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At least 55 records · Page 3

Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes

Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. We then applied this workflow to a sample of yet uncultured multicellular magnetotactic bacteria. In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes at single cell resolution.

Schaible, George↗

Dissolution kinetics of a sodium borosilicate glass in Tris buffer solutions: impact of Tris concentration and acid (HCl/HNO 3 ) identity

Here, understanding the corrosion behavior of glasses in near-neutral environments is crucial for many technologies including glasses for regenerative medicine and nuclear waste immobilization. To maintain consistent pH values throughout experiments in the pH = 7 to 9 regime, buffer solutions containing tris(hydroxymethyl)aminomethane (“Tris”, or sometimes called THAM) are recommended in ISO standards 10993-14 and 23317 for evaluating biomaterial degradation and utilized throughout glass dissolution behavior literature—a key advantage being the absence of dissolved alkali/alkaline earth cations (i.e. Na + or Ca 2+ ) that can convolute experimental results due to solution feedback effects. Although Tris is effective at maintaining the solution pH, it has presented concerns due to the adverse artificial effects it produces while studying glass corrosion, especially in borosilicate glasses. Therefore, many open questions still remain on the topic of borosilicate glass interaction with Tris-based solutions. We have approached this topic by studying the dissolution behavior of a sodium borosilicate glass in a wide range of Tris-based solutions at 65 °C with varied acid identity (Tris–HCl vs. Tris–HNO 3 ), buffer concentration (0.01 M to 0.5 M), and pH (7–9). The results have been discussed in reference to previous studies on this topic and the following conclusions have been made: (i) acid identity in Tris-based solutions does not exhibit a significant impact on the dissolution behavior of borosilicate glasses, (ii) ~0.1 M Tris-based solutions are ideal for maintaining solution pH in the absence of obvious undesirable solution chemistry effects, and (iii) Tris–boron complexes can form in solution as a result of glass dissolution processes. The complex formation, however, exhibits a distinct temperature-dependence, and requires further study to uncover the precise mechanisms by which Tris-based solutions impact borosilicate glass dissolution behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut

Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating > 200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G–U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G–C base pairs (G3:C70 and G5:C68).

59 BASIC BIOLOGICAL SCIENCES↗

Role of the chiral anomaly in polarized deeply inelastic scattering. III. Wess-Zumino-Witten contributions and chiral Ward identities for finite quark mass

We extend our prior results on the worldline computation of the axial vector-vector-vector (AVV) triangle anomaly in polarized deeply inelastic scattering (DIS) to the finite mass case by computing in addition the pseudoscalar-vector-vector (PVV) triangle graph. For the well-studied QED case, we show explicitly how the off-forward AVV pole exactly cancels an identical PVV pole. We then demonstrate the dramatic difference in QCD due to the chiral condensate, which qualitatively modifies anomalous Ward identities. As in the massless case, the anomaly pole in QCD is canceled by the dynamics of a primordial isosinglet pseudoscalar η ¯ -meson, whose Wess-Zumino-Witten coupling to the topological charge density shifts the pole to the physical η ′ mass, with the finite quark mass contribution differing by O ( 10 % ) from the Witten-Veneziano formula. We obtain a compact analytic expression for the finite mass corrections to Shore and Veneziano’s result that the proton’s net quark helicity Δ Σ ∝ χ QCD ′ | m = 0 ( 0 ) , the forward slope of the topological susceptibility in the chiral limit, and show they are of the order of a few percentages. Our prior prediction that the polarized DIS structure function g 1 is quenched by sphaleronlike topological transitions at small x is unaffected by quark mass effects. Our results illustrate how worldline computations of anomalous processes, in synergy with lattice computations and nonet chiral perturbation theory, can uncover novel nonperturbative features of QCD at the Electron-Ion Collider. Published by the American Physical Society 2025

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Gravitational memory and Ward identities in the local detector frame

Gravitational memory, which describes the permanent shift in the strain after the passage of gravitational waves, is directly related to Weinberg’s soft graviton theorems and the Bondi-Metzner-Sachs (BMS) symmetry group of asymptotically flat space-times. In this work, we provide an equivalent description of the phenomenon in local coordinates around gravitational wave detectors, such as transverse-traceless (TT) gauge. We show that gravitational memory is encoded in large residual diffeomorphisms in this gauge, which include time-dependent anisotropic spatial rescalings, and prove their equivalence to BMS transformations when translated to TT gauge. We then derive the associated Ward identities and associated soft theorems, for both scattering amplitudes and equal-time (in-in) correlation functions, and explicitly check their validity for planar gravitational waves. Furthermore, the in-in identities are recognized as the flat-space analog of the well-known inflationary consistency relations.

General relativity↗

Plant Cell Identity in the Era of Single-Cell Transcriptomics

High-throughput single-cell transcriptomic approaches have revolutionized our view of gene expression at the level of individual cells, providing new insights into their heterogeneity, identities, and functions. Recently, technical challenges to the application of single-cell transcriptomics to plants have been overcome, and many plant organs and tissues have now been subjected to analyses at single-cell resolution. In this review, we describe these studies and their impact on our understanding of the diversity, differentiation, and activities of plant cells. We particularly highlight their impact on plant cell identity, including unprecedented views of cell transitions and definitions of rare and novel cell types. Lastly, we also point out current challenges and future opportunities for the application and analyses of single-cell transcriptomics in plants.

59 BASIC BIOLOGICAL SCIENCES↗

Tuning Solvation Dynamics of Electrolytes at Their Eutectic Point Through Halide Identity

Deep eutectic solvents (DESs) are regarded as highly promising solvent systems for redox flow batteries. DESs, composed of choline halides (ChX, X = F − , Cl − , Br − , I − ) and ethylene glycol (EG), exhibit distinct physicochemical properties at their eutectic points, including halide-dependent phase behavior, viscosity, polarity, conductivity, and solvation dynamics. In this study, we investigate the effects of the halide identity on the solvation properties of ChX:EG mixtures at varying mol % of ChX salt content. The solvatochromic polarity based on ET(30) measurements indicates higher polarity for larger halides (I − > Br − ) than for smaller halides (Cl − > F − ), which exhibit larger compensating solvation shells. The ionic conductivity follows the trend of the solvent fluidity (the inverse of the viscosity), namely ChCl > ChBr > ChI > ChF, influenced by the ion mobility and solvodynamic radii. Measurements of the liquidus temperatures (T L ) reveal that the system with ChCl exhibits the deepest eutectic point (at ~20 mol % ChCl), while ChBr and ChI have shallower minima at ~10 mol % ChBr and ~3 mol % ChI, respectively. ChF does not display a eutectic transition but instead appears to readily supercool at salt concentrations above 30 mol % ChF. Consistent with the phase transition measurements, femtosecond transient absorption spectroscopy shows that in the ChCl system, the solvation dynamics become faster with an increasing salt concentration up to ~16.67 mol %, after which the dynamics slow down with further increases in the salt content. The ChF-based system exhibits similar behavior, though with slower dynamics. In contrast, the solvation dynamics of the systems containing ChBr and ChI monotonously slow down with an increasing salt concentration, in agreement with the phase transition measurements, which show that the eutectic points occur at low salt concentrations. These measurements suggest that the solvent composition and, in particular, the identity of the halide anion play a significant role in the solvation behavior of these ethylene-glycol-based DESs, offering a foundation for tuning the DES properties for specific applications.

Biochemistry & Molecular Biology↗

Symmetry considerations in the scattering of identical composite bodies

Previous studies of the interactions between composite particles were extended to the case in which the composites are identical. The form of the total interaction potential matrix elements was obtained, and guidelines for their explicit evaluation were given. For the case of elastic scattering of identical composites, the matrix element approach was shown to be equivalent to the scattering amplitude method.

Norbury, J. W.↗

Phase-space quantum mechanics study of two identical particles in an external oscillatory potential

This simple example is used to show how the formalism of Moyal works when it is applied to systems of identical particles. The symmetric and antisymmetric Moyal propagators are evaluated for this case; from them, the correct energy levels of energy are obtained, as well as the Wigner functions for the symmetric and antisymmetric states of the two identical particle system. Finally, the solution of the Bloch equation is straightforwardly obtained from the expressions of the Moyal propagators.

Nieto, Luis M.↗

Engineering roles and identities in the scientific community: toward participatory justice

This paper seeks to examine the roles and identities of engineers constituting one of the fundamental, but a completely indescribable community in modern big science with particle accelerators. Large communities of accelerator and detector specialists, which replaced experimenters and instrumentalists of the middle of the last century, themselves exhibit a complex structure and are divided. However, this division is in turn grounded on the division of those whose activities focus on the phenomena of nature considered independent of human beings and those who design processes and phenomena of an artificial, technical nature. Nevertheless, in terms of their modus operandi and identity, the kinship between engineers and experimental scientists is considerable. I argue that such exclusion of the engineering community from epistemic practices can serve as an example of participatory injustice. As one of the ways to transcend participatory injustice, I suggest that the communities should be encouraged to work together in epistemically tantamount roles while structural hindrances to the mobility between communities need to be alleviated.

Pronskikh, V.↗

Resolving Nanoscale Processes during Carbon Mineralization Using Identical Location Transmission Electron Microscopy

Basalt reservoirs offer the potential for carbon mineralization, aiding in achieving net-zero emissions. However, debates persist about microscopic crystallization mechanisms due to limited characterization techniques under high-temperature and pressure conditions. By using Identical Location Transmission Electron Microscopy (IL-TEM) and cryo-TEM, this study reveals nanoscale interfacial carbonation processes of forsterite and diopside nanoparticles in water-saturated supercritical carbon dioxide under realistic reservoir conditions. Further, both minerals undergo preferential metal cation dissolution into a thin water film, forming porous Si-rich amorphous layers, supporting the leached layer mechanism as the dominant mineral reactivity process. Diopside’s amorphous layer has lower porosity and growth rate relative to forsterite, likely related to the connectivity of silicate tetrahedra. Kinetically favorable nesquehonite and aragonite nanocrystals form on the amorphous layers. These findings support the development of accurate reservoir simulations and help enable commercial-scale carbon storage deployment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics

Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calculates the percent bases aligned between two bacterial genomes and their corresponding ANI values, to set threshold values for determining species consistent with the conventional identification methods of known species. The performance of species identification was evaluated using two datasets: the Reference Genome Dataset v2 (RGDv2), consisting of 43 enteric genome assemblies representing 32 species, and the Test Genome Dataset (TGDv1), comprising 454 genome assemblies which is designed to represent all species needed to query for identification, as well as rare and closely related species. The RGDv2 contains six Campylobacter spp., three Escherichia/Shigella spp., one Grimontia hollisae, six Listeria spp., one Photobacterium damselae, two Salmonella spp., and thirteen Vibrio spp., while the TGDv1 contains 454 enteric bacterial genomes representing 42 different species. The analysis showed that, when a standard minimum of 70% genome bases alignment existed, the ANI threshold values determined for these species were ≥95 for Escherichia/Shigella and Vibrio species, ≥93% for Salmonella species, and ≥92% for Campylobacter and Listeria species. Using these metrics, the RGDv2 accurately classified all validation strains in TGDv1 at the species level, which is consistent with the classification based on previous gold standard methods.

59 BASIC BIOLOGICAL SCIENCES↗

Zero Trust and Identity Access Management in Support of Service-Based Urban Air Mobility Applications

Urban Air Mobility environments will contain of a collection of service-based services, which will be typically hosted within cloud infrastructures. The underlying data for these UAM services will need to be secured. One approach to securing these UAM services would be to leverage the Zero Trust framework, that focuses on securing services and associated data, instead of securing the network. An early step in moving towards a Zero Trust framework is to standardize identity access manage support for an ever-widening set of services, where users must explicitly be granted access to each service.

UAM↗

Supersymmetry and the celestial Jacobi identity

In this paper we study the simplifying effects of supersymmetry on celestial OPEs at both tree and loop level. We find at tree level that theories with unbroken supersymmetry around a stable vacuum have celestial soft current algebras satisfying the Jacobi identity, and we show at one loop that celestial OPEs in these theories have no double poles.

Supersymmetric Gauge Theory↗

Noise-aware optimization in nominally identical manufacturing and measuring systems for high-throughput parallel workflows

Device-to-device variability in experimental noise critically impacts reproducibility, especially in automated, high-throughput systems like additive manufacturing farms. While manageable in small labs, such variability can escalate into serious risks at larger scales, such as architectural 3D printing, where noise may cause structural or economic failures. This contribution presents a noise-aware decision-making algorithm that quantifies and models device-specific noise profiles to manage variability adaptively. It uses distributional analysis and pairwise divergence metrics with clustering to choose between single-device and robust multi-device Bayesian optimization strategies. Unlike conventional methods that assume homogeneous devices or enforce generic robustness, the proposed framework explicitly determines whether shared optimization across devices is appropriate based on the degree of inter-device noise heterogeneity. This enables improved performance, reproducibility, and efficiency. An experimental case study involving three nominally identical 3D printers (same brand, model, and close serial numbers) demonstrates reduced redundancy, lower resource usage, and improved reliability, along with improved convergence stability and solution quality through the selection of the appropriate optimization strategy based on the degree of inter-device noise heterogeneity. Overall, this framework establishes a general approach for precision- and resource-aware optimization in scalable, automated experimental platforms, demonstrated here on a representative multi-device 3D printing case study.

Schenk, Christina↗

Transition state stabilization depends on solvent identity, pore size, and hydrophilicity for epoxidations in zeolites

Ti-silicates activate H 2 O 2 to form Ti-hydroperoxo and Ti-peroxo intermediates that can react with alkenes to form epoxide products. Comparisons of kinetics for 1-octene epoxidation with H 2 O 2 on Ti-BEA and Ti-MFI catalysts with different hydrophilicities in methanol (CH 3 OH) or acetonitrile (CH 3 CN) solvents show the significance of the solvent for stabilizing catalytically-relevant species and the complex interdependencies between solvent, catalyst topology, and hydrophilicity. Epoxidation turnover rates are higher in CH 3 CN than CH 3 OH for Ti-BEA, but the opposite trend is observed for Ti-MFI. Ti-silicates with greater silanol densities, however, give greater epoxidation turnover rates than their hydrophobic counterparts in both solvents. Kinetic, spectroscopic, and thermodynamic analyses show that differences in turnover rates mainly arise from changes in the stabilization of reactive surface species by solvent mediated interactions, because the mechanism of the reaction and stability of the fluid-phase reactants remain similar in CH 3 CN and CH 3 OH. Specifically, apparent activation free energy values ($ΔG^{‡}_{App}$) indicate that surface intermediates responsible for alkene epoxidation are stabilized to a greater extent in CH 3 CN on Ti-BEA and in CH 3 OH on Ti-MFI. Hydrophilic Ti-silicates present lower ($ΔG^{‡}_{App}$) values regardless of solvent identity, which suggests that these differences correspond to the number of hydrogen-bonding solvent molecules found near reactive species bound to Ti active sites. Finally, taken together, these findings demonstrate the role of solvent molecules in allowing reactive intermediates to recognize the properties of active sites beyond the length-scale of covalent bonds, which carry implications for epoxidation but also other reactions within solvent-filled pores of microporous materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Energy and environmental aspects in recycling lithium-ion batteries: Concept of Battery Identity Global Passport

The emergence and dominance of lithium-ion batteries in expanding markets such as consumer electronics, electric vehicles, and renewable energy storage are driving enormous interests and investments in the battery sector. The explosively growing demand is generating a huge number of spent lithium-ion batteries, thereby urging the development of cost-effective and environmentally sustainable recycling technologies to manage end-of-life batteries. Currently, the recycling of end-of-life batteries is still in its infancy, with many fundamental and technological hurdles to overcome. Here in this paper, the authors provide an overview of the current state of battery recycling by outlining and evaluating the incentives, key issues, and recycling strategies. The authors highlight a direct recycling strategy through discussion of its benefits, processes, and challenges. Perspectives on the future energy and environmental science of this important field is also discussed with respect to a new concept introduced as the Battery Identity Global Passport (BIGP).

25 ENERGY STORAGE↗

A Massively Parallel Implementation of the CCSD(T) Method Using the Resolution-of-the-Identity Approximation and a Hybrid Distributed/Shared Memory Parallelization Model

In this work, a parallel algorithm is described for the coupled-cluster singles and doubles method augmented with a perturbative correction for triple excitations [CCSD(T)] using the resolution-of-the-identity (RI) approximation for two-electron repulsion integrals (ERIs). The algorithm bypasses the storage of four-center ERIs by adopting an integral-direct strategy. The CCSD amplitude equations are given in a compact quasi-linear form by factorizing them in terms of amplitude-dressed three-center intermediates. A hybrid MPI/OpenMP parallelization scheme is employed, which uses the OpenMP-based shared memory model for intranode parallelization and the MPI-based distributed memory model for internode parallelization. Parallel efficiency has been optimized for all terms in the CCSD amplitude equations. Two different algorithms have been implemented for the rate-limiting terms in the CCSD amplitude equations that entail and -scaling computational costs, where N O and N V denote the number of correlated occupied and virtual orbitals, respectively. One of the algorithms assembles the four-center ERIs requiring N V 4 and N O 2 N V 2 -scaling memory costs in a distributed manner on a number of MPI ranks, while the other algorithm completely bypasses the assembling of quartic memory-scaling ERIs and thus largely reduces the memory demand. It is demonstrated that the former memory-expensive algorithm is faster on a few hundred cores, while the latter memory-economic algorithm shows a better strong scaling in the limit of a few thousand cores. The program is shown to exhibit a near-linear scaling, in particular for the compute-intensive triples correction step, on up to 8000 cores. The performance of the program is demonstrated via calculations involving molecules with 24–51 atoms and up to 1624 atomic basis functions. As the first application, the complete basis set (CBS) limit for the interaction energy of the π-stacked uracil dimer from the S66 data set has been investigated. This work reports the first calculation of the interaction energy at the CCSD(T)/aug-cc-pVQZ level without local orbital approximation. The CBS limit for the CCSD correlation contribution to the interaction energy was found to be -8.01 kcal/mol, which agrees very well with the value -7.99 kcal/mol reported by Schmitz, Hättig, and Tew [ Phys. Chem. Chem. Phys. 2014 , 16 , 22167-22178]. The CBS limit for the total interaction energy was estimated to be -9.64 kcal/mol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗