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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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DOE OSTI2020

DOE Express Quantum Computing Application Teams (QCAT FY20 Report)

The QCOR project consists of 4 main research tasks: 1) scientific applications and algorithm development for machine learning (ML) and quantum theories of condensed matter systems and lattice gauge theories; 2) high-level quantum-classical (HLQC) language and domain specific language (DSL) development; 3) compiler and interfaces development for the HLQC language; and 4) hardware-level control, optimization, and algorithms libraries. In the succeeding sections we report on progress towards our research tasks during the 2020 calendar year.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Dakota A Multilevel Parallel Object-Oriented Framework for Design Optimization Parameter Estimation Uncertainty Quantification and Sensitivity Analysis (V.6.14) (Theory Manual)

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quantification, and optimization under uncertainty that provide the foundation for many of Dakota's iterative analysis capabilities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Dakota A Multilevel Parallel Object-Oriented Framework for Design Optimization Parameter Estimation Uncertainty Quantification and Sensitivity Analysis (V.6.14) (User's Manual)

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a users manual for the Dakota software and provides capability overviews and procedures for software execution, as well as a variety of example studies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Version 6.13 Theory Manual

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quantification, and optimization under uncertainty that provide the foundation for many of Dakota's iterative analysis capabilities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Version 6.13 User's Manual

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a user’s manual for the Dakota software and provides capability overviews and procedures for software execution, as well as a variety of example studies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Version 6.15 User's Manual

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Theory Manual (V.6.15)

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quantification, and optimization under uncertainty that provide the foundation for many of Dakota's iterative analysis capabilities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis (V.6.16 User's Manual)

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a user's manual for the Dakota software and provides capability overviews and procedures for software execution, as well as a variety of example studies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Version 6.16 Theory Manual

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quantification, and optimization under uncertainty that provide the foundation for many of Dakota’s iterative analysis capabilities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

CRiSPPy: An advanced hydropower scheduling tool for the Colorado River Storage Project

The Western Area Power Administration (WAPA) plays a vital role in delivering reliable and cost-effective hydroelectric power to millions of customers across the western United States. The Colorado River Storage Project (CRSP) carries out WAPA’s mission in Arizona, Utah, Colorado, New Mexico, Nevada, Wyoming and Texas. Achieving this mission requires effective management of the Colorado River system, and depends on the use of advanced analytical tools and modeling methodologies. For many years, CRSP has relied on the Generation and Transmission Maximization Superlite (GTMax SL) model for its mid-term and long-term hydroscheduling needs. However, the evolving energy market, power system operations, environmental rules, and hydrology conditions, coupled with advancements in computational capabilities, have necessitated the development of a more modern and robust solution. This report introduces the Colorado River Storage Project Python-based (CRiSPPy) model, a new, advanced hydropower scheduling tool developed to address CRSP ever-evolving challenges. CRiSPPy represents a significant leap forward in our ability to model and optimize the operation of the Colorado River system. It incorporates state-of-the-art optimization algorithms, enhanced data management capabilities, and an advanced graphical user interface, providing WAPA CRSP personnel with unprecedented insights and decision-making support. This document details the development, capabilities, and implementation of CRiSPPy. It is intended to serve as a comprehensive resource for WAPA staff, stakeholders, and anyone interested in the future of hydropower scheduling in the Colorado River Basin. We are confident that CRiSPPy will enhance WAPA's mission while adapting to the challenges of a dynamic and increasingly complex environment. The version of CRiSPPy described in this report is the version 2.3. New versions of CRiSPPy will be developed as the tool keeps evolving to address CRSP challenges.

13 HYDRO ENERGY↗
DOE OSTI2025

A Data Science and Machine Learning Platform Supporting Large Particle Accelerator Control and Diagnostics Applications Final Report: SBIR Initial Phase II DE-SC0022583

The Machine Learning Data Platform (MLDP) is a product providing full-stack support for data science, Machine Learning, and Artificial Intelligence (ML/AI) applications at particle accelerator and large experimental physics facilities. It supports ML/AI applications from front-end, high-speed acquisition of heterogeneous, time-series data, through data archiving and management, to back-end analysis. The MLDP embodies a “data-science ready” platform for data analysis and ML/AI applications in diagnosis, modelling, control, and optimization of these facilities. It provides data scientists and applications a consistent, datacentric interface to archive data standardizing implementation and deployment of ML/AI algorithms to different operations configurations within the same facility, or between facilities. Being an open-source, public-domain project, the MLDP is intended for broadest possible impact by increasing accessibility and minimizing the required expertise for installation and operation. The MLDP can also be deployed at user facilities for experimental data collection, archiving, and analysis. It is capable of acquisition and archiving of heterogeneous data from experimental equipment (e.g., images, arrays, structures, etc.) along with system hardware configurations (e.g., scalars, tables), control system process variables, and any metadata required for provenance. Thus, the MLDP can manage experimental data through its entire lifecycle, from acquisition and archiving, through analysis and investigation, to release and final publication.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Stability Analysis of Coupled Advection-Diffusion Models with Bulk Interface Condition

Numerical stability is of critical importance in general circulation models because it affects the design of algorithms, time to solution, and computational costs associated with the simulations, which are very expensive in practice. In this paper we extend the stability analysis for ocean-atmosphere coupling proposed in [Zhang et al., J. Sci. Comput. 84, 44(2020)] to a more realistic model that includes horizontal advection. We analyze various time-stepping strategies. We find that advection has a stabilizing effect in scenarios common to climate models when bulk interface condition and explicit flux coupling are used. We also show that our method can be used to study the stability impact of advection for other interface conditions such as Dirichlet-Neumann conditions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A Geometric Volume of Fluid-Based Multiphase Flow Solver Extension to the Reacting Flow Solver, PeleLM

A new algorithm is presented to simulate multiphase flows with surface tension in a pathway for spray combustion simulation. The algorithm combines capabilities from two open-source packages, including the interface reconstruction library (IRL), a library of computational geometry routines to enable the volume of fluid (VOF) method, and PeleLM, a solver for the reacting Navier-Stokes equations. Additionally, surface tension is implemented using the continuum surface force (CSF) model with an improved height function technique in the volume fraction field. Spurious errors in volume fraction arising from our combined strategy are corrected through a topology-based method that improves both numerical stability and accuracy. Multiple validation simulations are conducted, including (i) translations and rotations of Zalesak's disk, (ii) a stationary circular droplet with surface tension, (iii) an oscillating elliptical droplet, and (iv) three-dimensional deformation of a spherical droplet. Results indicate that the combined scheme retains the favorable properties of each of the component algorithms.

42 ENGINEERING↗
DOE OSTI2021

A FETI approach to domain decomposition for meshfree discretizations of nonlocal problems

We propose a domain decomposition method for the efficient simulation of nonlocal problems. Our approach is based on a multi-domain formulation of a nonlocal diffusion problem where the subdomains share “nonlocal” interfaces of the size of the nonlocal horizon. This system of nonlocal equations is first rewritten in terms of minimization of a nonlocal energy, then discretized with a meshfree approximation and finally solved via a Lagrange multiplier approach in a way that resembles the finite element tearing and interconnect method. Specifically, we propose a distributed projected gradient algorithm for the solution of the Lagrange multiplier system, whose unknowns determine the nonlocal interface conditions between subdomains. Several two-dimensional numerical tests on problems as large as 191 million unknowns illustrate the strong and the weak scalability of our algorithm, which outperforms the standard approach to the distributed numerical solution of the problem. Finally, this work is the first rigorous numerical study in a two-dimensional multi-domain setting for nonlocal operators with finite horizon and, as such, it is a fundamental step towards increasing the use of nonlocal models in large scale simulations.

42 ENGINEERING↗
DOE OSTI2023

Introduction to ALERT: A User-Interface Tool for Resilient Optimization

As the cyber-physical systems grow in complexity, there is a need for proactive resilience strategies that involve online, adaptive control actions to best prepare for any impending adversarial events. In this technical effort, supported by RD2C LDRD initiative, the project team designed and demonstrated online strategies – referred to as ALERT controls – for proactive and adaptive tuning of existing optimal controls in a microgrid, with quantifiably assured margins of resilience to various cyber-physical adversarial events. This ALERT functionality is made available to the end-users, e.g., the system operators, via an interactive user-interface. The end-users will not only be able to use the interface to visualize the system’s operation under various cyber-physical adversarial scenarios, but also evaluate the amount of tolerance the system has against selected adversarial perturbations of interest (e.g., malfunctioning sensors, suspected attacked measurements) via the adversarial plots. In this technical report, we briefly outline the algorithmic modules of the developed ALERT control technology, and introduce the user-interface tool that allows end-users (e.g., microgrid operators) to enter their system description, specify various operational and resilience requirements, and evaluate the impact of the control decisions via illustrative plots.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction

Computational approaches for predicting protein-protein interfaces are extremely useful for understanding and modelling the quaternary structure of protein assemblies. In particular, partner-specific binding site prediction methods allow delineating the specific residues that compose the interface of protein complexes. In recent years, new machine learning and other algorithmic approaches have been proposed to solve this problem. However, little effort has been made in finding better training datasets to improve the performance of these methods. With the aim of vindicating the importance of the training set compilation procedure, in this work we present BIPSPI+, a new version of our original server trained on carefully curated datasets that outperforms our original predictor. We show how prediction performance can be improved by selecting specific datasets that better describe particular types of protein interactions and interfaces (e.g. homo/hetero). In addition, our upgraded web server offers a new set of functionalities such as the sequence-structure prediction mode, hetero- or homo-complex specialization and the guided docking tool that allows to compute 3D quaternary structure poses using the predicted interfaces. BIPSPI+ is freely available at https://bipspi.cnb.csic.es.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

DyG-DPCD: A Distributed Parallel Community Detection Algorithm for Large-Scale Dynamic Graphs

Dynamic (Temporal) graphs capture the valuable evolution of real-world systems, from the continuously evolving patterns of social interactions and genetic pathways to the dynamic fluctuations of economic forces. Detecting communities for such evolving networks poses unique challenges. Detecting and analyzing the evolution of communities within dynamic graphs unlocks valuable insights into the underlying structural and temporal patterns of real-world systems. However, the sheer volume of modern graph data and the inherent complexity of the temporal dimension pose significant challenges to scalable community detection algorithms. Addressing this gap, our work explores the limited landscape of scalable distributed-memory parallel methods specifically designed for dynamic network community detection. We propose a novel parallel algorithm, DyG-DPCD (Dynamic Graph Distributed Parallel Community Detection), to detect communities in dynamic networks using the Message Passing Interface (MPI) framework. We present a vertex-centric approach, allowing us to detect communities through local optimization. Furthermore, we enhance our baseline algorithm by incorporating three heuristics, which improve the algorithm’s performance significantly while maintaining the quality of the solutions. We demonstrate the efficiency of our algorithm by experimenting on several real-world large-scale networks with hundreds of millions of edges spanning diverse domains. Notably, DyG-DPCD achieves speedups between 25× and 30× for large networks that we experimented on using NERSC compute nodes. In conclusion, our algorithm outperforms the STINGER parallel re-agglomeration algorithm by 30×.

97 MATHEMATICS AND COMPUTING↗