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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 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Impact of Interfacial Structure on Heterogeneous Nucleation of Amorphous Carbonates

For this work, classical molecular dynamics simulations were performed to provide physical insight into the impact of interfacial structure on the heterogeneous nucleation of amorphous calcium carbonate (ACC, CaCO 3 ·H 2 O) and amorphous magnesium carbonate (AMC, MgCO 3 ·H 2 O) by using α-quartz as a model substrate. Interfacial structure and energies were computed for ACC and AMC in contact with the (100), (001), and (101) α-quartz surfaces. The simulations showed α-quartz surfaces drew water molecules out of the carbonate nuclei to form a partial hydration layer. The formation of a partial hydration layer and its disruption to the ACC/AMC structure meant the α-quartz–ACC/AMC interfaces were not energetically favored relative to separate α-quartz–water and ACC/AMC–water interfaces and, thus, homogeneous ACC/AMC nucleation was favored over heterogeneous nucleation. The CMD simulations hence provided an atomic-level explanation for a reported nonclassical growth mechanism whereby carbonate minerals grow via homogeneous nucleation and subsequent surface attachment of amorphous intermediates.

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

Heat Transfer Through a Passive Fire Protective Board from an Impinging Hydrogen Flame

This report documents analysis to determine whether a hydrogen jet flame impinging on a tunnel ceiling structure could result in permanent damage to the Callahan tunnel in Boston, Massachusetts. This tunnel ceiling structure consists of a passive fire protective board supported by stainless steel hangers anchored to the tunnel ceiling with epoxy. Three types of fire protective boards were considered to determine whether heat from the flame could reach the stainless-steel hangers and the epoxy and cause the ceiling structure to collapse. Heat transfer analyses performed showed that the temperature remains constant where the steel hangers are attached to the passive fire protective board. According to these results, the passive fire protective board should provide adequate protection to the tunnel structure in this release scenario. Tunnel structures with similar suspended fire-resistant liner board materials should protect the integrity of the structure against the extremely low probability of an impinging hydrogen jet flame.

08 HYDROGEN↗
DOE OSTI2025

Tuning the Properties of Lignin‐Derived Deep Eutectic Solvents for Biomass Processing

Lignin-derived deep eutectic solvents (DESs) have been investigated as sustainable green media for biomass processing. However, the properties and processability of DESs have not been fully understood with the chemical structures of their constituents for biomass fractionation. Here, in this article, the properties of the phenolic DESs are discussed with different numbers of functional groups, such as –OCH 3 and –CHO in their hydrogen bond donor (HBD) structures. The formation of DES is significantly related to the hydrogen bond between its constituents, identified by nuclear magnetic resonance (NMR) analysis and density functional theory calculation (DFT). Lower viscosity and net basicity of DES are achieved with fewer –OCH 3 on HBD structures, resulting in enhanced processability and fractionation efficiency. The thermal stability of the DES is also influenced by the –OCH 3 and –CHO of HBD, as indicated by its onset temperature. The recyclability of the phenolic DES is confirmed by the fractionation performance of the recycled DES. Understanding the structural impacts of DES constituents on the properties and performance is crucial for designing solvents in biorefinery applications.

Ryu, Jiae [State University of New York (SUNY), Sy↗
DOE OSTI2021

Coupling of regional geophysics and local soil-structure models in the EQSIM fault-to-structure earthquake simulation framework

Accurate understanding and quantification of the risk to critical infrastructure posed by future large earthquakes continues to be a very challenging problem. Earthquake phenomena are quite complex and traditional approaches to predicting ground motions for future earthquake events have historically been empirically based whereby measured ground motion data from historical earthquakes are homogenized into a common data set and the ground motions for future postulated earthquakes are probabilistically derived based on the historical observations. This procedure has recognized significant limitations, principally due to the fact that earthquake ground motions tend to be dictated by the particular earthquake fault rupture and geologic conditions at a given site and are thus very site-specific. Historical earthquakes recorded at different locations are often only marginally representative. There has been strong and increasing interest in utilizing large-scale, physics-based regional simulations to advance the ability to accurately predict ground motions and associated infrastructure response. However, the computational requirements for simulations at frequencies of engineering interest have proven a major barrier to employing regional scale simulations. In a U.S. Department of Energy Exascale Computing Initiative project, the EQSIM application development is underway to create a framework for fault-to-structure simulations. This framework is being prepared to exploit emerging exascale platforms in order to overcome computational limitations. This article presents the essential methodology and computational workflow employed in EQSIM to couple regional-scale geophysics models with local soil-structure models to achieve a fully integrated, complete fault-to-structure simulation framework. Here, the computational workflow, accuracy and performance of the coupling methodology are illustrated through example fault-to-structure simulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Non-Equilibrium Synthesis of Highly Active Nanostructured, Oxygen-Incorporated Amorphous Molybdenum Sulfide HER Electrocatalyst

Molybdenum sulfide emerged as promising hydrogen evolution reaction (HER) electrocatalyst thanks to its high intrinsic activity, however its limited active sites exposure and low conductivity hamper its performance. To address these drawbacks, the non-equilibrium nature of pulsed laser deposition (PLD) is exploited to synthesize self-supported hierarchical nanoarchitectures by gas phase nucleation and sequential attachment of defective molybdenum sulfide clusters. Furthermore, the physics of the process are studied by in situ diagnostics and correlated to the properties of the resulting electrocatalyst. The as-synthesized architectures have a disordered nanocrystalline structure, with nanodomains of bent, defective S-Mo-S layers embedded in an amorphous matrix, with excess sulfur and segregated molybdenum particles. Oxygen incorporation in this structure fosters the creation of amorphous oxide/oxysulfide nanophases with high electrical conductivity, enabling fast electron transfer to the active sites. The combined effect of the nanocrystalline pristine structure and the surface oxidation enhances the performance leading to small overpotentials, very fast kinetics (35.1 mV dec -1 Tafel slope) and remarkable long-term stability for continuous operation up to -1 A cm -2 . This work shows possible new avenues in catalytic design arising from a non-equilibrium technique as PLD and the importance of structural and chemical control to improve the HER performance of MoS-based catalysts.

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

Single-Crystalline Ni-Rich LiNi x Mn y Co 1– x – y O 2 Cathode Materials: A Perspective

To drive electrical vehicles for long-range, the energy density of Li-ion batteries must be further enhanced, which requires high-energy cathode materials. Among them, Ni-rich LiNi x Mn y Co 1–x–y O 2 (x > 0.5, NMC) is one of the most promising candidates. However, traditional poly-crystal (PC) NMC materials, whose particles are secondary clusters consisting of many primary crystalline particles, are susceptible to pulverization along the inter grain/particle boundaries, resulting in poor cycle stability. Recently, single crystal (SC)-NMC cathodes are proposed as they are believed to have several merits such as high structural integrity, lower interface with electrolyte, and potentially better energy storage performance. Nevertheless, several queries, such as the merits of SC structure and the mechanism for their structure degradation, are still controversial and required to be addressed. Here, in this study, the synthesis parameters, properties, energy storage as well as safety of SC- and PC-NMC cathodes with various Ni contents are critically reviewed, for clarifying the merits and drawbacks of SC. Furthermore, the study focuses on the recent advances of insight mechanisms and strategies for stabilizing the structure/interface by doping, morphology engineering, surface coating, and composition tailoring. The remaining challenges, safety concerns, and perspectives to enhance the electrochemical performance of SC-NMC cathodes for electric vehicle application are followed.

25 ENERGY STORAGE↗
DOE OSTI2020

Application and Certification of Comparative Vacuum Monitoring Sensors for Structural Health Monitoring of 737 Wing Box Fittings

Multi-site fatigue damage, hidden cracks in hard-to-reach locations, disbonded joints, erosion, impact, and corrosion are among the major flaws encountered in today's extensive fleet of aging aircraft and space vehicles. The use of in-situ sensors for real-time health monitoring of aircraft structures are a viable option to overcome inspection impediments stemming from accessibility limitations, complex geometries, and the location and depth of hidden damage. Reliable, structural health monitoring systems can automatically process data, assess structural condition, and signal the need for human intervention. Prevention of unexpected flaw growth and structural failure can be improved if on-board health monitoring systems are used to continuously assess structural integrity. Such systems are able to detect incipient damage before catastrophic failures occurs. Condition-based maintenance practices could be substituted for the current time-based maintenance approach. Other advantages of on-board distributed sensor systems are that they can eliminate costly, and potentially damaging, disassembly, improve sensitivity by producing optimum placement of sensors and decrease maintenance costs by eliminating more time- consuming manual inspections. This report presents a Sandia Labs-aviation industry effort to move SHM into routine use for aircraft maintenance. This program addressed formal SHM technology validation and certification issues so that the full spectrum of concerns, including design, deployment, performance and certification were appropriately considered. The Airworthiness Assurance NDI Validation Center (AANC) at Sandia Labs, in conjunction with Boeing, Delta Air Lines, Structural Monitoring Systems Ltd., Anodyne Electronics Manufacturing Corp. and the Federal Aviation Administration (FAA) carried out a certification program to formally introduce Comparative Vacuum Monitoring (CVM) as a structural health monitoring solution to a specific aircraft wing box application. Validation tasks were designed to address the SHM equipment, the health monitoring task, the resolution required, the sensor interrogation procedures, the conditions under which the monitoring will occur, the potential inspector population, adoption of CVM into an airline maintenance program and the document revisions necessary to allow for routine use of CVM as an alternate means of performing periodic structural inspects. To carry out the validation process, knowledge of aircraft maintenance practices was coupled with an unbiased, independent evaluation. Sandia Labs designed, implemented, and analyzed the results from a focused and statistically-relevant experimental effort to quantify the reliability of the CVM system applied to the Boeing 737 Wing Box fitting application. All factors that affect SHM sensitivity were included in this program: flaw size, shape, orientation and location relative to the sensors, as well as operational and environmental variables. Statistical methods were applied to performance data to derive Probability of Detection (POD) values for CVM sensors in a manner that agrees with current nondestructive inspection (NDI) validation requirements and also is acceptable to both the aviation industry and regulatory bodies. This report presents the use of several different statistical methods, some of them adapted from NDI performance assessments and some proposed to address the unique nature of damage detection via SHM systems, and discusses how they can converge to produce a confident quantification of SHM performance An important element in developing SHM validation processes is a clear understanding of the regulatory measures needed to adopt SHM solutions along with the knowledge of the structural and maintenance characteristics that may impact the operational performance of an SHM system. This report describes the major elements of an SHM validation approach and differentiates the SHM elements from those found in NDI validation. The activities conducted in this program demonstrated the feasibility of routine SHM usage in general and CVM in particular for the application selected. They also helped establish an optimum OEM-airline-regulator process and determined how to safely adopt SHM solutions. This formal SHM validation will allow aircraft manufacturers and airlines to confidently make informed decisions about the proper utilization of CVM technology. It will also streamline the regulatory actions and formal certification measures needed to assure the safe application of SHM solutions.

42 ENGINEERING↗
DOE OSTI2024

Probing nuclear structure of heavy ions at energies available at the CERN Large Hadron Collider

We perform high-statistics simulations to study the impacts of nuclear structure on the ratios of anisotropic flow observables in 208 Pb + 208 Pb and 129 Xe + 129 Xe collisions at the Large Hadron Collider. Even with 40% difference in atomic numbers between 208 Pb and 129 Xe nuclei, the ratios of anisotropic flow in the same centrality class between the two collision systems are strongly affected by the nuclear structure inputs in the initial state. The ratios of v 2 ⁡{4}/v 2 ⁡{2} in these collisions are sensitive to the nuclear skin thickness of the colliding nuclei, providing indirect constraints on the nuclei's neutron skin. In conclusion, our model predictions serve as a benchmark to compare with experimental measurements.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Reinforcement Learning of Structured Stabilizing Control for Linear Systems With Unknown State Matrix

This paper delves into designing feedback control gains for a continuous-time linear quadratic regulator (LQR) problem that is constrained to certain predefined structure with unknown state matrix. We bring forth the ideas from reinforcement learning (RL) in conjunction with sufficient stability and performance guarantees in order to design these structured gains using the trajectory measurements of states and controls. Here we first formulate a model-based framework using dynamic programming (DP) to embed the structural constraint to the LQR gain computation in the continuous-time setting, and then subsequently, formulate a policy iteration RL algorithm that can alleviate the requirement of known state matrix in conjunction with maintaining the feedback gain structure. The design enables a distributed learning control design which is necessary for many large-scale cyber-physical systems. Theoretical guarantees are provided for stability and convergence of the structured reinforcement learning (SRL) algorithm. We validate our theoretical results with numerical simulations on a multi-agent networked linear time-invariant (LTI) dynamic system.

42 ENGINEERING↗
DOE OSTI2022

Simulating Atmospheric Boundary Layer Turbulence with Nek5000/RS

We present large-eddy-simulation (LES) modeling approaches for the simulation of atmospheric boundary layer turbulence that are of direct relevance to wind energy production. In this report, we study a GABLS benchmark problem using high-order spectral element code Nek5000/RS, which is supported under the DOE’s Exascale Computing Project (ECP) Center for Efficient Exascale Discretizations (CEED) project, targeting application simulations on various acceleration-device based exascale computing platforms [1, 2]. We demonstrate our newly developed subgrid-scale (SGS) models based on high-pass filter (HPF), mean-field eddy viscosity (MFEV), and Smagorinsky (SMG) with no-slip and traction boundary conditions, provided with low-order statistics, convergence and turbulent structure analysis. The model fidelity and scaling performance of Nek5000/RS on DOE’s leadership computing platforms in comparison to those of AMR-Wind, a block-structured second-order finite-volume code with adaptive-mesh-refinement capabilities, are discussed in [3].

17 WIND ENERGY↗
DOE OSTI2021

Soft magnetic alloy embodiments for additive manufacturing and geometric structures formed therefrom

Disclosed herein are embodiments of soft magnetic alloy embodiments for use in additive manufacturing and structures fabricated from such alloys. In some embodiments, the fabricated structures comprise a continuous thin wall (or plurality thereof) having a geometry that promotes reduced eddy current losses and other performance enhancements. In some embodiments, the fabricated structures are used to make components, such as transformer cores and/or electric motors.

Plotkowski, Alexander↗
DOE OSTI2022

A Moving Embedded Boundary Approach for the Compressible Navier-Stokes Equations in a Block-Structured Adaptive Refinement Framework

A computational technique has been developed to perform compressible flow simulations involving moving boundaries using an embedded boundary approach within the block-structured adaptive mesh refinement (SAMR) framework of AMReX [1], [91], [92]. We leverage the SAMR capability to obtain quantitatively accurate results whilst using robust, second-order finite volume schemes. A conservative, unsplit, cut-cell approach is utilized and a ghost-cell approach is developed for computing the flux on the moving, embedded boundary faces. A third-order least-squares formulation has been developed to compute the wall velocity gradients, and was found to significantly improve the performance of the solver in terms of the quantitative comparison of surface quantities such as the skin friction coefficient. Various test cases are performed to validate the method, and compared with analytical, experimental, and other numerical results in literature. Inviscid and viscous test cases are performed that span a wide regime of flow speeds - acoustic (harmonically pulsating sphere), smooth flows (expansion fan created by a receding piston) and flows with shocks (shock-cylinder interaction, shock-wedge interaction, pitching NACA 0012 airfoil and shock-cone interaction). A closed system with moving boundaries - an oscillating piston in a cylinder, showed that the percentage error in mass within the system decreases with refinement, demonstrating that the numerical scheme is conservative with grid refinement, but is not discretely conservative. Viscous test cases involve that of a horizontally moving cylinder at Re = 40, an inline oscillating cylinder at Re = 100, and a transversely oscillating cylinder at Re = 185. The judicious use of adaptive mesh refinement with appropriate refinement criteria to capture the regions of interest leads to well-resolved flow features, and good quantitative comparison is observed with the results available in literature.

adaptive refinement↗
DOE OSTI2020

Adaptive Machine Learning for Bragg Coherent Diffraction Imaging (BCDI) of 3D Electron Density Maps with Application to La 2-x Ba x CuO 4 (LBCO) High Temperature Superconductor Studies [PowerPoint]

Understanding mesoscale heterogeneity is important for evaluating fatigue and failure of structural materials and for manufacturing processes. Data-driven tools can facilitate in guiding effort investment (measurements and computations) at various stages of the materials development. Our 3D reconstruction approach is to find a set of coefficients which define a bounding surface of the electron density. Data for training the 3D CNN was generated by sampling coefficients from uniform distributions. Test vs. prediction values are shown for the 28 even-valued coefficients for 1000 test structures, with the best and worst performers highlighted. The adaptive part of this work utilized a model independent extremum seeking (ES). The predictions of the CNN were used as the starting point for the ES algorithm. The convergence of the ES algorithm for 3 different structures is illustrated, and the robustness of the adaptive ML approach was demonstrated on experimentally measured 3D crystal from high energy diffraction microscopy. Reconstruction of a non-uniform density volume with different levels of Poisson noise is also shown. Preliminary attempts at reconstructing measured La 2-x Ba x CuO 4 diffraction patterns have so far failed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Explicit structural topology optimization using boundary element method‐based moving morphable void approach

Abstract This article presents an explicit topology optimization approach using boundary element method based moving morphable void (MMV). Structural analysis in the conventional MMV approach is performed on a fixed mesh over the entire design domain. However, in the proposed method structural boundaries are described using B‐splines and discretized with boundary elements making explicit representation of the boundaries possible. In this regard, the proposed approach has following merits: a) the use of weak material, which is often adopted to mimic voids can be completely avoided; b) exact and explicit description of voids in MMV allows the capture of tiny structural features in a robust and effective way; c) numerical instabilities stemming from the use of fixed meshes can be naturally avoided. Several numerical examples are provided to demonstrate the effectiveness of the proposed approach.

Zhang, Weisheng↗
DOE OSTI2025

Pb:Sn Ratio-Driven Polytypism and Band Modulation in Photoresponsive Hexagonal Perovskitoids

Three-dimensional (3D) perovskites of the formula AMX 3 are known for their excellent optoelectronic properties, but their design is limited by the narrow range of A-site cations that can template the 3D corner-sharing structure, and many of the viable options have already been explored. These materials also face structural instability under environmental conditions. In contrast, 3D hexagonal perovskitoids, with the same chemical formula, may offer enhanced stability and richer structural diversity through a range of corner- and face-sharing octahedral configuration options, providing greater opportunities for structural design; however, challenges such as synthesis complexity and wide band gaps have hindered optoelectronic performance achieved to date. Herein, we synthesized a structural homologous series of mixed-metal hexagonal perovskitoids with the formula APb 1-x Sn x I 3 (x = 0, 0.25, 0.50, 0.75, 1; A = ethylammonium, guanidinium) and identified three polytypes (9R, 12R, 6H) using single-crystal X-ray diffraction (SCXRD). These structures exhibited increasing corner-sharing connectivity with higher Sn content, revealing a previously unobserved relationship between metal composition and structural evolution in perovskitoid materials. The incorporation of Sn reduced the band gap (tunable from 2.51 eV to 1.87 eV) and drove structural transformations, a trend seen also in density functional theory (DFT) calculations, which suggest a thermodynamic preference for Pb at face-sharing sites and Sn at corner-sharing sites. DFT band structure calculations and optical spectroscopy also reveal an anomalous behavior in these materials, which we term polytypic band modulation. This phenomenon combines conventional band bowing with the structural transformations that occur as Sn content increases, as observed in the band gap and in photoluminescence spectra. Photodiodes fabricated from thin films of these materials exhibited stable and pronounced photoresponses across various light intensities over time. Furthermore, the combination of templating 3D perovskitoids with multiple cations and alloying Pb and Sn, suggests a vastly underexplored phase space that offers new parameters to tune perovskitoids.

Cations↗
DOE OSTI2024

HydraGNN_Predictive_GFM_2024 - Ensemble of predictive graph foundation models for ground state atomistic materials modeling

We provide the ensemble of fifteen pre-trained graph foundation models (GFMs) for atomistic materials modeling applications. Each one of the fifteen GFMs has been trained on five open-source datasets that (once aggregated) amount to over 154 million atomistic structures, which cover over two-thirds of the natural elements of the periodic table and that comprises a broad set of organic and inorganic compounds. This vast set of atomistic structures comprises ground state configurations that are dynamically stable (i.e., equilibrated structures with atomic forces approximately close to zero values) as well as dynamically unstable structures (i.e., non-equilibrium structures with non-negligible non-zero values of atomic forces). The ensemble of datasets aggregated does NOT include excited states. The datasets have been curated to remove atomistic structures with spectral norm of the force tensor above 100 eV/angstrom. Moreover, a linear term of the energy was computed for each dataset using a linear regression model that uses the chemical concentration of each natural element as regressor. The linear term predicted by the linear regression model has been subtracted from each original energy value to perform a re-alignment of the energy values across different electronic structures approximation theories performed to generate the diverse multi-source, multi-fidelity datasets. The folder "ADIOS_files" contains the set of pre-processed datasets in Adaptable I/O System (ADIOS) format (https://www.exascaleproject.org/research-project/adios/) that have been used for the development and training of GFMs in this work. The "ADIOS_files" directory contains 6 sub-directories named as follows: - ANI1x-v3.bp - MPTrj-v3.bp - OC2020-20M-v3.bp - OC2020-v3.bp - OC2022-v3.bp - qm7x-v3.bp Each sub-directory contains the pre-processed datasets converted in Adaptable I/O System (ADIOS) format (https://www.exascaleproject.org/research-project/adios/) that have been used to the development, training, and performance testing of the ensemble go predictive graph foundation models. Each GFM was developed using HydraGNN (https://github.com/ORNL/HydraGNN) as underlying graph neural network (GNN) architecture. The multi-task learning (MTL) capability of HydraGNN was used to simultaneously train the GFMs on labeled values for direct predictions of energy (a total system property of an atomistic structure that measures the chemical stability) and atomic forces (an atomic level property of an atomistic structure that measures the dynamical stability). The hyper parameters of the GFM have been tuned using scalable hyperparameter optimization (HPO) algorithms implemented in the software DeepHyper (https://github.com/deephyper/deephyper). The pre-training of each HPO trial was performed using distributed data parallelism (DDP) to scale the training across 128 compute nodes of the exascale OLCF supercomputer Frontier. Each HPO trial was trained only for 10 epochs and an early stopping was performed to avoid wasting significant computational resources on GNN architectures that were clearly underperforming. For each HPO trial, the 'omnistat' tool developed by (AMD Research - Advanced Micro Device) was used to measure the total energy consumption in kWh. The ensemble of GFMs was obtained by selecting the fifteen best performing HPO trials. Four models have been selected for their clear advantage in accuracy, and these are the GFMs with IDs 229, 156, 147, 260. Additional eleven models have been selected based on judicious balance between accuracy and energy consumption needed for training, and these are the GFMs with IDs 165, 78, 137, 1, 175, 171, 181, 67, 179, 167, 351. Each selected GFM of the ensemble was continued to cumulate a total of at most 30 epochs. In some cases, the total number of epochs actually performed was les than 30 due to two combined factors: (1) the size of the GFM (i.e., the number of model parameters to train) and (2) the total wall-clock time for which the computational resources could be allocated on OLCF-Frontier. The "Ensemble_of_models" directory contains 15 sub-directories named as follows: - gfm_0.229 - gfm_0.156 - gfm_0.147 - gfm_0.260 - gfm_0.165 - gfm_0.78 - gfm_0.137 - gfm_0.1 - gfm_0.175 - gfm_0.171 - gfm_0.181 - gfm_0.67 - gfm_0.179 - gfm_0.167 - gfm_0.351 Each one of these sub-directories refers to one of the fifteen HPO trials that have been selected to continue the pre-training with at most 30 epochs. With each sub-directory associated with a specific HPO trial, the following files can be found: - config.json: file for argument parsing to develop and train an HydraGNN architecture - gfm_0.ID_epoch_N.pk: file with model parameters for HPO ID trial after N epochs of training The ensemble of fifteen GFM architectures was used for (1) ensemble averaging to stabilize the predictions of energy and atomic forces after pre-training for post-processing analysis and (2) ensemble uncertainty quantification (UQ). The code used to develop, pre-train, and load the pre-trained models for post-processing analysis is available on the ORNL-GitHub at the following link: https://github.com/ORNL/HydraGNN/tree/Predictive_GFM_2024

36 MATERIALS SCIENCE↗
DOE OSTI2024

Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure

Bacteroides are often the most abundant, commensal species in the gut microbiome of industrialized human populations. One of the most commonly detected species is Bacteroides ovatus. It has been linked to benefits like the suppression of intestinal inflammation but is also correlated with some autoimmune disorders, for example irritable bowel disorder (IBD). Bacterial cell surface carbohydrates, like capsular polysaccharides (CPS), may play a role in modulating these varied host interactions. Recent studies have begun to explore the diversity of CPS loci in Bacteroides; however, there is still much unknown. Here, we present structural and functional characterization of a putative polysaccharide deacetylase from Bacteroides ovatus (BoPDA) encoded in a CPS biosynthetic locus. We solved four high resolution crystal structures (1.36-1.56 Å) of the enzyme bound to divalent cations Co 2+ , Ni 2+ , Cu 2+ , or Zn 2+ and performed carbohydrate binding and deacetylase activity assays. Structural analysis of BoPDA revealed an atypical domain architecture that is unique to this enzyme, with a carbohydrate esterase 4 (CE4) superfamily catalytic domain inserted into a carbohydrate binding module (CBM). Additionally, BoPDA lacks the canonical CE4 His-His-Asp metal binding motif and our structures show it utilizes a noncanonical His-Asp dyad to bind metal ions. BoPDA is the first protein involved in CPS biosynthesis from B. ovatus to be characterized, furthering our understanding of significant biosynthetic processes in this medically relevant gut microbe.

59 BASIC BIOLOGICAL SCIENCES↗