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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Deconvoluting Structures of Component Plant Biopolymers Using Deuterium Labeled Brassica oleracea Stems

Several Brassica species are cultivated globally for the production of seed oils as food, lubricants, and increasingly biofuels. The stem and leaf residues of these herbaceous dicotyledonous crops constitute another feedstock for biofuels and other products. Plant cell walls are complex, multipolymeric structures that consist primarily of polysaccharides and lignin. Cellulose chains coalesce to form crystalline microfibrils while the amorphous biopolymers, hemicellulose, and lignin form a network structure and fill the interstitial space. Neutron scattering has been used for the structural study of the assembly and deconstruction of the plant cell walls. However, similar neutron sensitivity of the different amorphous biopolymers has made structural association to individual component biopolymers nontrivial and ambiguous. To improve the association of structural features to specific biopolymer components, partial deuteration of the plant cell wall can be employed to increase the difference in the neutron scattering length density between amorphous carbohydrate and lignin plant polymers. Vegetative stems from partially deuterated Brassica oleracea acephala (kale) plants were obtained commercially, and the plant cell wall structures were studied by contrast-variation small-angle neutron scattering (CV-SANS) and Fourier-transform infrared spectroscopy (FTIR). FTIR results indicated that deuterium substitution for hydrogen in the carbohydrates was higher than that in lignin. By combining CV-SANS and FTIR results, the neutron scattering length density (nSLD) of the polysaccharides and lignin was determined to match nSLD of 65%:35% and 48%:52% D 2 O/H 2 O solvent mixtures, respectively. These nSLD values were higher than the nSLD values of polysaccharides and lignin for H 2 O grown biopolymers. The nSLD increase correlates to replacing about 42.5% of hydrogens present as both C–H and O–H groups in cellulose with deuterium atoms, while only 21% for lignin. In conclusion, this study lays the foundation to use partially deuterated plants to deconvolute structural features of the different component biopolymers, especially cellulose, hemicellulose, and lignin, of the plant cell wall without introducing unintended structural modifications due to the pretreatment extraction processes.

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

Insights into the Structure–Activity Relationship in Aerobic Alcohol Oxidation over a Metal–Organic-Framework-Supported Molybdenum(VI) Catalyst

The understanding of structure–activity relationships at the atomic level has played a profound role in heterogeneous catalysis, providing valuable insights into designing suitable heterogeneous catalysts. However, uncovering the detailed roles of how such active species’ structures affect their catalytic performance remains a challenge owing to the lack of direct structural information on a specific active species. Herein, we deposited molybdenum(VI), an active species in oxidation reactions, on the Zr 6 node of a mesoporous zirconium-based metal–organic framework (MOF) NU-1200, using solvothermal deposition in MOFs (SIM). Due to the high crystallinity of the NU-1200 support, the precise structure of the resulting molybdenum catalyst, Mo-NU-1200, was characterized through single-crystal X-ray diffraction (SCXRD). Two distinct anchoring modes of the molybdenum species were observed: one mode (Mo1), displaying an octahedral geometry, coordinated to the node through one terminal oxygen atom and the other mode (Mo2) coordinated to two adjacent Zr 6 node oxygen atoms in a tetrahedral geometry. To investigate the role of base in the catalytic activity of these Mo centers, we assessed the activity of Mo-NU-1200 for the aerobic oxidation of 4-methoxybenzyl alcohol as a model reaction. The results revealed that Mo-NU-1200 exhibited remarkably higher catalytic reactivity under base-free conditions, while the presence of base inhibited the catalytic reactivity of this species. SCXRD studies revealed that the molybdenum binding motifs (structures of the supported metal on the Zr 6 node in the MOF) changed over the course of the reactions. Following the oxidation without base, both pristine coordination modes (Mo1 and Mo2) evolved into a new coordination mode (Mo3), in which the molybdenum atom coordinated to two adjacent oxygen atoms from the Zr 6 node in an octahedral geometry, while in the presence of base, the pristine Mo1 coordination mode evolved entirely into the pristine Mo2. Here, this study demonstrates the direct observation of an active species’ structural evolution from metal installation to subsequent catalytic reaction. As a result, these subtle structural changes in catalyst binding motifs led to distinct differences in catalytic activities, providing a compelling strategy for elucidating structure–activity relationships.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structural Asymmetry and Chiral-Induced Spin Selectivity in Chiral Palladium-Halide Semiconductors

Chiral Pb-free metal-halide semiconductors (MHSs) have attracted considerable attention in the field of spintronics due to various interesting spin-related properties and chiral-induced spin selectivity (CISS) effect. Despite their excellent chemical and structural tunability, the material scope and crystal structure of Pb-free chiral MHSs exhibiting the CISS effect are still limited; chiral MHSs that have metal-halide structures of octahedra and tetrahedra are only reported. Here, we report a new class of chiral MHSs, of which palladium (Pd)-halides are formed in 1D square-pyramidal structures or 0D square-planar structures, with a general formula of ((R/S-MBA) 2 PdBr 4 ) 1-x ((R/S-MBA) 2 PdCl 4 ) x (MBA = methylbenzylammonium; x = 0, 0.25, 0.5, 0.75, and 1) for the first time. The crystals adopt the 1D helical chain of Pd-halide square-pyramid (for x = 0, 0.25, 0.5, and 0.75) and 0D structure of Pd-halide square-plane (for x = 1). All the Pd-halides are distorted by the interaction between the halide and the chiral organic ammonium and arranged in a noncentrosymmetric position. Circular dichroism (CD) for ((R/S-MBA) 2 PdBr 4 ) 1-x ((R/S-MBA) 2 PdCl 4 ) x indicates that chirality was transferred from chiral organic ammonium to Pd-halide inorganics. ((R-MBA) 2 PdBr 4 ) 1-x ((R-MBA) 2 PdCl 4 ) x (x = 0, 0.25, 0.5, and 0.75) shows a distortion index of 0.127-0.128, which is the highest value among the previously reported chiral MHSs to the best of our knowledge. We also find that (R/S-MBA) 2 Pd(Br 1-x Cl x ) 4 crystals grow along the out-of-plane direction during spin coating and have high c-axis orientation and crystallinity, and (R/S-MBA) 2 Pd(Br 1-x Cl x ) 4 (x = 0 and 0.5) crystals exhibit a CISS effect in polycrystalline bulk films. In conclusion, these results demonstrate the possibility of a new metal-halide series with square-planar structures or square-pyramidal structures for future spintronic applications.

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

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning

The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.

Artificial intelligence↗
DOE OSTI2023

Universal and interpretable classification of atomistic structural transitions via unsupervised graph learning

Materials processing often occurs under extreme dynamic conditions leading to a multitude of unique structural environments. These structural environments generally occur at high temperatures and/or high pressures, often under non-equilibrium conditions, which results in drastic changes in the material's structure over time. Computational techniques, such as molecular dynamics simulations, can probe the atomic regime under these extreme conditions. However, characterizing the resulting diverse atomistic structures as a material undergoes extreme changes in its structure has proved challenging due to the inherently non-linear relationship between structures as large-scale changes occur. Here, we introduce SODAS++, a universal graph neural network framework, that can accurately and intuitively quantify the atomistic structural evolution corresponding to the transition between any two arbitrary phases. We showcase SODAS++ for both solid–solid and solid–liquid transitions for systems of increasing geometric and chemical complexity, such as colloidal systems, elemental Al, rutile and amorphous TiO 2 , and the non-stoichiometric ternary alloy Ag 26 Au 5 Cu 19 . Finally, we show that SODAS++ can accurately quantify all transitions in a physically interpretable manner, showcasing the power of unsupervised graph neural network encodings for capturing the complex and non-linear pathway, a material's structure takes as it evolves.

36 MATERIALS SCIENCE↗
DOE OSTI2024

An idealized model for the crystal structure of intermetallic compounds isostructural with Mg 3 Cr 2 Al 18

Mg 3 Cr 2 Al 18 (abbreviated in this report as MCA) is the parent phase for a large class of intermetallic compounds that belong to the cubic crystal space group, $Fd\overline{3}m$. The purpose of this paper is to introduce an ideal, unrelaxed crystal structure for compounds isostructural with MCA. There are five distinct atomic sublattices in MCA compounds, which can be denoted, $A, B, C, D,$ and $E$. With this, a general description for MCA structures can be written as $A^{8a}_{1}B^{16c}_{2}C^{16d}_{2}D^{48f}_{6}E^{96g}_{12}$, where the superscripts represent the Wyckoff special equipoints associated with the various sublattices in MCA, and the subscripts indicate the contributions of each sublattice to the stoichiometry of one formula unit in an any given MCA structured compound. Sublattices D and E are where deviations from ideality occur in real, MCA-like compounds. This paper examines MCA bond lengths, nearest-neighbour polyhedral arrangements, 3-D sublattice crystal structures, 2-D atom tessellation patterns, and crystal chemical effects associated with atomic relaxations on the $D$ and $E$ sublattices. The ideal MCA crystal structure developed in this report provides an appropriate initial structure for use as input to crystal structure refinements of diffraction data for MCA-like phases being examined experimentally, or as input for computational, atomistic simulations of the structures of such compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structural stability, elemental ordering, and transport properties of layered ScTaN 2

Ternary transition metal (TM) nitrides have gained significant attention in thin film research due to their promising properties for a broad range of applications. Particularly, some of the ternary TM nitrides have been predicted to adopt layered structures that make them interesting for thermoelectric conversion and quantum materials applications. Unfortunately, synthesis of TM ternary nitride films by physical vapor deposition often favors disordered 3D structures rather than the predicted 2D-like layered structure. In this study, we investigate the structural interplay in the Sc-Ta-N ternary system using a combinatorial approach. Combinatorial libraries S⁢c 𝑥 ⁢T⁢a 1−𝑥 ⁢N are synthesized following a two-step method: First, deposit film precursors by cosputtering and then process the resulting 3D-structured samples with rapid thermal annealing. Synchrotron grazing-incidence wide-angle x-ray scattering on films annealed at 1200 ⁢°⁢C for 20 min leads to the nucleation of ScTaN 2 layered structure (𝑃⁢6 3 /𝑚⁢𝑚⁢𝑐) near stoichiometry. We find that the layered structure can accommodate large off-stoichiometry in the Ta-rich region (𝑥 < 0.5), facilitated by the alloying with quasi-isostructural Ta 5 ⁢N 6 compound that exists on a composition tie line at 𝑥 = 0. While focusing on ScTaN 2 , we estimate the long-range order parameter in near-stoichiometric films to be 0.86, corresponding to a fraction of Sc/Ta antisites of 7%. Transport measurements on ScTaN 2 reveal a nearly temperature-independent high carrier density (10 21 c⁢m −3 ), suggesting a heavily doped semiconductor or semimetallic character, consistent with a small positive Seebeck coefficient of +19 µV/K. The carrier mobility at 2 K is relatively small (9.5c⁢m 2 V −1 s −1 ) and the residual-resistivity ratio is minor, suggesting that electrical conduction is dominated by defects or disorder. Measured magnetoresistance suggests possible weak antilocalization at 2 K. This paper highlights the interplay between ScTaN 2 and Ta 5 ⁢N 6 crystal structures in stabilizing layered materials, emphasizes the importance of cation order/disorder for potential tunable alloys, and suggests that ScTaN 2 is a promising platform for exploring electronic properties.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Coexisting structural disorder and robust spin-polarization in half-metallic FeMnVAl

We report half-metallic ferromagnets (HMFs) are one of the most promising materials in the field of spintronics due to their unique band structure, consisting of one spin subband having metallic characteristics along with another subband with semiconductor-like behavior. In this work, we report the synthesis of a novel quaternary Heusler alloy—FeMnVAl—and we have studied the structural, magnetic, transport, and electronic properties complemented with first-principles calculations. Among different possible structurally ordered arrangements, the optimal structure is identified by theoretical energy minimization. The corresponding spin-polarized band-structure calculations indicate the presence of a half-metallic ferromagnetic ground state. A detailed and careful investigation of the x-ray diffraction data, Mössbauer spectra, and nuclear magnetic resonance spectra suggests the presence of site disorder between the Fe and Mn atoms in the stable ordered structure of the system. The magnetic susceptibility measurement clearly establishes a ferromagnetic-like transition below ~213 K. The Fe Mössbauer spectrometry measurements suggest that only the Mn spins could be responsible for the magnetic order, which is consistent with our theoretical calculation. Surprisingly, the density-functional-theory calculations reveal that the spin-polarization value is almost immunized (92.4% → 90.4%) from the Mn-Fe structural disorder, even when nonmagnetic Fe and moment-carrying Mn sites are entangled inseparably. The robustness of spin polarization and half-metallicity in the studied FeMnVAl compound comprising structural disorder is thus quite interesting and could provide a new direction to investigate and understand the exact role of disorders on spin polarization in this class of materials, beyond the available knowledge.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Fast event-based electron counting for small-molecule structure determination by MicroED

Electron counting helped realize the resolution revolution in single-particle cryoEM and is now accelerating the determination of MicroED structures. Its advantages are best demonstrated by new direct electron detectors capable of fast (kilohertz) event-based electron counting (EBEC). This strategy minimizes the inaccuracies introduced by coincidence loss (CL) and promises rapid determination of accurate structures. We used the Direct Electron Apollo camera to leverage EBEC technology for MicroED data collection. Given its ability to count single electrons, the Apollo collects high-quality MicroED data from organic small-molecule crystals illuminated with incident electron beam flux densities as low as 0.01–0.045 e − /Å 2 /s. Under even the lowest flux density (0.01 e − /Å 2 /s) condition, fast EBEC data produced ab initio structures of a salen ligand (268 Da) and biotin (244 Da). Each structure was determined from a 100° wedge of data collected from a single crystal in as few as 50 s, with a delivered fluence of only ∼0.5 e − /Å 2 . Fast EBEC data collected with a fluence of 2.25 or 3.33 e − /Å 2 also facilitated a 1.5 Å structure of thiostrepton (1665 Da). While refinement of these structures appeared unaffected by CL, a CL adjustment applied to EBEC data further improved the distribution of intensities measured from the salen ligand and biotin crystals. However, CL adjustment only marginally improved the refinement of their corresponding structures, signaling the already high counting accuracy of detectors with counting rates in the kilohertz range. Overall, by delivering low-dose structure-worthy data, fast EBEC collection strategies open new possibilities for high-throughput MicroED.

EBEC↗
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

Influence on Structural Loading of a Wave Energy Converter by Controlling Variable-Geometry Components and the Power Take-Off

Oceans are harsh environments and can impose significant loads on deployed structures. A wave energy converter (WEC) should be designed to maximize the energy absorbed while ensuring the operating wave condition does not exceed the failure limits of the device itself. Therefore, the loads endured by the support structure are a design constraint for the system. Furthermore, the WEC should be adaptable to different sea states. Herethis work uses a WEC-Sim model of a variable-geometry oscillating wave energy converter (VGOSWEC) mounted on a support structure simulated under different wave scenarios. A VGOSWEC resembles a paddle pitching about a fixed hinge perpendicular to the incoming wave fronts. The geometry of the VGOSWEC is varied by opening a series of controllable flaps on the pitching paddle when the structure experiences threshold loads. It is hypothesized that opening the flaps should result in load shedding at the base of the support structure by reducing the moments about the hinge axis. This work compares the hydrodynamic coefficients, natural periods, and response amplitude operators from completely closed to completely open configurations of the controllable flaps. This work shows that the completely open configuration can reduce the pitch and surge loads on the base of the support structure by as much as 80%. Increased loads at the structure’s natural period can be mitigated by an axial power take-off damping acting as an additional design parameter to control the loads at the WEC’s support structure.

16 TIDAL AND WAVE POWER↗
DOE OSTI2022

Influence on Structural Loading of a Wave Energy Converter by Controlling Variable-Geometry Components and the Power Take-Off

Oceans are harsh environments and can impose significant loads on deployed structures. The deployment of wave energy converters (WECs) faces a design challenge with apparently contradictory goals. A WEC should be designed to maximize the energy absorbed while ensuring the operating wave condition does not exceed the failure limits of the device itself. Therefore, the loads endured by the support structure are a design constraint for the system. Adaptability to different sea states is, therefore, highly desirable. This work uses a WEC-Sim model of a variable-geometry oscillating wave energy converter (VGOSWEC) mounted on a support structure simulated under different wave scenarios. A VGOSWEC resembles a paddle pitching about a fixed hinge perpendicular to the incoming wave fronts. Therefore, the hinge experiences loads perpendicular to its axis as it maintains its position. The geometry of the VGOSWEC is varied by opening a series of controllable flaps on the pitching paddle when the structure experiences threshold loads. Because opening the flaps lets the waves transmit through the paddle, it is hypothesized that opening the flaps should result in load shedding at the base of the support structure. The load shedding is achieved by reducing the moments about the hinge axis. This work compares the hydrodynamic coefficients, natural periods, and response amplitude operators from completely closed to completely open configurations of the controllable flaps. The comparisons quantify the effects of letting the waves transmit through the VGOSWEC. This work shows that the completely open configuration can reduce the pitch and surge loads on the base of the support structure by as much as 80%. It was observed that at the paddle's resonance frequency, the loads on the structure increased substantially. This increase in loads can be mitigated by a rotational power take-off damping about the hinge axis. Changing the rotational power take-off damping was identified as an additional design parameter that can be used to control the loads experienced by the WEC's support structure.

fixed and floating structures↗
DOE OSTI2024

Molecular Vision - Multimodal, multitask retrieval of molecular structure from measured signatures for reference-free compound identification

We are currently at risk of generating false conclusions based on limited methods to identify small molecules in biological systems and in chemical forensics. By definition, the chemical structures of novel small molecules have not been determined, let alone measured or synthesized. Currently, unambiguous structure determination of small molecules is constrained by the time and effort needed to isolate compounds and perform de novo structure elucidation using laboratory-based methods, significantly extending the time to inform mitigation strategies. To address this gap, we have developed a deep learning approach to directly map molecular structure to experimental signatures. We aim to unify measurement technologies employed in untargeted small molecule identification studies—such as infrared (IR) spectrometry, tandem mass spectrometry (MS/MS), ion mobility spectrometry-derived collision cross section (CCS)—through use of a multimodal, multitask deep learning architecture. Where existing methods require direct generation of information-rich spectra and/or properties, an inherently difficult task, we will simplify molecular signature-based identification by posing the problem as a recognition or retrieval task. The model is thus presented with relevant endpoints – structure and one or more molecular signatures – and need only determine whether they are semantically related. Thus, our approach offers the following advantages over existing techniques: (i) circumvents difficulties associated with direct generation of molecular signatures from structure and structure from signatures; (ii) incorporates multiple molecular signatures simultaneously, as available, to support identification; and (iii) enables rapid computation of structural embeddings toward broad coverage of known chemical space. Taken together, the approach removes the need to explicitly obtain or compute reference spectra, representing a powerful method for compound identification that requires only experimentally observed signatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Centriole and transition zone structures in photoreceptor cilia revealed by cryo-electron tomography

Primary cilia mediate sensory signaling in multiple organisms and cell types but have structures adapted for specific roles. Structural defects in them lead to devastating diseases known as ciliopathies in humans. Key to their functions are structures at their base: the basal body, the transition zone, the “Y-shaped links,” and the “ciliary necklace.” We have used cryo-electron tomography with subtomogram averaging and conventional transmission electron microscopy to elucidate the structures associated with the basal region of the “connecting cilia” of rod outer segments in mouse retina. The longitudinal variations in microtubule (MT) structures and the lumenal scaffold complexes connecting them have been determined, as well as membrane-associated transition zone structures: Y-shaped links connecting MT to the membrane, and ciliary beads connected to them that protrude from the cell surface and form a necklace-like structure. These results represent a clearer structural scaffold onto which molecules identified by genetics, proteomics, and superresolution fluorescence can be placed in our emerging model of photoreceptor sensory cilia.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Influence on Structural Loading of a Wave Energy Converter by Controlling Variable-Geometry Components and the Power Take-Off: Preprint

Oceans are a harsh environment and can impose significant loads on deployed structures. Deployment of wave energy converters (WECs) faces a design challenge with apparently contradictory goals. A WEC should be designed to maximize the energy absorbed while ensuring the operating wave condition does not exceed the failure limits of the device itself. Therefore, the loads endured by the support structure are a design constraint for the system. Adaptability to different sea states is, therefore, highly desirable. This work uses a WEC-Sim model of a Variable Geometry Oscillating Wave Energy Converter (VGOSWEC) mounted on a support structure simulated under different wave scenarios. A VGOSWEC resembles a paddle pitching about a fixed hinge perpendicular to the incoming waves-fronts. Therefore, the hinge experiences loads perpendicular to its axis as it maintains its position. The geometry of the VGOSWEC was varied by opening a series of controllable flaps on the pitching paddle when the structure experiences threshold loads. Since opening the flaps lets the waves transmit through the paddle, it is hypothesized that opening the flaps should result in load shedding at the base of the support structure. This load shedding is achieved by reducing the moments about the hinge axis. This work compares the hydrodynamic coefficients, natural periods, and Response Amplitude Operators (RAOs) from completely closed to completely open configurations of the controllable flaps. These comparisons quantify the effects of letting the waves transmit through the VGOSWEC. This work shows that the completely open configuration can reduce the pitch and surge loads on the base of the support structure by as much as 80%. It was observed that at the paddle's resonance frequency, the loads on the structure increased substantially. This increase in loads can be mitigated by a rotational Power Take-off (PTO) damping about the hinge axis. Changing the rotational PTO damping was identified as an additional design parameter that can be used to control the loads experienced by the WEC's support structure.

fixed and floating structures↗
DOE OSTI2025

Comparative Analysis of TCR and TCR-pMHC Complex Structure Prediction Tools

The rapid development of computational approaches for predicting the structures of T cell receptors (TCRs) and TCR-peptide-major histocompatibility (TCR-pMHC) complexes, accelerated by AI breakthroughs such as AlphaFold, has made it feasible to calculate these structures with increasing accuracy. Although these tools show great potential, their relative accuracy and limitations remain unclear due to the lack of standardized benchmarks. Here, we systematically evaluate seven tools for predicting isolated TCR structures together with six tools for predicting TCR-pMHC complex structures. The methods include homology-based approaches, general prediction tools using AlphaFold, TCR-specific tools derived from AlphaFold2, and the newly developed tFold-TCR model. The evaluation uses a post-training data set comprising 40 αβ TCRs and 27 TCR-pMHC complexes (21 Class I and 6 Class II). Model accuracy is assessed at global, local, and interface levels using a variety of metrics. We find that each tool offers distinct advantages in various aspects of its predictions. AlphaFold2, AlphaFold3, and tFold-TCR excel in overall accuracy of TCR structure prediction, and TCRmodel2 and AlphaFold2 perform well in overall accuracy of TCR-pMHC structure prediction. However, TCR-specific tools derived from AlphaFold2 show lower accuracy in the framework region than both homology-based methods and general-purpose tools such as AlphaFold, and challenges remain for all in modeling CDR3 loops, docking orientations, TCR-peptide interfaces, and Class II MHC-peptide interfaces. Furthermore, these findings will guide researchers in selecting appropriate tools, emphasize the importance of using multiple evaluation metrics to assess model performance, and offer suggestions for improving TCR and TCR-pMHC structure prediction tools.

Chemical structure↗
DOE OSTI2024

Benchmarking Guanidinium Organosulfonate Hydrogen-Bonded Frameworks for Structure Determination of Encapsulated Guests

Single crystal X-ray diffraction (SCXRD) is arguably the most definitive method for molecular structure determination, but it is often challenged by compounds that are liquids or oils at room temperature or do not form crystals adequate for analysis. Our laboratory previously reported a simple, cost-effective, single-step crystallization method based on guanidinium organosulfonate (GS) hydrogen bonded frameworks for structure determination of a wide range of encapsulated guest molecules, including assignment of the absolute configuration of chiral centers. Herein, we expand on those results and report a head-to-head comparison of the GS method with adamantoid “molecular chaperones”, which have been reported to be useful hosts for structure determination. Inclusion compounds limited to only two GS hosts are characterized by low R1 values and Flack parameters, infrequent disorder of the host and guest, and manageable disorder when it does exist. The structures of some target molecules that were not included or resolved using the adamantoid chaperones were successfully included and resolved by the GS hosts, and vice versa. Of the 32 guests attempted by the GS method, 31 inclusion compounds afforded successful guest structure solutions, a 97% success rate. The GS hosts and adamantoid chaperones are complementary with respect to guest inclusion, arguing that both should be employed in the arsenal of methods for structure determination. Furthermore, the low cost of organosulfonate host components promises an accessible route to molecular structure determination for a wide range of users.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Candidate structure for the H 2 -PRE phase of solid hydrogen

Experimental progress finally reached the metallic solid hydrogen phase, which was predicted by Wigner and Huntington over 80 years ago. However, the different structures in the phase diagram are still being debated due to the difficulty of diffraction experiments for high-pressured hydrogen. The determination of crystal structures under extreme condition is both of the basic condensed matter physics, and in planetary science: the behavior of giant gaseous planets (e.g., Jupiter and Saturn) strongly depends on the properties of inner high-pressured hydrogen. This work describes possible structures appearing under high pressures of 400~600 GPa. We applied a structural search using particle swarm optimization with density functional theory (DFT) to propose several candidate structures. For these structures, we performed fixed-node diffusion Monte Carlo simulations combined with DFT zero-point energy corrections to confirm their relative stability. We found P2 1 /c-8 as a promising candidate structure for the H 2 -PRE phase. P2 1 /c-8 is predicted the most stable at 400 and 500 GPa. P2 1 /c-8 reproduces qualitatively the IR spectrum peaks observed in the H 2 -PRE phase.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗