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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 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Preparing angular momentum eigenstates using engineered quantum walks

Coupled angular-momentum eigenstates are widely used in atomic and nuclear physics calculations and are building blocks for spin networks and the Schur transform. To combine two angular momenta J 1 and J 2 , forming eigenstates of their total angular momentum J=J 1 +J 2 , we develop a quantum-walk scheme that does not require inputting O(j 3 ) nonzero Clebsch–Gordan (CG) coefficients classically. In fact, our scheme may be regarded as a unitary method for computing CG coefficients on quantum computers with a typical complexity of O⁡(j) and a worst-case complexity of O⁡(j 3 ). Equivalently, our scheme provides decompositions of the dense CG unitary into sparser unitary operations. Our scheme prepares angular-momentum eigenstates using a sequence of Hamiltonians to move an initial state deterministically to desired final states, which are usually highly entangled states in the computational basis. In contrast with usual quantum walks, whose Hamiltonians are prescribed, we engineer the Hamiltonians in su⁡(2)×su⁡(2), which are inspired by, but different from, Hamiltonians that govern magnetic resonances and dipole interactions. To achieve a deterministic preparation of both ket and bra states, we use projection and destructive interference to double pinch the quantum walks, such that each step is a unit-probability population transfer within a two-level system. We test our state preparation scheme on classical computers, reproducing tables of CG coefficients. Finally, we also implement small test problems on current quantum hardware.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Mathematical foundations of the GraphBLAS

The GraphBLAS standard (GraphBlas.org) is being developed to bring the potential of matrix-based graph algorithms to the broadest possible audience. Mathematically, the GraphBLAS defines a core set of matrix-based graph operations that can be used to implement a wide class of graph algorithms in a wide range of programming environments. This study provides an introduction to the mathematics of the GraphBLAS. Graphs represent connections between vertices with edges. Matrices can represent a wide range of graphs using adjacency matrices or incidence matrices. Adjacency matrices are often easier to analyze while incidence matrices are often better for representing data. Fortunately, the two are easily connected by matrix multiplication. A key feature of matrix mathematics is that a very small number of matrix operations can be used to manipulate a very wide range of graphs. This composability of a small number of operations is the foundation of the GraphBLAS. A standard such as the GraphBLAS can only be effective if it has low performance overhead. Finally, performance measurements of prototype GraphBLAS implementations indicate that the overhead is low.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection

Background: In many applications, a family of nucleotide or protein sequences classified into several subfamilies has to be modeled. Profile Hidden Markov Models (pHMMs) are widely used for this task, modeling each subfamily separately by one pHMM. However, a major drawback of this approach is the difficulty of dealing with subfamilies composed of very few sequences. One of the most crucial bioinformatical tasks affected by the problem of small-size subfamilies is the subtyping of human immunodeficiency virus type 1 (HIV-1) sequences, i.e., HIV-1 subtypes for which only a small number of sequences is known. Results: To deal with small samples for particular subfamilies of HIV-1, we introduce a novel model-based information sharing protocol. It estimates the emission probabilities of the pHMM modeling a particular subfamily not only based on the nucleotide frequencies of the respective subfamily but also incorporating the nucleotide frequencies of all available subfamilies. To this end, the underlying probabilistic model mimics the pattern of commonality and variation between the subtypes with regards to the biological characteristics of HI viruses. In order to implement the proposed protocol, we make use of an existing HMM architecture and its associated inference engine. Conclusions: We apply the modified algorithm to classify HIV-1 sequence data in the form of partial HIV-1 sequences and semi-artificial recombinants. Thereby, we demonstrate that the performance of pHMMs can be significantly improved by the proposed technique. Moreover, we show that our algorithm performs significantly better than Simplot and Bootscanning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Mining locus tags in PubMed Central to improve microbial gene annotation

Background: The scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. We propose to utilize the Open Access (OA) subset of PubMed Central (PMC) as a gene annotation database and have developed an R package called pmcXML to automatically mine and extract locus tags from full text, tables and supplements. Results: We mined locus tags from 1835 OA publications in ten microbial genomes and extracted tags mentioned in 30,891 sentences in main text and 20,489 rows in tables. We identified locus tag pairs marking the start and end of a region such as an operon or genomic island and expanded these ranges to add another 13,043 tags. We also searched for locus tags in supplementary tables and publications outside the OA subset in Burkholderia pseudomallei K96243 for comparison. There were 168 publications containing 48,470 locus tags and 83% of mentions were from supplementary materials and 9% from publications outside the OA subset. Conclusions: B. pseudomallei locus tags within the full text and tables of OA publications represent only a small fraction of the total mentions in the literature. For microbial genomes with very few functionally characterized proteins, the locus tags mentioned in supplementary tables and within ranges like genomic islands contain the majority of locus tags. Significantly, the functions in the R package provide access to additional resources in the OA subset that are not currently indexed or returned by searching PMC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

ORBiT: Oak Ridge biosurveillance toolkit for public health dynamics

Background: The digitization of health-related information through electronic health records (EHR) and electronic healthcare reimbursement claims and the continued growth of self-reported health information through social media provides both tremendous opportunities and challenges in developing effective biosurveillance tools. With novel emerging infectious diseases being reported across different parts of the world, there is a need to build systems that can track, monitor and report such events in a timely manner. Further, it is also important to identify susceptible geographic regions and populations where emerging diseases may have a significant impact. Methods: In this paper, we present an overview of Oak Ridge Biosurveillance Toolkit (ORBiT), which we have developed specifically to address data analytic challenges in the realm of public health surveillance. In particular, ORBiT provides an extensible environment to pull together diverse, large-scale datasets and analyze them to identify spatial and temporal patterns for various biosurveillance-related tasks. Results: We demonstrate the utility of ORBiT in automatically extracting a small number of spatial and temporal patterns during the 2009-2010 pandemic H1N1 flu season using claims data. These patterns provide quantitative insights into the dynamics of how the pandemic flu spread across different parts of the country. We discovered that the claims data exhibits multi-scale patterns from which we could identify a small number of states in the United States (US) that act as “bridge regions” contributing to one or more specific influenza spread patterns. Similar to previous studies, the patterns show that the south-eastern regions of the US were widely affected by the H1N1 flu pandemic. Several of these south-eastern states act as bridge regions, which connect the north-east and central US in terms of flu occurrences. Conclusions: These quantitative insights show how the claims data combined with novel analytical techniques can provide important information to decision makers when an epidemic spreads throughout the country. Taken together ORBiT provides a scalable and extensible platform for public health surveillance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

Statistical ensemble analysis for simulating extrinsic noise-driven response in NF-κB signaling networks

Background: Gene expression profiles and protein dynamics in single cells have a large cell-to-cell variability due to intracellular noise. Intracellular fluctuations originate from two sources: intrinsic noise due to the probabilistic nature of biochemical reactions and extrinsic noise due to randomized interactions of the cell with other cellular systems or its environment. Presently, there is no systematic parameterization and modeling scheme to simulate cellular response at the single cell level in the presence of extrinsic noise. Results: In this paper, we propose a novel statistical ensemble method to simulate the distribution of heterogeneous cellular responses in single cells. We capture the effects of extrinsic noise by randomizing values of the model parameters. In this context, a statistical ensemble is a large number of system replicates, each with randomly sampled model parameters from biologically feasible intervals. We apply this statistical ensemble approach to the well-studied NF-κB signaling system. We predict several characteristic dynamic features of NF-κB response distributions; one of them is the dosage-dependent distribution of the first translocation time of NF-κB. Conclusion: The distributions of heterogeneous cellular responses that our statistical ensemble formulation generates reveal the effect of different cellular conditions, e.g., effects due to wild type versus mutant cells or between different dosages of external stimulants. Distributions generated in the presence of extrinsic noise yield valuable insight into underlying regulatory mechanisms, which are sometimes otherwise hidden.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

Background: The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience. Description: Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases. Conclusions: In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Monitoring installation of partially occluded subassemblies in modular construction factories using BIM, ray tracing, and computer vision

Modular and offsite construction methods are being increasingly adopted due to the advantages they offer in terms of project completion time, quality, and energy-efficiency. Despite these advantages, the current state of monitoring systems in modular construction factories highly relies on labor-intensive, subjective, and error-prone observational methods. A large body of research has aimed to automate the monitoring process using an array of sensors, such as IMUs and RFIDs, during the past two decades. Recently, computer vision-based methods have gained increasing interest as a non-intrusive technology to monitor the process inside modular construction factories. However, partial occlusion challenges have impeded their practical application on a large scale. This challenge is specifically important for monitoring the installation of subassemblies since they can obstruct the view of the monitoring camera, especially those that enable long-term monitoring like closed-circuit television (CCTV) fixed-view surveillance cameras. Here, this paper aims to address this challenge by proposing a novel computer vision-based method to monitor the installation of new subassemblies inside modular factories in highly occluded scenes. The proposed methodology identifies the subassemblies in the CCTV video footage using computer vision, analyzes the occlusions using BIM and ray casting techniques, and estimates the progress of assembly by comparing the BIM model with the detected subassemblies in the video. The proposed methodology was successfully validated on surveillance videos captured from a volumetric modular construction factory in the U.S., achieving 93% accuracy in identifying the installation of subassemblies. The results from this research show that the integration of BIM and computer vision is a promising method for monitoring the installation processes inside modular factories under severe occlusion.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

The cost of embedding

This report describes the cost of embedding and its implication for quantum computing.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Sub-grid scale model classification and blending through deep learning

In this article we detail the use of machine learning for spatio-temporally dynamic turbulence model classification and hybridization for large eddy simulations (LES) of turbulence. Here, our predictive framework is devised around the determination of local conditional probabilities for turbulence models that have varying underlying hypotheses. As a first deployment of this learning, we classify a point on our computational grid as that which requires the functional hypothesis, the structural hypothesis or no modelling at all. This ensures that the appropriate model is specified from a priori knowledge and an efficient balance of model characteristics is obtained in a particular flow computation. In addition, we also utilize the conditional-probability predictions of the same machine learning to blend turbulence models for another hybrid closure. Our test case for the demonstration of this concept is given by Kraichnan turbulence, which exhibits a strong interplay of enstrophy and energy cascades in the wavenumber domain. Our results indicate that the proposed methods lead to robust and stable closure and may potentially be used to combine the strengths of various models for complex flow phenomena prediction.

42 ENGINEERING↗
DOE OSTI2023

Decentralized digital twins of complex dynamical systems

Abstract In this article, we introduce a decentralized digital twin (DDT) modeling framework and its potential applications in computational science and engineering. The DDT methodology is based on the idea of federated learning, a subfield of machine learning that promotes knowledge exchange without disclosing actual data. Clients can learn an aggregated model cooperatively using this method while maintaining complete client-specific training data. We use a variety of dynamical systems, which are frequently used as prototypes for simulating complex transport processes in spatiotemporal systems, to show the viability of the DDT framework. Our findings suggest that constructing highly accurate decentralized digital twins in complex nonlinear spatiotemporal systems may be made possible by federated machine learning.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A numerical method for simulating variable density flows in membrane desalination systems

Here, we present a novel method for simulating unsteady, variable density, fluid flows in membrane desalination systems. By assuming the density varies only with concentration and temperature, the scheme decouples the solution of the governing equations into two sequential blocks. The first solves the governing equations for the temperature and concentration fields, which are used to compute all thermophysical properties. The second block solves the conservation of mass and momentum equations for the velocity and pressure. We show that this is computationally more efficient than schemes that iterate over the full coupled equations in one block. We verify that the method achieves second-order spatial-temporal accuracy, and we use the method to investigate buoyancy-driven convection in a desalination process called vacuum membrane distillation. Specifically, we show that with gravity properly oriented, variations in temperature and concentration can trigger a double-diffusive instability that enhances mixing and improves water recovery. We also show that the instability can be strengthened by providing external heating.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1990

Computer simulation of cardiovascular changes during extended duration space flights

The application of mathematical modeling and computer simulation to the study of spaceflight cardiovascular changes is examined using a multicompartment representation model of the entire human cardiovascular system including its control elements. The model simulates the beat-to-beat dynamic responses of the cardiovascular system to orthostatic stresses. Simulation results pertaining to long-term space flight, the combined effect of +G(z) and blood volume loss, and the effect of anti-G suit inflation are discussed, including past results on the original version of the model which has been used in a number of analysis applications at NASA. New results pertain to analysis of cardiovascular changes in extended duration space flights and demonstrate the use of this model in evaluation of physiological factors that contribute to orthostatic intolerance following an exposure to weightlessness, in particular, blood volume loss and changes in the sensitivity of baroreceptors.

Srinivasan, R. Srini↗
DOE OSTI2021

Machine learning with persistent homology and chemical word embeddings improves prediction accuracy and interpretability in metal-organic frameworks

Machine learning has emerged as a powerful approach in materials discovery. Its major challenge is selecting features that create interpretable representations of materials, useful across multiple prediction tasks. We introduce an end-to-end machine learning model that automatically generates descriptors that capture a complex representation of a material’s structure and chemistry. This approach builds on computational topology techniques (namely, persistent homology) and word embeddings from natural language processing. It automatically encapsulates geometric and chemical information directly from the material system. We demonstrate our approach on multiple nanoporous metal–organic framework datasets by predicting methane and carbon dioxide adsorption across different conditions. Our results show considerable improvement in both accuracy and transferability across targets compared to models constructed from the commonly-used, manually-curated features, consistently achieving an average 25–30% decrease in root-mean-squared-deviation and an average increase of 40–50% in R 2 scores. A key advantage of our approach is interpretability: Our model identifies the pores that correlate best to adsorption at different pressures, which contributes to understanding atomic-level structure–property relationships for materials design.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Numerical simulations of realistic grating compressors

Chirped pulse amplification (CPA), originally proposed by Strickland and Mourou, is a critical enabling technology for creating very short laser pulses with very high peak power. It consists of three optical components: a stretcher, an amplifier, and a compressor. An initial laser pulse of short duration and low energy content is first stretched out in time by the stretcher, resulting in a pulse with longer duration, low energy content, and very low peak power. The pulse is then amplified to increase its energy content without changing its duration in time. The amplified pulse is finally compressed in time in the compressor, resulting in a laser pulse with very short duration and very high peak power. The objective of this work is to develop numerical techniques that enable small-scale grating aberrations in the compressor to be analyzed through high performance computer simulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Differentiable Multiphysics Codes: A Breakthrough Technology for Simulation and Computing

This document summarizes the findings of a strategic planning exercise commissioned by the Weapons Simulation and Computing, Computational Physics (WSC/CP) program at the Lawrence Livermore National Laboratory (LLNL) in FY24. During the year, the committee met with multiple stakeholder communities to gather input, opinions, suggestions and concerns which have been incorporated throughout this document. The key findings from this exercise are summarized: • The development of multiphysics modelling and simulation (mod/sim) codes and software technologies, their deployment on exascale compute platforms, and their broad adoption across the NNSA is a major success of the Advanced Simulation and Computing (ASC) program and the Exascale Computing Project (ECP). Sustained investment in these core technologies is essential. • Today’s state of the art involves running ensembles of O(100K) simulations to perform uncertainty quantification (UQ) and design studies using multiple statistical methods such as Bayesian optimization to understand sensitivities of our models and explore parameterized design spaces. Even with exascale computing, we are practically limited to O(10) parameters in these studies since the number of simulations required to sample the space scales exponentially with the number of design parameters. • The data from these simulation ensembles is increasingly being used to train machine learned (ML) surrogates (or reduced order models, ROMs) which can then be used for optimization or real time design exploration. However, the trained surrogates are still limited in the number of parameters they can represent due to the sampling limitations previously noted. • Augmenting our suite of integrated multiphysics simulation codes, both current and emerging, with the ability to compute gradients (solution derivatives) of arbitrary simulation outputs with respect to (some or all) simulation inputs would be a breakthrough technology, opening the door to a new era of efficient and automated inverse design based on verified and validated mod/sim capabilities. • This capability, which we refer to as differentiable multiphysics codes (DMCs), would revolutionize both UQ and optimization studies by breaking the curse of dimensionality that presently limits our “gradient-free” ensemble based computing approach. A similar breakthrough occurred in the AI/ML community once the ability to compute gradients of arbitrary loss functions using back-propagation became commonplace. Gradient information from the multiphysics codes can also be used to dramatically improve the efficiency and scale of training of ML/ROM surrogates for rapid assessments. • Achieving this in our suite of codes will be a grand challenge, similar to the amount of effort that was required to transition from CPU to GPU computing. It will require buy-in from the entire WSC/CP program and beyond, including all integrated codes, physics and engineering models, third-party library dependencies and performance portability abstractions. It will also require investment in research and development of numerical methods for computing adjoints of coupled physics across multiple adaptively refined moving meshes and of stochastic (Monte Carlo) and mesh free (SPH) methods. • New software and numerical techniques, largely pioneered by the AI/ML community, make this feasible. Chief among these is automatic differentiation (AD), the ability to employ AD at point-wise locations in a physics calculation (instead of traditional black-box approaches) and the ability to perform “back-propagation in time” (or reverse mode AD) for non-linear partial differential equations (PDEs). Fundamentally, the conclusion of this strategic planning exercise is that the time is right to undertake a large scale effort in WSC, centered on the existing integrated codes, to continue the natural evolution of mod/sim in the age of AI/ML. Instead of attempting to replace mod/sim with purely data driven AI/ML models, we believe the key to success is to integrate AI/ML by building on top of the decades of hard-won knowledge and the verified/validated multiphysics modelling capability that is the hallmark of the ASC program.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Modifying the Asynchronous Jacobi Method for Data Corruption Resilience

Moving scientific computation from high-performance computing (HPC) and cloud computing (CC) environments to devices on the edge, i.e., physically near instruments of interest, has received tremendous interest in recent years. Such edge computing environments can operate on data in situ, offering enticing benefits over data aggregation to HPC and CC facilities that include avoiding costs of transmission, increased data privacy, and real-time data analysis. Because of the inherent unreliability of edge computing environments, new fault-tolerant approaches must be developed before the benefits of edge computing can be realized. Motivated by algorithm-based fault tolerance, a variant of the asynchronous Jacobi (ASJ) method is developed that achieves resilience to data corruption by rejecting solution approximations from neighbor devices according to a bound derived from convergence theory. Numerical results on a two-dimensional Poisson problem show that the new rejection criterion, along with a novel approximation to the shortest path length on which the criterion depends, restores convergence for the ASJ variant in the presence of certain types data corruption. Numerical results are obtained for when the singular values in the analytic bound are approximated. Additional linear systems are also explored, one with a more dense sparsity pattern and one that includes advection. All results indicate that successful resilience to data corruption depends on whether the bound tightens fast enough to reject corrupted data before the iteration evolution deviates significantly from that predicted by the convergence theory defining the bound. This observation generalizes to future work on algorithm-based fault tolerance for other asynchronous algorithms, including upcoming approaches that leverage Krylov subspaces.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Mathematical model and software complex for computer simulation of field emission electron sources

The software complex developed in MATLAB allows modelling of function of diode and triode structures based on field emission electron sources with complex sub-micron geometry, their volt-ampere characteristics, calculating distribution of electric field for educational and research needs. The goal of this paper is describing the physical-mathematical model, calculation methods and algorithms the software complex is based on, demonstrating the principles of its function and showing results of its work. For getting to know the complex, a demo version with graphical user interface is presented.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗