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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
NASA NTRS2018

Using Adaptive Mesh Refinement to Study Grid Resolution Effects for Shock/Boundary-Layer Interactions

Adaptive Mesh Refinement (AMR) promises a much more computationally efficient meansto obtain a discrete approximation to a continuous boundary value problem of a specifiedaccuracy than classic isotropic grid refinement. The AMR capability of OVERFLOW is utilizedto provide estimates of the exact analytical solutions to problems of interest to turbulencemodeling. Predictions of surface pressure and skin friction, essentially the state of stress at thesurface, shows little difference with grids believed to be "grid resolved." Velocity profiles, on theother hand, show marked differences in flows with shocks. The AMR method, as implementedin OVERFLOW2.2k, appears to provide the ability to produce arbitrarily accurate solutionsat a predictable cost much smaller than classic uniform mesh refinement.

Adaptive Mesh Refinement↗
NASA NTRS2023

Hot Cracking Behavior and Beam-Induced Grain Refinement in Electron Beam Freeform Fabricated Al 7075

Electron beam freeform fabrication (EBF 3 ) is a high deposition rate, wire-based directed energy deposition (DED) additive manufacturing (AM) process used to print metallic parts in a vacuum environment. While high specific strength 7xxx-series Al alloys are of interest in the aerospace and automotive industries, these alloys suffer from hot cracking issues during fusion welding and AM. In this work, linear deposits of Al 7075 were fabricated with EBF 3 to study the effects of baseplate thickness, preheat temperature, and beam focus on hot cracking behavior. Solidification cracks were observed in the first deposition layer, and by the third layer coalesced into large “macrocracks” running vertically through the build height. Fine, intergranular liquation “microcracks” appeared between macrocracks below the root of the final deposit layer fusion zone. Increasing the substrate preheat temperature from 165°C to 320°C deepened the partially melted zone and resulted in a more than twofold increase in the liquation microcrack density. Analysis of Scheil solidification diagrams revealed that fugitive losses of Zn and Mg during deposition increased the susceptibility to solidification cracking and promoted substrate liquation cracking. Focused electron beam (EB) conditions combined with a high aspect ratio elliptical raster pattern resulted in bands of refined, equiaxed grains. The refined microstructure suppressed solidification macrocracking and caused a nearly fivefold reduction in liquation crack density, demonstrating that beam-induced grain refinement may be a promising low-cost method for reducing hot cracking during AM.

aluminum↗
DOE OSTI2012

Influence of Aluminum Content on Grain Refinement and Strength of AZ31 Magnesium GTA Weld Metal

The goal is to characterize the effect of Al content on AZ31 weld metal, the grain size and strength, and examine role of Al on grain refinement. The approach is to systematically vary the aluminum content of AZ31 weld metal, Measure average grain size in weld metal, and Measure cross-weld tensile properties and hardness. Conclusions are that: (1) increased Al content in AZ31 weld metal results in grain refinement Reason: higher undercooling during solidification; (2) weld metal grain refinement resulted in increased strength & hardness Reason: grain boundary strengthening; and (3) weld metal strength can be raised to wrought base metal levels.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Enhanced Bioconversion in Herbaceous Feedstocks from Impregnation of Co-Catalytic Lewis Acid and Deacetylation and Mechanical Refining

Improvements in conversion processes are needed to further reduce process complexity, biorefinery capital and operating (CAPEX/OPEX) costs, lower enzyme usage. Previous work has demonstrated that deacetylation and mechanical refining (DMR) process effectively deconstructs herbaceous biomass while producing highly digestible lignocellulosic slurries, with high titers of monomeric sugars, at reduced enzyme loadings (Poster 553 Chen at al,). We evaluated a co-catalytic approach using three Lewis acids: Fe+2, Fe+3, and Al+3, in sulfate form, at 1 mM, 5 mM and 10 mM concentrations. Lewis acids were impregnated into corn stover, followed by deacetylation with NaOH, and mechanically refined, prior to enzymatic hydrolysis (EH). Lower concentrations of Lewis acid positively impacted EH yield, increasing concentration lowered EH yield. Likewise Lewis acid treatment was more effective when combined with deacetylation than with deacetylation or Lewis acid treatment, alone. Comparing the effectiveness of the three Lewis acids identified ferrous iron more effective than ferric or aluminum (Fe+2 > Fe+3> Al+3) sulfate. Enzymatic hydrolysis sugar (glucose and xylose) concentration was higher 8% and 13%, respectively, in Fe2+ impregnated corn stover compared to the control. Refining energy required for PFI milling was reduced by ~25% with Fe+2 impregnation. However, treatment with Fenton treatment of the Fe2+ impregnated, deacetylated and PFI milled corn stover resulted in lower yields. for monomeric glucose and xylose due to non-specific degradation of carbohydrates and lignin.

09 BIOMASS FUELS↗
DOE OSTI2013

Direct Reduction of Waste through Refining of DOE Metal Assets - 13632

CVMR{sup R} presents a technology for refining nickel from the enrichment barrier materials of the DOE that is proven through 100 years of use by the metals industry. CVMR{sup R} applies modern controls, instrumentation for process and monitoring of the system, and innovative production methods to produce a wide spectrum of products that generate new technology applications and improvements to our society and economy. CVMR{sup R} will receive barrier materials as a secure operation and size reduce the metal to a shred that is fed to a carbonylation reactor where nickel is reacted with carbon monoxide and generate nickel carbonyl. The carbonyl will be filtered and decomposed with heat to form a variety of products that include high value nano powders, coated substrates, net shapes and pure nickel. The residue from the reactor will retain radionuclides from enrichment activities. The carbon monoxide will only react and extract nickel under the operating conditions to leave volumetric contamination in the unreacted residue. A demonstration plant was designed and built by CVMR{sup R} and operated by BWXT, to demonstrate the systems capabilities to DOE in 2006. A pilot plant operation precedes the detailed design of the nickel refinery and provides essential data for design, safe work practices, waste characterizations and system kinetics and confirms the project feasibility. CVMR{sup R} produces nickel products that are cleaner than the nickel in U.S. commerce and used by industry today. The CVMR{sup R} process and systems for nickel refining is well suited for DOE materials and will provide value through environmental stewardship, recovery of high value assets, and support of the DOE environmental remediation programs as the refined nickel generates additional long term benefits to local communities. (authors)

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Space-Confined Polymerization: Controlled Fabrication of Nitrogen-Doped Polymer and Carbon Microspheres with Refined Hierarchical Architectures

The construction of refined architectures plays a crucial role in performance improvement and application expansion of advanced materials. The synthesis of carbon microspheres with a refined hierarchical structure is still a problem in synthetic methodology, because it is difficult to achieve the necessary delicate control of the interior structure and outer shell across the microscale to nanoscale. Nitrogen-doped multichamber carbon (MCC) microspheres with a refined hierarchical structure are realized here via a surfactant-directed space-confined polymerization strategy. The MCC precursor is not the traditional phenolic resol but a new kind of 2,6-diaminopyridine-based multichamber polymer (MCP) with a high nitrogen content up to 20 wt%. The morphology and sizes of MCP microspheres can be easily controlled by a dual-surfactant system. The as-synthesized MCC with a highly microporous shell, a multichamber inner core, and beneficial N-doping can serve as a promising supercapacitor material.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Multistage mixed precision iterative refinement

Abstract Low precision arithmetic, in particular half precision (16‐bit) floating point arithmetic, is now available in commercial hardware. Using lower precision can offer significant savings in computation and communication costs with proportional savings in energy. Motivated by this, there has been a renewed interest in mixed precision iterative refinement schemes for solving linear systems , and new variants of GMRES‐based iterative refinement have been developed. Each particular variant with a given combination of precisions leads to different condition number‐based constraints for convergence of the backward and forward errors, and each has different performance costs. The constraints for convergence given in the literature are, as an artifact of the analyses, often overly strict in practice, and thus could lead a user to select a more expensive variant when a less expensive one would have sufficed. In this work, we develop a multistage mixed precision iterative refinement solver which aims to combine existing mixed precision approaches to balance performance and accuracy and improve usability. For a user‐specified initial combination of precisions, the algorithm begins with the least expensive approach and convergence is monitored via inexpensive computations with quantities produced during the iteration. If slow convergence or divergence is detected using particular stopping criteria, the algorithm switches to use a more expensive, but more reliable variant. A novel aspect of our approach is that, unlike existing implementations, our algorithm first attempts to use “stronger” GMRES‐based solvers for the solution update before resorting to increasing the precision(s). In some scenarios, this can avoid the need to refactorize the matrix in higher precision. We perform extensive numerical experiments on a variety of random dense problems and problems from real applications which confirm the benefits of the multistage approach.

Oktay, Eda↗
DOE OSTI2019

Towards Adaptive Mesh Refinement for the Spectral Element Solver Nek5000

When performing computational fluid dynamics (CFD) simulations of complex flows, the a priori knowledge of the flow physics and the location of the dominant flow features are usually unknown. For this reason, the development of adaptive remeshing techniques is crucial for large-scale computational problems. Some work has been made recently to provide Nek5000 with adaptive mesh refinement (AMR) capabilities in order to facilitate the generation of the grid and push forward the limit in terms of problem size and complexity [10]. Nek5000 is an open-source, highly scalable and portable code based on the spectral element method (SEM) [4], which offers minimal dissipation and dispersion, high accuracy and exponential convergence. It is aimed at solving direct and large-eddy simulations of turbulent incompressible or low Mach-number flows with heat transfer and species transport. The approach chosen for adapting the mesh is the h-refinement method, where elements are split locally, which requires the relaxation of the conforming grid constraint currently imposed by Nek5000. Other challenges include the implementation of an efficient management of the grid as refinement is applied, the development of tools to localize the critical flow regions via error estimators and the extension of the current preconditioning strategy to non-conforming grids. In this paper, we present a new procedure to setup an algebraic multigrid solver used as part of the preconditioner for the pressure equation.

Offermans, N.↗
DOE OSTI2023

Revisiting the refined Distance Conjecture

The Distance Conjecture of Ooguri and Vafa holds that any infinite-distance limit in the moduli space of a quantum gravity theory must be accompanied by a tower of exponentially light particles, which places tight constraints on the low-energy effective field theories in these limits. One attempt to extend these constraints to the interior of moduli space is the refined Distance Conjecture, which holds that the towers of light particles predicted by the Distance Conjecture must appear any time a modulus makes a super-Planckian excursion in moduli space. In this note, however, we point out that a tower which satisfies the Distance Conjecture in an infinite-distance limit of moduli space may be parametrically heavier than the Planck scale for an arbitrarily long geodesic distance. This means that the refined Distance Conjecture, in its most naive form, does not place meaningful constraints on low-energy effective field theory. This motivates alternative refinements of the Distance Conjecture, which place an absolute upper bound on the tower mass scale in the interior of moduli space. We explore two possibilities, providing evidence for them and briefly discussing their implications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Adaptive mesh refinement for steady flows in Nek5000

Adaptive mesh refinement is performed in the framework of the spectral element method augmented by approaches to error estimation and control. The h-refinement technique is used for adapting the mesh, where selected grid elements are split by a quadtree (2D) or octree (3D) structure. Continuity between parent-child elements is enforced by high-order interpolation of the solution across the common faces. Parallel mesh partitioning and grid management respectively, are taken care of by the external libraries ParMETIS and p4est. Two methods are considered for estimating and controlling the error of the solution. The first error estimate is local and based on the spectral properties of the solution on each element. This method gives a local measure of the L-2-norm of the solution over the entire computational domain. The second error estimate uses the dual-weighted residuals method - it is based on and takes into account both the local properties of the solution and the global dependence of the error in the solution via an adjoint problem. The objective of this second approach is to optimize the computation of a given functional of physical interest. The simulations are performed by using the code Nek5000 and three steady-state test cases are studied: a two-dimensional lid-driven cavity at Re = 7, 500, a two-dimensional flow past a cylinder at Re = 40, and a three-dimensional lid-driven cavity at Re = 2,000 with a moving lid tilted by an angle of 30 degrees. Finally, the efficiency of both error estimators is compared in terms of refinement patterns and accuracy on the functional of interest. In the case of the adjoint error estimators, the trend on the error of the functional is shown to be correctly represented up to a multiplicative constant.

42 ENGINEERING↗
DOE OSTI2017

Highly Efficient Training, Refinement, and Validation of a Knowledge-based Planning Quality-Control System for Radiation Therapy Clinical Trials

Purpose: To demonstrate an efficient method for training and validation of a knowledge-based planning (KBP) system as a radiation therapy clinical trial plan quality-control system. Methods and Materials: We analyzed 86 patients with stage IB through IVA cervical cancer treated with intensity modulated radiation therapy at 2 institutions according to the standards of the INTERTECC (International Evaluation of Radiotherapy Technology Effectiveness in Cervical Cancer, National Clinical Trials Network identifier: 01554397) protocol. The protocol used a planning target volume and 2 primary organs at risk: pelvic bone marrow (PBM) and bowel. Secondary organs at risk were rectum and bladder. Initial unfiltered dose-volume histogram (DVH) estimation models were trained using all 86 plans. Refined training sets were created by removing sub-optimal plans from the unfiltered sample, and DVH estimation models… and DVH estimation models were constructed by identifying 30 of 86 plans emphasizing PBM sparing (comparing protocol-specified dosimetric cutpoints V{sub 10} (percentage volume of PBM receiving at least 10 Gy dose) and V{sub 20} (percentage volume of PBM receiving at least 20 Gy dose) with unfiltered predictions) and another 30 of 86 plans emphasizing bowel sparing (comparing V{sub 40} (absolute volume of bowel receiving at least 40 Gy dose) and V{sub 45} (absolute volume of bowel receiving at least 45 Gy dose), 9 in common with the PBM set). To obtain deliverable KBP plans, refined models must inform patient-specific optimization objectives and/or priorities (an auto-planning “routine”). Four candidate routines emphasizing different tradeoffs were composed, and a script was developed to automatically re-plan multiple patients with each routine. After selection of the routine that best met protocol objectives in the 51-patient training sample (KBP{sub FINAL}), protocol-specific DVH metrics and normal tissue complication probability were compared for original versus KBP{sub FINAL} plans across the 35-patient validation set. Paired t tests were used to test differences between planning sets. Results: KBP{sub FINAL} plans outperformed manual planning across the validation set in all protocol-specific DVH cutpoints. The mean normal tissue complication probability for gastrointestinal toxicity was lower for KBP{sub FINAL} versus validation-set plans (48.7% vs 53.8%, P<.001). Similarly, the estimated mean white blood cell count nadir was higher (2.77 vs 2.49 k/mL, P<.001) with KBP{sub FINAL} plans, indicating lowered probability of hematologic toxicity. Conclusions: This work demonstrates that a KBP system can be efficiently trained and refined for use in radiation therapy clinical trials with minimal effort. This patient-specific plan quality control resulted in improvements on protocol-specific dosimetric endpoints.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Rietveld refinement and ionic conductivity of Ca{sub 8.4}Bi{sub 1.6}(PO{sub 4}){sub 6}O{sub 1.8}

The structure of Ca{sub 8.4}Bi{sub 1.6}(PO{sub 4}){sub 6}O{sub 1.8}, isostructural with Fluoroapatite, was determined by X-ray powder diffraction methods. The results of Rietveld refinement revealed that the formula of this compound is [Ca{sub 4}]{sup 4f}[Ca{sub 4.4}Bi{sub 1.6}]{sup 6h}(PO{sub 4}){sub 6}[O{sub 1.8}]{sup 2a}, space group P63/m (a=9.468 (3) A, c=6.957 (3) A). A total substitution of Bi{sup 3+} ions in the (6h) sites was related particularly to the high polarizability of the Bi{sup 3+} ion compared to Ca{sup 2+}. The observed frequencies in the Raman and infrared spectra were explained and discussed on the basis of unit-cell group analyses and in comparison with Fluoroapatite and other oxyapatites. The ionic conductivity over a wide range of temperature was investigated according to the complex impedance method. The highest overall conductivity values were found at {sigma}{sub 700 Degree-Sign C} =5.03 Multiplication-Sign 10{sup -7} S cm{sup -1} and E{sub a}=0.50 eV. - Graphical abstract: The final Rietveld refinement plot of the Ca{sub 8.4}Bi{sub 1.6} (PO{sub 4}){sub 6}O{sub 1.8}. Highlights: Black-Right-Pointing-Pointer The Rietveld refinement revealed that the formula of this compound is Ca{sub 8.4}Bi{sub 1.6}(PO{sub 4}){sub 6}O{sub 1.8}. Black-Right-Pointing-Pointer Vibrational spectroscopy supports the high symmetry P63/m space group for this apatite. Black-Right-Pointing-Pointer This apatite contained channels where oxygen ions were located in 2a sites. Black-Right-Pointing-Pointer The possibility of anionic conduction along these channels was considered.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Structural studies of TiC{sub 1−x}O{sub x} solid solution by Rietveld refinement and first-principles calculations

The lattice parameters, structural stability and electronic structure of titanium oxycarbides (TiC{sub 1−x}O{sub x}, 0≤x≤1) solid solution were investigated by Rietveld refinement and first-principles calculations. Series of TiC{sub 1−x}O{sub x} were precisely synthesized by sintering process under the vacuum. Rietveld refinement results of XRD patterns show the properties of continuous solid solution in TiC{sub 1−x}O{sub x} over the whole composition range. The lattice parameters vary from 0.4324 nm to 0.4194 nm decreasing with increasing oxygen concentration. Results of first-principles calculations reveal that the disorder C/O structure is stable than the order C/O structure. Further investigations of the vacancy in Ti{sub 1−Va}(C{sub 1−x}O{sub x}){sub 1−Va} solid solution present that the structure of vacancy segregated in TiO-part is more stable than the disorder C/O structure, which can be ascribed to the Ti–Ti bond across O-vacancy and the charge redistributed around Ti-vacancy via the analysis of the electron density difference plots and PDOS. - Graphical abstract: XRD of series of titanium oxycarbides (TiC{sub 1−x}O{sub x}, 0≤x≤1) solid solution prepared by adjusting the proportion of TiO in the starting material. Highlights: • Titanium oxycarbides were obtained by sintering TiO and TiC under carefully controlled conditions. • Rietveld refinement results show continuous solid solution with FCC structure in TiC{sub 1−x}O{sub x}. • The disorder C/O structure is stable than the order C/O structure. • Introduction of vacancy segregated in TiO-part is more stable than disorder C/O structure. • Ti–Ti bond across O-vacancy and the charge redistributed around Ti-vacancy enhance structural stability.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Synthesis, structure refinement and chromate sorption characteristics of an Al-rich bayerite-based layered double hydroxide

“Imbibition” of Zn{sup 2+} ions into the cation vacancies of bayerite–Al(OH){sub 3} and NO{sub 3}{sup −} ions into the interlayer gallery yields an Al-rich layered double hydroxide with Al/Zn ratio ∼3. NO{sub 3}{sup −} ions are intercalated with their molecular planes inclined at an angle to the plane of the metal hydroxide slab and bonded to it by hydrogen bonds. Rietveld refinement of the structure shows that the monoclinic symmetry of the precursor bayerite is preserved in the product, showing that the imbibition is topochemical in nature. The nitrate ion is labile and is quantitatively replaced by CrO{sub 4}{sup 2−} ions from solution. The uptake of CrO{sub 4}{sup 2−} ions follows a Langmuir adsorption isotherm, thus showing that the hydroxide is a candidate material for green chemistry applications for the removal of CrO{sub 4}{sup 2−} ions from waste water. Rietveld refinement of the structure of the hydroxide after CrO{sub 4}{sup 2−} inclusion reveals that the CrO{sub 4}{sup 2−} ion is intercalated with one of its 2-fold axes parallel to the b-crystallographic axis of the crystal, also the principal 2 axis of the monoclinic cell. - Graphical abstract: The structure of the [Zn–Al4-nitrate] LDH viewed along the a-axis. - Highlights: • Synthesis of Al-rich layered double hydroxide with Al/Zn ratio ∼3. • Rietveld refinement indicates that the imbibition of Zn into Al(OH){sub 3} is topochemical in nature. • The uptake of CrO{sub 4}{sup 2−} ions follows a Langmuir adsorption isotherm.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

In situ synchrotron X-ray diffraction analysis of ultrasonically assisted microstructure refinement during laser melting process

This work investigates the effect of ultrasonic treatment (UST) on the microstructure of AA4043 alloy during laser melting process. Here, the study utilizes in situ synchrotron X-ray diffraction (SXRD) and postmortem electron backscatter diffraction (EBSD) techniques to examine the ultrasonic grain refinement mechanism. The SXRD diffraction patterns exhibit higher continuity of major diffraction rings in the UST-test pattern, indicating a more refined grain structure. The presence of new diffraction spots in the post-test diffraction pattern with UST suggests the breakdown of epitaxial growth of columnar dendrites during solidification. Thermal profiles determined by analyzing the lattice parameter evolution show a faster cooling rate with UST. The inverse pole figures and aspect ratio distribution from EBSD reveal that the UST samples exhibit a refined, more equiaxed grain structure along the weld centerline. UST sample also develops more fine-sized low angle grain boundaries (LAGBs). These features offer better hot-cracking resistance in aluminum alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Dara: Automated Multiple-Hypothesis Phase Identification and Refinement from Powder X-ray Diffraction

Powder X-ray diffraction (XRD) is a foundational technique for characterizing crystalline materials. However, the reliable interpretation of XRD patterns, particularly in multiphase systems, remains a manual and expertise-demanding task. As a characterization method that only provides structural information, multiple reference phases can often be fit to a single pattern, leading to potential misinterpretation when alternative solutions are overlooked. To ease humans’ efforts and address the challenge, we introduce Dara (data-driven automated Rietveld analysis), a framework designed to automate the robust identification and refinement of multiple phases from powder XRD data. Dara performs an exhaustive tree search over all plausible phase combinations within a given chemical space and validates each hypothesis using the BGMN Rietveld refinement routine. Key features include structural database filtering, automatic clustering of isostructural phases during tree expansion, and peak-matching-based scoring to identify promising phases for refinement. When ambiguity exists, Dara generates multiple hypothesis which can then be decided between by human experts or with further characterization tools. By enhancing the reliability and accuracy of phase identification, Dara enables scalable analysis of realistic complex XRD patterns and provides a foundation for integration into multimodal characterization workflows, moving toward fully self-driving materials discovery.

Biological databases↗
DOE OSTI2020

Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures

The first important step in a structure-based virtual screening is the judicious selection of a receptor protein. In cases where the holo protein receptor structure is unavailable, significant reduction in virtual screening performance has been reported. In this work, we present a robust method to generate reliable holo protein structure conformations from apo structures using molecular dynamics (MD) simulation with restraints derived from holo structure binding-site templates. We perform benchmark tests on two different datasets: 40 structures from a directory of useful decoy-enhanced (DUD-E) and 84 structures from the Gunasekaran dataset. Our results show successful refinement of apo binding-site structures toward holo conformations in 82% of the test cases. In addition, virtual screening performance of 40 DUD-E structures is significantly improved using our MD-refined structures as receptors with an average enrichment factor (EF), an EF1% value of 6.2 compared to apo structures with 3.5. Docking of native ligands to the refined structures shows an average ligand root mean square deviation (RMSD) of 1.97 Å (DUD-E dataset and Gunasekaran dataset) relative to ligands in the holo crystal structures, which is comparable to the self-docking (i.e., docking of the native ligand back to its crystal structure receptor) average, 1.34 Å (DUD-E dataset) and 1.36 Å (Gunasekaran dataset). On the other hand, docking to the apo structures yields an average ligand RMSD of 3.65 Å (DUD-E) and 2.90 Å (Gunasekaran). These results indicate that our method is robust and can be useful to improve virtual screening performance of apo structures.

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

AQuaRef: machine learning accelerated quantum refinement of protein structures

Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical data, which, in addition to being limited to known chemical entities, do not include meaningful noncovalent interactions. Quantum mechanical (QM) calculations could alleviate these issues but are too expensive for large molecules. Here we present a novel AI-enabled Quantum Refinement (AQuaRef) based on AIMNet2 machine learned interatomic potential (MLIP) mimicking QM at substantially lower computational costs. By refining 41 cryo-EM and 30 X-ray structures, we show that this approach yields atomic models with superior geometric quality compared to standard techniques, while maintaining an equal or better fit to experimental data. Notably, AQuaRef aids in determining proton positions, as illustrated in the challenging case of short hydrogen bonds in the parkinsonism-associated human protein DJ-1 and its bacterial homolog YajL.

Zubatyuk, Roman [Carnegie Mellon University, Pitts↗