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At least 217 records · Page 12

A Hybrid Approach Enabling Large-Scale Glycomic Analysis of Post-Golgi Vesicles Reveals a Transport Route for Polysaccharides

The plant endomembrane system facilitates the transport of polysaccharides, associated enzymes, and glycoproteins through its dynamic pathways. Although enzymes involved in cell wall biosynthesis have been identified, little is known about the endomembrane-based transport of glycan components. This is partially attributed to technical challenges in biochemically determining polysaccharide cargo in specific vesicles. Here, we introduce a hybrid approach addressing this limitation. By combining vesicle isolation with a large-scale carbohydrate antibody arraying technique, we charted an initial large-scale map describing the glycome profile of the SYNTAXIN OF PLANTS61 (SYP61) trans-Golgi network compartment in Arabidopsis (Arabidopsis thaliana). A library of antibodies recognizing specific noncellulosic carbohydrate epitopes allowed us to identify a range of diverse glycans, including pectins, xyloglucans (XyGs), and arabinogalactan proteins in isolated vesicles. Changes in XyG- and pectin-specific epitopes in the cell wall of an Arabidopsis SYP61 mutant corroborate our findings. Our data provide evidence that SYP61 vesicles are involved in the transport and deposition of structural polysaccharides and glycoproteins. Finally, adaptation of our methodology can enable studies characterizing the glycome profiles of various vesicle populations in plant and animal systems and their respective roles in glycan transport defined by subcellular markers, developmental stages, or environmental stimuli.

59 BASIC BIOLOGICAL SCIENCES↗

Earth Microbiome Project and Global Systems Biology

Recently, we published the first large-scale analysis of data from the Earth Microbiome Project (1, 2), a truly multidisciplinary research program involving more than 500 scientists and 27,751 samples acquired from 43 countries. These samples represent myriad specimen types and span a wide range of biotic and abiotic factors, geographic locations, and physicochemical properties. The database (https://qiita.ucsd.edu/emp/) is still growing, with over 90,000 amplicon datasets, >500 metagenomic runs, and metabolomics datasets from a similar number of samples. Importantly, the techniques, data and analytical tools are all standardized and publicly accessible, providing a framework to support research at a scale of integration that just 7 years ago seemed impossible.

Gilbert, Jack A.↗

Green’s functions on a renormalized lattice: An improved method for the integer quantum Hall transition

Highlights: • Speed up of numerical calculations by exact renormalization group steps. • Practical approach to handle delicate scaling analysis. • Absence of evidence to prefer marginal corrections over power-law corrections. We introduce a performance-optimized method to simulate localization problems on bipartite tight-binding lattices. It combines an exact renormalization group step to reduce the sparseness of the original problem with the recursive Green’s function method. We apply this framework to investigate the critical behavior of the integer quantum Hall transition of a tight-binding Hamiltonian defined on a simple square lattice. In addition, we employ an improved scaling analysis that includes two irrelevant exponents to characterize the shift of the critical energy as well as the corrections to the dimensionless Lyapunov exponent. We compare our findings with the results of a conventional implementation of the recursive Green’s function method, and we put them into broader perspective in view of recent development in this field.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Large eddy simulation of a supersonic lifted hydrogen flame: Impacts of Lewis, turbulent Schmidt and Prandtl numbers

Parametric large eddy simulations (LES) of a supersonic lifted hydrogen flame are reported. The emphases are on two aspects: impacts of (1) Lewis number (Lei of the ith species) and (2) turbulent Schmidt and Prandtl numbers (⁠Sc t and Pr t ⁠) on supersonic turbulent flame and flow structures. Five cases are considered: species-specific Le i , Sc t = Sr t = 1.0 (C 0 ); unity Le i , Sc t = Pr t = 1.0 (C 1 ); species-specific Sc t = 0.5, Pr t = 1.0 (C 2 ); species-specific Le i , Sc t = 1.0, Pr t = 0.5 (C 3 ); and species-specific Le i , Sc t = Pr t = 0.5 (C 4 ). Numerical results of instantaneous and/or time-averaged species mole fractions, mixture fraction, heat release rate, flame base location, and mixed modes of premixed and diffusion combustion are compared between cases C 0 and C 1 . Differences in auto-ignition locations and strengths and flame structures and stabilization specify the impacts of Lewis number. They are triggered by different predictions of species mass and thermal diffusions at fuel-coflow and/or coflow-ambient air mixing layers. These differences are rationalized by a scale analysis of mass/thermal diffusion and convection for case C 0 , which suggests the relatively low but non-negligible former against the latter. Cases C 0 and C 2 –C 4 barely see differences in terms of instantaneous and/or time-averaged temperature, velocity, and mixed combustion modes except for further downstream areas where combustion occurs. Both Sc t and Pr t impose less significant influences than Lewis number, as sub-grid scale mass/thermal diffusion is subordinate to its resolved counterpart according to their scale analysis for case C 4 .

42 ENGINEERING↗

Hydropower Infrastructure - LAkes, Reservoirs, and RIvers (HILARRI), v4

HILARRI is a database of links between major datasets of operational hydropower dams and powerplants, and inland water bodies. These connections are critical for conducting large-scale analysis of hydropower infrastructure and their associated natural and engineered water systems. Features include: – Dams from the National Inventory of Dams (2025) and the Global Reservoir and Dam Database (GRanD v1.3) – Hydropower plants from the Existing Hydropower Assets dataset (EHA 2025) – Power plants that are listed in the 2025 U.S. Hydropower Development Pipeline Data or were listed in previous versions of the dataset These hydropower infrastructure features are linked to several major datasets that provide hydrologic and hydraulic information relevant for analysis of hydropower systems that includes the integral water resources. That information comes from: – Products from the National Hydrography Dataset (NHD) – NHDPlusV2 Medium Resolution river network flowlines, – NHD waterbodies (limited to lakes and reservoirs), – NHD Watershed Boundary Dataset (HUC12-level for the Conterminous United States (CONUS)) – NHD High Resolution waterbodies – HydroLAKES water bodies (lakes and reservoirs) – LAGOS-US lakes and reservoirs – EPA National Lakes Assessment (2007, 2012, 2017, and 2022) – The Reservoir Sedimentation Database (RESSED) – EPA SuRGE sampling locations Unique identifiers are used to facilitate joining to the original full datasets. For example, characteristics of NHD flowlines such as estimated average flow rate can be joined from the NHDPlusV2 dataset to a dam or power plant listed in HILARRI based on the ID field, “COMID”, that is common to both datasets. HILARRI only includes basic information about identifiers, location, and data quality or usage notes. It does not contain the attributes or time series data associated with these sites. The HILARRI dataset incorporates information from several datasets to facilitate more effective and accurate analysis of hydropower infrastructure and their associated waterbodies. For example, dams were checked against the most recent American Rivers Dam Removal Database to identify and flag facilities that may no longer exist. Additionally, dams that are listed multiple times in the NID are identified and flagged to avoid double-counting when analyzing and summarizing information. Other quality flags include certainty of operational hydropower (i.e., if one or more datasets indicates hydropower at a particular location), whether an associated water body is accurate or composed of multiple polygons, or whether there is a known issue with reported characteristics in one of the underlying datasets. These additional data flags are designed to increase confidence in data usage for individual to large-scale analyses.

Hansen, Carly [ORNL] (ORCID:0000000193280838)↗

Non-monotonic resonance in a spatially forced Lengyel-Epstein model

We study resonant spatially periodic solutions of the Lengyel-Epstein model modified to describe the chlorine dioxide-iodine-malonic acid reaction under spatially periodic illumination. Using multiple-scale analysis and numerical simulations, we obtain the stability ranges of 2:1 resonant solutions, i.e., solutions with wavenumbers that are exactly half of the forcing wavenumber. We show that the width of resonant wavenumber response is a non-monotonic function of the forcing strength, and diminishes to zero at sufficiently strong forcing. We further show that strong forcing may result in a π/2 phase shift of the resonant solutions, and argue that the nonequilibrium Ising-Bloch front bifurcation can be reversed. We attribute these behaviors to an inherent property of forcing by periodic illumination, namely, the increase of the mean spatial illumination as the forcing amplitude is increased.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Climate Change Impacts on Natural Sulfur Production: Ocean Acidification and Community Shifts

Utilizing the reduced-complexity model Hector, a regional scale analysis was conducted quantifying the possible effects climate change may have on dimethyl sulfide (DMS) emissions within the oceans. The investigation began with a review of the sulfur cycle in modern Earth system models. We then expanded the biogeochemical representation within Hector to include a natural ocean component while accounting for acidification and planktonic community shifts. The report presents results from both a latitudinal and a global perspective. This new approach highlights disparate outcomes which have been inadequately characterized via planetary averages in past publications. Our findings suggest that natural sulfur emissions (ESN) may exert a forcing up to 4 times that of the CO 2 marine feedback, 0.62 and 0.15 Wm –2 , respectively, and reverse the radiative forcing sign in low latitudes. Additionally, sensitivity tests were conducted to demonstrate the need for further examination of the DMS loop. As a result, the present work attempts to include dynamic ESN within reduced-complexity simulations of the sulfur cycle, illustrating its impact on the global radiative budget.

54 ENVIRONMENTAL SCIENCES↗

Large-scale proteome analysis of abscisic acid and ABSCISIC ACID INSENSITIVE3-dependent proteins related to desiccation tolerance in Physcomitrella patens

Desiccation tolerance is an ancestral feature of land plants and is still retained in non-vascular plants such as bryophytes and some vascular plants. However, except for seeds and spores, this trait is absent in vegetative tissues of vascular plants. Although many studies have focused on understanding the molecular basis underlying desiccation tolerance using transcriptome and proteome approaches, the critical molecular differences between desiccation tolerant plants and non-desiccation plants are still not clear. The moss Physcomitrella patens cannot survive rapid desiccation under laboratory conditions, but if cells of the protonemata are treated by the phytohormone abscisic acid (ABA) prior to desiccation, it can survive 24 h exposure to desiccation and regrow after rehydration. The desiccation tolerance induced by ABA (AiDT) is specific to this hormone, but also depends on a plant transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3). Here we report the comparative proteomic analysis of AiDT between wild type and ABI3 deleted mutant (Δabi3) of P. patens using iTRAQ (Isobaric Tags for Relative and Absolute Quantification). From a total of 1980 unique proteins that we identified, only 16 proteins are significantly altered in Δabi3 compared to wild type after desiccation following ABA treatment. Among this group, three of the four proteins that were severely affected in Δabi3 tissue were Arabidopsis orthologous genes, which were expressed in maturing seeds under the regulation of ABI3. These included a Group 1 late embryogenesis abundant (LEA) protein, a short-chain dehydrogenase, and a desiccation-related protein. Our results suggest that at least three of these proteins expressed in desiccation tolerant cells of both Arabidopsis and the moss are very likely to play important roles in acquisition of desiccation tolerance in land plants. Furthermore, our results suggest that the regulatory machinery of ABA- and ABI3-mediated gene expression for desiccation tolerance might have evolved in ancestral land plants before the separation of bryophytes and vascular plants. - Highlights: • Large-scale proteomics highlighted proteins related to plant desiccation tolerance. • The proteins were regulated by both the phytohormone ABA and ABI3. • The proteins accumulated in desiccation tolerant cells of both Arabidopsis and moss. • Evolutionary origin of regulatory machinery for desiccation tolerance is proposed.

60 APPLIED LIFE SCIENCES↗

Understanding the breakdown of classic two-phase theory and spray atomization at engine-relevant conditions

We present a generalized framework for multi-component liquid injections to understand and predict the breakdown of classic two-phase theory and spray atomization at engine-relevant conditions. The analysis focuses on the thermodynamic structure and the immiscibility state of representative gas-liquid interfaces. The most modern form of Helmholtz energy mixture state equation is utilized which exhibits a unique and physically-consistent behavior over the entire two-phase regime of fluid densities. It is combined with generalized models for non-linear Gradient Theory and for liquid injections to quantify multi-component two-phase interface structures in global thermal equilibrium. Then, the Helmholtz free energy is minimized which determines the interfacial species distribution as a consequence. This minimal free energy state is demonstrated to validate the underlying assumptions of classic two-phase theory and spray atomization. However, under certain engine-relevant conditions for which corroborating experimental data is presented, this requirement for interfacial thermal equilibrium becomes unsustainable. A rigorously derived probability density function quantifies the ability of the interface to develop internal spatial temperature gradients in the presence of significant temperature differences between injected liquid and ambient gas. Then, the interface can no longer be viewed as an isolated system at minimal free energy. Instead, the interfacial dynamics become intimately connected to those of the separated homogeneous phases. Hence, the interface transitions toward a state in local equilibrium whereupon it becomes a dense-fluid mixing layer. A new conceptual view of a transitional liquid injection process emerges from a transition time scale analysis. Close to the nozzle exit, the two-phase interface still remains largely intact and more classic two-phase processes prevail as a consequence. Further downstream, however, the transition to dense- fluid mixing generally occurs before the liquid length is reached. The significance of the presented modeling expressions is established by a direct comparison to a reduced model, which utilizes widely-applied approximations but fundamentally fails to capture the physical complexity discussed in this paper.

42 ENGINEERING↗

Collaborative atomic-scale design, analysis, and nanofabrication for record breaking, single-crystal Zn(x)Cd(1-x)Te solar cell arrays

Cadmium telluride (CdTe) based photovoltaics provide a viable solar energy solution because of their short payback time, low manufacturing cost, and high theoretical efficiency ~29%. However, the highest record laboratory efficiency is only 22.1% and long-term performance degradation is ~1 % per year which hinders greater economic viability. Higher open circuit voltage (Voc) and fill factor (FF) are needed to increase the efficiency of the solar cell. Cells with record energy conversion efficiencies report short current (Jsc) values close to their theoretical maximum. However, Voc and FF in these devices remain well below their anticipated optimum. These electrical parameters depend on the quality of the various layers in the solar cell. In particular they depend on the crystalline quality including the defect and impurity concentrations. Therefore understanding how defects and impurities form and evolve in the material layers is important to design devices with higher efficiency and stability. The aim of this project is to create a novel path around the fundamental barriers to achieve high open-circuit voltages (VOC ≥ 1.0 V) in CdTe/CdS solar cells. The idea of the project was to combine nanopatterned crystal growth and alloy compositional grading (with concomitant lattice parameter and energy band gap grading) to reduce the defect density and dramatically improve spatial uniformity of ZnxCd(1-x)Te/CdS cells. The lattice mismatch between ZnTe and CdS is 3.9% compared to a much larger 9.2% between CdTe and CdS. Importantly, when crystal growth is contained to the nanoscale, the strain in each layer is reduced by a factor of two due to strain partitioning and 3D strain relief mechanisms that come into play. This reduces the strain in the ZnTe from 3.9% to 1.95% which is within the range of metamorphic crystal growth. In preliminary studies, molecular dynamics simulation of ZnTe/CdS islands predicted dislocation-free material when the patterning was reduced to ~80 nm in diameter. The energy band gap of ZnxCd(1-x)Te is also graded in conjunction with alloy composition. ZnTe has an energy band gap of 2.3 eV. Finally, an added benefit of patterned growth is that it enables direct one-to-one study of the relationships between fabrication, microstructure and performance of individual crystal grains within the array. Experimental characterization techniques such as atomic probe tomography (APT) and transmission electron microscopy (TEM) have elucidated much about the microstructure of the layers. However, the techniques are destructive, costly and have limitations on the information they convey. For example, TEM gives information with atomic scale resolution but on 2-dimensional substrates. On the other hand, APT gives 3-dimensional information but is not able to resolve atomic scale structure. Alternatively, Molecular Dynamics (MD) simulations offer a solution to rapidly generate time-resolved, 3-dimensional, atomic scale structures of crystal growth. Direct MD simulations of microstructures of Cu-doped II-VI compound multilayers can impact the research on CdTe/CdS solar cells. Such MD simulations require an interatomic potential database that includes at least four elements Cu, Cd, Te, and S. The Stillinger-Weber (SW) potential is the most widely used interatomic potential for semiconductors. However, while SW potentials have been developed for Ga-In-As-Se-Te, Al-Ga-In-P-As-Sb, Cd-Te-Zn-As-Si, In-Ga-N systems, no potentials existed to simulate Cd-Zn-Hg-Se-S-Te-Cu. The goal of this effort was to fill the knowledge gap by developing a Zn-Cd-Hg-S-Se-Te-Cu SW potential database to enable MD simulations of microstructures of Cu-doped CdTe/CdS solar cells. The new potential was then applied, via MD crystal growth simulations, to study the growth mechanisms and atomic structures of the ZnTe/Cu/CdTe/CdS multilayers under various conditions. The objective of the project was to inform the solar cell community on crystal growth and defect formation at the interface between CdTe-based epilayers grown on CdS substrates. MD simulations offered a unique opportunity to analyze the 3-dimensional crystal growth evolution of Cu doped ZnxCd(1-x)TeyS(1-y) alloys with atomic scale resolution under a variety of conditions. The effect of substrate orientation and polycrystallinity on crystal growth was studied. Substrates with grain boundaries were created and the growth evolution on these substrates were analyzed. Another focus was to elucidate the effect of dopant incorporation on the nature of polycrystallinity crystal growth. Dopants available through the Stillinger-Weber potential developed in this project included Cu, Zn, S, Se, Hg and native vacancies.

14 SOLAR ENERGY↗

Real-Time Atomic-Scale Structural Analysis Resolves the Amorphous to Crystalline CaCO 3 Mechanism Controversy

Amorphous calcium carbonate (ACC) occurs as a precursor to geological and biogenic calcium carbonate (CaCO 3 ), yet its transformation pathways and reaction mechanisms remain inconsistent and controversial. In this study, we investigated the transformation of ACC to calcite under both solution and dry conditions, in the presence and absence of impurity ions, utilizing operando time-resolved synchrotron X-ray diffraction (TRXRD) and reactive transport modeling. Results demonstrate that TRXRD techniques allow us to differentiate dissolution-reprecipitation versus solid-state transformation mechanisms for amorphous to crystalline phase transitions. Specifically, we observe that in environments with abundant water, ACC transforms to calcite through a dissolution-reprecipitation mechanism. This features an activation energy of 63 ± 2 kJ/mol and unit cell volume contraction during calcite crystal growth. Conversely, under water-limited conditions, ACC to calcite transformation proceeds via a solid-state transformation mechanism, with an activation energy of 210 ± 2 kJ/mol, three times greater than the dissolution-reprecipitation route, and a unit cell expansion during crystalline calcite growth. Further, to illustrate the magnitude of these effects, the rates of calcite growth were similar during dissolution-reprecipitation at 3 °C [0.00207(35) s –1 ] and solid-state transformation at 280 °C [0.00134(11) s –1 ]. Moreover, the incorporation of an impurity, strontium, significantly retards the rate of calcite growth while expanding its unit cell but whose incorporation is history dependent. Reactive transport modeling of the dissolution–precipitation kinetics suggests that ACC must be dissolving as compact aggregates. These various transformation mechanisms drive diverse geological and biological carbonate formations, impacting their use as paleoenvironmental markers and functional materials synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomic-Scale STEM Analysis Shows Structural Changes of Au–Pd Nanoparticles in Various Gaseous Environments

We report dynamical restructuring effects in free-standing Au 0.75 Pd 0.25 nanoparticles occurring in gaseous environments at elevated temperatures. The freshly prepared sample was found to have a core–shell structure with a Pd-rich phase on the surface. The evolution of sample composition and morphology under exposure to 1 bar of pure gases, namely O 2 , H 2 , air, CO, and CO 2 , at different temperatures was studied using in situ scanning transmission electron microscopy (STEM) and energy-dispersive X-ray spectroscopy (EDS). We observed sharper facets on the surface of the particles under O 2 or air at 400 °C. Small islands of Pd were present on the surface, although some Pd was redistributed inside the bulk when the temperature was increased under O 2 . Subtle changes in surface roughness were noted when O 2 was substituted with H 2 at 400 °C, an observation correlated to density functional theory (DFT) calculations. The particles lost clean surface facets when CO was introduced at room temperature and at 200 °C. No substantial changes could be observed after exposure to CO 2 at 250 °C. The adsorption of CO molecules on the surface modifies the surface of the particles and decreases the facet prevalence. Furthermore, these in situ observations show how gases can induce subtle modification of the surface of nanocatalysts, potentially impacting their chemical properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Large-scale proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation

Our understanding of Alzheimer’s disease (AD) pathophysiology remains incomplete. Here, for this work, we used quantitative mass spectrometry and coexpression network analysis to conduct the largest proteomic study thus far on AD. A protein network module linked to sugar metabolism emerged as one of the modules most significantly associated with AD pathology and cognitive impairment. This module was enriched in AD genetic risk factors and in microglia and astrocyte protein markers associated with an anti-inflammatory state, suggesting that the biological functions it represents serve a protective role in AD. Proteins from this module were elevated in cerebrospinal fluid in early stages of the disease. In this study of >2,000 brains and nearly 400 cerebrospinal fluid samples by quantitative proteomics, we identify proteins and biological processes in AD brains that may serve as therapeutic targets and fluid biomarkers for the disease.

60 APPLIED LIFE SCIENCES↗

Central speed of sound, the trace anomaly, and observables of neutron stars from a perturbative analysis of scaled Tolman-Oppenheimer-Volkoff equations

The central speed of sound (SS) measures the stiffness of the equation of state (EOS) of superdense neutron star (NS) matter. Its variations with density and radial coordinate in NSs in conventional analyses often suffer from uncertainties of the specific nuclear EOS used. Using the central SS and NS mass/radius scaling obtained from solving perturbatively the scaled Tolman-Oppenheimer-Volkoff (TOV) equations, we study the variations of SS, trace anomaly and several closely related properties of NSs in an EOSmodel- independent manner. We find that the SS increases with the reduced central pressure Pˆ c ≡ P c =ε c (scaled by the central energy density εc), and the conformal bound for SS tends to break down for NSs with masses higher than about 1.9M ⊙ . The ratio P=ε is upper bounded as P=ε ≲ 0.374 around the centers of stable NSs. We demonstrate that it is an intrinsic property of strong field gravity and is more relevant than the perturbative QCD bound on it. While a sharp phase transition at high densities characterized by a sudden vanishing of SS in cores of massive NSs are basically excluded, the probability for a continuous crossover signaled by a peaked radial profile of SS is found to be enhanced as Pˆ c decreases, implying it likely happens near the centers of massive NSs. Moreover, a new and more stringent causality boundary as R max =km ≳ 4.73$M$$^{max}_{NS}$ =M ⊙ þ 1.14 for the NS mass-radius curve is found to be excellently consistent with observational data on NS masses and radii. Here, new constraints on the ultimate energy density and pressure allowed in NSs before collapsing into black holes are obtained and compared with earlier predictions in the literature

79 ASTRONOMY AND ASTROPHYSICS↗