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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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At least 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering

Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. Cis SERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. Cis SERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, Cis SERS utilizes the REBASE enzyme database. Results from Cis SERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. Cis SERS is a java based graphical user interface built around a perl backbone. Several of the applications of Cis SERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool Cis SERSand results from in-silico and corresponding wet-lab analyses demonstrating that Cis SERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Robust, automated sleep scoring by a compact neural network with distributional shift correction

Studying the biology of sleep requires the accurate assessment of the state of experimental subjects, and manual analysis of relevant data is a major bottleneck. Recently, deep learning applied to electroencephalogram and electromyogram data has shown great promise as a sleep scoring method, approaching the limits of inter-rater reliability. As with any machine learning algorithm, the inputs to a sleep scoring classifier are typically standardized in order to remove distributional shift caused by variability in the signal collection process. However, in scientific data, experimental manipulations introduce variability that should not be removed. For example, in sleep scoring, the fraction of time spent in each arousal state can vary between control and experimental subjects. We introduce a standardization method, mixture z-scoring, that preserves this crucial form of distributional shift. Using both a simulated experiment and mouse in vivo data, we demonstrate that a common standardization method used by state-of-the-art sleep scoring algorithms introduces systematic bias, but that mixture z-scoring does not. We present a free, open-source user interface that uses a compact neural network and mixture z-scoring to allow for rapid sleep scoring with accuracy that compares well to contemporary methods. This work provides a set of computational tools for the robust automation of sleep scoring.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

GEO2D - Two-Dimensional Computer Model of a Ground Source Heat Pump System

This file contains a zipped file that contains many files required to run GEO2D. GEO2D is a computer code for simulating ground source heat pump (GSHP) systems in two-dimensions. GEO2D performs a detailed finite difference simulation of the heat transfer occurring within the working fluid, the tube wall, the grout, and the ground. Both horizontal and vertical wells can be simulated with this program, but it should be noted that the vertical wall is modeled as a single tube. This program also models the heat pump in conjunction with the heat transfer occurring. GEO2D simulates the heat pump and ground loop as a system. Many results are produced by GEO2D as a function of time and position, such as heat transfer rates, temperatures and heat pump performance. On top of this information from an economic comparison between the geothermal system simulated and a comparable air heat pump systems or a comparable gas, oil or propane heating systems with a vapor compression air conditioner. The version of GEO2D in the attached file has been coupled to the DOE heating and cooling load software called ENERGYPLUS. This is a great convenience for the user because heating and cooling loads are an input to GEO2D. GEO2D is a user friendly program that uses a graphical user interface for inputs and outputs. These make entering data simple and they produce many plotted results that are easy to understand. In order to run GEO2D access to MATLAB is required. If this program is not available on your computer you can download the program MCRInstaller.exe, the 64 bit version, from the MATLAB website or from the Geothermal Data Repository. This is a free download which will enable you to run GEO2D.

15 GEOTHERMAL ENERGY↗
DOE OSTI2023

MyCrunchGPT: A LLM Assisted Framework for Scientific Machine Learning

Scientific machine learning (SciML) has advanced recently across many different areas in computational science and engineering. Here, the objective is to integrate data and physics seamlessly without the need of employing elaborate and computationally taxing data assimilation schemes. However, preprocessing, problem formulation, code generation, postprocessing, and analysis are still time- consuming and may prevent SciML from wide applicability in industrial applications and in digital twin frameworks. Here, we integrate the various stages of SciML under the umbrella of ChatGPT, to formulate MyCrunchGPT, which plays the role of a conductor orchestrating the entire workflow of SciML based on simple prompts by the user. Specifically, we present two examples that demonstrate the potential use of MyCrunchGPT in optimizing airfoils in aerodynamics, and in obtaining flow fields in various geometries in interactive mode, with emphasis on the validation stage. To demonstrate the flow of the MyCrunchGPT, and create an infrastructure that can facilitate a broader vision, we built a web app based guided user interface, that includes options for a comprehensive summary report. The overall objective is to extend MyCrunchGPT to handle diverse problems in computational mechanics, design, optimization and controls, and general scientific computing tasks involved in SciML, hence using it as a research assistant tool but also as an educational tool. While here the examples focus on fluid mechanics, future versions will target solid mechanics and materials science, geophysics, systems biology, and bioinformatics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology

The TOPAS Monte Carlo (MC) system is used in radiation therapy and medical imaging research, having played a significant role in making Monte Carlo simulations widely available for proton therapy related research. While TOPAS provides detailed simulations of patient scale properties, the fundamental unit of the biological response to radiation is a cell. Thus, our goal was to develop TOPAS-nBio, an extension of TOPAS dedicated to advance understanding of radiobiological effects at the (sub-)cellular, (i.e., the cellular and sub-cellular) scale. TOPAS-nBio was designed as a set of open source classes that extends TOPAS to model radiobiological experiments. TOPAS-nBio is based on and extends Geant4-DNA, which extends the Geant4 toolkit, the basis of TOPAS, to include very low-energy interactions of particles down to vibrational energies, explicitly simulates every particle interaction (i.e., without using condensed histories) and propagates radiolysis products. To further facilitate the use of TOPAS-nBio, a graphical user interface was developed. TOPAS-nBio offers full track-structure Monte Carlo simulations, integration of chemical reactions within the first millisecond, an extensive catalogue of specialized cell geometries as well as sub-cellular structures such as DNA and mitochondria, and interfaces to mechanistic models of DNA repair kinetics. We compared TOPAS-nBio simulations to measured and published data of energy deposition patterns and chemical reaction rates (G values). Our simulations agreed well within the experimental uncertainties. Additionally, we expanded the chemical reactions and species provided in Geant4-DNA and developed a new method based on independent reaction times (IRT), including a total of 72 reactions classified into 6 types between neutral and charged species. Chemical stage simulations using IRT were a factor of 145 faster than with step-by-step tracking. Finally, we applied the geometric/chemical modeling to obtain initial yields of double-strand breaks (DSBs) in DNA fibers for proton irradiations of 3 and 50 MeV and compared the effect of including chemical reactions on the number and complexity of DSB induction. Over half of the DSBs were found to include chemical reactions with approximately 5% of DSBs caused only by chemical reactions. In conclusion, the TOPAS-nBio extension to the TOPAS MC application offers access to accurate and detailed multiscale simulations, from a macroscopic description of the radiation field to microscopic description of biological outcome for selected cells. TOPAS-nBio offers detailed physics and chemistry simulations of radiobiological experiments on cells simulating the initially induced damage and links to models of DNA repair kinetics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

CO2-SCREEN

CO2 Storage prospeCtive Resource Estimation Excel aNalysis (CO2-SCREEN) is a tool which was developed by the Department of Energy’s National Energy Technology Laboratory (DOE-NETL) to screen saline formations for prospective CO2 storage resources. CO2-SCREEN applies U.S. DOE methods and equations for estimating prospective CO2 storage resources for saline formations. This provides a dependable method for calculating prospective CO2 storage resources which allows for consistent comparison of results between different research efforts. CO2-SCREEN latest version (v5.0) is a python application that utilizes a Java front end user interface. The 3.0 version consists of an Excel spreadsheet containing geologic inputs and outputs, linked to a GoldSim Player model that calculates prospective CO2 storage resources via Monte Carlo simulation. https://www.youtube.com/watch?v=lhakk-HYfOI

CO2 Storage Resource,Prospective Storage,Screening↗
DOE OSTI2023

CCSI Toolset 3.18 Release

CCSI Toolset 3.18 Release Highlights FOQUS was updated to allow installation for users using MacOS on Apple silicon. FOQUS Cloud support was added for user plugins. The Optimality-Based Design of Experiments tutorials were updated to reflect the latest changes in the user interface flow. The plot discrete sliders were fixed for CDF and 3D plots within Uncertainty Quantification, which were not working due to a matplotlib depreciation. The installation was updated to set the default location for the PSUADE executable if found in the environment. Updates were made to allow compatibility with NumPy 1.25. Additional documentation changes were made to fix typographical errors and fix a broken link to optional software.

AS↗
DOE OSTI2024

CCSI Toolset 3.22 Release

CCSI Toolset 3.22 Release Highlights The Sequential Design of Experiments user interface was updated to resolve an issue where the results would fail to plot in some cases (e.g., Non-Uniform Space Filling designs). The Machine Learning/Artificial Intelligence module was updated to support Keras 3 and to reflect changes made to dependencies’ syntax. A check was added to ensure PSUADE is installed and available at FOQUS startup. If PSUADE is not installed, a link to the FOQUS documentation is displayed and FOQUS is closed. The copyright year was updated to include 2024 in places where it had not previously been updated. Typographical errors were corrected to improve clarity in variable names and documentation. The FOQUS documentation was updated to reflect the fact that ALAMO can have two executables and indicates the correct executable to add to the Settings path. SimSinter was updated to version 3.1.0. This version removed gPROMS support and included security updates.

AS↗
DOE OSTI2024

CCSI Toolset 3.23 Release

CCSI Toolset 3.23 Release Highlights The user interface was updated to allow timeouts in Aspen Custom Modeler and AspenPlus. The installation was updated to use 64-bit versions of TurbineLite and SimSinter by default. The documentation was improved for clarity.

AS↗
DOE OSTI2019

LCLS-II Cryomodule and Cryogenic Distribution Control

The new superconducting Linear Coherent Light Source (LCLS-II) at the SLAC National Accelerator Laboratory will be an upgrade to LCLS, the world’s first hard X-ray free-electron laser. LCLS-II is in an advanced stage of construction with equipment for both Cryoplants as well as more than half of the 37 cryomodules onsite. Jefferson Lab (JLab) is a partner lab responsible for building half of the LCLS-II cryomodules. Hence the Low Energy Recirculation Facility (LERF) at JLab was used to stage and test LCLS-II cryomodules before shipping them to SLAC. LERF was set up to test two cryomodules at a time. LERF used LCLS-II cryogenic controls instrumentation racks, Programmable Logic Controllers (PLC) controls and Experimental Physics and Industrial Control System (EPICS) Input/Output Controllers (IOCs) with the intention to use the LERF setup to check-out and verify cryogenic controls for LCLS-II. The cryogenic controls first utilized at LERF would then be replicated for controlling all 37 cryomodules via an EPICS user interface. This paper discusses the cryogenic controls currently developed for implementation in the LCLS-II project.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Xopt and Badger: a machine learning ecosystem for real-time accelerator control and optimization

Machine learning (ML)-based black-box optimization algorithms have demonstrated significant improvements in accelerator optimization speed, often by orders of magnitude. However, deploying these algorithms in real-time facility control remains challenging due to the specialized expertise and infrastructure required. To bridge this gap, we introduce the Xopt ecosystem, a versatile suite of tools designed to make advanced ML-based optimization accessible to the broader accelerator community. This ecosystem includes Xopt, a modular Python framework that facilitates the integration of ML-based optimization algorithms with arbitrary control problems, and Badger, a graphical user interface built on top of Xopt, which enables seamless deployment of ML algorithms in real-time control systems. The Xopt ecosystem has been successfully applied towards solving challenging real-time control problems at leading international accelerator facilities, including SLAC, LBNL, Argonne, Fermilab, BNL, DESY, and ESRF, demonstrating its effectiveness in real-world optimization tasks. In this presentation, we provide an overview of Xopt’s capabilities and illustrate its impact through case studies from SLAC accelerator facilities including LCLS, LCLS-II, and FACET-II.

Roussel, Ryan [SLAC]↗
DOE OSTI2021

Performance of the LLRF System for the Fermilab PIP-II Injector Test

PIP-II IT is a test facility for the PIP-II project where the injector, warm front-end, and the first two superconducting cryomodules are being tested. The 8-cavity half-wave-resonator (HWR) cryomodule operating at 162.5 MHz is followed by the 8-cavity single-spoke resonator(SSR1) cryomodule operating at 325 MHz. The LLRF systems for both cryomodules are based on a common SOC FPGA-based hardware platform. The resonance control systems for the two cryomodules are quite different, the first being a pneumatic system based on helium pressure and the latter a piezo/stepper motor type control. The data acquisition and control system can support both CW and Pulsed mode operations. Beam loading compensation is available which can be used for both manual/automatic control in the LLRF system. The user interfaces include EPICS, Labview, and ACNET. Testing of the RF system has progressed to the point of being ready for a 2 mA beam to be accelerated to 25 MeV. The design and performance of the field control and resonance control system operation with beam are presented in this paper.

43 PARTICLE ACCELERATORS↗
DOE OSTI2019

The Latest Code Development Progress of JSPEC

The JLab Simulation Package on Electron Cooling (JSPEC) is an open source software developed at Jefferson Lab for electron cooling and intrabeam scattering (IBS) simulations. IBS is an important factor that leads to the growth of the beam emittance and hence the reduction of the luminosity in a high density ion collider ring. Electron cooling is an effective measure to overcome the IBS effect. Although JSPEC is initiated to fulfill the simulation needs in JLab Electron Ion Collider project, it can be used as a general design tool for other accelerators. JSPEC provides various models of the ion beam and the electron beam and it calculates the expansion rate and simulates the evolution of the ion beam under the IBS and/or electron cooling effect. In this report, we will give a brief introduction of JSPEC and then present the latest code development progress of JSPEC, including new models, algorithms, and the user interface.

Zhang, Y.↗
DOE OSTI2022

Hardware-Control: Instrument control and automation package

Conducting experimental research often relies on the control of laboratory instruments to, for example, control power supplies, move stages, and measure data. Tasks, such as data logging or parameter scans, often need to be automated. Being able to easily create a user interface to the hardware and to be able to reuse code is highly desirable.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

A Python Object Oriented & Data Driven Testing Infrastructure for an Environmental Information Management System

Software systems such as TEIMS, the Taurus Environmental Information Management System evolve in size and complexity making manual testing no longer sufficient or feasible, becoming a performance and quality risk. TEIMS is a system of systems comprised of dynamic, data-driven web-based applications that support planning, operational monitoring, data collection, sample management, reporting and, scientific findings for LLNL’s Environmental Restoration Department (ERD). Selenium’s Integrated Development Environment (IDE) was previously used to support TEIMS testing. An approach with limited flexibility for future software development. As a student intern I was assigned the task to develop an object oriented testing infrastructure for TEIMS. A critical resource in this approach is the development of a catalogue of page elements. To accomplish this I created a comma separated value file, which is comprised of key identifiers based on page elements. Using the Python language and the Selenium Web driver I then developed the object mapping structure, which serves as a wrapper for exposure of each element allowing interaction with the tests and test suites. A master driver “Module” allowed the web driver to be shared among the objects and tests. I then developed a web-based graphical user interface (GUI) for test history, metrics and searching. This data driven approach provides flexibility and extensibility, allowing changes to the structure to be performed in a single place. The result is an object oriented/data driven infrastructure that allows tests to be simpler, flexible, and maintainable, with searchable results.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

DAKOTA JAGUAR User's Manual (V.3.0)

JAGUAR (JAva GUi for Applied Research) is a Java software tool providing an advanced text editor and graphical user interface (GUI) to manipulate DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) input specifications. This document focuses on the features necessary to use JAGUAR.

Adams, Brian M.↗
DOE OSTI2013

Recovery Act: Advanced Interaction, Computation, and Visualization Tools for Sustainable Building Design

Current building energy simulation technology requires excessive labor, time and expertise to create building energy models, excessive computational time for accurate simulations and difficulties with the interpretation of the results. These deficiencies can be ameliorated using modern graphical user interfaces and algorithms which take advantage of modern computer architectures and display capabilities. To prove this hypothesis, we developed an experimental test bed for building energy simulation. This novel test bed environment offers an easy-to-use interactive graphical interface, provides access to innovative simulation modules that run at accelerated computational speeds, and presents new graphics visualization methods to interpret simulation results. Our system offers the promise of dramatic ease of use in comparison with currently available building energy simulation tools. Its modular structure makes it suitable for early stage building design, as a research platform for the investigation of new simulation methods, and as a tool for teaching concepts of sustainable design. Improvements in the accuracy and execution speed of many of the simulation modules are based on the modification of advanced computer graphics rendering algorithms. Significant performance improvements are demonstrated in several computationally expensive energy simulation modules. The incorporation of these modern graphical techniques should advance the state of the art in the domain of whole building energy analysis and building performance simulation, particularly at the conceptual design stage when decisions have the greatest impact. More importantly, these better simulation tools will enable the transition from prescriptive to performative energy codes, resulting in better, more efficient designs for our future built environment.

99 GENERAL AND MISCELLANEOUS↗