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All sources NASA NTRS DOE OSTI

DOE OSTI2021

Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering

Biology has changed radically in the past two decades, growing from a purely descriptive science into also a design science. The availability of tools that enable the precise modification of cells, as well as the ability to collect large amounts of multimodal data, open the possibility of sophisticated bioengineering to produce fuels, specialty and commodity chemicals, materials, and other renewable bioproducts. However, despite new tools and exponentially increasing data volumes, synthetic biology cannot yet fulfill its true potential due to our inability to predict the behavior of biological systems. Here, we showcase a set of computational tools that, combined, provide the ability to store, visualize, and leverage multiomics data to predict the outcome of bioengineering efforts. We show how to upload, visualize, and output multiomics data, as well as strain information, into online repositories for several isoprenol-producing strain designs. We then use these data to train machine learning algorithms that recommend new strain designs that are correctly predicted to improve isoprenol production by 23%. This demonstration is done by using synthetic data, as provided by a novel library, that can produce credible multiomics data for testing algorithms and computational tools. In short, this paper provides a step-by-step tutorial to leverage these computational tools to improve production in bioengineered strains.

09 BIOMASS FUELS↗

DOE OSTI2023

Perspectives on biorefineries in microbial production of fuels and chemicals

Microbes drive our complex biosphere by regulating the global ecosystem through cycling elements and energy. Humankind has barely begun leveraging this biotransformation capacity to impact global economies and ecologies. Advances in genetic engineering, molecular analysis, metabolic flux modeling, microbial consortia/biome mapping and engineering, cell-free bioproduction, artificial intelligence/machine learning and the ever expanding -omics frontiers have set the stage for paradigm changes to how humankind produces, uses, transforms, and recycles carbon and energy through microbes. Harnessing this enormous potential could drive a global bioeconomy and manage carbon at a planetary level but requires understanding and application at a grand scale across a broad range of science and engineering disciplines. The penultimate manifestation of these advances is the “bio-refinery”, which is often referenced, but is a long way from being fully developed as a global carbon management platform. Broadening the feed stocks, processing operations, and product portfolio to a sequential cascade optimizing the conversion as a whole instead of limited outputs could greatly advance deployment and stability of a bioeconomy.

09 BIOMASS FUELS↗

DOE OSTI2024

Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective

Stoichiometric genome-scale metabolic models (generally abbreviated GSM, GSMM, or GEM) have had many applications in exploring phenotypes and guiding metabolic engineering interventions. Nevertheless, these models and predictions thereof can become limited as they do not directly account for protein cost, enzyme kinetics, and cell surface or volume proteome limitations. Lack of such mechanistic detail could lead to overly optimistic predictions and engineered strains. Initial efforts to correct these deficiencies were by the application of precursor tools for GSMs, such as flux balance analysis with molecular crowding. In the past decade, several frameworks have been introduced to incorporate proteome-related limitations using a genome-scale stoichiometric model as the reconstruction basis, which herein are called resource allocation models (RAMs). This review provides a broad overview of representative or commonly used existing RAM frameworks. This review discusses increasingly complex models, beginning with stoichiometric models to precursor to RAM frameworks to existing RAM frameworks. RAM frameworks are broadly divided into two categories: coarse-grained and fine-grained, with different strengths and challenges. Discussion includes pinpointing their utility, data needs, highlighting framework strengths and limitations, and appropriateness to various research endeavors, largely through contrasting their mathematical frameworks. Finally, promising future applications of RAMs are discussed.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Radiation Belt Response to Fast Reverse Shock at Geosynchronous Orbit

Fast reverse shocks (FRSs) cause the magnetosphere to expand, by contrast to the well-known compressions caused by the impact of fast forward shocks (FFS). Usually, FFSs are more geoeffective than FRSs, and consequently the inner magnetosphere dynamic responses to both shock types can be quite different. In this study, we investigate for the first time the radiation belt response to an FRS impact using multi-satellite observations and numerical simulations. Spacecraft on the dayside observed decreases in magnetic field strength and energetic (~40–475 keV) particle fluxes. Timing analysis shows that the magnetic field signature propagated from the dayside to the nightside magnetosphere. Particles with different energies vary simultaneously at each spacecraft, implying a non-dispersive particle response to the shock. Spacecraft located at lower L-shells did not record any significant signatures. The observations indicate a local time dependence of the response associated with the shock inclination, with the clearest signatures being observed in the dusk–midnight sector. Simulations underestimate the amplitude of the magnetic field variations observed on the nightside. The observed decreases in the electron intensities result from a combination of radial gradient and adiabatic effects. The radial gradients in the spectral index appear to be the dominant contributor to the observed variations of electrons seen on the dayside (near noon and dusk) and on the nightside (near midnight). This work shows that even an FRS can affect the radiation belts significantly and provides an opportunity to understand their dynamic response to a sudden expansion of the magnetosphere.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics

Abstract. Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes and that can integrate genome-scale microbial metabolic information into a dynamically changing, spatially explicit representation of environmental conditions. The model couples a lattice Boltzmann implementation of Navier–Stokes (flow) and advection–diffusion-reaction (mass conservation) equations. Reaction formulations can include both kinetic rate expressions and flux balance analysis, thereby integrating reactive transport modeling and systems biology. We also show that the use of surrogate models such as neural network representations of in silico cell models can speed up computations significantly, facilitating applications to complex environmental systems. Parallelization enables simulations that resolve heterogeneity at multiple scales, and a cellular automaton module provides additional capabilities to simulate biofilm dynamics. The code thus constitutes a platform suitable for a range of environmental, engineering and – potentially – medical applications, in particular ones that involve the simulation of microbial dynamics.

58 GEOSCIENCES↗

NASA NTRS1983

A multiwavelength study of the short-period cataclysmic variable V442 Ophiuchi

The results of a program of observations of the cataclysmic variable V442 Oph from UV to IR wavelengths are reported. The observations comprise IUE SWP and LWR-camera spectra from October, 1981; UBVr and R photometry at Manastash Ridge Observatory from August, 1980; UBV photometry and IR measurements at Kitt Peak from July, 1981; and Coudespectroscopy at Mt. Wilson from June, 1980, and at Mt Lemmon from July, 1982. Tables of data, plots of H-alpha and He-II radial velocity, sample spectra, light curves, and a log-log diagram of F(lambda) vs lambda are given. Flux-ratio analysis of the IR data indicates a disk with very little optically thin material anad an outer-edge temperature of about 7920 K. The calculated period (3.37 h) and mass-accretion rate (1 x 10 to the -8th solar mass/yr) are compared to those of similar objects, and V442 Oph is found to be similar in this respect to systems like H2252-035. Its lack of a rotational period and the weakness of the optical and UV line emissions, however, are more like the old nova V603 Aql.

Shafter, A. W.↗

NASA NTRS1988

Variation in sulfur dioxide emissions related to earth tides, Halemaumau crater, Kilauea volcano, Hawaii

Variation in SO2 emissions from Halemaumau crater, Kilauea volcano, Hawaii is analyzed using a set of techniques known as exploratory data analysis. SO2 flux was monitored using a correlation spectrometer. A total of 302 measurements were made on 73 days over a 90-day period. The mean flux was 171 t/d with a standard deviation of 52 t/d. A significant increase in flux occurs during increased seismic activity beneath the caldera. SO2 flux prior to this change varies in a systematic way and may be related to variation in the tidal modulation envelope.

Connor, Charles B.↗

NASA NTRS1988

Nonpotential magnetic fields at sites of gamma ray flares

The relation between the degree of nonpotentiality of photospheric magnetic fields and the occurrence of gamma ray flares is examined. The parameter delta phi (magnetic shear) and the strength of the magnetic field intensity are used as measures of the degree of nonpotentiality, where delta phi is defined as the angular difference between the observed direction of the transverse component of the photospheric field and the direction of the potential field prescribed by the distribution of measured photospheric flux. An analysis of the great flare of April 24 to 25, 1984 is presented as an example of this technique to quantify the nonpotential characteristics of the pre-flare magnetic field. For this flare, which produced a large gamma ray event, strong shear and high field strengths prevailed over an extended length of the magnetic neutral line where the flare occurred. Moreover, the flare began near the area of strongest measured shear (89 to 90 deg). Four other flaring regions were analyzed; one of these produced a moderate gamma ray event while the other three did not produce detectable gamma rays. For all four regions the flares were located in the area where the field was not nonpotential, regardless of the class of flare. The fields of the gamma ray flares were compared with those associated with the flares without gamma rays, and little distinction was found in the degree of magnetic shear. The major difference is seen in the extent of the sheared field: for gamma ray events, the field is sheared over a longer length of the neutral line.

Hagyard, M. J.↗

NASA NTRS1991

A phenomenological approach to multisource data integration: Analysing infrared and visible data

A new method is described for combining multisensory data for remote sensing applications. The approach uses phenomenological models which allow the specification of discriminatory features that are based on intrinsic physical properties of imaged surfaces. Thermal and visual images of scenes are analyzed to estimate surface heat fluxes. Such analysis makes available a discriminatory feature that is closely related to the thermal capacitance of the imaged objects. This feature provides a method for labelling image regions based on physical properties of imaged objects. This approach is different from existing approaches which use the signal intensities in each channel (or an arbitrary linear or nonlinear combination of signal intensities) as features - which are then classified by a statistical or evident approach.

Nandhakumar, N.↗

NASA NTRS1993

Quasi-periodic transverse plasma flow associated with an evolving MHD vortex street in the outer heliosphere

We study a transverse plasma flow induced by the evolution of a Karman vortex street using a Chebyshev-Fourier spectral algorithm to solve both the compressible Navier-Stokes and MHD equations. The evolving vortex street is formed by the nonlinear interaction of two vortex sheets initially in equilibrium. We study spatial profiles of the total plasma velocity, the density, the meridional flow angle and the location of sector boundaries and find generally good agreement with Voyager 2 measurements of quasi-periodic transverse flow in the outer heliosphere. The pressure pulses associated with the meridional flows in the simulation are too small, although they are correctly located, and this may be due to the lack of any 'warp' in the current sheet in this model. A strong, flow-aligned magnetic field, such as would occur in the inner heliosphere, is shown to lead to weak effects that would be masked by the background interplanetary turbulence. We also study the plasma and magnetic transport resulting from the meridional flow and find that deficits of magnetic quantities do occur near the ecliptic. While the effect is relatively small, it is in general agreement with the most recent analysis of 'flux deficit' in the outer heliosphere.

Siregar, Edouard↗

NASA NTRS1998

Numerical Analysis of a Radiant Heat Flux Calibration System

A radiant heat flux gage calibration system exists in the Flight Loads Laboratory at NASA's Dryden Flight Research Center. This calibration system must be well understood if the heat flux gages calibrated in it are to provide useful data during radiant heating ground tests or flight tests of high speed aerospace vehicles. A part of the calibration system characterization process is to develop a numerical model of the flat plate heater element and heat flux gage, which will help identify errors due to convection, heater element erosion, and other factors. A 2-dimensional mathematical model of the gage-plate system has been developed to simulate the combined problem involving convection, radiation and mass loss by chemical reaction. A fourth order finite difference scheme is used to solve the steady state governing equations and determine the temperature distribution in the gage and plate, incident heat flux on the gage face, and flat plate erosion. Initial gage heat flux predictions from the model are found to be within 17% of experimental results.

Jiang, Shanjuan↗

NASA NTRS2004

The Soft Excess Emission in the Hercules Supercluster Observed with the ROSAT Position Sensitive Proportional Counter

Recent observations with the XMM-Newton satellite confirmed the existence of the soft excess phenomenon in galaxy clusters, earlier discovered in several EUVE, ROSAT and BeppoSAX observations. Excess of soft X-ray radiation in the spectra of several clusters -- above the contribution from the well-known hot intra-cluster gas -- is normally interpreted as emission from cooler gas (T~10^6 K) in the vicinity of galaxy clusters. In this paper we investigate the emission from three clusters in the Hercules concentration, MKW~S, A2052 and A2063. Available XMM observations for two of them (MKW~3s and A2052) indicate the presence of the excess emission, also associated with O VII emission lines. The clusters lie close to the North Polar Spur region, a portion of the sky which features strong soft X-ray emission. We analyze the ROSAT PSPC data of the three clusters and of eight other neighboring locations, in order to study the level of the local soft X-ray background and its influence on the determination of soft excess fluxes. Our analysis reveals that the North Polar Spur region has strong gradients in the soft X-ray emission, which render the background subtraction process quite cumbersome. Despite these complications, we are able to provide evidence for the presence of soft excess emission in the PSPC data of MKW~S, A2052 and A2063.

Bonamente, Massimiliana↗

NASA NTRS2013

Hybrid Large-Eddy/Reynolds-Averaged Simulation of a Supersonic Cavity Using VULCAN

Simulations of a supersonic recessed-cavity flow are performed using a hybrid large-eddy/Reynolds-averaged simulation approach utilizing an inflow turbulence recycling procedure and hybridized inviscid flux scheme. Calorically perfect air enters a three-dimensional domain at a free stream Mach number of 2.92. Simulations are performed to assess grid sensitivity of the solution, efficacy of the turbulence recycling, and the effect of the shock sensor used with the hybridized inviscid flux scheme. Analysis of the turbulent boundary layer upstream of the rearward-facing step for each case indicates excellent agreement with theoretical predictions. Mean velocity and pressure results are compared to Reynolds-averaged simulations and experimental data for each case and indicate good agreement on the finest grid. Simulations are repeated on a coarsened grid, and results indicate strong grid density sensitivity. Simulations are performed with and without inflow turbulence recycling on the coarse grid to isolate the effect of the recycling procedure, which is demonstrably critical to capturing the relevant shear layer dynamics. Shock sensor formulations of Ducros and Larsson are found to predict mean flow statistics equally well.

Quinlan, Jesse↗

NASA NTRS2017

Kepler Fine Guidance Sensor Data

The Kepler and K2 missions collected Fine Guidance Sensor (FGS) data in addition to the science data, as discussed in the Kepler Instrument Handbook (KIH, Van Cleve and Caldwell 2016). The FGS CCDs are frame transfer devices (KIH Table 7) located in the corners of the Kepler focal plane (KIH Figure 24), which are read out 10 times every second. The FGS data are being made available to the user community for scientific analysis as flux and centroid time series, along with a limited number of FGS full frame images which may be useful for constructing a World Coordinate System (WCS) or otherwise putting the time series data in context. This document will describe the data content and file format, and give example MATLAB scripts to read the time series. There are three file types delivered as the FGS data.1. Flux and Centroid (FLC) data: time series of star signal and centroid data. 2. Ancillary FGS Reference (AFR) data: catalog of information about the observed stars in the FLC data. 3. FGS Full-Frame Image (FGI) data: full-frame image snapshots of the FGS CCDs.

Kepler↗

NASA NTRS2019

Fine Guidance Sensor Data

FGS↗

DOE OSTI2024

Probabilistic Analysis of Uncertainty in ATRC Flux Profiles

ATRC is a replica of the larger ATR design and is used to conduct research and obtain data such as flux measurements, excess reactivity, and loading requirements before being loaded into ATR. One method for determining the impact an experiment will have at ATR is by looking at the axial flux profile along the fuel rod in the corresponding ATRC experiment; however, flux wand measurements includes large amounts of variation which makes drawing conclusions from the data difficult. This poster describes a definitive method to propagate the uncertainty from ATRC measurements using Python code.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2024

Measurement of D-T Neutron Source Flux by SelfNeutron Activation Analysis with a LaBr3 Detector

Conclusions: • Decay of 78Br produced from the 79Br(n,2n) reaction in LaBr3 is present in the spectrum plotted in the time domain. • The neutron production rate reconstructed from preliminary LaBr3 estimate is smaller than the generator output. • Generator characterization may become more routine if a simple and robust method is made available for applications. Ongoing work: • Implementing bootstrapping to improve error estimates. • Examining threshold and edge effects of LaBr3

SMITH, MURRY↗

NASA NTRS1962

Combined Radiation and Forced Convection for Flow of a Transparent Gas in a Tube with Sinusoidal Axial Wall Heat Flux Distribution

An analysis is made of the influence that radiation exchanges between elements on the inside surface of a tube have on the wall and gas temperature distributions for forced-convection flow. The wall heat generation has a chopped sine distribution with length along the tube, which is a distribution often encountered in nuclear-reactor channels. The flowing gas is assumed transparent to thermal radiation and hence does not participate directly in the radiative exchange process. Axial heat conduction is neglected in the gas and tube wall, and the convective-heat-transfer coefficient and fluid properties are assumed constant. Several numerical examples are given to illustrate the effects of eight independent parameters such as wall emissivity, Stanton number, and length-diameter ratio. In some instances the radiation exchanges reduced the peak wall temperature or caused a reduction in the exit gas temperature because of radiation losses from the tube end openings.

TUBE↗