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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

scMicrobe PTA: near complete genomes from single bacterial cells

Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Handheld Biosensor for COVID-19 Screening

We have made significant progress toward the development of an integrated nucleic acid amplification system for Autonomous Medical Devices Incorporated (AMDIs) Optikus handheld diagnostic device. In this effort, we developed a set of loop-mediated isothermal amplification (LAMP) primers for SARS-CoV-2 and then demonstrate amplification directly on a surface acoustic wave (SAW) sensor. We built associated hardware and developed a C-code to control the amplification process. The goal of this project was to develop a nucleic amplification assay that is compatible with SAW sensors to enable both nucleic and serological testing in a single handheld diagnostic device. Toward this goal, AMDI is collaborating Sandia National Laboratories to develop a rapid, portable diagnostic screening device that utilizes Sandias unique surface acoustic wave biosensor (SAW) for COVID-19 detection. Previously, the SANDIA- AMDI SAW sensor has successfully detected multiple high-profile bacteria viruses, including Ebola, HIV, Sin Nombre, and Anthrax. Over the last two years, AMDI and SANDIA have significantly improved the sensitivity and detection capability of the SAW biosensor and have also developed a modular hand-held, portable platform called the Optikus, which uses CD microfluidics and handheld instrumentation to automate all sample preparation, reagent introduction, sample delivery, and measurement for a number of different assay targets. We propose to use this platform for the development of a rapid (%3C30 minutes), point-of-care diagnostic test for detection of COVID-19 from nasal swab samples.

47 OTHER INSTRUMENTATION↗
NASA NTRS1988

'Flux conservation' by a Schwarzschild gravitational lens

It is demonstrated, by an explicit calculation, that a single, isolated Schwarzschild gravitational lens leads to a vanishing net total amplification on its own, without any 'help' from other lenses. It is shown that, in the limit of small M/R (where M is the mass of the lens in geometrical units and R is the distance from the source to the observers), the positive net total amplification, obtained from the classical approximation of the amplification for small impact angle lensing, is balanced by a negative net total amplification from the first-order term in M/R in an approximation of the amplification for large impact angle lensing derived here. The relation of these results to the common interpretation of average flux conservation by gravitational lenses is discussed as due to the collective action of many lenses in a cosmological framework.

Shulami, I.↗
NASA NTRS2012

Molecular Technique to Understand Deep Microbial Diversity

Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

Vaishampayan, Parag A.↗
NASA NTRS2012

Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity

Current planetary protection policies require that spacecraft targeted to sensitive solar system bodies be assembled and readied for launch in controlled cleanroom environments. A better understanding of the distribution and frequency at which high-risk contaminant microbes are encountered on spacecraft surfaces would significantly aid in assessing the threat of forward contamination. However, despite a growing understanding of the diverse microbial populations present in cleanrooms, less abundant microbial populations are probably not adequately taken into account due to technological limitations. This novel approach encompasses a wide spectrum of microbial species and will represent the true picture of spacecraft cleanroom-associated microbial diversity. All of the current microbial diversity assessment techniques are based on an initial PCR amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of a minor template appears to be suppressed by the amplification of a more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck overlooks the presence of the less abundant minority population and may underestimate their role in the ecosystem maintenance. DNA intercalating agents such as propidium monoazide (PMA) covalently bind with DNA molecules upon photolysis using visible light, and make it unavailable for DNA polymerase enzyme during polymerase chain reaction (PCR). Environmental DNA samples will be treated with suboptimum PMA concentration, enough to intercalate with 90 99% of the total DNA. The probability of PMA binding with DNA from abundant bacterial species will be much higher than binding with DNA from less abundant species. This will increase the relative DNA concentration of previously "shadowed" less abundant species available for PCR amplification. These PCR products obtained with and without PMA treatment will then be subjected to downstream diversity analyses such as sequencing and DNA microarray. It is expected that PMA-coupled PCR will amplify the "minority population" and help in understanding microbial diversity spectrum of an environmental sample at a much deeper level. This new protocol aims to overcome the major potential biases faced when analyzing microbial 16S rRNA gene diversity. This study will lead to a technological advancement and a commercial product that will aid microbial ecologists in understanding microbial diversity from various environmental niches. Implementation of this technique may lead to discoveries of novel microbes and their functions in sustenance of the ecosystem.

Vaishampayan, Parag A.↗
NASA NTRS2021

Hypersonic Boundary-Layer Transition on Blunted Cones at Angle of Attack

Experimental studies of cones at several high-speed facilities have demonstrated that, for small nosetip bluntness, transition onset over a circular cone moves upstream along the leeward side and downstream along the windward side, but this trend may be reversed at large bluntness values, where transition onset moves downstream along the leeward side and upstream along the windward side. A theoretical and numerical investigation is performed to characterize the effects of nose bluntness on disturbance amplification over the circular cone for several angles of attack, with the goal of understanding the potential physical mechanisms behind the experimental observations. The three-dimensional laminar basic states over a 1.5 m long, 7-degree half-angle cone with 9.525 mm nosetip radius are computed for selected angles of attack values and freestream conditions that are selected to match the Mach 10 experiments conducted within the Hypervelocity Wind Tunnel 9 at the Arnold Engineering Development Complex (AEDC). The solutions at a freestream unit Reynolds number of 17.1 million per meter are used to perform detailed instability analyses for angles of attack equal to 0, 1, 3, and 5 degrees. Results indicate that the linear amplification of stationary crossflow waves along inflection lines may begin to influence transition along the acreage of the cone for angles of attack equal to or larger than 5 degrees. The measured trend in transition front with respect to increasing angle of attack is found to be consistent with the predicted increase in the amplification factors for Mack mode disturbances along the streamline trajectories. The increase in Mack mode amplification along the windward ray for higher angles of attack is shown to be the result of a progressively earlier entropy-layer swallowing. Computations also indicate that the transition amplification factor along the windward ray is not constant and increases with the angle of attack and that the transition #-factors along the leeward ray are rather small. The nonmodal analysis for zero degrees angle of attack shows that entropy-layer disturbances with appreciably strong energy growth can coexist with Mack mode instabilities at the measured transition location.

boundary layer transition↗
NASA NTRS2021

Hypersonic Boundary-Layer Transition on Blunted Cones at Angle of Attack

Experimental studies of cones at several high-speed facilities have demonstrated that, for small nosetip bluntness, transition onset over a circular cone moves upstream along the leeward side and downstream along the windward side, but this trend may be reversed at large bluntness values, where transition onset moves downstream along the leeward side and upstream along the windward side. A theoretical and numerical investigation is performed to characterize the effects of nose bluntness on disturbance amplification over the circular cone for several angles of attack, with the goal of understanding the potential physical mechanisms behind the experimental observations. The three-dimensional laminar basic states over a 1.5 m long, 7-degree half-angle cone with 9.525 mm nosetip radius are computed for selected angles of attack values and freestream conditions that are selected to match the Mach 10 experiments conducted within the Hypervelocity Wind Tunnel 9 at the Arnold Engineering Development Complex (AEDC). The solutions at a freestream unit Reynolds number of 17.1 million per meter are used to perform detailed instability analyses for angles of attack equal to 0, 1, 3, and 5 degrees. Results indicate that the linear amplification of stationary crossflow waves along inflection lines may begin to influence transition along the acreage of the cone for angles of attack equal to or larger than 5 degrees. The measured trend in transition front with respect to increasing angle of attack is found to be consistent with the predicted increase in the amplification factors for Mack mode disturbances along the streamline trajectories. The increase in Mack mode amplification along the windward ray for higher angles of attack is shown to be the result of a progressively earlier entropy-layer swallowing. Computations also indicate that the transition amplification factor along the windward ray is not constant and increases with the angle of attack and that the transition #-factors along the leeward ray are rather small. The nonmodal analysis for zero degrees angle of attack shows that entropy-layer disturbances with appreciably strong energy growth can coexist with Mack mode instabilities at the measured transition location.

Boundary Layer Transition↗
DOE OSTI2020

Magnetic field generation in a laser-irradiated thin collisionless plasma target by return current electrons carrying orbital angular momentum

Abstract Magnetized high energy density physics offers new opportunities for observing magnetic field-related physics for the first time in the laser–plasma context. We focus on one such phenomenon, which is the ability of a laser-irradiated magnetized plasma to amplify a seed magnetic field. We performed a series of fully kinetic 3D simulations of magnetic field amplification by a picosecond-scale relativistic laser pulse of intensity 4.2 × 10 18 W cm −2 incident on a thin overdense target. We observe axial magnetic field amplification from an initial 0.1 kT seed to 1.5 kT over a volume of several cubic microns, persisting hundreds of femtoseconds longer than the laser pulse duration. The magnetic field amplification is driven by electrons in the return current gaining favorable orbital angular momentum from the seed magnetic field. This mechanism is robust to laser polarization and delivers order-of-magnitude amplification over a range of simulation parameters.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Reducing host DNA contamination in 16S rRNA gene surveys of anthozoan microbiomes using PNA clamps

Efforts to study the microbial communities associated with corals can be limited by inefficiencies in the sequencing process due to high levels of host amplification by universal bacterial 16S rRNA gene primers. Here, we develop an inexpensive peptide nucleic acid (PNA) clamp that binds to a target sequence of host DNA during PCR and blocks amplification. We then test the ability of this PNA clamp to mitigate host contamination and increase overall microbial sequence coverage on samples from three coral species: the gorgonians Eunicea flexuosa and Gorgonia ventalina, and the scleractinian Porites panamensis. The 20-bp PNA clamp was designed using DNA from E. flexuosa. Adding the PNA clamp during PCR increased the percentage of microbial reads in E. flexuosa samples more than 11-fold. Microbial community diversity was similar without- and with-PNA clamps, as were the relative frequencies of the ten most abundant ASVs (amplicon sequence variants), indicating that the clamps successfully blocked host DNA amplification while simultaneously increasing microbial DNA amplification proportionally across the most abundant taxa. The reduction of E. flexuosa DNA correlated with an increase in the abundance of rarer taxa. The clamp also increased the average percentage of microbial reads in another gorgonian, G. ventalina, by 8.6-fold without altering the microbial community beta diversity, and in a distantly related scleractinian coral, P. panamensis, by nearly double. The reduction of host contamination correlated with the number of nucleotide mismatches between the host amplicon and the PNA clamp. The PNA clamp costs as little as $0.48 per sample, making it an efficient and cost-effective solution to increase microbial sequence coverage for high-throughput sequencing of coral microbial communities.

16S rRNA gene sequencing↗
DOE OSTI2020

Intensity measure adequacy assessment for nonlinear site response using Information Theory

Nonlinear site response modeling is a crucial aspect of Probabilistic Seismic Hazard Analysis. Site amplification models routinely rely on a rock intensity measure to characterize the strength of the bedrock motion. However, the adequacy of such intensity measures towards predicting amplifications across the oscillator period range has not been investigated in the literature. This paper analyzes the adequacy of rock intensity measures using state of the art criterion established in Performance-Based Earthquake Engineering and techniques from Information Theory. The efficiency and the sufficiency of several rock intensity measure are assessed. It was found that spectral accelerations at low periods usually are adequate for predicting amplifications across the period range. This supports the current practice of using Peak Ground Acceleration in Ground Motion Models. However, for extremely soft sites, which demonstrate nonlinear effects well into the period range, it is better practice to ensure that amplification and spectral acceleration share the same oscillator period. Lastly, for predicting the peak shear strain (an important parameter that controls nonlinearity of site response), Peak Ground Velocity is generally adequate, and this conclusion is in line with the definition of proxy shear strain.

42 ENGINEERING↗
DOE OSTI2020

Energy Transfer from Large to Small Scales in Turbulence by Multiscale Nonlinear Strain and Vorticity Interactions

An intrinsic feature of turbulent flows is an enhanced rate of mixing and kinetic energy dissipation due to the rapid generation of small-scale motions from large-scale excitation. The transfer of kinetic energy from large to small scales is commonly attributed to the stretching of vorticity by the strain rate, but strain self-amplification also plays a role. Previous treatments of this connection are phenomenological or inexact, or cannot distinguish the contribution of vorticity stretching from that of strain self-amplification. In this Letter, an exact relationship is derived which quantitatively establishes how intuitive multiscale mechanisms such as vorticity stretching and strain self-amplification together actuate the interscale transfer of energy in turbulence. Further, numerical evidence verifies this result and uses it to demonstrate that the contribution of strain self-amplification to energy transfer is higher than that of vorticity stretching, but not overwhelmingly so.

42 ENGINEERING↗
DOE OSTI2020

Significance of the Direct Excitation Mechanism for High-Frequency Response of Premixed Flames to Flow Oscillations

Premixed flames are sensitive to flow disturbances, which can arise from acoustic or vortical fluctuations. For transverse instabilities, it is known that a dominant mechanism for flame response is “injector coupling,” whereby pressure oscillations associated with transverse waves excite axial flow disturbances. These axial flow disturbances then excite heat release oscillations. The objective of this paper is to consider another mechanism—the direct sensitivity of the unsteady heat release to transverse acoustic waves—and to compare its significance relative to the induced axial disturbances, in a linear framework. The rate at which the flame adds energy to the disturbance field is quantified using the Rayleigh criterion and evaluated over a range of control parameters, such as flame length and swirl number. The results show that radial modes induce heat release fluctuations that always add energy to the acoustic field, whereas heat release fluctuations induced by mixed radial-azimuthal modes can add or remove energy. These amplification rates are then compared to the flame response from induced axial fluctuations. For combustor-centered flames, these results show that the direct excitation mechanism has negligible amplification rates relative to the induced axial mechanism for radial modes. For transverse modes, the fact that the nozzle is located at a pressure node indicates that negligible induced axial velocity disturbances are excited; as such, the direct mechanism dominates. As a result, for flames that are not centered on pressure nodes, the direct mechanism for mixed modes dominates for certain nozzle locations and flame angles.

42 ENGINEERING↗
DOE OSTI2022

Development of planar P-type point contact germanium detectors for low-mass dark matter searches

The detection of low-energy deposition in the range of sub-eV through ionization using germanium (Ge) with a bandgap of ~ 0.7 eV requires internal amplification of the charge signal. This can be achieved through high electric field that accelerates charge carriers, which can then generate more charge carriers. The minimum electric field required to generate internal charge amplification is derived for different temperatures. We report the development of a planar point contact Ge detector in terms of its fabrication and the measurements of its leakage current and capacitance as a function of applied bias voltage. With the determination of the measured depletion voltage, the field distribution is calculated using GeFiCa, which predicts that the required electric field for internal charge amplification can be achieved in proximity to the point contact. The energy response to an Am-241 source is characterized and discussed. We conclude that such a detector with internal charge amplification can be used to search for low-mass dark matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS1979

On the stability of the boundary layer on a transonic swept wing

Both incompressible and compressible linear stability theory are applied to the three-dimensional compressible boundary layer on a particular transonic sweptback wing of infinite span. A spatial stability theory is used which identifies the growth direction with the real part of the complex angle of the group velocity. It is found that in the forward, but not the rear, crossflow instability region, the maximum amplification rates of the steady disturbances may be calculated to within about 10% by the incompressible stability theory. There is little difference between the sixth and eighth-order compressible theories. The maximum amplification rate of the steady disturbances at any chordwise station is closely related to the maximum crossflow at that station independent of the Reynolds number. For other than crossflow instability, there can be large differences between the incompressible and compressible theories, both as to the amplification rate and the angle of the wavenumber vector for maximum instability. Amplitude ratios of individual wave components are obtained by integrating the spatial amplification rate along the growth direction subject to the constraint that the wavenumber vector is irrotational. This procedure yields steady disturbances aligned with the local potential flow direction whose wavelengths are nearly independent of downstream distance.

Mack, L. M.↗
NASA NTRS1979

Analysis of flight effects on noise radiation from dual-flow coaxial jets

A theoretical study has been made of the effects of flight on noise from dual-flow coaxial jets. The theory is based on an instability free, vortex sheet flow model. It is shown that the flight effects are more favorable (and hence produce less forward-arc amplification) for coaxial jets than for single-stream jets. Further, the theory predicts that, like the single-stream jet case, flight effects induce noise amplification in the forward quadrant and attenuation in the aft quadrant and have virtually no effect at theta = 90 deg to the jet axis, where theta is the angle between the directions of convection and emission at the retarded time. Amplification in the forward quadrant diminishes as the inner flow velocity increases and becomes optimum when the outer-to-inner velocity ratio is about 0.5. The theory also shows that the higher the outer-to-inner area ratio, the lower the forward-arc amplification due to flight.

Dash, R.↗
NASA NTRS1981

Compressible boundary-layer stability calculations for sweptback wings with suction

The stability of the laminar boundary layers on two transonic wings of infinite span with distributed suction is investigated with the compressible, parallel-flow stability theory. Both wings have supercritical airfoil sections; one has a sweep angle of 23 deg, the other of 35 deg. Zero-frequency disturbances are used to represent cross-flow instability, and disturbances with the wavenumber vector aligned with the local flow direction represent traveling-wave instability. In both cases, the maximum spatial amplification rate is used as a measure of the instability. For the suction, distributions with constant mass flux downstream of the starting point are used. The main objective is to determine how the maximum amplification rate varies with the magnitude and starting point of the suction. It is found for both types of disturbances that the maximum amplification rate varies almost linearly with the suction magnitude up to at least the point where the amplification rate is halved. Different starting locations for the suction in the first 4% of the chord were found to affect cross-flow instability, but to have little influence on traveling-wave instability.

Mack, L. M.↗
NASA NTRS1984

Large-scale coherent structure and far-field jet noise

The phenomenon of broadband noise amplification/suppression under controlled excitation is investigated. The suppression is found to occur only at low jet speeds when the exit boundary layer is laminar; excitation at a Strouhal St(theta) number of about 0.017 results in optimum suppression of the far-field broadband noise as well as of the near-flow-field turbulence. The noise amplification is found to be a function of the Mach number, the amplification is higher at higher Mach number for a given excitation Strouhal number and level. The amplification also depends on the Strouhal number (St D), the maximum occurring in the range 0.65-0.85. Vortex pairing induced by the excitation appears to be at the heart of the noise amplification phenomenon under excitation.

Zaman, K. B. M. Q.↗