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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
NASA NTRS2021

Modeling the Effects of a Backward-Facing Step on Boundary-Layer Transition

We model transition to turbulence in a two-dimensional boundary layer downstream of a backward-facing step (BFS) along a flat plate. With the goal of evaluating the available engineering models for predicting the effects of step excrescences on the transition characteristics, two separate methodologies are used to monitor the streamwise shift in the transition onset location as the step height and the flow speed are varied across the range of a previously reported experiment involving step-height-to-local-displacement-thickness ratios of 0 < h/δ* < 1.6. Unlike the variable N -factor method from the previous literature, both of these methods are general in scope and do not involve any empirical correlations that are specific to step excrescences. The first of these techniques involves an N -factor method that directly accounts for the change in boundary-layer instability characteristics due to the step. Stability computations using the harmonic linearized Navier-Stokes equations (HLNSE), which fully account for the nonparallel-mean-flow effects close to the BFS, indicate that the measured transition locations at nearly all test conditions ( h/δ* < 1.3) correlate well with a computed N -factor of N tr = 7.6, demonstrating a successful stability-based transition criterion related to step excrescences. Linear stability theory, which does not account for nonparallel effects, demonstrates reasonable agreement with the HLNSE results, yielding good predictions for the overall trends, but predicts a somewhat earlier onset of transition than HLNSE. The other methodology used in this work involves transport-equation-based transition models. We first show that the Langtry-Menter y - Re θt transition model cannot accurately predict the location of transition onset for moderate BFS heights because it is unable to accurately account for the flow history effects. Along with the Langtry-Menter transition model, we also show the amplification factor transport model does not produce accurate transition locations for subsonic flow over steps even though it accounts for some flow history effects.

Transition↗
DOE OSTI2025

Development and application of two-step uncertainty propagation and sensitivity analysis methodology for fast reactor safety analysis

Uncertainty quantification (UQ) in nuclear reactors for transients is directly linked with safety assessment through the cross-sections uncertainties, provided as a covariance matrix, which are propagated through the reactor system to output of interest pertaining to reactor safety, such as peak temperatures in fuel/clad/coolant. Using a two-step approach, uncertainties are first quantified and propagated from basic input variables (such as reaction cross-sections) to intermediate quantities (such as reactivity feedback coefficients) through lattice level calculations. Uncertainties of intermediate quantities (from the first step) are then propagated through the system transient calculations, in the second step, to obtain uncertainties on reactor safety output parameters of interest. The scope of this work consists of Uncertainty Quantification & Propagation of nuclear data uncertainties that are highly correlated through unprotected transient overpower and unprotected loss of flow to assess their impact on core safety parameters. This two-step approach in the presence of covariance renders the sensitivity analysis very challenging. In fact, usually the sensitivity analysis is restricted to each step, which limits its application since the sensitivities between the system output quantities and the basic input variables are difficult to obtain. Here, in this work, we address this issue by proposing a simple, general methodology to combine the sensitivity indices obtained in each step by assuming the model behavior being linear. For the first step Generalized Perturbation theory based indices are used while in the second step the recently studied Johnson indices. The uncertainty quantification and sensitivity methodologies discussed here are demonstrated on a generic LFR design which is based on the 500 MWth demonstration Lead-cooled fast reactor (DLFR) using oxide fuel, developed by Westinghouse Electric Company (WEC).

42 - ENGINEERING↗
DOE OSTI2020

Experimental studies of the two-step scheme with an intense radioactive 132 Sn beam for next-generation production of very neutron-rich nuclei

The study of nuclei in the yet-unexplored, very neutron-rich, mid- to heavy-mass region of the nuclear chart, comprising perhaps half of all nuclei predicted to exist, is leading to new and/or upgraded facilities, as well as to research into the underlying production processes. In the present study, the usefulness of the two-step scheme, an alternate method to produce very neutron-rich nuclei, by a combination of an isotope-separation online (ISOL) system as a first step, and in-beam fragmentation of re-accelerated radioactive isotopes (RIs) as a second step, was investigated with a 132 Sn beam. In this work, very neutron-rich RIs around the neutron-rich neutron number N = 82 region were produced from the 278-MeV/nucleon 132 Sn beam impinging on a 5.97-mm Be target, and their production cross sections were measured. Yields were then estimated for the two-step scheme with the 132 Sn beam relative to the ones by a one-step scheme, in-flight fission of a 238 U beam, for 1-MW proton and 238 U beams at respective RI-beam facilities. This comparison suggests that the two-step scheme with the 132 Sn beam provides yields >40-times higher than those with the one-step scheme for the very neutron-rich N = 82 region. Moreover, by using various RI beams over the nuclear chart from ISOL, certain kinds of very neutron-rich RIs around the supernova r-process path can be produced with greater yields than by the one-step approach.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Quantifying and attributing time step sensitivities in present-day climate simulations conducted with EAMv1

Abstract. This study assesses the relative importance of time integration error in present-day climate simulations conducted with the atmosphere component of the Energy Exascale Earth System Model version 1 (EAMv1) at 1∘ horizontal resolution. We show that a factor-of-6 reduction of time step size in all major parts of the model leads to significant changes in the long-term mean climate. Examples of changes in 10-year mean zonal averages include the following: up to 0.5 K of warming in the lower troposphere and cooling in the tropical and subtropical upper troposphere, 1 %–10 % decreases in relative humidity throughout the troposphere, and 10 %–20 % decreases in cloud fraction in the upper troposphere and decreases exceeding 20 % in the subtropical lower troposphere. In terms of the 10-year mean geographical distribution, systematic decreases of 20 %–50 % are seen in total cloud cover and cloud radiative effects in the subtropics. These changes imply that the reduction of temporal truncation errors leads to a notable although unsurprising degradation of agreement between the simulated and observed present-day climate; to regain optimal climate fidelity in the absence of those truncation errors, the model would require retuning. A coarse-grained attribution of the time step sensitivities is carried out by shortening time steps used in various components of EAM or by revising the numerical coupling between some processes. Our analysis leads to the finding that the marked decreases in the subtropical low-cloud fraction and total cloud radiative effect are caused not by the step size used for the collectively subcycled turbulence, shallow convection, and stratiform cloud macrophysics and microphysics parameterizations but rather by the step sizes used outside those subcycles. Further analysis suggests that the coupling frequency between the subcycles and the rest of EAM significantly affects the subtropical marine stratocumulus decks, while deep convection has significant impacts on trade cumulus. The step size of the cloud macrophysics and microphysics subcycle itself appears to have a primary impact on cloud fraction in the upper troposphere and also in the midlatitude near-surface layers. Impacts of step sizes used by the dynamical core and the radiation parameterization appear to be relatively small. These results provide useful clues for future studies aiming at understanding and addressing the root causes of sensitivities to time step sizes and process coupling frequencies in EAM. While this study focuses on EAMv1 and the conclusions are likely model-specific, the presented experimentation strategy has general value for weather and climate model development, as the methodology can help researchers identify and understand sources of time integration error in sophisticated multi-component models.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1978

Flight-measured pressure characteristics of aft-facing steps in thick boundary layer flow for transonic and supersonic Mach numbers

Aft-facing step base pressure flight data were obtained for three step heights for nominal transonic Mach numbers of 0.80, 0.90, and 0.95, and for supersonic Mach numbers of 2.2, 2.5, and 2.8 with a Reynolds number, based on the fuselage length ahead of the step, of about 10 to the 8th power. Surface static pressures were measured ahead of the step, behind the step, and on the step face (base), and a boundary layer rake was used to obtain boundary layer reference conditions. A comparison of the data from the present and previous experiments shows the same trend of increasing base pressure ratio (decreasing drag) with increasing values of momentum thickness to step height ratios. However, the absolute level of these data does not always agree at the supersonic Mach numbers. For momentum thickness to height ratios near 1.0, the differences in the base pressure ratios appear to be primarily a function of Reynolds number based on the momentum thickness. Thus, for Mach numbers above 2, the data analyzed show that the base pressure ratio decreases (drag increases) as Reynolds number based on momentum thickness increases for a given momentum thickness and step height.

Powers, S. G.↗
NASA NTRS1935

The effect of depth of step on the water performance of a flying-boat hull model

NACA model 11-C was tested with four different depths of step to obtain information as to the effect of the depth of step on the water performance. The depths of step were selected to cover the practicable range of depths and in each case the included angle between the forebody and afterbody keels was kept the same 6-1/2 degrees. Small depths of step were found to give lower resistance at speeds below and at the hump speed of the model and greater depths of step lower resistance at high speeds. For low resistance throughout the speed range of the model investigated the most desirable depth of step is from 2.5 to 4.0 percent of the beam. The change of the best trim angle caused by variation of the depth of step was not appreciable. Increased depth of step caused increases in the maximum positive trimming moments at all trim angles investigated.

Bell, Joe W↗
NASA NTRS1997

Application of the Two-Step Filter to Process Ranging Measurements for Relative Navigation in an Elliptical Orbit

This estimator breaks a nonlinear estimation problem into a set of over determined 'first step' states which are linear in the observations and 'second step' states which are ultimately the states of interest. Linear estimation methods are applied to filter the observations and produce the optimal first step state estimate. The 'second step' states are obtained through iterative nonlinear parameter estimation considering the first step states as observations. It has been shown that this process exactly minimizes the least squares cost function for static problems and provides a better solution than the iterated extended Kalman filter (EKF) for dynamic problems. The two step filter is applied in this paper to process range and range rate measurements between the two spacecraft. Details of the application of the two step estimator to this problem will be given, highlighting the use of a test for ill-conditioned covariance estimates that can result from the first order covariance propagation. A comparison will be made between the performance of the two step filter and the IEKF.

Garrison, James L.↗
NASA NTRS1997

Unsteady Crystal Growth Due to Step-Bunch Cascading

Based on our experimental findings of growth rate fluctuations during the crystallization of the protein lysozym, we have developed a numerical model that combines diffusion in the bulk of a solution with diffusive transport to microscopic growth steps that propagate on a finite crystal facet. Nonlinearities in layer growth kinetics arising from step interaction by bulk and surface diffusion, and from step generation by surface nucleation, are taken into account. On evaluation of the model with properties characteristic for the solute transport, and the generation and propagation of steps in the lysozyme system, growth rate fluctuations of the same magnitude and characteristic time, as in the experiments, are obtained. The fluctuation time scale is large compared to that of step generation. Variations of the governing parameters of the model reveal that both the nonlinearity in step kinetics and mixed transport-kinetics control of the crystallization process are necessary conditions for the fluctuations. On a microscopic scale, the fluctuations are associated with a morphological instability of the vicinal face, in which a step bunch triggers a cascade of new step bunches through the microscopic interfacial supersaturation distribution.

Vekilov, Peter G.↗
NASA NTRS2003

Step Bunch Evolution on Vicinal Faces of KDP

For in-situ studies of the formation and evolution of step patterns in solution growth, we have assembled an experimental setup based on Michelson interferometry with the growing crystal surface as one of the reflective surfaces. The device allows data collection over a relatively large area (approximately 4 sq. mm) in situ and in real time during growth. The depth resolution is improved over traditional interferometry using phase-shifted images combining by a suitable algorithm. We achieve a depth resolution of approximately 50 Angstroms. Lateral resolution, dependent on the degree of magnification, is around 0.3 to 5 microns. The crystal chosen as a model in this work is potassium dihydrogen phosphate (KDP), the optically non-linear material widely used in frequency doubling applications. Kinetics of KDP crystallization is well studied so that KDP can serve as a benchmark for our investigations. We present quantitative results on the onset, initial stages and development of instabilities in moving step trains on vicinal crystal surfaces at varying supersaturation, flow rate, and flow direction. The kinetics data suggest that at low supersaturations, step bunching is caused by impurity retardation of the steps, while at higher supersaturations, we link the non-linearity during growth to interdependence of the velocity and density of the steps evidenced in independent experiments. The behavior on the surface is very dynamic, small bunches both merge and split from larger bunches as they travel across the facet. We present evidence that despite these dynamics, under steady conditions there exists a limiting value to step bunch height. This height is reached at distances between 600 and 1000 microns from the step source. In our experiments, we observed the retention of this step bunch height limit up to the path of 1500 microns.

Booth, N. A.↗
NASA NTRS1947

Aerodynamic Characteristics of Three Deep-Stepped Planing-Tail Flying-Boat Hulls

An investigation was made in the Langley 300 MPH 7- by 10-foot tunnel to determine the aerodynamic characteristics of three deep-stepped planing-tail flying-boat hulls differing only in the amount of step fairing. The hulls were derived by increasing the unfaired step depth of a planing-tail hull of a previous aerodynamic investigation to a depth about 92 percent of the hull beam. Tests were also made on a transverse-stepped hull with an extended afterbody for the purpose of comparison and in order to extend and verify the results of a previous investigation. The investigation indicated that the extended afterbody hull had a minimum drag coefficient about the same as a conventional hull, 0.0066, and an angle-of-attack range for minimum drag coefficient of 0.0057 which was 14 percent less than the transverse stepped hull with extended afterbody; the hulls with step fairing had up to 44 percent less minimum drag coefficient than the transverse-stepped hull, or slightly more drag than a streamlined body having approximately the same length and volume. Longitudinal and lateral instability varied little with step fairing and was about the same as a conventional hull.

Riebe, John M.↗
NASA NTRS2006

Recent Results from Epitaxial Growth on Step Free 4H-SiC Mesas

This paper updates recent progress made in growth, characterization, and understanding of high quality homoepitaxial and heteroepitaxial films grown on step-free 4H-SiC mesas. First, we report initial achievement of step-free 4H-SiC surfaces with carbon-face surface polarity. Next, we will describe further observations of how step-free 4H-SiC thin lateral cantilever evolution is significantly impacted by crystal faceting behavior that imposes non-uniform film thickness on cantilever undersides. Finally, recent investigations of in-plane lattice constant mismatch strain relief mechanisms observed for heteroepitaxial growth of 3C-SiC as well as 2H-AlN/GaN heterofilms on step-free 4H-SiC mesas will be reviewed. In both cases, the complete elimination of atomic heterointerface steps on the mesa structure enables uniquely well-ordered misfit dislocation arrays to form near the heterointerfaces with remarkable lack of dislocations threading vertically into the heteroepilayers. In the case of 3C-SiC heterofilms, it has been proposed that dislocation half-loops nucleate at mesa edges and glide laterally along the step-free 3C/4H interfaces. In contrast, 3C-SiC and 2H-AlN/GaN heterofilms grown on 4H-SiC mesas with steps exhibit highly disordered interface misfit dislocation structure coupled with 100X greater density of dislocations threading through the thickness of the heteroepilayers. These results indicate that the presence of steps at the heteroepitaxial interface (i.e., on the initial heteroepitaxial nucleation surface) plays a highly important role in the defect structure, quality, and relaxation mechanisms of single-crystal heteroepitaxial films.

Neudeck, Philip G.↗
DOE OSTI2022

High-order multirate explicit time-stepping schemes for the baroclinic-barotropic split dynamics in primitive equations

In order to treat the multiple time scales of ocean dynamics in an efficient manner, the baroclinic-barotropic splitting technique has been widely used for solving the primitive equations for ocean modeling. Based on the framework of strong stability-preserving Runge-Kutta approach, we propose two high-order multirate explicit time-stepping schemes (SSPRK2-SE and SSPRK3-SE) for the resulting split system in this paper. The proposed schemes allow for a large time step to be used for the three-dimensional baroclinic (slow) mode and a small time step for the two-dimensional barotropic (fast) mode, in which each of the two mode solves just need to satisfy their respective CFL conditions for numerical stability. Specifically, at each time step, the baroclinic velocity is first computed by advancing the baroclinic mode and fluid thickness of the system with the large time-step and the assistance of some intermediate approximations of the barotropicmode obtained by substepping with the small time step; then the barotropic velocity is corrected by using the small time step to re-advance the barotropic mode un-der an improved barotropic forcing produced by interpolation of the forcing terms from the preceding baroclinic mode solves; lastly, the fluid thickness is updated by coupling the baroclinic and barotropic velocities. Additionally, numerical inconsistencies on the discretized sea surface height caused by the mode splitting are relieved via a reconciliation process with carefully calculated flux deficits. Here, two benchmark tests from the “MPAS-Ocean” platform are carried out to numerically demonstrate the performance and parallel scalability of the proposed SSPRK-SE schemes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Mechanistic Pathways for the Molecular Step Growth of Calcium Oxalate Monohydrate Crystal Revealed by In Situ Liquid-Phase Atomic Force Microscopy

Calcium oxalate monohydrate (COM) crystal is the most common crystalline component of human kidney stones. The molecular-scale inhibitory mechanisms of COM crystal growth by urinary biomolecules such as citrate and osteopontin adsorbed onto the crystal surface are now well understood. However, the pathways by which dissolved calcium and oxalate ions are incorporated into the molecular step of the COM crystal surface, leading to COM crystal growth—a prerequisite to be elucidated for developing effective therapeutics to inhibit COM stones—remain unknown. Here, using in situ liquid-phase atomic microscopy along with a step kinetic model, we reveal the pathways of the calcium and oxalate ions into the COM molecular step via the growth speed analysis of the molecular steps with respect to their step width at the nanoscale. Our results show that, primarily, the ions are adsorbed onto the terrace of the crystal surface from the solution—the rate-controlling stage for the molecular step growth, i.e., COM crystal growth—and then diffuse over it and are eventually incorporated into the steps. This primary pathway of the ions is unaffected by the model peptide D-Asp6 adsorbed on the COM crystal surface, suggesting that urinary biomolecules will not alter the pathway. These new findings rendering an essential understanding of the fundamental growth mechanism of COM crystal at the nanoscale provide crucial insights beneficial to the development of effective therapeutics for COM kidney stones.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Explicit Monotone Stable Super-Time-stepping Methods for Finite Time Singularities

We explore a novel way to numerically resolve the scaling behavior of finite-time singularities in solutions of nonlinear parabolic PDEs. The Runge–Kutta–Legendre (RKL) and Runge–Kutta–Gegenbauer (RKG) super-time-stepping methods were originally developed for nonlinear complex physics problems with diffusion. These are multistage single step second-order, forward-in-time methods with no implicit solves. The advantage is that the time-step size for stability scales with stage number 𝑠 as $\mathcal{O}$⁡(𝑠 2 ). Many interesting nonlinear PDEs have finite-time singularities, and the presence of diffusion often limits one to using implicit or semi-implicit time-step methods for stability constraints. Finite-time singularities are particularly challenging due to the large range of scales that one desires to resolve, often with adaptive spatial grids and adaptive time steps. Here, in this study, we show two examples of nonlinear PDEs for which the self-similar singularity structure has time and space scales that are resolvable using the RKL and RKG methods, without forcing even smaller time steps. Compared to commonly used implicit numerical methods, we achieve a significantly smaller run time while maintaining comparable accuracy. We also prove numerical monotonicity for both the RKL and RKG methods under their linear stability conditions for the constant coefficient heat equation, in the case of infinite domain and periodic boundary condition, leading to a theoretical guarantee of the superiority of the RKL and RKG methods over traditional super-time-stepping methods, such as the Runge-Kutta-Chebyshev and the orthogonal Runge-Kutta-Chebyshev methods. Code can be found at https://github.com/ZT220501/SRK-Singularity.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Mixed precision s –step Lanczos and conjugate gradient algorithms

Compared to the classical Lanczos algorithm, the s-step Lanczos variant has the potential to improve performance by asymptotically decreasing the synchronization cost per iteration. However, this comes at a price; despite being mathematically equivalent, the s-step variant may behave quite differently in finite precision, potentially exhibiting greater loss of accuracy and slower convergence relative to the classical algorithm. It has previously been shown that the errors in the s-step version follow the same structure as the errors in the classical algorithm, but are amplified by a factor depending on the square of the condition number of the O(s)-dimensional Krylov bases computed in each outer loop. As the condition number of these s-step bases grows (in some cases very quickly) with s, this limits the s values that can be chosen and thus can limit the attainable performance. In this work, we show that if a select few computations in s-step Lanczos are performed in double the working precision, the error terms then depend only linearly on the conditioning of the s-step bases. This has the potential for drastically improving the numerical behavior of the algorithm with little impact on per-iteration performance. Our numerical experiments demonstrate the improved numerical behavior possible with the mixed precision approach, and also show that this improved behavior extends to mixed precision s-step CG. Here, we present preliminary performance results on NVIDIA V100 GPUs that show that the overhead of extra precision is minimal if one uses precisions implemented in hardware.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Shapiro steps and stability of skyrmions interacting with alternating anisotropy under the influence of ac and dc drives

Here we use atomistic simulations to examine the sliding dynamics of a skyrmion in a two-dimensional system containing a periodic one-dimensional stripe pattern of variations between low and high values of the perpendicular magnetic anisotropy. The skyrmion changes in size as it crosses the interface between two anisotropy regions. On applying combined dc and ac driving in either parallel or perpendicular directions, we observe a wide variety of Shapiro steps, Shapiro spikes, and phase-locking phenomena. The phase-locked orbits have two-dimensional dynamics due to the gyrotropic or Magnus dynamics of the skyrmions and are distinct from the phase-locked orbits found for strictly overdamped systems. Along a given Shapiro step when the ac drive is perpendicular to the dc drive, the velocity parallel to the ac drive is locked while the velocity in the perpendicular direction increases with increasing drive to form Shapiro spikes. At the transition between adjacent Shapiro steps, the parallel velocity jumps up to the next step value, and the perpendicular velocity drops. The skyrmion Hall angle shows a series of spikes as a function of increasing dc drive, where the jumps correspond to the transition between different phase-locked steps. At high drives, the Shapiro steps and Shapiro spikes are lost. When both the ac and dc drives are parallel to the stripe periodicity direction, Shapiro steps appear, while if the dc drive is parallel to the stripe periodicity direction and the ac drive is perpendicular to the stripe periodicity, then there are only two locked phases, and the skyrmion motion consists of a combination of sliding along the interfaces between the two anisotropy values and jumping across the interfaces.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

First Solar Thermal Energy Planner (STEP 1) and Nationwide Industrial Heat and Power Analysis

The First Solar Thermal Energy Planner (STEP 1) and Nationwide Industrial Heat and Power Analysis (aka the STEP 1 Project or the Project) aimed to (1) developed a brand-new web tool that could provide decision support through free, rapid techno-economic analysis of behind-the-meter solar+storage systems for industrial process heat and (2) conduct high-level analyses of the cost-competitiveness of the same systems across the US in key sectors. The STEP 1 web tool collects key location, land availability, thermal load profile, proccess heat temperature and media, and other key parameters through an easy-to-use user interface (UI). The UI was designed to meet the user at their level of understanding by minimizing the number of required inputs as much as possible while including options for more nuanced inputs if the user desires. STEP 1 advises users on which solar thermal tehcnologies that could fit their needs based on the inputs provided (namely process media and temperature). The tool can model a wide range of solar thermal technologies including flat plate collectors, evacuated tubes, parabolic troughs, linear Fresnel, and molten salt towers all with corresponding thermal energy storage (TES) - solar PV with resistive heating and TES is also included. Once the parameters are collected, a nominal thermal energy production profile for the facility's location is generated using NREL's System Advisory Model (SAM) and then passed to a modified version of NREL's REopt platform to optimize the size (capacity) and dispatch of the solar+storage system to minimize lifecycle costs subject to energy balance, fuel and electricity rates, emission reductions goals, and other constraints. This entire process takes less than 20 minutes, is completely free, requires zero coding skills, and provides the user with a high-level assessment on the techno-economic feasability of deploying solar+storage systems for their energy needs. In addition to the development of the STEP 1 web tool, the project completed two complementary analyses focused on leveraging the backend code of STEP 1, public industrial facility locations and fuel consumption data, and key sector information to assess the economic opportunity of reducing fuel costs at various levels of capacity factor around the US. Both analyses found that there are key markets, locations, industrial sectors (namely food and beverage), and degrees of offset where solar thermal technologies could be cost-effectively deployed, highlighting a key market entry point for these technologies, and assessing deployment potential. In summary, the STEP 1 project improved the opportunities for solar+storage systems to expand into the industrial process heat market through breaking down barriers to assessing these technologies.

14 SOLAR ENERGY↗
DOE OSTI2021

A Two-Step PCR Protocol Enabling Flexible Primer Choice and High Sequencing Yield for Illumina MiSeq Meta-Barcoding

High-throughput amplicon sequencing that primarily targets the 16S ribosomal DNA (rDNA) (for bacteria and archaea) and the Internal Transcribed Spacer rDNA (for fungi) have facilitated microbial community discovery across diverse environments. A three-step PCR that utilizes flexible primer choices to construct the library for Illumina amplicon sequencing has been applied to several studies in forest and agricultural systems. The three-step PCR protocol, while producing high-quality reads, often yields a large number (up to 46%) of reads that are unable to be assigned to a specific sample according to its barcode. Here, we improve this technique through an optimized two-step PCR protocol. We tested and compared the improved two-step PCR meta-barcoding protocol against the three-step PCR protocol using four different primer pairs (fungal ITS: ITS1F-ITS2 and ITS1F-ITS4, and bacterial 16S: 515F-806R and 341F-806R). We demonstrate that the sequence quantity and recovery rate were significantly improved with the two-step PCR approach (fourfold more read counts per sample; determined reads ≈90% per run) while retaining high read quality (Q30 > 80%). Given that synthetic barcodes are incorporated independently from any specific primers, this two-step PCR protocol can be broadly adapted to different genomic regions and organisms of scientific interest.

16S rDNA↗