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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 sources NASA NTRS DOE OSTI

DOE OSTI2015

Sirocco Storage Server v. pre-alpha 0.1

Sirocco is a parallel storage system under development, designed for write-intensive workloads on large-scale HPC platforms. It implements a keyvalue object store on top of a set of loosely federated storage servers that cooperate to ensure data integrity and performance. It includes support for a range of different types of storage transactions. This software release constitutes a conformant storage server, along with the client-side libraries to access the storage over a network.

Curry, Matthew L.↗

DOE OSTI2016

EPICS Channel Access Server for LabVIEW

It can be challenging to interface National Instruments LabVIEW (http://www.ni.com/labview/) with EPICS (http://www.aps.anl.gov/epics/). Such interface is required when an instrument control program was developed in LabVIEW but it also has to be part of global control system. This is frequently useful in big accelerator facilities. The Channel Access Server is written in LabVIEW, so it works on any hardware/software platform where LabVIEW is available. It provides full server functionality, so any EPICS client can communicate with it.

Zhukov, Alexander P.↗

DOE OSTI2025

MOOSE Web Server Interface: A Message-based External Interface for Multiphysics Simulations

The Multiphysics Object-Oriented Simulation Environment (MOOSE) framework is a C++ toolkit designed to streamline the development of finite element and finite volume applications. It offers an interface for input-based coupling of these applications to create multiscale, multiphysics models. We introduce a new capability that enables external applications to integrate with MOOSE-based applications in situ via a web server using HTTP requests. An example of this integration is provided, where a MOOSE thermal-fluids solve has a boundary condition that is driven by an external Python application. Additionally, the coupling of the Python-based OpenMC depletion solver with the Cardinal application is demonstrated. A multiphysics model of a pressurized water reactor, incorporating neutronics, heat conduction, thermal-fluids, and depletion, is presented to showcase this new Cardinal capability that is enabled by the MOOSE web server capability.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

MOOSE Web Server Interface: A Message-based External Interface for Multiphysics Simulations

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2019

The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation

To assess the chemical reactivity, toxicity, and mobility of pollutants in the environment, knowledge of their species distributions is critical. Because their direct measurement is often infeasible, speciation modeling is widely adopted. Mercury (Hg) is a representative pollutant for which study of its speciation benefits from modeling. However, Hg speciation modeling is often hindered by a lack of reliable thermodynamic constants. Although computational chemistry (e.g., density functional theory [DFT]) can generate these constants, methods for directly coupling DFT and speciation modeling are not available. Here, we combine computational chemistry and continuum-scale modeling with curated online databases to ameliorate the problem of unreliable inputs to Hg speciation modeling. Our AQUA-MER databases and web server (https://aquamer.ornl.gov) provides direct speciation results by combining web-based interfaces to a speciation calculator, databases of thermodynamic constants, and a computational chemistry toolkit to estimate missing constants. Lastly, although Hg is presented as a concrete use case, AQUA-MER can also be readily applied to other elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Comprehensive Metabolite Identification Strategy Using Multiple Two-Dimensional NMR Spectra of a Complex Mixture Implemented in the COLMARm Web Server

Identification of metabolites in complex mixtures represents a key step in metabolomics. A new strategy is introduced, which is implemented in a new public web server, COLMARm, that permits the co-analysis of up to three 2D NMR spectra, namely 13C-1H HSQC, 1H-1H TOCSY, and 13C-1H HSQC-TOCSY for the comprehensive, accurate, and efficient performance of this task. The highly versatile and interactive nature of COLMARm permits its application to a wide range of metabolomics samples independent of the magnetic field. Database query is performed using the HSQC spectrum and the top metabolite hits are then validated against the TOCSY-type experiment(s) by superimposing the expected cross-peaks on the mixture spectrum. In this way the user can directly accept or reject candidate metabolites by taking advantage of the complementary spectral information offered by these experiments and their different sensitivities. The power of COLMARm is demonstrated for a human serum sample uncovering the existence of 14 metabolites that hitherto were not identified by NMR.

Bingol, Kerem↗

DOE OSTI2023

TeraChem protocol buffers ( TCPB ): Accelerating QM and QM/MM simulations with a client–server model

The routine use of electronic structures in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. Here, we describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by third-party client programs. We exploit Google’s protocol buffer framework for data serialization and communication. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages, such as C++, Fortran, and Python. To demonstrate the ease of coupling third-party programs with electronic structures using TCPB, we have incorporated the TCPB client into Amber for quantum mechanics/molecular mechanics (QM/MM) simulations. The TCPB interface saves time with GPU initialization and I/O operations, achieving a speedup of more than 2× compared to a prior file-based implementation for a QM region with ~250 basis functions. We demonstrate the practical application of TCPB by computing the free energy profile of p-hydroxybenzylidene-2,3-dimethylimidazolinone (p-HBDI - )—a model chromophore in green fluorescent proteins—on the first excited singlet state using Hamiltonian replica exchange for enhanced sampling. All calculations in this work have been performed with the non-commercial freely-available version of TeraChem, which is sufficient for many QM region sizes in common use.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

BioTransformer 3.0 – A Web Server for Accurately Predicting Metabolic Transformation Products

BioTransformer 3.0 is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. It combines machine learning approaches with a rule-based system to predict small-molecule metabolism in human tissues, the human gut as well as the external environment (soil and water microbiota). Simply stated, BioTransformer takes a molecular structure as input (SMILES or SDF) and outputs an interactively viewable/sortable table of the predicted metabolites or transformation products (SMILES, PNG images) along with the enzymes that are predicted to be responsible for those reactions and richly annotated downloadable files (CSV and JSON). The entire process typically takes a few seconds. Previous versions of BioTransformer focused exclusively on predicting the metabolism of xenobiotics (such as plant natural products, drugs, cosmetics and other synthetic compounds) using a limited number of pre-defined steps and somewhat limited rule-based methods. BioTransformer 3.0, uses much more sophisticated methods and incorporates new databases, new constraints and new prediction modules to not only more accurately predict the metabolic transformation products of exogenous xenobiotics but also the transformation products of endogenous metabolites, such as amino acids, peptides, carbohydrates, organic acids, and lipids. BioTransformer 3.0 can also support customized sequential combinations of these transformations along with multiple iterations to simulate multi-step human and/or environmental biotransformation events. Performance tests indicate that BioTransformer 3.0 is 40-50% more accurate, much less prone to combinatorial “explosions” and far more comprehensive in terms of metabolite coverage/capabilities than previous versions of BioTransformer.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

The PhyloFacts ‘Fast Approximate Tree Classification’ (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT’s high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts’ broad taxonomic and functional coverage, with >7.3 M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyperlinked to various external databases.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Double crystallographic groups and their representations on the Bilbao Crystallographic Server

A new section of databases and programs devoted to double crystallographic groups (point and space groups) has been implemented in the Bilbao Crystallographic Server (http://www.cryst.ehu.es). The double crystallographic groups are required in the study of physical systems whose Hamiltonian includes spin-dependent terms. In the symmetry analysis of such systems, instead of the irreducible representations of the space groups, it is necessary to consider the single- and double-valued irreducible representations of the double space groups. The new section includes databases of symmetry operations ( DGENPOS ) and of irreducible representations of the double (point and space) groups ( REPRESENTATIONS DPG and REPRESENTATIONS DSG ). The tool DCOMPREL provides compatibility relations between the irreducible representations of double space groups at different k vectors of the Brillouin zone when there is a group–subgroup relation between the corresponding little groups. The program DSITESYM implements the so-called site-symmetry approach, which establishes symmetry relations between localized and extended crystal states, using representations of the double groups. As an application of this approach, the program BANDREP calculates the band representations and the elementary band representations induced from any Wyckoff position of any of the 230 double space groups, giving information about the properties of these bands. Recently, the results of BANDREP have been extensively applied in the description of and the search for topological insulators.

Chemistry↗

DOE OSTI2024

Determining magnetic structures in GSAS-II using the Bilbao Crystallographic Server tool k-SUBGROUPSMAG

The embedded call to a special version of the web-based Bilbao Crystallographic Server tool k-SUBGROUPSMAG from within GSAS-II to form a list of all possible commensurate magnetic subgroups of a parent magnetic grey group is described. It facilitates the selection and refinement of the best commensurate magnetic structure model by having all the analysis tools including Rietveld refinement in one place as part of GSAS-II. It also provides the chosen magnetic space group as one of the 1421 possible standard Belov–Neronova–Smirnova forms or equivalent non-standard versions.

36 MATERIALS SCIENCE↗

DOE OSTI2015

SU-E-I-75: Development of New Biological Fingerprints for Patient Recognition to Identify Misfiled Images in a PACS Server

Purpose: We are trying to develop an image-searching technique to identify misfiled images in a picture archiving and communication system (PACS) server by using five biological fingerprints: the whole lung field, cardiac shadow, superior mediastinum, lung apex, and right lower lung. Each biological fingerprint in a chest radiograph includes distinctive anatomical structures to identify misfiled images. The whole lung field was less effective for evaluating the similarity between two images than the other biological fingerprints. This was mainly due to the variation in the positioning for chest radiographs. The purpose of this study is to develop new biological fingerprints that could reduce influence of differences in the positioning for chest radiography. Methods: Two hundred patients were selected randomly from our database (36,212 patients). These patients had two images each (current and previous images). Current images were used as the misfiled images in this study. A circumscribed rectangular area of the lung and the upper half of the rectangle were selected automatically as new biological fingerprints. These biological fingerprints were matched to all previous images in the database. The degrees of similarity between the two images were calculated for the same and different patients. The usefulness of new the biological fingerprints for automated patient recognition was examined in terms of receiver operating characteristic (ROC) analysis. Results: Area under the ROC curves (AUCs) for the circumscribed rectangle of the lung, upper half of the rectangle, and whole lung field were 0.980, 0.994, and 0.950, respectively. The new biological fingerprints showed better performance in identifying the patients correctly than the whole lung field. Conclusion: We have developed new biological fingerprints: circumscribed rectangle of the lung and upper half of the rectangle. These new biological fingerprints would be useful for automated patient identification system because they are less affected by positioning differences during imaging.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

mDNS to support local price server discovery with OpenADR 3 (mDNS for OpenADR 3) v1.0

This software contains a template VEN with local VTN service discovery over mDNS. It provides common starter code for an OpenADR3.0 VEN that advertises itself over mDNS, conducts local VTN service discovery over mDNS, connects to the VTN over HTTP(S), and regularly polls and acts on energy prices and events hosted on the VTN. The software is written to be easily modified to accommodate different VEN appliances, VEN-VTN networking protocols, user interfaces, and default responses, given the wide range of possible use cases for local price server discovery. OpenADR3.0 is an open communications standard from the OpenADR Alliance that is designed to provide two-way information exchange regarding e.g., dynamic price and event signals to utility applications, so that customers can modify their energy usage to save money and reduce their carbon footprint.

Nordman, Bruce [Lawrence Berkeley National Laborat↗

DOE OSTI2016

CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking

RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS) motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

NREL Energy Performance Testing of Asetek's RackCDU System on a Single Rack of Twin Blade Servers: Cooperative Research and Development Final Report, CRADA Number CRD-13-518

The project will entail Asetek retrofitting 1 - 2 compute racks of servers at the National Renewable Energy Laboratory (NREL) to test and validate RackCDU's cooling performance and long-term reliability. The project will also entail measuring and reporting energy savings under a real workload by comparing total power input to the system vs. total heat removed by liquid and air. Direct measurements will be made to compare and contrast energy consumption and performance both before and after RackCDU installation. The scope of this project is strictly demonstration and feedback on the system. No development work will be performed under this CRADA.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2019

Client-side and Server-side Programming in Sirepo Framework

Sirepo [1] is an interactive simulation environment for accelerator and beamline design. It is integrated with numbers of widely used scientific codes, including Synchrotron Radiation Workshop (SRW) [2] for accurate X–ray source and optics simulations. Sirepo is a fully open source and could be quickly extended to support the codes from different scientific domains. Sirepo framework covers both client and server–side simulation job management, user management and front–end data presentation. In this present note, we extend Sirepo by adding a new SRW source type for the beamline simulations.

36 MATERIALS SCIENCE↗

DOE OSTI2020

An Integrated Two-Factor Authentication Solution Using Pulse Connect Secure and Apache HTTP Server

Complex system requirements can often lead to a situation wherein no single product or platform can provide a solution. In these cases, a solution integrating the features of multiple products and platforms is needed. Recently, a program sponsor required discontinued use of a third-party Security Assertion Markup Language Identity Provider that was being used to implement a two-factor authentication (2FA) solution that fully integrated with Pulse Connect Secure (PCS). PCS alone could not provide the features necessary to meet all the requirements of a new 2FA solution. The challenge was to leverage the features of additional platforms to design an integrated solution to meet all requirements. This paper presents a solution that integrates the features of PCS, Apache HyperText Transfer Protocol Server, and a custom application that meets all requirements, including a requirement to defend against Uniform Resource Locator manipulation as means to gain unauthorized access to backend applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Meshing, Language Server Protocol, and other User-Oriented MOOSE Framework Improvements to Enhance Reactor Analysis Capabilities and Workflows

The open-source Multiphysics Object-Oriented Simulation Environment (MOOSE) framework underpins most of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) physics applications and coupling methods. Users interact with MOOSE in multiple ways to enable the construction of complex multiphysics models, including but not limited to compilation, input creation and syntax validation, meshing, solving the physics problem via MOOSE-based solvers and coupling, and output inspection. In FY23, numerous enhancements have been made to MOOSE to enhance the user experience. Reactor-oriented meshing capabilities in MOOSE have been expanded, an online tutorial was created and hosted on the MOOSE site, and a hands-on workshop was held for more than 100 users. The Language Server Protocol (LSP) capability has been implemented in MOOSE to better communicate correct syntax to the NEAMS Workbench user interface which is commonly used to validate input and submit jobs by users. Finally, several other user-facing improvements were made including the implementation of improved screen output and logging control, enhancements to the initial condition system, and enhancements of the MultiApp system commonly used for coupling. Collectively, these enhancements were driven by user needs and directly improve user ability to construct complex multiphysics models for nuclear reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗