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DOE OSTI2021

Characterization data of an (AlFeNiTiVZr) 1-x Cr x multi-principal element alloy continuous composition spread library

The data provided in this article is related to the research article entitled “Phase stabilization and oxidation of a continuous composition spread multi-principal element (AlFeNiTiVZr) 1-x Cr x alloy”. This data article describes the high-throughput synthesis and characterization processes of an (AlFeNiTiVZr) 1-x Cr x alloy system. Continuous composition spread (CCS) thin-film libraries were synthesized by co-depositing an AlFeNiTiVZr metal alloy target and Cr target via magnetron sputtering. Post-processing was performed on the sample libraries with a vacuum anneal at 873 K and an air anneal at 873 K. Compositional data was determined via WDS in order to verify parameters provided by an in-house sputter model. Crystallographic data was captured via synchrotron diffraction and diffractograms were compared as a function of the change in Cr concentration. These measurements were taken in order to observe phase behavior after oxidation throughout the composition library. Furthermore, vibrational spectrographic data is provided of the oxidized library to show surface speciation along the composition gradient of the alloy system. The structural and oxidative behavior of the (AlFeNiTiVZr) 1-x Cr x alloy can be analysed using the data provided in this article. Additionally, this characterization dataset can be utilized in machine learning algorithms for determining important features and parameters for future hypothesis generation of functional multi-principal element alloys (MPEAs).

36 MATERIALS SCIENCE↗

DOE OSTI2020

Calculations of Astrophysical Reaction Rates Using ENDF/B-VIII.0 Library

Recent observations of neutron stars merger (GW170817) renewed interest in stellar nucleosynthesis. Stellar nucleosynthesis modeling requires fully traceable, unbiased, high fidelity nuclear data. The Evaluated Nuclear Data File (ENDF) libraries contain complete collections of reaction data sets over the nuclear industry standard 10 -5 eV - 20 MeV energy span. For the first time, the (n,γ), (n,fission), (n,p), and (n,α) astrophysical reaction rates were computed within the 0.01-10 GK range of temperatures using the ENDF/B-VIII.0 library, and nuclear Reaction rate Library for astrophysics (REACLIB) fit parameters were deduced. The present results were used to estimate the slow neutron capture timescale. These findings demonstrate the potential astrophysical applications of the ENDF libraries and the complementary relations between the nuclear industry and astrophysics data developments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Computational design and analysis of modular cells for large libraries of exchangeable product synthesis modules

Microbial metabolism can be harnessed to produce a large library of useful chemicals from renewable resources such as plant biomass. However, it is laborious and expensive to create microbial biocatalysts to produce each new product. To tackle this challenge, we have recently developed modular cell (ModCell) design principles that enable rapid generation of production strains by assembling a modular (chassis) cell with exchangeable production modules to achieve overproduction of target molecules. Previous computational ModCell design methods are limited to analyze small libraries of around 20 products. In this study, we developed a new computational method, named ModCell-HPC, that can design modular cells for large libraries with hundreds of products with a highly-parallel and multi-objective evolutionary algorithm and enable us to elucidate modular design properties. We demonstrated ModCell-HPC to design Escherichia coli modular cells towards a library of 161 endogenous production modules. From these simulations, we identified E. coli modular cells with few genetic manipulations that can produce dozens of molecules in a growth-coupled manner with different types of fermentable sugars. These designs revealed key genetic manipulations at the chassis and module levels to accomplish versatile modular cells, involving not only in the removal of major by-products but also modification of branch points in the central metabolism. We further found that the effect of various sugar degradation on redox metabolism results in lower compatibility between a modular cell and production modules for growth on pentoses than hexoses. To better characterize the degree of compatibility, we developed a method to calculate the minimal set cover, identifying that only three modular cells are all needed to couple with up 85 compatible production modules. By determining the unknown compatibility contribution metric, we further elucidated the design features that allow an existing modular cell to be re-purposed towards production of new molecules. Altogether, ModCell-HPC is a useful tool for understanding modularity of biological systems and guiding more efficient and generalizable design of modular cells that help reduce research and development cost in biocatalysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples

Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties of molecules in complex mixtures and, in concert, are sensitive enough to resolve even stereoisomers. Despite these experimental advances, small molecule identification is inhibited by (i) chemical reference libraries (e.g. mass spectra, collision cross section, and other measurable property libraries) representing <1% of known molecules, limiting the number of possible identifications, and (ii) the lack of a method to generate candidate matches directly from experimental features (i.e. without a library). To this end, we developed a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. We extended the VAE to include a chemical property decoder, trained as a multitask network, in order to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, with its focus on properties that can be obtained from experimental measurements (m/z, CCS) paired with its training paradigm, which involved a cascade of transfer learning iterations. First, molecular representation is learned from a large dataset of structures with m/z labels. Next, in silico property values are used to continue training, as experimental property data is limited. Finally, the network is further refined by being trained with the experimental data. This allows the network to learn as much as possible at each stage, enabling success with progressively smaller datasets without overfitting. Once trained, the network can be used to predict chemical properties directly from structure, as well as generate candidate structures with desired chemical properties. Our approach is orders of magnitude faster than first-principles simulation for CCS property prediction. Additionally, the ability to generate novel molecules along manifolds, defined by chemical property analogues, positions DarkChem as highly useful in a number of application areas, including metabolomics and small molecule identification, drug discovery and design, chemical forensics, and beyond.

Colby, Sean M.↗

DOE OSTI2022

Augmentation of MS/MS Libraries with Spectral Interpolation for Improved Identification

Tandem mass spectrometry (MS/MS) is a primary tool for identification of small molecules and metabolites where resultant spectra are most commonly identified by matching them with spectra in MS/MS reference libraries. The high degree of variability in MS/MS spectrum acquisition techniques and parameters creates a significant challenge for building standardized reference libraries. Here we present a method to improve the usefulness of existing MS/MS libraries by augmenting available experimental spectra datasets with statistically interpolated spectra at unreported collision energies. We find that highly accurate spectral approximations can be interpolated from as few as three experimental spectra and that the interpolated spectra will be consistent with true spectra gathered from the same instrument as the experimental spectra. Supplementing existing spectral databases with interpolated spectra yields consistent improvements to identification accuracy on a range of instruments and precursor types. Applying this method yields significant improvements (~10% more spectra correctly identified) on large datasets (2,000 - 10,000 spectra), indicating this is a quick yet adept tool for improving spectral matching in situations where available reference libraries are not yet sufficient. We also find improvements of matching spectra across instrument types (between an Agilent Q-TOF and an Orbitrap Elite), at high collision energies (50 - 90 eV), and with smaller datasets available through MassBank.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Combinatorial Exploration and Mapping of Phase Transformation in a Ni–Ti–Co Thin Film Library

Combinatorial synthesis and high-throughput characterization of a Ni–Ti–Co thin film materials library are reported for exploration of reversible martensitic transformation. The library was prepared by magnetron co-sputtering, annealed in vacuum at 500 °C without atmospheric exposure, and evaluated for shape memory behavior as an indicator of transformation. Composition, structure, and transformation behavior of the 177 pads in the library were characterized using high-throughput wavelength dispersive spectroscopy (WDS), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and four-point probe temperature-dependent resistance (R(T)) measurements. A new, expanded composition space having phase transformation with low thermal hysteresis and Co > 10 at. % is found. Unsupervised machine learning methods of hierarchical clustering were employed to streamline data processing of the large XRD and XPS data sets. Through cluster analysis of XRD data, we identified and mapped the constituent structural phases. Finally, composition–structure–property maps for the ternary system are made to correlate the functional properties to the local microstructure and composition of the Ni–Ti–Co thin film library.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Development of the MPACT 69-group Library for Magnox Reactor Analysis using CASL VERA

The Consortium for Advanced Simulation of Light Water Reactors (CASL) has developed the CASL toolset, Virtual Environment for Reactor Analysis (VERA), for pressurized water reactor (PWR) analysis. Recently the CASL VERA was improved for Magnox reactor analysis, which required the development of a new cross section library and new geometrical and thermal feedback capabilities for graphite-moderated Magnoxreactors. The MPACT neutronics module of the CASL core simulator is a 3D whole core transport code, which requires a new cross section library with a different energy group structure due to the different neutronic characteristics of Magnox compared with PWR. A new 69-group structure was developed based on the MPACT 51-group structure to have more thermal energy groups and to be a subset of the SCALE 252-group structure. The ENDF/B-VII.1 MPACT 69-group library was developed for Magnox reactor analysis using the SCALE/AMPX and VERA-XSTools for which a super-homogenization method was applied, and transport cross sections were generated for graphite using a neutron leakage conservation method. Benchmark results show that new MPACT 69-group library works reasonably well for Magnox reactor analysis.

Kim, Kang Seog↗

DOE OSTI2026

Automated scanning probe microscopy of combinatorial ferroelectric libraries: Gaussian-process-guided exploration and noise-aware experiment planning

Combinatorial materials libraries provide an efficient route for mapping composition–property relationships, but their broader impact depends on rapid, quantitative, and functionally relevant characterization. Scanning Probe Microscopy (SPM), including piezoresponse force microscopy (PFM), offers significant potential for quantitative, functionally relevant combi-library readouts. Here, we implement a fully automated SPM workflow for ferroelectric combinatorial libraries and benchmark Gaussian-process-based Bayesian optimization strategies for autonomous experiment planning. The workflow integrates automated probe motion, contact optimization, imaging, and dual amplitude resonance tracking-PFM spectroscopy, and uses scalarized spectroscopic observables to guide subsequent measurements. Stage motion, probe engagement, in-contact tuning, imaging, spectroscopy, and the choice of the next measurement location all proceed without human input. We demonstrate the approach on Sm-doped BiFeO 3 and Zn x Mg 1−x O libraries. By comparing vanilla Bayesian optimization with a measured-noise variant, we show that explicit treatment of local reproducibility can improve modeling of composition-dependent response when the measured variance is physically meaningful, but can also reduce robustness when variability is dominated by outliers or topographic artifacts. Furthermore, these results establish automated SPM as a bridge between combinatorial synthesis and quantitative functional characterization.

Liu, Yu [University of Tennessee, Knoxville, TN (U↗

DOE OSTI2013

Modelica buildings library

This paper describes the Buildings library, a free open-source library that is implemented in Modelica, an equation-based object-oriented modeling language. The library supports rapid prototyping, as well as design and operation of building energy and control systems. First, we describe the scope of the library, which covers HVAC systems, multi-zone heat transfer and multi-zone airflow and contaminant transport. Next, we describe differentiability requirements and address how we implemented them. We describe the class hierarchy that allows implementing component models by extending partial implementations of base models of heat and mass exchangers, and by instantiating basic models for conservation equations and flow resistances. We also describe associated tools for pre- and post-processing, regression tests, co-simulation and real-time data exchange with building automation systems. Furthermore, the paper closes with an example of a chilled water plant, with and without water-side economizer, in which we analyzed the system-level efficiency for different control setpoints.

42 ENGINEERING↗

DOE OSTI2014

On the construction of a new stellar classification template library for the LAMOST spectral analysis pipeline

The LAMOST spectral analysis pipeline, called the 1D pipeline, aims to classify and measure the spectra observed in the LAMOST survey. Through this pipeline, the observed stellar spectra are classified into different subclasses by matching with template spectra. Consequently, the performance of the stellar classification greatly depends on the quality of the template spectra. In this paper, we construct a new LAMOST stellar spectral classification template library, which is supposed to improve the precision and credibility of the present LAMOST stellar classification. About one million spectra are selected from LAMOST Data Release One to construct the new stellar templates, and they are gathered in 233 groups by two criteria: (1) pseudo g – r colors obtained by convolving the LAMOST spectra with the Sloan Digital Sky Survey ugriz filter response curve, and (2) the stellar subclass given by the LAMOST pipeline. In each group, the template spectra are constructed using three steps. (1) Outliers are excluded using the Local Outlier Probabilities algorithm, and then the principal component analysis method is applied to the remaining spectra of each group. About 5% of the one million spectra are ruled out as outliers. (2) All remaining spectra are reconstructed using the first principal components of each group. (3) The weighted average spectrum is used as the template spectrum in each group. Using the previous 3 steps, we initially obtain 216 stellar template spectra. We visually inspect all template spectra, and 29 spectra are abandoned due to low spectral quality. Furthermore, the MK classification for the remaining 187 template spectra is manually determined by comparing with 3 template libraries. Meanwhile, 10 template spectra whose subclass is difficult to determine are abandoned. Finally, we obtain a new template library containing 183 LAMOST template spectra with 61 different MK classes by combining it with the current library.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

IRIS-BLAS: Towards a Performance Portable and Heterogeneous BLAS Library

This paper presents IRIS-BLAS, a novel heterogeneous and performance portable BLAS library. IRIS-BLAS is built on top of the IRIS runtime and multiple vendor and open-source BLAS libraries. It can transparently use all the architectures/devices available in a heterogeneous system, using the appropriate BLAS library based on the task mapping at run time. Thus, IRIS-BLAS is portable across a broad spectrum of architectures and BLAS libraries, alleviating the worry of application developers about modifying the application source code. Even though the emphasis is on portability, IRIS-BLAS provides competitive or even better performance than other state-of-the-art references. Moreover, IRIS-BLAS offers new features such as efficiently using extremely heterogeneous systems composed of multiple GPUs from different hardware vendors.

Miniskar, Narasinga Rao↗

DOE OSTI2015

SU-E-J-93: Development of Pre-Contoured Human Model Library in DICOM-RT Format for the Epidemiological Study of the Radiotherapy Patients

Purpose: Prior to 3D conformal radiation therapy planning, patient anatomy information was mostly limited to 2D beams-eye-view from the conventional simulator. To analyze the outcomes of such treatments for radiation late effects, 3D computational human models are often used in commercial treatment planning systems (TPSs). However, several underlying difficulties such as time-consuming manual delineation procedures of a large number of structures in the model have always limited its applications. Primary objective of this work was to develop a human model library for the epidemiological study by converting 3D-surface model organs to DICOM-RT format (DICOM-RT structure) using an in-house built software. We converted the ICRP reference human models to DICOM-RT models, which can be readily adopted for various dose calculations. Methods: MATLAB based code were utilized to convert the contour drawings extracted in text-format from the 3D graphic-tool, Rhinoceros into DICOM-RT structure format for 50 different organs of each model using a 16GB dual-core processor. The conversion periods were measured for each DICOM-RT models, and the reconstructed structure volumes were validated against the original 3D-surface models in the TPS. Ten reference hybrid whole-body models (8-pediatric and 2-adults) were automatically processed to create DICOM-RT computational human model library. Results: Mean contour conversion period was found to be 580 (N=2) and 394.5 (N=8) seconds for 50 organs in the adult and pediatric models respectively. A good agreement for large organs (NRMSD <1.0%) and small organs (NRMSD <7.7%) was also observed between the original volumes and corresponding DICOM-RT structure volumes of the organs. Conclusion: The ICRP reference human models were converted into DICOM-RT format to support the epidemiological study using a large cohort of conventional radiotherapy patients. Due to its DICOM-compatibility, the library may be implemented to many other different applications. We also expect to develop the library by including additional models in future.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Building and exploring libraries of atomic defects in graphene: Scanning transmission electron and scanning tunneling microscopy study

The presence and configurations of defects are primary components determining materials functionality. Their population and distribution are often nonergodic and dependent on synthesis history, and therefore rarely amenable to direct theoretical prediction. Here, dynamic electron beam–induced transformations in Si deposited on a graphene monolayer are used to create libraries of possible Si and carbon vacancy defects. Deep learning networks are developed for automated image analysis and recognition of the defects, creating a library of (meta) stable defect configurations. Density functional theory is used to estimate atomically resolved scanning tunneling microscopy (STM) signatures of the classified defects from the created library, allowing identification of several defect types across imaging platforms. This approach allows automatic creation of defect libraries in solids, exploring the metastable configurations always present in real materials, and correlative studies with other atomically resolved techniques, providing comprehensive insight into defect functionalities.

36 MATERIALS SCIENCE↗

DOE OSTI2019

MPI Stages : A Serializable MPI Library

MPI library that supports serializing (and check-pointing) its MPI Stages is a communication library that allows nodes and programs in a computer cluster to communicate via the Message-Passing Interface (MPI). The internal data objects of the library are serializable, i.e., the user can convert the MPI state or objects, such as groups or communicators, into byte streams and save them into a checkpoint file. Later users can load the checkpoint file and de-serialize previous objects into the library. Serialization/de-serialization is useful in MPI applications to recover from node failures.

Ruefenacht, Martin↗

DOE OSTI2020

Certification Validation Libraries

“The code “Certificate Validation Libraries” provides the ability to validate x509 certificates in python using a simple library. These libraries validate certificates in 3 ways: 1) validation that certificate has not expired. 2) validation that certificate has not been revoked and 3) validation of certificate's digital signature. The benefits of this code is that one can properly validate x509 certificates, thus strengthening the security of systems using these libraries.”

Maerz, StefanA↗

DOE OSTI2020

Java Software Extensibility Library

The Java Software Extensibility Library provides tools that help Java software developers produce flexible and extensible Java applications. The major components include a Plugin Library and a Polymorphic Map data structure. The Plugin Library provides developers with a Plugin Registry and a standard pattern for designing, versioning, registering, retrieving, and annotating plugins. It also enables advanced capabilities such as loading plugins at runtime, and creating/loading encrypted plugin packages. The Polymorphic Map data structure facilitates the storage and retrieval of objects of varying types within a single data structure; while maintaining type safety. The library also provides a standard design pattern for producing application-specific "Domain Maps" and "Closed Domain Maps".SAND2020-3816 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Fleschute, Christopher↗

DOE OSTI2021

NRWAL (NLR formerly known as NREL Wind Analysis Library) [SWR-21-26]

NRWAL (NLR (National Laboratory of the Rockies) formerly known as NREL (National Renewable Energy Laboratory) Wind Analysis Library: A library of offshore wind cost equations (plus new energy technologies like marine hydro!) Easy equation manipulation without editing source code Full continental-scale integration with the NREL Renewable Energy Potential Model (reV) https://nrel.github.io/reV/ Ready-to-use configs for basic users Dynamic python tools for intuitive equation handling One seriously badass sea unicorn To get started with NRWAL, check out the NRWAL Config documentation or the NRWAL example notebook. You can also launch the notebook in an interactive jupyter shell right in your browser without any downloads or software using binder. Ready to build a model with NRWAL but don't want to contribute to the library? No problem! Check out the example getting started project here. Here is the important stuff: The NRWAL Equation Library. Default NRWAL Configs

Nunemaker, Jacob↗

DOE OSTI2026

Scientific Core Library Stack (SCLS) v2026

SCLS (Scientific Core Library Stack) is an opinionated build and packaging system for scientific computing libraries developed at Lawrence Berkeley National Laboratory. It produces a coherent, reproducible stack of numerical libraries — including BLAS/LAPACK, MPI, sparse direct and iterative solvers, graph partitioners, and parallel I/O libraries (e.g., PETSc, SLEPc, HDF5, NetCDF, MUMPS, OpenBLAS) — that work together without manual repair by downstream scientific software. From a single recipe-and-flavor model, SCLS produces native RPM packages for RHEL-family Linux, DEB packages for Debian/Ubuntu, direct Unix-style prefix installs for HPC and locked-down environments, and native macOS builds. Multiple build "flavors" (e.g., GCC+OpenBLAS, GCC+MKL, Intel+MKL, debug) coexist in distinct prefixes on the same host. Compared to general-purpose meta-build frameworks, SCLS is deliberately curated rather than infinitely configurable. It enforces deterministic, audit-friendly behavior: explicit build dependencies, no silent feature autodetection, a clear open-source license policy, and rpath-based runtime linkage so installs integrate cleanly with standard package-manager workflows.

Messe, Christian [Lawrence Berkeley National Labor↗