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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,657 records · Page 92
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Robustness of the Stochastic Parameterization of Subgrid-Scale Wind Variability in Sea Surface Fluxes

Abstract High-resolution numerical models have been used to develop statistical models of the enhancement of sea surface fluxes resulting from spatial variability of sea surface wind. In particular, studies have shown that flux enhancement is not a deterministic function of the resolved state. Previous studies focused on single geographical areas or used a single high-resolution numerical model. This study extends the development of such statistical models by considering six different high-resolution models, four different geographical regions, and three different 10-day periods, allowing for a systematic investigation of the robustness of both the deterministic and stochastic parts of the data-driven parameterization. Results indicate that the deterministic part, based on regressing the unresolved normalized flux onto resolved-scale normalized flux and precipitation, is broadly robust across different models, regions, and time periods. The statistical features of the stochastic part of the model (spatial and temporal autocorrelation and parameters of a Gaussian process fit to the regression residual) are also found to be robust and not strongly sensitive to the underlying model, modeled geographical region, or time period studied. Best-fit Gaussian process parameters display robust spatial heterogeneity across models, indicating potential for improvements to the statistical model. These results illustrate the potential for the development of a generic, explicitly stochastic parameterization of sea surface flux enhancements dependent on wind variability.

Endo, Kota↗
DOE OSTI2023

An Interactive Spectral Analysis Tool for Chemical Identification and Quantification of Gas-Phase Species in Complex Spectra

A spectral analysis tool has been developed to interactively identify and quantify individual gas-phase species from complex infrared absorbance spectra obtained from laboratory or field data. The SpecQuant program has an intuitive graphical interface that accommodates both reference and experimental data with varying resolution and instrumental lineshape, as well as algorithms to readily align the wavenumber axis of a sample spectrum with the raster of a reference spectrum. Using a classical least squares model in conjunction with reference spectra such as those from the Pacific Northwest National Laboratory (PNNL) gas-phase infrared database or simulated spectra derived from the HITRAN line-by-line database, the mixing ratio of each identified species is determined along with its associated estimation error. After correcting the wavelength and intensity of the field data, SpecQuant displays the calculated mixing ratio versus the experimental data for each analyte along with the residual spectrum with any or all analyte fits subtracted for visual inspection of the fit and residuals. The software performance for multianalyte quantification was demonstrated using moderate resolution (0.5 cm –1 ) infrared spectra that were collected during the time-resolved infrared photolysis of methyl iodide.

Thompson, Christopher J.↗
DOE OSTI2021

Empirical Estimation of Shortest Route Length along U.S. Interstate Highways Based on Great Circle Distance

In this study, 98 regression models were specified for easily estimating shortest distances based on great circle distances along the U.S. interstate highways nationwide and for each of the continental 48 states. This allows transportation professionals to quickly generate distance, or even distance matrix, without expending significant efforts on complicated shortest path calculations. For simple usage by all professionals, all models are present in the simple linear regression form. Only one explanatory variable, the great circle distance, is considered to calculate the route distance. For each geographic scope (i.e., the national or one of the states), two different models were considered, with and without the intercept. Based on the adjusted R-squared, it was observed that models without intercepts generally have better fitness. Additionally, all these models generally have good fitness with the linear regression relationship between the great circle distance and route distance. At the state level, significant variations in the slope coefficients between the state-level models were also observed. Furthermore, a preliminary analysis of the effect of highway density on this variation was conducted.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2024

Exploration of Factors That Influence Willingness to Consider Pooled Rideshare

Ridesharing has become an increasingly prevalent form of transportation. Although transportation network companies such as Uber and Lyft initially started as a personal rideshare service where individuals ride alone or with people they know, rideshare services have been expanded to pooled rideshare—a dynamic rideshare system where an individual rides with passengers they do not know. Despite the growth in rideshare services worldwide, the use of pooled rideshare in the U.S.A. is relatively low compared to other forms of transportation. A national U.S. survey (N = 5385) was conducted to investigate reasons why individuals are willing or unwilling to consider pooled rideshare. Exploratory and confirmatory factor analyses were performed, where the exploratory factor analysis suggests five factors, specifically,service experience,time/cost,traffic/environment,privacy, andsafety. Model fit indices of the confirmatory factor analysis verified that these five factors can represent the factors behind riders’ willingness to consider pooled rideshare. Furthermore, a binomial logistic regression was conducted to explore how the five factors influence riders’ willingness to consider pooled rideshare. The three factors that influence riders’ willingness to consider pooled rideshare wereservice experience(B = 1.05),traffic/environment(B = .38), andtime/cost(B = .26), while a lack ofprivacy(B = −1.46) can be a deterrent for pooled rideshare.Safetyis important for those who are both willing and unwilling to consider the use of pooled rideshare. Understanding these factors is important for the future of pooled rideshare services in the U.S.A.

Engineering↗
DOE OSTI2025

Misclassification in Workers’ Telecommuting Frequency Choices Using a Generalized Extreme Value Model

Telecommuting frequency is a response variable collected in travel surveys and is, therefore, prone to errors leading to mismeasurements or misclassification. Misclassification of explanatory variables is a common risk when using statistical modeling techniques. We define “misclassification” as a response reported or recorded in the wrong category; for example, a variable is recorded as a 1 when it should be 0. Here, in this context, this study aims to develop a statistical model to analyze telecommuting data which accounts for potential misclassification errors by building on existing literature in econometrics. The empirical analysis was undertaken using the 2017 National Household Travel Survey (NHTS) and the general extreme value (GEV) models available in the literature. Specifically, the frequency of telecommuting days was analyzed using the negative binomial (NB) model recast as the multinomial logit (MNL) model. By nature—and consistent with other studies—NHTS data are prone to errors that can be classified as intentional or unintentional misinformation provided by the person being interviewed. Ignoring these errors while modeling telecommuting frequencies using standard discrete count models can result in biased parameter estimates. The misclassification parameter was calculated for both over-reporting and under-reporting scenarios. The misclassification errors can be as high as 14% over-reported and 10% under-reported, particularly for the neighboring values. Statistical fit comparison between the models shows that models that ignore misclassification have worse data fit and biased parameter estimates with significant policy implications.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2018

An Evaluation of Army Wellness Center Clients’ Health-Related Outcomes

Purpose: To examine whether Army community members participating in a best-practice based workplace health promotion program (WHPP) experience goal-moderated improvements in health-related outcomes. Design: Pretest/posttest outcome evaluation examining an autonomously participating client cohort over 1 year. Setting: Army Wellness Center facilities on 19 Army installations. Participants: Army community members sample (N = 5703), mostly Active Duty Soldiers (64%). Intervention: Assessment of health risks with feedback, health assessments, health education classes, and health coaching sessions conducted by health educators at a recommended frequency of once a month for 3 to 12 months. Measures: Initial and follow-up outcome assessments of body mass index (BMI), body fat, cardiorespiratory fitness, blood pressure, and perceived stress. Analysis: Mixed model linear regression testing for goal-moderated improvements in outcomes. Results: Clients experienced significant improvements in body fat (−2% change), perceived stress (−6% to −12% change), cardiorespiratory fitness (+6% change), and blood pressure (−1% change) regardless of health-related goal. Only clients with a weight loss goal experienced BMI improvement (−1% change). Follow-up outcome assessment rates ranged from 44% (N = 2509) for BMI to 6% (N = 342) for perceived stress. Conclusion: Army Wellness Center clients with at least 1 follow-up outcome assessment experienced improvements in military readiness correlates and chronic disease risk factors. Evaluation design and follow-up-related limitations notwithstanding results suggest that best practices in WHPPs can effectively serve a globally distributed military force.

Rivera, L. Omar↗
DOE OSTI2020

A phenomenological rate of injection model for predicting fuel injection with application to mixture formation in light-duty diesel engines

Fuel injection rate laws are one of the most important pieces of information needed when modeling engine combustion with computational fluid dynamics. In this study, a simple phenomenological model of a common-rail injector was developed and calibrated for the Bosch CRI2.2 platform. The model requires three tunable parameter fits, making it relatively easy to calibrate and suitable for injector modeling when high-fidelity information about the internal injector’s geometry and electrical circuit details are not available. Each injection pulse is modeled as a sequence of up to four stages: an injection needle mechanical opening transient, a full-lift viscous flow inertial transient, a Bernoulli steady-state stage, and a needle descent transient. Parameters for each stage are obtained as polynomial fits from measured injection rate properties. The model enforces total injected mass, and the intermediate stages are only introduced if the injection pulse duration is long enough. Experimental rates of injection from two separate campaigns on the same injector were used to calibrate the model. The model was first validated against measured injection rate laws featuring pilot injections, short partially premixed combustion pulses, and conventional diesel combustion injection strategies. Then, it was employed as an input to engine computational fluid dynamics simulations, which were run to simulate experiments of mixture formation in an optically accessible light-duty diesel engine. It was found that, though simple, this model is capable of predicting both pilot and main injection pulse mass flow rates well: the simulations yielded accurate predictions of in-cylinder equivalence ratio distributions from injection strategies for both partially premixed combustion and pilot injections. Also, once calibrated, the model produced appropriate results for a wide range of injected mass and rail pressure values. Finally, it was observed that usage of such a relatively simple model can be a good choice when high-fidelity injection rate input and highly detailed information of the injector’s geometry and operation are not available, particularly as noticeable discrepancies can be present also among different experimental campaigns on similar hardware.

42 ENGINEERING↗
DOE OSTI2021

Learning curves for drug response prediction in cancer cell lines

Motivated by the size and availability of cell line drug sensitivity data, researchers have been developing machine learning (ML) models for predicting drug response to advance cancer treatment. As drug sensitivity studies continue generating drug response data, a common question is whether the generalization performance of existing prediction models can be further improved with more training data. We utilize empirical learning curves for evaluating and comparing the data scaling properties of two neural networks (NNs) and two gradient boosting decision tree (GBDT) models trained on four cell line drug screening datasets. The learning curves are accurately fitted to a power law model, providing a framework for assessing the data scaling behavior of these models. The curves demonstrate that no single model dominates in terms of prediction performance across all datasets and training sizes, thus suggesting that the actual shape of these curves depends on the unique pair of an ML model and a dataset. The multi-input NN (mNN), in which gene expressions of cancer cells and molecular drug descriptors are input into separate subnetworks, outperforms a single-input NN (sNN), where the cell and drug features are concatenated for the input layer. In contrast, a GBDT with hyperparameter tuning exhibits superior performance as compared with both NNs at the lower range of training set sizes for two of the tested datasets, whereas the mNN consistently performs better at the higher range of training sizes. Moreover, the trajectory of the curves suggests that increasing the sample size is expected to further improve prediction scores of both NNs. These observations demonstrate the benefit of using learning curves to evaluate prediction models, providing a broader perspective on the overall data scaling characteristics. A fitted power law learning curve provides a forward-looking metric for analyzing prediction performance and can serve as a co-design tool to guide experimental biologists and computational scientists in the design of future experiments in prospective research studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

tRNA functional signatures classify plastids as late-branching cyanobacteria

Eukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data. Using Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies (“phyloclassifies”) cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data. Phylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

Zymomonas mobilis is a natural ethanologen being developed and deployed as an industrial biofuel producer. To date, eight Z. mobilis strains have been completely sequenced and found to contain 2-8 native plasmids. However, systematic verification of predicted Z. mobilis plasmid genes and their contribution to cell fitness has not been hitherto addressed. Moreover, the precise number and identities of plasmids in Z. mobilis model strain ZM4 have been unclear. The lack of functional information about plasmid genes in ZM4 impedes ongoing studies for this model biofuel-producing strain. In this study, we determined the complete chromosome and plasmid sequences of ZM4 and its engineered xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4 chromosome sequences, the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well as a 2400-bp insertion. Four plasmids were identified in all three strains, with 150 plasmid genes predicted in strain ZM4 and 2032, and 153 plasmid genes predicted in strain 8b due to the insertion of heterologous DNA for expanded substrate utilization. Plasmid genes were then annotated using Blast2GO, InterProScan, and systems biology data analyses, and most genes were found to have apparent orthologs in other organisms or identifiable conserved domains. To verify plasmid gene prediction, RNA-Seq was used to map transcripts and also compare relative gene expression under various growth conditions, including anaerobic and aerobic conditions, or growth in different concentrations of biomass hydrolysates. Overall, plasmid genes were more responsive to varying hydrolysate concentrations than to oxygen availability. Additionally, our results indicated that although all plasmids were present in low copy number (about 1-2 per cell), the copy number of some plasmids varied under specific growth conditions or due to heterologous gene insertion. The complete genome of ZM4 and two xylose-utilizing derivatives is reported in this study, with an emphasis on identifying and characterizing plasmid genes. Furthermore, plasmid gene annotation, validation, expression levels at growth conditions of interest, and contribution to host fitness are reported for the first time.

09 BIOMASS FUELS↗
DOE OSTI2019

A two-phase substrate model for enzymatic hydrolysis of lignocellulose: application to batch and continuous reactors

Abstract Background Enzymatic hydrolysis continues to have a significant projected production cost for the biological conversion of biomass to fuels and chemicals, motivating research into improved enzyme and reactor technologies in order to reduce enzyme usage and equipment costs. However, technology development is stymied by a lack of accurate and computationally accessible enzymatic-hydrolysis reaction models. Enzymatic deconstruction of cellulosic materials is an exceedingly complex physico-chemical process. Models which elucidate specific mechanisms of deconstruction are often too computationally intensive to be accessible in process or multi-physics simulations, and empirical models are often too inflexible to be effectively applied outside of their batch contexts. In this paper, we employ a phenomenological modeling approach to represent rate slowdown due to substrate structure (implemented as two substrate phases) and feedback inhibition, and apply the model to a continuous reactor system. Results A phenomenological model was developed in order to predict glucose and solids concentrations in batch and continuous enzymatic-hydrolysis reactors from which liquor is continuously removed by ultrafiltration. A series of batch experiments were performed, varying initial conditions (solids, enzyme, and sugar concentrations), and best-fit model parameters were determined using constrained nonlinear least-squares methods. The model achieved a good fit for overall sugar yield and insoluble solids concentration, as well as for the reduced rate of sugar production over time. Additionally, without refitting model coefficients, good quantitative agreement was observed between results from continuous enzymatic-hydrolysis experiments and model predictions. Finally, the sensitivity of the model to its parameters is explored and discussed. Conclusions Although the phenomena represented by the model correspond to behaviors that emerge from clusters of mechanisms, and hence a set of model coefficients are unique to the substrate and the enzyme system, the model is efficient to solve and may be applied to novel reactor schema and implemented in computational fluid dynamics (CFD) simulations. Hence, this modeling approach finds the right balance between model complexity and computational efficiency. These capabilities have broad application to reactor design, scale-up, and process optimization.

09 BIOMASS FUELS↗
DOE OSTI2025

The impact of kidney function on Alzheimer’s disease blood biomarkers: implications for predicting amyloid-β positivity

Impaired kidney function has a potential confounding effect on blood biomarker levels, including biomarkers for Alzheimer’s disease (AD). Given the imminent use of certain blood biomarkers in the routine diagnostic work-up of patients with suspected AD, knowledge on the potential impact of comorbidities on the utility of blood biomarkers is important. We aimed to evaluate the association between kidney function, assessed through estimated glomerular filtration rate (eGFR) calculated from plasma creatinine and AD blood biomarkers, as well as their influence over predicting Aβ-positivity. We included 242 participants from the Translational Biomarkers in Aging and Dementia (TRIAD) cohort, comprising cognitively unimpaired individuals (CU; n = 124), mild cognitive impairment (MCI; n = 58), AD dementia (n = 34), and non-AD dementia (n = 26) patients all characterized by [ 18 F] AZD-4694. Plasma samples were analyzed for Aβ42, Aβ40, glial fibrillary acidic protein (GFAP), neurofilament light chain (NfL), tau phosphorylated at threonine 181 (p-tau181), 217 (p-tau217), 231 (p-tau231) and N-terminal containing tau fragments (NTA-tau) using Simoa technology. Kidney function was assessed by eGFR in mL/min/1.73 m 2 , based on plasma creatinine levels, age, and sex. Participants were also stratified according to their eGFR-indexed stages of chronic kidney disease (CKD). We evaluated the association between eGFR and blood biomarker levels with linear models and assessed whether eGFR provided added predictive value to determine Aβ-positivity with logistic regression models. Biomarker concentrations were highest in individuals with CKD stage 3, followed by stages 2 and 1, but differences were only significant for NfL, Aβ42, and Aβ40 (not Aβ42/Aβ40). All investigated biomarkers showed significant associations with eGFR except plasma NTA-tau, with stronger relationships observed for Aβ40 and NfL. However, after adjusting for either age, sex or Aβ-PET SUVr, the association with eGFR was no longer significant for all biomarkers except Aβ40, Aβ42, NfL, and GFAP. When evaluating whether accounting for kidney function could lead to improved prediction of Aβ-positivity, we observed no improvements in model fit (Akaike Information Criterion, AIC) or in discriminative performance (AUC) by adding eGFR to a base model including each plasma biomarker, age, and sex. While covariates like age and sex improved model fit, eGFR contributed minimally, and there were no significant differences in clinical discrimination based on AUC values. We found that kidney function seems to be associated with AD blood biomarker concentrations. However, these associations did not remain significant after adjusting for age and sex, except for Aβ40, Aβ42, NfL, and GFAP. While covariates such as age and sex improved prediction of Aβ-positivity, including eGFR in the models did not lead to improved prediction for any biomarker. Our findings indicate that renal function, within the normal to mild impairment range, does not seem to have a clinically relevant impact when using highly accurate blood biomarkers, such as p-tau217, in a biomarker-supported diagnosis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

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↗
DOE OSTI2019

Fast approximate STEM image simulations from a machine learning model

Abstract Accurate quantum mechanical scanning transmission electron microscopy image simulation methods such as the multislice method require computation times that are too large to use in applications in high-resolution materials imaging that require very large numbers of simulated images. However, higher-speed simulation methods based on linear imaging models, such as the convolution method, are often not accurate enough for use in these applications. We present a method that generates an image from the convolution of an object function and the probe intensity, and then uses a multivariate polynomial fit to a dataset of corresponding multislice and convolution images to correct it. We develop and validate this method using simulated images of Pt and Pt–Mo nanoparticles and find that for these systems, once the polynomial is fit, the method runs about six orders of magnitude faster than parallelized CPU implementations of the multislice method while achieving a 1 − R 2 error of 0.010–0.015 and root-mean-square error/standard deviation of dataset being predicted of about 0.1 when compared to full multislice simulations.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

An adaptable technique for comparative image assessment: Application to crosswell electromagnetic survey design for fluid monitoring

Reservoir integrity stewardship accompanying carbon capture and sequestration considers fluid extraction and reinjection as a risk-mitigating method against overpressuring that could lead to caprock damage and ensuing [Formula: see text] leakage. Crosswell electromagnetics offers a technically viable monitoring method with the spatial volume coverage necessary for reservoir-encompassing pressure management. However, a certain logistic dilemma for deep gas sequestration into saline and thus electrically conductive aquifers is that crosswell magnetic-field measurements underperform in the imaging of more resistive plume bodies, further exacerbated when vertical arrays intersect, as opposed to surround, plumes. Furthermore, comparative synthetic-data plume imaging of such scenarios rates the information content of magnetic-field versus electric-field 3D crosswell layouts for reservoir and infrastructure conditions of a representative pilot site in a coastal area in Florida. The image quality of the resulting plume replications can be ranked numerically through a newly proposed semblance qualifier, appraising the model goodness of fit to a given reference. In contrast to common least-squares measures for goodness of fit, the semblance formulation uses classifying logistic function types, thus enabling a better distinction of predefined anomaly features.

58 GEOSCIENCES↗
DOE OSTI2022

Early arrival waveform inversion using data uncertainties and matching filters with application to near-surface seismic refraction data

We develop an early arrival waveform inversion (EAWI) technique for high-resolution near-surface velocity estimation by iteratively updating the P-wave velocity model to minimize the difference between the observed and calculated seismic refraction data. Traditional EAWI uses a least-squares penalty function and an acoustic forward-modeling engine. Conventional least-squares error is sensitive to data with low signal-to-noise ratio (S/N) and iterations of EAWI stop at a local-minimum data misfit or at the preassigned maximum number of iterations. These stopping criteria can result in overfitting the data. In addition, fitting the elastic field data with an acoustic modeling engine can introduce artifacts in velocity estimation, especially in land data with significant elastic effects. To overcome these challenges, we develop a robust EAWI (REAWI) method by (1) incorporating the data uncertainties into the penalty function and (2) mitigating the elastic effects using a matching filter workflow. The data uncertainties are estimated from waveform reciprocal errors. When full-waveform reciprocity is not available, trace interpolation is applied. The proposed method prevents closely fitting data with low S/N, avoids overall overfitting by stopping the iterations when a normalized chi-square ([Formula: see text]) waveform misfit of one is achieved, and is less affected by elastic effects. Numerical examples and application to near-surface refraction data at a groundwater contamination site suggest that the final REAWI models are more accurate than the corresponding EAWI models, at the same level of misfit. This is the first known application of a matching filter workflow to real land data. The final REAWI models satisfy an appropriate misfit between the real data and predicted elastic P-wave data, making this approach in this respect equivalent to elastic waveform inversion. We also develop a method to analyze model constraint by examining the energy of the wavefield Fréchet derivative thereby avoiding the influence of the data residuals in traditional Fréchet kernels.

Geochemistry & Geophysics↗
DOE OSTI2026

Data for A Generalized Platform for Artificial Intelligence-powered Autonomous Protein Engineering

Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-foldimprovement in substrate preference and 16-fold improvement in ethyl-transferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.

AI/ML↗
DOE OSTI2026

Data for "Examining Organic Acid Production Potential and Growth-Coupled Strategies in Issatchenkia orientalis Using Constraint-Based Modeling"

Growth-coupling product formation can facilitate strain stability by aligning industrial objectives with biological fitness. Organic acids make up many building block chemicals that can be produced from sugars obtainable from renewable biomass. Issatchenkia orientalis is a yeast strain tolerant to acidic conditions and is thus a promising host for industrial production of organic acids. Here, we use constraint-based methods to assess the potential of computationally designing growth-coupled production strains for I. orientalis that produce 22 different organic acids under aerobic or microaerobic conditions. We explore native and engineered pathways using glucose or xylose as the carbon substrates as proxy constituents of hydrolyzed biomass. We identified growth-coupled production strategies for 37 of the substrate-product pairs, with 15 pairs achieving production for any growth rate. We systematically assess the strain design solutions and categorize the underlying principles involved.

Bioproducts↗