Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “data replication”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Assessment of Potential Dose and Environmental Impacts from Proposed Testing at the INL Radiological Response Training Range

This assessment uses screening level models to calculate potential environmental impacts from proposed tests at the Idaho National Laboratory (INL) Radiological Response Training Range (RRTR) site. Proposed tests could be conducted using 11 different radioactive material types that include K 2 O, LaBr 3 , KBr, Cu, Zr, F, Ga, Ga 2 O 3 , NaNO 2 , Ga-68, and Tc-99m. The tests could potentially release radioactive material to the atmosphere and radionuclides and other contaminants to the soil, which could leach into the unsaturated zone and migrate to the aquifer. Atmospheric transport of radionuclides to potential human receptors and time-integrated air concentrations were calculated with a Gaussian plume model and three years of hourly meteorological data. Potential surface-soil impacts were calculated with the computer program Mixing-Cell Model (MCM). Groundwater impacts were calculated with the computer programs MCM and GWSCREEN. Radiological doses from potential atmospheric releases were calculated for public receptors off the INL Site and for workers at nearby INL facilities. Results were compared to regulatory dose limits. Maximum potential groundwater concentrations were estimated in the aquifer below the NSTR site and compared to drinking water standards or risk-based screening levels for resident tap water. Soil concentrations were calculated and compared to risk-based screening levels for workers and potential future residents. All impacts were estimated based on the assumption that 12 tests are conducted annually using all 11 material types for a period of 15 years. This document provides the resources to enable a subject matter expert in the field of environmental assessments to replicate the modeling and calculations. The methodology and parameters are presented in the text. All electronic files, including computer code input, output, executable files, batch files, scripts, and spreadsheet files are contained in a zip file that can be accessed by selecting “Additional Information” (select Native File) in the INL Electronic Document Management System (EDMS).

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2023

A physics-driven Σ-Y atomization model for heavy-duty engine simulations

The atomization of a liquid jet is a multi-scale and multi-physics problem of interest for many engineering applications. Particularly, it drives the fuel-oxidizer mixing and dictates the efficiency of combustion engines. High-fidelity multi-phase simulations remain challenging due to the excessive computational cost required to capture all the atomization scales. Thus, atomization models are necessary to represent sub-grid liquid structures. Here, in this work, a modified Σ-Y model in the context of Eulerian-Lagrangian Spray Atomization (ELSA) is used to transport the surface area density of the spray. The model's predictive performance is assessed under various operating conditions relevant to heavy-duty engines using the Engine Combustion Network (ECN) Spray C and Spray D research-grade injectors. The classic droplet collision formulation of the Σ-Y model alone does not replicate the response of the measured spray surface area to changes in injector, ambient pressure, and injection pressure, requiring individual tuning of the model's parameters. Instead, a transition between dense and dilute spray breakup mechanisms is proposed in terms of the average droplet spacing. The collision breakup mechanism represents the dilute spray, whereas the droplet size in the dense spray is driven by a competition between the integral scale of turbulence and the balance between the turbulent kinetic energy and the surface energy of the droplets. Such an approach minimizes the requirements for model tuning. Moreover, the role of the constants of a compressible standard k-ε RANS model is assessed in the injector's internal flow and external spray simulation framework, and an updated set is proposed. The results are validated against x-ray radiography and Ultra-Small Angle X-ray Scattering (USAXS) data and highlight the predictive capabilities of the proposed physics-driven Σ-Y model, which is compatible with engine simulation turnaround times.

42 ENGINEERING↗
DOE OSTI2021

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

Abstract Temperate phages are viruses of bacteria that can establish two types of infection: a lysogenic infection in which the virus replicates with the host cell without producing virions, and a lytic infection where the host cell is eventually destroyed, and new virions are released. While both lytic and lysogenic infections are routinely observed in the environment, the ecological and evolutionary processes regulating these viral dynamics are still not well understood, especially for uncultivated virus-host pairs. Here, we characterized the long-term dynamics of uncultivated viruses infecting green sulfur bacteria (GSB) in a model freshwater lake (Trout Bog Lake, TBL). As no GSB virus has been formally described yet, we first used two complementary approaches to identify new GSB viruses from TBL; one in vitro based on flow cytometry cell sorting, the other in silico based on CRISPR spacer sequences. We then took advantage of existing TBL metagenomes covering the 2005–2018 period to examine the interactions between GSB and their viruses across years and seasons. From our data, GSB populations in TBL were constantly associated with at least 2-8 viruses each, including both lytic and temperate phages. The dominant GSB population in particular was consistently associated with two prophages with a nearly 100% infection rate for >10 years. We illustrate with a theoretical model that such an interaction can be stable given a low, but persistent, level of prophage induction in low-diversity host populations. Overall, our data suggest that lytic and lysogenic viruses can readily co-infect the same host population, and that host strain-level diversity might be an important factor controlling virus-host dynamics including lytic/lysogeny switch.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Forest response to increased disturbance in the central Amazon and comparison to western Amazonian forests

Uncertainties surrounding vegetation response to increased disturbance rates associated with climate change remains a major global change issue for Amazonian forests. Additionally, turnover rates computed as the average of mortality and recruitment rates in the western Amazon basin are doubled when compared to the central Amazon, and notable gradients currently exist in specific wood density and aboveground biomass (AGB) between these two regions. This study investigates the extent to which the variation in disturbance regimes contributes to these regional gradients. To address this issue, we evaluated disturbance–recovery processes in a central Amazonian forest under two scenarios of increased disturbance rates using first ZELIG-TROP, a dynamic vegetation gap model which we calibrated using long-term inventory data, and second using the Community Land Model (CLM), a global land surface model that is part of the Community Earth System Model (CESM). Upon doubling the mortality rate in the central Amazon to mirror the natural disturbance regime in the western Amazon of ~2% mortality, the two regions continued to differ in multiple forest processes. With the inclusion of elevated natural disturbances, at steady state, AGB significantly decreased by 41.9% with no significant difference between modeled AGB and empirical AGB from the western Amazon data sets (104 vs. 107 Mg C ha -1 , respectively). However, different processes were responsible for the reductions in AGB between the models and empirical data set. The empirical data set suggests that a decrease in wood density is a driver leading to the reduction in AGB. While decreased stand basal area was the driver of AGB loss in ZELIG-TROP, a forest attribute that does not significantly vary across the Amazon Basin. Further comparisons found that stem density, specific wood density, and basal area growth rates differed between the two Amazonian regions. Last, to help quantify the impacts of increased disturbances on the climate and earth system, we evaluated the fidelity of tree mortality and disturbance in CLM. Similar to ZELIG-TROP, CLM predicted a net carbon loss of 49.9%, with an insignificant effect on aboveground net primary productivity (ANPP). Decreased leaf area index (LAI) was the driver of AGB loss in CLM, another forest attribute that does not significantly vary across the Amazon Basin, and the temporal variability in carbon stock and fluxes was not replicated in CLM. Our results suggest that (1) the variability between regions cannot be entirely explained by the variability in disturbance regime, but rather potentially sensitive to intrinsic environmental factors; or (2) the models are not accurately simulating all tropical forest characteristics in response to increased disturbances.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Directional solidification of aqueous TiO 2 suspensions under reduced gravity

Porous materials exhibiting aligned, elongated pore structures can be created by directional solidification of aqueous suspensions—where particles are rejected from a propagating ice front and form interdendritic, particle-packed walls—followed by sublimation of the ice, and sintering of the particle walls. Theoretical models that predict dendritic lamellae spacing—and thus wall and pore width in the final materials—are currently limited due to an inability to account for gravity-driven convective effects during solidification. In this work, aqueous suspensions of 10–30 nm TiO 2 nanoparticles are solidified on parabolic flights under micro-, lunar (~0.17 g; g l = 1.62 m/s 2 ), and Martian (~0.38 g; g m = 3.71 m/s 2 ) gravity and compared to terrestrially-solidified samples. After ice sublimation and sintering, all resulting TiO 2 materials exhibit elongated lamellar pores replicating the ice dendrites. Furthermore, increasing the TiO 2 fraction in the suspensions leads to decreased lamellar spacing in all samples, regardless of gravitational acceleration. Consistent with previous studies of microgravity solidification of binary metallic alloys, lamellar spacing decreases with increasing gravitational acceleration. Furthermore, mean lamellar spacing for 20 wt% TiO 2 nanoparticles suspensions under micro-, lunar, Martian, and terrestrial gravity are, respectively: 50 ± 8, 34 ± 11, 30 ± 6, and 23 ± 9 μm, indicating that gravity-driven convection strongly affects lamellae spacing under terrestrial gravity conditions. Gravitational effects on lamellar spacing are highest at low TiO 2 fractions in the suspension; for 5 wt% TiO 2 suspensions, the microgravity lamellar spacing is more than twice that under terrestrial gravity (182 ± 21 vs. 81 ± 23 μm). Results of this study are in good agreement with previous studies of binary metallic alloy solidification where primary dendrite spacing increases under microgravity. Additionally, literature data from ice-templating systems are used to discuss a dependence on lamellae spacing of the density ratio of particles and fluid.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A section 110 evaluation of the huron king test chamber, area 3, nevada national security site, nye county, nevada

The U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office tasked Desert Research Institute (DRI) with the identification and evaluation of the Huron King Test Chamber as part of their cultural resources program obligations under Section 110 of the National Historic Preservation Act. The Huron King nuclear test was a vertical line-of-sight weapons effects test that took place in Area 3 on June 24, 1980. Unique to this event was a specially designed aboveground test chamber that held a model defense communications satellite in a vacuum tank meant to replicate the space environment. Sponsored by the Defense Nuclear Agency, the purpose of the experiment was to understand the response of the satellite and its materials and equipment to an electromagnetic pulse and attendant radiation. Between July and August 2022, DRI conducted an archival review on the Huron King experiment and its associated test chamber. Subsequently, pedestrian fieldwork was undertaken at the Huron King Test Chamber by DRI on September 29, 2022. During fieldwork, the outside of the test chamber was documented using a Nevada State Historic Preservation Office Architectural Resource Assessment form. This effort included verifying the substructures that compose the test chamber as determined by the archival review, as well as obtaining a detailed photographic recordation of the exterior and assessing its current condition. Notably, the site where the Huron King test took place has been abandoned and almost entirely naturalized. All of the portable instrumentation trailers, communications and data cabling, and winch systems used to retract the test chamber following the detonation were removed after completion of the experiment in 1980. Only the subsidence crater and the test chamber remain as physical evidence of this experiment. Based on these findings, DRI recommends that the Huron King Test Chamber is eligible for listing in the National Register of Historic Places (NRHP) at the local level under Significance Criteria A and C and that it meets Criteria Consideration G for properties less than 50 years old.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

From observation to replication: machine-learning-driven quantification and replication of fine-scale fish kinematics and behavior

Long-term quantification of fish behavior is essential for aquatic ecology, wildlife telemetry, and biomechanical device development. However, the observation duration required to obtain reliable behavioral and kinematic metrics remains unclear, and few tools exist to physically reproduce natural swimming motion for controlled experimentation. We address these challenges by developing a generalizable framework that models behavioral reliability (Spearman–Brown reliability index) as a function of observation duration and derives metric-specific monitoring thresholds. Using juvenile white sturgeon (Acipenser transmontanus) as a case study, we demonstrate that the minimum duration needed for reliable estimates varies substantially across kinematic features: to exceed a reliability of 0.8, total distance traveled requires 12 days, average curvature (mm?¹) 15 days, tail-beat frequency (Hz) 8 days, and average speed (body length/s) 17 days. We further bridge digital analysis and physical testing by developing a hardware-in-the-loop simulator that reconstructs machine-learning-derived swimming kinematics with high fidelity (correlation coefficient 0.98–0.99, RMSE 1.22–1.27 mm over a 5-minute segment). This platform enables realistic, repeatable motion stimuli for evaluating aquatic sensing technologies and bio-integrated devices under controlled conditions. Together, these contributions provide a scalable approach for designing long-term behavioral studies and a data-driven connection between ecological observation and robotic experimentation.

Hwang, SungJoo↗
DOE OSTI2020

SO(3)-invariance of informed-graph-based deep neural network for anisotropic elastoplastic materials

This work examines the frame-invariance (and the lack thereof) exhibited in simulated anisotropic elasto-plastic responses generated from supervised machine learning of classical multi-layer and informed-graph-based neural networks, and proposes different remedies to fix this drawback. The inherent hierarchical relations among physical quantities and state variables in an elasto-plasticity model are first represented as informed, directed graphs, where three variations of the graph are tested. While feed-forward neural networks are used to train path-independent constitutive relations (e.g., elasticity), recurrent neural networks are used to replicate responses that depends on the deformation history, i.e. or path dependent. In dealing with the objectivity deficiency, we use the spectral form to represent tensors and, subsequently, three metrics, the Euclidean distance between the Euler Angles, the distance from the identity matrix, and geodesic on the unit sphere in Lie algebra, can be employed to constitute objective functions for the supervised machine learning. In this, the aim is to minimize the measured distance between the true and the predicted 3D rotation entities. Following this, we conduct numerical experiments on how these metrics, which are theoretically equivalent, may lead to differences in the efficiency of the supervised machine learning as well as the accuracy and robustness of the resultant models. Neural network models trained with tensors represented in component form for a given Cartesian coordinate system are used as a benchmark. Our numerical tests show that, even given the same amount of information and data, the quality of the anisotropic elasto-plasticity model is highly sensitive to the way tensors are represented and measured. The results reveal that using a loss function based on geodesic on the unit sphere in Lie algebra together with an informed, directed graph yield significantly more accurate rotation prediction than the other tested approaches.

42 ENGINEERING↗
DOE OSTI2022

Detection of Airborne Influenza A and SARS-CoV-2 Virus Shedding following Ocular Inoculation of Ferrets

Despite reports of confirmed human infection following ocular exposure with both influenza A virus (IAV) and SARS-CoV-2, the dynamics of virus spread throughout oculonasal tissues and the relative capacity of virus transmission following ocular inoculation remain poorly understood. Furthermore, the impact of exposure route on subsequent release of airborne viral particles into the air has not been examined previously. To assess this, ferrets were inoculated by the ocular route with A(H1N1)pdm09 and A(H7N9) IAVs and two SARS-CoV-2 (early pandemic Washington/1 and Delta variant) viruses. Virus replication was assessed in both respiratory and ocular specimens, and transmission was evaluated in direct contact or respiratory droplet settings. Viral RNA in aerosols shed by inoculated ferrets was quantified with a two-stage cyclone aerosol sampler (National Institute for Occupational Safety and Health [NIOSH]). All IAV and SARS-CoV-2 viruses mounted a productive and transmissible infection in ferrets following ocular inoculation, with peak viral titers and release of virus-laden aerosols from ferrets indistinguishable from those from ferrets inoculated by previously characterized intranasal inoculation methods. Viral RNA was detected in ferret conjunctival washes from all viruses examined, though infectious virus in this specimen was recovered only following IAV inoculation. Low-dose ocular-only aerosol exposure or inhalation aerosol exposure of ferrets to IAV similarly led to productive infection of ferrets and shedding of aerosolized virus. Viral evolution during infection was comparable between all inoculation routes examined. Furthermore, these data support that both IAV and SARS-CoV-2 can establish a high-titer mammalian infection following ocular exposure that is associated with rapid detection of virus-laden aerosols shed by inoculated animals.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Importance of sample preparation on reliable surface characterisation of nano-objects: ISO Standard 20579-4

The international ISO Standard 20579-4, dealing with the history and preparation of nano-objects for surface analysis, has been developed to help address some of the replication and reproducibility issues caused by the fundamental nature of nano-objects. Although all types of samples requiring surface analysis need thoughtful preparation, nano-objects, for which many properties are controlled by their surfaces, present additional challenges in order to avoid variations and artefacts due to the handling and preparation of materials prior to analysis. This international standard is part of a series of standards related to preparation of samples for surface chemical analysis. Parts 1 and 2 of ISO Standard series 20579 address general issues that apply to many samples. Part 4 specifically considers issues that arise due to the inherent nature of nano-objects. Because of sensitivity to their environment, the standard indicates the minimum information that needs to be reported about the handling and preparation of nano-objects prior to surface analysis. This information should become part of sample provenance information that helps assure the reliability and usefulness of data obtained from surface-analysis in the context of the synthesis, processing and analysis history of a batch of material. Application of this standard can help address reproducibility and traceability issues associated with synthesis, processing, and characterization of nano-objects in research and commercial applications.

nano-object characterization, surface analysis, sa↗
DOE OSTI2021

Post-landing major element quantification using SuperCam laser induced breakdown spectroscopy

The SuperCam instrument on the Perseverance Mars 2020 rover uses a pulsed 1064 nm laser to ablate targets at a distance and conduct laser induced breakdown spectroscopy (LIBS) by analyzing the light from the resulting plasma. SuperCam LIBS spectra are preprocessed to remove ambient light, noise, and the continuum signal present in LIBS observations. Prior to quantification, spectra are masked to remove noisier spectrometer regions and spectra are normalized to minimize signal fluctuations and effects of target distance. In some cases, the spectra are also standardized or binned prior to quantification. To determine quantitative elemental compositions of diverse geologic materials at Jezero crater, Mars, we use a suite of 1198 laboratory spectra of 334 well-characterized reference samples. The samples were selected to span a wide range of compositions and include typical silicate rocks, pure minerals (e.g., silicates, sulfates, carbonates, oxides), more unusual compositions (e.g., Mn ore and sodalite), and replicates of the sintered SuperCam calibration targets (SCCTs) onboard the rover. For each major element (SiO 2 , TiO 2 , Al 2 O 3 , FeO T , MgO, CaO, Na 2 O, K 2 O), the database was subdivided into five “folds” with similar distributions of the element of interest. One fold was held out as an independent test set, and the remaining four folds were used to optimize multivariate regression models relating the spectrum to the composition. We considered a variety of models, and selected several for further investigation for each element, based primarily on the root mean squared error of prediction (RMSEP) on the test set, when analyzed at 3 m. In cases with several models of comparable performance at 3 m, we incorporated the SCCT performance at different distances to choose the preferred model. Shortly after landing on Mars and collecting initial spectra of geologic targets, we selected one model per element. Subsequently, with additional data from geologic targets, some models were revised to ensure results that are more consistent with geochemical constraints. The calibration discussed here is a snapshot of an ongoing effort to deliver the most accurate chemical compositions with SuperCam LIBS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Accurate Optical Constants for Liquids in the Near-Infrared: Improved Methods for Obtaining the n and k Constants from 1 to 4 Microns

Other than open bodies of water, bulk liquids are rarely encountered in the environment. Rather, liquids are typically found as aerosols, liquid droplets, or liquid layers on sundry substrates: glass, concrete, metals, etc. The layers can be of varying thicknesses, from micron-level to millimeter thick deposits. The infrared (IR) reflectance spectra of such deposits vary greatly, approximating the bulk reflectance for thicker deposits and for thinner layers on reflective surfaces, producing “transflectance” spectra that more closely replicate simple transmission of the IR light twice traversing the absorptive medium. Rather than recording large numbers of such spectra to serve as endmembers of a spectral reflectance library, we have recognized that the spectra can be modeled so long as the complex optical constants n(?) and k(?) are known as a function of frequency, ?. Here n is the real (dispersion) part and k is the imaginary (absorption) component of the complex index of refraction. However, in many cases the bands in the longwave IR (7 to 13 µm) can become saturated, and better signal-to-noise and specificity can be realized at shorter wavelengths. In earlier studies, we obtained the n/k values from 1.28 to 25 µm for a series of liquids, but are now expanding those measurements to include additional liquid species and extending the spectral range to lower wavelengths. In this paper we describe the methodologies for compiling and fusing the two data sets collected to provide better and more complete spectral coverage from 1 to 25 µm (10,000 to 400 cm-1). The broad spectral range means that one needs to account for both strong and weak spectral features, all of which can be useful for detection, depending on the scenario. To account for the large dynamic range, both long and short path length transmission cells are required for accurate measurements.

optical constants, refractive index, liquids, mid ↗
DOE OSTI2021

Validation of Oregon State University High Temperature Test Facility Experiments Using Pronghorn

The OSU High Temperature Test Facility is a quarter-scale diameter, 1/64 scale volume test facility meant to replicate thermophysical phenomena in the prototypical General Atomics Modular High Temperature Gas Reactor. Tests pertaining to conduction cooldown events were performed from 2016-2019, providing a large database by which computational methods that are applicable to different length scales can be validated. One of these codes is Pronghorn, which is a coarse-meshed, porous-based subchannel thermal hydraulics code based on the MOOSE application, with the intention of better capturing the physics of both conduction and convection heat transfer within the OSU HTTF core. The goal of this summer project is to develop the framework by which Pronghorn can perform validation exercises of the HTTF core for benchmarking, by generating a mesh appropriate to the geometry of the HTTF core, developing input decks that accurately capture the initial and boundary conditions, materials, and relevant equations to the physics seen in the HTTF core, and using a postprocessor to compare simulation results to various experimental data. While validation of codes is a multi-year project, a mesh has been generated and tested in Pronghorn that meets mass conservation and basic heat transfer principles. The next step is to accurate depict the fluid inlet and outlet boundary conditions, which will be performed using computational fluid dynamics software.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2016

The bright end of the z ∼ 9 and z ∼ 10 UV luminosity functions using all five candels fields

The deep, wide-area (∼800–900 arcmin{sup 2}) near-infrared/WFC3/IR + Spitzer/IRAC observations over the CANDELS fields have been a remarkable resource for constraining the bright end of high-redshift UV luminosity functions. However, the lack of Hubble Space Telescope (HST) 1.05 μm observations over the CANDELS fields has made it difficult to identify z ∼ 9–10 sources robustly, since such data are needed to confirm the presence of an abrupt Lyman break at 1.2 μm. Here, we report on the successful identification of many such z ∼ 9–10 sources from a new HST program (z9-CANDELS) that targets the highest-probability z ∼ 9–10 galaxy candidates with observations at 1.05 μm, to search for a robust Lyman-break at 1.2 μm. The potential z ∼ 9–10 candidates were preselected from the full HST, Spitzer/IRAC S-CANDELS observations, and the deepest-available ground-based optical+near-infrared observations (CFHTLS-DEEP+HUGS+UltraVISTA+ZFOURGE). We identified 15 credible z ∼ 9–10 galaxies over the CANDELS fields. Nine of these galaxies lie at z ∼ 9 and five are new identifications. Our targeted follow-up strategy has proven to be very efficient in making use of scarce HST time to secure a reliable sample of z ∼ 9–10 galaxies. Through extensive simulations, we replicate the selection process for our sample (both the preselection and follow-up) and use it to improve current estimates for the volume density of bright z ∼ 9 and z ∼ 10 galaxies. The volume densities we find are 5{sub −2}{sup +3}× and 8{sub −3}{sup +9}× lower, respectively, than those found at z ∼ 8. When compared with the best-fit evolution (i.e., d log{sub 10} ρ{sub UV}/dz=−0.29±0.02) in the UV luminosity densities from z ∼ 8 to z ∼ 4 integrated to 0.3L{sub z=3}{sup ∗} (−20 mag), these luminosity densities are 2.6{sub −0.9}{sup +1.5}× and 2.2{sub −1.1}{sup +2.0}× lower, respectively, than the extrapolated trends. Our new results are broadly consistent with the “accelerated evolution” scenario at z > 8, consistent with that seen in many models.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Antiretroviral therapy for HIV and intrahepatic hepatitis C virus replication

HIV alters host responses to hepatitis C virus (HCV). However, the impact of antiretroviral therapy (ART) on HCV is rarely understood in relevant tissues and never before within individual hepatocytes. HIV and HCV kinetics were studied before and after ART initiation among 19 HIV/HCV co-infected persons. From five persons with the largest decline in plasma HCV RNA, liver tissues collected before and during ART, when plasma HIV RNA was undetectable, were studied. Here we used single-cell laser capture microdissection and quantitative PCR to assess intrahepatic HCV. Immunohistochemistry was performed to characterize intrahepatic immune cell populations. Plasma HCV RNA declined by 0.81 (0.52–1.60) log 10 IU/ml from a median (range) 7.26 (6.05–7.29) log 10 IU/ml and correlated with proportions of HCV-infected hepatocytes (r = 0.89, P = 2 × 10 -5 ), which declined from median (range) of 37% (6–49%) to 23% (0.5–52%) after plasma HIV clearance. Median (range) HCV RNA abundance within cells was unchanged in four of five participants. Liver T-cell abundance unexpectedly decreased, whereas natural killer (NK) and NK T-cell infiltration increased, correlating with changes in proportions of HCV-infected hepatocytes (r = -0.82 and r = -0.73, respectively). Hepatocyte expression of HLA-E, an NK cell restriction marker, correlated with proportions of HCV-infected hepatocytes (r = 0.79). These are the first data to show that ART control of HIV reduces the intrahepatic burden of HCV. Furthermore, our data suggest that HIV affects the pathogenesis of HCV infection by an NK/NK T-cell-mediated mechanism that may involve HLA-E and can be rescued, at least in part, by ART.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data

High-throughput RNA sequencing (RNA-seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages - protonema, gametophore and sporophyte - allowed us to define both general transcriptional patterns and stage-specific transcripts. As an example of variation of physico-chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter-laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Expanding the capability of reaction-diffusion codes using pseudo traps and temperature partitioning: Applied to hydrogen uptake and release from tungsten

Simulating the implantation and thermal desorption evolution in a reaction-diffusion model requires solving a set of coupled differential equations that describe the trapping and release of atomic species in Plasma Facing Materials (PFMs). These fundamental equations are well outlined by the Tritium Migration Analysis Program (TMAP) which can model systems with no more than three active traps per atomic species. To overcome this limitation, we have developed a Pseudo Trap and Temperature Partition (PTTP) scheme allowing us to lump multiple inactive traps into one pseudo trap, simplifying the system of equations to be solved. For all temperatures, we show the trapping of atoms from solute is exactly accounted for when using a pseudo trap. However, a single effective pseudo trap energy can not well replicate the release from multiple traps, each with its own detrapping energy. However, atoms held in a high energy trap will remain trapped at relatively low temperatures, and thus there is a temperature range in which release from high energy traps is effectively inactive. By partitioning the temperature range into segments, a pseudo trap can be defined for each segment to account for multiple high energy traps that are actively trapping but are effectively not releasing atoms. With increasing temperature, as in controlled thermal desorption, the lowest energy trap is nearly emptied and can be removed from the set of coupled equations, while the next higher energy trap becomes an actively releasing trap. Each segment is thus calculated sequentially, with the last time step of a given segment solution being used as an initial input for the next segment as only the pseudo and actively releasing traps are modeled. This PTTP scheme is then applied to experimental thermal desorption data for tungsten (W) samples damaged with heavy ions, which display six distinct release peaks during thermal desorption. Without modifying the TMAP7 source code the PTTP scheme is shown to successfully model the D retention in all six traps. In conclusion, we demonstrate the full reconstruction from the plasma implantation phase through the controlled thermal desorption phase with detrapping energies near 0.9, 1.1, 1.4, 1.7, 1.9 and 2.1 eV for a W sample damaged at room temperature.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗