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DOE OSTI2022

High–throughput measurement of plant fitness traits with an object detection method using Faster R–CNN

Revealing the contributions of genes to plant phenotype is frequently challenging because loss-of-function effects may be subtle or masked by varying degrees of genetic redundancy. Such effects can potentially be detected by measuring plant fitness, which reflects the cumulative effects of genetic changes over the lifetime of a plant. However, fitness is challenging to measure accurately, particularly in species with high fecundity and relatively small propagule sizes such as Arabidopsis thaliana. An image segmentation-based method using the software ImageJ and an object detection-based method using the Faster Region-based Convolutional Neural Network (R-CNN) algorithm were used for measuring two Arabidopsis fitness traits: seed and fruit counts. The segmentation-based method was error-prone (correlation between true and predicted seed counts, r 2 = 0.849) because seeds touching each other were undercounted. By contrast, the object detection-based algorithm yielded near perfect seed counts (r 2 = 0.9996) and highly accurate fruit counts (r 2 = 0.980). Comparing seed counts for wild-type and 12 mutant lines revealed fitness effects for three genes; fruit counts revealed the same effects for two genes. Our study provides analysis pipelines and models to facilitate the investigation of Arabidopsis fitness traits and demonstrates the importance of examining fitness traits when studying gene functions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population’s mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

A Dynamic Trajectory Fit to Multisensor Fireball Observations

Meteorites with known orbital origins are key to our understanding of solar system formation and the source of life on Earth. Fireball networks have been developed globally in a unified effort to record and ultimately retrieve these cosmic samples. However, the accuracy of the determined orbit and the likelihood of meteorite recovery depend directly on the accuracy of the chosen meteoroid triangulation method. There are three leading techniques for meteoroid triangulation discussed in the literature: the method of planes, the straight-line least-squares method, and the multiparameter fit method. Here we describe an alternative method to meteoroid triangulation, called the dynamic trajectory fit. This approach uses the meteoroid’s 3D dynamic equations of motion to fit a realistic trajectory directly to multisensor line-of-sight observations. This method has the ability to resolve fragmentation events, fit systematic observatory timing offsets, and determine mass estimates of the meteoroid along its observable trajectory. Through a comprehensive Monte Carlo analysis of over 100,000 trajectory simulations, we find this new method to more accurately estimate meteoroid trajectories of slow entry events (<25 km s{sup −1}) and events observed from low convergence angles (<10°) compared to existing meteoroid triangulation techniques. Additionally, we triangulate an observed fireball event with visible fragmentation using the various triangulation methods to show that the proposed dynamic trajectory fit implementing fragmentation to best match the captured multisensor line-of-sight data.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

A combinatorially complete epistatic fitness landscape in an enzyme active site

Protein engineering often targets binding pockets or active sites which are enriched in epistasis—nonadditive interactions between amino acid substitutions—and where the combined effects of multiple single substitutions are difficult to predict. Few existing sequence-fitness datasets capture epistasis at large scale, especially for enzyme catalysis, limiting the development and assessment of model-guided enzyme engineering approaches. We present here a combinatorially complete, 160,000-variant fitness landscape across four residues in the active site of an enzyme. Assaying the native reaction of a thermostable β-subunit of tryptophan synthase (TrpB) in a nonnative environment yielded a landscape characterized by significant epistasis and many local optima. These effects prevent simulated directed evolution approaches from efficiently reaching the global optimum. There is nonetheless wide variability in the effectiveness of different directed evolution approaches, which together provide experimental benchmarks for computational and machine learning workflows. The most-fit TrpB variants contain a substitution that is nearly absent in natural TrpB sequences—a result that conservation-based predictions would not capture. Thus, although fitness prediction using evolutionary data can enrich in more-active variants, these approaches struggle to identify and differentiate among the most-active variants, even for this near-native function. Overall, this work presents a large-scale testing ground for model-guided enzyme engineering and suggests that efficient navigation of epistatic fitness landscapes can be improved by advances in both machine learning and physical modeling.

biocatalysis↗

DOE OSTI2020

Modelling the Milky Way – I. Method and first results fitting the thick disc and halo with DES-Y3 data

ABSTRACT We present a technique to fit the stellar components of the Galaxy by comparing Hess Diagrams (HDs) generated from trilegal models to real data. We apply this technique, which we call mwfitting, to photometric data from the first 3 yr of the Dark Energy Survey (DES). After removing regions containing known resolved stellar systems such as globular clusters, dwarf galaxies, nearby galaxies, the Large Magellanic Cloud, and the Sagittarius Stream, our main sample spans a total area of ∼2300 deg2. We further explore a smaller subset (∼1300 deg2) that excludes all regions with known stellar streams and stellar overdensities. Validation tests on synthetic data possessing similar properties to the DES data show that the method is able to recover input parameters with a precision better than 3 per cent. We fit the DES data with an exponential thick disc model and an oblate double power-law halo model. We find that the best-fitting thick disc model has radial and vertical scale heights of 2.67 ± 0.09 kpc and 925 ± 40 pc, respectively. The stellar halo is fit with a broken power-law density profile with an oblateness of 0.75 ± 0.01, an inner index of 1.82 ± 0.08, an outer index of 4.14 ± 0.05, and a break at 18.52 ± 0.27 kpc from the Galactic centre. Several previously discovered stellar overdensities are recovered in the residual stellar density map, showing the reliability of mwfitting in determining the Galactic components. Simulations made with the best-fitting parameters are a promising way to predict Milky Way star counts for surveys such as the LSST and Euclid.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Abridged spectral matrix inversion: parametric fitting of X-ray fluorescence spectra following integrative data reduction

Recent improvements in both X-ray detectors and readout speeds have led to a substantial increase in the volume of X-ray fluorescence data being produced at synchrotron facilities. This in turn results in increased challenges associated with processing and fitting such data, both temporally and computationally. Herein an abridging approach is described that both reduces and partially integrates X-ray fluorescence (XRF) data sets to obtain a fivefold total improvement in processing time with negligible decrease in quality of fitting. The approach is demonstrated using linear least-squares matrix inversion on XRF data with strongly overlapping fluorescent peaks. This approach is applicable to any type of linear algebra based fitting algorithm to fit spectra containing overlapping signals wherein the spectra also contain unimportant (non-characteristic) regions which add little (or no) weight to fitted values, e.g. energy regions in XRF spectra that contain little or no peak information.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Dry heat sterilization as a method to recycle N95 respirator masks: The importance of fit

In times of crisis, including the current COVID-19 pandemic, the supply chain of filtering facepiece respirators, such as N95 respirators, are disrupted. To combat shortages of N95 respirators, many institutions were forced to decontaminate and reuse respirators. While several reports have evaluated the impact on filtration as a measurement of preservation of respirator function after decontamination, the equally important fact of maintaining proper fit to the users’ face has been understudied. In the current study, we demonstrate the complete inactivation of SARS-CoV-2 and preservation of fit test performance of N95 respirators following treatment with dry heat. We apply scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDS), X-ray diffraction (XRD) measurements, Raman spectroscopy, and contact angle measurements to analyze filter material changes as a consequence of different decontamination treatments. We further compared the integrity of the respirator after autoclaving versus dry heat treatment via quantitative fit testing and found that autoclaving, but not dry heat, causes the fit of the respirator onto the users face to fail, thereby rendering the decontaminated respirator unusable. Our findings highlight the importance to account for both efficacy of disinfection and mask fit when reprocessing respirators to for clinical redeployment.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2020

Analytic fits to atom-in-jellium shear modulus predictions

Fits to AJ shear modulus calculations from ρ0 to the limit of the corresponding AJ EOS table (usually 1000 ρ0), adjusted to reproduce STP shear modulus where possible. Fitting minimized the fractional difference, so low-pressure points would be reproduced accurately despite the wide-ranging tabulation. AJ calculations were at T=0. Isochoric variation G(T) has been small for all cases spot-tested so far, and may have either sign. The fitted equation usually matches the AJ data to within a few percent. Between numerical noise in the AJ calculation and probably-physical structure not captured by the equation, the deviation could be up to 20% in some places in most models, and 30% in a few. AJ does not capture structural phase transitions or phases stabilized by directional bonds, where the shear modulus may vary by a greater amount. Where possible, STP ρ,G were used as parameters, and low pressure AJ points were de-weighted or removed if necessary. Otherwise, such as where AJ fails to capture solid phases with a significantly different shear modulus, the AJ data were fitted as far down in pressure as possible, G0 was also fitted if necessary, and ρ0 was also adjusted if needed to keep G0>0. The resulting models are not intended for use at low pressure, though some are probably adequate for practical purposes

36 MATERIALS SCIENCE↗

DOE OSTI2025

GADRAS-DRF Validation for Safeguards and Custom Peak Fit Enhancements

In previous years, SGTech funded enhancements to the isotopics routine in the software called Gamma Detector Response and Analysis Software-Detector Response Function (GADRAS-DRF), including the addition of peak fit customization capabilities. A project was also funded that focused on implementing a peak-based model fitting routine, allowing model fitting to be performed without dependence on export-controlled cross-sections. In FY25 significant improvements were made to the custom peak fitting interface, accompanied by several validation studies within GADRAS-DRF. These studies encompassed IsotopeID performance, distributed source analysis, isotopics validation, and activity estimation. Additionally, the peak-only model fitting option was validated using an HPGe measurement of a rotating drum with line sources.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Quantitative analysis of Cu XANES spectra using linear combination fitting of binary mixtures simulated by FEFF9

We report x-ray absorption near edge structure (XANES) is a powerful tool to probe the fingerprint of local structures, and when coupled with X-ray microscopy, the small spot size enables one to probe very specific regions of interest in a device or material, e.g. interfaces/bulk, different grains, good/bad electrical areas. In this work, we investigate the use of linear combination fitting (LCF) of XANES spectra for the particular case of Cu doping in CdTe. We show that the experimental data seem to be accurately represented by standards of Cu 2 Te and its substoichiometric counterpart, Cu 1.43 Te. We use Cu in CdTe as a case study to evaluate the accuracy of linear combination fitting using simulated standards, given that experimental standards for certain phases (e.g. Cu 1.43 Te) or defect structures (e.g. vacancies) cannot be readily obtained. We discuss how spectral features of the FEFF9-simulated standards, fitting ranges, and noise levels all dictate the accuracy of this type of analysis. We show that the greater the spectral difference between the two standards, the better the LCF is able to differentiate between the two structures and to tolerate experimental noise. Finally, we estimate the error of the fitted weights for different spectral features and noise levels and propose a framework to study local structures semi-quantitatively by using binary mixtures of FEFF9-simulated standards.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Robust Automatic EXAFS First-Shell Fits

Extended X-ray absorption fine structure (EXAFS) is a widely used technique for atomic structure determination. Fourier transformation connects EXAFS in k space and R space. However, determining the appropriate k-range for the transformation can be challenging, but critical for the first-shell fit. In this study, we present an automatic method to determine the k-range using the Larch package and a Python program. The first step is to estimate spectral noise across a series of k-ranges with a fixed minimum value and identify the optimal maximum value in the k-range (k max ). The k max is determined by an empirical noise threshold that marks the point where the noise level in the Fourier transformed spectrum changes dramatically. Using the obtained k max value, the first shell is modeled to determine the minimum k value (k min ) by optimizing the background function through alignment of the spectrum with theory. The optimal k min corresponds to the point of the minimum R-factor, which quantifies the difference between the experimental and fitted spectrum. Our method was tested on various typical datasets and yielded suitable k-ranges for Fourier transformation and accurate first-shell fits. This approach helps avoid unreliable, irreproducible data analysis, especially for noisy data from diluted samples, and enables robust automatic first-shell EXAFS fitting.

EXAFS analysis↗

DOE OSTI2024

The 300 Marines: characterizing the US Marines with perfect scores on their physical and combat fitness tests

Few US Marines earn perfect 300 scores on both their Physical Fitness Test (PFT) and Combat Fitness Test (CFT). The number 300 invokes the legendary 300 Spartans that fought at the Battle of Thermopylae, which inspired high physical fitness capabilities for elite ground forces ever since. Purpose: Determine distinguishing characteristics of the “300 Marines” (perfect PFT and CFT scores) that may provide insights into the physical and physiological requirements associated with this capability. These tests have been refined over time to reflect physical capabilities associated with Marine Corps basic rifleman performance. Materials and methods: Data were analyzed from US Marines, including 497 women (age, 29 ± 7 years; height 1.63 ± 0.07 m; body mass, 67.4 ± 8.4 kg) and 1,224 men (30 ± 8 years; 1.77 ± 0.07 m; 86.1 ± 11.1 kg). Marines were grouped by whether they earned perfect 300 scores on both the PFT and CFT (300 Marines) or not. We analyzed group differences in individual fitness test events and body composition (dual-energy x-ray absorptiometry). Results: Only 2.5% (n = 43) of this sample earned perfect PFT and CFT scores (n = 21 women; n = 22 men). Compared to sex-matched peers, 300 Marines performed more pull-ups, with faster three-mile run, maneuver-under-fire, and movement-to-contact times (each p < 0.001); 300 Marines of both sexes had lower fat mass, body mass index, and percent body fat (each p < 0.001). The lower percent body fat was explained by greater lean mass (p = 0.041) but similar body mass (p = 0.085) in women, whereas men had similar lean mass (p = 0.618), but lower total body mass (p = 0.025). Conclusion: Marines earning perfect PFT and CFT scores are most distinguished from their peers by their maneuverability, suggesting speed and agility capabilities. While both sexes had considerably lower percent body fat than their peers, 300 Marine women were relatively more muscular while men were lighter.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Energy Efficiency Package for Tenant Fit-Out: Laboratory Testing and Validation of Energy Savings and Indoor Environmental Quality

Approximately 40% of the total U.S. office floor space of 1.5 billion sq.m (16 billion sq.ft.) is leased space occupied by tenants. Tenant fit-out presents a key opportunity to incorporate energy efficiency within the real estate business cycle. We designed a package of energy efficiency measures tailored to the scope of a tenant fit-out. This tenant fit-out package (TFP) includes advanced lighting and heating, ventilating and air-conditioning (HVAC) controls as core measures, with ceiling fans, automated shading, and plug load controls as additional optional measures. We conducted laboratory testing of six configurations of the package to evaluate energy savings, indoor environmental quality, and identify installation, commissioning, and operational issues. Combined savings for HVAC, lighting, and plug loads ranged from 33–40%. Lighting savings ranged from 69–83%, and HVAC savings from 20–40%. The laboratory testing also revealed some minor but tractable challenges with installation and commissioning of HVAC controls. Overall, the results demonstrate that significant savings can be realized in existing office buildings by incorporating relatively low-risk, proven measures at the time of a tenant fit-out.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

Is selfing a reproductive assurance promoting polyploid establishment? Reduced fitness, leaky self‐incompatibility and lower inbreeding depression in neotetraploids

Premise Newly formed polyploids face significant obstacles to persistence and population establishment because of fitness costs of intercytotype mating. Selfing provides the opportunity to escape mate limitation, enabling production of new individuals and increasing the likelihood of fixation of new polyploid lineages. Still, association between self‐compatibility and polyploidy is not always clear. We compared self‐incompatibility and inbreeding depression in neotetraploids and their diploid progenitor to explore the direct effects of whole genome duplications on self‐incompatibility and the implications of ploidy‐driven changes for polyploid establishment. Methods Outcross and self‐pollinations were performed in diploids and synthetic neotetraploids of Jasione maritima var. maritima , and reproductive success was measured through fruit and seed production and seed germination. Self‐ and outcross offspring were grown under controlled conditions, and plant performance was measured through several fitness parameters. Results Neotetraploids showed an overall lower performance than diploids. Reproductive success was negatively affected by selfing in both cytotypes. However, greater variation in the expression of self‐incompatibility was observed in neotetraploids; additionally, developmental and physiological parameters were not affected by selfing on neotetraploids, with an overall similar fitness of outcrossed and selfed individuals, resulting in lower inbreeding depression indexes. Conclusions Neotetraploids might have benefited from selfing at initial stages after their formation. Genome duplications resulted in leaky self‐incompatibility, enabling the production of offspring under minority cytotype disadvantage with similar fitness as outcrossed offspring. Our results support theoretical assumptions that selfing might be important for neopolyploid establishment, although changes in self‐incompatibility might not be abrupt.

Siopa, Catarina↗

DOE OSTI2023

High-Order Mesh hr-adaptivity for Surface Fitting to Implicit Geometries

We present an ℎ𝑟-adaptivity framework for morphing a given mesh to fit a target surface prescribed as the zero isocontour of a discrete function. In this framework, high-order meshing is posed as a variational minimization problem that depends on the mesh quality prescribed via the target matrix optimization paradigm (TMOP) and position of a subset of mesh nodes with respect to the target surface. The proposed formulation ensures that the variational problem is converged and mesh quality degradation near the surface is limited, even when the mesh topology is incompatible with the target surface. Additionally, a mesh subset-based approach and ℎ-refinement is introduced to efficiently increase fitting accuracy while reducing the computational cost of the mesh morphing problem. The ℎ𝑟-adaptivity technique extends to different element types in two- and three-dimensions, and can be used in existing finite element and spectral element frameworks to obtain high-order body-fitted meshes. Various numerical experiments demonstrate the robustness and accuracy of the fitting approach for problems of practical interest such as Lagrangian hydrodynamics and topology optimization.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Beyond traditional diagnostics: Identifying active galactic nuclei using spectral energy distribution fitting in DESI data

Active galactic nuclei (AGN) are typically identified through their distinctive X-ray or radio emissions, mid-infrared (MIR) colors, or emission lines. However, each method captures different subsets of AGN due to signal-to-noise (S/N) limitations, redshift coverage, and extinction effects, underscoring the necessity for a multiwavelength approach for comprehensive AGN samples. This study explores the effectiveness of spectral energy distribution (SED) fitting as a robust method for AGN identification. Using CIGALE optical-MIR SED fits on DESI Early Data Release galaxies, we compare SED-based AGN selection (AGNFRAC ≥ 0.1) with traditional methods including BPT diagrams, WISE colors, X-ray, and radio diagnostics. The SED fitting identifies ∼70% of narrow- and broad-line AGN and 87% of WISE-selected AGN. Incorporating high S/N WISE photometry reduces star-forming galaxy contamination from 62% to 15%. Initially, ∼50% of SED-AGN candidates are undetected by standard methods, but additional diagnostics classify ∼85% of these sources, revealing low-ionization nuclear emission-line regions and retired galaxies potentially representing evolved systems with weak AGN activity. Further spectroscopic and multiwavelength analysis will be essential to determine the true AGN nature of these sources. SED fitting provides complementary AGN identification, unifying multiwavelength AGN selections. This approach enables more complete – albeit somewhat contaminated – AGN samples, which are essential for upcoming large-scale surveys where spectroscopic diagnostics may be limited.

Seyfert↗

DOE OSTI2020

A generalized forward fit for neutron detectors with energy-dependent response functions

To date, most analysis of neutron time-of-flight data from inertial confinement fusion experiments has focused on the relatively small range of energies corresponding to the primary neutrons from DD and DT fusion, and have therefore employed instrument response functions (IRF’s) corresponding to monoenergetic 2.45-MeV or 14.03-MeV neutrons. For analysis of time-of-flight signals corresponding to broader ranges of neutron energies, accurate treatment of the data requires the use of an energy-dependent IRF. Here, this work describes interpolation of the IRF for neutrons of arbitrary energy, construction of an energy-dependent IRF, and application of this IRF in a forward fit via matrix multiplication. As an example of the application of this method, an analysis of synthetic data relevant to TT fusion experiments at the Omega Laser Facility is discussed. This example is used to illustrate the differences between a forward fit that uses an energy-dependent IRF and a forward fit that uses a monoenergetic IRF. Use of the energy-dependent IRF is shown to result in accurate inference of the fit parameters of interest.

47 OTHER INSTRUMENTATION↗