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At least 883 records · Page 49

Biogenic-to-lithogenic handoff of particulate Zn affects the Zn cycle in the Southern Ocean

Zinc (Zn) is vital to marine organisms. Its active uptake by phytoplankton results in a substantial depletion of dissolved Zn, and Zn bound to particulate organic matter replenishes dissolved Zn in the ocean through remineralization. However, we found that particulate Zn changes from Zn bound to phosphoryls in cells to recalcitrant inorganic pools that include biogenic silica, clays, and iron, manganese, and aluminum oxides in the Southern Ocean water column. The abundances of inorganic pools increase with depth and are the only phases preserved in sediments. Changes in the particulate-Zn speciation influence Zn bioavailability and explain the decoupling of Zn and phosphorus and the correlation of Zn and silicon in the water column. Here, these findings reveal a new dimension to the ocean Zn cycle, implicating an underappreciated role of inorganic Zn particles and their impact on biological productivity.

Duan, J.↗

Electrode strain dynamics in layered intercalation battery cathodes

Rechargeable batteries using electrodes based on intercalation chemistry exhibit notable cyclability, yet their performance still suffers from chemomechanical degradation. In this study, by combining a suite of operando microscopy methods, we explored electrode strain evolution and observed intricate particle cluster rearrangement under electrochemical stimuli. We show that early-stage strain accumulation in intercalation cathodes occurs during the period of interparticle charge transfer and redox reactions stemming from asynchronous coupling and decoupling between chemical (de)intercalation and physical grain motion. This interplay drives heterogeneous redox activity, localized charge equilibration, and multiscale strain cascades that propagate through an asynchronous network of chemical-mechanical interactions. Together, these findings reveal how collective particle dynamics and hierarchical strain transmission dictate electrode deformation and degradation in intercalation cathodes.

25 ENERGY STORAGE↗

Linking the Salmonella enterica 1,2-Propanediol Utilization Bacterial Microcompartment Shell to the Enzymatic Core via the Shell Protein PduB

Bacterial microcompartments (MCPs) are protein-based organelles that house the enzymatic machinery for metabolism of niche carbon sources, allowing enteric pathogens to outcompete native microbiota during host colonization. While much progress has been made toward understanding MCP biogenesis, questions still remain regarding the mechanism by which core MCP enzymes are enveloped within the MCP protein shell. Here, we explore the hypothesis that the shell protein PduB is responsible for linking the shell of the 1,2-propanediol utilization (Pdu) MCP from Salmonella enterica serovar Typhimurium LT2 to its enzymatic core. Using fluorescent reporters, we demonstrate that all members of the Pdu enzymatic core are encapsulated in Pdu MCPs. We also demonstrate that PduB is critical for linking the entire Pdu enzyme core to the MCP shell. Using MCP purifications, transmission electron microscopy, and fluorescence microscopy, we find that shell assembly can be decoupled from the enzymatic core, as apparently empty MCPs are formed in Salmonella strains lacking PduB. Mutagenesis studies reveal that PduB is incorporated into the Pdu MCP shell via a conserved, lysine-mediated hydrogen bonding mechanism. Finally, growth assays and system-level pathway modeling reveal that unencapsulated pathway performance is strongly impacted by enzyme concentration, highlighting the importance of minimizing polar effects when conducting these functional assays. Together, these results provide insight into the mechanism of enzyme encapsulation within Pdu MCPs and demonstrate that the process of enzyme encapsulation and shell assembly are separate processes in this system, a finding that will aid future efforts to understand MCP biogenesis.

1, 2-propanediol utilization↗

Soil Origin and Plant Genotype Modulate Switchgrass Aboveground Productivity and Root Microbiome Assembly

Switchgrass (Panicum virgatum) is a model perennial grass for bioenergy production that can be productive in agricultural lands that are not suitable for food production. There is growing interest in whether its associated microbiome may be adaptive in low- or no-input cultivation systems. However, the relative impact of plant genotype and soil factors on plant microbiome and biomass are a challenge to decouple. To address this, a common garden greenhouse experiment was carried out using six common switchgrass genotypes, which were each grown in four different marginal soils collected from long-term bioenergy research sites in Michigan and Wisconsin. We characterized the fungal and bacterial root communities with high-throughput amplicon sequencing of the ITS and 16S rDNA markers, and collected phenological plant traits during plant growth, as well as soil chemical traits. At harvest, we measured the total plant aerial dry biomass. Significant differences in richness and Shannon diversity across soils but not between plant genotypes were found. Generalized linear models showed an interaction between soil and genotype for fungal richness but not for bacterial richness. Community structure was also strongly shaped by soil origin and soil origin × plant genotype interactions. Overall, plant genotype effects were significant but low. Random Forest models indicate that important factors impacting switchgrass biomass included NO 3 – , Ca 2+ , PO 4 3– , and microbial biodiversity. We identified 54 fungal and 52 bacterial predictors of plant aerial biomass, which included several operational taxonomic units belonging to Glomeraceae and Rhizobiaceae, fungal and bacterial lineages that are involved in provisioning nutrients to plants.

plant biomass↗

Metabolic Model of the Nitrogen-Fixing Obligate Aerobe Azotobacter vinelandii Predicts Its Adaptation to Oxygen Concentration and Metal Availability

There is considerable interest in promoting biological nitrogen fixation (BNF) as a mechanism to reduce the inputs of nitrogenous fertilizers in agriculture, but considerable fundamental knowledge gaps still need to be addressed. BNF is catalyzed by nitrogenase, which requires a large input of energy in the form of ATP and low potential electrons. Diazotrophs that respire aerobically have an advantage in meeting the ATP demands of BNF but face challenges in protecting nitrogenase from inactivation by oxygen. Here, we constructed a genome-scale metabolic model of the nitrogen-fixing bacterium Azotobacter vinelandii, which uses a complex respiratory protection mechanism to consume oxygen at a high rate to keep intracellular conditions microaerobic. Our model accurately predicts growth rate under high oxygen and substrate concentrations, consistent with a large electron flux directed to the respiratory protection mechanism. While a partially decoupled electron transport chain compensates for some of the energy imbalance under high-oxygen conditions, it does not account for all substrate intake, leading to increased maintenance rates. Interestingly, the respiratory protection mechanism is required for accurate predictions even when ammonia is supplemented during growth, suggesting that the respiratory protection mechanism might be a core principle of metabolism and not just used for nitrogenase protection. We have also shown that rearrangement of flux through the electron transport system allows A. vinelandii to adapt to different oxygen concentrations, metal availability, and genetic disruption, which cause an ammonia excretion phenotype. Accurately determining the energy balance in an aerobic nitrogen-fixing metabolic model is required for future engineering approaches.

59 BASIC BIOLOGICAL SCIENCES↗

Whole-lithosphere shear during oblique rifting

Processes controlling the formation of continental whole-lithosphere shear zones are debated, but their existence requires that the lithosphere is mechanically coupled from base to top. We document the formation of a dextral, whole-lithosphere shear zone in the Death Valley region (DVR), southwest United States. Dextral deflections of depth gradients in the lithosphere-asthenosphere boundary and Moho are stacked vertically, defining a 20–50-km-wide, lower lithospheric shear zone with ~60 km of shear. These deflections underlie an upper-crustal fault zone that accrued ~60 km of dextral slip since ca. 8–7 Ma, when we infer that whole-lithosphere shear began. This dextral offset is less than net dextral offset on the upper-crustal fault zone (~90 km, ca. 13–0 Ma) and total upper-crustal extension (~250 km, ca. 16–0 Ma). We show that, before ca. 8–7 Ma, weak middle crust decoupled upper-crustal deformation from deformation in the lower crust and mantle lithosphere. Between 16 and 7 Ma, detachment slip thinned, uplifted, cooled, and thus strengthened the middle crust, which is exposed in metamorphic core complexes collocated with the whole-lithosphere shear zone. Midcrustal strengthening coupled the layered lithosphere vertically and therefore enabled whole-lithosphere dextral shear. Where thick crust exists (as in pre–16 Ma DVR), midcrustal strengthening is probably a necessary condition for whole-lithosphere shear.

58 GEOSCIENCES↗

Synchronous and Concurrent Multidomain Computing Method for Cloud Computing Platforms

We present a numerical method for synchronous and concurrent solution of transient elastodynamics problem where the computational domain is divided into subdomains that may reside on separate computational platforms. Here, this work employs the variational multiscale discontinuous Galerkin (VMDG) method to develop interdomain transmission conditions for transient problems. The fine-scale modeling concept leads to variationally consistent coupling terms at the common interfaces. The method admits a large class of time discretization schemes, and decoupling of the solution for each subdomain is achieved by selecting any explicit algorithm. Numerical tests with a manufactured solution problem show optimal convergence rates. The energy history in a free vibration problem is in agreement with that of the solution from a monolithic computational domain.

97 MATHEMATICS AND COMPUTING↗

FROSch Preconditioners for Land Ice Simulations of Greenland and Antarctica

Numerical simulations of Greenland and Antarctic ice sheets involve the solution of large-scale highly nonlinear systems of equations on complex shallow geometries. This work is concerned with the construction of Schwarz preconditioners for the solution of the associated tangent problems, which are challenging for solvers mainly because of the strong anisotropy of the meshes and wildly changing boundary conditions that can lead to poorly constrained problems on large portions of the domain. In this study, two-level generalized Dryja--Smith--Widlund (GDSW)--type Schwarz preconditioners are applied to different land ice problems, i.e., a velocity problem, a temperature problem, as well as the coupling of the former two problems. We employ the message passing interface (MPI)--parallel implementation of multilevel Schwarz preconditioners provided by the package FROSch (fast and robust Schwarz) from the Trilinos library. The strength of the proposed preconditioner is that it yields out-of-the-box scalable and robust preconditioners for the single physics problems. To the best of our knowledge, this is the first time two-level Schwarz preconditioners have been applied to the ice sheet problem and a scalable preconditioner has been used for the coupled problem. The preconditioner for the coupled problem differs from previous monolithic GDSW preconditioners in the sense that decoupled extension operators are used to compute the values in the interior of the subdomains. Additionally, several approaches for improving the performance, such as reuse strategies and shared memory OpenMP parallelization, are explored. In our numerical study we target both uniform meshes of varying resolution for the Antarctic ice sheet as well as nonuniform meshes for the Greenland ice sheet. We present several weak and strong scaling studies confirming the robustness of the approach and the parallel scalability of the FROSch implementation. Among the highlights of the numerical results are a weak scaling study for up to 32,K processor cores (8,K MPI ranks and 4 OpenMP threads) and 566,M degrees of freedom for the velocity problem as well as a strong scaling study for up to 4,K processor cores (and MPI ranks) and 68,M degrees of freedom for the coupled problem.

97 MATHEMATICS AND COMPUTING↗

Neutrino emission from binary neutron star mergers: characterising light curves and mean energies

Abstract Neutrinos are copiously emitted by neutron star mergers, due to the high temperatures reached by dense matter during the merger and its aftermath. Neutrinos influence the merger dynamics and shape the properties of the ejecta, including the resulting r -process nucleosynthesis and kilonova emission. In this work, we analyse neutrino emission from a large sample of binary neutron star merger simulations in Numerical Relativity, covering a broad range of initial masses, nuclear equation of state and viscosity treatments. We extract neutrino luminosities and mean energies, and compute quantities of interest such as the peak values, peak broadnesses, time averages and decrease time scales. We provide a systematic description of such quantities, including their dependence on the initial parameters of the system. We find that for equal-mass systems the total neutrino luminosity (several $$10^{53}{\hbox {erg}~{\hbox {s}}^{-1}}$$ 10 53 erg s - 1 ) decreases as the reduced tidal deformability increases, as a consequence of the less violent merger dynamics. Similarly, tidal disruption in asymmetric mergers leads to systematically smaller luminosities. Peak luminosities can be twice as large as the average ones. Electron antineutrino luminosities dominate (initially by a factor of 2-3) over electron neutrino ones, while electron neutrinos and heavy flavour neutrinos have similar luminosities. Mean energies are nearly constant in time and independent on the binary parameters. Their values reflect the different decoupling temperature inside the merger remnant. Despite present uncertainties in neutrino modelling, our results provide a broad and physically grounded characterisation of neutrino emission, and they can serve as a reference point to develop more sophisticated neutrino transport schemes.

79 ASTRONOMY AND ASTROPHYSICS↗

$\Sigma (1385)^{\pm }$ resonance production in Pb–Pb collisions at $\sqrt{s_{\textrm{NN}}} = 5.02$ TeV

Hadronic resonances are used to probe the hadron gas produced in the late stage of heavy-ion collisions since they decay on the same timescale, of the order of 1–10 fm/c, as the decoupling time of the system. In the hadron gas, (pseudo)elastic scatterings among the products of resonances that decayed before the kinetic freeze-out and regeneration processes counteract each other, the net effect depending on the resonance lifetime, the duration of the hadronic phase, and the hadronic cross sections at play. In this context, the Σ(1385) ± particle is of particular interest as models predict that regeneration dominates over rescattering despite its relatively short lifetime of about 5.5 fm/c. The first measurement of the Σ(1385) ± resonance production at midrapidity in Pb–Pb collisions at $\sqrt{s_{NN}}$=5.02 TeV with the ALICE detector is presented in this Letter. The resonances are reconstructed via their hadronic decay channel, Λπ, as a function of the transverse momentum (p T ) and the collision centrality. The results are discussed in comparison with the measured yield of pions and with expectations from the statistical hadronization model as well as commonly employed event generators, including PYTHIA8/Angantyr and EPOS3 coupled to the UrQMD hadronic cascade afterburner. None of the models can describe the data. For Σ(1385) ± , a similar behaviour as K*(892) 0 is observed in data unlike the predictions of EPOS3 with afterburner.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Cold freeze out of superheavy dark matter and Hubble tension

We present a unified framework, the "X miracle", in which dark matter consists of superheavy, nonthermal X particles whose relic abundance is determined not by the conventional weak-scale, semi-relativistic ("hot") freeze-out of WIMPs, but by annihilation or decay occurring within the smallest and earliest gravitationally bound objects. Unlike thermal WIMPs, which decouple at velocities of order 0.3c with relic abundance ρ∞ set by weak-scale interactions, X particles are produced nonthermally with an initial overabun dance ρ ini >> ρ ∞ . They become nonrelativistic extremely early, redshift to ultra-cold velocities, allowing collapse into compact bound structures characterized by a novel quantum gravitational scale, r X = 4$\hbar$ 2 $/Gm^3_X$ = 10 −13 m $\hbar$$/m_Xc$, much larger than the Compton wavelength. The framework predicts a particle mass of 10 12 GeV and an enhanced cross section of 10 −21 m 3 /s. Overlapping particle wavefunctions in these compact structures drive annihilation or decay into additional radiation, leading to a "cold" freeze-out that converts most of ρ ini into radiation while leaving a relic density ρ ∞ . Solutions to the Boltzmann equation indicate that an extreme ("big") depletion, with only one particle in a billion surviving, yields an additional radiation contribution $ΔN_{eff}$ ≈ 0.4, which could help alleviate the Hubble tension. For particles of 10 12 GeV, the scenario predicts a dark coupling constant α X = 0.09 that is responsible for an instanton-induced decay process, consistent with current UHECR bounds. Early collapse at 10 −6 s may release binding energy as high-frequency (100kHz) gravitational waves or ultralight GUT-scale axions (10 −9 eV). Superheavy sterile neutrinos provide a natural particle realization, linking dark matter to neutrino mass and baryogenesis. If gravitationally produced, this framework favors high-scale inflation and effi cient reheating. The "X miracle" thus demonstrates that dark matter need not be weak-scale: gravitational dynamics can control freeze-out and evolution, producing multi-messenger observational signatures in UHECRs, axions, gravitational waves, and small-scale structures.

Xu, Zhijie Jay [Pacific Northwest National Laborat↗

Non-Wilsonian ultraviolet completion via transseries

We study some of the implications for the perturbative renormalization program when augmented with the Borel–Ecalle resummation. We show the emergence of a new kind of nonperturbative fixed point for the scalar [Formula: see text] model, representing an ultraviolet self-completion by transseries. We argue that this completion is purely non-Wilsonian and it depends on one arbitrary constant stemming from the transseries solution of the renormalization group equation. On the other hand, if no fixed points are demanded through the adjustment of this arbitrary constant, we end up with an effective theory in which the scalar mass is quadratically-sensitive to the cutoff, even working in dimensional regularization. Complete decoupling of the scalar mass to this energy scale can be used to determine a physical prescription for the Borel–Laplace resummation of the renormalons in nonasymptotically free models. We also comment on possible orthogonal scenarios available in the literature that might play a role when no fixed points exist.

Physics↗

Quantum gravity phenomenology in the infrared

Quantum gravity effects are traditionally tied to short distances and high energies. In this essay, we argue that, perhaps surprisingly, quantum gravity may have important consequences for the phenomenology of the infrared. We center our discussion around a conception of quantum gravity involving a notion of quantum spacetime that arises in metastring theory. This theory allows for an evolution of a cosmological Universe in which string-dual degrees of freedom decouple as the Universe ages. Importantly, such an implementation of quantum gravity allows for the inclusion of a fundamental length scale without introducing the fundamental breaking of Lorentz symmetry. The mechanism seems to have potential for an entirely novel source for dark matter/energy. The simplest observational consequences of this scenario may very well be residual infrared modifications that emerge through the evolution of the Universe.

Astronomy & Astrophysics↗

Towards Superior Software Portability with SHAD and HPX C++ Libraries

As hardware architectures and software stacks complexity grows, development productivity, performance and software portability, quickly evolve from desirable features to actual needs. SHAD, the Scalable High-performance Algorithms and Data-structures C++ library is designed to mitigate these issues: it provides general purpose building blocks as well as high-level custom utilities, and offers a shared-memory programming abstraction which facilitates the programming of complex systems, scaling up to High Performance Computing clusters. SHAD’s portability is achieved through an abstract runtime interface, which decouples the upper layers of the library and hides the low level details of the underlying architecture. This layer enables SHAD to interface with different runtime/threading systems, e.g. Intel TBB and Global Memory and Threading (GMT). However, current backends targeting distributed systems, rely on a centralized controller which may possibly limit scalability up to hundreds of nodes and creates a network hot spot due to all to one communication for synchronization, and possibly resulting in degraded performance at high process counts. In this research, we explore HPX, the C++ standard library for parallelism and concurrency, as an additional backend in support of the SHAD library, and present the methodologies in support of local and remote task executions in SHAD with respect to HPX. Finally, we evaluate the proposed system by comparing against existing backends of SHAD and analyzing their performance on C++ Standard Template Library algorithms.

Wu, Nanmiao↗

QuComm: Optimizing Collective Communication for Distributed Quantum Computing

Distributed quantum computing (DQC) is a scalable way to build a large-scale quantum computing system while the error-prone nonlocal communication between DQC nodes may heavily degrade the fidelity of the distributed quantum program and thus demands specific compiler optimizations. Previous compilers on DQC communication optimization either assumes unlimited communication resource or a few communication qubits due to the hardware limitation. The former compilers may not be efficient when interfacing with communication-resource-constrained DQC hardware while the latter compilers lose the opportunities of optimizing collective communication and routing concurrent communication as they unnecessarily couple limited communication qubits with the implementation of expensive inter-node operations. In this paper, we invent the communication buffer, a communication facility consisting of idle qubits in each compute node, to decouple the execution of inter-node quantum operations from communication qubits: communication qubits are devoted to generating inter-node entanglement while internode operations are conducted in the communication buffer. The communication buffer provides an intermediate layer for inter-node communication and paves the way for collective communication optimization. We then propose QuComm, a buffer-based compiler framework that first performs smart buffer allocation according to communication characteristics of the distributed quantum program and then optimizes and collectively routes inter-node quantum operations. Experimental results on a hierarchical DQC system show that the proposed QuComm can reduce the most expensive inter-node communication request and the latency of various distributed quantum programs by 50.4% and 47.6% on average, respectively.

Wu, Anbang↗

Increasing the Measured Effective Quantum Volume with Zero Noise Extrapolation

Quantum volume is a full-stack benchmark for near-term quantum computers. It quantifies the largest size of a square circuit which can be executed on the target device with reasonable fidelity. Error mitigation is a set of techniques intended to remove the effects of noise present in the computation of noisy quantum computers when computing an expectation value of interest. Effective quantum volume is a proposed metric that applies error mitigation to the quantum volume protocol to evaluate the effectiveness not only of the target device but also of the error mitigation algorithm. Digital zero-noise extrapolation is an error mitigation technique that estimates the noiseless expectation value using circuit folding to amplify errors by known scale factors and then extrapolating computed expectation values to the zero-noise limit. Here we demonstrate that zero-noise extrapolation, with global and local unitary folding with fractional scale factors, in conjunction with dynamical decoupling, can increase the effective quantum volume over the vendor-measured quantum volume. Specifically, we measure the effective quantum volume of four IBM Quantum superconducting processor units, obtaining values that are larger than the vendor-measured quantum volume on each device. This is the first such increase reported.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

OmniFed: A Modular Framework for Configurable Federated Learning from Edge to HPC

Federated Learning (FL) is critical for edge and High Performance Computing (HPC) where data is not centralized and privacy is crucial. We present OmniFed, a modular framework designed around decoupling and clear separation of concerns for configuration, orchestration, communication, and training logic. Its architecture supports configuration-driven prototyping and code-level override-what-you-need customization. We also support different topologies, mixed communication protocols within a single deployment, and popular training algorithms. It also offers optional privacy mechanisms including Differential Privacy (DP), Homomorphic Encryption (HE), and Secure Aggregation (SA), as well as compression strategies. These capabilities are exposed through well-defined extension points, allowing users to customize topology and orchestration, learning logic, and privacy/compression plugins, all while preserving the integrity of the core system. We evaluate multiple models and algorithms to measure various performance metrics. By unifying topology configuration, mixed-protocol communication, and pluggable modules in one stack, OmniFed streamlines FL deployment across heterogeneous environments. Github repository is available at https://github.com/at-aaims/OmniFed.

Tyagi, Sahil [ORNL] (ORCID:0009000783144745)↗

QProR: An Efficient Framework for Quantity-of-Interest Based Progressive Retrieval with Guaranteed Error Control

Scientific applications generate an unprecedented volume of data, overwhelming the network and file systems’ bandwidth and posing challenges for efficient and scalable data retrieval and analysis. Progressive data compression offers a promising solution by enabling on-demand retrieval at reduced size. However, existing progressive methods either fail to bound the errors in essential quantities of interest (QoIs) derived from raw data or suffer from suboptimal retrieval efficiency. In this work, we propose QProR, an efficient QoI-based progressive framework that optimizes progressive retrieval for target QoIs. Our key contributions include: (1) a systematic framework that integrates error-controlled lossy compressors with bitplane encoding while decoupling the two processes for high flexibility and adaptability; (2) a novel weighted bitplane encoding method which incorperates QoI knowledge into data refactoring to enhance retrieval efficiency; (3) an optimized retrieval strategy that accounts for the varying impacts of different variables on multivariate QoIs; (4) comprehensive evaluations using six real-world datasets from multiple scientific applications and thorough comparisons against state of the arts. Experimental results demonstrate that QProR achieves up to 80.38% reduction in the retrieval size under the same requested QoI error tolerance, when compared with the best-performing existing methods. When transferring 384 GB of scientific data to remote sites, QProR delivers up to 1.68 × speedup in the end-to-end data transfer performance.

Li, Wenbo [University of Kentucky]↗