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At least 199 records · Page 11

Toward a First-Principles Framework for Predicting Collective Properties of Electrolytes

Conspectus Given the universal importance of electrolyte solutions, it is natural to expect that we have a nearly complete understanding of the fundamental properties of these solutions (e.g., the chemical potential) and that we can therefore explain, predict, and control the phenomena occurring in them. In fact, reality falls short of these expectations. But, recent advances in the simulation and modeling of electrolyte solutions indicate that it should soon be possible to make progress toward these goals. In this Account, we will discuss the use of first-principles interaction potentials based in quantum mechanics (QM) to enhance our understanding of electrolyte solutions. Specifically, we will focus on the use of quantum density functional theory (DFT) combined with molecular dynamics simulation (DFT-MD) as the foundation for our approach. The overarching concept is to understand and accurately reproduce the balance between local or short-ranged (SR) structural details and long-range (LR) correlations, allowing the prediction of the thermodynamics of both single ions in solution as well as the collective interactions characterized by activity/osmotic coefficients. In doing so, relevant collective motions and driving forces characterized by chemical potentials can be determined. Here, in this Account, we will make the case that understanding electrolyte solutions requires a faithful QM representation of the SR nature of the ion–ion, ion–water, and water–water interactions. However, the number of molecules that is required for collective behavior makes the direct application of high-level QM methods that contain the best SR physics untenable, making methods that balance accuracy and efficiency a practical goal. Alternatives such as continuum solvent models (CSMs) and empirically based classical molecular dynamics have been extensively employed to resolve this problem but without yet overcoming the fundamental issue of SR accuracy. We will demonstrate that accurately describing the SR interaction is imperative for predicting both intrinsic properties, namely, at infinite dilution, and collective properties of electrolyte solutions. DFT has played an important role in our understanding of condensed phase systems, e.g., bulk liquid water, the air–water interface, ions in bulk, and at the air–water interface. This approach holds huge promise to provide benchmark calculations of electrolyte solution properties that will allow for the development and improvement of more efficient methods, as well as an enhanced understanding of fundamental phenomena. However, the standard protocol using the generalized gradient approximation with van der Waals (vdW) correction requires improvement in order to achieve a high level of quantitative accuracy. Simply simulating with higher level DFT functionals may not be the best route considering the significant computational cost. Alternative methods of incorporating information from higher levels of QM should be explored; e.g., using force matching techniques on small clusters, where high level benchmark calculations are possible, to develop ideal correction terms to the DFT functional is a promising possibility. We argue that DFT with statistical mechanics is becoming an increasingly useful framework enabling the prediction of collective electrolyte properties.

Duignan, Timothy T.↗

A positive feedback loop involving the Spa2 SHD domain contributes to focal polarization

Focal polarization is necessary for finely arranged cell-cell interactions. The yeast mating projection, with its punctate polarisome, is a good model system for this process. We explored the critical role of the polarisome scaffold protein Spa2 during yeast mating with a hypothesis motivated by mathematical modeling and tested by in vivo experiments. Our simulations predicted that two positive feedback loops generate focal polarization, including a novel feedback pathway involving the N-terminal domain of Spa2. We characterized the latter using loss-of-function and gain-of-function mutants. The N-terminal region contains a Spa2 Homology Domain (SHD) which is conserved from yeast to humans, and when mutated largely reproduced the spa2Δ phenotype. Our work together with published data show that the SHD domain recruits Msb3/4 that stimulates Sec4-mediated transport of Bud6 to the polarisome. There, Bud6 activates Bni1-catalyzed actin cable formation, recruiting more Spa2 and completing the positive feedback loop. We demonstrate that disrupting this loop at any point results in morphological defects. Gain-of-function perturbations partially restored focal polarization in a spa2 loss-of-function mutant without restoring localization of upstream components, thus supporting the pathway order. Thus, we have collected data consistent with a novel positive feedback loop that contributes to focal polarization during pheromone-induced polarization in yeast.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of flow and transport in a fracture network at the EGS Collab field experiment through stochastic modeling of tracer recovery

Energy extraction from subsurface reservoirs is important for addressing the increasing energy demand and environmental concerns such as global warming. However, the characterization of subsurface reservoirs, particularly reservoirs dominated by fracture networks remains a challenge due to the lack of means to directly observe subsurface processes. This study explores the feasibility and efficacy of characterizing fracture flow and transport processes in an enhanced geothermal system (EGS) testbed through stochastic tracer modeling. There are two enabling factors that allow application of stochastic modeling to characterize a subsurface reservoir. First, an abundance of geological and geophysical measurements enables the development of a high-fidelity and well-constrained fracture network model. Second, high-performance computing (HPC) allows running massive realizations efficiently. Six conservative tracer tests were stochastically modeled and produced satisfactory realizations that successfully reproduce field tracer recovery data from each tracer test. The evolution of flow and transport processes in the fracture network was then analyzed from these satisfactory realizations. This work demonstrates that stochastic tracer modeling on a high-fidelity fracture network model is feasible and can provide important insights regarding flow and transport characteristics in subsurface fractured reservoirs.

58 GEOSCIENCES↗

Community-Driven Methods for Open and Reproducible Software Tools for Analyzing Datasets from Atom Probe Microscopy

Atom probe tomography, and related methods, probe the three-dimensional architecture of a material. The software tools that microscopists use, and how these tools are connected into workflows, makes a substantial contribution to the accuracy and precision of such a material characterization experiment. Typically, we adapt methods from other communities like mathematics, data science, computational geometry, artificial intelligence, or scientific computing. We also realize that improving on research data management is a challenge when it comes to align with the FAIR data stewardship principles. Faced with this global challenge, we are convinced that collaborating is useful. Here, we report the results and challenges with an inter-laboratory call for developing test cases for several types of atom probe software tools. The results support why defining detailed recipes of software workflows and sharing these recipes is necessary and rewarding: Open source tools and (meta)data exchange can help to make our day-to-day data processing tasks become more efficient, the training of new users and knowledge transfer become easier, and assist us with automated quantification of uncertainties to gain access to substantiated results.

36 MATERIALS SCIENCE↗

Characterizing Ice Nucleating Particles Over the Southern Ocean Using Simultaneous Aircraft and Ship Observations

Abstract Supercooled liquid clouds are ubiquitous over the Southern Ocean (SO), even to temperatures below −20°C, and comprise a large fraction of the marine boundary layer (MBL) clouds. Earth system models and reanalysis products have struggled to reproduce the observed cloud phase distribution and occurrence of cloud ice in the region. Recent simulations found the microphysical representation of ice nucleation and growth has a large impact on these properties, however, measurements of SO ice nucleating particles (INPs) to validate simulations are sparse. This study presents measurements of INPs from simultaneous aircraft and ship campaigns conducted over the SO in austral summer 2018, which include the first in situ observations in and above cloud in the region. Our results confirm recent observations that INP concentrations are uniformly lower than measurements made in the late 1960s. While INP concentrations below and above cloud are similar, higher ice nucleation efficiency above cloud supports model simulations that the dominant INP composition varies with height. Model parameterizations based solely on aerosol properties capture the mean relationship between INP concentration and temperature but not the observed variability, which is likely related to the only modest correlations observed between INPs and environmental or aerosol metrics. Including wind speed in addition to activation temperature in a marine INP parameterization reduces bias but does not explain the large range of observed INP concentrations. Direct and indirect inference of marine INP size suggests MBL INPs, at least during Austral summer, are dominated by particles with diameters smaller than 500 nm.

Meteorology & Atmospheric Sciences↗

Powder‐to‐Film Conversion of Nickel Single‐Atom Catalysts into Binder‐Free and Resistant Electrodes

Although a few binder-free and self-supported single-atom electrodes have been reported, achieving mechanically robust, defect-engineered, and reproducible films that preserve atomic dispersion under electrochemical operation remains challenging. This work addresses this limitation by presenting a versatile and generalizable strategy to transform powders into standalone, defect-engineered thin films hosting atomically dispersed Ni centers within conductive 2D frameworks. The physicochemical and electronic properties of these materials are thoroughly characterized using a comprehensive set of spectroscopic and microscopic techniques and confirmed the homogeneous dispersion and monoatomic nature of the Ni centers (0.94 wt.%) on the electrode films. Electrochemical testing via cyclic voltammetry and electrochemical impedance spectroscopy under a range of experimental conditions revealed that integration of Ni single atoms markedly enhanced performance and stability compared to carbon nanotube-only electrodes, maintaining integrity after 15 h of continuous operation. This improvement is accompanied by a notable reduction in charge transfer resistance (30.50 Ω) and an increase in double-layer capacitance (295.45 µF). Post-electrochemical analyses corroborated the structural integrity and robustness of the electrodes. Overall, this work bridges atomically precise catalysis and device-level electrochemistry, opening a route toward reproducible and scalable single-atom electrodes for sensing and energy conversion.

36 MATERIALS SCIENCE↗

Sediment Mineralogy Data Review for the Hanford Central Plateau

The compendium of Hanford site sediment mineralogy data provided in this report was initiated in 2012 to support flux mitigation technologies and real-time monitoring that could limit contaminant fluxes to the groundwater in the Central Plateau. Recent efforts in advancing spectral induced polarization as a method for monitoring contaminant transformations for active biogeochemical remedies have underscored the need for a published compendium of sediment characterization data. Although the data are primarily focused on the mineralogical composition of Hanford sediments, other soil measurements such as particle size distribution such as particle size distribution and carbon content are provided. The data have been reproduced from the original reports and are provided here for information only (FIO).

58 GEOSCIENCES↗

Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi

Abstract Extraradical hyphae (ERH) of arbuscular mycorrhizal fungi (AMF) extend from plant roots into the soil environment and interact with soil microbial communities. Evidence of positive and negative interactions between AMF and soil bacteria point to functionally important ERH-associated communities. To characterize communities associated with ERH and test controls on their establishment and composition, we utilized an in-growth core system containing a live soil–sand mixture that allowed manual extraction of ERH for 16S rRNA gene amplicon profiling. Across experiments and soils, consistent enrichment of members of the Betaproteobacteriales, Myxococcales, Fibrobacterales, Cytophagales, Chloroflexales, and Cellvibrionales was observed on ERH samples, while variation among samples from different soils was observed primarily at lower taxonomic ranks. The ERH-associated community was conserved between two fungal species assayed, Glomus versiforme and Rhizophagus irregularis, though R. irregularis exerted a stronger selection and showed greater enrichment for taxa in the Alphaproteobacteria and Gammaproteobacteria. A distinct community established within 14 days of hyphal access to the soil, while temporal patterns of establishment and turnover varied between taxonomic groups. Identification of a conserved ERH-associated community is consistent with the concept of an AMF microbiome and can aid the characterization of facilitative and antagonistic interactions influencing the plant-fungal symbiosis.

59 BASIC BIOLOGICAL SCIENCES↗

Improved Simulation of East Asian Summer Monsoon in the High-resolution CESM1 and Its Causes

Based on the high- and low-resolution Community Earth System Model, version 1 (CESM1), and corresponding simulations from phase 6 of the Coupled Model Intercomparison Project (CMIP6), we compare the interannual variability of the East Asian summer monsoon (EASM). The EASM interannual variability is characterized by the anomalous western North Pacific anticyclone (WNPAC) circulation and the dipole rainfall pattern with a negative southern lobe over the western North Pacific and a positive northern lobe along the Meiyu–Baiu region, which is better reproduced by the high-resolution models. Here, the reason for the improvement in the high-resolution models has been attributed to the better simulation of the warm temperature advection from the wind anomalies on the climatological temperature gradient. Positive sea surface temperature (SST) anomalies over the tropical Indian Ocean are the key to the improved wind anomalies featuring a WNPAC in the high-resolution models. The warm SST anomalies over the tropical Indian Ocean strengthen the WNPAC by triggering a Kelvin-wave response to the enhanced heat release induced by the increased precipitation. Based on the mixed-layer heat budget analysis, the warm SST anomalies over the western Indian Ocean in the high-resolution CESM1 are tied to the anomalous easterly wind along the equator, which reduces surface evaporation and upwelling. Therefore, the better simulations of air-sea feedback and the oceanic mesoscale eddy over the western Indian Ocean are the key for the improved simulation of the EASM interannual variations in the high-resolution CESM1.

54 ENVIRONMENTAL SCIENCES↗

TRISO SiC Failure Probability for Reactivity Initiated Accidents in High-Temperature Gas-Cooled Reactors

This work analyzes the failure process of the silicon carbide (SiC) layer in tristructural isotropic (TRISO) during reactivity-initiated accident scenarios for a high-temperature gas-cooled reactor (HTGR) with BISON. Two cases are considered—a group control rod withdrawal (CRW) and a control rod ejection (CRE)—reproduced from a previous study. Failure probability is modeled using Weibull statistics, and worst-case scenario Weibull parameters are adopted to simulate the envelopes in BISON with a one-dimensional TRISO model. CRW scenario results are characterized by higher values of maximum energy deposition and final temperature and volumetric strain with respect to the CRE ones, but the latter have remarkably higher SiC failure probability, mainly due to the offset in strain rates between the two cases. This work also confirms the validity and conservatism of the performance envelopes produced in a previous work by replicating the envelope formulation using RELAP5-3D and RAVEN with a different sampling technique and obtaining consistent results. A sensitivity analysis using the Sobol variance decomposition method on SiC failure probability is then performed involving a set of inputs on both CRW and CRE. The two most important parameters are Weibull modulus and characteristic stress, and their relative importance depends on the specific case. The proposed interpretation of the results is that both energy deposition and strain rate influence the relative degree of importance of the failure parameters. Computation of 95% confidence intervals around worst-case scenario SiC failure probability values is also carried out for four different sets of Weibull parameters. Heren a new criterion for SiC TRISO quality classification built upon safety-based ranges of Weibull parameters is proposed to be integrated in future Fuel-Production Quality Assurance Plans.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Nonlinear elasticity and short-range mechanical coupling govern the rate and symmetry of mouth opening in Hydra

Hydra has a tubular bilayered epithelial body column with a dome-shaped head on one end and a foot on the other. Hydra lacks a permanent mouth: its head epithelium is sealed. Upon neuronal activation, a mouth opens at the apex of the head which can exceed the body column diameter in seconds, allowing Hydra to ingest prey larger than itself. While the kinematics of mouth opening are well characterized, the underlying mechanism is unknown. We show that Hydra mouth opening is generated by independent local contractions that require tissue-level coordination. We model the head epithelium as an active viscoelastic nonlinear spring network. The model reproduces the size, timescale and symmetry of mouth opening. It shows that radial contractions, travelling inwards from the outer boundary of the head, pull the mouth open. Nonlinear elasticity makes mouth opening larger and faster, contrary to expectations. Here, the model correctly predicts changes in mouth shape in response to external forces. By generating innervated : nerve-free chimera in experiments and simulations, we show that nearest-neighbor mechanical signaling suffices to coordinate mouth opening. Hydra mouth opening shows that in the absence of long-range chemical or neuronal signals, short-range mechanical coupling is sufficient to produce long-range order in tissue deformations.

59 BASIC BIOLOGICAL SCIENCES↗

Investigation of a U(IV)/U(III) Thermodynamic Reference Electrode for High-Temperature Molten Fluoride Salts

While thermodynamic reference electrodes with known and stable potentials are common in traditional aqueous systems, the high temperature and corrosive environment of a molten fluoride salt makes achieving long term stability with a thermodynamic reference electrode challenging, especially at temperatures of 600°C or higher. In this work, a thermodynamic reference electrode consisting of U(IV)/U(III) in a boron nitride compartment was evaluated for use in FLiBe at temperatures ≥ 600°C. FLiBe used in the study was purified by AlphaTech's proprietary process and characterized by ICP-MS and square wave voltammetry. The free oxide concentration was <2 ppm. Using the purified FLiBe, the U(IV)/U(III) thermodynamic reference electrode was shown to provide a stable, well-defined, and reproducible potential for more than 600+ hours of use in different tests. Moreover, the thermodynamic reference electrode showed a consistent potential with no signs of failure, even after being cooled between tests and then reheated for reuse. Thus, the U(IV)/U(III) reference electrode is suitable for use in rigorous electrochemical studies in molten fluoride salts. As a result, it may be useful as a common standard, facilitating the advancement of nuclear applications such as isotope separation or online monitoring of reactor systems through improved certainty in the measurement of thermodynamic potentials.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Assessing impacts of selective logging on water, energy, and carbon budgets and ecosystem dynamics in Amazon forests using the Functionally Assembled Terrestrial Ecosystem Simulator

Abstract. Tropical forest degradation from logging, fire, and fragmentation not only alters carbon stocks and carbon fluxes, but also impacts physical land surface properties such as albedo and roughness length. Such impacts are poorly quantified to date due to difficulties in accessing and maintaining observational infrastructures, as well as the lack of proper modeling tools for capturing the interactions among biophysical properties, ecosystem demography, canopy structure, and biogeochemical cycling in tropical forests. As a first step to address these limitations, we implemented a selective logging module into the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) by mimicking the ecological, biophysical, and biogeochemical processes following a logging event. The model can specify the timing and aerial extent of logging events, splitting the logged forest patch into disturbed and intact patches; determine the survivorship of cohorts in the disturbed patch; and modifying the biomass and necromass (total mass of coarse woody debris and litter) pools following logging. We parameterized the logging module to reproduce a selective logging experiment at the Tapajós National Forest in Brazil and benchmarked model outputs against available field measurements. Our results suggest that the model permits the coexistence of early and late successional functional types and realistically characterizes the seasonality of water and carbon fluxes and stocks, the forest structure and composition, and the ecosystem succession following disturbance. However, the current version of FATES overestimates water stress in the dry season and therefore fails to capture seasonal variation in latent and sensible heat fluxes. Moreover, we observed a bias towards low stem density and leaf area when compared to observations, suggesting that improvements are needed in both carbon allocation and establishment of trees. The effects of logging were assessed by different logging scenarios to represent reduced impact and conventional logging practices, both with high and low logging intensities. The model simulations suggest that in comparison to old-growth forests the logged forests rapidly recover water and energy fluxes in 1 to 3 years. In contrast, the recovery times for carbon stocks, forest structure, and composition are more than 30 years depending on logging practices and intensity. This study lays the foundation to simulate land use change and forest degradation in FATES, which will be an effective tool to directly represent forest management practices and regeneration in the context of Earth system models.

54 ENVIRONMENTAL SCIENCES↗

A rapid assay for assessing bacterial effects on Arabidopsis thermotolerance

Abstract Background The role of beneficial microbes in mitigating plant abiotic stress has received considerable attention. However, the lack of a reproducible and relatively high-throughput screen for microbial contributions to plant thermotolerance has greatly limited progress in this area, this slows the discovery of novel beneficial isolates and the processes by which they operate. Results We designed a rapid phenotyping method to assess the effects of bacteria on plant host thermotolerance. After testing multiple growth conditions, a hydroponic system was selected and used to optimize an Arabidopsis heat shock regime and phenotypic evaluation. Arabidopsis seedlings germinated on a PTFE mesh disc were floated onto a 6-well plate containing liquid MS media, then subjected to heat shock at 45 °C for various duration. To characterize phenotype, plants were harvested after four days of recovery to measure chlorophyll content. The method was extended to include bacterial isolates and to quantify bacterial contributions to host plant thermotolerance. As an exemplar, the method was used to screen 25 strains of the plant growth promoting Variovorax spp. for enhanced plant thermotolerance. A follow-up study demonstrated the reproducibility of this assay and led to the discovery of a novel beneficial interaction. Conclusions This method enables rapid screening of individual bacterial strains for beneficial effects on host plant thermotolerance. The throughput and reproducibility of the system is ideal for testing many genetic variants of Arabidopsis and bacterial strains.

59 BASIC BIOLOGICAL SCIENCES↗

Atomic‐Scale Surface Imaging of Bulk Epitaxial CsPbBr 3 Perovskite Single Crystals on Mica Using Light Assisted Scanning Tunneling Microscopy at Low‐Temperature (80 K)

Epitaxial single-crystalline CsPbBr 3 perovskite films on mica, prepared ex situ, are explored using a low-temperature scanning tunneling microscope (STM) by probing the unoccupied electronic states of their surface in ultra-high vacuum (UHV) at 80 K. Light-assisted STM measurements under a broadband illumination with visible light were employed to enhance and stabilize surface conductivity. STM imaging across the surface of macroscopic bulk CsPbBr 3 films reveals large flat terraces characterized by a specific type of surface reconstruction, consisting of parallel rows of U-shaped atomic nanostructures. These structures are spaced by 12 Å and exhibit an internal feature size of 5.1 Å. Density functional theory (DFT) calculations reproduce the experimental observations and reveal a competition between different orthorhombic CsPbBr 3 (110) surface reconstructions: a Cs-rich structure, identified as the most energetically stable, and three alternative Pb–Br-rich reconstructions, which are slightly higher in energy yet remain consistent with the STM data. Additional analyses that explicitly account for the mica substrate exclude the cubic CsPbBr 3 phase and other orthorhombic surface orientations, while showing that variations in the mica surface termination do not alter the preferred CsPbBr 3 (110) reconstruction. In conclusion, this combined approach thereby confirms our assignment and resolves previous STM interpretations of CsPbBr 3 .

36 MATERIALS SCIENCE↗

CQM-Analysis v1.0

This repository contains the data and code necessary to reproduce the primary analysis and figures for the manuscript "Pathways to productivity: mapping the relationship between multimodal transportation infrastructure, commute quality, and economic vitality for the United States workforce". The analysis demonstrates a newly defined commute quality metric (CQM) characterizing the quality, as a monetized consumer surplus, of travel for the purpose of work for every census tract in the continental United States. The analysis additionally demonstrates the correlation of that CQM with key economic vitality indicators. Specifically median household income and unemployment rate.

Spurlock, C Anna [Lawrence Berkeley National Labor↗

Gaussian Process Modeling For Experimental Procedure Uncertainty

Many laboratory experiments generate data that are characterized by a form of uncertainty that differs from noise: experimental procedure uncertainty. The origin of this type of uncertainty is the difficulty in controlling a subset of experimental conditions in such a way that the experiment is perfectly reproducible within noise. In this report, we describe a Gaussian Process modeling-based method that accounts for experimental procedure uncertainty. The method accounts for variations in conditions from experiment to experiment that are independent between experiments, but correlated within each experiment, and incorporates the resulting uncertainty into predictions at future experimental settings. The method is discussed in the context of a specific chemistry application in which Raman scattering spectra are measured from three-component mixtures.

42 ENGINEERING↗

Characterizing Families of Spectral Similarity Scores and Their Use Cases for Gas Chromatography–Mass Spectrometry Small Molecule Identification

Metabolomics provides a unique snapshot into the world of small molecules and the complex biological processes that govern the human, animal, plant, and environmental ecosystems encapsulated by the One Health modeling framework. However, this “molecular snapshot” is only as informative as the number of metabolites confidently identified within it. The spectral similarity (SS) score is traditionally used to identify compound(s) in mass spectrometry approaches to metabolomics, where spectra are matched to reference libraries of candidate spectra. Unfortunately, there is little consensus on which of the dozens of available SS metrics should be used. This lack of standard SS score creates analytic uncertainty and potentially leads to issues in reproducibility, especially as these data are integrated across other domains. In this work, we use metabolomic spectral similarity as a case study to showcase the challenges in consistency within just one piece of the One Health framework that must be addressed to enable data science approaches for One Health problems. Here, using a large cohort of datasets comprising both standard and complex datasets with expert-verified truth annotations, we evaluated the effectiveness of 66 similarity metrics to delineate between correct matches (true positives) and incorrect matches (true negatives). We additionally characterize the families of these metrics to make informed recommendations for their use. Our results indicate that specific families of metrics (the Inner Product, Correlative, and Intersection families of scores) tend to perform better than others, with no single similarity metric performing optimally for all queried spectra. This work and its findings provide an empirically-based resource for researchers to use in their selection of similarity metrics for GC-MS identification, increasing scientific reproducibility through taking steps towards standardizing identification workflows.

59 BASIC BIOLOGICAL SCIENCES↗