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All sourcesNASA NTRSDOE OSTI
NASA NTRS2002

The Mars Exploration Rover/Collaborative Information Portal

Astrology has long argued that the alignment of the planets governs human affairs. Science usually scoffs at this. There is, however, an important exception: sending spacecraft for planetary exploration. In late May and early June, 2003, Mars will be in position for Earth launch. Two Mars Exploration Rovers (MER) will rocket towards the red planet. The rovers will perform a series of geological and meteorological experiments, seeking to examine geological evidence for water and conditions once favorable for life. Back on earth, a small army of surface operations staff will work to keep the rovers running, sending directions for each day's operations and receiving the files encoding the outputs of the Rover's six instruments. (Mars is twenty light minutes from Earth. The rovers must be robots.) The fundamental purpose of the project is, after all, Science. Scientists have experiments they want to run. Ideally, scientists want to be immediately notified when the data products of their experiments have been received, so that they can examine their data and (collaboratively) deduce results. Mars is an unpredictable environment. We may issue commands to the rovers but there is considerable uncertainty in how the commands will be executed and whether what the rovers sense will be worthy of further pursuit. The steps of what is, to a scientist, conceptually an individual experiment may be scattered over a large number of activities. While the scientific staff has an overall strategic idea of what it would like to accomplish, activities are planned daily. The data and surprises of the previous day need to be integrated into the negotiations for the next day's activities, all synchronized to a schedule of transmission windows . Negotiations is the operative term, as different scientists want the resources to run possibly incompatible experiments. Many meetings plan each day's activities.

Walton, Joan↗
DOE OSTI2021

Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants

The second and third steps of the histidine biosynthetic pathway (HBP) in plants are catalyzed by a bifunctional enzyme–HISN2. The enzyme consists of two distinct domains, active respectively as a phosphoribosyl-AMP cyclohydrolase (PRA-CH) and phosphoribosyl-ATP pyrophosphatase (PRA-PH). The domains are analogous to single-domain enzymes encoded by bacterial hisI and hisE genes, respectively. The calculated sequence similarity networks between HISN2 analogs from prokaryotes and eukaryotes suggest that the plant enzymes are closest relatives of those in the class of Deltaproteobacteria. In this work, we obtained crystal structures of HISN2 enzyme from Medicago truncatula (MtHISN2) and described its architecture and interactions with AMP. The AMP molecule bound to the PRA-PH domain shows positioning of the N1-phosphoribosyl relevant to catalysis. AMP bound to the PRA-CH domain mimics a part of the substrate, giving insights into the reaction mechanism. The latter interaction also arises as a possible second-tier regulatory mechanism of the HBP flux, as indicated by inhibition assays and isothermal titration calorimetry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Progressive Tree-Based Compression of Large-Scale Particle Data

Scientific simulations and observations using particles have been creating large datasets that require effective and efficient data reduction to store, transfer, and analyze. However, current approaches either compress only small data well while being inefficient for large data, or handle large data but with insufficient compression. Toward effective and scalable compression/decompression of particle positions, we introduce new kinds of particle hierarchies and corresponding traversal orders that quickly reduce reconstruction error while being fast and low in memory footprint. Our solution to compression of large-scale particle data is a flexible block-based hierarchy that supports progressive, random-access, and error-driven decoding, where error estimation heuristics can be supplied by the user. For low-level node encoding, we introduce new schemes that effectively compress both uniform and densely structured particle distributions. Our proposed methods thus target all three phases of a tree-based particle compression pipeline, namely tree construction, tree traversal, and node encoding. In conclusion, the improved efficacy and flexibility of these methods over existing compressors are demonstrated through extensive experimentation, using a wide range of scientific particle datasets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Domain architecture and catalysis of the Staphylococcus aureus fatty acid kinase

Fatty acid kinase (Fak) is a two-component enzyme that generates acyl-phosphate for phospholipid synthesis. Fak consists of a kinase domain protein (FakA) that phosphorylates a fatty acid enveloped by a fatty acid binding protein (FakB). The structural basis for FakB function has been established, but little is known about FakA. Here, we used limited proteolysis to define three separate FakA domains: the amino terminal FakA_N, the central FakA_L, and the carboxy terminal FakA_C. The isolated domains lack kinase activity, but activity is restored when FakA_N and FakA_L are present individually or connected as FakA_NL. The X-ray structure of the monomeric FakA_N captures the product complex with ADP and two Mg 2+ ions bound at the nucleotide site. The FakA_L domain encodes the dimerization interface along with conserved catalytic residues Cys240, His282, and His284. AlphaFold analysis of FakA_L predicts the catalytic residues are spatially clustered and pointing away from the dimerization surface. Furthermore, the X-ray structure of FakA_C shows that it consists of two subdomains that are structurally related to FakB. Analytical ultracentrifugation demonstrates that FakA_C binds FakB, and site-directed mutagenesis confirms that a positively charged wedge on FakB meshes with a negatively charged groove on FakA_C. Finally, small angle X-ray scattering analysis is consistent with freely rotating FakA_N and FakA_C domains tethered by flexible linkers to FakA_L. These data reveal specific roles for the three independently folded FakA protein domains in substrate binding and catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2003

Block QCA Fault-Tolerant Logic Gates

Suitably patterned arrays (blocks) of quantum-dot cellular automata (QCA) have been proposed as fault-tolerant universal logic gates. These block QCA gates could be used to realize the potential of QCA for further miniaturization, reduction of power consumption, increase in switching speed, and increased degree of integration of very-large-scale integrated (VLSI) electronic circuits. The limitations of conventional VLSI circuitry, the basic principle of operation of QCA, and the potential advantages of QCA-based VLSI circuitry were described in several NASA Tech Briefs articles, namely Implementing Permutation Matrices by Use of Quantum Dots (NPO-20801), Vol. 25, No. 10 (October 2001), page 42; Compact Interconnection Networks Based on Quantum Dots (NPO-20855) Vol. 27, No. 1 (January 2003), page 32; Bit-Serial Adder Based on Quantum Dots (NPO-20869), Vol. 27, No. 1 (January 2003), page 35; and Hybrid VLSI/QCA Architecture for Computing FFTs (NPO-20923), which follows this article. To recapitulate the principle of operation (greatly oversimplified because of the limitation on space available for this article): A quantum-dot cellular automata contains four quantum dots positioned at or between the corners of a square cell. The cell contains two extra mobile electrons that can tunnel (in the quantummechanical sense) between neighboring dots within the cell. The Coulomb repulsion between the two electrons tends to make them occupy antipodal dots in the cell. For an isolated cell, there are two energetically equivalent arrangements (denoted polarization states) of the extra electrons. The cell polarization is used to encode binary information. Because the polarization of a nonisolated cell depends on Coulomb-repulsion interactions with neighboring cells, universal logic gates and binary wires could be constructed, in principle, by arraying QCA of suitable design in suitable patterns. Heretofore, researchers have recognized two major obstacles to realization of QCA-based logic gates: One is the need for (and the difficulty of attaining) operation of QCA circuitry at room temperature or, for that matter, at any temperature above a few Kelvins. It has been theorized that room-temperature operation could be made possible by constructing QCA as molecular-scale devices. However, in approaching the lower limit of miniaturization at the molecular level, it becomes increasingly imperative to overcome the second major obstacle, which is the need for (and the difficulty of attaining) high precision in the alignments of adjacent QCA in order to ensure the correct interactions among the quantum dots.

Firjany, Amir↗
NASA NTRS2003

Bit-Serial Adder Based on Quantum Dots

A proposed integrated circuit based on quantum-dot cellular automata (QCA) would function as a bit-serial adder. This circuit would serve as a prototype building block for demonstrating the feasibility of quantum-dots computing and for the further development of increasingly complex and increasingly capable quantum-dots computing circuits. QCA-based bit-serial adders would be especially useful in that they would enable the development of highly parallel and systolic processors for implementing fast Fourier, cosine, Hartley, and wavelet transforms. The proposed circuit would complement the QCA-based circuits described in "Implementing Permutation Matrices by Use of Quantum Dots" (NPO-20801), NASA Tech Briefs, Vol. 25, No. 10 (October 2001), page 42 and "Compact Interconnection Networks Based on Quantum Dots" (NPO-20855), which appears elsewhere in this issue. Those articles described the limitations of very-large-scale-integrated (VLSI) circuitry and the major potential advantage afforded by QCA. To recapitulate: In a VLSI circuit, signal paths that are required not to interact with each other must not cross in the same plane. In contrast, for reasons too complex to describe in the limited space available for this article, suitably designed and operated QCA-based signal paths that are required not to interact with each other can nevertheless be allowed to cross each other in the same plane without adverse effect. In principle, this characteristic could be exploited to design compact, coplanar, simple (relative to VLSI) QCA-based networks to implement complex, advanced interconnection schemes. To enable a meaningful description of the proposed bit-serial adder, it is necessary to further recapitulate the description of a quantum-dot cellular automation from the first-mentioned prior article: A quantum-dot cellular automaton contains four quantum dots positioned at the corners of a square cell. The cell contains two extra mobile electrons that can tunnel (in the quantum-mechanical sense) between neighboring dots within the cell. The Coulomb repulsion between the two electrons tends to make them occupy antipodal dots in the cell. For an isolated cell, there are two energetically equivalent arrangements (denoted polarization states) of the extra electrons. The cell polarization is used to encode binary information. Because the polarization of a nonisolated cell depends on Coulomb-repulsion interactions with neighboring cells, universal logic gates and binary wires could be constructed, in principle, by arraying QCA of suitable design in suitable patterns. Again, for reasons too complex to describe here, in order to ensure accuracy and timeliness of the output of a QCA array, it is necessary to resort to an adiabatic switching scheme in which the QCA array is divided into subarrays, each controlled by a different phase of a multiphase clock signal. In this scheme, each subarray is given time to perform its computation, then its state is frozen by raising its inter-dot potential barriers and its output is fed as the input to the successor subarray. The successor subarray is kept in an unpolarized state so it does not influence the calculation of preceding subarray. Such a clocking scheme is consistent with pipeline computation in the sense that each different subarray can perform a different part of an overall computation. In other words, QCA arrays are inherently suitable for pipeline and, moreover, systolic computations. This sequential or pipeline aspect of QCA would be utilized in the proposed bit-serial adders.

Fijany, Amir↗
DOE OSTI2023

Identifying COVID-19 cases and extracting patient reported symptoms from Reddit using natural language processing

We used social media data from “covid19positive” subreddit, from 03/2020 to 03/2022 to identify COVID-19 cases and extract their reported symptoms automatically using natural language processing (NLP). We trained a Bidirectional Encoder Representations from Transformers classification model with chunking to identify COVID-19 cases; also, we developed a novel QuadArm model, which incorporates Question-answering, dual-corpus expansion, Adaptive rotation clustering, and mapping, to extract symptoms. Our classification model achieved a 91.2% accuracy for the early period (03/2020-05/2020) and was applied to the Delta (07/2021–09/2021) and Omicron (12/2021–03/2022) periods for case identification. We identified 310, 8794, and 12,094 COVID-positive authors in the three periods, respectively. The top five common symptoms extracted in the early period were coughing (57%), fever (55%), loss of sense of smell (41%), headache (40%), and sore throat (40%). During the Delta period, these symptoms remained as the top five symptoms with percent authors reporting symptoms reduced to half or fewer than the early period. During the Omicron period, loss of sense of smell was reported less while sore throat was reported more. Our study demonstrated that NLP can be used to identify COVID-19 cases accurately and extracted symptoms efficiently.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Space Nuclear Power Autonomous Control Algorithm and Control Element Test Bed

Nuclear thermal rockets are currently NASA’s preferred option for use in a manned mission to Mars in the 2040s. The communication delay between an Earth ground station and a spacecraft heading toward Mars can be up to 20 min. Therefore, controlling the nuclear rocket engine would require either a full-time reactor operator on the mission or an autonomous control system for the reactor. The latter idea of making space nuclear reactors fully autonomous has drawn more interest from stakeholders, but such an autonomous control system must be rigorously tested and validated before it is certified for human use. The cost of a full ground test for a space nuclear reactor is tremendous, so a nonnuclear mock reactor test bed was created to test and validate control elements and control algorithms for space nuclear reactors. The test bed consists of control element hardware that inputs physical measurement data into a reactor emulator to produce the reactor’s performance under steady-state, transient, and fault conditions. The control element hardware consists of six full-sized control drums equipped with servo drives and motors and is instrumented with optical encoders, resolvers, and torque sensors for drum movement characterization. In addition to the drums, a two-phase flow loop was designed and built to mimic the valves and turbomachinery associated with the propellant flow through a nuclear thermal rocket engine; components such as pressure sensors, flow meters, thermocouples, and tachometers are instrumented throughout the loop to characterize the fluid flow, valve, and turbomachinery behavior of the system. The data from the physical hardware (e.g., drum position, propellant flow rates) are input to a nuclear reactor simulator to determine the actual nuclear reactor parameters, and the data are sent back to a control algorithm to complete the control loop. The ability to conduct numerous tests of the control systems and autonomous algorithms can help validate the instrumentation and control aspects for a space nuclear reactor for every possible fault situation.

Wilson, Brandon↗
DOE OSTI2025

An Evaluation of Representation Learning Methods in Particle Physics Foundation Models

We present a systematic evaluation of representation learning objectives for particle physics within a unified framework. Our study employs a shared transformer-based particle-cloud encoder with standardized preprocessing, matched sampling, and a consistent evaluation protocol on a jet classification dataset. We compare contrastive (supervised and self-supervised), masked particle modeling, and generative reconstruction objectives under a common training regimen. In addition, we introduce targeted supervised architectural modifications that achieve state-of-the-art performance on benchmark evaluations. This controlled comparison isolates the contributions of the learning objective, highlights their respective strengths and limitations, and provides reproducible baselines. We position this work as a reference point for the future development of foundation models in particle physics, enabling more transparent and robust progress across the community.

Chen, Michael [Caltech]↗
DOE OSTI2021

Improved Localization Precision and Angular Resolution of a Cylindrical, Time-Encoded Imaging System From Adaptive Detector Movements

To the first order, the localization precision and angular resolution of a cylindrical, time-encoded imaging (c-TEI) system is governed by the geometry of the system. Improving either measure requires increasing the mask radius or decreasing the detector diameter, both of which are undesirable. Here, we propose an alternative option of repositioning the detector within the mask to increase the detector-to-mask distance in the direction of a source, thereby improving the localization precision and angular resolution in that direction. Since the detector-to-mask distance only increases for a small portion of the field of view (FOV), we propose implementing adaptive imaging where one leverages data collected during the measurement to optimize the system configuration. This article utilizes both simulations and experiments to set upper bounds on the potential gain from adaptive detector movements for one and two sources in the FOV. When only one source is present, adaptive detector movements can improve the localization precision and angular resolution by 20% for a source at 90 cm and by 32% for a far-field source. When two sources are present, adaptive detector movements can improve localization precision and angular resolution by up to 50% for sources that are ~10° apart (90 cm from the system). We experimentally verify these results through maximum likelihood estimation of the source position(s) and image reconstruction of point sources that are close together. As a demonstration of an adaptive imaging algorithm, we image a complex arrangement of special nuclear material at the Zero Power Physics Reactor facility at Idaho National Laboratory.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗
NASA NTRS2000

First-Generation Jet Propulsion Laboratory "Hockey-Puck" Free-Flying Magnetometers for Distributed In-Situ Multiprobe Measurement of Current Density Filamentation in the Northern Auroral Zone: Enstrophy Mission

The sub-orbital rocket mission was a collaborative project between the University of New Hampshire, Cornell University, and the Jet Propulsion Laboratory (JPL) to study filamentation phenomena in the northern Auroral zone. The Enstrophy mission test flies the JPL Free-Flying Magnetometer (FFM) concept. The FFM technology development task has been funded by NASA develop miniaturized, low-power, integrated "sensorcrafts". JPL's role was to design, integrate, test, and deliver four FFMs for deployment from the sounding rocket, allowing a unique determination of curl-B. This provides a direct measurement of magnetic-field-aligned current density along the rocket trajectory. A miniaturized three-axis fluxgate magnetometer was integrated with a 4-channel 22-bit sigma-delta Analog to Digital Converter (ADC), four temperature sensors, digital control electronics, seven (Li-SOCl2) batteries, two (4 deg x 170 deg field of view) sun-sensors, a fan-shaped-beam laser diode beacon, a (16 MHz) stable Temperature Compensated Crystal Oscillator (TCXO) clock, Radio Frequency (RF) communication subsystem, and an antenna for approximately 15 minutes of operation where data was collected continuously and transmitted in three (3) bursts (approximately 26 seconds each) to ground station antennas at Poker Flat, Alaska. FFMs were stowed within two trays onboard the rocket during the rocket launch and were released simultaneously using the spinning action of the rocket at approximately 300 km altitude (approximately 100 sec. into the flight). FFMs were deployed with spin rate of approximately 17 Hz and approximately 3 m/sec linear velocity with respect to the rocket. For testing purposes while the rocket was in the launch pad and during flight prior to release of FFMs from the rocket, commands (such as "power on", "test", "flight", "power off', and clock "Reset" signal) were transmitted via a infrared Light Emitting Diode to an infrared detector in the FFM. Special attention was paid to low magnetic signature electronic design and choice of materials in packaging. The miniaturized fluxgate magnetometers had a range of 1-60000 nT with 0.1% full-scale linearity. The frequency range of interest for magnetic measurement was 10 mHz - 50 Hz. Digital data from the magnetometer's three axes were placed in a 4MB Static Random Access Memory (SRAM) in data packages (frames) formatted together with time tags and frame ID. After a specified time was elapsed, the data were Viterbi encoded and transmitted at a rate of 100 kbps (BPSK). Each of the four FFMs transmitted at different frequency. These carrier frequencies were in the range of 2200-2300 MHz. The antenna was a single patch on a high dielectric constant substrate covering one end-plate of the hockey-puck-sized unit. The local clocks aboard the FFMs were reset at the start of the mission and stayed synchronized within 3 msec during the mission. Position of each FFM with respect to the rocket is calculated by the knowledge of its release velocity (measured at exit point of the FFM launcher tract) providing an accuracy of 1 m over the maximum range of 3 km. Spatial and temporal nature of observants can be separated to within 3 m in space or 3 msec time interval.

Javadi, H.↗
DOE OSTI2026

Quantum computing approach for building surface sunlit in urban-scale energy modeling

Solar shadow calculations are needed in building energy modeling and performance simulation of PV systems installed on roofs or facades of buildings. We present a quantum computing approach for calculation of building surface sunlit fractions by recasting solar visibility as a binary optimization problem solved by quantum annealing. Each triangulated surface centroid is encoded as a binary qubit indicating sunlit or shaded status. Geometric visibility constraints are derived from the Möller-Trumbore intersection algorithm and converted into a constrained quadratic binary model compatible with contemporary quantum annealers. The coefficients were embedded to D-Wave quantum computer. To demonstrate feasibility, we conducted a case study in San Francisco for a target building with 52 triangles and roughly 2700 nearby triangles within 50 m evaluated at representative winter and summer solar positions. The results demonstrated that quantum annealing can reliably calculate and distinguish sunlit from shaded surfaces. Quantum samples achieved average accuracy exceeding 92.4 %, with the aggregate surface-level agreement approaching 99.9 %. The outputs of quantum computers agreed closely with classical algorithms, indicating practical feasibility and promising scalability. Finally, the hourly sunlit fractions of building surfaces can be obtained for urban energy modelling. This is the first study to apply quantum computing to the solar shadow and building surface sunlit calculation. It introduces a new paradigm that differs fundamentally from traditional approaches.

Deng, Zhipeng↗
DOE OSTI2021

Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut ( Arachis hypogaea L.)

Abstract The fatty acid composition of seed oil is a major determinant of the flavor, shelf-life, and nutritional quality of peanuts. Major QTLs controlling high oil content, high oleic content, and low linoleic content have been characterized in several seed oil crop species. Here, we employ genome-wide association approaches on a recently genotyped collection of 787 plant introduction accessions in the USDA peanut core collection, plus selected improved cultivars, to discover markers associated with the natural variation in fatty acid composition, and to explain the genetic control of fatty acid composition in seed oils. Overall, 251 single nucleotide polymorphisms (SNPs) had significant trait associations with the measured fatty acid components. Twelve SNPs were associated with two or three different traits. Of these loci with apparent pleiotropic effects, 10 were associated with both oleic (C18:1) and linoleic acid (C18:2) content at different positions in the genome. In all 10 cases, the favorable allele had an opposite effect—increasing and lowering the concentration, respectively, of oleic and linoleic acid. The other traits with pleiotropic variant control were palmitic (C16:0), behenic (C22:0), lignoceric (C24:0), gadoleic (C20:1), total saturated, and total unsaturated fatty acid content. One hundred (100) of the significantly associated SNPs were located within 1000 kbp of 55 genes with fatty acid biosynthesis functional annotations. These genes encoded, among others: ACCase carboxyl transferase subunits, and several fatty acid synthase II enzymes. With the exception of gadoleic (C20:1) and lignoceric (C24:0) acid content, which occur at relatively low abundance in cultivated peanuts, all traits had significant SNP interactions exceeding a stringent Bonferroni threshold (α = 1%). We detected 7682 pairwise SNP interactions affecting the relative abundance of fatty acid components in the seed oil. Of these, 627 SNP pairs had at least one SNP within 1000 kbp of a gene with fatty acid biosynthesis functional annotation. We evaluated 168 candidate genes underlying these SNP interactions. Functional enrichment and protein-to-protein interactions supported significant interactions (P-value < 1.0E−16) among the genes evaluated. These results show the complex nature of the biology and genes underlying the variation in seed oil fatty acid composition and contribute to an improved genotype-to-phenotype map for fatty acid variation in peanut seed oil.

Otyama, Paul I.↗
DOE OSTI2023

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

Climate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred “active” vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth’s destabilized and rapidly disappearing cryosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Charge completeness and the massless charge lattice in F-theory models of supergravity

We prove that, for every 6D supergravity theory that has an F-theory description, the property of charge completeness for the connected component of the gauge group (meaning that all charges in the corresponding charge lattice are realized by massive or massless states in the theory) is equivalent to a standard assumption made in F-theory for how geometry encodes the global gauge theory by means of the Mordell-Weil group of the elliptic fibration. This result also holds in 4D F-theory constructions for the parts of the gauge group that come from sections and from 7-branes. We find that in many 6D F-theory models the full charge lattice of the theory is generated by massless charged states; this occurs for each gauge factor where the associated anomaly coefficient satisfies a simple positivity condition. We describe many of the cases where this massless charge sufficiency condition holds, as well as exceptions where the positivity condition fails, and analyze the related global structure of the gauge group and associated Mordell-Weil torsion in explicit F-theory models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

River Delta Morphotypes Emerge From Multiscale Characterization of Shorelines

Abstract Delta shoreline structure has long been hypothesized to encode information on the relative influence of fluvial, wave, and tidal processes on delta formation and evolution. We introduce here a novel multiscale characterization of shorelines by defining three process‐informed morphological metrics. We show that this characterization yields self‐emerging classes of morphologically similar deltas, that is, delta morphotypes, and also predicts the dominant forcing of each morphotype. Then we show that the dominant forcings inferred from shoreline structure generally align with those estimated via relative sediment fluxes, while positing that misalignments arise from spatiotemporal heterogeneity in deltaic sediment fluxes not captured in their estimates. The proposed framework for shoreline characterization advances our quantitative understanding of how shoreline features reflect delta forcings, and may aid in deciphering paleoclimate from images of ancient deposits and projecting delta morphologic response to changes in sediment fluxes.

Vulis, L.↗
DOE OSTI2021

Cation and Anion Channelrhodopsins: Sequence Motifs and Taxonomic Distribution

Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as optogenetic tools to control cell membrane potential with light. We mined algal and other protist polynucleotide sequencing projects and metagenomic samples to identify 75 channelrhodopsin homologs from four channelrhodopsin families, including one revealed in dinoflagellates in this study. We carried out electrophysiological analysis of 33 natural channelrhodopsin variants from different phylogenetic lineages and 10 metagenomic homologs in search of sequence determinants of ion selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins. Our results show that association of a reduced number of glutamates near the conductance path with anion selectivity depends on a wider protein context, because prasinophyte homologs with a glutamate pattern identical to that in cryptophyte ACRs are cation selective. Desensitization is also broadly context dependent, as in one branch of stramenopile ACRs and their metagenomic homologs, its extent roughly correlates with phylogenetic relationship of their sequences. Regarding spectral tuning, we identified two prasinophyte CCRs with red-shifted spectra to 585 nm. They exhibit a third residue pattern in their retinal-binding pockets distinctly different from those of the only two types of red-shifted channelrhodopsins known (i.e., the CCR Chrimson and RubyACRs). In cryptophyte ACRs we identified three specific residue positions in the retinal-binding pocket that define the wavelength of their spectral maxima. Lastly, we found that dinoflagellate rhodopsins with a TCP motif in the third transmembrane helix and a metagenomic homolog exhibit channel activity. Channelrhodopsins are widely used in neuroscience and cardiology as research tools and are considered prospective therapeutics, but their natural diversity and mechanisms remain poorly characterized. Genomic and metagenomic sequencing projects are producing an ever-increasing wealth of data, whereas biophysical characterization of the encoded proteins lags behind. In this study, we used manual and automated patch clamp recording of representative members of four channelrhodopsin families, including a family in dinoflagellates that we report in this study. Our results contribute to a better understanding of molecular determinants of ionic selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome

Small molecules encoded by biosynthetic pathways mediate cross-species interactions and harbor untapped potential, which has provided valuable compounds for medicine and biotechnology. Since studying biosynthetic gene clusters in their native context is often difficult, alternative efforts rely on heterologous expression, which is limited by host-specific metabolic capacity and regulation. Here, in this work, we describe a computational-experimental technology to redesign genes and their regulatory regions with hybrid elements for cross-species expression in Gram-negative and -positive bacteria and eukaryotes, decoupling biosynthetic capacity from host-range constraints to activate silenced pathways. These synthetic genetic elements enabled the discovery of a class of microbiome-derived nucleotide metabolites—tyrocitabines—from Lactobacillus iners. Tyrocitabines feature a remarkable orthoester-phosphate, inhibit translational activity, and invoke unexpected biosynthetic machinery, including a class of “Amadori synthases” and “abortive” tRNA synthetases. Our approach establishes a general strategy for the redesign, expression, mobilization, and characterization of genetic elements in diverse organisms and communities.

59 BASIC BIOLOGICAL SCIENCES↗