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At least 1,783 records · Page 99
All sourcesNASA NTRSDOE OSTI
NASA NTRS2001

Effects of Convective Transport of Solute and Impurities on Defect-Causing Kinetics Instabilities

For in-situ studies of the formation and evolution of step patterns during the growth of protein crystals, we have designed and assembled an experimental setup based on Michelson interferometry with the surface of the growing protein crystal as one of the reflective surfaces. The crystallization part of the device allows optical monitoring of a face of a crystal growing at temperature stable within 0.05 C in a developed solution flow of controlled direction and speed. The reference arm of the interferometer contains a liquid-crystal element that allows controlled shifts of the phase of the interferograms. We employ an image processing algorithm which combines five images with a pi/2 phase difference between each pair of images. The images are transferred to a computer by a camera capable of capturing 6-8 frames per second. The device allows data collection data regarding growth over a relatively large area (approximately .3 sq. mm) in-situ and in real time during growth. The estimated dept resolution of the phase shifting interferometry is about 100 A. The lateral resolution, depending on the zoom ratio, varies between 0.3 and 0.6 micrometers. We have now collected quantitative results on the onset, initial stages and development of instabilities in moving step trains on vicinal crystal surfaces at varying supersaturation, position on the facet, crystal size and temperature with the proteins ferritin, apoferritin and thaumatin. Comparisons with theory, especially with the AFM results on the molecular level processes, see below, allow tests of the rational for the effects of convective flows and, as a particular case, the lack thereof, on step bunching.

Vekilov, Peter G.↗
NASA NTRS1994

The FU Orionis Outburst as a Thermal Disk Accretion Event: Detailed Calculations and Comparison to Observations

FU Orionis outbursts are temporary large increases in luminosity: x (40 - 250) thought to occur repeatedly in all low mass young stellar systems. We discuss detailed calculations of viscous accretion disks suggesting that FU Ori events signify the existence of a protostellar disk transporting mass at a rate of (1 - 10) x 10(exp 6) solar mass / yr, in agreement with theoretical and observational estimates of molecular cloud core collapse rates. Accretion through the inner edge of disks subject to outburst is self-regulated through the thermal ionization instability such that long periods (approx. 1000 yrs) of low mass flux: (1 - 10) x 10(exp -5) solar mass / yr, are punctuated by short periods (approx. 100 yrs) of high mass flux: (1-10) x 10(exp -5) solar mass / yr. The unstable region of the disk extends radially only to a distance of approx. = 1/4 AU. Beyond this region matter is transported stably at the infall rate. In systems for which M(sum *) = 1 solar mass with an inner disk edge of 3 solar radius, the critical rate for outbursts is 5 x 10(exp -7) solar mass / yr independent of the magnitude of the viscous ce parameter consistent with estimates of boundary layer mass flux in T Tauri stars. We use timescales of observed outbursts to constrain the magnitude of the alpha parameter to be 10(exp -4) where hydrogen is neutral and 10(exp -3) where ionized. Light curves of V1515 Cyg, FU Ori, and V1057 Cya are reproduced; the latter two require application of a small perturbation in surface density to produce observed rapid rise times. Detailed reply is made to objections to the accretion disk model for outbursts. Comparison to observations are made of time dependent spectral energy distributions, colors, and line-width velocity evolution.

Bell, K. R.↗
DOE OSTI2021

In vivo evolution of lactic acid hyper-tolerant Clostridium thermocellum

Lactic acid (LA) has several applications in the food, cosmetics and pharmaceutical industries, as well as in the production of biodegradable plastic polymers, namely polylactides. Industrial production of LA is essentially based on microbial fermentation. Recent reports have shown the potential of the cellulolytic bacterium Clostridium thermocellum for direct LA production from inexpensive lignocellulosic biomass. However, C. thermocellum is highly sensitive to acids and does not grow at pH < 6.0. Improvement of LA tolerance of this microorganism is pivotal for its application in cost-efficient production of LA. In the present study, the LA tolerance of C. thermocellum strains LL345 (wild-type fermentation profile) and LL1111 (high LA yield) was increased by adaptive laboratory evolution. At large inoculum size (10 %), the maximum tolerated LA concentration of strain LL1111 was more than doubled, from 15 g/L to 35 g/L, while subcultures evolved from LL345 showed 50–85 % faster growth in medium containing 45 g/L LA. Gene mutations (pyruvate phosphate dikinase, histidine protein kinase/phosphorylase) possibly affecting carbohydrate and/or phosphate metabolism have been detected in most LA-adapted populations. Although improvement of LA tolerance may sometimes also enable higher LA production in microorganisms, C. thermocellum LA-adapted cultures showed a yield of LA, and generally of other organic acids, similar to or lower than parental strains. Based on its improved LA tolerance and LA titer similar to its parent strain (LL1111), mixed adapted culture LL1630 showed the highest performing phenotype and could serve as a framework for improving LA production by further metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Kinetic Monte Carlo simulations of aging in δ -Pu

We have developed a first-passage kinetic Monte Carlo approach for materials aging to investigate the sensitivity of void swelling to model parameters, including helium bubble density and size distribution. In addition to explicitly accounting for the spatial distribution of individual point defects, bubbles, and voids, our approach can simulate total doses equivalent to 100 years of natural aging on statistically representative volumes of materials. This technique enables us to study the effects on swelling and radiation damage evolution due to temperature and dose rate (as altered in artificially aged experiments), differences in effective interaction radii between vacancies and interstitials, and varying defect diffusion activation energies, while providing more detailed information than previous rate-equation based approaches. In conclusion, our results indicate that spatial effects that are not modeled in mean-field rate theories could play a significant role in void swelling initiation and growth for certain regimes of model parameters.

Actinides↗
DOE OSTI2020

Resonant propagation of x rays from the linear to the nonlinear regime

We present a theoretical study of temporal, spectral, and spatial reshaping of intense, ultrafast x-ray pulses propagating through a resonant medium. Our calculations are based on the solution of a three-dimensional time-dependent Schrodinger-Maxwell equation, with the incident x-ray photon energy on resonance with the core-level is-3p transition in neon. We study the evolution of the combined incident and medium-generated field, including the effects of stimulated emission, absorption, ionization, and Auger decay, as a function of the input pulse energy and duration. We find that stimulated Raman scattering between core-excited states 1s -1 3p and 2p -1 3p occurs at high x-ray intensity, and that the emission around this frequency is strongly enhanced when also including the similar 1s -1 -2p -1 response of the ion. We also explore the dependence of x-ray self-induced transparency (SIT) and self-focusing on the pulse intensity and duration, and we find that the stimulated Raman scattering plays an important role in both effects. Finally, we discuss how these nonlinear effects may potentially be exploited as control parameters for pulse properties of x-ray free-electron laser sources.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRSDate not supplied

From the Interstellar Medium to Ocean Worlds: new challenges for Laboratory Astrophysics

From the Interstellar Medium to Ocean Worlds: new challenges for Laboratory Astrophysics For the past 35+ years, laboratory experiments in Astrophysics have been focusing on identifying and understanding the molecular species and chemistry occurring in interstellar environments, such as the diffuse interstellar medium (ISM) and dense molecular clouds. A significant portion of these laboratory efforts concerns investigations of carbon-based molecules ranging in size from a single carbon atom (e.g., CO, CO2, H2CO) to large polycyclic aromatic hydrocarbon (PAH) molecules potentially consisting of more than one hundred carbon atoms as well as their reactions with H2O and other interstellar species. The laboratory facilities built to conduct these investigations are capable of monitoring the chemistry and measuring the spectra under a wide range of interstellar conditions (e.g., low temperatures and pressures). The past 15 years of space exploration revealed the presence of at least nine other Ocean Worlds, besides Earth, in our Solar System. These worlds include moons and dwarf planets, ice-covered surfaces, subsurface oceans, as well as geysers venting H2O and other compounds, including organics in at least one environment, into space. Although these worlds represent environments that are significantly different from those traditionally considered the realm of Laboratory Astrophysics, their facilities are well situated to provide insight into the chemistry occurring in and around these worlds as well as experimental data for the interpretation of observations from missions visiting these Ocean World. This presentation will discuss the areas where Laboratory Astrophysics can provide experimental data to help understand the chemistry, and mission data of Ocean Worlds, and the challenges research into Ocean Worlds presents to our current facilities and how they can be overcome. Lastly, this presentation will introduce the new ICEE (In-situ Carbon Evolution Experiments) facility at NASA Ames Research Center as an example of how a lab dedicated to Laboratory Astrophysics can adapt itself to also meet the needs for Ocean Worlds research.

Andrew Lige Mattioda↗
DOE OSTI2024

The plant cell wall—dynamic, strong, and adaptable—is a natural shapeshifter

Mythology is replete with good and evil shapeshifters, who, by definition, display great adaptability and assume many different forms—with several even turning themselves into trees. Cell walls certainly fit this definition as they can undergo subtle or dramatic changes in structure, assume many shapes, and perform many functions. In this review, we cover the evolution of knowledge of the structures, biosynthesis, and functions of the 5 major cell wall polymer types that range from deceptively simple to fiendishly complex. Along the way, we recognize some of the colorful historical figures who shaped cell wall research over the past 100 years. The shapeshifter analogy emerges more clearly as we examine the evolving proposals for how cell walls are constructed to allow growth while remaining strong, the complex signaling involved in maintaining cell wall integrity and defense against disease, and the ways cell walls adapt as they progress from birth, through growth to maturation, and in the end, often function long after cell death. We predict the next century of progress will include deciphering cell type–specific wall polymers; regulation at all levels of polymer production, crosslinks, and architecture; and how walls respond to developmental and environmental signals to drive plant success in diverse environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Herbig–Haro Outflows in Circinus W

We report the discovery of new Herbig–Haro (HH) outflows in the Western Circinus molecular cloud. They were found using a color-composite imaging method that reveals faint Hα emission in complex environments. Follow-up observations in [S ii] confirmed their classification as HH objects. Nearly half of the newly discovered objects are part of the HH 76 outflow and are associated with a likely young stellar object (YSO) candidate. We also identify the source of a second outflow. Three newly discovered objects are part of a third outflow whose origin is unknown. Four more HH objects are also discovered, each of which has a location and morphology that does not suggest an origin. In total there must be at least five YSOs in the field currently producing outflows. The discovery of new HH objects and associated driving sources in this cloud complex provides more evidence for active star formation and a relatively young age in this seldom-studied region.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Geometric integration of classical spin dynamics via a mean-field Schrödinger equation

The Landau-Lifshitz equation describes the time evolution of magnetic dipoles and can be derived by taking the classical limit of a quantum mechanical spin Hamiltonian. To take this limit, one constrains the many-body quantum state to a tensor product of coherent states, thereby neglecting entanglement between sites. Expectation values of the quantum spin operators produce the usual classical spin dipoles. One may also consider expectation values of polynomials of the spin operators, leading to quadrupole and higher-order spin moments, which satisfy a dynamical equation of motion that generalizes the Landau-Lifshitz dynamics [Zhang and Batista, Phys. Rev. B 104, 104409 (2021)]. Here we reformulate the dynamics of these N 2 –1 generalized spin components as a mean-field Schrödinger equation on the N-dimensional coherent state. Furthermore, this viewpoint suggests efficient integration methods that respect the local symplectic structure of the classical spin dynamics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Slip-free multiplication and complexity of dislocation networks in FCC metals

Abstract During plastic deformation of crystalline solids, intricate networks of dislocation lines form and evolve. To capture dislocation density evolution, prominent theories of crystal plasticity assume that 1) multiplication is driven by slip in active slip systems and 2) pair-wise slip system interactions dominate network evolution. In this work, we analyze a massive database of over 100 discrete dislocation dynamics simulations (with cross-slip suppressed), and our findings bring both of these assumptions into question. We demonstrate that dislocation multiplication is commonly observed on slip systems with no applied stress and no plastic strain rate, a phenomenon we refer to as slip-free multiplication. We show that while the formation of glissile junctions provides one mechanism for slip-free multiplication, additional mechanisms which account for the influence of coplanar interactions are needed to fully explain the observations. Unlike glissile junction formation which results from a binary reaction between a pair of slip systems, these new multiplication mechanisms require higher order reactions that lead to complex network configurations. While these complex configurations have not been given much attention previously, they account for about 50% of the line intersections in our database.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Changes in leaf economic trait relationships across a precipitation gradient are related to differential gene expression in a C 4 perennial grass

Summary The leaf economics spectrum (LES) describes a suite of functional traits that consistently covary at large spatial and taxonomic scales. Despite its importance at these larger scales, few studies have examined the major drivers of intraspecific variation in the LES – phenotypic plasticity and standing genetic variation. Using experimental precipitation manipulations, we examined whether covariation among leaf economics traits and selection on leaf economics traits and trait combinations change as diverse genotypes of the widespread perennial grass Panicum virgatum are exposed to differences in precipitation. We also used RNA‐Seq to examine whether groups of co‐expressed genes that align with leaf economics traits function in processes hypothesized to underlie the LES. Water availability impacted leaf economics trait covariation in important ways – covariation between leaf economics traits and selection on covariation between traits (i.e. correlational selection) tended to be strongest when water availability was high. Additionally, many genes associated with leaf economics traits functioned in processes that may explain how the LES originates, such as chloroplasts, cell walls, and nitrogen metabolism. Water availability is likely an important modulator of selection and evolution of the LES in P. virgatum that can be better understood by examining gene expression.

Heckman, Robert W. [Department of Integrative Biol↗
DOE OSTI2021

Multi-fluid and kinetic models of partially ionized magnetic reconnection

Magnetic reconnection in partially ionized plasmas is a ubiquitous and important phenomenon in both laboratory and astrophysical systems. Here, simulations of partially ionized magnetic reconnection with well-matched initial conditions are performed using both multi-fluid and fully-kinetic approaches. Despite similar initial conditions, the time-dependent evolution differs between the two models. In multi-fluid models, the reconnection rate locally obeys either a decoupled Sweet–Parker scaling, where neutrals are unimportant, or a fully coupled Sweet–Parker scaling, where neutrals and ions are strongly coupled, depending on the resistivity. In contrast, kinetic models show a faster reconnection rate that is proportional to the fully-coupled, bulk Alfvén speed, $v^*_A$. In this work, these differences are interpreted as the result of operating in different collisional regimes. Multi-fluid simulations are found to maintain $ν_{ni}L/v^*_A$ ≳1, where $ν_{ni}$ is the neutral–ion collision frequency and L is the time-dependent current sheet half-length. This strongly couples neutrals to the reconnection outflow, while kinetic simulations evolve to allow $ν_{ni}L/v^*_A$ <1, decoupling neutrals from the reconnection outflow. Differences in the way reconnection is triggered may explain these discrepancies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Microbial Diversity and Sulfur Cycling in an Early Earth Analogue: From Ancient Novelty to Modern Commonality

Life emerged and diversified in the absence of molecular oxygen. The prevailing anoxia and unique sulfur chemistry in the Paleo-, Meso-, and Neoarchean and early Proterozoic eras may have supported microbial communities that differ from those currently thriving on the earth’s surface. Zodletone spring in southwestern Oklahoma represents a unique habitat where spatial sampling could substitute for geological eras namely, from the anoxic, surficial light-exposed sediments simulating a preoxygenated earth to overlaid water column where air exposure simulates oxygen intrusion during the Neoproterozoic era. We document a remarkably diverse microbial community in the anoxic spring sediments, with 340/516 (65.89%) of genomes recovered in a metagenomic survey belonging to 200 bacterial and archaeal families that were either previously undescribed or that exhibit an extremely rare distribution on the current earth. Such diversity is underpinned by the widespread occurrence of sulfite, thiosulfate, tetrathionate, and sulfur reduction and the paucity of sulfate reduction machineries in these taxa.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Structure, Function, Self-Assembly and Origin of Simple Membrane Proteins

Integral membrane proteins perform such essential cellular functions as transport of ions, nutrients and waste products across cell walls, transduction of environmental signals, regulation of cell fusion, recognition of other cells, energy capture and its conversion into high-energy compounds. In fact, 30-40% of genes in modem organisms codes for membrane proteins. Although contemporary membrane proteins or their functional assemblies can be quite complex, their transmembrane fragments are usually remarkably simple. The most common structural motif for these fragments is a bundle of alpha-helices, but occasionally it could be a beta-barrel. In a series of molecular dynamics computer simulations we investigated self-organizing properties of simple membrane proteins based on these structural motifs. Specifically, we studied folding and insertion into membranes of short, nonpolar or amphiphatic peptides. We also investigated glycophorin A, a peptide that forms sequence-specific dimers, and a transmembrane aggregate of four identical alpha-helices that forms an efficient and selective voltage-gated proton channel was investigated. Many peptides are attracted to water-membrane interfaces. Once at the interface, nonpolar peptides spontaneously fold to a-helices. Whenever the sequence permits, peptides that contain both polar and nonpolar amino also adopt helical structures, in which polar and nonpolar amino acid side chains are immersed in water and membrane, respectively. Specific identity of side chains is less important. Helical peptides at the interface could insert into the membrane and adopt a transmembrane conformation. However, insertion of a single helix is unfavorable because polar groups in the peptide become completely dehydrated upon insertion. The unfavorable free energy of insertion can be regained by spontaneous association of peptides in the membrane. The first step in this process is the formation of dimers, although the most common are aggregates of 4-7 helices. The helices could arrange themselves such that they formed pores capable of transporting ions and small molecules across membranes. Stability of transmembrane aggregates of simple proteins is often only marginal and, therefore, it can be regulated by environmental signals or small sequence modifications in the region of interhelical interactions. A key step in the earliest evolution of membrane proteins was the emergence of selectivity for specific substrates. Many channels could become selective if one or only a few properly chosen amino acids are properly placed along the channel, acting as filters or gates. This is a convenient evolutionary solution because it does not require imposing conditions on the whole sequence.

Pohorille, Andrew↗
NASA NTRS2010

History of Nebular Processing Traced by Silicate Stardust in IDPS

Chondritic porous interplanetary dust particles (CP-IDPs) may be the best preserved remnants of primordial solar system materials, in part because they were not affected by parent body hydrothermal alteration. Their primitive characteristics include fine grained, unequilibrated, anhydrous mineralogy, enrichment in volatile elements, and abundant molecular cloud material and silicate stardust. However, while the majority of CP-IDP materials likely derived from the Solar System, their formation processes and provenance are poorly constrained. Stardust abundances provide a relative measure of the extent of processing that the Solar System starting materials has undergone in primitive materials. For example, among primitive meteorites silicate stardust abundances vary by over two orders of magnitude (less than 10-200 ppm). This range of abundances is ascribed to varying extents of aqueous processing in the meteorite parent bodies. The higher average silicate stardust abundances among CP-IDPs (greater than 375 ppm) are thus attributable to the lack of aqueous processing of these materials. Yet, silicate stardust abundances in IDPs also vary considerably. While the silicate stardust abundance in IDPs having anomalous N isotopic compositions was reported to be 375 ppm, the abundance in IDPs lacking N anomalies is less than 10 ppm. Furthermore, these values are significantly eclipsed among some IDPs with abundances ranging from 2,000 ppm to 10,000 ppm. Given that CP-IDPs have not been significantly affected by parent body processes, the difference in silicate stardust abundances among these IDPs must reflect varying extents of nebular processing. Here we present recent results of a systematic coordinated mineralogical/isotopic study of large cluster IDPs aimed at (1) characterizing the mineralogy of presolar silicates and (2) delineating the mineralogical and petrographic characteristics of IDPs with differing silicate stardust abundances. One of the goals of this study is to better understand the earliest stages of evolution of the Solar System starting materials.

Messenger, Scott R.↗
DOE OSTI2020

Diffusional growth of cloud droplets in homogeneous isotropic turbulence: DNS, scaled-up DNS, and stochastic model

This paper presents a novel methodology to use direct numerical simulation (DNS) to study the impact of isotropic homogeneous turbulence on the condensational growth of cloud droplets. As shown by previous DNS studies, the impact of turbulence increases with the computational domain size, that is, with the Reynolds number, because larger eddies generate higher and longer-lasting supersaturation fluctuations that affect growth of individual cloud droplets. The traditional DNS can only simulate a limited range of scales because of the excessive computational cost that comes from resolving all scales involved, that is, from large scales at which the turbulent kinetic energy (TKE) is introduced down to the Kolmogorov microscale, and from following every single droplet. The novel approach is referred to as the “scaled-up DNS”. The scaling up is done in two parts, first by increasing both the computational domain and the Kolmogorov microscale and second by using super-droplets instead of real droplets. To ensure proper dissipation of TKE and scalar variance at small scales, molecular transport coefficients are appropriately scaled up with the grid length. For the scaled-up domains, say, meters and tens of meters, one needs to follow billions of real droplets. This is not computationally feasible, and so-called super-droplets are applied in scaled-up DNS simulations. Each super-droplet represents an ensemble of identical real droplets, and the number of real droplets represented by a super-droplet is referred to as the multiplicity attribute. After simple tests showing the validity of the methodology, scaled-up DNS simulations are conducted for five domains, the largest of 64 3 m 3 volume using a DNS of 256 3 grid points and various multiplicities. All simulations are carried out with vanishing mean vertical velocity and with no mean supersaturation, similarly to past DNS studies. As expected, the supersaturation fluctuations as well as the spread in droplet size distribution increase with the domain size, with the droplet radius variance increasing in time t as t 1∕2 as identified in previous DNS studies. Scaled-up simulations with different multiplicities document numerical convergence of the scaled-up solutions. Finally, we compare the scaled-up DNS results with a simple stochastic model that calculates supersaturation fluctuations based on the vertical velocity fluctuations updated using the Langevin equation. Overall, the results document similar scaling to previous small-domain DNS simulations and support the notion that the stochastic subgrid-scale model is a valuable tool for the multi-scale simulation of droplet spectral evolution applying a large-eddy simulation model.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2000

Dynamics of Molecular Hydrogen in Hypersaline Microbial Mars

Early Earth microbial communities that centered around the anaerobic decomposition of organic molecular hydrogen as a carrier of electrons, regulator of energy metabolism, and facilitator of syntroph'c microbial interactions. The advent of oxygenic photosynthetic organisms added a highly dynamic and potentially dominant term to the hydrogen economy of these communities. We have examined the daily variations of hydrogen concentrations in cyanobacteria-dominated microbial mats from hypersaline ponds in Baja California Sur, Mexico. These mats bring together phototrophic and anaerobic bacteria (along with virtually all other trophic groups) in a spatially ordered and chemically dynamic matrix that provides a good analog for early Earth microbial ecosystems. Hydrogen concentrations in the photic zone of the mat can be three orders of magnitude or more higher than in the photic zone, which are, in turn, an order of magnitude higher than in the unconsolidated sediments underlying the mat community. Within the photic zone, hydrogen concentrations can fluctuate dramatically during the diel (24 hour day-night) cycle, ranging from less than 0.001% during the day to nearly 10% at night. The resultant nighttime flux of hydrogen from the mat to the environment was up to 17% of the daytime oxygen flux. The daily pattern observed is highly dependent on cyanobacterial species composition within the mat, with Lyngbya-dominated systems having a much greater dynamic range than those dominated by Microcoleus; this may relate largely to differing degrees of nitrogen-fixing and fermentative activity in the two mats. The greatest H2 concentrations and fluxes were observed in the absence of oxygen, suggesting an important potential feedback control in the context of the evolution of atmospheric composition. The impact of adding this highly dynamic photosynthetic term to the hydrogen economy of early microbial ecosystems must have been substantial. From an evolutionary standpoint, the H2 generated in mats could have represented a very important new source of electrons and energy - but one that could not be harnessed without substantial adaptation to the highly variable chemistry of the mat surface. In addition, the emergent chemistry of anaerobic communities is often highly dependent on ambient hydrogen concentrations, so that incorporation of these communities into photosynthetic mats could have significantly affected the composition and flux of reduced "biosignature' gases to the environment.

Hoehler, Tori M.↗