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DOE OSTI2018

Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards

Selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), is a data acquisition technique used in targeted analysis of molecules, including targeted proteomic studies. It exploits the unique capability of triple-quadrupole (QQQ) mass spectrometers to monitor the predefined precursor and fragment ion pairs of specific molecules of interest throughout a liquid chromatography (LC) elution profile. Compared to shotgun proteomics, targeted proteomics using SRM has high selectivity, high sensitivity, and a wide linear dynamic range,(1-3) which makes it especially useful in the accurate and reproducible quantification of low-abundance proteins in highly complex biological samples. SRM has been widely used in the fields of biomarker discovery,(4-7) analysis of protein post-translational modifications(8) and characterization of biological protein networks.(4,9) In the recent years, multiple technical advances have greatly improved the throughput of SRM analyses, allowing for the quantification of hundreds of peptides in a single analysis.(6,7,10) For example, a single 800-plex SRM assay (e.g., 400 unlabeled and heavy-labeled peptide pairs and 2400 transitions with retention time scheduling) using ultrahigh-performance liquid chromatography (UHPLC) has been developed to quantify proteins in plasma.(11) Advanced labeling techniques utilizing in vitro proteome-assisted MRM for protein absolute quantification (iMPAQT) demonstrated the capability of SRM in genome-wide protein quantification of over 18?000 human proteins.(12) Moreover, the scan speed of QQQ instrumentation has been greatly improved in recent releases of commercial instrumentation. The newly developed TSQ Altis (released in 2017) can scan more than 600 transitions per second, which is 6 times more than a traditional QQQ scan speed of 100 transitions per second. The breadth of measurement enabled by these technological improvements to QQQ mass spectrometry has increased the feasibility and popularity of large scale targeted proteomics studies,(13) a major application of which will be in clinical studies in which up to hundreds of protein candidates need to be quantified in hundreds of clinical specimens.(14) Quantitative accuracy is a primary motivating factor for utilizing a targeted proteomics protocol. The precise and reproducible absolute quantification produced by SRM assays is essential to many clinical and laboratory experiments.(15,16) Because the abundance of an endogenous peptide is calculated from the measurement of the spiked-in reference standard, it is essential to assess the data quality of these references.(17) In early applications of targeted proteomics, when instrument speed greatly limited the number of transitions that could be monitored, much of this quality assessment was done manually. However, recent improvements in instrument performance and experimental design have enabled a dramatic increase in the number of target peptides and associated SRM transitions, which makes manual quality assessment an untenable and laborious task. A variety of computational tools assist in SRM experiment design and data analysis. The first task in creating an SRM experiment is the choice of proteins and representative peptides to monitor. Achieving a reliable protein abundance requires appropriately choosing peptides that have a strong signal and are free from interferences in the biological matrix. Numerous computational tools exist to facilitate assay design by identifying peptides and refining SRM transitions.(18-21) To help share these assays and eliminate time spent designing the same transitions at multiple institutions, community portals have begun to host well-designed and vetted assays.(22-24) Analyzing the experimental data requires significant computational effort to align files across replicates and experimental conditions, pick peaks and produce quantitative values, normalize data and perform statistical tests, etc.(25-27)

Gibbons, Bryson C.↗

NASA NTRS1990

Parallelization of implicit finite difference schemes in computational fluid dynamics

Implicit finite difference schemes are often the preferred numerical schemes in computational fluid dynamics, requiring less stringent stability bounds than the explicit schemes. Each iteration in an implicit scheme involves global data dependencies in the form of second and higher order recurrences. Efficient parallel implementations of such iterative methods are considerably more difficult and non-intuitive. The parallelization of the implicit schemes that are used for solving the Euler and the thin layer Navier-Stokes equations and that require inversions of large linear systems in the form of block tri-diagonal and/or block penta-diagonal matrices is discussed. Three-dimensional cases are emphasized and schemes that minimize the total execution time are presented. Partitioning and scheduling schemes for alleviating the effects of the global data dependencies are described. An analysis of the communication and the computation aspects of these methods is presented. The effect of the boundary conditions on the parallel schemes is also discussed.

Decker, Naomi H.↗

DOE OSTI2019

The Transactive Network Template Metamodel

While transactive energy—an allocation of electricity based on dynamically discovered values or prices—has been extensively studied, its uptake and use has been slow. This report describes a tool, the transactive network template, which should hasten the creation and uptake of transactive energy networks. The transactive network template is a metamodel meant to guide implementers as they configure their own transactive agent within a network of such agents. The transactive network template’s object–oriented design approach provides implementers basic code object types, which may be used and extended to represent each of the assets in the implementer’s circuit region. These objects further facilitate the transactive agent’s necessary computations, which are divided among responsibilities to schedule assets’ power usage, to balance electric supply and demand, and to coordinate the exchange of electricity with the other transactive agents. This report addresses the conceptual transactive network template design. Implementers are directed to more formal design documents and reference implementations. A Python™-based [Python 2018] reference implementation of the transactive network template has been coded, and three implementations have been configured to represent a national laboratory and two university campuses. In the future, the author wishes to make the transactive network template more generally applicable to networks that require more accurate power flow and those employing alternative transactive coordination mechanisms.

24 POWER TRANSMISSION AND DISTRIBUTION↗

NASA NTRS1978

A mechanical, thermal and electrical packaging design for a prototype power management and control system for the 30 cm mercury ion thruster

A prototype Electric Power Management and Thruster Control System for a 30 cm ion thruster has been built and is ready to support a first mission application. The system meets all of the requirements necessary to operate a thruster in a fully automatic mode. Power input to the system can vary over a full two to one dynamic range (200 to 400 V) for the solar array or other power source. The Power Management and Control system is designed to protect the thruster, the flight system and itself from arcs and is fully compatible with standard spacecraft electronics. The system is designed to be easily integrated into flight systems which can operate over a thermal environment ranging from 0.3 to 5 AU. The complete Power Management and Control system measures 45.7 cm x 15.2 cm x 114.8 cm and weighs 36.2 kg. At full power the overall efficiency of the system is estimated to be 87.4 percent. Three systems are currently being built and a full schedule of environmental and electrical testing is planned.

Sharp, G. R.↗

NASA NTRS1998

Lift Fan Nozzle for Joint Strike Fighter Tested in NASA Lewis' Powered Lift Rig

Under a nonreimbursable space act agreement between the NASA Lewis Research Center and the Allison Advanced Development Company, Allison tested a lift fan nozzle in Lewis' Powered Lift Rig. This test was in support of the Joint Strike Fighter program (formerly the Joint Advanced Strike Technology) sponsored by the Department of Defense, which will develop and field an affordable, multirole, next-generation, strike fighter aircraft for the Navy, Air Force, Marine Corps, and foreign allies. Allison, along with Pratt & Whitney Company, is part of the Lockheed Martin Corporation team that is scheduled to build a concept demonstrator aircraft by fiscal year 2001. The test was initiated in April and successfully completed in mid-July of 1997. Allison supplied a one-third-scale model of the lift fan nozzle, and Lewis provided the facility and the necessary support team. Various configurations, including pitching vectored angles ranging from 15deg forward to 60deg backward, were tested over a range of nozzle pressure ratios. Nozzle flow rates, thrust, and static pressures were measured for each of the configurations. Results from the test met the design requirements for the Joint Strike Fighter program and were in agreement with Allison's internal computational fluid dynamics (CFD) analyses. Data obtained from this test will also be used in the full-scale design of the lift fan system.

Lam, David W.↗

DOE OSTI2016

Radar Wind Profiler for Cloud Forecasting at Brookhaven National Laboratory (BNL) Field Campaign Report

The Radar Wind Profiler for Cloud Forecasting at Brookhaven National Laboratory (BNL) [http://www.arm.gov/campaigns/osc2013rwpcf] campaign was scheduled to take place from 15 July 2013 through 15 July 2015 (or until shipped for the next U.S. Department of Energy Atmospheric Radiation Measurement [ARM] Climate Research Facility first Mobile Facility [AMF1] deployment). The campaign involved the deployment of the AMF1 Scintec 915 MHz Radar Wind Profiler (RWP) at BNL, in conjunction with several other ARM, BNL and National Weather Service (NWS) instruments. The two main scientific foci of the campaign were: 1) To provide profiles of the horizontal wind to be used to test and validate short-term cloud advection forecasts for solar-energy applications and 2) to provide vertical profiling capabilities for the study of dynamics (i.e., vertical velocity) and hydrometeors in winter storms. This campaign was a serendipitous opportunity that arose following the deployment of the RWP at the Two-Column Aerosol Project (TCAP) campaign in Cape Cod, Massachusetts and restriction from participation in the Green Ocean Amazon 2014/15 (GoAmazon 2014/15) campaign due to radio-frequency allocation restriction for international deployments. The RWP arrived at BNL in the fall of 2013, but deployment was delayed until fall of 2014 as work/safety planning and site preparation were completed. The RWP further encountered multiple electrical failures, which eventually required several shipments of instrument power supplies and the final amplifier to the vendor to complete repairs. Data collection began in late January 2015. The operational modes of the RWP were changed such that in addition to collecting traditional profiles of the horizontal wind, a vertically pointing mode was also included for the purpose of precipitation sensing and estimation of vertical velocities. The RWP operated well until the end of the campaign in July 2015 and collected observations for more than 20 precipitation events.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Radar Wind Profiler for Cloud Forecasting at Brookhaven National Laboratory (BNL) Field Campaign Report

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2004

Total Water Measurements Using In Situ UV Fragment Fluorescence Spectroscopy in Support of CRYSTAL-FACE

Given both the powerful diagnostic importance of the condensed phases of water for dynamics and the impact of phase changes in water on the radiation field, the accurate, in situ observation of total water is of central importance to CRYSTAL-FACE. This is clear both from the defined scientific objectives of the NRA and from developments in the coupled fields of stratosphere/troposphere exchange, cirrus cloud formation/removal and mechanisms for the distribution of water vapor in the middle/upper troposphere. Accordingly, we were funded under NASA Grant NAG5-115487 to perform the following tasks for the CRYSTAL-FACE mission that took place in Key West, Florida, during July 2001: 1) Prepare the Total Water instrument for integration into the WB57F and test flights scheduled for Spring 2002. 2) Calibrate and prepare the Total Water instrument for the Summer 2002 CRYSTAL-FACE science flights based in Jacksonville, Florida. 3) Provide both science and engineering support for the above-mentioned efforts. 4) Analyze and interpret the CRYSTAL-FACE data in collaboration with the other mission scientists. 5) Attend the proposed science workshop in Spring 2003. 6) Publish the data and analysis in peer-reviewed journals.

Anderson, James G.↗

NASA NTRS2011

LADEE Satellite Modeling and Simulation Development

As human activity on and around the Moon increases, so does the likelihood that our actions will have an impact on its atmosphere. The Lunar Atmosphere and Dust Environment Explorer (LADEE), a NASA satellite scheduled to launch in 2013, will orbit the Moon collecting composition, density, and time variability data to characterize the current state of the lunar atmosphere. LADEE will also test the concept of the "Modular Common Bus" spacecraft architecture, an effort to reduce both development time and cost by designing reusable, modular components for use in multiple missions with similar requirements. An important aspect of this design strategy is to both simulate the spacecraft and develop the flight code in Simulink, a block diagram-style programming language that allows easy algorithm visualization and performance testing. Before flight code can be tested, however, a realistic simulation of the satellite and its dynamics must be generated and validated. This includes all of the satellite control system components such as actuators used for force and torque generation and sensors used for inertial orientation reference. My primary responsibilities have included designing, integrating, and testing models for the LADEE thrusters, reaction wheels, star trackers, and rate gyroscopes.

Adams, Michael↗

NASA NTRS1991

General circulation of the South Atlantic between 5 deg N and 35 deg S

The TOPEX/POSEIDON altimeter will provide the temporal mean seal level. So, secondly, we propose to compute the difference between these two surfaces (mean sea level minus general circulation dynamic topography). The result will be an estimate of the marine geoid, which is time invariant for the 5-year period under consideration. If this geoid is precise enough, it will permit a description of seasonal variability of the large-scale surface circulation. If there happens to be enough float data, it may be possible to infer the first vertical modes of this variability. Thus the main goal of our investigation is to determine the 3-D general circulation of the South Atlantic and the large-scale seasonal fluctuations. This last objective, however, may be restricted to the western part of the South Atlantic because float deployments have been scheduled only in the Brasil basin.

Ollitrault, Michel↗

NASA NTRS2012

A Sounding Rocket Mission Concept to Acquire High-Resolution Radiometric Spectra Spanning the 9 nm - 31 nm Wavelength Range

When studying Solar Extreme Ultraviolet (EUV) emissions, both single-wavelength, two- dimensional (2D) spectroheliograms and multi-wavelength, one-dimensional (1D) line spectra are important, especially for a thorough understanding of the complex processes in the solar magnetized plasma from the base of the chromosphere through the corona. 2D image data are required for a detailed study of spatial structures, whereas radiometric (i.e., spectral) data provide information on relevant atomic excitation/ionization state densities (and thus temperature). Using both imaging and radiometric techniques, several satellite missions presently study solar dynamics in the EUV, including the Solar Dynamics Observatory (SDO), Hinode, and the Solar-Terrestrial Relations Observatory (STEREO). The EUV wavelengths of interest typically span 9 nm to 31 nm, with the shorter wavelengths being associated with the hottest features (e.g., intense flares and bright points) and the longer wavelengths associated with cooler features (e.g., coronal holes and filaments). Because the optical components of satellite instruments degrade over time, it is not uncommon to conduct sounding rocket underflights for calibration purposes. The authors have designed a radiometric sounding rocket payload that could serve as both a calibration underflight for and a complementary scientific mission to the upcoming Solar Ultraviolet Imager (SUVI) mission aboard the GOES-R satellite (scheduled for a 2015 launch). The challenge to provide quality radiometric line spectra over the 9-31 nm range covered by SUVI was driven by the multilayer coatings required to make the optical components, including mirrors and gratings, reflective over the entire range. Typically, these multilayers provide useful EUV reflectances over bandwidths of a few nm. Our solution to this problem was to employ a three-telescope system in which the optical components were coated with multilayers that spanned three wavelength ranges to cover the three pairs of SUVI bands. The complete system was designed to fit within the Black Brandt-IX 22.-diameter payload skin envelope. The basic optical path is that of a simple parabolic telescope in which EUV light is focused onto a slit and shutter assembly and imaged onto a normal-incidence diffraction grating, which then disperses the light onto a 2048 2048 CCD sensor. The CCD thus records 1D spatial information along one axis and spectral information along the other. The slit spans 40 arc-minutes in length, thus covering a solar diameter out to +/- 1.3 solar radii. Our operations concept includes imaging at three distinct positions: the north-south meridian, the northeast-southwest diagonal, and real-time pointing at an active region. Six 10-second images will be obtained at each position. Fine pointing is provided by the SPARCS-VII attitude control system typically employed on Black Brandt solar missions. Both before and after launch, all three telescopes will be calibrated with the EUV line emission source and monochromater system at NASA's Stray Light Facility at Marshall Spaceflight Center. Details of the payload design, operations concept, and data application will be presented.

Krause, L. Habash↗

DOE OSTI2019

Resilient Disaster Recovery Logistics of Distribution Systems: Co-Optimize Service Restoration With Repair Crew and Mobile Power Source Dispatch

Repair crews (RCs) and mobile power sources (MPSs) are critical resources for distribution system (DS) outage management after a natural disaster. However, their logistics have not been well investigated. We propose a resilient scheme for disaster recovery logistics to co-optimize DS restoration with the dispatch of RCs and MPSs. A novel co-optimization model is formulated to route RCs and MPSs in the transportation network, schedule them in the DS, and reconfigure the DS for microgrid formation coordinately, etc. The model incorporates different timescales of DS restoration and RC/MPS dispatch, the coupling of transportation and power networks, etc. To ensure radiality of the DS with variable physical structure and MPS allocation, we also model topology constraints based on the concept of spanning forest. The model is convexified equivalently and linearized into a mixed-integer linear programming. To reduce its computation time, preprocessing methods are proposed to preassign a minimal set of repair tasks to depots and reduce the number of candidate nodes for MPS connection. Resilient recovery strategies thus are generated to enhance service restoration, especially by dynamic formation of microgrids that are powered by MPSs and topologized by repair actions of RCs and network reconfiguration of the DS. Case studies demonstrate the proposed methodology.

Disaster recovery logistics↗

NASA NTRS2018

Dynamic Shared Computing Resources for Multi-Robot Mars Exploration

The NASA roadmap for 2020 and beyond includes several key technologies which will have a game-changing impact on planetary exploration. The ﬁrst of these is High Performance Spaceﬂight Computing (HPSC), which will provide orders of magnitude increases in processing power for next-generation rovers and orbiters (Doyle et al. 2013). The second is Delay Tolerant Networking, which overlays the Deep Space Network, providing internet-like abstractions and store-forward to route data through intermittent delays in connectivity. The third is a trend toward small, co-dependent robots included in ﬂagship missions (MarCO, PUFFER, and Mars Heli). Taken together, these imply an increasing amount of communication and computing heterogeneity on Mars in coming decades. Motivated by these technological trends, we study the concept of Mars on-site shared analysis, information, and communication (MOSAIC) for Mars exploration. The key algorithmic problem associated with MOSAIC networks is simultaneous scheduling of computation, communication, and caching of data, which we illustrate using the three scenarios. We present models, preliminary solutions, and simulation results for two scenarios, showing how mission efﬁciency relates to communication bandwidth, processing power, geography of the environment, and optimal scheduling of computation, communication, and data caching. The third scenario illustrates future directions of this work.

Chien, Steve↗

NASA NTRS1978

A mechanical, thermal and electrical packaging design for a prototype power management and control system for the 30 cm mercury ion thruster

A prototype electric power management and thruster control system for a 30 cm ion thruster is described. The system meets all of the requirements necessary to operate a thruster in a fully automatic mode. Power input to the system can vary over a full two to one dynamic range (200 to 400 V) for the solar array or other power source. The power management and control system is designed to protect the thruster, the flight system and itself from arcs and is fully compatible with standard spacecraft electronics. The system is easily integrated into flight systems which can operate over a thermal environment ranging from 0.3 to 5 AU. The complete power management and control system measures 45.7 cm (18 in.) x 15.2 cm (6 in.) x 114.8 cm (45.2 in.) and weighs 36.2 kg (79.7 lb). At full power the overall efficiency of the system is estimated to be 87.4 percent. Three systems are currently being built and a full schedule of environmental and electrical testing is planned.

Sharp, G. R.↗

NASA NTRS2001

Computational Analysis of the Combustion Processes in an Axisymmetric, RBCC Flowpath

Computational fluid dynamic simulations have been used to study the combustion processes within an axisymmetric, RBCC flowpath. Two distinct operating modes have been analyzed to date, including the independent ramjet stream (IRS) cycle and the supersonic combustion ramjet (scramJet) cycle. The IRS cycle investigation examined the influence of fuel-air ratio, fuel distribution, and rocket chamber pressure upon the combustion physics and thermal choke characteristics. Results indicate that adjustment of the amount and radial distribution of fuel can control the thermal choke point. The secondary massflow rate was very sensitive to the fuel-air ratio and the rocket chamber pressure. The scramjet investigation examined the influence of fuel-air ratio and fuel injection schedule upon combustion performance estimates. An analysis of the mesh-dependence of these calculations was presented. Jet penetration data was extracted from the three-dimensional simulations and compared favorably with experimental correlations of similar flows. Results indicate that combustion efficiency was very sensitive to the fuel schedule.

Steffen, Christopher J., Jr.↗

NASA NTRS1992

An X-band spacecraft transponder for deep space applications - Design concepts and breadboard performance

The design concepts and measured performance characteristics are summarized of an X band (7162 MHz/8415 MHz) breadboard deep space transponder (DSP) for future spacecraft applications, with the first use scheduled for the Comet Rendezvous Asteroid Flyby (CRAF) and Cassini missions in 1995 and 1996, respectively. The DST consists of a double conversion, superheterodyne, automatic phase tracking receiver, and an X band (8415 MHz) exciter to drive redundant downlink power amplifiers. The receiver acquires and coherently phase tracks the modulated or unmodulated X band (7162 MHz) uplink carrier signal. The exciter phase modulates the band (8415 MHz) downlink signal with composite telemetry and ranging signals. The receiver measured tracking threshold, automatic gain control, static phase error, and phase jitter characteristics of the breadboard DST are in good agreement with the expected performance. The measured results show a receiver tracking threshold of -158 dBm and a dynamic signal range of 88 dB.

Mysoor, Narayan R.↗

NASA NTRS2000

Computational Analysis of the Combustion Processes in an Axisymmetric, RBCC Flowpath

Computational fluid dynamic simulations have been used to study the combustion processes within an axisymmetric, RBCC flowpath. Two distinct operating modes have been analyzed to date, including the independent ramjet stream (IRS) cycle and the supersonic combustion ramjet (scramjet) cycle. The IRS cycle investigation examined the influence of fuel-air ratio, fuel distribution, and rocket chamber pressure upon the combustion physics and thermal choke characteristics. Results indicate that adjustment of the amount and radial distribution of fuel can control the thermal choke point The secondary mass flow rate was very sensitive to the fuel-air ratio and the rocket chamber pressure. The scramjet investigation examined the influence of fuel-air ratio and fuel injection schedule upon combustion performance estimates An analysis of the mesh-dependence of these calculations was presented. Jet penetration data was extracted from the three-dimensional simulations and compared favorably with experimental correlations of similar flows. Results indicate that combustion efficiency was very sensitive to the fuel schedule.

Steffen, Christopher J., Jr.↗

NASA NTRS1991

Design concepts and performance of NASA X-band (7162 MHz/8415 MHz) transponder for deep-space spacecraft applications

The design concepts and measured performance characteristics are summarized of an X band (7162 MHz/8415 MHz) breadboard deep space transponder (DSP) for future spacecraft applications, with the first use scheduled for the Comet Rendezvous Asteroid Flyby (CRAF) and Cassini missions in 1995 and 1996, respectively. The DST consists of a double conversion, superheterodyne, automatic phase tracking receiver, and an X band (8415 MHz) exciter to drive redundant downlink power amplifiers. The receiver acquires and coherently phase tracks the modulated or unmodulated X band (7162 MHz) uplink carrier signal. The exciter phase modulates the X band (8415 MHz) downlink signal with composite telemetry and ranging signals. The receiver measured tracking threshold, automatic gain control, static phase error, and phase jitter characteristics of the breadboard DST are in good agreement with the expected performance. The measured results show a receiver tracking threshold of -158 dBm and a dynamic signal range of 88 dB.

Mysoor, N. R.↗