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At least 271 records · Page 15

The embedded feature model for the interpretation of chromospheric contrast profiles

Contrast profiles obtained from chromospheric filtergrams and spectra of bright and dark mottles have to date been interpreted almost exclusively in terms of Becker's cloud model. Here we demonstrate the failure of this model to account in a physically consistent way for the observed contrasts. As an alternative, we introduce an embedded-feature model, restricting our discussion in this paper to stationary features. Our model is then characterized by three independent parameters: the density of absorbing atoms, the geometrical depth, and the profile of the absorption coefficient. An analytic approximation to the contrast resulting from such a model reproduces well the observed behavior of all types of contrast profiles.

Steinitz, R.↗

Electrical-transport properties and microwave device performance of sputtered TlCaBaCuO superconducting thin films

The paper describes the processing and electrical transport measurements for achieving reproducible high-Tc and high-Jc sputtered TlCaBaCuO thin films on LaAlO3 substrates, for microelectronic applications. The microwave properties of TlCaBaCuO thin films were investigated by designing, fabricating, and characterizing microstrip ring resonators with a fundamental resonance frequency of 12 GHz on 10-mil-thick LaAlO3 substrates. Typical unloaded quality factors for a ring resonator with a superconducting ground plane of 0.3 micron-thickness and a gold ground plane of 1-micron-thickness were above 1500 at 65 K. Typical values of penetration depth at 0 K in the TlCaBaCuO thin films were between 7000 and 8000 A.

Subramanyam, G.↗

Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline

Abstract As genomic databases expand and artificial intelligence tools advance, there is a growing demand for efficient characterization of large numbers of proteins. To this end, here we describe a generalizable pipeline for high-throughput protein purification using small-scale expression in E. coli and an affordable liquid-handling robot. This low-cost platform enables the purification of 96 proteins in parallel with minimal waste and is scalable for processing hundreds of proteins weekly per user. We demonstrate the performance of this method with the expression and purification of the leading poly(ethylene terephthalate) hydrolases reported in the literature. Replicate experiments demonstrated reproducibility and enzyme purity and yields (up to 400 µg) sufficient for comprehensive analyses of both thermostability and activity, generating a standardized benchmark dataset for comparing these plastic-degrading enzymes. The cost-effectiveness and ease of implementation of this platform render it broadly applicable to diverse protein characterization challenges in the biological sciences.

36 MATERIALS SCIENCE↗

Improved Performance of Cu(InGa)(SeS) 2 PV Modules Using the Reaction of Metal Precursors. Final Report

This project “Improved Performance of Cu(InGa)(SeS) 2 PV Modules using the Reaction of Metal Precursors” was a partnership led by the Institute of Energy Conversion (IEC) at the University of Delaware with Columbia University and the Molecular Foundry at the Lawrence Berkeley National Laboratory. The aim was to develop pathways to improve Cu(InGa)(SeS) 2 (CIGSS) thin film photovoltaic modules using processes compatible with low manufacturing cost. The CIGSS approach investigated was a two-step process including deposition of metal precursor films following by reaction in hydride gases utilizing IEC’s novel reactor. The process was similar to that under commercial development by the project’s industry partner Stion. When Stion went out of business mid-project the focus changed to a rapid thermal process considered more commercially viable. Approaches to improve the performance of solar cells using the reacted films focused on two material innovations. First, the overall Ga content was increased to increase the operating voltage, which is desirable for scale-up to commercial modules. Second, the processing and performance advantages arising from Ag alloying were investigated. Advanced characterization guided process and material development including control of relative composition gradients. Research on the formation of Cu-Ga-In metal precursors utilized sputtering deposition which is normally used in commercial applications. The work resulted in processes for deposition of precursor stacks with increased relative Ga content and effects of deposition parameters on morphology and phase composition were established. It was shown that the metal precursor films have comparable phase composition and morphology so subsequent reaction follows from the same starting point. The addition of Ag to the metal precursors gave more uniform morphology and improved adhesion of reacted films which enable higher reaction temperature for faster processing. A novel outcome was the discovery of a previously undocumented material phase in sputter-deposited and evaporated Ag-Cu-In-Ga thin films. Hydride gas reaction processes including time-temperature-concentration profiles were developed for different precursor compositions. This enables control of composition profiles to engineer through-film gradients for solar cell optimization with characterization and simulations used to correlate measured film composition profiles to measurements of devices. In particular, the gradient of sulfur at the front of the CIGSS film was found to be critical. The simulations guided process development leading to improved reproducibility of devices improved performance with higher Ga content and higher voltage. With Ag-alloyed precursors, the reaction pathways leading were determined. A significant finding was that Ag-alloying increases the reaction rate to completely convert precursor films to the final chalcopyrite which could enable reduced reaction time to benefit manufacturability. To maintain potential commercial viability, the process under investigation was refocused to a rapid thermal process that could potentially be incorporated into an in-line process for manufacturing. Precursors with different composition were capped with an extra selenium layer and reacted in hydrogen sulfide 5-15 minutes, compared to typically 2 hours in the previous multi-step batch process. Critical RTP parameters were identified to control the reaction. Further optimization would be needed for high efficiency solar cells but pathways to high quality devices with further optimization and improved heating uniformity were developed. The project also developed new optoelectronic characterization approaches with a focus on development and application of spatial- and time-resolved photoluminescence and a custom mapping photoluminescence microscope built. It was shown how critical electronic transport properties strongly depend on the chemical composition of the material and that a wide range of samples show inhomogeneity on a length scale larger than the grains in the films. Additionally, two-photon excitation capability was developed to distinguish bulk vs surface losses. The project advances the state-of-the -art for precursor reaction processes in several ways that could impact manufacturing. This includes validation of approaches to increase voltage and establishment of model-guided control to form optimal composition profiles. The application of process control approaches with knowledge of phase formation and reaction pathways can be critically valuable in designing a large-scale process.

14 SOLAR ENERGY↗

Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N -1-Phenylethyl Sidechains

N-substituted glycines (polypeptoids) containing chiral hydrophobic sidechains are known to fold into biomimetic alpha helices. These helix formers often produce conformationally heterogeneous structures and are difficult to characterize at a sub-nanometer resolution. Previously, peptoid N-1-phenylethyl (S)-enantiomer sidechains (Nspe) were inferred from various experiments to form right-handed helices and (R)-enantiomers (Nrpe), left-handed helices. Prior computational work for N(s/r)pe oligomers has struggled to reproduce this trend. Herein, quantum mechanics calculations and molecular dynamics simulations are used to understand the origins of this discrepancy. Results from DFT and molecular mechanics calculations on a variety of Nspe and Nrpe oligomers as a function of chain length are in agreement, showing that Nspe and Nrpe prefer left- and right-handed helices, respectively. Additional metadynamics simulations are used to study Nrpe and Nspe oligomers folding in water. These results show that the free-energy driving forces for assembly into a helical backbone configuration are very small (within ~k B T). Lastly, we compare DFT calculations for other experimentally characterized peptoid sidechains, N(r/s)sb, N(r/s)tbe, and N(r/s)npe. In this analysis, we show that peptoid sidechains determined to be more robust experimentally (tbe and npe) have helical preferences opposite the trend seen in less robust assemblies formed by N(r/s)pe and N(r/s)sb chemistries. Furthermore, the more robust tbe and nnpe favor the (S)-enantiomer to right-handed and the (R)-enantiomers to left-handed helices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimal adjustment sets for causal query estimation in partially observed biomolecular networks

Abstract Causal query estimation in biomolecular networks commonly selects a ‘valid adjustment set’, i.e. a subset of network variables that eliminates the bias of the estimator. A same query may have multiple valid adjustment sets, each with a different variance. When networks are partially observed, current methods use graph-based criteria to find an adjustment set that minimizes asymptotic variance. Unfortunately, many models that share the same graph topology, and therefore same functional dependencies, may differ in the processes that generate the observational data. In these cases, the topology-based criteria fail to distinguish the variances of the adjustment sets. This deficiency can lead to sub-optimal adjustment sets, and to miss-characterization of the effect of the intervention. We propose an approach for deriving ‘optimal adjustment sets’ that takes into account the nature of the data, bias and finite-sample variance of the estimator, and cost. It empirically learns the data generating processes from historical experimental data, and characterizes the properties of the estimators by simulation. We demonstrate the utility of the proposed approach in four biomolecular Case studies with different topologies and different data generation processes. The implementation and reproducible Case studies are at https://github.com/srtaheri/OptimalAdjustmentSet.

59 BASIC BIOLOGICAL SCIENCES↗

Biogeochemistry simulations for the Salt Marsh Accretion Response to Temperature eXperiment (SMARTX)

Coastal ecosystems have been largely ignored in Earth system models but are important zones for carbon and nutrient processing. Interactions between water, microbes, soil, sediments, and vegetation are important for mechanistic representation of coastal processes and ecosystem function. To investigate the role of these feedbacks, we used a reactive transport model (PFLOTRAN) that has the capability to be connected to the Energy Exascale Earth System Model (E3SM). PFLOTRAN was used to incorporate redox reactions and track chemical species important for coastal ecosystems as well as define simple representations of vegetation dynamics. Our goal was to incorporate oxygen flux, salinity, pH, sulfur cycling, and methane production along with plant-mediated transport of gases and tidal flux. Using porewater profile and incubation data for model calibration and evaluation, we were able to create depth-resolved biogeochemical soil profiles for saltmarsh habitat and use this updated representation to simulate direct and indirect effects of elevated CO2 and temperature on subsurface biogeochemical cycling. We found that simply changing the partial pressure of CO2 or increasing temperature in the model did not fully reproduce observed changes in the porewater profile, but the inclusion of plant or microbial responses to CO2 and temperature manipulations was more accurate in representing porewater concentrations. This indicates the importance of characterizing tightly coupled vegetation-subsurface processes for developing predictive understanding and the need for measurement of plant-soil interactions on the same time scale to understand how hotspots or moments are generated.Included in this data package are PFLOTRAN input (PFLOTRAN input files and chemical database) files for simulating single column biogeochemistry, root, and tide interactions at the Global Change Research Wetland (Kirkpatrick Marsh; Edgewater, MD). The biogeochemical network includes soil organic matter decomposition, nitrogen, iron, and sulfur cycling, and methanogenesis. Reduced species can be oxidized and plant processes include oxygen and nutrient priming, methane release, and nutrient uptake.Inputs:TAI_database.dat - geochemical database for reactions, more information on database structure and variables can be found here https://www.pflotran.org/documentation/user_guide/cards/pages/geochemical_database.htmlswamp.in - input file for biogeochemical network in PFLOTRANswamp_eCO2.in - input file for biogeochemical network in PFLOTRAN with input gas partial pressures/concentrations adjusted for elevated CO2 treatmentsOutputs:swamp_obs_0.tec - hourly porewater concentrations from from multiple depths in the soil columnswamp_eCO2_obs_0.tec - hourly porewater concentrations from multiple depths in the soil column for elevated CO2 treatmentsPFLOTRAN code access: https://github.com/fmyuan/pflotran-elm-interface.git

54 ENVIRONMENTAL SCIENCES↗

X-ray scattering and fluorescence in the wind of a massive X-ray binary

Spectral data from the binary X-ray pulsar 4 U 0900 - 40 obtained with the Ginga satellite and covering a range of orbital phases are presented and interpreted using simulated spectra created with a Monte Carlo scattering code. It is found that scattering and fluorescence in a simple spherically symmetric distribution of matter surrounding the companion star can reproduce the eclipse spectrum, as well as the 'soft X-ray-excess' observed during egress and other orbital phases. Reasonably secure values are found for a number of the parameters that characterize the density profile of the stellar wind and atmosphere of the companion star. The Fe abundance is within a factor of about 1.3 of that in the solar neighborhood. It is shown that ionization zones are not critical to understanding the orbital-phase-resolved spectra in this source. It is also found that the contribution by scattering from interstellar dust grains to the observed spectra during eclipse is negligible, while that from diffuse emission from the 'Galactic ridge' is significant.

Lewis, W.↗

A crystal plasticity finite element model embedding strain-rate sensitivities inherent to deformation mechanisms: Application to alloy AZ31

We report the fundamental power-law relationship representing the flow rule in crystal visco-plasticity ensures uniqueness in the selection of slip systems accommodating imposed plastic strain-rates. The power-law relationship also introduces an artificially high strain-rate sensitivity in crystal plasticity simulations, unless a high value of the power-law exponent is used. However, the use of high values for the exponent is limited by numerical tractability. This paper presents a numerical method implemented in a crystal plasticity finite element (CPFE) model for embedding any value of the power-law exponent reflecting the true material strain-rate sensitivity. Importantly, the method does not increase computation time involved in the simulations. The enhanced CPFE model is used to interpret and predict a complex strain-rate sensitive response and microstructural evolution of AZ31 Mg alloy. Measured values of strain-rate sensitivity for slip and twinning modes are used in the simulations. Calculations show that the model successfully captures the phenomena pertaining to the effect of changing applied strain-rate on the mechanical response including flow stress and evolution of texture and twinning for a broad range of strain-rates ranging from 10 -3 s -1 to 10 3 s -1 and loading orientations in tension and compression. It is shown that such predictions are a consequence of not only relative amounts of slip and twinning activities driven by a set of accurately characterized hardening law parameters but also values of the strain-rate sensitivities inherent to individual deformation mechanisms. Besides, the model validates the measured strain-rate dependency of deformation mechanisms while accurately reproducing the mechanical data. Hence, the model can be used to verify and further refine or infer measured strain-rate sensitivity per deformation mechanism by reproducing experimental data.

36 MATERIALS SCIENCE↗

Developing a Redox Network for Coastal Saltmarsh Systems in the PFLOTRAN Reaction Model

Coastal ecosystems have been largely ignored in Earth system models but are important zones for carbon and nutrient processing. Interactions between water, microbes, soil, sediments, and vegetation are important for mechanistic representation of coastal processes and ecosystem function. To investigate the role of these feedbacks, we used a reactive transport model (PFLOTRAN) that has the capability to be connected to the Energy Exascale Earth System Model (E3SM). PFLOTRAN was used to incorporate redox reactions and track chemical species important for coastal ecosystems as well as define simple representations of vegetation dynamics. Here our goal was to incorporate oxygen flux, salinity, pH, sulfur cycling, and methane production along with plant-mediated transport of gases and tidal flux. Using porewater profile and incubation data for model calibration and evaluation, we were able to create depth-resolved biogeochemical soil profiles for saltmarsh habitat and use this updated representation to simulate direct and indirect effects of elevated CO 2 and temperature on subsurface biogeochemical cycling. We found that simply changing the partial pressure of CO 2 or increasing temperature in the model did not fully reproduce observed changes in the porewater profile, but the inclusion of plant or microbial responses to CO 2 and temperature manipulations was more accurate in representing porewater concentrations. This indicates the importance of characterizing tightly coupled vegetation-subsurface processes for developing predictive understanding and the need for measurement of plant-soil interactions on the same time scale to understand how hotspots or moments are generated.

54 ENVIRONMENTAL SCIENCES↗

Estimates of the wavenumber wavelet power spectrum of magnetic fluctuations during magnetic reconnection

Fluctuation analyses of experimental observations generally lack high temporal resolution and are in frequency-space f, contrary to theoretical efforts in wavenumber-space k. This is due to the inherent limits of the Fourier transform, though it is prominent due to the ease of diagnostic implementation. Advances in wavelet-based analysis have provided relief due to its temporal resolution, but in its common use, is still hard to compare to theoretical models. By using the two-point correlation technique in conjunction with large data sets, a wavelet power spectrum in wavenumber-space can be created. Dubbed the wavenumber wavelet power spectrum, this spectrum relates wavenumber to power in time. Further, this analysis technique more closely connects characterizations of experimentally observed fluctuations with other system parameters and theoretical predictions. In this article, we develop the wavenumber wavelet power spectrum using magnetic fluctuations caused by tearing instability driven magnetic reconnection in reproducible, high temperature laboratory plasmas. These dynamic magnetic fluctuations generated in reversed field pinch plasmas are broadband, ranging from the low frequency, 10's of kHz, up to the ion gyroradii frequencies, 100's of kHz. The dominant fluctuations have poloidal and toroidal mode numbers (m,n)=(1,6−10) and can grow to 2%–3% of the mean magnetic field. During these reconnection events, ions, and electrons are energized, magnetic fluctuation amplitudes increase, plasma flow is halted, and the toroidal magnetic flux increases, all on a semi-periodic basis. The newly developed spectrum provides better temporal resolution of spectrum characteristics to correlate with these particle energization phenomena.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dark Matter Velocity Distributions for Direct Detection: Astrophysical Uncertainties Are Smaller Than They Appear

The sensitivity of direct detection experiments depends on the phase-space distribution of dark matter near the Sun, which can be modeled theoretically using cosmological hydrodynamical simulations of Milky Way–like galaxies. However, capturing the halo-to-halo variation in the local dark matter speeds—a necessary step for quantifying the astrophysical uncertainties that feed into experimental results—requires a sufficiently large sample of simulated galaxies, which has been a challenge. In this Letter, we quantify this variation with nearly 100 Milky Way–like galaxies from the tng50 simulation, the largest sample to date at this resolution. Moreover, we introduce a novel phase-space scaling procedure that endows every system with a reference frame that accurately reproduces the local standard-of-rest speed of our Galaxy, providing a principled way of extrapolating the simulation results to real-world data. The ensemble of predicted speed distributions is well characterized by the standard halo model, a Maxwell-Boltzmann distribution truncated at the escape speed, though the individual distributions can deviate from it, especially at high speeds. The dark matter–nucleon cross section limits placed by these speed distributions vary by ∼ 60% about the median. This places the 1⁢𝜎 astrophysical uncertainty at or below the level of the systematic uncertainty of current ton-scale detectors, even down to the energy threshold. The predicted uncertainty remains unchanged when subselecting on those TNG 50 galaxies with merger histories similar to the Milky Way. Tabulated speed distributions, as well as Maxwell-Boltzmann fits, are provided for use in computing direct detection bounds or projecting sensitivities.

Milky Way↗

A high-throughput experimentation platform for data-driven discovery in electrochemistry

Automating electrochemical analyses combined with artificial intelligence is poised to accelerate discoveries in renewable energy sciences and technologies. This study presents an automated high-throughput electrochemical characterization (AHTech) platform as a cost-effective and versatile tool for rapidly assessing liquid analytes. The Python-controlled platform combines a liquid handling robot, potentiostat, and customizable microelectrode bundles for diverse, reproducible electrochemical measurements in microtiter plates, minimizing chemical consumption and manual effort. To showcase the capability of AHTech, we screened a library of 180 small molecules as electrolyte additives for aqueous zinc metal batteries, generating data for training machine learning models to predict Coulombic efficiencies. Key molecular features governing additive performance were elucidated using Shapley Additive exPlanations and Spearman’s correlation, pinpointing high-performance candidates like cis-4-hydroxy-d-proline, which achieved an average Coulombic efficiency of 99.52% over 200 cycles. The workflow established herein is highly adaptable, offering a powerful framework for accelerating the exploration and optimization of extensive chemical spaces across diverse energy storage and conversion fields.

Lin, Dian-Zhao [Johns Hopkins University, Baltimor↗

Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT

We previously described X-ray histotomography, a high-resolution, non-destructive form of X-ray microtomography (micro-CT) imaging customized for three-dimensional (3D), digital histology, allowing quantitative, volumetric tissue and organismal phenotyping (Ding et al., 2019). Here, we have combined micro-CT with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. The resulting images enabled whole-body, computational analyses of regional melanin content and morphology. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and further allowed direct quantitative comparisons of melanin content across wild-type and mutant samples, including subtle phenotypes not previously noticed. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, 3D computational phenomic analysis of a specific cell type at cellular resolution, with potential applications in other model organisms and melanocytic neoplasms. Advances such as this in whole-organism, high-resolution phenotyping provide superior context for studying the phenotypic effects of genetic, disease, and environmental variables.

59 BASIC BIOLOGICAL SCIENCES↗

On the Properties of Cosmological Ionization Fronts

We investigate the properties of cosmological ionization fronts during the epoch of reionization using the Cosmic Reionization on Computers simulations. By analyzing reionization timing maps, we characterize ionization front velocities and curvatures and their dependence on the density structure of the intergalactic medium (IGM). The velocity distribution of ionization fronts in the simulations indicates that while the barrier-crossing analytical model captures the overall shape in high-velocity regions, it fails to reproduce the low-velocity tail, highlighting the non-Gaussian nature of the IGM’s density field. Ionization front velocities are inversely correlated with local density, propagating faster in underdense regions and more slowly in overdense environments. Faster ionization fronts also lead to higher postionization temperatures, reaching a plateau at ∼2 × 10$^{4}$ K for velocities exceeding 3000 km s$^{−1}$. Examining curvature statistics further establishes a connection between ionization front structure and the normalized density contrast ν, with trends in overdense regions aligning well with barrier-crossing model predictions, while deviations appear in underdense environments due to model limitations. These results provide a detailed characterization of ionization front dynamics and their interaction with the underlying density field, bridging small-scale reionization physics with large-scale observables such as the 21 cm signal and the IGM’s thermal history.

79 ASTRONOMY AND ASTROPHYSICS↗

Automated scanning probe microscopy of combinatorial ferroelectric libraries: Gaussian-process-guided exploration and noise-aware experiment planning

Combinatorial materials libraries provide an efficient route for mapping composition–property relationships, but their broader impact depends on rapid, quantitative, and functionally relevant characterization. Scanning Probe Microscopy (SPM), including piezoresponse force microscopy (PFM), offers significant potential for quantitative, functionally relevant combi-library readouts. Here, we implement a fully automated SPM workflow for ferroelectric combinatorial libraries and benchmark Gaussian-process-based Bayesian optimization strategies for autonomous experiment planning. The workflow integrates automated probe motion, contact optimization, imaging, and dual amplitude resonance tracking-PFM spectroscopy, and uses scalarized spectroscopic observables to guide subsequent measurements. Stage motion, probe engagement, in-contact tuning, imaging, spectroscopy, and the choice of the next measurement location all proceed without human input. We demonstrate the approach on Sm-doped BiFeO 3 and Zn x Mg 1−x O libraries. By comparing vanilla Bayesian optimization with a measured-noise variant, we show that explicit treatment of local reproducibility can improve modeling of composition-dependent response when the measured variance is physically meaningful, but can also reduce robustness when variability is dominated by outliers or topographic artifacts. Furthermore, these results establish automated SPM as a bridge between combinatorial synthesis and quantitative functional characterization.

Liu, Yu [University of Tennessee, Knoxville, TN (U↗

Verification of Coupled Hydraulic Fracturing Simulators Using Laboratory-Scale Experiments

In this work, we aim to verify the predictions of the numerical simulators, which are used for designing field-scale hydraulic stimulation experiments. Although a strong theoretical understanding of this process has been gained over the past few decades, numerical predictions of fracture propagation in low-permeability rocks still remains a challenge. Against this background, we performed controlled laboratory-scale hydraulic fracturing experiments in granite samples, which not only provides high-quality experimental data but also a well-characterized experimental set-up. Using the experimental pressure responses and the final fracture sizes as benchmark, we compared the numerical predictions of two coupled hydraulic fracturing simulators—CSMP and GEOS. Both the simulators reproduced the experimental pressure behavior by implementing the physics of Linear Elastic Fracture Mechanics (LEFM) and lubrication theory within a reasonable degree of accuracy. The simulation results indicate that even in the very low-porosity (1–2 %) and low-permeability (10 -18 m 2 - 10 -19 m 2 ) crystalline rocks, which are usually the target of EGS, fluid-loss into the matrix and unsaturated flow impacts the formation breakdown pressure and the post-breakdown pressure trends. Therefore, underestimation of such parameters in numerical modeling can lead to significant underestimation of breakdown pressure. The simulation results also indicate the importance of implementing wellbore solvers for considering the effect of system compressibility and pressure drop due to friction in the injection line. The varying injection rate as a result of decompression at the instant of fracture initiation affects the fracture size, while the entry friction at the connection between the well and the initial notch may cause an increase in the measured breakdown pressure.

15 GEOTHERMAL ENERGY↗