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At least 667 records · Page 37

Modeling the dynamic response of rock masses with multiple compliant fluid saturated joint sets—Part I: Mesoscale simulations

Recently a mesoscale model was developed that includes thermomechanically consistent constitutive equations with dissipation due to porous compaction, inelastic distortional deformation rate, and slipping on persistent dry joint surfaces. In this Part I of a two-part paper, we describe enhancements of the mesoscale model which include: normal compliance with hysteresis, non-persistent joints with finite area, joint sets with angular deviation, and the weakening effect of fluid pressure in the joints. Examples study the influences of these effects on average strength. These computationally expensive simulations are used to inspire functional forms in a continuum model, described in Part II, which is needed for large scale simulations of real applications.

42 ENGINEERING↗

Low-dose high-resolution $\mathrm{TOF}$-$\mathrm{PET}$ using ionization-activated multi-state low-$\mathrm{Z}$ detector media

We propose PET scanners using low atomic number media that undergo a persistent local change of state along the paths of the Compton recoil electrons. Measurement of the individual scattering locations and angles, deposited energies, and recoil electron directions allows using the kinematical constraints of the 2-body Compton scattering process to perform a statistical time-ordering of the scatterings, with a high probability of precisely identifying where the gamma first interacted in the detector. In these cases the Line-of-Response is measured with high resolution, determined by the underlying physics processes and not the detector segmentation. There are multiple such media that act through different mechanisms. As an example in which the change of state is quantum-mechanical through a change in molecular configuration, rather than thermodynamic, as in a bubble chamber, we present simulations of a two-state photoswitchable organic dye, a ‘Switchillator’, that is activated to a fluorescent-capable state by the ionization of the recoil electrons. The activated state is persistent, and can be optically excited multiple times to image individual activated molecules. Energy resolution is provided by counting the activated molecules. Location along the LOR is implemented by large-area time-of-flight MCP-PMT photodetectors with single photon time resolution in the tens of ps and sub-mm spatial resolution. Simulations indicate a large reduction of dose.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Decadal survival of tropical pioneer seeds in the soil seed bank is accompanied by fungal infection and dormancy release

Pioneer trees require high-light environments for successful seedling establishment. Consequently, seeds of these species often persist in the soil seed bank (SSB) for periods ranging from several weeks to decades. How they survive despite extensive pressure from seed predators and soil-borne pathogens remains an intriguing question. Here this study aims to test the hypotheses that decades-old seeds collected from the SSB in a lowland tropical forest remain viable by (i) escaping infection by fungi, which are major drivers of seed mortality in tropical soils, and/or (ii) maintaining high levels of seed dormancy and seed coat integrity when compared to inviable seeds. We collected seeds of Trema micrantha and Zanthoxylum ekmanii at Barro Colorado Island, Panama, from sites where adult trees previously occurred in the past 30 years. We used carbon dating to measure seed age and characterized seed coat integrity, seed dormancy and fungal communities. Viable seeds from the SSB ranged in age from 9 to 30 years for T. micrantha, and 5 to 33 years for Z. ekmanii. We found no evidence that decades-old seeds maintain high levels of seed dormancy or seed coat integrity. Fungi were rarely detected in fresh seeds (no soil contact), but phylogenetically diverse fungi were detected often in seeds from the SSB. Although fungal infections were more commonly detected in inviable seeds than in viable seeds, a lack of differences in fungal diversity and community composition between viable and inviable seeds suggested that viable seeds are not simply excluding fungal species to survive long periods in the SSB. Synthesis. Our findings reveal the importance of a previously understudied aspect of seed survival, where the impact of seed–microbial interactions may be critical to understand long-term persistence in the SSB.

54 ENVIRONMENTAL SCIENCES↗

Optimizing Irregular Communication with Neighborhood Collectives and Locality-Aware Parallelism

Irregular communication often limits both the performance and scalability of parallel applications. Typically, applications individually implement irregular communication as point-to-point, and any optimizations are integrated directly into the application. As a result, these optimizations lack portability. It is difficult to optimize point-to-point messages within MPI, as the interface for single messages provides no information on the collection of all communication to be performed. However, the persistent neighbor collective API, released in the MPI 4 standard, provides an interface for portable optimizations of irregular communication within MPI libraries. This paper presents methods for implementing existing optimizations for irregular communication within neighborhood collectives, analyzes the impact of replacing point-to-point communication in existing codebases such as Hypre BoomerAMG with neighborhood collectives, and finally shows up to a 1.38x speedup on sparse matrix-vector multiplication communication within a BoomerAMG solve through the use of our optimized neighbor collectives. Here, the authors analyze three implementations of persistent neighborhood collectives for Alltoallv: an unoptimized wrapper of standard point-to-point communication, and two locality-aware aggregating methods. The second locality-aware implementation exposes an non-standard interface to perform additional optimization, and the authors present the additional 0.07x speedup from the extended interface. All optimizations are available in an open-source codebase, MPI Advance, which sits on top of MPI, allowing for optimizations to be added into existing codebases regardless of the system MPI install.

AMG↗

Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources

Salmonella enterica is one of the most common bacterial foodborne pathogens in the United States, causing illnesses that range from self-limiting gastroenteritis to more severe, life threatening invasive disease. Many Salmonella strains contain plasmids that carry virulence, antimicrobial resistance, and/or transfer genes which allow them to adapt to diverse environments, and these can include incompatibility group (Inc) FIB plasmids. This study was undertaken to evaluate the genomic and phenotypic characteristics of IncFIB-positive Salmonella enterica serovar Typhimurium isolates from food animal sources, to identify their plasmid content, assess antimicrobial resistance and virulence properties, and compare their genotypic isolates with more recently isolated S. Typhimurium isolates from food animal sources. Methods: We identified 71 S. Typhimurium isolates that carried IncFIB plasmids. These isolates were subjected to whole genome sequencing and evaluated for bacteriocin production, antimicrobial susceptibility, the ability to transfer resistance plasmids, and a subset was evaluated for their ability to invade and persist in intestinal human epithelial cells. Results: Approximately 30% of isolates (n = 21) displayed bacteriocin inhibition of Escherichia coli strain J53. Bioinformatic analyses using PlasmidFinder software confirmed that all isolates contained IncFIB plasmids along with multiple other plasmid replicon types. Comparative analyses showed that all strains carried multiple antimicrobial resistance genes and virulence factors including iron acquisition genes, such as iucABCD (75%), iutA (94%), sitABCD (76%) and sitAB (100%). In 17 cases (71%), IncFIB plasmids, along with other plasmid replicon types, were able to conjugally transfer antimicrobial resistance and virulence genes to the susceptible recipient strain. For ten strains, persistence cell counts (27%) were noted to be significantly higher than invasion bacterial cell counts. When the genome sequences of the study isolates collected from 1998–2003 were compared to those published from subsequent years (2005–2018), overlapping genotypes were found, indicating the perseverance of IncFIB positive strains in food animal populations. This study confirms that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species.

59 BASIC BIOLOGICAL SCIENCES↗

The C‐Terminal Domain of α‐Synuclein Confers Steric Stabilization on Synaptic Vesicle‐Like Surfaces

Abstract While α‐synuclein, an intrinsically disordered protein linked to Parkinson's disease, has been shown to associate with membrane organelles, its overall cellular function remains nebulous. α‐Synuclein binds to membranes through its amino‐terminal domain (first ≈100 residues), but there is no consensus on the biophysical function of the carboxyl‐terminal domain (last ≈40 residues) due, in part, to its lack of strong interaction partners and persisting intrinsic disorder even when membrane bound. Here, by directly applying force on α‐synuclein bound to spherical nanoparticle‐supported lipid bilayers (SSLBs) and tracking higher‐order structural changes through small‐angle X‐ray scattering, strong evidence is presented that α‐synuclein sterically stabilizes membrane surfaces through its carboxyl‐terminal domain. Full‐length α‐synuclein dramatically increases the critical osmotic pressure at which SSLBs cluster ( P C ≈ 1.3 × 10 5 Pa) compared to α‐synuclein without the carboxyl‐terminal domain ( P C ≈ 1.9 × 10 4 Pa) at physiological salt and temperature conditions. This clustering of α‐synuclein‐bound SSLBs is shown to be reversible and sensitive to monovalent/divalent salt, both features of grafted polyelectrolyte‐mediated steric stabilization. In elucidating the biophysical function of α‐synuclein in the framework of polymer science, it is demonstrated that the carboxyl‐terminal domain can potentially utilize its persisting intrinsic disorder to functionalize membrane surfaces.

Chung, Peter J.↗

Abiotic and biotic factors jointly influence the contact and environmental transmission of a generalist pathogen

The joint influence of abiotic and biotic factors is important for understanding the transmission of generalist pathogens. Abiotic factors such as temperature can directly influence pathogen persistence in the environment and will also affect biotic factors, such as host community composition and abundance. At intermediate spatial scales, the effects of temperature, community composition, and host abundance are expected to contribute to generalist pathogen transmission. We use a simple transmission model to explain and predict how host community composition, host abundance, and environmental pathogen persistence times can independently and jointly influence transmission. Our transmission model clarifies how abiotic and biotic factors can synergistically support the transmission of a pathogen. The empirical data show that high community competence, high abundance, and low temperatures correlate with high levels of transmission of ranavirus in larval amphibian communities. Discrete wetlands inhabited by larval amphibians in the presence of ranavirus provide a compelling case study comprising distinct host communities at a spatial scale anticipated to demonstrate abiotic and biotic influence on transmission. We use these host communities to observe phenomena demonstrated in our theoretical model. These findings emphasize the importance of considering both abiotic and biotic factors, and concomitant direct and indirect mechanisms, in the study of pathogen transmission and should extend to other generalist pathogens with the capacity for environmental transmission.

59 BASIC BIOLOGICAL SCIENCES↗

Temporal Patterns in Soil Redox Potential Vary Across a Freshwater Coastal Delta

Widespread and persistent flooding is submerging coastal ecosystems, particularly along the Louisiana Gulf coast, where flooding results from the compounding effects of ground subsidence and rising sea level. Restoration projects aim to mitigate land loss by diverting sediment loads from rivers into degraded areas to increase ground elevation. To predict how coastal ecosystems will change over time in response to projected changes in relative sea level and restoration, it is necessary to understand how subsurface biogeochemical processes respond to dynamic hydrologic forcings. Here, this study evaluates how environmental parameters that integrate biogeochemical processes vary with water table fluctuations in the freshwater Wax Lake Delta (WLD) in Louisiana, USA, where water diversions have formed one of the only active deltas along the coast. High‐frequency observations of water level, soil redox potential, specific conductance and pH were made for 1 year along elevation transects located on the older, proximal and younger, distal ends of a deltaic island. Redox responded rapidly to changing water tables, with fluctuations occurring primarily in shallow soils (< 20 cm) and at higher elevations. Deeper soils and those at lower elevation remained inundated and reduced. Semi‐diurnal tidal fluctuations were pronounced in younger, distal soils, presumably due to rapid groundwater exchange with the river channel. Tidal signals were muted in older soils that instead exhibited seasonal variability associated with river discharge and evapotranspiration. Although much of the delta sediments are persistently reducing and anoxic, redox fluctuations in the natural levees that border the deltaic islands likely drive high rates of biogeochemical activity. Evaluating how hydrology drives the frequency and duration of redox fluctuations provides a basis for understanding how biogeochemical processes might vary with complex hydrological interactions in coastal systems.

Herndon, Elizabeth [Oak Ridge National Laboratory ↗

Implications from Monitoring Gopher Tortoises at Two Spatial Scales

A problem that conservation biologists face is how to monitor species, given both resource limitations and the inherent challenges of assessing long-term demographic processes. We assessed gopher tortoise (Gopherus polyphemus) abundance at a landscape scale and at the scale of 3 local populations within the Conecuh National Forest (CNF).USA between 1991 and 2017. Landscape-level data were collected 26 from line transect distance sampling arranged uniformly across the CNF and collected during a single season (2011); data for local populations were generated from long-term mark-recapture of individuals at three sites selected based on prior knowledge of high density at each. At a landscape scale, we estimated 5,242 (95% CI = 3,538-7,768) tortoises occurred across the approximately 34,000-ha forest, yielding a density of 0.14-0.32 tortoises/ ha. These low densities across the landscape suggest that, on average, management activities across the property have not allowed tortoise populations to retain social structure needed for long-term persistence. The three local populations, however, contained 25-60 individuals and densities of 1.9–6.9 tortoises/ha. Over the study period, populations at two sites were stable and the third experienced significant population growth. Mean annual survival of individuals was 0.89 and invariant across size classes. Altogether, line transect distance sampling is important for assessing landscape-scale abundance of tortoises but may fail to detect local clusters of high-density sites important for population persistence. Our mark-recapture efforts at the local scale revealed that small populations on these high-density sites can exhibit long-term stability or growth even though they do not meet current established criteria for viability. Improved models that incorporate immigration and emigration and better reflect dynamics of peripheral populations would assist in determining how such populations best contribute to species recovery and regional conservation targets.

59 BASIC BIOLOGICAL SCIENCES↗

On the Equilibrium Electrostatic Potential and Light-Induced Charge Redistribution in Halide Perovskite Structures

Lead halide perovskites are semiconductor materials which are employed as nonintentionally doped absorbers inserted between two selective carrier transport layers (SCTL), realizing a p-i-n or n-i-p heterojunction. In our study, we have developed and investigated a lateral device, based on methylammonium lead iodide (MAPbI3) in which the p-i-n heterojunction develops in the horizontal direction. Our research suggests that the effective doping level in the MAPbI3 film should be very low, below 1012 cm-3. Along the vertical direction, this doping level is not enough to screen the electric field of the buried heterojunction with the SCTL. The perovskite work function is therefore affected by the work function of the SCTL underneath. From drift-diffusion simulations, we show that intrinsic perovskite-SCTL structures develop mV range surface photovoltages (SPVs) under continuous illumination. However, perovskite-SCTL structures can develop SPVs of hundreds of mV, as confirmed by our measurements. We therefore analyzed the compatibility between low doping and low defect densities in the perovskite layer and such high SPV values using numerical modeling. It is shown that these high SPV values could originate from electronic processes due to large band offsets in the buried perovskite-SCTL heterojunctions, or at the SCTL-transparent conductive oxide (TCO) buried heterojunction. However, such electronic processes can hardly explain the long SPV persistence after switching off the illumination.

defects↗

Antisolvent‐Mediated Air Quench for High‐Efficiency Air‐Processed Carbon‐Based Planar Perovskite Solar Cells

Perovskite solar cells (PSCs) have becoma a leading low‐cost photovoltaic technology, achieving power conversion efficiencies (PCEs) of up to 26.1%. However, their commercialization is hindered by stability issues and the need for controlled processing environments. Carbon‐electrode‐based PSCs (C‐PSCs) offer enhanced stability and cost‐effectiveness compared to traditional metal‐electrode PSCs, i.e., Au and Ag. However, processing challenges persist, particularly in air conditions where moisture sensitivity poses a significant hurdle. Herein, a novel air processing technique is presented for planar C‐PSCs that incorporates antisolvent vapors, such as chlorobenzene, into a controlled air‐quenching process. This method effectively mitigates moisture‐induced instability, resulting in champion PCEs exceeding 20% and robust stability under ambient conditions. The approach retains 80% of initial efficiency after 30 h of operation at maximum power point without encapsulation. This antisolvent‐mediated air‐quenching technique represents a significant advancement in the scalable production of C‐PSCs, paving the way for future large‐scale deployment.

14 SOLAR ENERGY↗

Extrapolating Contaminant Effects from Individuals to Populations: A Case Study on Nanoparticle Toxicity to Daphnia Fed Environmentally Relevant Food Levels

Ecological risk assessment (ERA) is charged with assessing the likelihood a chemical will have adverse environmental or ecological effects. When assessing the risk of a potential contaminant to biological organisms, ecologists are most concerned with the sustainability of populations of organisms, rather than protecting every individual. However, ERA most commonly relies on data on the effect of a potential contaminant on individuals because these experiments are more feasible than costly population-level exposures. In this work, we address the challenge of extrapolating these individual-level results to predict population-level effects. Previous per-capita population growth rate estimates calculated from individual-level exposures of Daphnia pulicaria to silver nanoparticles (AgNPs) at different food rations predict a critical daily food requirement for daphnid populations exposed to 200 μg/L AgNPs to avoid extinction. To test this, we exposed daphnid populations to the same AgNP concentration at three different food inputs, with the lowest ration close to the extinction threshold predicted from data on individuals. The two populations with the higher food inputs persisted, and the population with the lowest food input went extinct after 50 days but did persist through two generations. Further, we demonstrate that we can extrapolate between these levels of biological organization by parameterizing an individual-level biomass model with data on individuals’ response to AgNPs and using these parameters to predict the outcome for control and AgNP-exposed populations. Key to successful extrapolation is careful modeling of temporal changes in resource density, driven by both the experimental protocols and feedback from the consumer. The implication for ecotoxicology is that estimates of extinction thresholds based on studies of individuals may be reliable predictors of population outcomes, but only with careful treatment of resource dynamics.

54 ENVIRONMENTAL SCIENCES↗

Assessing microbial residues in soil as a potential carbon sink and moderator of carbon use efficiency

Abstract A longstanding assumption of glucose tracing experiments is that all glucose is microbially utilized during short incubations of ≤2 days to become microbial biomass or carbon dioxide. Carbon use efficiency (CUE) estimates have consequently ignored the formation of residues (non-living microbial products) although such materials could represent an important sink of glucose that is prone to stabilization as soil organic matter. We examined the dynamics of microbial residue formation from a short tracer experiment with frequent samplings over 72 h, and conducted a meta-analysis of previously published glucose tracing studies to assess the generality of these experimental results. Both our experiment and meta-analysis indicated 30–34% of amended glucose-C ( 13 C or 14 C) was in the form of residues within the first 6 h of substrate addition. We expand the conventional efficiency calculation to include residues in both the numerator and denominator of efficiency, thereby deriving a novel metric of the potential persistence of glucose-C in soil as living microbial biomass plus residues (‘carbon stabilization efficiency’). This new metric indicates nearly 40% of amended glucose-C persists in soil 180 days after amendment, the majority as non-biomass residues. Starting microbial biomass and clay content emerge as critical factors that positively promote such long term stabilization of labile C. Rapid residue production supports the conclusion that non-growth maintenance activity can illicit high demands for C in soil, perhaps equaling that directed towards growth, and that residues may have an underestimated role in the cycling and sequestration potential of C in soil.

Geyer, Kevin (ORCID:0000000252182745)↗

Hydrogen Bonding Stiffens Peptide Amphiphile Supramolecular Filaments by Aza-Glycine Residues

Peptide amphiphiles (PAs) are a class of molecules comprised of short amino acid sequences conjugated to hydrophobic moieties that may exhibit self-assembly in water into supramolecular structures. Here, we investigate here how mechanical properties of hydrogels formed by PA supramolecular nanofibers are affected by hydrogen bond densities within their internal structure by substituting glycine for aza-glycine (azaG) residues. We found that increasing the number of PA molecules that contain azaG up to 5 mol% in PA supramolecular nanofibers increases their persistence length fivefold and decreases their diffusion coefficients as measured by fluorescence recovery after photobleaching. When these PAs are used to create hydrogels, their bulk storage modulus (G') was found to increase as azaG PA content in the supramolecular assemblies increases up to a value of 10 mol% and beyond this value a decrease was observed, likely due to diminished levels of nanofiber entanglement in the hydrogels as a direct result of increased supramolecular rigidity. Interestingly, we found that the bioactivity of the scaffolds toward dopaminergic neurons derived from induced pluripotent stem cells can be enhanced directly by persistence length independently of storage modulus. We hypothesize that this is due to interactions between the cells and the extracellular environment across different size scales: from filopodia adhering to individual nanofiber bundles to cell adhesion sites that interact with the hydrogel as a bulk substrate. Fine tuning of hydrogen bond density in self-assembling peptide biomaterials such as PAs provides an approach to control nanoscale stiffness as part of an overall strategy to optimize bioactivity in these supramolecular systems. supramolecular biomaterials.

36 MATERIALS SCIENCE↗

Timing Value of Marine Renewable Energy Resources for Potential Grid Applications

In this paper, the applicability of marine renewable energy for potential grid applications is presented. We show that many of the unique value streams from marine-based electricity generation stem from their inherent temporal characteristics, especially when compared to wind and solar. Specifically, in this work, we evaluate the timing value for three types of marine energy resources - (a) tidal (b) wave and (c) ocean currents. Firstly, through a suite of novel metrics such as resource availability, persistence and versatility, we evaluate the temporal value characteristics of these resources. Secondly, through a more grid-oriented numerical study, we comment on the potential ramifications of those temporal characteristics in context of energy balancing and effective load carrying capability, for one marine-based resource i.e. wave. Subsequently, we further our understanding of the relative advantages which may be leveraged by operating wave-based generation resources in tandem with more established renewable choices, such as solar and wind. Our results indicate that compared to wind and solar, marine energy resources are consistently more available and persistent on an hourly level, throughout an entire year of operation. In addition to this, wave resources are also seen to reduce both the magnitudes and the degree of volatility in balancing requirements within the power system. Our work not only focuses on sites specific to the Unites States (US), but also includes a parallel study for a location in Great Britain (GB). Results are found to be consistent for sites in both the US and GB, implying that the grid benefits discussed in this work could apply to a number of locations globally.

Bhattacharya, Saptarshi↗

The value of adding black carbon to community monitoring of particulate matter

Low-cost particulate matter (PM) sensors are increasingly used by researchers, public health agencies, and the public to measure spatial and temporal variations in air pollution, which can inform strategies for community air pollution reduction. While low-cost PM sensors provide a valuable measure of harmful fine particulate matter (PM 2.5 ), a significant portion of ambient PM 2.5 is typically the secondary product of air pollution emitted by varied sources outside of community boundaries. In contrast, concentrations of black carbon (BC), a component of PM 2.5 , are directly emitted by a few specific sources, such as diesel engines within communities. Motivated by community organizations seeking to understand persistent sources of local pollution, this study deployed a suite of custom-built BC sensors alongside a network of low-cost PM sensors for four weeks in two seasons at 50 stationary locations in the adjacent cities of Richmond, North Richmond, and San Pablo, California, east of the San Francisco Bay. Concentrations of BC varied more than PM 2.5 both temporally and spatially. Monthly network-average BC was 3×higher in winter than late spring, while PM 2.5 was only 10% lower. In both seasons, average PM 2.5 concentrations at two-thirds of sites were within ±10% of the network average, whereas two-thirds of sites had BC levels outside of ±10% of the network-average concentration. The most and least polluted locations were more persistent across seasons for BC than PM 2.5 , and the temporal dynamics of BC at these sites were similar, signifying that they are impacted by the same emission sources. Together, these spatiotemporal trends show that BC is a better indicator of the proximity and activity of local pollution sources than PM 2.5 . Thus, including BC in addition to PM 2.5 in community monitoring networks can provide additional insights about local sources of air pollution.

54 ENVIRONMENTAL SCIENCES↗

Intrinsic self-stressing and low carbon Engineered Cementitious Composites (ECC) for improved sustainability

Highlights: • A self-stressing criterion for ECC was established and experimentally verified. • An intrinsic self-stressing ECC was developed by utilizing LC3 and CSA cement. • Initial maximum expansion and later expansion loss were successfully tailored. • Expansion mechanism was identified by XRD patterns. • Self-stressing ECC has 64% of the carbon footprint of conventional concrete. Engineered Cementitious Composites (ECC) is an emerging cementitious composite material with ultra-high ductility. However, its higher cement dosage limits its material greenness and leads to concerns with drying shrinkage. In this research, an ECC utilizing limestone calcined clay cement (LC3) and calcium sulphoaluminate cement (CSA) is investigated, focusing on minimizing the material's embodied carbon while enhancing its durability with intrinsic self-stressing functionality. A self-stressing criterion is theoretically established and experimentally verified. X-ray diffraction patterns reveal an ettringite quantity that modulates the initial expansion and later expansion-reversal of LC3-CSA-ECC to support a persistent self-stressing mechanism. LC3-CSA-ECC has a lower (64%) carbon footprint and similar embodied energy compared to conventional concrete. When combined with the durability advantage (tiny crack, high ductility of 5.5%, and self-stressing function), this low carbon self-stressing ECC holds promise as a sustainable repair material that lowers the embodied and operational carbon in civil infrastructure.

36 MATERIALS SCIENCE↗