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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Molecular Viscosity and Diffusivity Effects in Transitional and Shock-Driven Mixing Flows

Here, this paper investigates the importance of molecular viscosity and diffusivity for the prediction of transitional and shock-driven mixing flows featuring high and low Reynolds and Mach number regions. Two representative problems are computed with implicit large-eddy simulations using the inviscid Euler equations (EE) and viscous Navier-Stokes equations (NSE): the Taylor-Green vortex at Reynolds number Re = 3000 and initial Mach number Ma = 0.28, and an air- SF 6 -air gas curtain subjected to two shock waves at Ma = 1.2. The primary focus is on differences between NSE and EE predictions due to viscous effects. The outcome of the paper illustrates the advantages of utilizing NSE. In contrast to the EE, where the effective viscosity decreases upon grid refinement, NSE predictions can be assessed for simulations of flows with transition to turbulence at prescribed constant Re. The NSE can achieve better agreement between solutions and reference data, and the results converge upon grid refinement. On the other hand, the EE predictions do not converge with grid refinement, and can only exhibit similarities with the NSE results at coarse grid resolutions. We also investigate the effect of viscous effects on the dynamics of the coherent and turbulent fields, as well as on the mechanisms contributing to the production and diffusion of vorticity. The results show that nominally inviscid calculations can exhibit significantly varying flow dynamics driven by changing effective resolution-dependent Reynolds number, and highlight the role of viscous processes affecting the vorticity field. These tendencies become more pronounced upon grid refinement. The discussion of the results concludes with the assessment of the computational cost of inviscid and viscous computations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Symmetry-mode analysis for local structure investigations using pair distribution function data

Symmetry-adapted distortion modes provide a natural way of describing distorted structures derived from higher-symmetry parent phases. Structural refinements using symmetry-mode amplitudes as fit variables have been used for at least ten years in Rietveld refinements of the average crystal structure from diffraction data; more recently, this approach has also been used for investigations of the local structure using real-space pair distribution function (PDF) data. Here, the value of performing symmetry-mode fits to PDF data is further demonstrated through the successful application of this method to two topical materials: TiSe2, where a subtle but long-range structural distortion driven by the formation of a charge-density wave is detected, and MnTe, where a large but highly localized structural distortion is characterized in terms of symmetry-lowering displacements of the Te atoms. Here, the analysis is performed using fully open-source code within the DiffPy framework via two packages developed for this work: isopydistort, which provides a scriptable interface to the ISODISTORT web application for group theoretical calculations, and isopytools, which converts the ISODISTORT output into a DiffPy-compatible format for subsequent fitting and analysis. These developments expand the potential impact of symmetry-adapted PDF analysis by enabling high-throughput analysis and removing the need for any commercial software.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Detector alignment for X-ray crystallography using Millepede-II

I describe a method for accurately refining the geometrical parameters of segmented X-ray area detectors on the basis of serial crystallography data, using 'Millepede' – an algorithm created for a very similar problem in high-energy physics. The Millepede method for serial crystallography builds on the approach of Brewster et al. [Acta Cryst. (2018), D74, 877–894], in which the detector parameters are refined simultaneously with the parameters for each individual crystal. This accounts for the mutual dependency between the parameters and thereby avoids the bias and slow convergence problems that have afflicted older approaches in which the deviations between observed and calculated Bragg peak positions were taken directly as the updates for the detector panel positions. The Millepede method uses the special structure of the least-squares normal equations to reduce them to a much smaller form that can be solved very quickly, even compared with the sparse matrix methods used previously. This makes it practical to refine the detector geometry frequently and thereby maintain accurate calibration without specialized alignment campaigns. Tilts of detector panels out of the plane can be reliably refined, as can the overall distance of the detector in the beam direction. With a simulated test case, the new method produced panel shifts within 7% of the correct values with only one iteration, and produced almost exactly correct shifts after a second iteration. A simulated out-of-plane panel rotation was correctly determined to within 0.001°. Applied to experimental data from an X-ray free-electron laser, the method increased the indexable fraction of frames from 30% to 91% in a single iteration, and to 96% after two further iterations. Computing the geometry updates on the basis of 2060 crystals took only 0.819 s on desktop computing hardware, including the time taken to read the required data from disk. The scaling was found to be very close to linear for up to 100 980 sets of crystal parameters, which took only 78.2 s to process under the same conditions. The method has been applied as part of a real-time feedback system at a synchrotron radiation beamline, in which an out-of-plane detector tilt of 0.04° was detected and corrected. Possible further applications are also described here.

Millepede-II↗
DOE OSTI2021

Energy Exascale Earth System Model v2.0

First release of version 2 of the Energy Exascale Earth System Model. The atmosphere component remains EAM. Major changes since version 1 include: all column-physics parameterizations are computed on a separate grid that has approximately half the number of points of the dynamics grid, a new nonhydrostatic dynamical core (running in hydrostatic mode) with semi-Lagrangian tracer transport, CLUBB updated from v1 to v2, a new convective trigger (dCAPE/ULL) based on the dynamic Convective Available Potential Energy (CAPE) (dCAPE) and the Unrestricted Launch Level (ULL) concepts is used in ZM. minimum cloud droplet number changed, gravity wave drag energy conservation fixed and new tunings used, dust emission size distribution changed to emit more coarse dust particles The land component is still ELM. Major changes since version 1 include: using SNICAR-AD for radiation in snow to match the sea-ice model and fixing bugs in snow compaction and water state calculation. The ocean component remains MPAS-ocean. Major change since version 1 include: Redi isopycnal mixing has been updated, tested, and tuned in combination with the Gent-McWilliams parameterization, a sign error was fixed in the 3rd-order flux routines, the mesh used in low-resolution coupled cases was modified and the time steps adjusted, new regionally refined meshes were created, one focused on North America and another on the Southern Ocean, including ice shelf cavities. The sea-ice component remains MPAS-seaice. Major changes since version 1 include: A new heat- and freshwater-conserving coupling of frazil ice, turning off of SSH filtering, addition of SNICAR-AD and snow grain aging. The land-ice component remains MPAS-Albany-landIce (MALI) and is a static ice sheet. There is more out-of-the-box support for cryosphere configurations including the new regionally refined configuration around Antarctica with ice shelf cavities. The river model is MOSART. The half-degree river mesh was redone so it no longer treats Black and Caspian seas as ocean. The coupler remains cpl7/MCT. Major changes since version 1 include handling of ice shelf melt fluxes (heat / freshwater exchange with the ocean), and data icebergs. All components allow regional refinement of their meshes and two separate example of refinement, one in and around North America and one around Antarctica and the Southern Ocean, are provided.

E3SM Project, DOE↗
DOE OSTI2020

The arbitrary-order virtual element method for linear elastodynamics models. Convergence, stability and dispersion-dissipation analysis.

We design the conforming virtual element method for the numerical approximation of the two dimensional elastodynamics problem. We prove stability and convergence of the semi-discrete approximation and derive optimal error estimates under $\textit{h}$-refinement in both the energy and the $L^2$ norms, and optimal error estimates under $\textit{p}$-refinement in the energy norm. The performance of the proposed virtual element method is assessed on a set of different computational meshes, including non-convex cells up to order four in the h-refinement setting. Exponential convergence is also experimentally observed under p-refinement. Finally, we present a dispersion-dissipation analysis for both the semi-discrete and fully-discrete schemes, showing that polygonal meshes behave as classical simplicial/quadrilateral grids in terms of dispersion-dissipation properties.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Enabling Real-time Scattering Data Analysis with Scalable Optimization [Slides]

Diffraction experiments produce datasets with rich multidimensional physics information such as microstructure, equations of state, crystal structure, elastoplastic properties, and other key inputs to LANL mission-essential multiphysics models. This information is typically extracted through a process called Rietveld refinement, which involves selecting appropriate models of the instrument, crystal structure, and microstructure, identifying suitable starting values, and then fitting often hundreds of model parameters using a sequence of empirical parameter turnon/off sequences within a non-global gradient-based optimization. Extensive user expertise is required to properly setup a refinement, identify appropriate models, and select initial parameter values close to truth, such that the refinement will yield parameter values that are optimally predictive. This is a very tedious manual process performed far after the beamline campaign has ended. As facilities have become capable of generating larger volumes of data, the limitation in throughput due to Rietveld refinement has led to a dramatic increase in unanalyzed data as opposed to an intended increase in new science. In our FY22 TED, we demonstrated an integrated toolset providing near real-time automated Rietveld analysis. If this toolset can be optimized to provide automated Rietveld analysis in real-time, this could alleviate the bottleneck in unanalyzed diffraction data, aid in decision-making during experiments, and increase efficiency of the facility.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Preserving Superconvergence of Spectral Elements for Curved Domains

Spectral element methods (SEM), extensions of finite element methods (FEM), have emerged as significant techniques for solving partial differential equations in physics and engineering. SEM can potentially deliver superior accuracy due to the potential superconvergence in nodal solutions for well-shaped tensor-product elements. However, the accuracy of SEM often degrades in complex geometries due to geometric inaccuracies near curved boundaries and the loss of superconvergence with simplicial or non-tensor-product elements. To overcome the first issue, we propose using geometric refinement, which both refines the mesh near high-curvature regions and increases the degree of geometric basis functions. We show that when using mixed-element meshes with tensor-product elements in the interior of the domain, curvature-based geometric refinement near boundaries can improve the accuracy of the interior elements by reducing pollution errors and preserving the superconvergence in nodal solutions. To address the second issue, we introduce ApSEM, a post-processing technique using the adaptive extended stencil finite element method (AES-FEM) to recover the accuracy near the curved boundaries. The combination of curvature-based geometric refinement and accurate post-processing offers an effective and easier-to-implement alternative to methods reliant on exact geometries. We demonstrate our techniques by solving the convection-diffusion equation in 2D and 3D and show up to two orders of magnitude of improvement in the solution accuracy, even when the elements are poorly shaped near boundaries. We also show the efficiency of ApSEM as it can recover superconvergence in nodal solutions without drastically increasing the computational cost.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Southwest Regional Partnership on Carbon Sequestration: Phase III (Final Scientific/Technical Report)

The Southwest Regional Partnership on Carbon Sequestration (SWP) is one of 7 regional partnerships formed in 2003 under the U.S. Department of Energy’s (DOE) Regional Carbon Sequestration Partnerships (RCSPs) initiative. The overall purpose of the initiative was to help determine and implement the technology, infrastructure, and regulations most appropriate to promote carbon storage in different regions of the country. Covering Arizona, Colorado, New Mexico, Oklahoma, Utah, and parts of Texas, Wyoming, and Kansas, the SWP evaluated regional carbon storage and utilization potential and focused on technologies and sites that could complement the region’s strong position in energy production. The project progressed through three phases: • Phase I (2003–2005): Characterized regional geologic formations and CO 2 sources, assessed sequestration potential, and identified pilot test sites. • Phase II (2005–2013): Conducted small-scale field tests to validate sequestration methods, including geologic and terrestrial projects. • Phase III (2008–2022): Demonstrated large-scale CO 2 injection at a commercial oil field to test monitoring, verification, and long-term storage strategies. This report covers Phase III. The final project site, the Farnsworth Unit (FWU) in Texas, provided real-world testing of reservoir characterization, monitoring, and risk evaluation tools and processes that could be used in any commercial scale carbon capture, utilization, and storage (CCUS) project. Extensive data collection and analysis helped refine best practices for reservoir characterization, injection monitoring, and storage verification. The SWP contributed to national databases, DOE best practice manuals, and regional geological assessments to support future sequestration efforts. Key lessons learned include the importance of robust data management, strategic site selection, regulatory navigation, and effective industry collaboration. The project’s findings will inform ongoing and future carbon storage initiatives. Task 1 (Regional Characterization) • The SWP continued to participate in national outreach efforts and NATCARB. • The SWP evaluated multiple potential sites before selecting the FWU as the primary field test location. Task 2 (Public Outreach and Education) • The SWP contributed to national databases, DOE best practice manuals, and regional geological assessments to support future sequestration efforts. Task 3 (Permitting and Regulatory Compliance) • The SWP ensured compliance with federal and state regulations, including National Environmental Policy Act (NEPA) requirements. • The SWP obtained all necessary permits for drilling, injection, and monitoring activities. Task 4 (Site Characterization and Planning) • The SWP developed work plans for four key activities: characterization, simulation, monitoring and verification, and risk evaluation. • The SWP collected and synthesized legacy data from multiple sources to build initial static geological models and dynamic reservoir models demonstrating project feasibility. • The SWP conducted an initial risk evaluation and developed mitigation plans. Task 5 (Field Operations and Data Collection) • The SWP drilled, logged, and cored three characterization wells to gather critical subsurface data. • The SWP conducted multiple geophysical surveys, including 3D seismic, crosswell seismic, and vertical seismic profiling, to improve reservoir characterization. Task 6 (Monitoring and Verification) • The SWP performed extensive geological characterization using data from characterization wells and seismic surveys. • The SWP established a surface monitoring network to track CO 2 flux in soil gas, groundwater chemistry, and near-surface atmospheric CO 2 levels. • The SWP built and refined reservoir models to study the effects of relative permeability on simulation behavior and improve calibration with experimental data. Task 7 (Risk Assessment and Model Refinement) • The SWP conducted multiple studies to evaluate reservoir integrity, predict CO 2 plume behavior and improve predictive modeling capabilities. • The SWP refined geological models and used them to enhance the accuracy of simulation models. • The SWP continued quantitative risk assessment of top-ranked risks and strengthened the link between qualitative and quantitative risk methodologies.

02 PETROLEUM↗
DOE OSTI2022

Effect of Cooling Rate on Nano-Eutectic Formation in Laser Surface Remelted and Rare Earth Modified Hypereutectic Al-20Si Alloys

Laser Surface Remelting (LSR) was applied to arc-melted Al-20Si-0.2Sr, Al-20Si-0.2Ce, and Al-20Si hypereutectic alloys to refine microstructures. Experiments revealed that microstructures in the melt pool varied from fully eutectic to a mixture of Al dendrites and inter-dendritic eutectic. We calculated cooling rates using the Eagar-Tsai model and correlated cooling rates with characteristic microstructures, revealing that a cooling rate on the order of 104 K/s could lead to maximized fully eutectic microstructure morphology. Due to rapid solidification, the Si composition in the LSR eutectic was measured at 18.2 wt.%, higher than the equilibrium eutectic composition of 12.6 wt.%Si. Compared to Al-20Si, Ce addition had no significant effect on the volume fraction of the fully eutectic structure but refined Si fibers to approximately 30 nm in diameter. Sr addition did not further refine the diameter of eutectic Si fibers compared to Al-20Si but increased the volume fraction of the fully eutectic microstructure morphology. The refinement ratio (φ) of the Si fiber diameter from the bottom of the melt pool to the surface for the three alloys was similar, at around 28%. The established correlation between the cooling rate and the size and morphology of the microstructure within the melt pool will enable tailoring of the microstructure in laser-processed as well as deposited alloys for high strength and plasticity.

36 MATERIALS SCIENCE↗
DOE OSTI2021

New insights into the drainage of inundated ice-wedge polygons using fundamental hydrologic principles

Abstract. The pathways and timing of drainage from the inundated centers of ice-wedge polygons in a warming climate have important implications for carbon flushing, advective heat transport, and transitions from methane to carbon dioxide dominated emissions. Here, we expand on previous research using a recently developed analytical model of drainage from a low-centered polygon. Specifically, we perform (1) a calibration to field data identifying necessary model refinements and (2) a rigorous model sensitivity analysis that expands on previously published indications of polygon drainage characteristics. This research provides intuition on inundated polygon drainage by presenting the first in-depth analysis of drainage within a polygon based on hydrogeological first principles. We verify a recently developed analytical solution of polygon drainage through a calibration to a season of field measurements. Due to the parsimony of the model, providing the potential that it could fail, we identify the minimum necessary refinements that allow the model to match water levels measured in a low-centered polygon. We find that (1) the measured precipitation must be increased by a factor of around 2.2, and (2) the vertical soil hydraulic conductivity must decrease with increasing thaw depth. Model refinement (1) accounts for runoff from rims into the ice-wedge polygon pond during precipitation events and possible rain gauge undercatch, while refinement (2) accounts for the decreasing permeability of deeper soil layers. The calibration to field measurements supports the validity of the model, indicating that it is able to represent ice-wedge polygon drainage dynamics. We then use the analytical solution in non-dimensional form to provide a baseline for the effects of polygon aspect ratios (radius to thaw depth) and coefficient of hydraulic conductivity anisotropy (horizontal to vertical hydraulic conductivity) on drainage pathways and temporal depletion of ponded water from inundated ice-wedge polygon centers. By varying the polygon aspect ratio, we evaluate the relative effect of polygon size (width), inter-annual increases in active-layer thickness, and seasonal increases in thaw depth on drainage. The results of our sensitivity analysis rigorously confirm a previous analysis indicating that most drainage through the active layer occurs along an annular region of the polygon center near the rims. This has important implications for transport of nutrients (such as dissolved organic carbon) and advection of heat towards ice-wedge tops. We also provide a comprehensive investigation of the effect of polygon aspect ratio and anisotropy on drainage timing and patterns, expanding on previously published research. Our results indicate that polygons with large aspect ratios and high anisotropy will have the most distributed drainage, while polygons with large aspect ratios and low anisotropy will have their drainage most focused near their periphery and will drain most slowly. Polygons with small aspect ratios and high anisotropy will drain most quickly. These results, based on parametric investigation of idealized scenarios, provide a baseline for further research considering the geometric and hydraulic complexities of ice-wedge polygons.

Harp, Dylan R. (ORCID:0000000197778000)↗
DOE OSTI2022

Mechanically robust high magnetic-performance Sm-Co sintered magnets through microstructure engineering

Samarium-cobalt (Sm-Co) sintered magnets have high magnetic energy densities, great resistance to demagnetization and corrosion, and excellent thermal stability in a wide temperature range (–50–550 °C). However, the utilization of these magnets is restricted by their brittleness. Based on micromechanical and the Zener pinning model, Sm-Co sintered magnets with improved mechanical properties have been designed and fabricated via microstructure engineering. A small amount of fine Sm 2 O 3 particulates (0–3 wt%) has been incorporated into Sm 2 (CoFeCuZr) 17 sintered magnets to refine the grain size by up to approximately 50% (from 45 to 22 µm) and narrow the grain size distribution. Doping with 3 wt% Sm 2 O 3 increased the flexural strength by 62% while maintaining magnetic performance. Both grain-refined unimodal microstructure and heterogeneous laminated coarse/fine grain microstructure were formed by strategically designed assemblies of Sm 2 O 3 -added Sm-Co powder feedstock mixtures. The technology is compatible with existing magnet manufacturing processes. Numerical micromechanics simulation indicates that the fracture is dominated by intragranular mode. The mechanical strength is mainly enhanced by the additive-induced grain refinement, while the small amount of Sm 2 O 3 addition has a small direct positive contribution. Finally, these magnets will be more cost-effective, efficient, and robust for various functional applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Toughening Sm–Co sintered magnets via microstructure modification with additives

We report the mechanical properties of the brittle Smsingle bondCo permanent magnets are of great practical significance. However, studies on the magnets have mostly focused on their magnetic properties. This paper reports the modified microstructure and refined unimodal grain size, enhanced flexural strength, and magnetic properties of Sm 2 (Co,Fe,Cu,Zr) 17 sintered magnets doped with La 2 O 3 , MgO, and CaF 2 fine particulates. The correlations between microstructure, phase composition, and mechanical and magnetic properties were studied. Doping of a small amount (e.g., 0.5–3 wt%) of La 2 O 3 , MgO, or CaF 2 fine particulates could significantly refine the unimodal grain sizes of the Smsingle bondCo magnets via the Zener pinning effect. Moreover, doping significantly improved the flexural strengths σ of the magnets. For example, the σ values of the magnets with 0.5 wt% MgO, 1 wt% La 2 O 3 , and 1 wt% CaF 2 were approximately 65%, 63%, and 42% higher than that of the reference magnet, respectively. Micromechanical simulations revealed that the fine particles of La 2 O 3 could deflect crack growth, while the CaF 2 particles could attract or arrest cracks during the fracture process. The mechanical strengthening effect was mainly due to grain size refinement. The Smsingle bondCo magnets with 0.5–1.5 wt% CaF2 and 0.5 wt% La 2 O 3 exhibited excellent magnetic properties while doping 1–3 wt% La2O3 and 0.5–3 wt% MgO deteriorated magnetic performance. The rational design of CaF 2 - or La 2 O 3 -doped microstructure can be an economical and effective method for producing toughened Sm–Co sintered magnets with high magnetic performance.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Effect of heat treatment on the microstructure of medium burn-up U-Mo monolithic fuel foils

Using scanning electron microscopy (SEM), this study evaluates the microstructure evolution of U-Mo fuel foils made with and without heat treatment at medium burn-up (of approximately 5 x 10 21 f/cm 3 ). The impact of annealing treatments on critical microstructural properties of the U-Mo fuel foils, including porosity, grain structure, Mo homogeneity, and fuel interaction with the Zr interlayer, was examined using large area lift outs (LALOs). The heat-treated specimens presented less grain refining at these burnups when compared to the un-heated specimens. Grain refinement was associated with porosities and fission products precipitation. Heat treatment can reduce fuel swelling during irradiation. Chemical inhomogeneity (Mo banding) was found to persist in the un-heated samples but was not present in the heat-treated samples. Thus, heat-treated U-Mo foils allows for more predictable fuel behavior under irradiation with respect to un-heated foils. The U-Mo and Zr interaction layer appears to be thicker and more continuous in the heat-treated sample which has been associated with stronger interface integrity during irradiation, as also observed in previous studies. These observations may indicate an overall improved performance of heat-treated fuel foil in a reactor. Further, the effect of local burn-up on grain size/refinement and porosities in each LALO specimen, sampled from different positions in the fuel foil, was difficult to analyze due to the large standard deviation of these parameters. Finally, evidence of grain refinement by polygonization may be present in these specimens.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Angular-spatial hp -adaptivity for radiative transfer with discontinuous Galerkin spectral element methods

Radiative transfer is important for many science and engineering applications, and numerical simulations of radiative transfer can be challenging. For instance, the radiation field is seven-dimensional – three spatial, two angular, one wavelength, and one temporal – and often features steep gradients. Therefore, memory usage is a key issue. To reduce memory, some past work has investigated the use of adaptive mesh refinement (AMR), typically for either the spatial or angular coordinate, and typically for only h -adaptivity. Here, we propose the use of AMR for the spatial and angular coordinates together, and the use of h - and p -adaptivity together as hp -AMR for the potential for further memory savings. We implemented the proposed method for several test cases in two spatial and one angular dimension, with the discontinuous Galerkin spectral element method. These test cases featured highly anisotropic angular radiation, with or without steep spatial gradients. Our primary findings from these test cases were: (1) Angular hp -adaptivity can deliver the radiation solution with the same accuracy as, and with much less computational memory than, uniform angular h - or p -refinements, or angular h -adaptivity alone. This is most obvious when the incoming radiation is highly anisotropic, in which case the savings can be orders of magnitude. (2) Full spatial-angular hp -adaptivity is more efficient in solution representation, compared to solely spatial or solely angular -adaptivity. This is most evident when steep gradients are present in both the spatial and angular distribution. These results suggest that adaptive spatial- hp angular-refinement may perform well in large-scale seven-dimensional applications.

Adaptive refinement↗
DOE OSTI2021

Dynamic recrystallization of a wrought magnesium alloy: Grain size and texture maps and their application for mechanical behavior predictions

Effect of dynamic recrystallization (DRX) on the grain refinement and texture modification was studied by conducting a series of hot compression on AZ31B Mg alloy. Processing-grain size-texture maps were established as a function of temperature, strain rate, strain, and the Zener-Hollomon parameter (Z). Moreover, influence of simultaneous changes in the grain size and texture on tensile yield strength and ductility of the hot-worked Mg alloy was studied using the grain size and texture maps established. The processing-grain size map showed that the DRX grain size decreased with the increase in Z, also revealing various characteristics ranging from a grain growth, grain refinement, to a bimodal distribution of ultrafine grains and partially recrystallized grains. The effect of twinning on the grain refinement was also evident at high Z conditions. The processing-texture map revealed that the initial fiber texture was altered significantly to a shear, off-normal, or extension-twin texture with the increase in Z. The Schmid-factor maps were calculated to identify a dominant deformation mode during a subsequent tensile deformation of the hot-worked samples. Finally, a corresponding Hall-Petch relationship for each dominant deformation mode was used to establish tensile yield-strength maps, which agree well with the measured data.

36 MATERIALS SCIENCE↗
DOE OSTI2026

pyDiSCaMB : enabling the use of multipolar scattering factors in Phenix

Multipolar scattering models, such as the transferable aspherical atom model, account for atomic chemical interactions and provide a more accurate representation of experimental data. However, the simpler independent atom model (IAM), which assumes non-interacting atoms, is the only model available in the most widely used macromolecular refinement programs. This is primarily because IAM offers a hard-to-beat combination of computational efficiency and modelling power at typical macromolecular resolutions. By contrast, more accurate multipolar modelling has historically been limited due to its computational cost and the absence of an interface between software capable of calculating structure factors and gradients based on multipolar models and software designed for macromolecular refinement. This work introduces pyDiSCaMB , a Python software package designed to integrate between the computational crystallography toolbox ( cctbx ) and the quantum crystallography library DiSCaMB ( Densities in Structural Chemistry and Molecular Biology ), thus enabling multipolar scattering models in Phenix 's toolkit. The implementation, features and capabilities of pyDiSCaMB are presented, the runtimes for the calculation of structure factor and target gradients with respect to atomic parameters are explored, and Fourier images of electrostatic potential, electron density and deformation maps are computed as illustrative examples. The pyDiSCaMB library will make multipolar modelling widely available to the structural biology community, potentially transforming refinement and model-building for both crystallography and cryogenic electron microscopy (cryoEM).

MATTS data bank↗
DOE OSTI2024

Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors

Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen–Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen–Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen–Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Arginine off-kilter: guanidinium is not as planar as restraints denote

Crystallographic refinement of macromolecular structures relies on stereochemical restraints to mitigate the typically poor data-to-parameter ratio. For proteins, each amino acid has a unique set of geometry restraints which represent stereochemical information such as bond lengths, valence angles, torsion angles, dihedrals and planes. It has been shown that the geometry in refined structures can differ significantly from that present in libraries; for example, it was recently reported that the guanidinium moiety in arginine is not symmetric. In this work, the asymmetry of the N ∊ —C ζ —N η1 and N ∊ —C ζ —N η2 valence angles in the guanidinium moiety is confirmed. In addition, it was found that the C δ atom can deviate significantly (more than 20°) from the guanidinium plane. This requires the relaxation of the planar restraint for the C δ atom, as it otherwise causes the other atoms in the group to compensate by distorting the guanidinium core plane. A new set of restraints for the arginine side chain have therefore been formulated, and are available in the software package Phenix , that take into account the asymmetry of the group and the planar deviation of the C δ atom. This is an example of the need to regularly revisit the geometric restraint libraries used in macromolecular refinement so that they reflect the best knowledge of the structural chemistry of their components available at the time.

59 BASIC BIOLOGICAL SCIENCES↗