A.V. Shubnikov Institute of Crystallography

A program suite for one-dimensional small-angle scattering data processing running on IBM-compatible PCs under Windows 9 x /NT/2000/XP is presented. The main program, PRIMUS , has a menu-driven graphical user interface calling computational modules to perform data manipulation and analysis. Experimental data in binary OTOKO format can be reduced by calling the program SAPOKO , which includes statistical analysis of time frames, averaging and scaling. Tools to generate the angular axis and detector response files from diffraction patterns of calibration samples, as well as binary to ASCII transformation programs, are available. Several types of ASCII files can be directly imported into PRIMUS , in particular, sasCIF or ILL-type files are read without modification. PRIMUS provides basic data manipulation functions (averaging, background subtraction, merging of data measured in different angular ranges, extrapolation to zero sample concentration, etc. ) and computes invariants from Guinier and Porod plots. Several external modules coupled with PRIMUS via pop-up menus enable the user to evaluate the characteristic functions by indirect Fourier transformation, to perform peak analysis for partially ordered systems and to find shape approximations in terms of three-parametric geometrical bodies. For the analysis of mixtures, PRIMUS enables model-independent singular value decomposition or linear fitting if the scattering from the components is known. An interface is also provided to the general non-linear fitting program MIXTURE , which is designed for quantitative analysis of multicomponent systems represented by simple geometrical bodies, taking shape and size polydispersity as well as interparticle interference effects into account.

DAMMIF , a revised implementation of the ab - initio shape-determination program DAMMIN for small-angle scattering data, is presented. The program was fully rewritten, and its algorithm was optimized for speed of execution and modified to avoid limitations due to the finite search volume. Symmetry and anisometry constraints can be imposed on the particle shape, similar to DAMMIN . In equivalent conditions, DAMMIF is 25–40 times faster than DAMMIN on a single CPU. The possibility to utilize multiple CPUs is added to DAMMIF . The application is available in binary form for major platforms.

Lipid monolayers on the surface of water have been studied for over a hundred years, but in the last decade there has been a dramatic evolution in our understanding of the structures and phase transitions of these systems, driven by new experimental techniques and theoretical advances. In this review, dense monolayers of simple lipids are described in detail, including structures revealed by x-ray-diffraction experiments, computer simulations, molecular models, and a phenomenological theory of phase transitions. The effects of chirality and the structures of phospholipid monolayers are considered. Open questions and possible approaches to finding answers are discussed.

A method is presented for automated best-matching alignment of three-dimensional models represented by ensembles of points. A normalized spatial discrepancy (NSD) is introduced as a proximity measure between three-dimensional objects. Starting from an inertia-axes alignment, the algorithm minimizes the NSD; the final value of the NSD provides a quantitative estimate of similarity between the objects. The method is implemented in a computer program. Simulations have been performed to test its performance on model structures with specified numbers of points ranging from a few to a few thousand. The method can be used for comparative analysis of structural models obtained by different methods, e.g. of high-resolution crystallographic atomic structures and low-resolution models from solution scattering or electron microscopy.

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.

Polyelectrolyte multilayers were deposited onto polystyrene and melamine formaldehyde latex particles by means of consecutive adsorption. Two different methods of multilayer growth were employed. First, adsorption of polyelectrolytes at a concentration exceeding saturation amounts was combined with the removal of the nonbound polyelectrolyte by means of centrifugation. Second, adsorption of polyelectrolyte was performed at a concentration just sufficient for saturation coverage. Both methods yielded continuous layer growth. The process of film formation was followed by electrophoresis, dynamic light scattering, single particle light scattering and fluorescence intensity measurements. Layer deposition onto partially crosslinked melamine resin latex particles, which were soluble at pH values of less than 1.6, resulted in the production of three-dimensional thin polyelectrolyte shells upon dissolving the core. The ultrathin shells were observed by means of scanning and transmission electron microscopy. © 1998 John Wiley & Sons, Ltd.

The program package ATSAS 2.1 for small-angle X-ray and neutron scattering data analysis is presented. The programs included in the package cover the major processing and interpretation steps from primary data reduction to three-dimensional modelling. This system is primarily oriented towards the analysis of biological macromolecules, but could also be used for non-biological isotropic and partially ordered objects (nanoparticle systems, colloidal solutions, polymers in solution and bulk). Recent developments in the programs included in ATSAS 2.1 are highlighted. The main programs run on multiple hardware platforms, including Windows PC, Linux RedHat and Suse, DEC Alpha, SGI IRIX and Mac OSX.

1. Introduction 148 2. Basics of X-ray and neutron scattering 149 2.1 Elastic scattering of electromagnetic radiation by a single electron 149 2.2 Scattering by assemblies of electrons 151 2.3 Anomalous scattering and long wavelengths 153 2.4 Neutron scattering 153 2.5 Transmission and attenuation 155 3. Small-angle scattering from solutions 156 3.1 Instrumentation 156 3.2 The experimental scattering pattern 157 3.3 Basic scattering functions 159 3.4 Global structural parameters 161 3.4.1 Monodisperse systems 161 3.4.2 Polydisperse systems and mixtures 163 3.5 Characteristic functions 164 4. Modelling 166 4.1 Spherical harmonics 166 4.2 Shannon sampling 169 4.3 Shape determination 170 4.3.1 Modelling with few parameters: molecular envelopes 171 4.3.2 Modelling with many parameters: bead models 173 4.4 Modelling domain structure and missing parts of high-resolution models 178 4.5 Computing scattering patterns from atomic models 184 4.6 Rigid-body refinement 187 5. Applications 190 5.1 Contrast variation studies of ribosomes 190 5.2 Structural changes and catalytic activity of the allosteric enzyme ATCase 191 6. Interactions between molecules in solution 203 6.1 Linearizing the problem for moderate interactions: the second virial coefficient 204 6.2 Determination of the structure factor 205 7. Time-resolved measurements 211 8. Conclusions 215 9. Acknowledgements 216 10. References 216 A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies – on ribosomes and on the allosteric protein aspartate transcarbamoylase – illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.

We demonstrate that rotationally symmetric chiral metasurfaces can support sharp resonances with the maximum optical chirality determined by precise shaping of bound states in the continuum (BICs). Being uncoupled from one circular polarization of light and resonantly coupled to its counterpart, a metasurface hosting the chiral BIC resonance exhibits a narrow peak in the circular dichroism spectrum with the quality factor limited by weak dissipation losses. We propose a realization of such chiral BIC metasurfaces based on pairs of dielectric bars and validate the concept of maximum chirality by numerical simulations.

Small-angle scattering (SAS) is frequently employed for screening large numbers of samples and for studying these samples under different conditions, including space- and time-resolved analysis. These measurements produce immense amounts of data, especially on modern high-flux and high-brilliance sources (e.g. third-generation synchrotrons). In biological SAS, like high-throughput macromolecular crystallography, large-scale analysis of proteins and macromolecular complexes is also emerging. Automation of data analysis becomes an indispensable prerequisite for adequate evaluation of high-throughput SAS experiments. Here a prototype of an automated data-analysis system for isotropic solution scattering based on the further development of the programs belonging to the package ATSAS 2.1 is reported. This system allows the major analysis tasks starting from the raw data processing and, for monodisperse systems, finishing with a three-dimensional model, to be performed automatically. Convenient web interfaces for the online use of individual ATSAS programs are also provided.

Abstract Pressure‐stabilized hydrides are a new rapidly growing class of high‐temperature superconductors, which is believed to be described within the conventional phonon‐mediated mechanism of coupling. Here, the synthesis of one of the best‐known high‐ T C superconductors—yttrium hexahydride ‐YH 6 is reported, which displays a superconducting transition at ≈224 K at 166 GPa. The extrapolated upper critical magnetic field B c2 (0) of YH 6 is surprisingly high: 116–158 T, which is 2–2.5 times larger than the calculated value. A pronounced shift of T C in yttrium deuteride YD 6 with the isotope coefficient 0.4 supports the phonon‐assisted superconductivity. Current–voltage measurements show that the critical current I C and its density J C may exceed 1.75 A and 3500 A mm −2 at 4 K, respectively, which is higher than that of the commercial superconductors, such as NbTi and YBCO. The results of superconducting density functional theory (SCDFT) and anharmonic calculations, together with anomalously high critical magnetic field, suggest notable departures of the superconducting properties from the conventional Migdal–Eliashberg and Bardeen–Cooper–Schrieffer theories, and presence of an additional mechanism of superconductivity.

Proteins with intrinsically disordered domains are implicated in a vast range of biological processes, especially in cell signaling and regulation. Having solved the quaternary structure of the folded domains in the tumor suppressor p53 by a multidisciplinary approach, we have now determined the average ensemble structure of the intrinsically disordered N-terminal transactivation domain (TAD) by using residual dipolar couplings (RDCs) from NMR spectroscopy and small-angle x-ray scattering (SAXS). Remarkably, not only were we able to measure RDCs of the isolated TAD, but we were also able to do so for the TAD in both the full-length tetrameric p53 protein and in its complex with a specific DNA response element. We determined the orientation of the TAD ensemble relative to the core domain, found that the TAD was stiffer in the proline-rich region (residues 64-92), which has a tendency to adopt a polyproline II (PPII) structure, and projected the TAD away from the core. We located the TAD in SAXS experiments on a complex between tetrameric p53 and four Taz2 domains that bind tightly to the TAD (residues 1-57) and acted as "reporters." The p53-Taz2 complex was an extended cross-shaped structure. The quality of the SAXS data enabled us to model the disordered termini and the folded domains in the complex with DNA. The core domains enveloped the response element in the center of the molecule, with the Taz2-bound TADs projecting outward from the core.

The theory and the experimental characteristics of the bulk photovoltaic effect in ferroelectric and piezoelectric crystals first observed at the Institute of Crystallography have been reviewed. I dedicate this review to the memory of B.K. Vainshtein whose help in performing these works was really inestimable.

One of the most important overall parameters, which can be derived from small-angle X-ray scattering (SAXS) experiments on macromolecular solutions is the molecular mass (MM) of the solute. In particular, for a monodisperse protein solution, MM of the solute is calculated from the extrapolated scattering intensity at zero angle I(0). Assessing MM by SAXS provides valuable information about the oligomeric state and absence of unspecific aggregation in solution. The value of MM can either be estimated by comparison with a protein standard with a known MM or by determining the absolute scattering intensity using, e.g., water scattering. In both cases, knowledge about the solute concentration and about the partial specific volume of the protein is required. By measuring 13 well characterized globular proteins with MMs ranging from 13.7 to 669 kDa we analyze the sources of possible systematic deviations and assess the accuracy of MM determination using SAXS. The data indicate that all these proteins have approximately the same `effective' value of the partial specific volume of about 0.7425 cm3 g−1. It is shown that both inter-protein and water calibration can be used for molecular mass determination by SAXS and in most cases the errors do not exceed 10%.

The Landau-Ginzburg theory of ferroelectricity predicts the intrinsic coercive field for polarization reversal, but the observed extrinsic coercive field is always much smaller as a result of nucleation, dynamic processes not covered by the static theory. We have realized the intrinsic coercive field for the first time, in two-dimensional Langmuir-Blodgett polymer films as thin as 1 nm. The measured coercive field is in good agreement with the theoretical intrinsic value, exhibits the expected dependence on temperature, and does not depend on thickness below 15 nm.

Zinc doping is shown to reduce the photorefraction in LiNbO(3):Zn. The damage-resistant crystal LiNbO(3):Zn has demonstrated a conversion efficiency of approximately 50% for frequency doubling of 1.06-microm radiation. The dependence of optical characteristics on the ZnO concentration in the melt reveals a sharp change of the optical properties at the threshold concentration of 4-6 mol % Zn. The optical and nonlinear-optical data of LiNbO(3):Zn are similar to those of LiNbO(3):Mg, but the former shows better optical performance.

Spectroscopic, laser, and chi((3)) nonlinear optical properties of tetragonal PbWO(4), NaY(WO(4))(2), CaWO(4), and monoclinic CdWO(4) and ZnWO(4) were investigated. Particular attention was paid to Nd(3+)-doped and undoped PbWO(4) and NaY(WO(4))(2) crystals. Their absorption and luminescence intensity characteristics, including the peak cross sections of induced transitions, were determined. Pulsed and continuous-wave lasing in the two 4F(3/2)-->4I(11/2) and 4F(3/2)-->4I(13/2) channels was excited. For these five tungstates, highly efficient (greater than 50%) multiple Stokes generation and anti-Stokes picosecond generation were achieved. All the observed scattered laser components were identified. These results were analyzed and compared with spectroscopic data from spontaneous Raman scattering. A new crystalline Raman laser based on PbWO(4) was developed for the chi((3)) conversion frequency of 1-microm pump radiation to the first Stokes emission with efficiency up to 40%. We classify all the tungstates as promising media for lasers and neodymium-doped crystals for self-stimulated Raman scattering lasers.

In the present work, a method for adjusting a crystal analyzer to separate two characteristic lines from the spectrum of a conventional X-ray tube for simultaneous registration of tomographic projections is proposed. The experimental implementation of this method using radiation of a molybdenum anode ( K α 1 , K β lines) and a silicon Si(111) crystal analyzer in Laue geometry is presented. Projection images at different wavelengths are separated in space and can be recorded independently for further processing. Potential uses of this scheme are briefly discussed.

Abstract A new electrooptic mode of operation of ferroelectric chiral smectic C liquid crystal displays (LCDs) is proposed and demonstrated. The effect, which is called the deformed helical ferroelectric (DHF) effect, is based on the deformation of the helical structure by weak electric fields. In the unbiased device the smectic layers are arranged in the bookshelf geometry with the helix axis parallel to the electrodes [1]. Systems with a very small pitch (<1 μm) and a large tilt angle are especially well suited for this mode. The key characteristics of DHF-LCDs are: (a) low driving fields (1 Vp-pμm−1 for maximum contrast); (b) grey scale which is approximately linear with the applied electric field; (c) easy alignment even for thick cells using standard wall-aligning methods; and (d) response times at room temperature of 300 μs.

The voltage generated in a noncentrosymmetric crystal due to the bulk photovoltaic effect (BPE) can greatly exceed the energy gap, however, the light energy conversion efficiency is extremely low. Here we show that the BPE is remarkably enhanced in the case of thin films. The measurements of the BPE in heteroepitaxial single domain ferroelectric ${\mathrm{BaTiO}}_{3}$ thin films reveal the enhancement of both photoinduced electric field and conversion efficiencies of the BPE by more than 4 orders of magnitude. Besides the fundamental aspect, our results indicate the potential for the use of the BPE in photovoltaic applications.