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DOE OSTI2022

Efficient and interpretable graph network representation for angle-dependent properties applied to optical spectroscopy

Abstract Graph neural networks are attractive for learning properties of atomic structures thanks to their intuitive graph encoding of atoms and bonds. However, conventional encoding does not include angular information, which is critical for describing atomic arrangements in disordered systems. In this work, we extend the recently proposed ALIGNN (Atomistic Line Graph Neural Network) encoding, which incorporates bond angles, to also include dihedral angles (ALIGNN-d). This simple extension leads to a memory-efficient graph representation that captures the complete geometry of atomic structures. ALIGNN-d is applied to predict the infrared optical response of dynamically disordered Cu(II) aqua complexes, leveraging the intrinsic interpretability to elucidate the relative contributions of individual structural components. Bond and dihedral angles are found to be critical contributors to the fine structure of the absorption response, with distortions that represent transitions between more common geometries exhibiting the strongest absorption intensity. Future directions for further development of ALIGNN-d are discussed.

36 MATERIALS SCIENCE↗

NASA NTRS1985

Voyager-Uranus at our doorstep

Following the encounter of Voyager 2 with Saturn and the subsequent approach, in January 1986, to the planet Uranus, the NASA Deep Space Network (DSN) undertook a reshaping of Voyager's end-to-end data system to provide communication to earth with a sufficient number of images for Uranus characterization. In-flight evolution of the spacecraft and ground system is described, with particular attention given to the aspects of target motion compensation, line enhancement, arraying, and encoding data streams. Solutions to the on-board problems encountered during the flight are presented. Voyager and its principal elements, an actuator for the scan platform, and the coding diagram are among the illustrations included.

Laeser, R. P.↗

NASA NTRSDate not supplied

Space-based UV Spectropolarimetry for Chromospheric Magnetic Field Measurements

High-resolution observations with space-and ground-based telescopes, along with advanced numerical modeling, have highlighted the intricate coupling between the chromosphere, transition region, and corona, and the critical role the chromosphere plays in the mass and energy balance of the outer solar atmosphere. Despite these recent advances, a major impediment to better understanding the solar atmosphere is our lack of empirical knowledge regarding the direction and strength of the magnetic field in the upper chromosphere (Decadal Survey, 2012). Such measurements are crucial to address several major unresolved issues in solar physics: for example, to constrain the energy flux carried by the Alfvén waves propagating through the chromosphere, and to determine the height at which the plasma β = 1 transition occurs, which has important consequences for the braiding of magnetic fields, for propagation and mode conversion of waves and for non-linear force-free extrapolation methods that are key to determining what drives instabilities such as flares or coronal mass ejections. Probing the magnetic nature of the Sun’s atmosphere requires measurement of the Stokes I, Q, U and V profiles of relevant spectral lines (of which Q, U and V encode the magnetic field information). Many of the magnetically sensitive lines formed in the chromosphere and transition region are in the ultraviolet spectrum, necessitating observations above the absorbing terrestrial atmosphere. The Chromospheric Layer Spectro-Polarimeter (“CLASP2”) sounding rocket was flown successfully in April 2019, as a follow-on to the successful flight in September 2015 of the Chromospheric Lyman-Alpha Spectro-Polarimeter (“CLASP1”). In October of 2021, we re-flew the CLASP2 experiment with a modified observing program to further demonstrate the maturity of the UV spectropolarimetry techniques, and readiness for development into a satellite observatory. During the reflight, called “CLASP2.1”, the spectrograph slit was scanned across an active region plage to acquire a two-dimensional map of Stokes V/I, to demonstrate the ability of UV spectropolarimetry to yield chromospheric magnetic fields over a large area.

David E McKenzie↗

DOE OSTI2026

Data for Expression of a Bacterial Trehalose 6-Phosphate Synthase Gene otsA in Camelina sativa Seeds Promotes the Channelling of Carbon Towards Oil Accumulation

Improving seed oil yield is essential for developing Camelina sativa as a sustainable biofuel crop. Fatty acid synthesis depends on the production of acetyl-CoA from photosynthetically derived sugars. Trehalose 6-phosphate (T6P), a proxy for sucrose availability, can link sugar status to plant growth and development. Synthesised by trehalose 6-phosphate synthase (TPS) from UDP-glucose and glucose-6-phosphate, T6P plays a regulatory role in metabolism. Our previous studies on Arabidopsis transgenic lines constitutively expressing the E. coli otsA (encoding TPS) showed increased T6P levels and seed triacylglycerol, along with stunted growth. In the present study we express otsA in camelina under the control of a seed-specific Phaseolin promoter. Seeds of the resulting transgenic lines accumulated high levels of T6P, and a 15%–20% increase in total fatty acids and triacylglycerol compared to wild-type. Molecular analysis showed the transgenic seeds had reduced SnRK1 activity, elevated WRI1 protein levels, and increased the levels of WRI1 and its target genes, along with enhanced rates of fatty acid synthesis that increased seed weights relative to wild type. Notably, the increase in oil did not affect seed protein levels but did reduce the soluble metabolite fraction. Crucially, seed-specific expression of otsA mitigated the growth defects associated with constitutive otsA expression, and the transgenic lines showed normal seed development and germination. These findings demonstrate that targeted T6P modulation via seed-specific otsA expression is an effective metabolic engineering strategy to boost oil production in camelina and potentially in other oilseed crops and bioenergy crops such as energycane, sorghum and miscanthus.

Lipids↗

DOE OSTI2024

A versatile high-speed x-ray microscope for sub-10 nm imaging

We have developed a next-generation scanning x-ray microscope RASMI (RApid Scanning Microscopy Instrument) for high-throughput tomographic imaging. RASMI is installed at the hard x-ray nanoprobe beamline at NSLS-II and is capable of manipulating 1D multilayer Laue lenses (MLLs) and 2D optics (both zone plates and monolithically assembled 2D MLLs). The sample scanning stage utilizes line-focusing interferometry as an encoder while performing fly-scanning data acquisition. The system can be configured for both position- and time-triggering modes during fly-scanning. The microscope demonstrated a detector-limited data acquisition rate of 1.25 kHz during ptychography measurements. The initial x-ray results yielded a sample-limited resolution of ∼6 nm in 2D. RASMI can be adopted for in-vacuum applications and is a foundation for the next-generation scanning microscopy systems to be developed and commissioned at NSLS-II.

36 MATERIALS SCIENCE↗

NASA NTRS1980

Bandwidth compression of color video signals

The different encoder/decoder strategies to digitally encode video using an adaptive delta modulation are described. The techniques employed are: (1) separately encoding the R, G, and B components; (2) separately encoding the I, Y, and Q components; and (3) encoding the picture in a line sequential manner.

Schilling, D. L.↗

DOE OSTI2025

Expression of a Bacterial Trehalose 6-Phosphate Synthase Gene otsA in Camelina sativa Seeds Promotes the Channelling of Carbon Towards Oil Accumulation

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Altered cell wall hydroxycinnamate composition impacts leaf- and canopy-level CO2 uptake and water use in rice

Abstract Cell wall properties play a major role in determining photosynthetic carbon uptake and water use through their impact on mesophyll conductance (CO2 diffusion from substomatal cavities into photosynthetic mesophyll cells) and leaf hydraulic conductance (water movement from xylem, through leaf tissue, to stomata). Consequently, modification of cell wall (CW) properties might help improve photosynthesis and crop water use efficiency (WUE). We tested this using 2 independent transgenic rice (Oryza sativa) lines overexpressing the rice OsAT10 gene (encoding a “BAHD” CoA acyltransferase), which alters CW hydroxycinnamic acid content (more para-coumaric acid and less ferulic acid). Plants were grown under high and low water levels, and traits related to leaf anatomy, CW composition, gas exchange, hydraulics, plant biomass, and canopy-level water use were measured. Alteration of hydroxycinnamic acid content led to statistically significant decreases in mesophyll CW thickness (−14%) and increased mesophyll conductance (+120%) and photosynthesis (+22%). However, concomitant increases in stomatal conductance negated the increased photosynthesis, resulting in no change in intrinsic WUE (ratio of photosynthesis to stomatal conductance). Leaf hydraulic conductance was also unchanged; however, transgenic plants showed small but statistically significant increases in aboveground biomass (AGB) (+12.5%) and canopy-level WUE (+8.8%; ratio of AGB to water used) and performed better under low water levels than wild-type plants. Our results demonstrate that changes in CW composition, specifically hydroxycinnamic acid content, can increase mesophyll conductance and photosynthesis in C3 cereal crops such as rice. However, attempts to improve photosynthetic WUE will need to enhance mesophyll conductance and photosynthesis while maintaining or decreasing stomatal conductance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Generative BigSMILES CLI

Generative BigSMILES CLI is a command-line interface for handling polymer string encoding formats such as BigSMILES and GenerativeBigSMILES.

Salij, Andrew↗

NASA NTRS1972

Radio astronomy Explorer B antenna aspect processor

The antenna aspect system used on the Radio Astronomy Explorer B spacecraft is described. This system consists of two facsimile cameras, a data encoder, and a data processor. Emphasis is placed on the discussion of the data processor, which contains a data compressor and a source encoder. With this compression scheme a compression ratio of 8 is achieved on a typical line of camera data. These compressed data are then convolutionally encoded.

Miller, W. H.↗

NASA NTRS1978

Confidence about line features in Her X-1 spectrum

A balloon borne X-ray telescope was flown Aire-surl'Adour, France to search for pulsation of the X-ray source HER X1. The source was measured for about 3500 s relative exposure larger than 0.75 and features were detected at 57.5 plus or minus 7.5 keV and 135 plus or minus 10 keV in the spectrum. Data were reanalyzed in terms of possibility of gain shift encoder. The very strong dependence of the line features on such a shift is discussed.

Durouchoux, P.↗

NASA NTRS1992

Structure and strategy in encoding simplified graphs

Tversky and Schiano (1989) found a systematic bias toward the 45-deg line in memory for the slopes of identical lines when embedded in graphs, but not in maps, suggesting the use of a cognitive reference frame specifically for encoding meaningful graphs. The present experiments explore this issue further using the linear configurations alone as stimuli. Experiments 1 and 2 demonstrate that perception and immediate memory for the slope of a test line within orthogonal 'axes' are predictable from purely structural considerations. In Experiments 3 and 4, subjects were instructed to use a diagonal-reference strategy in viewing the stimuli, which were described as 'graphs' only in Experiment 3. Results for both studies showed the diagonal bias previously found only for graphs. This pattern provides converging evidence for the diagonal as a cognitive reference frame in encoding linear graphs, and demonstrates that even in highly simplified displays, strategic factors can produce encoding biases not predictable solely from stimulus structure alone.

Schiano, Diane J.↗

DOE OSTI2021

Locality-aware and sharing-aware cache coherence for collections of processors

A cache coherence technique for operating a multi-processor system including shared memory includes allocating a cache line of a cache memory of a processor to a memory address in the shared memory in response to execution of an instruction of a program executing on the processor. The technique includes encoding a shared information state of the cache line to indicate whether the memory address is a shared memory address shared by the processor and a second processor, or a private memory address private to the processor, in response to whether the instruction is included in a critical section of the program, the critical section being a portion of the program that confines access to shared, writeable data.

Farmahini Farahani, Amin↗

DOE OSTI2025

Commuting Line Defects At $q^N$ = 1

Here, we explain the physical origin of a curious property of algebras $\mathcal{A}_{\mathfrak{q}}$ which encode the rotation-equivariant fusion ring of half-BPS line defects in four-dimensional $\mathcal{N}$ = 2 supersymmetric quantum field theories. These algebras are a quantization of the algebras of holomorphic functions on the three-dimensional Coulomb branch of the SQFTs, with deformation parameter log $\mathfrak{q}$. They are known to acquire a large center, canonically isomorphic to the undeformed algebra, whenever $\mathfrak{q}$ is a root of unity. We give a physical explanation of this fact. We also generalize the construction to characterize the action of this center in the $\mathcal{A}_{\mathfrak{q}}$-modules associated to three-dimensional $\mathcal{N}$ = 2 boundary conditions. Finally, we use dualities to relate this construction to a construction in the Kapustin–Witten twist of four-dimensional $\mathcal{N}$ = 4 gauge theory. These considerations give simple physical explanations of certain properties of quantized skein algebras and cluster varieties, and quantum groups, when the deformation parameter is a root of unity.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS2017

CLASP2: The Chromospheric LAyer Spectro-Polarimeter

A major remaining challenge for heliophysicsis to decipher the magnetic structure of the chromosphere, due to its "large role in defining how energy is transported into the corona and solar wind" (NASA's Heliophysics Roadmap). Recent observational advances enabled by the Interface Region Imaging Spectrometer (IRIS) have revolutionized our view of the critical role this highly dynamic interface between the photosphere and corona plays in energizing and structuring the outer solar atmosphere. Despite these advances, a major impediment to better understanding the solar atmosphere is our lack of empirical knowledge regarding the direction and strength of the magnetic field in the upper chromosphere. Such measurements are crucial to address several major unresolved issues in solar physics: for example, to constrain the energy flux carried by the Alfven waves propagating through the chromosphere (De Pontieuet al., 2014), and to determine the height at which the plasma Beta = 1 transition occurs, which has important consequences for the braiding of magnetic fields (Cirtainet al., 2013; Guerreiroet al., 2014), for propagation and mode conversion of waves (Tian et al., 2014a; Straus et al., 2008) and for non-linear force-free extrapolation methods that are key to determining what drives instabilities such as flares or coronal mass ejections (e.g.,De Rosa et al., 2009). The most reliable method used to determine the solar magnetic field vector is the observation and interpretation of polarization signals in spectral lines, associated with the Zeeman and Hanle effects. Magnetically sensitive ultraviolet spectral lines formed in the upper chromosphere and transition region provide a powerful tool with which to probe this key boundary region (e.g., Trujillo Bueno, 2014). Probing the magnetic nature of the chromosphere requires measurement of the Stokes I, Q, U and V profiles of the relevant spectral lines (of which Q, U and V encode the magnetic field information).

Chromosphere↗

NASA NTRS2017

CLASP2: The Chromospheric LAyer Spectro-Polarimeter

A major remaining challenge for heliophysicsis to decipher the magnetic structure of the chromosphere, due to its 'large role in defining how energy is transported into the corona and solar wind' (NASA's Heliophysics Roadmap). Recent observational advances enabled by the Interface Region Imaging Spectrometer (IRIS) have revolutionized our view of the critical role this highly dynamic interface between the photosphere and corona plays in energizing and structuring the outer solar atmosphere. Despite these advances, a major impediment to better understanding the solar atmosphere is our lack of empirical knowledge regarding the direction and strength of the magnetic field in the upper chromosphere. Such measurements are crucial to address several major unresolved issues in solar physics: for example, to constrain the energy flux carried by the Alfven waves propagating through the chromosphere (De Pontieuet al., 2014), and to determine the height at which the plasma β = 1 transition occurs, which has important consequences for the braiding of magnetic fields (Cirtainet al., 2013; Guerreiroet al., 2014), for propagation and mode conversion of waves (Tian et al., 2014a; Straus et al., 2008) and for non-linear force-free extrapolation methods that are key to determining what drives instabilities such as flares or coronal mass ejections (e.g., De Rosa et al., 2009). The most reliable method used to determine the solar magnetic field vector is the observation and interpretation of polarization signals in spectral lines, associated with the Zeeman and Hanle effects. Magnetically sensitive ultraviolet spectral lines formed in the upper chromosphere and transition region provide a powerful tool with which to probe this key boundary region (e.g., Trujillo Bueno, 2014). Probing the magnetic nature of the chromosphere requires measurement of the Stokes I, Q, U and V profiles of the relevant spectral lines (of which Q, U and V encode the magnetic field information).

Solar; Chromosphere; Polarization↗

NASA NTRS1993

A high-speed lossless data compression system for space applications

This paper reports on the integration of a lossless data compression/decompression chipset into a space data system architecture. For its compression engine, the data system incorporates the Universal Source Encoder (USE) designed for the NASA/Goddard Space Flight Center. Currently, the data compression testbed generates video frames consisting of 512 lines of 512 pixels having 8-bit resolution. Each image is passed through the USE where the lines are internally partitioned into 16-word blocks. These blocks are adaptively encoded across widely varying entropy levels using a Rice 12-option set coding algorithm. The current system operates at an Input/Output rate of 10 Msamples/s or 80 Mbits/s for each buffered input line. Frame and line synchronization for each image are maintained through the use of uniquely decodable command words. Length information of each variable length compressed image line is also included in the output stream. The data and command information are passed to the next stage of the system architecture through a serial fiber-optic transmitter. The initial segment of this stage consists of packetizer hardware which adds an appropriate CCSDS header to the received source data. An uncompressed mode is optionally available to pass image lines directly to the packetizer hardware. A data decompression testbed has also been developed to confirm the data compression operation.

Miko, Joe↗

NASA NTRS1979

Telephone multiline signaling using common signal pair

An operator can rapidly and automatically produce coded electrical signals by manipulating mechanical thumb wheel switches so as to instruct a service center to connect any number of telephone lines to the console thus enabling the operator to listen and/or talk over several lines simultaneously. The system includes an on-site console having several mechanically operated thumb wheel switches to which the desired lines to be connected can be dialed in. Electrical coded signals are fed to a number of banks of line AND gates representing units, tens and hundreds, a group of channel gates, and a command gate. These signals are gated out in a controlled manner to an encoder which generates tones that are transmitted over a single line to a communication service center.

Goodloe, R. R.↗