SEARCH · Engineering Papers
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.
We developed models to predict the photoactivity of organic molecules for photocatalytic hydrogen evolution by integrating experiment, computation, and machine learning. This marks a step toward the data-driven discovery of molecular photocatalysts.
The African swine fever virus (ASFV) is currently causing a world-wide pandemic of a highly lethal disease in domestic swine and wild boar. Currently, recombinant ASF live-attenuated vaccines based on a genotype II virus strain are commercially available in Vietnam. With 25 reported ASFV genotypes in the literature, it is important to understand the molecular basis and usefulness of ASFV genotyping, as well as the true significance of genotypes in the epidemiology, transmission, evolution, control, and prevention of ASFV. Historically, genotyping of ASFV was used for the epidemiological tracking of the disease and was based on the analysis of small fragments that represent less than 1% of the viral genome. The predominant method for genotyping ASFV relies on the sequencing of a fragment within the gene encoding the structural p72 protein. Genotype assignment has been accomplished through automated phylogenetic trees or by comparing the target sequence to the most closely related genotyped p72 gene. To evaluate its appropriateness for the classification of genotypes by p72, we reanalyzed all available genomic data for ASFV. We conclude that the majority of p72-based genotypes, when initially created, were neither identified under any specific methodological criteria nor correctly compared with the already existing ASFV genotypes. Based on our analysis of the p72 protein sequences, we propose that the current twenty-five genotypes, created exclusively based on the p72 sequence, should be reduced to only six genotypes. To help differentiate between the new and old genotype classification systems, we propose that Arabic numerals (1, 2, 8, 9, 15, and 23) be used instead of the previously used Roman numerals. Furthermore, we discuss the usefulness of genotyping ASFV isolates based only on the p72 gene sequence.
Study of the evolutionary developments that occurred subsequent to the origin of ancestral cells. Microbial physiology and ecology are potential sharp tools for shaping concepts of microbial evolution. Some popular unjustified assumptions are discussed. It is considered that certain principles derived mainly from the advances of molecular biology can be used to order the natural groups (genera) of extant prokaryotes and their patterns phylogenetically.
Detailed, time-dependent, two-dimensional numerical simulations of premixed laminar flames have been used to study the initiation and subsequent development of cellular structures in lean hydrogen-air flames. The model includes detailed hydrogen-oxygen combustion with 24 elementary reactions of eight reactive species and a nitrogen diluent, molecular diffusion of all species, thermal conduction, viscosity, and convection. This model has been used to study the nonlinear evolution of cellular flame structure and shows that cell splitting, as observed in experiments, can be predicted numerically for sufficiently reactive mixtures. The structures that evolved also resembled the cellular structures observed in experiments. The present study shows that the 'cell-split limit' postulated from experimental observations is an intrinsic property of the mixture and that external factors such as heat losses are not necessary to cause this limit.
The present Mars atmosphere is relatively thin and cold. It is not at all like that which is presumed to have been responsible for the formation of valley networks and the heavy erosion of craters during the earliest epochs of martian history. An important goal of Mars exploration is to try to understand the properties of the early atmosphere, the initial inventory of volatiles at the planet's surface, the processes by which the atmosphere and climate have evolved over time, and the current location of volatiles presumed to have been in the atmosphere in the earlier times. The current status of understanding of the escape of volatiles to space over geologic time and the resulting fractionation of isotopes of stable atoms remaining in the atmosphere are described, and a scenario for volatile abundance and evolution that is consistent with the available information on the escape and fractionation of each species is constructed. In particular, the evolution of hydrogen, carbon, oxygen, and nitrogen, as contained in atmospheric (and non-atmospheric) water, carbon dioxide, and molecular nitrogen, is examined.
Analyses of of high-redshift ultraluminous infrared OR) galaxies traditionally use the observed optical to submillimeter spectral energy distribution (SED) and estimates of the dynamical mass as observational constraints to derive the star formation rate (SFR), the stellar mass, and age of these objects. In this lecture we add this constraint to the analysis of AzTEC-3, a starburst galaxy at z=5.3. We construct different stellar and chemical evolutionary scenarios, constrained to produce the inferred dust mass and observed luminosity before the associated stellar mass exceeds the observational limit. A robust result of our models is that all scenarios require most of the radiating dust mass to have been accreted in molecular clouds. Our new procedure highlights the importance of a multi wavelength approach, and of the use of dust evolution models in constraining the age and the star formation activity and history in galaxies.
Analyses of of high-redshift ultraluminous infrared (IR) galaxies traditionally use the observed optical to submillimeter spectral energy distribution (SED) and estimates of the dynamical mass as observational constraints to derive the star formation rate (SFR), the stellar mass, and age of these objects. In this lecture we add this constraint to the analysis of AzTEC-3, a starburst galaxy at z=5.3. We construct different stellar and chemical evolutionary scenarios, constrained to produce the inferred dust mass and observed luminosity before the associated stellar mass exceeds the observational limit. A robust result of our models is that all scenarios require most of the radiating dust mass to have been accreted in molecular clouds. Our new procedure highlights the importance of a multi wavelength approach, and of the use of dust evolution models in constraining the age and the star formation activity and history in galaxies.
Single-strand RNA (ssRNA) Fiersviridae phages cause host lysis with a product of single gene (sgl for single-gene lysis; product Sgl) that induces autolysis. Many different Sgls have been discovered, but the molecular targets of only a few have been identified. In this study, we used a high-throughput genetic screen to uncover genome-wide host suppressors of diverse Sgls. In addition to validating known molecular mechanisms, we discovered that the Sgl of PP7, an ssRNA phage of Pseudomonas aeruginosa, targets MurJ, the flippase responsible for lipid II export, previously shown to be the target of the Sgl of coliphage M. These two Sgls, which are unrelated and predicted to have opposite membrane topology, thus represent a case of convergent evolution. We extended the genetic screens to other uncharacterized Sgls and uncovered a common set of multicopy suppressors, suggesting that these Sgls act by the same or similar mechanism.
The mechanical behavior of two-dimensional (2D) materials across 2D phase changes is unknown, and the finite temperature (T) elasticity of paradigmatic SnSe monolayers—ferroelectric 2D materials turning paraelectric as their unit cell turns from a rectangle into a square—is described here in a progressive manner. To begin with, their zero–T total energy landscape gives way to (Boltzmann-like) averages from which the elastic behavior is determined. Furthermore, these estimates are complemented with results from the strain-fluctuation method, which employs the energy landscape or ab initio molecular dynamics data. All approaches capture the coalescence of elastic moduli < C 11 (T) > = < C 22 (T) > due to the structural transformation. The broad evolution and sudden changes of elastic parameters < C 11 (T) >, < C 22 (T) >, and < C 12 (T) > of these atomically thin phase-change membranes establishes a heretofore overlooked connection among 2D materials and soft matter.
The chemistry evolution in a laser ablation plume depends strongly on its initial physical conditions. In this article, we investigate the impact of plasma generation conditions on the interrelated phenomena of expansion dynamics, plasma chemistry, and physical conditions. Plasmas are produced from a uranium metal target in air using nanosecond, femtosecond, and femtosecond filament-assisted laser ablation. Time-resolved two-dimensional spectral imaging was performed for evaluating the spatio-temporal evolu-tion of atoms, diatoms, polyatomic molecules, and nanoparticles in situ. Emission spectral features reveal that molecular formation occurs at early times in both femtosecond and filament ablation plumes, although with different temporal decay. In contrast, mo-lecular formation is found to occur at much later times in nanosecond plasma evolution. Spectral modeling is used to infer tem-poral behavior of plasma excitation temperature, and results highlighted that nanosecond plume temperatures decay rapidly while plumes generated by filament ablation show slowest decay. In this work, we find U atoms and UO molecules co-exist in ultrafast laser produced plasmas even at early times after plasma onset owing to favorable temperatures for molecular formation. Regardless of irradiation conditions, plume emission features showed presence of higher oxides (i.e. UxOy), although with different temporal histories. Our study provides insight into the impact of plasma generation conditions on chemistry evolution in plasmas produced from traditional focused femtosecond, nanosecond, and filament-assisted laser ablation.
In this work, real space pair-distribution function (PDF) analysis in conjunction with molecular dynamics (MD) simulations was applied to characterize crystal structure, shape and surface structure of diamond nanoparticles annealed in air up to 880 °C. MD simulated models of individual nanodiamond particles of various shapes and sizes were used to calculate theoretical radial distribution functions G(r) for powders with different grain size distributions. The calculated curves, showing distinct differences for the explored parameter space, were compared to the experimental G(r) functions obtained from neutron scattering for annealed detonated nanodiamond samples in a search for a model best describing the actual powders. It was found that as-synthesized nanodiamond grains are terminated by equally abundant (100), (110) and (111) crystallographic faces and their structure does not change upon annealing in air up to 280 °C. The shape and size of grains annealed above 480 °C changes due to surface etching. The etching rate differs between crystals faces and depends on temperature, resulting in the observed differences in grain shape. Below 680 °C the share of the (110) facets gradually increases and at 680 °C the grains become rhombic dodecahedra terminated solely by (110) surfaces. Further increase of the annealing temperature promotes formation of (111) surfaces and at 880 °C the preferred grain shape becomes an octahedron terminated by a variant of (111) surfaces possessing three dangling sp3 bonds per atom. At lower temperatures all grains become smaller and the size distribution moves towards the lower values. Furthermore, as the annealing temperature increases, the smallest grains disappear entirely and the average grain size grows back.
Understanding activation barriers controlling structural relaxation in glass-forming liquids, molecular transport, and ionic conductivity in amorphous polymers is a grand challenge of fundamental scientific and materials engineering interest across disciplines. Over decades, intriguing but puzzling empirical correlations between the elementary time scale of activated barrier crossing and the apparent Arrhenius activation energy, the so-called Meyer−Neldel (MN) rules, have been discovered in diverse liquids and glasses. Here, in this study, we formulate and successfully apply a new experimental analysis and an explicitly dynamical theoretical framework which provides an understanding of the origin, validity, and failure of such correlations, that bridge and unify the three fields of structural relaxation, molecular transport, and ionic conductivity in liquids and quenched glasses. Distinct quasi-universal laws are predicted in equilibrated liquids and nonequilibrium glasses, consistent with experiments. Our analysis reveals that even if the relaxation appears Arrhenius over a limited temperature range, the physical activation barrier is generally temperature-dependent in polymeric systems even below glass transition temperature. In addition, we show that the approximate validity of classical MN rules hinges on a linear temperature dependence of this barrier and the temperature range probed in experiments. Our findings are relevant for controlling the activation barrier in functional soft polymeric materials relevant to molecular separations, barrier coatings, and charge transport, and also provide new constraints on the theoretical understanding of the mechanism underlying slow activated dynamics in glass-forming condensed matter.
A telescopic and laboratory investigation of water distribution among low albedo asteroids in the outer belt, using the 3-micron reflectance absorption of molecular H2O and structural OH ions (coincident with the 3-micron spectral signature of meteorite and asteroid hydrated silicates) shows that 66 percent of the C-class asteroids in the sample have hydrated silicate surfaces. In conjunction with the apparently anhydrous P and D surfaces, this pronounced hydration difference between C-class asteroids and the more distant P and D classes points to an original outer belt asteroid composition of anhydrous silicates, water ice, and complex organic material. Early solar-wind induction heating of protoasteroids, declining in intensity with distance from the sun, is conjectured to have produced the observed diminution of hydrated silicate abundance.
To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology.
Two X-ray images were obtained with the XMM-Newton spacecraft of more than 300 members of the NGC 2264 Open Cluster and its associated molecular cloud in order to investigate their magnetic activity. The X-ray fluxes extracted from those observations were used to study the dependence of stellar dynamo activity upon age and rotation for the optically revealed T Tauri stars and to place empirical constraints on theoretical models of angular momentum/dynamo evolution. The observations were also used to study the role of magnetic fields in the formation of low mass stars through the observation of very young protostars that are deeply embedded in the molecular cloud located behind the visible open cluster.
During the past two decades observations combined with laboratory simulations, have revolutionized our understanding of interstellar ice and dust, the raw materials from which planets, comets and stars form. Most interstellar material is concentrated in large molecular clouds where simple molecules are formed by dust-grain and gas-phase reactions. Gaseous species striking the cold (10K) dust stick, forming an icy grain mantle. This accretion, coupled with UV photolysis, produces a complex chemical mixture containing volatile, non-volatile, and isotopically fractionated species. Ices in molecular clouds contain the very simple molecules H2O, CH3OH, CO, CO2, H2, and perhaps some NH3 and H2CO, as well as more complex species. The evidence for these compounds, as well as carbon-rich materials, will be reviewed and the possible connections with comets and meteorites will be presented in the first part of the talk . The second part of the presentation will focus on interstellar/precometary ice photochemical evolution and the species likely to be found in comets. The chemical composition and photochemical evolution of realistic interstellar/pre-cometary ice analogs will be discussed. Ultraviolet photolysis of these ices produces H2, H2CO, CO2, CO, CH4, HCO, and more complex molecules. When ices representative of interstellar grains and comets are exposed to UV radiation at low temperature a series of moderately complex organic molecules are formed in the ice including: CH3CH2OH (ethanol), HC(=O)NH2 (formamide), CH3C(=O)NH2 (acetamide), and R-C=N (nitriles). Several of these are already known to be in the interstellar medium, and their presence indicates the importance of grain processing. After warming to room temperature an organic residue remains. This is composed primarily of hexamethylenetetramine (HMT, C6H12N4), with lesser amounts of polyoxymethylene-related species (POMs), amides, and ketones. This is in sharp contrast to the organic residues produced by irradiating unrealistic interstellar ice analogs or thermally promoted polymerization-type reactions in unirradiated realistic ice mixtures.
While most phase transformations, e.g., ferroelectric or ferromagnetic, can be first or second order depending on external applied fields, martensitic transformations in metallic alloys are nearly universally first order. We demonstrate that epitaxial stress originating from the incorporation of a tailored second phase can modify the free energy landscape that governs the phase transition and change its order from first to second. High-fidelity molecular dynamics simulations show a remarkable change in the character of the martensitic transformation in Ni–Al alloys near the critical point. We observe the continuous evolution of the transformation order parameter and scaling with power-law exponents comparable to those in other ferroic transitions exhibiting critical behavior. Our theoretical work provides a foundation for recent experimental and computational results on martensites near critical points.
Abstract Autotrophic microorganisms that convert inorganic carbon into organic matter were key players in the evolution of life on Earth. As the early atmosphere became oxygenated, microorganisms needed to develop mechanisms for oxygen protection, especially those relying on enzymes containing oxygen-sensitive metal clusters (e.g., Fe-S). Here we investigated how 4-hydroxybutyryl-CoA dehydratase (4HBD) - the key enzyme of the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle for CO 2 -fixation - adapted as conditions shifted from anoxic to oxic. 4HBD is found in both anaerobic bacteria and aerobic ammonia-oxidizing archaea (AOA). The oxygen-sensitive bacterial 4HBD and oxygen-tolerant archaeal 4HBD share 59 % amino acid identity. To examine the structural basis of oxygen tolerance in archaeal 4HBD, we determined the atomic resolution structure of the enzyme. Two tunnels providing access to the canonical [4Fe-4S] cluster in oxygen-sensitive bacterial 4HBD were closed with four conserved mutations found in all aerobic AOA and other archaea. Further biochemical experiments and molecular dynamics simulations support our findings that restricting access to the active site is the key to oxygen tolerance, explaining how active site evolution drove a major evolutionary transition. Significance statement Autotrophy (primary production) was the first life strategy on Earth. Before photosynthesis (using solar energy to fix carbon dioxide), life relied on chemical reactions for energy. These chemosynthetic reactions are present in all domains of life, including archaea possessing the most energy-efficient carbon fixation pathway - the 3-hydroxypropionate/4-hydroxybutyrate cycle. This efficiency results from enzyme modifications, including enhanced enzyme stability and catalysis of multiple reactions. We reveal the first structure of aerobic 4-hydroxybutyryl-CoA dehydratase (4HBD) from ammonia-oxidizing archaea. These archaea are among the most abundant organisms on the planet, and their 4HBD active site evolved oxygen tolerance to support aerobic metabolism. This modification can provide further insight into enzyme evolution on early earth, as photosynthesis developed and began oxygenating the atmosphere.