Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “LIBRARIES”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Patching EAF-2010 into CINDER2008 Cross Section Libraries

CINDER2008 [1] comes with multi-group cross section libraries using most recent evaluated cross section data. The multi-group cross sections are weighted with three spectra: fission, fusion and flat. However, due to data format incompatibilities with the CINDER2008library maker tool, many of the reaction cross sections adapted from EAF-2010 [2] are either truncated or completely missing. Therefore it is essential to regenerate the CINDER2008 libraries with compatible EAF-2010 data. The updated cross section libraries are compared to those of the current cross section libraries in the sections below following a brief introduction of the CINDER2008 cross section libraries and a description of the method of generating cross sections for the CINDER2008 code. In the remainder of this document, we will refer to the libraries distributed with CINDER2008before October 2016 as the "current" libraries, and those described in this work as the "updated" libraries. In figures, the current library data may be shown with the library namewith or without “cur” appended, while the updated library data may be shown with "mod" appended.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
NASA NTRS2000

Constructing high complexity synthetic libraries of long ORFs using in vitro selection

We present a method that can significantly increase the complexity of protein libraries used for in vitro or in vivo protein selection experiments. Protein libraries are often encoded by chemically synthesized DNA, in which part of the open reading frame is randomized. There are, however, major obstacles associated with the chemical synthesis of long open reading frames, especially those containing random segments. Insertions and deletions that occur during chemical synthesis cause frameshifts, and stop codons in the random region will cause premature termination. These problems can together greatly reduce the number of full-length synthetic genes in the library. We describe a strategy in which smaller segments of the synthetic open reading frame are selected in vitro using mRNA display for the absence of frameshifts and stop codons. These smaller segments are then ligated together to form combinatorial libraries of long uninterrupted open reading frames. This process can increase the number of full-length open reading frames in libraries by up to two orders of magnitude, resulting in protein libraries with complexities of greater than 10(13). We have used this methodology to generate three types of displayed protein library: a completely random sequence library, a library of concatemerized oligopeptide cassettes with a propensity for forming amphipathic alpha-helical or beta-strand structures, and a library based on one of the most common enzymatic scaffolds, the alpha/beta (TIM) barrel. Copyright 2000 Academic Press.

Non-NASA Center↗
DOE OSTI2026

LibraryX: A Framework for Cross-Library-Call Optimization

Scientific applications utilize performance libraries as a software engineering concept: these libraries encapsulate important and well-understood (mathematical) operations, allow for reuse, and are implemented and tuned by experts. Domain scientists then implement complex algorithms based on these domainspecific libraries. While individual library calls are optimized, larger performance gains across sequences of calls—sometimes spanning multiple libraries—are often unrealized, forcing a trade-off between performance and implementation complexity.To overcome this issue, we propose LibraryX, an approach and a system that allows for cross-library-call optimization even when library calls stem from multiple performance libraries. LibraryX annotates library calls with semantic information and optimizes entire directed acyclic graphs (DAGs) of calls dynamically using the SPIRAL code generation system. We demonstrate its effectiveness across a range of memory bound workloads, achieving significant speedups on Nvidia, AMD, and Intel accelerators compared to code using native libraries without cross-call optimization.

Rao, Sanil [Carnegie Mellon University,Department ↗
DOE OSTI2017

CHEMICAL EVOLUTION LIBRARY FOR GALAXY FORMATION SIMULATION

We have developed a software library for chemical evolution simulations of galaxy formation under the simple stellar population (SSP) approximation. In this library, all of the necessary components concerning chemical evolution, such as initial mass functions, stellar lifetimes, yields from Type II and Type Ia supernovae, asymptotic giant branch stars, and neutron star mergers, are compiled from the literature. Various models are pre-implemented in this library so that users can choose their favorite combination of models. Subroutines of this library return released energy and masses of individual elements depending on a given event type. Since the redistribution manner of these quantities depends on the implementation of users’ simulation codes, this library leaves it up to the simulation code. As demonstrations, we carry out both one-zone, closed-box simulations and 3D simulations of a collapsing gas and dark matter system using this library. In these simulations, we can easily compare the impact of individual models on the chemical evolution of galaxies, just by changing the control flags and parameters of the library. Since this library only deals with the part of chemical evolution under the SSP approximation, any simulation codes that use the SSP approximation—namely, particle-base and mesh codes, as well as semianalytical models—can use it. This library is named “CELib” after the term “Chemical Evolution Library” and is made available to the community.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1998

Architectural Optimization of Digital Libraries

This work investigates performance and scaling issues relevant to large scale distributed digital libraries. Presently, performance and scaling studies focus on specific implementations of production or prototype digital libraries. Although useful information is gained to aid these designers and other researchers with insights to performance and scaling issues, the broader issues relevant to very large scale distributed libraries are not addressed. Specifically, no current studies look at the extreme or worst case possibilities in digital library implementations. A survey of digital library research issues is presented. Scaling and performance issues are mentioned frequently in the digital library literature but are generally not the focus of much of the current research. In this thesis a model for a Generic Distributed Digital Library (GDDL) and nine cases of typical user activities are defined. This model is used to facilitate some basic analysis of scaling issues. Specifically, the calculation of Internet traffic generated for different configurations of the study parameters and an estimate of the future bandwidth needed for a large scale distributed digital library implementation. This analysis demonstrates the potential impact a future distributed digital library implementation would have on the Internet traffic load and raises questions concerning the architecture decisions being made for future distributed digital library designs.

Biser, Aileen O.↗
DOE OSTI2016

Generation of the V4.2m5 and AMPX and MPACT 51 and 252-Group Libraries with ENDF/B-VII.0 and VII.1

The evaluated nuclear data file (ENDF)/B-7.0 v4.1m3 MPACT 47-group library has been used as a main library for the Consortium for Advanced Simulation of Light Water Reactors (CASL) neutronics simulator in simulating pressurized water reactor (PWR) problems. Recent analysis for the high void boiling water reactor (BWR) fuels and burnt fuels indicates that the 47-group library introduces relatively large reactivity bias. Since the 47- group structure does not match with the SCALE 6.2 252-group boundaries, the CASL Virtual Environment for Reactor Applications Core Simulator (VERA-CS) MPACT library must be maintained independently, which causes quality assurance concerns. In order to address this issue, a new 51-group structure has been proposed based on the MPACT 47- g and SCALE 252-g structures. In addition, the new CASL library will include a 19-group structure for gamma production and interaction cross section data based on the SCALE 19- group structure. New AMPX and MPACT 51-group libraries have been developed with the ENDF/B-7.0 and 7.1 evaluated nuclear data. The 19-group gamma data also have been generated for future use, but they are only available on the AMPX 51-g library. In addition, ENDF/B-7.0 and 7.1 MPACT 252-g libraries have been generated for verification purposes. Various benchmark calculations have been performed to verify and validate the newly developed libraries.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2018

A novel lentiviral scFv display library for rapid optimization and selection of high affinity antibodies

Highlights: • We constructed a novel scFv display library based on lentivirus vector. • Stable transduced cell lines were obtained. • Characterization of mutants showed approximately upto three fold increase in antibody affinity. Antibody display libraries have become a popular technique to screen monoclonal antibodies for therapeutic purposes. An important aspect of display technology is to generate an optimization library by changing antibody affinity to antigen through mutagenesis and screening the high affinity antibody. In this study, we report a novel lentivirus display based optimization library antibody in which Agtuzumab scFv is displayed on cell membrane of HEK-293T cells. To generate an optimization library, hotspot mutagenesis was performed to achieve diverse antibody library. Based on sequence analysis of randomly selected clones, library size was estimated approximately to be 1.6 × 10{sup 6}. Lentivirus display vector was used to display scFv antibody on cell surface and flow cytometery was performed to check the antibody affinity to antigen. Membrane bound scFv antibodies were then converted to secreted antibody through cre/loxP recombination. One of the mutant clones, M8 showed higher affinity to antigen in flow cytometery analysis. Further characterization of cellular and secreted scFv through western blot showed that antibody affinity was increased by three fold after mutagenesis. This study shows successful construction of a novel antibody library and suggests that hotspot mutagenesis could prove a useful and rapid optimization tool to generate similar libraries with various degree of antigen affinity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

DeCOIL: Optimization of Degenerate Codon Libraries for Machine Learning-Assisted Protein Engineering

With advances in machine learning (ML)-assisted protein engineering, models based on data, biophysics, and natural evolution are being used to propose informed libraries of protein variants to explore. Synthesizing these libraries for experimental screens is a major bottleneck, as the cost of obtaining large numbers of exact gene sequences is often prohibitive. Degenerate codon (DC) libraries are a cost-effective alternative for generating combinatorial mutagenesis libraries where mutations are targeted to a handful of amino acid sites. However, existing computational methods to optimize DC libraries to include desired protein variants are not well suited to design libraries for ML-assisted protein engineering. To address these drawbacks, we present DEgenerate Codon Optimization for Informed Libraries (DeCOIL), a generalized method which directly optimizes DC libraries to be useful for protein engineering: to sample protein variants that are likely to have both high fitness and high diversity in the sequence search space. Using computational simulations and wet-lab experiments, we demonstrate that DeCOIL is effective across two specific case studies, with potential to be applied to many other use cases. DeCOIL offers several advantages over existing methods, as it is direct, easy-to-use, generalizable, and scalable. With accompanying software, DeCOIL can be readily implemented to generate desired informed libraries.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules

A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sublibraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

MT71x: Multi-Temperature Library Based on ENDF/B-VII.1

The Nuclear Data Team has released a multitemperature transport library, MT71x, based upon ENDF/B-VII.1 with a few modifications as well as additional evaluations for a total of 427 isotope tables. The library was processed using NJOY2012.39 into 23 temperatures. MT71x consists of two sub-libraries; MT71xMG for multigroup energy representation data and MT71xCE for continuous energy representation data. These sub-libraries are suitable for deterministic transport and Monte Carlo transport applications, respectively. The SZAs used are the same for the two sub-libraries; that is, the same SZA can be used for both libraries. This makes comparisons between the two libraries and between deterministic and Monte Carlo codes straightforward. Both the multigroup energy and continuous energy libraries were verified and validated with our checking codes checkmg and checkace (multigroup and continuous energy, respectively) Then an expanded suite of tests was used for additional verification and, finally, verified using an extensive suite of critical benchmark models. We feel that this library is suitable for all calculations and is particularly useful for calculations sensitive to temperature effects.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2017

Software Quality Assurance and Verification for the MPACT Library Generation Process

This report fulfills the requirements for the Consortium for the Advanced Simulation of Light-Water Reactors (CASL) milestone L2:RTM.P14.02, “SQA and Verification for MPACT Library Generation,” by documenting the current status of the software quality, verification, and acceptance testing of nuclear data libraries for MPACT. It provides a brief overview of the library generation process, from general-purpose evaluated nuclear data files (ENDF/B) to a problem-dependent cross section library for modeling of light-water reactors (LWRs). The software quality assurance (SQA) programs associated with each of the software used to generate the nuclear data libraries are discussed; specific tests within the SCALE/AMPX and VERA/XSTools repositories are described. The methods and associated tests to verify the quality of the library during the generation process are described in detail. The library generation process has been automated to a degree to (1) ensure that it can be run without user intervention and (2) to ensure that the library can be reproduced. Finally, the acceptance testing process that will be performed by representatives from the Radiation Transport Methods (RTM) Focus Area prior to the production library’s release is described in detail.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Verification of the ENDF/B-VII.1 Based MC 2 -3 Library Rev.1

The MC 2 -3 code, developed by Argonne National Laboratory under the DOE-NE NEAMS program, is a multigroup cross section generation code for fast reactor applications. Last year, the ENDF/B-VII.0 (E70) MC 2 -3 library, which has been extensively used, verified, and validated over a long period, was intensively reverified and updated to support the commercial grade dedication (CGD) requirement of the TerraPower Natrium project. This year, the ENDF/B-VII.1 (E71) MC 2 -3 library, the preliminary version of which was generated several years ago, was regenerated and rigorously verified to support the Natrium project as well as the completion of verification of the E71 library. The E71 library was verified using the process developed during the verification of the E70 library, including comparisons of cross sections with the NJOY-generated cross sections, comparisons of the resolved resonance cross sections with those using the PEDNF library, and comparison of total cross sections with the sum of partial cross sections. Additional verifications were conducted to ensure that the benchmark problem solutions with the E71 library are reasonable compared to the corresponding Monte Carlo solutions. Furthermore, the E71 gamma library was generated, which includes data for prompt gamma, delayed gamma, and delayed beta as well as neutron and gamma heating. The gamma library was verified at the level of individual isotopes. The EBR-II core solutions from MC 2 -3/ DIF3D and MCNP were compared, demonstrating that those solutions in terms of k-effective and assembly powers were in good agreement.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
NASA NTRS1999

Field Encapsulation Library The FEL 2.2 User Guide

This document describes version 2.2 of the Field Encapsulation Library (FEL), a library of mesh and field classes. FEL is a library for programmers - it is a "building block" enabling the rapid development of applications by a user. Since FEL is a library intended for code development, it is essential that enough technical detail be provided so that one can make full use of the code. Providing such detail requires some assumptions with respect to the reader's familiarity with the library implementation language, C++, particularly C++ with templates. We have done our best to make the explanations accessible to those who may not be completely C++ literate. Nevertheless, familiarity with the language will certainly help one's understanding of how and why things work the way they do. One consolation is that the level of understanding essential for using the library is significantly less than the level that one should have in order to modify or extend the library. One more remark on C++ templates: Templates have been a source of both joy and frustration for us. The frustration stems from the lack of mature or complete implementations that one has to work with. Template problems rear their ugly head particularly when porting. When porting C code, successfully compiling to a set of object files typically means that one is almost done. With templated C++ and the current state of the compilers and linkers, generating the object files is often only the beginning of the fun. On the other hand, templates are quite powerful. Used judiciously, templates enable more succinct designs and more efficient code. Templates also help with code maintenance. Designers can avoid creating objects that are the same in many respects, but not exactly the same. For example, FEL fields are templated by node type, thus the code for scalar fields and vector fields is shared. Furthermore, node type templating allows the library user to instantiate fields with data types not provided by the FEL authors. This type of flexibility would be difficult to offer without the support of the language. For users who may be having template-related problems, we offer the consolation that support for C++ templates is destined to improve with time. Efforts such as the Standard Template Library (STL) will inevitably drive vendors to provide more thorough, optimized tools for template code development. Furthermore, the benefits will become harder to resist for those who currently subscribe to the least-common-denominator "code it all in C" strategy. May FEL bring you both increased productivity and aesthetic satisfaction.

Moran, Patrick J.↗
DOE OSTI2016

Revised Extended Grid Library

The Revised Eolus Grid Library (REGL) is a mesh-tracking library that was developed for use with the MCNP6TM computer code so that (radiation) particles can track on an unstructured mesh. The unstructured mesh is a finite element representation of any geometric solid model created with a state-of-the-art CAE/CAD tool. The mesh-tracking library is written using modern Fortran and programming standards; the library is Fortran 2003 compliant. The library was created with a defined application programmer interface (API) so that it could easily integrate with other particle tracking/transport codes. The library does not handle parallel processing via the message passing interface (mpi), but has been used successfully where the host code handles the mpi calls. The library is thread-safe and supports the OpenMP paradigm. As a library, all features are available through the API and overall a tight coupling between it and the host code is required. Features of the library are summarized with the following list: Can accommodate first and second order 4, 5, and 6-sided polyhedra; any combination of element types may appear in a single geometry model; parts may not contain tetrahedra mixed with other element types; pentahedra and hexahedra can be together in the same part; robust handling of overlaps and gaps; tracks element-to-element to produce path length results at the element level; finds element numbers for a given mesh location; finds intersection points on element faces for the particle tracks; produce a data file for post processing results analysis; reads Abaqus .inp input (ASCII) files to obtain information for the global mesh-model; supports parallel input processing via mpi; and support parallel particle transport by both mpi and OpenMP.

Martz, Roger L.↗
DOE OSTI2018

Verification and Validation of the ENDF/B-VII.1 v4.3m1 MPACT 51-Group Cross Section Library

The MPACT neutronics module of the Consortium for Advanced Simulation of Light Water Reactors (CASL) core simulator is a 3-D whole core transport code being developed for the Virtual Environment for Reactor Analysis (VERA) CASL toolset. Key characteristics of the MPACT code include (1) a subgroup method for resonance selfshielding and (2) a whole-core transport solver with a 2-D/1-D synthesis method. The MPACT code requires a cross section library to support all of its core simulation capabilities; a cross section library would be MPACT’s most influencing component for simulation accuracy. Due to the limitation of computing capacity even in high performance computing, the cross section library must be developed to enhance computational efficiency in memory and computing time without losing accuracy and generality. This requires a very coarse energy group structure with about 50 groups. Multigroup (MG) neutron cross section libraries for the CASL VERA-CS neutronics simulator MPACT have been created by using the AMPX/SCALE code package developed at Oak Ridge National Laboratory (ORNL). A new 51-group structure was developed for efficient simulation to be applicable for both pressurized water reactor (PWR) and boiling water reactor (BWR) simulations. New v4.3m1 MPACT 51-group library with the ENDF/B- VII.1 nuclear data were developed for MPACT. Since SCALE KENO has some issues in the probability table and has a low cutoff energy for the free gas model, this issue has been corrected. This study focused on the development of the ENDF/B-VII.1 v4.3m1 MPACT MG library, including verification and validation. This document includes the library generation methodology and procedure, the verification procedure, and benchmark results compared to continuous energy Monte Carlo results using newly developed cross section libraries.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2022

Singe Library Review: XCAP Review Report

Singe is a computational library for simulating thermonuclear reactions written in C++14. It was inspired by the earlier Singe library, developed by Joann Campbell. From the beginning of the Singe project, the goal has been to create a library that provides the necessary functionality, runs efficiently, and is flexible enough to connect to a variety of multi-physics host codes. Such a library allows subject-matter experts to focus on development within the library, while library staff can support host-code staff in integrating Singe into their multi-physics codes. A common library used across multiple multi-physics codes allows those subject-matter experts to roll out new features to all host codes simultaneously, and eases the process of code-to-code comparison between codes that are leveraging the same physics in different ways. The Singe effort was established by Joann Campbell, who provided significant guidance on the goals, requirements, and philosophy of the library. It has been developed by Brendan K. Krueger, CJ Solomon, Jesse Canfield, and Terry Adams, with computer science support from Tyler Reddy and Karen Tsai. Discussions with multiple potential stakeholders have been critical to the planning of such a cross-cutting project, including representatives from multiple host codes and Brian Haines who helped define usage and needs for the inertial confinement fusion (ICF) program. This document is based on the XCAP review process. It is an updated version of the initial document distributed to the reviewers, memo XCP-2:21-005. We want to acknowledge the time and effort of the reviewers who participated in this process: Philipp Edelmann, Alan Harrison, Christopher Malone, Edward Norris, Ryosuke Park, Galen Shipman, CJ Solomon, and any others who may have contributed to the feedback that was provided to us.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

SDSS-IV MaStar: A Large and Comprehensive Empirical Stellar Spectral Library—First Release

In this work, we present the first release of the MaNGA Stellar Library (MaStar), which is a large, well-calibrated, high-quality empirical library covering the wavelength range 3622-10354 Å at a resolving power of R ~ 1800. The spectra were obtained using the same instrument as used by the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) project, by piggybacking on the Sloan Digital Sky Survey (SDSS-IV)/Apache Point Observatory Galaxy Evolution Experiment 2-N (APOGEE-2N) observations. Compared to previous empirical libraries, the MaStar library will have a higher number of stars and a more comprehensive stellar-parameter coverage, especially of cool dwarfs, low-metallicity stars, and stars with different [α/Fe], achieved by a sophisticated target-selection strategy that takes advantage of stellar-parameter catalogs from the literature. This empirical library will provide a new basis for stellar-population synthesis and is particularly well suited for stellar-population analysis of MaNGA galaxies. The first version of the library contains 8646 high-quality per-visit spectra for 3321 unique stars. Compared to photometry, the relative flux calibration of the library is accurate to 3.9% in g-r, 2.7% in r-i, and 2.2% in i-z. The data are released as part of SDSS Data Release 15. We expect the final release of the library to contain more than 10,000 stars.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1994

Application Reuse Library for Software, Requirements, and Guidelines

Better designs are needed for expert systems and other operations automation software, for more reliable, usable and effective human support. A prototype computer-aided Application Reuse Library shows feasibility of supporting concurrent development and improvement of advanced software by users, analysts, software developers, and human-computer interaction experts. Such a library expedites development of quality software, by providing working, documented examples, which support understanding, modification and reuse of requirements as well as code. It explicitly documents and implicitly embodies design guidelines, standards and conventions. The Application Reuse Library provides application modules with Demo-and-Tester elements. Developers and users can evaluate applicability of a library module and test modifications, by running it interactively. Sub-modules provide application code and displays and controls. The library supports software modification and reuse, by providing alternative versions of application and display functionality. Information about human support and display requirements is provided, so that modifications will conform to guidelines. The library supports entry of new application modules from developers throughout an organization. Example library modules include a timer, some buttons and special fonts, and a real-time data interface program. The library prototype is implemented in the object-oriented G2 environment for developing real-time expert systems.

Malin, Jane T.↗