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At least 127 records · Page 7

Scaling patch analysis of turbulent planar plume

Proper scaling in turbulent planar plumes is investigated in this study using a scaling patch approach. Based on the scaled boundary conditions, a proper velocity scale for the mean axial flow is the plume centerline velocity U ref = U ctr , and a proper temperature scale for the temperature excess is Θ ref = T ctr – T ∞ , where T ctr is the plume centerline temperature and T ∞ is the ambient fluid temperature. By seeking an admissible scaling, a key concept in the scaling patch approach, for the mean continuity, mean momentum, and mean energy equations, respectively, the following is found: (1) a proper scale for the mean transverse flow is V ref = ( d δ / d x ) U ctr , where d δ / d x is the growth rate of the plume width. (2) A proper scale for the Reynolds shear stress is R vu , ref = U ctr V ref = ( d δ / d x ) U ctr 2 , a mix of the scales for the mean axial and transverse flows. (3) A proper scale for the turbulent heat flux is R v θ , ref = V ref Θ ctr , a mix of the scales for the mean transverse flow and mean temperature excess. The mean transverse flow thus plays a critical role in the scaling of turbulent planar plumes. Approximate functions are developed for the scaled mean transverse flow, Reynolds shear stress, and turbulent temperature flux, and are found to agree favorably with experimental and numerical simulation data. The integral analysis of the mean momentum equation yields a Richardson number Ri, which remains invariant in the axial direction. The Richardson number is defined as Ri = def g β Θ ctr δ t / ( U ctr V ref ) ≈ 1 / 2 , where g is the gravitational acceleration, β is the thermal expansion coefficient, and δ t is the plume half-width based on the mean temperature profile. This Richardson number arises directly from the scaling patch analysis of the mean momentum equation, including both the streamwise and transverse velocity scales.

42 ENGINEERING↗

Biorefinery siting and sizing to achieve the US Billion‐Ton Bioeconomy vision: A case study using a gasification–Fischer–Tropsch process

Achieving a secure, abundant, and affordable energy future requires a robust and adaptable energy strategy, with bioenergy playing a pivotal role. Biomass-based energy presents a promising pathway to use domestic resources while fostering economic opportunities in rural areas. Despite the potential to source more than 1 billion dry short tons of biomass annually in the US, significant infrastructure and economic barriers hinder full utilization for energy production. This study used the Biofuel Infrastructure, Logistics, and Transportation (BILT) model to assess biorefinery siting and scale and determine the number and size of facilities required to maximize use of the US biomass potential. A spatially agnostic approach first assessed the effects of facility capacity and transportation constraints on biomass use. Then, a spatially explicit analysis integrated county-level biomass availability from the US Department of Energy's 2023 Billion-Ton Report and technoeconomic assessments to evaluate different biorefinery deployment scenarios. The results indicate that an optimized mix of facility sizes is essential to leverage biomass resources fully across varying regional production densities to maximize use of the US biomass potential. Larger biorefineries or co-located smaller facilities significantly enhance biomass use while reducing costs through economies of scale. These findings underscore the importance of strategically balancing facility capacity and spatial distribution to optimize the bioenergy supply chain. In conclusion, this study provides critical insights for advancing the US bioenergy economy by aligning biorefinery deployment with biomass resource availability and economic viability.

BILT Model↗

Optimization of well design and CO 2 injection strategy for risk reduction in Class VI geological carbon sequestration wells

The safety and durability of Class VI wells are critical for geological carbon sequestration (GCS). However, current GCS operations face unique challenges: unlike traditional Class II wells, Class VI CO 2 injection wells operate at rates up to 100 times higher, dramatically increasing the risk of wellbore leakage and structural compromise due to severe temperature drops and associated mechanical stresses. Despite existing guidelines on material selection, there remains a substantial gap in understanding how rapid CO 2 injection rates, low surface temperatures, and variable reservoir conditions interact to threaten long-term well integrity. This study presents a comprehensive, original workflow integrating advanced analytical and numerical models for both well flow and well integrity analysis. By systematically simulating a wide range of field-relevant scenarios—including variations in injection rate, CO 2 temperature, and reservoir pressure—this work provides the first cross-validated assessment of cooling effects on wellbore. The results reveal that extreme temperature drops, up to 60 °C, can occur under high injection rates, particularly in depleted reservoirs, significantly increasing the risk of cement failure. Building on these insights, the study proposes innovative, practical well design and operational strategies, including ductile cement formulations, pre-stressing techniques, advanced insulation coatings, and proactive management of injection rates. The safety of Class VI well extends beyond simply using CO 2 resistant materials. Cement materials should possess optimal thermo-hydraulic-mechanical-chemical properties for effective performance. This work provides a scientific basis for optimizing Class VI well designs, with direct benefits for minimizing environmental risk, lowering operational costs, and enhancing the long-term reliability of GCS.

25 ENERGY STORAGE↗

Kinetics of Pyrolysis and Thermal Evolution of Negev Desert Lithologies

The Negev desert in Israel is home to large quantities of organic-rich, shallow marine sedimentary lithologies that could potentially accommodate the disposal of spent nuclear fuel. Previous thermal analyses of Negev carbonates have focused on industrially relevant considerations such as natural gas and oil extraction or pyrolysis for recovering hydrocarbon fuels. Here, this study addresses thermal evolution of the Negev organic-rich carbonate, siliceous, and phosphorite rocks and associated chemical, mineralogical, and microstructural changes that may occur under prolonged thermal loading in the vicinity of spent nuclear fuel disposal systems. Our employed methods include high-temperature X-ray diffraction, high-temperature infrared spectroscopy, and thermal analysis integrating thermogravimetry, differential scanning calorimetry, and mass spectrometry. Further, we apply iterative iso-conversional model-free methods to derive kinetic parameters for thermal decomposition of the Negev organic-rich carbonate rocks from 200 to 550 °C. Our results have provided mechanistic insights into the thermal evolution encompassing water desorption, decomposition of organic matter, and decarbonation of carbonate phases.

58 GEOSCIENCES↗

Predicting Cement-Sheath Integrity with Consideration of Initial State of Stress and Thermoporoelastic Effects

In conventional wellbore-integrity analysis, the cement sheath’s initial state of stress and transient thermoporoelastic effects are often neglected. However, the initial state of stress is prerequisite information for accurately predicting the safe operating conditions that prevent a cemented well from being damaged. In addition, transient thermoporoelastic effects can have a profound effect on when damage will occur. Here in this paper, we propose a model that includes these effects to predict the safe operating pressures and temperatures that will prevent cement-sheath failure. For the initial state of stress, we proposed an empirical model using measurements. Subsequent stress changes are evaluated by a fully coupled transient thermoporoelastic model to analyze the mechanical behavior of the cement sheath. We predict the safe operating envelope (SOE) for shear, tensile, and debonding cement-sheath failures caused by pressure and temperature perturbations after the cement sets. Our model predicts that pore pressure is a key factor for cement failure, especially for rapid temperature changes. If the formation is low permeability, the transient pore pressures are amplified, causing the risk of damage to increase. Compared with conventional thermoelastic models, the thermoporoelastic model predicts a smaller SOE when heating the internal casing fluid and a larger envelope when cooling the internal casing fluid. Finally, the heating rate was considered with respect to field applications. The heating rate was also considered, and slower heating/cooling rates can prevent damage to the cement sheath. Finally, the thermoporoelastic model was applied to explain several laboratory and field experiments and achieved good matches.

02 PETROLEUM↗

Single-cell profiling of Arabidopsis leaves to Pseudomonas syringae infection

Plant response to pathogen infection varies within a leaf, yet this heterogeneity is not well resolved. We expose Arabidopsis to Pseudomonas syringae or mock treatment and profile >11,000 individual cells using single-cell RNA sequencing. Integrative analysis of cell populations from both treatments identifies distinct pathogen-responsive cell clusters exhibiting transcriptional responses ranging from immunity to susceptibility. Pseudotime analyses through pathogen infection reveals a continuum of disease progression from an immune to a susceptible state. Confocal imaging of promoter-reporter lines for transcripts enriched in immune cell clusters shows expression surrounding substomatal cavities colonized or in close proximity to bacterial colonies, suggesting that cells within immune clusters represent sites of early pathogen invasion. Susceptibility clusters exhibit more general localization and are highly induced at later stages of infection. Overall, our work shows cellular heterogeneity within an infected leaf and provides insight into plant differential response to infection at a single-cell level.

59 BASIC BIOLOGICAL SCIENCES↗

Spent fuel nondestructive assay integrated characterization from active neutron, passive neutron, and passive gamma

Spent nuclear fuel comprises a wide range of irradiated isotopic material compositions, and characterization through nondestructive measurements is beneficial in verifying declared parameters before the fuel is placed in storage, final disposal, and/or reprocessed. This paper discusses results from three nondestructive assay instruments, including passive gamma, passive neutron, and active neutron methods, that measured fifty spent fuel assemblies at the Clab interim storage facility in Sweden. Here, integrated analysis of the measurements from the three different instruments allowed parametric assessments of cooling time, burnup, neutron multiplication, fissile mass, initial enrichment, and decay heat of each individual fuel assembly. Passive gamma measurements were found to be the most beneficial in predicting cooling time, passive neutron for determining burnup, active neutron in estimating initial enrichment, and both passive and total neutron for multiplication correlations. Fissile mass was best estimated using any combination of any two of the instruments such that corrections for isotopic changes in the fuel could be accounted for with the first set of measurements and multiplication of the assembly in the second. In conclusion, the nondestructive assay technologies demonstrated through this effort enhance the characterization of spent nuclear fuel assemblies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Thermally Stable Co@C3N4 Single-Atom Catalysts for CO Oxidation: Atomic-Level Insights into Structure and Activity

Single Co atoms supported on C3N4 (Co@C3N4) have demonstrated high activity and selectivity in photocatalysis. However, the investigation of structure–function relationships and reaction mechanisms under photocatalytic conditions is very challenging due to the complex conditions of light absorption, charge transfer, and catalysis. In this study, we employed thermal CO oxidation as a prototypical probe reaction to benchmark the intrinsic catalytic performance and track the active-site evolution of Co@C3N4. Single Co atoms were identified and shown to be the catalytically active sites for CO oxidation based on control experiments and isotope-labeling experiments. The Co sites remained atomically dispersed before, during, and after the reaction with temperatures up to 400 °C, as established by in situ X-ray absorption fine structure (XAFS) combined with density functional theory (DFT), FDMNES simulations, and dynamic-time-warping (DTW)-assisted X-ray absorption near edge structure (XANES) matching. Together with theoretical calculations, the integrated analysis reveals a stable coordination environment under reaction conditions, which correlates with sustained activity, establishing Co@C3N4 single-atom catalysts as thermally stable CO oxidation catalysts. Beyond these findings, the current study provides a workflow for unambiguously assigning active sites in Co@C3N4 for thermal CO oxidation. This workflow will aid the understanding of their behavior in photocatalysis in the future, where light-driven dynamics obscure direct structure–function links. Notably, this study provides fundamental insights for the rational design of robust single-atom catalysts and a foundation for the broader application of Co@C3N4 catalysts in oxidation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An atlas of dynamic chromatin landscapes in mouse fetal development

The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP–seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC–seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.

59 BASIC BIOLOGICAL SCIENCES↗

Evolution of neuronal cell classes and types in the vertebrate retina

The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs1. Retinal cell types may have evolved to accommodate these varied needs, but this has not been systematically studied. Here we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a bird, a reptile, a teleost fish and a lamprey. We found high molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells (RGCs) and Müller glia), with transcriptomic variation across species related to evolutionary distance. Major subclasses were also conserved, whereas variation among cell types within classes or subclasses was more pronounced. However, an integrative analysis revealed that numerous cell types are shared across species, based on conserved gene expression programmes that are likely to trace back to an early ancestral vertebrate. The degree of variation among cell types increased from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified rodent orthologues of midget RGCs, which comprise more than 80% of RGCs in the human retina, subserve high-acuity vision, and were previously believed to be restricted to primates. By contrast, the mouse orthologues have large receptive fields and comprise around 2% of mouse RGCs. Projections of both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but are descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.

59 BASIC BIOLOGICAL SCIENCES↗

Tracking ion intercalation into layered Ti 3 C 2 MXene films across length scales

Enhancing the energy stored and power delivered by layered materials relies strongly on improved understanding of the intricate interplay of electrolyte ions, solvents, and electrode interactions as well as the role of confinement. Here we report a highly integrated study with multiscale theory/modelling and experiments to track the intercalation of aqueous Li + , Na + , K + , Cs + , and Mg 2+ ions into Ti 3 C 2 MXene. The integrated analysis of experiments assisted by theory/modelling allows for a deep understanding of energy storage processes highlighting the importance of the dynamics of cations, their positionings between MXene sheets, their effects on mechanical properties and capacitive energy storage. Computational simulations and operando calorimetry measurements prove the processes involving cation dehydration and H+ rehydration, showing a good correlation for heat variations between experiments and theory. Operando liquid AFM mapped energy dissipation of ions appears non-uniformly across the MXene surface, indicating heterogeneities of ions inside the MXene and confirming partially the ion behaviour obtained in theory. We directly demonstrate that the average distance between the cation and MXene surface follows a modified two-sided Helmholtz model when plotted versus the open circuit potential capacitance, revealing a different electrical double layer mechanism in confinement. This new fundamental understanding lays the foundation for improved functional devices utilizing electrodes and membranes made of two-dimensional materials.

36 MATERIALS SCIENCE↗

High-throughput Single-Cell Proteomics and Transcriptomics from the Same Cells with a Nanoliter-Scale Spin-Transfer Approach

Single-cell multiomic platforms provide a comprehensive snapshot of cellular states and cell types by offering critical insights into the spatiotemporal regulation of biomolecular networks at a systems level, thereby defining the basis of multicellularity. Here, we introduce nanoSPINS, an advanced platform that enables high-throughput profiling and integrative analysis of the transcriptome and proteome from the same single cells using RNA sequencing and isobaric labeling LC-MS-based proteomics, respectively. NanoSPINS can efficiently transfer mRNA-containing droplets across two microarrays via a centrifugation-based approach, while proteins are retained on the initial platform. Benchmarking of nanoSPINS on two cell lines demonstrates its ability to generate global proteomic and transcriptomic profiles that align well with previously established methodologies/platforms. The incorporation of isobaric TMTpro labeling into this single-cell multiomics platform significantly enhances the throughput of single-cell proteomic analyses. Through the high-throughput quantification of the proteome and transcriptome, nanoSPINS not only facilitates the identification of molecular features at both mRNA and protein level but also provides larger sample sizes for improved statistical power in clustering and differential abundance. Given the broad applicability of single-cell multiomics in biological research and clinical settings, we believe nanoSPINS represents a powerful platform for the characterization of heterogeneous cell populations.

multi 'omics↗

Spatial profiling of the interplay between cell type- and vision-dependent transcriptomic programs in the visual cortex

How early sensory experience during “critical periods” of postnatal life affects the organization of the mammalian neocortex at the resolution of neuronal cell types is poorly understood. We previously reported that the functional and molecular profiles of layer 2/3 (L2/3) cell types in the primary visual cortex (V1) are vision-dependent [S. Chenget al.,Cell185, 311–327.e24 (2022)]. Here, we characterize the spatial organization of L2/3 cell types with and without visual experience. Spatial transcriptomic profiling based on 500 genes recapitulates the zonation of L2/3 cell types along the pial–ventricular axis in V1. By applying multitasking theory, we suggest that the spatial zonation of L2/3 cell types is linked to the continuous nature of their gene expression profiles, which can be represented as a 2D manifold bounded by three archetypal cell types. By comparing normally reared and dark reared L2/3 cells, we show that visual deprivation-induced transcriptomic changes comprise two independent gene programs. The first, induced specifically in the visual cortex, includes immediate-early genes and genes associated with metabolic processes. It manifests as a change in cell state that is orthogonal to cell-type-specific gene expression programs. By contrast, the second program impacts L2/3 cell-type identity, regulating a subset of cell-type-specific genes and shifting the distribution of cells within the L2/3 cell-type manifold. Through an integrated analysis of spatial transcriptomics with single-nucleus RNA-seq data, we describe how vision patterns cortical L2/3 cell types during the critical period.

Science & Technology - Other Topics↗

Creb5 controls its own expression and directly induces the joint interzone regulatory program

Prior studies have indicated that the transcription factor Creb5 is expressed in the joint interzone, which contains the progenitors for all synovial joint tissues in both mouse and human embryos. In the absence of Creb5 function, most synovial joint interzones fail to form and the cartilage templates in the long bones remain fused. This earlier work did not clarify whether Creb5 initiates a cascade of signaling molecules, such as growth and differentiation factor 5 (Gdf5) and Wnt-family members, that in turn induce the formation of the joint interzone, or instead directly activates the expression of joint interzone markers. In the present study, an integrative analysis of the transcriptome, chromatin accessibility, and Creb5-occupancy in joint progenitors revealed that Creb5 directly binds to both its own two promoters and to the regulatory regions of Gdf5 and Sfrp2, each of whose expression in the joint interzone is Creb5-dependent. Functional enhancer analysis indicated that Creb5 binding sites in either the two Creb5 promoters, or in Gdf5 and Sfrp2 regulatory elements are necessary for these sequences to drive transgene expression in the developing synovial joints. While Creb5 directly drives Gdf5 and Sfrp2 expression in the inner joint interzone, Creb5 activates Barx1 expression specifically in the outer joint interzone. Our findings indicate that Creb5 initiates a regulatory network that both promotes the formation of synovial joints, and subsequently activates distinct transcriptional targets in the inner versus the outer regions of the joint interzone, thus regionalizing gene expression in the developing joint.

Zhang, Cheng-Hai↗

Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils

Abstract Peatlands are among the largest natural sources of atmospheric methane (CH 4 ) worldwide. Microbial processes play a key role in regulating CH 4 emissions from peatland ecosystems, yet the complex interplay between soil substrates and microbial communities in controlling CH 4 emissions as a function of global change remains unclear. Herein, we performed an integrated analysis of multi‐omics data sets to provide a comprehensive understanding of the molecular processes driving changes in greenhouse gas (GHG) emissions in peatland ecosystems with increasing temperature and sulfate deposition in a laboratory incubation study. We sought to first investigate how increasing temperatures (4, 21, and 35°C) impact soil microbiome–metabolome interactions; then explore the competition between methanogens and sulfate‐reducing bacteria (SRBs) with increasing sulfate concentrations at the optimum temperature for methanogenesis. Our results revealed that peat soil organic matter degradation, mediated by biotic and potentially abiotic processes, is the main driver of the increase in CO 2 production with temperature. In contrast, the decrease in CH 4 production at 35°C was linked to the absence of syntrophic communities and the potential inhibitory effect of phenols on methanogens. Elevated temperatures further induced the microbial communities to develop high growth yield and stress tolerator trait‐based strategies leading to a shift in their composition and function. On the other hand, SRBs were able to outcompete methanogens in the presence of non‐limiting sulfate concentrations at 21°C, thereby reducing CH 4 emissions. At higher sulfate concentrations, however, the prevalence of communities capable of producing sufficient low‐molecular‐weight carbon substrates for the coexistence of SRBs and methanogens was translated into elevated CH 4 emissions. The use of omics in this study enhanced our understanding of the structure and interactions among microbes with the abiotic components of the system that can be useful for mitigating GHG emissions from peatland ecosystems in the face of global change.

AminiTabrizi, Roya↗

Unraveling design principles of protein landscapes in photosynthetic membranes in plant chloroplasts

The supramolecular organization of proteins within photosynthetic membranes is crucial for energy conversion in plants. Here, we introduce an analytical and computational pipeline that integrates high-resolution cryo–scanning electron microscopy, biochemical quantification, advanced Monte Carlo computer simulations, and statistical methods to elucidate the elusive protein landscapes of grana membranes in intact Arabidopsis leaves. Our integrated analysis challenges the prevailing view that particles on the exoplasmic fracture faces in freeze-fracture samples represent photosystem II exclusively. Instead, these particles also include cytochrome b 6 f complexes. Furthermore, our steric clash analysis demonstrates that stacked membranes contain a mixture of larger PSII supercomplexes (C 2 S 2 M 2 and C 2 S 2 ) in addition to a smaller complex (C 2 ). This suggests that in vivo PSII supercomplexes exist in an equilibrium distribution of differing sizes. Furthermore, we discovered that, although size exclusion effects govern the global protein arrangement, local packing exhibits orientational order indicative of lateral attractive protein-protein interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon

The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation in environmental acclimation are underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating the transcriptome-wide locations of transcript processing sites (TPSs) and SmAP1 binding, the genome-wide locations of antisense RNAs (asRNAs), and the consequences of RNase_2099C knockout on the differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely being regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (transcriptome sequencing [RNA-Seq]) and protein levels (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry [SWATH-MS]) for 2,579 genes over four phases of batch culture growth in complex medium generated additional evidence for the conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation under anoxic conditions and modulate the frequency of transposition by insertion sequence (IS) elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public Web resource (https://halodata.systemsbiology.net).

59 BASIC BIOLOGICAL SCIENCES↗

IOMiner v0.3

Modern HPC systems are collecting large amounts of I/O performance data. The massive volume and heterogeneity of this data, however, have made timely performance of in-depth integrated analysis difficult. To overcome this difficulty and to allow users to identify the root causes of poor application I/O performance, we developed IOMiner, an I/O log analytics framework.

Byna, Suren↗