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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis

Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restrains for non-protein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in Chlorophyll (Chl) proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C 2 symmetry of Photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and Cryogenic electron microscopy (CryoEM) PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restrains play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested, from cyanobacteria to algae. Furthermore, these results highlight both the opportunities and limitations inherent in the structure-based analysis of the bioenergetic and optical properties of CPs and other protein-ligand complexes.

14 SOLAR ENERGY↗
DOE OSTI2023

Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge

Elucidating protein–ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein–ligand interaction is traditionally tackled by molecular docking and simulation, which is based on physical forces and statistical potentials and cannot effectively leverage cryo-EM data and existing protein structural information in the protein–ligand modeling process. In this work, we developed a deep learning bioinformatics pipeline (DeepProLigand) to predict protein–ligand interactions from cryo-EM density maps of proteins and ligands. DeepProLigand first uses a deep learning method to predict the structure of proteins from cryo-EM maps, which is averaged with a reference (template) structure of the proteins to produce a combined structure to add ligands. The ligands are then identified and added into the structure to generate a protein–ligand complex structure, which is further refined. The method based on the deep learning prediction and template-based modeling was blindly tested in the 2021 EMDataResource Ligand Challenge and was ranked first in fitting ligands to cryo-EM density maps. These results demonstrate that the deep learning bioinformatics approach is a promising direction for modeling protein–ligand interactions on cryo-EM data using prior structural information.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Benchmarking structural evolution methods for training of machine learned interatomic potentials

When creating training data for machine-learned interatomic potentials (MLIPs), it is common to create initial structures and evolve them using molecular dynamics (MD) to sample a larger configuration space. Here, we benchmark two other modalities of evolving structures, contour exploration (CE) and dimer-method (DM) searches against MD for their ability to produce diverse and robust density functional theory training data sets for MLIPs. We also discuss the generation of initial structures which are either from known structures or from random structures in detail to further formalize the structure-sourcing processes in the future. The polymorph-rich zirconium-oxygen composition space is used as a rigorous benchmark system for comparing the performance of MLIPs trained on structures generated from these structural evolution methods. Using Behler–Parrinello neural networks as our MLIP models, we find that CE and the DM searches are generally superior to MD in terms of spatial descriptor diversity and statistical accuracy.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Structural constraint integration in a generative model for the discovery of quantum materials

Billions of organic molecules have been computationally generated, yet functional inorganic materials remain scarce due to limited data and structural complexity. Here, in this work, we introduce Structural Constraint Integration in a GENerative model (SCIGEN), a framework that enforces geometric constraints, such as honeycomb and kagome lattices, within diffusion-based generative models to discover stable quantum materials candidates. SCIGEN enables conditional sampling from the original distribution, preserving output validity while guiding structural motifs. This approach generates ten million inorganic compounds with Archimedean and Lieb lattices, over 10% of which pass multistage stability screening. High-throughput density functional theory calculations on 26,000 candidates shows over 95% convergence and 53% structural stability. A graph neural network classifier detects magnetic ordering in 41% of relaxed structures. Furthermore, we synthesize and characterize two predicted materials, TiPd 0.22 Bi 0.88 and Ti 0.5 Pd 1.5 Sb, which display paramagnetic and diamagnetic behaviour, respectively. Our results indicate that SCIGEN provides a scalable path for generating quantum materials guided by lattice geometry.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Contributions to Lignomics: Stochastic Generation of Oligomeric Lignin Structures for Interpretation of MALDI–FT‐ICR‐MS Results

The lack of standards to identify oligomeric molecules is a challenge for the analysis of complex organic mixtures. High-resolution mass spectrometry—specifically, Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS)—offers new opportunities for analysis of oligomers with the assignment of formulae (C x H y O z ) to detected peaks. However, matching a specific structure to a given formula remains a challenge due to the inability of FT-ICR MS to distinguish between isomers. Additional separation techniques and other analyses (e.g., NMR spectroscopy) coupled with comparison of results to those from pure compounds is one route for assignment of MS peaks. Unfortunately, this strategy may be impractical for complete analysis of complex, heterogeneous samples. In this study we use computational stochastic generation of lignin oligomers to generate a molecular library for supporting the assignment of potential candidate structures to compounds detected during FT-ICR MS analysis. Furthermore, this approach may also be feasible for other macromolecules beyond lignin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Effects of Al:Si and (Al+Na):Si Ratios on the Properties of the International Simple Glass, Part II: Structure

High-alumina containing high-level waste (HLW) will be vitrified at the Waste Treatment Plant at the Hanford Site. The resulting glasses, high in alumina, will have distinct composition-structure-property (C-S-P) relationships compared to previously studied HLW glasses. These C-S-P relationships determine the processability and product durability of glasses and therefore must be understood. The main purpose of this study is to understand the detailed structural changes caused by Al:Si and (Al+Na):Si substitutions in a simplified nuclear waste model glass (ISG, International Simple Glass) by combining experimental structural characterizations and molecular dynamics (MD) simulations. The structures of these two series of glasses were characterized by neutron total scattering and 27Al, 23Na, 29Si, and 11B solid-state nuclear magnetic resonance (NMR) spectroscopy. Additionally, MD simulations were used to generate atomistic structural models of the borosilicate glasses and simulation results were validated by the experimental structural data. Short-range (e.g., bond distance, coordination number, etc.) and medium-range (e.g., oxygen speciation, network connectivity, polyhedral linkages) structural features of the borosilicate glasses were systematically investigated as a function of the degree of substitution. The results show that bond distance and coordination number of the cation-oxygen pairs are relatively insensitive to Al:Si and (Al+Na):Si substitutions with the exception of the B-O pair. Additionally, the Al:Si substitution results in an increase of tri-bridging oxygen species, while (Al+Na):Si substitution creates non-bridging oxygen species. Charge compensator preferences were found for Si-[NBO] (Na+), [3]B-[NBO] (Na+), [4]B (mostly Ca2+), [4]Al (nearly equally split Na+ and Ca2+), and [6]Zr (mostly Ca2+). The network former-BO-network former linkages preferences were also tabulated; Si-O-Al and Al-O-Al were preferred at the expense of lower Si-O-[3]B and [3]B-O-[3]B linkages. These results provide insights on the structural origins of property changes such as glass transition temperature caused by the substitutions, providing a basis for future improvements of theoretical and computer simulation models.

Lu, Xiaonan↗
DOE OSTI2026

Crystal generation using the fully differentiable pipeline and latent space optimization

We present a materials generation framework that couples a symmetry-conditioned variational autoencoder with a differentiable SO(3) power spectrum objective to steer candidates toward a specified local environment under the crystallographic constraints. In particular, we implement a fully differentiable pipeline that performs batch-wise optimization on both direct and latent crystallographic representations. Using the GPU acceleration, the implementation achieves about fivefold speed compared to our previous CPU workflow, while yielding comparable outcomes. In addition, we introduce the optimization strategy that alternatively performs optimization on the direct and latent crystal representations. This dual-level relaxation approach can effectively escape local minima defined by different objective gradients, thus increasing the success rate of generating complex structures satisfying the target local environments. This framework can be extended to systems consisting of multi-components and multi-environments, providing a scalable route to generate material structures with the target local environment.

conditional VAE↗
DOE OSTI2022

AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome

Intrinsically disordered proteins/regions (IDPRs) are a very large and functionally important class of proteins that participate in weak multivalent interactions in protein complexes. They are recalcitrant for interrogations using X-ray crystallography and cryo-EM. The IDPRs observed at the interface of the photosynthetic pigment protein complexes (PPCs) remain much less clear, e.g., the major cyanobacterial light-harvesting complex (PBS) contains an unstructured PB-loop insertion in the phycocyanobilin domain (PB domain) of ApcE (the largest polypeptide in PBS). Here, a joint platform is built to probe such structural domains. This platform is characterized by two-round progressive justifications of in silico models by using the structural mass spectrometry data. First, the AlphaFold-generated 3D structure of the PB domain (containing PB-loop) was justified in the context of PBS. Second, docking the AlphaFold-generated ApcG (a ligand) into the first-step justified structure (a receptor). The final ligand-receptor complex was then subjected to a second-round justification, again, by using unequivocal isotopically-encoded cross-links identified in LC-MS/MS. This work reveals a full-length PB-loop structure modelled in the PBS basal cylinder, free from any spatial conflicts against the other subunits in PBS. The structure of PB domain highlights the close associations of the intrinsically disordered PB-loop with its binding partners in PBS, including ApcG, another IDPR. The PB-loop region involved in the binding of photosystem II (PSII) is also discussed in the context of excitation energy transfer regulation. Finally, this work calls attention to the highly disordered, yet interrogatable interface between the light-harvesting antenna complexes and the reaction centers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Quadrupolar NMR crystallography guided crystal structure prediction (QNMRX-CSP) of zwitterionic organic HCl salts

In this work, we benchmark quadrupolar NMR crystallography guided crystal structure prediction (QNMRX-CSP) for determining the crystal structures of two zwitterionic organic HCl salts, L-ornithine HCl ( Orn ) and L-histidine HCl·H 2 O ( Hist ). These salts present an interesting challenge for QNMRX-CSP, as gas-phase geometry optimizations used to generate starting structures for the organic zwitterionic fragments fail to capture their correct solid-state geometries. To overcome this limitation, geometry optimizations using the COSMO water-solvation model are employed to generate initial structural models. Using this approach, QNMRX-CSP yields structural models of the two zwitterionic organic HCl salts that closely match experimentally determined crystal structures. In addition, the application of QNMRX-CSP to Hist represents a further step toward the de novo structural determination of solvated organic HCl salts, as Hist is the first benchmark system of this type to include a water molecule as a component of its crystal structure. This work is significant for its potential application to the structural determination of active pharmaceutical ingredients, which often feature complex organic components and solvated solid forms.

Fleischer, Carl H. [Florida State Univ., Tallahass↗
DOE OSTI2020

Multiobjective and categorical global optimization of photonic structures based on ResNet generative neural networks

Abstract We show that deep generative neural networks, based on global optimization networks (GLOnets), can be configured to perform the multiobjective and categorical global optimization of photonic devices. A residual network scheme enables GLOnets to evolve from a deep architecture, which is required to properly search the full design space early in the optimization process, to a shallow network that generates a narrow distribution of globally optimal devices. As a proof-of-concept demonstration, we adapt our method to design thin-film stacks consisting of multiple material types. Benchmarks with known globally optimized antireflection structures indicate that GLOnets can find the global optimum with orders of magnitude faster speeds compared to conventional algorithms. We also demonstrate the utility of our method in complex design tasks with its application to incandescent light filters. These results indicate that advanced concepts in deep learning can push the capabilities of inverse design algorithms for photonics.

Jiang, Jiaqi↗
DOE OSTI2025

GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability

Aptamers are oligonucleotide receptors that bind to their targets with high affinity. Here, we consider aptamers comprised of single-stranded DNA that undergo target-binding-induced conformational changes, giving rise to unique secondary and tertiary structures. Given a specific aptamer primary sequence, there are well-established computational tools (notably mfold) to predict the secondary structure via free energy minimization algorithms. While mfold generates secondary structures for individual sequences, there is a need for a high-throughput process whereby thousands of DNA structures can be predicted in real-time for use in an interactive setting, when combined with aptamer selections that generate candidate pools that are too large to be experimentally interrogated. We developed a new Python code for high-throughput aptamer secondary structure determination (GMfold). GMfold uses subgraph matching methods to group aptamer candidates by secondary structure similarities. We also improve an open-source code, SeqFold, to incorporate subgraph matching concepts. We represent each secondary structure as a lowest-energy bipartite subgraph matching of the DNA graph to itself. These new tools enable thousands of DNA sequences to be compared based on their secondary structures, using machine-learning algorithms. This process is advantageous when analyzing sequences that arise from aptamer selections via systematic evolution of ligands by exponential enrichment (SELEX). This work is a building block for future machine-learning-informed DNA-aptamer selection processes to identify aptamers with improved target affinity and selectivity and advance aptamer biosensors and therapeutics.

Aptamer↗
DOE OSTI2025

AI-Assisted Conceptual Development of a Pre-Geometric Cosmological Model - An Exercise in AI-Assisted Conceptual Framework Generation, Paper III: Cosmological Structure and Predictions

This paper develops the cosmological consequences of the replication-driven cosmogenesis framework introduced in Paper I and the emergent geometric structure established in Paper II. After the replication epoch freezes out, the coherent sector occupies a finite spectral band and contains a population of excited states. The relaxation of these excited coherent configurations does not produce coherent radiation; instead, all released energy flows into the incoherent substrate, where the randomizer acts as a rapid phase-scrambling mechanism. This process generates an effectively thermal radiation bath, providing a natural reheating mechanism that requires neither inflaton oscillations nor scalar-field potentials, and can be contrasted with standard scenarios of nonperturbative reheating dynamics. Subsequent symmetry-breaking transitions in the coherent vacuum inject additional radiation, yielding a multi-stage thermal history with well-defined energy transfers. We derive the effective equations of state for each component—the cosmological vacuum, the coherent vacuum, and the radiation bath—and show how their interplay produces an FRW-like expansion. The discrete sequence of coherent-state relaxations imprints a distinctive multi-peaked stochastic gravitational-wave background, whose spectral structure reflects the underlying hierarchy of coherent frequencies. Potential observational signatures in the LISA and mid-band frequency ranges are highlighted, providing concrete avenues to test this replication-based cosmological framework in the context of standard cosmological gravitational-wave backgrounds and LISA-oriented forecasts.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

AlphaFold -assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography

Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.

molecular replacement↗
DOE OSTI2023

Optically controlled single-valley exciton doublet states with tunable internal spin structures and spin magnetization generation

Manipulating quantum states through light–matter interactions has been actively pursued in two-dimensional materials research. Significant progress has been made toward the optical control of the valley degrees of freedom in semiconducting monolayer transition-metal dichalcogenides, based on doubly degenerate excitons from their two distinct valleys in reciprocal space. Here, we introduce a type of optically controllable doubly degenerate exciton states that come from a single valley, dubbed as single-valley exciton doublet (SVXD) states. They are unique in that their constituent holes originate from the same valence band, making possible the direct optical control of the spin structure of the excited constituent electrons. Combining ab initio GW plus Bethe–Salpeter equation ( GW -BSE) calculations and a theoretical analysis method, we demonstrate such SVXD in substrate-supported monolayer bismuthene—which has been successfully grown using molecular beam epitaxy. In each of the two distinct valleys in the Brillouin zone, strong spin–orbit coupling and C 3 v symmetry lead to a pair of degenerate 1s exciton states (the SVXD states) with opposite spin configurations. Any coherent linear combinations of the SVXD in a single valley can be excited by light with a specific polarization, enabling full manipulation of their internal spin configurations. In particular, a controllable net spin magnetization can be generated through light excitation. Our findings open routes to control quantum degrees of freedom, paving the way for applications in spintronics and quantum information science.

2D materials↗
DOE OSTI2024

Electron-impact excitation data for W 2+ in support of tungsten spectroscopy and re-deposition measurements for magnetically-confined plasmas

Abstract To better understand plasma wall interactions involving tungsten, accurate atomic structure and electron-impact driven collisional processes for near-neutral ion stages of tungsten are required. Complementing existing work on neutral and singly ionised tungsten, atomic structure and collisional calculations for W 2+ electron-impact excitation have been completed. These excitation calculations are an important component of S/XB coefficients for near-neutral charge states, which may be used to spectroscopically infer re-deposition of tungsten at the plasma-solid boundary of fusion relevant devices. With W 2+ in particular having emission lines that can be observed at ultraviolet (UV) wavelengths, while higher charge states of tungsten are unlikely to have lines possible to observe outside of the vacuum UV range. The atomic structure was generated using the General-purpose Relativistic Atomic Structure Package (GRASP 0 ), implementing the Multi-configuration Dirac Fock approach. This structure was the basis for a subsequent Dirac R -matrix electron-impact excitation calculation to provide Maxwellian averaged rate coefficients. A synthetic spectrum was generated from this data using a collisional-radiative model to predict the strongest W III spectral lines and these lines were compared to emission from the Compact Toroidal Hybrid (CTH) plasma device. Several of the strongest W III lines are observed in CTH and agree well with the modelled line wavelengths and intensities, a table of these lines is provided that could be observed in other devices.

McCann, M. (ORCID:0000000215321240)↗
DOE OSTI2024

Studying Wind Loading on CSP Collectors to Improve Performance and Reliability

Electricity generation through Concentrating Solar-thermal Power (CSP) adds the advantage of thermal energy storage and heat production. CSP collector costs constitute nearly one-third of total plant costs. Managing wind loading, especially dynamic wind loading caused by the turbulent wind flow, is a significant design challenge. Traditional collector designs rely on wind tunnel experiments and numerical simulations, which do not fully capture dynamic effects. Here, we provide an overview of NREL's activities on wind loading on CSP collectors, aiming to improve their reliability and cost-efficiency. We present insights from field measurements at operational parabolic trough and power-tower CSP plants. Over two years, we measured turbulent wind fields and resulting structural loads in a parabolic trough plant, revealing wind, turbulence, and collector field interactions. Similar measurements are ongoing at the Crescent Dunes heliostat field. These campaigns show how atmospheric turbulence, wind direction, and collector orientation affect dynamic wind loading. Upwind collector structures can generate turbulent structures, causing fluctuating loads at downstream collectors, impacting fatigue lifetime and optical efficiency. Preliminary results indicate that interior collectors experience higher turning moments than those at the edges, suggesting higher drive wear. At Crescent Dunes, we use instrumented heliostats at the field's edge and interior to study the translation of turbulent wind to dynamic structural loads. The campaign is still ongoing, and we will present first findings. Another focus of our work is tying the experimental wind loading findings to optical performance of the collectors, using simulation tools. For example, we derive torsional errors of the parabolic troughs - the angular offset from the sun position along a collector row. This error is impacted by wind-induced mirror deformations. Future work will focus on continuing the measurement efforts and combining them with computational fluid dynamic simulations. By providing detailed field measurements and validated models, our efforts aim to enhance understanding of wind loading on CSP collectors, improving their structural integrity and optical performance.

CSP↗
DOE OSTI2026

Ionic Precursors Transformed Into Vinyl Acetate Synthesis Catalyst via Reaction-Driven Restructuring

Conventional preparation of supported bimetallic catalysts relies on solution-mediated metal salt immobilization and pre-formation of alloy nanoparticles before reaction. Here, we report a fundamentally different synthesis strategy of using a physical mixture of salt precursors to generate an active catalyst during reaction. The catalytic structure is generated in situ from Pd3(OAc)6, Au(OH)3, and KOAc through H2 treatment and reaction-driven restructuring under vinyl acetate monomer (VAM) synthesis conditions. Ascertained from in situ X-ray diffraction and operando infrared spectroscopy analyses, reduction treatment produces segregated Pd and Au domains, and subsequent exposure to a VAM reaction mixture triggers dynamic extraction of Pd from the metal surface. This latter process, mediated by acetate-assisted redox cycles, facilitates Pd migration toward Au domains to form a near-surface localized Pd50Au50 alloy phase. Monometallic Pd domains serve as a reservoir of Pd to the alloy phase, leading to and sustaining a more Pd-enriched active surface and a higher population of accessible Pd sites, compared to a conventionally prepared K-PdAu/SiO2 catalyst. Consequently, this leads to a twofold increase in the VAM formation rate, demonstrating highly active bimetallic catalysts can be generated through the gas-phase treatment of physically mixed ionic precursors.

Cha, Byeong Jun [Rice University]↗
DOE OSTI2021

A theoretical calculation of stacking fault energy of Ni alloys: The effects of temperature and composition

Combining cluster expansion (CE) method with one dimensional axial Ising model, this work investigated the effects of alloying elements and configurational variations due to temperature on the stacking fault energy (SFE) of FCC Ni binary alloys. Ensembles of large numbers of atomistic structures, each with more than ~400 atoms, were generated to consider sufficient long-range chemical disorder and temperature effects due to configurational entropy. Here, a Monte Carlo Metropolis algorithm was used to generate these structures, whose energies were then evaluated based on the effective cluster interactions obtained from CE. As a baseline, this work had shown the SFE of pure Ni and Al to be 127 mJ/m 2 and 137 mJ/m 2 , respectively, which agreed with the experimental values of 125 mJ/m 2 and 150 mJ/m 2 reported in the literature. Additions of Al, Ti, Cr and Co to pure Ni were found to decrease the SFE to different extents. Although temperature does not strongly influence the SFE of the FCC Ni-Al and Ni-Cr binary alloys, it can lead to significant changes to the SFE of the FCC Ni-Ti and Ni-Co alloys. While effects of temperature and composition on SFE observed in this work were calculated from binary Ni alloys, the general trends are nonetheless expected to be valid in the γ phase of multicomponent Ni superalloys.

36 MATERIALS SCIENCE↗