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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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All sourcesNASA NTRSDOE OSTI
NASA NTRS2010

Seasonal Change on Saturn from Cassini/CIRS Observations, 2004-2009

Five years of thermal infrared spectra from the Cassini Composite Infrared Spectrometer (CIRS) are analyzed to determine the response of Saturn's atmosphere to seasonal changes in insolation. Hemispheric mapping sequences at 15.0 cm-1 spectral resolution are used to retrieve the variation in the zonal mean temperatures in the stratosphere (0.5-5.0 mbar) and upper troposphere (75-800 mbar) between October 2004 (shortly after the summer solstice in the southern hemisphere) and July 2009 (shortly before the autumnal equinox). Saturn's northern mid-latitudes show signs of dramatic warming in the stratosphere (by 6-10 K) as they emerge from ring-shadow into springtime conditions, whereas southern mid-latitudes show evidence for cooling (4-6 K). The 40-K asymmetry in stratospheric temperatures between northern and southern hemispheres (at 1 mbar) slowly decreased during the timespan of the observations. Tropospheric temperatures also show temporal variations but with a smaller range, consistent with the increasing radiative time constant of the atmospheric response with increasing pressure. The tropospheric response to the insolation changes shows the largest magnitude at the locations of the broad retrograde jets. Saturn's warm south-polar stratospheric hood has cooled over the course of the mission, but remains present. Stratospheric temperatures are compared to a radiative climate model which accounts for the spatial distribution of the stratospheric coolants. The model successfully predicts the magnitude and morphology of the observed changes at most latitudes. However, the model fails at locations where strong dynamical perturbations dominate the temporal changes in the thermal field, such as the hot polar vortices and the equatorial semi-annual oscillation (Orton, G., and 27 colleagues [2008]. Nature 453, 196-198). Furthermore, observed temperatures in Saturn's ring-shadowed regions are larger than predicted by all radiative-climate models to date due to the incomplete characterization of the dynamical response to the shadow. Finally, far-infrared CIRS spectra are used to demonstrate variability of the para-hydrogen distribution over the 5-year span of the dataset, which may be related to observed changes in Saturn's tropospheric haze in the spring hemisphere.

Fletcher, Leigh N.↗
NASA NTRS2009

Broad Search Solar Electric Propulsion Trajectories to Saturn with Gravity Assists

Solar electric propulsion (SEP) trajectories to Saturn using multiple gravity assists are explored for the joint NASA and ESA Titan Saturn System Mission study. Results show that these new trajectories enable greater performance compared to chemical propulsion with similar gravity assists or SEP without gravity assists. This paper describes the method used in finding these interplanetary trajectories and examines variations in the performance for different SEP systems, flight times, and flyby sequences. The benefits of the SEP trajectories for a mission to Saturn are also discussed.

Titan↗
DOE OSTI2024

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome

ABSTRACT Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change. IMPORTANCE Microbiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus ), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein

The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1978

Lava flow materials in the Tharsis region of Mars

Lava-flow materials in the Tharsis region of Mars were studied from moderate-resolution (100-280 m/pixel) Viking Orbiter imagery. Individual eruptive sequences were recognized primarily by stratigraphic relations, density of superimposed impact craters, flow morphology, flow trend, and variations in surface albedo. Nine detailed maps of lava flows based on delineation of flow scarps were compiled for a total area of 7.25 million sq km. Two thirds of this area was covered by mappable flows representing at least 14 distinct eruptive sequences. Assuming a rate of crater production twice that of the moon, the observed range of superimposed crater densities (90 to 3200 craters at least 1 km in diameter per sq km) indicates an age range of 100 m.y. to several billion years for these flows. The youngest lavas are associated with flood lavas filling the depression surrounding the Olympus Mons shield. Flow thicknesses range from less than 5 meters to 20 meters on steeper shield slopes (0.5 to 4.5 deg) and from 20 to 65 meters on relatively flat (less than 0.5 deg slope) terrain.

Schaber, G. G.↗
NASA NTRS1995

A simulation to study the feasibility of improving the temporal resolution of LAGEOS geodynamic solutions by using a sequential process noise filter

A key drawback to estimating geodetic and geodynamic parameters over time based on satellite laser ranging (SLR) observations is the inability to accurately model all the forces acting on the satellite. Errors associated with the observations and the measurement model can detract from the estimates as well. These 'model errors' corrupt the solutions obtained from the satellite orbit determination process. Dynamical models for satellite motion utilize known geophysical parameters to mathematically detail the forces acting on the satellite. However, these parameters, while estimated as constants, vary over time. These temporal variations must be accounted for in some fashion to maintain meaningful solutions. The primary goal of this study is to analyze the feasibility of using a sequential process noise filter for estimating geodynamic parameters over time from the Laser Geodynamics Satellite (LAGEOS) SLR data. This evaluation is achieved by first simulating a sequence of realistic LAGEOS laser ranging observations. These observations are generated using models with known temporal variations in several geodynamic parameters (along track drag and the J(sub 2), J(sub 3), J(sub 4), and J(sub 5) geopotential coefficients). A standard (non-stochastic) filter and a stochastic process noise filter are then utilized to estimate the model parameters from the simulated observations. The standard non-stochastic filter estimates these parameters as constants over consecutive fixed time intervals. Thus, the resulting solutions contain constant estimates of parameters that vary in time which limits the temporal resolution and accuracy of the solution. The stochastic process noise filter estimates these parameters as correlated process noise variables. As a result, the stochastic process noise filter has the potential to estimate the temporal variations more accurately since the constraint of estimating the parameters as constants is eliminated. A comparison of the temporal resolution of solutions obtained from standard sequential filtering methods and process noise sequential filtering methods shows that the accuracy is significantly improved using process noise. The results show that the positional accuracy of the orbit is improved as well. The temporal resolution of the resulting solutions are detailed, and conclusions drawn about the results. Benefits and drawbacks of using process noise filtering in this type of scenario are also identified.

Hartman, Brian Davis↗
DOE OSTI2023

Phylogeography of the blacklegged tick ( Ixodes scapularis ) throughout the USA identifies candidate loci for differences in vectorial capacity

Abstract The blacklegged tick ( Ixodes scapularis ( Journal of the Academy of Natural Sciences of Philadelphia , 1821, 2 , 59)) is a vector of Borrelia burgdorferi sensu stricto ( s.s .) ( International Journal of Systematic Bacteriology , 1984, 34 , 496), the causative bacterial agent of Lyme disease, part of a slow‐moving epidemic of Lyme borreliosis spreading across the northern hemisphere. Well‐known geographical differences in the vectorial capacity of these ticks are associated with genetic variation. Despite the need for detailed genetic information in this disease system, previous phylogeographical studies of these ticks have been restricted to relatively few populations or few genetic loci. Here we present the most comprehensive phylogeographical study of genome‐wide markers in I. scapularis , conducted by using 3RAD (triple‐enzyme restriction‐site associated sequencing) and surveying 353 ticks from 33 counties throughout the species' range. We found limited genetic variation among populations from the Northeast and Upper Midwest, where Lyme disease is most common, and higher genetic variation among populations from the South. We identify five spatially associated genetic clusters of I. scapularis . In regions where Lyme disease is increasing in frequency, the I. scapularis populations genetically group with ticks from historically highly Lyme‐endemic regions. Finally, we identify 10 variable DNA sites that contribute the most to population differentiation. These variable sites cluster on one of the chromosome‐scale scaffolds for I. scapularis and are within identified genes. Our findings illuminate the need for additional research to identify loci causing variation in the vectorial capacity of I. scapularis and where additional tick sampling would be most valuable to further understand disease trends caused by pathogens transmitted by I. scapularis .

3RAD↗
DOE OSTI2026

Predicting river turbidity in Pine Island Bayou using machine learning techniques coupled with variational mode decomposition

Elevated turbidity levels pose significant public health risks by facilitating the transport of harmful pollutants, including metals, organic compounds, and pathogenic microorganisms into the surface water. These conditions create serious challenges for public recreational water use and drinking water treatment, leading to economic losses and health risks. This study utilizes water monitoring data in Pine Island Bayou, Texas, and develops a Sequence-to-Sequence (S2S) model to predict turbidity using Attention-based Gated Recurrent Units with Encoder-Decoder (AT-GRU-ED) and Long Short-Term Memory (LSTM), coupled with Variational Mode Decomposition (VMD). Compared to the model without VMD, the model demonstrates satisfactory 72-hour turbidity prediction performance, achieving MAEs of 2.60 and 3.29 NTU (reductions of 53% and 58%), RMSEs of 21.08 and 31.49 NTU (reductions of 82% and 80%), and R² values of 0.96 and 0.84 on the validation and test sets, respectively. Feature importance analysis reveals that water temperature is the dominant factor influencing seasonal turbidity patterns, while real-time hourly rainfall significantly contributes to short-term variability. Turbidity typically peaks within 48 hours after rainfall events due to lagged effects from surface runoff and upstream flow. Findings suggest suspending recreational water use and water supply pumping for three days after heavy rainfall can benefit public health and improve water treatment processes. Discharges above 100 m3/s are found to accelerate sediment dilution and transport, reducing turbidity levels more quickly after the peak. In conclusion, the proposed model demonstrates reliable 72-hour turbidity prediction, supporting decision-making for water treatment plant operations and providing early warning for public recreational water use.

Deep learning↗
NASA NTRS2012

Multi-Sensors Observations of Pre-Earthquake Signals. What We Learned from the Great Tohoku Earthquake?

The lessons learned from the Great Tohoku EQ (Japan, 2011) will affect our future observations and an analysis is the main focus of this presentation. Multi-sensors observations and multidisciplinary research is presented in our study of the phenomena preceding major earthquakes Our approach is based on a systematic analysis of several physical and environmental parameters, which been reported by others in connections with earthquake processes: thermal infrared radiation; temperature; concentration of electrons in the ionosphere; radon/ion activities; and atmospheric temperature/humidity [Ouzounov et al, 2011]. We used the Lithosphere-Atmosphere-Ionosphere Coupling (LAIC) model, one of several possible paradigms [Pulinets and Ouzounov, 2011] to interpret our observations. We retrospectively analyzed the temporal and spatial variations of three different physical parameters characterizing the state of the atmosphere, ionosphere the ground surface several days before the March 11, 2011 M9 Tohoku earthquake Namely: (i) Outgoing Long wave Radiation (OLR) measured at the top of the atmosphere; (ii) Anomalous variations of ionospheric parameters revealed by multi-sensors observations; and (iii) The change in the foreshock sequence (rate, space and time); Our results show that on March 8th, 2011 a rapid increase of emitted infrared radiation was observed and an anomaly developed near the epicenter with largest value occurring on March 11 at 07.30 LT. The GPS/TEC data indicate an increase and variation in electron density reaching a maximum value on March 8. Starting from this day in the lower ionosphere there was also observed an abnormal TEC variation over the epicenter. From March 3 to 11 a large increase in electron concentration was recorded at all four Japanese ground-based ionosondes, which returned to normal after the main earthquake. We use the Japanese GPS network stations and method of Radio Tomography to study the spatiotemporal structure of ionospheric perturbations, and to distinguish ionospheric responses to processes of EQ preparation against the effects of other factors. The 2-D snapshots of the electron density over Japan showed abnormal increase over the maximum stress during the night, a few hours before the main shock. Our results from recording atmospheric and ionospheric conditions during the earthquake indicate the presence of anomalies in the atmosphere and ionospheres occurring consistently over regions of maximum stress near the epicenter. Due to their long duration (hours and days) and spatial appearance (only over the Sendai region) these results do not appear to be caused by meteorological or magnetic activity. They reveal the existence of atmospheric and ionospheric phenomena occurring prior to the earthquake, which indicates new evidence of a distinct coupling between the lithosphere and atmosphere/ionosphere. Similar results have been reported before the catastrophic events in Chile (M8.8, 2010), Italy (M6.3, 2009) and Sumatra (M9.3, 2004).

Ouzonounov, D.↗
DOE OSTI2018

A comparison of methods used to unveil the genetic and metabolic pool in the built environment

BACKGROUND:A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting. RESULTS:We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community. CONCLUSIONS:Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies

The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Variation of Structure and Cellular Functions of Type IA Topoisomerases across the Tree of Life

Topoisomerases regulate the topological state of cellular genomes to prevent impediments to vital cellular processes, including replication and transcription from suboptimal supercoiling of double-stranded DNA, and to untangle topological barriers generated as replication or recombination intermediates. The subfamily of type IA topoisomerases are the only topoisomerases that can alter the interlinking of both DNA and RNA. In this article, we provide a review of the mechanisms by which four highly conserved N-terminal protein domains fold into a toroidal structure, enabling cleavage and religation of a single strand of DNA or RNA. We also explore how these conserved domains can be combined with numerous non-conserved protein sequences located in the C-terminal domains to form a diverse range of type IA topoisomerases in Archaea, Bacteria, and Eukarya. There is at least one type IA topoisomerase present in nearly every free-living organism. The variation in C-terminal domain sequences and interacting partners such as helicases enable type IA topoisomerases to conduct important cellular functions that require the passage of nucleic acids through the break of a single-strand DNA or RNA that is held by the conserved N-terminal toroidal domains. In addition, this review will exam a range of human genetic disorders that have been linked to the malfunction of type IA topoisomerase.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1978

Meteorological control of lower stratospheric minor species variations - An observational example

Lower stratospheric air trajectories entering the region over Alaska at the approximately 125 mb level during late May, 1975 indicate a substantial shift in the geographical source regions for the air masses present during that time. This shift coincides with an approximately 25% decrease in the observed halocarbon mixing ratios at the 125 mb level as determined from a daily sequence of halocarbon profiles. Since the halocarbon species measured are essentially chemically inactive at this level, the observed variation is linked to the changing meteorological pattern.

Alyea, F. N.↗
DOE OSTI2019

Rare variants contribute disproportionately to quantitative trait variation in yeast

How variants with different frequencies contribute to trait variation is a central question in genetics. We use a unique model system to disentangle the contributions of common and rare variants to quantitative traits. We generated ~14,000 progeny from crosses among 16 diverse yeast strains and identified thousands of quantitative trait loci (QTLs) for 38 traits. We combined our results with sequencing data for 1011 yeast isolates to show that rare variants make a disproportionate contribution to trait variation. Evolutionary analyses revealed that this contribution is driven by rare variants that arose recently, and that negative selection has shaped the relationship between variant frequency and effect size. We leveraged the structure of the crosses to resolve hundreds of QTLs to single genes. These results refine our understanding of trait variation at the population level and suggest that studies of rare variants are a fertile ground for discovery of genetic effects.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases

Family 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These important enzymes are often bimodular, including a catalytic domain and carbohydrate binding module (CBM) attached via a flexible linker, and exhibit an active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain data-driven insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, trained only on the number of residues in the active-site loops as features, were able discriminate GH7 CBHs and EGs with up to 99% accuracy, demonstrating that the lengths of loops A4, B2, B3, and B4 strongly correlate with functional subtype across the GH7 family. Classification rules were derived such that specific residues at 42 different sequence positions each predicted the functional subtype with accuracies surpassing 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. Our ML results recapitulate, as top-performing features, a substantial number of the sequence positions determined by previous experimental studies to play vital roles in GH7 activity. We surmise that the yet-to-be-explored sequence positions among the top-performing features also contribute to GH7 functional variation and may be exploited to understand and manipulate function.

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

Aftershocks of the 2012 Off-Coast of Sumatra Earthquake Sequence

Aftershocks of the 2012 Off-Coast of Sumatra Earthquake Sequence exhibit a complex and diffuse spatial distribution. The first-order complexity in aftershock distribution is clear and well beyond the influence of typical earthquake location uncertainty. The sequence included rupture of multiple fault segments, spatially separated. We use surface-wave based relative centroid locations to examine whether, at the small scale, the distribution of the aftershocks was influenced by location errors. Surface-wave based relative location has delineated precise oceanic transform fault earthquake locations in multiple regions. However, the relocated aftershocks off the coast of Sumatra seldom align along simple linear trends that are compatible with the corresponding fault strikes as estimated for the GCMT catalog. The relocation of roughly 60 moderate-earthquake epicentroids suggests that the faulting involved in the 2012 earthquake aftershock sequence included strain release along many short fault segments. Statistical analysis and temporal variations of aftershocks show a typical decay of the aftershocks but a relatively low number of aftershocks, as is common for intraplate oceanic earthquakes. Coulomb stress calculations indicate that most of the moderate-magnitude aftershocks are compatible with stress changes predicted by the large-event slip models. Furthermore the patterns in the aftershocks suggest that the formation of the boundary and eventual localization of deformation between the Indian and Australian plate is a complicated process.

2012 Sumatra Earthquake↗
DOE OSTI2019

Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi

Fungi that decay wood have characteristic associations with certain tree species, but the mechanistic bases for these associations are poorly understood. We studied substrate-specific gene expression and RNA editing in six species of wood-decaying fungi from the 'Antrodia clade' (Polyporales, Agaricomycetes) on three different wood substrates (pine, spruce, and aspen) in submerged cultures. We identified dozens to hundreds of substrate-biased genes (i.e., genes that are significantly upregulated in one substrate relative to the other two substrates) in each species, and these biased genes are correlated with their host ranges. Evolution of substrate-biased genes is associated with gene family expansion, gain and loss of genes, and variation in cis- and trans- regulatory elements, rather than changes in protein coding sequences. We also demonstrated widespread RNA editing events in the Antrodia clade, which differ from those observed in the Ascomycota in their distribution, substitution types, and the genomic environment. Moreover, we found that substrates could affect editing positions and frequency, including editing events occurring in mRNA transcribed from wood-decay-related genes. Finally, this work shows the extent to which gene expression and RNA editing differ among species and substrates, and provides clues into mechanisms by which wood-decaying fungi may adapt to different hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Numerical simulations of the ablative Rayleigh-Taylor instability in planar inertial-confinement-fusion targets using the FastRad3D code

The ablative Rayleigh-Taylor (RT) instability is a central issue in the performance of laser-accelerated inertial-confinement-fusion targets. Historically, the accurate numerical simulation of this instability has been a challenging task for many radiation hydrodynamics codes, particularly when it comes to capturing the ablatively stabilized region of the linear dispersion spectrum and modeling ab initio perturbations. Here, we present recent results from two-dimensional numerical simulations of the ablative RT instability in planar laser-ablated foils that were performed using the Eulerian code FastRad3D. Our study considers polystyrene, (cryogenic) deuterium-tritium, and beryllium target materials, quarter- and third-micron laser light, and low and high laser intensities. An initial single-mode surface perturbation is modeled in our simulations as a small modulation to the target mass density and the ablative RT growth-rate is calculated from the time history of areal-mass variations once the target reaches a steady-state acceleration. By performing a sequence of such simulations with different perturbation wavelengths, we generate a discrete dispersion spectrum for each of our examples and find that in all cases the linear RT growth-rate γ is well described by an expression of the form γ=α [kg/(1+ϵ kLm)]1/2−βkVa, where k is the perturbation wavenumber, g is the acceleration of the target, Lm is the minimum density scale-length, Va is the ablation velocity, and ϵ is either one or zero. The dimensionless coefficients α and β in the above formula depend on the particular target and laser parameters and are determined from two-dimensional simulation results through the use of a nonlinear curve-fitting procedure. While our findings are generally consistent with those of Betti et al. (Phys. Plasmas 5, 1446 (1998)), the ablative RT growth-rates predicted in this investigation are somewhat smaller than the values previously reported for the same target and laser parameters. It is speculated that differences in the equation-of-state and opacity models are largely responsible for the discrepancy. Resolution of this issue awaits the development of better experimental diagnostics capable of measuring small-wavelength (5–20 μm) perturbation growth due to the ablative RT instability in the linear regime.

Bates, J. W. (ORCID:0000000188087240)↗