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At least 577 records · Page 32

Binding mechanism and binding free energy of amino acids and citrate to hydroxyapatite surfaces as a function of crystallographic facet, pH, and electrolytes

Hydroxyapatite (HAP) is the major mineral phase in bone and teeth. The interaction of individual amino acids and citrate ions with different crystallographic HAP surfaces has remained uncertain for decades, creating a knowledge gap to rationally design interactions with peptides, proteins, and drugs. In this contribution, we quantify the binding mechanisms and binding free energies of the 20 end-capped natural amino acids and citrate ions on the basal (001) and prismatic (010)/(020) planes of hydroxyapatite at pH values of 7 and 5 for the first time at the molecular scale. We utilized over 1500 steered molecular dynamics simulations with highly accurate potentials that reproduce surface and hydration energies of (hkl) hydroxyapatite surfaces at different pH values. Charged residues demonstrate a much higher affinity to HAP than charge-neutral species due to the formation of superficial ion pairs and ease of penetration into layers of water molecules on the mineral surface. Binding free energies range from 0 to -60 kJ/mol and were determined with ~10% uncertainty. The highest affinity was found for citrate, followed by Asp(-) and Glu(-), and followed after a gap by Arg(+), Lys(+), as well as by His(+) at pH 5. The (hkl)-specific area density of calcium ions, the protonation state of phosphate ions, and subsurface directional order of the ions in HAP lead to surface-specific binding patterns. Amino acids without ionic side groups exhibit weak binding, between -3 and 0 kJ/mol, due to difficulties to penetrate the first layer of water molecules on the apatite surfaces. We explain recognition processes that remained elusive in experiments, in prior simulations, discuss agreement with available data, and reconcile conflicting interpretations. In conclusion, the findings can serve as useful input for the design of peptides, proteins, and drug molecules for the modification of bone and teeth-related materials, as well as control of apatite mineralization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Temperature, Humidity, and Time-Lapse Video Data from the East River Watershed, Water Year 2024

A new version of this dataset is available at doi:10.15485/3001338 and is the first citation in the 'Related References' section. It is expands on this dataset by appending another water year of data collection and additional logger sites.This dataset contains time-lapse imagery and distributed measurements of air temperature, relative humidity, dew point, and soil temperature across the East River basin from 3 October 2023 to 12 August 2024. Instruments were deployed at 14 sites as part of the DOE Grant: Seasonal Cycles Unravel Mysteries of Missing Mountain Water organized by Jessica Lundquist (University of Washington), Rosemary Carroll (Desert Research Institute), and Ethan Gutmann (National Center for Atmospheric Research). The data are published to support studies of surface climate or hydrologic processes in complex terrain. Measurements were collected with low-cost data loggers installed 2 m high on evergreen trees or buried just below the soil surface. Time-lapse cameras were deployed at three sites. Imagery from sites AP BONUS and AP5 provides insight into large-scale seasonal snow cover variability. Imagery from site EL2 shows smaller-scale snow patterns across a nearby meadow.Dataset files are organized by site and variable (air measurements, ground measurements, or time-lapse video). Air and ground measurements are packaged in LoggerData.zip, and time-lapse imagery is compiled into short videos stored in TimelapseVideos.zip. File-level metadata contains details for each file included in the dataset. A data dictionary provides units and descriptions for column or row names in all files. The locations metadata file describes site characteristics, locations, and associated GPS methods.Dataset update 2025-03-03: Resolved header and datetime formatting inconsistencies within LoggerData.zip files KP1_Air, KP3_Air, KP3_Ground, KP6_Ground, AP3_Ground, AP4_Air, and AP6_Air.Dataset update 2025-11-18: Modified abstract and related references sections to include new version of dataset.

54 ENVIRONMENTAL SCIENCES↗

Qualitative and quantitative analysis of neutron irradiation effects in SiC/SiC composites using X-ray computed tomography

Silicon carbide fiber-reinforced silicon carbide matrix (SiC/SiC) composites are candidate materials for cladding of light water reactor (LWR) fuels. Loss of fission product gas retention due to the formation of microcrack networks is considered a potential failure mechanism for SiC/SiC-cladded fuels. In this work, a variety of SiC/SiC composite tubes were irradiated with and without an LWR-relevant radial heat flux in the High Flux Isotope Reactor, followed by detailed characterization with X-ray computed tomography (XCT). This first set of XCT data for neutron-irradiated samples confirmed that the internal stresses arising from a combination of temperature gradients and irradiation-induced swelling act as the primary driver for cracking. Consequently, while the observed cracking patterns varied depending on the tube architectures, the sharp edges of relatively large pores were found to be the common stress concentrator. These findings are useful to help improve the design and manufacturing of SiC/SiC fuel claddings for reduced failure probability.

42 ENGINEERING↗

2D-EFICACY: Control of Metastable 2D Carbide Chalcogenide Heterolayers: Strain and Moire Engineering

The experimental isolation of graphene led to the discovery of an entirely new world of two-dimensional (2D) materials in which the 2D nature often leads to emergent behaviors not seen in bulk systems. 2D transition metal dichalcogenides (TMDs) exhibit physico-chemical properties that depend on the transition metal, polymorph, thickness, and presence and type of defects. Recently, a group of thin (10-100nm) transition metal carbides (TMCs), such as Mo 2 C, has been synthesized that exhibit a thickness-dependent superconducting critical temperature (Tc). These thin TMCs are different from MXenes, another class of 2D materials consisting of few layers of nitrides or carbides (<5nm) produced by chemical etching and delamination. The goal of this renewal proposal is to combine experiment and computation to synthesize and elucidate the guiding principles that control the growth, orientation and strain of heterostacks of thin TMCs and TMDs composed with Nb, Ti and W. We expect to stabilize metastable hybrid phases of TMCs sandwiched between TMDs (H-TMD/Cs) with unprecedented physico-chemical properties. As part of previous DOE-funded work by the Terrones/Sinnott groups, thin (10-100 nm thick) Mo 2 C flakes were successfully synthesized by chemical vapor deposition (CVD). By subsequently exposing Mo 2 C to H 2 S, partial chalcogenization was achieved, resulting in heterostacks of MoCx phases and MoS 2 . The formation of MoS 2 led to a deficiency of Mo atoms in the underlying Mo 2 C, resulting in an inhomogeneous phase change from α-Mo 2 C to γ’-MoCx and then to γ-MoC. The γ’-MoCx is a strained metastable phase and the heterostack of all three phases demonstrated an increased Tc relative to that of α-Mo 2 C, from 4 to 6K; its interleaved layered structure consisting of superconducting and semiconducting phases is ideal for future studies of Josephson junction series arrays. Moiré patterns in these heterostacked systems could result in new phenomena, as moiré patterns in bilayer graphene showed unconventional superconductivity and moiré excitons have been observed in twisted TMD heterobilayers. The scientific hypothesis of the proposed synergistic computational and experimental research is that orientation and strain control within confined thin metastable TMCs, sandwiched by stable phases of TMCs and layered TMDs, will depend on kinetic and thermodynamic “knobs” that include fast temperature changes, chalcogen diffusion through preferred crystallographic planes, reaction times, pressure, reactive atmosphere, precursors, and surfactants, which will also tailor properties such as superconductivity, magnetism, ferroelectricity, piezoelectricity, and catalytic performance. We will develop the guiding principles for the synthesis and stabilization of metastable H-TMD/Cs based on Nb, Ti and W. In order to validate the hypothesis, four tasks are proposed: The first task will synthesize ultra-thin TMCs based on Nb, W and Ti, by: 1) adapting the CVD method used for Mo 2 C, 2) plasma assisted CVD, 3) defect-mediated CVD processes, and 4) cryo-milling of carbide powders. The second task will accomplish the synthesis and basic physico-chemical characterizations of H-TMD/Cs by chalcogenization of the materials synthesized in task one, and by carbonization of TMDs. H-TMD/Cs will also be investigated for their suitability in energy conversion applications such as supercapacitors, Li and multivalent ion batteries, and electrocatalysts, topics of interest to DoE. These tasks will be carried out in close conjunction with density functional theory (DFT) calculations with insights into energetics, lattice parameters, stability, phase diagrams, band structures, and density of states of H-TMD/Cs. The third task will characterize and evaluate strain and moiré patterns at the interfaces of different H-TMD/Cs by high-resolution scanning transmission electron microscopy (HR-STEM), scanning tunneling microscopy (STM), and conductive tip atomic force microscopy. Nudged elastic band calculations with DFT will be performed to understand the chalcogen diffusion process, which will provide insights into the interfaces between different phases of TMCs and TMDs. The fourth task aims at quantifying the stability and dynamics of H-TMD/Cs by in-situ TEM and Raman studies under heating, strain, and electrical biasing. Phonon calculations using DFT will provide a basis for interpreting Raman spectra. This coherent framework involving synthesis, characterization, and computation will result in a broad scientific impact for energy related applications. The ability to develop new H-TMD/Cs will enhance a range of applications that include batteries, catalysts, switches, sensors, quantum computing components and smart coatings.

2-Dimensional Materials↗

Ionic Pairs-Engineered Fluorinated Covalent Organic Frameworks Toward Direct Air Capture of CO 2

The covalent organic frameworks (COFs) possessing high crystallinity and capability to capture low-concentration CO 2 (400 ppm) from air are still underdeveloped. The challenge lies in simultaneously incorporating high-density active sites for CO 2 insertion and maintaining the ordered structure. Herein, a structure engineering approach is developed to afford an ionic pair-functionalized crystalline and stable fluorinated COF (F-COF) skeleton. The ordered structure of the F-COF is well maintained after the integration of abundant basic fluorinated alcoholate anions, as revealed by synchrotron X-ray scattering experiments. The breakthrough test demonstrates its attractive performance in capturing (400 ppm) CO 2 from gas mixtures via O$-$C bond formation, as indicated by the in situ spectroscopy and operando nuclear magnetic resonance spectroscopy using 13 C-labeled CO 2 sources. Both theoretical and experimental thermodynamic studies reveal the reaction enthalpy of ≈-40 kJ mol -1 between CO 2 and the COF scaffolds. This implies weaker interaction strength compared with state-of-the-art amine-derived sorbents, thus allowing complete CO 2 release with less energy input. The structure evolution study from synchrotron X-ray scattering and small-angle neutron scattering confirms the well-maintained crystalline patterns after CO 2 insertion. In conclusion, the as-developed proof-of-concept approach provides guidance on anchoring binding sites for direct air capture (DAC) of CO 2 in crystalline scaffolds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamics and lipid membrane coupling of the RAS-RAF complex revealed via multiscale simulations

To gain molecular and mechanistic insights into initiation of the RAS-RAF signaling cascade, we developed and used a combination of multiscale simulation and experimental approaches. The influence and impact of the membrane on RAS and RAF proteins is a factor we are just beginning to understand and appreciate in more detail. Molecular simulation is an ideal methodology to further study this complicated relationship between the membrane and associated proteins. Our previous work using Multiscale Machine-learned Modeling Infrastructure investigated different lipid compositions solely around the KRAS4b protein and the interplay between protein behavior and these membrane environments. Multiscale Machine-learned Modeling Infrastructure uses machine learning to couple adjacent simulation scales and has been efficiently scaled across some of the world’s largest high-performance computers. Recently, we have expanded this multiresolution framework to include the all-atom simulation scale and to incorporate the RAF RBDCRD domains. Here, we present the overall analysis results from this new simulation campaign comprising a mixture of RAS and RAF RBDCRD proteins. Approximately 35,000 coarse-grained and 10,000 all-atom molecular dynamics simulations were completed, sampled from a variety of protein/lipid composition configurations that were generated from a micron-scale continuum simulation containing hundreds of copies of the proteins. Our studies suggest that orientations of the RAS-RBDCRD complex on the membrane occupy distinct configurational states, and the spatial patterns of lipid arrangements around these different protein states are unique to each state. The extent and size of lipid “fingerprints” imposed on the membrane by the RAS-RBDCRD protein complex are significantly larger than observed for just the RAS protein on its own. These protein complexes strongly associate, but we do not observe statistically significant preferred protein-protein orientations. These observations indicate that spatial colocalization of RAS-RBDCRD proteins in the same vicinity may be assisted by specific membrane environments, acting to increase the probability of signaling complex formation.

Carpenter, Timothy S. [Lawrence Livermore National↗

Streamflow measurements from four sites on the Tuolumne River in Yosemite National Park from Water Years 2002 to 2021

Regions with remote and complex terrain experience spatially varying streamflow patterns, but are often poorly sampled due to difficult access. This data package includes streamflow measurements collected using low-visibility and low-impact installations at four sites on the Tuolumne River in Yosemite National Park, for water years 2002 to 2021. The resulting data set offers a unique opportunity to explore hydrologic processes in complex terrain.This data package contains half-hourly recordings of unvented pressure, vented pressure, and water temperature are measured and used to estimate discharge and stage height. Discharge flags provide insight into data anomalies. This dataset is formatted in accordance with ESS-Dive's Hydrologic Monitoring and File Level Metadata Formats. It contains the following files:1) Folder containing four csv files of time series streamflow measurements (unvented pressure, vented pressure, estimated discharge, water temperature, stage height, and discharge flag) from four locations on the Tuolumne River2) Data dictionary (dd.csv) containing units, definitions, human readable column names, and data type for all column headers throughout the dataset3) File-level metadata (FLMD.csv) containing metadata for files contained in the dataset4) Installation methods (InstallationMethods.csv) containing metadata on sensor installation

54 ENVIRONMENTAL SCIENCES↗

A spatial-statistical investigation of surface expressions associated with cyclic steaming in the Midway-Sunset Oil Field, California

In the Midway Sunset Oil Field in Central California, operators inject steam into the shallow diatomite formation to enhance heavy oil recovery through imbibition, wettability alteration, and viscosity reduction, among other mechanisms. The injected steam, however, does not always remain in the reservoir or return through the wells. In two zones in the study area, the steam comes out at the surface, creating sinkholes, seeps, and steam outlets. These phenomena, called “surface expressions,” pose safety and environmental hazards. Even though these surface expressions are a widespread problem in Central California, they are not well documented and understood. Possible causes of the surface expressions include: high injection pressure, structurally controlled flow patterns, leakage of steam through old improperly abandoned wells, high injection volumes, or flow along naturally occurring faults, among other possible factors. This work examines attributes of the zones with surface expressions in order to determine factors that may contribute to their occurrence. Spatial statistical analysis using logistic regression, random forests, and classification trees is used to explore the relationship between the surface expressions and geological and production-related attributes. The results point to a significant spatial correlation between the surface expressions and two predictors: concentration of plugged wells and geologic seal thickness. The results guide follow-up studies to further investigate the role of well abandonment and seal thickness in the occurrence of surface expressions.

02 PETROLEUM↗

Higher-order topology induced by structural buckling

Abstract Higher-order topological insulator (HOTI) states, such as two-dimension (2D) HOTI featured with topologically protected corner modes at the intersection of two gapped crystalline boundaries, have attracted much recent interest. However, the physical mechanism underlying the formation of HOTI states is not fully understood, which has hindered our fundamental understanding and discovery of HOTI materials. Here we propose a mechanistic approach to induce higher-order topological phases via structural buckling of 2D topological crystalline insulators (TCIs). While in-plane mirror symmetry is broken by structural buckling, which destroys the TCI state, the combination of mirror and rotation symmetry is preserved in the buckled system, which gives rise to the HOTI state. We demonstrate that this approach is generally applicable to various 2D lattices with different symmetries and buckling patterns, opening a horizon of possible materials to realize 2D HOTIs. The HOTIs so generated are also shown to be robust against buckling height fluctuation and in-plane displacement. A concrete example is given for the buckled $\beta $-Sb monolayer from first-principles calculations. Our finding not only enriches our fundamental understanding of higher-order topology, but also opens a new route to discovering HOTI materials.

42 ENGINEERING↗

Building a Framework to Understand Transition Metals' Behavior in Euxinic Conditions (Final Technical Report)

This project focuses first and foremost on metal sulfide geochemistry and mineralogy as controlled by a complex matrix of environmental factors. The principal investigator’s group aim to illuminate the metal-sulfide reaction mechanisms, rates, and pathways through systematic experimentation and data collection and analyzing the relationships between the characteristics of the produced metal sulfide solid-phase/aqueous complexes and the environmental factors. This understanding is essential for obtaining a full picture of the complex cycling patterns of single or multi metal species in sulfidic environments ranging from deep-see basins, hydrothermal vents, inland seas, terrestrial water bodies, to engineered remediation systems. The specific goal of this past project was to illuminate the reaction mechanisms and kinetics of metal anions and sulfide in mixed metal cation-metal anion-sulfide systems under various aqueous conditions (which resembled a range of naturally occurring euxinic settings). For the period of this contract, we investigated the molybdenum-iron-sulfide system, with an emphasis on the conditions that caused solid phase formation. We focused on quantifying the mobility/sequestration of molybdenum under each experimental condition and identified the changes of valence states for each involved element (i.e., Mo, Fe, and S) in the precipitate. We also proposed pathways for the electron transfer that occurred in aqueous chemistry. The major analytical tools used for this study include UV-visible light spectroscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, and synchrotron-based X-ray absorption spectroscopy (access gained through facility proposals to the Canadian Light Source). The biggest finding of this project was that besides pH, the iron-sulfur chemistry has a dominant control of the thiolation kinetics and subsequent reduction of Mo(VI), which are likely prerequisites of molybdenum sequestration in anoxic conditions. The results have been written up as manuscript by the end of this project (see Phillips et al.). The experimental results of this project may be critical for advancing our understanding of (1) basic chemistry involving transition metals and reduced sulfur species, (2) the validity of certain geochemical proxies, and (3) the stability and evolution of euxinic geochemical environments. It is noted that the basic results obtained through this project also have implications for Mo-S cluster-based catalyst development in inorganic chemistry and materials sciences.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Accurate determination of chemical abundances near a supermassive black hole

The metal abundances in galactic nuclei carry key information on the history of star formation and mass transfer in central regions of galaxies. X-ray fluorescence analysis is a unique tool to reliably measure the abundances of various elements via simple physics. Here we present a new observation of the active nucleus in the Circinus galaxy with the XRISM satellite at unprecedented X-ray energy resolution. The fluorescent iron Kα line profile modified by Compton scattering indicates that the material responsible for its emission is cold and metal rich and is located ≳0.024 pc from the supermassive black hole, consistent with the dusty torus region. The abundance pattern derived from comparing fluorescent line intensities of different metals shows subsolar ratios of argon- and calcium-to-iron and a supersolar ratio of nickel-to-iron. This abundance pattern is best produced by a combination in number fraction of 92$^{+2}_{–4}$% core-collapse supernovae from progenitor stars less massive than 20$^{+3}_{–2}$ M ⊙ and 8$^{+4}_{–2}$% type Ia supernovae. This suggests that gas feeding the supermassive black hole was enriched by recent core-collapse supernovae. Our findings imply that in metal-rich environments stars more massive than about 20 M ⊙ directly collapse into black holes or make faint supernovae without ejecting heavy metals into the space.

Astronomy and AstroPhysics↗

SDSS-IV MaNGA: stellar rotational support in disc galaxies versus central surface density and stellar population age

ABSTRACT We investigate how the stellar rotational support changes as a function of spatially resolved stellar population age ($D_n4000$) and relative central stellar surface density ($\Delta \Sigma _1$) for MaNGA isolated/central disc galaxies. We find that the galaxy rotational support indicator $\lambda _{R_\mathrm{e}}$ varies smoothly as a function of $\Delta \Sigma _1$ and $D_n4000$. $D_n4000$ versus $\Delta \Sigma _1$ follows a ‘J-shape’, with $\lambda _{R_\mathrm{e}}$ contributing to the scatters. In this ‘J-shaped’ pattern rotational support increases with central $D_n4000$ when $\Delta \Sigma _1$ is low but decreases with $\Delta \Sigma _1$ when $\Delta \Sigma _1$ is high. Restricting attention to low-$\Delta \Sigma _1$ (i.e. large-radius) galaxies, we suggest that the trend of increasing rotational support with $D_n4000$ for these objects is produced by a mix of two different processes, a primary trend characterized by growth in $\lambda _{R_\mathrm{e}}$ along with mass through gas accretion, on top of which disturbance episodes are overlaid, which reduce rotational support and trigger increased star formation. An additional finding is that star-forming galaxies with low $\Delta \Sigma _1$ have relatively larger radii than galaxies with higher $\Delta \Sigma _1$ at fixed stellar mass. Assuming that these relative radii rankings are preserved while galaxies are star forming then implies clear evolutionary paths in central $D_n4000$ versus $\Delta \Sigma _1$. The paper closes with comments on the implications that these paths have for the evolution of pseudo-bulges versus classical bulges. The utility of using $\rm D_n4000$–$\Delta \Sigma _1$ to study $\lambda _{R_\mathrm{e}}$ reinforces the notion that galaxy kinematics correlate both with structure and with stellar-population state, and indicates the importance of a multidimensional description for understanding bulge and galaxy evolution.

Wang, Xiaohan (ORCID:0009000283121002)↗

An optimized FM-index library for nucleotide and amino acid search

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

59 BASIC BIOLOGICAL SCIENCES↗

Data and code for Daily and Multi-Day Extreme Rainfall Analysis Under Future Climates Using Stochastic Storm Transposition and NEX-GDDP-CMIP6 Over CONUS

This data package provides inputs, codes, and outputs for a comprehensive analysis of projected changes in extreme precipitation across 10 regions of the continental United States, using 34 downscaled Earth System Models (ESMs) from the NASA Earth Exchange Global Daily Downscaled Projections, Coupled Model Intercomparison Project Phase 6 (NEX-GDDP-CMIP6) dataset. These models are part of the Coupled Model Intercomparison Project Phase 6 (CMIP6), a coordinated climate modeling framework widely used to assess climate change impacts. The analysis applies a stochastic storm transposition method to quantify changes in extreme rainfall under two Shared Socioeconomic Pathway (SSP) climate scenarios—SSP2-4.5 (moderate emissions) and SSP5-8.5 (high emissions)—compared to historical conditions (1995–2014 vs. 2081–2100). The dataset includes rainfall depth estimates for extreme events with return periods from 2 to 500 years across multiple storm durations (1, 3, and 5 days) for each of the 10 U.S. regions. Weighted ensemble statistics are derived from individual ESM performance against historical precipitation patterns, enabling robust uncertainty quantification through both sign-based and permutation-test-based model agreement assessments. Key analyses address: (1) relative changes in extreme precipitation for each climate scenario, (2) differences between SSP scenarios (SSP5-8.5 vs. SSP2-4.5), (3) contrasts between rare and frequent events, and (4) variations between multi-day and daily storm durations. The workflow produces ensemble statistics—median, 5th, 25th, 75th, and 95th percentiles—along with model agreement metrics that identify regions and event types with robust climate change signals. The dataset includes: processed rainfall depth outputs (netCDF format) from the RainyDay Python package, ESM weights from historical performance evaluation using DayMet observations, ensemble statistics across all storm dimensions, and figures summarizing key findings.

54 ENVIRONMENTAL SCIENCES↗

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica , a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.

59 BASIC BIOLOGICAL SCIENCES↗

The DECam MAGIC Survey: Spectroscopic Follow-up of the Most Metal-poor Stars in the Distant Milky Way Halo *

In this work, we present high-resolution spectroscopic observations for six metal-poor stars with [Fe/H] < –3 (including one with [Fe/H] < –4), selected using narrowband Ca ii HK photometry from the DECam MAGIC Survey. The spectroscopic data confirm the accuracy of the photometric metallicities and allow for the determination of chemical abundances for 16 elements, from carbon to barium. The program stars have chemical abundances consistent with the [Fe/H] < –3 range. A kinematic/dynamical analysis suggests that all program stars belong to the distant Milky Way halo population (heliocentric distances 35 < d helio /kpc ≲ 55), including three with high-energy orbits that might have been associated with the Magellanic system and one, J0026−5445, having parameters consistent with being a member of the Sagittarius stream. The remaining two stars show kinematics consistent with the Gaia-Sausage/Enceladus dwarf galaxy merger. J0433−5548, with [Fe/H] = –4.12, is a carbon-enhanced ultra metal-poor star, with [C/Fe] = +1.73. This star is believed to be a bona fide second-generation star, and its chemical abundance pattern was compared with yields from metal-free supernova models. Results suggest that J0433−5548 could have been formed from a gas cloud enriched by a single supernova explosion from an ∼11 M ⊙ star in the early Universe. The successful identification of such objects demonstrates the reliability of photometric metallicity estimates, which can be used for target selection and statistical studies of faint targets in the Milky Way and its satellite population. These discoveries illustrate the power of measuring chemical abundances of metal-poor Milky Way halo stars to learn more about early galaxy formation and evolution.

CEMP stars↗

A computational model tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit dissemination

Mycobacterium tuberculosis (Mtb), the causative infectious agent of tuberculosis (TB), kills more individuals per year than any other infectious agent. Granulomas, the hallmark of Mtb infection, are complex structures that form in lungs, composed of immune cells surrounding bacteria, infected cells, and a caseous necrotic core. While granulomas serve to physically contain and immunologically restrain bacteria growth, some granulomas are unable to control Mtb growth, leading to bacteria and infected cells leaving the granuloma and disseminating, either resulting in additional granuloma formation (local or non-local) or spread to airways or lymph nodes. Dissemination is associated with development of active TB. It is challenging to experimentally address specific mechanisms driving dissemination from TB lung granulomas. Herein, we develop a novel hybrid multi-scale computational model, MultiGran, that tracks Mtb infection within multiple granulomas in an entire lung. MultiGran follows cells, cytokines, and bacterial populations within each lung granuloma throughout the course of infection and is calibrated to multiple non-human primate (NHP) cellular, granuloma, and whole-lung datasets. We show that MultiGran can recapitulate patterns of in vivo local and non-local dissemination, predict likelihood of dissemination, and predict a crucial role for multifunctional CD8+ T cells and macrophage dynamics for preventing dissemination.

59 BASIC BIOLOGICAL SCIENCES↗

Multiscale modeling of hydrogenolysis of ethane and propane on Ru(0001): Implications for plastics recycling

Plastic waste presents an environmental threat. Chemical recycling via hydrogenolysis can convert plastic waste into waxes, lubricants, and fuels. Among catalysts, Ru stands out for its superior activity and selectivity. The chemistry of light alkane hydrogenolysis can help understanding plastics deconstruction. Here, we perform first-principles calculations, develop descriptor-based relations, and conduct microkinetic modeling and analysis on ethane and propane. Predictions are in excellent agreement with experimental data. We identify a similar cracking pattern for both hydrocarbons entailing a deeply dehydrogenated species with the removal of four hydrogen atoms: CHCH*+* → 2CH* for ethane and CH 3 CCH*+2* → CH 3 C* + CH* for propane. We find that the rate-determining step is the C-C cracking for ethane and the first dehydrogenation from the terminal carbon (CH 3 CH 2 CH 3 *+* → CH 3 CH 2 CH 2 *+H*) for propane. The vinyl species CH 2 CH* produced from propane cracking is responsible for whether a single or multiple cracking events occur and effectively controls the selectivity. Specifically, ethane formation in propane hydrogenolysis is suppressed at elevated temperatures due to over-cracking via multiple (two here) cracking events being preferred over hydrogenation and desorption of ethane from the catalyst. Our workflow and models provide a baseline for future studies on heavier hydrocarbons. Insights into recent experimental studies of polyethylene over Ru-based catalysts are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗