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  • International Union of Crystallography  (46,860)
  • Annual Reviews
  • 2020-2022  (3,074)
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  • 1
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    Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: In the past two decades, most of the steps in a macromolecular crystallography experiment have undergone tremendous development with respect to speed, feasibility and increase of throughput. The part of the experimental workflow that is still a bottleneck, despite significant efforts, involves the manipulation and harvesting of the crystals for the diffraction experiment. Here, a novel low‐cost device is presented that functions as a cover for 96‐well crystallization plates. This device enables access to the individual experiments one at a time by its movable parts, while minimizing evaporation of all other experiments of the plate. In initial tests, drops of many typically used crystallization cocktails could be successfully protected for up to 6 h. Therefore, the manipulation and harvesting of crystals is straightforward for the experimenter, enabling significantly higher throughput. This is useful for many macromolecular crystallography experiments, especially multi‐crystal screening campaigns.
    Description: A simple and low‐cost device has been developed to minimize evaporation in microtiter plates for easy crystal handling and harvesting. image
    Keywords: 548 ; evaporation reduction ; crystal handling ; crystal harvesting ; crystallographic fragment screening
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  • 2
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    Cation distribution in Cu2ZnSnSe4, Cu2FeSnS4 and Cu2ZnSiSe4 by multiple‐edge anomalous diffraction (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-30
    Description: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Semiconductors from this group of materials are promising candidates for photovoltaic applications. Their properties strongly depend on point defects, in particular related to cation order–disorder. However, Cu+, Zn2+ and Fe2+ have very similar scattering factors and are all but indistinguishable in usual X‐ray diffraction experiments. Anomalous diffraction utilizes the dependency of the atomic scattering factors f′ and f′′ of the energy of the radiation, especially close to the element‐specific absorption edges. In the MEAD technique, individual Bragg peaks are tracked over an absorption edge. The intensity changes depending on the structure factor can be highly characteristic for Miller indices selected for a specific structural problem, but require very exact measurements. Beamline KMC‐2 at synchrotron BESSY II, Berlin, has been recently upgraded for this technique. Anomalous X‐ray powder diffraction and XAFS compliment the data. Application of this technique confirmed established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS). In contrast to the literature, cation distribution in Cu2ZnSiSe4 (CZSiSe) is shown to adopt a highly ordered wurtz‐kesterite structure type.
    Description: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Application of this technique confirms established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS), but in Cu2ZnSiSe4 (CZSiSe) the cation distribution is shown to adopt a highly ordered wurtz‐kesterite structure type in contrast to the literature. image
    Keywords: 548 ; synchrotron ; anomalous diffraction ; semiconductor ; MEAD
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  • 3
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    The copper(II)‐binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: The growth of diffraction‐quality crystals and experimental phasing remain two of the main bottlenecks in protein crystallography. Here, the high‐affinity copper(II)‐binding tripeptide GHK was fused to the N‐terminus of a GFP variant and an MBP‐FG peptide fusion. The GHK tag promoted crystallization, with various residues (His, Asp, His/Pro) from symmetry molecules completing the copper(II) square‐pyramidal coordination sphere. Rapid structure determination by copper SAD phasing could be achieved, even at a very low Bijvoet ratio or after significant radiation damage. When collecting highly redundant data at a wavelength close to the copper absorption edge, residual S‐atom positions could also be located in log‐likelihood‐gradient maps and used to improve the phases. The GHK copper SAD method provides a convenient way of both crystallizing and phasing macromolecular structures, and will complement the current trend towards native sulfur SAD and MR‐SAD phasing.
    Description: A novel three‐residue tag containing the residues GHK that can be used to promote crystallization and in SAD phasing experiments using its tightly bound copper ion is described. image
    Keywords: 548 ; phasing ; crystallization ; GHK ; SAD
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  • 4
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    Determining paracrystallinity in mixed‐tacticity polyhydroxybutyrates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: Recently, the authors reported on the development of crystallinity in mixed‐tacticity polyhydroxybutyrates. Comparable values reported in the literature vary depending on the manner of determination, the discrepancies being partially attributable to scattering from paracrystalline portions of the material. These portions can be qualified by peak profile fitting or quantified by allocation of scattered X‐ray intensities. However, the latter requires a good quality of the former, which in turn must additionally account for peak broadening inherent in the measurement setup, and due to limited crystallite sizes and the possible presence of microstrain. Since broadening due to microstrain and paracrystalline order both scale with scattering vector, they are easily confounded. In this work, a method to directionally discern these two influences on the peak shape in a Rietveld refinement is presented. Allocating intensities to amorphous, bulk and paracrystalline portions with changing tactic disturbance provided internal validations of the obtained directional numbers. In addition, the correlation between obtained thermal factors and Young's moduli, determined in earlier work, is discussed.
    Description: A method to robustly determine paracrystalline contents from Rietveld‐refined powder X‐ray data is presented and discussed for the example of mixed‐tacticity polyhydroxybutyrates. image
    Keywords: 548 ; polyhydroxybutyrates ; mixed tacticity ; paracrystallinity ; Rietveld refinement ; thermal factors
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  • 5
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    Concepts for nondestructive and depth‐resolved X‐ray residual stress analysis in the near‐surface region of nearly single crystalline materials with mosaic structure (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: Two evaluation concepts for nondestructive depth‐resolved X‐ray residual stress analysis in the near‐surface region of materials with cubic symmetry and nearly single crystalline structure are introduced by simulated examples. Both concepts are based on the same data acquisition strategy, which consists in the determination of lattice‐spacing depth profiles along the ⟨hkl⟩ poles by stepwise sample rotation around the scattering vector. Segmentation of these profiles parallel to the sample surface provides the lattice strain state as a function of depth. The first evaluation concept extends the crystallite group method developed for materials with pronounced crystallographic texture by the feature of depth resolution and can be applied to samples with arbitrary orientation. The second evaluation concept, which adapts the linear regression approach of the sin2ψ method for the case of single crystalline materials, is restricted to samples with (001) orientation. The influence of the strain‐free lattice parameter a0 on residual stress analysis using both evaluation concepts is discussed on the basis of explicitly derived relations.
    Description: Two data evaluation concepts are proposed for nondestructive and depth‐resolved X‐ray residual stress analysis by means of energy‐dispersive diffraction on materials featuring cubic symmetry and a nearly single crystalline structure. image
    Keywords: 548 ; residual stress ; X‐ray diffraction ; depth‐resolved analysis ; mosaic crystals
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  • 6
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    X‐ray dichroism in polyimide caused by non‐resonant scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: Dichroism is one of the most important optical effects in both the visible and the X‐ray range. Besides absorption, scattering can also contribute to dichroism. This paper demonstrates that, based on the example of polyimide, materials can show tiny dichroism even far from electronic resonances due to scattering. Although the effect is small, it can lead to a measurable polarization change and might have influence on highly sensitive polarimetric experiments.
    Description: Aligned molecules, for example in polyimide foils, lead to small dichroism even far from resonances, which can be revealed by high‐precision X‐ray polarimetry. image
    Keywords: 548 ; polyimide ; polarization ; X‐ray polarimetry ; wide‐angle scattering ; X‐ray dichroism
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  • 7
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    Elastic stiffness coefficients of thiourea from thermal diffuse scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: The complete elastic stiffness tensor of thiourea has been determined from thermal diffuse scattering (TDS) using high‐energy photons (100 keV). Comparison with earlier data confirms a very good agreement of the tensor coefficients. In contrast with established methods to obtain elastic stiffness coefficients (e.g. Brillouin spectroscopy, inelastic X‐ray or neutron scattering, ultrasound spectroscopy), their determination from TDS is faster, does not require large samples or intricate sample preparation, and is applicable to opaque crystals. Using high‐energy photons extends the applicability of the TDS‐based approach to organic compounds which would suffer from radiation damage at lower photon energies.
    Description: The elastic stiffness coefficients of thiourea are determined from thermal diffuse scattering. image
    Keywords: 548 ; thermal diffuse scattering ; elastic stiffness ; thiourea
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  • 8
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    Fast fitting of reflectivity data of growing thin films using neural networks (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-07-03
    Description: X‐ray reflectivity (XRR) is a powerful and popular scattering technique that can give valuable insight into the growth behavior of thin films. This study shows how a simple artificial neural network model can be used to determine the thickness, roughness and density of thin films of different organic semiconductors [diindenoperylene, copper(II) phthalocyanine and α‐sexithiophene] on silica from their XRR data with millisecond computation time and with minimal user input or a priori knowledge. For a large experimental data set of 372 XRR curves, it is shown that a simple fully connected model can provide good results with a mean absolute percentage error of 8–18% when compared with the results obtained by a genetic least mean squares fit using the classical Parratt formalism. Furthermore, current drawbacks and prospects for improvement are discussed.
    Description: Artificial neural networks trained with simulated data are shown to correctly and quickly determine film parameters from experimental X‐ray reflectivity curves.
    Keywords: 548 ; X‐ray reflectivity ; machine learning ; organic semi‐conductors ; neural networks
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  • 9
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    Numerically stable form factor of any polygon and polyhedron (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-05
    Description: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Apparent singularities, all removable, are discussed in detail. Cancellation near the singularities causes a loss of precision that can be avoided by using series expansions. An important application domain is small‐angle scattering by nanocrystals.
    Description: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Series expansions are used to ensure numeric precision close to apparent singularities. image
    Keywords: 548 ; form factors ; polyhedra ; Fourier shape transform
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  • 10
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    ROBL‐II at ESRF: a synchrotron toolbox for actinide research (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-30
    Description: ROBL‐II provides four different experimental stations to investigate actinide and other alpha‐ and beta‐emitting radionuclides at the new EBS storage ring of ESRF within an energy range of 3 to 35 keV. The XAFS station consists of a highly automatized, high sample throughput installation in a glovebox, to measure EXAFS and conventional XANES of samples routinely at temperatures down to 10 K, and with a detection limit in the sub‐p.p.m. range. The XES station with its five bent‐crystal analyzer, Johann‐type setup with Rowland circles of 1.0 and 0.5 m radii provides high‐energy resolution fluorescence detection (HERFD) for XANES, XES, and RIXS measurements, covering both actinide L and M edges together with other elements accessible in the 3 to 20 keV energy range. The six‐circle heavy duty goniometer of XRD‐1 is equipped for both high‐resolution powder diffraction as well as surface‐sensitive CTR and RAXR techniques. Single crystal diffraction, powder diffraction with high temporal resolution, as well as X‐ray tomography experiments can be performed at a Pilatus 2M detector stage (XRD‐2). Elaborate radioprotection features enable a safe and easy exchange of samples between the four different stations to allow the combination of several methods for an unprecedented level of information on radioactive samples for both fundamental and applied actinide and environmental research.
    Description: ROBL‐II at ESRF provides four experimental stations to investigate actinides with X‐ray absorption and emission spectroscopy, and with surface, high‐resolution powder, and single‐crystal X‐ray diffractometry.
    Keywords: 549 ; actinides ; EXAFS ; XANES ; HERFD‐XANES ; XAS ; XES ; RIXS ; XRD ; CTR ; RAXR ; surface diffraction
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  • 11
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    ATSAS 3.0: expanded functionality and new tools for small‐angle scattering data analysis (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small‐angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus‐based concentration‐independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi‐atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy – a PyMOL plugin to run a subset of ATSAS tools – to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl‐hamburg.de/biosaxs/software.html.
    Description: ATSAS is a comprehensive software suite for the processing, visualization, analysis and modelling of small‐angle scattering data. This article describes developments in the ATSAS 3.0 release, including new programs for data simulation and for the structural modelling of lipids, nucleic acids and polydisperse systems. image
    Keywords: 548 ; small‐angle scattering ; data analysis ; biological macromolecules ; structural modelling ; ATSAS
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  • 12
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    XGANDALF – extended gradient descent algorithm for lattice finding (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real‐time feedback during serial crystallography experiments. It is implemented in an open‐source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.
    Description: A description and evaluation are given of XGANDALF, extended gradient descent algorithm for lattice finding, an algorithm developed for fast and accurate indexing of snapshot diffraction patterns. image
    Keywords: 548 ; indexing ; XGANDALF ; CrystFEL ; multiple lattices ; serial crystallography
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  • 13
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    pinkIndexer – a universal indexer for pink‐beam X‐ray and electron diffraction snapshots (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink‐beam X‐ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit‐cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink‐beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi‐monochromatic X‐rays and with electrons the algorithm indexed more patterns than other programs tested.
    Description: pinkIndexer, an algorithm developed for indexing of snapshot diffraction patterns recorded with pink‐beam X‐rays, monochromatic X‐rays and electrons, is described and its use evaluated. image
    Keywords: 548 ; indexing ; pinkIndexer ; CrystFEL ; pink X‐ray beam ; serial electron diffraction
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  • 14
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    Crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-17
    Description: CRM1 is a nuclear export receptor that has been intensively targeted over the last decade for the development of antitumor and antiviral drugs. Structural analysis of several inhibitor compounds bound to CRM1 revealed that their mechanism of action relies on the covalent modification of a critical cysteine residue (Cys528 in the human receptor) located in the nuclear export signal‐binding cleft. This study presents the crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP at 2.58 Å resolution. The results demonstrate that buffer components can interfere with the characterization of cysteine‐dependent inhibitor compounds.
    Description: The covalent modification of human CRM1 by 2‐mercaptoethanol interferes with the characterization of cysteine‐dependent inhibitor compounds. image
    Keywords: 548 ; nuclear export ; cancer ; exportin 1 ; cysteine modification
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  • 15
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    Staircase array of inclined refractive multi‐lenses for large field of view pixel super‐resolution scanning transmission hard X‐ray microscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-26
    Description: Owing to the development of X‐ray focusing optics during the past decades, synchrotron‐based X‐ray microscopy techniques allow the study of specimens with unprecedented spatial resolution, down to 10 nm, using soft and medium X‐ray photon energies, though at the expense of the field of view (FOV). One of the approaches to increase the FOV to square millimetres is raster‐scanning of the specimen using a single nanoprobe; however, this results in a long data acquisition time. This work employs an array of inclined biconcave parabolic refractive multi‐lenses (RMLs), fabricated by deep X‐ray lithography and electroplating to generate a large number of long X‐ray foci. Since the FOV is limited by the pattern height if a single RML is used by impinging X‐rays parallel to the substrate, many RMLs at regular intervals in the orthogonal direction were fabricated by tilted exposure. By inclining the substrate correspondingly to the tilted exposure, 378000 X‐ray line foci were generated with a length in the centimetre range and constant intervals in the sub‐micrometre range. The capability of this new X‐ray focusing device was first confirmed using ray‐tracing simulations and then using synchrotron radiation at BL20B2 of SPring‐8, Japan. Taking account of the fact that the refractive lens is effective for focusing high‐energy X‐rays, the experiment was performed with 35 keV X‐rays. Next, by scanning a specimen through the line foci, this device was used to perform large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy (PSR‐STHXM) with a 780 ± 40 nm spatial resolution within an FOV of 1.64 cm × 1.64 cm (limited by the detector area) and a total scanning time of 4 min. Biomedical implant abutments fabricated via selective laser melting using Ti–6Al–4V medical alloy were measured by PSR‐STHXM, suggesting its unique potential for studying extended and thick specimens. Although the super‐resolution function was realized in one dimension in this study, it can be expanded to two dimensions by aligning a pair of presented devices orthogonally.
    Description: A new X‐ray focusing device generates hundreds of thousands of line foci, periodically spaced in the sub‐micrometre range, with centimetre length. It enables to achieve large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy. image
    Keywords: 502.82 ; inclined refractive X‐ray multi‐lens array ; pixel super‐resolution ; scanning transmission hard X‐ray microscopy ; deep X‐ray lithography and electroplating
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  • 16
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    A new concept for temporal gating of synchrotron X‐ray pulses (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-07-02
    Description: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented. First experimental tests of the concept yield a diffraction efficiency of 0.18%; however, the calculations indicate a theoretical efficiency and contrast of 〉30% and 10−5, respectively. The full efficiency of the pulse picker has not been reached yet due to a long‐range thermal deformation of the sample after absorption of the excitation laser. This method can be implemented in a broad spectral range (100 eV to 20 keV) and is only minimally invasive to an existing setup.
    Description: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented.
    Keywords: 548 ; synchrotron ; time‐resolved ; thermal deformation ; transient grating ; pulse picking
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  • 17
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    The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP at BESSY II (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-06
    Description: The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP for optical pump/X‐ray probe experiments at the electron storage ring BESSY II is dedicated to investigating the structural response of thin film samples and heterostructures after their excitation with ultrashort laser pulses and/or electric field pulses. It enables experiments with access to symmetric and asymmetric Bragg reflections via a four‐circle diffractometer and it is possible to keep the sample in high vacuum and vary the sample temperature between ∼15 K and 350 K. The femtosecond laser system permanently installed at the beamline allows for optical excitation of the sample at 1028 nm. A non‐linear optical setup enables the sample excitation also at 514 nm and 343 nm. A time‐resolution of 17 ps is achieved with the `low‐α' operation mode of the storage ring and an electronic variation of the delay between optical pump and hard X‐ray probe pulse conveniently accesses picosecond to microsecond timescales. Direct time‐resolved detection of the diffracted hard X‐ray synchrotron pulses use a gated area pixel detector or a fast point detector in single photon counting mode. The range of experiments that are reliably conducted at the endstation and that detect structural dynamics of samples excited by laser pulses or electric fields are presented.
    Description: The KMC‐3 XPP endstation of the synchrotron BESSY II is dedicated to time‐resolved studies of structural dynamics of matter upon optical and/or electrical excitation using hard X‐ray diffraction with an accessible time range from 17 ps to several microseconds. image
    Keywords: 548 ; beamline instrumentation ; time‐resolved X‐ray diffraction ; optical excitation ; thermal transport ; ferroelectric switching
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  • 18
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    Disordered sodium alkoxides from powder data: crystal structures of sodium ethoxide, propoxide, butoxide and pentoxide, and some of their solvates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: The crystal structures of sodium ethoxide (sodium ethanolate, NaOEt), sodium n‐propoxide (sodium n‐propanolate, NaOnPr), sodium n‐butoxide (sodium n‐butanolate, NaOnBu) and sodium n‐pentoxide (sodium n‐amylate, NaOnAm) were determined from powder X‐ray diffraction data. NaOEt crystallizes in space group P421m, with Z = 2, and the other alkoxides crystallize in P4/nmm, with Z = 2. To resolve space‐group ambiguities, a Bärnighausen tree was set up, and Rietveld refinements were performed with different models. In all structures, the Na and O atoms form a quadratic net, with the alkyl groups pointing outwards on both sides (anti‐PbO type). The alkyl groups are disordered. The disorder becomes even more pronounced with increasing chain length. Recrystallization from the corresponding alcohols yielded four sodium alkoxide solvates: sodium ethoxide ethanol disolvate (NaOEt·2EtOH), sodium n‐propoxide n‐propanol disolvate (NaOnPr·2nPrOH), sodium isopropoxide isopropanol pentasolvate (NaOiPr·5iPrOH) and sodium tert‐amylate tert‐amyl alcohol monosolvate (NaOtAm·tAmOH, tAm = 2‐methyl‐2‐butyl). Their crystal structures were determined by single‐crystal X‐ray diffraction. All these solvates form chain structures consisting of Na+, –O− and –OH groups, encased by alkyl groups. The hydrogen‐bond networks diverge widely among the solvate structures. The hydrogen‐bond topology of the iPrOH network in NaOiPr·5iPrOH shows branched hydrogen bonds and differs considerably from the networks in pure crystalline iPrOH.
    Description: The crystal structures of NaOEt, NaOPr, NaOBu and NaOAm (Am = amyl = pentyl) were determined from powder data. These compounds crystallize in an anti‐PbO structure in the space groups P21m and P4/nmm. Additionally, solvates with the composition NaOEt·2EtOH, NaOPr·2PrOH, NaOiPr·5iPrOH and NaOtAm·tAmOH were synthesized, and their structures were determined from single crystals. They form interesting chain structures of different compositions and topologies. image
    Keywords: 548 ; sodium alkoxide ; powder data ; solvate ; isopropanol ; Bärnighausen tree ; PXRD
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  • 19
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    Small‐angle X‐ray scattering from GaN nanowires on Si(111): facet truncation rods, facet roughness and Porod's law (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: Small‐angle X‐ray scattering from GaN nanowires grown on Si(111) is measured in the grazing‐incidence geometry and modelled by means of a Monte Carlo simulation that takes into account the orientational distribution of the faceted nanowires and the roughness of their side facets. It is found that the scattering intensity at large wavevectors does not follow Porod's law I(q) ∝ q−4. The intensity depends on the orientation of the side facets with respect to the incident X‐ray beam. It is maximum when the scattering vector is directed along a facet normal, reminiscent of surface truncation rod scattering. At large wavevectors q, the scattering intensity is reduced by surface roughness. A root‐mean‐square roughness of 0.9 nm, which is the height of just 3–4 atomic steps per micrometre‐long facet, already gives rise to a strong intensity reduction.
    Description: The intensity of small‐angle X‐ray scattering from GaN nanowires on Si(111) depends on the orientation of the side facets with respect to the incident beam. This reminiscence of truncation rod scattering gives rise to a deviation from Porod's law. A roughness of just 3–4 atomic steps per micrometre‐long side facet notably changes the intensity curves. image
    Keywords: 548 ; nanowires ; Porod's law ; facet truncation rods ; small‐angle X‐ray scattering ; SAXS ; grazing‐incidence small‐angle X‐ray scattering ; GISAXS
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    The accuracy of protein models automatically built into cryo‐EM maps with ARP/wARP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-28
    Description: Recent developments in cryogenic electron microscopy (cryo‐EM) have enabled structural studies of large macromolecular complexes at resolutions previously only attainable using macromolecular crystallography. Although a number of methods can already assist in de novo building of models into high‐resolution cryo‐EM maps, automated and reliable map interpretation remains a challenge. Presented here is a systematic study of the accuracy of models built into cryo‐EM maps using ARP/wARP. It is demonstrated that the local resolution is a good indicator of map interpretability, and for the majority of the test cases ARP/wARP correctly builds 90% of main‐chain fragments in regions where the local resolution is 4.0 Å or better. It is also demonstrated that the coordinate accuracy for models built into cryo‐EM maps is comparable to that of X‐ray crystallographic models at similar local cryo‐EM and crystallographic resolutions. The model accuracy also correlates with the refined atomic displacement parameters.
    Keywords: 548 ; ARP/wARP ; model building ; cryo‐EM ; model accuracy ; sequence assignment
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    Synthesis, crystal structure and structure–property relations of strontium orthocarbonate, Sr2CO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-05
    Description: Carbonates containing CO4 groups as building blocks have recently been discovered. A new orthocarbonate, Sr2CO4 is synthesized at 92 GPa and at a temperature of 2500 K. Its crystal structure was determined by in situ synchrotron single‐crystal X‐ray diffraction, selecting a grain from a polycrystalline sample. Strontium orthocarbonate crystallizes in the orthorhombic crystal system (space group Pnma) with CO4, SrO9 and SrO11 polyhedra as the main building blocks. It is isostructural to Ca2CO4. DFT calculations reproduce the experimental findings very well and have, therefore, been used to predict the equation of state, Raman and IR spectra, and to assist in the discussion of bonding in this compound.
    Description: A new orthocarbonate, Sr2CO4, was synthesized under extreme pressure and temperature conditions of 92 GPa and 2500 K, respectively. The crystal structure of the compound s fully characterized in situ by synchrotron single‐crystal X‐ray diffraction and DFT calculations were employed to provide insight into its equation of state, Raman and IR spectra, and bonding. image
    Keywords: 548 ; orthocarbonates ; crystal structure ; single‐crystal X‐ray diffraction ; high pressure ; Sr2CO4
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  • 22
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    Anomalous SAXS at P12 beamline EMBL Hamburg: instrumentation and applications (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-28
    Description: Small‐angle X‐ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element‐specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X‐rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline.
    Keywords: 548 ; ASAXS ; biological SAXS ; metalloproteins ; gold nanoparticles ; anomalous scattering ; beamline development
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  • 23
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    Symmetry relations in wurtzite nitrides and oxide nitrides and the curious case of Pmc21 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-27
    Description: Binary III–V nitrides such as AlN, GaN and InN in the wurtzite‐type structure have long been considered as potent semiconducting materials because of their optoelectronic properties, amongst others. With rising concerns over the utilization of scarce elements, a replacement of the trivalent cations by others in ternary and multinary nitrides has led to the development of different variants of nitrides and oxide nitrides crystallizing in lower‐symmetry variants of wurtzite. This work presents the symmetry relationships between these structural types specific to nitrides and oxide nitrides and updates some prior work on this matter. The non‐existence of compounds crystallizing in Pmc21, formally the highest subgroup of the wurtzite type fulfilling Pauling's rules for 1:1:2 stoichiometries, has been puzzling scientists for a while; a rationalization is given, from a crystallographic basis, of why this space group is unlikely to be adopted.
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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    Comparison and evaluation of pair distribution functions, using a similarity measure based on cross‐correlation functions (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-20
    Description: An approach for the comparison of pair distribution functions (PDFs) has been developed using a similarity measure based on cross‐correlation functions. The PDF is very sensitive to changes in the local structure, i.e. small deviations in the structure can cause large signal shifts and significant discrepancies between the PDFs. Therefore, a comparison based on pointwise differences (e.g. R values and difference curves) may lead to the assumption that the investigated PDFs as well as the corresponding structural models are not in agreement at all, whereas a careful visual inspection of the investigated structural models and corresponding PDFs may reveal a relatively good match. To quantify the agreement of different PDFs for those cases an alternative approach is introduced: the similarity measure based on cross‐correlation functions. In this paper, the power of this application of the similarity measure to the analysis of PDFs is highlighted. The similarity measure is compared with the classical Rwp values as representative of the comparison based on pointwise differences as well as with the Pearson product‐moment correlation coefficient, using polymorph IV of barbituric acid as an example.
    Description: A novel approach to the quantification of the agreement between pair distribution functions by a similarity measure based on cross‐correlation functions is introduced and evaluated. image
    Keywords: 548 ; pair distribution functions ; similarity measures ; total scattering techniques ; cross‐correlation functions ; R values
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  • 25
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    Novel experimental setup for megahertz X‐ray diffraction in a diamond anvil cell at the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser (EuXFEL) (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: The high‐precision X‐ray diffraction setup for work with diamond anvil cells (DACs) in interaction chamber 2 (IC2) of the High Energy Density instrument of the European X‐ray Free‐Electron Laser is described. This includes beamline optics, sample positioning and detector systems located in the multipurpose vacuum chamber. Concepts for pump–probe X‐ray diffraction experiments in the DAC are described and their implementation demonstrated during the First User Community Assisted Commissioning experiment. X‐ray heating and diffraction of Bi under pressure, obtained using 20 fs X‐ray pulses at 17.8 keV and 2.2 MHz repetition, is illustrated through splitting of diffraction peaks, and interpreted employing finite element modeling of the sample chamber in the DAC.
    Description: The high‐precision X‐ray diffraction (XRD) setup for work with diamond anvil cells (DACs) in Interaction Chamber 2 of the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser is described. image
    Keywords: 548 ; diamond anvil cells ; X‐ray free‐electron lasers ; high‐precision X‐ray diffraction ; finite element modeling
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  • 26
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    The anisotropy in the optical constants of quartz crystals for soft X‐rays (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from orientation‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. Owing to the anisotropy of the crystal structure in the (100) and (001) directions, a significant deviation of the measured reflectance at the Si L2,3 and O K absorption edges is observed. The anisotropy in the optical constants reconstructed from these data is also confirmed by ab initio Bethe–Salpeter equation calculations for the O K edge. This new experimental data set expands the existing literature data for quartz crystal optical constants significantly, particularly in the near‐edge regions.
    Description: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from polarization‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. The reconstructed anisotropy in the optical constants is also confirmed by ab initio Bethe–Salpeter equation calculations of the O K edge. image
    Keywords: 548 ; optical constants ; quartz ; anisotropy ; soft X‐ray reflectometry
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  • 27
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    Unravelling the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ mixed ionic electronic conductors (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-07-05
    Description: Mixed ionic electronic conducting ceramics Nd6−yWO12−δ (δ is the oxygen deficiency) provide excellent stability in harsh environments containing strongly reactive gases such as CO2, CO, H2, H2O or H2S. Due to this chemical stability, they are promising and cost‐efficient candidate materials for gas separation, catalytic membrane reactors and protonic ceramic fuel cell technologies. As in La6−yWO12−δ, the ionic/electronic transport mechanism in Nd6−yWO12−δ is expected to be largely controlled by the crystal structure, the conclusive determination of which is still lacking. This work presents a crystallographic study of Nd5.8WO12−δ and molybdenum‐substituted Nd5.7W0.75Mo0.25O12−δ prepared by the citrate complexation route. High‐resolution synchrotron and neutron powder diffraction data were used in combined Rietveld refinements to unravel the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ. Both investigated samples crystallize in a defect fluorite crystal structure with space group Fm3m and doubled unit‐cell parameter due to cation ordering. Mo replaces W at both Wyckoff sites 4a and 48h and is evenly distributed, in contrast with La6−yWO12−δ. X‐ray absorption spectroscopy as a function of partial pressure pO2 in the near‐edge regions excludes oxidation state changes of Nd (Nd3+) and W (W6+) in reducing conditions: the enhanced hydrogen permeation, i.e. ambipolar conduction, observed in Mo‐substituted Nd6−yWO12−δ is therefore explained by the higher Mo reducibility and the creation of additional – disordered – oxygen vacancies.
    Description: The crystal structures of non‐substituted and Mo‐substituted neodymium tungstates are described in detail through neutron diffraction and high‐resolution X‐ray diffraction. Combined X‐ray and neutron diffraction refinements and electron probe micro‐analysis were employed to locate Mo atoms in the crystal structure of Nd6−yW1−zMozO12−δ (z = 0, 0.25), while X‐ray absorption spectroscopy in the near‐edge regions confirmed no changes in the oxidation states of Nd and W.
    Keywords: 548 ; powder diffraction ; mixed conductors ; X‐ray absorption spectroscopy (XAS) ; Nd6−yWO12−δ
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  • 28
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    High‐temperature treatments of niobium under high vacuum, dilute air‐ and nitrogen‐atmospheres as investigated by in situ X‐ray absorption spectroscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-30
    Description: Niobium metal foils were heat‐treated at 900°C under different conditions and in situ investigated with time‐resolved X‐ray absorption fine‐structure (EXAFS and XANES) measurements. The present study aims to mimic the conditions usually applied for heat treatments of Nb materials used for superconducting radiofrequency cavities, in order to better understand the evolving processes during vacuum annealing as well as for heat treatments in controlled dilute gases. Annealing in vacuum in a commercially available cell showed a substantial amount of oxidation, so that a designated new cell was designed and realized, allowing treatments under clean high‐vacuum conditions as well as under well controllable gas atmospheres. The experiments performed under vacuum demonstrated that the original structure of the Nb foils is preserved, while a detailed evaluation of the X‐ray absorption fine‐structure data acquired during treatments in dilute air atmospheres (10−5 mbar to 10−3 mbar) revealed a linear oxidation with the time of the treatment, and an oxidation rate proportional to the oxygen (air) pressure. The structure of the oxide appears to be very similar to that of polycrystalline NbO. The cell also permits controlled exposures to other reactive gases at elevated temperatures; here the Nb foils were exposed to dilute nitrogen atmospheres after a pre‐conditioning of the studied Nb material for one hour under high‐vacuum conditions, in order to imitate typical conditions used for nitrogen doping of cavity materials. Clear structural changes induced by the N2 exposure were found; however, no evidence for the formation of niobium nitride could be derived from the EXAFS and XANES experiments. The presented results establish the feasibility to study the structural changes of the Nb materials in situ during heat treatments in reactive gases with temporal resolution, which are important to better understand the underlaying mechanisms and the dynamics of phase formation during those heat treatments in more detail.
    Keywords: 548 ; in situ EXAFS ; high temperature ; time‐resolved EXAFS ; niobium
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    Pressure‐induced Pb–Pb bonding and phase transition in Pb2SnO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: High‐pressure single‐crystal to 20 GPa and powder diffraction measurements to 50 GPa, show that the structure of Pb2SnO4 strongly distorts on compression with an elongation of one axis. A structural phase transition occurs between 10 GPa and 12 GPa, with a change of space group from Pbam to Pnam. The resistivity decreases by more than six orders of magnitude when pressure is increased from ambient conditions to 50 GPa. This insulator‐to‐semiconductor transition is accompanied by a reversible appearance change from transparent to opaque. Density functional theory‐based calculations show that at ambient conditions the channels in the structure host the stereochemically‐active Pb 6s2 lone electron pairs. On compression the lone electron pairs form bonds between Pb2+ ions. Also provided is an assignment of irreducible representations to the experimentally observed Raman bands.
    Description: The structure of Pb2SnO4 is found to strongly distort on compression and a structural phase transition with a change of space group from Pbam to Pnam occurs at ∼11 GPa. Our complementary DFT‐based calculations show that at ambient conditions, the channels in the structure host the stereochemically active Pb 6s2 lone electron pairs which form bonds between the Pb2+ ions with increasing pressure. image
    Keywords: 548 ; lead stannate (Pb2SnO4) ; density functional theory ; high‐pressure X‐ray diffraction ; pressure‐induced phase transition ; insulator–semiconductor transition
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  • 30
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    A discussion on `Domain formation and phase transitions in the wurtzite‐based heterovalent ternaries: a Landau theory analysis' (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-05
    Description: Heterovalent ternary nitrides are considered one of the promising classes of materials for photovoltaics, combining attractive physical properties with low toxicity and element abundance. One of the front‐runner systems under consideration is ZnSnN2. Although it is nominally a ternary compound, no clear crystallographic evidence for cation ordering has been observed so far. An attempt to elucidate this discrepancy [Quayle (2020). Acta Cryst. A76, 410–420] was the trigger for an intensive discussion between the authors, and an agreement was reached to elaborate on some points in order to set things in perspective. Rather than using a conventional comment–answer scheme, this is published in the form of a joint discussion to celebrate constructive criticism and collegiality.
    Description: A scientific exchange on an earlier paper [Quayle (2020). Acta Cryst. A76, 410–420] has led to the clarification of some of the points. image
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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    X‐SPEC: a 70 eV to 15 keV undulator beamline for X‐ray and electron spectroscopies (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: X‐SPEC is a high‐flux spectroscopy beamline at the KIT (Karlsruhe Institute of Technology) Synchrotron for electron and X‐ray spectroscopy featuring a wide photon energy range. The beamline is equipped with a permanent magnet undulator with two magnetic structures of different period lengths, a focusing variable‐line‐space plane‐grating monochromator, a double‐crystal monochromator and three Kirkpatrick–Baez mirror pairs. By selectively moving these elements in or out of the beam, X‐SPEC is capable of covering an energy range from 70 eV up to 15 keV. The flux of the beamline is maximized by optimizing the magnetic design of the undulator, minimizing the number of optical elements and optimizing their parameters. The beam can be focused into two experimental stations while maintaining the same spot position throughout the entire energy range. The first experimental station is optimized for measuring solid samples under ultra‐high‐vacuum conditions, while the second experimental station allows in situ and operando studies under ambient conditions. Measurement techniques include X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS).
    Description: X‐SPEC is a high‐flux undulator beamline for electron and X‐ray spectroscopy with an energy range from 70 eV to 15 keV. It offers X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS) for in vacuo, in situ and operando sample environments. image
    Keywords: 548 ; undulator beamline ; soft X‐ray ; tender X‐ray ; hard X‐ray ; in situ ; operando ; HAXPES ; RIXS ; XAS ; XES
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    Role of carbon cycle observations and knowledge in carbon management (2005)
    Annual Reviews
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2003. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Environment and Resources 28 (2003): 521-558, doi:10.1146/annurev.energy.28.011503.163443.
    Description: Agriculture and industrial development have led to inadvertent changes in the natural carbon cycle. As a consequence, concentrations of carbon dioxide and other greenhouse gases have increased in the atmosphere and may lead to changes in climate. The current challenge facing society is to develop options for future management of the carbon cycle. A variety of approaches has been suggested: direct reduction of emissions, deliberate manipulation of the natural carbon cycle to enhance sequestration, and capture and isolation of carbon from fossil fuel use. Policy development to date has laid out some of the general principles to which carbon management should adhere. These are summarized as: how much carbon is stored, by what means, and for how long. To successfully manage carbon for climate purposes requires increased understanding of carbon cycle dynamics and improvement in the scientific capabilities available for measurement as well as for policy needs. The specific needs for scientific information to underpin carbon cycle management decisions are not yet broadly known. A stronger dialogue between decision makers and scientists must be developed to foster improved application of scientific knowledge to decisions. This review focuses on the current knowledge of the carbon cycle, carbon measurement capabilities (with an emphasis on the continental scale) and the relevance of carbon cycle science to carbon sequestration goals.
    Description: The National Center for Atmospheric Research is supported by the National Science Foundation.
    Keywords: Carbon sequestration ; Measurement techniques ; Climate ; Kyoto protocol
    Repository Name: Woods Hole Open Access Server
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    Long nonlinear internal waves (2006)
    Annual Reviews
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    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2006. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Fluid Mechanics 38 (2006): 395-425, doi:10.1146/annurev.fluid.38.050304.092129.
    Description: Over the past four decades, the combination of in situ and remote sensing observations has demonstrated that long nonlinear internal solitary-like waves are ubiquitous features of coastal oceans. The following provides an overview of the properties of steady internal solitary waves and the transient processes of wave generation and evolution, primarily from the point of view of weakly nonlinear theory, of which the Korteweg-de Vries equation is the most frequently used example. However, the oceanographically important processes of wave instability and breaking, generally inaccessible with these models, are also discussed. Furthermore, observations often show strongly nonlinear waves whose properties can only be explained with fully nonlinear models.
    Description: KRH acknowledges support from NSF and ONR and an Independent Study Award from the Woods Hole Oceanographic Institution. WKM acknowledges support from NSF and ONR, which has made his work in this area possible, in close collaboration with former graduate students at Scripps Institution of Oceanography and MIT.
    Keywords: Solitary waves ; Nonlinear waves ; Stratified flow ; Physical Oceanography
    Repository Name: Woods Hole Open Access Server
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    Design and function of superfast muscles : new insights into the physiology of skeletal muscle (2005)
    Annual Reviews
    Details
    Publication Date: 2022-05-25
    Description: First published online as a Review in Advance on October 24, 2005. (Some corrections may occur before final publication online and in print)
    Description: Author Posting. © Annual Reviews, 2005. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Physiology 68 (2006): 22.1-22.29, doi:10.1146/annurev.physiol.68.040104.105418.
    Description: Superfast muscles of vertebrates power sound production. The fastest, the swimbladder muscle of toadfish, generates mechanical power at frequencies in excess of 200 Hz. To operate at these frequencies, the speed of relaxation has had to increase approximately 50-fold. This increase is accomplished by modifications of three kinetic traits: (a) a fast calcium transient due to extremely high concentration of sarcoplasmic reticulum (SR)-Ca2+ pumps and parvalbumin, (b) fast off-rate of Ca2+ from troponin C due to an alteration in troponin, and (c) fast cross-bridge detachment rate constant (g, 50 times faster than that in rabbit fast-twitch muscle) due to an alteration in myosin. Although these three modifications permit swimbladder muscle to generate mechanical work at high frequencies (where locomotor muscles cannot), it comes with a cost: The high g causes a large reduction in attached force-generating cross-bridges, making the swimbladder incapable of powering low-frequency locomotory movements. Hence the locomotory and sound-producing muscles have mutually exclusive designs.
    Description: This work was made possible by support from NIH grants AR38404 and AR46125 as well as the University of Pennsylvania Research Foundation.
    Keywords: Parvalbumin ; Ca2+ release ; Ca2+ uptake ; Cross-bridges ; Adaptation ; Sound production ; Whitman Center
    Repository Name: Woods Hole Open Access Server
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  • 35
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    Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called `PDF‐Global‐Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross‐correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF‐Global‐Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF‐Global‐Fit is in excellent agreement with the published crystal structure data.
    Keywords: 548 ; pair distribution function analysis ; structure determination ; total scattering technique ; similarity measures ; PDF‐Global‐Fit
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    Structural basis of chitin utilization by a GH20 β‐N‐acetylglucosaminidase from Vibrio campbellii strain ATCC BAA‐1116 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-07-01
    Description: Vibrio species play a crucial role in maintaining the carbon and nitrogen balance between the oceans and the land through their ability to employ chitin as a sole source of energy. This study describes the structural basis for the action of the GH20 β‐N‐acetylglucosaminidase (VhGlcNAcase) in chitin metabolism by Vibrio campbellii (formerly V. harveyi) strain ATCC BAA‐1116. Crystal structures of wild‐type VhGlcNAcase in the absence and presence of the sugar ligand, and of the unliganded D437A mutant, were determined. VhGlcNAcase contains three distinct domains: an N‐terminal carbohydrate‐binding domain linked to a small α+β domain and a C‐terminal (β/α)8 catalytic domain. The active site of VhGlcNAcase has a narrow, shallow pocket that is suitable for accommodating a small chitooligosaccharide. VhGlcNAcase is a monomeric enzyme of 74 kDa, but its crystal structures show two molecules of enzyme per asymmetric unit, in which Gln16 at the dimeric interface of the first molecule partially blocks the entrance to the active site of the neighboring molecule. The GlcNAc unit observed in subsite −1 makes exclusive hydrogen bonds to the conserved residues Arg274, Tyr530, Asp532 and Glu584, while Trp487, Trp546, Trp582 and Trp505 form a hydrophobic wall around the −1 GlcNAc. The catalytic mutants D437A/N and E438A/Q exhibited a drastic loss of GlcNAcase activity, confirming the catalytic role of the acidic pair (Asp437–Glu438).
    Description: Crystal structures of a GH20 β‐N‐acetylglucosaminidase from V. campbellii reveal substrate specificity in chitin utilization.
    Keywords: 577.14 ; GH20 β‐N‐acetylglucosaminidase ; chitin recycling ; Vibrio spp ; marine bacteria
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    Resolution of a bent‐crystal spectrometer for X‐ray free‐electron laser pulses: diamond versus silicon (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: The resolution function of a spectrometer based on a strongly bent single crystal (bending radius of 10 cm or less) is evaluated. It is shown that the resolution is controlled by two parameters: (i) the ratio of the lattice spacing of the chosen reflection to the crystal thickness and (ii) a single parameter comprising crystal thickness, its bending radius, distance to a detector, and anisotropic elastic constants of the chosen crystal. The results allow the optimization of the parameters of bent‐crystal spectrometers for the hard X‐ray free‐electron laser sources.
    Description: The resolution function of a bent‐crystal spectrometer for pulses of an X‐ray free‐electron laser is evaluated. Under appropriate conditions, the energy resolution reaches the ratio of the lattice spacing to the crystal thickness. image
    Keywords: 548 ; X‐ray free‐electron lasers ; X‐ray spectroscopy ; bent crystals ; diamond crystal optics ; femtosecond X‐ray diffraction
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    Separation of the inelastic and elastic scattering in time‐of‐flight mode on the pinhole small‐angle neutron scattering diffractometer KWS‐2 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: To study and control the incoherent inelastic background in small‐angle neutron scattering, which makes a significant contribution to the detected scattering from hydrocarbon systems, the KWS‐2 small‐angle neutron scattering diffractometer operated by the Jülich Centre for Neutron Science (JCNS) at Heinz‐Maier Leibnitz Zentrum (MLZ), Garching, Germany, was equipped with a secondary single‐disc chopper that is placed in front of the sample stage. This makes it possible to record in time‐of‐flight mode the scattered neutrons in the high‐Q regime of the instrument (i.e. short incoming wavelengths and detection distances) and to discard the inelastic component from the measured data. Examples of measurements on different materials routinely used as standard samples, sample containers and solvents in the experiments at KWS‐2 are presented. When only the elastic region of the spectrum is used in the data‐reduction procedure, a decrease of up to two times in the incoherent background of the experimentally measured scattering cross section may be obtained. The proof of principle is demonstrated on a solution of bovine serum albumin in D2O.
    Description: A new chopper has been installed at the sample position in front of the sample stage at the KWS‐2 small‐angle neutron‐scattering diffractometer of the Jülich Centre for Neutron Science. The pulsed beam and the time‐of‐flight data acquisition enable the separation of elastic and inelastic scattering from hydrogenous samples.
    Keywords: 548 ; TOF‐SANS ; incoherent neutron scattering ; inelastic neutron scattering ; hydrocarbon systems
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    Czochralski growth of mixed cubic sesquioxide crystals in the ternary system Lu2O3–Sc2O3–Y2O3 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: Cubic rare‐earth sesquioxide crystals are strongly demanded host materials for high power lasers, but due to their high melting points investigations on their thermodynamics and the growth of large‐size crystals of high optical quality remain a challenge. Detailed thermal investigations of the ternary system Lu2O3–Sc2O3–Y2O3 revealing a large range of compositions with melting temperatures below 2200°C and a minimum of 2053°C for the composition (Sc0.45Y0.55)2O3 are presented. These reduced temperatures enable for the first time the growth of high optical quality mixed sesquioxide crystals with disordered structure by the conventional Czochralski method from iridium crucibles. An (Er0.07Sc0.50Y0.43)2O3 crystal is successfully grown and characterized with respect to its crystallographic properties as well as its composition, thermal conductivity and optical absorption in the 1 µm range.
    Description: The phase diagram of the ternary system Lu2O3–Sc2O3–Y2O3 is investigated and compositions with melting points below 2200°C are found. This allows for the first successful growth of the mixed cubic sesquioxide crystal (Er0.07Sc0.50Y0.43)2O3 by the Czochralski method from an iridium crucible. image
    Keywords: 548 ; crystal growth ; optical materials ; phase diagrams ; melting points ; rare earth sesquioxides
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    Solid-State NMR Approaches for Studying Membrane Protein Structure (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 25-47 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.21.060192.000325
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    Approaching Atomic Resolution in Crystallography of Ribosomes (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 77-93 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Atomic and Nuclear Probes of Enzyme Systems (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 1-26 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Structure and Function of Actin (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 49-76 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Microtubule Dynamic Instability and GTP Hydrolysis (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 145-166 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    The Mechanism of alpha-Helix Formation by Peptides (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 95-118 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    NMR Structure Determination in Solution: A Critique and Comparison with X-Ray Crystallography (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 167-198 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Rubisco: Structure and Mechanism (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 119-143 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Femtosecond Biology (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 199-222 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Intramembrane Helix-Helix Association in Oligomerization and Transmembrane Signaling (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 223-242 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    The Permeation Pathway of Neurotransmitter-Gated Ion Channels (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 267-292 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Protein Folding Studied Using Hydrogen-Exchange Labeling and Two-Dimensional NMR (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 243-265 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Solubilization and Functional Reconstitution of Biomembrane Components (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 323-348 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Pathway Analysis of Protein Electron-Transfer Reactions (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 349-377 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Protein Folding in the Cell: The Role of Molecular Chaperones Hsp70 and Hsp60 (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 293-322 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    The Single-Nucleotide Addition Cycle in Transcription: a Biophysical and Biochemical Perspective (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 379-415 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Protein Involvement in Transmembrane Lipid Asymmetry (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 417-439 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Structure and Mechanism of Alkaline Phosphatase (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 21 (1992), S. 441-483 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Interaction of Proteins With Lipid Headgroups: Lessons from Protein Kinase C (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 1-25 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Macromolecular Crowding: Biochemical, Biophysical, and Physiological Consequences (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 27-65 
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    The Control of Protein Stability and Association by Weak Interactions with Water: How Do Solvents Affect These Processes? (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 67-97 
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    The Two-Dimensional Transferred Nuclear Overhauser Effect: Theory and Practice (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 99-122 
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    Prolyl Isomerase: Enzymatic Catalysis of Slow Protein-Folding Reactions (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 123-143 
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    ISSN: 1056-8700
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    Models of Lipid-Protein Interactions in Membranes (1993)
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    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 145-171 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    The Effects of Phosphorylation on the Structure and Function of Proteins (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 199-232 
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    Functional Bases for Interpreting Amino Acid Sequences of Voltage-Dependent K+ Channels (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 173-198 
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    The Design of Metal-Binding Sites in Proteins (1993)
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    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 257-281 
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    What Does Electron Cryomicroscopy Provide that X-Ray Crystallography and NMR Spectroscopy Cannot? (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 233-255 
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    Artificial Neural Networks for Pattern Recognition in Biochemical Sequences (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 283-298 
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    The Structure of the Four-Way Junction in DNA (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 299-328 
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    Structure and Function of Human Growth Hormone: Implications for the Hematopoietins (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 329-351 
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    Realistic Simulations of Native-Protein Dynamics in Solution and Beyond (1993)
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    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 353-380 
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    Hydrogen Bonding, Hydrophobicity, Packing, and Protein Folding (1993)
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    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 381-415 
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    Glycoprotein Motility and Dynamic Domains in Fluid Plasma Membranes (1993)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 417-431 
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    Fast Crystallography and Time-Resolved Structures (1993)
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    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 467-498 
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    Mechanisms of Membrane Fusion (1993)
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    Annual Review of Biophysics and Biomolecular Structure 22 (1993), S. 433-466 
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    Field Gradient ESR and Molecular Diffusion in Model Membranes (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 1-25 
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    Hydration and Steric Pressures between Phospholipid Bilayers (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 27-51 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.000331
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    DNA Branched Junctions (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 53-86 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.000413
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    Biomolecular Imaging with the Atomic Force Microscope (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 115-140 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.000555
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    Nonresonance Raman Difference Spectroscopy: A General Probe of Protein Structure, Ligand Binding, Enzymatic Catalysis, and the Structures of Other Biomacromolecules (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 215-245 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.001243
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    Molecular Diversity and Functions of Glutamate Receptors (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 319-348 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.001535
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    Molecular Nanomachines: Physical Principles and Implementation Strategies (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 377-405 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.002113
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    Evolution of the EF-Hand Family of Proteins (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 473-507 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.002353
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    The Bacterial Flagellar Motor (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 509-539 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.002453
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    Conformational and Thermodynamic Properties of Supercoiled DNA (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 609-643 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.003141
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    G-Quartet Structures in Telomeric DNA (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 703-730 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.003415
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    Polypeptide Interactions with Molecular Chaperones and their Relationship to in Vivo Protein Folding (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 645-669 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.003241
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    The beta-Ribbon DNA Recognition Motif (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 671-701 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.003323
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    Molecular Dynamics Simulations of the Gramicidin Channel (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 731-761 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.003503
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    Mechanical Properties of the Red Cell Membrane in Relation to Molecular Structure and Genetic Defects (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 787-818 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.004035
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    Voltage-Dependent Gating of Ionic Channels (1994)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 23 (1994), S. 819-846 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.bb.23.060194.004131
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    TOROIDAL DNA CONDENSATES: Unraveling the Fine Structure and the Role of Nucleation in Determining Size (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 295-318 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Toroidal DNA condensates have attracted the attention of biophysicists, biochemists, and polymer physicists for more than thirty years. In the biological community, the quest to understand DNA toroid formation has been motivated by its relevance to gene packing in certain viruses and by the potential use of DNA toroids in artificial gene delivery (e.g., gene therapy). In the physical sciences, DNA toroids are appreciated as a superb model system for studying particle formation by the collapse of a semiflexible, polyelectrolyte polymer. This review focuses on experimental studies from the past few years that have significantly increased our understanding of DNA toroid structure and the mechanism of their formation. Highlights include structural studies that show the DNA strands within toroids to be packed in an ideal hexagonal lattice, and also in regions with a nonhexagonal lattice that are required by the topological constraints associated with winding DNA into a toroid. Recent studies of DNA toroid formation have also revealed that toroid size limits result from a complex interplay between kinetic and thermodynamic factors that govern both toroid nucleation and growth. The work discussed in this review indicates that it will ultimately be possible to obtain substantial control over DNA toroid dimensions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144500
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    STRUCTURAL AND SEQUENCE MOTIFS OF PROTEIN (HISTONE) METHYLATION ENZYMES (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 267-294 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: With genome sequencing nearing completion for the model organisms used in biomedical research, there is a rapidly growing appreciation that proteomics, the study of covalent modification to proteins, and transcriptional regulation will likely dominate the research headlines in the next decade. Protein methylation plays a central role in both of these fields, as several different residues (Arg, Lys, Gln) are methylated in cells and methylation plays a central role in the "histone code" that regulates chromatin structure and impacts transcription. In some cases, a single lysine can be mono-, di-, or trimethylated, with different functional consequences for each of the three forms. This review describes structural aspects of methylation of histone lysine residues by two enzyme families with entirely different structural scaffolding (the SET proteins and Dot1p) and methylation of protein arginine residues by PRMTs.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144452
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    ION CONDUCTION AND SELECTIVITY IN K+ CHANNELS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 153-171 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Potassium (K+) channels are tetrameric membrane-spanning proteins that provide a selective pore for the conductance of K+ across the cell membranes. These channels are most remarkable in their ability to discriminate K+ from Na+ by more than a thousandfold and conduct at a throughput rate near diffusion limit. The recent progress in the structural characterization of K+ channel provides us with a unique opportunity to understand their function at the atomic level. With their ability to go beyond static structures, molecular dynamics simulations based on atomic models can play an important role in shaping our view of how ion channels carry out their function. The purpose of this review is to summarize the most important findings from experiments and computations and to highlight a number of fundamental mechanistic questions about ion conduction and selectivity that will require further work.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144655
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    CHEMICAL SYNTHESIS OF PROTEINS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 91-118 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Proteins have become accessible targets for chemical synthesis. The basic strategy is to use native chemical ligation, Staudinger ligation, or other orthogonal chemical reactions to couple synthetic peptides. The ligation reactions are compatible with a variety of solvents and proceed in solution or on a solid support. Chemical synthesis enables a level of control on protein composition that greatly exceeds that attainable with ribosome-mediated biosynthesis. Accordingly, the chemical synthesis of proteins is providing previously unattainable insight into the structure and function of proteins.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144700
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    THE STRUCTURE-FUNCTION DILEMMA OF THE HAMMERHEAD RIBOZYME (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 415-440 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: A powerful approach to understanding protein enzyme catalysis is to examine the structural context of essential amino acid side chains whose deletion or modification negatively impacts catalysis. In principle, this approach can be even more powerful for RNA enzymes, given the wide variety and subtlety of functionally modified nucleotides now available. Numerous recent success stories confirm the utility of this approach to understanding ribozyme function. An anomaly, however, is the hammerhead ribozyme, for which the structural and functional data do not agree well, preventing a unifying view of its catalytic mechanism from emerging. To delineate the hammerhead structure-function comparison, we have evaluated and distilled the large body of biochemical data into a consensus set of functional groups unambiguously required for hammerhead catalysis. By examining the context of these functional groups within available structures, we have established a concise set of disagreements between the structural and functional data. The number and relative distribution of these inconsistencies throughout the hammerhead reaffirms that an extensive conformational rearrangement from the fold observed in the crystal structure must be necessary for cleavage to occur. The nature and energetic driving force of this conformational isomerization are discussed.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.34.122004.184428
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    SINGLE-MOLECULE RNA SCIENCE (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 399-414 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: The development of single-molecule detection and manipulation has allowed us to monitor the behavior of individual biological molecules and molecular complexes in real time. This approach significantly expands our capability to characterize complex dynamics of biological processes, allowing transient intermediate states and parallel kinetic pathways to be directly observed. Exploring this capability to elucidate complex dynamics, recent single-molecule experiments on RNA folding and catalysis have improved our understanding of the folding energy landscape of RNA and allowed us to better dissect complex RNA catalytic reactions, including translation by the ribosome.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144641
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    MODELING WATER, THE HYDROPHOBIC EFFECT, AND ION SOLVATION (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 173-199 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Water plays a central role in the structures and properties of biomoleculesĐ??proteins, nucleic acids, and membranesĐ??and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global propertiesĐ??water's thermodynamics, phase diagram, and solvation properties, for exampleĐ??and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of waterĐ??as a pure liquid and as a solventĐ??derive from the geometric and hydrogen bonding properties of water.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144517
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    PROTEIN-DNA RECOGNITION PATTERNS AND PREDICTIONS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 379-398 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Although the structures of a large number of protein-DNA complexes are known, the mechanisms underlying their specific binding are still only poorly understood. Analysis of these structures has shown that there is no simple one-to-one correspondence between bases and amino acids within protein-DNA complexes; nevertheless, the observed patterns of interaction carry important information on the mechanisms of protein-DNA recognition. In this review, we show how the patterns of interaction, either observed in known structures or derived from computer simulations, confer recognition specificity, and how they can be used to examine the relationship between structure and specificity and to predict target DNA sequences used by regulatory proteins.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144537
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    THE LYMPHATIC VASCULATURE: Recent Progress and Paradigms (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 21 (2005), S. 457-483 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The field of lymphatic research has been recently invigorated by the identification of genes and mechanisms that control various aspects of lymphatic development. We are beginning to understand how, starting from a subgroup of embryonic venous endothelial cells, the whole lymphatic system forms in a stepwise manner. The generation of genetically engineered mice with defects in different steps of the lymphangiogenic program has provided models that are increasing our understanding of the lymphatic system in health and disease. This knowledge, in turn, should lead to the development of better diagnostic methods and treatments of lymphatic disorders and tumor metastasis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.cellbio.21.012704.132338
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