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At least 1,333 records · Page 74

RNAseq data for P. putida with vanillate

Illumina sequencing reads from RNA sequencing of vanillate-utilizing strains of Pseudomonas putida, described in Evolution and engineering of pathways for aromatic O-demethylation in Pseudomonas putida KT2440 by A. Bleem, et al. (2024)

Adaptive laboratory evolution↗

Feature Engineering and Process Mining to Enable Hazard Detection in Health Information Technology

Motivation for this work originates from a recognized need for developing data-driven approaches through analysis of complex electronic health records. Specifically, we aim to enhance the reliability of health information technology (HIT) systems by detection of plausible HIT hazards in clinical order transactions. In the absence of well-defined event logs in corporate data warehouses, our proposed approach identifies relevant timestamped data fields that could indicate transactions in the clinical order life cycle generating raw event sequences. Subsequently, we adopt state transitions of the OASIS Human Task standard to map the raw event sequences and simplify the complex process that clinical radiology orders go through. We describe how the current approach provides the potential to investigate areas of improvement and potential hazards in HIT systems. The discussion concludes with a use case and opportunities for future applications.

Ozmen, Ozgur↗

Engineering custom morpho- and chemotypes of Populus for sustainable production of biofuels, bioproducts, and biomaterials

Humans have been modifying plant traits for thousands of years, first through selection (i.e., domestication) then modern breeding, and in the last 30 years, through biotechnology. These modifications have resulted in increased yield, more efficient agronomic practices, and enhanced quality traits. Precision knowledge of gene regulation and function through high-resolution single-cell omics technologies, coupled with the ability to engineer plant genomes at the DNA sequence, chromatin accessibility, and gene expression levels, can enable engineering of complex and complementary traits at the biosystem level. Populus spp., the primary genetic model system for woody perennials, are among the fastest growing trees in temperate zones and are important for both carbon sequestration and global carbon cycling. Ample genomic and transcriptomic resources for poplar are available including emerging single-cell omics datasets. To expand use of poplar outside of valorization of woody biomass, chassis with novel morphotypes in which stem branching and tree height are modified can be fabricated thereby leading to trees with altered leaf to wood ratios. These morphotypes can then be engineered into customized chemotypes that produce high value biofuels, bioproducts, and biomaterials not only in specific organs but also in a cell-type-specific manner. For example, the recent discovery of triterpene production in poplar leaf trichomes can be exploited using cell-type specific regulatory sequences to synthesize high value terpenes such as the jet fuel precursor bisabolene specifically in the trichomes. By spatially and temporally controlling expression, not only can pools of abundant precursors be exploited but engineered molecules can be sequestered in discrete cell structures in the leaf. The structural diversity of the hemicellulose xylan is a barrier to fully utilizing lignocellulose in biomaterial production and by leveraging cell-type-specific omics data, cell wall composition can be modified in a tailored and targeted specific manner to generate poplar wood with novel chemical features that are amenable for processing or advanced manufacturing. Precision engineering poplar as a multi-purpose sustainable feedstock highlights how genome engineering can be used to re-imagine a crop species.

09 BIOMASS FUELS↗

Evaluated Nuclear Structure Data File (ENSDF)

Contains recommended nuclear structure and decay data for all the known nuclides, which are obtained following a critical review of all available experimental data, supplemented with systematic trend studies and theoretical models. ENSDF data include (i) nuclear level properties, such as observation source, energy, half-life, decay modes, spin and parity; (ii) gamma ray energies, intensities, multipolarities, mixing ratios and conversion coefficients; (iii) nuclear radiation energy and intensity as well as radiation-specific data for different radiation types, such as such as gammas, alphas, betas and neutrons. Data for about 220 nuclides are fully evaluated each year; additionally, many datasets are partially updated each year. Nearly all the evaluation work is supported by the US Nuclear Data Program. The National Nuclear Data Center at Brookhaven National Laboratory is responsible for coordinating the evaluation effort as well as its web and journal dissemination.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Understanding the trade-offs of national municipal solid waste estimation methods for circular economy policy

Policies embracing circular economy concepts have taken hold in national legislation around the world. As the number of governments and organizations adopting circular economy policies increases, so does the need for accurate and timely measurement of material resource flows. Since many countries do not have access to centrally reported municipal solid waste (MSW) data, estimation and modeling are critical in evaluating circular economy policy effectiveness. The purpose of this paper is to examine three modeling approaches estimating national MSW data in the United States, including industry-based material flow analysis, waste-extended input-output modeling, and aggregated regional waste reporting. We establish five criteria to guide the analysis through the context of policy monitoring (data quality, flow totality, update frequency, sensitivity to disruption, and product granularity) and use these criteria to analyze and score each model. We then use a literature search to identify five, internationally-implemented options for circular economy policy and determine the data and modeling components that are most helpful in evaluating policy effectiveness. Finally, we provide a crosswalk of the model scores and policy needs to inform the suitability of model selection by policy type. We found that data quality and update frequency are identified as critical components for evaluating circular economy policies within the models evaluated, and can both be fulfilled by aggregated regional waste reporting. Flow totality, sensitivity to disruption, and product granularity requirements vary by both model and policy types. While none of the evaluated models satisfy the combination of requirements for any of the five policies, industry-based material flow analysis offers flow totality for extended producer responsibility, landfill bans, and recycling rate target policies that typically require it. Here, the waste-extended input-output model can provide disruption sensitivity and product granularity as needed for policies like minimum recycled content and market restrictions. Policy developers in areas where strong centralized data collection is not an option should design policy action(s) with modeling tradeoffs in mind, including the potential hybridization of modeling approaches that may provide the most accurate national MSW estimates.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Modular Subsurface Sensors and Integrated Software for Advanced Subsurface Characterization and Monitoring using Unoccupied Vehicles

The advent and subsequent proliferation of autonomous airborne, waterborne, and groundbased vehicles (i.e., “drones”) promises to broadly transform the geosciences and associated industries, including fossil energy exploration and development, mineral resource exploration and development, water-resource management, and environmental remediation. For geophysical characterization and monitoring, the prospect of programming highly repeatable and low-cost drone missions for subsurface imaging will allow for deployments in hazardous and previously inaccessible areas. Coupled with autonomous workflows for data processing, management, and visualization, drone-based geophysical characterization and monitoring will enable unprecedented, real-time insight into diverse subsurface properties and processes of scientific and engineering importance. Toward this end, the objectives of this Lab Directed Research and Development (LDRD) project were to develop new (1) instrumentation for dronebased electromagnetic induction (EMI) geophysical imaging, including separated transmitter and receivers and associated electronics, (2) software for real-time data telemetry, processing, management, and visualization. Although EMI has been previously deployed using unoccupied aerial systems (UASs), these applications failed to capitalize on the game-changing capabilities of drone platforms. Whereas drone-based data acquisition allows for collection of rich, three-dimensional (3D) multi-offset/multi-angle configurations between transmitters and receivers, past efforts have relied on conventional instrumentation that was designed for ground-based data collection with the transmitter and a single receiver housed in the same unit; nor did these previous applications demonstrate real-time delivery of results to support rapid management decisions in the field. In this 1-year project, we (1) designed and constructed new lightweight independent transmitter and receiver antenna platforms that communicate with a laptop computer; (2) developed software to control data acquisition, manage/transfer data, and visualize data as its collected; and (3) demonstrated the operation of the new hardware and software systems in a ground-based field test. Our work entails major technological advances for EMI and established a foundation on which to build a new drone-based, real-time geophysical EMI imaging capability to support diverse challenges facing the nation.

47 OTHER INSTRUMENTATION↗

Advanced Drying Cycle Simulator Thermal Response to Commercial Drying Conditions

The purpose of this report is to document updates on testing of the apparatus built to simulate commercial drying procedures for spent nuclear fuel at the Nuclear Energy Work Complex at Sandia National Laboratories. Validation of the extent of water removal in a dry spent nuclear fuel storage system based on drying procedures used at nuclear power plants is needed to close existing technical gaps. Operational conditions leading to incomplete drying may have potential impacts on the fuel, cladding, and other components in the system during subsequent storage and disposal. A general lack of data suitable for model validation of commercial nuclear canister drying processes necessitates well-designed investigations of drying process efficacy and water retention that incorporate relevant physics and well-controlled boundary conditions. This report documents testing updates for the Advanced Drying Cycle Simulator (ADCS). This apparatus was built to simulate commercial drying procedures and quantify the amount of residual water remaining in a pressurized water reactor (PWR) fuel assembly after drying. The ADCS was constructed with a prototypic 17×17 PWR fuel skeleton and waterproof heater rods to simulate decay heat. These waterproof heaters are the next generation design to heater rods developed and tested at Sandia National Laboratories in FY20. This report describes preliminary testing of the ADCS through measurement and analysis of the thermal response of the system to a subset of commercial drying conditions that exclude the introduction of water, namely simulated decay heats and pressures relevant to commercial drying. This test series, referred to as a “dry” test series in this report, spans three uniform waterproof heater rod powers (representing spent fuel decay heats), four helium fill pressures, and six vacuum levels. This test series was conducted to cover the range of expected ADCS testing conditions for upcoming “wet” testing, where water will be introduced and a simulated commercial drying cycle will be performed. The dry test conditions were derived from the commercial drying conditions seen in the High Burnup Demonstration and the vacuum drying conditions chosen for a smaller scale Dashpot Drying Apparatus tested at Sandia National Laboratories in FY22. For a given uniform power and pressure/vacuum level, the ADCS was operated at constant power and pressure and allowed to reach steady state conditions. The thermal data obtained from these tests were analyzed, and the results can inform computational models built to simulate commercial drying processes by providing baseline thermal data prior to the introduction of water. Following the preliminary dry tests, a test plan for the ADCS will be developed to implement a drying procedure that begins with the introduction of water to the system and is based on measurements from the drying process used for the High Burnup Demonstration Project. While applying power to the simulated fuel rods, this procedure is expected to consist of filling the ADCS vessel with water, draining the water with applied pressure and multiple helium blowdowns, evacuating additional water with a vacuum drying sequence at successively lower pressures, and backfilling the vessel with helium. Additional investigations are expected to feature failed fuel rod simulators with engineered cladding defects and guide tubes with obstructed dashpots to challenge the drying system with multiple water retention sites. The data from these investigations is expected to inform the efficacy of commercial drying operations through the quantification of residual water in a prototypic-length dry storage canister.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Featureless adaptive optimization accelerates functional electronic materials design

Electronic materials that exhibit phase transitions between metastable states (e.g., metal-insulator transition materials with abrupt electrical resistivity transformations) are challenging to decode. For these materials, conventional machine learning methods display limited predictive capability due to data scarcity and the absence of features that impede model training. In this article, we demonstrate a discovery strategy based on multi-objective Bayesian optimization to directly circumvent these bottlenecks by utilizing latent variable Gaussian processes combined with high-fidelity electronic structure calculations for validation in the chalcogenide lacunar spinel family. We directly and simultaneously learn phase stability and bandgap tunability from chemical composition alone to efficiently discover all superior compositions on the design Pareto front. Previously unidentified electronic transitions also emerge from our featureless adaptive optimization engine. Our methodology readily generalizes to optimization of multiple properties, enabling co-design of complex multifunctional materials, especially where prior data is sparse.

36 MATERIALS SCIENCE↗

Optimal economic operation of liquid petroleum products pipeline systems

The majority of overland transport needs for crude petroleum and refined petroleum products are met using pipelines. Numerous studies have developed optimization methods for design of these systems in order to minimize construction costs while meeting capacity requirements. Here, we formulate problems to optimize the operations of existing single liquid commodity pipeline systems subject to physical flow and pump engineering constraints. The objectives are to maximize the economic value created for users of the system and to minimize operating costs. We present a general computational method for this class of continuous, non-convex nonlinear programs, and examine the use of pump operating settings and flow allocations as decision variables. Furthermore, the approach is applied to compute optimal operating regimes and perform engineering economic sensitivity analyses for a case study of a crude oil pipeline developed using publicly available data.

02 PETROLEUM↗

Characterizing Hydrated Polymers via Dielectric Relaxation Spectroscopy: Connecting Relative Permittivity, State of Water, and Salt Transport Properties of Sulfonated Polysulfones

Sulfonated polysulfone is a promising membrane material for separation and energy generation processes that rely on membranes to control the rates of small-molecule (e.g., water and ions) transport. The interactions among water molecules, ions, and the sulfonate groups in these polymers play a key role in controlling these rates of transport, but much remains unknown about these fundamental interactions in sulfonated polymers. In this study, we used dielectric relaxation spectroscopy to characterize water molecule dynamics in sulfonated polysulfone and Nafion. We found that the charged sulfonate groups contribute to a restriction of water molecule dynamics (i.e., a reduction in the characteristic time scale of dipolar motions) in a manner that is governed by the concentration and nature (i.e., conjugate base strength) of the sulfonate group. Additionally, we develop strategies to use these data to aid in modeling ion transport in sulfonated polysulfone. These results may be useful to guide engineering strategies for polymeric membranes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography

Candida boidinii NAD + -dependent formate dehydrogenase (CbFDH) has gained significant attention for its potential application in the production of biofuels and various industrial chemicals from inorganic carbon dioxide. The present study reports the atomic X-ray crystal structures of wild-type CbFDH at cryogenic and ambient temperatures, as well as that of the Val120Thr mutant at cryogenic temperature, determined at the Turkish Light Source ‘Turkish DeLight’. The structures reveal new hydrogen bonds between Thr120 and water molecules in the active site of the mutant CbFDH, suggesting increased stability of the active site and more efficient electron transfer during the reaction. Further experimental data is needed to test these hypotheses. Collectively, these findings provide invaluable insights into future protein-engineering efforts that could potentially enhance the efficiency and effectiveness of CbFDH.

59 BASIC BIOLOGICAL SCIENCES↗

Disaster risk and artificial intelligence: A framework to characterize conceptual synergies and future opportunities

Artificial intelligence (AI) methods have revolutionized and redefined the landscape of data analysis in business, healthcare, and technology. These methods have innovated the applied mathematics, computer science, and engineering fields and are showing considerable potential for risk science, especially in the disaster risk domain. The disaster risk field has yet to define itself as a necessary application domain for AI implementation by defining how to responsibly balance AI and disaster risk. (1) How is AI being used for disaster risk applications; and how are these applications addressing the principles and assumptions of risk science, (2) What are the benefits of AI being used for risk applications; and what are the benefits of applying risk principles and assumptions for AI-based applications, (3) What are the synergies between AI and risk science applications, and (4) What are the characteristics of effective use of fundamental risk principles and assumptions for AI-based applications? This study develops and disseminates an online survey questionnaire that leverages expertise from risk and AI professionals to identify the most important characteristics related to AI and risk, then presents a framework for gauging how AI and disaster risk can be balanced. This study is the first to develop a classification system for applying risk principles for AI-based applications. This classification contributes to understanding of AI and risk by exploring how AI can be used to manage risk, how AI methods introduce new or additional risk, and whether fundamental risk principles and assumptions are sufficient for AI-based applications.

97 MATHEMATICS AND COMPUTING↗

Sandia Injury Biomechanics Laboratory Library

The Sandia Injury Biomechanics Laboratory (SIBL) Library is a collection of scripts and tools used to preprocess, process, and postprocess data for analysis of injury biomechanics data. SAND2020-3663 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Hovey, Chad↗

Code for the manuscript "Mori-Zwanzig Modal Decomposition"

We would like to create an open source repository in LANL's github on code written in Julia, in which we implement and extend the data-driven Mori-Zwanzig method for extracting large-scale spatio-temporal structures from data, which we call MZMD. This method is an extension of Dynamic Mode Decomposition (DMD) in which Mori-Zwanzig memory kernels are included into the associated companion matrix. In the code we would like to release, we apply MZMD to a flow over a cylinder with Reynolds number 100 rather than the much larger data set used in the associated manuscript. DMD is used extensively in the fluid dynamics community mainly for extracting large scale spatio-temporal structures (patters) from flow data. This is useful for understanding the key mechanisms that generate certain complex dynamical process relevant in engineering design. In MZMD, we improve upon DMD by adding the Mori-Zwanzig memory kernels, and show this improvement is especially important in strongly nonlinear regions of the flow.

Woodward, Michael↗