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At least 469 records · Page 26

Persistence Control of Engineered Functions in Complex Soil Microbiomes (PerCon SFA), Secure Biosystems Design Project Data Catalog at PNNL DataHub

The Persistence Control of Engineered Functions in Complex Soil Microbiomes Project (PerCon SFA) at Pacific Northwest National Laboratory (PNNL) is a Genomic Sciences Program Biosystems Design, Science Focus Area research project consortium. Collaborating across highly integrated institutions, PerCon SFA scientists are exploring how environmental niches can be sculpted using the mechanisms of genome reduction and metabolic addiction to drive secure rhizosphere community design for robust biomass cropping in challenging environments. The PerCon SFA DataHub project repository contains publication-relevant digital dataset and metadata DOI packages, enabling exploration and download of integrated experimental dataset catalogs publicly available to a global scientific community. and metadata repository allow for exploring and downloading integrated experimental biodesign omics dataset catalogs, including experimental protocols and/or workflows, raw and/or processed data, as required by the repository, and other relevant supporting materials and/or metadata required for research reproducibility and reporting.

59 BASIC BIOLOGICAL SCIENCES↗

Microstructure-Sensitive Uncertainty Quantification for Crystal Plasticity Finite Element Constitutive Models Using Stochastic Collocation Methods

Uncertainty quantification (UQ) plays a major role in verification and validation for computational engineering models and simulations, and establishes trust in the predictive capability of computational models. In the materials science and engineering context, where the process-structure-property-performance linkage is well known to be the only road mapping from manufacturing to engineering performance, numerous integrated computational materials engineering (ICME) models have been developed across a wide spectrum of length-scales and time-scales to relieve the burden of resource-intensive experiments. Within the structure-property linkage, crystal plasticity finite element method (CPFEM) models have been widely used since they are one of a few ICME toolboxes that allows numerical predictions, providing the bridge from microstructure to materials properties and performances. Several constitutive models have been proposed in the last few decades to capture the mechanics and plasticity behavior of materials. While some UQ studies have been performed, the robustness and uncertainty of these constitutive models have not been rigorously established. In this work, we apply a stochastic collocation (SC) method, which is mathematically rigorous and has been widely used in the field of UQ, to quantify the uncertainty of three most commonly used constitutive models in CPFEM, namely phenomenological models (with and without twinning), and dislocation-density-based constitutive models, for three different types of crystal structures, namely face-centered cubic (fcc) copper (Cu), body-centered cubic (bcc) tungsten (W), and hexagonal close packing (hcp) magnesium (Mg). Our numerical results not only quantify the uncertainty of these constitutive models in stress-strain curve, but also analyze the global sensitivity of the underlying constitutive parameters with respect to the initial yield behavior, which may be helpful for robust constitutive model calibration works in the future.

36 MATERIALS SCIENCE↗

Seismic source characterization of the Arabian Peninsula and Zagros Mountains from regional moment tensor and coda envelopes

Reliable estimates of moment magnitude and source mechanism for seismic events in the Middle East can be challenging due to a small number of openly available stations, the complex tectonic setting, and regions of high attenuation. Access to high-quality waveform data from well-calibrated regional seismic stations is fundamental in producing robust and stable estimates of earthquake source parameters, particularly when measurements of absolute ground motion amplitudes are required. Earthquake source mechanism and moment magnitude are invaluable information in the assessment of seismic hazard, plate motions, and the characterization of faults and regional stress field. The expansion of the Kingdom of Saudi Arabia’s national seismic network in the past several decades provides an opportunity to develop the capabilities of routine focal mechanism and moment magnitude estimations. In this study, we use time-domain full waveform moment tensor inversion and coda envelope–derived amplitude measurements to solve for earthquake source mechanism, moment magnitudes, and their source type. Furthermore, we compared the moment magnitudes calculated from the two methods and publicly available earthquake catalogs and discuss the implications of the obtained source parameters.

58 GEOSCIENCES↗

In-situ visualization of the transition metal dissolution in layered cathodes

Transition metal dissolution in layered cathodes is one of the most intractable issues that deteriorates the battery performance and lifetime. It not only aggravates the structure degradation in cathode, but also damages the solid electrolyte interphase in anode and even induce the formation of lithium dendrites. In this work, we investigate the dissolution behaviors of polycrystalline and single-crystalline layered cathode via operando X-ray imaging techniques. The described cathode particle morphology appears to have a significant impact on the evolution of the dissolution dynamics. As a mitigation strategy, we reveal that doping with trace amount of Zr in the layered cathode could improve its robustness against the transition metal dissolution. Our finding provides valuable insights for designing the next-generation highly-stable layered battery cathodes.

25 ENERGY STORAGE↗

Freestanding and Flexible Micrometer-Thick PEDOT:PSS Film with High Power Factor

High-efficiency thermoelectric materials are vital for sustainable energy. This work presents a reliable method to fabricate freestanding, flexible micrometer-thick films of poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS), achieving a power factor of 204 μW m –1 K –2 , 4 orders of magnitude higher than pristine films. Furthermore, this improvement stems from polymer chain realignment and enhanced charge transport via solvent doping, coupled with PSS reduction during post-treatment, which also strengthens film mechanics. Crucially, the freestanding nature ensures transferability, making them ideal for versatile applications. Besides thermoelectrics, these highly conductive, robust, and flexible PEDOT:PSS films provide attractive solutions for organic solar cells, battery electrodes, and flexible electronics.

Conjugated Polymers↗

Enabling robust offline active learning for machine learning potentials using simple physics-based priors

Abstract Machine learning surrogate models for quantum mechanical simulations have enabled the field to efficiently and accurately study material and molecular systems. Developed models typically rely on a substantial amount of data to make reliable predictions of the potential energy landscape or careful active learning (AL) and uncertainty estimates. When starting with small datasets, convergence of AL approaches is a major outstanding challenge which has limited most demonstrations to online AL. In this work we demonstrate a Δ-machine learning (ML) approach that enables stable convergence in offline AL strategies by avoiding unphysical configurations with initial datasets as little as a single data point. We demonstrate our framework’s capabilities on a structural relaxation, transition state calculation, and molecular dynamics simulation, with the number of first principle calculations being cut down anywhere from 70%–90%. The approach is incorporated and developed alongside AMP torch , an open-source ML potential package, along with interactive Google Colab notebook examples.

Shuaibi, Muhammed↗

Measurements of dihadron correlations relative to the event plane in Au+Au collisions at $\sqrt{s_{NN}} =200$ GeV*

Dihadron azimuthal correlations containing a high transverse momentum ($ p_{T} $) trigger particle are sensitive to the properties of the nuclear medium created at RHIC through the strong interactions occurring between the traversing parton and the medium, i.e. jet-quenching. Previous measurements revealed a strong modification to dihadron azimuthal correlations in Au+Au collisions with respect to p+p and d+Au collisions. The modification increases with the collision centrality, suggesting a path-length or energy density dependence to the jet-quenching effect. This paper reports STAR measurements of dihadron azimuthal correlations in mid-central (20%-60%) Au+Au collisions at $ \sqrt{s_{\rm{NN}}} = 200 $ GeV as a function of the trigger particle's azimuthal angle relative to the event plane, $ \phi_{s} = | \phi_{t}- \psi_{{\rm{EP}}}| $. The azimuthal correlation is studied as a function of both the trigger and associated particle $ p_{T} $. The subtractions of the combinatorial background and anisotropic flow, assuming Zero Yield At Minimum (ZYAM), are described. The correlation results are first discussed with subtraction of the even harmonic (elliptic and quadrangular) flow backgrounds. The away-side correlation is strongly modified, and the modification varies with $ \phi_{s} $, with a double-peak structure for out-of-plane trigger particles. The near-side ridge (long range pseudo-rapidity $ \Delta\eta $ correlation) appears to drop with increasing $ \phi_{s} $ while the jet-like component remains approximately constant. The correlation functions are further studied with the subtraction of odd harmonic triangular flow background arising from fluctuations. It is found that the triangular flow, while responsible for the majority of the amplitudes, is not sufficient to explain the $ \phi_{s} $-dependence of the ridge or the away-side double-peak structure. The dropping ridge with $ \phi_{s} $ could be attributed to a $ \phi_{s} $-dependent elliptic anisotropy; however, the physics mechanism of the ridge remains an open question. Even with a $ \phi_{s} $-dependent elliptic flow, the away-side correlation structure is robust. These results, with extensive systematic studies of the dihadron correlations as a function of $ \phi_{s} $, trigger and associated particle $ p_{T} $, and the pseudo-rapidity range $ \Delta\eta $, should provide stringent inputs to help understand the underlying physics mechanisms of jet-medium interactions in high energy nuclear collisions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Emergent unitarity in de Sitter from matrix integrals

We study Jackiw-Teitelboim gravity with positive cosmological constant as a model for de Sitter quantum gravity. We focus on the quantum mechanics of the model at past and future infinity. There is a Hilbert space of asymptotic states and an infinite-time evolution operator between the far past and far future. This evolution is not unitary, although we find that it acts unitarily on a subspace up to non-perturbative corrections. These corrections come from processes which involve changes in the spatial topology, including the nucleation of baby universes. There is significant evidence that this 1+1 dimensional model is dual to a 0+0 dimensional matrix integral in the double-scaled limit. So the bulk quantum mechanics, including the Hilbert space and approximately unitary evolution, emerge from a classical integral. We find that this emergence is a robust consequence of the level repulsion of eigenvalues along with the double scaling limit, and so is rather universal in random matrix theory.

2D gravity↗

Breeding of microbiomes conferring salt tolerance to plants

Microbiome breeding through host-mediated selection is a technique to artificially select for microbiomes conferring beneficial properties to plants. Using a systematic selection protocol that maximises the heritability of microbiome effects, transmission fidelity, and microbiome stability through multiple selection cycles, we previously developed root-associated microbial communities conferring sodium and aluminium tolerance to Brachypodium distachyon, a model for cereal crops. Here, we explore the physiological mechanisms underlying our selected microbiomes’ effect on plant fitness and analyse how our selection protocol shaped the composition and structure of these microbiomes. We analysed the effects of our selected microbiomes on plant fitness and tissue-nutrient concentration, then used 16S rRNA amplicon sequencing to examine microbial community composition and co-occurrence network patterns. Our sodium-selected microbiomes reduced leaf sodium concentration by ~ 50%, whereas the aluminium-selected microbiomes had no effect on leaf-tissue nutrient concentration, suggesting different mechanisms underlying the microbiome-mediated stress tolerance. By testing the selected microbiomes in a cross-fostering experiment, we show that our artificially selected microbiomes attained (a) ecological robustness contributing to transplantability (i.e. inheritance) of microbiome-encoded effects between plants; and (b) network features identifying key bacteria promoting salt-stress tolerance. Combined, these findings elucidate critical mechanisms underlying host-mediated artificial selection as a framework to breed microbiomes with targeted benefits for plants under salt stresses, with significant implications for sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗

Understanding and Harnessing the Robustness of Undomesticated Yarrowia lipolytica Strains for Biosynthesis of Designer Bioesters (Final Report)

This project seeks to elucidate and harness the exceptional robustness of novel and undomesticated Y. lipolytica isolates, which were identified from a genetic diversity screening for compatibility with bioenergy development. Bioenergy-relevant isolates were further developed as microbial platforms for efficient conversion of undetoxified biomass hydrolysates into designer bio-esters continuously recovered by solvent extraction. The project has three major goals. Goal 1. Elucidate and enhance the endogenous metabolism of Y. lipolytica for superior growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates under hypoxic conditions. Goal 2. Understand and enhance the underlying mechanism of exceptional tolerance of Y. lipolytica to organic solvents. Goal 3. Elucidate and rewire endogenous metabolism of the most robust Y. lipolytica strains for effective conversion of accumulating lipids to designer bio-esters. Significant progress has been made toward completing all research goals. We elucidated and optimized the robustness of Y. lipolytica by utilizing mixed C5 and C6 sugars in switchgrass hydrolysates (SGH) for lipid production (Aim 1). We conducted extensive omics analysis to investigate how genetic diversity among Yarrowia strains, derived from natural isolates or developed through adaptive laboratory evolution, influences lipid production when utilizing SGH. In Aim 2, novel mechanisms and underlying genetics were discovered that enabled Yarrowia strains to thrive in cultures containing high ionic liquid (IL) concentrations. Amongst other novel findings, it was found that sterols strengthened cell membranes to confer IL toxicity resistance, specifically via increased ergosterol content upon exposure to IL. In Aim 3, mechanistic studies elucidated how Y. lipolytica utilized intracellular lipids and alkanes/alkenes, leading to our discovery of novel enzymes and pathways for making short-chain esters. Most notably, thermostable chloramphenicol transferases were repurposed to function as alcohol acetyltransferases in Y. lipolytica, as well as the Gram-negative and Gram-positive bacteria Escherichia coli and thermophile Clostridium thermocellum, respectively.

09 BIOMASS FUELS↗

Unlocking multiphysics design guidelines on Si/C composite nanostructures for high-energy-density and robust lithium-ion battery anode

In general, current material fabrication guidance for novel designs of Si/C composite particle materials focuses on electrochemical behavior and redox reactions at the nano/micro level. However, such guidance cannot provide detailed information for predicting mechanical deformations of the composite particles, especially when the mechanical field coupled with electrochemical and thermal fields. Here, we establish an electro-chemo-mechanical model and implement it to quantitatively analyze the multiphysics behavior of five representative Si/C composite nanostructures. Modeling and computation discover that yolk-shell and dual-shell structures are more robust in terms of particle fractures. When considering electrochemical performance, the yolk-shell structure is the best among the compared five Si/C composites. Finally, we map design guidance to further illustrate quantitative structure-property relationships. This study provides novel insights on Si/C composite nanostructure anode material design and additional powerful design tools for next-generation high-energy-density lithium-ion batteries.

25 ENERGY STORAGE↗

Alpha ketoacid decarboxylases: Diversity, structures, reaction mechanisms, and applications for biomanufacturing of platform chemicals and fuels

In living cells, alpha-ketoacid decarboxylases (KDCs, EC 4.1.1.-) are a class of enzymes that convert alpha-ketoacids into aldehydes through decarboxylation. These aldehydes serve as either drop-in chemicals or precursors for the biosynthesis of alcohols, carboxylic acids, esters, and alkanes. These compounds play crucial roles in cellular metabolism and fitness and the bioeconomy, facilitating the sustainable and renewable biomanufacturing of platform chemicals and fuels. This review explores the diversity and classification of KDCs, detailing their structures, mechanisms, and functions. We highlight recent advancements in repurposing KDCs to enhance their efficiency and robustness for biomanufacturing. Additionally, we present modular KDC-dependent metabolic pathways for the microbial biosynthesis of aldehydes, alcohols, carboxylic acids, esters, and alkanes. Lastly, we discuss recent developments in the modular cell engineering technology that can potentially be applied to harness the diversity of KDC-dependent pathways for biomanufacturing platform chemicals and fuels.

09 BIOMASS FUELS↗

Probing the Formation of Cathode-Electrolyte Interphase on Lithium Iron Phosphate Cathodes via Operando Mechanical Measurements

Interfacial instabilities in electrodes control the performance and lifetime of Li-ion batteries. While the formation of solid-electrolyte interface (SEI) on anodes has received much attention, there is still lack of understanding about the formation of cathode-electrolyte interface (CEI) on the cathodes. To fill this gap, we report on dynamic deformations on lithium iron phosphate, LiFePO 4 cathodes during charge / discharge by utilizing in-operando digital image correlation, impedance spectroscopy and Cryo X-ray photoelectron spectroscopy. LiFePO4 cathodes were cycled in either LiPF 6 , LiClO 4 or LiTFSI- containing organic liquid electrolytes. Beyond the first cycle, Li-ion intercalation results in a nearly linear correlation between electrochemical strains and the state of (dis)-charge, regardless of the electrolyte chemistry. However, during the first charge in LiPF 6 - containing electrolyte, there is a distinct irreversible positive strain evolution at the onset of anodic current rise as well as current decay at around 4.0V. Impedance studies show the increase in surface resistance in the same potential window, suggesting the formation of CEI layers on the cathode. The chemistry of the CEI layer was characterized by X-ray photoelectron spectroscopy. LiF is detected in CEI layer starting as early as 3.4 V and Li $x$ PO $y$ F $z$ appeared at voltages higher than 4.0 V during the first charge. In conclusion, our approach offers new insights into the formation mechanism of CEI layers on the cathode electrodes, which is crucial for the development of robust cathode and electrolyte chemistries for higher performance batteries.

25 ENERGY STORAGE↗

X-ray Micro-Computed Tomography for Structural Analysis of All-Solid-State Battery at Pouch Cell Level

Characterizing the microstructure of all-solid-state batteries (ASSBs) during fabrication and operation is vital for their advancement, particularly as scaling to pouch cell levels introduces challenges in probing large-scale microstructural evolution. This work highlights the potential of synchrotron X-ray micro-computed tomography (sXCT) as a nondestructive, rapid (<30 min), and high-resolution technique for visualizing and quantifying key microstructural features, including overhang, porosity, contact loss, active surface area, and tortuosity, in all-solid-state pouch cells. The large field of view (up to millimeters) of sXCT enables detailed analysis at an industry-relevant scale, bridging the gap between laboratory research and commercial applications. Furthermore, integrating realistic sXCT-derived 3D models into multiphysics simulations could provide insights into chemo-mechanical degradation, particularly at the edges of the pouch cells, offering a pathway for designing robust, high-performance ASSBs. This perspective establishes sXCT as an indispensable tool for advancing both the understanding and the engineering of next-generation energy storage systems.

25 ENERGY STORAGE↗

A Donor–Acceptor [2]Catenane for Visible Light Photocatalysis

Colored charge-transfer complexes can be formed by the association between electron-rich donor and electron-deficient acceptor molecules, bringing about the narrowing of HOMO–LUMO energy gaps so that they become capable of harnessing visible light. In an effort to facilitate the use of these widespread, but nonetheless weak, interactions for visible light photocatalysis, it is important to render the interactions strong and robust. Furthermore, we employ a well-known donor–acceptor [2]catenane—formed by the mechanical interlocking of cyclobis(paraquat-p-phenylene) and 1,5-dinaphtho[38]crown-10—in which the charge-transfer interactions between two 4,4'-bipyridinium and two 1,5-dioxynaphthalene units are enhanced by mechanical bonding, leading to increased absorption of visible light, even at low concentrations in solution. As a result, since this [2]catenane can generate persistent bipyridinium radical cations under continuous visible-light irradiation without the need for additional photosensitizers, it can display good catalytic activity in both photo-reductions and -oxidations, as demonstrated by hydrogen production—in the presence of platinum nanoparticles—and aerobic oxidation of organic sulfides, such as l-methionine, respectively. This research, which highlights the usefulness of nanoconfinement present in mechanically interlocked molecules for the reinforcement of weak interactions, can not only expand the potential of charge-transfer interactions in solar energy conversion and synthetic photocatalysis but also open up new possibilities for the development of active artificial molecular shuttles, switches, and machines.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural basis for dimerization quality control

Most quality control pathways target misfolded proteins to prevent toxic aggregation and neurodegeneration 1 . Dimerization quality control further improves proteostasis by eliminating complexes of aberrant composition 2 , but how it detects incorrect subunits remains unknown. Here we provide structural insight into target selection by SCF-FBXL17, a dimerization-quality-control E3 ligase that ubiquitylates and helps to degrade inactive heterodimers of BTB proteins while sparing functional homodimers. We find that SCF-FBXL17 disrupts aberrant BTB dimers that fail to stabilize an intermolecular β-sheet around a highly divergent β-strand of the BTB domain. Furthermore, complex dissociation allows SCF-FBXL17 to wrap around a single BTB domain, resulting in robust ubiquitylation. SCF-FBXL17 therefore probes both shape and complementarity of BTB domains, a mechanism that is well suited to establish quality control of complex composition for recurrent interaction modules.

59 BASIC BIOLOGICAL SCIENCES↗

How earthquakes organize stress

Stress is not uniform in the Earth. Therefore, we must use natural experiments to measure the distribution of stresses and related quantities, rather than single values. For instance, dynamic triggering shows that faults are uniformly distributed over their loading cycles in Southern California. The probability that a fault ruptures across a barrier measures the in situ energy distribution. Fault roughness reflects the distribution of strength. These natural experiments produce observable distributions that are surprisingly consistent and suggest some degree of self-organization in the Earth’s crust. Once established, the functional form of the distributions can be used to track changes in response to earthquakes as well as to distinguish fundamentally different fault systems. Transient fault locking before stress release in laboratory experiments can be interpreted as a consequence of self-organization of fault stress. The robust self-organization of multiple variables in earthquake systems suggests that the most consequential mechanical outcome of earthquakes may be the redistribution of stress and the strain energy associated with it. The low friction on a fault during seismic slip as inferred by temperature measurements of the Tohoku earthquake is consistent with dissipation playing a secondary role to this redistribution process. Through stress redistribution and interaction, subduction zone faults tend to synchronize, perhaps due to their geometric simplicity, while the continental system of Southern California cannot synchronize, perhaps due to the complexity of the fault network. Earthquakes organize stress in the crust and produce a suite of well-defined, consistent distributions.

earthquakes↗

Molecular bond stabilization in the strong-field dissociation of O 2 +

We theoretically examine the rotational and vibrational dynamics of O 2 + molecular ions exposed to intense, short laser pulses for conditions realized in contemporary pump-probe experiments. We solve the time-dependent Schrödinger equation within the Born-Oppenheimer approximation for an initial distribution of randomly aligned molecular ions. For fixed peak intensities, our numerical results show that total, angle-integrated O 2 + → O( 3 P) + O + ( 4 S 0 ) dissociation yields do not monotonically increase with increasing infrared-probe pulse duration. We find this pulse-duration-dependent stabilization to be consistent with the transient trapping of nuclear probability density in a light-induced (bond-hardening) potential-energy surface and robust against rotational excitation. We analyze this stabilization effect and its underlying bond-hardening mechanism (i) in the time domain, by following the evolution of partial nuclear probability densities associated with the dipole-coupled O 2 + (a 4 Π u ) and O 2 + (f 4 Π g ) cationic states, and (ii) in the frequency domain, by examining rovibrational quantum-beat spectra for the evolution of the partial nuclear probability densities associated with these states. In this work, our analysis reveals the characteristic timescale for the bond-hardening mechanism in O 2 + and explains the onset of bond stabilization for sufficiently long pulse durations.

74 ATOMIC AND MOLECULAR PHYSICS↗