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NASA NTRS2017

Biosignatures in the Context of Low Energy Flux

Many of the features that are thought of as biosignatures - including the mediation of chemical and physical processes with speed, specificity, and selectivity - result directly or indirectly from life's unique capability to mediate and direct energy flux. As such, it is important to consider the impact that differences in energy flux may have on the quantity and quality of evidence for life. Earth differs from every other body in our solar system in the magnitude of biologically-usable energy flux into a liquid water environment. On a global basis, the capture of light energy into photosynthesis and the flux of chemical energy represented in the products of that photosynthesis (organic material + O2) are about six and four orders of magnitude larger, respectively, than the flux of energy represented in geochemical sources. Our conception of what an inhabited world "looks like" and our intuition about how to search for life are based in this high-energy context. Energy fluxes on worlds beyond Earth may be better approximated by the million-fold smaller flux provided to Earth's biosphere by geochemical sources. As a result, the nature, abundance, and quality of evidence for life that could be expected on an inhabited extraterrestrial world within our solar system may differ profoundly from that found on Earth. Understanding this potential difference in quantitative terms provides important context for the formulation of life detection strategies. The influence of energy flux on biosignatures can be evaluated through reference to the two basic purposes into which life partitions energy flux: (1) Life expends energy to sustain existing biomass in a metabolic steady state (metabolically functional but non-growing). The formal representation of this relationship in the traditional microbiology literature equates biomass directly with energy flux. The direct implication is that worlds having lower energy flux will have correspondingly lower potential to support biomass. Life detection strategies that directly target extant organisms should therefore be prepared to encounter average biomass densities that may be many orders of magnitude smaller than those found in most of Earth's surface environments (2) Life expends energy to synthesize new biomass. An end-member case in which new biomass is created at the energy-limited rate and the corresponding cells are immediately destroyed (so that the energy partitioned to cell maintenance is minimized) establishes an upper bound on the rate at which biological material can enter a bulk global pool. For a specified bulk concentration [i] of any particular biological compound, i, or for biologically produced matter overall, this synthesis rate, R (sub i), defines a characteristic time scale tau (sub i) equals [i] divided by R (sub i). tau (sub i) can be thought of as (a) the minimum time required for biosynthesis to yield a specific bulk concentration (e.g., a detection threshold) of i, and (b) the average residence time of i within a bulk pool when [i] is held in steady state through a balance between biosynthesis and attrition by physical, chemical, or biological consumption. tau (sub i) becomes an important quantity in considering the potential utility of enantiomeric excess (as a product of homochiral biosynthesis) as a biosignature. Spontaneous racemization of amino acids acts to "erase" the signature of homochiral synthesis over time scales that may range from hundreds to hundreds of thousands of years, depending on temperature. For environments in which low energy flux translates to low rates of biosynthesis, including the synthesis of homochiral amino acids, amino acid residence times in pools having detectable concentrations may compare to or significantly exceed the time scale for racemization. This and similar consequences of long residence times should be considered in the formulation of life detection strategies based on detection of biologically-produced species. Fluxes of biologically-useful energy on potentially habitable worlds within our solar system are, at present, not well constrained. Improving such constraint has the potential to inform priorities in the formulation and targeting of search-for-life strategies, based on the implications of energy flux for the abundance and quality of biosignatures overall, and in specific categories.

ENERGY FLUX↗

NASA NTRS2009

Atomic References for Measuring Small Accelerations

Accelerometer systems that would combine the best features of both conventional (e.g., mechanical) accelerometers and atom interferometer accelerometers (AIAs) have been proposed. These systems are intended mainly for use in scientific research aboard spacecraft but may also be useful on Earth in special military, geological, and civil-engineering applications. Conventional accelerometers can be sensitive, can have high dynamic range, and can have high frequency response, but they lack accuracy and long-term stability. AIAs have low frequency response, but they offer high sensitivity, and high accuracy for measuring small accelerations. In a system according to the proposal, a conventional accelerometer would be used to perform short-term measurements of higher-frequency components of acceleration, while an AIA would be used to provide consistent calibration of, and correction of errors in, the measurements of the conventional accelerometer in the lower-frequency range over the long term. A brief description of an AIA is prerequisite to a meaningful description of a system according to the proposal. An AIA includes a retroreflector next to one end of a cell that contains a cold cloud of atoms in an ultrahigh vacuum. The atoms in the cloud are in free fall. The retroreflector is mounted on the object, the acceleration of which is to be measured. Raman laser beams are directed through the cell from the end opposite the retroreflector, then pass back through the cell after striking the retroreflector. The Raman laser beams together with the cold atoms measure the relative acceleration, through the readout of the AIA, between the cold atoms and the retroreflector.

Maleki, Lute↗

DOE OSTI2024

phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids

Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range of structural and dynamic properties of biomolecules, such as ligand binding, enzyme-reaction mechanisms, and protein folding. However, the development of force field parameters for the simulation of proteins containing phosphorylated amino acids using the Amber program has not kept pace with the development of parameters for standard amino acids, and it is challenging to model these modified amino acids with accuracy comparable to proteins containing only standard amino acids. In particular, the popular ff14SB and ff19SB models do not contain parameters for phosphorylated amino acids. Here, the dihedral parameters for the side chains of the most common phosphorylated amino acids are trained against reference data from QM calculations adopting the ff14SB approach, followed by validation against experimental data. Finally, library files and corresponding parameter files are provided, with versions that are compatible with both ff14SB and ff19SB.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2022

Structure-Based Design and Antigenic Validation of Respiratory Syncytial Virus G Immunogens

Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease of children, the elderly, and immunocompromised individuals. Currently, there are no FDA-approved RSV vaccines. The RSV G glycoprotein is used for viral attachment to host cells and impairment of host immunity by interacting with the human chemokine receptor CX3CR1. Antibodies that disrupt this interaction are protective against infection and disease. Nevertheless, development of an RSV G vaccine antigen has been hindered by its low immunogenicity and safety concerns. A previous study described three engineered RSV G proteins containing single-point mutations that induce higher levels of IgG antibodies and have improved safety profiles compared to wild-type RSV G. However, it is unclear if the mutations affect RSV G protein folding and display of its conformational epitopes. In this study, we show that the RSV G S177Q protein retains high-affinity binding to protective human and mouse monoclonal antibodies and has equal reactivity as wild-type RSV G protein to human reference immunoglobulin to RSV. Additionally, we determined the high-resolution crystal structure of RSV G S177Q protein in complex with the anti-RSV G antibody 3G12, further validating its antigenic structure. These studies show for the first time that an engineered RSV G protein with increased immunogenicity and safety retains conformational epitopes to high-affinity protective antibodies, supporting its further development as an RSV vaccine immunogen. Respiratory syncytial virus (RSV) causes severe lower respiratory diseases of children, the elderly, and immunocompromised populations. There currently are no FDA-approved RSV vaccines. Most vaccine development efforts have focused on the RSV F protein, and the field has generally overlooked the receptor-binding antigen RSV G due to its poor immunogenicity and safety concerns. However, single-point mutant RSV G proteins have been previously identified that have increased immunogenicity and safety. In this study, we investigate the antibody reactivities of three known RSV G mutant proteins. We show that one mutant RSV G protein retains high-affinity binding to protective monoclonal antibodies, is equally recognized by anti-RSV antibodies in human sera, and forms the same three-dimensional structure as the wild-type RSV G protein. Our study validates the structure-guided design of the RSV G protein as an RSV vaccine antigen.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1994

Cosmic heavy ion tracks in mesoscopic biological test objects

Since more than 20 years ago, when the National Academy of Sciences and the National Research Council of the U.S.A. released their report on 'HZE particle effects in manned spaced flight', it has been emphasized how difficult - if not even impossible - it is to assess their radiobiological impact on man from conventional studies where biological test organisms are stochastically exposed to 'large' fluences of heavy ions. An alternative, competing approach had been realized in the BIOSTACK experiments, where the effects of single cosmic as well as accelerator - heavy ions on individual biological test organisms could be investigated. Although presented from the beginning as the preferable approach for terrestrial investigations with accelerator heavy ions too ('The BIOSTACK as an approach to high LET radiation research'), only recently this insight is gaining more widespread recognition. In space flight experiments, additional constraints imposed by the infrastructure of the vehicle or satellite further impede such investigations. Restrictions concern the physical detector systems needed for the registration of the cosmic heavy ions' trajectories as well as the biological systems eligible as test organisms. Such optimized procedures and techniques were developed for the investigations on chromosome aberrations induced by cosmic heavy ions in cells of the stem meristem of lettuce seeds (Lactuca sativa) and for the investigation of the radiobiological response of Wolffia arriza, which is the smallest flowering (water) plant. The biological effects were studied by the coworkers of the Russian Institute of Biomedical Problems (IBMP) which in cooperation with the European Space Agency ESA organized the exposure in the Biosatellites of the Cosmos series. Since biological investigations and physical measurements of particle tracks had to be performed in laboratories widely separated, the preferred fixed contact between biological test objects and the particle detectors until the geometrical correlation between tracks and organisms has been established could not be maintained. This gave rise to half a dozen of coordinate systems for different measurements which finally had to be related to a single stack reference system.

Facius, R.↗

DOE OSTI2025

Constraints on light QCD and CP-violating axions from the death line of rotation-powered pulsars

For axions that couple to nucleons, the presence of dense nuclear matter can displace the axion from its vacuum minimum, sourcing large field gradients around neutron stars (and, more generally, compact objects). These gradients, which we refer to as axion hair, couple to the local background magnetic field, inducing a large voltage drop near the surface of the star; here, we demonstrate that the presence of axion hair decouples local near-field particle acceleration in the open magnetic field line bundle from the rotational frequency of the pulsar itself. This is significant as the non-observation of old slowly-rotating pulsars is attributed to the fact the rotationally-induced electric fields are not strong enough to sustain $e^\pm$ pair production. In this work, we review the evidence for the existence for `pulsar death', i.e. the threshold at which $e^\pm$ pair production (and thus, by association, coherent radio emission) ceases, and demonstrate using both semi-analytics and particle-in-cell simulations that the existence of axion hair can dramatically extend pulsar lifetimes. We show that the non-observation of extremely old, slowly rotating, pulsars allows for a new probe of light QCD and CP-violating axions. We also demonstrate how the observation of emission from both poles of pulsars with nearly orthogonal rotational and magnetic axes, as seen e.g. in PSR J1906+0746, can be used to set competitive limits on CP-violating axion-nucleon interactions.

Witte, Samuel J. [Oxford U., Theor. Phys.; DESY; H↗

DOE OSTI2024

Subject-specific multi-scale modeling of the fate of inhaled aerosols

Determining the fate of inhaled aerosols in the respiratory system is essential in assessing the potential toxicity of inhaled airborne materials, responses to airborne pathogens, or in improving inhaled drug delivery. The availability of high-resolution clinical lung imaging and advances in the reconstruction of lung airways from CT images have led to the development of subject-specific in-silico 3D models of aerosol dosimetry, often referred to as computational fluid-particle-dynamics (CFPD) models. As CFPD models require extensive computing resources, they are typically confined to the upper and large airways. These models can be combined with lower-dimensional models to form multiscale models that predict the transport and deposition of inhaled aerosols in the entire respiratory tract. Understanding where aerosols deposit is only the first of potentially several key events necessary to predict an outcome, being a detrimental health effect or a therapeutic response. To that end, multiscale approaches that combine CFPD with physiologically-based pharmacokinetics (PBPK) models have been developed to evaluate the absorption, distribution, metabolism, and excretion (ADME) of toxic or medicinal chemicals in one or more compartments of the human body. CFPD models can also be combined with host cell dynamics (HCD) models to assess regional immune system responses. Here, this paper reviews the state of the art of these different multiscale approaches and discusses the potential role of personalized or subject-specific modeling in respiratory health.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1999

A Real Time Investigation of Morphological Evolution During Solidification of Different Alloy Systems

Solidification phenomenon which occur at the solid/liquid (s/I) interface play a major role in the determination of structure and hence the technologically important properties of a casting. However, metals being opaque, conclusions related to several important phenomenon such as boundary layer thickness, morphological evolution, and eutectic and cell spacing are deduced from quenching experiments and subsequent post solidification metallographic analysis. Consequently, limited information is obtained about the dynamics of the process. This paper will discuss the recent efforts at the Space Science Laboratory, NASA Marshall Space Flight Center, to view and quantify in-situ and in real time the dynamics of the solidification process and to measure interfacial undercooling. First, a high resolution x-ray transmission microscope (XTM) has been developed to monitor fundamental interfacial phenomena during directional solidification of metals and alloys. The XTM operates in the range of 10-100 KeV and through projection is capable of achieving magnification of up to 16OX. Secondly, an innovative collapsible furnace has been designed to quantify interfacial undercooling by measuring the temperature of a moving s/I interface in reference to a fixed s/l interface. This measurement technique is non-intrusive in nature and is based on the Seebeck principle. In this paper real time results obtained to characterize the dynamics of irregular eutectic spacing will be presented. As an example fiber to lamella or plate transition in the Al-Al2Au eutectic system will be discussed. Further, a resolution limit of 25 micron has permitted viewing in real time morphological instability and cellular growth in Al-Au and Al-Ag systems. Simultaneously, a systematic investigation has been carried out to measure interfacial undercooling for Pb-1 wt.% Sn at and near the marginal stability regime. In conjunction with the XTM observations this study attempts to validate existing relationships between undercooling and growth velocity during plane front growth, marginal stability regime, and stable cellular growth.

Sen, S.↗

DOE OSTI2022

Transcriptional networks underlying a primary ovarian insufficiency disorder in alligators naturally exposed to EDCs

Interactions between the endocrine system and environmental contaminants are responsible for impairing reproductive development and function. Despite the taxonomic diversity of affected species and attendant complexity inherent to natural systems, the underlying signaling pathways and cellular consequences are mostly studied in lab models. To resolve the genetic and endocrine pathways that mediate affected ovarian function in organisms exposed to endocrine disrupting contaminants in their natural environments, we assessed broad-scale transcriptional and steroidogenic responses to exogenous gonadotropin stimulation in juvenile alligators (Alligator missippiensis) originating from a lake with well-documented pollution (Lake Apopka, FL) and a nearby reference site (Lake Woodruff, FL). Here, we found that individuals from Lake Apopka are characterized by hyperandrogenism and display hyper-sensitive transcriptional responses to gonadotropin stimulation when compared to individuals from Lake Woodruff. Site-specific transcriptomic divergence appears to be driven by wholly distinct subsets of transcriptional regulators, indicating alterations to fundamental genetic pathways governing ovarian function. Consistent with broad-scale transcriptional differences, ovaries of Lake Apopka alligators displayed impediments to folliculogenesis, with larger germinal beds and decreased numbers of late-stage follicles. After resolving the ovarian transcriptome into clusters of co-expressed genes, most site-associated modules were correlated to ovarian follicule phenotypes across individuals. However, expression of two site-specific clusters were independent of ovarian cellular architecture and are hypothesized to represent alterations to cell-autonomous transcriptional programs. Collectively, our findings provide high resolution mapping of transcriptional patterns to specific reproductive function and advance our mechanistic understanding regarding impaired reproductive health in an established model of environmental endocrine disruption.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Chemical contributions to silicon anode calendar aging are dominant over mechanical contributions

Silicon (Si) anodes are a promising candidate for increasing the energy density of lithium (Li)-ion batteries for electric vehicles. However, they have recently been identified as having poor calendar life that is insufficient for commercial needs, in addition to the well-known issue of their poor cycle life resulting from large volume expansion. Here, a specially designed protocol with variable rest periods between intermittent cycling is used to evaluate the impact of the mechanical disruption of Si and solid electrolyte interphase (SEI) from cycling on calendar aging measurements. Si was found to undergo more mechanical degradation during calendar aging with intermittent cycling than graphite. However, Si anode capacity fade was still dominated by time, especially for rest periods greater than or equal to 1 month between cycling. Postmortem dQ/dV half-cell analysis indicated this was mainly due to Li inventory loss and an increase in electrode resistance. Isothermal microcalorimetry further demonstrated that Si passivation is more disrupted than graphite passivation with intermittent cycling and suggested that there may be a chemical buildup of a detrimental species in the electrolyte, leading to a large spike in heat after the Si and SEI are disrupted by cycling.

25 ENERGY STORAGE↗

NASA NTRS2024

Biofabrication in Space - A Perspective

Human exploration of Mars is one of the primary goals of NASA. A three-year human exploration mission to Mars is a viable design reference mission (Design Reference Mission). If we are sending a four member crew, comprehensive understanding of the health conditions of the crew is important. Based on the biomedical results of long-duration crew members at ISS, and during gravitational transitions, a few maladaptation have been observed. Discovering the root-cause of these aberrations and finding suitable mitigations at the molecular and cellular levels are of importance for a successful mission. Developing and executing the technologies to carry out tissue generation in space as well as the development of an analog hardware for tissue generation under terrestrial conditions will be discussed. These tissues were typically used to develop disease models and drug toxicology studies for several weeks and many other applications. The significant progress made during the last two decades have unfolded developments in organ generation, stem cell generation in space. When you remove the gravitational force during these cellular building processes while in space, other forces like surface tension, intermolecular forces, Coriolis force, loss of convection, reduced shear force, dominate the environment leading to behavior that we may not observe under terrestrial conditions. Based on these discoveries, the fundamental mechanisms could be better understood and new insights into bioprocesses could be developed for an exciting future.

Antony Jeevarajan↗

NASA NTRS1982

Jet noise suppression by porous plug nozzles

Jet noise suppression data presented earlier by Maestrello for porous plug nozzles were supplemented by the testing of a family of nozzles having an equivalent throat diameter of 11.77 cm. Two circular reference nozzles and eight plug nozzles having radius ratios of either 0.53 or 0.80 were tested at total pressure ratios of 1.60 to 4.00. Data were taken both with and without a forward motion or coannular flow jet, and some tests were made with a heated jet. Jet thrust was measured. The data were analyzed to show the effects of suppressor geometry on nozzle propulsive efficiency and jet noise. Aerodynamic testing of the nozzles was carried out in order to study the physical features that lead to the noise suppression. The aerodynamic flow phenomena were examined by the use of high speed shadowgraph cinematography, still shadowgraphs, extensive static pressure probe measurements, and two component laser Doppler velocimeter studies. The different measurement techniques correlated well with each other and demonstrated that the porous plug changes the shock cell structure of a standard nozzle into a series of smaller, periodic cell structures without strong shock waves. These structures become smaller in dimension and have reduced pressure variations as either the plug diameter or the porosity is increased, changes that also reduce the jet noise and decrease thrust efficiency.

Bauer, A. B.↗

DOE OSTI2022

Best Practices in PEC Water Splitting: How to Reliably Measure Solar-to-Hydrogen Efficiency of Photoelectrodes

Photoelectrochemical (PEC) water splitting, which utilizes sunlight and water to produce hydrogen fuel, is potentially one of the most sustainable routes to clean energy. One challenge to success is that, to date, similar materials and devices measured in different labs or by different operators lead to quantitatively different results, due to the lack of accepted standard operating procedures and established protocols for PEC efficiency testing. With the aim of disseminating good practices within the PEC community, we provide a vetted protocol that describes how to prepare integrated components and accurately measure their solar-to-hydrogen (STH) efficiency (η STH ). This protocol provides details on electrode fabrication, η STH test device assembly, light source calibration, hydrogen evolution measurement, and initial material qualification by photocurrent measurements under monochromatic and broadband illumination. Common pitfalls in translating experimental results from any lab to an accurate STH efficiency under an AM1.5G reference spectrum are discussed. A III–V tandem photocathode is used to exemplify the process, though with small modifications, the protocol can be applied to photoanodes as well. Dissemination of PEC best practices will help those approaching the field and provide guidance for comparing the results obtained at different lab sites by different groups.

08 HYDROGEN↗

NASA NTRS1991

Data analysis and interpretation related to space system/environment interactions at LEO altitude

Several studies made on the interaction of active systems with the LEO space environment experienced from orbital or suborbital platforms are covered. The issue of high voltage space interaction is covered by theoretical modeling studies of the interaction of charged solar cell arrays with the ionospheric plasma. The theoretical studies were complemented by experimental measurements made in a vacuum chamber. The other active system studied was the emission of effluent from a space platform. In one study the emission of plasma into the LEO environment was studied by using initially a 2-D model, and then extending this model to 3-D to correctly take account of plasma motion parallel to the geomagnetic field. The other effluent studies related to the releases of neutral gas from an orbiting platform. One model which was extended and used determined the density, velocity, and energy of both an effluent gas and the ambient upper atmospheric gases over a large volume around the platform. This model was adapted to study both ambient and contaminant distributions around smaller objects in the orbital frame of reference with scale sizes of 1 m. The other effluent studies related to the interaction of the released neutral gas with the ambient ionospheric plasma. An electrostatic model was used to help understand anomalously high plasma densities measured at times in the vicinity of the space shuttle orbiter.

Raitt, W. John↗

NASA NTRS2003

The Effect of Spaceflight on the Ultrastructure of the Cerebellum

In weightlessness, astronauts and cosmonauts may experience postural illusions as well as motion sickness symptoms known as the space adaptation syndrome. Upon return to Earth, they have irregularities in posture and balance. The adaptation to microgravity and subsequent re-adaptation to Earth occurs over several days. At the cellular level, a process called neuronal plasticity may mediate this adaptation. The term plasticity refers to the flexibility and modifiability in the architecture and functions of the nervous system. In fact, plastic changes are thought to underlie not just behavioral adaptation, but also the more generalized phenomena of learning and memory. The goal of this experiment was to identify some of the structural alterations that occur in the rat brain during the sensory and motor adaptation to microgravity. One brain region where plasticity has been studied extensively is the cerebellar cortex-a structure thought to be critical for motor control, coordination, the timing of movements, and, most relevant to the present experiment, motor learning. Also, there are direct as well as indirect connections between projections from the gravity-sensing otolith organs and several subregions of the cerebellum. We tested the hypothesis that alterations in the ultrastructural (the structure within the cell) architecture of rat cerebellar cortex occur during the early period of adaptation to microgravity, as the cerebellum adapts to the absence of the usual gravitational inputs. The results show ultrastructural evidence for neuronal plasticity in the central nervous system of adult rats after 24 hours of spaceflight. Qualitative studies conducted on tissue from the cerebellar cortex (specifically, the nodulus of the cerebellum) indicate that ultrastructural signs of plasticity are present in the cerebellar zones that receive input from the gravity-sensing organs in the inner ear (the otoliths). These changes are not observed in this region in cagematched ground control animals. The specific changes include the formation of lamellar bodies, profoundly enlarged Purkinje cell mitochondria, the presence of inter-neuronal cellular protrusions in the molecular layer, and signs of degeneration in the distal dendrites of the Purkinje cells. Since these morphologic signs are not apparent in the control animals, they are not likely to be due to caging or tissue processing effects. The particular nature of the structural alterations in the nodulus, most notably the formation of lamellar bodies and the presence of degeneration, further suggests that excitotoxicity (damaging overstimulation of neurons) may play a role in the short-term neural response to spaceflight. These findings suggest a structural basis for the neuronal and synaptic plasticity accompanying the central nervous system response to altered gravity and help identify the cellular bases underlying the vestibular abnormalities experienced by astronauts during periods of adaptation and re-adaptation to different gravitational forces. Also, since the short- and long-term changes in neural structure occurring during such periods of adaptation resemble the neuronal alterations that occur in some neurologic disorders such as stroke, these findings may offer guidance in the development of strategies for rehabilitation and treatment of such disorders.

Holstein, Gay R.↗

NASA NTRS2004

The Southern Hemisphere Additional Ozonesondes (SHADOZ) 1998-2002 Tropical Ozone Climatology: Instrumentation and Station-to-Station Variability - 3

Abstract: Since 1998 the Southern Hemisphere ADditional OZonesondes (SHADOZ) project has collected more than 2000 ozone profiles from a dozen tropical and subtropical sites using balloon-borne electrochemical concentration cell (ECC) ozonesondes. The data (with accompanying pressure-temperature-humidity soundings) are archived. Analysis of ozonesonde imprecision within the SHADOZ dataset revealed that variations in ozonesonde technique could lead to station-to-station biases in the measurements. In this paper imprecisions and accuracy in the SHADOZ dataset are examined in light of new data. When SHADOZ total ozone column amounts are compared to version 8 TOMS (2004 release), discrepancies between sonde and satellite datasets decline 1-2 percentage points on average, compared to version 7 TOMS. Variability among stations is evaluated using total ozone normalized to TOMS and results of laboratory tests on ozonesondes (JOSE-2O00, Julich Ozonesonde Intercomparison Experiment). Ozone deviations from a standard instrument in the JOSE flight simulation chamber resemble those of SHADOZ station data relative to a SHADOZ-defined climatological reference. Certain systematic variations in SHADOZ ozone profiles are accounted for by differences in solution composition, data processing and instrument (manufacturer). Instrument bias leads to a greater ozone measurement above 25 km over Nairobi and to lower total column ozone at three Pacific sites compared to other SHADOZ stations at 0-20 deg.S.

Thompson, Anne M.↗

DOE OSTI2023

NbTaV_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution ternary alloys niobium-tantalum-vanadium (Nb-Ta-V). The first-principle code that has been used to run the calculations is the closed-source Vienna Ab-Initio Simulation Package (VASP). The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 8. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 10,500 randomized atomic structures over 105 chemical compositions. The calculations have been collected on NERSC-Perlmutter using the VASP 6.3.2. The VASP calculations for every atomic structure have been performed in 2 main steps: 1. Starting from an ideal body-centered-cubic (BCC) structure, geometry optimization with low precision has been executed to perform a preliminary optimization of the atomic structure. The output for this calculations is available in the files 0.CONTCAR, 0.OUTCAR, rlx1.out. 2. Using the atomic structure resulting from the preliminary geometry optimization, a second geometry optimization has been performed using normal precision. The output for this calculations is available in the files CONTCAR, OUTCAR, rlx2.out, vaspout.h5, and vasprun.xml. Every chemical composition sampled across the composition range in the dataset has its own directory. The convention used to name the directories for ternary alloys is AXBYCZ, where A, B, and C refer to the constituents, and X, Y, and Z are positive integers that represent the number of atoms for each constituent and their values still sum up to 128. Each atomic structure associated with a specific chemical composition has its own sub-directory within the directory of the corresponding chemical composition. The sub-directories for each atomic structure for each chemical composition are named 'case-*', where * is a positive integer that spans all the values from 1 through 100, extremes included. The files contained in each sub-directory 'case-*' for each atomic structure are as follows: 1. INCAR: input file that contains various parameters and settings for controlling the behavior of the electronic structure calculations 2. 0.POSCAR: input file that defines the atomic structure of a system 3. 0.CONTCAR: output file that provides the atomic positions and cell parameters after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 4. 0.OUTCAR: output file that contains detailed information about the progress of a calculation after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 5. rlx1.out: file with diagnostic information about the execution of the first geometry optimization with precision variable set to PREC=Low in the INCAR file 6. POSCAR: input file that defines the atomic structure of a system after the first geometry optimization has been run at low precision. This represents the input for the second geometry optimization run with the precision variable set to PREC=Normal in the INCAR file 7. CONTCAR: output file that provides the atomic positions and cell parameters after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 8. OUTCARL: output file that contains detailed information about the progress of a calculation after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 9. rlx2.out: file with diagnostic information about the execution of the second geometry optimization with precision variable set to PREC=Normal in the INCAR file 10. vaspout.h5: hierarchical HDF5 file containing the inputs and outputs of a VASP calculation. To analyze the data in this file we recommend using py4vasp. This file is only produced if the VASP version used is compiled with HDF5 support 11. vasprun.xml: contains similar information to OUTCAR, but in an xml format. This research is sponsored by the Artificial Intelligence Initiative as part of the Laboratory Directed Research and Development (LDRD) Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the US Department of Energy under contract DE-AC05-00OR22725. This work used resources of the Oak Ridge Leadership Computing Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725, under Directorate Discretionary awards MAT025 (Materials Science) and LRN026 (Machine Learning), and INCITE award MAT201. This work also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, under award ERCAP0025216.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

ABSTRACT Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8–2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life. IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers’ efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

59 BASIC BIOLOGICAL SCIENCES↗