Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Base Sequence”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,477 records · Page 82
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Biogenic carbon capture at pulp mills via sodium spiking and oxy-fuel calcination

Over 13 million metric tons of biogenic carbon dioxide (CO 2 ) are mineralized yearly in United States (US) pulp mill recovery boilers as molten sodium carbonate. The mineralized CO 2 is released downstream in the rotary lime kiln where it can be captured at a relatively low cost for permanent sequestration. The use of biocarbon and bioenergy at pulp mills enables the possibility for atmospheric carbon removal when biogenic CO2 is captured and sequestered. We demonstrate the feasibility of capturing biogenic CO 2 via sodium spiking coupled with oxy-fuel calcination in the rotary lime kiln at existing kraft pulp mills. Sodium (Na) spiking elevates the Na ion loading in the kraft chemical looping process by replacing chlorine-based bleaching with a highly alkaline bleaching sequence. Chemical pulping processes are modeled and simulated to understand the technical limits of implementing sodium spiking in existing pulp mills. Each 1 % of sodium added to the bleaching operations increases the rate of CO 2 mineralization by 4 %, and the maximum increase in sodium content in the kraft process is 9 %. Without sodium spiking, estimated CO 2 capture costs are $131 and $107/mt CO 2 for air and oxy-fuel combustion, respectively. With the implementation of sodium spiking, the cost of CO 2 captured decreases by 27 % and 31 %, showing costs of $96 and $74/mt CO 2 for air and oxy-fuel combustion, respectively. Oxy-fuel combustion reduces the costs of CO 2 capture compared to air combustion, but merged deployment with sodium spiking seems to be the most cost-effective pathway to integrate carbon capture.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

MR-OPERA: A Multicenter/Multivendor Validation of Magnetic Resonance Imaging–Only Prostate Treatment Planning Using Synthetic Computed Tomography Images

Purpose: To validate the dosimetric accuracy and clinical robustness of a commercially available software for magnetic resonance (MR) to synthetic computed tomography (sCT) conversion, in an MR imaging–only workflow for 170 prostate cancer patients. Methods and Materials: The 4 participating centers had MriPlanner (Spectronic Medical), an atlas-based sCT generation software, installed as a cloud-based service. A T2-weighted MR sequence, covering the body contour, was added to the clinical protocol. The MR images were sent from the MR scanner workstation to the MriPlanner platform. The sCT was automatically returned to the treatment planning system. Four MR scanners and 2 magnetic field strengths were included in the study. For each patient, a CT-treatment plan was created and approved according to clinical practice. The sCT was rigidly registered to the CT, and the clinical treatment plan was recalculated on the sCT. The dose distributions from the CT plan and the sCT plan were compared according to a set of dose-volume histogram parameters and gamma evaluation. Treatment techniques included volumetric modulated arc therapy, intensity modulated radiation therapy, and conventional treatment using 2 treatment planning systems and different dose calculation algorithms. Results: The overall (multicenter/multivendor) mean dose differences between sCT and CT dose distributions were below 0.3% for all evaluated organs and targets. Gamma evaluation showed a mean pass rate of 99.12% (0.63%, 1 SD) in the complete body volume and 99.97% (0.13%, 1 SD) in the planning target volume using a 2%/2-mm global gamma criteria. Conclusions: Results of the study show that the sCT conversion method can be used clinically, with minimal differences between sCT and CT dose distributions for target and relevant organs at risk. The small differences seen are consistent between centers, indicating that an MR imaging–only workflow using MriPlanner is robust for a variety of field strengths, vendors, and treatment techniques.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Ancestral archaea expanded the genetic code with pyrrolysine

The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNA Pyl ) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNA Pyl pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNA Pyl and reveal the emergence of tRNA Pyl sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNA Pyl species with the more common G73-containing tRNA Pyl will enable future efforts to engineer PylRS systems for further genetic code expansion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Distinct evolutionary lineages of Schistocephalus parasites infecting co-occurring sculpin and stickleback fishes in Alaska

Sculpins (coastrange and slimy) and sticklebacks (ninespine and threespine) are widely distributed fishes cohabiting 2 south-central Alaskan lakes (Aleknagik and Iliamna), and all these species are parasitized by cryptic diphyllobothriidean cestodes in the genus Schistocephalus. The goal of this investigation was to test for host-specific parasitic relationships between sculpins and sticklebacks based upon morphological traits (segment counts) and sequence variation across the NADH1 gene. A total of 446 plerocercoids was examined. Large, significant differences in mean segment counts were found between cestodes in sculpin (mean = 112; standard deviation [S.D.] = 15) and stickleback (mean = 86; S.D. = 9) hosts within and between lakes. Nucleotide sequence divergence between parasites from sculpin and stickleback hosts was 20.5%, and Bayesian phylogenetic analysis recovered 2 well-supported clades of cestodes reflecting intermediate host family (i.e. sculpin, Cottidae vs stickleback, Gasterosteidae). Our findings point to the presence of a distinct lineage of cryptic Schistocephalus in sculpins from Aleknagik and Iliamna lakes that warrants further investigation to determine appropriate evolutionary and taxonomic recognition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Reproducing Natural Spider Silks' Copolymer Behavior in Synthetic Silk Mimics

Dragline silk from orb-weaving spiders is a copolymer of two large proteins, major ampullate spidroin 1 (MaSp1) and 2 (MaSp2). The ratio of these proteins is known to have a large variation across different species of orb-weaving spiders. NMR results from gland material of two different species of spiders, N. clavipes and A. aurantia, indicates that MaSp1 proteins are more easily formed into β-sheet nanostructures, while MaSp2 proteins form random coil and helical structures. To test if this behavior of natural silk proteins could be reproduced by recombinantly produced spider silk mimic protein, recombinant MaSp1/MaSp2 mixed fibers as well as chimeric silk fibers from MaSp1 and MaSp2 sequences in a single protein were produced based on the variable ratio and conserved motifs of MaSp1 and MaSp2 in native silk fiber. Mechanical properties, solid-state NMR, and XRD results of tested synthetic fibers indicate the differing roles of MaSp1 and MaSp2 in the fiber and verify the importance of postspin stretching treatment in helping the fiber to form the proper spatial structure.

An, Bo↗
DOE OSTI2017

Rational design of molecular crystals for enhanced charge transfer properties

Here, using solution based self-assembly, we contrast a three-dimensional co-crystal, where a [1]benzothieno[3,2-b][1]benzothiophene (BTBT) based donor and a tetracyanoquinodimethane (TCNQ) based acceptor leads to a mixed stacking sequence with pronounced intermolecular hybridization, with the donor–acceptor bilayer. Despite a comparable increase in conductivity, we observe a co-crystal with unique mechano-pyro-electric coupling properties.

Guan, Ying-Shi↗
DOE OSTI2026

High-throughput Single-Cell Proteomics and Transcriptomics from the Same Cells with a Nanoliter-Scale Spin-Transfer Approach

Single-cell multiomic platforms provide a comprehensive snapshot of cellular states and cell types by offering critical insights into the spatiotemporal regulation of biomolecular networks at a systems level, thereby defining the basis of multicellularity. Here, we introduce nanoSPINS, an advanced platform that enables high-throughput profiling and integrative analysis of the transcriptome and proteome from the same single cells using RNA sequencing and isobaric labeling LC-MS-based proteomics, respectively. NanoSPINS can efficiently transfer mRNA-containing droplets across two microarrays via a centrifugation-based approach, while proteins are retained on the initial platform. Benchmarking of nanoSPINS on two cell lines demonstrates its ability to generate global proteomic and transcriptomic profiles that align well with previously established methodologies/platforms. The incorporation of isobaric TMTpro labeling into this single-cell multiomics platform significantly enhances the throughput of single-cell proteomic analyses. Through the high-throughput quantification of the proteome and transcriptome, nanoSPINS not only facilitates the identification of molecular features at both mRNA and protein level but also provides larger sample sizes for improved statistical power in clustering and differential abundance. Given the broad applicability of single-cell multiomics in biological research and clinical settings, we believe nanoSPINS represents a powerful platform for the characterization of heterogeneous cell populations.

multi 'omics↗
DOE OSTI2012

Narrowing of the coherent population trapping resonance under zone pumping in cells with different characteristics of the wall coating

It is shown that when coherent population trapping (CPT) resonance is excited by a narrow laser beam, the presence of elastic collisions with the cell wall significantly affects the line shape of the CPT-resonance. We have constructed a theoretical model, which is based on averaging over the random Ramsey sequences of the atom dwell time in the beam and dark zones and takes into account the probability of elastic bounce of an atom from the wall.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex

The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup133 55–502 ) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup1332–1157. Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

AN AUTOMATIC DETECTION METHOD FOR EXTREME-ULTRAVIOLET DIMMINGS ASSOCIATED WITH SMALL-SCALE ERUPTION

Small-scale extreme-ultraviolet (EUV) dimming often surrounds sites of energy release in the quiet Sun. This paper describes a method for the automatic detection of these small-scale EUV dimmings using a feature-based classifier. The method is demonstrated using sequences of 171 Angstrom-Sign images taken by the STEREO/Extreme UltraViolet Imager (EUVI) on 2007 June 13 and by Solar Dynamics Observatory/Atmospheric Imaging Assembly on 2010 August 27. The feature identification relies on recognizing structure in sequences of space-time 171 Angstrom-Sign images using the Zernike moments of the images. The Zernike moments space-time slices with events and non-events are distinctive enough to be separated using a support vector machine (SVM) classifier. The SVM is trained using 150 events and 700 non-event space-time slices. We find a total of 1217 events in the EUVI images and 2064 events in the AIA images on the days studied. Most of the events are found between latitudes -35 Degree-Sign and +35 Degree-Sign . The sizes and expansion speeds of central dimming regions are extracted using a region grow algorithm. The histograms of the sizes in both EUVI and AIA follow a steep power law with slope of about -5. The AIA slope extends to smaller sizes before turning over. The mean velocity of 1325 dimming regions seen by AIA is found to be about 14 km s{sup -1}.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

White dwarf cosmochronology in the solar neighborhood

The study of the stellar formation history in the solar neighborhood is a powerful technique to recover information about the early stages and evolution of the Milky Way. We present a new method that consists of directly probing the formation history from the nearby stellar remnants. We rely on the volume complete sample of white dwarfs within 20 pc, where accurate cooling ages and masses have been determined. The well characterized initial-final mass relation is employed in order to recover the initial masses (1 ≲ M {sub initial}/M {sub ☉} ≲ 8) and total ages for the local degenerate sample. We correct for moderate biases that are necessary to transform our results to a global stellar formation rate, which can be compared to similar studies based on the properties of main-sequence stars in the solar neighborhood. Our method provides precise formation rates for all ages except in very recent times, and the results suggest an enhanced formation rate for the solar neighborhood in the last 5 Gyr compared to the range 5 < Age (Gyr) < 10. Furthermore, the observed total age of ∼10 Gyr for the oldest white dwarfs in the local sample is consistent with the early seminal studies that have determined the age of the Galactic disk from stellar remnants. The main shortcoming of our study is the small size of the local white dwarf sample. However, the presented technique can be applied to larger samples in the future.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Hamiltonian simulation in Zeno subspaces

Here, we investigate the quantum Zeno effect as a framework for designing and analyzing quantum algorithms for Hamiltonian simulation. We show that frequent projective measurements of an ancilla qubit register can be used to simulate quantum dynamics on a target qubit register with a circuit complexity similar to randomized approaches. The classical sampling overhead in the latter approaches is traded for ancilla qubit overhead in Zeno-based approaches. A second-order Zeno sequence is developed to improve scaling and implementations through unitary kicks are discussed. We derive rigorous error bounds that allow for identifying the associated circuit complexities for the first- and second-order Zeno sequences. We show that the circuits over the combined register can be identified as a subroutine commonly used in post-Trotter Hamiltonian simulation methods. We build on this observation to reveal connections between different Hamiltonian simulation algorithms.

Hamiltonian simulation↗
DOE OSTI2014

Constraining the neutrino magnetic dipole moment from white dwarf pulsations

Pulsating white dwarf stars can be used as astrophysical laboratories to constrain the properties of weakly interacting particles. Comparing the cooling rates of these stars with the expected values from theoretical models allows us to search for additional sources of cooling due to the emission of axions, neutralinos, or neutrinos with magnetic dipole moment. In this work, we derive an upper bound to the neutrino magnetic dipole moment (μ{sub ν}) using an estimate of the rate of period change of the pulsating DB white dwarf star PG 1351+489. We employ state-of-the-art evolutionary and pulsational codes which allow us to perform a detailed asteroseismological period fit based on fully DB white dwarf evolutionary sequences. Plasmon neutrino emission is the dominant cooling mechanism for this class of hot pulsating white dwarfs, and so it is the main contributor to the rate of change of period with time (Pidot) for the DBV class. Thus, the inclusion of an anomalous neutrino emission through a non-vanishing magnetic dipole moment in these sequences notably influences the evolutionary timescales, and also the expected pulsational properties of the DBV stars. By comparing the theoretical Pidot value with the rate of change of period with time of PG 1351+489, we assess the possible existence of additional cooling by neutrinos with magnetic dipole moment. Our models suggest the existence of some additional cooling in this pulsating DB white dwarf, consistent with a non-zero magnetic dipole moment with an upper limit of μ{sub ν} ∼< 10{sup -11} μ{sub B}. This bound is somewhat less restrictive than, but still compatible with, other limits inferred from the white dwarf luminosity function or from the color-magnitude diagram of the Globular cluster M5. Further improvements of the measurement of the rate of period change of the dominant pulsation mode of PG 1351+489 will be necessary to confirm our bound.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

A DYNAMICAL SIGNATURE OF MULTIPLE STELLAR POPULATIONS IN 47 TUCANAE

Based on the width of its main sequence, and an actual observed split when viewed through particular filters, it is widely accepted that 47 Tucanae contains multiple stellar populations. In this contribution, we divide the main sequence of 47 Tuc into four color groups, which presumably represent stars of various chemical compositions. The kinematic properties of each of these groups are explored via proper motions, and a strong signal emerges of differing proper-motion anisotropies with differing main-sequence color; the bluest main-sequence stars exhibit the largest proper-motion anisotropy which becomes undetectable for the reddest stars. In addition, the bluest stars are also the most centrally concentrated. A similar analysis for Small Magellanic Cloud stars, which are located in the background of 47 Tuc on our frames, yields none of the anisotropy exhibited by the 47 Tuc stars. We discuss implications of these results for possible formation scenarios of the various populations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

The relationship between the incidence of X-ray selected AGN in nearby galaxies & star-formation rate

ABSTRACT We present the identification and analysis of an X-ray selected AGN sample that lie within the local (z < 0.35) galaxy population. From a parent sample of 22 079 MPA-JHU (based on SDSS DR8) galaxies, we identified 917 galaxies with central, excess X-ray emission (from 3XMM-DR7) likely originating from an AGN. We measured the host galaxies’ star formation rates and classified them as either star-forming or quiescent based on their position relative to main sequence of star formation. Only 72 per cent of the X-ray selected sample were identified as AGN using BPT selection; this technique is much less effective in quiescent hosts, only identifying 50 per cent of the X-ray AGN. We also calculated the growth rates of the black holes powering these AGN in terms of their specific accretion rate (∝ LX/M*) and found quiescent galaxies, on average, accrete at a lower rate than star-forming galaxies. Finally, we measured the sensitivity function of 3XMM so we could correct for observational bias and construct probability distributions as a function of accretion rate. AGN were found in galaxies across the full range of star formation rates ($\log _{10} \, \mathrm{SFR/M_\odot \ yr^{-1}} = -3\ \mathrm{to}\ 2$) in both star-forming and quiescent galaxies. The incidence of AGN was enhanced by a factor 2 (at a 3.5σ significance) in star-forming galaxies compared to quiescent galaxies of equivalent stellar mass and redshift, but we also found a significant population of AGN hosted by quiescent galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data

In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and on-going oceanographic sequencing efforts. In Planet Microbe, each ‘omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same sample collection event, to provide a broader environmental context. This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Theory of topological defects and textures in two-dimensional quantum orders with spontaneous symmetry breaking

In this article, we consider two-dimensional (2d) quantum many-body systems with long-range orders, where the only gapless excitations in the spectrum are Goldstone modes of spontaneously broken continuous symmetries. To understand the interplay between classical long-range order of local order parameters and quantum order of long-range entanglement in the ground states, we study the topological point defects and textures of order parameters in such systems. We show that the universal properties of point defects and textures are determined by the remnant symmetry enriched topological order in the symmetry-breaking ground states with a nonfluctuating order parameter, and provide a classification for their properties based on the inflation-restriction exact sequence. We highlight a few phenomena revealed by our theory framework. First, in the absence of intrinsic topological orders, we show a connection between the symmetry properties of point defects and textures to deconfined quantum criticality. Second, when the symmetry-breaking ground state has intrinsic topological orders, we show that the point defects can permute different anyons when braided around. They can also obey projective fusion rules in the sense that multiple vortices can fuse into an Abelian anyon, a phenomenon for which we coin “defect fractionalization.” Finally, we provide a formula to compute the fractional statistics and fractional quantum numbers carried by textures (skyrmions) in Abelian topological orders.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

High-Power Clock Laser Spectrally Tailored for High-Fidelity Quantum State Engineering

Highly frequency-stable lasers are ubiquitous tools for optical-frequency metrology, precision interferometry, and quantum information science. While making a universally applicable laser is unrealistic, spectral noise can be tailored for specific applications. Here we report a high-power 698-nm clock laser with a maximum output of 4W and minimized frequency noise up to a few kHz Fourier frequency, together with long-term instability of 3.5 × 10 −17 at one to thousands of seconds. The laser-frequency noise is precisely characterized with atom-based spectral analysis that employs a pulse sequence designed to suppress sensitivity to intensity noise. This method provides universally applicable tunability of the spectral response and analysis of quantum sensors over a wide frequency range. With the optimized laser system characterized by this technique, we achieve an average single-qubit Clifford gate fidelity of up to 𝐹$^2_1$ = 0.999⁢64⁢(3) when simultaneously driving 3000 optical qubits with a homogeneous Rabi frequency ranging from 10 Hz to 1 kHz. This result represents the highest single optical-qubit-gate fidelity for a large number of atoms.

atomic gases↗