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Results for “sequence alignment”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Octet: A coherent qubit control system for trapped-ion quantum computers

This is firmware and software designed for a Zynq UltraScale+ RFSoC chip made by Xilinx, specifically targeted to laser-based individual addressing of trapped ion qubits via a multi-channel AOM. The design features 8 dual-tone outputs with frequencies up to 409 MHz that can be controlled statically or dynamically via on-chip cubic spline interpolation engines that allow one to generate sequences of output waveforms with fast modulation of frequency, phase, amplitude, and z-rotations that are smooth/discrete and can run simultaneously across all parameters/tones. It also features global phase alignment on all tones regardless of frequency and the ability to return to a known phase/frequency at any later time on a per-tone basis without the need for manual bookkeeping. Acoustic and optical cross-talk can also be destructively canceled by adding neighboring outputs with variable amplitude/phase/delay. Each tone can be optionally frequency locked to an external RF source. SAND2020-12703 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Lobser, Daniel↗
DOE OSTI2023

Insensitivity to propagation timing in a preview-enabled wind turbine control experiment

Lidar scanners are capable of taking measurements of a wind field upstream of a wind turbine. The wind turbine controller can use these measurements as a “preview” of future disturbances impacting the turbine. Such preview-enabled (or feedforward) controllers show superior performance to standard wind turbine control configurations based purely on a feedback architecture. To capitalize on the performance improvements that preview wind measurements can provide, feedforward control actions should be timed to coincide with the arrival of the wind field at the wind turbine location. However, the time of propagation of the wind field between the lidar measurement location and the wind turbine is not perfectly known. Moreover, the best time to take feedforward control action may not perfectly coincide with the true arrival time of the wind disturbance. This contribution presents results from an experiment where preview-enabled model predictive control was deployed on a fully-actuated, scaled model wind turbine operating in a wind tunnel testbed. In the study, we investigate the sensitivity of the controller performance to the assumed propagation delay using a range of wind input sequences. We find that the preview-enabled controller outperforms the feedback only case across a wide range of assumed propagation delays, demonstrating a level of robustness to the time alignment of the incoming disturbances.

17 WIND ENERGY↗
NASA NTRS1993

Generating local addresses and communication sets for data-parallel programs

Generating local addresses and communication sets is an important issue in distributed-memory implementations of data-parallel languages such as High Performance FORTRAN. We show that, for an array A affinely aligned to a template that is distributed across p processors with a cyclic(k) distribution and a computation involving the regular section A(l:h:s), the local memory access sequence for any processor is characterized by a finite state machine of at most k states. We present fast algorithms for computing the essential information about these state machines, and extend the framework to handle multidimensional arrays. We also show how to generate communication sets using the state machine approach. Performance results show that this solution requires very little run-time overhead and acceptable preprocessing time.

Chatterjee, Siddhartha↗
NASA NTRS2002

Protein Kinase Classification with 2866 Hidden Markov Models and One Support Vector Machine

The main application considered in this paper is predicting true kinases from randomly permuted kinases that share the same length and amino acid distributions as the true kinases. Numerous methods already exist for this classification task, such as HMMs, motif-matchers, and sequence comparison algorithms. We build on some of these efforts by creating a vector from the output of thousands of structurally based HMMs, created offline with Pfam-A seed alignments using SAM-T99, which then must be combined into an overall classification for the protein. Then we use a Support Vector Machine for classifying this large ensemble Pfam-Vector, with a polynomial and chisquared kernel. In particular, the chi-squared kernel SVM performs better than the HMMs and better than the BLAST pairwise comparisons, when predicting true from false kinases in some respects, but no one algorithm is best for all purposes or in all instances so we consider the particular strengths and weaknesses of each.

Weber, Ryan↗
NASA NTRS1995

Spin-Orbit Interaction in Neutron Star/Main Sequence Binaries and Implications for Pulsar Timing

The spin-induced quadrupole moment of a rapidly rotating star changes the orbital dynamics in a binary system, giving rise to advance (or regression) of periastron and precession of the orbital plane. We show that these effects are important in the recently discovered radio pulsar/mail sequence star binary system PSR J0045-7319, and reliably account for the observed peculiar timing residuals. Precise measurements of the apsidal motion and orbital plane precession can yield valuable information on the internal structure and rotation of the star. The detection of orbital precession implies that the spin of the companion star is not aligned with the orbital angular momentum, and suggests that the supernova gave the pulsar a kick out of the original orbital plane. Excitations of g-mode oscillations near periastron (the dynamical tide) can induce measurable changes in the orbital period and eccentricity at each passage for this system. We also discuss the spin-orbit coupling effects for the accreting X-ray pulsars and the other know radio pulsar/main sequence binary, PSR B1259-63.

neutron stars↗
DOE OSTI2021

Deformation and fracture behavior of a laser powder bed fusion processed stainless steel: In situ synchrotron x-ray computed microtomography study

Tensile plastic deformation and fracture behavior of a laser powder bed fusion processed 316L stainless steel alloy was investigated in situ using high-resolution synchrotron x-ray computed microtomography (sXCT). Three different cases were studied: (1) specimen A1, near full-density with initial porosity of 0.04%, (2) specimen B1, initial lack-of-fusion (LOF) porosity of about 3% with the major axis of defects aligned nearly perpendicular to the tensile loading direction (LD), and (3) specimen B, similar to B1 but with the major axis of LOF defects aligned nearly parallel to LD. The effects of type, density, and orientation of defects in as-printed samples on plastic deformation and failure modes were studied by analyzing sXCT image sequences and quantitative defect properties. Specifically, the evolutions of porosity, size, aspect ratio, and angle of gas pores and LOF defects were characterized as a function of applied strain. Moreover, interactions between as-printed defects and deformation-induced crack propagation were investigated. The tensile behavior of specimen A1 was comparable to that of a commercial wrought plate. Furthermore, the quantitative in-situ sXCT results showed a void-growth phenomenon in A1 but without noticeable coalescence, resulting in a ductile cup-cone failure. Specimen B1 showed damage-driven brittle failure with limited plasticity due to early and rapid propagation of open voids. On the other hand, specimen B, with a similar amount of LOF defects as B1, showed deceivingly strong and ductile tensile behavior similar to A1 without any major crack propagations due to the favorable orientation relationship between LOF defects and the LD.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Diagnosing the representation of surface and layered soil moisture in Earth system models

Surface soil moisture (mrsos) and vertically integrated soil moisture (mrsol) over the top 10 cm should, by definition, be physically consistent in Earth System Models (ESMs). However, an evaluation of nine CMIP6 models reveals substantial inconsistencies: in some models, mrsos and integrated mrsol agree globally; in others, they align only in specific regions; and in a few, they diverge across all grid cells. These discrepancies arise from a combination of factors, including metadata errors, inconsistent variable definitions, or diagnostic sequencing within the model. We demonstrate how such issues can lead to significant biases, even when both variables are present and seemingly well-defined. As model complexity increases and multi-model comparisons become more common, assumptions about variable equivalence may lead to flawed conclusions. This study highlights the need for routine consistency checks, improved metadata standards, and community-wide practices that ensure reliability of derived variables across ESM outputs, particularly in preparation for CMIP7.

Earth system models↗
DOE OSTI2021

Development of an inexpensive matrix-assisted laser desorption—time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize

Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety contained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.

dereplication↗
NASA NTRS2019

KELT-24b: A 5M(J) Planet on a 5.6 day Well-aligned Orbit around the Young V=8.3 F-star HD 93148

We present the discovery of KELT-24 b, a massive hot Jupiter orbiting a bright (V=8.3 mag, K=7.2 mag) young F-star with a period of 5.6 days. The host star, KELT-24 (HD 93148), has a Teff=-+65094950K, a mass of M*=+1.4600.0590.055Me, a radius of R*=1.506±0.022Re, and an age of +0.780.420.61Gyr. Its planetary companion (KELT-24 b) has a radius of RP=1.272±0.021RJ and a mass of MP=-+5.180.220.21MJ, and from Doppler tomographic observations, we find that the planet’s orbit is well aligned to its host star’s projected spin axis (l=-+2.63.65.1). The young age estimated for KELT-24 suggests that it only recently started to evolve from the zero-age main sequence. KELT-24 is the brightest star known to host a transiting giant planet with a period between 5 and 10 days. Although the circularization timescale is much longer than the age of the system, we do not detect a large eccentricity or significant misalignment that is expected from dynamical migration. The brightness of its host star and its moderate surface gravity make KELT-24b an intriguing target for detailed atmospheric characterization through spectroscopic emission measurements since it would bridge the current literature results that have primarily focused on lower mass hot Jupiters and a few brown dwarfs.

Transit photometry↗
DOE OSTI2020

Probing the Consequences of Cubic Particle Shape and Applied Field on Colloidal Crystal Engineering with DNA

Abstract In a magnetic field, cubic Fe 3 O 4 nanoparticles exhibit assembly behavior that is a consequence of a competition between magnetic dipole–dipole and ligand interactions. In most cases, the interactions between short hydrophobic ligands dominate and dictate assembly outcome. To better tune the face‐to‐face interactions, cubic Fe 3 O 4 nanoparticles were functionalized with DNA. Their assembly behaviors were investigated both with and without an applied magnetic field. Upon application of a field, the tilted orientation of cubes, enabled by the flexible DNA ligand shell, led to an unexpected crystallographic alignment of the entire superlattice, as opposed to just the individual particles, along the field direction as revealed by small and wide‐angle X‐ray scattering. This observation is dependent upon DNA length and sequence and cube dimensions. Taken together, these studies show how combining physical and chemical control can expand the possibilities of crystal engineering with DNA.

Urbach, Zachary J.↗
NASA NTRS1986

A systolic architecture for the correlation and accumulation of digital sequences

A fully systolic architecture for the implementation of digital sequence correlator/accumulators is described. These devices consist of a two-dimensional array of processing elements that are conceived for efficient fabrication in Very Large Scale Integrated (VLSI) circuits. A custom VLSI chip that was implemented using these concepts is described. The chip, which contains a four-lag three-level sequence correlator and four bits of accumulation with overflow detection, was designed using the Integrated UNIX-Based Computer Aided Design (CAD) System. Applications of such devices include the synchronization of coded telemetry data, alignment of both real time and non-real time Very Large Baseline Interferometry (VLBI) signals, and the implementation of digital filters and processes of many types.

Deutsch, L. J.↗
DOE OSTI2026

Small Signaling Peptides in Sorghum bicolor : Integrating Phylogeny and Gene Expression to Characterize Roles in Stem Development

Small signaling peptides (SSPs) are important regulators of plant growth, development, and responses to biotic and abiotic stress, yet their role in the C4 grass Sorghum bicolor is largely uncharacterized. To help fill this knowledge gap, 219 sorghum genes that encode SSPs were identified based on SSP sequences previously identified in Arabidopsis thaliana, Zea mays, Oryza sativa, Triticum aestivum , and Brachypodium distachyon . The 219 sorghum SSP-encoding genes were assigned to 19 gene families, analyzed for the presence of motifs, and aligned with genes that encode SSPs in other plants using phylogenetic analysis. Sorghum genes in 12 of the 19 SSP gene families had not been previously characterized. Expression of the 219 SSP-encoding genes in sorghum organs, during stem development, and in stem tissues and cell types revealed distinct spatial, temporal, and developmental patterns of expression. Genes associated with the SbCEP and SbRGF families were preferentially expressed in roots, whereas SbEPF genes were expressed in stem epidermal and pith parenchyma cells and panicles. The expression of genes during bioenergy sorghum stem growth and development was investigated because stems account for ~80% of harvested biomass and serve as conduits for water and nutrient transport between leaves and roots. During stem development, 28 SSP genes in several families ( CLE, EPF, CEP, GASS, PSY, ES, PSK, CAPE, POE ) were expressed at higher levels in zones of cell proliferation. For example, the TDIF homologs SbCLE41 and SbCLE42 were expressed at high levels in nascent stem nodes where they may regulate vascular bundle cambial activity and cell differentiation. A different set of 15 genes in the CIF, POE, CAPE, PSY, CEP, RALF , and CLE families were expressed at higher levels in zones of stem tissue differentiation highlighted by elevated expression of five SbRALFR s in the stem nodal plexus. Cell type–specific expression of many sorghum genes that encode SSPs was observed in fully elongated internodes indicating gene expression is regulated with high spatial resolution. Overall, the results provide a foundation of information for analysis of SSP function in sorghum that can be integrated with knowledge of sorghum gene regulatory networks to modulate traits important for production of sorghum crops.

bioenergy sorghum↗
DOE OSTI2024

OrthoPhyl—streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales

Abstract There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large-scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity-spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use cases: E. coli/Shigella, Brucella/Ochrobactrum and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Determination of the spins and parities for the 0$^{+}_{4}$ and 0$^{+}_{5}$ states in 100 Zr

Here, two 0 + states at 1294.5 and 1774.0 keV, together with three 2 + and one 4 + levels, were identified or unambiguously spin-parity assigned for the first time in 100 Zr utilizing γ-ray spectroscopy and γ–γ angular correlation techniques with the Gammasphere spectrometer, following the β – decay of neutron-rich, mass-separated 100,100m Y isotopes. Comparisons with recent Monte Carlo shell-model calculations indicate that these two states are candidates for the bandhead of a sequence in a shape-coexisting spherical minimum predicted to be located around ≈1500 keV. According to the measured relative B(E2) relative transition probabilities, the 0$^+_5$ state exhibits decay properties which more closely align with those predicted for a spherical shape, while the 0$^+_4$ level is suggested to be associated with a weakly deformed shape similar to one related to the 0$^+_2$ state.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Enter the AHU (36th Chamber of ASHRAE): A Multi-site Field Study of ASHRAE G36

Despite being recognized as the best practice for advanced building controls, ASHRAE Guideline 36 (G36) has seen slow adoption in retrofit cases. Decisionmakers lack credible field evidence to justify the time and person-power investment. Most prior analyses have relied on software simulations, which overlook implementation challenges and fail to persuade owners to move from models to real-world deployment. This paper presents a multi-site field study of G36 performance, drawing on measured results from 17 projects across diverse building types and climate zones. The analysis disaggregates outcomes by the most widely adopted air handling unit (AHU) based G36 strategies, including trim-and-respond approaches to supply air temperature (SAT) and duct static pressure (DSP) reset, and economizer controls. Results for controls re programming implementations are encouraging, with HVAC savings ranging from 2% - 49%, with a median of 18%. The range aligns with simulation study findings showing 1% - 46% savings through these three strategies. These findings show that even without capital investment in control infrastructure upgrades, existing building owners are reaping significant benefits from updating HVAC sequences of operation to industry best-practice solutions. The results give practitioners and decisionmakers a reference point on what to expect, which strategies deliver, and how field performance may compare to simulation.

Deshpande, Reva↗
DOE OSTI2024

Determination of the spins and parities for the $0^+_4$ and $0^+_5$ states in $^{100}Zr$

Two 0 + states at 1294.5 and 1774.0 keV, together with three 2 + and one 4 + levels, were identified or unambiguously spin-parity assigned for the first time in 100 Zr utilizing γ-ray spectroscopy and γ-γ angular correlation techniques with the Gammasphere spectrometer, following the β - decay of neutron-rich, mass separated 100,100m Y isotopes. Comparisons with recent Monte Carlo Shell-Model (MCSM) calculations indicate that these two states are candidates for the bandhead of a sequence in a shape-coexisting spherical minimum predicted to be located around ≈1500 keV. According to the measured relative B(E2) relative transition probabilities, the 0+ 5 state exhibits decay properties which more closely align with those predicted for a spherical shape, while the $0^+_4$ level is suggested to be associated with a weakly-deformed shape similar to one related to the $0^+_2$ state.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Determination of the spins and parities for the $0$$^{+}_{4}$ and $0$$^{+}_{5}$ states in 100 Zr

Two 0 + states at 1294.5 and 1774.0 keV, together with three 2 + and one 4 + levels, were identified or unambiguously spin-parity assigned for the first time in 100 Zr utilizing γ-ray spectroscopy and γ-γ angular correlation techniques with the Gammasphere spectrometer, following the β¯ decay of neutron-rich, mass separated 100,100m Y isotopes. Comparisons with recent Monte Carlo Shell-Model (MCSM) calculations indicate that these two states are candidates for the bandhead of a sequence in a shape-coexisting spherical minimum predicted to be located around ≈1500 keV. According to the measured relative B(E2) relative transition probabilities, the $0$$^{+}_{5}$ state exhibits decay properties which more closely align with those predicted for a spherical shape, while the $0$$^{+}_{4}$ level is suggested to be associated with a weakly-deformed shape similar to one related to the $0$$^{+}_{2}$ state.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1991

Fiber optic phase stepping system for interferometry

A closed loop phase control system using an all-fiber optical configuration has been developed for use in phase-stepping interferometry. This system drives the relative phase of two interfering beams through a sequence of pi/2 rad increments so that the initial relative phase of these beams can be determined. This phase-stepping system uses optical fibers to provide spatially uniform phase steps from a flexible, easily aligned optical configuration. In addition, this system uses phase feedback to eliminate phase modulator errors and to compensate for phase drifts caused by environmental disturbances.

Mercer, Carolyn R.↗