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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

MultiPhATE2: code for functional annotation and comparison of phage genomes

To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes

While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Web Based Beamline Control System (Bluesky Web) v0.1.0

Bluesky Web is a web based interface that provides beam line controls to the end user. It allows users to issue commands to various physical devices at a beam line end station like motors and cameras. It utilizes an open source Python library (Bluesky) as the controller. It uses Bluesky to also allow for running "plans" or a sequence of device operations that can be used when running an experiment. This program is different from other controls technologies because it is intended to be open source and can be accessed from a web browser, as opposed to other paid software that is run as a stand-alone application on a computer.

De Leon, Seij↗
DOE OSTI2026

Establishing Data Analysis Pipeline for Bulk ATAC-Seq Datasets

We developed an analysis pipeline for transposase-accessible chromatin sequencing (ATAC-Seq) data derived from bulk samples, which brings together publicly available R packages in addition to command-line tools designed for analysis of bulk ATAC-Seq data and can be run on any computer running a Linux-like operating system such as Ubuntu or Apple OSX.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Learning reference governor for cycle-to-cycle combustion control with misfire avoidance in spark-ignition engines at high exhaust gas recirculation–diluted conditions

Cycle-to-cycle feedback control is employed to achieve optimal combustion phasing while maintaining high levels of exhaust gas recirculation by adjusting the spark advance and the exhaust gas recirculation valve position. The control development is based on a control-oriented model that captures the effects of throttle position, exhaust gas recirculation valve position, and spark timing on the combustion phasing. Under the assumption that in-cylinder pressure information is available, an adaptive extended Kalman filter approach is used to estimate the exhaust gas recirculation rate into the intake manifold based on combustion phasing measurements. The estimation algorithm is adaptive since the cycle-to-cycle combustion variability (output covariance) is not known a priori and changes with operating conditions. A linear quadratic regulator controller is designed to maintain optimal combustion phasing while maximizing exhaust gas recirculation levels during load transients coming from throttle tip-in and tip-out commands from the driver. During throttle tip-outs, however, a combination of a high exhaust gas recirculation rate and an overly advanced spark, product of the dynamic response of the system, generates a sequence of misfire events. In this work, an explicit reference governor is used as an add-on scheme to the closed-loop system in order to avoid the violation of the misfire limit. The reference governor is enhanced with model-free learning which enables it to avoid misfires after a learning phase. Experimental results are reported which illustrate the potential of the proposed control strategy for achieving an optimal combustion process during highly diluted conditions for improving fuel efficiency.

42 ENGINEERING↗
DOE OSTI2023

Development of a High-Pressure Fuel Injection System for Use with Propane-DME

Paper details the design approach and performance of a high-pressure common rail fuel injection system used with Propane-DME mixtures targeting high injection pressures on a light duty 2.2L inline-4 compression ignition engine. The study estimates the bulk modulus of elasticity based on the hardware geometry and operating pressures to assess the compressibility of Propane and DME across a range of pressures typical of the LD engine application. The compressibility factor ranges from 500 to 3000 bar, significantly lower than the theoretical values for the conditions tested. The high-pressure pump performance is optimized via the implementation of an inlet metering valve operated on a crank-angle open/close sequence to control pressure at the common rail. The application of a model-based controller and the use of high-speed sampling of rail pressure indicate that pressure at the rail can be attained with the pump metering valve, and without use of the pressure relieve valve present in the rail. Results show a significant reduction on pumping work parasitics and of fuel heating, on the order of 40°C, at typical working conditions with the proposed approach. Injector rates of injection with Propane-DME are very similar to those of Diesel. Paper compares bench data of rates of injection versus simulation predictions across operating pressures of 200 to 1000bar and from injection commands spanning 0.20 to 2.0ms. Furthermore, the accuracy of the model predictions are attributed in part by to the updated fuel compressibility modulus descriptions attained during the testing.

42 ENGINEERING↗
DOE OSTI2023

Maximum-impact Adversary Design for Network-based Control System: A Case Study on Grid-interactive Efficient Buildings

The Internet of Things (IoT) technology has dramatically improved the efficiency of today's building operation and management. By connecting controllable devices into a communication network, control signals can be easily passed to the devices, and operating status can be acquired from measurable ends with minimal effort. However, this all-connected configuration could also expose the network-based control system (NBCS) to malicious actions, such as cyberattacks. One of the common NBCSs is the building automation system. With the promotion of grid-interactive efficient buildings (GEBs), there has been increasing attention on securing the buildings from the network perspective. This research proposes a maximum-impact adversary design framework so that the adversary can provide the most adversarial impact on the controlled system while remaining stealthy. The proposed framework is numerically demonstrated on a network-based building energy and control system. The building energy system is built in a Modelica-based simulation environment and controlled by the state-of-the-art ASHRAE Guideline 36 control sequences. The control commands at the supervisory level, generated from the Guideline 36 controller, are assumed to be sent to local devices through communication networks using the BACnet protocol. Simulation results show that the proposed maximum-impact adversary on such a system can stealthily affect the building system's performance to its maximum extent. It is anticipated that results can be used by researchers and practitioners in the building automation industry to design efficient and robust cyber-attack detection algorithms, especially for stealthy attacks.

Chu, Mengyuan↗