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Results for “Mathematics of computing”

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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This ‘GO Phylogenetic Annotation’ approach integrates GO annotations from evolutionarily related genes across 100 different organisms in the context of a gene family tree, in which curators build an explicit model of the evolution of gene functions. GO Phylogenetic Annotation models the gain and loss of functions in a gene family tree, which is used to infer the functions of uncharacterized (or incompletely characterized) gene products, even for human proteins that are relatively well studied. Here, we report our results from applying this paradigm to two well-characterized cellular processes, apoptosis and autophagy. This revealed several important observations with respect to GO annotations and how they can be used for function inference. Notably, we applied only a small fraction of the experimentally supported GO annotations to infer function in other family members. The majority of other annotations describe indirect effects, phenotypes or results from high throughput experiments. In addition, we show here how feedback from phylogenetic annotation leads to significant improvements in the PANTHER trees, the GO annotations and GO itself. Thus GO phylogenetic annotation both increases the quantity and improves the accuracy of the GO annotations provided to the research community. We expect these phylogenetically based annotations to be of broad use in gene enrichment analysis as well as other applications of GO annotations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability

The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true ‘machine-actionable interoperability’, which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources

The ever-increasing metagenomic data necessitate appropriate cataloguing in a way that facilitates the comparison and better contextualization of the underlying investigations. To this extent, information associated with the sequencing data as well as the original sample and the environment where it was obtained from is crucial. To date, there are not any publicly available repositories able to capture environmental metadata pertaining to hydrocarbon-rich environments. As such, contextualization and comparative analysis among sequencing datasets derived from these environments is to a certain degree hindered or cannot be fully evaluated. The metagenomics data management system for hydrocarbon resources (MetaHCRs) enables the capturing of marker gene and whole metagenome sequencing data as well as over 300 contextual attributes associated with samples, organisms, environments and geological properties, among others. Moreover, MetaHCR implements the Minimum Information about any Sequence–hydrocarbon resource specification from the Genomic Standards Consortium; it integrates a user-friendly web interface and relational database model, and it enables the generation of complex custom search. MetaHCR has been tested with 36 publicly available metagenomic studies, and its modular architecture can be easily customized for other types of environmental and metagenomics studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Physiological fidelity or model parsimony? The relative performance of reverse-toxicokinetic modeling approaches

Physiologically-based toxicokinetic (PBTK) models are often developed to facilitate in vitro to in vivo extrapolation (IVIVE) using a top-down, compartmental approach, favoring architectural simplicity over physiological fidelity despite the lack of general guidelines relating model design to dynamical predictions. Here we explore the impact of design choice (high vs. low fidelity) on chemical distribution throughout an animal’s organ system. Results We contrast transient dynamics and steady states of three previously proposed PBTK models of varying complexity in response to chemical exposure. The steady states for each model were determined analytically to predict exposure conditions from tissue measurements. Steady state whole-body concentrations differ between models, despite identical environmental conditions, which originates from varying levels of physiological fidelity captured by the models. These differences affect the relative predictive accuracy of the inverted models used in exposure reconstruction to link effects-based exposure data with whole-organism response thresholds obtained from in vitro assay measurements. Conclusions Our results demonstrate how disregarding physiological fideltiy in favor of simpler models affects the internal dynamics and steady state estimates for chemical accumulation within tissues, which, in turn, poses significant challenges for the exposure reconstruction efforts that underlie many IVIVE methods. Developing standardized systems-level models for ecological organisms would not only ensure predictive consistency among future modeling studies, but also ensure pragmatic extrapolation of in vivo effects from in vitro data or modeling exposure-response relationships.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1973

Research in mathematical theory of computation

Research progress in the following areas is reviewed: (1) new version of computer program LCF (logic for computable functions) including a facility to search for proofs automatically; (2) the description of the language PASCAL in terms of both LCF and in first order logic; (3) discussion of LISP semantics in LCF and attempt to prove the correctness of the London compilers in a formal way; (4) design of both special purpose and domain independent proving procedures specifically program correctness in mind; (5) design of languages for describing such proof procedures; and (6) the embedding of ideas in the first order checker.

Mccarthy, J.↗
NASA NTRS1982

Description of a mathematical model and computer simulation of separation of the nose cap from the solid rocket booster

A system of equations which models the motion of the Solid Rocket Booster Nose Cap upon separation is described. The computer program which utilizes these equations to generate nose cap trajectories is described in detail. Application of the program to simulate a rocket sled test of the nose cap separation is discussed and the results of the applications are presented. With the information given a user should be able to exercise the computer program with a minimum of effort.

Schwaniger, A. J., Jr.↗
NASA NTRS1990

Research in progress in applied mathematics, numerical analysis, and computer science

Research conducted at the Institute in Science and Engineering in applied mathematics, numerical analysis, and computer science is summarized. The Institute conducts unclassified basic research in applied mathematics in order to extend and improve problem solving capabilities in science and engineering, particularly in aeronautics and space.

Source record↗
DOE OSTI2022

A weighted state redistribution algorithm for embedded boundary grids

State redistribution is an algorithm that stabilizes cut cells for embedded boundary grid methods. This work extends the earlier algorithm in several important ways. First, state redistribution is extended to three spatial dimensions. Second, we discuss several algorithmic changes and improvements motivated by the more complicated cut cell geometries that can occur in higher dimensions. In particular, we introduce a weighted version with less dissipation in an easily generalizable framework. Third, we demonstrate that state redistribution can also stabilize a solution update that includes both advective and diffusive contributions. Notably, the stabilization algorithm is shown to be effective for incompressible as well as compressible reacting flows. Finally, we discuss the implementation of the algorithm for several exascale-ready simulation codes based on AMReX, demonstrating ease of use in combination with domain decomposition, hybrid parallelism and complex physics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Scalability of high-performance PDE solvers

Performance tests and analyses are critical to effective high-performance computing software development and are central components in the design and implementation of computational algorithms for achieving faster simulations on existing and future computing architectures for large-scale application problems. In this article, we explore performance and space-time trade-offs for important compute-intensive kernels of large-scale numerical solvers for partial differential equations (PDEs) that govern a wide range of physical applications. We consider a sequence of PDE-motivated bake-off problems designed to establish best practices for efficient high-order simulations across a variety of codes and platforms. We measure peak performance (degrees of freedom per second) on a fixed number of nodes and identify effective code optimization strategies for each architecture. In addition to peak performance, we identify the minimum time to solution at 80% parallel efficiency. The performance analysis is based on spectral and p-type finite elements but is equally applicable to a broad spectrum of numerical PDE discretizations, including finite difference, finite volume, and h-type finite elements.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Ensemble‐Based, Large‐Eddy Reconstruction of Wind Turbine Inflow in a Near‐Stationary Atmospheric Boundary Layer Through Generative Artificial Intelligence

ABSTRACT To validate the second‐by‐second dynamics of turbines in field experiments, it is necessary to accurately reconstruct the winds going into the turbine. Current time‐resolved inflow reconstruction techniques estimate wind behavior in unobserved regions using relatively simple spectral‐based models of the atmosphere. Here, we develop a technique for time‐resolved inflow reconstruction that is rooted in a large‐eddy simulation model of the atmosphere. Our “large‐eddy reconstruction” technique blends observations and atmospheric model information through a diffusion model machine learning algorithm, allowing us to generate probabilistic ensembles of reconstructions for a single 10‐min observational period. Our generated inflows can be used directly by aeroelastic codes or as inflow boundary conditions in a large‐eddy simulation. We verify the second‐by‐second reconstruction capability of our technique in three synthetic field campaigns, finding positive Pearson correlation coefficient values () between ground‐truth and reconstructed streamwise velocity, as well as smaller positive correlation coefficient values for unobserved fields (spanwise velocity, vertical velocity, and temperature). We validate our technique in three real‐world case studies by driving large‐eddy simulations with reconstructed inflows and comparing to independent inflow measurements. The reconstructions are visually similar to measurements, follow desired power spectra properties, and track second‐by‐second behavior ().

17 WIND ENERGY↗
DOE OSTI2025

Benchmark study of the DTU OWC chamber with both two-way and one-way absorption

This paper reports on a benchmark study based on small-scale (1:50) measurements of a single, oscillating water column chamber mounted sideways in a long flume. The geometry of the OWC chamber is extracted from a barge-like, attenuator-type floating concept “KNSwing” with 40 chambers targeted for deployment in the Danish part of the North Sea. In addition to traditional two-way energy extraction we also consider one-way energy extraction with passive venting and compare chamber response, pressures and total absorbed energy between the two methods. A blind study was established for the numerical modeling, with participants applying several implementations of weakly nonlinear potential flow theory and commercial Navier–Stokes solvers (CFD). Both compressible and incompressible models were used for the air phase. Potential flow calculations predict more energy absorption near the chamber resonance for one-way absorption than for two-way absorption, but the opposite is found from the experimental measurements. This outcome is mainly attributed to energy losses in the experimental passive valve system, but this conclusion must be confirmed by better experimental measurements. Modeling the one-way valve in CFD proved to be very challenging and only one team was able to provide results which were generally closer to the experiments. The study illustrates the challenges associated with both numerical and experimental analysis of OWC chambers. Air compressibility effects were not found to be important at this scale, even with the large volume of additional air used for the one-way case.

16 TIDAL AND WAVE POWER↗
DOE OSTI2025

Automatic building energy model development and debugging using large language models agentic workflow

Building energy modeling (BEM) is a complex process that demands significant time and expertise, limiting its broader application in building design and operations. While Large Language Models (LLMs) agentic workflow have facilitated complex engineering processes, their application in BEM has not been specifically explored. This paper investigates the feasibility of automating BEM using LLM agentic workflow. Here, we developed a generic LLM-planning-based workflow that takes a building description as input and generates an error-free EnergyPlus building energy model. Our robust workflow includes four core agents: 1) Building Description Pre-Processing, 2) IDF Object Information Extraction, 3) Single IDF Object Generator Suite, and 4) IDF Debugging Agent. These agents divide the complex tasks into manageable sub-steps, enabling LLMs to generate accurate and reliable results at each stage. The case study demonstrates the successful translation of a building description into an error-free EnergyPlus model for the iUnit modular building at the National Renewable Energy Laboratory. The effectiveness of our workflow surpasses: 1) naive prompt engineering, 2) other LLM-based workflows, and 3) manual modeling, in terms of accuracy, reliability, and time efficiency. The paper concludes with a discussion on the interplay between foundational models and LLM agent planning design, advocating for the use of fine-tuned, specialized models to advance this field.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Novel artificial neural network model for instantaneous power losses and operational efficiency mapping of MW-scale vanadium redox flow battery for improved technoeconomic analysis

A novel data-driven, machine-learning-based method for modeling the instantaneous power losses of a distribution-sited 2 MW/8MWh vanadium redox flow battery (VRFB), a grid-scale electrochemical storage technology, is introduced and compared against benchmark empirical modeling approaches, including symmetric and asymmetric models, as well as a recent convex hull modeling approach. The novel loss modeling method introduces several advantages over the benchmark models and over simplistic efficiency estimates, the most significant of which is that the model can accurately reflect the stepwise and non-linear parasitic losses associated with the duty cycles of mechanical auxiliary systems like pump motor drives and blower fans. Residuals of the models are compared; the proposed data driven model features significantly improved accuracy over the benchmark models. The model's coefficient of determination is also improved relative to that of the benchmark models. Furthermore, a novel method for visualization of operational efficiency of the grid-scale storage technology is introduced. To demonstrate the benefits of the novel data-driven method for modeling the VRFB, the benchmark models and the proposed models are embedded into an Open DSS distribution network model to study two applications of the grid-scale electrical storage system: load leveling for grid support and energy arbitrage. This article demonstrates that the accuracy of the instantaneous power loss model significantly impacts the understanding of the state of charge of the VRFB. In turn, the accuracy of the efficiency modeling of the VRFB impacts the understanding of the potential economic value and technical benefits to the distribution network operators. In conclusion, the presented power loss modeling approach is, therefore, highly relevant for utility-stakeholders, battery asset owners, system engineers, system designers, and financial planners interested in evaluating or optimizing the operation of grid-scale VRFBs.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2018

Hardware-efficient fermionic simulation with a cavity–QED system

In digital quantum simulation of fermionic models with qubits, non-local maps for encoding are often encountered. Such maps require linear or logarithmic overhead in circuit depth which could render the simulation useless, for a given decoherence time. In this, we show how one can use a cavity–QED system to perform digital quantum simulation of fermionic models. In particular, we show that highly nonlocal Jordan–Wigner or Bravyi–Kitaev transformations can be efficiently implemented through a hardware approach. The key idea is using ancilla cavity modes, which are dispersively coupled to a qubit string, to collectively manipulate and measure qubit states. Our scheme reduces the circuit depth in each Trotter step of the Jordan–Wigner encoding by a factor of N 2 , comparing to the scheme for a device with only local connectivity, where N is the number of orbitals for a generic two-body Hamiltonian. Additional analysis for the Fermi–Hubbard model on an N × N square lattice results in a similar reduction. We also discuss a detailed implementation of our scheme with superconducting qubits and cavities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Understanding Peelle’s Pertinent Puzzle bias in generalized least squares regression through eigenspectrum analysis

Certain correlation structures in the data covariance matrix (DCM) used for generalized least squares (GLS) regression can result in biased estimates, commonly known in the field of nuclear data evaluation as Peele’s Pertinent Puzzle (PPP). This article introduces a generative, forward modeling framework within which the PPP bias is characterized through an eigenspectrum analysis of the DCM. This analysis highlights the root cause of the bias, generalizes the problem beyond the nuclear data field, and provides insight to the problem regimes where it can occur. What follows is an understanding that the bias can show up for any experimental neutron time-of-flight data for which systematic uncertainties have been quantified. Lastly, a discussion of the adaptation of cross validation approaches that require pre-whitening to incorporate the known ‘fix’ to the PPP bias in the GLS estimator.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗