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At least 829 records · Page 46

Multiomics and deep learning dissect regulatory syntax in human development

Transcription factors establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility and regulating gene expression1. Mapping accessible chromatin offers critical insights into transcriptional control, but available datasets for human development are restricted to bulk tissue, single organs or single modalities2. Here we present the Human Development Multiomic Atlas, a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types and more than 1 million candidate cis-regulatory elements, many of which exhibit organ-specific in vivo enhancer activity. Deep learning models trained to predict accessibility from local DNA sequence unravel a comprehensive lexicon of motifs that influence accessibility, including composite motifs exhibiting distinct syntactic constraints that are predicted to mediate transcription factor cooperativity. We identify ‘hard’ syntactic rules requiring precise motif spacing and orientation, ‘soft’ rules allowing flexible motif arrangements, and ubiquitous motifs inhibiting accessibility. Model-based interpretation of genetic variants reveals that disruption of motifs with positive and negative effects is associated with concordant effects on gene expression. Our work delineates how motif syntax governs cell-type-specific chromatin accessibility and provides a foundational resource for decoding cis-regulatory logic and interpreting genetic variation during human development.

59 BASIC BIOLOGICAL SCIENCES↗

Sizing Accuracy of Low-Cost Optical Particle Sensors Under Controlled Laboratory Conditions

Low-cost particulate matter sensors have seen increased use for monitoring at personal and local levels due to their affordability, ease of operation, and high time resolution. However, the quality of data reported by these sensors can be questionable, and a thorough evaluation of their performance is necessary. This study evaluated the particle sizing accuracy of several commonly used optical sensors, including the Alphasense optical particle counter (OPC), TSI DustTrak DRX aerosol monitor, Plantower PMS5003 sensor, and Sensirion SPS30 sensor, using laboratory-generated monodisperse particles. The OPC and DRX agreed partially with reference instruments and showed promise in detecting coarse-size particles. However, the PMS5003 and SPS30 did not correctly size fine and coarse particles. Furthermore, their reported mass distributions do not directly correspond to their number distribution. Despite these limitations, field measurements involving a dust storm period showed that the SPS30 correlated reasonably well with reference instruments for both PM2.5 and PM10, though the regression slopes differed significantly. These findings underscore the need for caution when interpreting data from low-cost optical sensors, particularly for coarse particles. Recommendations for improving the performance of these sensors are also provided.

Gautam, Prakash↗

Allosteric control of olefin isomerization kinetics via remote metal binding and its mechanochemical analysis

Abstract Allosteric control of reaction thermodynamics is well understood, but the mechanisms by which changes in local geometries of receptor sites lower activation reaction barriers in electronically uncoupled, remote reaction moieties remain relatively unexplored. Here we report a molecular scaffold in which the rate of thermal E-to-Z isomerization of an alkene increases by a factor of as much as 10 4 in response to fast binding of a metal ion to a remote receptor site. A mechanochemical model of the olefin coupled to a compressive harmonic spring reproduces the observed acceleration quantitatively, adding the studied isomerization to the very few reactions demonstrated to be sensitive to extrinsic compressive force. The work validates experimentally the generalization of mechanochemical kinetics to compressive loads and demonstrates that the formalism of force-coupled reactivity offers a productive framework for the quantitative analysis of the molecular basis of allosteric control of reaction kinetics. Important differences in the effects of compressive vs. tensile force on the kinetic stabilities of molecules are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tuning MXene Surface Terminations for Strategic Control of Physical Properties

Scientific Achievement • Ti3C2Tx surfaces with a higher hydroxyl group concentration play a pivotal role in surface properties and were found to be thermodynamically stable. • From the electronic bonding analysis, the charge density difference and electron localization function demonstrated a significant electron localization at the hydroxyl group, which results in a locally induced dipole on the surface. • A large tunability in the work function is found from different concentrations of functional groups on the surface which can be controlled by the concentration of HF used for etching of the MAX phase to produce the resulting MXene. Research Details • The influence of termination group distribution on the surface of Ti3C2Tx MXenes from various etching concentrations of HF was evaluated • The work functions of Ti3C2Tx MXenes with differing concentrations of functional groups were determined • The influence of termination group clustering on the surface of Ti3C2Tx MXenes was investigated by visualization of the electron localization function and charge density difference

Ward, Patrick A.↗

Assessing turbulence and mixing parameterizations in the gray-zone of multiscale simulations over mountainous terrain during the METEX21 field experiment

Multiscale numerical weather prediction models transition from mesoscale, where turbulence is fully parameterized, to microscale, where the majority of highly energetic scales of turbulence are resolved. The turbulence gray-zone is situated between these two regimes and multiscale models must downscale through these resolutions. Here, we compare three multiscale simulations which vary by the parameterization used for turbulence and mixing within the gray-zone. The three parameterizations analyzed are the Mellor-Yamada Nakanishi and Niino (MYNN) Level 2.5 planetary boundary layer scheme, the TKE-1.5 large eddy simulation (LES) closure scheme, and a recently developed three-dimensional planetary boundary layer scheme based on the Mellor-Yamada model. The simulation domain includes complex (i.e., mountainous) terrain in Nevada that was instrumented with meteorological towers, profiling and scanning lidars, a tethered balloon, and a surface flux tower. Simulations are compared to each other and to observations, with assessment of model skill at predicting wind speed, wind direction and TKE, and qualitative evaluations of transport and dispersion of smoke from controlled releases. This analysis demonstrates that microscale predictions of transport and dispersion can be significantly influenced by the choice of turbulence and mixing parameterization in the terra incognita , particularly over regions of complex terrain and with strong local forcing. This influence may not be apparent in the analysis of model skill, and motivates future field campaigns involving controlled tracer releases and corresponding modeling studies of the turbulence gray-zone.

54 ENVIRONMENTAL SCIENCES↗

Increased AGE Cross-Linking Reduces the Mechanical Properties of Osteons

Abstract The osteon is the primary structural component of bone, contributing significantly to its unique toughness and strength. Despite extensive research on osteonal structure, the properties of osteons have not been fully investigated, particularly within the context of bone fragility diseases like type 2 diabetes mellitus (T2DM). This study aims to isolate osteons from bovine bone, simulate the effects of increased advanced glycation end-products (AGEs) in T2DM through ribosylation, and evaluate the mechanical properties of isolated osteons. Osteons extracted from the posterior section of bovine femur mid-diaphysis were processed to achieve a sub-millimeter scale for microscale imaging. Subsequently, synchrotron radiation micro-computed tomography was employed to precisely localize and isolate the osteon internally. While comparable elastic properties were observed between control and ribosylated osteons, the presence of AGEs led to decreased strain to failure. Young’s modulus was quantified (9.9 ± 4.9 GPa and 8.7 ± 3 GPa, respectively), aligning closely with existing literature. This study presents a novel method for the extraction and isolation of osteons from bone and shows the detrimental effect of AGEs at the osteonal level.

Materials Science↗

Proppant embedment in coal and shale: Impacts of stress hardening and sorption

During methane production in CBM reservoirs, the influence of proppant embedment and permeability damage cannot be neglected – especially where the wall-rock is soft. Effective stresses are elevated during methane recovery, increasing both normal loading stress and confinement and simultaneously overprinting sorption-induced volumetric strains. Experiments and analytic modeling are conducted to define key mechanisms controlling these competitive effects. We independently measure overall sample compaction (external LVDT) and local strain (strain gauge) in the matrix to deconvolve proppant embedment in a propped fracture for different conditions of confining stress. The results show symptomatic behaviors of elastic (shale) and elastoplastic (coal) responses of embedment. Different from shale, the evolution of embedment is convex upwards with increased stress where indented depth increases more rapidly as loading stress increases under constant confinement. In addition, a stress-hardening effect is found to play a pivotal role in determining the characteristics of indentation, which are examined in terms of evolution profiles, deformation regimes, embedment slopes, curvatures, yield points and irreversible indentations. Based on the experimental observations a semianalytical model predicts indentation and the evolution of propped permeability under recreated in-situ stress conditions. A simplified case study is conducted to further illustrate the evolution of aperture and permeability of a propped fracture in CBM reservoirs. The modeling results suggest that proppant embedment is significantly overestimated if the variable stress-hardening (VSH) effect is neglected, especially when effective stress is large. Moreover, a decrease in indentation depth possibly occurs during late stage methane production, resulting in a reversal/recovery in fracture closure. This is because desorption-induced shrinkage becomes the predominant effect, causing an increase in aperture and a reduction in the indented volume of proppant. The resulting recovery in permeability implies that the propped coal fracture has the potential to optimally facilitate methane production as a pathway, even at high closure stresses generated by methane drainage.

01 COAL, LIGNITE, AND PEAT↗

Spatial and temporal variability of tritium in precipitation within South Africa and it's bearing on hydrological studies

Tritium, the radioactive isotope of hydrogen, has been used to understand groundwater recharge processes for decades. The current variation of tritium in the atmosphere is largely attributed to stratospheric production and fall out rates as well as global circulation phenomena controlling the hydrological cycle. Global controls on the variability in atmospheric tritium activity are poorly suited to explain local variation and tritium activities in precipitation are often assumed to be uniform over both local and regional catchments and watersheds. This assumption can result in both over and under estimation of modern recharge within an aquifer when using tritium as the recharge proxy. In order to minimize the inherent prediction residuals associated with tritium based recharge investigations, the variability of tritium in precipitation was modelled from 127 spatial precipitation samples taken over a two year period, combined with a 76 precipitation sample group-set taken over a one year period in a single location. Precipitation events were traced backward in time, from the point of collection, using HYSPLIT modelling to ascertain the origins of moisture content as well as the altitudes of moisture origin reached along the particle track. Tritium activities, collected over a one year period in Paarl, range from 0.45 to 4.16 TU and have a mean of 1.59 TU. Spatial storm events in the Western Cape in 2017 and 2018 had a range from 0 to 2.2 and 0.37 to 3.27 TU, respectively, with mean activities of 1.18 (n = 34) and 1.25 TU (n = 32). Both storm events had similar tritium variability (σ = 0.5 n = 35 and 0.48 n = 32). Regional precipitation events had the largest range of tritium activities (0.55–12.2 TU). Although not all tritium activities can be explained by interrogating the water mass origin, this study suggests that approximately 90% of events can be completely or partially attributed to the origin of the water mass. The variability of tritium, both spatially and temporally, was higher than expected, confirming that when uniform tritium inputs are used, the groundwater system would provide inaccurate modern recharge estimates. Higher spatial resolution of tritium variation in precipitation for a particular region will improve our ability to relate tritium activities in groundwater to local precipitation.

54 ENVIRONMENTAL SCIENCES↗

Cosolvent-tuned interactions in ionic liquids: A vibrational and quantum-chemical study of ethylene glycol ratio effects

Ionic liquids (ILs) are attractive media for CO 2 capture but remain limited by viscosity and cost. Blending ILs with ethylene glycol (EG) is a practical route to mitigate these constraints, yet the molecular origins of cosolvent effects and their dependence on composition are not well resolved. We combine Fourier-transform infrared (FT-IR) spectroscopy with quantum-chemical (DFT) analysis to elucidate how the IL:EG molar ratio modulates intermolecular interactions and electronic structure. Computed vibrational frequencies enable mode assignment and deconvolution of overlapping bands, revealing systematic, ratio-dependent shifts and broadenings in (i) EG O–H stretching, (ii) cation and EG C–H stretchings (imidazolium C2–H, C4–H, C5–H, methyl and ethyl groups, -CH2 of EG), (iii) anion signature modes (e.g., CN motifs), and (iv) EG C–O and C–C stretchings, consistent with the redistribution of hydrogen-bonding networks. Molecular electrostatic potential (MESP) maps quantify attenuation of extreme potential regions with increasing EG, indicating progressive screening of cation–anion electrostatic interactions. Quantum Theory of Atoms in Molecules (QTAIM) identifies emergent bond critical points between EG and the IL ions, while Reduced Density Gradient–Noncovalent Interaction (RDG–NCI) analysis differentiates strong directional hydrogen bonds from dispersive contacts across compositions. Together, these results show that EG fraction controls a switch from predominantly ion–ion to mixed ion–EG coordination, altering local polarity and polarizability that underlie the observed FT-IR trends. The framework provides composition–structure–spectrum relationships that can guide rational selection of IL:EG ratios to balance favorable molecular interactions with practical performance targets in scalable CO 2 capture systems.

DAC↗

How Fast Can a Li-Ion Battery Be Charged? Determination of Limiting Fast Charging Conditions

Fast-charge protocols that prevent lithium plating are needed to extend the life span of lithium-ion batteries. Here, we describe a simple experimental method to estimate the minimum charging time below which it is simply impossible to avoid plating at a given temperature. We demonstrate that, by gauging and correcting the ohmic drop that is intrinsic to reference electrodes, the local potential at the anode surface can be reasonably approximated. This finer anode control enables the determination of the maximum average rate at which lithium deposition can be mitigated, establishing realistic boundaries that can inform the development of advanced charging protocols.

25 ENERGY STORAGE↗

Recycling of Post-Consumer Waste Polystyrene Using Commercial Plastic Additives

Photothermal conversion can promote plastic depolymerization (chemical recycling to a monomer) through light-to-heat conversion. The highly localized temperature gradient near the photothermal agent surface allows selective heating with spatial control not observed with bulk pyrolysis. However, identifying and incorporating practical photothermal agents into plastics for end-of-life depolymerization have not been realized. Interestingly, plastics containing carbon black as a pigment present an ideal opportunity for photothermal conversion recycling. Herein, we use visible light to depolymerize polystyrene plastics into styrene monomers by using the dye in commercial black plastics. A model system is evaluated by synthesizing polystyrene–carbon black composites and depolymerizing under white LED light irradiation, producing styrene monomer in up to 60% yield. Excitingly, unmodified postconsumer black polystyrene samples are successfully depolymerized to a styrene monomer without adding catalysts or solvents. Using focused solar irradiation, yields up to 80% are observed in just 5 min. Furthermore, combining multiple types of polystyrene plastics with a small percentage of black polystyrene plastic enables full depolymerization of the mixture. This simple method leverages existing plastic additives to actualize a closed-loop economy of all-colored plastics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charge Delocalization and Vibronic Couplings in Quadrupolar Squaraine Dyes

Squaraines are prototypical quadrupolar charge-transfer chromophores that have recently attracted much attention as building blocks for solution-processed photovoltaics, fluorescent probes with large two-photon absorption cross sections, and aggregates with large circular dichroism. Their optical properties are often rationalized in terms of phenomenological essential state models, considering the coupling of two zwitterionic excited states to a neutral ground state. As a result, optical transitions to the lowest S 1 excited state are one-photon allowed, whereas the next higher S 2 state can only be accessed by two-photon transitions. A further implication of these models is a substantial reduction of vibronic coupling to the ubiquitous high-frequency vinyl-stretching modes of organic materials. Here, in this study, we combine time-resolved vibrational spectroscopy, two-dimensional electronic spectroscopy, and quantum-chemical simulations to test and rationalize these predictions for nonaggregated molecules. We find small Huang–Rhys factors below 0.01 for the high-frequency, 1500 cm –1 modes in particular, as well as a noticeable reduction for those of lower frequency modes in general for the electronic S 0 → S 1 transition. The two-photon allowed state S 2 is well separated energetically from S 1 and has weak vibronic signatures as well. Thus, the resulting pronounced concentration of the oscillator strength in a narrow region relevant to the lowest electronic transition makes squaraines and their aggregates exceptionally interesting for strong and ultrastrong coupling of excitons to localized light modes in external resonators with chiral properties that can largely be controlled by the molecular architecture.

36 MATERIALS SCIENCE↗

Wigner polarons probe the dynamics of a Wigner crystal in a monolayer semiconductor

Wigner crystals—lattices made purely of electrons—provide a platform for studying correlation-driven quantum phase transitions. Despite extensive research, accessing the internal dynamics of Wigner crystals has remained challenging, with most experiments probing only static order or collective motion. Here we demonstrate optical probing and the manipulation of zero-field Wigner crystals and elucidate their static and dynamic properties in the frequency domain. We observe optical resonances that we identify as Wigner polarons—quasiparticles formed when the electron lattice is locally distorted by exciton–Wigner crystal coupling. We further achieve all-optical control of spins in the Wigner crystal, thereby directly probing valley-dependent Wigner polaron scattering well above the magnetic ordering temperature and in the absence of any external magnetic field. Lastly, we show optical melting of the Wigner crystal and observe different responses of the umklapp (static) and Wigner polaron (dynamic) resonances to optical excitation. Our results provide an avenue for understanding electron dynamics and achieving ultrafast optical control of interaction-driven quantum phase transitions in strongly correlated electron systems.

2D materials↗

Solution structures in alkali nitrates and nitrites at high concentrations

In highly concentrated electrolyte solutions, where classical models often fail, specific ion–solvent interactions dictate bulk properties. Here, in this study, we combine small-angle X-ray scattering (SAXS) and Raman spectroscopy to link molecular coordination to mesoscale structure across alkali nitrate and nitrite solutions. Our results reveal a structural hierarchy driven by cation identity in that smaller cations (Li + , Na + ) form discrete contact ion pairs, while larger cations (K + , Rb + ) promote increasingly disordered local coordination and extended solute–solvent networks. Using nitrite salts as a structural control, we confirm this organizing principle across different anion geometries. Cs + undergoes a concentration-induced transition to a uniquely ordered state, resulting in a highly structured solution. This work provides a direct, mechanistic explanation for how cation choice dictates the ‘rules’ of solution architecture, offering a predictive basis for understanding phase behavior in complex industrial and environmental systems.

Mergelsberg, Sebastian T. [Pacific Northwest Natio↗

Contact-free reversible switching of improper ferroelectric domains by electron and ion irradiation

Focused ion beam (FIB) and scanning electron microscopy (SEM) are used to reversibly switch improper ferroelectric domains in the hexagonal manganite ErMnO 3 . Surface charging is achieved by local ion (positive charging) and electron (positive and negative charging) irradiation, which allows controlled polarization switching without the need for electrical contacts. Polarization cycling reveals that the domain walls tend to return to the equilibrium configuration obtained in the as-grown state. The response of sub-surface domains is studied by FIB cross-sectioning, enabling imaging in the direction perpendicular to the applied electric field. The results clarify how the polarization reversal in hexagonal manganites progresses at the level of domains, resolving both domain wall movements and the nucleation and growth of new domains. Our FIB-SEM based switching approach is applicable to all ferroelectrics where a sufficiently large electric field can be built up via surface charging, facilitating contact-free high-resolution studies of the domain and domain wall response to electric fields in 3D.

36 MATERIALS SCIENCE↗

Rheo–Electric Foundations and Engineering of Carbon Slurry Flow Electrodes

Flowable carbon slurry electrodes promise continuous, scalable electrochemical desalination and energy storage when their rheology (flow and stability) and electronic connectivity are jointly optimized. This report integrates six complementary thrusts that we executed under the Laboratory Directed Research and Development (LDRD) project: (i) a fast, ex situ, centrifuge-compatible method to quantify pellet (packed slurry) electronic conductivity, with a validated cell constant (“shape factor”) and quantitative structure–property insights for carbon mixtures; (ii) a controlled circulation study showing that peristaltic pumping can irreversibly alter particle size and morphology over laboratory-relevant durations; (iii) development of a miniature jet pump that preserves particle integrity while achieving entrainment ratios of 2–4 at practical flow rates; (iv) a comprehensive mapping of how a representative non-ionic surfactant (Tween 20) collapses the carbon gel network, separating network-percolation losses from intrinsic particle contact resistance; (v) in-situ visualization revealing how gravitational settling and flow-driven mixing compete to control charge transport, with dynamic bed layers preventing saturation while achieving 30-fold local concentration enhancement; and (vi) a simple, widely adoptable fabrication route to structured, gas-nitrided titanium nitride (TiN) titanium current collectors that dramatically lower interfacial losses and enable geometry-driven performance gains. Together, these results provide a coherent toolchain and design rules to accelerate formulation screening, de-risk device prototyping, and standardize characterization for carbon slurry electrodes in flow-electrode capacitive deionization (FCDI), electrochemical flow capacitor (EFC), and related systems.

25 ENERGY STORAGE↗

Deep Learning and Photogrammetric Reconstruction for Automated Crack Detection and Dimensional Measurement in Mining Operations

Surface crack detection and dimensional measurement at active mining sites present significant safety and operational challenges. Manual inspection methods are labor-intensive, spatially incomplete, and expose personnel to hazardous environments, while existing automated approaches have been developed primarily for concrete civil infrastructure and have not been validated on the complex, variable surfaces characteristic of mining environments. This dissertation presents an automated pipeline that integrates deep learning semantic segmentation with Structure-from-Motion photogrammetry to detect surface cracks and measure their aperture, length, and vertical displacement from standard RGB imagery acquired during routine Uncrewed Aerial Vehicle (UAV) survey operations, without requiring additional sensor hardware or manual measurement. The pipeline combines a U-Net architecture with an EfficientNet-B0 encoder, pretrained on the SDNET2018 concrete crack dataset and fine-tuned on a mining-specific dataset spanning laboratory concrete specimens, coal refuse impoundment embankments, and post-blast limestone quarry benches. Photogrammetric reconstruction is performed using COLMAP Structure-from-Motion and Multi-View Stereo, with crack segmentation masks projected into the reconstructed point cloud to enable three-dimensional vertical displacement measurement through local plane fitting and bimodal surface detection. The pipeline was validated across 36 controlled laboratory specimens at three imaging distances and four vertical displacement levels, achieving aperture measurement RMSE of 0.047 cm and R² of 0.954, and vertical displacement RMSE of 0.140 cm and R² of 0.966, against independent caliper measurements. Field application at a coal refuse impoundment in southwestern Pennsylvania detected 71 crack components across the embankment crest, with a dominant longitudinal crack exhibiting aperture values reaching 28 cm and a 95th percentile vertical displacement of 35.53 cm, consistent in magnitude and spatial distribution with simultaneously acquired LiDAR-derived estimates. Application across four post-blast limestone quarry bench datasets in California successfully characterized blast-induced fracture networks at ground sampling distances ranging from 0.59 to 1.23 cm/pixel, with detected crack geometries physically consistent with observable surface conditions at each site. The results demonstrate that deep learning-based crack detection and photogrammetric measurement can be integrated into routine UAV inspection workflows at mining sites, providing repeatable, scalable, and quantitative crack characterization across surface types, crack scales, and displacement magnitudes not previously addressed in the literature. The pipeline requires no dedicated surveying equipment beyond the UAV platforms already deployed at mine sites for survey and monitoring purposes, supporting practical adoption within existing operational workflows.

Crack detection, Dimensional Measurement↗