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DOE OSTI2022

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

Abstract Background Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. Results Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro - and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity ( π and θ ), and selective pressures (pN/pS and Tajima’s D ) within and fixation indices ( F ST ) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity ( π ) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better “bet hedge” in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. Conclusions These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro - and microdiversity across microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Cluster Dynamics Simulations of Intra-Granular Fission Gas Bubble Size and Pressure Evolution in UO 2

Fission gases such as xenon (Xe) play a critical role in determining the behavior and response of nuclear fuel. Given that Xe has little solubility in UO 2 , it accumulates and forms bubbles, which significantly impact fuel performance. Intra- and inter-granular bubble nucleation and growth can lead to fuel swelling, and once bubbles interconnect at grain boundaries, fission gas can be released into the plenum. At low temperatures, limited uranium vacancy mobility can restrict swelling, therefore causing the bubbles to become highly pressurized. Consequently, this can induce micro-cracking, promote fission gas release (increasing the likelihood of cladding failure), and even lead to fuel pulverization under accident conditions such as a loss of coolant accident. As bubble evolution is strongly influenced by local temperature and fission rate, markedly different behavior occurs across the radial profile of the fuel pellet. Capturing the mechanisms that underpin bubble evolution is therefore important to predict these behaviors in the fuel. Previous models describing important mechanisms informed by lower length scale simulations have been developed under the NEAMS program. These can describe the evolution of a single bubble type (i.e., single value for radius and pressure) at each position in the pellet, for instance using the Centipede cluster dynamic code. However, in reality, a full distribution in bubble sizes and pressures exists within the microstructure at a given position in the pellet. To address this the cluster dynamics code Xolotl, which can predict Xe and vacancy phase space (i.e., bubble distributions) for intra-granular bubbles, has been used before. Prior work benchmarked the Xolotl code against the Centipede cluster dynamics code to ensure compatibility and to verify that mobile defect properties are adequately transferred between the two codes, along with some physics improvements. In this work, we go further by introducing a physics-based set of improvements that will allow us to accurately predict bubble size distributions and internal bubble pressures under representative UO 2 irradiation conditions. The improvements include (i) coupling bubble-defect reaction energies to a virial equation of state (EOS), (ii) including a bubble surface tension contribution, (iii) incorporating radiation-induced re-solution of Xe and vacancies, (iv) enabling pressure-driven dislocation loop punching through an effective emission of interstitial clusters informed by interstitial loop energetics, (v) accounting for radiation induced athermal diffusion of Xe, and (vi) implementing a Booth-type grain boundary sink representation for all mobile defects and defect clusters. After these modifications, we observe good agreement of Xolotl fission gas bubble size and concentration predictions with legacy experimental measurements. Additionally, it allows the distribution of Xe bubble pressures and radius to also be predicted and compared to data produced through the Advanced Fuels Campaign (AFC) program. Here, we have done this by running simulations under conditions similar to the AFC post-irradiation examination (PIE) samples irradiated at North Anna 2 light water reactor (LWR). Our results shows excellent agreement with these experimental measurements.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

NASA NTRS1972

Ion drift velocities in gaseous mixtures at arbitrary field strengths.

A momentum-transfer theory is used to obtain an expression for the drift velocity of an ion in a multicomponent gas mixture. This is combined with an approximate calculation of the partition of the ion energy in the mixture to yield a formula for the drift velocity in terms of the drift velocities in the pure component gases. Positive deviations from Blanc's law at high fields are predicted, of magnitudes that should be easily measured experimentally.

Mason, E. A.↗

NASA NTRS1993

Multi-channel spatial auditory display for speech communications

A spatial auditory display for multiple speech communications was developed at NASA-Ames Research Center. Input is spatialized by use of simplified head-related transfer functions, adapted for FIR filtering on Motorola 56001 digital signal processors. Hardware and firmware design implementations are overviewed for the initial prototype developed for NASA-Kennedy Space Center. An adaptive staircase method was used to determine intelligibility levels of four letter call signs used by launch personnel at NASA, against diotic speech babble. Spatial positions at 30 deg azimuth increments were evaluated. The results from eight subjects showed a maximal intelligibility improvement of about 6 to 7 dB when the signal was spatialized to 60 deg or 90 deg azimuth positions.

Begault, Durand↗

NASA NTRS2005

Orbiter Repair Maneuver Contingency Separation Methods and Analysis

Repairing damaged thermal protection system tile requires the Space Shuttle to be oriented such that repair platform access from the International Space Station (ISS) is possible. To do this, the Space Shuttle uses the Orbiter Repair Maneuver (ORM), which utilizes the Shuttle Remote Manipulator System (SRMS) to rotate the Space Shuttle in relation to the ISS, for extended periods of time. These positions cause difficulties and challenges to performing a safe separation (no collision or thruster plume damage to sensitive ISS structures) should an inadvertent release occur or a contingency procedure require it. To help protect for an SRMS failure or other failures, a method for separating without collision and the ability to redock to ISS from the ORM configuration was needed. The contingency ORM separation solution elegantly takes advantage of orbital mechanics between ISS and the separating Space Shuttle. By pitching the ISS down approximately 45 degrees, in a majority of the ORM repair positions, the altitude difference between the ISS and Space Shuttle center of gravity is maximized. This altitude difference results in different orbital energies (orbital periods) causing objects to separate from each other without requiring translational firings. Using this method, a safe contingency ORM separation is made possible in many odd positions even though some separation positions point high powered thrusters directly at fragile ISS and Soyuz solar arrays. Documented in this paper are the development simulations and procedures of the contingency ORM separation and the challenges encountered with large constraints to work around. Lastly, a method of returning to redock with the ISS to pick up the stranded crew members (or transfer the final crew members) is explained as well as the thruster and ISS loads analysis.

Machula, Michael↗

NASA NTRS2011

Effects of Absorbing Aerosols on Accelerated Melting of Snowpack in the Hindu-Kush-Himalayas-Tibetan Plateau Region

The impacts of absorbing aerosol on melting of snowpack in the Hindu-Kush-Himalayas-Tibetan Plateau (HKHT) region are studied using in-situ, satellite observations, and GEOS-5 GCM. Based on atmospheric black carbon measurements from the Pyramid observation (~ 5 km elevation) in Mt. Everest, we estimate that deposition of black carbon on snow surface will give rise to a reduction in snow surface albedo of 2- 5 %, and an increased annual runoff of 12-34% for a typical Tibetan glacier. Examination of satellite reflectivity and re-analysis data reveals signals of possible impacts of dust and black carbon in darkening the snow surface, and accelerating spring melting of snowpack in the HKHT, following a build-up of absorbing aerosols in the Indo-Gangetic Plain. Results from GCM experiments show that 8-10% increase in the rate of melting of snowpack over the western Himalayas and Tibetan Plateau can be attributed to the elevated-heat-pump (EHP) feedback effect, initiated from the absorption of solar radiation by dust and black carbon accumulated to great height (~ 5 km) over the Indo-Gangetic Plain and Himalayas foothills in the pre-monsoon season (April-May). The accelerated melting of the snowpack is enabled by an EHP-induced atmosphere-land-snowpack positive feedback involving a) orographic forcing of the monsoon flow by the complex terrain, and thermal forcing of the HKHT region, leading to increased moisture, cloudiness and rainfall over the Himalayas foothills and northern India, b) warming of the upper troposphere over the Tibetan Plateau, and c) an snow albedo-temperature feedback initiated by a transfer of latent and sensible heat from a warmer atmosphere over the HKHT to the underlying snow surface. Results from ongoing modeling work to assess the relative roles of EHP vs. snow-darkening effects on accelerated melting of snowpack in HKHT region will also be discussed.

Lau, William K.↗

NASA NTRS2016

The Human Challenges of Remotely Piloted Aircraft Systems

Remotely Piloted Aircraft (RPA) range from small electric quadcopters that are flown close to the ground within visual range of the operator, to larger systems capable of extended flight in airspace shared with conventional aircraft. Before RPA can operate routinely and safely in civilian airspace, we need to understand the unique human factors associated with these aircraft. RPA pilots participated in focus groups where they were asked to recall critical incidents that either presented a threat to safety, or highlighted a case where the pilot contributed to system resilience or mission success. Ninety incidents were gathered from focus-groups. Human factor issues included the impact of reduced sensory cues, traffic separation in the absence of an out-the-window view, control latencies, vigilance during monotonous and ultra-long endurance flights, control station design considerations, transfer of control between control stations, the management of lost link procedures, and decision-making during emergencies. Some of these concerns have received significant attention in the literature, or are analogous to human factors of manned aircraft. Although many of the reported incidents were related to pilot error, the participants also provided examples of the positive contribution that humans make to the operation of highly-automated systems.

Hobbs, Alan↗

DOE OSTI2022

Structures of a phycobilisome in light-harvesting and photoprotected states

Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae 1,2 . These large protein complexes capture incident sunlight and transfer the energy through a network of embedded pigment molecules called bilins to the photosynthetic reaction centres. However, light harvesting must also be balanced against the risks of photodamage. A known mode of photoprotection is mediated by orange carotenoid protein (OCP), which binds to PBS when light intensities are high to mediate photoprotective, non-photochemical quenching 3-6 . Here we use cryogenic electron microscopy to solve four structures of the 6.2 MDa PBS, with and without OCP bound, from the model cyanobacterium Synechocystis sp. PCC 6803. The structures contain a previously undescribed linker protein that binds to the membrane-facing side of PBS. For the unquenched PBS, the structures also reveal three different conformational states of the antenna, two previously unknown. The conformational states result from positional switching of two of the rods and may constitute a new mode of regulation of light harvesting. Further, only one of the three PBS conformations can bind to OCP, which suggests that not every PBS is equally susceptible to non-photochemical quenching. In the OCP-PBS complex, quenching is achieved through the binding of four 34kDa OCPs organized as two dimers. The complex reveals the structure of the active form of OCP, in which an approximately 60Å displacement of its regulatory carboxy terminal domain occurs. Finally, by combining our structure with spectroscopic properties 7 , we elucidate energy transfer pathways within PBS in both the quenched and light-harvesting states. Collectively, our results provide detailed insights into the biophysical underpinnings of the control of cyanobacterial light harvesting. The data also have implications for bioengineering PBS regulation in natural and artificial light-harvesting systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Implementing Mixed Reality Tools to Support Mission Delivery at Hanford - 20520

Mission Support Alliance's (MSA) Public Works and Information Systems organizations have been working with Microsoft Corporation to develop and implement mixed reality operational solutions using their HoloLens technology. This collaborative effort is intended to drive innovative solutions and significantly improve MSA's efficiency in performing work at the Hanford Site. HoloLens, a mixed reality tool, is a commercial off-the-shelf technology that combines a head-mounted viewing screen with applications to help people and organizations learn, communicate, and collaborate more effectively through the use of mixed reality. https://microsoft.com/en-us/hololens MSA's initial pilot successfully demonstrated its ability to use mixed reality utilizing HoloLens' advanced features in a variety of ways, illustrating the potential efficiency gains previously stated as goals of this pilot. These achievements include the development of proprietary technology that allows synchronization between a HoloLens device and a mobile device or alternate global positioning system (GPS) device. This synchronization enables the HoloLens device to access real time GPS location data anywhere on the Hanford Site. This real time location data, combined with MSA's improved Hanford Geographical Information System (GIS) data, enables the mixed reality pilot application to identify underground utility systems as well as related utility attributes. This ability will aid utility workers in several areas, including excavation activities, the placement of large cranes, identifying interactions and conflicts with future underground utility placements and, eventually, recognizing and de-conflicting tank waste transfer system valve alignments. The HoloLens mixed reality application is also able to provide full or small scale holographic images of a facility's digital twin. This feature will allow MSA's Water and Sewer Utilities team to train and validate procedures associated with the new water treatment facility virtually, before it is constructed. This reduces the amount of time it takes to complete the training and procedure validation, and accelerates the overall construction schedule. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Structural and Mechanistic Advances in the Chemistry of Methyl-Coenzyme M Reductase (MCR)

Methane represents 34% of U.S. energy consumption and is a major greenhouse gas related to the global carbon cycle and energy production. However, current industrial practices significantly increase atmospheric methane levels, necessitating a deeper understanding of its biosynthesis and oxidation. Methyl-coenzyme M reductase (MCR) is central to biological methane metabolism, catalyzing the final step of methanogenesis and the first step in anaerobic methane oxidation. It is also a key target for strategies to capture and transform methane into value-added chemicals.The active site of MCR is a buried Ni-based cofactor only accessible by the substrates via a 50 Å long tunnel. Although the Ni(I) state is required to initiate catalysis, capturing this state remains a challenge for the current structural techniques. Recent advances in structural biology using X-ray Free-Electron Laser serial crystallography have provided insights into MCR's inactive Ni(II) state at room temperature and show promise for capturing its active Ni(I) form.Our team has established several critical aspects of the MCR mechanism using a combination of experimental and computational studies. MCR uses CH 3 -SCoM and CoBSH as substrates, producing methane and a disulfide product CoMSSCoB. Kinetic analysis showed that productive substrate binding requires CH 3 -SCoM to bind first, inducing conformational changes that optimize the active site for subsequent CoBSH binding. Following substrate binding, four proposed methane production/oxidation mechanisms were examined, establishing whether the reaction proceeds through an organometallic methyl-nickel(III), methyl anion ion, or methyl radical intermediate. Experimental measurements using CoBSH analogs successfully slowed the reaction, allowing for mechanistic insight that demonstrated the methyl radical pathway, where the initial interactions involve homolytic cleavage of the methyl-sulfur bond, generating a methyl radical that quickly abstracts the thiol hydrogen atom of CoBSH to form methane. Computational studies further confirmed that, compared to other mechanisms, the methyl radical mechanism is thermodynamically more favorable and accessible under physiological conditions.Spectroscopic and computational studies challenged the conventional understanding of substrate binding in MCR by proposing an alternative positioning of CH 3 -SCoM and CoMSSCoB in the active site pocket. The research suggested that CH 3 -SCoM (substrate) and CoMSSCoB (product) bind via their sulfonate groups to the Ni(I) center of cofactor F 430 . This binding allows for the reaction without substrate reorganization in the pocket but would require a long-range electron transfer. Altogether, the work summarized in this review reflects our current understanding of the enzyme's catalytic mechanism and structural dynamics. This is essential for developing efficient methane conversion technologies that could mitigate its environmental impact while harnessing energy-storage properties.

03 NATURAL GAS↗

DOE OSTI2020

EFRC Accomplishments 2014-2020: NorthEast Center for Chemical Energy Storage (NECCES)

The mission of NECCES is to develop an understanding of how key electrode reactions occur in cathode materials for Li based batteries, and how they can be controlled to improve electrochemical performance, from the atomistic level to the macroscopic level through the life-time of the operating battery. This mission will allow the determination of the ultimate limits of intercalation reactions for chemical energy storage. The approach and specific research goals of NECCES are to: 1. Attain reversible multi-electron transfer in a cathode material using lithium, using the model compound ε -VOPO 4 ; 2. Close the gap between the theoretical and practical energy density for intercalation compounds, using the model compound LiNi 0.85 Co 0 .10Al 0.05 O 2 ; 3. Understand the transition from cation redox to anion redox electrochemistry; 4. Understand performance limiting transport in positive electrode structures from the local through the meso to the macroscale.

25 ENERGY STORAGE↗

DOE OSTI2024

Support of the Third Summer School and Workshop Focused on Theory and Applications of Time-Dependent Density Functional Theory, Electronic Excited States, and Excited State Dynamics

To create a community of scholars with a deep understanding of TDDFT and excited state methods, both their capabilities and limitations, and how they can be used to model the excited state properties and charge transfer in materials and molecules, we are planning the third iteration of a summer school and workshop focusing on theory and applications of TDDFT, Excited States, and Excited State Dynamics to be offered in the summer of 2023. The two iterations of the US-based school that we previously organized have been very successful with overwhelmingly positive feedback. There is a high level of engagement, enthusiasm, and active participation and networking amongst the students of the school and the scientists of the workshop.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1982

Unprecented syntonization and syncronization accuracy via simultaneous viewing with GPS receivers: Construction characteristics of an NBS/GPS receiver

The National Bureau of Standards/Global Positioning System (NBS/GPS) receiver is discussed. It is designed around the concept of obtaining high accuracy, low cost time and frequency comparisons between remote frequency standards and clocks with the intent to aid international time and frequency coordination. Preliminary tests of this comparison technique between Boulder, CO and Washington, D.C indicate the ability to do accurate time transfer to better that 10 ns, and frequency measurements to better than 1 part in 10 to the 14th power. The hardware and software of the receiver is detailed. The receiver is fully automatic with a built-in 0.1 ns resolution time interval counter. A microprocessor does data processing. Satellite signal stabilities are routinely at the 5 ns level for 15 s averages, and the internal receiver stabilities are at the 1 ns level.

Davis, D. D.↗

NASA NTRS1986

Centroid tracking with area array detectors

A computer program (ALGEVAL) has been developed to simulate the position estimating behavior of a centroid estimator algorithm using data typical of optical point spread function data recorded by an area array detector. Typical results are shown of varying detector properties and optical point spread function types. The detector parameters currently available for study include read noise mean value, dark current mean value and spatial variation, charge transfer efficiency and point spread function location, saturation level, signal level and pixel size. The program is capable of calculating any order centroid using an array size from 2 x 2 to 15 x 15 pixels. The output of the program is either a performance map, histogram data or tabluar data. A number of further developments are recommended.

Glavich, T. A.↗

NASA NTRS1994

Multichannel Spatial Auditory Display for Speed Communications

A spatial auditory display for multiple speech communications was developed at NASA/Ames Research Center. Input is spatialized by the use of simplifiedhead-related transfer functions, adapted for FIR filtering on Motorola 56001 digital signal processors. Hardware and firmware design implementations are overviewed for the initial prototype developed for NASA-Kennedy Space Center. An adaptive staircase method was used to determine intelligibility levels of four-letter call signs used by launch personnel at NASA against diotic speech babble. Spatial positions at 30 degree azimuth increments were evaluated. The results from eight subjects showed a maximum intelligibility improvement of about 6-7 dB when the signal was spatialized to 60 or 90 degree azimuth positions.

Begault, Durand R.↗

NASA NTRS1994

Multichannel spatial auditory display for speech communications

A spatial auditory display for multiple speech communications was developed at NASA/Ames Research Center. Input is spatialized by the use of simplified head-related transfer functions, adapted for FIR filtering on Motorola 56001 digital signal processors. Hardware and firmware design implementations are overviewed for the initial prototype developed for NASA-Kennedy Space Center. An adaptive staircase method was used to determine intelligibility levels of four-letter call signs used by launch personnel at NASA against diotic speech babble. Spatial positions at 30 degrees azimuth increments were evaluated. The results from eight subjects showed a maximum intelligibility improvement of about 6-7 dB when the signal was spatialized to 60 or 90 degrees azimuth positions.

NASA Discipline Space Human Factors↗

NASA NTRS2019

Carbon Nanostructures in Biological Sensors for Space and Terrestrial Applications

Biosensing devices comprised of carbon nanotubes and nanofibers have been developed for astronaut crew point-of-care. Their inherent nanometer scale, high conductivity, wide potential window, good biocompatibility and well-defined surface chemistry make them ideal candidates as biosensor electrodes. Here, we report two studies using carbon nanotube and carbon nanofiber electrodes for biomedical applications. First, a 3x3 electrode device, with each electrode containing 40,000 carbon nanofiber nanoelectrodes was fabricated on silicon using traditional microfabrication processing. The device was demonstrated as a multiplexed immunosensor for simultaneous, label-free detection of cardiac troponin-I, C-reactive protein and myoglobin. Antibodies specific to cardiac troponin-I, C-reactive protein and myoglobin were covalently bound to the CNF surface and were characterized using electrochemical impedance spectroscopy and differential pulse voltammetry. Each step of the modification process resulted in changes in resistance to charge transfer due to the changes at the electrode surface upon antibody immobilization and binding to the specific cardiac protein. The real-time label free detection of the three cardiac markers from pure components and mixtures was demonstrated with high sensitivity, down to 0.2 ng/mL, and good selectivity. Detection in human blood serum did not present false positives from non-specific protein adsorption. More recently, this detection scheme has been applied to inkjet printed carbon nanotube electrodes on Kapton and paper. Printed devices have several unique advantages including simple and inexpensive fabrication. The results demonstrate that these sensors can serve a miniaturized, low cost device for detection of proteins in complex mixtures making this platform a good candidate for early stage diagnosis of myocardial infarction. Future inkjet printed devices can be fabricated have the added advantage in their suitability to be manufactured in an in-space, microgravity environment.

carbon nanotubes↗

NASA NTRS2019

Carbon Nanomaterials for Biosensing Applications

carbon nanotubes↗