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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Improving Peptide-Level Mass Spectrometry Analysis via Double Competition

A critical statistical task in the analysis of shotgun proteomics data involves controlling the false discovery rate (FDR) among the reported set of discoveries. This task is most commonly solved at the peptide-spectrum match (PSM) level by using target-decoy competition (TDC), in which a set of observed spectra are searched against a database containing a mixture of real (target) and decoy peptides. The PSM-level procedure can be adapted to the peptide level by selecting the top-scoring PSM per peptide prior to FDR estimation. Here, we investigate both PSM-level and peptide-level FDR control methods and come to two conclusions. First, although the TDC procedure is provably correct under certain assumptions, we observe that one of these assumptions - that incorrect PSMs are independent of one another - is frequently violated. Hence, we empirically demonstrate that TDC-based PSM-level FDR estimates can be liberally biased. Further, we propose that researchers avoid PSM-level results and instead focus on peptide-level analysis. Second, we investigate three ways to carry out peptide level TDC and show that the most common method ("PSM-only") offers the lowest statistical power in practice. The most powerful method, peptide-level FDR with PSM competition ("PSM-and-peptide"), carries out competition first at the PSM level and then again at the peptide level. In our experiments, this approach yields an average increase of 17% more discovered peptides at a1% FDR threshold relative to the PSM-only method.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

DESI mock challenge: Halo and galaxy catalogues with the bias assignment method

We present a novel approach to the construction of mock galaxy catalogues for large-scale structure analysis based on the distribution of dark matter halos obtained with effective bias models at the field level. We aim to produce mock galaxy catalogues capable of generating accurate covariance matrices for a number of cosmological probes that are expected to be measured in current and forthcoming galaxy redshift surveys (e.g. two- and three-point statistics). The construction of the catalogues shown in this paper is part of a mock-comparison project within the Dark Energy Spectroscopic Instrument (DESI) collaboration. We use the bias assignment method ( BAM ) to model the statistics of halo distribution through a learning algorithm using a few detailed N-body simulations, and approximated gravity solvers based on Lagrangian perturbation theory. We introduce cosmic-web-dependent corrections to modelling redshift-space distortions at the N-body level – both in the halo and galaxy distributions –, as well as a multi-scale approach for accurate assignment of halo properties. Using specific models of halo occupation distributions to populate halos, we generate galaxy mocks with the expected number density and central-satellite fraction of emission-line galaxies, which are a key target of the DESI experiment. BAM generates mock catalogues with per cent accuracy in a number of summary statistics, such as the abundance, the two- and three-point statistics of halo distributions, both in real and redshift space. In particular, the mock galaxy catalogues display ~3%-10% accuracy in the multipoles of the power spectrum up to scales of k ~ 0.4 h -1 Mpc. We show that covariance matrices of two- and three-point statistics obtained with BAM display a similar structure to the reference simulation. BAM offers an efficient way to produce mock halo catalogues with accurate two- and three-point statistics and is able to generate a variety of multi-tracer catalogues with precise covariance matrices of several cosmological probes. We discuss future developments of the algorithm towards mock production in DESI and other galaxy-redshift surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Discrete ordinates analysis of the forced-flight variance reduction technique in Monte Carlo neutral particle transport simulations

This paper presents mathematical formulations and methods to predict the effect of forced-flight variance reduction on Monte Carlo tally variance and calculation time. This includes deducing biasing operators that are then used to construct a history-score probability density function (HSPDF), which represents all possible Monte Carlo random walks and gives the probability of a Monte Carlo history scoring in a tally from a particular phase-space position. The history-score moment equations (HSMEs), the statistical moments of the HSPDF, are then derived to calculate the statistical behavior of the Monte Carlo tally when forced-flight variance reduction is applied. In addition, the future-time equation (FTE) is derived to predict the Monte Carlo computational time as a result of applying forced-flight variance reduction. The solutions of the HSMEs and FTE can be used to predict Monte Carlo computational cost. Furthermore, this work also describes a discrete ordinates method to solve the forced-flight HSMEs and FTE. Several 1-D and 2-D test problems verify that the derivations are performed and implemented correctly.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

NASA’s Pandora SmallSat Mission: Simulating the Impact of Stellar Photospheric Heterogeneity and Its Correction

Stellar photospheric heterogeneity is a dominant astrophysical systematic impacting exoplanet transmission spectroscopy. NASA’s Pandora SmallSat Mission is designed to address this challenge through contemporaneous visible-band photometry and near-infrared spectroscopy of exoplanet host stars. Here, we present an end-to-end simulation study quantifying Pandora’s ability to infer stellar photospheric properties and correct stellar contamination using out-of-transit observations. We construct eight representative stellar activity scenarios and generate 160 simulated Pandora datasets, incorporating time-dependent stellar spectra, instrument response, and noise. Given accurate models, Bayesian retrievals of joint visible photometry (0.4–0.7 μm) and near-infrared spectroscopy (0.9–1.6 μm, R ≈ 120) recover photospheric temperatures with typical uncertainties of ≈30 K, with no significant bias. Models with two spectral components (i.e., a quiescent photosphere and spots) are strongly favored in 95% of cases; one-component models are preferred when true spot filling factors fall below a detection threshold of ≈0.3%. We propagate the true and inferred stellar parameters to compute true, inferred, and residual contamination signals under physically motivated spot geometries. For simple spot distributions, contamination signals of 10 2 –10 3 ppm are reduced to ≲10 ppm—well below Pandora’s expected transmission spectroscopy precision (30–100 ppm). For more complex spot distributions, geometric degeneracies limit deterministic corrections, leaving residual contamination at the 10 3 ppm level that must be mitigated using additional constraints, such as spot-crossing events and joint stellar–planetary retrievals of transmission spectra. These results define regimes in which stellar contamination can be corrected from stellar observations alone and show how Pandora stellar observations can identify cases where additional information is required.

Astronomy and AstroPhysics↗
DOE OSTI2020

Enhancing nuclear data validation analysis by using machine learning

In this work, we demonstrate how machine learning (ML) techniques can be used as an auxiliary tool for nuclear data validation analysis. The output of the ML analysis can inform evaluators and validators on the quality, or lack thereof, of specific nuclear data and benchmark experiments with respect to simulating these experimental benchmark values. To this end, measured and simulated effective neutron multiplication factors, k eff , of 875 selected ICSBEP critical assemblies and the latter's sensitivities with respect to nuclear data as well as benchmarks' features (e.g., material nuclide, core geometry) are used as input for a random forest (RF) regression model. The RF is used to encode the complex inter-dependencies between thousands of nuclear data features (i.e., sensitivity profiles and aspects describing the measurements) and 875 simulated and experimental k eff values in order to understand what nuclear data features are most informative for predicting bias. The complexity of relationships and high-dimensional space is difficult-to-impossible to search fully using simply expert judgment. As a first proof-of-concept—step, it is demonstrated that this technique is able to correctly trace large discrepancies between simulated and experimental k eff back to fabricated shortcomings in nuclear data that were perturbed to simulated k eff values. In a second, real-case scenario, step, the RF algorithm is used to validate the ENDF/B-VIII.0 library in comparison to ENDF/B-VII.1 nuclear data. One case is showcased where the chosen ML algorithms highlighted nuclear data (the 19 F(n,inl) cross section from 0.4–0.9 MeV) that are shown to be problematic by comparing them to associated differential experimental data and nuclear data from other libraries. In addition to that, it is shown that the RF results point towards poor benchmark experiments and associated underestimated uncertainties (e.g., the PU-SOL-THERM-028 series). However, using the RF algorithm for validating nuclear data with respect to k eff is currently limited to pinpointing groups of questionable nuclear data due to the inherent correlations between features introduced by the nuclear data themselves and how k eff is simulated. Due to this, we recommend that the ML methods presented be used to augment—rather than replace—the expert knowledge of evaluators and validators.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

Stellar-reddening-based Extinction Maps for Cosmological Applications

Cosmological surveys must correct their observations for the reddening of extragalactic objects by Galactic dust. Existing dust maps, however, have been found to have spatial correlations with the large-scale structure of the Universe. Errors in extinction maps can propagate systematic biases into samples of dereddened extragalactic objects and into cosmological measurements such as correlation functions between foreground lenses and background objects and the primordial non-Gaussianity parameter f NL . Emission-based maps are contaminated by the cosmic infrared background, while maps inferred from stellar reddenings suffer from imperfect removal of quasars and galaxies from stellar catalogs. Thus, stellar-reddening-based maps using catalogs without extragalactic objects offer a promising path to making dust maps with minimal correlations with large-scale structure. We present two high-latitude integrated extinction maps based on stellar reddenings, with a point-spread functions of FWHMs 6'. 1 and 15'. We employ a strict selection of catalog objects to filter out galaxies and quasars and measure the spatial correlation of our extinction maps with extragalactic structure. Our galactic extinction maps have reduced spatial correlation with large-scale structure relative to most existing stellar-reddening-based and emission-based extinction maps.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Differential Measurements of Jet Substructure and Partonic Energy Loss in Au+Au Collisions at √ sNN = 200 GeV

The STAR collaboration presents jet substructure measurements related to both the momentum fraction and the opening angle within jets in p+p and Au+Au collisions at √sNN =200GeV. The substructure observables include SoftDrop groomed momentum fraction (zg), groomed jet radius (Rg), and subjet momentum fraction (zSJ) and opening angle (θSJ). The latter observable is introduced for the first time. Fully corrected subjet measurements are presented for p+p collisions and are compared to leading-order Monte Carlo models. The subjet θSJ distributions reflect the jets leading opening angle and are utilized as a proxy for the resolution scale of the medium in Au+Au collisions. We compare data from Au+Au collisions to those from p+p which are embedded in minimum-bias Au+Au events in order to include the effects of detector smearing and the heavy-ion collision underlying event. The subjet observables are shown to be more robust to the background than zg and Rg. We observe no significant modifications of the subjet observables within the two highest-energy, back-to-back jets, resulting in a distribution of opening angles and the splittings that are vacuumlike. We also report measurements of the differential dijet momentum imbalance (AJ) for jets of varying θSJ. We find no qualitative differences in energy loss signatures for varying angular scales in the range 0.1< θSJ<0.3, leading to the possible interpretation that energy loss in this population of high-momentum dijet pairs, is due to soft medium-induced gluon radiation from a single color charge as it traverses the medium.

Abdallah, M. S.↗
DOE OSTI2026

Resolving root causes of experiment discrepancies guided by machine learning

Abstract Scientists rely on accurate experimental data to explain nature and then harness this knowledge for applications addressing human needs. However, discrepancies between experiments of the same observable can impede scientific progress if one does not understand the underlying causes. Here, we developed a process that unravels data discrepancies by first using Bayesian machine learning to relate discrepancies to few of many, potentially biasing metadata features that encode experiment procedures. This machine learning output guides human experts to study discrepancy causes by simulating suspicious aspects of historical experiments or designing modern ones to address open questions. The study findings then lead to rejecting or correcting historical data on firm scientific bases. This process is demonstrated for the energy spectrum of neutrons emitted promptly (<1 ns) after fission of 252 Cf, a trusted nuclear physics Standard. It reduces the spread in experimental 252 Cf spectra by up to a factor of 6.

Neudecker, D. (ORCID:0000000339200627)↗
DOE OSTI2021

The persistence of large scale structures. Part I. Primordial non-Gaussianity

Abstract We develop an analysis pipeline for characterizing the topology of large scale structure and extracting cosmological constraints based on persistent homology . Persistent homology is a technique from topological data analysis that quantifies the multiscale topology of a data set, in our context unifying the contributions of clusters, filament loops, and cosmic voids to cosmological constraints. We describe how this method captures the imprint of primordial local non-Gaussianity on the late-time distribution of dark matter halos, using a set of N-body simulations as a proxy for real data analysis. For our best single statistic, running the pipeline on several cubic volumes of size 40 (Gpc/h) 3 , we detect f NL loc =10 at 97.5% confidence on ~ 85% of the volumes. Additionally wetest our ability to resolve degeneracies betweenthe topological signature of f NL loc and variation of σ 8 and argue that correctly identifying nonzero f NL loc in this case is possible via an optimal template method. Our method relies on information living at $\mathcal{O}$(10) Mpc/h, a complementary scale with respect to commonly used methods such as the scale-dependent bias in the halo/galaxy power spectrum. Therefore, while still requiring a large volume, our method does not require sampling long-wavelength modes to constrain primordial non-Gaussianity. Moreover, our statistics are interpretable: we are able to reproduce previous results in certain limits and we make new predictions for unexplored observables, such as filament loops formed by dark matter halos in a simulation box.

Astronomy & Astrophysics↗
DOE OSTI2025

Global models predict clouds at the wrong time of day: Does it matter for radiation and climate?

Accurate prediction of future climate change hinges upon the ability of Earth system models (ESMs) to simulate clouds and their radiative effects. Even if an ESM can simulate the correct clouds, a systematic error in the amount of sunlight reflected by clouds (and, thus, cloud radiative effect) can exist if the clouds are simulated at the incorrect time of day. In this work, we develop an analytical model connecting diurnal cloud biases to emergent mean state radiative biases. With the use of satellite observations, we demonstrate that there are errors in the time of day that clouds are occurring in ESMs that would cause bias in shortwave cloud radiative effect (SWCRE) that is greater than 45% of the total SWCRE bias, but such errors in the cloud diurnal cycle are masked by other compensating errors, indicating that these ESMs are getting the right answer for the wrong reasons.

Geosciences↗
DOE OSTI2025

Urban weather modeling using WRF: linking physical assumptions, code implementation, and observational needs

The Weather Research and Forecasting (WRF) model includes urban schemes that simulate the influence of urban surfaces on the atmosphere using parameterizations for flux, and radiative exchanges. Three core schemes – the Bulk urban parameterization, Single-Layer Urban Canopy Model (SLUCM), and Multi-Layer Urban Canopy Model (MLUCM) – represent increasing levels of complexity. Although the parameterizations within these urban schemes are described in the literature, their specific implementation remains poorly documented, thus slowing down model development efforts. This manuscript provides a roadmap to the three urban schemes in WRF version 4.5.2, presenting equations using the same symbols as in the model code, along with references to code lines, and including graphics and explanations that connect the code to its physical foundations. Our thorough review of the urban parameterizations implemented in WRF version 4.5.2 highlighted a handful of parameters that may introduce discontinuities in simulations: (i) in the SLUCM, a 1 mm h −1 rain rate threshold is employed to switch between two minimum moisture availability parameterizations, thus impacting latent heat flux calculations; (ii) in the SLUCM a threshold is used to partition shortwave radiation into direct and diffuse components; (iii) in all three urban schemes, the bulk Richardson number is employed to select the similarity function, which influences the vertical distribution of heat and momentum. We also identified a highly simplified treatment of the radiative balance on roof surfaces. The implications of these simplifications can be assessed through targeted observations across relevant conditions, including varying precipitation rates, cloud cover, and transitions between stability regimes. Furthermore, the widespread application of the Monin-Obukhov similarity theory in these urban schemes warrants model evaluation under highly stable and unstable conditions and in heterogeneous urban settings with variable land cover and building heights on scales finer than model resolution. To address these challenges, we offer guidance on observational strategies, emphasizing the need for multi-parametric measurements to capture potential compensating biases and multi-height measurements that align with the levels where quantities are diagnostic and prognosed in the model (i.e., the lowest atmospheric level of the WRF model). Finally, our inspection of the code revealed implementation bugs that have now been corrected in WRF versions 4.6.0 and 4.6.1. Sensitivity tests over the Atlanta urban area show that these corrections affect surface temperatures, underscoring the importance of performing rigorous documentation and verification of the implementation of parameterizations in model code.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A Compound Poisson Generator Approach to Point-source Inference in Astrophysics

Abstract The identification and description of point sources is one of the oldest problems in astronomy, yet even today the correct statistical treatment for point sources remains one of the field’s hardest problems. For dim or crowded sources, likelihood-based inference methods are required to estimate the uncertainty on the characteristics of the source population. In this work, a new parametric likelihood is constructed for this problem using compound Poisson generator (CPG) functionals that incorporate instrumental effects from first principles. We demonstrate that the CPG approach exhibits a number of advantages over non-Poissonian template fitting (NPTF)—an existing method—in a series of test scenarios in the context of X-ray astronomy. These demonstrations show that the effect of the point-spread function, effective area, and choice of point-source spatial distribution cannot, generally, be factorized as they are in NPTF, while the new CPG construction is validated in these scenarios. Separately, an examination of the diffuse-flux emission limit is used to show that most simple choices of priors on the standard parameterization of the population model can result in unexpected biases: when a model comprising both a point-source population and diffuse component is applied to this limit, nearly all observed flux will be assigned to either the population or to the diffuse component. A new parameterization is presented for these priors that properly estimates the uncertainties in this limit. In this choice of priors, CPG correctly identifies that the fraction of flux assigned to the population model cannot be constrained by the data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Improving Effective Mass Estimations in Pu-Metal Annuli

Determining the effective mass of 240 Pu in a plutonium metal item can be achieved through a number of destructive and non-destructive assay techniques. However, these techniques have one or more shortcomings. These include the need for large quantities of plutonium, long measurement time, or lack of sufficient accuracy. While efforts have been made to mitigate these issues by estimating 240 Pu quantities through neutron coincidence counting techniques, these estimates are subject to systematic bias, and their estimates are not well characterized when other factors of the annulus’ physical form and composition are accounted for. In this work, we expand upon these non-destructive assay techniques via the implementation of random forest machine learning models, which produce correction functions that augment and improve the effective mass estimates derived from classical leakage multiplication, singles, doubles, and triples multiplicity counting equations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics

Understanding the driving forces behind the nucleation of different polymorphs is of great importance for material sciences and the pharmaceutical industry. This includes understanding the reaction coordinate that governs the nucleation process and correctly calculating the relative free energies of different polymorphs. Here, we demonstrate, for the prototypical case of urea nucleation from the melt, how one can learn such a one-dimensional reaction coordinate as a function of prespecified order parameters and use it to perform efficient biased all-atom molecular dynamics simulations. The reaction coordinate is learnt as a function of the generic thermodynamic and structural order parameters using the “spectral gap optimization of order parameters (SGOOP)” approach [Tiwary, P. and Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. (2016)] and is biased using well-tempered metadynamics simulations. The reaction coordinate gives insights into the role played by different structural and thermodynamics order parameters, and the biased simulations obtain accurate relative free energies for different polymorphs. This includes an accurate prediction of the approximate pressure at which urea undergoes a phase transition and one of the metastable polymorphs becomes the most stable conformation. Here, we believe the ideas demonstrated in this work will facilitate efficient sampling of nucleation in complex, generic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Assessing the accuracy of compound formation energies with quantum Monte Carlo

Accurately predicting the formation energy of a compound, which describes its thermodynamic stability, is a key challenge in materials physics. Here, we employ a many-body quantum Monte Carlo (QMC) with single-reference trial functions to compute the formation energy of two electronically disparate compounds, the intermetallic VPt2 and the semiconductor CuI, for which standard density functional theory (DFT) predictions using both the Perdew-Burke-Ernzerhof (PBE) and the strongly constrained and appropriately normed (SCAN) density functional approximations deviate markedly from available experimental values. For VPt2, we find an agreement between QMC, SCAN, and PBE0 estimates, which therefore remain in disagreement with the much less exothermic experimental value. For CuI, the QMC result agrees with neither SCAN nor PBE pointing towards DFT exchange-correlation biases, likely related to the localized Cu 3d electrons. Compared to the behavior of some density functional approximations within DFT, spin-averaged QMC exhibits a smaller but still appreciable deviation when compared to experiment. The QMC result is slightly improved by incorporating spin-orbit corrections for CuI and solid I 2 , so that experiment and theory are brought into imperfect but reasonable agreement within about 120 meV/atom.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Improved temperature control for measuring the humidity dependence of aerosol optical properties

Aerosols impact climate and cloud formation by their ability to take up water, which leads to changes in their optical properties. To better characterize the interactions of aerosol with water vapor, a humidification section has been added to the Cavity Attenuation Phase-shift Spectrometry (CAPS) instrument. The CAPS is a diode based method that provides simultaneous measurements of both aerosol total optical extinction and scattering in real-time. We are improving the humidity controlled sample line with new temperature controls. The current system suffers from particlelosses and poorly controlled humidity profiles, both of which were corrected for in the systems redesign. This improved wet-CAPS system has been integrated with a dry-CAPS to simultaneously measure the wet and dry aerosol optical properties. The two CAPS monitors were operated in a dry collection mode to ensure there were no biases between the instruments. Initial calibrations and data were collected to test the functionality of the dual CAPS system (wet + dry). The new two channel CAPS system improves our ability to measure the effects of humidity on aerosol optical properties.

58 GEOSCIENCES↗
DOE OSTI2023

A Gridded Solar Irradiance Ensemble Prediction System Based on WRF-Solar EPS and the Analog Ensemble

The WRF-Solar Ensemble Prediction System (WRF-Solar EPS) and a calibration method, the analog ensemble (AnEn), are used to generate calibrated gridded ensemble forecasts of solar irradiance over the contiguous United States (CONUS). Global horizontal irradiance (GHI) and direct normal irradiance (DNI) retrievals, based on geostationary satellites from the National Solar Radiation Database (NSRDB) are used for both calibrating and verifying the day-ahead GHI and DNI predictions (GDIP). A 10-member ensemble of WRF-Solar EPS is run in a re-forecast mode to generate day-ahead GDIP for three years. The AnEn is used to calibrate GDIP at each grid point independently using the NSRDB as the “ground truth”. Performance evaluations of deterministic and probabilistic attributes are carried out over the whole CONUS. The results demonstrate that using the AnEn calibrated ensemble forecast from WRF-Solar EPS contributes to improving the overall quality of the GHI predictions with respect to an AnEn calibrated system based only on the deterministic run of WRF-Solar. In fact, the calibrated WRF-Solar EPS’s mean exhibits a lower bias and RMSE than the calibrated deterministic WRF-Solar. Moreover, using the ensemble mean and spread as predictors for the AnEn allows a more effective calibration than using variables only from the deterministic runs. Finally, it has been shown that the recently introduced algorithm of correction for rare events is of paramount importance to obtain the lowest values of GHI from the calibrated ensemble (WRF-Solar EPS AnEn), qualitatively consistent with those observed from the NSRDB.

14 SOLAR ENERGY↗
DOE OSTI2020

Unfolding quantum computer readout noise

Abstract In the current era of noisy intermediate-scale quantum computers, noisy qubits can result in biased results for early quantum algorithm applications. This is a significant challenge for interpreting results from quantum computer simulations for quantum chemistry, nuclear physics, high energy physics (HEP), and other emerging scientific applications. An important class of qubit errors are readout errors. The most basic method to correct readout errors is matrix inversion, using a response matrix built from simple operations to probe the rate of transitions from known initial quantum states to readout outcomes. One challenge with inverting matrices with large off-diagonal components is that the results are sensitive to statistical fluctuations. This challenge is familiar to HEP, where prior-independent regularized matrix inversion techniques (“unfolding”) have been developed for years to correct for acceptance and detector effects, when performing differential cross section measurements. We study one such method, known as iterative Bayesian unfolding, as a potential tool for correcting readout errors from universal gate-based quantum computers. This method is shown to avoid pathologies from commonly used matrix inversion and least squares methods.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗