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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 NTRS2015

BioSentinel: Mission Development of a Radiation Biosensor to Gauge DNA Damage and Repair Beyond Low Earth Orbit on a 6U Nanosatellite

We are designing and developing a 6U (10 x 22 x 34 cm; 14 kg) nanosatellite as a secondary payload to fly aboard NASAs Space Launch System (SLS) Exploration Mission (EM) 1, scheduled for launch in late 2017. For the first time in over forty years, direct experimental data from biological studies beyond low Earth orbit (LEO) will be obtained during BioSentinels 12- to 18-month mission. BioSentinel will measure the damage and repair of DNA in a biological organism and allow us to compare that to information from onboard physical radiation sensors. In order to understand the relative contributions of the space environments two dominant biological perturbations, reduced gravity and ionizing radiation, results from deep space will be directly compared to data obtained in LEO (on ISS) and on Earth. These data points will be available for validation of existing biological radiation damage and repair models, and for extrapolation to humans, to assist in mitigating risks during future long-term exploration missions beyond LEO. The BioSentinel Payload occupies 4U of the spacecraft and will utilize the monocellular eukaryotic organism Saccharomyces cerevisiae (yeast) to report DNA double-strand-break (DSB) events that result from ambient space radiation. DSB repair exhibits striking conservation of repair proteins from yeast to humans. Yeast was selected because of 1) its similarity to cells in higher organisms, 2) the well-established history of strains engineered to measure DSB repair, 3) its spaceflight heritage, and 4) the wealth of available ground and flight reference data. The S. cerevisiae flight strain will include engineered genetic defects to prevent growth and division until a radiation-induced DSB activates the yeasts DNA repair mechanisms. The triggered culture growth and metabolic activity directly indicate a DSB and its successful repair. The yeast will be carried in the dry state within the 1-atm PL container in 18 separate fluidics cards with each card having 16 independent culture microwells, with integral microchannels and filters to supply nutrients and reagents, confine the yeast to the wells, and enable optical measurement. The measurement subsystem will monitor each subgroup of culture wells continuously for several weeks, optically tracking DSB-triggered cell growth and metabolism. BioSentinel will also include physical radiation sensors based on the TimePix sensor, as implemented by JSCs RadWorks group, which record individual radiation events including estimates of their linear-energy-transfer (LET) values. Radiation-dose and LET data will be compared directly to the rate of DSB-and-repair events measured by the S. cerevisiae biosentinels.

Radiation Biosensor↗
DOE OSTI2015

New prospects for PV powered water desalination plants: case studies in Saudi Arabia: New prospects for PV powered water desalination plants

Increased water demand and increased drought episodes in the Middle East and other regions necessitate an expansion in desalination projects and create a great market opportunity for photovoltaics (PV). PV-powered desalination has previously been regarded as not being a cost-competitive solution when compared with conventionally powered desalination; however, the decline in PV costs over the last few years has changed this outlook. Here, this article presents up-to-date performance and cost analysis of reverse osmosis (RO) desalination powered with PV connected to the Saudi Arabian grid. Reference cases include relatively small (i.e., producing 6550 m 3 water per day) and large (i.e., 190 000 m 3 /day) desalination plants using seawater at a salinity of 40 000 ppm. We used data from a King Abdullah University for Science and Technology presentation and Hybrid Optimization Model for Electric Renewables 2.81 Energy Modeling Software (HOMER Energy LLC) in tandem with Desalination Economic Evaluation Program 4.0 (International Atomic Energy Agency) desalination software to analyze the techno-economic feasibility of these plants. The first phase of our work entailed a comparison between dual-axis high concentration PV (CPV) equipped with triple junction III/V solar cells and CdTe PV-powered RO systems. The estimated levelized cost of electricity from CPV is 0.16/kWh dollars, whereas that from CdTe PV is $0.10/kWh dollars and 0.09/kWh dollars for fixed-tilt and one-axis tracking systems, respectively. These costs are higher than the price of diesel-based grid electricity in the region because diesel fuel is heavily subsidized in Saudi Arabia.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

Engineering the green algae Chlamydomonas incerta for recombinant protein production

Chlamydomonas incerta , a genetically close relative of the model green alga Chlamydomonas reinhardtii , shows significant potential as a host for recombinant protein expression. Because of the close genetic relationship between C. incerta and C. reinhardtii , this species offers an additional reference point for advancing our understanding of photosynthetic organisms, and also provides a potential new candidate for biotechnological applications. This study investigates C. incerta ’s capacity to express three recombinant proteins: the fluorescent protein mCherry, the hemicellulose-degrading enzyme xylanase, and the plastic-degrading enzyme PHL7. We have also examined the capacity to target protein expression to various cellular compartments in this alga, including the cytosol, secretory pathway, cytoplasmic membrane, and cell wall. When compared directly with C. reinhardtii , C. incerta exhibited a distinct but notable capacity for recombinant protein production. Cellular transformation with a vector encoding mCherry revealed that C. incerta produced approximately 3.5 times higher fluorescence levels and a 3.7-fold increase in immunoblot intensity compared to C. reinhardtii . For xylanase expression and secretion, both C. incerta and C. reinhardtii showed similar secretion capacities and enzymatic activities, with comparable xylan degradation rates, highlighting the industrial applicability of xylanase expression in microalgae. Finally, C. incerta showed comparable PHL7 activity levels to C. reinhardtii , as demonstrated by the in vitro degradation of a polyester polyurethane suspension, Impranil® DLN. Finally, we also explored the potential of cellular fusion for the generation of genetic hybrids between C. incerta and C. reinhardtii as a means to enhance phenotypic diversity and augment genetic variation. We were able to generate genetic fusion that could exchange both the recombinant protein genes, as well as associated selectable marker genes into recombinant offspring. These findings emphasize C. incerta ’s potential as a robust platform for recombinant protein production, and as a powerful tool for gaining a better understanding of microalgal biology.

cell membranes↗
NASA NTRS2004

Optical Diagnostic System for Solar Sails: Phase 1 Final Report

NASA's In-Space Propulsion program recently selected AEC-ABLE Engineering and L'Garde, Inc. to develop scale-model solar sail hardware and demonstrate its functionality on the ground. Both are square sail designs with lightweight diagonal booms (<100 g/m) and ultra-thin membranes (<10 g/sq m). To support this technology, the authors are developing an integrated diagnostics instrumentation package for monitoring solar sail structures such as these in a near-term flight experiment. We refer to this activity as the "Optical Diagnostic System (ODS) for Solar Sails" project. The approach uses lightweight optics and photogrammetric techniques to measure solar sail membrane and boom shape and dynamics, thermography to map temperature, and non-optical sensors including MEMS accelerometers and load cells. The diagnostics package must measure key structural characteristics including deployment dynamics, sail support tension, boom and sail deflection, boom and sail natural frequencies, sail temperature, and sail integrity. This report summarizes work in the initial 6-month Phase I period (conceptual design phase) and complements the final presentation given in Huntsville, AL on January 14, 2004.

Pappa, Richard S.↗
DOE OSTI2013

A model to simulate the oxygen distribution in hypoxic tumors for different vascular architectures

Purpose: As hypoxic cells are more resistant to photon radiation, it is desirable to obtain information about the oxygen distribution in tumors prior to the radiation treatment. Noninvasive techniques are currently not able to provide reliable oxygenation maps with sufficient spatial resolution; therefore mathematical models may help to simulate microvascular architectures and the resulting oxygen distributions in the surrounding tissue. Here, the authors present a new computer model, which uses the vascular fraction of tumor voxels, in principle measurable noninvasively in vivo, as input parameter for simulating realistic PO2 histograms in tumors, assuming certain 3D vascular architectures.Methods: Oxygen distributions were calculated by solving a reaction-diffusion equation in a reference volume using the particle strength exchange method. Different types of vessel architectures as well as different degrees of vascular heterogeneities are considered. Two types of acute hypoxia (ischemic and hypoxemic) occurring additionally to diffusion-limited (chronic) hypoxia were implemented as well.Results: No statistically significant differences were observed when comparing 2D- and 3D-vessel architectures (p > 0.79 in all cases) and highly heterogeneously distributed linear vessels show good agreement, when comparing with published experimental intervessel distance distributions and PO2 histograms. It could be shown that, if information about additional acute hypoxia is available, its contribution to the hypoxic fraction (HF) can be simulated as well. Increases of 128% and 168% in the HF were obtained when representative cases of ischemic and hypoxemic acute hypoxia, respectively, were considered in the simulations.Conclusions: The presented model is able to simulate realistic microscopic oxygen distributions in tumors assuming reasonable vessel architectures and using the vascular fraction as macroscopic input parameter. The model may be used to generate PO2 histograms, which are needed as input in models predicting the radiation response of hypoxic tumors.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

Carbide-Modified Pd on ZrO2 as Active Phase for CO2-Reforming of Methane—A Model Phase Boundary Approach

Starting from subsurface Zr0-doped “inverse” Pd and bulk-intermetallic Pd0Zr0 model catalyst precursors, we investigated the dry reforming reaction of methane (DRM) using synchrotron-based near ambient pressure in-situ X-ray photoelectron spectroscopy (NAP-XPS), in-situ X-ray diffraction and catalytic testing in an ultrahigh-vacuum-compatible recirculating batch reactor cell. Both intermetallic precursors develop a Pd0–ZrO2 phase boundary under realistic DRM conditions, whereby the oxidative segregation of ZrO2 from bulk intermetallic PdxZry leads to a highly active composite layer of carbide-modified Pd0 metal nanoparticles in contact with tetragonal ZrO2. This active state exhibits reaction rates exceeding those of a conventional supported Pd–ZrO2 reference catalyst and its high activity is unambiguously linked to the fast conversion of the highly reactive carbidic/dissolved C-species inside Pd0 toward CO at the Pd/ZrO2 phase boundary, which serves the role of providing efficient CO2 activation sites. In contrast, the near-surface intermetallic precursor decomposes toward ZrO2 islands at the surface of a quasi-infinite Pd0 metal bulk. Strongly delayed Pd carbide accumulation and thus carbon resegregation under reaction conditions leads to a much less active interfacial ZrO2–Pd0 state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1996

The August Krogh principle applies to plants

The Krogh principle refers to the use of a large number of animals to study the large number of physiological problems, rather than limiting study to a particular organism for all problems. There may be organisms that are more suited to study of a particular problem than others. This same principle applies to plants. The authors are concerned with the recent trend in plant biology of using Arabidopsis thaliana as the "organism of choice." Arabidopsis is an excellent organism for molecular genetic research, but other plants are superior models for other research areas of plant biology. The authors present examples of the successful use of the Krogh principle in plant cell biology research, emphasizing the particular characteristics of the selected research organisms that make them the appropriate choice.

NASA Discipline Plant Biology↗
DOE OSTI2018

Towards district scale flood simulations using conventional and anisotropic porosity shallow water models with high-resolution topographic information

Current topographic survey technology provides high-resolution (HR) datasets for urban environments. Incorporating this HR information in models aiming to provide flood risk assessment is desirable because the flood wave propagation is depending on the urban topographic features, i.e. buildings, bridges and street networks. Conceptual, numerical and practical challenges arise from the application of shallow water models to HR urban flood modeling. For example, numerical challenges are occurrence of wet-dry fronts, geometric discontinuities in the urban environment and discontinuous solutions, i.e. shock waves. These challenges can be overcome by using a Godunov-type scheme. However, the computational cost of this type of schemes is high, such that HR two-dimensional shallow water simulations with practical relevance have to be run on supercomputers. The porous shallow water model is an alternative approach that aims to reduce computational cost by using a coarse resolution and accounting for unresolved processes by means of the porosity terms. Usually, a speedup between two and three orders of magnitude in comparison to HR simulations can be obtained. This study presents preliminary results of a practical test case concerning pluvial flooding in a district of the city of Nice, France, caused by the intense rainfall event on October 3rd, 2015. HR topography data set on a 1 m resolution is available for the district, whereby street features of infra-metric dimensions have been included. A reference solution is calculated by a HR shallow water model on a 1 m by 1 m structured computational grid. The porous shallow water model is run on a 10 m by 10 m grid and the influence of the drag source term is studied. The model calculations show a large deviation, which is caused by the poor meshing strategy of the porous shallow water (AP) model. The study also summarizes practical challenges that arise during the application of the AP and HR models to a large urban catchment. The main difficulty is to obtain a good mesh. In smaller scale investigations, the mesh is currently constructed by hand such that the cell edges align with buildings. This approach is not feasible for large scale urban catchments with a large number of buildings. Future steps that have to be taken, such as a strategy for automatic mesh generation, are reported on.

42 ENGINEERING↗
DOE OSTI2020

Correlated insulating phases of twisted bilayer graphene at commensurate filling fractions: A Hartree-Fock study

Motivated by the recently observed insulating states in twisted bilayer graphene, we study the nature of the correlated insulating phases of the twisted bilayer graphene at commensurate filling fractions. Iin this work, we use the continuum model and project the Coulomb interaction onto the flat bands to study the ground states by using a Hartree-Fock approximation. In the absence of the hexagonal boron nitride substrate, the ground states are the intervalley coherence states at charge neutrality (filling $\textit{ν}$ = 0 , or four electrons per moiré cell) and at $\textit{ν}$ = –1/4 and –1/2 (three and two electrons per cell, respectively) and the $C_2\mathcal{T}$ symmetry-broken state at $\textit{ν}$ = –3/4 (one electron per cell). The hexagonal boron nitride substrate drives the ground states at all $\textit{ν}$ into $C_2\mathcal{T}$ symmetry broken-states. Our results provide good reference points for further study of the rich correlated physics in the twisted bilayer graphene.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS2001

The effect of acute microgravity on mechanically-induced membrane damage and membrane-membrane fusion events

Although it is unclear how a living cell senses gravitational forces there is no doubt that perturbation of the gravitational environment results in profound alterations in cellular function. In the present study, we have focused our attention on how acute microgravity exposure during parabolic flight affects the skeletal muscle cell plasma membrane (i.e. sarcolemma), with specific reference to a mechanically-reactive signaling mechanism known as mechanically-induced membrane disruption or "wounding". Both membrane rupture and membrane resealing events mediated by membrane-membrane fusion characterize this response. We here present experimental evidence that acute microgravity exposure can inhibit membrane-membrane fusion events essential for the resealing of sarcolemmal wounds in individual human myoblasts. Additional evidence to support this contention comes from experimental studies that demonstrate acute microgravity exposure also inhibits secretagogue-stimulated intracellular vesicle fusion with the plasma membrane in HL-60 cells. Based on our own observations and those of other investigators in a variety of ground-based models of membrane wounding and membrane-membrane fusion, we suggest that the disruption in the membrane resealing process observed during acute microgravity is consistent with a microgravity-induced decrease in membrane order.

Parabolic Flight↗
DOE OSTI2014

Fat Composition Changes in Bone Marrow During Chemotherapy and Radiation Therapy

Purpose: To quantify changes in bone marrow fat fraction and determine associations with peripheral blood cell counts. Methods and Materials: In this prospective study, 19 patients received either highly myelotoxic treatment (radiation therapy plus cisplatin, 5-fluorouracil mitomycin C [FU/MMC], or cisplatin/5-FU/cetuximab) or less myelotoxic treatment (capecitabine-radiation therapy or no concurrent chemotherapy). Patients underwent MR imaging and venipuncture at baseline, midtreatment, and posttreatment visits. We performed mixed effects modeling of the mean proton density fat fraction (PDFF[%]) by linear time, treatment, and vertebral column region (lumbar [L]4-sacral [S]2 vs thoracic [T]10-L3 vs cervical[C]3-T9), while controlling for cumulative mean dose and other confounders. Spearman rank correlations were performed by white blood cell (WBC) counts versus the differences in PDFF(%) before and after treatment. Results: Cumulative mean dose was associated with a 0.43% per Gy (P=.004) increase in PDFF(%). In the highly myelotoxic group, we observed significant changes in PDFF(%) per visit within L4-S2 (10.1%, P<.001) and within T10-L3 (3.93%, P=.01), relative to the reference C3-T9. In the less myelotoxic group, we did not observe significant changes in PDFF(%) per visit according to region. Within L4-S2, we observed a significant difference between treatment groups in the change in PDFF(%) per visit (5.36%, P=.04). Rank correlations of the inverse log differences in WBC versus the differences in PDFF(%) overall and within T10-S2 ranged from 0.69 to 0.78 (P<.05). Rank correlations of the inverse log differences in absolute neutrophil counts versus the differences in PDFF(%) overall and within L4-S2 ranged from 0.79 to 0.81 (P<.05). Conclusions: Magnetic resonance imaging fat quantification is sensitive to marrow composition changes that result from chemoradiation therapy. These changes are associated with peripheral blood cell counts. This study supports a rationale for bone marrow-sparing treatment planning to reduce the risk of hematologic toxicity.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Computational analysis of metal–metal bonded dimetal tetrabenzoate redox potentials in the context of ammonia oxidation electrocatalysis

Metal–metal bonded complexes are promising candidates for catalyzing redox transformations. Of particular interest is the oxidation of ammonia to dinitrogen, an important half reaction for the potential utilization of ammonia as a fuel or hydrogen carrier. This work computationally explores 30 different metal–metal bonded dimers (5 different metal centers and 6 different benzoate ligand derivatives) to explore the tunability of the redox potential when ammonia is bound to the complexes as an axial ligand, modeling the first step in ammonia oxidation electrocatalysis. We calculate the redox potentials of these compounds, making reference to experimental data when appropriate, identifying two degrees of tunability: a coarse adjustment, changing the metal center, allows for a wide range of redox potentials to be accessed (from +1.0 to –2.0 V vs. ferrocene/ferrocenium in acetonitrile solution) and a fine adjustment, the para-substituent of the benzoate derivative, which affects the redox potential in a smaller range based on the electron donating/withdrawing effects of the substituent. Ruthenium and osmium tetrabenzoate catalysts are prime candidates for next generation ammonia oxidation catalysts because their redox potentials fall within the direct ammonia fuel cell “viability zone” bracketed by the thermodynamic potentials of oxygen reduction (ORR) and nitrogen reduction (NRR). Rhodium tetrabenzoate species fall above the ORR potential, suggesting ammonia oxidation promoted by Rh 2 catalysts could instead be used to facilitate hydrogen production through coupling to hydrogen evolution at a cathode. The redox potentials of rhenium and iridium tetrabenzoate catalysts fall below the NRR potential suggesting that these compounds could be further investigated in the context of electrochemical ammonia synthesis. Each redox event studied involves electron transfer from the M–M δ* orbital regardless of choice of metal or benzoate ligand derivative; this leads us to believe that the chemical reactivity of the various studied compounds will be similar in the context of ammonia oxidation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2001

The Effect of Acute Microgravity on Mechanically-Induced Membrane Damage and Membrane-Membrane Fusion Events

Although it is unclear how a living cell senses gravitational forces there is no doubt that perturbation of the gravitational environment results in profound alterations in cellular function. In the present study, we have focused our attention on how acute microgravity exposure during parabolic flight affects the skeletal muscle cell plasma membrane (i.e. sarcolemma), with specific reference to a mechanically-reactive signaling mechanism known as mechanically-induced membrane disruption or "wounding". This response is characterized by both membrane rupture and membrane resealing events mediated by membrane-membrane fusion. We here present experimental evidence that acute microgravity exposure can inhibit membrane-membrane fusion events essential for the resealing of sarcolemmal wounds in individual human myoblasts. Additional evidence to support this contention comes from experimental studies that demonstrate acute microgravity exposure also inhibits secretagogue-stimulated intracellular vesicle fusion with the plasma membrane in HL-60 cells. Based on our own observations and those of other investigators in a variety of ground-based models of membrane wounding and membrane-membrane fusion, we suggest that the disruption in the membrane resealing process observed during acute microgravity is consistent with a microgravity-induced decrease in membrane order.

Clarke, Mark, S. F.↗
DOE OSTI2023

Single-crystal elasticity of (Al,Fe)-bearing bridgmanite up to 82 GPa

Abstract Thermoelastic properties of mantle candidate minerals are essential to our understanding of geophysical phenomena, geochemistry, and geodynamic evolutions of the silicate Earth. However, the lower-mantle mineralogy remains much debated due to the lack of single-crystal elastic moduli (Cij) and aggregate sound velocities of (Al,Fe)-bearing bridgmanite, the most abundant mineral of the planet, at the lower mantle pressure-temperature (P-T) conditions. Here we report single-crystal Cij of (Al,Fe)-bearing bridgmanite, Mg0.88Fe0.1Al0.14Si0.90O3 (Fe10-Al14-Bgm) with Fe3+/ΣFe = ~0.65, up to ~82 GPa using X-ray diffraction (XRD), Brillouin light scattering (BLS), and impulsive stimulated light scattering (ISLS) measurements in diamond-anvil cells (DACs). Two crystal platelets with orientations of (–0.50, 0.05, –0.86) and (0.65, –0.59, 0.48), that are sensitive to deriving all nine Cij, are used for compressional and shear wave velocity (νP and νS) measurements as a function of azimuthal angles over 200° at each experimental pressure. Our results show that all Cij of singe-crystal Fe10-Al14-Bgm increase monotonically with pressure with small uncertainties of 1–2% (±1σ), except C55 and C23, which have uncertainties of 3–4%. Using the third-order Eulerian finite-strain equations to model the elasticity data yields the aggregate adiabatic bulk and shear moduli and respective pressure derivatives at the reference pressure of 25 GPa: KS = 326 ± 4 GPa, µ = 211 ± 2 GPa, KS′ = 3.32 ± 0.04, and µ′ = 1.66 ± 0.02 GPa. The high-pressure aggregate νS and νP of Fe10-Al14-Bgm are 2.6–3.5% and 3.1–4.7% lower than those of MgSiO3 bridgmanite end-member, respectively. These data are used with literature reports on bridgmanite with different Fe and Al contents to quantitatively evaluate pressure and compositional effects on their elastic properties. Comparing with one-dimensional seismic profiles, our modeled velocity profiles of major lower-mantle mineral assemblages at relevant P-T suggest that the lower mantle could likely consist of about 89 vol% (Al,Fe)-bearing bridgmanite. After considering uncertainties, our best-fit model is still indistinguishable from pyrolitic or chondritic models.

Geochemistry & Geophysics↗
NASA NTRS2001

A Structural and Molecular Approach for the Study Biomarkers

Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life, is referred to as organic synthesis on mineral surfaces. Furthermore, it is suggested that the interaction between mineral surfaces and simple organic molecules resulted in the formation of amino acids, RNA, and perhaps other more complex molecules such as proteins. On the other hand, in natural systems, it is recognized that functional groups on cell walls or membranes of microorganisms serve as sites of nucleation and crystallization. The precise replication of biominerals with controlled structure, morphology, size and texture is not confined to higher organisms as it also occurs in primitive prokaryotic cells such as magnetotactic bacteria and cyanobacteria. This suggests that the principal strategies of biomineralization were established early on in the evolutionary history of organisms. It is critical, therefore, to search for common mechanisms within diverse biological systems. One such common factor is the capability for organization and self-assembly. Organic macromolecules such as proteins and lipids can aggregate and polymerize forming membranes or extracellular matrix. At the organic-inorganic interface, several factors such as lattice geometry, polarity, stereochemistry and topography may act in concert to control nucleation and growth of crystals. Although several models have been proposed that discuss the significance of these factors for biomineralization, no comprehensive experimental data are available. In contrast to crystallization in exclusively inorganic systems, the kinetics of reaction and structural relationships between organic and inorganic phases in biominerals or biomimetic material is poorly understood. For example, it is not clear if the concept of epitactic growth (geometrical matching of unit cells at the interface of a secondary crystal growing on a primary crystal) applies to organic-inorganic systems. In contrast to inorganic templates that often have a smooth and rigid surface that promotes epitactic growth, biological substrates are usually rough and result in a large degree of mismatch. It is apparent that factors controlling the reaction at the crystal-matrix interface are strongly dependent upon the nature of the substrate. Therefore, characterization of the assembled organic surface and surface structure of the inorganic phase is crucial to understanding the processes of biomineralization. The focus of our research is the investigation of the processes leading to the nucleation and growth of crystals on both natural and synthetic systems through an interdisciplinary approach that integrates molecular biology, morphology and mineralogy using advanced preparation and analytical techniques. We have studied run-products, particularly magnetite, siderite and other carbonates, that resulted from extracellular biomineralization by extremophiles isolated from a variety of extreme environments ranging from permafrost to hydrothermal vent systems. The results of this study are critical to recognizing biomarkers in terrestrial and extraterrestrial environments.

Thomas-Keprta, Kathie↗
DOE OSTI2019

A reduced basis approach for PDEs on parametrized geometries based on the shifted boundary finite element method and application to a Stokes flow

Here we propose a model order reduction technique integrating the Shifted Boundary Method (SBM) with a POD-Galerkin strategy. This approach allows to deal with complex parametrized domains in an efficient and straightforward way. The impact of the proposed approach is threefold. First, problems involving parametrizations of complex geometrical shapes and/or large domain deformations can be efficiently solved at full-order by means of the SBM. This unfitted boundary method permits to avoid remeshing and the tedious handling of cut cells by introducing an approximate surrogate boundary. Second, the computational effort is reduced by the development of a Reduced Order Model (ROM) technique based on a POD-Galerkin approach. Third, the SBM provides a smooth mapping from the true to the surrogate domain, and for this reason, the stability and performance of the reduced order basis are enhanced. This feature is the net result of the combination of the proposed ROM approach and the SBM. Similarly, the combination of the SBM with a projection-based ROM gives the great advantage of an easy and fast to implement algorithm considering geometrical parametrization with large deformations. The transformation of each geometry to a reference geometry (morphing) is in fact not required. These combined advantages will allow the solution of PDE problems more efficiently. We illustrate the performance of this approach on a number of two-dimensional Stokes flow problems.

42 ENGINEERING↗
DOE OSTI2015

Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

Background: Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. Results: Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. Conclusions: In this first genome-wide analysis of a modified histone in a woody tissue, we optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2000

Simulation and Experimental Measurements of Inductively Coupled CF4 and CF4/Ar Plasmas

The recently developed code SEMS (semiconductor equipment modeling software)is applied to the simulation of CF4 and CF4/Ar inductively coupled plasmas (ICP). This work builds upon the earlier nitrogen, transformer coupled plasma (TCP) SEMS research by demonstrating its accuracy for more complex reactive mixtures, moving closer to the realization of a virtual plasma reactor. Attention is given to the etching of and/or formation of carbonaceous films on the quartz dielectric window and diagnostic aperatures. The simulations are validated through comparisons with experimental measurements using FTIR (Fourier Transform Infrared) and UV absorption spectroscopy for CFx and SiFx neutral radicals, QMS (quadrupole mass spectrometry) for the ions, and Langmuir probe measurements of electron number density and temperature in an ICP GEC reference cell.

Hash, D. B.↗