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DOE OSTI2025

Physics-Driven Construction of Compact Primitive Gaussian Density Fitting Basis Sets

We present a model-assisted density fitting (MADF) basis set generator, an algorithm for generating primitive atomic Gaussian density fitting (DF) basis sets (DFBSs) from a contracted Gaussian orbital basis set (OBS). The MADF algorithm produces DFBSs suitable for accurate robust DF approximation of 2-particle interactions in mean-field and correlated electronic structures. The algorithm is designed to (a) saturate the OBS product space by a large regularized set of primitive solid-harmonic Gaussian shells with nonuniform distribution of exponents, followed by (b) pruning of the shells according to their contributions to the 2- body energy of a correlated atomic ensemble. Building the DFBS generator model almost exclusively on mathematical and physical principles allows one to limit the number of parameters that control the density fitting error to three, with a single set of parameters sufficient for computations with all basis cardinal numbers, with and without correlation of core electrons, with and without scalar and spin-dependent relativistic effects, spanning almost all of the Periodic Table. Performance assessment included basis sets up to quadruple-ζ quality from several major basis set families, using molecules composed of main-group, d-block, and f-block elements. The resulting DF errors in Hartree−Fock and second-order MP2 energies (with relativistic all-electron treatments, when appropriate) were on the order of 20 and 10 μE h per electron, respectively.

Approximation↗

DOE OSTI2022

Fitness Landscape-Guided Engineering of Locally Supercharged Virus-like Particles with Enhanced Cell Uptake Properties

Protein-based nanoparticles are useful models for the study of self-assembly and attractive candidates for drug delivery. Virus-like particles (VLPs) are especially promising platforms for expanding the repertoire of therapeutics that can be delivered effectively as they can deliver many copies of a molecule per particle for each delivery event. However, their use is often limited due to poor uptake of VLPs into mammalian cells. In this study, we use the fitness landscape of the bacteriophage MS2 VLP as a guide to engineer capsid variants with positively charged surface residues to enhance their uptake into mammalian cells. By combining mutations with positive fitness scores that were likely to produce assembled capsids, we identified two key double mutants with internalization efficiencies as much as 67-fold higher than that of wtMS2. Internalization of these variants with positively charged surface residues depends on interactions with cell surface sulfated proteoglycans, and yet, they are biophysically similar to wtMS2 with low cytotoxicity and an overall negative charge. Additionally, the best-performing engineered MS2 capsids can deliver a potent anticancer small-molecule therapeutic with efficacy levels similar to antibody-drug conjugates. Through this work, we were able to establish fitness landscape-based engineering as a successful method for designing VLPs with improved cell penetration. These findings suggest that VLPs with positive surface charge could be useful in improving the delivery of small-molecule- and nucleic acid-based therapeutics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

SDSS-IV MaStar: Stellar parameter determination with continuum-supplemented full-spectrum fitting

We present a stellar parameter catalog built to accompany the MaStar Stellar Library, which is a comprehensive collection of empirical, medium-resolution stellar spectra. We constructed this parameter catalog by using a multicomponent χ 2 fitting approach to match MaStar spectra to models generated by interpolating the ATLAS9-based BOSZ model spectra. The total χ 2 for a given model is defined as the sum of components constructed to characterize narrow-band features of observed spectra (e.g., absorption lines) and the broadband continuum shape separately. Extinction and systematics due to flux calibration were taken into account in the fitting. The χ 2 distribution for a given region of model space was sampled using a Markov chain Monte Carlo (MCMC) algorithm, the data from which were then used to extract atmospheric parameter estimates (T eff , log g, [Fe/H], and [α/Fe]), their corresponding uncertainties, and direct extinction measurements. Two methods were used to extract parameters and uncertainties: one that accepts the MCMC’s prescribed minimum-χ 2 result, and one that uses Bayesian inference to compute a likelihood-weighted mean from the χ 2 distribution sampled by the MCMC. Results were evaluated for internal consistency using repeat observations where available and by comparing them with external data sets (e.g., APOGEE-2 and Gaia DR2). Our spectral-fitting exercise reveals possible deficiencies in current theoretical model spectra, illustrating the potential power of MaStar spectra for helping to improve the models. This paper represents an update to the parameters that were originally presented with SDSS-IV DR17. The MaStar parameter catalog containing our BestFit results is available on the SDSS-IV DR17 website as part of version 2 of the MaStar stellar parameter value-added catalog.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

MB-Fit: Software infrastructure for data-driven many-body potential energy functions

Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Quantitative assessment of fitting errors associated with streak camera noise in Thomson scattering data analysis

Thomson scattering measurements in high energy density experiments are often recorded using optical streak cameras. In the low-signal regime, noise introduced by the streak camera can become an important and sometimes the dominant source of measurement uncertainty. In this paper, we present a formal method of accounting for the presence of streak camera noise in our measurements. We present a phenomenological description of the noise generation mechanisms and present a statistical model that may be used to construct the covariance matrix associated with a given measurement. This model is benchmarked against simulations of streak camera images. We demonstrate how this covariance may then be used to weight fitting of the data and provide quantitative assessments of the uncertainty in the fitting parameters determined by the best fit to the data and build confidence in the ability to make statistically significant measurements in the low-signal regime, where spatial correlations in the noise become apparent. These methods will have general applicability to other measurements made using optical streak cameras.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Fit-free optical determination of electronic thermalization time in nematic iron-based superconductors

We present a nematic response function model (NRFM) for fit-free direct extraction of the characteristic time of ultrafast electronic thermalization in iron-based superconductors, materials with electronic nematicity. By combining the NRFM for polarization-dependent pump–probe measurements of electronic nematic response with the two-temperature model (TTM) for sub-picosecond quasiparticle relaxation, we quantify the electronic thermalization timescales and their anisotropy. The nematic response function is modeled as the difference in normalized reflectivity signals, revealing a pronounced sub-picosecond extremum in signal evolution that directly yields the characteristic electronic thermalization time. This method demonstrates that the NRFM is consistent with TTM fits of transient optical response, yielding electronic thermalization time constants on the order of 110–230 fs for the FeSe 1−x Te x and Ba(Fe 0.92 Co 0.08 ) 2 As 2 thin films. Here, the proposed approach can be applied to any material that exhibits electronic nematicity, providing a powerful tool for direct mapping of the relaxation time in nematic materials, avoiding complex experimental data-fitting procedures.

Bartenev, Alexander [University of Puerto Rico, Ma↗

DOE OSTI2022

The PDF4LHC21 combination of global PDF fits for the LHC Run III

A precise knowledge of the quark and gluon structure of the proton, encoded by the parton distribution functions (PDFs), is of paramount importance for the interpretation of high-energy processes at present and future lepton–hadron and hadron–hadron colliders. Motivated by recent progress in the PDF determinations carried out by the CT, MSHT, and NNPDF groups, we present an updated combination of global PDF fits: PDF4LHC21. It is based on the Monte Carlo combination of the CT18, MSHT20, and NNPDF3.1 sets followed by either its Hessian reduction or its replica compression. Extensive benchmark studies are carried out in order to disentangle the origin of the differences between the three global PDF sets. In particular, dedicated fits based on almost identical theory settings and input datasets are performed by the three groups, highlighting the role played by the respective fitting methodologies. We compare the new PDF4LHC21 combination with its predecessor, PDF4LHC15, demonstrating their good overall consistency and a modest reduction of PDF uncertainties for key LHC processes such as electroweak gauge boson production and Higgs boson production in gluon fusion. We study the phenomenological implications of PDF4LHC21 for a representative selection of inclusive, fiducial, and differential cross sections at the LHC. The PDF4LHC21 combination is made available via the LHAPDF library and provides a robust, user-friendly, and efficient method to estimate the PDF uncertainties associated to theoretical calculations for the upcoming Run III of the LHC and beyond.

quantum chromodynamics↗

DOE OSTI2023

A comparison of template vs. direct model fitting for redshift-space distortions in BOSS

The growth of large-scale structure, as revealed in the anisotropic of clustering of galaxies in the low redshift Universe at z < 2, provides a stringent test of our cosmological model. The strongest current constraints come from the BOSS and eBOSS surveys, with uncertainties on σ 8 , the amplitude of clustering on an 8 h –1 Mpc scale, of less than 10 per cent. A number of different approaches have been taken to fitting this signal, leading to discrepancies of up to 1σ in the measurements of the amplitude of fluctuations at late times. We compare in some detail two of the leading approaches, one based on fitting a template cosmology whose amplitude and length scales are allowed to float with one based on varying the underlying parameters of a cosmological model directly, when fitting to the BOSS DR12 data. Holding the input data, scale cuts, window functions and modeling framework fixed we are able to isolate the cause of the differences and discuss the implications for future surveys.

redshift surveys↗

DOE OSTI2021

Fitness cost of vancomycin-resistant Enterococcus faecium plasmids associated with hospital infection outbreaks

Abstract Background Vancomycin resistance is mostly associated with Enterococcus faecium due to Tn1546-vanA located on narrow- and broad-host plasmids of various families. This study’s aim was to analyse the effects of acquiring Tn1546-carrying plasmids with proven epidemicity in different bacterial host backgrounds. Methods Widespread Tn1546-carrying plasmids of different families RepA_N (n = 5), Inc18 (n = 4) and/or pHTβ (n = 1), and prototype plasmids RepA_N (pRUM) and Inc18 (pRE25, pIP501) were analysed. Plasmid transferability and fitness cost were assessed using E. faecium (GE1, 64/3) and Enterococcus faecalis (JH2-2/FA202/UV202) recipient strains. Growth curves (Bioscreen C) and Relative Growth Rates were obtained in the presence/absence of vancomycin. Plasmid stability was analysed (300 generations). WGS (Illumina-MiSeq) of non-evolved and evolved strains (GE1/64/3 transconjugants, n = 49) was performed. SNP calling (Breseq software) of non-evolved strains was used for comparison. Results All plasmids were successfully transferred to different E. faecium clonal backgrounds. Most Tn1546-carrying plasmids and Inc18 and RepA_N prototypes reduced host fitness (–2% to 18%) while the cost of Tn1546 expression varied according to the Tn1546-variant and the recipient strain (9%–49%). Stability of Tn1546-carrying plasmids was documented in all cases, often with loss of phenotypic resistance and/or partial plasmid deletions. SNPs and/or indels associated with essential bacterial functions were observed on the chromosome of evolved strains, some of them linked to increased fitness. Conclusions The stability of E. faecium Tn1546-carrying plasmids in the absence of selective pressure and the high intra-species conjugation rates might explain the persistence of vancomycin resistance in E. faecium populations despite the significant burden they might impose on bacterial host strains.

Tedim, Ana P.↗

DOE OSTI2023

Monte Carlo goodness-of-fit tests for degree corrected and related stochastic blockmodels

Abstract We construct Bayesian and frequentist finite-sample goodness-of-fit tests for three different variants of the stochastic blockmodel for network data. Since all of the stochastic blockmodel variants are log-linear in form when block assignments are known, the tests for the latent block model versions combine a block membership estimator with the algebraic statistics machinery for testing goodness-of-fit in log-linear models. We describe Markov bases and marginal polytopes of the variants of the stochastic blockmodel and discuss how both facilitate the development of goodness-of-fit tests and understanding of model behaviour. The general testing methodology developed here extends to any finite mixture of log-linear models on discrete data, and as such is the first application of the algebraic statistics machinery for latent-variable models.

Karwa, Vishesh↗

DOE OSTI2022

Semi-analytic spectral fitting: simultaneously modelling the mass accumulation and chemical evolution in MaNGA spiral galaxies

We develop a novel semi-analytic spectral fitting approach to quantify the star formation histories (SFHs) and chemical enrichment histories (ChEHs) of individual galaxies. We construct simple yet general chemical evolution models that account for gas inflow and outflow processes as well as star formation, to investigate the evolution of merger-free star-forming systems. These models are fitted directly to galaxies’ absorption-line spectra, while their emission lines are used to constrain current gas phase metallicity and star formation rate. We apply this method to spiral galaxies selected from the SDSS-IV Mapping Nearby Galaxies at Apache Point Observatory survey. By fitting the co-added absorption-line spectra for each galaxy, and using the emission-line constraints on present-day metallicity and star formation, we reconstruct both the SFHs and the ChEHs for all objects in the sample. We can use these reconstructions to obtain archaeological measures of derived correlations such as the mass–metallicity relation at any redshift, which compare favourably with direct observations. We find that both the SFHs and ChEHs have strong mass dependence: massive galaxies accumulate their stellar masses and become enriched earlier. This mass dependence causes the observed flattening of the mass–metallicity relation at lower redshifts. The model also reproduces the observed gas-to-stellar mass ratio and its mass dependence. Moreover, we are able to determine that more massive galaxies have earlier gas infall times and shorter infall time-scales, and that the early chemical enrichment of low-mass galaxies is suppressed by strong outflows, while outflows are not very significant in massive galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Differentiable vertex fitting for jet flavor tagging

This work explores the use of differentiable programming to integrate domain knowledge, in the form of domain specific software, into neural networks to develop scientific machine learning systems. We propose a differentiable vertex fitting algorithm that estimates the crossing point of multiple curves. In the high energy physics setting, these curves are defined by particle equations of motion and the crossing point represents the origin of particle production. This differentiable vertex fitting algorithm can be seamlessly integrated into neural networks, and we show its utility and efficacy in the high energy physics application of the classification of jets, i.e., collimated streams of particles in particle detectors whose originating parent particle we aim to classify. We demonstrate how differentiable vertex fitting can be integrated into larger transformer-based models for jet flavor tagging and show improvements in heavy flavor jet classification when compared to baseline models. Published by the American Physical Society 2024

Smith, Rachel E. C. (ORCID:0000000335851262)↗

DOE OSTI2025

time-resolved spectroscopy fit (trspecfit) v0.01

Analyze 2D time- and energy-resolved data, such as from a pump-probe spectroscopy experiment. User can select and input different peak shapes/ functions and background types to first fit a ground state/ unperturbed spectrum. This would be similar to how standard spectroscopy data is fit. Subsequently, to describe the time domain, users can choose functions that describe the temporal dynamics of one or more spectral features, such as a peak amplitude, peak position, etc. These time dynamics functions can be added or convoluted (e.g. describing an instrument response function) with each other. Functionality to integrate implicit variables leading to distributions of certain parameters/ functions is in development. Alternatively, 2D data can be analyzed one time step at a time to get an idea of the time dynamics of the system before deploying the global 2D fit described above. Typically people write custom software for this purpose. During my PhD I've seen five internal LBL and external researchers write one-off code in different languages to analyze time- and energy-resolved spectra. While this was specifically was for a laser pump - X-ray probe spectroscopy experiment, I'm trying to write a general package for the time-resolved spectroscopy community.

Mahl, Johannes [Lawrence Berkeley National Laborat↗

DOE OSTI2023

Predicting partner fitness based on spatial structuring in a light-driven microbial community

Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology ( e . g ., personalized probiotics, bioproduction of high-value products, biosensing). The capacity to monitor and model metabolite exchange in dynamic microbial consortia can provide foundational information important to understand the community level behaviors that emerge, a requirement for building novel consortia. Where experimental approaches for monitoring metabolic exchange are technologically challenging, computational tools can enable greater access to the fate of both chemicals and microbes within a consortium. In this study, we developed an in-silico model of a synthetic microbial consortia of sucrose-secreting Synechococcus elongatus PCC 7942 and Escherichia coli W. Our model was built on the NUFEB framework for Individual-based Modeling (IbM) and optimized for biological accuracy using experimental data. We showed that the relative level of sucrose secretion regulates not only the steady-state support for heterotrophic biomass, but also the temporal dynamics of consortia growth. In order to determine the importance of spatial organization within the consortium, we fit a regression model to spatial data and used it to accurately predict colony fitness. We found that some of the critical parameters for fitness prediction were inter-colony distance, initial biomass, induction level, and distance from the center of the simulation volume. We anticipate that the synergy between experimental and computational approaches will improve our ability to design consortia with novel function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites

Trichoderma spp. are ubiquitous rhizosphere fungi capable of producing several classes of secondary metabolites that can modify the dynamics of the plant-associated microbiome. However, the bacterial-fungal mechanisms that mediate these interactions have not been fully characterized. Here, a random barcode transposon-site sequencing (RB-TnSeq) approach was employed to identify bacterial genes important for fitness in the presence of Trichoderma atroviride exudates. We selected three rhizosphere bacteria with RB-TnSeq mutant libraries that can promote plant growth: the nitrogen fixers Klebsiella michiganensis M5aI and Herbaspirillum seropedicae SmR1, and Pseudomonas simiae WCS417. As a non-rhizosphere species, Pseudomonas putida KT2440 was also included. From the RB-TnSeq data, nitrogen-fixing bacteria competed mainly for iron and required the siderophore transport system TonB/ExbB for optimal fitness in the presence of T . atroviride exudates. In contrast, P . simiae and P . putida were highly dependent on mechanisms associated with membrane lipid modification that are required for resistance to cationic antimicrobial peptides (CAMPs). A mutant in the Hog1-MAP kinase (Δ tmk 3) gene of T . atroviride showed altered expression patterns of many nonribosomal peptide synthetase (NRPS) biosynthetic gene clusters with potential antibiotic activity. In contrast to exudates from wild-type T . atroviride , bacterial mutants containing lesions in genes associated with resistance to antibiotics did not show fitness defects when RB-TnSeq libraries were exposed to exudates from the Δ tmk3 mutant. Unexpectedly, exudates from wild-type T . atroviride and the Δ tmk 3 mutant rescued purine auxotrophic mutants of H . seropedicae , K . michiganensis and P . simiae . Metabolomic analysis on exudates from wild-type T . atroviride and the Δ tmk 3 mutant showed that both strains excrete purines and complex metabolites; functional Tmk3 is required to produce some of these metabolites. This study highlights the complex interplay between Trichoderma -metabolites and soil bacteria, revealing both beneficial and antagonistic effects, and underscoring the intricate and multifaceted nature of this relationship.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Quantifying uncertainties in crystal electric field Hamiltonian fits to neutron data

We systematically examine uncertainties from fitting rare earth single-ion crystal electric field (CEF) Hamiltonians to inelastic neutron scattering data. Using pyrochlore and delafossite structures as test cases, we find that uncertainty in CEF parameters can be large despite visually excellent fits. These results show Yb ^{3+} 3 + compounds have particularly large g g -tensor uncertainty because of the few available peaks. In such cases, additional constraints are necessary for meaningful fits.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

PMK 1000 cone-socket ventilator fittings force testing to ISO 5356-1:2015 Standard

This memo summarizes the results of verification tests on a cone-socket fitting to the ISO 5356-1:2015 standard, annexes B and F. The components were found to meet requirements holding 50N tensile force and more than 35 N-cm of torque for 10 seconds without separating at 35°C with a fresh socket. Humidity control was unavailable; consequently, humidity was significantly lower than the values in the ISO standard. Several repeat tests of the fitting with force, torque, and time excursions give us confidence that the fittings perform suitably to the ISO standard. Force overload tests suggest that the samples will disengage under tension at around 69 N, while torque overload tests under a force of 50 N will fail at 79 N-cm of torque. If repeated tests are performed on the same component, the socket can deform and lead to the connection failing the standard requirements. However, such failures only occur with repeated testing, and the gripping of such units can be modified so that they pass the standard. This observation demonstrates that socket gripping is responsible for those failures and would not be a problem in application.

42 ENGINEERING↗

DOE OSTI2026

Bayesian Fit to NOvA Data Subsamples for Three Flavor Oscillation Analysis

NOvA (NuMI Off-Axis $\nu_e$ Appearance) is a long baseline neutrino experiment designed to measure the oscillation of muon neutrinos to electron neutrinos over a distance of 810 km. NOvA uses a near and far detector to observe $\nu_\mu$ disappearance and $\nu_e$ appearance of neutrinos produced by the NuMI beam at Fermilab. NOvA uses a Bayesian analysis framework in addition to its Frequentist method to measure neutrino oscillation parameters such as the mixing angles, mass ordering, and CP-violating phase. We report preliminary results of Bayesian fits to representative NOvA datasets. Comparison of fits to $\nu_\mu$ disappearance and $\nu_e$ appearance enables a cross-check of NOvA results with reactor $\bar{\nu_e}$ disappearance measurements. NOvA also searches for violation of Lorentz invariance by analyzing fits of forward horn current (FHC) versus reverse horn current (RHC) samples. The results validate and advance NOvA's contributions to precision measurements of neutrino properties.

Zhao, Larry [Fermilab]↗