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Li, Bing

Publications and source records attributed to Li, Bing.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Comparative genomics reveals the high diversity and adaptation strategies of Polaromonas from polar environments

Abstract Background Bacteria from the genus Polaromonas are dominant phylotypes found in a variety of low-temperature environments in polar regions. The diversity and biogeographic distribution of Polaromonas have been largely expanded on the basis of 16 S rRNA gene amplicon sequencing. However, the evolution and cold adaptation mechanisms of Polaromonas from polar regions are poorly understood at the genomic level. Results A total of 202 genomes of the genus Polaromonas were analyzed, and 121 different species were delineated on the basis of average nucleotide identity (ANI) and phylogenomic placements. Remarkably, 8 genomes recovered from polar environments clustered into a separate clade (‘polar group’ hereafter). The genome size, coding density and coding sequences (CDSs) of the polar group were significantly different from those of other nonpolar Polaromonas . Furthermore, the enrichment of genes involved in carbohydrate and peptide metabolism was evident in the polar group. In addition, genes encoding proteins related to betaine synthesis and transport were increased in the genomes from the polar group. Phylogenomic analysis revealed that two different evolutionary scenarios may explain the adaptation of Polaromonas to cold environments in polar regions. Conclusions The global distribution of the genus Polaromonas highlights its strong adaptability in both polar and nonpolar environments. Species delineation significantly expands our understanding of the diversity of the Polaromonas genus on a global scale. In this study, a polar-specific clade was found, which may represent a specific ecotype well adapted to polar environments. Collectively, genomic insight into the metabolic diversity, evolution and adaptation of the genus Polaromonas at the genome level provides a genetic basis for understanding the potential response mechanisms of Polaromonas to global warming in polar regions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Quantifying Streambed Grain Size, Uncertainty, and Hydrobiogeochemical Parameters Using Machine Learning Model YOLO

Abstract Streambed grain sizes control river hydro‐biogeochemical (HBGC) processes and functions. However, measuring their quantities, distributions, and uncertainties is challenging due to the diversity and heterogeneity of natural streams. This work presents a photo‐driven, artificial intelligence (AI)‐enabled, and theory‐based workflow for extracting the quantities, distributions, and uncertainties of streambed grain sizes from photos. Specifically, we first trained You Only Look Once, an object detection AI, using 11,977 grain labels from 36 photos collected from nine different stream environments. We demonstrated its accuracy with a coefficient of determination of 0.98, a Nash–Sutcliffe efficiency of 0.98, and a mean absolute relative error of 6.65% in predicting the median grain size of 20 ground‐truth photos representing nine typical stream environments. The AI is then used to extract the grain size distributions and determine their characteristic grain sizes, including the 10th, 50th, 60th, and 84th percentiles, for 1,999 photos taken at 66 sites within a watershed in the Northwest US. The results indicate that the 10th, median, 60th, and 84th percentiles of the grain sizes follow log‐normal distributions, with most likely values of 2.49, 6.62, 7.68, and 10.78 cm, respectively. The average uncertainties associated with these values are 9.70%, 7.33%, 9.27%, and 11.11%, respectively. These data allow for the computation of the quantities, distributions, and uncertainties of streambed HBGC parameters, including Manning's coefficient, Darcy‐Weisbach friction factor, top layer interstitial velocity magnitude, and nitrate uptake velocity. Additionally, major sources of uncertainty in grain sizes and their impact on HBGC parameters are examined.

58 GEOSCIENCES↗
DOE OSTI2024

Transient energy dissipation at the Fermi velocity in a magnetocaloric metal

Realizing fast energy dissipation in crystalline materials over macroscopic length scales is critical for energy-efficient devices and applications toward a carbon-neutral society but is usually dominated by electron-lattice interactions that cap the energy dissipation at the phonon velocity. Going beyond this velocity has been the focus of many studies, and the physical limit is the Fermi velocity where the energy is predominantly carried away by electrons throughout the materials. However, whether and how the Fermi velocity can be reached over macroscopic distances experimentally remain largely elusive. Here we show ultrafast energy dissipation at the Fermi velocity in the magnetocaloric metal LaFe 10.6 Co 1.0 Si 1.4 . Using time-resolved powder x-ray diffraction, we observe negative thermal expansion of the lattice throughout the micron-sized crystals in less than 600 fs with an incident optical fluence higher than 8 J cm -2 . The ultrafast timescale is in sharp contrast to the normal energy dissipation and shows the existence of a macroscopic momentum-relaxing electron mean free path immediately after the optical excitation. In conclusion, our findings open a different regime in energy dissipation and demonstrate the possibility of manipulating macroscopic material properties by strong optical pulses.

Chen, Yanna↗
DOE OSTI2024

Mechanistic definition and prediction of the mass exchange coefficient between rivers and hyporheic zones: The $α$ of two $Ω$s

Solute transport in interconnected rivers and hyporheic zones is typically modeled through dual-domain models where first-order solute mass transfer between the two domains, Ω R and Ω HZ , is represented by a coefficient α. The transient storage model (TSM) is an example of such an approach. In practice, α is determined by fitting the tails of solute tracer breakthrough curves using a TSM. This approach has led to ambiguity regarding α’s physical meaning and transferability. Here, in this work, we investigated the physical basis for α and tested it with virtual experiments through the fully coupled multiphysics model hyporheicFoam for the Ω R – Ω HZ system. hyporheicFoam explicitly simulated coupled flow and solute transport over a kilometer with centimeter-scale resolution. Model results were analyzed to calculate α following its theoretical definition directly. Using the determined α within a TSM enables accurate reproduction of solute transport, underscoring α’s physical relevance and precision.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Magnetic interactions and excitations in SrMnSb 2

The magnetic interactions in the antiferromagnetic (AFM) Dirac semimetal candidate SrMnSb 2 are investigated using ab initio linear response theory and inelastic neutron scattering (INS). Our calculations reveal that the first two nearest in-plane couplings (J 1 and J 2 ) are both AFM in nature, indicating a significant degree of spin frustration, which aligns with experimental observations. The orbital resolution of exchange interactions shows that J 1 and J 2 are dominated by direct and superexchange, respectively. In a broader context, a rigid-band model suggests that electron doping fills the minority spin channel and results in a decrease in the AFM coupling strength for both J 1 and J 2 . To better compare with INS measurements, we calculate the spin-wave spectra within a linear spin-wave theory, utilizing the computed exchange parameters. Although the calculated spin-wave spectra somewhat overestimate the magnon bandwidth, they exhibit overall good agreement with measurements from INS experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Integrated Effects of Site Hydrology and Vegetation on Exchange Fluxes and Nutrient Cycling at a Coastal Terrestrial‐Aquatic Interface

Abstract The complex interactions among soil, vegetation, and site hydrologic conditions driven by precipitation and tidal cycles control the biogeochemical transformations and bi‐directional exchange of carbon and nutrients across the terrestrial–aquatic interfaces (TAIs) in coastal regions. This study uses a highly mechanistic model, Advanced Terrestrial Simulator (ATS)‐PFLOTRAN, to explore how these interactions affect exchanges of materials and carbon and nitrogen cycling. We used a transect in the Chesapeake Bay region that spans zones of open water, coastal wetland, transition, and upland forest. We designed several simulation scenarios to parse the effects of the individual controlling factors and the sensitivity of carbon cycling to reaction rate parameters derived from laboratory experiments. Our simulations reveal an active zone for carbon cycling under the transition zones between the wetland and the upland. Evapotranspiration is found to enhance the exchange fluxes between the surface and subsurface domains, resulting in a higher dissolved oxygen concentration in the TAIs. The transport of organic carbon derived from plant leaves and roots provide an additional source of organic carbon needed for the aerobic respiration and denitrification processes in the TAIs. The variability in reaction rate parameters associated with microbial activities is also found to play a dominant role in controlling the heterogeneity and dynamics of the simulated redox conditions. This modeling‐focused exploratory study enabled us to better understand the complex interactions among soil, water and microbes that govern the hydro‐biogeochemical processes at the TAIs, which is an important step toward representing coastal ecosystems in larger‐scale Earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Transition from an incommensurate spin density wave to a commensurate magnetic order in a triangular lattice compound Ho 2 PdAl 6 Ge 4

Rare-earth (RE) intermetallics on a triangular lattice are promising candidates for generating interesting magnetic phases due to the complex interplay between Ruderman-Kittel-Kasuya-Yoshida (RKKY) interaction and geometrical frustration. Here, in this work, we report the exotic magnetic structure of a layered compound Ho 2 PdAl 6 Ge 4 with triangular lanthanide nets. Magnetization and heat capacity measurements in zero magnetic field reveal two magnetic phase transitions at T N1 = 10.8 K and T N2 = 6.0 K. Neutron powder diffraction demonstrates a commensurate antiferromagnetic phase with k 1 = (0, 0, 1.5) below T N2 . With increasing temperature, another incommensurate vector appears and therefore, the magnetic structure of the intermediate state is identified as an unusual incommensurate spin density wave with two propagation vectors k 1 = (0, 0, 1.5) and k 2 = (0.0492, 0.0492, 1.5). The magnetic moments in the intermediate state rotate continuously and form an unusual S-shaped wave arrangement in the ab plane, sharing similarities with typical cycloid and helix magnetic orders. These results identify Ho 2 PdAl 6 Ge 4 as a candidate for exploring field-induced topological magnetic phases such as skyrmions, opening the way for further investigations on the family of RE 2 PdAl 6 Ge 4 materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

High-order harmonics and the reverse of the squaring up process in the triangular-lattice magnet HoPdAl 4 ⁢Ge 2

We uncover high-order harmonics and the reverse of the squaring-up process, in terms of analyzing the evolution of magnetic orders in a centrosymmetric layered triangular-lattice magnet HoPdAl 4 ⁢Ge 2 , based on a detailed study of the crystal structure, magnetic susceptibility, magnetization, heat capacity, and magnetic structure. Temperature dependencies of magnetic susceptibility and heat capacity show two magnetic transitions at T N = 10.5 K and T t = 5.5 K. Below T N , Ho 3+ spins order antiferromagnetically as a transverse spin-density wave with the propagation vector k 1 = (001.5 – δ) with δ ≈ 0.18. Upon further cooling through T t , the high-order harmonics with k n = (001.5 – nδ), n = 3, 5, 7 develop, suggesting a squaring-up process. It is surprising that the squaring-up process does not continue down to 0 K but reverses the trend below 3 K. Magnetic-field-induced metastable transitions were observed in M⁡(H) curves with the fields applied both parallel and perpendicular to the triangular-lattice plane. Neutron-diffraction results suggest that the magnetization process in HoPdAl 4 ⁢Ge 2 involves the conversion of k n = (001.5 – n⁢δ) with n = 1, 3, 5, 7, to a ferromagnetic k F = (000) component. It is worth noting that the already weak seventh harmonic magnetic peak is enhanced by applying a small magnetic field in the ab plane at 1.5 K or warming up to 3 K, accompanied by a slight decrease of δ.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Genomic surveillance indicates clonal replacement of hypervirulent Klebsiella pneumoniae ST881 and ST29 lineage strains in vivo

The emergence of hypervirulent Klebsiella pneumoniae (hvKp) poses a significant public health threat, particularly regarding its carriage in the healthy population. However, the genomic epidemiological characteristics and population dynamics of hvKp within a single patient across distinct infection episodes remain largely unknown. This study aimed to investigate the clonal replacement of hvKp K2-ST881 and K54-ST29 lineage strains in a single patient experiencing multiple-site infections during two independent episodes. Two strains, designated EDhvKp-1 and EDhvKp-2, were obtained from blood and cerebrospinal fluid during the first admission, and the strain isolated from blood on the second admission was named EDhvKp-3. Whole-genome sequencing, utilizing both short-read Illumina and long-read Oxford Nanopore platforms, was conducted. In silico multilocus sequence typing (MLST), identification of antimicrobial resistance and virulence genes, and the phylogenetic relationship between our strains and other K. pneumoniae ST881 and ST29 genomes retrieved from the public database were performed. Virulence potentials were assessed through a mouse lethality assay. Our study indicated that the strains were highly susceptible to multiple antimicrobial agents. Plasmid sequence analysis confirmed that both virulence plasmids, pEDhvKp-1 (166,008 bp) and pEDhvKp-3 (210,948 bp), belonged to IncFIB type. Multiple virulence genes, including rmpA , rmpA2 , rmpC , rmpD , iroBCDN , iucABCD , and iutA , were identified. EDhvKp-1 and EDhvKp-2 showed the closest relationship to strain 502 (differing by 51 SNPs), while EDhvKp-3 exhibited 69 SNPs differences compared to strain TAKPN-1, which all recovered from Chinese patients in 2020. In the mouse infection experiment, both ST881 EDhvKp-1 and ST29 EDhvKp-3 displayed similar virulence traits, causing 90 and 100% of the mice to die within 72 h after intraperitoneal infection, respectively. Our study expands the spectrum of hvKp lineages and highlights genomic alterations associated with clonal switching between two distinct lineages of hvKP that successively replaced each other in vivo . The development of novel strategies for the surveillance, diagnosis, and treatment of high-risk hvKp is urgently needed.

Liu, Ning↗
DOE OSTI2024

Data and scripts associated with the manuscript "A Hydrogeophysical Framework to Assess Infiltration During a Simulated Ecosystem-Scale Flooding Experiment”

This package contains the data and scripts used in "A hydrogeophysical framework to assess infiltration during a simulated ecosystem-scale flooding experiment" (Adebayo et al., 2023). The Geophysics folder contains two subfolders containing Ground Penetrating Radar (GPR) and Electrical Resistivity Imaging (ERI) datasets acquired between August 23 and August 26, 2021. The GPR subfolder contains raw data (Tempest_Project.GPZ) and processed results using the Sensors and Software EKKO Project software. The ERI subfolder contains two additional subfolders named Static and Timelapse. The Static subfolder contains background resistivity datasets acquired before infiltration, both raw and inverted results using the ResIpy code. The Timelapse subfolder contains repeated resistivity datasets acquired during infiltration on two profiles, along with raw and inverted results using the ResIpy code. The Flow model folder contains ATS model simulation files. The Geophysics-informed subfolder contains simulation datasets for two profiles generated using information from the geophysics data. The National_database-informed subfolder contains simulation datasets for two profiles generated using information from a national soil database. Each subfolder contains initial simulation results, multiple ensembles, and final simulation files. The Sensitivity_analysis folder contains the observation files exported from the flow model, notebooks used in running the code, and sensitivity analysis results showing the sensitivity of different parameters over a 48-hour period. We used mutual information-based global sensitivity analysis for the sensitivity analysis, following Jiang et al., 2022. This study shows a novel approach that integrates geophysical data with hydrological modeling to understand subsurface flow during coastal flooding.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Competing magnetic fluctuations and orders in a multiorbital model of doped SrCo 2 ⁢As 2

We revisit the intriguing magnetic behavior of the paradigmatic itinerant frustrated magnet Sr⁢Co 2 ⁢As 2 , which shows strong and competing magnetic fluctuations yet does not develop long-range magnetic order. By calculating the static spin susceptibility Χ⁡(q) within a realistic 16-orbital Hubbard-Hund model, we determine the leading instability to be ferromagnetic (FM). We then explore the effect of doping and calculate the critical Hubbard interaction strength U c that is required for the development of magnetic order. We find that U c decreases under electron doping and with increasing Hund's coupling J, but increases rapidly under hole doping. This suggests that magnetic order could possibly emerge under electron doping but not under hole doping, which agrees with experimental findings. We map out the leading magnetic instability as a function of doping and Hund's coupling and find several antiferromagnetic phases in addition to FM. We also quantify the degree of itinerant frustration in the model and resolve the contributions of different orbitals to the magnetic susceptibility. Lastly, we discuss the dynamic spin susceptibility Χ⁡(q,ω) at finite frequencies, where we recover the anisotropy of the peaks at Q π = (π,0) and (0,π) observed by inelastic neutron scattering that is associated with the phenomenon of itinerant magnetic frustration. By comparing results between theory and experiment, we conclude that the essential experimental features of doped SrCo 2 ⁢As 2 are well captured by an itinerant Hubbard-Hund multiorbital model if one considers a small shift of the chemical potential towards hole doping.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

A hydrogeophysical framework to assess infiltration during a simulated ecosystem-scale flooding experiment

This study presents a framework to quantify changes in soil saturation in response to flooding caused by extreme hydrologic perturbation on coastal ecosystems at the interfaces and transition between terrestrial and aquatic systems. Subsurface heterogeneity limits the use of in situ measurements to quantify subsurface flow during flooding due to the spatial discontinuity in the measured data. While geophysical methods, including time-lapse electrical resistivity imaging (ERI), are increasingly used to monitor soil hydrological processes, their abilities to parameterize flow models have been underutilized. This study combines background ERI, ground penetrating radar (GPR), time-lapse ERI, soil characterization, and a numerical flow model developed using an Advanced Terrestrial Simulator (ATS) code to quantify the infiltration pathway and describe the hydrological dynamics during a simulated flooding experiment. We assessed the use of two conceptual models developed using [1] ERI and GPR data that described the stratigraphic distribution, and time-lapse ERI that mapped permeability contrast, and [2] information from a national soil database for capturing changes in saturation. Combining the ERI and GPR results with soil core data revealed the stratigraphic heterogeneity at the site with a silty clay layer from 1 to 2 m between an overlying loamy topsoil and an underlying saturated silty sand. This silty clay layer could restrict deep infiltration. The time-lapse ERI showed up to a 35% decrease in resistivity, which correlated with soil moisture data (R 2 value > 0.53) and revealed preferential infiltration zones used to inform the flow model. Numerical simulation results from both the geophysics- and soil database-informed models quantified changes in soil saturation with calculated soil moistures that agreed with field data. The geophysics-informed model captured more of the system’s variability, reflective of shallow subsurface heterogeneities. The framework presented will serve as a precursor for a robust ecohydrological model that can describe the impacts of extreme events induced by climate change on coastal ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Data and scripts associated with the manuscript evaluating the hydrologic responses of the Pacific Northwest watersheds to wildfires (v2)

This data package is associated with the publication “Evaluating Post-fire Watershed Response to Varying Burn Severity and Precipitation Regimes Using Fully-distributed and Integrated Hydrologic Models” submitted to Journal of Hydrology (Li et al. 2025). In this study, we employed the Advanced Terrestrial Simulator (ATS), an integrated watershed model that couples surface flow, subsurface flow, and canopy biophysical processes, to investigate post-fire hydrologic responses in a few selected watersheds with varying burn severity.The data package contains the required input data (meteorological forcing, Leaf Area Index, wildfire burn severities, etc.) to run the model, configuration files, the Jupyter notebooks in Python to pre-process and post-process data, the figures in the manuscript, and the modeling output files. The variables include watershed-averaged evapotranspiration, watershed-averaged surface/subsurface/canopy water content, and river discharge at watershed outlet.The data package contains a file-level metadata that lists and describes all the files contained in the data package (ATS_flmd.csv), a data dictionary file that defines columns headers across all csv files contained in the data package (ATS_dd.csv), a data package level readme file (the current file), and four zipped folders.The ‘data’ folder provides data needed to run the model in .h5, .i2s, .xyz, .shp, and .exo formats. The sub-folders are for each data types. The ‘model’ folder provides input files (.xml format) and essential model outputs. Each sub-folder provides the files from each simulated watershed. The ‘notebooks’ folder provides the Jupyter notebooks (.ipynb format) for pre- and post- processing model files, and for producing the figures in the manuscript. The ‘figures’ folder provides the figures associated with manuscript in .pdf and .png formats.The ‘model’ folder and the ‘data’ folder have been split into 5GB-large pieces using the Linux command ‘split -b 5120m model.zip model.zip.’ and ‘split -b 5120m data.zip data.zip.’, respectively. They can be merged back using the Linux command ‘cat model.zip.* > model.zip’ and ‘cat data.zip.* > data.zip’, respectively.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Artificial intelligence models, photos, and data associated with the manuscript “Quantifying Streambed Grain Size, Uncertainty, and Hydrobiogeochemical Parameters Using Machine Learning Model YOLO” (v2)

This data package is associated with the manuscript “Quantifying Streambed Grain Size, Uncertainty, and Hydrobiogeochemical Parameters Using Machine Learning Model YOLO” published in Water Resources Research (Chen et al., 2024). This data package includes the training, validation, testing, and prediction data used by the artificial intelligence (AI) model for automated grain size and hydro-biogeochemistry quantification using streambed photos. The grain size data are extracted for each photo using You Look Only Once (YOLO), a pre-trained object detection model. This data package was originally published in October 2023. It was updated August 2025 (v2; new and modified files). File and folder names were not revised to indicate changes. See the change history section in the readme for more details. Please see flmd.csv for a list of all files contained in this data package and descriptions for each. Please see dd.csv for a data dictionary that defines the column headers of .csv files in the data package. This dataset is comprised of one data folder containing (1) file-level metadata; (2) data dictionary; (3) readme; and (4) six subfolders. Subfolders 1 to 4 include the training, validation, testing, and prediction data. Subfolder 5_Summary includes the summary results of different combinations of training, validation, testing, and prediction data. Subfolder 6_SupplementalData includes additional data downloaded from public sources (Kaufman et al., 2023a; Kaufman et al., 2023b; Garefalakis et al., 2023; Mair et al., 2024; https://github.com/river-corridors-sfa/Geospatial_variables). In total, the data package includes 110 folders and 44,283 files. These files include 9,047 .jpg photos, 1 .png photo, 3 .tif photos; 26,639 photo labels and individual grain sizes and probability from AI (.txt); 8,447 grain size distribution data (.dat); and 126 CSV files for results summary, and 14 required metadata files (.xlsx). The summary CSV files contain 68 columns and approximately 2,200 rows that represent photo names, site locations, recording time, GPS coordinates, grains sizes (D10, D50, D60, and D84), number of grains, and additional hydro-biogeochemical data such as water depth, flow velocity, Manning’s coefficient, friction factor, hydraulic conductivity, permeability, streambed interstitial velocity magnitude, mass transfer rate, and nitrate uptake velocity. The photos were obtained from 75 sites in the Yakima River Basin and the Columbia River shorelines, and other associated data from samples and sensors obtained when the photos were taken are publicly available (Fulton et al. 2022; Grieger et al. 2023). All files are .csv, .txt, .dat, .jpg, or .pdf. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected some of these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗