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At least 1,477 records · Page 82

Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Background: Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat. Results: Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages. Conclusions: Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale.

59 BASIC BIOLOGICAL SCIENCES↗

Data System Implications Derived from User Application Requirements for Satellite Data

An investigation of the data system needs as driven by users of space acquired Earth observation data is documented. Two major categories of users, operational and research, are identified. Limiting data acquisition alleviates some of the delays in processing thus improving timeliness of the delivered product. Trade offs occur between timeliness and data distribution costs, and between data storage and reprocessing. The complexity of the data system requirements to apply space data to users' needs is such that no single analysis suffices to design and implement the optimum system. A series of iterations is required with analyses of the salient problems in a general way, followed by a limited implementation of benefit to some users with a continual upgrade in system capacity, functions, and applications served. The resulting most important requirement for the data system is flexibility to accommodate changing requirements as the system is implemented.

Neiers, J.↗

The Growth of Protein Crystals Using McDUCK

Most of the current microgravity crystal growth hardware is optimized to produce crystals within the limited time available on orbit. This often results in the actual nucleation and growth process being rushed or the system not coming to equilibrium within the limited time available. Longer duration hardware exists, but one cannot readily pick out crystals grown early versus those which nucleated and grew more slowly. We have devised a long duration apparatus, the Multi-chamber Dialysis Unit for Crystallization Kinetics, or McDUCK. This apparatus-is a series of protein chambers, stacked upon a precipitant reservoir chamber. All chambers are separated by a dialysis membrane, which serves to pass small molecules while retaining the protein. The volume of the Precipitant chamber is equal to the sum of the volumes of the protein chamber. In operation, the appropriate chambers are filled with precipitant solution or protein solution, and the McDUCK is placed standing upright, with the precipitant chamber on the bottom. The precipitant diffuses upwards over time, with the time to reach equilibration a function of the diffusivity of the precipitant and the overall length of the diffusion pathway. Typical equilibration times are approximately 2-4 months, and one can readily separate rapid from slow nucleation and growth crystals. An advantage on Earth is that the vertical precipitant concentration gradient dominates that of the solute, thus dampening out solute density gradient driven convective flows. However, large Earth-grown crystals have so far tended to be more two dimensional. Preliminary X-ray diffraction analysis of lysozyme crystals grown in McDUCK have indicated that the best, and largest, come from the middle chambers, suggesting that there is an optimal growth rate. Further, the improvements in diffraction resolution have been better signal to noise ratios in the low resolution data, not an increase in resolution overall. Due to the persistently large crystals grown we are currently proposing McDUCK for the growth of macromolecule crystals for use in neutron diffraction studies.

Ewing, Felicia↗

Future Model-Based Systems Engineering Vision and Strategy Bridge for NASA

A vision for the future of model-based systems engineering (MBSE) at NASA in 2029 and a strategy bridge towards that future are presented. Strategic thinking and leading change concepts were used to analyze reports and presentations on global trends and visionary thinking about the future of systems and digital engineering. The context, strategic time horizon, stakeholders, strategic challenges, strategic advantages, driving forces, and opportunities were considered. The analysis resulted in a future vision of MBSE that shows what NASA systems engineers and digital machines will do to perform rapid, extraordinary, and unprecedented missions. The NASA systems engineer, in this future vision, works with a global project team in a virtual and collaborative environment, engineers the system, and uses digital approaches as the routine and default way of working. The digital machines provide data-driven and automated mission designs; have a backbone of program and project management, systems engineering, and product life-cycle management; and are a knowledge-sharing infrastructure. The NASA systems engineer and the systems engineering team are envisioned to use digital machines to plan and perform rapid exploration missions, develop a digital twin that lasts across the life cycle, and develop enduring and adaptable systems. NASA has an engineering enterprise and a life-cycle management framework that endure, adapt, and respond. A strategy bridge based on the Baldrige Criteria for Performance Excellence Framework and lessons learned from a recent MBSE initiative illuminates a way forward from today to this desired future. The bridge lays out a strategy for leaders and recommends investments of today for immediate benefits and for benefits in 2029.

model-based systems engineering, digital engineeri↗

Towards a New nCTEQ global nPDF release

We discuss the foundation for a new global nCTEQ nuclear PDF analysis, combining a number of our previous analyses into one consistent framework with updates to the underlying theoretical treatment as well as the addition of new available data. In particular, the new global release will be the first nCTEQ release containing neutrino DIS scattering data in a consistent manner together with JLab high-x DIS data and new LHC p-Pb data. These additions will improve the data-driven description of nuclear PDFs in new regions, especially the strange quark and the gluon PDF at low-x.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Scaling and Design Analysis of a Sub-Scale, Reduced Temperature Stratified Flow Separate Effects Test Facility for the Experimental Investigation of Air Ingress in a High Temperature Reactor System

High temperature gas reactors (HTGR) are poised to spearhead the next generation of nuclear reactors, due to their passive safety characteristics and their applications flexibility. Able to provide base load power or process heat for industrial applications, HGTRs may be a critical component to reducing greenhouse gas emissions in the United States and abroad. However, increased interest and development has also highlighted areas requiring further investigation, one of which being the air-ingress accident. Air ingress may occur following a break in the coaxial cross duct and pressure vessel depressurization. The initial mode of ingress is hypothesized to be density driven cross flow as the cold air enters the lower plenum, at which point molecular diffusion and/or local buoyancy phenomena will dominate until a global natural circulation current is established. While computational simulations support this progression, little or no experimental data exists to validate and support this phenomenology. Therefore, it is necessary to generate such data; this research seeks to do so through the use of a sub-scale separate effects test facility - the Stratified Flow Separate Effects Test Facility (SFSETF). The goal of this facility is more specifically to focus on the transition to global natural circulation starting from air ingress after a double-ended guillotine break (DEGB) while neglecting depressurization. This paper will provide analyses performed in the design of this facility, including the geometric and hydraulic scaling analyses, safety analysis and instrumentation selection. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Data Driven Smart Proxy for CFD: Application of Big Data Analytics & Machine Learning in Computational Fluid Dynamics (Part 1)

Simulation technologies can reduce the time and cost of the development and deployment of advanced technologies and allow rapid scale-up of these technologies for fossil fuel based energy systems. However, to ensure their usefulness in practice, the credibility of the simulations needs to be established with Uncertainty Quantification (UQ) methods. National Energy Technology Laboratory (NETL) has been applying non-intrusive UQ methodologies to categorize and quantify uncertainties in CFD simulations of gas-solid multiphase flows. To reduce the computational cost associated with gas-solid flow simulations required for UQ analysis, techniques commonly used in the area of Artificial Intelligence (AI) and Data Mining (DM) are used to construct smart proxy models, which can reduce the computational cost of conducting large number of multiphase CFD simulations.

97 MATHEMATICS AND COMPUTING↗

Overcoming persistent challenges in putting environmental flow policy into practice: a systematic review and bibliometric analysis

The implementation of environmental flows (e-flows) aims to reduce the negative impacts of hydrological alteration on freshwater ecosystems. Despite the growing attention to the importance of e-flows since the 1970s, actual implementation has lagged. Therefore, we explore the limitations in e-flows implementation, their systemic reasons, and solutions. We conducted a systematic review and a bibliometric analysis to identify peer-reviewed articles published on the topic of e-flows implementation research in the last two decades, resulting in 68 research and review papers. Co-occurrence of terms, and geographic and temporal trends were analyzed to identify the gaps in environmental water management and propose recommendations to address limitations on e-flows implementation. We identify the underlying causes and potential solutions to such challenges in environmental water management. The limitations to e-flow implementation identified were categorized into 21 classes. The most recognized limitation was the competing priorities of human uses of water (n = 29). Many secondary limitations, generally co-occurring in co-causation, were identified as limiting factors, especially for implementing more nuanced and sophisticated e-flows. The lack of adequate hydrological data (n = 24) and ecological data (n = 28) were among the most mentioned, and ultimately lead to difficulties in starting or continuing monitoring/adaptive management (n = 28) efforts. The lack of resource/capacity (n = 21), experimentation (n = 19), regulatory enforcement (n = 17), and differing authorities involved (n = 18) were also recurrent problems, driven by the deficiencies in the relative importance given to e-flows when facing other human priorities. In order to provide a clearer path for successful e-flow implementation, system mapping can be used as a starting point and general-purpose resource for understanding the sociohydrological problems, interactions, and inherited complexity of river systems. Secondly, we recommend a system analysis approach to address competing demands, especially with the use of coupled water-energy modeling tools to support decision-making when hydropower generation is involved. Such approaches can better assess the complex interactions among the hydrologic, ecological, socioeconomic, and engineering dimensions of water resource systems and their effective management. Lastly, given the complexities in environmental water allocation, implementation requires both scientific rigor and proven utility. Consequently, and where possible, we recommend a move from simplistic flow allocations to a more holistic approach informed by hydroecological principles. To ease conflicts between competing water demands, water managers can realize more 'pop per drop' by supporting key components of a flow regime that include functional attributes and processes that enhance biogeochemical cycling, structural habitat formation, and ecosystem maintenance.

54 ENVIRONMENTAL SCIENCES↗

Global teleconnections influencing large-scale drought in the United States using SVDI

Understanding recent large-scale drought patterns and the mechanisms producing extreme drought events is vital for future drought forecasts and understanding future drought risks. Increasingly, vapor pressure deficit (VPD) has been used as an important measure of evaporative demand and proxy for drought detection. In this study, VPD is used to calculate the new Standardized VPD Drought Index (SVDI) with NASA North American Land Data Assimilation System (NLDAS) data. Previous studies have shown that SVDI accurately identifies the timing and magnitude short-term droughts in the United States (U.S). In the present study, SVDI is now used to identify large-scale drought patterns between 1980 and 2021 and drought variability driven by selected global teleconnections originating in the Pacific and Atlantic Oceans. Spatial drought characteristics were extracted from SVDI using empirical orthogonal function (EOF) analysis. Then a k-means clustering algorithm was applied to both EOF principal components and primary teleconnections, including the El Nino-Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO) to identify drought events driven by the Pacific Ocean. Results show that the SVDI is useful in evaluating large-scale drought variability in the U.S. related to global teleconnections, and that mechanisms influencing summer drought patterns in the Western and Southwestern U.S. are driven by a tropical-extratropical interactions originating in the equatorial Pacific Ocean related to ENSO dynamics with interdecadal variability modulated by PDO. The large-scale droughts in the Central and Southern U.S., like those in 2011 and 2012, on the other hand, are driven by the North Pacific Ocean warm pool during a strong negative PDO, which subsequently influenced variability in the Bermuda-Azores High in the Atlantic Ocean. In summer 2011, the Bermuda-Azores High weakened, reducing the onshore winds and moisture transport along the eastern Gulf of Mexico and contributing to ongoing drought in the region. The Northern Pacific and Atlantic Ocean sea surface temperatures (SSTs) have increased between 1980 and 2021. In conclusion, as SSTs continue to rise in the Northern Pacific Ocean, one consequence of the coupled North Pacific warm pool and atmospheric dynamics, is to increase summer drought variability over a large region in the southern and midwestern U.S. under global warming.

54 ENVIRONMENTAL SCIENCES↗

Revealing the Structure and Dynamics of Self-Generated Electric and Magnetic Fields Near Plasma Stagnation in Laser-Driven Hohlraums

By coupling newly developed triparticle charged particle radiography with radiography reconstruction algorithms and novel reconstruction postprocessing techniques, the spatial structure and time evolution of self-generated electric and magnetic fields in laser-driven vacuum hohlraums have been quantitatively revealed. Through high-fidelity data from a series of experiments, it is shown that late in the hohlraum evolution (after the end of laser drive) these fields are strongly correlated in both space and time, providing evidence that their evolution is primarily dominated by advection with the plasma flow. At these late times, plasma flow velocities inferred from both gross radiography analysis and field reconstructions (and corroborated with Thomson scattering measurements) indicate that the plasma is approaching stagnation near the hohlraum axis. Finally, these experiments provide not only new physical insight into spontaneously generated hohlraum fields, but also provide important spatially and temporally resolved information for future benchmarking of numerical codes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Unlocking the distinctive enzymatic functions of the early plant biomass deconstructive genes in a brown rot fungus by cell-free protein expression

ABSTRACT Saprotrophic fungi that cause brown rot of woody biomass evolved a distinctive mechanism that relies on reactive oxygen species (ROS) to kick-start lignocellulosic polymers’ deconstruction. These ROS agents are generated at incipient decay stages through a series of redox relays that shuttle electrons from fungus’s central metabolism to extracellular Fenton chemistry. A list of genes has been suggested encoding the enzyme catalysts of the redox processes involved in ROS’s function. However, navigating the functions of the encoded enzymes has been challenging due to the lack of a rapid method for protein synthesis. Here, we employed cell-free expression system to synthesize four redox or degradative enzymes, which were identified, by transcriptomic data, as conserved players of the ROS oxidation phase across brown rot fungal species. All four enzymes were successfully expressed and showed activities that enable confident assignment of function, namely, benzoquinone reductase (BQR), ferric reductase, α-L-arabinofuranosidase (ABF), and heme-thiolate peroxidase (HTP). Detailed analysis of their catalytic features within the context of brown rot environments allowed us to interpret their roles during ROS-driven wood decomposition. Specifically, we validated the functions of BQR as the driver redox enzyme of Fenton cycles and reconstructed its interactions with the co-occurring HTP or laccase and ABF. Taken together, this research demonstrated that the cell-free expression platform is adequate for synthesizing functional fungal enzymes and provided an alternative route for the rapid characterization of fungal proteins, escalating our understanding of the distinctive biocatalyst system for plant biomass conversion. IMPORTANCE Brown rot fungi are efficient wood decomposers in nature, and their unique degradative systems harbor untapped catalysts pursued by the biorefinery and bioremediation industries. While the use of “omics” platforms has recently uncovered the key “oxidative-hydrolytic” mechanisms that allow these fungi to attack lignocellulose, individual protein characterization is lagging behind due to the lack of a robust method for rapid synthesis of crucial fungal enzymes. This work delves into the studies of biochemical functions of brown rot enzymes using a rapid, cell-free expression platform, which allowed the successful depictions of enzymes’ catalytic features, their interactions with Fenton chemistry, and their roles played during the incipient stage of brown rot when fungus sets off the reactive oxygen species for oxidative degradation. We expect this research could illuminate cell-free protein expression system’s use to fulfill the increasing need for functional studies of fungal enzymes, advancing the discoveries of novel biomass-converting catalysts.

60 APPLIED LIFE SCIENCES↗

Multiscale Electricity Modeling for Evaluating Carbon Capture and Sequestration Technologies (MEME-CCS)

This effort employs and adapts an existing, rigorous multiscale electricity modeling platform at the National Renewable Energy Laboratory (NREL) to evaluate carbon capture and sequestration (CCS) and negative emissions technologies (NET) from the ARPA-E FLECCS program. NREL's modeling platform includes the Regional Energy Deployment System (ReEDS) electric sector capacity expansion model, which projects future electricity generation mixes at sub-state-level resolution that are downscaled to the unit-level to enable hourly, zonal or nodal electricity production cost modeling in the PLEXOS model. The resulting hourly price data from PLEXOS is provided to technology developers under the ARPA-E FLECCS program to enable technology-specific economic analysis. The ReEDS-PLEXOS modeling suite is well-established for examining electric sector futures with high renewable energy penetrations, energy storage, electrification, and distributed generation. The key advancement proposed herein utilizes collaboration with CCS experts at the University of Wyoming and the FLECCS teams to create innovative methods for representing CCS and NET in the ReEDS and PLEXOS models. Expanded technology options, new operational parameterizations, and detailed data defining CO2 capture, transportation, and storage systems are being integrated into these models to allow an unprecedented combination of scope and resolution for exploring the future of CCS and NET. The resulting capabilities will take advantage of high-performance computing resources to permit wide-ranging scenario analysis to assess CCS and NET deployment under alternative CO2 prices, fossil fuel prices, electricity demand growth, and other electric sector characteristics. Final outcomes will include publicly available hourly grid operation and price data for any U.S. region of interest along with open-access capacity expansion tools for evaluating CCS/NET systems. These products will help an emerging CCS/NET industry in the United States by providing economics-driven guidance to technology developers while informing policy and investment decisions in the public and private sectors.

air capture↗

Frequency domain model for analysis of paralleled, series-output-connected Mapham inverters

The Mapham resonant inverter is characterized as a two-port network driven by a selected periodic voltage. The two-port model is then used to model a pair of Mapham inverters connected in series and employing phasor voltage regulation. It is shown that the model is useful for predicting power output in paralleled inverter units, and for predicting harmonic current output of inverter pairs, using standard power flow techniques. Some examples are compared to data obtained from testing hardware inverters.

Brush, Andrew S.↗

Accelerating particle-in-cell kinetic plasma simulations via reduced-order modeling of space-charge dynamics using dynamic mode decomposition

We present a data-driven reduced-order modeling of the space-charge dynamics for electromagnetic particle-in-cell (EMPIC) plasma simulations based on dynamic mode decomposition (DMD). The dynamics of the charged particles in kinetic plasma simulations such as EMPIC is manifested through the plasma current density defined along the edges of the spatial mesh. We showcase the efficacy of DMD in modeling the time evolution of current density through a low-dimensional feature space. Not only do such DMD based predictive reduced-order models help accelerate EMPIC simulations, they also have the potential to facilitate investigative analysis and control applications. Here, we demonstrate the proposed DMD-EMPIC scheme for reduced-order modeling of current density and speedup in EMPIC simulations involving electron beam under the influence of magnetic field, virtual cathode oscillations, and backward wave oscillator.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Spatio-temporal multivariate cluster evolution analysis for detecting and tracking climate impacts

Recent years have seen a growing concern about climate change and its impacts. While Earth System Models (ESMs) can be invaluable tools for studying the impacts of climate change, the complex coupling processes encoded in ESMs and the large amounts of data produced by these models, together with the high internal variability of the Earth system, can obscure important source-to-impact relationships. Here, this paper presents a novel and efficient unsupervised data-driven approach for detecting statistically-significant impacts and tracing spatio-temporal source-impact pathways in the climate through a unique combination of ideas from anomaly detection, clustering and Natural Language Processing (NLP). Using as an exemplar the 1991 eruption of Mount Pinatubo in the Philippines, we demonstrate that the proposed approach is capable of detecting known post-eruption impacts/events. We additionally describe a methodology for extracting meaningful sequences of post-eruption impacts/events by using NLP to efficiently mine frequent multivariate cluster evolutions, which can be used to confirm or discover the chain of physical processes between a climate source and its impact(s).

Anomaly detection↗

Phase change material-to-refrigerant heat exchangers: Experimental validation and uneven melting analysis

Thermal energy storage (TES) using phase change materials (PCMs) enables load shifting and reduces mismatches between the building's thermal demand and the heat pump (HP) system's thermal capacity. While most TES studies have focused on single-phase heat transfer fluids, PCM-to-refrigerant heat exchangers (PRHX), in which the refrigerant undergoes liquid-vapor phase change, remain largely underexplored. Here, to address this gap, this study systematically investigates a shell-and-tube PRHX operating as the condenser in an HP through experiments and simulations. A two-dimensional enthalpy-based finite-volume PRHX model was developed and validated against experimental data, including refrigerant and PCM temperature profiles, PRHX capacity, and system-level performance. Results show three characteristic stages: Stage I, the condenser temperature rapidly increases with PCM in the solid state absorbing sensible heat; Stage II, stable operation during PCM phase change; and Stage III, performance decline once part of the PCM becomes fully melted. Heat transfer analysis revealed that uneven PCM melting along the condenser length was driven primarily by variations in the refrigerant-side heat transfer coefficient, rather than local approach temperature differences. Further study demonstrated that minimizing refrigerant outlet subcooling led to more uniform PCM melting and extended Stages I and II by up to 89%. This paper provides a validated PRHX model, clarifies the mechanisms of uneven PCM melting, and highlights subcooling control as an effective strategy to improve TES performance in HP systems without requiring secondary loops.

Graphite matrix↗

Reshock analysis for PMMA driven above the threshold for chemical decomposition

Polymethyl methacrylate (PMMA) is a transparent thermoplastic often used in shock compression science. Previous proceedings (AIP Conf. Proc. 845, 131 (2006)) described plate impact experiments in which PMMA was reshocked to pressures of up to ~130 GPa, well above that at which it decomposes on its principal Hugoniot. Because some of the conclusions of the original analysis were surprising, the results were reanalyzed in a later proceeding (ibid. 1426, 771 (2012)). In addition to our own reanalysis of the data, we performed hydrodynamic simulations of the experiments based on a new equation of state for PMMA shocked above its threshold for decomposition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗