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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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

On-lattice kinetic Monte Carlo approaches for modeling molecular anisotropy in resveratrol crystallization

Stilbenes are a class of organic compounds with broad-ranging pharmaceutical and agricultural applications, which are typically isolated and purified through recrystallization. We are motivated by reducing experimental waste and optimizing yield via developing predictive simulations for processing-dependent crystal morphologies. Using resveratrol as a model stilbene system, we have developed an approach for simulating crystallization with molecular resolution using on-lattice kinetic Monte Carlo. In this work, we highlight modifications to the Stochastic Parallel PARticle Kinetic Simulator (SPPARKS) software package, which were essential to this application. Key enhancements include the incorporation of non-orthogonal cell shapes and monomer anisotropy approximations using bound hard spheres. This new SPPARKS application has been applied to resveratrol with attachment energy libraries obtained from density functional theory, resulting in excellent agreement with experimental morphology prediction.

crystallization↗
DOE OSTI2022

CoLoRe: fast cosmological realisations over large volumes with multiple tracers

We present CoLoRe, a public software package to efficiently generate synthetic realisations of multiple cosmological surveys.CoLoRe can simulate the growth of structure with different degrees of accuracy, with the current implementation supporting lognormal fields, first, and second order Lagrangian perturbation theory.CoLoRe simulates the density field on an all-sky light-cone up to a desired maximum redshift, and uses it to generate multiple 2D and 3D maps: galaxy positions and velocities, lensing (shear, magnification, convergence), integrated Sachs-Wolfe effect, line intensity mapping, and line of sight skewers for simulations of the Lyman-α forest. We test the accuracy of the simulated maps against analytical theoretical predictions, and showcase its performance with a multi-survey simulation including DESI galaxies and quasars, LSST galaxies and lensing, and SKA intensity mapping and radio galaxies. We expect CoLoRe to be particularly useful in studies aiming to characterise the impact of systematics in multi-experiment analyses, quantify the covariance between different datasets, and test cross-correlation pipelines for near-future surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Color Transformations of Photometric Measurements of Galaxies in Optical and Near-infrared Wide-field Imaging Surveys*

Abstract Over the past 2 decades, wide-field photometric surveys in optical and infrared domains reached a nearly all-sky coverage thanks to numerous observational facilities operating in both hemispheres. However, subtle differences among exact realizations of Johnson and SDSS photometric systems require one to convert photometric measurements into the same system prior to analysis of composite data sets originating from multiple surveys. It turns out that the published photometric transformations lead to substantial biases when applied to integrated photometry of galaxies from the corresponding catalogs. Here we present photometric transformations based on piece-wise linear approximations of integrated photometry of galaxies in the optical surveys SDSS, DECaLS, BASS, MzLS, DES, DELVE, KiDS, VST ATLAS, and the near-infrared surveys UKIDSS, UHS, VHS, and VIKING. We validate our transformations by constructing k -corrected color–magnitude diagrams of non-active galaxies and measuring the position and tightness of the “red sequence.” We also provide transformations for aperture magnitudes and show how they are affected by the image quality difference among the surveys. We present the implementation of the derived transformations in python and idl and also a web-based color transformation calculator for galaxies. By comparing DECaLS and DES, we identified systematic issues in DECaLS photometry for extended galaxies, which we attribute to the photometric software package used by DECaLS. As an application of our method, we compiled two multi-wavelength photometric catalogs for over 200,000 low- and intermediate-redshift galaxies originating from CfA FAST and Hectospec spectral archives.

Astronomy & Astrophysics↗
DOE OSTI2021

Neoclassical toroidal viscosity torque prediction via deep learning

GPECnet is a densely connected neural network that has been trained on GPEC data, to predict the plasma stability, neoclassical toroidal viscosity (NTV) torque, and optimized 3D coil current distributions for desired NTV torque profiles. Using NTV torque, driven by non-axisymmetric field perturbations in a tokamak, can be vital in optimizing pedestal performance by controlling the rotation profile in both the core, to ensure tearing stability, and the edge, to avoid edge localized modes (ELMs). The generalized perturbed equilibrium code (GPEC) software package can be used to calculate the plasma stability to 3D perturbations and the NTV torque profile generated by applied 3D magnetic fields. These calculations, however, involve complex integrations over space and energy distributions, which takes time to compute. Initially, GPECnet has been trained solely on data representative of the quiescent H-mode (QH) scenario, in which neutral beams are often balanced and toroidal rotation is low across the plasma profile. Lastly, this work provides the foundation for active control of the rotation shear using a combination of beams and 3D fields for robust and high performance QH mode operation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Next generation experimental data access at NSLS-II

The NSLS-II network and computing infrastructure has been significantly updated recently. The re-IP process in 2020-2021 enabled the NSLS-II network to be routable to the rest of the BNL campus. Then, standardization of the operating systems and deployment procedures helped to deliver a consistent environment to workstations and servers used by all NSLS-II beamlines. In particular, the RedHat Enterprise Linux 8 was deployed to 700+ machines using the RedHat Satellite infrastructure management product, and all critical services (IOCs, databases, etc.) were migrated to the new OS. NFS users’ home directories are consistent across all of the machines, which eliminates the need for the individual configuration of the user environment on each host. The standard suite of software packages is available to the beamline staff and users, which includes the system packages (deployed via RPM) as well as the conda environments for data acquisition and analysis. Security measures were implemented to comply with the industry standards, which include multi-factor authentication (using Duo), secure screen lock for the beamline machines, and advanced access control to the experimental data that is stored in shared central storage available on all hosts. These major enhancements facilitated sharing the experimental data (currently for a number of selected beamlines, with a plan to extend it to the whole facility in the nearest future) with the users via an externally facing JupyterHub instance. The beamlines keep using the Bluesky data acquisition framework to orchestrate their experiments, and the new infrastructure enabled them to use a next-generation data access library called tiled.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Combining diagnostics, modeling, and control systems for automated alignment of the TES beamline

X-ray beamlines are essential components of all synchrotron light sources. Practical operations involve frequent variation in beamline component positions and orientation, particularly when photon beam parameters shift due to experimental needs, or due to variations in the incoming photon beam. The alignment process can be time consuming and takes away from valuable beam time for experimental data collection. We describe progress in the automation of certain alignment tasks on the tender-energy X-ray spectroscopy (TES) beamline at the National Synchrotron Light Source II (NSLS-II). The beamline is controlled using the BlueSky software in which high level experimental plans guide the beamline components during an experiment. Numerous software packages exist for beamline modeling, and they may be tied to the beamline control system using a package we are continuing to develop called Sirepo-Bluesky. The photon beam distribution may be measured with fluorescent screens, and a relation between beam and machine state can be found by varying the mirror and aperture settings over a multi-dimensional range. We describe the results of such parameter varying measurements and how we are combining Sirepo-Bluesky with machine learning methods and reduced models to automate mirror alignment on the TES beamline.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Developments in SRW Code and Sirepo Framework Supporting Simulation of Time-Dependent Coherent X-ray Scattering Experiments

Physical optics simulations for beamlines and experiments are essential for the effective use of synchrotron light source facilities such as NSLS-II at BNL. The SRW software package supports such source-to-detector simulations for coherent X-ray scattering and imaging experiments through its Python interface and Sirepo browser-based graphical user interface. This allows one to define custom sample models, assess the feasibility of an experiment, and estimate most appropriate beamline settings before using valuable beamtime. We discuss the recent use of general-purpose GPU resources and coherent mode decomposition algorithms in SRW to accelerate physical optics simulations with partially coherent X-rays. To illustrate these new capabilities, we describe simulations of typical time series of partially coherent scattering images used in X-ray Photon Correlation Spectroscopy (XPCS) experiments; aiming to characterize the nanoscale dynamics of a disordered sample, representing a solution of nanoparticles undergoing Brownian diffusion.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Nanosecond machine learning regression with deep boosted decision trees in FPGA for high energy physics

We present a novel application of the machine learning / artificial intelligence method called boosted decision trees to estimate physical quantities on field programmable gate arrays (FPGA). The software package fwXmachina features a new architecture called parallel decision paths that allows for deep decision trees with arbitrary number of input variables. It also features a new optimization scheme to use different numbers of bits for each input variable, which produces optimal physics results and ultraefficient FPGA resource utilization. Problems in high energy physics of proton collisions at the Large Hadron Collider (LHC) are considered. Estimation of missing transverse momentum (E T miss ) at the first level trigger system at the High Luminosity LHC (HL-LHC) experiments, with a simplified detector modeled by Delphes, is used to benchmark and characterize the firmware performance. The firmware implementation with a maximum depth of up to 10 using eight input variables of 16-bit precision gives a latency value of $\mathcal{O}$(10) ns, independent of the clock speed, and $\mathcal{O}$(0.1)% of the available FPGA resources without using digital signal processors.

Instruments & Instrumentation↗
DOE OSTI2025

Tools for unbinned unfolding

Machine learning has enabled differential cross section measurements that are not discretized. Going beyond the traditional histogram-based paradigm, these unbinned unfolding methods are rapidly being integrated into experimental workflows. Here, in order to enable widespread adaptation and standardization, we develop methods, benchmarks, and software for unbinned unfolding. For methodology, we demonstrate the utility of boosted decision trees for unfolding with a relatively small number of high-level features. This complements state-of-the-art deep learning models capable of unfolding the full phase space. To benchmark unbinned unfolding methods, we develop an extension of existing dataset to include acceptance effects, a necessary challenge for real measurements. Additionally, we directly compare binned and unbinned methods using discretized inputs for the latter in order to control for the binning itself. Lastly, we have assembled two software packages for the OmniFold unbinned unfolding method that should serve as the starting point for any future analyses using this technique. One package is based on the widely-used RooUnfold framework and the other is a standalone package available through the Python Package Index (PyPI).

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Probing quantum processor performance with pyGSTi

PyGSTi is a Python software package for assessing and characterizing the performance of quantum computing processors. It can be used as a standalone application, or as a library, to perform a wide variety of quantum characterization, verification, and validation (QCVV) protocols on as-built quantum processors. In this work, we outline pyGSTi's structure, and what it can do, using multiple examples. We cover its main characterization protocols with end-to-end implementations. These include gate set tomography, randomized benchmarking on one or many qubits, and several specialized techniques. We also discuss and demonstrate how power users can customize pyGSTi and leverage its components to create specialized QCVV protocols and solve user-specific problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Phoebe: a high-performance framework for solving phonon and electron Boltzmann transport equations

Understanding the electrical and thermal transport properties of materials is critical to the design of electronics, sensors, and energy conversion devices. Computational modeling can accurately predict material properties but, in order to be reliable, requires accurate descriptions of electron and phonon states and their interactions. While first-principles methods are capable of describing the energy spectrum of each carrier, using them to compute transport properties is still a formidable task, both computationally demanding and memory intensive, requiring integration of fine microscopic scattering details for estimation of macroscopic transport properties. To address this challenge, we present Phoebe—a newly developed software package that includes the effects of electron–phonon, phonon–phonon, boundary, and isotope scattering in computations of electrical and thermal transport properties of materials with a variety of available methods and approximations. This open source C++ code combines MPI-OpenMP hybrid parallelization with GPU acceleration and distributed memory structures to manage computational cost, allowing Phoebe to effectively take advantage of contemporary computing infrastructures. We demonstrate that Phoebe accurately and efficiently predicts a wide range of transport properties, opening avenues for accelerated computational analysis of complex crystals.

36 MATERIALS SCIENCE↗
DOE OSTI2024

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗
DOE OSTI2021

Improving deep learning-based protein distance prediction in CASP14

Abstract Motivation Accurate prediction of residue–residue distances is important for protein structure prediction. We developed several protein distance predictors based on a deep learning distance prediction method and blindly tested them in the 14th Critical Assessment of Protein Structure Prediction (CASP14). The prediction method uses deep residual neural networks with the channel-wise attention mechanism to classify the distance between every two residues into multiple distance intervals. The input features for the deep learning method include co-evolutionary features as well as other sequence-based features derived from multiple sequence alignments (MSAs). Three alignment methods are used with multiple protein sequence/profile databases to generate MSAs for input feature generation. Based on different configurations and training strategies of the deep learning method, five MULTICOM distance predictors were created to participate in the CASP14 experiment. Results Benchmarked on 37 hard CASP14 domains, the best performing MULTICOM predictor is ranked 5th out of 30 automated CASP14 distance prediction servers in terms of precision of top L/5 long-range contact predictions [i.e. classifying distances between two residues into two categories: in contact (<8 Angstrom) and not in contact otherwise] and performs better than the best CASP13 distance prediction method. The best performing MULTICOM predictor is also ranked 6th among automated server predictors in classifying inter-residue distances into 10 distance intervals defined by CASP14 according to the precision of distance classification. The results show that the quality and depth of MSAs depend on alignment methods and sequence databases and have a significant impact on the accuracy of distance prediction. Using larger training datasets and multiple complementary features improves prediction accuracy. However, the number of effective sequences in MSAs is only a weak indicator of the quality of MSAs and the accuracy of predicted distance maps. In contrast, there is a strong correlation between the accuracy of contact/distance predictions and the average probability of the predicted contacts, which can therefore be more effectively used to estimate the confidence of distance predictions and select predicted distance maps. Availability and implementation The software package, source code and data of DeepDist2 are freely available at https://github.com/multicom-toolbox/deepdist and https://zenodo.org/record/4712084#.YIIM13VKhQM. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

GENTANGLE: integrated computational design of gene entanglements

The design of two overlapping genes in a microbial genome is an emerging technique for adding more reliable control mechanisms in engineered organisms for increased stability. The design of functional overlapping gene pairs is a challenging procedure, and computational design tools are used to improve the efficiency to deploy successful designs in genetically engineered systems. GENTANGLE (Gene Tuples ArraNGed in overLapping Elements) is a high-performance containerized pipeline for the computational design of two overlapping genes translated in different reading frames of the genome. This new software package can be used to design and test gene entanglements for microbial engineering projects using arbitrary sets of user-specified gene pairs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies

Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking and dependency management. To manage these processes, a diverse set of tools is required, from command-line utilities to powerful ontology-engineering environmentsr. Particularly in the biomedical domain, which has developed a set of highly diverse yet inter-dependent ontologies, standardizing release practices and metadata and establishing shared quality standards are crucial to enable interoperability. The Ontology Development Kit (ODK) provides a set of standardized, customizable and automatically executable workflows, and packages all required tooling in a single Docker image. In this paper, we provide an overview of how the ODK works, show how it is used in practice and describe how we envision it driving standardization efforts in our community.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2021

Analysis of Early Science observations with the CHaracterising ExOPlanets Satellite ( CHEOPS ) using pycheops

ABSTRACT CHEOPS (CHaracterising ExOPlanet Satellite) is an ESA S-class mission that observes bright stars at high cadence from low-Earth orbit. The main aim of the mission is to characterize exoplanets that transit nearby stars using ultrahigh precision photometry. Here, we report the analysis of transits observed by CHEOPS during its Early Science observing programme for four well-known exoplanets: GJ 436 b, HD 106315 b, HD 97658 b, and GJ 1132 b. The analysis is done using pycheops, an open-source software package we have developed to easily and efficiently analyse CHEOPS light-curve data using state-of-the-art techniques that are fully described herein. We show that the precision of the transit parameters measured using CHEOPS is comparable to that from larger space telescopes such as Spitzer Space Telescope and Kepler. We use the updated planet parameters from our analysis to derive new constraints on the internal structure of these four exoplanets.

Maxted, P. F. L. (ORCID:0000000337941317)↗
DOE OSTI2023

Empirically Driven multiwavelength K-c orrections at low redshift

K -corrections – a necessary ingredient for converting between flux in observed bands to flux in rest-frame bands – are critical for comparing galaxies at differing redshifts. These corrections often rely on fits to empirical or theoretical spectral energy distribution (SED) templates of galaxies. However, templates can only produce reliable K-corrections in regimes where SED models are robust. For instance, the templates utilized in some popular software packages are not well-constrained in some bands (e.g. WISE W4 in KCORRECT ), which results in ill-behaved K -corrections. We address this shortcoming by developing an empirically driven approach to K -corrections that limits the dependence on SED templates. We perform a polynomial fit for the K -correction as a function of a galaxy’s rest-frame colour determined in a pair of well-constrained bands (e.g. 0 (g − r)) and redshift, exploiting the fact that galaxy SEDs can be approximated as a one-parameter family at low redshift. For bands well-constrained by SED templates, our empirically driven K -corrections yield results comparable to the SED fitting methods used by KCORRECT and the GSWLC-M2 catalogue (the updated medium-deep GALEX–SDSS–WISE Legacy Catalogue). However, our method dramatically outperforms Kcorrect derived K -corrections for WISE W4 . Our method is also robust to incorrect template assumptions outside of the optical bands and enforces that the K -correction must be zero at z = 0. Our K -corrected photometry and code are publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗