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DOE OSTI2026

Energy Partition in Collisionless Counterstreaming Plasmas

Fast, counterstreaming plasma outflows drive magnetic field amplification, plasma heating, and particle acceleration in numerous astrophysical environments, from supernova remnant shocks to active galactic nuclei jets. Understanding how, in the absence of Coulomb collisions, energy is redistributed between the different plasma species remains a fundamental open question. We use three-dimensional, fully kinetic simulations to investigate energy partition in weakly magnetized counterpropagating plasmas. Our results reveal a complex interplay between different processes, where at early times the Weibel instability drives a first stage of magnetic field amplification and at late times the kinking of current filaments drives a second amplification stage via a dynamo-type mechanism. Electrons are heated primarily during the latter phase through magnetic pumping. By the time the flows thermalize, we observe that the final temperature ratio T e /T i and energy partition depend on the ion-to-electron mass ratio. For electron–proton flows, the electron thermal energy only reaches up to a few percent of the initial ion kinetic energy.

Marret, Alexis [SLAC National Accelerator Laborato↗

DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗

DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods: Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results: . Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions: PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗

DOE OSTI2019

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1980

Coherent substructure of turbulence near the stagnation zone of a bluff body

The evolution of freestream turbulence in crossflow about a circular cylinder was studied in order to identify the existence of a coherent substructure which is the outcome of the amplification of freesteam turbulence by the stretching mechanism in diverging flow about a bluff body. Visualization of the flow events revealed the selective stretching of cross-vortex tubes and the emergence of an organized turbulent flow pattern near the cylinder stagnation zone. Significant amplification of the total turbulent energy of the streamwise fluctuating velocity was consistently monitored. Realization of selective amplification at scales larger than the neutral scale of the stagnation flow was indicated by the variation of the discrete streamwise turbulent energy. A most amplified scale, characteristic of the energy containing eddies within the coherent substructure and commensurate with the boundary-layer thickness, was detected. Penetration of the amplified turbulence into the cylinder boundary layer led to the retardation of separation and to a concurrent decrease in the drag coefficient at subcritical cylinder-diameter Reynolds numbers.

Sadeh, W. Z.↗

NASA NTRS1980

Strouhal number influence on flight effects on jet noise radiated from convecting quadrupoles

The paper reports a complementary extension of previous work to include the high-frequency features reflected in the discussion of the higher Strouhal number influence on flight effects. It is found that, in addition to the usual features of flight effects on noise from ordinary flows, the high Strouhal number flows exhibit some more interesting features which are uniquely characteristic to them. The additional features are as follows: (1) Flight effects are more favorable to hot jets than to cold jets; (2) the higher the Strouhal number of the jet flow, the lesser the forward arc amplification due to flight; (3) as the Strouhal number increases, the peak amplification angle in the forward quadrant and the peak suppression angle in the aft quadrant move toward 90 deg and get closer, thus reducing the amplification exposure to a constricted angular region; (4) the silence zone is disturbed and displaced from its normal position parallel to the jet flow to give rise to multiple crossings of flight curves with the static line; and (5) the occurrence of multiple crossings is a strange phenomenon solely characteristic of high Strouhal number with high subcritical jet flows in flight.

Dash, R.↗

NASA NTRS1981

Gortler vortices and transition in wall boundary layers of two Mach 5 nozzles

The onset of transition in the wall boundary layers of two axisymmetric Mach 5 wind-tunnel nozzles has been measured under conditions of extremely low incident disturbance levels. The range of test unit Reynolds numbers, based on conditions at the nozzle exit, was from 6 x 10 to the 6th power m to 2.5 x 10 to the 7th power m. When the nozzle walls were maintained in a polished and clean condition, transition moved gradually upstream as the test Reynolds number was increased. When transition occurred in the supersonic concave wall region, the values of the local Gortler parameter at transition varied from about 5 to 6, whereas the momentum thickness Reynolds number varied from about 750 to 1050. Oil flow patterns obtained near the exit of the nozzles indicated that Gortler vortices were always present when the wall boundary layers were laminar. Calculations for the growth of Gortler vortices based on new results from linear theory for supersonic flat-plate profiles gave amplification ratios to transition from e to the 4th power to e to the 15th power. Possible reasons for this wide range in amplification ratios are discussed, but no definite conclusions are yet possible regarding the values of n in a simple e to the nth power type theory for the assumed linear amplification of Gortler vortices to transition in supersonic nozzles.

Beckwith, I. E.↗

NASA NTRS1981

Jet oscillations caused by vorticity interactions with shock waves

A linear theory is developed for the amplification of disturbances along a jet containing shock waves. The theory indicates that near grazing angles (i.e., wave angles near 90 deg) horizontal vorticity is greatly amplified after passing through the two shock waves that exist in a shock cell. The cumulative amplification and the mode that is amplified most can be obtained if the changes in shock parameters from cell to cell are known. Rapid rates of growth of disturbances are exhibited by shadowgraphs and rates of angular displacement of about 10 are observed. The linear two-dimensional theory also indicates that such rates of amplification occur, and that the behavior of a two-dimensional jet is qualitatively similar to that of a round jet.

Parthasarathy, S. P.↗

NASA NTRS1982

Tone-excited jet: Theory and experiments

A detailed study to understand the phenomenon of broadband jet-noise amplification produced by upstream discrete-tone sound excitation has been carried out. This has been achieved by simultaneous acquisition of the acoustic, mean velocity, turbulence intensities, and instability-wave pressure data. A 5.08 cm diameter jet has been tested for this purpose under static and also flight-simulation conditions. An open-jet wind tunnel has been used to simulate the flight effects. Limited data on heated jets have also been obtained. To improve the physical understanding of the flow modifications brought about by the upstream discrete-tone excitation, ensemble-averaged schlieren photographs of the jets have also been taken. Parallel to the experimental study, a mathematical model of the processes that lead to broadband-noise amplification by upstream tones has been developed. Excitation of large-scale turbulence by upstream tones is first calculated. A model to predict the changes in small-scale turbulence is then developed. By numerically integrating the resultant set of equations, the enhanced small-scale turbulence distribution in a jet under various excitation conditions is obtained. The resulting changes in small-scale turbulence have been attributed to broadband amplification of jet noise. Excellent agreement has been found between the theory and the experiments. It has also shown that the relative velocity effects are the same for the excited and the unexcited jets.

Ahuja, K. K.↗

NASA NTRS1984

Jet noise modification by the 'whistler nozzle'

The farfield noise characteristics of a subsonic whistler nozzle jet are measured as a function of Mach number (0.25, 0.37, and, 0.51), emission angle, and excitation mode. It is shown that a whistler nozzle has greater total and broadband acoustic power than an excited contraction nozzle; and that the intensity of far-field noise is a function of emission angle, Mach number, and whistler excitation stage. The whistler nozzle excitation produces broadband noise amplification with constant spectral shape; the broadband noise amplification (without associated whistler tones and harmonics) increases omnidirectionally with emission angle at all Mach numbers; and the broadband amplification factor decreases as Mach number and emission angle increase. Finally the whistler nozzle is described as a very efficient but inexpensive siren with applications in not only jet excitation but also acoustics.

Hasan, M. A. Z.↗

NASA NTRS1985

Far-field noise of a subsonic jet under controlled excitation

The role of large-scale coherent structures in broadband jet noise suppression and amplification under controlled excitation are studied experimentally. It is found that suppression occurs only at low Reynolds and Mach numbers, when the boundary layer at the jet exit is laminar; the optimum St(Theta) (St, based on the initial shear-layer momentum thickness) value is 0.017, at which the excitation results in a quick roll-up and transition of the laminar shear-layer vortices, yielding coherent structures similar to those existing at high speeds. At the asymptotic level the broadband jet noise can only be amplified by the excitation. The amplification is inferred to be maximum for excitation in the St(D) (St based on the jet diameter) range of 0.65-0.85. Finally, it is noted that the pairing process induced by the excitation is at the origin of the broadband noise amplification.

Zaman, K. B. M. Q.↗

NASA NTRS1986

The influrence of an optical receiving system on statistical characteristics of a lidar signal

The effects connected with correlation of direct and backward waves propagating through the same randomly inhomogeneous media can be observed along the path with refection in a turbulent atmosphere. In particular, the mean intensity of the reflected wave can increase in comparison with the wave propagating in the forward direction at a doubled distance; the intensity fluctuations can become stronger. These effects depend on the strength of optical turbulence, as well as on the diffraction sizes of the exit apertures of the source and the reflector. However, the focusing of radiation reflected with a receiving telescope leads, in some cases, to the fact that the dependence of amplification effects on the parameters becomes essentially different. This should be taken into account when alayzing the lidar signals. The effect of backscattering amplification and amplification of the intensity fluctuations is discussed.

Zuev, A. E.↗

NASA NTRS1988

Application of finite element and remeshing technique to shock interference on a cylindrical leading edge

The problem of planar oblique shock impingement on a cylindrical leading edge in hypersonic flow is modeled using a Galerkin-Runge Kutta finite element method. The method utilizes a four stage Runge-Kutta time stepping scheme to solve the compressible Euler equations. Freestream Mach numbers of 6.5, 8.0 and 16.0 are studied. The computed surface pressure distributions consistently agree well with available experimental data. The peak pressure amplification ranges from 5.45 at M = 6.5 to approximately 17.0 at M = 16.0. Stagnation point heat transfer rate amplifications are calculated from the inviscid solution using the method of Fay and Riddell. The value and wall location of the peak pressure and heat transfer rate amplifications are extremely sensitive to the location of the impinging shock/bow shock intersection point.

Stewart, James R.↗

NASA NTRS1988

Effect of bulges on the stability of boundary layers

The instability of flows around hump and dip imperfections is investigated. The mean flow is calculated using interacting boundary layers, thereby accounting for viscous/inviscid interaction and separation bubbles. Then, the two-dimensional linear stability of this flow is analyzed, and the amplification factors are computed. Results are obtained for several height/width ratios and locations. The theoretical results have been used to correlate the experimental results of Walker and Greening (1942). The observed transition locations are found to correspond to amplification factors varying between 7.4 and 10.0, consistent with previous results for flat plates. The method accounts for both viscous and shear-layer instabilities. Separation is found to increase significantly the amplification factor.

Nayfeh, Ali H.↗

NASA NTRS1988

Light propagation in inhomogeneous universes - The ray-shooting method

The propagation of light in a clumpy universe is studied using the ray-shooting method. It is found that 'empty cones' in a clumpy universe are rare, which points out the limitation of frequently used distance measures in an inhomogeneous universe. The results show some qualitatively new features of multiple-gravitational-lens geometry, and a likely explanation for these features is presented. A statistical analysis of the simulations give amplification probability distributions for extended sources, as well as the distribution for the ratio of amplifications of compact sources to amplifications of more extended sources. Sample light curves of individual sources are obtained. Finally, the results support the validity of recent investigations on the influence of gravitational light deflection on source counts of compact extragalactic objects.

Schneider, Peter↗

NASA NTRS1991

Unified aeroacoustics analysis for high speed turboprop aerodynamics and noise. Volume 5: Propagation of propeller tone noise through a fuselage boundary layer

An analysis of tone noise propagation through a boundary layer and fuselage scattering effects was derived. This analysis is a three dimensional and the complete wave field is solved by matching analytical expressions for the incident and scattered waves in the outer flow to a numerical solution in the boundary layer flow. The outer wave field is constructed analytically from an incident wave appropriate to the source and a scattered wave in the standard Hankel function form. For the incident wave, an existing function - domain propeller noise radiation theory is used. In the boundary layer region, the wave equation is solved by numerical methods. The theoretical analysis is embodied in a computer program which allows the calculation of correction factors for the fuselage scattering and boundary layer refraction effects. The effects are dependent on boundary layer profile, flight speed, and frequency. Corrections can be derived for any point on the fuselage, including those on the opposite side from the source. The theory was verified using limited cases and by comparing calculations with available measurements from JetStar tests of model prop-fans. For the JetStar model scale, the boundary layer refraction effects produce moderate fuselage pressure reinforcements aft of and near the plane of rotation and significant attenuation forward of the plane of rotation at high flight speeds. At lower flight speeds, the calculated boundary layer effects result in moderate amplification over the fuselage area of interest. Apparent amplification forward of the plane of rotation is a result of effective changes in the source directivity due to boundary layer refraction effects. Full scale effects are calculated to be moderate, providing fuselage pressure amplification of about 5 dB at the peak noise location. Evaluation using available noise measurements was made under high-speed, high-altitude flight conditions. Comparisons of calculations made of free field noise, using a current frequency-domain propeller noise prediction method, and fuselage effects using this new procedure show good agreement with fuselage measurements over a wide range of flight speeds and frequencies. Correction factors for the JetStar measurements made on the fuselage are provided in an Appendix.

Magliozzi, B.↗

NASA NTRS1990

Three-dimensional instability of rotating flows with oscillating axial strain

The equations of motion for perturbed uniformly rotating flows with uniform axial-time periodic strain, are derived from the Navier-Stokes equations in the low Mach number limit. The perturbation equations admit exponentially growing three-dimensional solutions for which the amplification factors per period are computed for a range of compression and swirl ratios. It is found that for a given compression ratio, the flow is stable for swirl ratios, but at high swirl ratios the flow is unstable with the amplification factor dependent on wave angle but independent of wavelength. For an unstable swirl ratio, higher compression ratios yield larger amplification factors.

Mansour, Nagi N.↗

NASA NTRS1993

Stochastic forcing of perturbation variance in unbounded shear and deformation flows

An alternative mechanism for growth and maintenance of perturbation variance - amplification in a straining flow of stochastically forced perturbations in the absence of exponential instabilities - is explored, using as examples unbounded constant shear and pure deformation flow for which closed-form solutions are available and neither of which support a nonsingular mode. With diffusive dissipation, amplification of isotropic band-limited stochastic driving is found to be unbounded for the case of pure deformation and to be bounded by a threefold increase at large shear for the case of a linear velocity profile. It is concluded that amplification of stochastic forcing in a straining field can maintain a variance field substantially more energetic than that resulting from the same forcing in the absence of a background straining flow.

Farrell, Brian F.↗