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

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

De novo design of protein structure and function with RFdiffusion

Abstract There has been considerable recent progress in designing new proteins using deep-learning methods 1–9 . Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher-order symmetric architectures, has yet to be described. Diffusion models 10,11 have had considerable success in image and language generative modelling but limited success when applied to protein modelling, probably due to the complexity of protein backbone geometry and sequence–structure relationships. Here we show that by fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal-binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryogenic electron microscopy structure of a designed binder in complex with influenza haemagglutinin that is nearly identical to the design model. In a manner analogous to networks that produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications.

Science & Technology - Other Topics↗
DOE OSTI2025

Calculation of ion–ion mutual neutralization rate constants using Landau–Zener theory coupled with trajectory simulations for Ar + –Cl − , Br − , I −

In this computational study, we self-consistently calculate the rate constants of mutual neutralization reactions by incorporating the electron transfer probability, using Landau–Zener state transition theory with inputs derived from ab initio quantum chemistry calculations, into classical trajectory simulations. Electronic structure calculations are done using correlation consistent basis sets with multi-reference configuration interaction to map all the molecular electronic states below the ion-dissociation limit as a function of the distance between the reacting species. Our electronic structure calculations have been significantly improved from our previous work through improved selection of molecular electronic configurations maintaining a fine grid of 1a 0 over a wide range of bond lengths and accurate treatment of spin–orbit couplings. Non-adiabatic coupling matrix elements are calculated with the three-point central difference method near each avoided crossing to estimate the exact crossing point R x and coupling parameter H if , which are inputs to the multi-channel Landau–Zener theory to calculate the electron transition probability. Our approach is applied to estimate the mutual neutralization rate constants for the following ion pairs: Ar + –Cl − , Ar + –Br − , Ar + –I − at ∼133 Pa. Furthermore, our predictions are compared against the experimental data reported. It is seen that the improvement in the electronic structure calculation results in excellent agreement between the simulation results and the available experimental data to within a factor of ∼2 or ∼±50%.

Complete-active space self-consistent field↗
DOE OSTI2025

Probabilistic flux limiters

The stable numerical integration of shocks in compressible flow simulations relies on the reduction or elimination of Gibbs phenomena (unstable, spurious oscillations). A popular method to virtually eliminate Gibbs oscillations caused by numerical discretization in under-resolved simulations is to use a flux limiter. A wide range of flux limiters have been studied in the literature, with recent interest in their optimization via machine learning methods trained on high-resolution datasets. The common use of flux limiters in numerical codes as plug-and-play blackbox components makes them key targets for design improvement. Even for deterministic dynamical models, numerical uncertainty is introduced via coarse-graining required by insufficient computational power to solve all scales of motion. Conventional flux limiters are deterministic and lack the capacity to address uncertainties, both aleatoric (inherent randomness) and epistemic (modeling uncertainty due to limited knowledge), which arise in coarse-grained numerical simulations. Here, we introduce a conceptually distinct type of flux limiter that is designed to handle the effects of randomness in the model and uncertainty in model parameters. Unlike traditional single-function flux limiters, these new probabilistic flux limiters incorporate multiple flux limiting functions, each applied with a learned probability drawn from high-resolution data to mitigate the effects of uncertainty in numerical simulations. This approach departs from traditional single-function limiters by explicitly modeling and incorporating uncertainty into the shock capturing process. Using the example of Burgers' equation as a testbed, we show that a machine learned, probabilistic flux limiter may be used in a shock capturing code to more accurately capture shock profiles. In particular, we show that our probabilistic flux limiter outperforms standard limiters and can be successively improved upon (up to a point) by expanding the set of probabilistically chosen flux limiting functions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Correcting for fibre assignment incompleteness in the DESI Bright Galaxy Survey

The Dark Energy Spectroscopic Instrument (DESI) Bright Galaxy Survey (BGS) will be a survey of bright, low-redshift galaxies, which is planned to cover an area of ~14000 square degrees in three passes. Each pass will cover the survey area with ~2000 pointings, each of area ~8 square degrees. The BGS is currently proposed to consist of a bright high priority sample to an r-band magnitude limit r ~ 19.5, with a fainter low priority sample to r ~ 20. The geometry of the DESI fibre positioners in the focal plane of the telescope affects the completeness of the survey and has a non-trivial impact on clustering measurements. Using a BGS mock catalogue, we demonstrate that completeness due to fibre assignment primarily depends on the surface density of galaxies. Completeness is high (>95 per cent) in low-density regions, but very low (<10 per cent) in the centre of massive clusters. We apply the pair inverse probability (PIP) weighting correction to clustering measurements from a BGS mock which has been through the fibre assignment algorithm. This method is only unbiased if it is possible to observe every galaxy pair. To expedite this, we randomly promote a small fraction of the fainter sample to be high priority, and dither the set of tile positions by a small angle. We show that inverse pair weighting combined with angular upweighting provides an unbiased correction to galaxy clustering measurements for the complete three pass survey, and also after one pass, which is highly incomplete.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

Wildfire Risk Mapping over the State of Mississippi: Land Surface Modeling Approach

Three fire risk indexes based on soil moisture estimates were applied to simulate wildfire probability over the southern part of Mississippi using the logistic regression approach. The fire indexes were retrieved from: (1) accumulated difference between daily precipitation and potential evapotranspiration (P-E); (2) top 10 cm soil moisture content simulated by the Mosaic land surface model; and (3) the Keetch-Byram drought index (KBDI). The P-E, KBDI, and soil moisture based indexes were estimated from gridded atmospheric and Mosaic-simulated soil moisture data available from the North American Land Data Assimilation System (NLDAS-2). Normalized deviations of these indexes from the 31-year mean (1980-2010) were fitted into the logistic regression model describing probability of wildfires occurrence as a function of the fire index. It was assumed that such normalization provides more robust and adequate description of temporal dynamics of soil moisture anomalies than the original (not normalized) set of indexes. The logistic model parameters were evaluated for 0.25 x0.25 latitude/longitude cells and for probability representing at least one fire event occurred during 5 consecutive days. A 23-year (1986-2008) forest fires record was used. Two periods were selected and examined (January mid June and mid September December). The application of the logistic model provides an overall good agreement between empirical/observed and model-fitted fire probabilities over the study area during both seasons. The fire risk indexes based on the top 10 cm soil moisture and KBDI have the largest impact on the wildfire odds (increasing it by almost 2 times in response to each unit change of the corresponding fire risk index during January mid June period and by nearly 1.5 times during mid September-December) observed over 0.25 x0.25 cells located along the state of Mississippi Coast line. This result suggests a rather strong control of fire risk indexes on fire occurrence probability over this region.

forest fire risk↗
DOE OSTI2020

Measurement of 3-Flavour Neutrino Oscillation Parameters in the NOvA Experiment

NOvA is a long-baseline neutrino oscillation experiment consisting of two functionally identical tracking calorimeters, a Near and Far Detector, that measure neutrino interactions induced by the Fermi National Accelerator Laboratory’s NuMI beam at baselines of 1 km and 810 km, respectively. The NuMI beam can be configured to produce either a primary ν µ neutrino or $\bar{ν}$ µ anti-neutrino beam. Neutrino oscillations are observed and measured by the analysis of ν µ + $\bar{ν}$ µ disappearance and νe + $\bar{ν}$ e appearance in the beam, comparing the neutrino energy spectra in the Near and Far detectors means that neutrino oscillation parameters sin 2 θ 23 , |Δ$m^2_{32}$|, and δ CP can be constrained. This thesis presents the 2018 NOvA ν µ +$\bar{ν}$ µ disappearance, ν e +$\bar{ν}$ e appearance, and combined analyses using both neutrino and anti-neutrino data, where oscillation fits have been performed, where possible, on an event-by-event basis rather than on a bin-by-bin basis as has conventionally been used in NOvA oscillation analyses. This allows for better precision in applying both neutrino oscillation probabilities and systematic uncertainties. Furthermore, oscillation analyses for the disappearance, appearance, and combined channels are presented using an unbinned likelihood fit and compared with the equivalent binned χ 2 likelihood fit used in the standard analysis. The 14 ktonne detector equivalent beam exposures used for this thesis are 8.85 × 10 20 and 6.91 × 10 20 protons on target for neutrino and antineutrino data respectively, corresponding to 5 years of NOvA data taking. A combined ν µ + $\bar{ν}$ µ disappearance and ν e + $\bar{ν}$ e appearance fit to the Far Detector data, assuming normal mass ordering and using the event-by-event oscillation and unbinned fitting methodologies, produces oscillation parameter constraints of Δ$m^2_{32}$ = (2.50$^{+0.08}_{-0.06}$) × 10 -3 eV 2 , sin 2 θ 23 = 0.59$^{+0.02}_{-0.04}$, and δ CP = 0.72$^{+0.5}_{-0.9}$π.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Development of a bayesian belief network model for the software reliability assessment of nuclear digital I and C safety systems - 206

Since the digital instrumentation and control systems are expected to play an important role for the safety systems in nuclear power plants (NPPs), the need has emerged to not only establish a basis for incorporating software behavior into digital I and C system reliability models, but also to quantify the failure probability of the software used in NPP digital protection systems. In this study, a Bayesian belief network (BBN) model is developed to quantitatively assess software reliability by estimating the number of faults in a software program considering its software development life cycle (SDLC). The model structure and parameters are established based on the information applicable to NPP safety-related systems and the evidence used to construct and quantify the BBN model was collected from three stages of expert elicitation. The software failure probability is estimated from the number of residual defects in a software program at the end of SDLC phase. As a case study, the BBN model was applied to quantify the software reliability of a typical digital protection software having the size of 50 function points and having the Medium development and validation and verification (V and V) qualities. The developed model can be applied to estimate the failure probability for both developing and deployed safety-related NPP software, and such results can be used to evaluate the quality of the digital I and C systems in addition to estimating potential reactor risk due to software failure. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2015

Correlation function induced by a generalized diffusion equation with the presence of a harmonic potential

An integro-differential diffusion equation with linear force, based on the continuous time random walk model, is considered. The equation generalizes the ordinary and fractional diffusion equations, which includes short, intermediate and long-time memory effects described by the waiting time probability density function. Analytical expression for the correlation function is obtained and analyzed, which can be used to describe, for instance, internal motions of proteins. The result shows that the generalized diffusion equation has a broad application and it may be used to describe different kinds of systems. - Highlights: • Calculation of the correlation function. • The correlation function is connected to the survival probability. • The model can be applied to the internal dynamics of proteins.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Uncertainty analysis for VERA problem 2 using the cell-code Condor v2.8.05

Condor is a cell-level neutronic calculation code that applies multi-group collision probabilities with heterogeneous response coupling method within generic geometry configurations. Under the Condor's code continuous development, the incorporation of up-to-date methodologies and state-of-the-art practices in reactor analysis represents a driving force. In this work, the capabilities of Condor v2.8.05 to develop an uncertainty analysis for realistic PWR-kind fuel assemblies are studied. The Total Monte Carlo approach is applied to quantify the impact of fabrication tolerances in the code's results for reactivity and power distributions, by means of randomly sampled input values using the VERA problem 2 as basis. The VERA problem 2 proposes a series of Westinghouse 2D 17 x 17-type fuel lattices, to be calculated reflected at beginning-of-life without Xe. The configurations correspond to a modern PWR. Selected neutronic parameters from Condor runs are thus analyzed in terms of the observed spread as well as the obtained distributions for the randomly perturbed cases, showing the capability of the code to handle the required input data, as well as its ability to provide valuable insights regarding uncertainty quantification.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2025

Converting sWeights to probabilities with density ratios

The use of machine learning approaches continues to have many benefits in experimental nuclear and particle physics. One common issue is generating training data which is sufficiently realistic to give reliable results. Here we advocate using real experimental data as the source of training data and demonstrate how one might subtract background contributions through the use of probabilistic weights which can be readily applied to training data. The sPlot formalism is a common tool used to isolate distributions from different sources. However, the negative sWeights produced by the sPlot technique can cause training problems and poor predictive power. This article demonstrates how density ratio estimation can be applied to convert sWeights to event probabilities, which we call drWeights. The drWeights can then be applied to produce the distributions of interest and are consistent with direct use of the sWeights. This article will also show how decision trees are particularly well suited to convert sWeights, with the benefit of fast prediction rates and adaptability to aspects of experimental data such as the data sample size and proportions of different event sources. We also show that a density ratio product approach in which the initial drWeights are reweighted by an additional converter gives substantially better results.

Glazier, Derek I. [Univ. of Glasgow, Scotland (Uni↗
DOE OSTI2023

An Analysis of the Johnson-Lindenstrauss Lemma with the Bivariate Gamma Distribution

Probabilistic proofs of the Johnson-Lindenstrauss lemma imply that random projection can reduce the dimension of a data set and approximately preserve pairwise distances. If a distance being approximately preserved is called a success, and the complement of this event is called a failure, then such a random projection likely results in no failures. Assuming a Gaussian random projection, the lemma is proved by showing that the no-failure probability is positive using a combination of Bonferroni's inequality and Markov's inequality. This paper modifies this proof in two ways to obtain a greater lower bound on the no-failure probability. First, Bonferroni's inequality is applied to pairs of failures instead of individual failures. Second, since a pair of projection errors has a bivariate gamma distribution, this probability of a pair of successes is bounded using an inequality from [Jensen, 1969]. If n is the number of points to be embedded and μ is the probability of success, then this leads to an increase in the lower bound on the no-failure probability of $\frac{1}{2}$ ($\genfrac{}{}{0pt}{}{n}{2}$) (1- μ ) 2 is ($\genfrac{}{}{0pt}{}{n}{2}$) is even and $\frac{1}{2}$ (($\genfrac{}{}{0pt}{}{n}{2}$)-1) (1- μ ) 2 if ($\genfrac{}{}{0pt}{}{n}{2}$) is odd. For example, if n =10 5 points are to be embedded in k =10 4 dimensions with a tolerance of ϵ=0.1, then the improvement in the lower bound is on the order of 10 -14 . We also show that further improvement is possible if the inequality in [Jensen, 1969] extends to three successes, though we do not have a proof of this result.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2013

Maximizing the biological effect of proton dose delivered with scanned beams via inhomogeneous daily dose distributions

Purpose: Biological effect of radiation can be enhanced with hypofractionation, localized dose escalation, and, in particle therapy, with optimized distribution of linear energy transfer (LET). The authors describe a method to construct inhomogeneous fractional dose (IFD) distributions, and evaluate the potential gain in the therapeutic effect from their delivery in proton therapy delivered by pencil beam scanning. Methods: For 13 cases of prostate cancer, the authors considered hypofractionated courses of 60 Gy delivered in 20 fractions. (All doses denoted in Gy include the proton's mean relative biological effectiveness (RBE) of 1.1.) Two types of plans were optimized using two opposed lateral beams to deliver a uniform dose of 3 Gy per fraction to the target by scanning: (1) in conventional full-target plans (FTP), each beam irradiated the entire gland, (2) in split-target plans (STP), beams irradiated only the respective proximal hemispheres (prostate split sagittally). Inverse planning yielded intensity maps, in which discrete position control points of the scanned beam (spots) were assigned optimized intensity values. FTP plans preferentially required a higher intensity of spots in the distal part of the target, while STP, by design, employed proximal spots. To evaluate the utility of IFD delivery, IFD plans were generated by rearranging the spot intensities from FTP or STP intensity maps, separately as well as combined using a variety of mixing weights. IFD courses were designed so that, in alternating fractions, one of the hemispheres of the prostate would receive a dose boost and the other receive a lower dose, while the total physical dose from the IFD course was roughly uniform across the prostate. IFD plans were normalized so that the equivalent uniform dose (EUD) of rectum and bladder did not increase, compared to the baseline FTP plan, which irradiated the prostate uniformly in every fraction. An EUD-based model was then applied to estimate tumor control probability (TCP) and normal tissue complication probability (NTCP). To assess potential local RBE variations, LET distributions were calculated with Monte Carlo, and compared for different plans. The results were assessed in terms of their sensitivity to uncertainties in model parameters and delivery. Results: IFD courses included equal number of fractions boosting either hemisphere, thus, the combined physical dose was close to uniform throughout the prostate. However, for the entire course, the prostate EUD in IFD was higher than in conventional FTP by up to 14%, corresponding to the estimated increase in TCP to 96% from 88%. The extent of gain depended on the mixing factor, i.e., relative weights used to combine FTP and STP spot weights. Increased weighting of STP typically yielded a higher target EUD, but also led to increased sensitivity of dose to variations in the proton's range. Rectal and bladder EUD were same or lower (per normalization), and the NTCP for both remained below 1%. The LET distributions in IFD also depended strongly on the mixing weights: plans using higher weight of STP spots yielded higher LET, indicating a potentially higher local RBE. Conclusions: In proton therapy delivered by pencil beam scanning, improved therapeutic outcome can potentially be expected with delivery of IFD distributions, while administering the prescribed quasi-uniform dose to the target over the entire course. The biological effectiveness of IFD may be further enhanced by optimizing the LET distributions. IFD distributions are characterized by a dose gradient located in proximity of the prostate's midplane, thus, the fidelity of delivery would depend crucially on the precision with which the proton range could be controlled.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A novel framework for increasing research transparency: Exploring the connection between diversity and innovation

A split sample/dual method research protocol is demonstrated to increase transparency while reducing the probability of false discovery. We apply the protocol to examine whether diversity in ownership teams increases or decreases the likelihood of a firm reporting a novel innovation using data from the 2018 United States Census Bureau’s Annual Business Survey. Transparency is increased in three ways: 1) all specification testing and identifying potentially productive models is done in an exploratory subsample that 2) preserves the validity of hypothesis test statistics fromde novoestimation in the holdout confirmatory sample with 3) all findings publicly documented in an earlier registered report and in this journal publication. Bayesian estimation procedures that leverage information from the exploratory stage included in the confirmatory stage estimation replace traditional frequentist null hypothesis significance testing. In addition to increasing statistical power by using information from the full sample, Bayesian methods directly estimate a probability distribution for the magnitude of an effect, allowing much richer inference. Estimated magnitudes of diversity along academic discipline, race, ethnicity, and foreign-born status dimensions are positively associated with innovation. A maximally diverse ownership team on these dimensions would be roughly six times more likely to report new-to-market innovation than a homophilic team.

Science & Technology - Other Topics↗
DOE OSTI2014

Neutron star masses and radii from quiescent low-mass x-ray binaries

We perform a systematic analysis of neutron star radius constraints from five quiescent low-mass X-ray binaries and examine how they depend on measurements of their distances and amounts of intervening absorbing material, as well as their assumed atmospheric compositions. We construct and calibrate to published results a semi-analytic model of the neutron star atmosphere which approximates these effects for the predicted masses and radii. Starting from mass and radius probability distributions established from hydrogen-atmosphere spectral fits of quiescent sources, we apply this model to compute alternate sets of probability distributions. We perform Bayesian analyses to estimate neutron star mass-radius curves and equation of state (EOS) parameters that best-fit each set of distributions, assuming the existence of a known low-density neutron star crustal EOS, a simple model for the high-density EOS, causality, and the observation that the neutron star maximum mass exceeds 2 M {sub ☉}. We compute the posterior probabilities for each set of distance measurements and assumptions about absorption and composition. We find that, within the context of our assumptions and our parameterized EOS models, some absorption models are disfavored. We find that neutron stars composed of hadrons are favored relative to those with exotic matter with strong phase transitions. In addition, models in which all five stars have hydrogen atmospheres are found to be weakly disfavored. Our most likely models predict neutron star radii that are consistent with current experimental results concerning the nature of the nucleon-nucleon interaction near the nuclear saturation density.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Small-Noise Analysis and Symmetrization of Implicit Monte Carlo Samplers

Implicit samplers are algorithms for producing independent, weighted samples from multivariate probability distributions. These are often applied in Bayesian data assimilation algorithms. We use Laplace asymptotic expansions to analyze two implicit samplers in the small noise regime. Our analysis suggests a symmetrization of the algorithms that leads to improved implicit sampling schemes at a relatively small additional cost. Here, computational experiments confirm the theory and show that symmetrization is effective for small noise sampling problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

A note on the logistic equation subject to uncertainties in parameters

This paper discusses the logistic equation subject to uncertainties in the intrinsic growth rate, α, in the initial population density, N{sub 0}, and in the environmental carrying capacity, K. These parameters are treated as independent random variables. The random variable transformation method is applied to compute the first probability density function of the time–population density, N(t), and of its inflection point, t{sup ∗}. Results for the density functions of N(t), for a fixed t>0, and t{sup ∗} are also provided for α, N{sub 0} and K uniformly distributed. Finally, numerical experiments illustrate the proposed theoretical results.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

A computationally efficient ductile damage model accounting for nucleation and micro-inertia at high triaxialities

The computational formulation of a micro-mechanical material model for the dynamic failure of ductile metals is presented in this paper. The statistical nature of porosity initiation is accounted for by introducing an arbitrary probability density function which describes the pores nucleation pressures. Each micropore within the representative volume element is modeled as a thick spherical shell made of plastically incompressible material. The treatment of porosity by a distribution of thick-walled spheres also allows for the inclusion of micro-inertia effects under conditions of shock and dynamic loading. The second order ordinary differential equation governing the microscopic porosity evolution is solved with a robust implicit procedure. A new Chebyshev collocation method is employed to approximate the porosity distribution and remapping is used to optimize memory usage. The adaptive approximation of the porosity distribution leads to a reduction of computational time and memory usage of up to two orders of magnitude. Moreover, the proposed model affords consistent performance: changing the nucleation pressure probability density function and/or the applied strain rate does not reduce accuracy or computational efficiency of the material model. The numerical performance of the model and algorithms presented is tested against three problems for high density tantalum: single void, one-dimensional uniaxial strain, and two-dimensional plate impact. Here, the results using the integration and algorithmic advances suggest a significant improvement in computational efficiency and accuracy over previous treatments for dynamic loading conditions.

42 ENGINEERING↗