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DOE OSTI2023

A constitutive model for sheared dense fiber suspensions

Here we propose a constitutive model to predict the viscosity of fiber suspensions, which undergoes shear thinning, at various volume fractions, aspect ratios, and shear stresses/rates. We calibrate the model using the data from direct numerical simulation and prove the accuracy by predicting experimental measurements from the literature. We use a friction coefficient decreasing with the normal load between the fibers to quantitatively reproduce the experimentally observed shear thinning in fiber suspensions. In this model, the effective normal contact force, which is directly proportional to the bulk shear stress, determines the effective friction coefficient. A rise in the shear stress reduces the effective friction coefficient in the suspension. As a result, the jamming volume fraction increases with the shear stress, resulting in a shear thinning in the suspension viscosity. Moreover, we extend the model to quantify the effects of fiber volume fraction and aspect ratio in the suspension. We calibrate this model using the data from numerical simulations for the rate-controlled shear flow. Once calibrated, we show that the model can be used to predict the relative viscosity for different volume fractions, shear stresses, and aspect ratios. The model predictions are in excellent agreement with the available experimental measurements from the literature. The findings of this study can potentially be used to tune the fiber size and volume fraction for designing the suspension rheology in various applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

On the functional dependence of transition-potential coupled cluster

Orbital relaxation of the core region is a primary source of error in the computation of core ionization and core excitation energies. Recently, Transition-Potential Coupled Cluster (TP-CC) methods have been used to explicitly treat orbital relaxation using non-variational molecular orbitals determined by reoccupation of orbitals optimized for a fractional core occupation. The amount of fractional occupation is governed by parameter λ, and recommended values for accurate TP-CCSD and XTP-CCSD computations of carbon, nitrogen, oxygen, and fluorine K edges were previously determined. Herein, we explore the performance of several density functionals for generating the fractionally occupied orbitals used in TP-CCSD. These functionals include HF, BP86, BH&HLYP, B3LYP, M06-2X, and ωB97m-V. The fractionally occupied orbitals computed across the various functionals were subsequently employed as the initial orbitals for our TP-CCSD calculations of organic K-edge x-ray absorption and photoelectron spectra. Regardless of the functional used to generate the fractionally occupied orbitals, the TP-CCSD calculations yield accurate and comparable core ionization energies, core excitation energies, and oscillator strengths.

Coupled-cluster methods↗
DOE OSTI2022

Impact of CH 4 addition on the electron properties and electric field dynamics in a Ar nanosecond-pulsed dielectric barrier discharge

Non-equilibrium plasmas derive their low temperature reactivity from producing and driving energetic electrons and active species under large electric fields. Therefore, the impact of reactants on the plasma properties including electron number density, electric field, and electron temperature is critical for applications such as plasma CH 4 reforming. Due to experimental complexity, electron properties and the electric field are rarely measured together in the same discharge. Here, we combine time-resolved Thomson scattering and electric field induced second harmonic generation (EFISH) to probe electron temperature, electron density, and electric field strength in a 60 Torr CH 4 /Ar nanosecond-pulsed dielectric barrier discharge (ns-DBD) while varying the CH 4 mole fraction from 0 to 8%. These measurements are compared to a 1-D numerical model to benchmark its predictions and identify areas of uncertainty. Nonlinear coupling between CH 4 addition, electron temperature, electron density, and the electric field was directly observed. Contrary to previous measurements in He, the electron temperature increased with CH 4 mole fraction. This rise in electron temperature is identified as electron heating by residual electric fields that increased with larger CH 4 mole fraction. Moreover, the electron number density has been found to decrease rapidly with the increase of methane mole fraction. Comparison of these measurements with the model yielded better agreement at higher CH 4 mole fractions and with the usage of ab initio calculated Ar electron-impact cross-sections from the B-spline R-matrix (BSR) database. Furthermore, the calculated plasma properties are shown to be sensitive to the residual surface charge implanted on the quartz dielectric surfaces. Without considering surface charge in the simulations, the calculated electric field profiles agreed well with the measurements, but the electron properties were underpredicted by more than a factor of three. Therefore, measurements of either the electric field or electron properties measurements alone are insufficient to fully validate modelling predictions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Abundance and properties of dark radiation from the cosmic microwave background

We study the cosmological signatures of new light relics that are collisionless like standard neutrinos or are strongly interacting. We provide a simple and succinct rephrasing of their physical effects in the cosmic microwave background, as well as the resulting parameter degeneracies with other cosmological parameters, in terms of the total radiation abundance and the fraction thereof that freely streams. In these more general terms, interacting and noninteracting light relics are differentiated by their respective decrease and increase of the free-streaming fraction, and, moreover, the scale-dependent interplay thereof with a common, correlated reduction of the fraction of matter in baryons. We then derive updated constraints on various dark-radiation scenarios with the latest cosmological observations, employing this language to identify the physical origin of the impact of each dataset. The “PR4” reanalyses of Planck CMB data prefer a larger primordial helium yield and therefore also slightly more radiation than the 2018 analysis; we investigate the differences between the two releases that drives these shifts. Smaller free-streaming fractions are disfavored by the excess lensing of the CMB measured in lensing reconstruction data from Planck and the Atacama Cosmology Telescope. On the other hand, baryon acoustic oscillation measurements from the Dark Energy Spectroscopic Instrument drive marginal detections of new, strongly interacting light relics due to that data's preference for lower matter fractions. Finally, we forecast measurements from the CMB-S4 experiment.

cosmological parameters from CMBR↗
DOE OSTI2021

Correcting correlation functions for redshift-dependent interloper contamination

ABSTRACT The construction of catalogues of a particular type of galaxy can be complicated by interlopers contaminating the sample. In spectroscopic galaxy surveys this can be due to the misclassification of an emission line; for example in the Hobby–Eberly Telescope Dark Energy Experiment (HETDEX) low-redshift [O ii] emitters may make up a few per cent of the observed Ly α emitter (LAE) sample. The presence of contaminants affects the measured correlation functions and power spectra. Previous attempts to deal with this using the cross-correlation function have assumed sources at a fixed redshift, or not modelled evolution within the adopted redshift bins. However, in spectroscopic surveys like HETDEX, where the contamination fraction is likely to be redshift dependent, the observed clustering of misclassified sources will appear to evolve strongly due to projection effects, even if their true clustering does not. We present a practical method for accounting for the presence of contaminants with redshift-dependent contamination fractions and projected clustering. We show using mock catalogues that our method, unlike existing approaches, yields unbiased clustering measurements from the upcoming HETDEX survey in scenarios with redshift-dependent contamination fractions within the redshift bins used. We show our method returns autocorrelation functions with systematic biases much smaller than the statistical noise for samples with at least as high as 7 per cent contamination. We also present and test a method for fitting for the redshift-dependent interloper fraction using the LAE–[O ii] galaxy cross-correlation function, which gives less biased results than assuming a single interloper fraction for the whole sample.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Star-spots and magnetism: testing the activity paradigm in the Pleiades and M67

We measure star-spot filling fractions for 240 stars in the Pleiades and M67 open star clusters using APOGEE high-resolution H-band spectra. For this work, we developed a modified spectroscopic pipeline which solves for star-spot filling fraction and star-spot temperature contrast. We exclude binary stars, finding that the large majority of binaries in these clusters (80 per cent) can be identified from Gaia DR3 and APOGEE criteria – important for field star applications. Our data agree well with independent activity proxies, indicating that this technique recovers real star-spot signals. In the Pleiades, filling fractions saturate at a mean level of 0.248 ± 0.005 for active stars with a decline at slower rotation; we present fitting functions as a function of Rossby number. In M67, we recover low mean filling fractions of 0.030 ± 0.008 and 0.003 ± 0.002 for main sequence GK stars and evolved red giants, respectively, confirming that the technique does not produce spurious spot signals in inactive stars. Star-spots also modify the derived spectroscopic effective temperatures and convective overturn time-scales. Effective temperatures for active stars are offset from inactive ones by −109 ± 11 K, in agreement with the Pecaut & Mamajek empirical scale. Star-spot filling fractions at the level measured in active stars changes their inferred overturn time-scale, which biases the derived threshold for saturation. Finally, we identify a population of stars statistically discrepant from mean activity–Rossby relations and present evidence that these are genuine departures from a Rossby scaling. Our technique is applicable to the full APOGEE catalogue, with broad applications to stellar, galactic, and exoplanetary astrophysics.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Time variability of ultra fast BAL outflows using SALT: C IV equivalent width analysis

We study the time variability (over ≤7.3 yr) of ultra fast outflows (UFOs) detected in a sample of 64 C IV broad absorption line (BAL) quasars (with 80 distinct BAL components) monitored using the Southern African Large Telescope. By comparing the properties of the quasar in our sample with those of a control sample of non-BAL quasars, we show that the distributions of black hole mass are different and the bolometric luminosities and optical photometric variations of UFO BAL quasars are slightly smaller compared to that of non-BAL quasars. The detection fraction of C IV equivalent width (W) variability (∼95 per cent), the fractional variability amplitude $\left(\frac{\Delta W}{W}\right)$ and the fraction of ‘highly variable’ BAL (i.e. $\big|$$\frac{\Delta W}{W}$$\big|$ > 0.67) components (∼33 per cent) are higher in our sample compared to the general BAL population. The scatter in $\frac{\Delta W}{W}$ and the fraction of ‘highly variable’ BALs increase with the time-scale probed. The $\frac{\Delta W}{W}$ distribution is asymmetric at large time scales. We attribute this to the BAL strengthening time-scales being shorter than the weakening time-scales. The BAL variability amplitude correlates strongly with the BAL properties compared to the quasar properties. BALs with low W, high-velocity, shallow profiles, and low-velocity width tend to show more variability. When multiple BAL components are present, a correlated variability is seen between low- and high-velocity components with the latter showing a larger amplitude variations. We find an anticorrelation between the fractional variations in the continuum flux and W. While this suggests photoionization induced variability, the scatter in continuum flux is much smaller than that of W.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Emergence of the temperature–density relation in the low-density intergalactic medium

We examine the evolution of the phase diagram of the low-density intergalactic medium during the Epoch of Reionization in simulation boxes with varying reionization histories from the Cosmic Reionization on Computers project. The probability density function (PDF) of gas temperature at fixed density exhibits two clear modes: a warm and a cold temperature mode, corresponding to the gas inside and outside of ionized bubbles. We find that the transition between the two modes is ‘universal’ in the sense that its timing is accurately parametrized by the value of the volume-weighted neutral fraction for any reionization history. This ‘universality’ is more complex than just a reflection of the fact that ionized gas is warm and neutral gas is cold: it holds for the transition at a fixed value of gas density, and gas at different densities transitions from the cold to the warm mode at different values of the neutral fraction, reflecting a non-trivial relationship between the ionization history and the evolving gas density PDF. Furthermore, the ‘emergence’ of the tight temperature–density relation in the warm mode is also approximately ‘universally’ controlled by the volume-weighted neutral fraction for any reionization history. In particular, the ‘emergence’ of the temperature–density relation (as quantified by the rapid decrease in its width) occurs when the neutral fraction is 10 –4 ≲ X HI ≲ 10 –3 for any reionization history. Our results indicate that the neutral fraction is a primary quantity controlling the various properties of the temperature–density relation, regardless of reionization history.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Study of the decay D s + → π + π + π - η and observation of the W -annihilation decay D s + → a 0 ( 980 ) + ρ 0

The decay $D^+_s$ → $π^+π^+π^-η$ is observed for the first time, using e + e - collision data corresponding to an integrated luminosity of 6.32 fb -1 collected by the BESIII detector at center-of-mass energies between 4.178 and 4.226 GeV. The absolute branching fraction for this decay is measured to be $\mathscr{B}$($D^+_s$ → $π^+π^+π^-η$) = (3.12 ± 0.13 stat ± 0.90 syst )%. The first amplitude analysis of this decay reveals the substructures in $D^+_s$ → $π^+π^+π^-η$ nd determines the relative fractions and the phases among these substructures. The dominant intermediate process is $D^+_s$ → $a_1$(1260) + $η,a_1$(1260) + → ρ(770) 0 $π^+$ with a branching fraction of (1.73 ± 0.14 stat ±0.08 syst )%. We also observe the W-annihilation process $D^+_s$ → $a_0$(980) + ρ(770) 0 , $a_0$(980) + → $π^+η$ with a branching fraction of (0.21 ± 0.08 stat ± 0.05 syst )%, which is larger than the branching fractions of other measured pure W-annihilation decays by 1 order of magnitude.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Observation of D → K ¯ 1 ( 1270 ) μ + ν μ and test of lepton flavor universality with D → K ¯ 1 ( 1270 ) ℓ + ν ℓ

By analyzing 7.93 fb − 1 of e + e − collision data collected at the center-of-mass energy of 3.773 GeV with the BESIII detector operated at the BEPCII collider, we report the observation of the semimuonic decays of D + → K ¯ 1 ( 1270 ) 0 μ + ν μ and D 0 → K 1 ( 1270 ) − μ + ν μ with statistical significances of 12.5 σ and 6.0 σ , respectively. Their decay branching fractions are determined to be B [ D + → K ¯ 1 ( 1270 ) 0 μ + ν μ ] = ( 2.36 ± 0.2 0 − 0.27 + 0.18 ± 0.48 ) × 10 − 3 and B [ D 0 → K 1 ( 1270 ) − μ + ν μ ] = ( 0.78 ± 0.1 1 − 0.09 + 0.05 ± 0.15 ) × 10 − 3 , where the first and second uncertainties are statistical and systematic, respectively, and the third originates from the input branching fraction of K ¯ 1 ( 1270 ) 0 → K − π + π 0 or K 1 ( 1270 ) − → K − π + π − . Combining our branching fractions with the previous measurements of B [ D + → K ¯ 1 ( 1270 ) 0 e + ν e ] and B [ D 0 → K 1 ( 1270 ) − e + ν e ] , we determine the branching fraction ratios to be B [ D + → K ¯ 1 ( 1270 ) 0 μ + ν μ ] / B [ D + → K ¯ 1 ( 1270 ) 0 e + ν e ] = 1.03 ± 0.14 − 0.15 + 0.11 and B [ D 0 → K 1 ( 1270 ) − μ + ν μ ] / B [ D 0 → K 1 ( 1270 ) − e + ν e ] = 0.74 ± 0.13 − 0.13 + 0.08 . Using the branching fractions measured in this work and the world-average lifetimes of the D + and D 0 mesons, we determine the semimuonic partial decay width ratio to be Γ [ D + → K ¯ 1 ( 1270 ) 0 μ + ν μ ] / Γ [ D 0 → K 1 ( 1270 ) − μ + ν μ ] = 1.22 ± 0.10 − 0.09 + 0.06 , which is consistent with unity as predicted by isospin conservation. Published by the American Physical Society 2025

Ablikim, M.↗
DOE OSTI2022

Simulation and Reynolds-averaged Navier-Stokes modeling of a three-component Rayleigh-Taylor mixing problem with thermonuclear burn

Rayleigh-Taylor mixing in the presence of a third component with intermediate density is investigated through three-dimensional large-eddy simulation (LES) with a high-order compact finite-difference code. Two configurations are considered: (1) a symmetric configuration in which the Atwood number between the heavy and intermediate components matches the Atwood number between the intermediate and light components and (2) an asymmetric configuration in which the Atwood number between the heavy and intermediate components is an order of magnitude greater than the Atwood number between the intermediate and light components. Mass fraction covariances are extracted, and proposed Reynolds-averaged Navier-Stokes (RANS) closures for density-specific-volume and density-mass-fraction covariances are evaluated in an a priori fashion. Additionally, a multicomponent extension of the k - Φ - L - a - V RANS model [Morgan, Phys. Rev. E 104, 015107 (2021)] is presented which includes model equations for the upper-triangular elements of the mass fraction covariance matrix. This model, referred to as the k - Φ - L - a - C model, is compared against results from LES and against other RANS models. Profiles of average mass fraction, mass-fraction covariance, and density-specific-volume covariance obtained with the k - Φ - L - a - C model are found to agree well with LES data. Finally, the impact of three-component turbulent mixing on average reaction rate is investigated in both premixed and nonpremixed cases by heating the mixing layer and allowing it to undergo thermonuclear (TN) burn. A closure model for average reaction rate is proposed for use with the k - Φ - L - a - C model, and when this model is applied, improved agreement is obtained between LES and RANS in total TN neutron production.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Observation of the W -Annihilation Process D s + → ω ρ + and Measurement of D s + → ϕ ρ + in D s + → π + π + π − π 0 π 0 Decays

We present the first amplitude analysis and branching fraction measurement of the decay D s + → π + π + π − π 0 π 0 , using e + e − collision data collected with the BESIII detector at center-of-mass energies between 4.128 and 4.226 GeV corresponding to an integrated luminosity of 7.33 fb − 1 , and report the first observation of the pure W -annihilation decay D s + → ω ρ + with a branching fraction of ( 0.99 ± 0.0 8 stat − 0.07 + 0.05 syst ) % . In comparison to the low significance of the D wave in the decay D s + → ϕ ρ + , the dominance of the D wave over the S and P waves, with a fraction of ( 51.85 ± 7.2 8 stat − 7.90 + 4.83 syst ) % observed in the decay D s + → ω ρ + , provides crucial information for the “polarization puzzle,” as well as for the understanding of charm meson decays. The branching fraction of D s + → π + π + π − π 0 π 0 is measured to be ( 4.41 ± 0.1 5 stat ± 0.1 3 syst ) % . Moreover, the branching fraction of D s + → ϕ ρ + is measured to be ( 3.98 ± 0.3 3 stat − 0.19 + 0.21 syst ) % , and the R ϕ = B ( ϕ → π + π − π 0 ) / B ( ϕ → K + K − ) is determined to be ( 0.222 ± 0.01 9 stat − 0.016 + 0.016 syst ), which is consistent with the previous measurement based on charm meson decays, but deviates from the results from e + e − annihilation and K − N scattering experiments by more than 3 σ . Published by the American Physical Society 2025

Ablikim, M.↗
DOE OSTI2024

Lipid droplet-associated proteins in alcohol-associated fatty liver disease: A proteomic approach

The earliest manifestation of alcohol-associated liver disease (ALD) is steatosis characterized by deposition of fat in specialized organelles called lipid droplets (LDs). While alcohol administration causes a rise in LD numbers in the hepatocytes, little is known regarding their characteristics that allow their accumulation and size to increase. The aim of the present study is to gain insights into underlying pathophysiological mechanisms by investigating the ethanol-induced changes in hepatic LD proteome as a function of LD size. Adult male Wistar rats (180–200 g BW) were fed with ethanol liquid diet for 6 weeks. At sacrifice, large-, medium-, and small-sized hepatic LD subpopulations (LD1, LD2, and LD3, respectively) were isolated and subjected to morphological and proteomic analyses. Morphological analysis of LD1-LD3 fractions of ethanol-fed rats clearly demonstrated that LD1 contained larger LDs compared with LD2 and LD3 fractions. Our preliminary results from principal component analysis showed that the proteome of different-sized hepatic LD fractions was distinctly different. Proteomic data analysis identified over 2000 proteins in each LD fraction with significant alterations in protein abundance among the three LD fractions. Among the altered proteins, several were related to fat metabolism, including synthesis, incorporation of fatty acid, and lipolysis. Ingenuity pathway analysis revealed increased fatty acid synthesis, fatty acid incorporation, LD fusion, and reduced lipolysis in LD1 compared to LD3. Overall, the proteomic findings indicate that the increased level of protein that facilitates fusion of LDs combined with an increased association of negative regulators of lipolysis dictates the generation of large-sized LDs during the development of alcohol-associated hepatic steatosis. Several significantly altered proteins were identified in different-sized LDs isolated from livers of ethanol-fed rats. Ethanol-induced increases in specific proteins that hinder LD lipid metabolism led to the accumulation and persistence of large-sized LDs in the liver.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

The ionic conductivity of Sm‐doped ceria

Abstract The oxygen ion conductivity of polycrystalline samples of Sm‐doped ceria and of Gd‐doped ceria is studied as a function of doping fraction and temperature using impedance spectroscopy allowing the separation of bulk and grain boundary conductivity. The introduction of a fine spacing for the Sm dopant fraction allows the clear identification of the dopant fraction leading to the largest bulk conductivity. At 267°C, the largest bulk conductivity is shown for Ce 0.93 Sm 0.07 O 1.965 . With increasing temperature, indications of an increase in the dopant fraction, which leads to the maximum in conductivity, are found. For the grain boundary conductivity, the maximum appears at larger dopant fractions compared to the bulk conductivity. The largest total conductivity for both dopants is again found for Sm‐doped ceria. In literature, different syntheses and sample preparation methods led to larger total conductivities for Gd‐doped ceria. In this work, we demonstrate that the variation of sintering conditions leads to scattering in the conductivity over one order of magnitude. Finally, we demonstrate that, in nominally pure cerium oxide, impurities dominate the ionic conductivity.

Koettgen, Julius↗
DOE OSTI2020

Magnesium isotopes of the bulk solar wind from Genesis diamond-like carbon films

–NASA’s Genesis Mission returned solar wind (SW) to the Earth for analysis to derive the composition of the solar photosphere from solar material. SW analyses control the precision of the derived solar compositions, but their ultimate accuracy is limited by the theoretical or empirical models of fractionation due to SW formation. Mg isotopes are “ground truth” for these models since, except for CAIs, planetary materials have a uniform Mg isotopic composition (within ≤1&) so any significant isotopic fractionation of SW Mg is primarily that of SW formation and subsequent acceleration through the corona. This study analyzed Mg isotopes in a bulk SW diamond-like carbon (DLC) film on silicon collector returned by the Genesis Mission. A novel data reduction technique was required to account for variable ion yield and instrumental mass fractionation (IMF) in the DLC. The resulting SW Mg fractionation relative to the DSM-3 laboratory standard was ( 14.4&, 30.2&) (4.1&, 5.5&), where the uncertainty is 2σ SE of the data combined with a 2.5& (total) error in the IMF determination. Two of the SW fractionation models considered generally agreed with our data. Their possible ramifications are discussed for O isotopes based on the CAI nebular composition of McKeegan et al. (2011).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Erratum to: Search for single top-quark production via flavour-changing neutral currents at 8 TeV with the ATLAS detector

One correction is noted for the paper. The branching fraction ($\mathcal{B}$($W →{ℓv}$) = 0.3246 was not included in the conversion of the observed cross-section limit, σ x $\mathcal{B}$( $t →Wb$) x ($\mathcal{B}$($W →{ℓv}$) < 2.9to the coupling constants $κ_{ugt}$ and $κ_{cgt}$ and the branching fractions $\mathcal{B}$( $t →ug$) and $\mathcal{B}$( $t →cg$). The inclusion leads to weaker observed exclusion limits on the coupling constants divided by the scale of new physics of $k_{ugt}$/ Λ <10 x 10 -3 TeV -1 and $k_{cgt}$/Λ <23 x 10 -3 TeV -1 and on the branching fractions $\mathcal{B}$( $t →ug$) < 1.2 x10 -4 and $\mathcal{B}$( $t →cg$) < 6.4 x 10 -4 . The predicted exclusion limits on the coupling constants divided by the scale of new physics are $k_{ugt}$/ Λ < 9.5 x 10 -3 TeV -1 and $\mathcal{B}$( $t →cg$)/ Λ < 22 x 10 -3 TeV -1 and on the branching fractions $\mathcal{B}$( $t →ug$) < 1.1 x 10 -4 and $\mathcal{B}$( $t →cg$) < 5.7 x 10 -4 . Updated distributions of the observed upper limits on the coupling constants for combinations of cgt and ugt channels are shown in Figure 10a and on the branching fractions in Figure 10b.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Variation in sugarcane biomass composition and enzymatic saccharification of leaves, internodes and roots

The composition of biomass determines its suitability for different applications within a biorefinery system. The proportion of the major biomass fractions (sugar, cellulose, hemicellulose and lignin) may vary in different sugarcane genotypes and growth environments and different parts of the plant. This study investigated the composition of mature and immature internodes, roots and mature leaves of sugarcane. Internodes were found to have a significantly larger alcohol-soluble component than leaves and roots. The primary difference between the immature and mature internodes was the ratio of soluble sugars. In mature tissues, sucrose content was significantly higher, whereas in immature internodal tissues there was lower sucrose and heightened concentrations of reducing sugars. Carbon (C) partitioning in leaf tissues was characterised by low levels of soluble components and high “other” and cell wall fractions. Root tissue had low ratios of soluble fractions relative to their cell wall contents, indicating a lack of storage of soluble carbon. There was no significant difference in the ratio of the major cell wall fractions between the major organ types. Characterisation of individual non-cellulosic monomers indicated leaf and root tissues had significantly higher arabinose and galactose fractions. Significantly larger proportions of syringyl lignin compounds and the hydroxycinnamic compound, p-coumaric acid were observed in mature internodal tissues compared to the other tissue types. Tissue-specific differences in composition were shown to greatly affect the recalcitrance of the cell wall to enzymatic saccharification. Overall, this study displayed clear evidence of the differential partitioning of C throughout the sugarcane plant in specific organs. These organ-specific differences have major implications in their utility as a bioproduct feedstock. For example, the inclusion of trash (leaves) with the culms (internodes) may alter processing efficiency.

09 BIOMASS FUELS↗
DOE OSTI2022

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Abstract Background Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing—SIP—remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance—the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling. Results Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13 C-AMF hyphosphere DNA from a 13 CO 2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10–33 atom% 13 C), even though the soils’ overall enrichment was low (1.8 atom% 13 C). We assembled 212 13 C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13 C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera . Conclusions Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP—fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat—generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs’ phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling.

59 BASIC BIOLOGICAL SCIENCES↗