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DOE OSTI2021

UEMtomaton: A Source-Available Platform to Aid in Start-up of Ultrafast Electron Microscopy Labs

The steady rise in the number of ultrafast electron microscopy (UEM) labs, in addition to the opacity and lack of detailed descriptions of current approaches that would enable point-by-point construction, has created an opportunity for sharing common methods and instrumentation for (for example) automating data acquisition to assist in efficient lab start-up and to learn about common and robust protocols. In the spirit of open sharing of methods, we provide here a description of an entry-level method and user interface (UI) for automating UEM experiments, and we provide access to the source code and scripts (source-available) for ease of implementation or as a starting reference point for those entering or seeking to enter the field (https://github.com/CEMSFlannigan/UEMtomaton/releases/tag/v1.0). Core instrumentation and physical connections in the UEM lab at Minnesota are described. Interface communication schemes consisting of duo server-client pairs between critical components – the optical delay stage and the UEM digital camera – are presented, with emphasis placed on describing the logic and communications sequence designed to conduct automated series acquisitions. An application designed and programmed with C++/CLI as Windows Forms in Microsoft Visual Studio – dubbed UEMtomaton – is also presented. Key to the UI layout is centralization of the automation tasks and establishment of communication within the software rather than by interfacing with each individual workstation. It is our hope that this note provides useful insight for current and future UEM researchers, particularly with respect to generalizability and portability of the approach to emerging labs. Here, we note that while this basic, entry-level approach is certainly not the most sophisticated or comprehensive of those currently in use, we feel there is nevertheless value in clearly communicating a proven straightforward method to hopefully lower the barrier to entry into the field.

47 OTHER INSTRUMENTATION↗

DOE OSTI2018

In situ spectroscopic analysis and quantification of [Tc(CO)3]+ in Hanford tank waste

A Pretreatment Protocol is demonstrated for the quantitative conversion and subsequent in situ spectroscopic analysis of non-pertechnetate [Tc(CO)3]+ in tank 241-AN-102 at the Hanford Site. This conversion technique is based on a test method demonstrated using [Re(CO)3]+ in simulated Hanford tank waste. The Protocol entails adding a real waste sample containing the non-pertechnetate [Tc(CO)3]+ species to a developer solution that facilitates the rapid, quantitative conversion of the non-emissive species to a luminescent species which can then be detected spectroscopically. Three AN-102 samples were tested by the standard addition method: (1) a 5 M Na adjusted sample, (2) a sample depleted 137Cs by resin column ion exchange, (3) and an acid-stripped column eluate. The concentrations of non-pertechnetate [Tc(CO)3]+ in these samples were 7.78 × 10-6 M, 6.53 × 10-7 M, and 2.46 × 10-6 M, respectively.

Branch, Shirmir D.↗

DOE OSTI2026

Carbamoylation as an Effective Tool in the Analysis of the Soman Nerve Agent Marker Pinacolyl Alcohol in Soil Matrices by EI-GC-MS and LC-HRMS

Pinacolyl alcohol (PA) is a Schedule 2 chemical commonly featured in most proficiency tests (PTs) administered by the Organisation for the Prohibition of Chemical Weapons (OPCW) due to its direct as well as forensic link to the nerve agent Soman. Therefore, its detection by Chemical Weapons Convention (CWC) inspection teams during on-site investigations is a strong indicator of the past or latent presence of Soman in the environment. Its small molecular weight (102), early elution time, and poor ionization profile make PA a challenging analyte to detect particularly at low concentrations (∼1–10 μg/g). In this work, 1,1′-carbonyldimidazole (CDI) has been used to effectively modify PA for the first time in two different soil matrices (Virginia type A soil and silt sediment) at two separate concentrations (1 and 10 μg/g) for its subsequent detection by EI-GC-MS and LC-HRMS methods. For the EI-GC-MS analysis, the PA carbamate derivative (PIC) exhibits improved chromatography relative to PA such as improved peak shape, increased molecular weight (196 for PIC and 102 for PA) and increased retention time (16.9 min for PIC and ∼4.1 min for PA). In addition, the derivatization also improves the detection of PA by LC-HRMS as the PIC product possesses protonation sites (i.e., imidazole ring) relative to none exhibited by PA. More importantly, the carbamoylation proceeds under mild conditions (55 °C, no base) and rapidly (3 h), characteristics that make it an appealing protocol for the analysis of PA during OPCW PTs or real case scenarios particularly in instances where it is present at low concentrations. It is anticipated that the protocol can be applied to the forensic analysis of this important Soman marker in various environmental matrices.

Chemistry↗

NASA NTRS1990

CCSDS - An approach to the definition of common standards for space data and information systems

The Consultative Committee for Space Data Systems (CCSDS) was formed in 1982 to develop common space system data structures, protocols, and interfaces which would facilitate mutual international support and interoperability. It soon emerged that CCSDS's activities exerted synergistic forces on systems development efforts. Currently, CCSDS is composed of both member-status and observer-status agencies; while only one member agency is admitted from any one country, multiple additional agencies may participate as observers. CCSDS recommendations to date have identified a common architectural approach for the handling and processing of space data.

Greene, Edward P.↗

NASA NTRS1993

Thermal-vacuum response of polymer matrix composites in space

This report describes a thermal-vacuum outgassing model and test protocol for predicting outgassing times and dimensional changes for polymer matrix composites. Experimental results derived from 'control' samples are used to provide the basis for analytical predictions to compare with the outgassing response of Long Duration Exposure Facility (LDEF) flight samples. Coefficient of thermal expansion (CTE) data are also presented. In addition, an example is given illustrating the dimensional change of a 'zero' CTE laminate due to moisture outgassing.

Tennyson, R. C.↗

NASA NTRS2007

Developing Carbon Nanotube Standards at NASA

Single wall carbon nanotubes (SWCNTs) are currently being produced and processed by several methods. Many researchers are continuously modifying existing methods and developing new methods to incorporate carbon nanotubes into other materials and utilize the phenomenal properties of SWCNTs. These applications require availability of SWCNTs with known properties and there is a need to characterize these materials in a consistent manner. In order to monitor such progress, it is critical to establish a means by which to define the quality of SWCNT material and develop characterization standards to evaluate of nanotube quality across the board. Such characterization standards should be applicable to as-produced materials as well as processed SWCNT materials. In order to address this issue, NASA Johnson Space Center has developed a protocol for purity and dispersion characterization of SWCNTs (Ref.1). The NASA JSC group is currently working with NIST, ANSI and ISO to establish purity and dispersion standards for SWCNT material. A practice guide for nanotube characterization is being developed in cooperation with NIST (Ref.2). Furthermore, work is in progress to incorporate additional characterization methods for electrical, mechanical, thermal, optical and other properties of SWCNTs.

Nikolaev, Pasha↗

NASA NTRS2011

CCSDS Advanced Orbiting Systems Virtual Channel Access Service for QoS MACHETE Model

To support various communications requirements imposed by different missions, interplanetary communication protocols need to be designed, validated, and evaluated carefully. Multimission Advanced Communications Hybrid Environment for Test and Evaluation (MACHETE), described in "Simulator of Space Communication Networks" (NPO-41373), NASA Tech Briefs, Vol. 29, No. 8 (August 2005), p. 44, combines various tools for simulation and performance analysis of space networks. The MACHETE environment supports orbital analysis, link budget analysis, communications network simulations, and hardware-in-the-loop testing. By building abstract behavioral models of network protocols, one can validate performance after identifying the appropriate metrics of interest. The innovators have extended the MACHETE model library to include a generic link-layer Virtual Channel (VC) model supporting quality-of-service (QoS) controls based on IP streams. The main purpose of this generic Virtual Channel model addition was to interface fine-grain flow-based QoS (quality of service) between the network and MAC layers of the QualNet simulator, a commercial component of MACHETE. This software model adds the capability of mapping IP streams, based on header fields, to virtual channel numbers, allowing extended QoS handling at link layer. This feature further refines the QoS v existing at the network layer. QoS at the network layer (e.g. diffserv) supports few QoS classes, so data from one class will be aggregated together; differentiating between flows internal to a class/priority is not supported. By adding QoS classification capability between network and MAC layers through VC, one maps multiple VCs onto the same physical link. Users then specify different VC weights, and different queuing and scheduling policies at the link layer. This VC model supports system performance analysis of various virtual channel link-layer QoS queuing schemes independent of the network-layer QoS systems.

Jennings, Esther H.↗

NASA NTRS2019

MERRA-2 Ocean: The NASA Global Modeling and Assimilation Office's Weakly Coupled Atmosphere-Ocean Reanalysis Using GEOS-S2S Version 3

The NASA Modern Era Reanalysis for Research and Applications (MERRA2) has been a respected and widely used reanalysis that has so far been restricted to the atmosphere. Now a newly released version of the atmosphere/ocean coupled data assimilation system (AODAS) has been developed by the NASA/Goddard Global Modeling and Assimilation Office to perform a retrospective ocean reanalysis from 1982 to present. In addition to assimilating all available in situ data (e.g. Argo, mooring, XBT and CTD data) and altimetry information into the ocean, the new version (GEOS-S2S Version 3) model includes a higher resolution, eddy-permitting ocean model than previous versions, a more realistic implementation of the atmosphere-ocean interface layer, and an improved coupling between glacier and ocean (among other improvements). In addition, this ocean data assimilation was expanded to include the assimilation of satellite sea surface salinity. The MERRA-2 AODAS will be described, and preliminary results will be shown from the assimilation reanalysis and from retrospective forecasts issued using a new ensemble strategy. Following the Global Ocean Data Assimilation Experiment (GODAE) protocols, we will present Class 1 through Class 4 validation results from the ocean reanalysis. Results indicate an improved ocean mixed layer depth, improved salinity near Greenland, an improved diurnal cycle of the sea surface skin temperature, an improved estimate of ocean evaporation, and better representation of western boundary currents (e.g. Gulf Stream) from our new ocean reanalysis. One of the motivations of this project is to provide optimal initial states for ENSO forecasting. Therefore, we will also present some preliminary results of retrospective ENSO forecasts. After thorough testing, it is expected that the GEOS-S2S Version 3 will replace our contributions to North American Multi-Model Ensemble (NMME), WCRP Subseasonal to Seasonal (S2S), and IRI seasonal prediction forecast projects.

Molod, Andrea↗

DOE OSTI2024

A Typing Discipline for High-Assurance Control Systems

This poster describes a typing discipline for high-assurance industrial systems based on three novel type systems. The first type system, information flow control (IFC), controls the flow of data through the system. The second system, dependent session types, restricts messages exchanged during the execution of a communication protocol to avoid dangerous states. The third system uses dimensional analysis to avoid subtle bugs that adversaries can exploit to cause the system to enter a dangerous state. This poster describes how a combination of these approaches can prevent sophisticated cyber attacks, such as the infamous Stuxnet incident, from occurring. In addition, we provide experimental evidence to support the claim that these approaches can be applied in control systems that are resource-constrained.

42 - ENGINEERING↗

NASA NTRS2013

Fifteen-minute Extravehicular Activity Prebreathe Protocol Using NASA's Exploration Atmosphere (8.2 psia/ 34% 02)

A TBDM DCS probability model based on an existing biophysical model of inert gas bubble growth provides significant prediction and goodness-of-fit with 84 cases of DCS in 668 human altitude exposures. 2. Model predictions suggest that 15-minute O2 prebreathe protocols used in conjunction with suit ports and an 8.2 psi, 34% O2, 66% N2 atmosphere may enable rapid EVA capability for future exploration missions with the risk of DCS ≤ 12%.  EVA could begin immediately at 6.0 psi, with crewmembers decreasing suit pressure to 4.3 psi after completing the 15-minute in-suit prebreathe. 3. Model predictions suggest that intermittent recompression during exploration EVA may reduce decompression stress by 1.8% to 2.3% for 6 hours of total EVA time. Savings in gas consumables and crew time may be accumulated by abbreviating the EVA suit N2 purge to 2 minutes (20% N2) compared with 8 minutes (5% N2) at the expense of an increase in estimated decompression risk of up to 2.4% for an 8-hour EVA.  Increased DCS risk could be offset by IR or by spending additional time at 6 psi at the beginning of the EVA.  Savings of 0.48 lb of gas and 6 minutes per person per EVA corresponds to more than 31 hours of crew time and 1800 lb of gas and tankage under the Constellation lunar architecture. 6. Further research is needed to characterize and optimize breathing mixtures and intermittent recompression across the range of environments and operational conditions in which astronauts will live and work during future exploration missions. 7. Development of exploration prebreathe protocols will begin with definition of acceptable risk, followed by development of protocols based on models such as ours, and, ultimately, validation of protocols through ground trials before operational implementation.

Abercromby, Andrew F. J.↗

DOE OSTI2025

Multimodal In Situ Characterization Uncovers Unexpected Stability of a Cobalt Electrocatalyst for Acidic Sustainable Energy Technologies

An accelerated development of durable and affordable sustainable energy technologies is often hindered by a limited understanding of how non-precious materials within these systems degrade. In acidic proton exchange membrane fuel cells and water electrolyzers, metallic cobalt (Co) is considered an unstable component that is often combined with precious metals or other stabilizers. To understand the mechanisms behind Co instability, we employ an experimental platform that quantifies dissolution with on-line inductively coupled plasma mass spectrometry and product formation with electrochemical mass spectrometry during electrochemical testing, along with ex- situ characterization. Under varied conditions (electrocatalysis, time, gas-type saturation, and ion concentration), windows of Co stability are observed that are different than predicted with classical chemical thermodynamics, suggesting new stabilization and degradation mechanisms than previously understood. Notably, Co is active for the hydrogen evolution reaction (HER), with prolonged stability that is ~300 mV different than thermodynamically projected. Additionally, in an oxygenated environment, Co concurrently performs the HER and oxygen reduction reaction (ORR) yet undergoes different morphology changes and dissolution mechanisms. Interestingly, in the absence of electrocatalysis, there is a 22x decrease in dissolution in an oxygen-free environment, proposing a route to decrease Co losses during device shutdown protocols. Lastly, under more extreme operating conditions, Co becomes stable after a substantial amount of dissolution, suggesting that high concentrations of Co 2+ ions in the microenvironment induce the formation of a stable CoHO 2 surface. Altogether, these results can be leveraged to improve the design and development of more robust and cost-effective sustainable energy technologies, as well as promote strategic strategies for prolonged material utilization.

Dissolution↗

DOE OSTI2014

Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling

Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.

60 APPLIED LIFE SCIENCES↗

NASA NTRSDate not supplied

Open-source Wireless Sensor Network (Wi-Se Net) for Flexible Deployment

Wireless sensors, especially if battery powered, have a number of advantages over wired sensors for flexible or temporary diagnostic deployment in a field or lab setting. Recent advances in wireless technology and microprocessor boards have produced a variety of inexpensive off-the shelf chips which can communicate wirelessly with simple protocols. This paper describes the design and implementation of a highly customizable wireless sensor network (called WiSe Net) using inexpensive open-source hardware components as wireless nodes. These wireless sensor nodes can transmit data at a rate <250 Hz, can be battery powered, and have a small footprint (2x5 cm). In addition, a preliminary over-the-air programming system was developed to allow for simple wireless configuration when active. The network performance was demonstrated by taking distributed and electrically isolated temperature measurements on a high-voltage lab apparatus. Although this test case is in a laboratory setting, this network architecture could be easily repurposed for various other forms of monitoring

Wireless Sensor Network↗

NASA NTRSDate not supplied

Open-source Wireless Sensor Network (Wi-Se Net) for Flexible Deployment

Wireless Sensor Network↗

DOE OSTI2011

Global Arrays Parallel Programming Toolkit

The two predominant classes of programming models for parallel computing are distributed memory and shared memory. Both shared memory and distributed memory models have advantages and shortcomings. Shared memory model is much easier to use but it ignores data locality/placement. Given the hierarchical nature of the memory subsystems in modern computers this characteristic can have a negative impact on performance and scalability. Careful code restructuring to increase data reuse and replacing fine grain load/stores with block access to shared data can address the problem and yield performance for shared memory that is competitive with message-passing. However, this performance comes at the cost of compromising the ease of use that the shared memory model advertises. Distributed memory models, such as message-passing or one-sided communication, offer performance and scalability but they are difficult to program. The Global Arrays toolkit attempts to offer the best features of both models. It implements a shared-memory programming model in which data locality is managed by the programmer. This management is achieved by calls to functions that transfer data between a global address space (a distributed array) and local storage. In this respect, the GA model has similarities to the distributed shared-memory models that provide an explicit acquire/release protocol. However, the GA model acknowledges that remote data is slower to access than local data and allows data locality to be specified by the programmer and hence managed. GA is related to the global address space languages such as UPC, Titanium, and, to a lesser extent, Co-Array Fortran. In addition, by providing a set of data-parallel operations, GA is also related to data-parallel languages such as HPF, ZPL, and Data Parallel C. However, the Global Array programming model is implemented as a library that works with most languages used for technical computing and does not rely on compiler technology for achieving parallel efficiency. It also supports a combination of task- and data-parallelism and is available as an extension of the message passing (MPI) model. The GA model exposes to the programmer the hierarchical memory of modern high-performance computer systems, and by recognizing the communication overhead for remote data transfer, it promotes data reuse and locality of reference. Virtually all the scalable architectures possess non-uniform memory access characteristics that reflect their multi-level memory hierarchies. These hierarchies typically comprise processor registers, multiple levels of cache, local memory, and remote memory. Over time, both the number of levels and the cost (in processor cycles) of accessing deeper levels has been increasing. It is important for any scalable programming model to address memory hierarchy since it is critical to the efficient execution of scalable applications.

ARMCI↗

DOE OSTI2021

Microwave-Assisted Synthesis of Cu@IrO 2 Core-Shell Nanowires for Low-Temperature Methane Conversion

A facile microwave-assisted synthesis was developed for the tunable fabrication of a novel Cu@IrO 2 core@shell nanowire motif. Experimental parameters, such as (i) reaction time, (ii) the method of addition of the Ir precursor, (iii) capping agent, (iv) reducing agent, as well as (v) the capping agent-to-reducing agent ratio, were subsequently optimized. The viability of other methods based on previously reported literature, such as refluxing, stirring, and physical sonication, was studied and compared with our optimized microwave-assisted protocol in creating our as-prepared materials. It should be noted that the magnitude of the IrO 2 shell could be tailored based on varying the Cu: Ir ratio coupled with judicious variations in the amounts of capping agent and reducing agent. Structural characterization techniques, such as XRD, XPS, and HRTEM (including HRTEM-EDS), were used to analyze our Cu@IrO 2 motifs. Specifically, the shell could be reliably tailored from sizes of 10 nm, 8 nm, 6 nm, and 3.5 nm with corresponding Cu: Ir ratios of 10:1, 15:1, 20:1, and 25:1, respectively. Moreover, the structural integrity of the motifs was probed and found to have been maintained after not only heat treatment but also the post-methane conversion process, indicative of an intrinsically high stability. Both components within the CuO-IrO 2 interface were able to activate methane at temperatures between 400 to 500 K with a reduction of the associated metal cations (Cu 2+ → Cu 1+ ; Ir 4+ → Ir 3+ ) and the deposition of CH x fragments on the surface, as clearly observed in the ambient-pressure XPS results. Thus, on the basis of their stability and chemical activity, these core-shell materials could be very useful for the catalytic conversion of methane into 'higher value" chemicals.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor

Colletotrichum sublineola is an aggressive fungal pathogen that causes anthracnose in sorghum [ Sorghum bicolor (L.) Moench]. The obvious symptoms of anthracnose are leaf blight and stem rot. Sorghum, the fifth most widely grown cereal crop in the world, can be highly susceptible to the disease, most notably in hot and humid environments. In the southeastern United States the acreage of sorghum has been increasing steadily in recent years, spurred by growing interest in producing biofuels, bio-based products, and animal feed. Resistance to anthracnose is, therefore, of paramount importance for successful sorghum production in this region. To identify anthracnose resistance loci present in the highly resistant cultivar ‘Bk7’, a biparental mapping population of F 3:4 and F 4:5 sorghum lines was generated by crossing ‘Bk7’ with the susceptible inbred ‘Early Hegari-Sart’. Lines were phenotyped in three environments and in two different years following natural infection. The population was genotyped by sequencing. Following a stringent custom filtering protocol, totals of 5186 and 2759 informative SNP markers were identified in the two populations. Segregation data and association analysis identified resistance loci on chromosomes 7 and 9, with the resistance alleles derived from ‘Bk7’. Both loci contain multiple classes of defense-related genes based on sequence similarity and gene ontologies. In addition, genetic analysis following an independent selection experiment of lines derived from a cross between ‘Bk7’ and sweet sorghum ‘Mer81-4’ narrowed the resistance locus on chromosome 9 substantially, validating this QTL. As observed in other species, sorghum appears to have regions of clustered resistance genes. Further characterization of these regions will facilitate the development of novel germplasm with resistance to anthracnose and other diseases.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

WHONDRS Surface Water Dissolved Organic Carbon and FTICR-MS across Glacial Features in Svalbard 2022

This dataset supports a broader study examining climatic forcing of terrestrial greenhouse gas emission through permafrost and glaciers in Svalbard. The dataset provides geochemistry and organic matter characterization data generated from surface water collected from 11 sites across central Svalbard. Data were also collected in 2021 and can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1888571. Additional related data were collected and will be published separately in collaboration with Yde and Kleber.This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved organic carbon (DOC; measured as non-purgeable organic carbon; NPOC); (5) surface water sampling protocol; (6) readme; (7) methods codes; (8) international geo-sample number (IGSN) mapping file; (9) a folder of field photos; and (10) folder of high resolution characterization of organic matter via 7 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) generated through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). The FTICR folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml.

54 ENVIRONMENTAL SCIENCES↗