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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Meeting report for the 1st skin microbiota workshop, Boulder, CO, October 15-16, 2012

This report details the outcome of the 1st Skin Microbiota Workshop, Boulder, CO, held on October 15th-16th 2012. The workshop was arranged to bring Department of Defense personnel together with experts in microbial ecology, human skin physiology and anatomy, and computational techniques for interrogating the microbiome to define research frontiers at the intersection of these important areas. The workshop outlined a series of questions and created several working groups to address those questions, specifically to promote interdisciplinary activity and potential future collaboration. The US Army provided generous grant support and the meeting was organized and hosted by the University of Colorado at Boulder. A primary forward vision of the meeting was the importance of understanding skin microbial communities to improve the health and stealth of US Army warfighters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Development of models for predicting Torsade de Pointes cardiac arrhythmias using perceptron neural networks

Background: Blockage of some ion channels and in particular, the hERG (human Ether-a’-go-go-Related Gene) cardiac potassium channel delays cardiac repolarization and can induce arrhythmia. In some cases it leads to a potentially life-threatening arrhythmia known as Torsade de Pointes (TdP). Therefore recognizing drugs with TdP risk is essential. Candidate drugs that are determined not to cause cardiac ion channel blockage are more likely to pass successfully through clinical phases II and III trials (and preclinical work) and not be withdrawn even later from the marketplace due to cardiotoxic effects. The objective of the present study is to develop an SAR (Structure-Activity Relationship) model that can be used as an early screen for torsadogenic (causing TdP arrhythmias) potential in drug candidates. The method is performed using descriptors comprised of atomic NMR chemical shifts (13C and 15N NMR) and corresponding interatomic distances which are combined into a 3D abstract space matrix. The method is called 3D-SDAR (3-dimensional spectral data-activity relationship) and can be interrogated to identify molecular features responsible for the activity, which can in turn yield simplified hERG toxicophores. A dataset of 55 hERG potassium channel inhibitors collected from Kramer et al. consisting of 32 drugs with TdP risk and 23 with no TdP risk was used for training the 3D-SDAR model. Results: An artificial neural network (ANN) with multilayer perceptron was used to define collinearities among the independent 3D-SDAR features. A composite model from 200 random iterations with 25% of the molecules in each case yielded the following figures of merit: training, 99.2%; internal test sets, 66.7%; external (blind validation) test set, 68. 4%. In the external test set, 70.3% of positive TdP drugs were correctly predicted. Moreover, toxicophores were generated from TdP drugs. Conclusion: A 3D-SDAR was successfully used to build a predictive model for drug-induced torsadogenic and non-torsadogenic drugs based on 55 compounds. The model was tested in 38 external drugs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

The Perchlorate Reduction Genomic Island: Mechanisms and Pathways of Evolution by Horizontal Gene Transfer

Background: Perchlorate is a widely distributed anion that is toxic to humans, but serves as a valuable electron acceptor for several lineages of bacteria. The ability to utilize perchlorate is conferred by a horizontally transferred piece of DNA called the perchlorate reduction genomic island (PRI). Methods: We compared genomes of perchlorate reducers using phylogenomics, SNP mapping, and differences in genomic architecture to interrogate the evolutionary history of perchlorate respiration. Results: Here we report on the PRI of 13 genomes of perchlorate-reducing bacteria from four different classes of Phylum Proteobacteria (the Alpha-, Beta-, Gamma- and Epsilonproteobacteria). Among the different phylogenetic classes, the island varies considerably in genetic content as well as in its putative mechanism and location of integration. However, the islands of the densely sampled genera Azospira and Magnetospirillum have striking nucleotide identity despite divergent genomes, implying horizontal transfer and positive selection within narrow phylogenetic taxa. We also assess the phylogenetic origin of accessory genes in the various incarnations of the island, which can be traced to chromosomal paralogs from phylogenetically similar organisms. Conclusion: These observations suggest a complex phylogenetic history where the island is rarely transferred at the class level but undergoes frequent and continuous transfer within narrow phylogenetic groups. This restricted transfer is seen directly by the independent integration of near-identical islands within a genus and indirectly due to the acquisition of lineage-specific accessory genes. The genomic reversibility of perchlorate reduction may present a unique equilibrium for a metabolism that confers a competitive advantage only in the presence of an electron acceptor, which although widely distributed, is generally present at low concentrations in nature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Lassa virus protein–protein interactions as mediators of Lassa fever pathogenesis

Viral hemorrhagic Lassa fever (LF), caused by Lassa virus (LASV), is a significant public health concern endemic in West Africa with high morbidity and mortality rates, limited treatment options, and potential for international spread. Despite advances in interrogating its epidemiology and clinical manifestations, the molecular mechanisms driving pathogenesis of LASV and other arenaviruses remain incompletely understood. This review synthesizes current knowledge regarding the role of LASV host-virus interactions in mediating the pathogenesis of LF, with emphasis on interactions between viral and host proteins. Through investigation of these critical protein–protein interactions, we identify potential therapeutic targets and discuss their implications for development of medical countermeasures including antiviral drugs. This review provides an update in recent literature of significant LASV host-virus interactions important in informing the development of targeted therapies and improving clinical outcomes for LF patients. Knowledge gaps are highlighted as opportunities for future research efforts that would advance the field of LASV and arenavirus pathogenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets

Abstract Background Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. Results We optimized and employed a pipeline integrating various “guilt-by-association” (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum . Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum . In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. Conclusions This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.

09 BIOMASS FUELS↗
DOE OSTI2025

The anaerobic fungus Neocallimastix californiae shifts metabolism and produces melanin in response to lignin-derived aromatic compounds

Biological deconstruction of lignocellulose for sustainable chemical production offers an opportunity to harness evolutionarily specialized enzymes and organisms for industrial bioprocessing. While hydrolysis of cellulose and hemicellulose by CAZymes yields fermentable sugars, ligninolysis releases a heterogeneous mix of aromatic compounds that likely play a crucial role in shaping microbial communities and microbial metabolism. Here, we interrogated the metabolomic and transcriptomic response of a lignocellulolytic anaerobic fungus, Neocallimastix californiae, to a heterogeneous mixture of aromatic compounds derived from lignin. Through exposing the fungus to both a concentration it might experience in its native environment and an elevated concentration of alkaline lignin, we observe that N. californiae transforms vanillin and that supplying alkaline lignin at 0.125 g/L, alongside cellulose, enhances the growth and polysaccharide-degrading activity of N. californiae. Altogether, our results further suggest that vanillin consumption, increased polymer-degrading activity, increased metabolic activity, and transcriptomic remodeling of amino acid synthesis genes all coincide with increased melanin production by fungal cells. These observations challenge previous notions that aromatics from lignocellulose only inhibit the growth and polymer deconstruction capabilities of the biomass-degrading anaerobic fungi (Neocallimastigomycetes). This study demonstrates that anaerobic fungi have a complex relationship with aromatic chemicals derived from lignin and hemicellulose and shift their metabolism in response to the addition of lignocellulose-derived aromatics to their growth medium. Further, as no known pathways for the biochemical transformation of aromatics were detected in these organisms despite observed transcriptome remodeling in the presence of aromatics, we suggest they might encode novel biochemical routes for scavenging amino acid building blocks from aromatic monomers derived from hemicellulose side chains and lignin.

Anaerobic fungi↗
DOE OSTI2023

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research

Abstract As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how “microbiomes within microbiomes” affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Zero-crosstalk silicon photonic refractive index sensor with subwavelength gratings

Abstract Silicon photonic index sensors have received significant attention for label-free bio and gas-sensing applications, offering cost-effective and scalable solutions. Here, we introduce an ultra-compact silicon photonic refractive index sensor that leverages zero-crosstalk singularity responses enabled by subwavelength gratings. The subwavelength gratings are precisely engineered to achieve an anisotropic perturbation-led zero-crosstalk, resulting in a single transmission dip singularity in the spectrum that is independent of device length. The sensor is optimized for the transverse magnetic mode operation, where the subwavelength gratings are arranged perpendicular to the propagation direction to support a leaky-like mode and maximize the evanescent field interaction with the analyte space. Experimental results demonstrate a high wavelength sensitivity of − 410 nm/RIU and an intensity sensitivity of 395 dB/RIU, with a compact device footprint of approximately 82.8 μm 2 . Distinct from other resonant and interferometric sensors, our approach provides an FSR-free single-dip spectral response on a small device footprint, overcoming common challenges faced by traditional sensors, such as signal/phase ambiguity, sensitivity fading, limited detection range, and the necessity for large device footprints. This makes our sensor ideal for simplified intensity interrogation. The proposed sensor holds promise for a range of on-chip refractive index sensing applications, from gas to biochemical detection, representing a significant step towards efficient and miniaturized photonic sensing solutions. Graphical Abstract

Materials Science↗
DOE OSTI2019

Geomechanical modeling of distributed fiber-optic sensor measurements

Fiber-optic-based distributed acoustic sensors (DAS) are a new technology that can be deployed in a well and are continuously interrogated during operations. These sensors calculate the strain (or strain rate) at all points along the fiber and have been used extensively to monitor hydraulic stimulations. The data from these sensors indicate that they are sensitive to high-frequency signals associated with microseismicity and low-frequency signals associated with fracture growth. We have developed a set of idealized models to simulate these signals and to identify interpretation methods that may be used to estimate fracture location, geometry, and extent. We use a multiphysics code that includes rock physics, fluid flow, and elastic-wave propagation to generate synthetic DAS measurements from a set of simple models that mimic hydraulic fracturing. We then relate the signals observed in the synthetic DAS to specific features in the model such as fracture height, width, and aperture. Our results demonstrate that the synthetic DAS measurements may be used to determine field DAS measurements and to optimize the design of future sensor deployments for sensitivity to fracture attributes.

03 NATURAL GAS↗
DOE OSTI2023

Methods for Continuously Resolving Spectral Shifts in Distributed Optical Fiber Sensors Irradiated to Extreme Neutron Fluence

Optical frequency domain reflectometry (OFDR) is a technique for interrogating distributed optical fiber sensors (DOFS) and involves correlating changes in the Rayleigh backscatter fingerprint for a fiber under test (FUT) with a reference measurement. Recently, under the WIRE-21 experiment sponsored by Nuclear Science User Facilities (NSUF) and performed at the High-Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL), silica optical fibers were irradiated to a fast neutron fluence of 1x10^21 n/cm^2/s at temperatures from 200--400 C. As in the cases of high-temperature and high-strain conditions, such high levels of neutron bombardment result in a highly dynamic RBS that evades analysis with conventional methods. This work describes the further development and application of graphical signal processing techniques applied to OFDR-based distributed optical fiber sensors specifically deployed in in-pile applications. While the signal processing techniques developed in this work are applied to DOFS in nuclear environments, they provide a general framework for the analysis of OFDR measurements and a tangible method to yield higher quality data, without imposing additional hardware requirements.

Sweeney, Dan↗
DOE OSTI2013

Non-destructive Assay Measurements Using the RPI Lead Slowing Down Spectrometer

The use of a Lead Slowing-Down Spectrometer (LSDS) is consid- ered as a possible option for non-destructive assay of fissile material of used nuclear fuel. The primary objective is to quantify the 239Pu and 235U fissile content via a direct measurement, distinguishing them through their characteristic fission spectra in the LSDS. In this pa- per, we present several assay measurements performed at the Rensse- laer Polytechnic Institute (RPI) to demonstrate the feasibility of such a method and to provide benchmark experiments for Monte Carlo cal- culations of the assay system. A fresh UOX fuel rod from the RPI Criticality Research Facility, a 239PuBe source and several highly en- riched 235U discs were assayed in the LSDS. The characteristic fission spectra were measured with 238U and 232Th threshold fission cham- bers, which are only sensitive to fission neutron with energy above the threshold. Despite the constant neutron and gamma background from the PuBe source and the intense interrogation neutron flux, the LSDS system was able to measure the characteristic 235U and 239Pu responses. All measurements were compared to Monte Carlo simula- tions. It was shown that the available simulation tools and models are well suited to simulate the assay, and that it is possible to calculate the absolute count rate in all investigated cases.

Lead Slowing Down Spectrometer↗
DOE OSTI2014

Quantifying tissue mechanical properties using photoplethysmography

Photoplethysmography (PPG) is a non-invasive optical method that can be used to detect blood volume changes in the microvascular bed of tissue. The PPG signal comprises two components; a pulsatile waveform (AC) attributed to changes in the interrogated blood volume with each heartbeat, and a slowly varying baseline (DC) combining low frequency fluctuations mainly due to respiration and sympathetic nervous system activity. In this report, we investigate the AC pulsatile waveform of the PPG pulse for ultimate use in extracting information regarding the biomechanical properties of tissue and vasculature. By analyzing the rise time of the pulse in the diastole period, we show that PPG is capable of measuring changes in the Young s Modulus of tissue mimicking phantoms with a resolution of 4 KPa in the range of 12 to 61 KPa. In addition, the shape of the pulse can potentially be used to diagnose vascular complications by differentiating upstream from downstream complications. A Windkessel model was used to model changes in the biomechanical properties of the circulation and to test the proposed concept. The modeling data confirmed the response seen in vitro and showed the same trends in the PPG rise and fall times with changes in compliance and vascular resistance.

Akl, Tony↗
DOE OSTI2016

Imaging theory of structured pump-probe microscopy

With sub-micron spatial resolution and femtosecond temporal resolution, pump probe microscopy provides a powerful spectroscopic probe of complex electronic environments in bulk and nanoscale materials. However, the electronic structure of many materials systems are governed by compositional and morphological heterogeneities on length scales that lie below the diffraction limit. We have recently demonstrated Structured Pump Probe Microscopy (SPPM), which employs a patterned pump excitation field to provide spectroscopic interrogation of sub-diffraction limited sample volumes. Herein, we develop the imaging theory of SPPM in two dimensions to accompany the previously published experimental methodology. We show that regardless of pump and probe wavelengths, a nearly two-fold reduction in spectroscopic probe volume can be achieved. We also examine the limitations of the approach, with a detailed discussion of ringing in the point spread function that can reduce imaging performance.

47 OTHER INSTRUMENTATION↗
DOE OSTI2017

Ultrabroadband 2D electronic spectroscopy with high-speed, shot-to-shot detection

Two-dimensional electronic spectroscopy (2DES) is an incisive tool for disentangling excited state energies and dynamics in the condensed phase by directly mapping out the correlation between excitation and emission frequencies as a function of time. Despite its enhanced frequency resolution, the spectral window of detection is limited to the laser bandwidth, which has often hindered the visualization of full electronic energy relaxation pathways spread over the entire visible region. Here, we describe a high-sensitivity, ultrabroadband 2DES apparatus. We report a new combination of a simple and robust setup for increased spectral bandwidth and shot-to-shot detection. We utilize 8-fs supercontinuum pulses generated by gas filamentation spanning the entire visible region (450 – 800 nm), which allows for a simultaneous interrogation of electronic transitions over a 200-nm bandwidth, and an all-reflective interferometric delay system with angled nanopositioner stages achieves interferometric precision in coherence time control without introducing wavelength-dependent dispersion to the ultrabroadband spectrum. To address deterioration of detection sensitivity due to the inherent instability of ultrabroadband sources, we introduce a 5-kHz shot-to-shot, dual chopping acquisition scheme by combining a high-speed line-scan camera and two optical choppers to remove scatter contributions from the signal. Comparison of 2D spectra acquired by shot-to-shot detection and averaged detection shows a 15-fold improvement in the signal-to-noise ratio. In conclusion, this is the first direct quantification of detection sensitivity on a filamentation-based ultrabroadband 2DES apparatus.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Multi-parameter distributed fiber optic sensing using double-Brillouin peak fiber in Brillouin optical time domain analysis

In this paper, we demonstrate a multi-parameter fiber sensing system based on stimulated Brillouin scattering in a double-Brillouin peak specialty fiber with enhanced Brillouin gain response. The amplitude level of the second Brillouin gain peak, which originated from the higher-order acoustic modes, has been improved with an approximately similar amplitude level to the first Brillouin gain peak from the fundamental acoustic mode. Compared to other multi-Brillouin peak fibers presented in the literature, the proposed fiber significantly reduces the measured Brillouin frequency shift error, thus improving strain and temperature accuracies. By utilizing the sensitivity values of the strain and temperature associated with each Brillouin gain spectrum (BGS) peak, a successful discriminative measurement of strain and temperature is performed with an accuracy of ±13 μɛ, and ±0.5 °C, respectively. The proposed double-Brillouin peak fiber appears to be a possible alternative to other multi-BGS peak fibers, for instance, large effective area fiber and dispersion compensating fibers, which are inherently accompanied by large measurement errors due to the weak Brillouin gain values originating from the higher-order acoustic modes. The demonstrated results show different strain and temperature coefficients of 47 kHz/µɛ, 1.15 MHz/°C for peak 1 and 51 kHz/µɛ, 1.37 MHz/°C for peak 2. Moreover, the enhanced BGS peak gains having nearly the same amplitude levels enable the discriminative measurement of strain and temperature. Such fibers in Brillouin interrogation eliminate the need for complex monitoring setups and reduce measurement errors. We recommend that for long-distance natural gas pipeline monitoring, where discriminative strain and temperature measurement is crucial, the proposed double-Brillouin peak fiber can be highly beneficial.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Microwave–photonic low-coherence interferometry for dark zone free distributed optical fiber sensing

A microwave–photonic low-coherence interferometry (MPLCI) system is proposed for fully distributed optical fiber sensing. Assisted by an unbalanced Michelson interferometer, a low-coherence laser source is used to interrogate cascaded Fabry–Perot interferometers along with an optical fiber for a dark zone free (or spatially continuous) distributed measurement. Here, by combining the advantages of microwaves and photonics, the MPLCI system can synergistically achieve high sensitivity and high spatial resolution. Our tests have confirmed a strain resolution of 95 nε at the spatial resolution of 10 cm.

42 ENGINEERING↗