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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Comparison of Energetic Electron Fluxes Measured by GPS and THEMIS Spacecraft in the Inner Magnetosphere

Key elements of space weather models are energetic electron fluxes in the inner magnetosphere and the outer radiation belt. Flux depletion is driven by various loss processes: scattering into atmosphere, magnetopause shadowing. Flux enhancement is driven by various acceleration processes: local wave-particle interactions, radial transport, plasma sheet injections. Many of these processes operate on ~ hour timescales. Such mesoscale flux variations are not well traced by equatorial spacecraft with much longer orbits. Energetic electron detectors onboard the Global Positioning System (GPS) constellation provide a unique opportunity for probing such ~ hour-scale flux variations. Measurements from up to 23 identically instrumented GPS satellites cover a wide energy and L-shell range with a subhour time resolution. However, their orbits are inclined and thus all measurements at L-shell >4.3 are off-equatorial. Here, in this report, we present a comparison of equatorial THEMIS and nonequatorial GPS measurements of omnidirectional ≤600 keV electron fluxes. Such a comparison allows us to derive coefficients for using off-equatorial GPS fluxes to infer the equatorial values. These coefficients depend on particle energy and L-shell. We demonstrate a new data set derived from GPS measurements and discuss how it can be used to investigate mesoscale dynamics of energetic electron fluxes in the inner magnetosphere.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Cross-platform comparison of arbitrary quantum states

As we approach the era of quantum advantage, when quantum computers (QCs) can outperform any classical computer on particular tasks, there remains the difficult challenge of how to validate their performance. While algorithmic success can be easily verified in some instances such as number factoring or oracular algorithms, these approaches only provide pass/fail information of executing specific tasks for a single QC. On the other hand, a comparison between different QCs preparing nominally the same arbitrary circuit provides an insight for generic validation: a quantum computation is only as valid as the agreement between the results produced on different QCs. Such an approach is also at the heart of evaluating metrological standards such as disparate atomic clocks. In this paper, we report a cross-platform QC comparison using randomized and correlated measurements that results in a wealth of information on the QC systems. We execute several quantum circuits on widely different physical QC platforms and analyze the cross-platform state fidelities.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Bond dissociation energies of low-valent lanthanide hydroxides: lower limits from ion–molecule reactions and comparisons with fluorides

Despite that bond dissociation energies (BDEs) are among the most fundamental and relevant chemical properties they remain poorly characterized for most elementary lanthanide hydroxides and halides. Lanthanide ions Ln + = Eu + , Tm + and Yb + are here shown to react with H 2 O to yield hydroxides LnOH + . Additionally, under low-energy conditions such reactions must be exothermic, which implies a lower limit of 499 kJ mol -1 for the Ln + –OH BDEs. This limit is significantly higher than previously reported for YbOH + and is unexpectedly similar to the BDE for Yb + –F. To explain this apparent anomaly, it is considered feasible that the inefficient hydrolysis reactions observed here in a quadrupole ion trap mass spectrometer may actually be endothermic. More definitive and broad-based evaluations and comparisons require additional and more reliable BDEs and ionization energies for key lanthanide molecules, and/or energies for ligand-exchange reactions like LnF + OH ↔ LnOH + F. The hydroxide results motivated an assessment of currently available lanthanide monohalide BDEs. Among several intriguing relationships is the distinctively higher BDE for neutral LuF versus cationic LuF + , though quantifying this comparison awaits a more accurate value for the anomalously high ionization energy of LuF.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Large eddy simulation of atmospheric boundary layer flow over complex terrain in comparison with RANS simulation and on-site measurements under neutral stability condition

Large eddy simulation (LES) of the atmospheric boundary layer (ABL) flow over complex terrain is presented with a validation using meteorological tower (met-tower) data through an improved neutral stability sampling approach. The proposed stability sampling procedure includes a condition based on the most-likely occurrence time-periods of the neutral ABL and reduces the variabilities of the conditional wind statistics calculated at the met-towers in comparison to our previous work. The ABL flow simulations are carried out over a potential wind site with a prominent hill based using the OpenFOAM-based simulator for on/off-shore wind farm applications by applying the Lagrangian-averaged scale-invariant dynamic sub-grid scale turbulence model. A low-dissipative scale-selective discretization scheme for the non-linear convection term in the LES governing equation is adopted implicitly to ensure both the second-order accuracy and bounded solution. The LES inflow is generated through a precursor method with a “tiling” approach based on the flow driving parameters obtained from a corresponding Reynolds-averaged Navier–Stokes (RANS) simulation. Overall, the averaged wind velocity profiles predicted by the LES approach at all met-tower locations show a similar tendency as the RANS results, which are also in reasonable agreement with the met-tower data. An obvious difference in wind speed standard deviation profiles is seen between LES and RANS, especially at regions downstream of the hill edge, where the LES shows under-predicted results at the highest measurement levels in comparison to the tower data. The computational costs of the LES are found to be about 20 times higher than the RANS simulations.

Energy & Fuels↗
DOE OSTI2023

Self-consistent calculations of the electric charge, ion drag force, and the drift velocity of spherical grains using Langevin dynamics and comparisons against canonical experiments

We present trajectory simulation-based modeling to capture the interactions between ions and charged grains in dusty or complex plasmas. Our study is motivated by the need for a self-consistent and experimentally validated approach for accurately calculating the ion drag force and grain charge that determine grain collective behavior in plasmas. We implement Langevin dynamics in a computationally efficient predictor–corrector approach to capture multiscale ion and grain dynamics. Predictions of grain velocity, grain charge, and ion drag force are compared with prior measurements to assess our approach. The comparisons reveal excellent agreement to within ±20% between predicted and measured grain velocities [Yaroshenko et al., Phys. Plasmas 12, 093503 (2005) and Khrapak et al., Europhys. Lett. 97, 35001 (2012)] for 0.64, 1.25 μm grains at ∼20−500 Pa. Comparisons with the measured grain charge [Khrapak et al., Phys. Rev. E 72, 016406 (2005)] under similar conditions reveal agreement to within ∼20% as well. Measurements of the ion drag force [Hirt et al., Phys. Plasmas 11, 5690 (2004); IEEE Trans. Plasma Sci. 32, 582 (2004)] are used to assess the viability of the presented approach to calculate the ion drag force experienced by grains exposed to ion beams of well-defined energy. Excellent agreement between calculations and measurements is obtained for beam energies >10 eV, and the overprediction below 10 eV is attributed to the neglect of charge exchange collisions in our modeling. Along with critical assessments of our approach, suggestions for future experimental design to probe charging of and momentum transfer onto grains that capture the effect of space charge concentration and external fields are outlined.

Physics↗
DOE OSTI2024

Code-to-code comparison between FLASH and HYDRA in gas-puff Z-pinch modeling

The numerical modeling of gas-puff Z pinches involves the nonlinear coupling of a broad range of complex, multi-physics phenomena that makes such simulations challenging. The challenge is further compounded by nonlinear instabilities that can impact the dynamics of imploding gas-puff Z pinches, such as the magneto Rayleigh–Taylor instability (MRTI). If the growth rate and amplitude of the latter is comparable to the relevant timescales and properties of the imploding plasma, the MRTI can dramatically alter implosion dynamics, dictate pinch stability, and govern the plasma properties achievable in pulsed-power-driven laboratory experiments. National Laboratories and academic teams have developed numerical tools that can accurately model Z-pinch configurations and provide reliable design capabilities that can guide experimental choices and assist in interpreting experimental results. Most such tools, however, are not broadly available. Here, we present newly developed Z-pinch simulation capabilities of the publicly available FLASH code, applied in the study of MRTI growth and dynamical effects in gas-puff implosions. To verify the new implementations, we perform a comparison of FLASH gas-puff implosion simulations with previously published calculations with the HYDRA code from Lawrence Livermore National Laboratory, which have been validated with experimental data from the CESZAR pulsed-power driver at the University of California, San Diego. The experiments involved double- and triple-nozzle configurations, in an experimental attempt to stabilize the pinch to the MRTI. The code-to-code comparison shows similar results between the FLASH and HYDRA simulations, supporting the use of FLASH in the modeling of future gas-puff Z-pinch experiments at CESZAR.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Modeling nanoparticle charge distribution in the afterglow of non-thermal plasmas and comparison with measurements

Particle charging in the afterglows of non-thermal plasmas typically take place in a non-neutral space charge environment. We model the same by incorporating particle-ion collision rate constant models, developed in prior work by analyzing particle-ion trajectories calculated using Langevin Dynamics simulations, into species transport equations for ions, electrons and charged particles in the afterglow. A scaling analysis of particle charging and additional Langevin Dynamics calculations of the particle-ion collision rate constant are presented to extend the range of applicability to ion electrostatic to thermal energy ratios of 300 and diffusive Knudsen number (that scales inversely with gas pressure) up to 2000. The developed collision rate constant models are first validated by comparing predictions of particle charge against measured values in a stationary, non-thermal DC plasma from past PK-4 campaigns published in Phys. Rev. Lett. 93(8): 085001 and Phys. Rev. E 72(1): 016406). The comparisons reveal excellent agreement within ±35% for particles of radius 0.6,1.0,1.3 μm in the gas pressure range of ~20-150 Pa. The experiments to probe particle charge distributions by Sharma et al. (J. Physics D: Appl. Phys. 53(24): 245204) are modeled using the validated particle-ion collision rate constant models and the calculated charge fractions are compared with measurements. The comparisons reveal that the ion/electron concentration and gas temperature in the afterglow critically influence the particle charge and the predictions are generally in qualitative agreement with the measurements. Along with critical assessment of the modeling assumptions, several recommendations are presented for future experimental design to probe charging in afterglows.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

First multi-institutional systematic comparison of the neutron ambient dose equivalent produced by proton therapy systems

Objective. Isochronous cyclotrons, synchrocyclotrons, and synchrotrons are used to accelerate protons for proton therapy. An accurate measurement of neutron doses generated by these accelerators and associated delivery systems and its clinical relevance requires systematic protocols and proper neutron dosimetry for a meaningful assessment. We present the first comprehensive comparison of neutron ambient dose equivalent (H*(10)) produced by clinically operational proton therapy systems. Approach. Treatment plans with 10 cm modulation-depth and ranges of 10 cm (R10M10) and 25 cm (R25M10) were created to cover a 10 × 10 × 10 cm 3 water target. The pencil beam scanning proton therapy machines studied were: two gantry-mounted synchrocyclotrons (Hyperscan, Mevion, half-gantry), two isochronous cyclotrons (ProBeam, Varian, full-gantry), one isochronous cyclotron (Proteus, IBA, full-gantry), and two synchrotrons (PROBEAT, Hitachi, full- and half-gantry). Proton beams were delivered to 30 × 30 × 40 cm 3 plastic water phantoms. WENDI-II and LUPIN-BF3-NP neutron rem-meters were positioned at three angles (0°, 45°, 90°) relative to the beam direction to measure the neutron H*(10) at distances between 50–300 cm from the isocenter. Main results. H*(10) showed dependence on beam energy, machine type, and measurement location. The highest reading was for the gantry-mounted synchrocyclotron, whereas other systems produced approximately comparable neutron doses. In all cases, the H*(10) reduced with distance from the isocenter. The H*(10) drop at 2 m distance compared to that at 0.5 m was a factor of ∼5 for the gantry-mounted synchrocyclotron whereas in other systems the decrease was a factor of 10. The WENDI-II device suffered from dead-time-associated under-estimation of the dose by a factor of ∼2–3 under the synchrocyclotron beam due to its high dose-per-pulse. However, WENDI-II and LUPIN-BF3-NP results were within reasonable agreement in isochronous cyclotron and synchrotron beams, indicating that both devices are suitable for those systems. Significance. Neutron H*(10) is dependent on various parameters including beam energy, measurement location, as well as machine design. Caution must be exercised in choosing the appropriate neutron-dose-measurement device to be used for low-duty-factor, particularly in high-instantaneous-rate proton delivery systems. By delivering the same volumetric proton dose across different machines, this work provides a benchmark for inter-system comparisons and serves as a foundation for future studies.

LUPIN↗
DOE OSTI2025

A comparison of effective field theory models of redshift space galaxy power spectra for DESI 2024 and future surveys

In preparation for the next generation of galaxy redshift surveys, and in particular the year-one data release from the Dark Energy Spectroscopic Instrument (DESI), we investigate the consistency of a variety of effective field theory models that describe the galaxy-galaxy power spectra in redshift space into the quasi-linear regime using 1-loop perturbation theory. These models are employed in the pipelines velocileptors, PyBird, and Folpsν. While these models have been validated independently, a detailed comparison with consistent choices has not been attempted. After briefly discussing the theoretical differences between the models we describe how to provide a more apples-to-apples comparison between them. We present the results of fitting mock spectra from the AbacusSummit suite of N-body simulations provided in three redshift bins to mimic the types of dark time tracers targeted by the DESI survey. We show that the theories behave similarly and give consistent constraints in both the forward-modeling and ShapeFit compressed fitting approaches. We additionally generate (noiseless) synthetic data from each pipeline to be fit by the others, varying the scale cuts in order to show that the models agree within the range of scales for which we expect 1-loop perturbation theory to be applicable. Finally, this work lays the foundation of Full-Shape analysis with DESI Y1 galaxy samples where in the tests we performed, we found no systematic error associated with the modeling of the galaxy redshift space power spectrum for this volume.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Lensing without borders – I. A blind comparison of the amplitude of galaxy–galaxy lensing between independent imaging surveys

ABSTRACT Lensing without borders is a cross-survey collaboration created to assess the consistency of galaxy–galaxy lensing signals (ΔΣ) across different data sets and to carry out end-to-end tests of systematic errors. We perform a blind comparison of the amplitude of ΔΣ using lens samples from BOSS and six independent lensing surveys. We find good agreement between empirically estimated and reported systematic errors which agree to better than 2.3σ in four lens bins and three radial ranges. For lenses with zL > 0.43 and considering statistical errors, we detect a 3–4σ correlation between lensing amplitude and survey depth. This correlation could arise from the increasing impact at higher redshift of unrecognized galaxy blends on shear calibration and imperfections in photometric redshift calibration. At zL > 0.54, amplitudes may additionally correlate with foreground stellar density. The amplitude of these trends is within survey-defined systematic error budgets that are designed to include known shear and redshift calibration uncertainty. Using a fully empirical and conservative method, we do not find evidence for large unknown systematics. Systematic errors greater than 15 per cent (25 per cent) ruled out in three lens bins at 68 per cent (95 per cent) confidence at z < 0.54. Differences with respect to predictions based on clustering are observed to be at the 20–30 per cent level. Our results therefore suggest that lensing systematics alone are unlikely to fully explain the ‘lensing is low’ effect at z < 0.54. This analysis demonstrates the power of cross-survey comparisons and provides a promising path for identifying and reducing systematics in future lensing analyses.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

A comparison of the baryonic Tully–Fisher relation in MaNGA and IllustrisTNG

We compare an observed baryonic Tully–Fisher relation (BTFR) from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) and HI-MaNGA surveys to a simulated BTFR from the cosmological magnetohydrodynamical simulation, IllustrisTNG. To do so, we calibrate the BTFR of the local universe using 377 galaxies from the MaNGA and HI-MaNGA surveys, and perform mock 21 cm observations of matching galaxies from IllustrisTNG. The mock observations are used to ensure that the comparison with the observed galaxies is fair since it has identical measurement algorithms, observational limitations, biases, and uncertainties. For comparison, we also calculate the BTFR for the simulation without mock observations and demonstrate how mock observations are necessary to fairly and consistently compare between observational and theoretical data. We report a MaNGA BTFR of log$_{10} (M_{ \rm Bary}/M_\odot)= (2.97 \pm 0.18)$ log$_{10} V_{ \rm Rot} + (4.04 \pm 0.41)\, \log _{10}{M_{\odot }}$ and an IllustrisTNG BTFR of log$_{10} (M_{ \rm Bary}/M_\odot) = (2.94 \pm 0.23$) log$_{10} V_{ \rm Rot} + (4.15 \pm 0.44)\, \log _{10}{M_{\odot }}$. Thus, MaNGA and IllustrisTNG produce BTFRs that agree within uncertainties, demonstrating that IllustrisTNG has created a galaxy population that obeys the observed relationship between mass and rotation velocity in the observed universe.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Non-local contribution from small scales in galaxy–galaxy lensing: comparison of mitigation schemes

ABSTRACT Recent cosmological analyses with large-scale structure and weak lensing measurements, usually referred to as 3 × 2pt, had to discard a lot of signal to noise from small scales due to our inability to accurately model non-linearities and baryonic effects. Galaxy–galaxy lensing, or the position–shear correlation between lens and source galaxies, is one of the three two-point correlation functions that are included in such analyses, usually estimated with the mean tangential shear. However, tangential shear measurements at a given angular scale θ or physical scale R carry information from all scales below that, forcing the scale cuts applied in real data to be significantly larger than the scale at which theoretical uncertainties become problematic. Recently, there have been a few independent efforts that aim to mitigate the non-locality of the galaxy–galaxy lensing signal. Here, we perform a comparison of the different methods, including the Y-transformation, the point-mass marginalization methodology, and the annular differential surface density statistic. We do the comparison at the cosmological constraints level in a combined galaxy clustering and galaxy–galaxy lensing analysis. We find that all the estimators yield equivalent cosmological results assuming a simulated Rubin Observatory Legacy Survey of Space and Time (LSST) Year 1 like set-up and also when applied to DES Y3 data. With the LSST Y1 set-up, we find that the mitigation schemes yield ∼1.3 times more constraining S8 results than applying larger scale cuts without using any mitigation scheme.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Bound on hot-spot mix in high-velocity, high-adiabat direct-drive cryogenic implosions based on comparison of absolute x-ray and neutron yields

In laser-driven implosions for laboratory fusion, the comparison of hot-spot x-ray yield to neutron production can serve to infer hot-spot mix. For high-performance direct-drive implosions, this ratio depends sensitively on the degree of equilibration between the ion and electron fluids. A scaling for x-ray yield as a function of neutron yield and characteristic ion and electron hot-spot temperatures is developed on the basis of simulations with varying degrees of equilibration. We apply this model to hot-spot x-ray measurements of direct-drive cryogenic implosions typical of the direct-drive designs with best ignition metrics. Furthermore, the comparison of the measured x-ray and neutron yields indicates that hot-spot mix, if present, is below a sensitivity estimated as ~ 2% by-atom mix of ablator plastic into the hot spot.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Tropical forests and global change: biogeochemical responses and opportunities for cross-site comparisons, an organized INSPIRE session at the 108th Annual Meeting, Ecological Society of America, Portland, Oregon, USA, August 2023

In this study, tropical forests play a critical role in the global carbon (C) cycle. These ecosystems maintain the highest rates of net primary production (NPP) on Earth, contain c. 30% of terrestrial C stocks, and have some of the largest stores of fine-root biomass globally, as well as higher fine-root production and turnover rates compared with other biomes. Tropical forest responses to projected warming, altered rainfall regimes, and elevated CO 2 concentrations are likely to be different from other ecosystems because of their unique characteristics (Box 1), making targeted research and model development important for understanding tropical forest–climate feedbacks. There is now a critical mass of long-term global change field experiments and modeling efforts in tropical forests, yet thus far there has been little synthesis, cross-site comparison, or multi-site standardized experimentation among tropical forests to help us understand how these biomes are changing. An organized INSPIRE session at the 108th Annual Meeting of the Ecological Society of America set out to tackle just this. Speakers covered large-scale tropical forest field experiments and modeling efforts, with an emphasis on changes in ecosystem biogeochemistry under warming, drying, elevated atmospheric CO 2 , and changing nutrient status. In this Meeting report, we provide an overview of the large-scale global change experiments presented and highlight the main objectives and opportunities for tropical forest research that emerged, including cross-site comparisons and integration with ecosystem-scale models (Fig. 1).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Comparison of Thin Film Heat Flux Gauge Technologies Emphasizing Continuous-Duration Operation

Abstract Thin-film heat flux gauges (HFGs) have been used for decades to measure surface temperatures and heat flux in test turbines with the majority being used in facilities that are short-duration. These gauges are typically composed of two resistive temperature devices deposited on opposing sides of a dielectric. However, because these sensors have been traditionally applied for measurements in transient-type facilities, the challenges facing adaptation of this technology for a steady facility warrant investigation. These challenges are highlighted, and the solutions are presented throughout the paper. This paper describes the nanofabrication process for heat flux gauges and a new calibration method to address the potential deterioration of gauges over long runtimes in continuous-duration facilities. Because the primary uncertainty of these sensors arises from the ambiguity of the thermal properties, the emphasis is placed on the property determination. Also, this paper presents a discussion on the use of impulse response theory to process the data showing the feasibility of the method for steady-duration facilities after an initial settling time. The latter portion of the paper focuses on comparing well-established heat flux gauges developed for short-duration turbine test facilities to recently developed gauges fabricated using modern nanofabrication techniques for a continuous turbine test facility. The gauges were compared using the test case of an impinging jet over a range of Reynolds numbers. The comparison between the PSU gauge and the reference device indicated agreement within 14%, and similar results were achieved through comparison with established sensors from partner institutions.

Engineering↗
DOE OSTI2023

Wcomp (Wind Farm Wake Comparison Framework) [SWR-23-72]

The Wind Farm Wake Comparison Framework (Wcomp) is a software tool to facilitate the comparison of a specific collection of wind farm wake modeling tools: Python-based, steady-state, analytical wake modeling utilities. Wcomp integrates another software project, windIO, to create a consistent method for describing a wind farm flow control problem. Additionally, a data structure is included to represent the outputs a wind farm flow control simulation. Well-described interfaces allow existing wake modeling tools to plug into this framework.

Mudafort, Rafael↗
DOE OSTI2023

Assessment of an E10 gasoline surrogate: Qualitative and quantitative comparisons of in-cylinder spray morphology

A minimum-component gasoline fuel surrogate that captures both chemical and physical behaviors of a full-distillate fuel is needed for high-fidelity CFD simulations. This study evaluates gasoline spray characteristics in a direct-injection spark-ignition engine under motored operation. Two fuels are compared; PACE-20, which is a 9-component surrogate formulation of RD5-87, is compared with its target fuel RD5-87, which is a full-boiling range research grade E10 gasoline. The spray morphologies of both fuels are recorded for a centrally-located direct-injection 8-hole spray subject to intake air cross-flow during the early part of the intake stroke. High-speed imaging recorded scattered light of the side and axial projections of the liquid spray. Quantitative metrics were developed and employed to facilitate comparison of spray morphologies as well as to identify the transition in spray morphology due to flash boiling. This paper builds on a previous study of RD5-87 where coolant temperature (20°C–100°C), in-cylinder pressure (40–110 kPa), engine speed (650–1950 rpm), and injection pressure (60–180 bar) were systematically changed to span operating conditions with and without flash boiling. Images of the PACE-20 morphology are selected for a sub-set of operating conditions from the previous study where distinctive morphology changes occurred. Visual inspection of the images and quantitative metrics demonstrate that the PACE-20 spray morphology is equivalent to that of the RD5-87 in most cases. The exception was for changes in the ambient-gas pressure where the flash-boiling transition occurred at ∼5 kPa higher in-cylinder pressure for PACE-20. Three empirical metrics, Merging Index, Asymmetry, and Flash Index are proposed here and they were found to be useful both as quantitative comparisons of the fuel morphologies, and for identifying the transition in spray morphology due to flash boiling.

Kim, Namho↗
DOE OSTI2022

A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

Background: In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E. coli. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages. Results: In E. coli, the four software programs identified one of the supplementary sources of radiation (KCl) to evoke about 5 times more transcribed genes than the minus-radiation treatment (69–114 differentially expressed genes, DEGs), and so the rest of the analyses used this KCl vs “Minus” comparison. After imposing a 30-read minimum cutoff, one of the DNAStar options shared two of the three steps (mapping, normalization, and statistic) with Partek Flow (they both used median of ratios to normalize and the DESeq2 statistical package), and these two programs identified the highest number of DEGs in common with each other (53). In contrast, when the programs used different approaches in each of the three steps, between 31 and 40 DEGs were found in common. Regarding the extent of expression differences, three of the four programs gave high fold-change results (15–178 fold), but one (DNAstar’s DESeq2) resulted in more conservative fold-changes (1.5–3.5). In a parallel study comparing three qPCR commercial validation software programs, these programs also gave variable results as to which genes were significantly regulated. Similarly, the C. elegans analysis showed exaggerated fold-changes in CLC and DNAstar’s edgeR while DNAstar-D was more conservative. Conclusions: Regarding the extent of expression (fold-change), and considering the subtlety of the very low level radiation treatments, in E. coli three of the four programs gave what we consider exaggerated fold-change results (15 – 178 fold), but one (DNAstar’s DESeq2) gave more realistic fold-changes (1.5–3.5). When RT-qPCR validation comparisons to transcriptome results were carried out, they supported the more conservative DNAstar-D’s expression results. When another model organism’s (nematode) response to these radiation differences was similarly analyzed, DNAstar-D also resulted in the most conservative expression patterns. Therefore, we would propose DESeq2 (“DNAstar-D”) as an appropriate software tool for differential gene expression studies for treatments expected to give subtle transcriptome responses.

59 BASIC BIOLOGICAL SCIENCES↗