Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Population Structure”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Constraints on late-forming exploding black holes

Black holes can be produced in collapse of small-scale dark matter structures, which can happen at any time from the early to present-day Universe. Microstructure black holes (MSBHs) can have a wide range of masses. Here, small MSBHs evaporate via Hawking radiation with lifetimes shorter than the age of the Universe, but they are not subject to the usual early-Universe bounds on the abundance of small primordial black holes. We investigate the possible signal of such a population of exploding, late-forming black holes, constraining their abundance with observations from diffuse extragalactic gamma- and x-ray sources, the Galactic Center, and dwarf spheroidal galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems

The ecological drivers that concurrently act upon both a virus and its host and that drive community assembly are poorly understood despite known interactions between viral populations and their microbial hosts. Hydraulically fractured shale environments provide access to a closed ecosystem in the deep subsurface where constrained microbial and viral community assembly processes can be examined. Here, we used metagenomic analyses of time-resolved-produced fluid samples from two wells in the Appalachian Basin to track viral and host dynamics and to investigate community assembly processes. Hypersaline conditions within these ecosystems should drive microbial community structure to a similar configuration through time in response to common osmotic stress. However, viral predation appears to counterbalance this potentially strong homogeneous selection and pushes the microbial community toward undominated assembly. In comparison, while the viral community was also influenced by substantial undominated processes, it assembled, in part, due to homogeneous selection. When the overall assembly processes acting upon both these communities were directly compared with each other, a significant relationship was revealed, suggesting an association between microbial and viral community development despite differing selective pressures. These results reveal a potentially important balance of ecological dynamics that must be in maintained within this deep subsurface ecosystem in order for the microbial community to persist over extended time periods. More broadly, this relationship begins to provide knowledge underlying metacommunity development across trophic levels.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Structural analysis of platelet fragments and extracellular vesicles produced by apheresis platelets during storage

Platelets (PLTs) for transfusion can be stored for up to 7 days at room temperature (RT). The quality of apheresis PLTs decreases over storage time, which affects PLT hemostatic functions. Here, we characterized the membranous particles produced by PLT storage lesion (PSLPs), including degranulated PLTs, PLT ghosts, membrane fragments, and extracellular membrane vesicles (PEVs). The PSLPs generated in apheresis platelet units were analyzed on days 1, 3, 5, and 7 of RT storage. A differential centrifugation and a sucrose density gradient were used to separate PSLP populations. PSLPs were characterized using scanning and transmission electron microscopy (EM), flow cytometry (FC), and nanoparticle tracking analysis (NTA). PSLPs have different morphologies and a broad size distribution; FC and NTA showed that the concentration of small and large PSLPs increases with storage time. The density gradient separated 3 PSLP populations: (1) degranulated PLTs, PLT ghosts, and large PLT fragments; (2) PEVs originated from PLT activation and organelles released by necrotic PLTs; and (3) PEV ghosts. Most PSLPs expressed phosphatidyl serine and induced thrombin generation in the plasma. PSLPs contained extracellular mitochondria and some had the autophagosome marker LC3. PSLPs encompass degranulated PLTs, PLT ghosts, large PLT fragments, large and dense PEVs, and low-density PEV ghosts. The activation-related PSLPs are released, particularly during early stage of storage (days 1-3), and the release of apoptosis- and necrosis-related PSLPs prevails after that. No elevation of LC3- and TOM20-positive PSLPs indicates that the increase of extracellular mitochondria during later-stage storage is not associated with PLT mitophagy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dimming the Lights: 2D Simulations of Deflagrations of Hybrid C/O/Ne White Dwarfs Using FLASH

The dimmest and most numerous outlier of the Type Ia supernova population, the Type Iax event, is increasingly being found in the results of observational campaigns. There is currently no single accepted model to describe these events. This 2D study explores the viability of modeling Type Iax events as a hybrid C/O/Ne white dwarf progenitor undergoing a deflagration using the multiphysics software FLASH. This hybrid was created using the stellar evolution code MESA, and its C-depleted core and mixed structure have demonstrated lower yields than traditional C/O progenitors in previous deflagration-to-detonation studies. To generate a sample, 30 “realizations” of this simulation were performed, the only difference being the shape of the initial match head used to start the deflagration. Consistent with earlier work, these realizations produce the familiar hot dense bound remnant surrounded by sparse ejecta. Our results indicate that the majority of the star remains unburned (∼70%) and bound (>90%). Our realizations produce total ejecta yields on the order of 10 −2 –10 −1 M ☉ , ejected 56 Ni yields on the order of 10 −4 –10 −2 M ☉ , and ejecta kinetic energies on the order of 10 48 –10 49 erg. Compared to yields inferred from recent observations of the dimmest Type Iax events—SN 2007qd, SN 2008ha, SN 2010ae, SN 2019gsc, SN 2019muj, SN 2020kyg, and SN 2021fcg—our simulation produces comparable 56 Ni yields but too-small total yields and kinetic energies. Reignition of the remnant is also seen in some realizations.

Hydrodynamical simulations↗
DOE OSTI2020

Deep Learning Prediction of Interspecies Interactions from Self-organized Spatiotemporal Patterns of Co-evolving Organisms

Microorganisms colonizing natural habits such as soils co-evolve to form specific spatial patterns through interspecies interactions. These self-organized patterns are a key ecological phenotype, which provides critical information on their interaction mechanisms. However, conventional network inference techniques that analyze species population data in bulk have yet to be extended to account for such spatial heterogeneity. Here we proposed supervised deep learning as a new network inference tool for predicting interspecies interactions from spatiotemporal patterns of microbial evolution. Due to lack of biological imaging data that can be used for training deep learning networks, we used in silico data generated from high-fidelity agent-based models to determine model structure and parameters. Even though networks were trained under simple configurations where interaction coefficients are assumed to be spatially invariant, we demonstrated that the resulting model can be utilized to successfully predict spatial variation of interactions in more complex domains (i.e., configured with a context-dependent mixture of interaction coefficients) as well as in simple domains without further training. In the further test against real biological data obtained through imaging experiments of a binary consortium (Pseudomonas fluorescens and a mutant of Escherichia coli), our model also predicted the dramatic shifts in interactions of the two organisms across different environmental contexts. Through various successful demonstrations in this work, the combined use of the agent-based model and machine learning algorithm provides a means to use new type of data - microscopic images - for extracting microbial interactions, therefore presenting itself as a useful tool for the analysis of more complex microbial community interactions.

Lee, Joon-Yong↗
DOE OSTI2023

Cross-protective antibodies against common endemic respiratory viruses

Respiratory syncytial virus (RSV), human metapneumovirus (HMPV), and human parainfluenza virus types one (HPIV1) and three (HPIV3) can cause severe disease and death in immunocompromised patients, the elderly, and those with underlying lung disease. A protective monoclonal antibody exists for RSV, but clinical use is limited to high-risk infant populations. Hence, therapeutic options for these viruses in vulnerable patient populations are currently limited. Here, we present the discovery, in vitro characterization, and in vivo efficacy testing of two cross-neutralizing monoclonal antibodies, one targeting both HPIV3 and HPIV1 and the other targeting both RSV and HMPV. The 3 × 1 antibody is capable of targeting multiple parainfluenza viruses; the MxR antibody shares features with other previously reported monoclonal antibodies that are capable of neutralizing both RSV and HMPV. We obtained structures using cryo-electron microscopy of these antibodies in complex with their antigens at 3.62 Å resolution for 3 × 1 bound to HPIV3 and at 2.24 Å for MxR bound to RSV, providing a structural basis for in vitro binding and neutralization. Together, a cocktail of 3 × 1 and MxR could have clinical utility in providing broad protection against four of the respiratory viruses that cause significant morbidity and mortality in at-risk individuals.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands

Viruses shape microbial communities, food web dynamics, and carbon and nutrient cycling in diverse ecosystems. However, little is known about the patterns and drivers of viral community composition, particularly in soil, precluding a predictive understanding of viral impacts on terrestrial habitats. To investigate soil viral community assembly processes, here we analyzed 43 soil viromes from a rainfall manipulation experiment in a Mediterranean grassland in California. We identified 5,315 viral populations (viral operational taxonomic units [vOTUs] with a representative sequence ≥10 kbp) and found that viral community composition exhibited a highly significant distance–decay relationship within the 200-m 2 field site. This pattern was recapitulated by the intrapopulation microheterogeneity trends of prevalent vOTUs (detected in ≥90% of the viromes), which tended to exhibit negative correlations between spatial distance and the genomic similarity of their predominant allelic variants. Although significant spatial structuring was also observed in the bacterial and archaeal communities, the signal was dampened relative to the viromes, suggesting differences in local assembly drivers for viruses and prokaryotes and/or differences in the temporal scales captured by viromes and total DNA. Despite the overwhelming spatial signal, evidence for environmental filtering was revealed in a protein-sharing network analysis, wherein a group of related vOTUs predicted to infect actinobacteria was shown to be significantly enriched in low-moisture samples distributed throughout the field. Overall, our results indicate a highly diverse, dynamic, active, and spatially structured soil virosphere capable of rapid responses to changing environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

H-cluster Intermediates and Catalytic Properties of Clostridium pasteurianum [FeFe]-Hydrogenase III

[FeFe]-Hydrogenases are structurally diverse enzymes that catalyze reversible H2 activation at a catalytic cofactor or H-cluster. The H-cluster is a [4Fe-4S] cubane linked by a cysteine thiolate to a diiron subsite containing unique CO, CN-, and dithiomethylamine ligands. The established H-cluster resting state of [4Fe-4S]2+-[FeII-FeI], or Hox, functions in H2 binding and oxidation, or by proton-coupled reduction initiates H2 evolution. In contrast, in Clostridium pasteurianum [FeFe]-hydrogenase III (CpIII) the resting state of the H-cluster is fully oxidized, [4Fe-4S]2+-[FeII-FeII], or Hox+1. To begin to understand if Hox+1 has a role in the mechanism of CpIII, we determined the spectroscopic and redox properties of CpIII H-cluster states under catalytic conditions. CpIII poised in Hox+1 and either equilibrated under 1 atm of H2 or reduced with sodium dithionite, resulted in a mixture of reduced states including Hox (Em8 = -407 mV), Htrans-like [4Fe-4S]+-[FeII-FeII] (Em8 = -418 mV), Hred [4Fe-4S]+-[FeII-FeI], and HredH+ [4Fe-4S]2+-[FeI-FeI] (Em8 = -455-480 mV). Under H2 the population of the Htrans-like state was >20-fold higher than Hox, implicating a role in CpIII catalysis. Unlike other enzymes, there was no spectral evidence of fully reduced states, such as HsredH+ ([4Fe-4S]+-[FeI-FeI]) or Hhyd ([4Fe-4S]+-[FeII-FeII]-H-). Thus, while the H-cluster states of CpIII encompass most of the catalytic intermediates, it is either unable to form HsredH+ and Hhyd, or these states are highly destabilized in CpIII. Thus, these results demonstrate that catalytic intermediates of reduced CpIII differ from the typical intermediates of other catalytic [FeFe]-hydrogenases and may explain the catalytic preference for H2 production.

08 HYDROGEN↗
DOE OSTI2022

MgADP Promotes Myosin Head Movement toward Actin at Low [Ca 2+ ] to Increase Force Production and Ca 2+ -Sensitivity of Contraction in Permeabilized Porcine Myocardial Strips

Myosin cross-bridges dissociate from actin following Mg 2+ -adenosine triphosphate (MgATP) binding. Myosin hydrolyses MgATP into inorganic phosphate (P i ) and Mg 2+ -adenosine diphosphate (ADP), and release of these hydrolysis products drives chemo-mechanical energy transitions within the cross-bridge cycle to power muscle contraction. Some forms of heart disease are associated with metabolic or enzymatic dysregulation of the MgATP-MgADP nucleotide pool, resulting in elevated cytosolic [MgADP] and impaired muscle relaxation. We investigated the mechanical and structural effects of increasing [MgADP] in permeabilized myocardial strips from porcine left ventricle samples. Sarcomere length was set to 2.0 µm at 28 °C, and all solutions contained 3% dextran T-500 to compress myofilament lattice spacing to near-physiological values. Under relaxing low [Ca 2+ ] conditions (pCa 8.0, where pCa = -log 10 [Ca 2+ ]), tension increased as [MgADP] increased from 0-5 mM. Complementary small-angle X-ray diffraction measurements show that the equatorial intensity ratio, I 1,1 /I 1,0 , also increased as [MgADP] increased from 0 to 5 mM, indicating myosin head movement away from the thick-filament backbone towards the thin-filament. Ca 2+ -activated force-pCa measurements show that Ca 2+ -sensitivity of contraction increased with 5 mM MgADP, compared to 0 mM MgADP. These data show that MgADP augments tension at low [Ca 2+ ] and Ca 2+ -sensitivity of contraction, suggesting that MgADP destabilizes the quasi-helically ordered myosin OFF state, thereby shifting the cross-bridge population towards the disordered myosin ON state. Together, these results indicate that MgADP enhances the probability of cross-bridge binding to actin due to enhancement of both thick and thin filament-based activation mechanisms.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Emerging Per- and Polyfluoroalkyl Substances in Tap Water from the American Healthy Homes Survey II

Humans experience widespread exposure to anthropogenic per- and polyfluoroalkyl substances (PFAS) through various media, which can lead to a wide range of negative health impacts. Tap water is an important source of exposure in communities with any degree of contamination but routine or large-scale PFAS monitoring often depends on targeted analytical methods limited to measuring specific PFAS. We analyzed 680 tap water samples from the American Healthy Homes Survey II for PFAS using non-targeted analysis (NTA) to expand the range of detectable PFAS. Based on detection frequency and relative abundance, about half of the identified PFAS were found only by NTA. We identified (with varying degrees of confidence) 75 distinct PFAS, including 57 exclusively detected by NTA. The identified PFAS are members of seven structural subclasses differentiated by their head groups and degree of fluorination. Clustering analysis categorized the PFAS into four coabundance groups dominated by specific PFAS subclasses. One group uniquely identified by NTA contains zwitterionic PFAS and other PFAS transformation products which are likely associated with aqueous firefighting foam contaminants in a small number of spatially correlated samples. These results help further characterize the scope of exposure to emerging PFAS experienced by the U.S. population via tap water and augment nationwide targeted-PFAS monitoring programs.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2021

Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail

Seasonal flu is an acute respiratory disease that exacts a massive toll on human populations, healthcare systems and economies. The disease is caused by an enveloped Influenza virus containing eight ribonucleoprotein (RNP) complexes. Each RNP incorporates multiple copies of nucleoprotein (NP), a fragment of the viral genome (vRNA), and a viral RNA-dependent RNA polymerase (POL), and is responsible for packaging the viral genome and performing critical functions including replication and transcription. A complete model of an Influenza RNP in atomic detail can elucidate the structural basis for viral genome functions, and identify potential targets for viral therapeutics. In this work we construct a model of a complete Influenza A RNP complex in atomic detail using multiple sources of structural and sequence information and a series of homology-modeling techniques, including a motif-matching fragment assembly method. Our final model provides a rationale for experimentally-observed changes to viral polymerase activity in numerous mutational assays. Further, our model reveals specific interactions between the three primary structural components of the RNP, including potential targets for blocking POL-binding to the NP-vRNA complex. The methods developed in this work open the possibility of elucidating other functionally-relevant atomic-scale interactions in additional RNP structures and other biomolecular complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Characterization of Deformational Isomerization Potential and Interconversion Dynamics with Ultrafast X-ray Solution Scattering

Dimeric complexes composed of d 8 square planar metal centers and rigid bridging ligands provide model systems to understand the interplay between attractive dispersion forces and steric strain in order to assist the development of reliable methods to model metal dimer complexes more broadly. [Ir 2 (dimen) 4 ] 2+ (dimen = para-diisocyanomenthane) presents a unique case study for such phenomena, as distortions of the optimal structure of a ligand with limited conformational flexibility counteract the attractive dispersive forces from the metal and ligand to yield a complex with two ground state deformational isomers. Here, in this work, we use ultrafast X-ray solution scattering (XSS) and optical transient absorption spectroscopy (OTAS) to reveal the nature of the equilibrium distribution and the exchange rate between the deformational isomers. The two ground state isomers have spectrally distinct electronic excitations that enable the selective excitation of one isomer or the other using a femtosecond duration pulse of visible light. We then track the dynamics of the nonequilibrium depletion of the electronic ground state population—often termed the ground state hole—with ultrafast XSS and OTAS, revealing a restoration of the ground state equilibrium in 2.3 ps. This combined experimental and theoretical study provides a critical test of various density functional approximations in the description of bridged d 8 –d 8 metal complexes. The results show that density functional theory calculations can reproduce the primary experimental observations if dispersion interactions are added, and a hybrid functional, which includes exact exchange, is used.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

In anaerobic reactors the microbial community structure depends on feed type, with no “keystone” species tied to COD removal

Two-stage anaerobic digestion (AD) systems provide treatment for high strength wastewater with high stability and performance. Encapsulation technology can intensify AD to facilitate the separation of the solids retention time from the hydraulic retention time (HRT), offering lower HRTs, smaller reactors, and high effluent quality. To support successful deployment, however, the encapsulated community must contain all the needed microorganisms for successful treatment and be flexible enough to treat a variety of wastewaters. Here, a two-stage system was investigated in which microbial cultures were enriched on various high-strength wastewaters in suspended flow-through systems to determine how feed type influenced performance and microbial community structure. The hypothesis was that specific genera, or so-called “keystone species” would positively correlate to organic carbon degradation for a given feed, enabling construction of a well-functioning community for encapsulation. Results showed that the number of total bacteria (as 16S rRNA gene copies) did not correlate to soluble chemical oxygen demand (sCOD) removal, indicating that the community structure and/or members were important for good performance. Results also showed that feed type strongly influenced carbon removal and microbial community structure for 1st-stage fermenting communities, but not 2nd-stage methanogenic communities. In this study, the “core” community members were defined as organisms common to all of either the 1st- or 2nd-stage reactors irrespective of the feed they received and were present in at least 50% of the samples throughout the entire experiment. “Unique” community members were specific to a single feed, and hence, only present in either the 1st- or 2nd-stage reactors receiving that feed. In both 1st- and 2nd-stage communities, only one core genera and no unique genera were positively and significantly correlated to sCOD removal. Verification experiments performed with encapsulated communities showed that organisms identified in flow-through system and correlated with carbon degradation, though not significantly, seemed to be important for performance. Our results suggest that one cannot construct a community containing specific populations in lieu of enrichment. Nevertheless, a single diverse encapsulated anaerobic community should provide good (>80%) carbon removal when fed a variety of influents, if time is provided for enrichment after deployment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Slow light in a 2D semiconductor plasmonic structure

Spectrally narrow optical resonances can be used to generate slow light, i.e., a large reduction in the group velocity. In a previous work, we developed hybrid 2D semiconductor plasmonic structures, which consist of propagating optical frequency surface-plasmon polaritons interacting with excitons in a semiconductor monolayer. Here, we use coupled exciton-surface plasmon polaritons (E-SPPs) in monolayer WSe 2 to demonstrate slow light with a 1300 fold decrease of the SPP group velocity. Specifically, we use a high resolution two-color laser technique where the nonlinear E-SPP response gives rise to ultra-narrow coherent population oscillation (CPO) resonances, resulting in a group velocity on order of 105 m/s. Our work paves the way toward on-chip actively switched delay lines and optical buffers that utilize 2D semiconductors as active elements.

42 ENGINEERING↗
DOE OSTI2024

Landscape fragmentation overturns classical metapopulation thinking

Habitat loss and isolation caused by landscape fragmentation represent a growing threat to global biodiversity. Existing theory suggests that the process will lead to a decline in metapopulation viability. However, since most metapopulation models are restricted to simple networks of discrete habitat patches, the effects of real landscape fragmentation, particularly in stochastic environments, are not well understood. To close this major gap in ecological theory, we developed a spatially explicit, individual-based model applicable to realistic landscape structures, bridging metapopulation ecology and landscape ecology. This model reproduced classical metapopulation dynamics under conventional model assumptions, but on fragmented landscapes, it uncovered general dynamics that are in stark contradiction to the prevailing views in the ecological and conservation literature. Notably, fragmentation can give rise to a series of dualities: a) positive and negative responses to environmental noise, b) relative slowdown and acceleration in density decline, and c) synchronization and desynchronization of local population dynamics. Furthermore, counter to common intuition, species that interact locally (“residents”) were often more resilient to fragmentation than long-ranging “migrants.” This set of findings signals a need to fundamentally reconsider our approach to ecosystem management in a noisy and fragmented world.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Decay spectroscopy of an isomeric state in Md251

Excited states in Md251 have been populated by decay of an isomeric state at Ex≈1174 keV and studied via delayed γ-ray spectroscopy. We observe the population of two rotational bands, one of which we identify as the Nilsson π72[514] ground-state band and the other we propose is based on the π92[624] configuration. From the observed decay pattern, we suggest that the isomer spin parity is 232+, with the three-quasiparticle configuration π72[514]⊗{ν72[624]⊗ν92[734]}Kπ=8−. We compare our results to theoretical predictions of the single- and multi-quasiparticle structure of Md251.

Morse, C↗
DOE OSTI2021

Bio-inspired Bistable Piezoelectric Energy Harvester for Powering Animal Telemetry Tags: Concept Design and Preliminary Experimental Validation

This paper presents the concept design, preliminary experimental validation, and performance evaluation of a novel bio-inspired bi-stable piezoelectric energy harvester for self-powered animal telemetry tags. The overall concept design, which includes a bio-inspired attachment and a bi-stable piezoelectric energy harvester, is introduced firstly with a specific application example of marine fish tracking. The self-powered telemetry tag can be externally deployed on fish (dorsal fin) to monitor fish habitats, population, and underwater environment. Inspired by the Venus flytrap’s rapid shape transition, a bistable piezoelectric energy harvester is developed to scavenge energy from fish maneuvering and the surrounding fluid flow for a sustainable power supply. The bistability of the harvester is characterized by the measured force-displacement curve and double potential wells. A bluff body is integrated to the free end of the bistable piezoelectric energy harvester to enhance the structure-fluid interaction for the large-amplitude snap-through vibrations and higher voltage output. Controlled laboratory experiments are conducted in a water tank on the bio-inspired bi-stable piezoelectric energy harvester using a servo motor system to simulate fish swing motion at various conditions to evaluate the power generation performance. The preliminary underwater experimental results demonstrated that the proposed bio-inspired bi-stable piezoelectric could effectively converter fish swing motions into electricity. 17.25 mJ energy was obtained within 130 s under the peak-to-peak swing angle of 30o at 1.5 Hz in the capacitor charging experiments.

Qian, Feng↗