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At least 1,459 records · Page 81

An experimental and computational study of thin-layer Rayleigh–Taylor instability development during deceleration with and without an externally applied magnetic field

The importance of mitigating the Rayleigh–Taylor instability (RTI) in inertial confinement fusion (ICF) is critical to successfully achieve high gain fusion yield. Consequently, understanding the seed mechanisms of RTI and the potential evolution of RTI in ICF relevant conditions is crucial. Single feature perturbations consistently demonstrate non-linear RTI evolution, for which an experimental platform on OMEGA-EP is developed. Manufacturing defects introduced into the target design require exploration of unanticipated changes to RTI development and an identification of targets that will still render quantifiable physics results. Consequently, it is presented that the inherent 3D nature of experimental targets necessitates 3D modeling for accurate design work and predictive modeling of experimental targets, especially when high resolution imaging diagnostics, like Fresnel Zone Plates, are utilized. A study of the morphology of the RTI evolution due to changing initial conditions and the presence of an externally applied magnetic field are also explored. Experimental data show thin-layer RTI morphology comparable to resistive magneto hydrodynamic 3D results. A discussion on the impacts of an externally applied magnetic field makes the case for continued efforts to observe a magnetic field's impact on RTI morphology.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Pervasive iron limitation at subsurface chlorophyll maxima of the California Current

Subsurface chlorophyll maximum layers (SCMLs) are nearly ubiquitous in stratified water columns and exist at horizontal scales ranging from the submesoscale to the extent of oligotrophic gyres. These layers of heightened chlorophyll and/or phytoplankton concentrations are generally thought to be a consequence of a balance between light energy from above and a limiting nutrient flux from below, typically nitrate (NO 3 ). Here we present multiple lines of evidence demonstrating that iron (Fe) limits or with light colimits phytoplankton communities in SCMLs along a primary productivity gradient from coastal to oligotrophic offshore waters in the southern California Current ecosystem. SCML phytoplankton responded markedly to added Fe or Fe/light in experimental incubations and transcripts of diatom and picoeukaryote Fe stress genes were strikingly abundant in SCML metatranscriptomes. Using a biogeochemical proxy with data from a 40-y time series, we find that diatoms growing in California Current SCMLs are persistently Fe deficient during the spring and summer growing season. We also find that the spatial extent of Fe deficiency within California Current SCMLs has significantly increased over the last 25 y in line with a regional climate index. Finally, we show that diatom Fe deficiency may be common in the subsurface of major upwelling zones worldwide. Our results have important implications for our understanding of the biogeochemical consequences of marine SCML formation and maintenance.

54 ENVIRONMENTAL SCIENCES↗

Structural basis for activity of TRIC counter-ion channels in calcium release

Trimeric intracellular cation (TRIC) channels are thought to provide counter-ion currents that facilitate the active release of Ca 2+ from intracellular stores. TRIC activity is controlled by voltage and Ca 2+ modulation, but underlying mechanisms have remained unknown. Here we describe high-resolution crystal structures of vertebrate TRIC-A and TRIC-B channels, both in Ca 2+ -bound and Ca 2+ -free states, and we analyze conductance properties in structure-inspired mutagenesis experiments. The TRIC channels are symmetric trimers, wherein we find a pore in each protomer that is gated by a highly conserved lysine residue. In the resting state, Ca 2+ binding at the luminal surface of TRIC-A, on its threefold axis, stabilizes lysine blockage of the pores. During active Ca 2+ release, luminal Ca 2+ depletion removes inhibition to permit the lysine-bearing and voltage-sensing helix to move in response to consequent membrane hyperpolarization. Diacylglycerol is found at interprotomer interfaces, suggesting a role in metabolic control.

Wang, Xiao-hui↗

Emergence of topological electronic phases in elemental lithium under pressure

Lithium, a prototypical simple metal under ambient conditions, has a surprisingly rich phase diagram under pressure, taking up several structures with reduced symmetry, low coordination numbers, and even semiconducting character with increasing density. Using first-principles calculations, we demonstrate that some predicted high-pressure phases of elemental Li also host topological electronic structures. Beginning at 80 GPa and coincident with a transition to the previously predicted Pbca phase, we find Li to be a Dirac nodal line semimetal. We further calculate that Li retains linearly dispersing energy bands near the Fermi energy in subsequent predicted higher-pressure phases and that it exhibits a Lifshitz transition between two Cmca phases at 220 GPa. The Fd 3 ¯ m phase at 500 GPa forms buckled honeycomb layers that give rise to a Dirac crossing 1 eV below the Fermi energy. The well-isolated topological nodes near the Fermi level in these phases result from increasing p-orbital character with density at the Fermi level, itself a consequence of rising 1s core wavefunction overlap, and a preference for nonsymmorphic symmetries in the crystal structures favored at these pressures. Our results provide evidence that under pressure, bulk 3D materials with light elements, or even pure elemental systems, can undergo phase transitions hosting nontrivial topological phase transitions hosting nontrivial topological properties near the Fermi level with measurable consequences and that, through pressure, we can access these phases in elemental lithium.

36 MATERIALS SCIENCE↗

Asynchronous nitrogen supply and demand produce nonlinear plant allocation responses to warming and elevated CO 2

Terrestrial ecosystem responses to climate change are mediated by complex plant–soil feedbacks that are poorly understood, but often driven by the balance of nutrient supply and demand. We actively increased aboveground plant-surface temperature, belowground soil temperature, and atmospheric CO 2 in a brackish marsh and found nonlinear and nonadditive feedbacks in plant responses. Changes in root-to-shoot allocation by sedges were nonlinear, with peak belowground allocation occurring at +1.7 °C in both years. Above 1.7 °C, allocation to root versus shoot production decreased with increasing warming such that there were no differences in root biomass between ambient and +5.1 °C plots in either year. Elevated CO 2 altered this response when crossed with +5.1 °C, increasing root-to-shoot allocation due to increased plant nitrogen demand and, consequently, root production. We suggest these nonlinear responses to warming are caused by asynchrony between the thresholds that trigger increased plant nitrogen (N) demand versus increased N mineralization rates. The resulting shifts in biomass allocation between roots and shoots have important consequences for forecasting terrestrial ecosystem responses to climate change and understanding global trends.

54 ENVIRONMENTAL SCIENCES↗

The impact of long-range dispersal on gene surfing

Range expansions lead to distinctive patterns of genetic variation in populations, even in the absence of selection. These patterns and their genetic consequences have been well studied for populations advancing through successive short-ranged migration events. However, most populations harbor some degree of long-range dispersal, experiencing rare yet consequential migration events over arbitrarily long distances. Although dispersal is known to strongly affect spatial genetic structure during range expansions, the resulting patterns and their impact on neutral diversity remain poorly understood. Here, we systematically study the consequences of long-range dispersal on patterns of neutral variation during range expansion in a class of dispersal models which spans the extremes of local (effectively short-ranged) and global (effectively well-mixed) migration. We find that sufficiently long-ranged dispersal leaves behind a mosaic of monoallelic patches, whose number and size are highly sensitive to the distribution of dispersal distances. We develop a coarse-grained model which connects statistical features of these spatial patterns to the evolution of neutral diversity during the range expansion. We show that growth mechanisms that appear qualitatively similar can engender vastly different outcomes for diversity: Depending on the tail of the dispersal distance distribution, diversity can be either preserved (i.e., many variants survive) or lost (i.e., one variant dominates) at long times. Our results highlight the impact of spatial and migratory structure on genetic variation during processes as varied as range expansions, species invasions, epidemics, and the spread of beneficial mutations in established populations.

59 BASIC BIOLOGICAL SCIENCES↗

Measuring the effectiveness of high-performance Co-Optima biofuels on suppressing soot formation at high temperature

Soot emissions in combustion are unwanted consequences of burning hydrocarbon fuels. The presence of soot during and following combustion processes is an indication of incomplete combustion and has several negative consequences including the emission of harmful particulates and increased operational costs. Efforts have been made to reduce soot production in combustion engines through utilizing oxygenated biofuels in lieu of traditional nonoxygenated feedstocks. The ongoing Co-Optimization of Fuels and Engines (Co-Optima) initiative from the US Department of Energy (DOE) is focused on accelerating the introduction of affordable, scalable, and sustainable biofuels and high-efficiency, low-emission vehicle engines. The Co-Optima program has identified a handful of biofuel compounds from a list of thousands of potential candidates. In this study, a shock tube was used to evaluate the performance of soot reduction of five high-performance biofuels downselected by the Co-Optima program. Current experiments were performed at test conditions between 1,700 and 2,100 K and 4 and 4.7 atm using shock tube and ultrafast, time-resolve laser absorption diagnostic techniques. The combination of shock heating and nonintrusive laser detection provides a state-of-the-art test platform for high-temperature soot formation under engine conditions. Soot reduction was found in ethanol, cyclopentanone, and methyl acetate; conversely, an α-diisobutylene and methyl furan produced more soot compared to the baseline over longer test times. For each biofuel, several reaction pathways that lead towards soot production were identified. The data collected in these experiments are valuable information for the future of renewable biofuel development and their applicability in engines.

09 BIOMASS FUELS↗

Modeling the evolution of the US opioid crisis for national policy development

The opioid crisis remains one of the greatest public health challenges in the United States. The crisis is complex, with long delays and feedbacks between policy actions and their effects, which creates a risk of unintended consequences and complicates policy decision-making. We present SOURCE (Simulation of Opioid Use, Response, Consequences, and Effects), an operationally detailed national-level model of the opioid crisis, intended to enhance understanding of the crisis and guide policy decisions. Drawing on multiple data sources, SOURCE replicates how risks of opioid misuse initiation and overdose have evolved over time in response to behavioral and other changes and suggests how those risks may evolve in the future, providing a basis for projecting and analyzing potential policy impacts and solutions.

59 BASIC BIOLOGICAL SCIENCES↗

A distinct RNA recognition mechanism governs Np 4 decapping by RppH

Dinucleoside tetraphosphates, often described as alarmones because their cellular concentration increases in response to stress, have recently been shown to function in bacteria as precursors to nucleoside tetraphosphate (Np 4 ) RNA caps. Removal of this cap is critical for initiating 5' end-dependent degradation of those RNAs, potentially affecting bacterial adaptability to stress; however, the predominant Np 4 decapping enzyme in proteobacteria, ApaH, is inactivated by the very conditions of disulfide stress that enable Np 4 -capped RNAs to accumulate to high levels. Here, in this study, we show that, in Escherichia coli cells experiencing such stress, the RNA pyrophosphohydrolase RppH assumes a leading role in decapping those transcripts, preferring them as substrates over their triphosphorylated and diphosphorylated counterparts. Unexpectedly, this enzyme recognizes Np 4 -capped 5' ends by a mechanism distinct from the one it uses to recognize other 5' termini, resulting in a one-nucleotide shift in substrate specificity. The unique manner in which capped substrates of this kind bind to the active site of RppH positions the δ-phosphate, rather than the β-phosphate, for hydrolytic attack, generating triphosphorylated RNA as the primary product of decapping. Consequently, a second RppH-catalyzed deprotection step is required to produce the monophosphorylated 5' terminus needed to stimulate rapid RNA decay. The unconventional manner in which RppH recognizes Np 4 -capped 5' ends and its differential impact on the rates at which such termini are deprotected as a prelude to RNA degradation could have major consequences for reprogramming gene expression during disulfide stress.

59 BASIC BIOLOGICAL SCIENCES↗

Self-consistent dispersal puts tight constraints on the spatiotemporal organization of species-rich metacommunities

Dispersal can be critical to the maintenance of ecosystems as it allows local communities to be recolonized after extinction. However, it remains unclear whether the extinction-mitigating effect of dispersal persists when the number of competing species is large. Based on a spatially explicit mathematical description of metacommunities, we show that when many species coexist, each species operates near its extinction threshold, barely surviving due to dispersal. This has general consequences for spatiotemporal abundance patterns. For short-range dispersal, species organize into fractal spatiotemporal extinction patterns characteristic of a directed percolation phase transition. As species approach their extinction threshold, biodiversity is very sensitive to perturbation, suggesting that dispersal within a metacommunity puts tight constraints on the robustness and evolution of species-rich metacommunities. Biodiversity is often attributed to a dynamic equilibrium between the immigration and extinction of species. This equilibrium forms a common basis for studying ecosystem assembly from a static reservoir of migrants—the mainland. Yet, natural ecosystems often consist of many coupled communities (i.e., metacommunities), and migration occurs between these communities. The pool of migrants then depends on what is sustained in the ecosystem, which, in turn, depends on the dynamic migrant pool. This chicken-and-egg problem of survival and dispersal is poorly understood in communities of many competing species, except for the neutral case—the “unified neutral theory of biodiversity.” Employing spatiotemporal simulations and mean-field analyses, we show that self-consistent dispersal puts rather tight constraints on the dynamic migration–extinction equilibrium. When the number of species is large, species are pushed to the edge of their global extinction, even when competition is weak. As a consequence, the overall diversity is highly sensitive to perturbations in demographic parameters, including growth and dispersal rates. When dispersal is short range, the resulting spatiotemporal abundance patterns follow broad scale-free distributions that correspond to a directed percolation phase transition. The qualitative agreement of our results for short-range and long-range dispersal suggests that this self-organization process is a general property of species-rich metacommunities. Our study shows that self-sustaining metacommunities are highly sensitive to environmental change and provides insights into how biodiversity can be rescued and maintained.

54 ENVIRONMENTAL SCIENCES↗

Partial PdAu nanoparticle embedding into TiO 2 support accentuates catalytic contributions from the Au/TiO 2 interface

Despite the broad catalytic relevance of metal–support interfaces, controlling their chemical nature, the interfacial contact perimeter (exposed to reactants), and consequently, their contributions to overall catalytic reactivity, remains challenging, as the nanoparticle and support characteristics are interdependent when catalysts are prepared by impregnation. Here, we decoupled both characteristics by using a raspberry-colloid-templating strategy that yields partially embedded PdAu nanoparticles within well-defined SiO 2 or TiO 2 supports, thereby increasing the metal–support interfacial contact compared to nonembedded catalysts that we prepared by attaching the same nanoparticles onto support surfaces. Between nonembedded PdAu/SiO 2 and PdAu/TiO 2 , we identified a support effect resulting in a 1.4-fold higher activity of PdAu/TiO 2 than PdAu/SiO 2 for benzaldehyde hydrogenation. Notably, partial nanoparticle embedding in the TiO 2 raspberry-colloid-templated support increased the metal–support interfacial perimeter and consequently, the number of Au/TiO 2 interfacial sites by 5.4-fold, which further enhanced the activity of PdAu/TiO 2 by an additional 4.1-fold. Theoretical calculations and in situ surface-sensitive desorption analyses reveal facile benzaldehyde binding at the Au/TiO 2 interface and at Pd ensembles on the nanoparticle surface, explaining the connection between the number of Au/TiO 2 interfacial sites (via the metal–support interfacial perimeter) and catalytic activity. Our results demonstrate partial nanoparticle embedding as a synthetic strategy to produce thermocatalytically stable catalysts and increase the number of catalytically active Au/TiO 2 interfacial sites to augment catalytic contributions arising from metal–support interfaces.

Lim, Kang Rui Garrick (ORCID:0000000321599844)↗

Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na + and K + Ions and the Protonation State of Glu 290

Ions play key mechanistic roles in the gating dynamics of neurotransmitter:sodium symporters (NSSs). In other microsecond scale molecular dynamics simulations of a complete model of the dopamine transporter, a NSS protein, we observed a partitioning of K + ions from the intracellular side toward the unoccupied Na2 site of dopamine transporter following the release of the Na2-bound Na + . In this work, we evaluate with computational simulations and experimental measurements of ion affinities under corresponding conditions, the consequences of K+ binding in the Na2 site of LeuT, a bacterial homolog of NSS, when both Na + ions and substrate have left, and the transporter prepares for a new cycle. We compare the results with the consequences of binding Na + in the same apo system. Analysis of >50-μs atomistic molecular dynamics and enhanced sampling trajectories of constructs with Glu 290 , either charged or neutral, point to the Glu 290 protonation state as a main determinant in the structural reconfiguration of the extracellular vestibule of LeuT in which a “water gate” opens through coordinated motions of residues Leu 25 , Tyr 108 , and Phe 253 . The resulting water channel allows the binding/dissociation of the Na + and K + ions that are prevalent, respectively, in the extracellular and intracellular environments.

59 BASIC BIOLOGICAL SCIENCES↗

Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

As the capability of mass spectrometry-based proteomics has matured, tens of thousands of peptides can be measured simultaneously, which has the benefit of offering a systems view of protein expression. However, a major challenge is that with an increase in throughput, protein quantification estimation from the native measured peptides has become a computational task. A limitation to existing computationally-driven protein quantification methods is that most ignore protein variation, such as alternate splicing of the RNA transcript and post-translational modifications or other possible proteoforms, which will affect a significant fraction of the proteome. The consequence of this assumption is that statistical inference at the protein level, and consequently downstream analyses, such as network and pathway modeling, have only limited power for biomarker discovery. Here, we describe a Bayesian model (BP-Quant) that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern, or the existence of multiple over-expressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. We verify the approach using a dilution study from mouse plasma samples and demonstrate that BP-Quant achieves similar accuracy as the current state-of-the-art methods at proteoform identification with significantly better specificity. BP-Quant is available as a MatLab ® and R packages at https://github.com/PNNL-Comp-Mass-Spec/BP-Quant.

Protein Quantitation, proteomics↗

First-of-a-Kind Risk-Informed Digital Twin for Operational Decision Making

A digital twin (DT) is a digital model or a collection of models of a physical entity. DTs in the nuclear arena can be used from plant design through decommissioning. Decisions are typically a priori or made offline. Risk-informed decision making is identifying what can go wrong, its frequency, and the consequences of its failure. Ideally risk-informed decision making reflects the current state of the plant and provides a decision in real time. Traditionally, probabilistic risk assessments (PRAs) evaluate the failures of safety systems, the risk of core damage, and the offsite dose as the consequence. However, this DT evaluates the decisions on the control side rather than the protection side. It uses the same risk methods to probabilistically inform the decision-making process but in a different way. Rather than evaluating the risk of core damage, this DT evaluates the likelihood of avoiding a trip set point while maintaining plant safety. Performance-based assessments are identified via its probabilistic evaluation of operational alternatives based on system status. Because the purpose of the control system is to maintain system variables within prescribed operating ranges, upsets or challenges that can exceed a trip set point resulting in a plant transient and a challenge to plant mitigating systems based on actual plant conditions, are evaluated to safely maintain the plant within the operating ranges. The probabilistic portion of the model is autonomously and automatically adjusted, and the metric of interest (i.e. likelihood of avoiding a trip set point) is recalculated. The digital representation of the physical system (i.e. the DT) performs a deterministic performance–based assessment of the probabilistically identified alternatives identified to validate the probabilistic assessment. A decision-making algorithm selects the appropriate option based on the probabilistic and deterministic assessments and transmits a control signal to a component(s) to initiate a corrective action or informs an operator of its decision.

digital twin↗

Investigating the Role of Accident Tolerant Cladding on Source Term Reduction for High-Burnup PWRs Using MELCOR

The use of accident tolerant fuel (ATF) cladding can increase coping times during and beyond design basis accidents. While such gains may be incremental, they provide a margin that can potentially be recovered to enable high-burnup (HBU) operation. Realizing such a margin requires demonstrating that the combination of HBU and ATF has not led to an overall increase in source term. This study investigates the influence of cladding technology (Zr-based, Cr-coated Zr, and FeCrAl) and fuel cycle length (18 and 24 months) on radiological dose at the boundary of the exclusion zone for a four-loop pressurized water reactor to investigate whether ATF claddings can provide such benefits. We analyze a recovered large break loss-of-coolant accident scenario to investigate the impact of transient timescale on the benefits of such coping time increases. The simulations have been performed using the MELCOR and MELCOR Accident Consequence Code System codes. For the cases analyzed, increased fuel cycle length did not necessarily increase radionuclide release and hydrogen generation, as these were found to be sensitive to the core power distribution. Similarly, off-site dose consequence is dominated by short-lived radionuclides that tend to saturate earlier in the burnup, so higher burnup operation did not necessarily increase the source term for the phenomena and transients analyzed here. Delays in recovery of the lowpressure safety injection system increase hydrogen production and radionuclide release, especially between 780 s and 1620 s, due to the nonlinear oxidation and core degradation behavior. Results show that Cr-coated Zr enhances safety by delaying heatup and gap release. Here, when uncertainty propagation on oxidation properties is considered, FeCrAl exhibits the lowest overall radionuclide release and off-site dose throughout the spectrum. However, while the considered “base model” performance is superior under delayed injection scenarios, upper-bound cases display hydrogen generation risk comparable to the Zr-based cladding.

Accident Tolerant Fuel↗

Estimating viscosity of individual substrate-deposited particles from measurements of their height-to-width ratios

Airborne particles alter the radiative forcing of climate and have further consequences on air visibility, atmospheric chemistry, and human health. Recent studies reported the existence of highly viscous semisolid and even solid amorphous organic aerosol (OA) particles. Particle viscosity has an impact on the heterogeneous chemistry, gas-particle partitioning, and ice nucleation properties. Consequently, variations in particle viscosity must be considered when predicting the atmospheric impact of OA. Here, in this work, we use scanning electron microscopy (SEM) and scanning transmission X-ray microscopy (STXM) to estimate the viscosity of individual particles deposited on substrates based on their characteristic height-to-width ratios, which are affected by changes in morphology upon deposition. The height-to-width ratios obtained from SEM and STXM exhibit a strong correlation, demonstrating that both imaging approaches can be applied separately for viscosity assessment of the substrate-deposited particles. While these metrics are largely qualitative, this method enables rapid assessment of particle viscosity ranges, distinguishing between semisolid (>10 10 Pa·s), viscous (10 4– 10 8 Pa·s), and liquid (10°–10 1 Pa·s) particles within ensembles of ambient particles collected for microscopy studies.

54 ENVIRONMENTAL SCIENCES↗

Structural and functional differences between porcine brain and budding yeast microtubules

The cytoskeleton of eukaryotic cells relies on microtubules to perform many essential functions. We have previously shown that, in spite of the overall conservation in sequence and structure of tubulin subunits across species, there are differences between mammalian and budding yeast microtubules with likely functional consequences for the cell. Here we expand our structural and function comparison of yeast and porcine microtubules to show different distribution of protofilament number in microtubules assembled in vitro from these two species. The different geometry at lateral contacts between protofilaments is likely due to a more polar interface in yeast. We also find that yeast tubulin forms longer and less curved oligomers in solution, suggesting stronger tubulin:tubulin interactions along the protofilament. Finally, we observed species-specific plus-end tracking activity for EB proteins: yeast Bim1 tracked yeast but not mammalian MTs, and human EB1 tracked mammalian but not yeast MTs. These findings further demonstrate that subtle sequence differences in tubulin sequence can have significant structural and functional consequences in microtubule structure and behavior.

Cell Biology Tubulin↗

Socially-aware evaluation framework for transportation

Technological advancements are rapidly changing traffic management in cities. Navigation applications, in particular, have impacted cities in many ways by rerouting traffic. As different routing strategies distribute traffic differently, understanding these disparities across multiple city-relevant dimensions is extremely important for decision-makers. We develop a multi-themed framework called Socially- Aware Evaluation Framework for Transportation (SAEF), which assists in understanding how traffic routing and the resultant dynamics affect cities. The framework is presented for four Bay Area cities, for which we compare three routing strategies - user equilibrium travel time, system optimal travel time, and system optimal fuel. The results demonstrate that many neighborhood impacts, such as traffic load on residential streets and around minority schools, degraded with the system-optimal travel time and fuel routing in comparison to the user-equilibrium travel time routing. The findings also show that all routing strategies subject the city's disadvantaged neighborhoods to disproportionate traffic exposure. Our intent with this work is to provide an evaluation framework that enables reflection on the consequences of traffic routing and management strategies, allowing city planners to recognize the trade-offs and potential unintended consequences.

99 GENERAL AND MISCELLANEOUS↗