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36 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4 [Next/Last]

Instruments / Technical Area	Publication Details	Published
I04-1-Macromolecular Crystallography (fixed wavelength)	A molecular evolution algorithm for ligand design in DOCK Lauren E. Prentis , Courtney D. Singleton , John D. Bickel , William J. Allen , Robert C. Rizzo Journal Of Computational Chemistry 93 DOI: 10.1002/jcc.26993 Open Access Show Abstract ▼ Abstract: As a complement to virtual screening, de novo design of small molecules is an alternative approach for identifying potential drug candidates. Here, we present a new 3D genetic algorithm to evolve molecules through breeding, mutation, fitness pressure, and selection. The method, termed DOCK_GA, builds upon and leverages powerful sampling, scoring, and searching routines previously implemented into DOCK6. Three primary experiments were used during development: Single-molecule evolution evaluated three selection methods (elitism, tournament, and roulette), in four clinically relevant systems, in terms of mutation type and crossover success, chemical properties, ensemble diversity, and fitness convergence, among others. Large scale benchmarking assessed performance across 651 different protein-ligand systems. Ensemble-based evolution demonstrated using multiple inhibitors simultaneously to seed growth in a SARS-CoV-2 target. Key takeaways include: (1) The algorithm is robust as demonstrated by the successful evolution of molecules across a large diverse dataset. (2) Users have flexibility with regards to parent input, selection method, fitness function, and molecular descriptors. (3) The program is straightforward to run and only requires a single executable and input file at run-time. (4) The elitism selection method yields more tightly clustered molecules in terms of 2D/3D similarity, with more favorable fitness, followed by tournament and roulette.	Sep 2022
	Versatile automated domain mapping of 4D-STEM data utilizing ML algorithms and Bayesian statistics A. Bridger , M. Danaie , K. Butler , T. Wood , W. I. F. David Microscopy And Microanalysis 28, 3022 - 3023 Microscopy & Microanalysis 2022: C04 - Artificial Intelligence, Instrument Automation, and High-dimensional Data Analytics for Microscopy and Microanalysis DOI: 10.1017/S1431927622011308 Show Abstract ▼ Abstract: This work outlines the development of a workflow that combines both informed and data-driven approaches to process and classify 4D-STEM data utilising signal dimensionality reduction obtained from unsupervised machine learning algorithms. Using these ‘latent space’ representations of the scanned region, we can then apply clustering algorithms to identify regions of similar character. By combining the results of multiple autonomous computations, we would be able to map domains within the crystal and associate a level of confidence to given classifications. This confidence is then used to iteratively improve the learning algorithms and the performance of their dimensionality reduction. Incorporating this as a pre-processing unsupervised workflow would drastically improve the ability to characterise the nano-scale structure of materials, both through production of significantly signal-boosted diffraction data and reduction in laborious manual investigation.	Aug 2022
Theoretical Physics	Magnetic properties of RuO2 and charge-magnetic interference in Bragg diffraction of circularly polarized x-rays S. W. Lovesey , D. D. Khalyavin , G. Van Der Laan Physical Review B 105, 014403 DOI: 10.1103/PhysRevB.105.014403 Show Abstract ▼ Abstract: Rutile-type RuO2 likely supports a simple antiferromagnetic structure which can be verified by x-ray Bragg diffraction. Three magnetic motifs that do not break translation symmetry are explored in calculations of amplitudes suitable for diffraction enhanced by tuning the primary x-ray energy to a ruthenium atomic resonance. Coupling to x-ray helicity through a charge-magnetic interference is common to all motifs, together with magnetic and charge intensities in quadrature in the rotated channel of polarization. Necessary conditions for these diffraction phenomena are a centrosymmetric crystal structure, null magnetic propagation vector, and absence of a linear magnetoelectric effect. Published x-ray diffraction data for RuO2 were analyzed by the authors against a magnetic motif that does not satisfy the conditions. A polarized neutron study of antiferromagnetic domains can be achieved with a sample that meets the stated crystal and magnetic symmetries.	Jan 2022
I07-Surface & interface diffraction	Quantitative powder diffraction using a (2 + 3) surface diffractometer and an area detector Giuseppe Abbondanza , Alfred Larsson , Francesco Carla , Edvin Lundgren , Gary S. Harlow Journal Of Applied Crystallography 54, 1140 - 1152 DOI: 10.1107/S1600576721006245 Open Access Show Abstract ▼ Abstract: X-ray diffractometers primarily designed for surface X-ray diffraction are often used to measure the diffraction from powders, textured materials and fiber-texture samples in 2θ scans. Unlike in high-energy powder diffraction, only a fraction of the powder rings is typically measured, and the data consist of many detector images across the 2θ range. Such diffractometers typically scan in directions not possible on a conventional laboratory diffractometer, which gives enhanced control of the scattering vector relative to the sample orientation. There are, however, very few examples where the measured intensity is directly used, such as for profile/Rietveld refinement, as is common with other powder diffraction data. Although the underlying physics is known, converting the data is time consuming and the appropriate corrections are dispersed across several publications, often not with powder diffraction in mind. This paper presents the angle calculations and correction factors required to calculate meaningful intensities for 2θ scans with a (2 + 3)-type diffractometer and an area detector. Some of the limitations with respect to texture, refraction and instrumental resolution are also discussed, as is the kind of information that one can hope to obtain.	Aug 2021
Theoretical Physics	Electronic multipoles in second harmonic generation and neutron scattering G. Van Der Laan , S. W. Lovesey Physical Review B 103, 125124 DOI: 10.1103/PhysRevB.103.125124 Show Abstract ▼ Abstract: Nonlinear optics, and particularly second harmonic generation (SHG), is increasingly used in many modern disciplines from material characterization in physical sciences to bioimaging in medicine and optical signal processing in information technology. We present a theoretical analysis yielding a strong estimate of the energy integrated SHG response. Compact spherical multipoles are provided for the corresponding natural and magnetic circular dichroic signals. Like symmetry requirements in time and space are traced in the amplitude for magnetic neutron scattering, which includes all axial and polar (Dirac) contributions. Our method of working in terms of,now standard, electronic multipoles and Racah algebra, with full implementation of discrete symmetries, could be of use in a variety of other probes of matter.	Mar 2021
Theoretical Physics	Diffraction by multipoles in a 5d2 rhenium double perovskite S. W. Lovesey , D. D. Khalyavin , G. Van Der Laan , G. J. Nilsen Physical Review B 103, 104429 DOI: 10.1103/PhysRevB.103.104429 Show Abstract ▼ Abstract: A recent polarized neutron diffraction experiment on the 5d2 rhenium double perovskite Ba2YReO6 held at a low temperature uncovered weak magnetic diffraction peaks. Data analysis inferred a significantly reduced Re dipole moment, and long-range order compatible with an antiferromagnetic, noncollinear motif. To interpret the experimental findings, we present a model wave function for Re ions derived from the crystal field potential, Coulomb interaction, and spin-orbit coupling that fully respects the symmetry of the low temperature ordered state. It is used to calculate in analytic form all multipole moments visible in neutron and resonance enhanced x-ray diffraction. A minimal model consistent with available neutron diffraction data predicts significant multipolar moments up to the hexadecapole and, in particular, a dominant charge like quadrupole moment. Calculated diffraction patterns embrace single crystal x-ray diffraction at the Re L edge, and renewed neutron diffraction, to probe the presumed underlying multipolar order.	Mar 2021
Theoretical Physics	Magnetic multipoles and correlation shortage in the pyrochlore cerium stannate Ce2Sn2O7 S. W. Lovesey , G. Van Der Laan Physical Review B 101, 144419 DOI: 10.1103/PhysRevB.101.144419 Show Abstract ▼ Abstract: Cerium electronic multipoles in trigonal symmetry viewed in magnetic neutron diffraction are investigated. Analytic expressions for all the magnetic multipoles, and radial integrals calculated with an established atomic code, are used to scrutinize a recent claim to have observed an octupole-ice configuration in a powder sample of pyrochlore Ce2Sn2O7. Three equally plausible suites of multipoles belonging to uncorrelated cerium ions give equally satisfactory accounts of the available diffraction pattern. Our multipoles are suitable for future experiments using Bragg diffraction from a compound that supports long-range magnetic order.	Apr 2020
	Review and analysis of CO2 photoreduction kinetics Warren Athol Thompson , Eva Sanchez Fernandez , M. Mercedes Maroto-Valer Acs Sustainable Chemistry & Engineering DOI: 10.1021/acssuschemeng.9b06170 Open Access Show Abstract ▼ Abstract: Microkinetic, in situ analytics and empirical modeling approaches for developing intrinsic CO2 photoreduction kinetics are presented in this perspective. Intrinsic kinetic models that are independent of photoreactor geometry are critical for scaling CO2 photoreduction photoreactors. Successfully scaling CO2 photoreduction is limited using the current extrinsic CO2 photoreduction kinetic models described in this perspective as they are dependent on the photoreactor geometry and scale used. The impact of different photoreactor geometries and light transport that lead to extrinsic kinetic models is reviewed. The impacts of temperature and pressure on surface diffusion is highlighted as additional important process parameters. The current Langmuir-Hinshelwood based kinetic models are discussed and their limitations highlighted with respect to modeling the possible deactivation of the photocatalyst. With a view on developing an intrinsic kinetic model, the challenges for developing CO2 photoreduction kinetics are highlighted and discussed with reference to the current extrinsic CO2 photoreduction kinetic model examples found in the literature. Robust analytical methods for collecting CO2 photoreduction kinetic data and for confirming the carbon source are discussed. The false positive production from adventitious carbon and organic impurities introduced during the synthesis and/or coating of photocatalysts with solvents and degradation of photoreactor components is highlighted as a challenge to collecting CO2 photoreduction kinetic data. It is shown that a wide range of the kinetic model coefficient values are possible when using a multi-start, genetic algorithm or particle swarm approach for estimating nonlinear model coefficients. Finally, an easy to test and implement approach using a mean median multi-start and trust-region reflective algorithm method is presented for the estimation of nonlinear CO2 photoreduction kinetic model coefficients.	Mar 2020
Theoretical Physics	Circular dichroism of second harmonic generation response S. W. Lovesey , G. Van Der Laan Physical Review B 100, 245112 DOI: 10.1103/PhysRevB.100.245112 Open Access Show Abstract ▼ Abstract: Polarization-dependent photon spectroscopy (dichroism) of the second-harmonic generation response is shown to reveal chiral and magnetic properties of a sample. Two dichroic signals are allowed with electric-dipole and electric-quadrupole scattering events, and both require circular polarization in the primary beam. Explicit expressions for the signals are derived using theoretical techniques from atomic physics.	Dec 2019
Theoretical Physics	Field-induced magnetic charge in a cubic Laves compound UAl2 S. W. Lovesey , D. D. Khalyavin , G. Van Der Laan Journal Of Physics: Conference Series 1316, 012004 PNCMI 2018 DOI: 10.1088/1742-6596/1316/1/012004 Open Access Show Abstract ▼ Abstract: Magnetic diffraction of polarized neutrons by the cubic Laves compound UAl2 in a magnetic field has unveiled weak Bragg spots that are nominally forbidden. On the one hand, they can be viewed as magnetic analogues of the basis-forbidden (2, 2, 2) reflection in diamond-type structures that has been painstakingly and frequently investigated over almost a century. Alternatively, the pattern of weak intensities can be assigned to Dirac multipoles imbedded in field-induced magnetic charge. To this end, a published diffraction pattern is successfully confronted with intensities calculated from the appropriate magnetic space-group (Imm'a') that includes Dirac dipoles (anapoles) to describe the basis-forbidden magnetic reflections (Ho+Ko+Lo = 4n+2), and conventional (axial) dipole and octupole multipoles to describe basis-allowed magnetic reflections.	Dec 2019

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