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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 NTRS1997

Fatigue Debonding Characterization in Composite Skin/Stringer Configurations

The objective of this work was to investigate the fatigue damage mechanisms and to identify the influence of skin stacking sequence in carbon epoxy composite bonded skin/stringer constructions. A simple 4-point-bending test fixture originally designed for previously performed monotonic tests was used to evaluate the fatigue debonding mechanisms between the skin and the bonded frame when the dominant loading in the skin is flexure along the edge of the frame. The specimens consisted of a tapered flange, representing the stringer, bonded onto a skin. Based on the results of previous monotonic tests two different skin lay-ups in combination with one flange lay-up were investigated. The tests were performed at load levels corresponding to 40%, 50%, 60%, 70%, and 80% of the monotonic fracture loads. Microscopic investigations of the specimen edges were used to document the onset of matrix cracking and delamination, and subsequent fatigue delamination growth. Typical damage patterns for both specimen configurations were identified. The observations showed that failure initiated near the tip of the flange in the form of matrix cracks at one of two locations, one in the skin and one in the flange. The location of the 90 deg flange and skin plies relative to the bondline was identified as the dominant lay-up feature that controlled the location and onset of matrix cracking and subsequent delamination. The fatigue delamination growth experiments yielded matrix cracking and delamination onset as a function of fatigue cycles as well as delamination length as a function of the number of cycles.

Cvitkovich, Michael K.↗
DOE OSTI2023

PETSc/TAO Users Manual (Rev. 3.19)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and opti mization that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started). PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than packages such as MATLAB or a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or lldb, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself. For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. There are several packages, built on PETSc, that may satisfy your needs without requiring directly using PETSc. We recommend reviewing these packages functionality before starting to code directly with PETSc. PETSc can be used to provide a “MPI parallel linear solver” in an otherwise sequential, or OpenMP parallel code. This approach cannot provide extremely large improvements in the application time by utilizing large numbers of MPI processes but can still improve the performance. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect true scalability to large numbers of MPI processes. See PCMPI for details on how to utilize the PETSc MPI linear solver server. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc has been supported for twenty-five years; see mailing list information on our website for information on contacting support.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Crystallization of Long-Spaced Precision Polyacetals I: Melting and Recrystallization of Rapidly Formed Crystallites

Rapidly melt-crystallized polyethylenes with acetal groups (-O-CH 2 -O-) precisely spaced by 12, 18, 19, or 23 backbone carbons exhibit two reorganizations and three melting endotherms on heating at relatively low heating rates. Real-time WAXD experiments further confirm that these transitions are associated with reorganization to a different crystalline structure. Here, the DSC endotherms are associated with melting of the initially formed disordered phase, followed by melting of Form I and by melting of Form II crystals with increasing temperature. In parallel with these structural changes, the long spacing undergoes a discrete step increase at the polymorphic transitions. Upon the transition from disordered to Form I crystals, the core crystal thickness increases by one repeating unit, whereas the crystal thickness remains basically unchanged during the transition from Form I to Form II crystallites. The effect of even vs. odd CH2 spacer on the observed melting temperatures is prevalent for spacer < 10 CH 2 units. The even or odd number of methylenes between acetals also affects the type and kinetics of packing assembly in layered crystallites. While a disordered mesomorphic-like structure develops under fast cooling in odd-spaced polyacetals (PA-19, PA-23), the formation of Form I crystals cannot be bypassed in PA-12 and PA-18. Furthermore, some differences are also found in the WAXD patterns of Form II between odd and even-spaced polyacetals, denoting that staggering of the acetals in the crystallites is affected by the configuration of consecutive acetals with respect to the methylene sequence.

36 MATERIALS SCIENCE↗
NASA NTRS2001

Substantial reservoirs of molecular hydrogen in the debris disks around young stars

Circumstellar accretion disks transfer matter from molecular clouds to young stars and to the sites of planet formation. The disks observed around pre-main-sequence stars have properties consistent with those expected for the pre-solar nebula from which our own Solar System formed 4.5 Gyr ago. But the 'debris' disks that encircle more than 15% of nearby main-sequence stars appear to have very small amounts of gas, based on observations of the tracer molecule carbon monoxide: these observations have yielded gas/dust ratios much less than 0.1, whereas the interstellar value is about 100 (ref. 9). Here we report observations of the lowest rotational transitions of molecular hydrogen (H2) that reveal large quantities of gas in the debris disks around the stars beta Pictoris, 49 Ceti and HD135344. The gas masses calculated from the data are several hundreds to a thousand times greater than those estimated from the CO observations, and yield gas/dust ratios of the same order as the interstellar value.

unmanned↗
DOE OSTI2021

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Abstract Background Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Results Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH 4 and CO 2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Conclusions Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

High-efficiency Agrobacterium-mediated transformation of Norway spruce (Picea abies) and loblolly pine (Pinus taeda)

Agrobacterium-mediated gene transfer is the method of choice for many plant biotechnology laboratories; however, large-scale use of this organism in conifer transformation has been limited by difficult propagation of explant material, selection efficiencies and low transformation frequency. We have analyzed co-cultivation conditions and different disarmed strains of Agrobacterium to improve transformation. Additional copies of virulence genes were added to three common disarmed strains. These extra virulence genes included either a constitutively active virG or extra copies of virG and virB, both from pTiBo542. In experiments with Norway spruce, we increased transformation efficiencies 1000-fold from initial experiments where little or no transient expression was detected. Over 100 transformed lines expressing the marker gene beta-glucuronidase (GUS) were generated from rapidly dividing embryogenic suspension-cultured cells co-cultivated with Agrobacterium. GUS activity was used to monitor transient expression and to further test lines selected on kanamycin-containing medium. In loblolly pine, transient expression increased 10-fold utilizing modified Agrobacterium strains. Agrobacterium-mediated gene transfer is a useful technique for large-scale generation of transgenic Norway spruce and may prove useful for other conifer species.

NASA Discipline Plant Biology↗
DOE OSTI2020

Validation of Continuous-Energy ENDF/B-VIII.0 16 O, 56 Fe, and 63,65 Cu Cross Sections for Nuclear Criticality Safety Applications

Recently completed cross-section evaluations sponsored in part by the Nuclear Criticality Safety Program were incorporated into the 2018 release of the ENDF/B-VIII.0 cross-section library. Evaluated isotopes of interest to the nuclear data and criticality safety community include 16 O, 56 Fe, and 63,65 Cu. For performance validation, benchmark models defined in the International Criticality Safety Benchmark Evaluation Project Handbook were selected based on energy-integrated k eff sensitivities to total cross sections of interest and compared with experimental values. Of the 102 benchmark configurations that were utilized, 63 are sensitive to 16 O, 32 sensitive to 63,65 Cu, and 25 sensitive to 56 Fe. Selected benchmarks were modeled in SCALE 6.2.3 Criticality Safety Analysis Sequence (CSAS) continuous-energy Monte Carlo k eff calculations with ENDF/B-VII.1, with a hybrid ENDF/B-VII.1 with ENDF/B-VIII.0 data substituted for individual isotopes of interest, and with ENDF/B-VIII.0. ENDF/B-VIII.0 showed improved agreement with experimental k eff for 56 Fe, 63 Cu, elemental copper, and full library substitution while producing lessened agreement for 16 O and 65 Cu. Furthermore, with full library and isotope-specific ENDF/B-VIII.0 performance, a best-case ENDF library was formed by excluding underperforming isotopes’ ENDF/B-VIII.0 data, reverting 16 O and 65 Cu cross sections to ENDF/B-VII.1. This resulted in the average relative deviation between calculated and experimental data improving from 1.45σ for the ENDF/B-VIII.0 library to 1.32σ for the best-case library, relative to benchmark uncertainty.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗
DOE OSTI2023

Accuracy and precision of ESI-Orbitrap-IRMS observations of hours to tens of hours via reservoir injection

Here, orbitrap isotope ratio mass spectrometry (Orbitrap-IRMS) has recently been applied to high-precision, natural-abundance isotope ratio measurements of a diverse range of compounds, including amino acids, oxyanions, fatty acids, and metals. These measurements can characterize many isotope ratios simultaneously at high (≈1.0‰) precision. In a successful experiment, observed precision will track the shot-noise limit and be limited by experimental time. Some isotope ratios, for example those involving 17 O in organic compounds or multiply-substituted (‘clumped’) isotopologues, require experimental times of hours to tens of hours to achieve desired precision, while current sample introduction techniques focus on observations on the order of seconds to tens of minutes. In this study, we characterize Orbitrap-IRMS performance for three long duration measurements (individual acquisitions ≥1 h and as long as 24 h) using an automated reservoir injection system coupled to a Q Exactive HF Orbitrap with an electrospray ionization (ESI) source. First, we characterize long-term intra-measurement stability through a 24-h long measurement of acetone. We report the following isotope ratios and precisions (as acquisition errors, errors on the observed ratio within this measurement (σ AE )): 13 C/ 12 C (σ AE = 0.07‰), 17 O/ 16 O (σ AE = 1.1‰), 18 O/ 16 O (σ AE = 0.3‰), and 13 C 13 C/ 12 C (σ AE = 0.65‰). The σ AE of each tracks the shot noise limit throughout and is limited by the challenging conditions (high resolution and low numbers of ions per scan) required for 17 O/ 16 O measurement in the presence of 13 C via Orbitrap. Second, we characterize inter-measurement stability via a sequence of seven 75-min analyses of perchlorate. We observe the following ratios and acquisition errors: 37 Cl/ 35 Cl (σ AE = 0.09‰); 17 O/ 16 O (σ AE = 1.6‰); 18 O/ 16 O (σ AE = 0.7‰), 37 Cl 17 O/ 35 Cl 16 O (σ AE = 2.7‰), and 37 Cl 18 O/ 35 Cl 16 O (σ AE = 1.2‰). However, we find that inter-measurement drift between acquisitions limits our accuracy and precision for standardized measurements (i.e., error on reported δ values) to ≈1‰ for the 37 Cl/ 35 Cl measurement. Hence, the benefits of low σ AE may not be fully realized. Third, we demonstrate accuracy via sample/standard comparisons of a methionine sample with 13 C enrichment of ≈20‰ relative to a known standard. Using a sequence of seven 60-min analyses, we recover the following isotope ratios and standardized precisions (i.e., error on reported δ values, denoted propagated acquisition errors, σ PAE ): 33 S/ 32 S (σ PAE = 1.0‰), 34 S/ 32 S (σ PAE = 0.7‰), 15 N/ 14 N (σ PAE = 2.1‰), 2 H/ 1 H (σ PAE = 3.2‰), 13 C/ 12 C (σ PAE = 0.4‰), 18 O/ 16 O (σ PAE = 1.6‰), & 13 C 13 C/ 12 C (σ PAE = 2.8‰) with confirmation of accurate results for the known 13 C/ 12 C and 13 C 13 C/ 12 C enrichments. Together, our results demonstrate the viability of Orbitrap-IRMS for long duration measurements of diverse sample types via an automated reservoir injection system. Inter-measurement stability remains a challenge; we expect our methods to be most applicable to extended measurements of hard-to-observe properties, such as 17 O in organics and clumped isotopologues.

58 GEOSCIENCES↗
DOE OSTI2024

Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean

ABSTRACT Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome-assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon-degrading microbes with clade-specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all Cycloclasticus . Furthermore, all Bermanella encoded and expressed genes for non-gaseous n -alkane degradation; however, DWH Bermanella encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume member in the SAR324 and UBA11654 have the capacity for aromatic hydrocarbon degradation. In contrast, Colwellia were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provides missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment. IMPORTANCE Microbial degradation of hydrocarbons is a critically important process promoting ecosystem health, yet much of what is known about this process is based on physiological experiments with a few hydrocarbon substrates and cultured microbes. Thus, the ability to degrade the diversity of hydrocarbons that comprise oil and gas by microbes in the environment, particularly in the ocean, is not well characterized. Therefore, this study aimed to utilize non-cultivation-based ‘omics data to explore novel genomes of uncultured marine microbes involved in degradation of oil and gas. Analyses of newly assembled metagenomic data and previously existing genomes from other marine data sets, with metagenomic and metatranscriptomic read recruitment, revealed globally distributed hydrocarbon-degrading marine microbes with clade-specific substrate degradation potentials that have not been previously reported. This new understanding of oil and gas degradation by uncultured marine microbes suggested that the global ocean harbors a diversity of hydrocarbon-degrading bacteria, which can act as primary agents regulating ecosystem health.

Howe, Kathryn L.↗
NASA NTRS2013

SequenceL: Automated Parallel Algorithms Derived from CSP-NT Computational Laws

With the introduction of new parallel architectures like the cell and multicore chips from IBM, Intel, AMD, and ARM, as well as the petascale processing available for highend computing, a larger number of programmers will need to write parallel codes. Adding the parallel control structure to the sequence, selection, and iterative control constructs increases the complexity of code development, which often results in increased development costs and decreased reliability. SequenceL is a high-level programming language that is, a programming language that is closer to a human s way of thinking than to a machine s. Historically, high-level languages have resulted in decreased development costs and increased reliability, at the expense of performance. In recent applications at JSC and in industry, SequenceL has demonstrated the usual advantages of high-level programming in terms of low cost and high reliability. SequenceL programs, however, have run at speeds typically comparable with, and in many cases faster than, their counterparts written in C and C++ when run on single-core processors. Moreover, SequenceL is able to generate parallel executables automatically for multicore hardware, gaining parallel speedups without any extra effort from the programmer beyond what is required to write the sequen tial/singlecore code. A SequenceL-to-C++ translator has been developed that automatically renders readable multithreaded C++ from a combination of a SequenceL program and sample data input. The SequenceL language is based on two fundamental computational laws, Consume-Simplify- Produce (CSP) and Normalize-Trans - pose (NT), which enable it to automate the creation of parallel algorithms from high-level code that has no annotations of parallelism whatsoever. In our anecdotal experience, SequenceL development has been in every case less costly than development of the same algorithm in sequential (that is, single-core, single process) C or C++, and an order of magnitude less costly than development of comparable parallel code. Moreover, SequenceL not only automatically parallelizes the code, but since it is based on CSP-NT, it is provably race free, thus eliminating the largest quality challenge the parallelized software developer faces.

Cooke, Daniel↗
NASA NTRS2006

AERCam Autonomy: Intelligent Software Architecture for Robotic Free Flying Nanosatellite Inspection Vehicles

The NASA Johnson Space Center has developed a nanosatellite-class Free Flyer intended for future external inspection and remote viewing of human spacecraft. The Miniature Autonomous Extravehicular Robotic Camera (Mini AERCam) technology demonstration unit has been integrated into the approximate form and function of a flight system. The spherical Mini AERCam Free Flyer is 7.5 inches in diameter and weighs approximately 10 pounds, yet it incorporates significant additional capabilities compared to the 35-pound, 14-inch diameter AERCam Sprint that flew as a Shuttle flight experiment in 1997. Mini AERCam hosts a full suite of miniaturized avionics, instrumentation, communications, navigation, power, propulsion, and imaging subsystems, including digital video cameras and a high resolution still image camera. The vehicle is designed for either remotely piloted operations or supervised autonomous operations, including automatic stationkeeping, point-to-point maneuvering, and waypoint tracking. The Mini AERCam Free Flyer is accompanied by a sophisticated control station for command and control, as well as a docking system for automated deployment, docking, and recharge at a parent spacecraft. Free Flyer functional testing has been conducted successfully on both an airbearing table and in a six-degree-of-freedom closed-loop orbital simulation with avionics hardware in the loop. Mini AERCam aims to provide beneficial on-orbit views that cannot be obtained from fixed cameras, cameras on robotic manipulators, or cameras carried by crewmembers during extravehicular activities (EVA s). On Shuttle or International Space Station (ISS), for example, Mini AERCam could support external robotic operations by supplying orthogonal views to the intravehicular activity (IVA) robotic operator, supply views of EVA operations to IVA and/or ground crews monitoring the EVA, and carry out independent visual inspections of areas of interest around the spacecraft. To enable these future benefits with minimal impact on IVA operators and ground controllers, the Mini AERCam system architecture incorporates intelligent systems attributes that support various autonomous capabilities. 1) A robust command sequencer enables task-level command scripting. Command scripting is employed for operations such as automatic inspection scans over a region of interest, and operator-hands-off automated docking. 2) A system manager built on the same expert-system software as the command sequencer provides detection and smart-response capability for potential system-level anomalies, like loss of communications between the Free Flyer and control station. 3) An AERCam dynamics manager provides nominal and off-nominal management of guidance, navigation, and control (GN&C) functions. It is employed for safe trajectory monitoring, contingency maneuvering, and related roles. This paper will describe these architectural components of Mini AERCam autonomy, as well as the interaction of these elements with a human operator during supervised autonomous control.

Fredrickson, Steven E.↗
DOE OSTI2024

Functional role of myosin-binding protein H in thick filaments of developing vertebrate fast-twitch skeletal muscle

Myosin-binding protein H (MyBP-H) is a component of the vertebrate skeletal muscle sarcomere with sequence and domain homology to myosin-binding protein C (MyBP-C). Whereas skeletal muscle isoforms of MyBP-C (fMyBP-C, sMyBP-C) modulate muscle contractility via interactions with actin thin filaments and myosin motors within the muscle sarcomere “C-zone,” MyBP-H has no known function. This is in part due to MyBP-H having limited expression in adult fast-twitch muscle and no known involvement in muscle disease. Quantitative proteomics reported here reveal that MyBP-H is highly expressed in prenatal rat fast-twitch muscles and larval zebrafish, suggesting a conserved role in muscle development and prompting studies to define its function. We take advantage of the genetic control of the zebrafish model and a combination of structural, functional, and biophysical techniques to interrogate the role of MyBP-H. Transgenic, FLAG-tagged MyBP-H or fMyBP-C both localize to the C-zones in larval myofibers, whereas genetic depletion of endogenous MyBP-H or fMyBP-C leads to increased accumulation of the other, suggesting competition for C-zone binding sites. Does MyBP-H modulate contractility in the C-zone? Globular domains critical to MyBP-C’s modulatory functions are absent from MyBP-H, suggesting that MyBP-H may be functionally silent. However, our results suggest an active role. In vitro motility experiments indicate MyBP-H shares MyBP-C’s capacity as a molecular “brake.” These results provide new insights and raise questions about the role of the C-zone during muscle development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Stochastic Optimization for Grid Resilience. FY18 Final Technical Report

The optimal restoration problem lies at the foundation of the evaluation and improvement of resilience in power systems. In this report we present a scalable decomposition algorithm for solving this problem for realistic power systems. The algorithm has been developed in three major research threads, corresponding to the chapters in the present report. Chapter 1 studies mixed-integer programming (MIP) formulations for the requirement that each electrical island that appears after a recon guration must have at least one energized generator. We provide three alternative MIP formulations for this restriction, show their equivalence, and prove that two of them are stronger in terms of their linear programming relaxation than the formulation most commonly used in the power systems literature. Since the time to solve MIPs can vary signi cantly between equivalent formulations, we also present computational experiments on IEEE test systems for the Intentional Controlled Islanding (ICI) and the Black Start Allocation (BSA) problems. We observe that a polynomially separable, exponential in size, strong formulation yields the best performance for the BSA problem and exhibits a comparable performance to a linear in size, weak formulation for the ICI problem. Chapter 2 presents a methodology to generate mixed-integer linear approximations of the AC power ow equations governing lines, transformers (including tap regulators and phase shifters), shunt and series compensators, and consumption responsive to voltage. Our approximations are capable of capturing limitations for power grids under abnormal or uncommon operating conditions where common assumptions used in power ow relaxations may not hold. Particularly, the approximation captures overvoltages under almost no load, which is a major concern when energizing lines after a blackout. The method constructs piecewise linear approximations of the non-linear power ow equations by minimizing the squared approximation error over a subset of the feasible domain. We test the method using a realistic database for the Chilean system (1548 buses, 1114 lines, 564 transformers). The resulting approximations yield root mean square errors in the order of 0.05pu and are successfully applied to solve a transmission switching instance for the Chilean system. Chapter 3 presents our algorithm for optimal restoration. The algorithm works by partitioning the problem into a master problem and a slave problem. The master problem optimizes over energization sequences of generators, buses and branches, for the entire restoration horizon, while respecting the energization requiments studied in Chapter 1. The slave problem veri es that there exist power ow solutions supporting the energization sequences proposed by the master problem, adding cuts to the master if an infeasible sequence is detected.

24 POWER TRANSMISSION AND DISTRIBUTION↗
NASA NTRS2013

Science Opportunity Analyzer (SOA) Version 8

SOA allows scientists to plan spacecraft observations. It facilitates the identification of geometrically interesting times in a spacecraft s orbit that a user can use to plan observations or instrument-driven spacecraft maneuvers. These observations can then be visualized multiple ways in both two- and three-dimensional views. When observations have been optimized within a spacecraft's flight rules, the resulting plans can be output for use by other JPL uplink tools. Now in its eighth major version, SOA improves on these capabilities in a modern and integrated fashion. SOA consists of five major functions: Opportunity Search, Visualization, Observation Design, Constraint Checking, and Data Output. Opportunity Search is a GUI-driven interface to existing search engines that can be used to identify times when a spacecraft is in a specific geometrical relationship with other bodies in the solar system. This function can be used for advanced mission planning as well as for making last-minute adjustments to mission sequences in response to trajectory modifications. Visualization is a key aspect of SOA. The user can view observation opportunities in either a 3D representation or as a 2D map projection. Observation Design allows the user to orient the spacecraft and visualize the projection of the instrument field of view for that orientation using the same views as Opportunity Search. Constraint Checking is provided to validate various geometrical and physical aspects of an observation design. The user has the ability to easily create custom rules or to use official project-generated flight rules. This capability may also allow scientists to easily assess the cost to science if flight rule changes occur. Data Output allows the user to compute ancillary data related to an observation or to a given position of the spacecraft along its trajectory. The data can be saved as a tab-delimited text file or viewed as a graph. SOA combines science planning functionality unique to both JPL and the sponsoring spacecraft. SOA is able to ingest JPL SPICE Kernels that are used to drive the tool and its computations. A Percy search engine is then included that identifies interesting time periods for the user to build observations. When observations are then built, flight-like orientation algorithms replicate spacecraft dynamics to closely simulate the flight spacecraft s dynamics. SOA v8 represents large steps forward from SOA v7 in terms of quality, reliability, maintainability, efficiency, and user experience. A tailored agile development environment has been built around SOA that provides automated unit testing, continuous build and integration, a consolidated Web-based code and documentation storage environment, modern Java enhancements, and a focus on usability

Witoff, Robert J.↗
DOE OSTI2021

Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. Additionally, in geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T–A and U–A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2000

Section on Observed Impacts on El Nino

Agricultural applications of El Nino forecasts are already underway in some countries and need to be evaluated or re-evaluated. For example, in Peru, El Nino forecasts have been incorporated into national planning for the agricultural sector, and areas planted with rice and cotton (cotton being the more drought-tolerant crop) are adjusted accordingly. How well are this and other such programs working? Such evaluations will contribute to the governmental and intergovernmental institutions, including the Inter-American Institute for Global Change Research and the US National Ocean and Atmospheric Agency that are fostering programs to aid the effective use of forecasts. As El Nino climate forecasting grows out of the research mode into operational mode, the research focus shifts to include the design of appropriate modes of utilization. Awareness of and sensitivity to the costs of prediction errors also grow. For example, one major forecasting model failed to predict the very large El Nino event of 1997, when Pacific sea-surface temperatures were the highest on record. Although simple correlations between El Nino events and crop yields may be suggestive, more sophisticated work is needed to understand the subtleties of the interplay among the global climate system, regional climate patterns, and local agricultural systems. Honesty about the limitations of an forecast is essential, especially when human livelihoods are at stake. An end-to-end analysis links tools and expertise from the full sequence of ENSO cause-and-effect processes. Representatives from many disciplines are needed to achieve insights, e.g, oceanographers and atmospheric scientists who predict El Nino events, climatologists who drive global climate models with sea-surface temperature predictions, agronomists who translate regional climate connections in to crop yield forecasts, and economists who analyze market adjustments to the vagaries of climate and determine the value of climate forecasts. Methods include historical studies to understand past patterns and to test hindcasts of the prediction tools, crop modeling, spatial analysis and remote sensing. This research involves expanding, deepening, and applying the understanding of physical climate to the fields of agronomy and social science; and the reciprocal understanding of crop growth and farm economics to climatology. Delivery of a regional climate forecast with no information about how the climate forecast was derived limits its effectiveness. Explanation of a region's major climate driving forces helps to place a seasonal forecast in context. Then, a useful approach is to show historical responses to previous El Nino events, and projections, with uncertainty intervals, of crop response from dynamic process crop growth models. Regional ID forecasts should be updated with real-time weather conditions. Since every El Nino event is different, it is important to track, report and advise on each new event as it unfolds. The stability of human enterprises depends on understanding both the potentialities and the limits of predictability. Farmers rely on past experience to anticipate and respond to fluctuations in the biophysical systems on which their livelihoods depend. Now scientists are improving their ability to predict some major elements of climate variability. The improvements in the reliability of El Nino forecasts are encouraging, but seasonal forecasts for agriculture are not, and will probably never be completely infallible, due to the chaotic nature of the climate system. Uncertainties proliferate as we extend beyond Pacific sea-surface temperatures to climate teleconnections and agricultural outcomes. The goal of this research is to shed as a clear light as possible on these inherent uncertainties and thus to contribute to the development of appropriate responses to El Nino and other seasonal forecasts for a range of stakeholders, which, ultimately, includes food consumers everywhere.

Rosenzweig, Cynthia↗
DOE OSTI2018

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments

Microbes in Guaymas Basin (Gulf of California) hydrothermal sediments thrive on hydrocarbons and sulfur and experience steep, fluctuating temperature and chemical gradients. The functional capacities of communities inhabiting this dynamic habitat are largely unknown. Here, we reconstructed 551 genomes from hydrothermally influenced, and nearby cold sediments belonging to 56 phyla (40 uncultured). These genomes comprise 22 unique lineages, including five new candidate phyla. In contrast to findings from cold hydrocarbon seeps, hydrothermal-associated communities are more diverse and archaea dominate over bacteria. Genome-based metabolic inferences provide first insights into the ecological niches of these uncultured microbes, including methane cycling in new Crenarchaeota and alkane utilization in ANME-1. These communities are shaped by a high biodiversity, partitioning among nitrogen and sulfur pathways and redundancy in core carbon-processing pathways. The dynamic sediments select for distinctive microbial communities that stand out by expansive biodiversity, and open up new physiological perspectives into hydrothermal ecosystem function.

54 ENVIRONMENTAL SCIENCES↗