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DOE OSTI2020

Fluorescent amplification for next generation sequencing (FA-NGS) library preparation

BACKGROUND: Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process. RESULTS: In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data. CONCLUSIONS: We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Multispectral and thermal surface imagery and surface elevation mosaics - SGP July 2022

This data set contains high-resolution image products (orthomosaics) acquired from midsized uncrewed aerial systems that have been processed for value-added quality. The instrument itself, a multispectral imager, the Altum by Micasense, captures six spectral bands (red, green blue, NIR, red edge, and LWIR/thermal1) as radiance, which is converted to reflectance via custom code. The code used to develop these images first uses tools from the Micasense Python library2 to apply dark level corrections, row gradient corrections, and radiometric corrections. Next, it uses the processing API from Agisoft Metashape software to align and mosaic the processed imagery, following the processes developed by the USGS' structure from motion workflow documentation.3 Captures at different altitudes (recorded in MSL) produce an orthomosaic, a tif image containing information related to the six spectral bands, and a digital elevation model (DEM), a tif image containing information related to the elevation of the surveyed terraine. Metadata included in every image can be used to extract lat, lon, and reflectance values. 1 https://www.arm.gov/publications/tech_reports/handbooks/doe-sc-arm-tr-281.pdf 2 https://micasense.github.io/imageprocessing/MicaSense%20Image%20Processing%20Setup.html 3 https://pubs.usgs.gov/of/2021/1039/ofr20211039.pdf

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Two (or more) for one: Identifying classes of household energy- and water-saving measures to understand the potential for positive spillover

A key component of behavior-based energy conservation programs is the identification of target behaviors. A common approach is to target behaviors with the greatest energy-saving potential. The concept of behavioral spillover introduces further considerations, namely that adoption of one energy-saving behavior may increase (or decrease) the likelihood of other energy-saving behaviors. This research aimed to identify and describe household energy- and water-saving measure classes within which positive spillover is likely to occur (e.g., adoption of energy-efficient appliances may correlate with adoption of water-efficient appliances), and explore demographic and psychographic predictors of each. Nearly 1,000 households in a California city were surveyed and asked to report whether they had adopted 75 different energy- and/or water-saving measures. Principal Component Analysis and Network Analysis based on correlations between adoption of these diverse measures revealed and characterized eight water-energy-saving measure classes: Water Conservation, Energy Conservation, Maintenance and Management, Efficient Appliance, Advanced Efficiency, Efficient Irrigation, Green Gardening, and Green Landscaping. Understanding these measure classes can help guide behavior-based energy program developers in selecting target behaviors and designing interventions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

PS3: The Pheno-Synthesis software suite for integration and analysis of multi-scale, multi-platform phenological data

Phenology is the study of recurring plant and animal life-cycle stages which can be observed across spatial and temporal scales that span orders of magnitude (e.g., organisms to landscapes). The variety of scales at which phenological processes operate is reflected in the range of methods for collecting phenologically relevant data, and the programs focused on these collections. Consideration of the scale at which phenological observations are made, and the platform used for observation, is critical for the interpretation of phenological data and the application of these data to both research questions and land management objectives. However, there is currently little capacity to facilitate access, integration and analysis of cross-scale, multi-platform phenological data. This paper reports on a new suite of software and analysis tools – the “Pheno-Synthesis Software Suite,” or PS3 – to facilitate integration and analysis of phenological and ancillary data, enabling investigation and interpretation of phenological processes at scales ranging from organisms to landscapes and from days to decades. We use PS3 to investigate phenological processes in a semi-aride, mixed shrub-grass ecosystem, and find that the apparent importance of seasonal precipitation to vegetation activity (i.e., “greenness”) is affected by the scale and platform of observation. We end by describing potential applications of PS3 to phenological modeling and forecasting, understanding patterns and drivers of phenological activity in real-world ecosystems, and supporting agricultural and natural resource management and decision-making.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

RouteE: A Vehicle Energy Consumption Prediction Engine

The emergence of connected and automated vehicles and smart cities technologies create the opportunity for new mobility modes and routing decision tools, among many others. To achieve maximum mobility and minimum energy consumption, it is critical to understand the energy cost of decisions and optimize accordingly. The Route Energy prediction model (RouteE) enables accurate estimation of energy consumption for a variety of vehicle types over trips or sub-trips where detailed drive cycle data are unavailable. Applications include vehicle route selection, energy accounting and optimization in transportation simulation, and corridor energy analyses, among others. The software is a Python package that includes a variety of pre-trained models from the National Renewable Energy Laboratory (NREL). However, RouteE also enables users to train custom models using their own data sets, making it a robust and valuable tool for both fast calculations and rigorous, data-rich research efforts. The pre-trained RouteE models are established using NREL’s Future Automotive Systems Technology Simulator paired with approximately 1 million miles of drive cycle data from the Transportation Secure Data Center, resulting in energy consumption behavior estimates over a representative sample of driving conditions for the United States. Validations have been performed using on-road fuel consumption data for conventional and electrified vehicle powertrains. Transferring the results of the on-road validation to a larger set of real-world origin-destination pairs, it is estimated that implementing the present methodology in a green-routing application would accurately select the route that consumes the least fuel 90% of the time. The novel machine learning techniques used in RouteE make it a flexible and robust tool for a variety of transportation applications.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2025

MTUQ: a framework for estimating moment tensors, point forces, and their uncertainties

SUMMARY We introduce MTUQ, an open-source Python package for seismic source estimation and uncertainty quantification, emphasizing flexibility and operational scalability. MTUQ provides MPI-parallelized grid search and global optimization capabilities, compatibility with 1-D and 3-D Green’s function database formats, customizable data processing, C-accelerated waveform and first-motion polarity misfit functions, and utilities for plotting seismic waveforms and visualizing misfit and likelihood surfaces. Applicability to a range of full- and constrained-moment tensor, point force, and centroid inversion problems is possible via a documented application programming interface, accompanied by example scripts and integration tests. We demonstrate the software using three different types of seismic events: (1) a 2009 intraslab earthquake near Anchorage, Alaska; (2) an episode of the 2021 Barry Arm landslide in Alaska; and (3) the 2017 Democratic People’s Republic of Korea underground nuclear test. With these events, we illustrate the well-known complementary character of body waves, surface waves, and polarities for constraining source parameters. We also convey the distinct misfit patterns that arise from each individual data type, the importance of uncertainty quantification for detecting multimodal or otherwise poorly constrained solutions, and the software’s flexible, modular design.

58 GEOSCIENCES↗

DOE OSTI2024

LEED: A Lightwave Energy-Efficient Datacenter

The Lightwave Energy-Efficient Datacenter (LEED) program is a disruptive “green-field” approach that provides a quantum leap in the energy efficiency of datacenters. LEED’s fundamental value proposition is that a novel and re-architected optical network—RotorNet— can deliver “more bandwidth per buck” as well as unique system-level attributes that significantly improve overall datacenter energy efficiency and performance. LEED has developed three system-level testbeds. The first testbed uses calibrated hardware and software power measurements to determine server energy efficiency as a function of network bandwidth and workload. These measurements have shown that increasing network communications bandwidth dramatically increases server energy efficiency providing a realistic path to the overall ENLITENED program goal of doubling the number of transactions per joule. The second testbed demonstrates key hardware: a prototype low-loss, high-port count optical “selector switch”. This switch was fabricated, racked, and tested. Measured switch characteristics include loss, bandwidth, crosstalk, switch time, system-level switch time (including the transceivers), and bit error rate. The third testbed demonstrates a fully working and manufactured pinwheel design which dramatically lowers the cost of design, while delivering high switch radix and low reconfiguration times. The LEED project has tied these three novel photonic switch prototypes together with production servers and software through the development of a novel FPGA-based NIC platform called Corundum. Corundum ensures that the packet-switched protocols supported by commodity operating systems and devices can interface with the Rotor switch design. The LEED group has used this combined hardware and software prototype to characterize applications running at a commercially relevant scale. The project has used a combination of enhanced optical modulation amplitude (OMA) modulators, broadband multiplexers and demultiplexers, avalanche photodiodes, and a novel burst-mode receivers to enable the insertion of LEED-developed optical switches without the need for expensive optical amplification. Our modeling has shown that measured LEED-developed device characteristics can achieve link characteristics of 2 pJ/bit including both transceivers and the Rotor switch. In summary, the LEED program has demonstrated a credible and practical path, through novel hardware and software, to realize the program objectives of ENLITENED. The net result will ensure that the United States maintains its strength in the crucial sector of Information Technology, which is vital to both our economic security and our national security.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

AmeriFlux FLUXNET-1F US-xDL NEON Dead Lake (DELA)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xDL NEON Dead Lake (DELA). This is the FLUXNET version of the carbon flux data for the site US-xDL NEON Dead Lake (DELA) produced by applying the standard ONEFlux (1F) software. Site Description - The Dead Lake site is just northeast of Demopolis, AL near the Black Warrior River. The site is in Major Land Resource Area (MLRA) 133A–Southern Coastal Plains, near the boundary of MLRA 135A–Alabama and Mississippi Blackland Prairie. Surrounded by woody wetlands and evergreen forest, DELA sits on the flood plain steps and stream terraces of an inside meander of the Black Warrior River in Greene Co., AL.

Network), NEON (National Ecological Observatory↗

DOE OSTI2023

Multispectral and thermal surface imagery and surface elevation mosaics - Pendleton Feb 2023

This data set contains high-resolution image products (orthomosaics) acquired from midsized uncrewed aerial systems that have been processed for value-added quality. The instrument Altum multispectral imager by Micasense, captures in six bands (blue - 475nm, green - 560nm, red - 668nm, red edge - 717nm, near-infrared - 840 and LWIR/thermal - 11000nm. The optical bands are converted to reflectance via custom code using the instantaneous band horizontal irradiance ratio to the radiance of the pixel. The code used to develop these images first uses tools from the Micasense Python library to apply dark level corrections, row gradient corrections, and radiometric corrections. Next, it uses the processing API from Agisoft Metashape software to align and mosaic the processed imagery, following the processes developed by the USGS' structure from motion workflow documentation. Captures from different altitudes are used to produce an orthomosaic at each height. A tif image containing information related to the six spectral bands, and a digital elevation model (DEM), a tif image containing information related to the elevation of the surveyed terrain. 1 https://www.arm.gov/publications/tech_reports/handbooks/doe-sc-arm-tr-281.pdf 2 https://micasense.github.io/imageprocessing/MicaSense%20Image%20Processing%20Setup.html 3 https://pubs.usgs.gov/of/2021/1039/ofr20211039.pdf

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Enabling Interoperable SCADA Communications for PV Inverters through Embedded Controllers

The percentage integration of photovoltaic (PV) inverters in the field has increased significantly in the past 5 years. Regardless of the size of the PV plants and the inverters (residential vs. commercial), it is becoming crucial that these devices have the capability to communicate with peers (other smart devices) and with components that are at a hierarchy above the inverters (e.g., supervisory control and data acquisition (SCADA) systems, distributed controllers, and data managers). This project aims to develop a standard SCADA software code for inverters’ embedded controllers that will enable interoperability with other components in the system. To achieve this, the code will be developed using two different protocols: Distributed Network Protocol 3 and International Electrotechnical Commission 61850. The developed code is aimed to be deployed in simple embedded controllers. It will be tested in the National Renewable Energy Laboratory’s (NREL’s) Energy Systems Integration Facility. The tested code will then be made available through Triangle MicroWorks’s (TMW’s) software platform. The primary objectives of this project include training the NREL team with TMW’s embedded controller libraries, developing an interoperable communication code for embedded controllers, successfully testing and deploying the code, and demonstrating the newly developed code in a conference.

14 SOLAR ENERGY↗

DOE OSTI2020

Low Temperature Oxidation of Methylpropyl Ether

Ethers are potential high-performance fuels that can be produced from renewable carbon sources such as biomass, but their combustion properties are not clearly understood. The cetane numbers (CN) for ethers, a measure of autoignition tendency, can range from less than 10 to greater than 100, and predictive tools based upon the molecular structures are desirable in order to focus fuel development research. In this study, we used molecular modeling, chemical kinetic modeling, and experimental measurements to understand the important reactions that lead to the autoignition of methylpropyl ether (MPE), a model for ethers containing alkyl chains long enough for intramolecular hydrogen transfer. These reactions are known to be important in the autoignition of alkanes and ethers and we propose to investigate the relationship between alkyl and ether reaction pathways. A reaction mechanism for MPE was created using MIT's Reaction Mechanism Generator (RMG) and G4 quantum calculation results and models were tested using the ChemKin Pro suite of software. Results from atmospheric pressure, flow tube reactor experiments and rapid compression machine (RCM) experiments were used to test the kinetic model and suggest refinements.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2021

Processed Surface Imagery & Raster Imagery taken onboard TigerShark (U3) UAS

Land-surface orthomosaic imagery derived from the images collected using the Micasense Altum Imager on board the UAS TigerShark (U3) on March 11th, 2021 at an altitude of 2000 ft. The Altum takes images of the land surface across five visible bands and one long wave infrared thermal band. The photogrametry software Agisoft PhotoScan v 1.4 is used to align and stitch the images into a larger composet image using the technique of structure from motion image capture to construct a dense cloud and 3-D model of the surface, which is used to produce a digital elevation model of the terraine surveyed and orthomosaic imagery. This dataset contains the raster calculated orthomosaics of various vegetative indicies, which are used to indicate plant health and land surface characteristics, including Normalized Difference Vegetation Index (NDVI), Green Normalized Difference Vegetation Index (GNDVI), Normalized Difference Water Index (NDWI), surface temperature, and Enhanced_vegetation_index (EVI). These orthomosaics were collected west of the Starkville, MS, airport, and include natural, agricultural, and industrial land coverage. The images have a resolution of 0.2 m/pix.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Simulation of a rapid compression machine for evaluation of ignition chemistry and soot formation using gasoline/ethanol blends

Due to the projected decline of demand for gasoline in light duty engines and the advent of ethanol as a green fuel, the use of gasoline/ethanol blend fuels in heavy duty applications are being investigated as they are projected to have lower cost and lower lifecycle green house gas (GHG) emissions. In heavy duty engines, the primary mode of combustion is mixing controlled combustion where wide range of mixture conditions (equivalence ratio) exist. Soot emissions of these fuels in richer conditions are not well understood. The goal of this research is to evaluate some commercially available soot modeling codes for the particulate matter emissions from gasoline/ethanol fuel blends, especially at fuel rich conditions. A Rapid Compression Machine (RCM) is modeled in a three-dimensional numerical simulation using CONVERGE computational software using a reduced chemical kinetic mechanism with SAGE chemistry solver and a RANS k-ϵturbulence model with a sector model including the creviced piston. The creviced piston is used in the experimental setup to reduce boundary layer effects and to maintain a homogeneous core in the reaction cylinder. Computational fluid dynamics simulations are conducted for different gasoline-ethanol fuel blends from E10 (10% ethanol v/v) to E100. The fuel blend is modeled as a surrogate mixture of toluene, iso-octane, n-heptane for gasoline content, and ethanol. The computational results were validated against experimental results using pressure measurements and laser extinction diagnostics. Different soot models are investigated to evaluate their capability of predicting the sooting tendencies of fuel blends, especially in richer conditions experienced during mixing-controlled combustion. The experimental combustion characteristics such as the ignition delay of different blends of fuel are reasonably well predicted. The Particulate Size Mimic (PSM) model accurately predicts the soot generation characteristics of the different fuels, but the Hiroyasu-NSC model falls short in this regard. For accurate prediction of soot with the PSM model, the thermodynamic conditions during combustion must be accurately modeled. While the current computational modeling tools can produce accurate results for the prediction of particulate matter emissions, there is much work to be done in improving our understanding of the underlying fundamental processes.

Energy & Fuels↗

DOE OSTI2023

Productivity frameworks for HPC

Productivity Frameworks for HPC will include container recipes, build recipes, continuous integration scripts, and other software aimed at testing the portability of containerized HPC software across platforms and interconnects. In particular, it tests the utility of bind-mounting at the MPI layer (rather than the underlying fabric layer) to leverage a standardized protocol and avoid various technical debt and vendor lock-in. Since MPIs are often ABI-incompatible, trampolines such as the open-source Wi4MPI will be tested when such cases arise.

Hanford, Nathan↗

DOE OSTI2022

Multispectral and Thermal Imager Onboard Aerial Platforms Instrument Handbook

The MicaSense Altum imager is an off-the-shelf, synchronized multispectral and thermal camera, combined with a Global Positioning System (GPS) unit and downwelling light sensor (DLS). The Altum takes images of the land surface within its field of view (FOV) across five visible bands and one longwave infrared thermal band. The sensor records the radiance and converts it to digital numbers. Imagery is radiometrically corrected, taking into account the sensor calibration, lens distortions, vignette effects, sun angle, and atmospheric effects (scattering and absorption). The photogrammetry software Agisoft PhotoScan v 1.4 is used to align and stitch the images into a larger composite image using the technique of structure from motion image capture to construct a dense cloud and 3D model of the surface, which is used to produce a digital elevation model of the terrain surveyed and orthomosaic imagery. Land surface leaf area index, albedo, and surface skin temperature are provided for the user. The user can perform raster calculations on the imagery to produce various other vegetative indices, which are used to indicate plant health and land surface characteristics, including Normalized Difference Vegetation Index (NDVI), Green Normalized Difference Vegetation Index (GNDVI), Normalized Difference Water Index (NDWI), surface temperature, and Enhanced_vegetation_index (EVI). This code is provided with the readme file for each data set. The images have a resolution of 20-60 cm/pixel, which are subsampled to 100 cm/pixel.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Automated reaction kinetics and network exploration (Arkane): A statistical mechanics, thermodynamics, transition state theory, and master equation software

The open-source statistical mechanics software described here, Arkane–Automated Reaction Kinetics and Network Exploration–facilitates computations of thermodynamic properties of chemical species, high-pressure limit reaction rate coefficients, and pressure-dependent rate coefficient over multi-well molecular potential energy surfaces (PES) including the effects of collisional energy transfer on phenomenological kinetics. Arkane can use estimates to fill in information for molecules or reactions where quantum chemistry information is missing. The software solves the internal energy master equation for complex unimolecular reaction systems. Inputs to the software include converged electronic structure computations performed by the user using a variety of supported software packages (Gaussian, Molpro, Orca, TeraChem, Q-Chem, Psi4). The software outputs high-pressure limit rate coefficients and pressure-dependent phenomenological rate coefficients, as well as computed thermodynamic properties (enthalpy, entropy, and constant pressure heat capacity) with added energy corrections. Some of the key features of Arkane include treatment of 1D, 2D or ND hindered internal rotation modes, treatment of free internal rotation modes, quantum tunneling effect consideration, transition state theory (TST) and Rice-Ramsperger-Kassel-Marcus (RRKM) rate coefficient computations, master equation solution with four implemented methods, inverse-Laplace transform of high-pressure limit rate coefficients into the energy domain, energy corrections based on bond-additivity or isodesmic reactions, automated and efficient PES exploration, and PES sensitivity analysis. The present work describes the design of Arkane, how it should be used, and refers to the theory that it employs. Arkane is distributed via the RMG-Py software suite (https://github.com/ReactionMechanismGenerator/RMG-Py).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

From Obsolete to Optimal (ATR Demineralized Water System)

My project was migrating a Human-Machine Interface (HMI) and Programmable Logic Controller (PLC) program from legacy software to a modern platform, enhancing operational efficiency and eliminating unsupported, obsolete equipment. Initially, I used a migration tool to transfer the programs to the new software, then manually updated variables to align with the new PLC. I optimized the PLC code by leveraging new scaling features in the I/O cards, removing over 45 obsolete rungs, and enhancing clarity with functional tag aliases. Next, I modernized the HMI's visuals with an updated color scheme and 3D buttons. I developed multiple interface versions iteratively refining them based on operator feedback. I also designed and created a dedicated "Rounds" screen incorporating insights from a previous intern’s project to streamline daily rounds. To improve clarity, consistency, and efficiency I redesigned the entire interface. Adding visual indicators to enhance operational awareness: red is used for values outside normal specifications, green for normal operating modes, yellow for manual mode, and grey for offline units. Additionally, I added a dynamic visual representation of tank levels, creating PLC logic to show the level in inches as well as inches and feet. I then incorporated a navigation sidebar to facilitate efficient screen transitions. Risk of human error was mitigated by defining narrow input ranges for tank level shutoff and password protecting setpoint changes. I also fixed issues with datatypes that caused inaccuracies in the original code. Overall, this comprehensive upgrade significantly enhanced the HMI's functionality, user experience, and operational reliability.

47 - OTHER INSTRUMENTATION↗

DOE OSTI2024

Grid Optimization Competition Challenge 3 Problem Formulation

This report contains the problem formulation for the Grid Optimization (GO) Competition Challenge 3. The Grid Optimization Competition is run by a team of researchers from a number of organizations, including the sponsor Advanced Research Projects Agency - Energy (ARPA-E), lead organization Pacific Northwest National Laboratory (PNNL), and technical contributors from Los Alamos National Laboratory (LANL), National Renewable Energy Laboratory (NREL), Texas A&M University (TAMU), Georgia Institute of Technology (GT), University of Wisconsin (UW), and others. The GO Competition poses challenge problems in the field of power grid management, invites entrants to develop solvers for these problems, invokes the solvers on a set of problem instances using common hardware, ranks the solvers according to their performance, and awards prizes according to the rankings. The overall goal of the GO Competition is to spur innovative research on high impact and computationally challenging problems in power grid management from initial development through commercial deployment. Complete information about the GO Competition can be found online at [2]. The webpage covers previous Challenges, rules, timeline, registration information, data formats, scoring methods, computational platform information, information on supported solvers and languages, sponsor information, frequently asked questions, administrator contact information, publicly available problem instances, computer code for reading and evaluating problem and solution data, a sandbox for testing solvers, and a solver submission interface, results, and publications.

24 POWER TRANSMISSION AND DISTRIBUTION↗