Recent advances toward the bioconversion of methane and methanol in synthetic methylotrophs
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Gregory, Gwendolyn J. (ORCID:0000000283919201)↗
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Ventilation and Indoor Air Quality in Recently Constructed U.S. Homes: Measured Data From Select Southeastern States
Little data is available that quantifies IAQ or associates contaminant levels with air exchange in U.S. homes. To address this gap, the U.S. Department of Energy (DOE) Building America Program conducted a study to characterize IAQ in U.S. homes constructed since 2013, along with presence, functionality, and occupant use of control measures. Specific objectives of this study effort included: Measuring time-integrated concentrations and temporal profiles of established contaminants of concern; monitoring the use of ventilation equipment; and tracking activities that impact air pollutant emissions and removal processes in typical homes in various climate zones; Characterizing the prevalence, type, and installed performance of mechanical ventilation equipment in new homes; exploring regional variations in system designs and performance; Investigating associations between contaminant levels and the presence of control measures including whole-house mechanical ventilation (WHMV). The study engaged research teams to collect data at a regional level. This report introduces the study protocol and presents and discusses high-level results obtained from Florida Solar Energy Center (FSEC) data collection efforts in the southeastern U.S. states of Florida, Georgia, and South Carolina.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Recent advances and applications of deep learning methods in materials science
Deep learning (DL) is one of the fastest-growing topics in materials data science, with rapidly emerging applications spanning atomistic, image-based, spectral, and textual data modalities. DL allows analysis of unstructured data and automated identification of features. The recent development of large materials databases has fueled the application of DL methods in atomistic prediction in particular. In contrast, advances in image and spectral data have largely leveraged synthetic data enabled by high-quality forward models as well as by generative unsupervised DL methods. In this article, we present a high-level overview of deep learning methods followed by a detailed discussion of recent developments of deep learning in atomistic simulation, materials imaging, spectral analysis, and natural language processing. For each modality we discuss applications involving both theoretical and experimental data, typical modeling approaches with their strengths and limitations, and relevant publicly available software and datasets. We conclude the review with a discussion of recent cross-cutting work related to uncertainty quantification in this field and a brief perspective on limitations, challenges, and potential growth areas for DL methods in materials science.
36 MATERIALS SCIENCE↗
C 12 ( n , n 1 ′ γ ) partial γ -ray cross section measured using the GENESIS array
Improved neutron inelastic scattering cross sections have repeatedly been identified as a top priority nuclear data need, important for basic science and a range of applications in nuclear energy, stockpile stewardship, and proliferation detection. For the C 12 ( n , n ′ γ ) reaction in particular, recent measurements have unveiled some structural discrepancies, demonstrating incongruities among themselves and in relation to the ENDF/B-VIII.0 nuclear data evaluation. To help resolve these disagreements, a measurement was performed at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory using a broad-spectrum neutron beam and a 99.8% pure natural carbon target. The Gamma Energy Neutron Energy Spectrometer for Inelastic Scattering (GENESIS) was employed to measure energy-differential γ -ray emission spectra as a function of incident neutron energy in the energy range of 5.5 to 16.7 MeV. The C 12 partial γ -ray cross sections were extracted at 63 ∘ , 122 . 5 ∘ , and 150 ∘ with respect to the incoming neutron beam and integrated using angular distribution data available in the literature. The data show agreement with a recent literature measurement and evaluation from 11 to 15 MeV, but indicate a larger cross section for incident neutron energies between 5.5 and 8.5 MeV. The measured relative angular distributions are also reported and were found to agree with evaluation. Published by the American Physical Society 2025
Gordon, J. M. (ORCID:0009000789886897)↗
Fostering Geothermal Machine Learning Success: Elevating Big Data Accessibility and Automated Data Standardization in the Geothermal Data Repository
The Department of Energy's (DOE's) Geothermal Data Repository (GDR) has implemented improvements to both its data lakes and its data standards and automated data pipelines. The GDR data lakes have reduced storage and compute-related barriers to using large geothermal datasets, enabling these large datasets to be accessed by anyone with a modern computer and internet access. More recently, the GDR has been working to further reduce barriers through streamlining the data intake process, educating users on the process and requirements, and helping users access data from the data lakes. These improvements have augmented the quantity of datasets the GDR is able to accept into its data lakes and have enabled users who are new to cloud tools to access these datasets more easily, overall increasing the accessibility of big geothermal data for use in machine learning and other projects. In addition, the GDR now has built-in data standards and pipelines for drilling data, geospatial data, and distributed acoustic sensing (DAS) data. These standardization efforts aim to enhance the real-world applicability of geothermal machine learning outcomes by improving the quality of training data. Specifically, through standardizing high-value datasets, the GDR is reducing project-specific data curation requirements, thus allowing more time for actual research. By automating this process, the burden of standardization is lifted from the user, ultimately increasing the availability of standardized data. This paper provides an update on recent improvements made to the GDR's data lakes and automated data pipelines, including: (1) streamlining the data lake intake process, (2) better educating users on the process and requirements through a new data lakes page, (3) adding data lake direct access links to GDR data lake submission pages, (4) implementing a DAS data pipeline to convert DAS data uploaded in SEG-Y format to a standardized hierarchical data format v5 (HDF5), (5) extending this pipeline to encompass data in the GDR data lake, (6) adding metadata requirements for geospatial data, (7) making user interface/user experience (UX) enhancements to the data pipelines' documentation pages, and (8) improving the GDR's data standards and pipelines pages to better guide users in ensuring that their data is standardized by the GDR's automated data pipelines. 2024 Geothermal Resources Council. All rights reserved.
accessibility↗
Nuclear Data Sheets for A=123
Experimental nuclear structure and decay data are evaluated for all of 15 known nuclides of mass 123 (Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe, Cs, Ba, La, Ce). For each nuclide, detailed evaluated spectroscopic information is presented in each reaction and decay, and the best values combining all available data are recommended for level properties, γ and β radiations, and other spectroscopic properties. No excited states have been identified in 123 Ru, 123 Rh and 123 Pd. For 123 Ag, the long-predicted 1/2 – β-emitting isomer has been identified at 60-keV by 2019Ch24 recently, resolving unknown excitation energies in the level scheme that was previously available only from isomeric decays of two isomers (202 ns and 393 ns) with the position and spin-parity of the former remaining unknown. Significant discrepancies exist between data on high-spin sequences based on 11/2 (–) isomer in 123 Cd (2002Hw01 and 2016Re05), which needs to be resolved with further experimental investigation. In 123 Cs, the 114-ns isomer as the πg 9/2 bandhead proposed at 231.6+x by 2000Gi12 has been resolved by 2004Si26 and 2004Si27 to be the 328-keV level that is proposed by 2000Gi12 as a separate level. Excited states in 123 La and 123 Ce have only been studied via (HI, xnγ) reactions, with their base levels and thus excitation energies remaining unknown. The β– decay schemes for daughter nuclide 123 Cd, 123 In and 123 Sn and the ε decay schemes for 123 Xe, 123 Cs and 123 Ba are considered incomplete due to large gaps between the highest observed excited levels and the Q-values. 123 Sn, 123 Sb, 123 Te and 123 I are the most extensively studied nuclides via various reactions and decays. Furthermore, this work supersedes earlier full evaluations of A=123 by 2004Oh11, 1993Oh12, 1980Ta02 and 1972Au10.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Calibration of Distributed Temperature Sensors Using Commercially Available SMF-28 Optical Fiber From 22 °C to 1000 °C
Optical frequency domain reflectometry (OFDR) is a family of optical techniques which can be used to produce distributed temperature measurements from the spectral shift of an interference pattern based on the Rayleigh backscatter signature of an optical fiber. Adaptive signal processing techniques have recently been used with OFDR to record meaningful spectral shift data from commercially available SMF-28 optical fibers heated beyond 950 °C. Furthermore, a correlation between the measured spectral shift and temperature has not yet been developed at these high temperatures. To extend the measurable temperature range of OFDR in SMF-28, this work describes the development of such a correlation from room temperature (22 °C) to 1000 °C. The relationship between spectral shift and temperature change over this range was found to be best characterized by the fourth-order polynomial ΔT=(-4.241 * 10 -11 )S 4 + (-2.017 * 10 -7 )S 3 + (-3.677 * 10 -4 )S 2 + (-0.8057)S, where ΔT represents the temperature difference compared to the reference temperature, and S represents the spectral shift measured by the fibers. The calibration developed in this work assumes that the fiber has been fully annealed by heating the fiber to 1000 °C for a few hours. This paper is the first to demonstrate the calibration and use of SMF-28 distributed optical fiber sensors up to 1000 °C, enabled using adaptive OFDR-based signal processing.
47 OTHER INSTRUMENTATION↗
Ion Mobility Spectrometry-Mass Spectrometry for High-Throughput Analysis
Ion mobility spectrometry is a widely used analytical technique providing gas phase separation of molecules. It has received increasing attention in the recent years with the advancement in technology development and the availability of commercial instruments. In this chapter, we introduced the ion mobility fundamental theory and provided examples of IMS applications, especially for isomer separation, collision cross section database generation, high throughput analysis workflows, software tools for IMS data analysis, and ongoing high resolution SLIM IMS development. While IMS is not yet routinely utilized in drug discovery and pharmaceutical industry, there has been increased interest in high throughput library screening and antibody characterization. With all the ongoing development in IMS technology and informatics, we foresee more and more exciting applications of high throughput IMS analysis in different fields including omics studies, drug discovery and clinical applications in the near future.
Ross, Dylan H.↗
Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution
A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution. (Model and code can be found at imageomics.github.io/phylo-diffusion)
Khurana, Mridul↗
Rethinking the Minamata Tragedy: What Mercury Species Was Really Responsible?
Industrial release of mercury into the local Minamata environment with consequent poisoning of local communities through contaminated fish and shellfish consumption is considered the classic case of environmental mercury poisoning. However, the mercury species in the factory effluent has proved controversial, originally suggested as inorganic, and more recently as methylmercury species. In this investigation, we used newly available methods to re-examine the cerebellum of historic Cat 717, which was fed factory effluent mixed with food to confirm the source. Synchrotron high-energy-resolution fluorescence detection-X-ray absorption spectroscopy revealed sulfur-bound organometallic mercury with a minor β-HgS phase. Density functional theory indicated energetic preference for α-mercuri-acetaldehyde as a waste product of aldehyde production. The consequences of this alternative species in the “classic” mercury poisoning should be re-evaluated.
54 ENVIRONMENTAL SCIENCES↗
Native Architecture of Wheat Straw Cell Walls: A Unified Model from X-ray Scattering and Solid-State NMR
Plant secondary cell walls constitute the dominant reservoir of renewable biomass, comprising tightly packed cellulose, hemicellulose, and lignin at the nanoscale. Recent advances in solid-state NMR spectroscopy and the availability of small-angle X-ray scattering for biomass characterization have led to an accumulation of experimental data on cell wall organization, yet no explicit structure model has simultaneously satisfied both Xray and NMR observations. Using wheat straw as a model system, we propose a structural framework consistent with current knowledge of cellulose biosynthesis, X-ray scattering data, and one- and two-dimensional 13 C solid-state NMR spectra. In this model, 18-chain elementary fibrils align in parallel and populate the cross-section at random. Arabinose-substituted xylan shows no conformational dependence for cellulose-binding in wheat, and only a minor fraction of 2-fold xylan appears in close proximity to cellulose, unlike in Arabidopsis, where xylan is more tightly attached to the cellulose surface. While NMR data cannot unambiguously resolve the internal arrangement of the 18 glucan chains, X-ray scattering profiles uniquely constrain the fibril size and exclude the possibility of tight bundling in the intact walls. The specific interaction between the matrix polymers and the cellulose elementary fibrils must be reconsidered in light of the small interfibril spaces, which bring the matrix components into spatial proximity with cellulose even in the absence of attractive interactions. These findings provide fundamental molecular-level insight into cellulose fibril architecture and matrix−polymer interactions, resolving longstanding discrepancies between spectroscopic and scattering data and advancing our understanding of biopolymer assembly into structurally and functionally versatile lignocellulosic biomaterials.
Carbohydrates↗
Evaluating the Potential and Challenges of an Uncertainty Quantification Method for Long Short–Term Memory Models for Soil Moisture Predictions
Recently, recurrent deep networks have shown promise to harness newly available satellite–sensed data for long–term soil moisture projections. However, to be useful in forecasting, deep networks must also provide uncertainty estimates. Here we evaluated Monte Carlo dropout with an input–dependent data noise term (MCD+N), an efficient uncertainty estimation framework originally developed in computer vision, for hydrologic time series predictions. MCD+N simultaneously estimates a heteroscedastic input–dependent data noise term (a trained error model attributable to observational noise) and a network weight uncertainty term (attributable to insufficiently constrained model parameters). Although MCD+N has appealing features, many heuristic approximations were employed during its derivation, and rigorous evaluations and evidence of its asserted capability to detect dissimilarity were lacking. To address this, we provided an in–depth evaluation of the scheme's potential and limitations. We showed that for reproducing soil moisture dynamics recorded by the Soil Moisture Active Passive (SMAP) mission, MCD+N indeed gave a good estimate of predictive error, provided that we tuned a hyperparameter and used a representative training data set. The input–dependent term responded strongly to observational noise, while the model term clearly acted as a detector for physiographic dissimilarity from the training data, behaving as intended. However, when the training and test data were characteristically different, the input–dependent term could be misled, undermining its reliability. Additionally, due to the data–driven nature of the model, data noise also influences network weight uncertainty, and therefore the two uncertainty terms are correlated. Altogether, this approach has promise, but care is needed to interpret the results.
54 ENVIRONMENTAL SCIENCES↗
Flexible metal–gas batteries: a potential option for next-generation power accessories for wearable electronics
Flexible metal–gas batteries have become increasingly attractive for use in wearable electronics in the recent years due to their large theoretical energy density and superior adaptability to irregular geometric surfaces, such as the human body. With continuous improvements in design strategies and assembly technologies, the fabrication of various advanced flexible metal–gas batteries has been attempted. In spite of these efforts, the synchronous integration of high flexibility, safety, comfort, and high performance into flexible metal–gas batteries with specifically functionalized configurations still remains a formidable challenge. To resolve these dilemmas, the redesign of cathode catalysts, gel polymer electrolyte, and battery configurations/components has been investigated. In this paper, we review the recent technical advances together with the major dilemmas facing currently available flexible metal–gas batteries, highlighting how flexible cathodes and gel polymer electrolytes with various structures and components can affect the electrochemical performance and functionality of flexible metal–gas batteries. Flexible Zn–air, Li–O 2 /air, and Li–CO 2 batteries are mainly exemplified to elucidate their promising potential. Finally, based on our considerations, unresolved technical hurdles and future research perspectives involving flexible metal–gas batteries for wearable electronics are proposed.
25 ENERGY STORAGE↗
Thermal Aging Effects on the Yield and Tensile Strength of 9Cr-1Mo-V (Grade 91)
The long-term exposure of 9Cr-1Mo-V (Grade 91) steel to elevated temperature can have a significant effect on reducing its yield and tensile strength. The yield and tensile strength changes, in turn, have potential implications to the assurance of the integrity of components constructed with this material over their design or intended lifetime. The ASME Boiler & Pressure Vessel Code (BPVC), Section III, Division 5 (III-5, high temperature reactors) provides tabulated reduction factors for Grade 91 yield and tensile strength as a function of exposure temperature and time up to 300,000 h. ASME BPVC III-5 s intent to extend these factors to an exposure duration of 500,000 h, the lack of available historic information to support the existing factors, and the recent development of a physics-based prediction model for ASME BPVC application are prime motivation for this study. This work describes results of the conventional time-temperature Hollomon–Jaffe parameter, strength reduction ratio prediction method using an updated, extensive Grade 91 unaged and related aged material strength database. The method, previously used by Oak Ridge National Laboratory in its evaluation of Grade 91 and likely used in development of the existing BPVC III-5 reduction factors, provides strength reduction ratio predictions useful for general component fitness-for-service assessments and for computing BPVC III-5 reduction factors as defined. Specific reduction factors to 500,000 h at 650 °C applicable to ASME BPVC III-5 are computed from the strength reduction ratios.
36 MATERIALS SCIENCE↗
Enhancement of harmonic generation by an intense driving laser with high-order waveguide modes in a high-pressure gas-filled hollow waveguide
High-order harmonics have been widely used as reliable tabletop coherent radiation sources recently, but their applications have often been limited by the available pulse energy. Here, we report that by using an overdriven intense laser in a long waveguide with high-pressure gas, phase matching can be achieved in three distinct “regimes”. In the third regime, favorable phase matching is achieved at near-axis positions to enhance harmonic yields. Our results are supported by a full theoretical analysis, and we demonstrate that coupling of the driving laser with the high-order waveguide modes (instead of the fundamental mode used in most prior experiments) is responsible for achieving phase matching. Furthermore, we establish that this phase matching (and harmonic enhancement) is robust, and a scaling relation is derived for the necessary waveguide and gas parameters, allowing our predictions to be tested immediately in any laboratory today.
Li, Baochang [Nanjing University of Science and Te↗
Assessing the release, transport, and retention of radioactive aerosols from hypothetical breaches in spent fuel storage canisters
Interim dry storage of spent nuclear fuel involves storing the fuel in welded stainless-steel canisters. Under certain conditions, the canisters could be subjected to environments that may promote stress corrosion cracking leading to a risk of breach and release of aerosol-sized particulate from the interior of the canister to the external environment through the crack. Research is currently under way by several laboratories to better understand the formation and propagation of stress corrosion cracks, however little work has been done to quantitatively assess the potential aerosol release. The purpose of the present work is to introduce a reliable generic numerical model for prediction of aerosol transport, deposition, and plugging in leak paths similar to stress corrosion cracks, while accounting for potential plugging from particle deposition. The model is dynamic (changing leak path geometry due to plugging) and it relies on the numerical solution of the aerosol transport equation in one dimension using finite differences. The model’s capabilities were also incorporated into a Graphical User Interface (GUI) that was developed to enhance user accessibility. Model validation efforts presented in this paper compare the model’s predictions with recent experimental data from Sandia National Laboratories (SNL) and results available in literature. We expect this model to improve the accuracy of consequence assessments and reduce the uncertainty of radiological consequence estimations in the remote event of a through-wall breach in dry cask storage systems.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
The Distinctive Evolution of orfX Clostridium parabotulinum Strains and Their Botulinum Neurotoxin Type A and F Gene Clusters Is Influenced by Environmental Factors and Gene Interactions via Mobile Genetic Elements
Of the seven currently known botulinum neurotoxin-producing species of Clostridium, C. parabotulinum, or C. botulinum Group I, is the species associated with the majority of human botulism cases worldwide. Phylogenetic analysis of these bacteria reveals a diverse species with multiple genomic clades. The neurotoxins they produce are also diverse, with over 20 subtypes currently represented. The existence of different bont genes within very similar genomes and of the same bont genes/gene clusters within different bacterial variants/species indicates that they have evolved independently. The neurotoxin genes are associated with one of two toxin gene cluster types containing either hemagglutinin (ha) genes or orfX genes. These genes may be located within the chromosome or extrachromosomal elements such as large plasmids. Although BoNT-producing C parabotulinum bacteria are distributed globally, they are more ubiquitous in certain specific geographic regions. Notably, northern hemisphere strains primarily contain ha gene clusters while southern hemisphere strains have a preponderance of orfX gene clusters. OrfX C. parabotulinum strains constitute a subset of this species that contain highly conserved bont gene clusters having a diverse range of bont genes. While much has been written about strains with ha gene clusters, less attention has been devoted to those with orfX gene clusters. The recent sequencing of 28 orfX C. parabotulinum strains and the availability of an additional 91 strains for analysis provides an opportunity to compare genomic relationships and identify unique toxin gene cluster characteristics and locations within this species subset in depth. The mechanisms behind the independent processes of bacteria evolution and generation of toxin diversity are explored through the examination of bacterial relationships relating to source locations and evidence of horizontal transfer of genetic material among different bacterial variants, particularly concerning bont gene clusters. Analysis of the content and locations of the bont gene clusters offers insights into common mechanisms of genetic transfer, chromosomal integration, and development of diversity among these genes.
59 BASIC BIOLOGICAL SCIENCES↗