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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Generalized parton distributions through universal moment parameterization: zero skewness case

We present a global analysis program for the generalized parton distributions (GPDs) based on conformal moment expansion. We apply the strategy of universal moment parameterization to fit both the collinear parton distribution functions (PDFs) from phenomenology and generalized form factors from lattice calculations, and show that the parameterization is flexible enough to accommodate these constraints. In addition, we can also fit direct lattice calculations of GPDs from large-momentum effective theory. In this work we focus on the analysis of t-dependent PDFs which correspond to GPDs in the ξ → 0 limit. The strategy also applies to the ξ ≠ 0 region with extra parameters, and therefore can be fitted to experimental observables in the future. With a demonstrative example of fitted GPDs, we exhibit the quark transverse angular momentum densities of the proton as well as the impact parameter space distributions of quarks in both unpolarized and transversely polarized protons.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Temporal covariance structure of multi-spectral phenotypes and their predictive ability for end-of-season traits in maize

Vegetation indices (VIs) derived from multi-spectral imaging (MSI) platforms can be used to study properties of crop canopy, providing non-destructive phenotypes that could be used to better understand growth curves throughout the growing season. To investigate the amount of variation present in several VIs and their relationship with important end-of-season traits, genetic and residual (co)variances for VIs, grain yield and moisture were estimated using data collected from maize hybrid trials. The VIs considered were Normalized Difference Vegetation Index (NDVI), Green NDVI, Red Edge NDVI, Soil-Adjusted Vegetation Index, Enhanced Vegetation Index and simple Ratio of Near Infrared to Red (Red) reflectance. Genetic correlations of VIs with grain yield and moisture were used to fit multi-trait models for prediction of end-of-season traits and evaluated using within site/year cross-validation. To explore alternatives to fitting multiple phenotypes from MSI, random regression models with linear splines were fit using data collected in 2016 and 2017. Heritability estimates ranging from (0.10 to 0.82) were observed, indicating that there exists considerable amount of genetic variation in these VIs. Furthermore, strong genetic and residual correlations of the VIs, NDVI and NDRE, with grain yield and moisture were found. Considerable increases in prediction accuracy were observed from the multi-trait model when using NDVI and NDRE as a secondary trait. Finally, random regression with a linear spline function shows potential to be used as an alternative to mixed models to fit VIs from multiple time points.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mapping Incidence and Prevalence Peak Data for SIR Modeling Applications

Infectious disease modeling and forecasting have played a key role in helping assess and respond to epidemics and pandemics. Recent work has leveraged data on disease peak infection and peak hospital incidence to fit compartmental models for the purpose of forecasting and describing the dynamics of a disease outbreak. Incorporating these data can greatly stabilize a compartmental model fit on early observations, where slight perturbations in the data may lead to model fits that forecast wildly unrealistic peak infection. We introduce a new method for incorporating historic data on the value and time of peak incidence of hospitalization into the fit for a Susceptible-Infectious-Recovered (SIR) model by formulating the relationship between an SIR model’s starting parameters and peak incidence as a system of two equations that can be solved computationally. We demonstrate how to calculate SIR parameter estimates – which describe disease dynamics such as transmission and recovery rates – using this method, and determine that there is a noticeable loss in accuracy whenever prevalence data is misspecified as incidence data. To exhibit the modeling potential, we update the Dirichlet-Beta State Space modeling framework to use hospital incidence data, as this framework was previously formulated to incorporate only data on total infections. This approach is assessed for practicality in terms of accuracy and speed of computation via simulation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Modification of conventional peak shapes to accurately represent spectral asymmetry: High-Resolution X-ray photoelectron spectra of [C 4 C 1 Pyrr][NTf 2 ] and [C 8 C 1 Im][NTf 2 ] ionic liquids

X-ray photoelectron spectroscopy (XPS) is one of the most widely used techniques for surface characterization. Analysis of XPS data is challenging and requires the analyst to fit the data with synthetic line shapes to reach physically meaningful interpretations. Experimental spectral envelopes, however, are complex and display asymmetric features that are often ignored or attributed to additional chemical components. The high-resolution XPS spectra of [C 4 C 1 Pyrr][NTf 2 ] and [C 8 C 1 Im][NTf 2 ] all exhibit a degree of asymmetry which is systematically observed at the higher binding energy side of photoemission envelopes. Here, we present the development of a refined fitting procedure for XPS spectra of these ionic liquid-based systems which include (a) Shirley background offset necessary to account for the insulator-like region and (b) spectral asymmetry in C 1s and N 1s regions. Further, Shirley and trapezoid components are applied to compensate for inelastic scattering taking place during electron transitions as high as 7.8 eV above the start of the fitting region in C 1s high-resolution spectrum. To demonstrate the fitness of this model, we present an analysis of a 2:1 mixture of [C 4 C 1 Pyrr][NTf 2 ]: [C 8 C 1 Im][NTf 2 ].

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Identification of crystal plasticity model parameters by multi-objective optimization integrating microstructural evolution and mechanical data

Crystal plasticity models evolve a polycrystalline yield surface using meso-scale descriptions of deformation mechanisms. The activation of deformation mechanisms is governed by crystallography and a set of model parameters, which are typically calibrated through the fitting of mechanical data such as stress–strain curves and elastic lattice strains. Microstructural data such as phase fractions and texture evolution are used for verifying crystal plasticity parameters. In this study, we use a multi-objective genetic algorithm to identify hardening parameters from flow stress curves with an option to incorporate texture into the optimization approach. Robust, generalized objective functions are developed and used to identify sets of parameters pertaining to dislocation density-based hardening laws in visco-plastic and elasto-plastic self-consistent (VPSC and EPSC) homogenization models. First, the parameters are identified for pure Nb directly from texture using an objective function based on generalized spherical harmonics. Since texture evolution is driven by the relative contribution of active slip systems, the parameters governing the evolution of slip resistance ratios can be recovered from fitting discrete textures at a series of strains. Next, a comprehensive set of load reversal data for dual phase (DP) 780 steel is used to fit a hardening law and a back-stress law in EPSC. Finally, parameters pertaining to a complex hardening law for the evolution of slip and twinning in pure α-Ti are identified. Remarkably, using texture as an objective in combination with stress–strain objectives constrains the model of Ti to fully reproduce not only stress–strain and texture evolution but also hierarchical twinning measurements as a function of initial grain size and texture. Furthermore, given an appropriate model fit to representative experimental texture evolution, underlying twin volume fractions contributing to texture evolution can be predicted.

42 ENGINEERING↗
DOE OSTI2020

Tight-binding study of beryllium

In this work, we have applied the Naval Research Laboratory Tight-binding (NRL-TB) Method to the hcp alkaline-earth metal Beryllium. This approach consists of fitting to energy band and total energy data generated by the Linearized Augmented Plane Wave (LAPW) for the fcc, bcc, sc, and hcp structures as a function of volume. First, we found that using the Generalized Gradient Approximation (GGA) for the input data secures a better agreement to experimental volumes than the LDA. Second, we found that including small volumes to the fit is needed to get TB parameters that are transferable enough to successfully predict the energies of structures that were not fitted, and to perform molecular dynamics (MD) simulations. The non-orthogonal Hamiltonian obtained, is successful in correctly predicting the hcp lattice as the ground state of Be and finding eight other structures, that were not fitted to LAPW, positioned at higher energies. In addition, the NRL-TB produces accurate energy bands, densities of states, elastic constants, the Bain path and several quantities derived from MD simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Joint estimation of biogeochemical model parameters from multiple experiments: A bayesian approach applied to mercury methylation

Here, to characterize complex biogeochemical systems, results from multiple experiments, where each targets a specific subprocess, are commonly combined. The resulting datasets are interpreted through the calibration of biogeochemical models for process inference and predictions. Commonly used calibration approaches of fitting datasets from individual experiments to subprocess models one at a time is prone to missing information shared between datasets and incomplete uncertainty propagation. We propose a Bayesian joint-fitting scheme addressing the above-mentioned concerns by jointly fitting all the available datasets, thus calibrating the entire biogeochemical model in one go using Markov Chain Monte Carlo (MCMC). The identification of null spaces in the parameter distributions from MCMC guided the simplification of certain subprocess models. For example, fast kinetic sorption was replaced by equilibrium sorption, and Monod demethylation was replaced by first-order demethylation. Joint fitting of datasets resulted in complete uncertainty propagation with parameter estimates informed by all available data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Thermalization of nuclear matter in heavy-ion collisions at Fermi energies

We analyze the time evolution of the kinetic properties of nuclear matter produced in heavy-ion collisions at Fermi energies. The collision system is simulated using Constrained Molecular Dynamics (CoMD) transport calculations whose output is the isospin, position, and momentum of the nucleons. Focusing on central 35 A·MeV 40 Ca+ 40 Ca collisions we utilize this information to extract localized momentum distributions in volume elements of 8 fm 3 and time steps of 5 fm/$c$. We then parameterize the single-particle momentum distributions with thermally motivated fit functions in the local rest frame of each cell. While the transverse-momentum distributions are well reproduced by thermal ones, the longitudinal ones carry a marked imprint of the initial nuclear motion which we capture by introducing a centroid motion into our fit functions. In particular, we find that Fermi distributions yield significantly better fits than Boltzmann ones, a consequence of the Pauli blocking implemented in CoMD. From the fits we extract the time dependence of the thermodynamic and collective properties of the excited nuclear medium. We find that the transverse temperature gradually rises to about 6 MeV, which is accompanied by a dissipation of the initial centroid motion of the incoming nuclei which vanishes at about 100 fm/c after initial impact. In conclusion, we are therefore able to track the transition of beam energy into random kinetic energy for nucleons, suggesting a three-dimensional equilibration of energy in the late stages of the collision.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Performance characterization of nanofiltration, reverse osmosis, and ion exchange technologies for acetic acid separation

A major obstacle to widespread implementation of bio-based fuels and chemicals is the lack of efficient and costeffective separation methods. To purify acetic acid produced by biochemical conversion of biomass via anaerobic digestion, this work employs two commonly used separation technologies: (1) ion-exchange (IX) resin and (2) pressure-driven membranes. This study tested five commercially available strong- and weak-base anion-exchange resins and five commercially available nanofiltration (NF) and reverse osmosis (RO) membranes. The pH of the feed solution significantly affected adsorption capacity. At pH 6.3, a strong-base IX resin (IRN-78) performed best (95.1% acetate removal). With strong-base IX resins, the Langmuir isotherm model fit well, whereas for weak-base IX resins, the Freundlich isotherm provided a better fit. A pseudo-second-order kinetic model fit well for both IRN-78 and IRA-67. Regarding membrane separation, RO (BW30XFR membrane) achieved the highest rejection (98.6% acetate rejection), whereas an NF membrane (NF*) achieved the best combination of permeate flux (105 L/(h∙m 2 )) and rejection (83.1% acetate rejection). For membrane performance, the experimental data were fit using the solution diffusion model. Increased pH in the feed solution lowered permeate flux but increased acetic acid rejection. Finally, then the acetic acid concentration in the feed solution increased, both permeate flux and acetic acid rejection decreased for membrane NF*.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

LASSO for CALPHAD Model Selection Enables Data-Efficient Thermodynamic Modeling: An Application in Thermochemical Hydrogen Production Materials

Phenomenological CALPHAD (CALculation of PHAse Diagrams) models, widely used for multicomponent materials, often contain a considerable number of parameters and require fitting using data from a relatively small number of experimental measurements or theoretical calculations. Sometimes these parameters are introduced for the purpose of improving model fits but without clear physical justification, which leads to overparametrized models with poor generalization performance. Automated approaches for optimal model selection based on the available data therefore become critical. Here, in this work, a least absolute shrinkage and selection operator (LASSO)-based approach is developed for model selection by leveraging the linearity of the CALPHAD model with respect to its parameters to convert the model selection and fitting to a LASSO minimization problem. We demonstrate its utility for thermodynamic modeling of thermochemical hydrogen (TCH) production materials using lanthanum strontium manganite (LSM) as an example. Various TCH-relevant properties, including oxygen stoichiometry as a function of oxygen partial pressure, enthalpy of reduction, and entropy of reduction, are successfully predicted with reasonable accuracy using a minimal set of model parameters. Importantly, the model selection and fitting involve minimal human decision; it can therefore be applied to high-throughput DFT defect calculations and yield efficient workflows for TCH material modeling and optimization.

CALPHAD↗
DOE OSTI2022

evSeq: Cost-Effective Amplicon Sequencing of Every Variant in a Protein Library

Widespread availability of protein sequence-fitness data would revolutionize both our biochemical understanding of proteins and our ability to engineer them. Unfortunately, even though thousands of protein variants are generated and evaluated for fitness during a typical protein engineering campaign, most are never sequenced, leaving a wealth of potential sequence-fitness information untapped. Primarily, this is because sequencing is unnecessary for many protein engineering strategies; the added cost and effort of sequencing is thus unjustified. It also results from the fact that, even though many lower cost sequencing strategies have been developed, they often require at least some sequencing or computational resources, both of which can be barriers to access. In this work, we present every variant sequencing (evSeq), a method and collection of tools/standardized components for sequencing a variable region within every variant gene produced during a protein engineering campaign at a cost of cents per variant. evSeq was designed to democratize low-cost sequencing for protein engineers and, indeed, anyone interested in engineering biological systems. Execution of its wet-lab component is simple, requires no sequencing experience to perform, relies only on resources and services typically available to biology labs, and slots neatly into existing protein engineering workflows. Analysis of evSeq data is likewise made simple by its accompanying software (found at github.com/fhalab/evSeq, documentation at fhalab.github.io/evSeq), which can be run on a personal laptop and was designed to be accessible to users with no computational experience. Here, low-cost and easy to use, evSeq makes collection of extensive protein variant sequence-fitness data practical.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Systematic Assessment of Retrieval Methods for Canopy Far-Red Solar-Induced Chlorophyll Fluorescence Using High-Frequency Automated Field Spectroscopy

Remote sensing of solar-induced chlorophyll fluorescence (SIF) offers potential to infer photosynthesis across scales and biomes. Many retrieval methods have been developed to estimate top-of-canopy SIF using ground-based spectroscopy. However, inconsistencies among methods may confound interpretation of SIF dynamics, eco-physiological/environmental drivers, and its relationship with photosynthesis. Using high temporal- and spectral resolution ground-based spectroscopy, we aimed to (1) evaluate performance of SIF retrieval methods under diverse sky conditions using continuous field measurements; (2) assess method sensitivity to fluctuating light, reflectance, and fluorescence emission spectra; and (3) inform users for optimal ground-based SIF retrieval. Analysis included field measurements from bi-hemispherical and hemispherical-conical systems and synthetic upwelling radiance constructed from measured downwelling radiance, simulated reflectance, and simulated fluorescence for benchmarking. Fraunhofer-based differential optical absorption spectroscopy (DOAS) and singular vector decomposition (SVD) retrievals exhibit convergent SIF-PAR relationships and diurnal consistency across different sky conditions, while O2A-based spectral fitting method (SFM), SVD, and modified Fraunhofer line discrimination (3FLD) exhibit divergent SIF-PAR relationships across sky conditions. We find that such behavior holds across system configurations, though hemispherical-conical systems diverge less across sky conditions. O 2 A retrieval accuracy, influenced by atmospheric distortion, improves with a narrower fitting window and when training SVD with temporally local spectra. This may impact SIF-photosynthesis relationships interpreted by previous studies using O 2 A-based retrievals with standard (759–767.76 nm) fitting windows. Fraunhofer-based retrievals resist atmospheric impacts but are noisier and more sensitive to assumed SIF spectral shape than O 2 A-based retrievals. We recommend SVD or SFM using reduced fitting window (759.5–761.5 nm) for robust far-red SIF retrievals across sky conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Quantifying the local adaptive landscape of a nascent bacterial community

Abstract The fitness effects of all possible mutations available to an organism largely shape the dynamics of evolutionary adaptation. Yet, whether and how this adaptive landscape changes over evolutionary times, especially upon ecological diversification and changes in community composition, remains poorly understood. We sought to fill this gap by analyzing a stable community of two closely related ecotypes (“L” and “S”) shortly after they emerged within the E. coli Long-Term Evolution Experiment (LTEE). We engineered genome-wide barcoded transposon libraries to measure the invasion fitness effects of all possible gene knockouts in the coexisting strains as well as their ancestor, for many different, ecologically relevant conditions. We find consistent statistical patterns of fitness effect variation across both genetic background and community composition, despite the idiosyncratic behavior of individual knockouts. Additionally, fitness effects are correlated with evolutionary outcomes for a number of conditions, possibly revealing shifting patterns of adaptation. Together, our results reveal how ecological and epistatic effects combine to shape the adaptive landscape in a nascent ecological community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Extracting structural motifs from pair distribution function data of nanostructures using explainable machine learning

Characterization of material structure with X-ray or neutron scattering using e.g. Pair Distribution Function (PDF) analysis most often rely on refining a structure model against an experimental dataset. However, identifying a suitable model is often a bottleneck. Recently, automated approaches have made it possible to test thousands of models for each dataset, but these methods are computationally expensive and analysing the output, i.e. extracting structural information from the resulting fits in a meaningful way, is challenging. Our Machine Learning based Motif Extractor (ML-MotEx) trains an ML algorithm on thousands of fits, and uses SHAP (SHapley Additive exPlanation) values to identify which model features are important for the fit quality. We use the method for 4 different chemical systems, including disordered nanomaterials and clusters. ML-MotEx opens for a type of modelling where each feature in a model is assigned an importance value for the fit quality based on explainable ML.

36 MATERIALS SCIENCE↗
DOE OSTI2025

CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d

Bacteriophages constitute one of the largest reservoirs of genes of unknown function in the biosphere. Even in well-characterized phages, the functions of most genes remain unknown. Experimental approaches to study phage gene fitness and function at genome scale are lacking, partly because phages subvert many modern functional genomics tools. Here we leverage RNA-targeting dCas13d to selectively interfere with protein translation and to measure phage gene fitness at a transcriptome-wide scale. We find CRISPR Interference through Antisense RNA-Targeting (CRISPRi-ART) to be effective across phage phylogeny, from model ssRNA, ssDNA and dsDNA phages to nucleus-forming jumbo phages. Using CRISPRi-ART, we determine a conserved role of diverse rII homologues in subverting phage Lambda RexAB-mediated immunity to superinfection and identify genes critical for phage fitness. CRISPRi-ART establishes a broad-spectrum phage functional genomics platform, revealing more than 90 previously unknown genes important for phage fitness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Potentiating antibiotic efficacy via perturbation of non-essential gene expression

Proliferation of multidrug-resistant (MDR) bacteria poses a threat to human health, requiring new strategies. Here we propose using fitness neutral gene expression perturbations to potentiate antibiotics. We systematically explored 270 gene knockout-antibiotic combinations in Escherichia coli, identifying 90 synergistic interactions. Identified gene targets were subsequently tested for antibiotic synergy on the transcriptomic level via multiplexed CRISPR-dCas9 and showed successful sensitization of E. coli without a separate fitness cost. These fitness neutral gene perturbations worked as co-therapies in reducing a Salmonella enterica intracellular infection in HeLa. Finally, these results informed the design of four antisense peptide nucleic acid (PNA) co-therapies, csgD, fnr, recA and acrA, against four MDR, clinically isolated bacteria. PNA combined with sub-minimal inhibitory concentrations of trimethoprim against two isolates of Klebsiella pneumoniae and E. coli showed three cases of re-sensitization with minimal fitness impacts. Our results highlight a promising approach for extending the utility of current antibiotics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Tracing the outflow kinematics in Type 2 active galactic nuclei

Here, we used a sample of 577 spectra of active galactic nuclei Type 1.8-2 (z < 0.25) taken from the Sloan Digital Sky Survey to trace the influence of the outflow kinematics on the profiles of different emission lines (Hβ, [O III], Hα, [N II], [S II]). All considered lines were fitted with two Gaussian components: one that fits the core of the line, and another that fits the wings. We provide a procedure for decomposition of the Hα+[N II] wavelength band for spectra where these lines overlap. The influence of the gravitational and non-gravitational kinematics on the line components is investigated by comparing the dispersions of the line components with stellar velocity dispersion. We find that wing components of all the considered emission lines have pure non-gravitational kinematics. The core components are consistent with gravitational kinematics for the Hα, [N II], and [S II] lines, while in the [O III] there is evidence for contribution from non-gravitational kinematics. We adopted the wing components as a proxy for the outflow contribution and investigated the outflow kinematics by analysing the correlations between the widths and shifts of the wing components of different lines. For this purpose, we used the subsets in which wing components are detected in both compared lines, and can be fitted independently. We find strong correlations between wing component shifts, as well as between wing component widths of all considered lines, with the exception of the Hβ wing component width. These correlations indicate that outflow dynamics systemically affect all emission lines in the spectrum. However, it reflects with a different strength in their profiles, which is observed as different widths of the wing components. This is investigated by comparison of the mean widths of the wing components in subsets where wing components are present in all lines. The strongest outflow signature is observed in the [O III] lines, which have the broadest wing components; weaker outflow signatures are found in Hα and [N II], and the weakest is found for [S II]. These results imply that the considered lines arise in different parts of an outflowing region.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Star formation rate and stellar mass calibrations based on infrared photometry and their dependence on stellar population age and extinction

The stellar mass (M $\star$ ) and the star formation rate (SFR) are among the most important features that characterize galaxies. Measuring these fundamental properties accurately is critical for understanding the present state of galaxies, their history, and future evolution. Infrared (IR) photometry is widely used to measure the M $\star$ and SFR of galaxies because the near-IR traces the continuum emission of the majority of their stellar populations (SPs), and the mid/far-IR traces the dust emission powered by star-forming activity. This work explores the dependence of the IR emission of galaxies on their extinction, and the age of their SPs. It aims to provide accurate and precise IR-photometry SFR and M $\star$ calibrations that account for SP age and extinction while providing quantification of their scatter. We used the CIGALE spectral energy distribution (SED) fitting code to create model SEDs of galaxies with a wide range of star formation histories, dust content, and interstellar medium properties. We fit the relations between M $\star$ and SFR with IR and optical photometry of the model-galaxy SEDs with the Markov chain Monte Carlo (MCMC) method. As an independent confirmation of the MCMC fitting method, we performed a machine-learning random forest (RF) analysis on the same data set. The RF model yields similar results to the MCMC fits, thus validating the latter. This work provides calibrations for the SFR using a combination of the WISE bands 1 and 3, or the JWST NIR-F200W and MIRI-F2100W. It also provides mass-to-light ratio calibrations based on the WISE band-1, the JWST NIR-F200W, and the optical u - r or g - r colors. These calibrations account for the biases attributed to the SP age, while they are given in the form of extinction-dependent and extinction-independent relations. The proposed calibrations show robust estimations while minimizing the scatter and biases throughout a wide range of SFRs and stellar masses. The SFR calibration offers better results, especially in dust-free or passive galaxies where the contributions of old SPs or biases from the lack of dust are significant. Similarly, the M $\star$ calibration yields significantly better results for dusty and high-SFR galaxies where dust emission can otherwise bias the estimations.

79 ASTRONOMY AND ASTROPHYSICS↗