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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 NTRS2020

Terrestrial Planets Comparative Climatology (TPCC) mission concept

The authors and co-signers of the Terrestrial Planets Comparative Climatology (TPCC) mission concept white paper advocate that planetary science in the next decade would greatly benefit from comparatively studying the fundamental behavior of the atmospheres of Venus and Mars, contemporaneously and with the same instrumentation, to capture atmospheric response to the same solar forcing, and with a minimum of instrument-related variability. NASA’s vision is to understand the effects of the Sun on the solar system and the potential for life elsewhere (Obj,1.1 of [1]). This vision directly motivates the study of terrestrial climate histories and evolution, with the ultimate goal of understanding what factors allow the emergence and sustainability of life/biosphere. It is widely accepted that Venus, Mars, and Earth were formed at the same time and in the same neighborhood of the solar nebula [2,3], and had water—a necessary ingredient for life. In spite of strong overlap in the atmospheric composition of these planets, their current climatic states are vastly different. While Earth retains water, both Mars and Venus’ surfaces are now dry. The manner in which these terrestrial bodies evolved, and whether Mars or Venus currently hosts or previously hosted life, are fundamental mysteries in planetary science. As such, the TPCC mission concept has been developed.The TPCC guiding science goals are:(1) to understand Venus’ evolutionary history compared to Mars and Earth, and (2) to elucidate the driving forces and mechanisms of global circulation at Mars and Venus. These goals address the science question: Why have Mars’ and Venus’ climates evolved so differently from each other and from Earth’s? Furthermore, a greater depth of understanding our own solar system, enables us to understand the variability and likelihood of habitable conditions within extra-solar planetary systems.We suggest a mission architecture and payload that would determine the noble gas content and isotopic ratios, including the D/H ratio, at Venus with sufficient accuracy to identify the timeline of Venus’ climatic evolution for comparison with Mars. In addition, our concept would systematically “follow the energy” at Mars and Venus, in order to establish how solar forcing on the two atmospheric systems leads to the current balance of dynamical, chemical, and radiative processes responsible for each planet’s climatic state.This would include acquisition of the first global atmospheric wind profiles on either planet;global, continuous profiles of aerosols, gases, and water vapor at vertical resolutions higher than any previous mission;and regular UV and IR night glow observations tracking global circulation on both planets.To increase the fidelity of the planned planetary comparisons, the TPCC mission concept baseline (estimated to be New Frontiers Class)would send a single spacecraft to visit one planet and then the next, allowing measurements of each planet with the same instrumentation within similar parts of the solar cycle. The concept uses commercial solar-electric propulsion (SEP; e.g., [4])similar to the Psyche mission [5], plus a probesent deep into Venus’ atmosphere(e.g., LLISSE concept; [6]).Alternatively, “twin” spacecraft (with added probe to the Venus craft),developed at the same time,and launched close in time,would increase the overlap in operation periods and should also be studied. Either architecture is a timely alternative to independently developed and launched spacecraft payloads, which ultimately are more costly and difficult to inter-calibrate.

Leslie K. Tamppari↗
NASA NTRS2021

An evolutionary system of mineralogy, Part IV: Planetesimal differentiation and impact mineralization (4566 to 4560 Ma)

The fourth installment of the evolutionary system of mineralogy considers two stages of planetesimal mineralogy that occurred early in the history of the solar nebula, commencing by 4.566 Ga and lasting for at least 5 million years: (1) primary igneous minerals derived from planetesimal melting and differentiation into core, mantle, and basaltic components and (2) impact mineralization resulting in shock-induced deformation, brecciation, melting, and high-pressure phase transformations. We tabulate 90 igneous differentiated asteroidal minerals, including the earliest known occurrences of minerals with Ba, Cl, Cu, F, and V as essential elements, as well as the first appearances of numerous phosphates, quartz, zircon, and amphibole group minerals. We also record 40 minerals formed through high-pressure impact alteration, commencing with the period of asteroid accretion and differentiation. These stages of mineral evolution thus mark the first time that high pressures, both static and dynamic, played a significant role in mineral paragenesis.

Shaunna M. Morrison↗
DOE OSTI2024

New Muon Campus Simulations for the Muon $g\textrm{-}2$ Experiment at Fermilab

The Muon $g\textrm{-}2$ Experiment (E989) at Fermilab conducted high-precision measurements of the muon anomalous magnetic moment $a_{\mu}$ using a storage ring from 2018 to 2023, achieving a remarkable precision of $200\:\mathrm{ppb}$ over Runs 1-3, with analyses for Runs 4-6 ongoing. A comprehensive understanding of the storage ring's beam dynamics and its accurate simulations are crucial for achieving the experiment's ambitious goals. One of the requirements for this effort is a very detailed knowledge of the phase space distribution of the beam. To address this requirement, we performed high-statistics simulations of the Muon $g\textrm{-}2$ Target Station (AP0) and the Muon Campus beamlines: M2 and M3, followed by the Delivery Ring, and then M4 and M5. The resulting muon distribution at the end of the M5 beamline from our previous $3\times10^{12}$ protons-on-target (PoT) simulation serves as an essential input for the storage ring simulations. In 2024, to facilitate the analyses of Runs 4-6, we have updated our Muon Campus models and re-optimised certain parameters to reflect the operational currents and wire chamber measurements of the beam. For these optimisations, we employed the heterogeneous island method, implemented in our evolutionary optimisation tool, glyfada. This key update addresses the need to use the best possible beam for the storage ring simulations and thus supports the experiment's overall precision. The Muon $g\textrm{-}2$ Experiment at Fermilab has successfully achieved its $70\:\mathrm{ppb}$ systematic uncertainty goal and collected 21 times more data than its predecessor at BNL. The updated and improved Muon Campus models and simulations not only facilitate the experiment's efforts to potentially resolve the current tension between experimental measurements and theoretical predictions of $a_{\mu}$, but also provide a basis for future simulations for the Mu2e Experiment (E-973), which utilises shared Muon Campus beamlines.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Relativistic gas accretion onto supermassive black hole binaries from inspiral through merger

Accreting supermassive black hole binaries are powerful multimessenger sources emitting both gravitational and electromagnetic (EM) radiation. Understanding the accretion dynamics of these systems and predicting their distinctive EM signals is crucial to informing and guiding upcoming efforts aimed at detecting gravitational waves produced by these binaries. To this end, accurate numerical modeling is required to describe both the spacetime and the magnetized gas around the black holes. In this paper, we present two key advances in this field of research. First, we have developed a novel 3D general relativistic magnetohydrodynamics (GRMHD) framework that combines multiple numerical codes to simulate the inspiral and merger of supermassive black hole binaries starting from realistic initial data and running all the way through merger. Throughout the evolution, we adopt a simple but functional prescription to account for gas cooling through photon emission. Next, we have applied our new computational method to follow the time evolution of a circular, equal-mass, nonspinning black hole binary for ∼200 orbits, starting from a separation of 20⁢𝑟 𝑔 and reaching the postmerger evolutionary stage of the system. We have shown how mass continues to flow toward the binary even after the binary “decouples” from its surrounding disk, but the accretion rate onto the black holes diminishes. We have identified how the minidisks orbiting each black hole are slowly drained and eventually dissolve as the binary compresses. We confirm previous findings that the system’s luminosity decreases by a factor of a few during inspiral; however, we observe an abrupt increase by ∼50% in this quantity at the time of merger, likely accompanied by an equally abrupt change in spectrum. Lastly, we have demonstrated that during the inspiral, fluid ram pressure regulates the fraction of the magnetic flux transported to the binary that attaches to the black holes’ horizons.

Accretion disk & black-hole plasma↗
DOE OSTI2025

Chemical templates of the Central Molecular Zone

Context . The Central Molecular Zone (CMZ) of the Milky Way exhibits extreme conditions, including high gas densities, elevated temperatures, enhanced cosmic-ray ionization rates, and large-scale dynamics. This makes it a perfect laboratory for astrochemical studies. With large-scale molecular surveys revealing increasing chemical and physical complexity in the CMZ, it is essential to develop robust methods to decode the chemical information embedded in this extreme region. Aims . A key step to interpreting the molecular richness found in the CMZ is building chemical templates tailored to its diverse conditions. In particular, understanding how CMZ environments affect shock and protostellar chemistry is crucial. The combined impact of high ionization, elevated temperatures, and dense gas remains insufficiently explored for observable tracers. Methods . For this study, we utilized UCLCHEM , a gas-grain time-dependent chemical model, to link physical conditions with their corresponding molecular signatures and identify key tracers of temperature, density, ionization, and shock activity. To achieve this, we ran a grid of models of shocks and protostellar objects representative of typical CMZ conditions, focusing on 24 species, including complex organic molecules. Results . Shocked and protostellar environments show distinct evolutionary timescales (≲10 4 vs. ≳10 4 years); 300 K emerges as a key temperature threshold for chemical differentiation. We find that cosmic-ray ionization and temperature are the main drivers of chemical trends. HCO + , H 2 CO, and CH 3 SH trace ionization, while HCO, HCO + , CH 3 SH, CH 3 NCO, and HCOOCH 3 show consistent abundance contrasts between shocks and protostellar regions over similar temperature ranges. Conclusions . We characterized the behavior of 24 species in protostellar and shock-related environments. While our models underpredict some complex organics in shocks, they reproduce observed trends for most species, supporting scenarios involving a need for recurring shocks in Galactic Center clouds and enhanced ionization toward Sgr B2(N2). Future work should assess the role of shock recurrence and metallicity in shaping chemistry.

Galaxy: center↗
NASA NTRS2002

On the Formation of Massive Stars

We calculate numerically the collapse of slowly rotating, nonmagnetic, massive molecular clumps of masses 30,60, and 120 Stellar Mass, which conceivably could lead to the formation of massive stars. Because radiative acceleration on dust grains plays a critical role in the clump's dynamical evolution, we have improved the module for continuum radiation transfer in an existing two-dimensional (axial symmetry assumed) radiation hydrodynamic code. In particular, rather than using "gray" dust opacities and "gray" radiation transfer, we calculate the dust's wavelength-dependent absorption and emission simultaneously with the radiation density at each wavelength and the equilibrium temperatures of three grain components: amorphous carbon particles. silicates, and " dirty ice " -coated silicates. Because our simulations cannot spatially resolve the innermost regions of the molecular clump, however, we cannot distinguish between the formation of a dense central cluster or a single massive object. Furthermore, we cannot exclude significant mass loss from the central object(s) that may interact with the inflow into the central grid cell. Thus, with our basic assumption that all material in the innermost grid cell accretes onto a single object. we are able to provide only an upper limit to the mass of stars that could possibly be formed. We introduce a semianalytical scheme for augmenting existing evolutionary tracks of pre-main-sequence protostars by including the effects of accretion. By considering an open outermost boundary, an arbitrary amount of material could, in principal, be accreted onto this central star. However, for the three cases considered (30, 60, and 120 Stellar Mass originally within the computation grid), radiation acceleration limited the final masses to 3 1.6, 33.6, and 42.9 Stellar Mass, respectively, for wavelength-dependent radiation transfer and to 19.1, 20.1, and 22.9 Stellar Mass. for the corresponding simulations with gray radiation transfer. Our calculations demonstrate that massive stars can in principle be formed via accretion through a disk. The accretion rate onto the central source increases rapidly after one initial free-fall time and decreases monotonically afterward. By enhancing the nonisotropic character of the radiation field, the accretion disk reduces the effects of radiative acceleration in the radial direction - a process we call the "flashlight effect." The flashlight effect is further amplified in our case by including the effects of frequency-dependent radiation transfer. We conclude with the warning that a careful treatment of radiation transfer is a mandatory requirement for realistic simulations of the formation of massive stars.

Yorke, Harold W.↗
NASA NTRSDate not supplied

Retrospectives: Intersection of Spaceflight Stressors and Microbial Risk to Crew and Craft

OVERVIEW The spaceflight environment has several unique stressors that affect the health of both the crew and the spacecraft. An area of continued, albeit incomplete, study is the interaction of these stressors on microbial populations inherent to both astronauts and spacecraft surfaces and systems. A primary concern is the potential for the spaceflight environment to perturb the phenotype of these populations towards negative outcomes for crew and craft. In order to effectively mitigate these potential risks, they must first be characterized. We performed a retrospective literature analysis to assess the current state of knowledge regarding the affects of ionizing radiation and elevated CO2 on relevant microbial populations. The results of these retrospectives will guide next steps in the decisions of what (if any) further studies should be pursued and to guide decisions of the need for countermeasures. STRESSORS Ionizing radiation. The health risk involved with increased exposure to cosmic radiation has been studied in crew for 35+ years, with human health and cancer risk being the main focus. However, space radiation could also affect both the resident microorganisms aboard the ISS and the normal, healthy astronaut microbiomes that are of direct concern for crew health. A retrospective review of over 250 publications was accomplished looking at the impact of cumulative ionizing radiation doses lower than 3 Gy (chronic or acute) on microbial populations. Elevated CO2. The health risk involved with elevated atmospheric CO2 in spacecraft, primarily focusing on human toxicological risks, is understudied. The current Spaceflight Maximum Allowance Concentration for 24-hour average CO2 is 0.4% (3 mm Hg), which is significantly higher than terrestrial levels (0.04%). Whether these elevated ambient CO2 levels aboard spacecraft influence the diversity and phenotypic responses of the resident microbial communities from both the spacecraft environment (air, surface, water) and crew members (gut, nasal,skin microbiomes) is not known. A retrospective review was accomplished looking at the impact of chronic CO2 exposure up to 0.7% (5 mm Hg) for up to 6 months and acute exposure up to 2.6% (20 mm Hg) for up to 24 hours. CONCLUSIONS: MICROBIOME OF THE BUILT ENVIRONMENT The microbiome of the built spacecraft environment has been sampled consistently over the course of human spaceflight and significant advancements have been made in identifying microbial populations on the ISS. The dominant source of microbes on spacecraft surfaces are human-derived. Once in the spacecraft built environment,the extreme environment selects for features that enhance survival. While efforts to understand potential antibiotic resistance and pathogenicity of ISS isolates is robust, there is little to no understanding of which spaceflight environmental stressors, to include ionizing radiation or elevated CO2, drive the evolutionary trajectory of spacecraft-associated microbial populations. CONCLUSIONS: MICROBE-HOST INTERACTIONS The host-microbiome field has emerged as an important factor in human health on Earth as well in spaceflight. The field is struggling with the complexity of the system under investigation as there is substantial taxonomic and functional heterogeneity in these communities, making it difficult to establish clear stimulus-response dynamics.Taxonomic characterization is the norm; however, the functional role of each community member is key to linking environmental perturbations to potential dysbiosis. For both ionizing radiation and elevated CO2, the likely target of the perturbation is the host tissue, not the microbes themselves.. Any resulting changes to the microbial community composition and/or function is likely a result of adapting to those changes in the host physiology. RECOMMENDATIONS Emphasize functional characterization as opposed to taxonomic characterization of microbial communities.Increase the number of investigations using chronic, spaceflight-relevant doses of ionizing radiation. MoBE studies should move away from observational studies towards predictive modeling of community dynamics. Continue to develop scale-down models, such as tissues-on-a-chip & defined microbial communities. Focus on the crew response to elevated CO2 over MoBE considerations. Assess how direct contact with the hypercapnic environment affects skin microbiome dynamics.

Countermeasures↗
DOE OSTI2024

Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon

Abstract Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determine the extant distribution of yeast enterobactin producers and cheaters.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1996

On the Dynamics of Small-Scale Solar Magnetic Elements

We report on the dynamics of the small-scale solar magnetic field, based on analysis of very high resolution images of the solar photosphere obtained at the Swedish Vacuum Solar Telescope. The data sets are movies from 1 to 4 hr in length, taken in several wavelength bands with a typical time between frames of 20 s. The primary method of tracking small-scale magnetic elements is with very high contrast images of photospheric bright points, taken through a 12 A bandpass filter centered at 4305 A in the Fraunhofer 'G band.' Previous studies have established that such bright points are unambiguously associated with sites of small-scale magnetic flux in the photosphere, although the details of the mechanism responsible for the brightening of the flux elements remain uncertain. The G band bright points move in the intergranular lanes at speeds from 0.5 to 5 km/s. The motions appear to be constrained to the intergranular lanes and are primarily driven by the evolution of the local granular convection flow field. Continual fragmentation and merging of flux is the fundamental evolutionary mode of small-scale magnetic structures in the solar photosphere. Rotation and folding of chains or groups of bright points are also observed. The timescale for magnetic flux evolution in active region plage is on the order of the correlation time of granulation (typically 6-8 minutes), but significant morphological changes can occur on timescales as short as 100 S. Smaller fragments are occasionally seen to fade beyond observable contrast. The concept of a stable, isolated subarcsecond magnetic 'flux tube' in the solar photosphere is inconsistent with the observations presented here.

Berger, T. E.↗
DOE OSTI2022

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Arp 58 and Arp 68: two M 51-type systems

ABSTRACT We study two M 51-type systems Arp 68 and Arp 58, which strongly differ by their stellar masses, gas content, and environment. Long-slit spectral observations obtained at the Russian 6-m telescope were used to trace the distributions of a line-of-sight (LOS) velocity and a gas-phase oxygen abundance along the spectral cuts. Two systems are compared by their observed properties. We found a very strong large-scale non-circular motion of gas in both systems and a kpc-size saw-edged velocity profile along the tidal spiral arm of Arp 68, probably caused by the gas outflow due to the stellar feedback. A deep decrease of LOS velocity is also found in the ‘hinge’ region in Arp 58, where the inner spiral arm transforms into the tidal spiral arm, which was predicted earlier for M 51-type galaxies. Local sites of star formation and the satellites are compared with the evolutionary models at the colour–colour diagrams. Unlike the spiral galaxy Arp 58, the main galaxy in Arp 68 system is experiencing an ongoing burst of star formation. Gas-phase metallicity estimates show that Arp 58 has a higher metal abundance and reveals a shallow negative radial gradient of the gas-phase oxygen abundance. The emission gas in Arp 68 has noticeably lower metallicity than it is expected for a given luminosity of this galaxy, which may be connected with its space position in the local void.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Dynamical Mass Estimates of the β Pictoris Planetary System through Gaussian Process Stellar Activity Modeling

Nearly 15 yr of radial velocity (RV) monitoring and direct imaging enabled the detection of two giant planets orbiting the young, nearby star β Pictoris. The δ Scuti pulsations of the star, which overwhelm planetary signals, need to be carefully suppressed. In this work, we independently revisit the analysis of the RV data following a different approach than available in the literature to model the activity of the star. We show that a Gaussian process (GP) with a stochastically driven damped harmonic oscillator kernel can model the δ Scuti pulsations. It provides similar results to parametric models but with a simpler framework, using only three hyperparameters. It also enables us to model poorly sampled RV data that were excluded from previous analyses, hence extending the RV baseline by nearly five years. Altogether, the orbit and mass of both planets can be constrained from RV only, which was not possible with the parametric modeling. To characterize the system more accurately, we also perform a joint fit of all available relative astrometry and RV data. Our orbital solutions for β Pic b favor a low eccentricity of 0.029$_{−0.024}^{+0.061}$ and a relatively short period of 21.1$_{−0.8}^{+2.0}$ yr. The orbit of β Pic c is eccentric with 0.206$_{−0.063}^{+0.074}$ with a period of 3.36 ± 0.03 yr. We find model-independent masses of 11.7 ± 1.4 and 8.5 ± 0.5 M Jup for β Pic b and c, respectively, assuming coplanarity. The mass of β Pic b is consistent with the hottest start evolutionary models, at an age of 25 ± 3 Myr. A direct detection of β Pic c would provide a second calibration measurement in a coeval system.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Updated HIV-1 Consensus Sequences Change but Stay Within Similar Distance From Worldwide Samples

HIV consensus sequences are used in various bioinformatic, evolutionary, and vaccine related research. Since the previous HIV-1 subtype and CRF consensus sequences were constructed in 2002, the number of publicly available HIV-1 sequences have grown exponentially, especially from non-EU and US countries. Here, we reconstruct 90 new HIV-1 subtype and CRF consensus sequences from 3,470 high-quality, representative, full genome sequences in the LANL HIV database. While subtypes and CRFs are unevenly spread across the world, in total 89 countries were represented. For consensus sequences that were based on at least 20 genomes, we found that on average 2.3% (range 0.8–10%) of the consensus genome site states changed from 2002 to 2021, of which about half were nucleotide state differences and the rest insertions and deletions. Interestingly, the 2021 consensus sequences were shorter than in 2002, and compared to 4,674 HIV-1 worldwide genome sequences, the 2021 consensuses were somewhat closer to the worldwide genome sequences, i.e., showing on average fewer nucleotide state differences. Some subtypes/CRFs have had limited geographical spread, and thus sampling of subtypes/CRFs is uneven, at least in part, due to the epidemiological dynamics. Thus, taken as a whole, the 2021 consensus sequences likely are good representations of the typical subtype/CRF genome nucleotide states. The new consensus sequences are available at the LANL HIV database.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2006

The Molecular Ecology of Guerrero Negro: Justifying the Need for Environmental Genomics

The record of life on the only planet where it is known to exist is contained in the biogeochemical processes that organisms catalyze for their survival, in the compounds that they produce, and in their phylogenetic (evolutionary) relationships to each other. We manipulated sulfate and nutrient concentrations in intact microbial mats over periods of time up to a year. The objectives of the manipulations were: 1) characterize the diversity of process-associated functional genes; 2) understand environmental conditions leading to shifts in microbial guilds; 3) monitor/identify competitive responses of organisms sharing a metabolic niche. Characterization of functional genes associated with carbon (mcrA), nitrogen (nifH, nirK) and sulfur (dsrkB) cycling performed to date provided insight into the diversity and metabolic potential of the system; however, we only identified broad scale correlations between gene abundances and changes in mat physiology. For instance, increases in methane production by mats subjected to lowered sulfate and salinity concentrations were correlated with an observed increase in abundance of hydrogenotroph-like mcrA genes. However, due to low sequence similarity to any cultured isolates, phylogenetic associations only allow order level taxonomic commentary, preventing any associations being made on the cellular level. In each of the genes characterized from these experiments, a significant portion of sequences recovered show minimal phylogenetic affiliation to cultured organisms, preventing any understanding of inter-community dynamics and the functional capacities of these unknown organisms. Environmental genomics may provide insight into mat systems by allowing the correlation of functional genes with phylogenetic markers.

Smith, Jason M.↗
NASA NTRS2001

High Resolution 4.7 Micron Keck/NIRSPEC Spectra of Protostars: Ices and Infalling Gas in the Disk of L1489 IRS - 1

We explore the infrared M band (4.7 micron) spectrum of the class I protostar L1489 IRS in the Taurus Molecular Cloud. This is the highest resolution wide coverage spectrum at this wavelength of a low mass protostar observed to date (R =25,000; (Delta)v =12 km s(exp -1). A large number of narrow absorption lines of gas phase (12)CO, (13)CO, and C(sup 18)O are detected, as well as a prominent band of solid (12)CO. The gas phase (12)CO lines have red shifted absorption wings (up to 100 km s(exp -1)), which likely originate from warm disk material falling toward the central object. Both the isotopes and the extent of the (12)CO line wings are successfully fitted with a contracting disk model of this evolutionary transitional object. This shows that the inward motions seen in millimeter wave emission lines continue to within approx. 0.1 AU from the star. The amount of high velocity infalling gas is however overestimated by this model, suggesting that only part of the disk is infalling, e.g. a hot surface layer or hot gas in magnetic field tubes. The colder parts of the disk are traced by the prominent CO ice band. The band profile results from CO in 'polar' ices (CO mixed with H2O), and CO in 'apolar' ices. At the high spectral resolution, the 'apolar' component is, for the first time, resolved into two distinct components, likely due to pure CO and CO mixed with CO2, O2 and/or N2. The ices have probably experienced thermal processing in the upper disk layer traced by our pencil absorption beam: much of the volatile 'apolar' ices has evaporated, the depletion factor of CO onto grains is remarkably low (approx. 7%), and the CO2 traced in the CO band profile was possibly formed energetically. This study shows that high spectral resolution 4.7 micron observations provide important and unique information on the dynamics and structure of protostellar disks and the origin and evolution of ices in these disks.

Boogert, A. C. A.↗
DOE OSTI2023

Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain

Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2005

How actin crosslinking and bundling proteins cooperate to generate an enhanced cell mechanical response

Actin-crosslinking proteins organize actin filaments into dynamic and complex subcellular scaffolds that orchestrate important mechanical functions, including cell motility and adhesion. Recent mutation studies have shown that individual crosslinking proteins often play seemingly non-essential roles, leading to the hypothesis that they have considerable redundancy in function. We report live-cell, in vitro, and theoretical studies testing the mechanical role of the two ubiquitous actin-crosslinking proteins, alpha-actinin and fascin, which co-localize to stress fibers and the basis of filopodia. Using live-cell particle tracking microrheology, we show that the addition of alpha-actinin and fascin elicits a cell mechanical response that is significantly greater than that originated by alpha-actinin or fascin alone. These live-cell measurements are supported by quantitative rheological measurements with reconstituted actin filament networks containing pure proteins that show that alpha-actinin and fascin can work in concert to generate enhanced cell stiffness. Computational simulations using finite element modeling qualitatively reproduce and explain the functional synergy of alpha-actinin and fascin. These findings highlight the cooperative activity of fascin and alpha-actinin and provide a strong rationale that an evolutionary advantage might be conferred by the cooperative action of multiple actin-crosslinking proteins with overlapping but non-identical biochemical properties. Thus the combination of structural proteins with similar function can provide the cell with unique properties that are required for biologically optimal responses.

Non-NASA Center↗
NASA NTRS1997

An Automated Method for Identifying Inconsistencies within Diagrammatic Software Requirements Specifications

The development of large-scale, composite software in a geographically distributed environment is an evolutionary process. Often, in such evolving systems, striving for consistency is complicated by many factors, because development participants have various locations, skills, responsibilities, roles, opinions, languages, terminology and different degrees of abstraction they employ. This naturally leads to many partial specifications or viewpoints. These multiple views on the system being developed usually overlap. From another aspect, these multiple views give rise to the potential for inconsistency. Existing CASE tools do not efficiently manage inconsistencies in distributed development environment for a large-scale project. Based on the ViewPoints framework the WHERE (Web-Based Hypertext Environment for requirements Evolution) toolkit aims to tackle inconsistency management issues within geographically distributed software development projects. Consequently, WHERE project helps make more robust software and support software assurance process. The long term goal of WHERE tools aims to the inconsistency analysis and management in requirements specifications. A framework based on Graph Grammar theory and TCMJAVA toolkit is proposed to detect inconsistencies among viewpoints. This systematic approach uses three basic operations (UNION, DIFFERENCE, INTERSECTION) to study the static behaviors of graphic and tabular notations. From these operations, subgraphs Query, Selection, Merge, Replacement operations can be derived. This approach uses graph PRODUCTIONS (rewriting rules) to study the dynamic transformations of graphs. We discuss the feasibility of implementation these operations. Also, We present the process of porting original TCM (Toolkit for Conceptual Modeling) project from C++ to Java programming language in this thesis. A scenario based on NASA International Space Station Specification is discussed to show the applicability of our approach. Finally, conclusion and future work about inconsistency management issues in WHERE project will be summarized.

Zhang, Zhong↗