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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Synthesis, Structure, and Properties of the Complex Zintl Phase Eu 9 Zn 4.5 As 9 : A Candidate Topological Insulator and Thermoelectric Material

Reported are the synthesis and detailed analysis of the crystal and electronic structure of the novel Zintl phase Eu 9 Zn 4.5 As 9 . This material was identified in the densely populated Eu–Zn–As compositional space. For structure determination and for property measurements, suitable single crystals of this compound were grown from either Sn- or Pb-flux. Single-crystal X-ray diffraction methods indicate that Eu 9 Zn 4.5 As 9 crystallizes in the orthorhombic crystal system with the space group Pnma (a = 12.1953(7) Å, b = 4.3730(2) Å, c = 42.674(2) Å) and is formally isostructural to Ca 9 Mn 4+x Sb 9 , the less common “9–4–9” type. The structure is heavily disordered, with multiple partially occupied sites, yet, according to the Zintl-Klemm formalism, a charge-balanced composition (Eu 2+ ) 9 (Zn 2+ ) 4.5 (As 3− ) 9 is attained. Electronic structure calculations for a model, disorder-free structure indicate no energy gap between the valence and the conduction bands and suggest (semi)metallic behavior. Preliminary susceptibility measurements confirm the expected divalent nature of Eu 2+ ([Xe] 4 f 7 ground state).

Zintl phases↗
DOE OSTI2021

The Population of H ii Regions in NGC 7020

The galaxy NGC 7020 displays an exotic hexagonal ringlike central structure with conspicuous ansae located at two opposite vertices and a tenuous external ring populated by H ii regions. Inside and around the hexagonal structure, Hα emission is also present at the inner disk. To characterize the population of the H ii regions, as well as their ionizing clusters, we imaged NGC 7020 with narrowband Hα and nearby continuum filters attached to GMOS-S installed on the Gemini South telescope. We found 202 H ii regions or complexes of H ii regions evenly distributed between the outer ring and the central disk The nucleus and ansae also present Hα emission. The equivalent width of the Hα line (W {sub Hα}) is systematically greater at the regions of the outer ring relative to those of the inner disk. We discuss the influence of the metallicity gradient of the disk and the upper limit of the masses of the initial mass function on W {sub Hα}, and we conclude that the data are still consistent with the occurrence of a younger burst of H ii region formation in the outer ring. The central regions present more massive clusters, M ≥ 10{sup 6} M {sub ⊙}, than those of the outer ring (M ≤ 10{sup 6} M {sub ⊙}). Three clusters within 5″ of the nucleus present masses higher than 10{sup 8} M {sub ⊙}. The presence of diffuse Hα emission in the inner 5″ suggests gas flows in the nuclear region.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Hydrogen Evolution on Electrode‐Supported Pt n Clusters: Ensemble of Hydride States Governs the Size Dependent Reactivity

Abstract We report the size‐dependent activity and stability of supported Pt 1,4,7,8 for electrocatalytic hydrogen evolution reaction, and show that clusters outperform polycrystalline Pt in activity, with size‐dependent stability. To understand the size effects, we use DFT calculations to study the structural fluxionality under varying potentials. We show that the clusters can reshape under H coverage and populate an ensemble of states with diverse stoichiometry, structure, and thus reactivity. Both experiment and theory suggest that electrocatalytic species are hydridic states of the clusters (≈2 H/Pt). An ensemble‐based kinetic model reproduces the experimental activity trend and reveals the role of metastable states. The stability trend is rationalized by chemical bonding analysis. Our joint study demonstrates the potential‐ and adsorbate‐coverage‐dependent fluxionality of subnano clusters of different sizes and offers a systematic modeling strategy to tackle the complexities.

Zhang, Zisheng↗
DOE OSTI2023

Hydrogen Evolution on Electrode–Supported Ptn Clusters: Ensemble of Hydride States Governs the Size Dependent Reactivity

We report the size-dependent activity and stability of supported Pt1,4,7,8 for electrocatalytic hydrogen evolution reaction, and show that clusters outperform polycrystalline Pt in activity, with sizedependent stability. To understand the size effects, we use DFT calculations to study the structural fluxionality under varying potentials. We show that the clusters can reshape under H coverage and populate an ensemble of states with diverse stoichiometry, structure, and thus reactivity. Both experiment and theory suggest that electrocatalytic species are hydridic states of the clusters (~2 H/Pt). An ensemble-based kinetic model reproduces the experimental activity trend and reveals the role of metastable states. Furthermore, the stability trend is rationalized by chemical bonding analysis. Our joint study demonstrates the potential- and adsorbate-coverage-dependent fluxionality of subnano clusters of different sizes and offers a systematic modeling strategy to tackle the complexities.

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

DEMOS (Demographic Microsimulator Tool for Longitudinal Synthetic Population) [SWR-25-135] related to NLR SWR-26-076

The Demographic Microsimulator (DEMOS) is an agent-based simulation framework used to model the evolution of population demographic characteristics and lifecycle events, such as education attainment, marital status, and other key transitions. DEMOS modules are designed to capture the interdependencies between short-term and long-term lifecycle events, which are often influential in downstream transportation and land-use modeling. A key feature of DEMOS is its ability to track changes in an agent’s demographic status from year t to year t + 1. This structure allows the model to evolve populations over any user-defined time horizon. As a result, DEMOS is well suited for analyzing medium- and long-term transportation-related decisions, including household vehicle transactions (e.g., purchasing, selling, or replacing vehicles) and work location choices. Core features of DEMOS include the modeling of more than ten lifecycle events, behaviorally realistic patterns informed by long-running panel data, explicit representation of interdependencies among lifecycle processes, and a flexible, modular simulation architecture. A technical memorandum describing DEMOS is available here. The memorandum provides an overview of the framework’s functionality, model structure, input and output data, and its applications in transportation planning and broader policy analysis contexts. Interested readers are also encouraged to consult the paper listed below for additional details on the DEMOS methodology. Sun, Bingrong, Shivam Sharda, Venu M. Garikapati, Mohamed Amine Bouzaghrane, Juan Caicedo, Srinath Ravulaparthy, Isabel Viegas de Lima, Ling Jin, C. Anna Spurlock, and Paul Waddell. "Demographic Microsimulator for Integrated Urban Systems: Adapting Panel Survey of Income Dynamics to Capture the Continuum of Life." Transportation Research Record (2025): 03611981251333339.

Sun, Bingrong [National Laboratory of the Rockies ↗
DOE OSTI2020

Effects of social structure and management on risk of disease establishment in wild pigs

Contact heterogeneity among hosts determines invasion and spreading dynamics of infectious disease, thus its characterization is essential for identifying effective disease control strategies. Yet, little is known about the factors shaping contact networks in many 28 wildlife species and how wildlife management actions might affect contact networks. Wild pigs in North America are an invasive, socially-structured species that pose a health concern for domestic swine given their ability to transmit numerous devastating diseases 2 such as African swine fever (ASF). Using proximity loggers and GPS data from 48 wild pigs in Florida and South Carolina, USA, we employed a probabilistic framework to estimate weighted contact networks. We determined the effects of sex, social group, and spatial distribution (monthly home range overlap and distance) on wild pig contact. We also estimated the impacts of management-induced perturbations on contact and inferred their effects on ASF establishment in wild pigs with simulation. Social group membership was the primary factor influencing contacts. Between-group contacts depended primarily on space use characteristics, with fewer contacts among groups separated by >2 km and no contacts among groups >4 km apart within a month. Modeling ASF dynamics on the contact network demonstrated that indirect contacts resulting from baiting (a typical method of attracting wild pigs or game species to a site to enhance recreational hunting) increased the risk of disease establishment by ~33% relative to direct contact. Low-intensity population reduction (<5.9% of the population) had no detectable impact on contact structure but reduced predicted ASF establishment risk relative to no population reduction. Here, we demonstrate an approach for understanding the relative role of spatial, social, and individual-level characteristics in shaping contact networks and predicting their effects on disease establishment risk, thus providing insight for optimizing disease control in spatially- and socially-structured wildlife species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Molecular Design Principles for Photosystem I-Based Biohybrid Solar Fuel Catalysts

Direct solar-to-chemical conversion offers a compelling route to clean, dispatchable energy. Photosystem I (PSI), an evolutionarily optimized light-driven oxidoreductase, can be repurposed for solar-fuel production by coupling its photochemistry to catalytic interfaces. However, the molecular determinants that govern productive electron transfer to abiotic catalysts remain poorly understood. Here, we present molecular structures of active PSI-Pt nanoparticle (PtNP) biohybrids that reveal how protein architecture controls catalyst access, binding geometry, and photocatalytic efficiency. Removal of stromal subunits exposes the electron transfer chain and enables PtNP binding proximal to the F X cluster, demonstrating that steric occlusion limits access to native acceptor regions in PSI. In contrast, in trimeric PSI, PtNPs bind at multiple sites per monomer, but only a subset are positioned within electron transfer distance of terminal cofactors, resulting in a heterogeneous population of productive and nonproductive configurations. Structural analyses and molecular dynamics simulations define the interface topology, electrostatics, and cofactor-to-nanoparticle distances that govern catalyst binding and electron transfer. These results establish that catalytic inefficiency arises not only from intrinsic electron transfer constraints but also from the distribution of binding geometries imposed by the protein scaffold. Together, these findings provide a molecular framework linking protein structure to biohybrid function and define design principles for engineering PSI-based solar fuel systems and protein-nanomaterial interfaces for light-driven catalysis.

biohybrid↗
DOE OSTI2025

A Safe Response to Renewable Energy Hazards

The International Association of Fire Fighters (IAFF) and Underwriters Laboratories, LLC (UL) in conjunction with UL Solutions initiated a joint project in 2022 under an agreement with the United States Department of Energy-Office of Energy Efficiency and Renewable Energy (DOE-EERE). This project focused on two separate and important initiatives related to energy efficiency in residential buildings. Initiative 1: Fire Performance on Energy Efficient Exterior Walls. Initiative 2: Firefighting Tactics in Residential Properties with Building Energy Storage Systems (BESS). The project’s first initiative addresses concerns surrounding new technologies with enhanced, energy-efficient exterior walls installed on residential properties. The concerns of fire rapidly traveling vertically up the exterior of these walls were examined. This addressed a growing concern from the first responder community that many times, the fires on the exterior of residential buildings have already evolved into an attic fire by the time of arrival – making it problematic to address the fire scenario. The test plan for Initiative 1 incorporated a modified version of an American Society for Testing and Materials (ASTM) test method, ASTM E2707, Standard Test Method for Determining Fire Penetration of Exterior Wall Assemblies Using a Direct Flame Impingement Exposure, as the foundation of the research. The test method involved a wall structure intended to represent retrofit construction to evaluate how fire would spread vertically or laterally. The second aspect of the UL-IAFF Project focuses on the fire service response to Residential Battery Energy Storage System (RBESS) incidents. These simulation tests were constructed in the large-scale fire test facility at UL Solutions’ Northbrook, IL campus. A baseline test was conducted that involved a test structure with no batteries—shelving units populated with standardized commodities, representing a typical garage with cellulosic and plastic contents. Three additional tests have been conducted to generate data with the contribution of energy storage system (ESS) batteries to compare fire and explosion hazards against the baseline test. Through this work, fire service tactical considerations can be explored. From the data, the team can determine 1) the visual indicators of a residential fire that has involved an RBESS (or, potentially, other large batteries) and 2) the impact of fire service-initiated ventilation of the structure on the fire conditions and explosion risks.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Beyond Galaxy Bimodality: The Complex Interplay between Kinematic Morphology and Star Formation in the Local Universe

It is generally assumed that galaxies are a bimodal population in both star formation and structure; star-forming galaxies are disks, while passive galaxies host large bulges or are entirely spheroidal. Here we test this scenario by presenting a full census of the kinematic morphologies of a volume-limited sample of galaxies in the local universe extracted from the MaNGA galaxy survey. We measure the integrated stellar line-of-sight velocity to velocity dispersion ratio (V/σ) for 4574 galaxies in the stellar mass range 9.75 < logM $\star$ [M ⊙ ] < 11.75. We show that at fixed stellar mass, the distribution of V/σ is not bimodal, and that a simple separation between fast and slow rotators is oversimplistic. Fast rotators are a mixture of at least two populations, referred to here as dynamically cold disks and intermediate systems, with disks dominating in both total stellar mass and number. When considering star-forming and passive galaxies separately, the star-forming population is almost entirely made up of disks, while the passive population is mixed, implying an array of quenching mechanisms. Passive disks represent ~30% (both in number and mass) of passive galaxies, nearly a factor of two higher than that of slow rotators, reiterating that these are an important population for understanding galaxy quenching. These results paint a picture of a local universe dominated by disky galaxies, most of which become somewhat less rotation-supported upon or after quenching. While spheroids are present to a degree, they are certainly not the evolutionary end point for the majority of galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The Critical Need for Innovations in Instruments and Techniques to Enable In-Situ Cold Ion and Cold Electron Measurements within the Magnetosphere

Relatively few studies have focused on the cold plasma populations of the magnetosphere due to difficulties associated with obtaining measurements. The cold particle populations are defined here as those with total energy approximately <100 eV which is an energy range for which measurements are difficult (regardless of species), but which often make up the bulk of the plasma density. These populations have known and suspected impacts on the structure and dynamics of the magnetosphere. Unfortunately, the lack of accurate measurements of the cold ion and cold electron populations through the magnetosphere makes closure of these science questions extremely difficult if not impossible. In a complex system of interconnected parts like the Earth’s magnetosphere, a lack of understanding of one part of the system (the cold electron and ion populations) is disabling. Hence, until cold electron and cold ion measurements are obtained robustly with every mission, the magnetospheric plasma environment cannot be completely understood. This will require innovations in plasma spectrometers and associated techniques required to obtain high-fidelity in-situ measurements of the cold ion and cold electron populations in the magnetosphere. This paper seeks to review the instruments and techniques that have been used to date and present possible options for future missions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach

Codon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to result from various selective pressures, including selection for efficient ribosome elongation, accurate translation, mRNA secondary structure, and/or protein folding. Given the critical link between protein folding and protein function, numerous studies have analyzed the relationship between codon usage and protein structure. The results from these studies have often been contradictory, likely reflecting the differing methods used for measuring codon usage and the failure to appropriately control for confounding factors, such as differences in amino acid usage between protein structures and changes in the frequency of different structures with gene expression. Here we take an explicit population genetics approach to quantify codon-specific shifts in natural selection related to protein structure in S. cerevisiae and E. coli. Unlike other metrics of codon usage, our approach explicitly separates the effects of natural selection, scaled by gene expression, and mutation bias while naturally accounting for a region’s amino acid usage. Bayesian model comparisons suggest selection on codon usage varies only slightly between helix, sheet, and coil secondary structures and, similarly, between structured and intrinsically-disordered regions. Similarly, in contrast to previous findings, we find selection on codon usage only varies slightly at the termini of helices in E. coli. Using simulated data, we show this previous work indicating “non-optimal” codons are enriched at the beginning of helices in S. cerevisiae was due to failure to control for various confounding factors (e.g. amino acid biases, gene expression, etc.), and rather than selection to modulate cotranslational folding. Our results reveal a weak relationship between codon usage and protein structure, indicating that differences in selection on codon usage between structures are slight. In addition to the magnitude of differences in selection between protein structures being slight, the observed shifts appear to be idiosyncratic and largely codon-specific rather than systematic reversals in the nature of selection. Overall, our work demonstrates the statistical power and benefits of studying selective shifts on codon usage or other genomic features from an explicitly evolutionary approach. Limitations of this approach and future potential research avenues are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Toggling Stereochemical Activity through Interstitial Positioning of Cations between 2D V 2 O 5 Double Layers

The 5/6s 2 lone-pair electrons of p-block cations in their lower oxidation states are a versatile electronic and geometric structure motif that can underpin lattice anharmonicity and often engender electronic and structural instabilities that underpin the function of active elements in nonlinear optics, thermochromics, thermoelectrics, neuromorphic computing, and photocatalysis. In contrast to periodic solids where lone-pair-bearing cations are part of the structural framework, installing lone-pair-bearing cations in the interstitial sites of intercalation hosts provides a means of a systematically modulating electronic structure through the choice of the group and the period of the inserted cation while preserving the overall framework connectivity. The extent of stereochemical activity and the energy positioning of lone-pair-derived mid-gap states depend on the cation identity, stoichiometry, and strength of anion hybridization. V 2 O 5 polymorphs are versatile insertion hosts that can accommodate a broad range of s-, p-, and d-block cations. However, the insertion of lone-pair-bearing cations remains largely underexplored. In this article, we examine the implications of varying the 6s 2 cations situated in interlayer sites between condensed [V 4 O 10 ] n double layers. Systematic modulations of lattice distortions, electronic structure, and magnetic ordering are observed with increasing strength of stereochemical activity from group 12 to group 14 cations. We compare and contrast p-block-layered M x V 2 O 5 (M = Hg, Tl, and Pb) compounds and map the significance of local off-centering arising from the stereochemical activity of lone-pair cations to the emergence of filled antibonding lone-pair 6s 2 –O 2p-hybridized mid-gap states mediated by second-order Jahn–Teller distortions. Crystallographic studies of cation coordination environments and the resulting modulation of V–V interactions have been used in conjunction with variable-energy hard X-ray photoelectron spectroscopy measurements, first-principles electronic structure calculations, and crystal orbital Hamilton population analyses to decipher the origins of stereochemical activity. Magnetic susceptibility measurements reveal antiferromagnetic signatures for all the three compounds. However, the differences in V–V interactions significantly affect the energy balance of the superexchange interactions, resulting in an ordering temperature of 160 and 260 K for Hg 0.5 V 2 O 5 and δ-Tl 0.5 V 2 O 5 , respectively, as compared to 7 K for δ-Pb 0.5 V 2 O 5 . In δ-Pb 0.5 V 2 O 5 , the strong stereochemical activity of electron lone pairs and the resulting electrostatic repulsions enforce superlattice ordering, which strongly modifies the electronic localization patterns along the [V 4 O 10 ] slabs, resulting in disrupted magnetic ordering and an anomalously low ordering temperature. The results demonstrate a versatile strategy for toggling the stereochemical activity of electron lone pairs to modify the electronic structure near the Fermi level and to mediate superexchange interactions.

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

Identification of more than 40 gravitationally magnified stars in a galaxy at redshift 0.725

Strong gravitational magnification enables the detection of faint background sources and allows researchers to resolve their internal structures and even identify individual stars in distant galaxies. Highly magnified individual stars are useful in various applications, including studies of stellar populations in distant galaxies and constraining dark matter structures in the lensing plane. However, these applications have been hampered by the small number of individual stars observed, as typically one or a few stars are identified from each distant galaxy. Here, we report the discovery of more than 40 microlensed stars in a single galaxy behind Abell 370 at redshift of 0.725 (dubbed ‘the Dragon arc’) when the Universe was half of its current age, using James Webb Space Telescope observations with the time-domain technique. These events were found near the expected lensing critical curves, suggesting that these are magnified stars that appear as transients from intracluster stellar microlenses. Through multi-wavelength photometry, we constrained their stellar types and found that many of them are consistent with red giants or supergiants magnified by factors of hundreds. Furthermore, this finding reveals a high occurrence of microlensing events in the Dragon arc and demonstrates that time-domain observations by the James Webb Space Telescope could lead to the possibility of conducting statistical studies of high-redshift stars.

Early universe↗
DOE OSTI2023

Deriving spatially explicit direct and indirect interaction networks from animal movement data

Abstract Quantifying spatiotemporally explicit interactions within animal populations facilitates the understanding of social structure and its relationship with ecological processes. Data from animal tracking technologies (Global Positioning Systems [“GPS”]) can circumvent longstanding challenges in the estimation of spatiotemporally explicit interactions, but the discrete nature and coarse temporal resolution of data mean that ephemeral interactions that occur between consecutive GPS locations go undetected. Here, we developed a method to quantify individual and spatial patterns of interaction using continuous‐time movement models (CTMMs) fit to GPS tracking data. We first applied CTMMs to infer the full movement trajectories at an arbitrarily fine temporal scale before estimating interactions, thus allowing inference of interactions occurring between observed GPS locations. Our framework then infers indirect interactions—individuals occurring at the same location, but at different times—while allowing the identification of indirect interactions to vary with ecological context based on CTMM outputs. We assessed the performance of our new method using simulations and illustrated its implementation by deriving disease‐relevant interaction networks for two behaviorally differentiated species, wild pigs ( Sus scrofa ) that can host African Swine Fever and mule deer ( Odocoileus hemionus ) that can host chronic wasting disease. Simulations showed that interactions derived from observed GPS data can be substantially underestimated when temporal resolution of movement data exceeds 30‐min intervals. Empirical application suggested that underestimation occurred in both interaction rates and their spatial distributions. CTMM‐Interaction method, which can introduce uncertainties, recovered majority of true interactions. Our method leverages advances in movement ecology to quantify fine‐scale spatiotemporal interactions between individuals from lower temporal resolution GPS data. It can be leveraged to infer dynamic social networks, transmission potential in disease systems, consumer–resource interactions, information sharing, and beyond. The method also sets the stage for future predictive models linking observed spatiotemporal interaction patterns to environmental drivers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Portable quantitative confocal Raman spectroscopy: Non-destructive approach of the carbonation chemistry and kinetics

Highlights: • Raman spectroscopy was used to monitor carbonation of portlandite • The approach was non-destructive, continuous, and performed within the material • Carbonation was identified coupling Raman spectroscopy and chemometrics • Kinetics was calculated for one portlandite thickness at different CO{sub 2}-percentages Carbonation is one major alteration process of cementitious materials. It can be monitored through several methods, all destructive. In this study, some preliminary investigations were conducted to monitor the carbonation process of pure portlandite with an in situ and non-destructive spectroscopic method. This complementary approach was motivated by a literature review indicating the benefits of Raman spectroscopy, but requiring innovative approaches for data acquisition and analysis. The material was selected to validate this spectroscopic monitoring, coupled with chemometrics tools to allowing an early detection of the carbonation reaction through a structure identified in the spectra data population. The carbonation occurred abruptly, and spectra analysis indicated the occurrence of phases synonymous of microstructural evolutions. Varying the atmospheric percentage of CO{sub 2} (0.04% - 4%) conducted to an appreciation of the kinetics of the carbonation front through the same thickness of portlandite.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Computational Investigation of the Role of Active Site Heterogeneity for aSupported Organovanadium(III) Hydrogenation Catalyst

A crucial consideration for supported heterogeneous catalysts is the nonuniformity of the active sites, particularly for supported organometallic catalysts. Standard spectroscopic techniques, such as X-ray absorption spectroscopy, reflect the nature of the most populated sites, which are often intrinsically structurally distinct from the most active catalytic sites. Additionally, with computational models, often, only a few representative structures are used to depict catalytic active sites on a surface, even though there are numerous observable factors of surface heterogeneity that contribute to the kinetically favorable active species. A previously reported study on the mechanism of a surface organovanadium-(III) catalyst [(SiO 2 )V III (Mes)(THF)] for styrene hydrogenation yielded two possible mechanisms: heterolytic cleavage and redox cycling. These two mechanistic scenarios are challenging to differentiate experimentally since the kinetic readouts of the catalyst are identical. To showcase the importance of modeling surface heterogeneity and its effect on catalytic activity, density functional theory (DFT) computational models of a series of potential active sites of [(SiO 2 )V III (Mes)(THF)] for the reaction pathways are applied in combination with kinetic Monte Carlo (kMC) simulations. Computed results were then compared to the previously reported experimental kinetic study: (1) DFT free-energy reaction pathways indicated the likely active site and pathway for styrene hydrogenation, a heterolytic cleavage pathway requiring a bare tripodal vanadium site. (2) From the kMC simulations, a mixture of different bond lengths from the support oxygen to the metal center was required to qualitatively describe the experimentally observed kinetic aspects of a supported organovanadium(III) catalyst for olefin hydrogenation. This work underscores the importance of modeling surface heterogeneity in computational catalysis.

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

Unsupervised learning of representative local atomic arrangements in molecular dynamics data

Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the right questions of MD data we may miss critical information hidden within it. Here we combine dimensionality reduction (UMAP) and unsupervised hierarchical clustering (HDBSCAN) to quantitatively characterize prevalent coordination environments of chemical species within MD data. By focusing on local coordination, we significantly reduce the amount of data to be analyzed by extracting all distinct molecular formulas within a given coordination sphere. We then efficiently combine UMAP and HDBSCAN with alignment or shape-matching algorithms to partition these formulas into structural isomer families indicating their relative populations. The method was employed to reveal details of cation coordination in electrolytes based on molecular liquids.

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

Robust reconstruction of single-cell RNA-seq data with iterative gene weight updates

Single-cell RNA-sequencing technologies have greatly enhanced our understanding of heterogeneous cell populations and underlying regulatory processes. However, structural (spatial or temporal) relations between cells are lost during cell dissociation. These relations are crucial for identifying associated biological processes. Many existing tissue-reconstruction algorithms use prior information about subsets of genes that are informative with respect to the structure or process to be reconstructed. When such information is not available, and in the general case when the input genes code for multiple processes, including being susceptible to noise, biological reconstruction is often computationally challenging. We propose an algorithm that iteratively identifies manifold-informative genes using existing reconstruction algorithms for single-cell RNA-seq data as subroutine. We show that our algorithm improves the quality of tissue reconstruction for diverse synthetic and real scRNA-seq data, including data from the mammalian intestinal epithelium and liver lobules.

59 BASIC BIOLOGICAL SCIENCES↗