Notes

Impact of age as well as gender upon lymphocyte subset matters within sufferers together with COVID-19.
Incoherent diffractive imaging (IDI) promises structural analysis with atomic resolution based on intensity interferometry of pulsed X-ray fluorescence emission. However, its experimental realization is still pending and a comprehensive theory of contrast formation has not been established to date. Explicit expressions are derived for the equal-pulse two-point intensity correlations, as the principal measured quantity of IDI, with full control of the prefactors, based on a simple model of stochastic fluorescence emission. The model considers the photon detection statistics, the finite temporal coherence of the individual emissions, as well as the geometry of the scattering volume. The implications are interpreted in view of the most relevant quantities, including the fluorescence lifetime, the excitation pulse, as well as the extent of the scattering volume and pixel size. Importantly, the spatiotemporal overlap between any two emissions in the sample can be identified as a crucial factor limiting the contrast and its dependency on the sample size can be derived. The paper gives rigorous estimates for the optimum sample size, the maximum photon yield and the expected signal-to-noise ratio under optimal conditions. Based on these estimates, the feasibility of IDI experiments for plausible experimental parameters is discussed. It is shown in particular that the mean number of photons per detector pixel which can be achieved with X-ray fluorescence is severely limited and as a consequence imposes restrictive constraints on possible applications.The power spectrum of proteins at high frequencies is remarkably well described by the flat Wilson statistics. Wilson statistics therefore plays a significant role in X-ray crystallography and more recently in electron cryomicroscopy (cryo-EM). Specifically, modern computational methods for three-dimensional map sharpening and atomic modelling of macromolecules by single-particle cryo-EM are based on Wilson statistics. Here the first rigorous mathematical derivation of Wilson statistics is provided. The derivation pinpoints the regime of validity of Wilson statistics in terms of the size of the macromolecule. learn more Moreover, the analysis naturally leads to generalizations of the statistics to covariance and higher-order spectra. These in turn provide a theoretical foundation for assumptions underlying the widespread Bayesian inference framework for three-dimensional refinement and for explaining the limitations of autocorrelation-based methods in cryo-EM.A real-space approach for the calculation of the moiré lattice parameters for superstructures formed by a set of rotated hexagonal 2D crystals such as graphene or transition-metal dichalcogenides is presented. Apparent moiré lattices continuously form for all rotation angles, and their lattice parameter to a good approximation follows a hyperbolical angle dependence. Moiré crystals, i.e. moiré lattices decorated with a basis, require more crucial assessment of the commensurabilities and lead to discrete solutions and a non-continuous angle dependence of the moiré-crystal lattice parameter. In particular, this lattice parameter critically depends on the rotation angle, and continuous variation of the angle can lead to apparently erratic changes of the lattice parameter. The solutions form a highly complex pattern, which reflects number-theoretical relations between formation parameters of the moiré crystal. The analysis also provides insight into the special case of a 30° rotation of the constituting lattices, for which a dodecagonal quasicrystalline structure forms.Deformation twinning on a plane is a simple shear that transforms a unit cell attached to the plane into another unit cell equivalent by mirror symmetry or 180° rotation. Thus, crystallographic models of twinning require the determination of the short unit cells attached to the planes, or hyperplanes for dimensions higher than 3. Here, a method is presented to find them. Equivalently, it gives the solutions of the N-dimensional Bézout's identity associated with the Miller indices of the hyperplane.The analytical expressions for coherent and diffuse components of the integrated reflection coefficient are considered in the case of Bragg diffraction geometry for single crystals containing randomly distributed microdefects. These expressions are analyzed numerically for the cases when the instrumental integration of the diffracted X-ray intensity is performed on one, two or three dimensions in the reciprocal-lattice space. The influence of dynamical effects, i.e. primary extinction and anomalously weak and strong absorption, on the integrated intensities of X-ray scattering is investigated in relation to the crystal structure imperfections.A phenomenological model of anisotropic lattice vibrations is proposed, using a temperature-dependent spectral cutoff and varying Debye temperatures for the vibrational normal components. The internal lattice energy, entropy and Debye-Waller B factors of non-cubic elemental crystals are derived. The formalism developed is non-perturbative, based on temperature-dependent linear dispersion relations for the normal modes. The Debye temperatures of the vibrational normal components differ in anisotropic crystals; their temperature dependence and the varying spectral cutoff can be inferred from the experimental lattice heat capacity and B factors by least-squares regression. The zero-point internal energy of the phonons is related to the low-temperature limits of the mean-squared vibrational amplitudes of the lattice measured by X-ray and γ-ray diffraction. A specific example is discussed, the thermodynamic variables of the hexagonal close-packed zinc structure, including the temperature evolution of the B factors of zinc. In this case, the lattice vibrations are partitioned into axial and basal normal components, which admit largely differing B factors and Debye temperatures. The second-order B factors defining the non-Gaussian contribution to the Debye-Waller damping factors of zinc are obtained as well. Anharmonicity of the oscillator potential and deviations from the uniform phonon frequency distribution of the Debye theory are modeled effectively by the temperature dependence of the spectral cutoff and Debye temperatures.The previously reported exact potential and multipole moment (EP/MM) method for fast and precise evaluation of the intermolecular electrostatic interaction energies in molecular crystals using the pseudoatom representation of the electron density [Nguyen, Macchi & Volkov (2020), Acta Cryst. A76, 630-651] has been extended to the calculation of the electrostatic potential (ESP), electric field (EF) and electric field gradient (EFG) in an infinite crystal. The presented approach combines an efficient Ewald-type summation (ES) of atomic multipoles up to the hexadecapolar level in direct and reciprocal spaces with corrections for (i) the net polarization of the sample (the `surface term') due to a net dipole moment of the crystallographic unit cell (if present) and (ii) the short-range electron-density penetration effects. The rederived and reported closed-form expressions for all terms in the ES algorithm have been augmented by the expressions for the surface term available in the literature [Stenhammar, Trulssoster than the DS calculations performed within the extended unit-cell limits but trails the DS calculations within the reduced summation ranges. Nonetheless, the described EP/MM-based ES algorithm is superior to the direct-space summations as it does not require the user to monitor continuously the convergence of the evaluated properties as a function of the summation limits and offers a better precision-performance balance.This article describes the simplest members of an infinite family of knots and links that have achiral piecewise-linear embeddings in which linear segments (sticks) meet at corners. The structures described are all corner- and stick-2-transitive - the smallest possible for achiral knots.The creation of knotted, woven and linked molecular structures is an exciting and growing field in synthetic chemistry. Presented here is a description of an extended family of structures related to the classical `Borromean rings', in which no two rings are directly linked. These structures may serve as templates for the designed synthesis of Borromean polycatenanes. Links of n components in which no two are directly linked are termed `n-Borromean' [Liang & Mislow (1994). J. Math. Chem. 16, 27-35]. In the classic Borromean rings the components are three rings (closed loops). More generally, they may be a finite number of periodic objects such as graphs (nets), or sets of strings related by translations as in periodic chain mail. It has been shown [Chamberland & Herman (2015). Math. Intelligencer, 37, 20-25] that the linking patterns can be described by complete directed graphs (known as tournaments) and those up to 13 vertices that are vertex-transitive are enumerated. In turn, these lead to ring-transitive (isonemal) n-Borromean rings. Optimal piecewise-linear embeddings of such structures are given in their highest-symmetry point groups. In particular, isonemal embeddings with rotoinversion symmetry are described for three, five, six, seven, nine, ten, 11, 13 and 14 rings. Piecewise-linear embeddings are also given of isonemal 1- and 2-periodic polycatenanes (chains and chain mail) in their highest-symmetry setting. Also the linking of n-Borromean sets of interleaved honeycomb nets is described.The bent structure of the water molecule, and its hydrogen-bonding properties, arguably rank among the most impactful discoveries in the history of chemistry. Although the fact that the H-O-H angle must deviate from linearity was inferred early in the 20th century, notably from the existence of the electric dipole moment, it was not clear what that angle should be and why. One hundred years ago, a young PhD student at the University of California, Berkeley, Eustace J. Cuy, rationalized the V-shape structure of a water molecule using the Lewis theory of a chemical bond, i.e. a shared electron pair, and its tetrahedral stereochemistry. He was inspired, in part, by the proposal of a weak (hydrogen) bond in water by two colleagues at Berkeley, Wendell Latimer and Worth Rodebush, who published their classic paper a year earlier. Cuy went on to suggest that other molecules, notably H2S and NH3, have similar structures, and presciently predicted that this architecture has broader consequences for the structure of water as a liquid. This short, but brilliant paper has been completely forgotten, perhaps due to the tragic death of the author at the age of 28; the hydrogen-bond study is also rarely recognized. One of the most impactful publications on the structure of liquid water, a classic treatise published in 1933 by John Bernal and Ralph Fowler, does not mention either of the two pioneering papers. In this essay, the background for the two discoveries is described, including the brief history of Lewis's research on the nature of the chemical bond, and the history of the discovery of the hydrogen bond, which inspired Cuy to look at the structure of the water molecule. This is - to the best of the author's knowledge - the first biographical sketch of Eustace J. Cuy.
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