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At least 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

A Systems Biology Platform for Characterizing Regulatory and Metabolic Pathways that Influence and Control Microbial Hydrogen Production

In this project, we created a novel systems biology technology platform and resources that can be used to reverse engineer and analyze gene regulatory networks and metabolic pathways that influence and control microbial hydrogen production. We constructed genome-scale transcriptional regulatory and metabolic models using automated model reconstruction methods, and subsequently integrated the regulatory and metabolic models for computational analysis. We devised novel algorithms for inferring putative regulatory architectures of metabolic pathways based on their topology, and for integrating gene expression information in flux balance analysis (FBA) models towards computing dynamical changes in metabolic objectives. From a metabolic engineering perspective, we improved and applied a method for predicting optimal environmental conditions and genetic modifications towards maximal productions of multiple desired metabolic outputs. We also developed and tested an improved flux balance approach for predicting the response of metabolic networks to genetic perturbations, proving that errors in model predictions are approaching the limit of experimental uncertainty. We also used the metabolic and regulatory models to identify relevant metabolic processes and pathways involved in hydrogen production. Below we provide a summary and details of our achievements.

Collins, James J.↗
NASA NTRS1990

A spectrum model for weakly anisotropic turbulence

A simple model, parameterized by the Reynolds stress anisotropy, is proposed for the spectrum of weakly anisotropic turbulence. It contains a model constant that affects its region of realizability. This spectrum model is used to derive a one-point closure to the rapid pressure-strain term. The derived pressure-strain model is linear in the Reynolds stress anisotropy and is of the same form as the closure model of Launder et al. (1975). The spectrum model becomes unrealizable in some regions of wave space for sufficiently large anisotropy of the Reynolds stress, and this is used to infer the region of validity of the linear closure model. It is found that the extent of the valid region is very small when the model constant is set to match rapid distortion theory, and largest for a model-constant set close to the value suggested by LRR. However, even the largest valid domain does not extend very far from isotropy, suggesting inherent weakness in the linear pressure-strain models.

Shih, Tsan-Hsing↗
DOE OSTI2025

An integrated integral projection model ( IPM 2 ) to disentangle size‐structured harvest and natural mortality

Abstract Body size is one of the most important traits governing individual‐level demographic rates and modulating population‐level processes. Multiple size‐dependent demographic rates can simultaneously change population structure, so distinguishing their individual contributions to overall population dynamics remains a challenge. Disentangling size‐dependent harvest rates from other demographic rates is critical for assessing the impact of removal on populations of invasive species. Inference about invasive populations can be difficult, however, as observations are often collected opportunistically as part of removal programs, rather than experimentally designed. Yet accurate inference is essential for understanding the feasibility of population suppression and optimising management decisions. We develop an integrated integral projection model (IPM 2 ) that leverages the strengths of the integrated population model and integral projection model to enable inference about complex, size‐structured demographic rates from imperfect observations. We apply the IPM 2 in the context of invasive European green crab ( Carcinus maenas ), a species for which individual body size strongly regulates both the observation‐generating process and latent, population dynamics. The IPM 2 facilitates the distinct estimation of green crab size‐structured harvest and natural mortality rates, parameters for which no explicit data is collected and that are unidentifiable in component datasets of the integrated population model. The model represents how the green crab population changes over time, providing the first estimates of size‐structured abundance of this high‐priority species. By forecasting the stable size distribution and equilibrium population size under varying removal efforts, we demonstrate that extremely high levels of removal effort can reduce the equilibrium green crab population size. Yet these high mortality rates also shift the stable size distribution and increase the equilibrium abundance of smaller crabs, since size‐selective removal alters intraspecific interactions. The ecological outcome of this shift in size structure will be variable, as green crab size modulates only some of its interactions with other species. These results highlight the value of the IPM 2 framework for inferring complex population dynamics with information needs that outpace information in individual observational datasets, providing a path forward for accurate assessment of conservation programs.

Keller, Abigail G. [Department of Environment Scie↗
DOE OSTI2017

The Atmospheric Response to High Nonthermal Electron Beam Fluxes in Solar Flares. I. Modeling the Brightest NUV Footpoints in the X1 Solar Flare of 2014 March 29

The 2014 March 29 X1 solar flare (SOL20140329T17:48) produced bright continuum emission in the far- and near-ultraviolet (NUV) and highly asymmetric chromospheric emission lines, providing long-sought constraints on the heating mechanisms of the lower atmosphere in solar flares. We analyze the continuum and emission line data from the Interface Region Imaging Spectrograph (IRIS) of the brightest flaring magnetic footpoints in this flare. We compare the NUV spectra of the brightest pixels to new radiative-hydrodynamic predictions calculated with the RADYN code using constraints on a nonthermal electron beam inferred from the collisional thick-target modeling of hard X-ray data from Reuven Ramaty High Energy Solar Spectroscopic Imager . We show that the atmospheric response to a high beam flux density satisfactorily achieves the observed continuum brightness in the NUV. The NUV continuum emission in this flare is consistent with hydrogen (Balmer) recombination radiation that originates from low optical depth in a dense chromospheric condensation and from the stationary beam-heated layers just below the condensation. A model producing two flaring regions (a condensation and stationary layers) in the lower atmosphere is also consistent with the asymmetric Fe ii chromospheric emission line profiles observed in the impulsive phase.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2017

The Atmospheric Response to High Nonthermal Electron Beam Fluxes in Solar Flares. I. Modeling the Brightest NUV Footpoints in the X1 Solar Flare of 2014 March 29

The 2014 March 29 X1 solar flare (SOL20140329T17:48) produced bright continuum emission in the far- and near-ultraviolet (NUV) and highly asymmetric chromospheric emission lines, providing long-sought constraints on the heating mechanisms of the lower atmosphere in solar flares. We analyze the continuum and emission line data from the Interface Region Imaging Spectrograph (IRIS) of the brightest flaring magnetic footpoints in this flare. We compare the NUV spectra of the brightest pixels to new radiative-hydrodynamic predictions calculated with the RADYN code using constraints on a nonthermal electron beam inferred from the collisional thick-target modeling of hard X-ray data from Reuven Ramaty High Energy Solar Spectroscopic Imager. We show that the atmospheric response to a high beam flux density satisfactorily achieves the observed continuum brightness in the NUV. The NUV continuum emission in this flare is consistent with hydrogen (Balmer) recombination radiation that originates from low optical depth in a dense chromospheric condensation and from the stationary beam-heated layers just below the condensation. A model producing two flaring regions (a condensation and stationary layers) in the lower atmosphere is also consistent with the asymmetric Fe II chromospheric emission line profiles observed in the impulsive phase.

Kowalski, Adam F.↗
DOE OSTI2015

The complex accretion geometry of GX 339–4 as seen by NuSTAR and Swift

We present spectral analyses of five Nuclear Spectroscopic Telescope Array and Swift observations of GX 339–4 taken during a failed outburst during the summer of 2013. These observations cover Eddington luminosity fractions in the range ≈0.9%–6%. Throughout this outburst GX 339–4 stayed in the hard state and all five observations show similar X-ray spectra, with a hard power law with a photon index near 1.6, and significant contribution from reflection. Using simple reflection models we find unrealistically high iron abundances. Allowing for different photon indices for the continuum incident on the reflector relative to the underlying observed continuum results in a statistically better fit and reduced iron abundances. With a photon index around 1.3, the input power law on the reflector is significantly harder than that which is directly observed. We study the influence of different emissivity profiles and geometries and consistently find an improvement when using separate photon indices. The inferred inner accretion disk radius is strongly model dependent, but we do not find evidence for a truncation radius larger than 100 r{sub g} in any model. The data do not allow independent spin constraints, but the results are consistent with the literature (i.e., a>0). Our best-fit models indicate an inclination angle in the range 40°–60°, consistent with limits on the orbital inclination but higher than reported in the literature using standard reflection models. The iron line around 6.4 keV is clearly broadened, and we detect a superimposed narrow core as well. This core originates from a fluorescent region outside the influence of the strong gravity of the black hole. Additionally, we discuss possible geometries.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

The Double-edged Sword of Data-driven Super-Resolution: Adversarial Super-resolution Models

Data-driven super-resolution (SR) methods are often integrated into imaging pipelines as preprocessing steps to improve downstream tasks such as classification and detection. However, these SR models introduce a previously unexplored attack surface into imaging pipelines. In this paper, we present AdvSR, a framework demonstrating that adversarial behavior can be embedded directly into SR model weights during training, requiring no access to inputs at inference time. Unlike prior attacks that perturb inputs or rely on backdoor triggers, AdvSR operates entirely at the model level. By jointly optimizing for reconstruction quality and targeted adversarial outcomes, AdvSR produces models that appear benign under standard image quality metrics while inducing downstream misclassification. We evaluate AdvSR on three SR architectures (SRCNN, EDSR, SwinIR) paired with a YOLOv11 classifier and demonstrate that AdvSR models can achieve high attack success rates with minimal quality degradation. These findings highlight a new model-level threat for imaging pipelines, with implications for how practitioners source and validate models in safety-critical applications.

Sullivan, Haley [ORNL] (ORCID:0000000274069217)↗
NASA NTRS1982

Investigation of MAGSAT and TRIAD magnetometer data to provide corrective information on high-lattitude external fields

Disturbances in the MAGSAT magnetometer data set due to high latitude phenomena were evaluated. Much of the categorization of disturbances due to Birkeland currents, ionospheric Hall currents, fine structure and wave phenomena was done with the MAGSAT data catalog. A color graphics technique was developed for the display of disturbances from multiple orbits, from which one can infer a 'global-image' of the current systems of the auroral zone. The MAGSAT 4/81 magnetic field model appears to represent the Earth's main field at high latitudes very well for the epoch 1980. MAGSAT's low altitude allows analysis of disturbances in the magnetometer data due to ionospheric electrojet currents. These current distributions were modeled properly for single events as a precursor to the inference of the Birkeland current system. MAGSAT's orbit was approximately shared with that of the Navy/APL TRIAD satellite. This allowed space-time studies of the magnetic disturbance signatures to be performed, the result being an approximately 75% agreement in, as well as high frequency of, signatures due to Birkeland currents. Thus the field-aligned currents are a steady-state participant in the Earth's magnetospheric current system.

Potemra, T. A.↗
NASA NTRS1972

Thermodynamic models in cosmochemical systems.

Generalized computer methods are developed for inferring details of the formation of cosmochemical systems. Compositions of ideal gas mixtures existing in equilibrium with multicomponent solid and liquid phases are calculated. A comparison of computed results with experimental data is made for the ternary system MgO-FeO-SiO2. While the ideal-solution approximation is shown to be inaccurate in dealing with the silicate melts, the stable phases and compositions can be accurately calculated in a system where there are only solids and gas. A model system containing the elements H, O, Si, Mg, S, C, Cl, and F is investigated over a range of compositions involving the gas and ten solid phases, to show the power of the technique in dealing with complex gas-solid equilibria. Systems close to cosmic composition are next considered, both with and without iron.

Griffiths, P. R.↗
DOE OSTI2021

Experimentally Inferred Fusion Yield Dependencies of OMEGA Inertial Confinement Fusion Implosions

Statistical modeling of experimental and simulation databases has enabled the development of an accurate predictive capability for deuterium-tritium layered cryogenic implosions at the OMEGA laser. Here, a physics-based statistical mapping framework is described and used to uncover the dependencies of the fusion yield. This model is used to identify and quantify the degradation mechanisms of the fusion yield in direct-drive implosions on OMEGA. The yield is found to be reduced by the ratio of laser beam to target radius, the asymmetry in inferred ion temperatures from the $l$ = 1 mode, the time span over which tritium fuel has decayed, and parameters related to the implosion hydrodynamic stability. When adjusted for tritium decay and $l$ = 1 mode, the highest yield in OMEGA cryogenic implosions is predicted to exceed 2 × 10 14 fusion reactions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Learning from Imperfections: Predicting Structure and Thermodynamics from Atomic Imaging of Fluctuations

In materials characterization, traditionally a single experimental sample is used to derive information about a single point in the composition space, while the imperfections, impurities, and stochastic details of material structure are deemed irrelevant or complicating factors in the analysis. Here we demonstrate that atomic-scale studies of a single nominal composition can provide information about microstructures and thermodynamic response over a finite area of chemical space. Using the principles of statistical inference, we develop a framework for incorporating structural fluctuations into statistical mechanical models and use it to solve the inverse problem of deriving effective interatomic interactions responsible for elemental segregation in a La 5/8 Ca 3/8 MnO 3 thin film. Here, the results are further analyzed by a variational autoencoder to detect anomalous behavior in the composition phase diagram. This study provides a framework for creating generative models from a combination of multiple experimental data and provides direct insight into the driving forces for cation segregation in manganites.

36 MATERIALS SCIENCE↗
NASA NTRS1981

Advantages of multigrid methods for certifying the accuracy of PDE modeling

Numerical techniques for assessing and certifying the accuracy of the modeling of partial differential equations (PDE) to the user's specifications are analyzed. Examples of the certification process with conventional techniques are summarized for the three dimensional steady state full potential and the two dimensional steady Navier-Stokes equations using fixed grid methods (FG). The advantages of the Full Approximation Storage (FAS) scheme of the multigrid technique of A. Brandt compared with the conventional certification process of modeling PDE are illustrated in one dimension with the transformed potential equation. Inferences are drawn for how MG will improve the certification process of the numerical modeling of two and three dimensional PDE systems. Elements of the error assessment process that are common to FG and MG are analyzed.

Forester, C. K.↗
DOE OSTI2022

Synthesis of observed and simulated rain microphysics to inform a new Bayesian statistical framework for microphysical parameterization in climate models (Final Scientific Report)

This project aimed to investigate a new approach to bulk microphysics schemes. We identified the need to move beyond the fixed structural assumptions and approximation of existing schemes. For example, most schemes assume some functional form for the rain drop size distribution (e.g. a gamma or exponential distribution). Most schemes then evolve some number of statistical moments of that distribution via various processes, such as evaporation, sedimentation, collision-coalescence, and collisional breakup. These microphysical processes, in turn, are typically some fixed functional form derived from either some other (more detailed) model, or using some single-particle rates that are then integrated over the size distribution. While these process rate functions may have some free parameters to adjust, in other cases doing so is impossible (e.g. when the process rates are analytical or piecewise solutions to some target function). Our goal was to build and test a scheme that assumed no size distribution form, and used a series of power laws as the basis for the process rates. Moments of the size distribution would be predicted, but no underlying size distribution would be specified. Any number or choice of size distribution moments could be used, and any number of power laws could be employed to model the process rates. Thus, our approach is flexible, and can seamlessly scale across levels of complexity, as demanded by the data. Bayesian inference then would provide the formalism to estimate the model parameters and structure, allowing for robust uncertainty quantification. We proposed testing this framework in idealized simulations using bin microphysical schemes as a data source. We also proposed using real data to inform our microphysics scheme, and also that we would integrate our scheme into WRF.

58 GEOSCIENCES↗
DOE OSTI2017

Shocks and Tides Quantified in the “Sausage” Cluster, CIZA J2242.8+5301 Using N-body/Hydrodynamical Simulations

The colliding cluster, CIZA J2242.8+5301, displays a spectacular, almost 2 Mpc long shock front with a radio based Mach number M≃5, that is puzzlingly large compared to the X-ray estimate of M≃2.5. The extent to which the X-ray temperature jump is diluted by cooler unshocked gas projected through the cluster currently lacks quantification. Here we apply our self-consistent N-body/hydrodynamical code (based on FLASH) to model this binary cluster encounter. We can account for the location of the shock front and also the elongated X-ray emission by tidal stretching of the gas and dark matter between the two cluster centers. The required total mass is 8.9×10{sup 14} M{sub ⊙} with a 1.3:1 mass ratio favoring the southern cluster component. The relative velocity we derive is ≃2500 km s{sup −1} initially between the two main cluster components, with an impact parameter of 120 kpc. This solution implies that the shock temperature jump derived from the low angular resolution X-ray satellite Suzaku is underestimated by a factor of two, due to cool gas in projection, bringing the observed X-ray and radio estimates into agreement. Finally, we use our model to generate Compton-y maps to estimate the thermal Sunyaev–Zel’dovich (SZ) effect. At 30 GHz, this amounts to ΔS{sub n}=−0.072 mJy/arcmin{sup 2} and ΔS{sub s}=−0.075 mJy/arcmin{sup 2} at the locations of the northern and southern shock fronts respectively. Our model estimate agrees with previous empirical estimates that have inferred the measured radio spectra of the radio relics can be significantly affected by the SZ effect, with implications for charged particle acceleration models.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2001

The Effect of Changes in the ASCA Calibration on the Fe-K Lines in Active Galaxies

The ASCA calibration has evolved considerably since launch and indeed, is still evolving. There have been concerns in the literature that changes in the ASCA calibration have resulted in the Fe-K lines in active galaxies (AGN) now being systematically narrower than was originally thought. If this were true, a large body of ASCA results would be impacted. In particular, it has been claimed that the broad red wing (when present) of the Fe-K line has been considerably weakened by changes in the ASCA calibration. We demonstrate explicitly that changes in the, ASCA calibration over a period of about eight years have a negligible effect on the width, strength, or shape of the Fe-K lines. The reduction in both width and equivalent width is only approximately 8% or less. We confirm this with simulations and individual sources, as well as sample average profiles. The average profile for type 1 AGN is still very broad, with the red wing extending down to approximately 4 keV. The reason for the claimed, apparently large, discrepancies is that in some sources the Fe-K line is complex, and a single-Gaussian model, being an inadequate description of the line profile, picks up different portions of the profile with different calibration. However, one cannot make inferences about calibration or astrophysics of the sources using models which do not describe the data. Better modeling of the Fe-K in such cases gives completely consistent results with both old and current calibration. Thus, inadequate modeling of the Fe-K line in these sources can seriously underestimate the line width and equivalent width, and therefore lead to incorrect deductions about the astrophysical implications.

Yaqoob, T.↗
DOE OSTI2020

Keck/NIRC2 L’-band Imaging of Jovian-mass Accreting Protoplanets around PDS 70

We present L’-band imaging of the PDS 70 planetary system with Keck/NIRC2 using the new infrared pyramid wave front sensor. We detected both PDS 70 b and c in our images, as well as the front rim of the circumstellar disk. After subtracting off a model of the disk, we measured the astrometry and photometry of both planets. Placing priors based on the dynamics of the system, we estimated PDS 70 b to have a semimajor axis of 20{sub −4}{sup +3} au and PDS 70 c to have a semimajor axis of 34{sub −6}{sup +12} au (95% credible interval). We fit the spectral energy distribution (SED) of both planets. For PDS 70 b, we were able to place better constraints on the red half of its SED than previous studies and inferred the radius of the photosphere to be 2–3 R {sub Jup}. The SED of PDS 70 c is less well constrained, with a range of total luminosities spanning an order of magnitude. With our inferred radii and luminosities, we used evolutionary models of accreting protoplanets to derive a mass of PDS 70 b between 2 and 4 M {sub Jup} and a mean mass accretion rate between 3 × 10{sup −7} and 8 × 10{sup −7} M {sub Jup}/yr. For PDS 70 c, we computed a mass between 1 and 3 M {sub Jup} and mean mass accretion rate between 1 × 10{sup −7} and 5 × 10{sup −7} M {sub Jup}/yr. The mass accretion rates imply dust accretion timescales short enough to hide strong molecular absorption features in both planets’ SEDs.

79 ASTRONOMY AND ASTROPHYSICS↗