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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Roots Mediate the Effects of Snowpack Decline on Soil Bacteria, Fungi, and Nitrogen Cycling in a Northern Hardwood Forest

Rising winter air temperature will reduce snow depth and duration over the next century in northern hardwood forests. Reductions in snow depth may affect soil bacteria and fungi directly, but also affect soil microbes indirectly through effects of snowpack loss on plant roots. We incubated root exclusion and root ingrowth cores across a winter climate-elevation gradient in a northern hardwood forest for 29 months to identify direct (i.e., winter snow-mediated) and indirect (i.e., root-mediated) effects of winter snowpack decline on soil bacterial and fungal communities, as well as on potential nitrification and net N mineralization rates. Both winter snowpack decline and root exclusion increased bacterial richness and phylogenetic diversity. Variation in bacterial community composition was best explained by differences in winter snow depth or soil frost across elevation. Root ingrowth had a positive effect on the relative abundance of several bacterial taxonomic orders (e.g., Acidobacterales and Actinomycetales). Nominally saprotrophic (e.g., Saccharomycetales and Mucorales) or mycorrhizal (e.g., Helotiales, Russalales, Thelephorales) fungal taxonomic orders were also affected by both root ingrowth and snow depth variation. However, when grouped together, the relative abundance of saprotrophic fungi, arbuscular mycorrhizal fungi, and ectomycorrhizal fungi were not affected by root ingrowth or snow depth, suggesting that traits in addition to trophic mode will mediate fungal community responses to snowpack decline in northern hardwood forests. Potential soil nitrification rates were positively related to ammonia-oxidizing bacteria and archaea abundance (e.g., Nitrospirales, Nitrosomondales, Nitrosphaerales). Rates of N mineralization were positively and negatively correlated with ectomycorrhizal and saprotrophic fungi, respectively, and these relationships were mediated by root exclusion. The results from this study suggest that a declining winter snowpack and its effect on plant roots each have direct effects on the diversity and abundance of soil bacteria and fungal communities that interact to determine rates of soil N cycling in northern hardwood forests.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Photoproduction of J /ψ in non-single-diffractive p+p collisions

Significant enhancements of $ J/\psi $ production at very low transverse momenta were recently observed by the ALICE and STAR collaborations in peripheral hadronic A+A collisions. The anomalous excess points to coherent photon-nucleus interactions in violent hadronic heavy-ion collisions, which were conventionally studied only in ultra-peripheral collisions. Assuming that the coherent photoproduction is the underlying mechanism responsible for the excess observed in peripheral A+A collisions, its contribution in p+p collisions with nuclear overlap, i.e. non-single-diffractive collisions, is of particular interest. In this paper, we perform a calculation of exclusive $ J/\psi $ photoproduction in non-single-diffractive p+p collisions at the RHIC and LHC energies based on the pQCD motivated parametrization using the world-wide experimental data, which could be further employed to improve the precision of the phenomenological calculations for photoproduction in A+A collisions. The differential rapidity and transverse momentum distributions of $ J/\psi $ from photoproduction are presented. In comparison with the $ J/\psi $ production from hadronic interactions, we find that the contribution of photoproduction is negligible.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins

Abstract RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron–electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Increasing temperatures reduce invertebrate abundance and slow decomposition

Decomposition is an essential ecosystem service driven by interacting biotic and abiotic factors. Increasing temperatures due to climate change can affect soil moisture, soil fauna, and subsequently, decomposition. Understanding how projected climate change scenarios will affect decomposition is of vital importance for predicting nutrient cycling and ecosystem health. In this study, we experimentally addressed the question of how the early stages of decomposition would vary along a gradient of projected climate change scenarios. Given the importance of biodiversity for ecosystem service provisioning, we measured the effect of invertebrate exclusion on red maple ( Acer rubrum ) leaf litter breakdown along a temperature gradient using litterbags in warming chambers over a period of five weeks. Leaf litter decomposed more slowly in the warmer chambers and in the litterbag treatment that minimized invertebrate access. Moreover, increasing air temperature reduced invertebrate abundance and richness, and altered the community composition, independent of exclusion treatment. Using structural equation models, we were able to disentangle the effects of average air temperature on leaf litter loss, finding a direct negative effect of warming on the early stages of decomposition, independent of invertebrate abundance. This result indicates that not only can climate change affect the invertebrate community, but may also directly influence how the remaining organisms interact with their environment and their effectiveness at provisioning ecosystem services. Overall, our study highlights the role of biodiversity in maintaining ecosystem services and contributes to our understanding of how climate change could disrupt nutrient cycling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Meson Photo-Production in GEANT4 for $E_\gamma = 0.225$ E γ = 0 . 225 -3.0 GeV using the $\gamma + p \rightarrow p + \pi^{0}$ reaction

The study of nuclear resonances in the intermediate energy regime requires accurate modeling of the experimental physics background. The cross sections in the GEANT4 toolkit do not adequately treat meson photo-production. The purpose of this study is to compare experimental data and theoretical models implemented in version 9.6.p02 of the GEANT4 Monte Carlo simulation toolkit for the exclusive and differential cross sections of $\pi^0$ photo-production. Two models were studied: the Chiral Invariant Phase Space (CHIPS) and Bertini Cascade (BERT). The cross section data from the models were compared to the experimental data from the CEBAF Large Acceptance Spectrometer (CLAS) of Jefferson Lab and the phenomenological Scattering Analysis Interactive Dial-in (SAID) model. Relativistic Breit-Wigner fits were used to compare the $\Delta(1232)$, N*(1520), N*(1650) and N*(1875) resonances from SAID, CLAS and CHIPS, giving agreements to within 3% for the mass of each resonance. The limited tabulated data set of BERT does not allow for an accurate description of the energy distribution, even following its improvement in version 10p02. The angular distributions of the cross sections show significant differences between CHIPS and both CLAS and SAID data, the latter being the most accurate model to describe the $\gamma p\rightarrow p\pi ^0$ exclusive cross section. Finally, the physics in CHIPS appears to be correct but it needs further development for the individual resonances contributions that could be useful since it is also the only model able to treat electromagnetically induced meson production for $A>1$.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Identification and characterization of a novel calmodulin binding site in Drosophila TRP C-terminus

Highlights: • Drosophila TRP 783–862 is a novel calmodulin binding site. • The shortest Ca{sup 2+}-CaM interaction region and core CaM binding sequences in TRP 783–862 were dissected. • Ca{sup 2+}-CaM binding induces helical structure formation of Drosophila TRP 783–862. Transient receptor potential (TRP) channels are a group of essential cation channels involved in many important sensory signal transduction processes, such as light, temperature, tastes and pressure sensing. Drosophila TRP channel is the first discovered family member and plays important roles in photo-transduction in Drosophila. Calmodulin (CaM), an important downstream effector of Ca{sup 2+} signal, was considered as a vital regulator of TRP activities. In this study, we discovered a novel Ca{sup 2+} dependent CaM binding site (TRP 783–862) in between the previously reported two calmodulin binding sites (CBSs). The isothermal titration calorimetry (ITC) and the size exclusion chromatography coupled with multi-angle static light scattering (SEC-MALS) results showed that the dissociation constant (Kd) between TRP 783–862 and Ca{sup 2+}-CaM is 0.10 ± 0.04 μM and their binding stoichiometry is 1:1. In addition, the shortest Ca{sup 2+}-CaM interaction region and core CaM binding sequences in TRP 783–862 were dissected by the boundary mapping and mutagenesis experiments. More interestingly, by comparing the circular dichroism (CD) spectra before and after Ca{sup 2+}-CaM binding, the TRP 783–862 fragment showed Ca{sup 2+}-CaM binding dependent secondary structure changes, indicating that the interaction between CaM and Drosophila TRP channel may have a conformational impact on TRP structure. In summary, by identifying and characterizing a novel CaM binding site in TRP C-terminus, our findings provided a biochemical and structural basis for further in vivo functional studies of Ca{sup 2+}-mediated TRP channel regulation through CaM/TRP interaction.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Perimatrix of middle ear cholesteatoma: A granulation tissue with a specific transcriptomic signature

Objectives/Hypothesis: To establish comprehensive transcriptomic profiles of cholesteatoma perimatrix tissue and granulation tissue from chronic otitis media (COM) that did not develop cholesteatoma, which can indicate molecular pathways involved in the cholesteatoma perimatrix pathology and invasiveness. Study Design: Retrospective Case Series. Methods: Transcriptome data were obtained from cholesteatoma perimatrix tissue and COM granulation tissue by an Illumina iScan microarray. Differentially expressed genes (DEGs) were subsequently analyzed using both bioinformatical functional annotation and network analysis. Expression of candidate genes (MMP9 and LCN2) was validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) on a larger group of samples. Results: Analysis of the transcriptome led to the identification of 169 differentially expressed genes between investigated tissues. Bioinformatic analysis suggested that most significant biological processes involving DEGs were previously described in cholesteatoma pathology. Network analysis identified ERBB2, TFAP2A, and TP63 as major hubs of the DEGs molecular network. Furthermore, it was observed that the cellular component most significantly enriched in DEGs was extracellular space containing 47 DEGs. Using qRT-PCR, it was confirmed that mRNA levels of the major extracellular hub (MMP9) are increased, whereas its interacting molecule (LCN2) mRNA levels were decreased in cholesteatoma perimatrix tissue compared to COM granulation tissue. Conclusions: The current study approach offers an overall look at molecular mechanisms that describe the cholesteatoma entity by focusing exclusively on the perimatrix processes in comparison to COM granulation tissue. The observed differences in gene expression between cholesteatoma perimatrix and COM granulation tissue could suggest novel markers potentially influenced by the perimatrix–matrix molecular interplay, which is not present in COM without cholesteatoma. Level of Evidence: NA. Laryngoscope, 130:E220–E227, 2020. © 2019 The American Laryngological, Rhinological and Otological Society, Inc.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Study of the Few Nucleon Systems at $\mathrm{CLAS}$

The study of few nucleon systems with electromagnetic probes is an essential component of the scientific program carried out at the Thomas Jefferson National Accelerator Facility (JLab). Here we present measurements of exclusive reactions on light nuclei using real photon beams with energies up to 3 GeV and the CEBAF Large Acceptance Spectrometer (CLAS), a nearly 4π magnetic spectrometer, in order to study the properties of strongly interacting matter and the transition from hadronic (i.e in terms of nucleons and mesons) to partonic (in terms of quark and gluons) degrees of freedom in nuclear interactions. We discuss the progress made in understanding the relevant degrees of freedom using polarisation observables and cross sections of deuteron and 3 He photodisintegration in the few-GeV photon-energy region. In addition, recent high-statistics experiments with the CLAS detector have provided us with sufficient counting rates to study the effects of initial- and final-state interactions in reactions off the deuteron. Such data allow us to extract a large set of polarisation observables for final-state interactions in hyperon photoproduction and to study the properties of the hyperon–nucleon interaction. Initial-state effects are studied by mapping the dependence of experimental observables on the spectator-nucleon momentum. We also present recent results for polarisation observables for quasi-free K + Λ off the bound proton in a deuteron as well as for final-state interactions in the reaction γd→K + Λn , and will discuss their impact on hyperon–nucleon studies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Search for dijet resonances in proton–proton collisions at $\sqrt{s}$ = 13 TeV and constraints on dark matter and other models

A search is presented for narrow resonances decaying to dijet final states in proton–proton collisions at s=13TeV using data corresponding to an integrated luminosity of 12.9 fb −1 . The dijet mass spectrum is well described by a smooth parameterization and no significant evidence for the production of new particles is observed. Upper limits at 95% confidence level are reported on the production cross section for narrow resonances with masses above 0.6 TeV. In the context of specific models, the limits exclude string resonances with masses below 7.4 TeV, scalar diquarks below 6.9 TeV, axigluons and colorons below 5.5 TeV, excited quarks below 5.4 TeV, color-octet scalars below 3.0 TeV, W′ bosons below 2.7 TeV, Z′ bosons below 2.1 TeV and between 2.3 and 2.6 TeV, and RS gravitons below 1.9 TeV. These extend previous limits in the dijet channel. Vector and axial-vector mediators in a simplified model of interactions between quarks and dark matter are excluded below 2.0 TeV. The first limits in the dijet channel on dark matter mediators are presented as functions of dark matter mass and are compared to the exclusions of dark matter in direct detection experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Benchmarking intra-nuclear cascade models for neutrino scattering with relativistic optical potentials

The description of final-state interactions (FSI) in the large phase space probed in neutrino experiments poses a great challenge. In neutrino experiments, which operate under semi-inclusive conditions, cascade models are commonly used for this task, while under exclusive conditions FSI can be treated with relativistic optical potentials (ROP). We formulate conditions under which the ROP approach and cascade model can be directly compared. We feed the NEUT cascade with events from a relativistic distorted-wave impulse approximation calculation that uses the real part of an optical potential. Cuts on the missing energy of the resulting events are applied to define a set of events that can be directly compared to RDWIA calculations with the full optical potential. The NEUT cascade and ROP agree for proton kinetic energies $T_p > 150$ MeV for carbon, oxygen and calcium nuclei when a realistic nuclear density is used to introduce events in the cascade. For $T_p < 100$ MeV the ROP and NEUT cross sections differ in shape and differences in magnitude are larger than 50 %. Single transverse variables allow to distinguish different approaches to FSI, but due to a large non-QE contribution the comparison to T2K data does not give an unambiguous view of FSI. We discuss electron scattering and argue that with a cut in missing energy FSI can be studied with minimal confounding factors in e.g. $e4\nu$. The agreement of the ROP and NEUT for T2K conditions lends confidence to these models as a tool in oscillation analyses for sufficiently large nucleon kinetic energies. These results urge for caution when a cascade model is applied for small nucleon energies. The assessment of model assumptions relevant to this region are strongly encouraged. This paper provides novel constraints on cascade models from proton-nucleus scattering that can be easily applied to other neutrino event generators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

The Detector Design of the Jefferson Lab EIC

The Electron-Ion Collider (EIC) is envisioned as the next-generation U.S. facility to study quarks and gluons in strongly interacting matter. The broad physics program of the EIC aims to precisely image gluons in nucleons and nuclei and to reveal the origin of the nucleon spin by colliding polarized electrons with polarized protons, polarized light ions, and heavy nuclei at high luminosity. The Jefferson Lab EIC (JLEIC) design is based on a figure-8 shaped ring-ring collider. The luminosity, exceeding 1033cm -2 s -1 in a broad range of the center-of-mass energy and maximum luminosity above 1034cm -2 s -1 , is achieved by high-rate collisions of short small-emittance low-charge bunches made possible by high-energy electron cooling of the ion beam and synchrotron radiation damping of the electron beam. The polarization of light ion species (p, d, 3He) can be easily preserved and manipulated due to the unique figure-8 shape of the collider rings. The focus of this presentation is put on the JLEIC primary detector that has been designed to support the full physics program of the EIC and to provide essentially full acceptance to all fragments produced in collisions. The detector has been fully integrated with the accelerator and extended to the forward electron and hadron regions to achieve exceptional small-angle acceptance and resolution as well as high-precision electron polarimetry and low-Q 2 tagging. The Central Detector design allows for excellent tracking up to small angles and excellent hadron PID resulting and offers a great performance, in particular for semi-inclusive and exclusive measurements. The combination of high luminosity, highly polarized lepton and ion beams, and a full acceptance, multi-purpose detector fully integrated with the accelerator will allow JLEIC a unique opportunity to make breakthroughs in the investigation of the strong interaction.

43 PARTICLE ACCELERATORS↗
DOE OSTI2016

A Perylene‐Based Microporous Coordination Polymer Interacts Selectively with Electron‐Poor Aromatics

Abstract The design, synthesis, and properties of the new microporous coordination polymer UMCM‐310 are described. The unique electronic character of the perylene‐based linker enables selective interaction with electron‐poor aromatics leading to efficient separation of nitroaromatics. UMCM‐310 possesses high surface area and large pore size and thus permits the separation of large organic molecules based on adsorption rather than size exclusion.

Tran, Ly D.↗
DOE OSTI2019

Chiral Recognition of Lipid Bilayer Membranes by Supramolecular Assemblies of Peptide Amphiphiles

On the basis of the exclusive existence of homochirality in biomolecules and the well-known phenomenon of chiral recognition, it is obvious that chirality is a crucial factor in biological events. We report here that supramolecular assemblies of peptide amphiphiles interact with lipid bilayer membranes in a stereospecific manner. When negatively charged chiral phospholipid bilayer vesicles were subjected to the assemblies, we found that peptide amphiphiles with l-amino acids show stronger affinity for the liposomes compared to the ones with d-amino acids. To examine their biological functions, we tested the cytotoxicity of nanofibers against mammalian primary cells using human bone marrow mesenchymal stem cells and murine astroglial cells. In this work, we demonstrated that cell viability increased when d-amino acids were incorporated in the structure of peptide amphiphiles, which is consistent with our finding of their weaker interactions with lipid bilayer membranes.

36 MATERIALS SCIENCE↗
DOE OSTI2016

LHC Forward Physics

The goal of this report is to give a comprehensive overview of the rich field of forward physics, with a special attention to the topics that can be studied at the LHC. The report starts presenting a selection of the Monte Carlo simulation tools currently available, chapter 2, then enters the rich phenomenology of QCD at low, chapter 3, and high, chapter 4, momentum transfer, while the unique scattering conditions of central exclusive production are analyzed in chapter 5. The last two experimental topics, Cosmic Ray and Heavy Ion physics are presented in the chapter 6 and 7 respectively. Chapter 8 is dedicated to the BFKL dynamics, multiparton interactions, and saturation. The report ends with an overview of the forward detectors at LHC. Each chapter is correlated with a comprehensive bibliography, attempting to provide to the interested reader with a wide opportunity for further studies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

Generation and Characterization of an IgG4 Monomeric Fc Platform

The immunoglobulin Fc region is a homodimer consisted of two sets of CH2 and CH3 domains and has been exploited to generate two-arm protein fusions with high expression yields, simplified purification processes and extended serum half-life. However, attempts to generate one-arm fusion proteins with monomeric Fc, with one set of CH2 and CH3 domains, are often plagued with challenges such as weakened binding to FcRn or partial monomer formation. Here, we demonstrate the generation of a stable IgG4 Fc monomer with a unique combination of mutations at the CH3-CH3 interface using rational design combined with in vitro evolution methodologies. In addition to size-exclusion chromatography and analytical ultracentrifugation, we used multi-angle light scattering (MALS) to show that the engineered Fc monomer exhibits excellent monodispersity. Furthermore, crystal structure analysis (PDB ID: 5HVW) reveals monomeric properties supported by disrupted interactions at the CH3-CH3 interface. Monomeric Fc fusions with Fab or scFv achieved FcRn binding and serum half-life comparable to wildtype IgG. These results demonstrate that this monomeric IgG4 Fc is a promising therapeutic platform to extend the serum half-life of proteins in a monovalent format.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Color Transparency and Light-Front Holographic QCD

Color transparency, the reduction of initial-state or final-state interactions in coherent nuclear processes, is a natural prediction of QCD (quantum chromodynamics) provided that small-sized or point-like configurations (PLCs) are formed in high-momentum transfer, high-energy, semi-exclusive processes. I use the Frankfurt-Miller-Strikman criteria for the existence of PLCs to show that the wave functions of light-front holographic QCD, as currently formulated, do not contain a PLC.

Miller, Gerald A. (ORCID:0000000324433639)↗
DOE OSTI2022

Spatial scales of competition and a growth–motility trade-off interact to determine bacterial coexistence

The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth–motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth–motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.

59 BASIC BIOLOGICAL SCIENCES↗