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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 1,351 records · Page 75
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Geographic patterns of genomic diversity and structure in the C4 grass Panicum hallii across its natural distribution

Abstract Geographic patterns of within-species genomic diversity are shaped by evolutionary processes, life history and historical and contemporary factors. New genomic approaches can be used to infer the influence of such factors on the current distribution of infraspecific lineages. In this study, we evaluated the genomic and morphological diversity as well as the genetic structure of the C4 grass Panicum hallii across its complex natural distribution in North America. We sampled extensively across the natural range of P. hallii in Mexico and the USA to generate double-digestion restriction-associated DNA (ddRAD) sequence data for 423 individuals from 118 localities. We used these individuals to study the divergence between the two varieties of P. hallii, P. hallii var. filipes and P. hallii var. hallii as well as the genetic diversity and structure within these groups. We also examined the possibility of admixture in the geographically sympatric zone shared by both varieties, and assessed distribution shifts related with past climatic fluctuations. There is strong genetic and morphological divergence between the varieties and consistent genetic structure defining seven genetic clusters that follow major ecoregions across the range. South Texas constitutes a hotspot of genetic diversity with the co-occurrence of all genetic clusters and admixture between the two varieties. It is likely a recolonization and convergence point of populations that previously diverged in isolation during fragmentation events following glaciation periods.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters

Abstract Motivation The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutation events in sequences relative to a reference. Two versions of this method are available as a webtool. Neither of these methods consider multistate characters or gaps in the sequence alignment. Results Here, we present an updated, user-friendly web and command-line version of Hypermut with functionality to handle multistate characters and gaps in the sequence alignment. This tool allows for straightforward integration of hypermutation detection into sequence analysis pipelines. As with the previous tool, while the main purpose is to identify G to A hypermutation events, any mutational pattern and context can be specified. Availability and implementation Hypermut 3 is written in Python 3. It is available as a command-line tool at https://github.com/MolEvolEpid/hypermut3 and as a webtool at https://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermutv3.html.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Patterns of genomic variation reveal a single evolutionary origin of the wild allotetraploid Mimulus sookensis

Abstract Polyploidy occurs across the tree of life and is especially common in plants. Because newly formed cytotypes are often incompatible with their progenitors, polyploidy is also said to trigger “instantaneous” speciation. If a polyploid can self-fertilize or reproduce asexually, it is even possible for one individual to produce an entirely new lineage, but how often this scenario occurs is unclear. Here, we investigate the evolutionary history of the wild allotetraploid Mimulus sookensis, which was formed through hybridization between self-compatible, diploid species in the Mimulus guttatus complex. We generate a chromosome-scale reference assembly for M. sookensis and define its distinct subgenomes. Despite previous reports suggesting multiple origins of this highly selfing polyploid, we discover patterns of population genomic variation that provide unambiguous support for a single origin. One M. sookensis subgenome is clearly derived from the selfer Mimulus nasutus, which organellar variation suggests is the maternal progenitor. The ancestor of the other subgenome is less certain, but it shares variation with both Mimulus decorus and M. guttatus, two outcrossing diploids with geographic ranges that overlap broadly with M. sookensis. This study establishes M. sookensis as an example of instantaneous speciation, likely facilitated by the polyploid’s predisposition to self-fertilize.

Environmental Sciences & Ecology↗
DOE OSTI2023

Biogeographic patterns in populations of marine Pseudoalteromonas atlantica isolates

Intra-specific genomic diversity is well documented in microbes. The question, however, remains whether natural selection or neutral evolution is the major contributor to this diversity. We undertook this study to estimate genomic diversity in Pseudoalteromonas atlantica populations and whether the diversity, if present, could be attributed to environmental factors or distance effects. Here, we isolated and sequenced twenty-three strains of P. atlantica from three geographically distant deep marine basins and performed comparative genomic analyses to study the genomic diversity of populations among these basins. Average nucleotide identity followed a strictly geographical pattern. In two out of three locations, the strains within the location exhibited >99.5% identity, whereas, among locations, the strains showed <98.11% identity. Phylogenetic and pan-genome analysis also reflected the biogeographical separation of the strains. Strains from the same location shared many accessory genes and clustered closely on the phylogenetic tree. Phenotypic diversity between populations was studied in ten out of twenty-three strains testing carbon and nitrogen source utilization and osmotolerance. A genetic basis for phenotypic diversity could be established in most cases but was apparently not influenced by local environmental conditions. Our study suggests that neutral evolution may have a substantial role in the biodiversity of P. atlantica.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Reducing stomatal density by expression of a synthetic epidermal patterning factor increases leaf intrinsic water use efficiency and reduces plant water use in a C4 crop

Abstract Enhancing crop water use efficiency (WUE) is a key target trait for climatic resilience and expanding cultivation on marginal lands. Engineering lower stomatal density to reduce stomatal conductance (gs) has improved WUE in multiple C3 crop species. However, reducing gs in C3 species often reduces photosynthetic carbon gain. A different response is expected in C4 plants because they possess specialized anatomy and biochemistry which concentrates CO2 at the site of fixation. This modifies the relationship of photosynthesis (AN) with intracellular CO2 concentration (ci), such that photosynthesis is CO2 saturated and reductions in gs are unlikely to limit AN. To test this hypothesis, genetic strategies were investigated to reduce stomatal density in the C4 crop sorghum. Constitutive expression of a synthetic epidermal patterning factor (EPF) transgenic allele in sorghum led to reduced stomatal densities, reduced gs, reduced plant water use, and avoidance of stress during a period of water deprivation. In addition, moderate reduction in stomatal density did not increase stomatal limitation to AN. However, these positive outcomes were associated with negative pleiotropic effects on reproductive development and photosynthetic capacity. Avoiding pleiotropy by targeting expression of the transgene to specific tissues could provide a pathway to improved agronomic outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Time-series elemental imaging reveals CAX-dependent redistribution patterns for anoxia recovery

Flooding-induced oxygen deprivation (anoxia) is a challenge to plant survival, necessitating adaptive mechanisms for recovery. This study investigated elemental redistribution during anoxia recovery using time-series elemental imaging to show changes in nutrient distribution. Focusing on the role of Cation/H + Exchangers (CAXs) in Arabidopsis thaliana, we show how mutants deficient in specific CAX transporters (cax1 and the cax1-4 quadruple mutant) respond to anoxia and metal stress. Mutants showed reduced lipid peroxidation and increased expression of flood-tolerance proteins during recovery. X-ray fluorescence microscopy and laser ablation–inductively coupled plasma mass spectrometry were used to show elemental redistribution over time. In wild-type plants (Col-0), post-anoxia elemental distribution resembled the elemental distribution of CAX mutants under normoxic conditions, suggesting that CAX-mediated elemental distribution before anoxia enables faster recovery post-anoxia, rather than affecting remobilization post-anoxia. Although CAX mutants had altered tolerance to excess manganese and copper, leaf metal distribution during metal stress was not altered. Here, these findings introduce the potential utility of time-series elemental imaging to show stress-response phenotypes and the importance of elemental distribution to recovery after anoxia. The novelty of this work lies in resolving spatial distribution patterns in a non-static system to gain insight into mechanisms of stress resilience in plants.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes

Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. Because many CAZyme families contain members of diverse molecular function (different EC-numbers), sophisticated tools are required to further delineate these enzymes. Such delineation is provided by the peptide-based clustering method CUPP, Conserved Unique Peptide Patterns. CUPP operates synergistically with the CAZy family/subfamily categorizations to allow systematic exploration of CAZymes by defining small protein groups with shared sequence motifs. The updated CUPP library contains 21,930 of such motif groups including 3,842,628 proteins. The new implementation of the CUPP-webserver, https://cupp.info/, now includes all published fungal and algal genomes from the Joint Genome Institute (JGI), genome resources MycoCosm and PhycoCosm, dynamically subdivided into motif groups of CAZymes. This allows users to browse the JGI portals for specific predicted functions or specific protein families from genome sequences. Thus, a genome can be searched for proteins having specific characteristics. All JGI proteins have a hyperlink to a summary page which links to the predicted gene splicing including which regions have RNA support. The new CUPP implementation also includes an update of the annotation algorithm that uses only a fourth of the RAM while enabling multi-threading, providing an annotation speed below 1 ms/protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids

Abstract Microtubule-based active fluids exhibit turbulent-like autonomous flows, which are driven by the molecular motor powered motion of filamentous constituents. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Search for New Physics in Jet Multiplicity Patterns of Multilepton Events at $\sqrt{s}$ = 13 TeV

A first search for beyond the standard model physics in jet multiplicity patterns of multilepton events is presented, using a data sample corresponding to an integrated luminosity of 138 fb −1 of 13 TeV proton-proton collisions recorded by the CMS detector at the LHC. The search uses observed jet multiplicity distributions in one-, two-, and four-lepton events to explore possible enhancements in jet production rate in three-lepton events with and without bottom quarks. The data are found to be consistent with the standard model expectation. The results are interpreted in terms of supersymmetric production of electroweak chargino-neutralino superpartners with cascade decays terminating in prompt hadronic 𝑅-parity violating interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Laning transitions in pattern-forming driven binary systems with competing interactions

A binary system of particles that move in opposite directions under an applied field can exhibit disordered states as well as laned states where the particles organize into oppositely moving high-mobility lanes to reduce collisions. Previous studies of laning transitions generally focused on particles with purely repulsive interactions. Here, in this study, we examine laning transitions for oppositely moving pattern-forming systems of particles with competing attractive and repulsive interactions, which in equilibrium form crystal, stripe, and bubble states. In addition to multiple types of laned states, we find jammed crystals, stripes, and bubbles, and generally observe a much richer variety of phases compared to the purely repulsive system. In the stripe-forming regime, the system can dynamically reorder into oppositely moving stripes that are aligned in the direction of the drive. The bubble phase can produce strongly polarized jammed states of elongated bubbles where particles in the individual bubbles segregate to opposite sides of the bubbles. We also find disordered states, segregated laned bubble states where the bubbles pass each other in lanes, and segregated bubbles that move through one another. In the compact bubble regime, we obtain a plastic bubble state in which the oppositely driven particles remain trapped in the bubbles but the bubbles move past each other at a slow velocity due to a net imbalance in the bubble population. At higher drives, individual particles begin to jump from bubble to bubble. We show that the different phases and the transitions between them produce signatures in the velocity-force and differential mobility curves. We demonstrate that the force for escaping from the jammed state is nonmonotonic, with stripes exhibiting the lowest unjamming force.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Temporal Pattern Recognition with Delayed-Feedback Spin-Torque Nano-Oscillators

The recent demonstration of neuromorphic computing with spin-torque nano-oscillators has opened a path to energy efficient data processing. The success of this demonstration hinged on the intrinsic short-term memory of the oscillators. We extend the memory of the spin-torque nano-oscillators through time-delayed feedback. We leverage this extrinsic memory to increase the efficiency of solving pattern recognition tasks that require memory to discriminate different inputs. Here, the large tunability of these nonlinear oscillators allows us to control and optimize the delayed-feedback memory using different operating conditions of applied current and magnetic field.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Nanoscale dynamics during self-organized ion beam patterning of Si. I. Ar + bombardment

X-ray photon correlation spectroscopy (XPCS) is used to investigate the fluctuation dynamics during self- organized nanopatterning of silicon by Ar + bombardment at 65° polar angle. Rich structure is observed in the development of the correlation dynamics as seen in the evolving correlation time τ(q || ) and fluctuation relaxation exponent n(q || ). Furthermore, on length scales of the ripple structure, local structure becomes ever more long lived as coarsening progresses. In addition, τ (q || ) develops a peak on length scales corresponding to the ripple wavelength. As patterning progresses, correlation times become asymmetric between the positive and negative directions, suggesting the possibility of different dynamics on the slopes facing toward and away from the ion beam. Relaxation exponents show evolution from linear dynamics at early times to compressed exponential relaxation at low wave numbers and stretched exponential relaxation at high wave numbers. Compressed exponential behavior is reminiscent of stress relaxation processes observed in glasses.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Three-mode coupling interference patterns in the dynamic structure factor of a relaxor ferroelectric

A long-standing controversy for relaxor ferroelectrics has been the origin of the waterfall effect in the phonon dispersion curves, in which low-energy transverse phonons cascade into vertical columns. Originally interpreted as phonons interacting with polar nanoregions (PNRs), it was later explained as an interference effect of coupling damped optic and acoustic phonons. In light of a recently discovered PNR vibrational mode near the waterfall wavevector [M. E. Manley, J. W. Lynn, D. L. Abernathy, E. D. Specht, O. Delaire, A. R. Bishop, R. Sahul, and J. D. Budai, Nat. Commun. 5, 3683 (2014)] we have reexamined this feature using neutron scattering on [100]-poled PMN-30%PT (0.6Pb(Mg 1/3 Nb 2/3 )O 3 0.3PbTiO 3 ). In addition, we find that the PNR mode couples to both optic and acoustic phonons, and that this results in complex patterns in the dynamic structure factor, including intensity pockets and peaks localized in momentum-energy space. These features are fully explained by extending the mode-coupling model to include three coupled damped harmonic oscillators representing the transverse optic, acoustic, and PNR modes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Nanoscale kinetics and dynamics during Ar + patterning of SiO 2

Broad-beam low-energy ion bombardment can lead to the spontaneous formation of nanoscale surface structures, but the dominant mechanisms driving evolution remain controversial. Using coherent x-ray scattering to examine the classic case of ion-beam rippling of SiO 2 surfaces, we study the relationship between the average kinetics of ripple formation and the underlying fluctuation dynamics. The early stage growth of fluctuations is well fit with a linear theory formalism employing a viscous relaxation term with full wave-number dependence. In this regime, the x-ray photon correlation spectroscopy two-time correlation function shows distinctive behavior with memory stretching back to the beginning of the bombardment. For a given length scale, correlation times do not grow significantly beyond the characteristic time associated with the early-stage ripple growth. In the late stages of patterning, when the average surface structure on a given length scale is no longer evolving, dynamical processes continue on the surface. Nonlinear processes dominate at long length scales, leading to compressed exponential decay of the speckle correlation functions, while at short length scales the dynamics appears to approach a linear behavior consistent with viscous flow relaxation. This behavior is found to be consistent with simulations of a recent nonlinear growth model. In addition, it is shown that the surface ripple velocity, an important parameter of the ion-driven surface evolution, can be measured with coherent x-ray scattering in conjunction with use of an inhomogeneous ion beam. The change in viewpoint exemplified by this study, from a focus on only average surface kinetics to one incorporating the underlying nanoscale dynamics, is rapidly becoming more widely applicable as new and upgraded x-ray sources with higher coherent flux come online.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Machine learning approach to pattern recognition in nuclear dynamics from the ab initio symmetry-adapted no-core shell model

A novel machine learning approach is used to provide further insight into atomic nuclei and to detect orderly patterns amid a vast data of large-scale calculations. The method utilizes a neural network that is trained on ab initio results from the symmetry-adapted no-core shell model (SA-NCSM) for light nuclei. We show that the SA-NCSM, which expands ab initio applications up to medium-mass nuclei by using dominant symmetries of nuclear dynamics, can reach heavier nuclei when coupled with the machine learning approach. In particular, we find that a neural network trained on probability amplitudes for s- and p-shell nuclear wave functions not only predicts dominant configurations for heavier nuclei but in addition, when tested for the 20 Ne ground state, accurately reproduces the probability distribution. The non-negligible configurations predicted by the network provide an important input to the SA-NCSM for reducing ultralarge model spaces to manageable sizes that can be, in turn, utilized in SA-NCSM calculations to obtain accurate observables. The neural network is capable of describing nuclear deformation and is used to track the shape evolution along the 20-42 Mg isotopic chain, suggesting a shape coexistence that is more pronounced toward the very neutron-rich isotopes. We provide first descriptions of the structure and deformation of 24 Si and 40 Mg of interest to x-ray burst nucleosynthesis, and even of the extremely heavy nuclei such as 166,168 Er and 236 U, that build on first-principles considerations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Determination of β -decay feeding patterns of 88 Rb and 88 Kr using the Modular Total Absorption Spectrometer at ORNL HRIBF

We report precise determination of ground-state feeding in the β decay of fission products is an important but challenging component in modeling reactor antineutrino flux and reactor decay heat. The Modular Total Absorption Spectrometer (MTAS) is a versatile NaI(Tl) detector array that determines the true β-decay pattern free from the pandemonium effect, including precise ground-state feeding intensities. In this paper, we report MTAS results of the β feeding intensities of 88 Rb and 88 Kr, fission products with large cumulative yields in nuclear reactors. By comparing MTAS results with previous measurements, 88 Rb provides a validation of MTAS's ability to determine ground-state feedings in β decays, while the precision of 88 Kr ground-state feeding is improved when compared with the Evaluated Nuclear Structure Data File (ENSDF). The investigation of sources that contribute to β feeding branching uncertainties in MTAS experiments is discussed in detail. Lastly, the deconvolution of 88 Rb decay spectra suggests that MTAS can distinguish an allowed β spectral shape from a first forbidden unique β spectral shape.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

Nucleon transverse momentum-dependent parton distributions in lattice QCD: Renormalization patterns and discretization effects

Lattice QCD calculations of transverse momentum-dependent parton distribution functions (TMDs) in nucleons are presented in this paper, based on the evaluation of nucleon matrix elements of quark bilocal operators with a staple-shaped gauge connection. Both time-reversal odd effects, namely, the generalized Sivers and Boer-Mulders transverse momentum shifts, as well as time-reversal even effects, namely, the generalized transversity and one of the generalized worm-gear shifts, are studied. Results are obtained on two different n f = 2 + 1 flavor ensembles with approximately matching pion masses but very different discretization schemes: domain-wall fermions (DWF) with lattice spacing a = 0.084 fm and pion mass 297 MeV, and Wilson-clover fermions with a = 0.114 fm and pion mass 317 MeV. Comparison of the results on the two ensembles yields insight into the length scales at which lattice discretization errors are small, and into the extent to which the renormalization pattern obeyed by the continuum QCD TMD operator continues to apply in the lattice formulation. For the studied TMD observables, the results are found to be consistent between the two ensembles at sufficiently large separation of the quark fields within the operator, whereas deviations are observed in the local limit and in the case of a straight link gauge connection, which is relevant to the studies of parton distribution functions. Finally and furthermore, the lattice estimates of the generalized Sivers shift obtained here are confronted with, and are seen to tend towards, a phenomenological estimate extracted from experimental data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Ring patterns generated by an expanding colloidal meniscus

The drop-and-dry is a common technique allowing for creation of periodic nanoparticle (NP) structures for sensing, photonics, catalysis, etc. However, the reproducibility and scalability of this approach for fabrication of NP-based structures faces serious challenges due to the complexity of the simple, at first glance, evaporation process. In this work we study the effect of the spatial confinement on the NP self-assembly under slow solvent evaporation, when the air-liquid-substrate contact line (CL) expands from the center towards the walls of a cylindrical cell, forming a toroid. Using in situ video monitoring of the stick-slip CL motion, we find regular hydrodynamic perturbations in the meniscus, and reveal fine details of the formation of quasiperiodic rings of close packed NP layers. We report that drying of the toroidal NP droplet has a number of important differences from drying of the classical hemispherical colloidal drops. In toroidal drops we observe linear-in-time average meniscus motion, in contrast to the hemispherical drops where the meniscus moves as a square root of time. While both droplet geometries produce NP ring patterns, the ring width for the toroidal drop decreases with increasing ring radius, while it decreases with decreasing the radius of the hemispherical drop. We suggest that free ligands are the main cause of the Marangoni instabilities driving the periodic vorticity in the meniscus. Finally, we show that the usually ignored contact line tension may yield a considerable contribution to the CL pinning causing the CL slip-stick motion and the ring formation.

36 MATERIALS SCIENCE↗