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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 1,189 records · Page 66
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Effective Ion Mobility Calculations for Macromolecules by Scattering off Electron Clouds

Broad commercialization and increasing resolving power of ion mobility spectrometry/mass spectrometry (IMS/MS) platforms has engendered an explosion of IMS applications to structural characterization of gas-phase biomolecules. That has renewed interest in more accurate and rapid ion mobility calculations needed to elicit ion geometries from the measurements. An approach based on scattering off electron density isosurfaces (SEDI) that mirrors the physics of molecular collisions was proven superior to the common methods involving atomic coordinates a decade ago, but has remained impractical for large ions because of extreme computational demands. Here, we accelerate SEDI by up to ~500 times using the fragment molecular orbital (FMO) approach for surface generation and the multiplexed scattering algorithm in conjunction with the new grid extrapolation procedure for cross section evaluations. Parallelization of the code on a supercomputer has produced major further speed gains, allowing SEDI calculations for proteins (defined by over a million surface points) with the precision of <0.1% in one minute. Initial tests reveal the anticipated dependences of mobility on the ion charge state and lower cross sections in view of reduced surface roughness. Present developments are expected to lead to broad application of SEDI in IMS studies of macromolecules, enabling more accurate and reliable structural assignments.

Alexeev, Yuri↗
DOE OSTI2014

Photoionization mass spectrometric measurements of initial reaction pathways in low-temperature oxidation of 2,5-dimethylhexane

The product formation from R + O 2 reactions relevant to low-temperature autoignition chemistry was studied for 2,5-dimethylhexane, a symmetrically branched octane isomer, at 550 and 650 K using Cl-atom initiated oxidation and multiplexed photoionization mass spectrometry (MPIMS). The interpretation of time- and photon-energy-resolved mass spectra led to three specific results important to characterizing the initial oxidation steps: (1) quantified isomer-resolved branching ratios for HO 2 + alkene channels; (2) 2,2,5,5-tetramethyltetrahydrofuran is formed in substantial yield from addition of O 2 to tertiary 2,5-dimethylhex-2-yl followed by isomerization of the resulting ROO adduct to tertiary hydroperoxyalkyl (QOOH) and exhibits a positive dependence on temperature over the range covered leading to a higher flux relative to aggregate cyclic ether yield. The higher relative flux is explained by a 1,5-hydrogen atom shift reaction that converts the initial primary alkyl radical (2,5-dimethylhex-1-yl) to the tertiary alkyl radical 2,5-dimethylhex-2-yl, providing an additional source of tertiary alkyl radicals. Furthermore, quantum-chemical and master-equation calculations of the unimolecular decomposition of the primary alkyl radical reveal that isomerization to the tertiary alkyl radical is the most favorable pathway, and is favored over O 2 -addition at 650 K under the conditions herein. The isomerization pathway to tertiary alkyl radicals therefore contributes an additional mechanism to 2,2,5,5-tetramethyltetrahydrofuran formation; (3) carbonyl species (acetone, propanal, and methylpropanal) consistent with β-scission of QOOH radicals were formed in significant yield, indicating unimolecular QOOH decomposition into carbonyl + alkene + OH.

2,2,5,5-tetramethyl-tetrahydrofuran↗
DOE OSTI2015

VUV Photoionization Cross Sections of HO 2 , H 2 O 2 , and H 2 CO

The absolute vacuum ultraviolet (VUV) photoionization spectra of the hydroperoxyl radical (HO2), hydrogen peroxide (H 2 O 2 ), and formaldehyde (H2CO) have been measured from their first ionization thresholds to 12.008 eV. HO 2 , H 2 O 2 , and H 2 CO were generated from the oxidation of methanol initiated by pulsed-laser-photolysis of Cl 2 in a low-pressure slow flow reactor. Reactants, intermediates, and products were detected by time-resolved multiplexed synchrotron photoionization mass spectrometry. Absolute concentrations were obtained from the time-dependent photoion signals by modeling the kinetics of the methanol oxidation chemistry. Photoionization cross sections were determined at several photon energies relative to the cross section of methanol, which was in turn determined relative to that of propene. These measurements were used to place relative photoionization spectra of HO 2 , H 2 O 2 , and H 2 CO on an absolute scale, resulting in absolute photoionization spectra.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Hyperbolic spoof plasmonic metasurfaces

Hyperbolic metasurfaces have recently emerged as a new research frontier because of the unprecedented capabilities to manipulate surface plasmon polaritons (SPPs) and many potential applications. But, thus far, the existence of hyperbolic metasurfaces has neither been observed nor predicted at low frequencies because noble metals cannot support SPPs at longer wavelengths. Here, we propose and experimentally demonstrate spoof plasmonic metasurfaces with a hyperbolic dispersion, where the spoof SPPs propagate on complementary H-shaped, perfectly conducting surfaces at low frequencies. Therefore, non-divergent diffractions, negative refraction and dispersion-dependent spin-momentum locking are observed as the spoof SPPs travel over the hyperbolic spoof plasmonic metasurfaces (HSPMs). The HSPMs provide fundamental new platforms to explore the propagation and spin of spoof SPPs. They show great capabilities for designing advanced surface wave devices such as spatial multiplexers, focusing and imaging devices, planar hyperlenses, and dispersion-dependent directional couplers, at both microwave and terahertz frequencies.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes

The structure and biological properties of RNAs are a function of changing cellular conditions, but comprehensive, simultaneous investigation of the effect of multiple interacting environmental variables is not easily achieved. We have developed an efficient, high-throughput method to characterize RNA structure and thermodynamic stability as a function of multiplexed solution conditions using Förster resonance energy transfer (FRET). In a single FRET experiment using conventional quantitative PCR instrumentation, 19,400 conditions of MgCl 2 , ligand and temperature are analysed to generate detailed empirical conformational and stability landscapes of the cyclic diguanylate (c-di-GMP) riboswitch. This method allows rapid comparison of RNA structure modulation by cognate and non-cognate ligands. Landscape analysis reveals that kanamycin B stabilizes a non-native, idiosyncratic conformation of the riboswitch that inhibits c-di-GMP binding. Our research demonstrates that allosteric control of folding, rather than direct competition with cognate effectors, is a viable approach for pharmacologically targeting riboswitches and other structured RNA molecules.

biological sciences↗
DOE OSTI2015

Engineering an allosteric transcription factor to respond to new ligands

Genetic regulatory proteins inducible by small molecules are useful synthetic biology tools as sensors and switches. Bacterial allosteric transcription factors (aTFs) are a major class of regulatory proteins, but few aTFs have been redesigned to respond to new effectors beyond natural aTF-inducer pairs. Altering inducer specificity in these proteins is difficult because substitutions that affect inducer binding may also disrupt allostery. In this paper, we engineered an aTF, the Escherichia coli lac repressor, LacI, to respond to one of four new inducer molecules: fucose, gentiobiose, lactitol and sucralose. Using computational protein design, single-residue saturation mutagenesis or random mutagenesis, along with multiplex assembly, we identified new variants comparable in specificity and induction to wild-type LacI with its inducer, isopropyl β-D-1-thiogalactopyranoside (IPTG). Finally, the ability to create designer aTFs will enable applications including dynamic control of cell metabolism, cell biology and synthetic gene circuits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data

Data-independent acquisition (DIA) is an emerging mass spectrometry (MS)-based technique for unbiased and reproducible measurement of protein mixtures. DIA tandem mass spectrometry spectra are often highly multiplexed, containing product ions from multiple cofragmenting precursors. Detecting peptides directly from DIA data is therefore challenging; most DIA data analyses require spectral libraries. Here we present PECECAN (http://pecan.maccosslab.org), a library-free, peptide-centric tool that robustly and accurately detects peptides directly from DIA data. PECECAN reports evidence of detection based on product ion scoring, which enables detection of low-abundance analytes with poor precursor ion signal. We demonstrate the chromatographic peak picking accuracy and peptide detection capability of PECECAN, and we further validate its detection with data-dependent acquisition and targeted analyses. Lastly, we used PECECAN to build a plasma proteome library from DIA data and to query known sequence variants.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2013

Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications

Reversible modifications on cysteine thiols play a significant role in redox signaling and regulation. A number of reversible redox modifications, including disulfide formation, S-nitrosylation, and S-glutathionylation, have been recognized for their significance in various physiological and pathological processes. Here we describe in detail a resin-assisted thiol-affinity enrichment protocol for both biochemical and proteomics applications. This protocol serves as a general approach for specific isolation of thiol-containing proteins or peptides derived from reversible redox-modified proteins. This approach utilizes thiol-affinity resins to directly capture thiol-containing proteins or peptides through a disulfide exchange reaction followed by on-resin protein digestion and on-resin multiplexed isobaric labeling to facilitate LC-MS/MS based quantitative site-specific analysis of redox modifications. The overall approach requires a much simpler workflow with increased specificity compared to the commonly used biotin switch technique. By coupling different selective reduction strategies, the resin-assisted approach provides the researcher with a useful tool capable of enriching different types of reversible modifications on protein thiols. Procedures for selective enrichment and analyses of S-nitrosylation and total reversible cysteine oxidation are presented to demonstrate the utility of this general strategy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Laser particles with omnidirectional emission for cell tracking

The ability to track individual cells in space over time is crucial to analyzing heterogeneous cell populations. Recently, microlaser particles have emerged as unique optical probes for massively multiplexed single-cell tagging. However, the microlaser far-field emission is inherently direction-dependent, which causes strong intensity fluctuations when the orientation of the particle varies randomly inside cells. Here, we demonstrate a general solution based on the incorporation of nanoscale light scatterers into microlasers. Two schemes are developed by introducing either boundary defects or a scattering layer into microdisk lasers. The resulting laser output is omnidirectional, with the minimum-to-maximum ratio of the angle-dependent intensity improving from 0.007 (-24 dB) to > 0.23 (-6 dB). After transfer into live cells in vitro, the omnidirectional laser particles within moving cells could be tracked continuously with high signal-to-noise ratios for 2 h, while conventional microlasers exhibited frequent signal loss causing tracking failure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

High-performance and scalable on-chip digital Fourier transform spectroscopy

Abstract On-chip spectrometers have the potential to offer dramatic size, weight, and power advantages over conventional benchtop instruments for many applications such as spectroscopic sensing, optical network performance monitoring, hyperspectral imaging, and radio-frequency spectrum analysis. Existing on-chip spectrometer designs, however, are limited in spectral channel count and signal-to-noise ratio. Here we demonstrate a transformative on-chip digital Fourier transform spectrometer that acquires high-resolution spectra via time-domain modulation of a reconfigurable Mach-Zehnder interferometer. The device, fabricated and packaged using industry-standard silicon photonics technology, claims the multiplex advantage to dramatically boost the signal-to-noise ratio and unprecedented scalability capable of addressing exponentially increasing numbers of spectral channels. We further explore and implement machine learning regularization techniques to spectrum reconstruction. Using an ‘elastic-D 1 ’ regularized regression method that we develop, we achieved significant noise suppression for both broad (>600 GHz) and narrow (<25 GHz) spectral features, as well as spectral resolution enhancement beyond the classical Rayleigh criterion.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

Abstract High titer, rate, yield (TRY), and scalability are challenging metrics to achieve due to trade-offs between carbon use for growth and production. To achieve these metrics, we take the minimal cut set (MCS) approach that predicts metabolic reactions for elimination to couple metabolite production strongly with growth. We compute MCS solution-sets for a non-native product indigoidine, a sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From the 63 solution-sets, our omics guided process identifies one experimentally feasible solution requiring 14 simultaneous reaction interventions. We implement a total of 14 genes knockdowns using multiplex-CRISPRi. MCS-based solution shifts production from stationary to exponential phase. We achieve 25.6 g/L, 0.22 g/l/h, and ~50% maximum theoretical yield (0.33 g indigoidine/g glucose). These phenotypes are maintained from batch to fed-batch mode, and across scales (100-ml shake flasks, 250-ml ambr®, and 2-L bioreactors).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts

Cell-free systems using crude cell extracts present appealing opportunities for designing biosynthetic pathways and enabling sustainable chemical synthesis. However, the lack of tools to effectively manipulate the underlying host metabolism in vitro limits the potential of these systems. Here, we create an integrated framework to address this gap that leverages cell extracts from host strains genetically rewired by multiplexed CRISPR-dCas9 modulation and other metabolic engineering techniques. As a model, we explore conversion of glucose to 2,3-butanediol in extracts from flux-enhanced Saccharomyces cerevisiae strains. We show that cellular flux rewiring in several strains of S. cerevisiae combined with systematic optimization of the cell-free reaction environment significantly increases 2,3-butanediol titers and volumetric productivities, reaching productivities greater than 0.9 g/L-h. We then show the generalizability of the framework by improving cell-free itaconic acid and glycerol biosynthesis. Our coupled in vivo/in vitro metabolic engineering approach opens opportunities for synthetic biology prototyping efforts and cell-free biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A functional map of HIV-host interactions in primary human T cells

Human Immunodeficiency Virus (HIV) relies on host molecular machinery for replication. Systematic attempts to genetically or biochemically define these host factors have yielded hundreds of candidates, but few have been functionally validated in primary cells. Here, we target 426 genes previously implicated in the HIV lifecycle through protein interaction studies for CRISPR-Cas9-mediated knock-out in primary human CD4+ T cells in order to systematically assess their functional roles in HIV replication. We achieve efficient knockout (>50% of alleles) in 364 of the targeted genes and identify 86 candidate host factors that alter HIV infection. 47 of these factors validate by multiplex gene editing in independent donors, including 23 factors with restrictive activity. Both gene editing efficiencies and HIV-1 phenotypes are highly concordant among independent donors. Importantly, over half of these factors have not been previously described to play a functional role in HIV replication, providing numerous novel avenues for understanding HIV biology. These data further suggest that host-pathogen protein-protein interaction datasets offer an enriched source of candidates for functional host factor discovery and provide an improved understanding of the mechanics of HIV replication in primary T cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A compact cold-atom interferometer with a high data-rate grating magneto-optical trap and a photonic-integrated-circuit-compatible laser system

Abstract The extreme miniaturization of a cold-atom interferometer accelerometer requires the development of novel technologies and architectures for the interferometer subsystems. Here, we describe several component technologies and a laser system architecture to enable a path to such miniaturization. We developed a custom, compact titanium vacuum package containing a microfabricated grating chip for a tetrahedral grating magneto-optical trap (GMOT) using a single cooling beam. In addition, we designed a multi-channel photonic-integrated-circuit-compatible laser system implemented with a single seed laser and single sideband modulators in a time-multiplexed manner, reducing the number of optical channels connected to the sensor head. In a compact sensor head containing the vacuum package, sub-Doppler cooling in the GMOT produces 15 μK temperatures, and the GMOT can operate at a 20 Hz data rate. We validated the atomic coherence with Ramsey interferometry using microwave spectroscopy, then demonstrated a light-pulse atom interferometer in a gravimeter configuration for a 10 Hz measurement data rate and T = 0–4.5 ms interrogation time, resulting in Δ g / g = 2.0 × 10 −6 . This work represents a significant step towards deployable cold-atom inertial sensors under large amplitude motional dynamics.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Low cost and massively parallel force spectroscopy with fluid loading on a chip

Current approaches for single molecule force spectroscopy are typically constrained by low throughput and high instrumentation cost. Herein, a low-cost, high throughput technique is demonstrated using microfluidics for multiplexed mechanical manipulation of up to ~4000 individual molecules via molecular fluid loading on-a-chip (FLO-Chip). The FLO-Chip consists of serially connected microchannels with varying width, allowing for simultaneous testing at multiple loading rates. Molecular force measurements are demonstrated by dissociating Biotin-Streptavidin and Digoxigenin-AntiDigoxigenin interactions along with unzipping of double stranded DNA of varying sequence under different dynamic loading rates and solution conditions. Rupture force results under varying loading rates and solution conditions are in good agreement with prior studies, verifying a versatile approach for single molecule biophysics and molecular mechanobiology. FLO-Chip enables straightforward, rapid, low-cost, and portable mechanical testing of single molecules that can be implemented on a wide range of microscopes to broaden access and may enable new applications of molecular force spectroscopy.

42 ENGINEERING↗
DOE OSTI2023

Orthogonal luminescence lifetime encoding by intermetallic energy transfer in heterometallic rare-earth MOFs

Lifetime-encoded materials are particularly attractive as optical tags, however examples are rare and hindered in practical application by complex interrogation methods. Here, we demonstrate a design strategy towards multiplexed, lifetime-encoded tags via engineering intermetallic energy transfer in a family of heterometallic rare-earth metal-organic frameworks (MOFs). The MOFs are derived from a combination of a high-energy donor (Eu), a low-energy acceptor (Yb) and an optically inactive ion (Gd) with the 1,2,4,5 tetrakis(4-carboxyphenyl) benzene (TCPB) organic linker. Precise manipulation of the luminescence decay dynamics over a wide microsecond regime is achieved via control over metal distribution in these systems. Demonstration of this platform’s relevance as a tag is attained via a dynamic double encoding method that uses the braille alphabet, and by incorporation into photocurable inks patterned on glass and interrogated via digital high-speed imaging. This study reveals true orthogonality in encoding using independently variable lifetime and composition, and highlights the utility of this design strategy, combining facile synthesis and interrogation with complex optical properties.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology

Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell Spatially resolved Metabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil, and endometrium tissues, respectively. The scSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet’s ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling

Abstract Metabolite identification in non-targeted mass spectrometry-based metabolomics remains a major challenge due to limited spectral library coverage and difficulties in predicting metabolite fragmentation patterns. Here, we introduce Multiplexed Chemical Metabolomics (MCheM), which employs orthogonal post-column derivatization reactions integrated into a unified mass spectrometry data framework. MCheM generates orthogonal structural information that substantially improves metabolite annotation through in silico spectrum matching and open-modification searches, offering a powerful new toolbox for the structure elucidation of unknown metabolites at scale.

Science & Technology - Other Topics↗