independent monomers in the asymmetric unit allowed additional means of estimation of Atomic Coordinate error. The structure of the mutant is essentially identical to that of the wild-type transthyretin (TTR). The largest deviations occur in surface loops and in the region of the substitution. The protein is a tetramer composed of identical subunits; each monomer has two four-stranded β-sheets which are extended to eight-stranded β-sheets when two monomers associate through hydrogen bonds forming a dimer, which is the crystallographic asymmetric unit. The replacement of valine for isoleucine introduces very small alterations in relation to the wild-type protein; nevertheless they seem to confirm a tendency for a less stable tetrameric structure. This would support the idea that the tetrameric structure might be disrupted in amyloid fibrils.
Bin Jiang - One of the best experts on this subject based on the ideXlab platform.
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Efficient and Accurate Simulations of Vibrational and Electronic Spectra with Symmetry-Preserving Neural Network Models for Tensorial Properties
The journal of physical chemistry. B, 2020Co-Authors: Yaolong Zhang, Jinxiao Zhang, Jun Jiang, Bin JiangAbstract:Machine learning has revolutionized the high-dimensional representations for molecular properties such as potential energy. However, there are scarce machine learning models targeting tensorial properties, which are rotationally covariant. Here, we propose tensorial neural network (NN) models to learn both tensorial response and transition properties in which Atomic Coordinate vectors are multiplied with scalar NN outputs or their derivatives to preserve the rotationally covariant symmetry. This strategy keeps structural descriptors symmetry invariant so that the resulting tensorial NN models are as efficient as their scalar counterparts. We validate the performance and universality of this approach by learning response properties of water oligomers and liquid water and transition dipole moment of a model structural unit of proteins. Machine-learned tensorial models have enabled efficient simulations of vibrational spectra of liquid water and ultraviolet spectra of realistic proteins, promising feasible and accurate spectroscopic simulations for biomolecules and materials.
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Efficient and Accurate Spectroscopic Simulations with Symmetry-Preserving Neural Network Models for Tensorial Properties
arXiv: Chemical Physics, 2020Co-Authors: Yaolong Zhang, Jinxiao Zhang, Jun Jiang, Bin JiangAbstract:Machine learning has revolutionized the high-dimensional representations for molecular properties such as potential energy. However, there are scarce machine learning models targeting tensorial properties, which are rotationally covariant. Here, we propose tensorial neural network (NN) models to learn both tensorial response and transition properties, in which Atomic Coordinate vectors are multiplied with scalar NN outputs or their derivatives to preserve the rotationally covariant symmetry. This strategy keeps structural descriptors symmetry invariant so that the resulting tensorial NN models are as efficient as their scalar counterparts. We validate the performance and universality of this approach by learning response properties of water oligomers and liquid water, and transition dipole moment of a model structural unit of proteins. Machine learned tensorial models have enabled efficient simulations of vibrational spectra of liquid water and ultraviolet spectra of realistic proteins, promising feasible and accurate spectroscopic simulations for biomolecules and materials.
Lee Makowski - One of the best experts on this subject based on the ideXlab platform.
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Predicting X‐ray solution scattering from flexible macromolecules
Protein science : a publication of the Protein Society, 2018Co-Authors: Hao Zhou, Hugo Guterres, Carla Mattos, Lee MakowskiAbstract:Wide-angle X-ray solution scattering (WAXS) patterns contain substantial information about the structure and dynamics of a protein. Solution scattering from a rigid protein can be predicted from Atomic Coordinate sets to within experimental error. However, structural fluctuations of proteins in solution can lead to significant changes in the observed intensities. The magnitude and form of these changes contain information about the nature and spatial extent of structural fluctuations in the protein. Molecular dynamics (MD) simulations based on a crystal structure and selected force field generate models for protein internal motions, and here we demonstrate that they can be used to predict the impact of structural fluctuations on solution scattering data. In cases where the observed and calculated intensities correspond, we can conclude that the X-ray scattering provides direct experimental validation of the structural and MD results. In cases where calculated and observed intensities are at odds, the inconsistencies can be used to determine the origins of these discrepancies. They may be because of overestimates or underestimates of structural fluctuations in MD simulations, under-sampling of the structural ensemble in the simulations, errors in the structural model, or a mismatch between the experimental conditions and the parameters used in carrying out the MD simulation.
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What Can We Learn from Wide-Angle Solution Scattering?
Advances in experimental medicine and biology, 2017Co-Authors: Yujing Wang, Hao Zhou, Emre Onuk, John Badger, Lee MakowskiAbstract:Extending collection of x-ray solution scattering data into the wide-angle regime (WAXS) can provide information not readily extracted from small angle (SAXS) data. It is possible to accurately predict WAXS scattering on the basis of Atomic Coordinate sets and thus use it as a means of testing molecular models constructed on the basis of crystallography, molecular dynamics (MD), cryo-electron microscopy or ab initio modeling. WAXS data may provide insights into the secondary, tertiary and quaternary structural organization of macromolecules. It can provide information on protein folding and unfolding beyond that attainable from SAXS data. It is particularly sensitive to structural fluctuations in macromolecules and can be used to generate information about the conformational make up of ensembles of structures co-existing in solution. Novel approaches to modeling of structural fluctuations can provide information on the spatial extent of large-scale structural fluctuations that are difficult to obtain by other means. Direct comparison with the results of MD simulations are becoming possible. Because it is particularly sensitive to small changes in structure and flexibility it provides unique capabilities for the screening of ligand libraries for detection of functional interactions. WAXS thereby provides an important extension of SAXS that can generate structural and dynamic information complementary to that obtainable by other biophysical techniques.
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Multi-Wavelength Anomalous Diffraction Using Medium-Angle X-Ray Solution Scattering (MADMAX)
Biophysical journal, 2012Co-Authors: Lee Makowski, Jaydeep P. Bardhan, David Gore, Diane J. Rodi, Robert F. FischettiAbstract:Proteins are dynamic molecules whose function in virtually all biological processes requires conformational motion. Direct experimental probes of protein structure in solution are needed to characterize these motions. Anomalous scattering from proteins in solution has the potential to act as a precise molecular ruler to determine the positions of specific chemical groups or atoms within proteins under conditions in which structural changes can take place free from the constraints of crystal contacts. In solution, anomalous diffraction has two components: a set of cross-terms that depend on the relative location of the anomalous centers and the rest of the protein, and a set of pure anomalous terms that depend on the distances between the anomalous centers. The cross-terms are demonstrated here to be observable and to provide direct information about the distance between the anomalous center and the center of mass of the protein. The second set of terms appears immeasurably small in the context of current experimental capabilities. Here, we outline the theory underlying anomalous scattering from proteins in solution, predict the anomalous differences expected on the basis of Atomic Coordinate sets, and demonstrate the measurement of anomalous differences at the iron edge for solutions of myoglobin and hemoglobin.