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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Detecting and Characterizing Fracture Zones Using a Convolutional Neural Network

This project directly supports the Geothermal Technologies Office (GTO) objectives outlined in the Multi-Year Program Plan (MYPP) by advancing two key research areas: “Exploration and Characterization” and “Data, Modeling, and Analysis.” This project has successfully demonstrated a pre-drilling ability to image and characterize the distribution and connectivity of subsurface faults and fractures, key parameters for identifying permeable pathways that enable geothermal fluids to circulate and produce energy. Specifically, we developed and implemented innovative machine learning methodologies to enhance geothermal exploration. Large-scale faults were detected using a Convolutional Neural Network (CNN), while small-scale fractures were characterized using a novel Double-Beam Neural Network (DBNN). These tools have proven both technically effective and cost-efficient by reducing reliance on expensive exploratory drilling. Through collaboration with our geothermal industry partner, this research has significantly advanced techniques for identifying hidden geothermal systems and extending the productive lifespan of existing geothermal fields. We applied our methods to two geothermal fields—Soda Lake (Nevada) and Lightning Dock (New Mexico)—to identify shallow steam-charged fracture zones and characterize deep faults at depths of 1.5-2 km. The steam zone identified at the Soda Lake geothermal field showed excellent agreement with prior drilling data, validating the effectiveness of our approaches. In addition, the analysis revealed three new prospective drilling targets for further development and verification. The outcomes of this project improve our scientific understanding of geothermal reservoir behavior, enhance exploration efficiency, extend the economic life of existing geothermal plants. Ultimately, these advancements contribute to GTO’s goal of achieving more sustainable, affordable, and data-driven geothermal energy development across the United States.

15 GEOTHERMAL ENERGY↗
DOE OSTI2020

Dynamic Bottlebrush Polymer Networks: Self-Healing in Super-Soft Materials

Here, we introduce a design strategy to expand the range of accessible mechanical properties in covalent adaptable networks (CANs) using bottlebrush polymer building blocks. Well-defined bottlebrush polymers with rubbery poly(4-methylcaprolactone) side-chains were crosslinked in formulations that include a bislactone and strong Lewis acid (tin ethylhexanoate). The resulting materials exhibit tunable stress relaxation rates at elevated temperatures (160–180 °C) due to dynamic ester crosslinks that undergo transesterification with residual hydroxy groups. Varying the crosslinker loading or bottlebrush backbone degree of polymerization yields predictable low-frequency shear moduli ca. 10–100 kPa, well below values typical of linear polymer CANs (1 MPa). These extensible networks can be stretched to strains as large as 350% before failure and undergo efficient self-healing to recover >85% of their original toughness upon repeated fracture and melt processing. In summary, molecular architecture creates new opportunities to tailor the mechanical properties of CANs in ways that are otherwise difficult to achieve.

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

Complex multicomponent spectrum analysis with Deep Neural Network

Here, in this paper, we present the use of deep neural networks to estimate physical parameters from complex optical emission spectra of the D β /H β transition. Specifically, we focus on estimating the radio frequency electric field vector of the lower hybrid wave and isotope ratio within the scrape-off-layer plasma of the WEST tokamak. Fitting the spectral data using a traditional non-linear least squares analysis requires many free parameters and is computationally expensive, rendering the data unusable for real-time control. By implementing relatively small neural networks, the physical parameters can be directly extracted from the spectral data with reasonable accuracy in a few milliseconds. The deep neural network prediction can serve as input for a reduced model using least-squares fitting or for real-time control. We show that deep neural networks can be an effective tool for analyzing complex multicomponent spectra, providing a speedup of more than 10 5 times compared to least residual analysis, with an accuracy of 0.5% for the isotope ratio, and 0.09 kV/cm and 0.38 kV/cm for the RF radial and poloidal electric field respectively.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Residual loss due to magnetic flux trapping in niobium superconducting microwave cavities

One of the significant source of radio frequency loss in superconducting microwave cavities is the trapped residual magnetic field during the cooldown due to the incomplete Messier effect. The sensitivity of flux trapping depends on the distribution of impurities, network of dislocations and defects which pin vortices. Recent advancement in cavity processing techniques resulted in very high quality factors with impurity doping, however the rf loss related to the flux trapping increases. High quality factor in SRF cavities is not only limited to particle accelerators but also emerging as an application to quantum computing and quantum information science. In this presentation, we present the results of measurements of flux trapping sensitivity on several 1.3 GHz elliptical accelerating cavities with different grain size, impurity content and surface preparations.

Dhakal, P.↗
DOE OSTI2026

Monitoring of Liquid Metal Reactor Heater Zones with Recurrent Neural Network Learning of Temperature Time Series

Advanced high-temperature fluid reactors (ARs), such as sodium fast reactors (SFRs) and molten salt cooled reactors (MSCRs) utilize high-temperature fluids at ambient pressure. To melt the fluid during reactor startup and prevent fluid freezing during cooldown, the thermal–hydraulic systems of such ARs include heater zones consisting of specific heaters with controllers, temperature sensors, and thermal insulation. The failure of heater zones due to insulation material degradation or improper installation, resulting in parasitic heat losses, can lead to fluid freezing. The detection of faults using a heat-transfer model is difficult because of a lack of knowledge of the experimental details. Data-driven machine learning of heater zone temperature time series offers a viable alternative. In this study, we benchmarked the performance of recurrent neural networks (RNNs) in an analysis of heat-up transient temperature time series of heater zones installed on a liquid sodium vessel. The RNN models include long short-term memory (LSTM) and gated recurrent unit (GRU) networks, as well as their bi-directional variants, BiLSTM and BiGRU. Anomalous temperature points were designated using a percentile-based threshold applied to residual fluctuations in the detrended temperature time series. Additionally, the impact of the exponentially weighted moving average (EWMA) method on detection accuracy was examined. The RNN models’ performance was assessed using precision, recall, and F 1 score metrics. Results demonstrated that RNN models effectively detect anomalies in temperature time series with the best models for each heater zone achieving F 1 scores of over 93%. To explain the variations in RNN model performance across different heater zones, we used Kullback–Leibler (KL) divergence to quantify the relative entropy between training and testing data, and the Detrended Fluctuation Analysis (DFA) to assess long-range temporal correlations. For datasets with strong long-range correlations and minimal relative entropy between training and testing data, GRU is the best-performing model. When the data exhibits weaker long-term correlations and a significant relative entropy between training and testing distributions, BiGRU shows the best performance. For the data sets with intermediate values of both KL divergence and DFA, the best performance is obtained with LSTM and BiLSTM, respectively.

gated recurrent unit↗
DOE OSTI2023

Chemical abrasion: the mechanics of zircon dissolution

Chemical abrasion is a technique that combines thermal annealing and partial dissolution in hydrofluoric acid (HF) to selectively remove radiation-damaged portions of zircon crystals prior to U–Pb isotopic analysis, and it is applied ubiquitously to zircon prior to U–Pb isotope dilution thermal ionization mass spectrometry (ID-TIMS). The mechanics of zircon dissolution in HF and the impact of different leaching conditions on the zircon structure, however, are poorly resolved. We present a microstructural investigation that integrates microscale X-ray computed tomography (µCT), scanning electron microscopy, and Raman spectroscopy to evaluate zircon dissolution in HF. We show that µCT is an effective tool for imaging metamictization and complex dissolution networks in three dimensions. Acid frequently reaches crystal interiors via fractures spatially associated with radiation damage zoning and inclusions to dissolve soluble high-U zones, some inclusions, and material around fractures, leaving behind a more crystalline zircon residue. Other acid paths to crystal cores include the dissolution of surface-reaching inclusions and the percolation of acid across zones with high defect densities. In highly crystalline samples dissolution is crystallographically controlled with dissolution proceeding almost exclusively along the c axis. Increasing the leaching temperature from 180 to 210 °C results in deeper etching textures, wider acid paths, more complex internal dissolution networks, and greater volume losses. How a grain dissolves strongly depends on its initial radiation damage content and defect distribution as well as the size and position of inclusions. As such, the effectiveness of any chemical abrasion protocol for ID-TIMS U–Pb geochronology is likely sample-dependent. We also briefly discuss the implications of our findings for deep-time (U-Th)/He thermochronology.

58 GEOSCIENCES↗
DOE OSTI2025

Elucidation of Local Ordering and Atomic-Scale Structure in Polymer-Derived SiOC

Silicon oxycarbide (SiOC) is a versatile ceramic material with tunable microstructure and compositions that can be modulated through precursor chemistry and processing conditions. Though there are several noteworthy uses of SiOC across a range of application spaces, the difficulties in elucidating the short- to medium-range order within these materials have limited the maturation of strategies to precisely control SiC x O 4–x compositions for user-tailored applications. In this contribution, we implement a range of synchrotron scattering and spectroscopy methods coupled with stochastic modeling techniques to elucidate changes in local chemistry and structure associated with the pyrolysis of a commercially available SiOC polymer precursor. Stochastic modeling approaches provide valuable insights into decoupling local Si–O and Si–C environments while confirming predominate heterogeneous phases in materials. Using pyrolysis temperatures between 250 to 800 °C results in a heterogeneous material predominately composed of SiOC and amorphous SiO 2 domains. At 1100 °C, redistribution of Si–C pairs in the SiOC network and Si–O from the SiO 2 domains create a more ordered SiOC phase with local cubic SiC-like ordering. In addition, residual carbon leads to a detectable carbon phases at 1100 °C that persist at higher temperatures. These efforts address the difficulties of obtaining atomic-scale insights into the local structure and nanoscale heterogeneities in SiOC, providing pathways toward establishing structure–property relationships for future materials development.

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

Combining direct ink writing with reactive melt infiltration to create architectured thermoelectric legs

Here, we present a new additive-reactive synthesis method where inks – cast into molds or 3D-additively extruded into architectured shapes – are reacted into intermetallic thermoelectric compounds. The new method, as demonstrated for equiatomic TiNiSn, combines: (i) extrusion printing (or casting) of inks containing Ni and Ti powders, (ii) debinding and reactive sintering to form a porous NiTi network, (iii) network infiltration with liquid Sn and subsequent reaction to synthesize the TiNiSn phase. Thin plates, created through this method, show high phase purity and low residual porosity. A thermoelectric figure of merit zT = 0.47 ± 0.05 is achieved at 800 K, within the broad range of values (zT= 0.3–1.0) reported for TiNiSn created via traditional powder hot-pressing methods. Layered TiNiSn microlattices – after 3D ink-extrusion printing and infiltration – exhibit high relative densities and minimal undesirable secondary phase content, with a Seebeck coefficient on par with the ink-cast TiNiSn plates, demonstrating that thermoelectric legs with far-ranging architectural freedom can be created additively with this novel reactive manufacturing method. Numerous other thermoelectric (and other) compounds, currently limited to basic geometries due to brittleness, are amenable to this new method based on a sequence of reactive sintering/infiltration of cast or ink-extruded precursors.

36 MATERIALS SCIENCE↗
DOE OSTI2025

CRN Modeling of Ammonia RQL Combustion using a Partially-Stirred Reactor Approach

Ammonia is a promising alternative to hydrogen with high energy density and favorable storage and transport characteristics. However low flammability and a propensity for high nitrogen oxide (NOx) emissions make direct utilization challenging. Recently, two-stage rich-quench-lean (RQL) combustion strategies have shown promise in achieving low NOx emissions with ammonia. In this approach, the rich stage serves to oxidize a portion of the fuel, while thermally decomposing as much of the remaining ammonia as possible, generating hydrogen. In the second (lean) stage, air is rapidly introduced, burning out the hydrogen and residual ammonia. Two-stage RQL combustion of ammonia has been investigated in the open literature both experimentally and numerically. In general, idealized chemical reactor network (CRN) models predict NOx concentrations below that of 2D/3D computational fluid dynamics models and experiments. The primary drivers of these discrepancies may be largely attributed to finite rate mixing non-adiabatic operation. The typical CRN model is comprised of a perfectly-stirred-reactor (PSR), followed by a plug-flow-reactor (PFR), meant to represent the flame, and post-flame zones, respectively. In the two-stage RQL approach two PSR-PFR networks are arranged sequentially, corresponding to the rich and lean stages, with secondary air injection in between. In the authors’ past work, this arrangement has demonstrated the significant sensitivity of exit NOx to the rich stage equivalence ratio, while the amount of secondary air injection was shown to be less critical. In this paper, the CRN model is extended to (1) include the impacts of heat loss and (2) utilize a partially-stirred-reactor (PaSR) approach to study the impacts of mixing on emissions performance. Varying amounts of heat loss are applied to the rich relaxation zone to understand emissions performance and changes to optimization of equivalence ratio and residence time. Premixed and non-premixed configurations are considered in the rich stage PaSR, with varying degrees of mixing intensity to study the interaction between mixing, transport, and kinetic timescales. Critically, the impact of mixing between hot products and secondary air injection is studied to understand practical injector needs. Results show unburnt ammonia leaving the rich stage as a primary contributor to NOx emissions – driven both by increased heat loss and reduced mixing rates. Furthermore, heat losses have shown to create conditions which are conducive to increased N2O formation in the lean stage. The results of this study will be considered in the context of developing optimized two-stage RQL combustors for ammonia..

advanced gas turbines↗
DOE OSTI2026

Temporal Convolutional Network Using Empirical Mode Decomposition to Detect Faults in Grid Connected Systems

Grid-connected power electronic systems require timely and reliable fault detection to prevent equipment damage and reduce downtime. This paper presents a forecasting-based anomaly detection pipeline that decomposes voltage and current measurements into intrinsic mode functions (IMFs) using empirical mode decomposition (EMD), then trains a causal temporal convolutional network (TCN) on normal-operation IMF data to predict short-horizon future dynamics. Deviations between forecasts and observations are summarized as reliability-weighted residual scores and thresholded per sensor using robust statistics with temporal persistence constraints to suppress false positives. To reduce runtime, EMD is performed on downsampled signals for detection, while raw-rate EMD is applied only within a short region of interest for high-frequency interpretability near detected events. Results on a simulated grid-connected converter system demonstrate that IMF-domain forecasting improves anomaly separability relative to raw-signal forecasting and provides interpretable evidence of faults across decomposition channels.

Sutton, Elizabeth [ORNL] (ORCID:0009000078885935)↗
DOE OSTI2023

A Methodology for Estimating the Energy and Moisture Budget of the Convective Boundary Layer Using Continuous Ground-Based Infrared Spectrometer Observations

Abstract Land–atmosphere interactions play a critical role in both the atmospheric water and energy cycles. Changes in soil moisture and vegetation alter the partitioning of surface water and energy fluxes, influencing diurnal evolution of the planetary boundary layer (PBL). The mixing-diagram framework has proven useful in understanding the evolution of the heat and moisture budget within the convective boundary layer (CBL). We demonstrate that observations from the Department of Energy Atmospheric Radiation Measurement (ARM) Southern Great Plains site provide all of the needed inputs needed for the mixing-diagram framework, allowing us to quantify the impact from the surface fluxes, advection, radiative heating, encroachment, and entrainment on the evolution of the CBL. Profiles of temperature and humidity retrieved from the ground-based infrared spectrometer [Atmospheric Emitted Radiance Interferometer (AERI)] are a critical component in this analysis. Large-eddy simulation results demonstrate that mean mixed-layer values derived are shown to be critical to close the energy and moisture budgets. A novel approach demonstrated here is the use of network of AERIs and Doppler lidars to quantify the advective fluxes of heat and moisture. The framework enables the estimation of the entrainment fluxes as a residual, providing a way to observe the entrainment fluxes without using multiple lidar systems. The high temporal resolution of the AERI observations enables the morning, midday, and afternoon evolution of the CBL to be quantified. This work provides a new way to use observations in this framework to evaluate weather and climate models. Significance Statement The energy and moisture budget of the planetary boundary layer (PBL) is influenced by multiple sources, and accurately representing this evolution in numerical models is critical for weather forecasts and climate predictions. The mixing-diagram approach, driven by profiling observations as illustrated here, provides a powerful way to quantify the contributions from each of these sources. In particular, the energy and moisture mixed into the PBL from above the PBL can be determined accurately from ground-based remote sensors using this approach.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Role of interfaces on the mechanical response of accumulative roll bonded nanometallic laminates investigated via dislocation dynamics simulations

Unraveling the effects of continuous dislocation interactions with interfaces, particularly at the nanometer length scales, is key to a broader understanding of plasticity, to material design and to material certification. To this end, this work proposes a novel discrete dislocation dynamics-based model for dislocation interface interactions tracking the fate of residual dislocation on interfaces. This new approach is used to predict the impact of dislocation/interface reactions on the overall mechanical behavior of accumulative roll bonded nanometallic laminates. The framework considers the dynamic evolution of the interface concurrent with a large network of dislocations, thus, accounting for the local short and long range effects of the dislocations under the external boundary conditions. Specifically, this study focuses on two-phase Fe/Cu nanometallic laminates, and investigates the role of the underlying elastic and plastic contrast of the Fe and the Cu layers on the composite response of the material. Moreover, the role of initial microstructures, resulting from processing is also investigated. Subsequently, the model is used to examine the effect of layer thickness and interface orientation relationship on the residual stresses of the relaxed microstructure. The associated mechanical response of these laminates are compared when loaded under normal direction compression, as well as shear compression. Finally, this work predicts a dominant effect of the layer thickness, as compared to the interface orientation relationship, on the macroscopic response and on the residual stresses of these nanolaminates, while the local dislocation transmission propensity through the interface is significantly influenced by the corresponding orientation relationship.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Mechanism and dynamics of fatty acid photodecarboxylase

Photoenzymes are rare biocatalysts driven by absorption of a photon at each catalytic cycle; they inspire development of artificial photoenzymes with valuable activities. Fatty acid photodecarboxylase (FAP) is a natural photoenzyme that has potential applications in the bio-based production of hydrocarbons, yet its mechanism is far from fully understood. RATIONALE To elucidate the mechanism of FAP, we studied the wild-type (WT) enzyme from Chlorella variabilis (CvFAP) and variants with altered active-site residues using a wealth of techniques, including static and time-resolved crystallography and spectroscopy, as well as biochemical and computational approaches. RESULTS A 1.8-Å-resolution CvFAP x-ray crystal structure revealed a dense hydrogen-bonding network positioning the fatty acid carboxyl group in the vicinity of the flavin adenine dinucleotide (FAD) cofactor. Structures solved from free electron laser and low-dose synchrotron x-ray crystal data further highlighted an unusual bent shape of the oxidized flavin chromophore, and showed that the bending angle (14°) did not change upon photon absorption (step 1) or throughout the photocycle. Calculations showed that bending substantially affected the energy levels of the flavin. Structural and spectroscopic analysis of WT and mutant proteins targeting two conserved active-site residues, R451 and C432, demonstrated that both residues were crucial for proper positioning of the substrate and water molecules and for oxidation of the fatty acid carboxylate by 1 FAD* (~300 ps in WT FAP) to form FAD ∙– (step 2). Time-resolved infrared spectroscopy demonstrated that decarboxylation occured quasi-instantaneously upon this forward electron transfer, consistent with barrierless bond cleavage predicted by quantum chemistry calculations and with snapshots obtained by time-resolved crystallography. Transient absorption spectroscopy in H 2 O and D 2 O buffers indicated that back electron transfer from FAD ∙– was coupled to and limited by transfer of an exchangeable proton or hydrogen atom (step 3). Unexpectedly, concomitant with FAD ∙– reoxidation (to a red-shifted form FAD RS ) in 100 ns, most of the CO 2 product was converted, most likely into bicarbonate (as inferred from FTIR spectra of the cryotrapped FAD RS intermediate). Calculations indicated that this catalytic transformation involved an active-site water molecule. Cryo-Fourier transform infrared spectroscopy studies suggested that bicarbonate formation (step 4) was preceded by deprotonation of an arginine residue (step 3). At room temperature, the remaining CO 2 left the protein in 1.5 μs (step 4'). The observation of residual electron density close to C432 in electron density maps derived from time-resolved and cryocrystallography data suggests that this residue may play a role in stabilizing CO 2 and/or bicarbonate. Three routes for alkane formation were identified by quantum chemistry calculations; the one shown in the figure is favored by the ensemble of experimental data. CONCLUSION Finally, we provide a detailed and comprehensive characterization of light-driven hydrocarbon formation by FAP, which uses a remarkably complex mechanism including unique catalytic steps. We anticipate that our results will help to expand the green chemistry toolkit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Revealing key structures for reversible sulfur redox in amorphous polymeric sulfur

Amorphous polymeric sulfur cathodes, such as sulfurized polyacrylonitrile (SPAN), enable high-energy lithium-sulfur batteries without cobalt or nickel, leveraging abundant sulfur. However, the limited in situ understanding of their synthesis and electrochemistry has impeded targeted optimization. Here, in this study, we integrate operando high-energy total scattering with sulfur K-edge X-ray absorption spectroscopy to monitor SPAN's formation and cycling in real time. Our results show that S-C bond formation halts further fusion of cyclized polyacrylonitrile, fostering π-π stacking and a transition from long-chain to short-chain sulfur-critical for reversible sulfur redox. These features synergistically minimize polysulfide dissolution and charge-transfer resistance, enabling optimized SPAN to achieve high capacity retention over 1,000 cycles. Operando X-ray absorption spectroscopy reveals that residual protons drive thiol-thione tautomerism, with lithium replacement during the first discharge causing ~20% irreversible capacity loss. To enhance performance, minimizing -NH groups and expanding pyridine networks are key. These findings transform SPAN optimization from empirical tuning to mechanism‑guided engineering and point the way towards sulfur loadings and energy densities competitive with state‑of‑the‑art Li‑ion cathodes.

25 ENERGY STORAGE↗
DOE OSTI2022

De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design

The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrel fold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel protein has been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the fold remains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold) symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbone sampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequence design protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences are highly stable and fold to the designed barrel curvature as determined by a 2.1 Å resolution crystal structure. The designs show robustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in the hydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diverse hydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major step towards the de novo design of functional TIM barrels.

Chu, Alexander E.↗
DOE OSTI2021

Impact of selenium addition to the cadmium-zinc-telluride matrix for producing high energy resolution X-and gamma-ray detectors

Abstract Both material quality and detector performance have been steadily improving over the past few years for the leading room temperature radiation detector material cadmium-zinc-telluride (CdZnTe). However, although tremendous progress being made, CdZnTe still suffers from high concentrations of performance-limiting defects, such as Te inclusions, networks of sub-grain boundaries and compositional inhomogeneity due to the higher segregation coefficient of Zn. Adding as low as 2% (atomic) Se into CdZnTe matrix was found to successfully mitigate many performance-limiting defects and provide improved compositional homogeneity. Here we report record-high performance of Virtual Frisch Grid (VFG) detector fabricated from as-grown Cd 0.9 Zn 0.1 Te 0.98 Se 0.02 ingot grown by the Traveling Heater Method (THM). Benefiting from superior material quality, we achieved superb energy resolution of 0.77% at 662 keV (as-measured without charge-loss correction algorithms) registered at room temperature. The absence of residual thermal stress in the detector was revealed from white beam X-ray topographic images, which was also confirmed by Infra-Red (IR) transmission imaging under cross polarizers. Furthermore, neither sub-grain boundaries nor their networks were observed from the X-ray topographic image. However, large concentrations of extrinsic impurities were revealed in as-grown materials, suggesting a high likelihood for further reduction in the energy resolution after improved purification of the starting material.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Binding and Translocation of Substrate Allosterically Promotes Functional Interactions Within the AlkB–AlkG Electron Transfer Complex

The alkane monooxygenase AlkB and rubredoxin AlkG form an electron transfer complex that hydroxylates terminal alkanes to produce alcohols. The recent cryoEM study of Fontimonas thermophila AlkB-AlkG complex revealed its architecture, including a dodecane (D12) substrate at the active site. However, FtAlkBG molecular mechanism of action of remains unknown. Here, in this study, we examined its dynamics and interactions by multiscale computations, including molecular dynamics simulations, elastic network models, and QM/MM of the oxygen activation mechanism at the AlkB catalytic site. D12 maintained stable interactions within the catalytic site during two MD runs, coordinated by hydrophobic residues L263-L264, I267, I133. A third extended run revealed that D12 could translocate to a membrane-exposed site near S49/F46 along a hydrophobic channel gated by I54. During this translocation, D12 was temporarily stabilized at intermediate sites IS1 (lined by I27/L30-G31/G50/L53-I54/P59/S124/A127-V128) and IS2 (I33-G34/L37/L45-F46/S49) before nearly exiting the protein, and diffused back to the active site, assisted by L30. Substrate binding and translocation across those intermediate sites affects the coupling between the iron centers in AlkBG, and interfacial interactions between AlkB-AlkG. The channel was further connected to the cytosol, near two surface-exposed arginines, potentially allowing for O 2 passage. The allosteric effects between D12 putative entry site, catalytic site and AlkB-AlkG interface were analyzed by ENM-based methods which confirmed the cooperative perturbation-responses and strongly correlated movements of residues belonging to those distal regions. Our study provides new mechanistic insights into key sites and their interactions that could be targeted for developing AlkB-variants with desirable alkane conversion functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

luoyunan/ECNet: First release

ECNet (evolutionary context-integrated neural network) is a deep learning model that guides protein engineering by predicting protein fitness from the sequence. It integrates local evolutionary context from homologous sequences that explicitly model residue-residue epistasis for the protein of interest with the global evolutionary context that encodes rich semantic and structural features from the enormous protein sequence universe.

Luo, Yunan↗