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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

ReaxFF Parameter Set for Boron Clusters and Icosahedral Boron Crystals: Comparison with Density Functional Theory and Machine-Learning Potentials

Icosahedral boron materials, which include regular icosahedra of 12 boron atoms have gained increasing attention due to their potential applications as superhard materials, semiconductors, and energy storage media. However, the synthesis of high quality crystals of these materials has been a major barrier to the development of these applications. To enable computational prediction of synthesis conditions yielding high-quality icosahedral boron crystals, herein we tested and refined a set of ReaxFF parameters for the nucleation and growth of such crystals. We focused on matching the relative energies of small boron clusters obtained by density functional theory since such small clusters and similar motifs are likely present in crystal nuclei and at the interface of growing crystals. Using a training set of B 80 clusters, including a low-energy core–shell structure containing a B 12 icosahedron core and a high-energy single-shell structure produced in preliminary ReaxFF simulations, the ReaxFF parameter set was refined to better reproduce energies calculated by density functional theory (DFT). Among existing ReaxFF parameter sets and the machine-learning interatomic potentials MACE-MP-0, MACE-MP-0b3, MACE-MPA-0, PFP v7.0.0, and SevenNet-MF-ompa, only our new parameter set and PFP v7.0.0 correctly ranked these B 80 clusters. This refinement led to improved agreement with DFT for a test set of 58 clusters consisting of 8–103 boron atoms. Furthermore, our refined parameter set yielded greater local icosahedral structure than the previously existing ReaxFF parameter set for larger scale simulations of crystallization from supercooled liquid boron. Additionally, simulations of solid boron in contact with molten nickel using our refined ReaxFF parameters yielded a boron solubility value that agrees moderately well with experimental expectations, while the previous boron parameters gave a value that was much too low.

boron↗
DOE OSTI2020

Influences of North Pacific Ocean Domain Extent on the Western U.S. Winter Hydroclimatology in Variable-Resolution CESM

Variable-resolution global climate models (VRGCMs) are a dynamical downscaling method that can reach spatiotemporal scales needed for regional climate assessments. Over the years, several users of VRGCMs have assumed where the location and extent of the refinement domain should be based on knowledge of the prevailing storm tracks and resolution dependence of important regional climate processes (e.g., atmospheric rivers [ARs] and orographic uplift), but the effect of high-resolution domain size and extent on the simulation of downstream hydroclimatic phenomena has not been systematically evaluated. Here, we use variable resolution in the Community Earth System Model (VR-CESM) to perform such a test. To do this, three VR-CESM grids were generated that span the entire, two thirds, and one third of the North Pacific and evaluated for a 30-year climatology using Atmospheric Model Intercomparison Project protocols. Simulations are compared with reanalysis products offshore (fifth-generation of the European Centre for Medium-Range Weather Forecasts atmospheric reanalysis [ERA5]) and onshore (Livneh, 2015, https://doi.org/10.1038/sdata.2015.42, and Parameter-elevation Regressions on Independent Slopes Model [PRISM]) of the western United States. The westward expansion of refinement domain influenced integrated vapor transport (IVT), which was generally high biased but minimally impacted AR characteristics. Due to slight differences in landfalling AR counts in the western United States, California winter precipitation generally improved with westward expansion of the refinement domain. Western U.S. mountain snowpack and surface temperatures were insensitive to refinement domain size and were more influenced by changes in topographic resolution and/or land surface model version. Here, given minimal dependence of simulated western U.S. hydroclimate on refinement domain size over the North Pacific, we advise future VR-CESM studies to focus grid resolution on better resolving land surface heterogeneity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Adaptive Grid Redistribution for a 1D Model of Turbulence and Clouds

In global atmospheric models, resolving stratocumulus (Sc) in the vertical is computationally expensive. However, Sc appear only under special meteorological conditions. Therefore, there is motivation to refine the vertical grid levels adaptively. In order to facilitate the possibility of parallelization on graphical processing units, our grid adaptation method prescribes the number of vertical levels a priori. Then grid levels are relocated toward altitude ranges in need of refinement. Because the method relocates existing grid levels, rather than adding extra levels, there is a risk of creating regions with overly coarse grid spacing, that is, voids in the grid mesh. To prevent such voids from forming, a simple method is developed to impose a maximum grid spacing. To decide where to place enhanced resolution, the authors develop an empirical mesh refinement criterion. It refines grid spacing near the ground, near strong temperature gradients, and within clouds. Our grid adaptation method is implemented in a single-column model and evaluated on four test cases: decaying stratocumulus, developing shallow cumulus, a quasi-stationary stratocumulus deck, and the diurnal cycle of a dry boundary layer. In the stratocumulus cases, mesh refinement leads to improvements in both the time evolution of fields and their time averages. The other two cases show smaller differences.

Carstensen, Steffen [Univ. of Wisconsin, Milwaukee↗
DOE OSTI2020

Two-way coupled particle-turbulence interaction: Effect of numerics and resolution on fluid and particle statistics

Euler-Lagrange point-particle simulation has emerged as a premier methodology for studying dispersed particle-laden flows. This method's popularity stems from its ability to resolve fine-scale fluid structures while also tracking individual particles at reduced cost using an appropriate particle acceleration model. However, the point-particle model has known convergence issues in that refinement of the fluid grid can lead to changes in the predicted statistics. The reasons for non-convergence are twofold: the point-particle two-way coupling force in the Navier-Stokes equations requires a numerical regularization and, without careful implementation, yields a singular force on the fluid with grid refinement. The second factor that yields grid-dependent statistics is that the point-particle force model in general depends on the undisturbed fluid velocity. When the undisturbed fluid velocity is not robustly modeled in a grid-insensitive way, the calculated force for both particles and fluid will be grid-dependent, contaminating their respective statistics. While the first issue regarding regularizing the point-particle source term has received attention in the literature, the consequences of robustly modeling the undisturbed velocity in the context of grid refinement of turbulence has received little attention. Here, we consider decaying homogeneous isotropic turbulence laden with particles at different Stokes numbers. For a given Stokes number, we systematically refine the grid and demonstrate that explicitly modeling the undisturbed fluid velocity yields relative grid insensitivity for the energy of the particle and fluid phases, as well as acceleration of the particles. We also demonstrate that an appropriately defined dissipation rate is also grid-insensitive when an undisturbed fluid velocity correction is used. In contrast, when the undisturbed fluid velocity is modeled using the conventional approach of interpolating the local fluid velocity to the particle location, we show this procedure yields divergent statistics with grid refinement. In particular, we show that higher-order interpolation of the fluid velocity in two-way coupled problems is worse than lower-order interpolation, in the absence of a correction procedure to estimate the undisturbed fluid velocity. We also examine velocity derivative statistics of the fluid phase and demonstrate that these statistics are not in general convergent even when the undisturbed fluid velocity is explicitly modeled. Collectively, the observations in this paper are used to present a philosophy on the types of questions which are answerable with point-particle methods.

42 ENGINEERING↗
DOE OSTI2024

Investigation of CAD-based Geometry Workflows for Multiphysics Fusion Problems Using OpenMC and MOOSE

Fusion system designs are complex and require intricate and accurate meshes to be properly modeled. In this study, we investigate the use of CAD-based geometry workflows in fusion systems multiphysics problems. A simplified tokamak was introduced and modeled in CAD using a multiphysics coupling of OpenMC Monte Carlo transport and MOOSE heat conduction. The meshed geometry was prepared using direct accelerated geometry Monte Carlo (DAGMC) for particle transport, and a volumetric mesh was also prepared to be used in MOOSE and to tally OpenMC results. Cardinal was used to run OpenMC Monte Carlo particle transport within MOOSE framework. The heat source distribution and tritium production were calculated in OpenMC. The data transfer system was used to transfer heat source and temperature distribution between OpenMC and MOOSE. Two computational studies related to mesh refinement were performed: (1) refining the DAGMC and volumetric meshes used for tallying results and solving heat conduction and (2) only refining the DAGMC particle transport mesh. The refinement of the tally mesh has a much larger effect on the runtime compared to the refinement of the DAGMC particle transport surface mesh.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Dyn$\mathrm{AMO}$: Multi-agent reinforcement learning for dynamic anticipatory mesh optimization with applications to hyperbolic conservation laws

Here we introduce DynAMO, a reinforcement learning paradigm for Dynamic Anticipatory Mesh Optimization. Adaptive mesh refinement is an effective tool for optimizing computational cost and solution accuracy in numerical methods for partial differential equations. However, traditional adaptive mesh refinement approaches for time-dependent problems typically rely only on instantaneous error indicators to guide adaptivity. As a result, standard strategies often require frequent remeshing to maintain accuracy. In the DynAMO approach, multi-agent reinforcement learning is used to discover new local refinement policies that can anticipate and respond to future solution states by producing meshes that deliver more accurate solutions for longer time intervals. By applying DynAMO to discontinuous Galerkin methods for the linear advection and compressible Euler equations in two dimensions, we demonstrate that this new mesh refinement paradigm can outperform conventional threshold-based strategies while also generalizing to different mesh sizes, remeshing and simulation times, and initial conditions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Localization of proteins involved in the biogenesis and repair of the photosynthetic apparatus to thylakoid subdomains in Arabidopsis

Abstract Thylakoid membranes in chloroplasts and cyanobacteria harbor the multisubunit protein complexes that catalyze the light reactions of photosynthesis. In plant chloroplasts, the thylakoid membrane system comprises a highly organized network with several subcompartments that differ in composition and morphology: grana stacks, unstacked stromal lamellae, and grana margins at the interface between stacked and unstacked regions. The localization of components of the photosynthetic apparatus among these subcompartments has been well characterized. However, less is known about the localization of proteins involved in the biogenesis and repair of the photosynthetic apparatus, the partitioning of proteins between two recently resolved components of the traditional margin fraction (refined margins and curvature), and the effects of light on these features. In this study, we analyzed the partitioning of numerous thylakoid biogenesis and repair factors among grana, curvature, refined margin, and stromal lamellae fractions of Arabidopsis thylakoid membranes, comparing the results from illuminated and dark‐adapted plants. Several proteins previously shown to localize to a margin fraction partitioned in varying ways among the resolved curvature and refined margin fractions. For example, the ALB3 insertase and FtsH protease involved in photosystem II (PSII) repair were concentrated in the refined margin fraction, whereas TAT translocon subunits and proteins involved in early steps in photosystem assembly were concentrated in the curvature fraction. By contrast, two photosystem assembly factors that facilitate late assembly steps were depleted from the curvature fraction. The enrichment of the PSII subunit OE23/PsbP in the curvature fraction set it apart from other PSII subunits, supporting the previous conjecture that OE23/PsbP assists in PSII biogenesis and/or repair. The PSII assembly factor PAM68 partitioned differently among thylakoid fractions from dark‐adapted plants and illuminated plants and was the only analyzed protein to convincingly do so. These results demonstrate an unanticipated spatial heterogeneity of photosystem biogenesis and repair functions in thylakoid membranes and reveal the curvature fraction to be a focal point of early photosystem biogenesis.

Chotewutmontri, Prakitchai↗
DOE OSTI2021

hr-Adaptivity for nonconforming high-order meshes with the target matrix optimization paradigm

In this study, we present an \(hr\) -adaptivity framework for optimization of high-order meshes. This work extends the r -adaptivity method by Dobrev et al. (Comput Fluids, 2020), where we utilized the Target-Matrix Optimization Paradigm (TMOP) to minimize a functional that depends on each element’s current and target geometric parameters: element aspect-ratio , size , skew , and rotation . Since fixed mesh topology limits the ability to achieve the target size and aspect-ratio at each position, in this paper, we augment the r -adaptivity framework with nonconforming adaptive mesh refinement to further reduce the error with respect to the target geometric parameters. The proposed formulation, referred to as \(hr\) -adaptivity, introduces TMOP-based quality estimators to satisfy the aspect-ratio target via anisotropic refinements and size target via isotropic refinements in each element of the mesh. The methodology presented is purely algebraic, extends to both simplices and hexahedra/quadrilaterals of any order, and supports nonconforming isotropic and anisotropic refinements in 2D and 3D. Using a problem with a known exact solution, we demonstrate the effectiveness of \(hr\) -adaptivity over both r - and \(h\) -adaptivity in obtaining similar accuracy in the solution with significantly fewer mesh nodes. We also present several examples that show that \(hr\) -adaptivity can help satisfy geometric targets even when \(r\) -adaptivity fails to do so, due to the topology of the initial mesh.

42 ENGINEERING↗
DOE OSTI2023

Extended isogeometric analysis of multi-material and multi-physics problems using hierarchical B-splines

Here, this paper presents an immersed, isogeometric finite element framework to predict the response of multi-material, multi-physics problems with complex geometries using locally refined discretizations. To circumvent the need to generate conformal meshes, this work uses an extended finite element method (XFEM) to discretize the governing equations on non-conforming, embedding meshes. A flexible approach to create truncated hierarchical B-splines discretizations is presented. This approach enables the refinement of each state variable field individually to meet field-specific accuracy requirements. To obtain an immersed geometry representation that is consistent across all hierarchically refined B-spline discretizations, the geometry is immersed into a single mesh, the XFEM background mesh, which is constructed from the union of all hierarchical B-spline meshes. An extraction operator is introduced to represent the truncated hierarchical B-spline bases in terms of Lagrange shape functions on the XFEM background mesh without loss of accuracy. The truncated hierarchical B-spline bases are enriched using a generalized Heaviside enrichment strategy to accommodate small geometric features and multi-material problems. The governing equations are augmented by a formulation of the face-oriented ghost stabilization enhanced for locally refined B-spline bases. We present examples for two- and three-dimensional linear elastic and thermo-elastic problems. The numerical results validate the accuracy of our framework. The results also demonstrate the applicability of the proposed framework to large, geometrically complex problems.

42 ENGINEERING↗
DOE OSTI2024

HHL algorithm with mapping function and enhanced sampling for model predictive control in microgrids

Here, this paper presents a refined quantum Harrow Hassidim Lloyd (HHL) algorithm for microgrid control. The first novelty of the developed method is that a mapping shift function enables the original HHL algorithm to handle general linear equations with non-singular and indefinite matrix. Second, a method of Matrix Extension for Amplifying Sampling Probabilities of Intended Solution (ME-ASPI) is proposed to design the reformulated linear algebraic equations, allowing for improved sampling efficiency of the quantum tomography in the refined HHL algorithm. Then, we applied the method to solve the model predictive control (MPC) problem in nonlinear dynamical microgrids. Specifically, with the ME-ASPI method, the refined HHL algorithm can effectively obtain the intended partial optimal control inputs for MPC. The optimization of quadratic programming problem in each time step of MPC is transformed into a linear system problem, which is addressed by the proposed quantum solver through using only partial information, with the time complexity improved from $\mathscr{O}(\mathscr{N}^{2.37286})$ classically to $\mathscr{O}(\mathscr{N}^{2} log \mathscr{N}$ x $p$ log $p)$ in quantum. Numerical examples have validated the effectiveness of the refined HHL algorithm with the proposed mapping function and the ME-ASPI method. By leveraging quantum properties, the proposed method provides a hybrid quantum–classical framework for microgrid control. This generic method can also potentially tackle many other challenges in analyzing and controlling general complex engineered systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Mass transport in a highly immiscible alloy on extended shear deformation

Forced mixing to a single phase or supersaturated solid solution (SSS) and its prerequisite microstructure evolution in immiscible systems has been a focus of research for both fundamental science and a variety of applications. Controlling the formation of SSS by shear deformation assisted processing could enable a material design beyond conventional equilibrium microstructure in immiscible systems. Here, a highly immiscible (mixing enthalpy of ~ 20 kJ·mol -1 ) Cu-50 at. % Cr binary alloy was employed to investigate the microstructure evolution and localized tendencies of SSS during severe shear deformation. The present results demonstrate distinctive microstructure refinement process in each phase and how they lead to localized SSS as a function of shear strain. Preferential dynamic recrystallization occurs in the softer Cu phase due to strain localization, leading to substantial grain refinement. The refinement of Cr phase in the top-most layer, however, is enabled by the progressive evolution of grain lamination, splitting, and fragmentation as a function of shear strain. The eventual SSS is found to be strongly dependent on the local environments that affect the dislocation activity, including the level of microstructure refinement, the interfacial orientation relationship, hardness difference, and supposed stability of oxidation. Ab initio simulations comfirm that it is more favorable to oxidize Cr than Cu at incoherent Cu/Cr interfaces which then limits the mass transport on an incoherent boundary. Our results shed light on the underpinning mechanism for non-equilibrium mass transport in immiscible systems upon severe deformation that can be applicable to a variety of processing techniques aimed at producing immiscible alloys with superior mechanical properties.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Synchrotron X-ray diffraction of pyrolusite (MnO 2 ) and rutile (TiO 2 ) during heating to ~1000 °C

To compare thermal expansion behaviors in isomorphic structures with different redox behaviors, we separately heated pyrolusite (Mn 4+ O 2 ) and rutile (Ti 4+ O 2 ) powders from 25 to ~1000 °C at a rate of 0.05 °C/s at ambient pressure and analyzed them using synchrotron X-ray diffraction and Rietveld refinement. The pyrolusite exhibited two reduction-induced phase decompositions. Between 531 and 583 °C, pyrolusite decomposed to bixbyite (Mn 3+ 2 O 3 ), and between 972 and 998 °C, bixbyite decomposed to hausmannite (Mn 2+ Mn 3+ 2 O 4 ). The rutile experienced no phase decompositions or transitions over this same temperature interval. The refined bond lengths and angles for pyrolusite showed that the Mn 4+ coordination octahedron became more distorted near the phase decomposition to bixbyite due to the approach of two coordinating oxygen atoms. The 3d electrons of each Mn 4+ ion in pyrolusite make π bonds with the 2p electrons of the surrounding O 2- ions, whereas the Ti 4+ of rutile has no 3d electrons. Thus, π bonding between octahedral Mn 4+ and the surrounding O 2- anions increases the strength of the Mn–O bonds of pyrolusite relative to the Ti–O bonds of rutile. However, we observed a small decrease in O–O distances in pyrolusite before the decomposition, suggesting that at high temperature, increased π bonding between adjacent O anions precedes the release of O 2 and the reduction of Mn 4+ to Mn 3+ . Analogous behavior was observed for bixbyite before its reductive phase decomposition to hausmannite. In contrast, no anomalous changes in the O–O distances occurred for rutile. Our X-ray diffraction analyses provided accurate thermal expansion coefficients for these materials over a broader temperature range than reported in previous studies. The Mn–O bond lengths in pyrolusite were shorter and stronger than the Ti–O bonds of rutile; for example, at 60 °C, bond distances in pyrolusite refined to 1.8854(6) Å whereas the bond lengths of rutile were 1.9575(4) Å. Accordingly, the axial and volumetric thermal expansion coefficients refined for rutile were greater than those for pyrolusite. Further, the axial coefficients of thermal expansion (CTE) for pyrolusite were 96% (a-axis) and 69% (c-axis) of the corresponding values for rutile, and the volumetric CTE for pyrolusite was 85% of that for rutile.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

An airfoil-based synthetic actuator disk model for wind turbine aerodynamic and structural analysis

Here, this study introduces an airfoil-based refinement technique to enhance the Actuator Disk Model (ADM) for improved wind turbine aerodynamic load prediction and structural simulation in conjunction with Large Eddy Simulations of the wind flow. While ADM offers higher computational efficiency than the more detailed but resource-intensive Actuator Line Model (ALM), it traditionally lacks the resolution needed to capture the localized blade forces accurately. To address this limitation, we introduce a refinement technique that uses airfoil-specific data and employs interpolation-based grid point refinement, achieving ALM-comparable accuracy while preserving ADM's efficiency. Unlike conventional ADM that provides only rotor-disk averaged forces, our synthetic method tracks transient aerodynamic load variations over multiple blade revolutions, allowing us to calculate the distributions of maximum and minimum loads during typical cycles. Applied to the NREL 5 MW reference turbine, our enhanced ADM accurately predicts key aerodynamic parameters (angle of attack, axial velocity, lift, drag, axial and tangential forces along the blades) as well as structural responses (blade tip deflection, maximum stress, and stress concentration). Our results show that the tip deflection ranges from 2.33m (3.69 % of blade length) to 4.28m (6.79 %), with maximum stress concentration occurring near the blade root. This research demonstrates that a refined synthetic ADM approach can serve as a computationally efficient alternative for both aerodynamic analysis and structural simulation of wind turbine blades subjected to realistic wind fields.

17 WIND ENERGY↗
DOE OSTI2025

Higher Dimensionality in the Mg–Co–B System: Synthesis and Structure of Incommensurate Composite Mg 1+ε Co 4 B 4

Guided by high-temperature in situ X-ray diffraction, the discovery and synthesis of Mg 1+ε Co 4 B 4 (ε ≈ 0.272) using a MgH 2 hydride precursor is reported, along with a detailed crystal structure description and measurement of magnetic properties. The mismatch in lattice periodicities between Mg and Co–B substructures places Mg 1+ε Co 4 B 4 in the family of incommensurate composite crystals and prompted structural refinement in a (3 + 1)-dimensional model. The structure of Mg 1+ε Co 4 B 4 (P4 2 /ncm(00γ)s00s, a = 6.75847(7) Å, c = 3.94007(8) Å, q = (0, 0, 1.2721(3))) was refined from neutron powder diffraction and high-resolution powder X-ray diffraction data and confirmed by scanning transmission electron microscopy and electron diffraction. Mg 1+ε Co 4 B 4 is isostructural to Nd 1+ε Fe 4 B 4 and several related ternary borides with 0.07 ≤ ε ≤ 0.17, with Mg occupying the rare-earth site. Satellite reflections in the electron diffraction patterns hinted at positional modulation of the transition metal–boron substructure by Mg atoms, but this could not be refined from the neutron or X-ray diffraction data. Low-temperature magnetic measurements show no indications of long-range magnetic ordering or superconductivity down to 5 K. DFT calculations confirmed the absence of a magnetically ordered ground state and the stability of a 5:4 supercell (ε = 0.25) relative to the fully commensurate structure. Neutron diffraction and synthesis from elemental Mg demonstrated that Mg 1+ε Co 4 B 4 is not a hydrogen-stabilized phase. Mg 1+ε Co 4 B 4 represents the second compound reported in the Mg–Co–B system and the first superspace symmetry model of a Nd 1+ε Fe 4 B 4 -type incommensurate composite compound refined from powder diffraction data.

chemical structure↗
DOE OSTI2024

The Collaborative Seismic Earth Model: Generation 2

Geological interpretations, earthquake source inversions and ground motion modeling, among other applications, require models that jointly resolve crustal and mantle structure. With the second generation of the Collaborative Seismic Earth Model (CSEM2), we present a global multi-resolution tomographic Earth model that serves this purpose. The model evolves through successive regional- and global-scale refinements. While the first generation aggregated regional models, with this study, we ensure consistency between all individual submodels, resulting in a model that accurately explains wave propagation across scales. Recent regional tomographic models were incorporated, comprising continental-scale inversions for Asia and Africa, as well as regional inversions for the Western US, Central Andes, Iran, and Southeast Asia. Across all regional refinements, over 793,000 source-receiver pairs contributed. Moreover, the long-wavelength Earth model (LOWE) introduces large-scale structures outside of pre-existing local refinements. A full-waveform inversion for global anisotropic P-and S-wave speed structure over a total of 194 iterations with a minimum period of 50 s on a large data set of 1 hr of waveform data from 2,423 earthquakes and over 6 million source-receiver pairs ensures that regional updates in the crust and uppermost mantle translate into updates of deeper, global-scale structure. To test the performance of CSEM2, we evaluate waveform fits between observed and synthetic seismograms at 50 s for an independent data set on the global scale, and on the regional scale for lower periods. We accurately simulate waveforms within and across regional refinements, maintaining the original resolution of the submodels embedded in the global framework.

58 GEOSCIENCES↗
DOE OSTI2025

Spotlight: efficient automated global optimization in rietveld analysis of diffraction data

Performing reliable Rietveld analysis on tens or hundreds of powder diffraction datasets from parametric or time-resolved experiments often poses a bottleneck in extracting meaningful results from the data. While automated analysis of data has recently been demonstrated, high temperature annealing studies, during which phase transformations occur and lattice parameters may change due to repartitioning of elements, are prime examples where automation by a simple phase identification from a database of room temperature structures or automation by sequential refinements is likely to fail. To enable reliable, efficient, automated Rietveld analysis, we present a Python package named Spotlight , building on established Rietveld packages such as MAUD, GSAS , or GSAS-II , which extends the refinement of best fit parameters to a global optimization using an ensemble of optimizers leveraging hierarchical parallel execution on high-performance computing clusters. Spotlight further enables the efficient design of refinement plans through the iterative automated machine-learning of a surrogate for the refinement on which the global optimizations are performed until results from the surrogate converge to the response surface data. We demonstrate Spotlight with the analysis of uranium molybdenum and Ti–6Al–4V datasets, as well as in two open-source tutorials analyzing aluminium oxide and lead sulphate.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Strengthening poly(lactic acid) composites with poly(methyl methacrylate) functionalized flax nanofibrils

Biobased reinforcements for poly(lactic acid) (PLA) are needed for more additive manufacturing applications requiring higher strength and sustainability. Flax nanofibrils (FNFs) produced through mechanical refining were explored as a lower energy alternative to cellulose nanofibril (CNF) reinforcements. To compatibilize the FNFs for the PLA matrix, a grafting-through surfactant free emulsion polymerization (SFEP) was performed to functionalize the FNF surface with poly(methyl methacrylate) (PMMA). FNFs produced using different refining energy were functionalized under varying solid contents in suspension. Polymerizations performed at 0.7 wt% FNFs in water yielded the highest degree of PMMA functionality. These optimal conditions were scaled up and the PMMA modified FNFs melt compounded into PLA yielding a 12% increase in tensile strength and 92% increase in the modulus of elasticity as compared to the original PLA. Interestingly, the FNFs with the lowest refining energy yielded the strongest composites using these methods, surpassing the higher refining energy CNF reinforcements. This increase was attributed to improved dispersion of the FNF reinforcements in the PLA matrix that was enabled by the PMMA coating on the FNF surface preventing interfibrillar adhesion and aggregation within the PLA matrix.

Mulligan, Abigail [University of Maine]↗