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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

GEAR-MC and Differential-Operator Methods Applied to Electron-Photon Transport in the Integrated TIGER Series

The sensitivity analysis algorithms that have been developed by the radiation transport community in multiple neutron transport codes, such as MCNP and SCALE, are extensively used by fields such as the nuclear criticality community. However, these techniques have seldom been considered for electron transport applications. In the past, the differential-operator method with the single scatter capability has been implemented in Sandia National Laboratories’ Integrated TIGER Series (ITS) coupled electron-photon transport code. This work is meant to extend the available sensitivity estimation techniques in ITS by implementing an adjoint-based sensitivity method, GEAR-MC, to strengthen its sensitivity analysis capabilities. To ensure the accuracy of this method being extended to coupled electron-photon transport, it is compared against the central-difference and differential-operator methodologies to estimate sensitivity coefficients for an experiment performed by McLaughlin and Hussman. Energy deposition sensitivities were calculated using all three methods, and the comparison between them has provided confidence in the accuracy of the newly implemented method. Unlike the current implementation of the differential-operator method in ITS, the GEAR-MC method was implemented with the option to calculate the energy-dependent energy deposition sensitivities, which are the sensitivity coefficients for energy deposition tallies to energy-dependent cross sections. The energy-dependent cross sections could be the cross sections for the material, elements in the material, or reactions of interest for the element. Further, these sensitivities were compared to the energy-integrated sensitivity coefficients and exhibited a maximum percentage difference of 2.15%.

42 ENGINEERING↗
DOE OSTI2011

A DIFFERENTIAL CHEMICAL ELEMENT ANALYSIS OF THE METAL-POOR GLOBULAR CLUSTER NGC 6397

We present chemical abundances in three red giants and two turnoff (TO) stars in the metal-poor Galactic globular cluster (GC) NGC 6397 based on spectroscopy obtained with the Magellan Inamori Kyocera Echelle high-resolution spectrograph on the Magellan 6.5 m Clay telescope. Our results are based on a line-by-line differential abundance analysis relative to the well-studied red giant Arcturus and the Galactic halo field star Hip 66815. At a mean of -2.10 {+-} 0.02 (stat.) {+-}0.07 (sys.), the differential iron abundance is in good agreement with other studies in the literature based on gf-values. As in previous differential works we find a distinct departure from ionization equilibrium in that the abundances of Fe I and Fe II differ by {approx}0.1 dex, with opposite signs for the red giant branch (RGB) and TO stars. The {alpha}-element ratios are enhanced to 0.4 (RGB) and 0.3 dex (TO), respectively, and we also confirm strong variations in the O, Na, and Al/Fe abundance ratios. Accordingly, the light-element abundance patterns in one of the red giants can be attributed to pollution by an early generation of massive Type II supernovae. TO and RGB abundances are not significantly different, with the possible exception of Mg and Ti, which are, however, amplified by the patterns in one TO star additionally belonging to this early generation of GC stars. We discuss interrelations of these light elements as a function of the GC metallicity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

MODELING OF DIFFERENTIAL ROTATION IN RAPIDLY ROTATING SOLAR-TYPE STARS

We investigate differential rotation in rapidly rotating solar-type stars by means of an axisymmetric mean field model that was previously applied to the Sun. This allows us to calculate the latitudinal entropy gradient with a reasonable physical basis. Our conclusions are as follows. (1) Differential rotation approaches the Taylor-Proudman state when stellar rotation is faster than solar rotation. (2) Entropy gradient generated by the attached subadiabatic layer beneath the convection zone becomes relatively small with a large stellar angular velocity. (3) Turbulent viscosity and turbulent angular momentum transport determine the spatial difference of angular velocity {Delta}{Omega}. (4) The results of our mean field model can explain observations of stellar differential rotation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

SOLAR CYCLE VARIABILITY AND SURFACE DIFFERENTIAL ROTATION FROM Ca II K-LINE TIME SERIES DATA

Analysis of over 36 yr of time series data from the NSO/AFRL/Sac Peak K-line monitoring program elucidates 5 components of the variation of the 7 measured chromospheric parameters: (a) the solar cycle (period {approx} 11 yr), (b) quasi-periodic variations (periods {approx} 100 days), (c) a broadband stochastic process (wide range of periods), (d) rotational modulation, and (e) random observational errors, independent of (a)-(d). Correlation and power spectrum analyses elucidate periodic and aperiodic variation of these parameters. Time-frequency analysis illuminates periodic and quasi-periodic signals, details of frequency modulation due to differential rotation, and in particular elucidates the rather complex harmonic structure (a) and (b) at timescales in the range {approx}0.1-10 yr. These results using only full-disk data suggest that similar analyses will be useful for detecting and characterizing differential rotation in stars from stellar light curves such as those being produced by NASA's Kepler observatory. Component (c) consists of variations over a range of timescales, in the manner of a 1/f random process with a power-law slope index that varies in a systematic way. A time-dependent Wilson-Bappu effect appears to be present in the solar cycle variations (a), but not in the more rapid variations of the stochastic process (c). Component (d) characterizes differential rotation of the active regions. Component (e) is of course not characteristic of solar variability, but the fact that the observational errors are quite small greatly facilitates the analysis of the other components. The data analyzed in this paper can be found at the National Solar Observatory Web site http://nsosp.nso.edu/cak{sub m}on/, or by file transfer protocol at ftp://ftp.nso.edu/idl/cak.parameters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

Differential rotation in solar-like stars from global simulations

To explore the physics of large-scale flows in solar-like stars, we perform three-dimensional anelastic simulations of rotating convection for global models with stratification resembling the solar interior. The numerical method is based on an implicit large-eddy simulation approach designed to capture effects from non-resolved small scales. We obtain two regimes of differential rotation, with equatorial zonal flows accelerated either in the direction of rotation (solar-like) or in the opposite direction (anti-solar). While the models with the solar-like differential rotation tend to produce multiple cells of meridional circulation, the models with anti-solar differential rotation result in only one or two meridional cells. Our simulations indicate that the rotation and large-scale flow patterns critically depend on the ratio between buoyancy and Coriolis forces. By including a sub-adiabatic layer at the bottom of the domain, corresponding to the stratification of a radiative zone, we reproduce a layer of strong radial shear similar to the solar tachocline. Similarly, enhanced super-adiabaticity at the top results in a near-surface shear layer located mainly at lower latitudes. The models reveal a latitudinal entropy gradient localized at the base of the convection zone and in the stable region, which, however, does not propagate across the convection zone. In consequence, baroclinicity effects remain small, and the rotation isocontours align in cylinders along the rotation axis. Our results confirm the alignment of large convective cells along the rotation axis in the deep convection zone and suggest that such 'banana-cell' pattern can be hidden beneath the supergranulation layer.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

On obliquely magnetized and differentially rotating stars

We investigate the interaction of differential rotation and a misaligned magnetic field. The incompressible magnetohydrodynamic equations are solved numerically for a free-decay problem. In the kinematic limit, differential rotation annihilates the non-axisymmetric field on a timescale proportional to the cube root of magnetic Reynolds number (Rm), as predicted by Rädler. Nonlinearly, the outcome depends upon the initial energy in the non-axisymmetric part of the field. Sufficiently weak fields approach axisymmetry as in the kinematic limit; some differential rotation survives across magnetic surfaces, at least on intermediate timescales. Stronger fields enforce uniform rotation and remain non-axisymmetric. The initial field strength that divides these two regimes does not follow the scaling Rm{sup −1/3} predicted by quasi-kinematic arguments, perhaps because our Rm is never sufficiently large or because of reconnection. We discuss the possible relevance of these results to tidal synchronization and tidal heating of close binary stars, particularly double white dwarfs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

DYNAMO EFFECTS NEAR THE TRANSITION FROM SOLAR TO ANTI-SOLAR DIFFERENTIAL ROTATION

Numerical MHD simulations play an increasingly important role for understanding the mechanisms of stellar magnetism. We present simulations of convection and dynamos in density-stratified rotating spherical fluid shells. We employ a new 3D simulation code for obtaining the solution of a physically consistent anelastic model of the process with a minimum number of parameters. The reported dynamo simulations extend into a “buoyancy-dominated” regime where the buoyancy forcing is dominant while the Coriolis force is no longer balanced by pressure gradients, and strong anti-solar differential rotation develops as a result. We find that the self-generated magnetic fields, despite being relatively weak, are able to reverse the direction of differential rotation from anti-solar to solar-like. We also find that convection flows in this regime are significantly stronger in the polar regions than in the equatorial region, leading to non-oscillatory dipole-dominated dynamo solutions, and to a concentration of magnetic field in the polar regions. We observe that convection has a different morphology in the inner and the outer part of the convection zone simultaneously such that organized geostrophic convection columns are hidden below a near-surface layer of well-mixed highly chaotic convection. While we focus our attention on the buoyancy-dominated regime, we also demonstrate that conical differential rotation profiles and persistent regular dynamo oscillations can be obtained in the parameter space of the rotation-dominated regime even within this minimal model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

SCATTER-DOMINATED INTERPLANETARY TRANSPORT OF SOLAR ENERGETIC PARTICLES IN LARGE GRADUAL EVENTS AND THE FORMATION OF DOUBLE POWER-LAW DIFFERENTIAL FLUENCE SPECTRA OF GROUND-LEVEL EVENTS DURING SOLAR CYCLE 23

The effects of scatter-dominated interplanetary transport on the spectral properties of the differential fluence of large gradual solar energetic particle (SEP) events are investigated analytically. The model assumes for simplicity radial constant solar wind and radial magnetic field. The radial diffusion coefficient is calculated with quasilinear theory by assuming a spectrum of Alfvén waves propagating parallel to the magnetic field. Cross-field transport is neglected. The model takes into consideration several essential features of gradual event transport: nearly isotropic ion distributions, adiabatic deceleration in a divergent solar wind, and particle radial scattering mean free paths increasing with energy. Assuming an impulsive and spherically symmetric injection of SEPs with a power-law spectrum near the Sun, the predicted differential fluence spectrum exhibits at 1 AU three distinctive power laws for different energy domains. The model naturally reproduces the spectral features of the double power-law proton differential fluence spectra that tend to be observed in extremely large SEP events. We select nine western ground-level events (GLEs) out of the 16 GLEs during Solar Cycle 23 and fit the observed double power-law spectra to the analytical predictions. The compression ratio of the accelerating shock wave, the power-law index of the ambient wave intensity, and the proton radial scattering mean free path are determined for the nine GLEs. The derived parameters are generally in agreement with the characteristic values expected for large gradual SEP events.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Multimodal differential emission measure in the solar corona

The Atmospheric Imaging Assembly (AIA) telescope on board the Solar Dynamics Observatory provides coronal extreme ultraviolet imaging over a broader temperature sensitivity range than the previous generations of instruments (Extreme Ultraviolet Imager; EUVI, EIT, and TRACE). Differential emission measure tomography (DEMT) of the solar corona based on AIA data is presented here for the first time. The main product of DEMT is the three-dimensional distribution of the local differential emission measure (LDEM). While in previous studies, based on EIT or EUVI data, there were three available EUV bands, the present study is based on the four cooler AIA bands (aimed at studying the quiet sun). The AIA filters allow exploration of new parametric LDEM models. Since DEMT is better suited for lower activity periods, we use data from Carrington Rotation 2099, when the Sun was in its most quiescent state during the AIA mission. Also, we validate the parametric LDEM models by using them to perform a bi-dimensional differential emission measure (DEM) analysis on sets of simultaneous AIA images, and comparing results with those obtained using other methods. Our study reveals a ubiquitous bimodal LDEM distribution in the quiet diffuse corona, characterized by two well-defined average centroid temperatures 〈T{sub 0,1}〉=(1.47±0.05) MK and 〈T{sub 0,2}〉=(2.57±0.05) MK. We argue that the nanoflare heating scenario is less likely to explain these results, and that alternative mechanisms, such as wave dissipation, appear better supported by our results.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings

SUMMARY: We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e. DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 28 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. AVAILABILITY AND IMPLEMENTATION: Model, codes, and data are publically available at https://github.com/MAGICS-LAB/DNABERT_S.

Zhou, Zhihan↗
DOE OSTI2020

Transporters and ascorbate–glutathione metabolism for differential cadmium accumulation and tolerance in two contrasting willow genotypes

Salix matsudana Koidz is a low cadmium (Cd)-accumulating willow, whereas its cultivated variety, Salix matsudana var. matsudana f. umbraculifera Rehd., is a high Cd-accumulating and tolerant willow (HCW). The physiological and molecular mechanisms underlying differential Cd accumulation and tolerance in the two Salix species are poorly understood. In this study, we confirmed that the differential Cd translocation capacity from roots to the shoots leads to the differential Cd accumulation in their aboveground parts between these two willow genotypes. Cadmium accumulation happens preferentially in the transport pathway, and Cd is mainly located in the vacuolar, cell wall and intercellular space in HCW bark by cadmium location analysis at tissue and subcellular levels. Comparative transcriptome analysis revealed that higher expressions of several metal transporter genes (ATP-binding cassette transporters, K + transporters/channels, yellow stripe-like proteins, zinc-regulated transporter/iron-regulated transporter-like proteins, etc.) are involved in root uptake and translocation capacity in HCW; meanwhile, ascorbate–glutathione metabolic pathways play essential roles in Cd detoxification and higher tolerance of the Cd-accumulator HCW. These results lay the foundation for further understanding the molecular mechanisms of Cd accumulation in woody plants and provide new insights into molecular-assisted-screening woody plant varieties for phytoremediation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

SODAs: sparse optimization for the discovery of differential and algebraic equations

Differential-algebraic equations (DAEs) integrate ordinary differential equations (ODEs) with algebraic constraints, providing a fundamental framework for developing models of dynamical systems characterized by time-scale separation, conservation laws and physical constraints. While sparse optimization has revolutionized model development by allowing data-driven discovery of parsimonious models from a library of possible equations, existing approaches for dynamical systems assume DAEs can be reduced to ODEs by eliminating variables before model discovery. This assumption limits the applicability of such methods for DAE systems with unknown constraints and time scales. We introduce sparse optimization for differential-algebraic systems (SODAs), a data-driven method for the identification of DAEs in their explicit form. By discovering the algebraic and dynamic components sequentially without prior identification of the algebraic variables, this approach leads to a sequence of convex optimization problems. It has the advantage of discovering interpretable models that preserve the structure of the underlying physical system. To this end, SODAs improves since SODAs is singular numerical stability when handling high correlations between library terms, caused by near-perfect algebraic relationships, by iteratively refining the conditioning of the candidate library. We demonstrate the performance of our method on biological, mechanical and electrical systems, showcasing its robustness to noise in both simulated time series and real-time experimental data.

DAE↗
DOE OSTI2025

Fast, differentiable, and extensible big bang nucleosynthesis package

Here, we introduce light isotope nucleosynthesis with JAX (LINX), a new differentiable public big bang nucleosynthesis code designed for fast parameter estimation. By leveraging JAX, LINX achieves both speed and differentiability, enabling the use of Bayesian inference, including gradient-based methods. We discuss the formalism used in LINX for rapid primordial elemental abundance predictions and give examples of how LINX can be used. When combined with differentiable cosmic microwave background power spectrum emulators, LINX can be used for joint cosmic microwave background and big bang nucleosynthesis analyses without requiring extensive computational resources, including on personal hardware.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Quantum advantage for differential equation analysis

Quantum algorithms for differential equation solving, data processing, and machine learning potentially offer an exponential speedup over all known classical algorithms. However, there also exist obstacles to obtaining this potential speedup in useful problem instances. The essential obstacle for quantum differential equation solving is that outputting useful information may require difficult postprocessing, and the essential obstacle for quantum data processing and machine learning is that inputting the data is a difficult task just by itself. In this study, we demonstrate that, when combined, these difficulties solve one another. We show how the output of quantum differential equation solving can serve as the input for quantum data processing and machine learning, allowing dynamical analysis in terms of principal components, power spectra, and wavelet decompositions. To illustrate this, we consider continuous-time Markov processes on epidemiological and social networks. These quantum algorithms provide an exponential advantage over existing classical Monte Carlo methods.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Differential study on molecular suppressed ionization in intense linearly and circularly polarized laser fields

We present a differential study on above-threshold ionization of the O{sub 2} (N{sub 2}) molecule as well as the companion atom Xe (Ar) (with close ionization potential) produced by linearly and circularly polarized laser fields (25 fs, 795 nm). The photoelectron angular distributions of the companion target are similar at the same laser condition. In both linearly and circularly polarized fields, we observe that the photoelectron yields of O{sub 2} are suppressed in the entire energy spectral range as compared with Xe with fully differential measurements, but not for the N{sub 2}-Ar pair. This is different from the prediction of photoelectron energy spectra by the model including the interference terms [Phys. Rev. Lett. 85, 2280 (2000)], from which the low-energy photoelectrons of O{sub 2} were expected to be strongly suppressed in both linearly and circularly polarized laser fields. Resorting to the basic strong-field ionization picture, we believe that the lower orbital-dependent multiphoton excitation or tunneling possibility of O{sub 2} as compared with Xe is responsible for this effect. High-resolution fully differential data pose a stringent test on the current strong-field calculations on molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

Torque Differential Magnetometry Using the qPlus Mode of a Quartz Tuning Fork

A quartz tuning fork is the key component of high-resolution atomic force microscope. Because of its high quality factor, a quartz tuning fork can also be used for high-sensitivity magnetometry. In this work, we develop a highly sensitive torque differential magnetometry using the qPlus mode of a quartz tuning fork. The tuning fork is driven by an ac voltage, and its deflection is measured by the resultant ac current. We observe a sharp resonance of the quartz tuning fork at low temperatures down to 1.6 K. We calibrate our torque differential magnetometry by measuring the angular dependence of the hysteresis loop in single-crystal Fe 0.25 TaS 2 . Furthermore, we demonstrate the high sensitivity of the torque differential magnetometry by measuring the quantum oscillations of a bismuth single crystal. The extracted Fermi-surface cross sections are consistent with those of bismuth crystals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Multiparticle integral and differential correlation functions

This paper formalizes the use of integral and differential cumulants for measurements of multiparticle event-by-event transverse momentum fluctuations, rapidity fluctuations, as well as net-charge fluctuations. This enables the introduction of multiparticle balance functions, defined based on differential correlation functions (factorial cumulants), that suppress two- and three-prong resonance decays effects and enable measurements of underlying long-range correlations obeying quantum number conservation constraints. These multiparticle balance functions satisfy simple sum rules determined by quantum number conservation. It is additionally shown that these multiparticle balance functions arise as an intrinsic component of high-order net-charge cumulants. This implies that the magnitude of these cumulants, measured in a specific experimental acceptance, is strictly constrained by charge conservation and primarily determined by the rapidity and momentum width of these balance functions. The paper also presents techniques to reduce the computation time of differential correlation functions up to order n = 10 based on the methods of moments. Published by the American Physical Society 2024

Physics↗