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DOE OSTI2019

Polaron and Exciton Delocalization in Oligomers of High-Performance Polymer PTB7

A key characteristic of organic photovoltaic cells is the efficient charge separation in the active layer. Sufficient delocalization of the positive polaron in organic photovoltaics is considered essential for the effective separation of the opposite charges and the suppression of recombination. Here we use light-induced EPR and ENDOR spectroscopy combined with DFT calculations to determine the electronic structure of the positive polaron in PTB7-type oligomers. Utilizing the superior spectral resolution of high-frequency (130 GHz) D-band EPR, the principal components of the g tensors were determined. Pulsed ENDOR spectroscopy at X-band allowed the measurement of H-1 hyperfine coupling constants. A comparison of g tensors and H-1 hyperfine coupling constants of the PTB7-type oligomers with the high-performance PTB7 polymer revealed a delocalization of the positive polaron in the polymer over about four monomeric units, corresponding to about 45 angstrom in length. Our current study thus not only determines the polaron delocalization length in PTB7 but also validates the approach combining EPR/ENDOR spectroscopy with DFT-calculated magnetic resonance parameters. This is of importance in those cases where oligomers of defined length are not easily obtained. In addition, the delocalization of the neutral triplet exciton was also determined in the oligomers and compared with polymer PTB7. The analysis revealed that the neutral triplet exciton is substantially more delocalized than the positive polaron, exceeding 10 monomeric units.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

A New Approach for Simultaneous Estimation of Entrainment and Detrainment Rates in Non- Precipitating Shallow Cumulus

A new approach is developed for estimating entrainment and detrainment rates in cumulus clouds based on aircraft observations. Equations relating entrainment and detrainment rates to gross entrainment and detrainment are derived. This approach is applied to the Holistic Interactions of Shallow Clouds, Aerosols, and Land-Ecosystems field campaign, supported by the U.S. Department of Energy's Atmospheric Radiation Measurement program. The results show that both entrainment and detrainment rates decrease with increasing height. Sensitivity tests with different detrained air assumptions yield similar results. The entrainment and detrainment rates can reproduce the cloud thermodynamic variables. Partial correlation analysis indicates that entrainment rate is positively correlated with environmental relative humidity (RH), and detrainment rate is negatively correlated with environmental RH and positively correlated with entrainment rate. This new approach can be applied to other cloud observations to obtain a data set of entrainment and detrainment rates in cumulus clouds.

Zhu, Lei↗

DOE OSTI2024

Observational Quantification of Tropical High Cloud Changes and Feedbacks

Abstract The response of tropical high clouds to surface warming and their radiative feedbacks are uncertain. For example, it is uncertain whether their coverage will contract or expand in response to surface warming and whether such changes entail a stabilizing radiative feedback (iris feedback) or a neutral feedback. Global satellite observations with passive and active remote sensing capabilities over the last two decades can now be used to address such effects that were previously observationally limited. Using these observations, we show that the vertically averaged coverage exhibits no significant contraction or expansion. However, we find a reduction in coverage at the altitude where high clouds peak and are particularly radiatively‐relevant. This results in a negative longwave (LW) feedback and a positive shortwave (SW) feedback which cancel to yield a near‐zero high‐cloud amount feedback, providing observational evidence against an iris feedback. Next, we find that tropical high clouds have risen but have also warmed, leading to a positive, but small, high‐cloud altitude feedback dominated by the LW feedback. Finally, we find that high clouds have been thinning, leading to a near‐zero high‐cloud optical depth feedback from a cancellation between negative LW and positive SW feedbacks. Overall, high clouds lead the total tropical cloud feedback to be small due to the negative LW‐positive SW feedback cancellations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Microbial Ecology and Site Characteristics Underlie Differences in Salinity-Methane Relationships in Coastal Wetlands

Methane (CH 4 ) is a potent greenhouse gas emitted by archaea in anaerobic environments such as wetland soils. Tidal freshwater wetlands are predicted to become increasingly saline as sea levels rise due to climate change. Previous work has shown that increases in salinity generally decrease CH 4 emissions, but with considerable variation, including instances where salinization increased CH 4 flux. We measured microbial community composition, biogeochemistry, and CH 4 flux from field samples and lab experiments from four different sites across a wide geographic range. We sought to assess how site differences and microbial ecology affect how CH 4 emissions are influenced by salinization. CH 4 flux was generally, but not always, positively correlated with CO 2 flux, soil carbon, ammonium, phosphate, and pH. Methanogen guilds were positively correlated with CH 4 flux across all sites, while methanotroph guilds were both positively and negatively correlated with CH 4 depending on site. There was mixed support for negative relationships between CH 4 fluxes and concentrations of alternative electron acceptors and abundances of taxa that reduce them. CH 4 /salinity relationships ranged from negative, to neutral, to positive and appeared to be influenced by site characteristics such as pH and plant composition, which also likely contributed to site differences in microbial communities. The activity of site-specific microbes that may respond differently to low-level salinity increases is likely an important driver of CH 4 /salinity relationships. Our results suggest several factors that make it difficult to generalize CH 4 /salinity relationships and highlight the need for paired microbial and flux measurements across a broader range of sites.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Molecular dynamics simulations of the secondary-binding site in disaccharide-modified glycopeptide antibiotics

Oritavancin is a semisynthetic glycopeptide antibiotic used to treat severe infections by multidrug-resistant Gram-positive pathogens. Oritavancin is known to be a thousand times more potent than vancomycin against Gram-positive bacteria due to the additional interactions with bacterial peptidoglycan (PG) facilitated by a secondary-binding site. The presence of this secondary-binding site is evident in desleucyl-oritavancin, an Edman degradation product of oritavancin, still retaining its potency against Gram-positive bacteria, whereas desleucyl-vancomycin is devoid of any antimicrobial activities. Herein, using explicit solvent molecular dynamics (MD) simulations, steered MD simulations, and umbrella sampling, we show evidence of a secondary-binding site mediated by the disaccharide-modified hydrophobic sidechain of oritavancin interactions with the pentaglycyl-bridge segment of the PG. The interactions were characterized through comparison to the interaction of PG with chloroeremomycin, vancomycin, and the desleucyl analogs of the glycopeptides. Our results show that the enhanced binding of oritavancin to PG over the binding of the other complexes studied is due to an increase in the hydrophobic effect, electrostatic and van der Waals interactions, and not the average number of hydrogen bonds. Our ranking of the binding interactions of the biomolecular complexes directly correlates with the order based on their experimental minimum inhibitory concentrations. The results of our simulations provide insight into the modification of glycopeptides to increase their antimicrobial activities or the design of novel antibiotics against pathogenic Gram-positive bacteria.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

The interplay between spatial and heliconical orientational order in twist-bend nematic materials

The helical pitch formed by organic molecules, such as the α-helix of proteins, usually requires hydrogen bonding between chiral units and long-range positional order. It was recently found that certain liquid crystal oligomers can have a twist-bend nematic (NTB) phase with nanoscale heliconical structure without hydrogen bonding, molecular chirality or positional order. To understand the nature of this unique structure, here we present hard and resonant tender X-ray scattering studies of two novel sulfur containing dimer materials. We simultaneously measure the temperature dependences of the helical pitch and the correlation length of both the helical and positional order. In addition to an unexpected strong variation of the pitch with the length of the spacer connecting the monomer units, we find that at the transition to the NTB phase the positional correlation length drops. Additionally, the helical structure was found not only in the NTB phase but observed even in the upper range of a smectic phase that forms just below the NTB state. The coexistence of smectic layering and the heliconical order indicates a layered (SmATB) phase wherein the rigid units of the dimers are tilted with respect to the smectic layer normal in order to accommodate the bent conformation of the dimers and the tilt direction rotates along the heliconical axis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Charges on a suspended silicon nitride membrane under a high-energy electron beam

Thin silicon nitride (SiN x ) membranes are widely used in gas and liquid phase transmission electron microscopy (TEM) and as phase plates to enhance imaging contrast. SiN x contains trap sites for both positive and negative charges, which can be manipulated by high-energy electron irradiation, external potential biasing, or light exposure. Charge accumulation on the membrane can significantly affect in situ TEM processes, including chemical and electrochemical reactions, nanoparticle dynamics, and catalytic activity, or introduce unwanted phase shifts when used as a phase plate. Here, in this study, charge accumulation on suspended SiN x membranes was investigated using off-axis electron holography combined with model-free charge analysis, supported by custom finite element analysis (FEA) simulations. An average residual positive charge density of approximately 2.8 × 10 −4 C m −2 was measured. Localized and stable regions of both positive and negative charges were identified on the membrane. The global positive and localized positive/negative charges give rise to strong electric fields and electroosmotic slip velocities at the membrane surface, which are sufficient to induce non-Brownian particle behavior and directional fluid flow, offering a physical explanation for previously observed anomalies in particle dynamics, nucleation, and growth during gas and liquid phase TEM experiments. These results provide a benchmark for understanding charge behavior at SiNx interfaces in gas and liquid phase TEM. Furthermore, the FEA simulations establish a framework for future investigations into charge distribution, electrostatic potentials, and electrical double layers at solid–liquid interfaces, particularly in complex geometries and chemically dynamic environments.

Suspended silicon↗

DOE OSTI2023

Sterically attenuated electronic communication in cobalt complexes of meridional isoquinoline-derived ligands for applications in electrocatalysis

The ability to synthetically tune the ligand frameworks of redox-active molecules is of critical importance to the economy of solar fuels because manipulating their redox properties can afford control over the operating potentials of sustained electrocatalytic or photoelectrocatalytic processes. The electronic and steric properties of 2,2′:6′,2″-terpyridine (Terpy) ligand frameworks can be tuned by functional group substitution on ligand backbones, and these correlate strongly to their Hammett parameters. The synthesis of a new series of tridentate meridional ligands of 2,4,6-trisubstituted pyridines that engineers the ability to finely tune the redox potentials of cobalt complexes to more positive potentials than that of their Terpy analogs is achieved by aryl-functionalizing at the four-position and by including isoquinoline at the two- and six-positions of pyridine (Aryl-DiQ). Their cobalt complex syntheses, their electronic properties, and their catalytic activity for carbon dioxide (CO2) reduction are reported and compared to their Terpy analogs. The cobalt derivatives generally experience a positive shift in their redox features relative to the Terpy-based analogs, covering a complementary potential range. Although those evaluated fail to produce any quantifiable products for the reduction of CO2 and suffer from long-term instability, these results suggest possible alternate strategies for stabilizing these compounds during catalysis. We speculate that lower equilibrium association constants to the cobalt center are intrinsic to these ligands, which originate from a steric interaction between protons on the pyridine and isoquinoline moieties. Nevertheless, the new Aryl-DiQ ligand framework has been engineered to selectively tune homoleptic cobalt complexes’ redox potentials.

Chemistry↗

DOE OSTI2024

RASPA3

RASPA3, a molecular simulation code for computing adsorption and diffusion in nanoporous materials and thermodynamic and transport properties of fluids. It implements force field based classical Monte Carlo/molecular dynamics in various ensembles. RASPA3 is rewritten from the ground up in C++23 with speed and code readability in mind. Transition-matrix Monte Carlo is added to compute the density of states and free energies. The Monte Carlo code for rigid molecules is based on quaternions, and the atomic positions needed in the energy evaluation are recreated from the center of mass position and quaternion orientation. The expanded ensemble methodology for fractional molecules, with a scaling parameter λ between 0 and 1, now also keeps track of analytic expressions of dU/dλ, allowing independent verification of the chemical potential using thermodynamic integration. The source code is freely available under the MIT license on GitHub.

Dubbeldam, David↗

DOE OSTI2024

Sound propagation in realistic interactive 3D scenes with parameterized sources using deep neural operators

We address the challenge of acoustic simulations in three-dimensional (3D) virtual rooms with parametric source positions, which have applications in virtual/augmented reality, game audio, and spatial computing. The wave equation can fully describe wave phenomena such as diffraction and interference. However, conventional numerical discretization methods are computationally expensive when simulating hundreds of source and receiver positions, making simulations with parametric source positions impractical. To overcome this limitation, we propose using deep operator networks to approximate linear wave-equation operators. This enables the rapid prediction of sound propagation in realistic 3D acoustic scenes with parametric source positions, achieving millisecond-scale computations. By learning a compact surrogate model, we avoid the offline calculation and storage of impulse responses for all relevant source/listener pairs. Our experiments, including various complex scene geometries, show good agreement with reference solutions, with root mean squared errors ranging from 0.02 to 0.10 Pa. Notably, our method signifies a paradigm shift as—to our knowledge—no prior machine learning approach has achieved precise predictions of complete wave fields within realistic domains.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Influence of discharge polarity on streamer breakdown criterion of ambient air in a non-uniform electric field

Streamer breakdown of atmospheric air with non-uniform dc electric field in a needle-to-plate electrode configuration is studied using a semi-analytic model and experimental measurements. A high voltage (either positive or negative) is applied to a hollow needle with 0.51 mm outer diameter and 0.25 mm inner diameter separated from a planar ground electrode by a gap distance of 0.1–1.4 cm. Breakdown voltages are recorded for both positive and negative discharge polarities. Empirical relations between the critical avalanche size for streamer breakdown and the gap distance are proposed. Using these empirical relations, a semi-analytic model based on Meek's criterion for streamer breakdown is developed to accurately predict the measured breakdown voltages. It is found that for pd > 380 Torr cm (or d > 0.5 cm at one atmosphere) streamer breakdown of ambient air occurs at a lower applied voltage for a positively biased needle compared to that with a negatively biased needle, referred as the polarity effect. For pd < 380 Torr cm breakdown is attained at a lower applied voltage with a negatively biased needle compared to that with a positively biased needle, and breakdown mode transits from the polarity effect to the so called inverted polarity effect.

42 ENGINEERING↗

DOE OSTI2024

Scintillation and cherenkov photon counting detectors with analog silicon photomultipliers for TOF-PET

Objective. Standard signal processing approaches for scintillation detectors in positron emission tomography (PET) derive accurate estimates for 511 keV photon time of interaction and energy imparted to the detection media from aggregate characteristics of electronic pulse shapes. The ultimate realization of a scintillation detector for PET is one that provides a unique timestamp and position for each detected scintillation photon. Detectors with these capabilities enable advanced concepts for three-dimensional (3D) position and time of interaction estimation with methods that exploit the spatiotemporal arrival time kinetics of individual scintillation photons. Approach. In this work, we show that taking into consideration the temporal photon emission density of a scintillator, the channel density of an analog silicon photomultiplier (SiPM) array, and employing fast electronic readout with digital signal processing, a detector that counts and timestamps scintillation photons can be realized. To demonstrate this approach, a prototype detector was constructed, comprising multichannel electronic readout for a bismuth germanate (BGO) scintillator coupled to an SiPM array. Main Results. In proof-of-concept measurements with this detector, we were able to count and provide unique timestamps for 66% of all optical photons, where the remaining 34% (two-or-more-photon pulses) are also independently counted, but each photon bunch shares a common timestamp. We show this detector concept can implement 3D positioning of 511 keV photon interactions and thereby enable corrections for time of interaction estimators. The detector achieved 17.6% energy resolution at 511 keV and 237 ± 10 ps full-width-at-half-maximum coincidence time resolution (CTR) (fast spectral component) versus a reference detector. We outline the methodology, readout, and approach for achieving this detector capability in first-ever, proof-of-concept measurements for scintillation photon counting detector with analog silicon photomultipliers. Significance. The presented detector concept is a promising design for large area, high sensitivity TOF-PET detector modules that can implement advanced event positioning and time of interaction estimators, which could push state-of-the-art performance.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2020

Measurement of space charge effects in the MicroBooNE LArTPC using cosmic muons

Large liquid argon time projection chambers (LArTPCs), especially those operating near the surface, are susceptible to space charge effects. In the context of LArTPCs, the space charge effect is the build-up of slow-moving positive ions in the detector primarily due to ionization from cosmic rays, leading to a distortion of the electric field within the detector. This effect leads to a displacement in the reconstructed position of signal ionization electrons in LArTPC detectors ("spatial distortions"), as well as to variations in the amount of electron-ion recombination experienced by ionization throughout the volume of the TPC. We present techniques that can be used to measure and correct for space charge effects in large LArTPCs by making use of cosmic muons, including the use of track pairs to unambiguously pin down spatial distortions in three dimensions. Finally, the performance of these calibration techniques are studied using both Monte Carlo simulation and MicroBooNE data, utilizing a UV laser system as a means to estimate the systematic bias associated with the calibration methodology.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

The 𝑚=2 amplituhedron and the hypersimplex: Signs, clusters, tilings, Eulerian numbers

The hypersimplex Δ <#comment/> k + 1 , n \Delta _{k+1,n} is the image of the positive Grassmannian G r k + 1 , n ≥ <#comment/> 0 Gr^{\geq 0}_{k+1,n} under the moment map. It is a polytope of dimension n − <#comment/> 1 n-1 in R n \mathbb {R}^n . Meanwhile, the amplituhedron A n , k , 2 ( Z ) \mathcal {A}_{n,k,2}(Z) is the projection of the positive Grassmannian G r k , n ≥ <#comment/> 0 Gr^{\geq 0}_{k,n} into the Grassmannian G r k , k + 2 Gr_{k,k+2} under a map Z ~ <#comment/> \tilde {Z} induced by a positive matrix Z ∈ <#comment/> M a t n , k + 2 > 0 Z\in Mat_{n,k+2}^{>0} . Introduced in the context of scattering amplitudes , it is not a polytope, and has full dimension 2 k 2k inside G r k , k + 2 Gr_{k,k+2} . Nevertheless, there seem to be remarkable connections between these two objects via T-duality , as conjectured by Łukowski, Parisi, and Williams [Int. Math. Res. Not. (2023)]. In this paper we use ideas from oriented matroid theory, total positivity, and the geometry of the hypersimplex and positroid polytopes to obtain a deeper understanding of the amplituhedron. We show that the inequalities cutting out positroid polytopes —images of positroid cells of G r k + 1 , n ≥ <#comment/> 0 Gr^{\geq 0}_{k+1,n} under the moment map—translate into sign conditions characterizing the T-dual Grasstopes —images of positroid cells of G r k , n ≥ <#comment/> 0 Gr^{\geq 0}_{k,n} under Z ~ <#comment/> \tilde {Z} . Moreover, we subdivide the amplituhedron into chambers , just as the hypersimplex can be subdivided into simplices, with both chambers and simplices enumerated by the Eulerian numbers. We use these properties to prove the main conjecture of Łukowski, Parisi, and Williams [Int. Math. Res. Not. (2023)]: a collection of positroid polytopes is a tiling of the hypersimplex if and only if the collection of T-dual Grasstopes is a tiling of the amplituhedron A n , k , 2 ( Z ) \mathcal {A}_{n,k,2}(Z) for all Z Z . Moreover, we prove Arkani-Hamed–Thomas–Trnka’s conjectural sign-flip characterization of A n , k , 2 \mathcal {A}_{n,k,2} , and Łukowski–Parisi–Spradlin–Volovich’s conjectures on m = 2 m=2 cluster adjacency and on positroid tiles for A n , k , 2 \mathcal {A}_{n,k,2} (images of 2 k 2k -dimensional positroid cells which map injectively into A n , k , 2 \mathcal {A}_{n,k,2} ). Finally, we introduce new cluster structures in the amplituhedron.

Parisi, Matteo↗

DOE OSTI2022

Disentangling Alzheimer’s disease neurodegeneration from typical brain ageing using machine learning

Abstract Neuroimaging biomarkers that distinguish between changes due to typical brain ageing and Alzheimer’s disease are valuable for determining how much each contributes to cognitive decline. Supervised machine learning models can derive multivariate patterns of brain change related to the two processes, including the Spatial Patterns of Atrophy for Recognition of Alzheimer’s Disease (SPARE-AD) and of Brain Aging (SPARE-BA) scores investigated herein. However, the substantial overlap between brain regions affected in the two processes confounds measuring them independently. We present a methodology, and associated results, towards disentangling the two. T1-weighted MRI scans of 4054 participants (48–95 years) with Alzheimer’s disease, mild cognitive impairment (MCI), or cognitively normal (CN) diagnoses from the Imaging-based coordinate SysTem for AGIng and NeurodeGenerative diseases (iSTAGING) consortium were analysed. Multiple sets of SPARE scores were investigated, in order to probe imaging signatures of certain clinically or molecularly defined sub-cohorts. First, a subset of clinical Alzheimer’s disease patients (n = 718) and age- and sex-matched CN adults (n = 718) were selected based purely on clinical diagnoses to train SPARE-BA1 (regression of age using CN individuals) and SPARE-AD1 (classification of CN versus Alzheimer’s disease) models. Second, analogous groups were selected based on clinical and molecular markers to train SPARE-BA2 and SPARE-AD2 models: amyloid-positive Alzheimer’s disease continuum group (n = 718; consisting of amyloid-positive Alzheimer’s disease, amyloid-positive MCI, amyloid- and tau-positive CN individuals) and amyloid-negative CN group (n = 718). Finally, the combined group of the Alzheimer’s disease continuum and amyloid-negative CN individuals was used to train SPARE-BA3 model, with the intention to estimate brain age regardless of Alzheimer’s disease-related brain changes. The disentangled SPARE models, SPARE-AD2 and SPARE-BA3, derived brain patterns that were more specific to the two types of brain changes. The correlation between the SPARE-BA Gap (SPARE-BA minus chronological age) and SPARE-AD was significantly reduced after the decoupling (r = 0.56–0.06). The correlation of disentangled SPARE-AD was non-inferior to amyloid- and tau-related measurements and to the number of APOE ε4 alleles but was lower to Alzheimer’s disease-related psychometric test scores, suggesting the contribution of advanced brain ageing to the latter. The disentangled SPARE-BA was consistently less correlated with Alzheimer’s disease-related clinical, molecular and genetic variables. By employing conservative molecular diagnoses and introducing Alzheimer’s disease continuum cases to the SPARE-BA model training, we achieved more dissociable neuroanatomical biomarkers of typical brain ageing and Alzheimer’s disease.

Hwang, Gyujoon↗

DOE OSTI2026

Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces

Coastal soils are dynamic systems where unique microbial niches are shaped by the intensity and duration of flooding between the terrestrial and aquatic boundaries of the terrestrial-aquatic interface (TAI). We aimed to understand the soil microbial community (16S rRNA gene) along the TAIs of a freshwater versus estuarine region and how it relates to organic matter (OM, via Fourier Transform Ion Cyclotron Resonance Mass Spectrometry). We studied the TAI gradients along a transect from upland (forested), transition (stressed forest), to wetland at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. Microbial communities differed significantly by region, transect position, and site. Contrary to expectations, given their dynamic hydrologies, transitions represented midpoints in microbial richness and diversity. We identified a core microbiome conserved across all transect positions within a region, highlighting potential microbial functions most resilient to environmental change. Indicator taxa unique to each transect position defined specific niches shaped by soil biogeochemistry. Co-expression networks of feature-level β-nearest-taxon indices revealed positive relationships in bacterial and OM feature contributions to community assembly. Our study provides critical insights into microbial communities at the forefront of hydrological changes in coastal areas that connect the land to lakes and oceans and remain vulnerable to changing weather patterns.

coastal ecosystems↗

DOE OSTI2021

Prevalence of gp160 polymorphisms known to be related to decreased susceptibility to temsavir in different subtypes of HIV-1 in the Los Alamos National Laboratory HIV Sequence Database

Fostemsavir, a prodrug of the gp120-directed attachment inhibitor temsavir, is indicated for use in heavily treatment-experienced individuals with MDR HIV-1. Reduced susceptibility to temsavir in the clinic maps to discrete changes at amino acid positions in gp160: S375, M426, M434 and M475.To query the Los Alamos National Laboratory (LANL) HIV Sequence Database for the prevalence of polymorphisms at gp160 positions of interest. Full-length gp160 sequences (N = 7560) were queried for amino acid polymorphisms relative to the subtype B consensus at positions of interest; frequencies were reported for all sequences and among subtypes/circulating recombinant forms (CRFs) with ≥10 isolates in the database. Among 239 subtypes in the database, the 5 most prevalent were B (n = 2651, 35.1%), C (n = 1626, 21.5%), CRF01_AE (n = 674, 8.9%), A1 (n = 273, 3.6%) and CRF02_AG (n = 199, 2.6%). Among all 7560 sequences, the most prevalent amino acids at positions of interest (S 375 , 73.5%; M 426 , 82.1%; M 434 , 88.2%; M 475 , 89.9%) were the same as the subtype B consensus. Specific polymorphisms with the potential to decrease temsavir susceptibility (S 375 H/I/M/N/T/Y, M 426 L/P, M 434 I/K and M475I) were found in <10% of isolates of subtypes D, G, A6, BC, F1, CRF07_BC, CRF08_BC, 02A, CRF06_cpx, F2, 02G and 02B. S 375 H and M 475 I were predominant among CRF01_AE (S375H, 99.3%; M 475 I, 76.3%; consistent with previously reported low temsavir susceptibility of this CRF) and 01B (S 375 H, 71.7%; M 475 I, 49.5%). Analysis of the LANL HIV Sequence Database found a low prevalence of gp160 amino acid polymorphisms with the potential to reduce temsavir susceptibility overall and among most of the common subtypes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

On the shear-current effect: toward understanding why theories and simulations have mutually and separately conflicted

ABSTRACT The shear-current effect (SCE) of mean-field dynamo theory refers to the combination of a shear flow and a turbulent coefficient β21 with a favourable negative sign for exponential mean-field growth, rather than positive for diffusion. There have been long-standing disagreements among theoretical calculations and comparisons of theory with numerical experiments as to the sign of kinetic ($\beta ^u_{21}$) and magnetic ($\beta ^b_{21}$) contributions. To resolve these discrepancies, we combine an analytical approach with simulations, and show that unlike $\beta ^b_{21}$, the kinetic SCE $\beta ^u_{21}$ has a strong dependence on the kinetic energy spectral index and can transit from positive to negative values at $\mathcal {O}(10)$ Reynolds numbers if the spectrum is not too steep. Conversely, $\beta ^b_{21}$ is always negative regardless of the spectral index and Reynolds numbers. For very steep energy spectra, the positive $\beta ^u_{21}$ can dominate even at energy equipartition urms ≃ brms, resulting in a positive total β21 even though $\beta ^b_{21}\lt 0$. Our findings bridge the gap between the seemingly contradictory results from the second-order-correlation approximation versus the spectral-τ closure, for which opposite signs for $\beta ^u_{21}$ have been reported, with the same sign for $\beta ^b_{21}\lt 0$. The results also offer an explanation for the simulations that find $\beta ^u_{21}\gt 0$ and an inconclusive overall sign of β21 for $\mathcal {O}(10)$ Reynolds numbers. The transient behaviour of $\beta ^u_{21}$ is demonstrated using the kinematic test-field method. We compute dynamo growth rates for cases with or without rotation, and discuss opportunities for further work.

79 ASTRONOMY AND ASTROPHYSICS↗