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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 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. Understanding the roles of these uncultivated populations has broad application in ecology, evolution, biotechnology and medicine. Accurate binning of assembled metagenomic sequences is an essential step in recovering the genomes and understanding microbial functions. We have developed a binning algorithm, MaxBin, which automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads. Binning of simulated metagenomic datasets demonstrated that MaxBin had high levels of accuracy in binning microbial genomes. MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. Application of MaxBin to metagenomes obtained from microbial consortia adapted to grow on cellulose allowed genomic analysis of new, uncultivated, cellulolytic bacterial populations, including an abundant myxobacterial population distantly related to Sorangium cellulosum that possessed a much smaller genome (5 MB versus 13 to 14 MB) but has a more extensive set of genes for biomass deconstruction. For the cellulolytic consortia, the MaxBin results were compared to binning using emergent self-organizing maps (ESOMs) and differential coverage binning, demonstrating that it performed comparably to these methods but had distinct advantages in automation, resolution of related genomes and sensitivity. The automatic binning software that we developed successfully classifies assembled sequences in metagenomic datasets into recovered individual genomes. The isolation of dozens of species in cellulolytic microbial consortia, including a novel species of myxobacteria that has the smallest genome among all sequenced aerobic myxobacteria, was easily achieved using the binning software. This work demonstrates that the processes required for recovering genomes from assembled metagenomic datasets can be readily automated, an important advance in understanding the metabolic potential of microbes in natural environments. MaxBin is available at https://sourceforge.net/projects/maxbin/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Sempervirens: A Fast Reconstruction Algorithm for Noisy and Incomplete Binary Matrix Representations of Trees

Applications such as reconstructing cell lineage trees (represented as phylogenetic trees) from single-cell sequencing data require reconstructing a {0,1}-matrix that has many errors and missing entries. We introduce Sempervirens, a very fast matrix reconstruction algorithm for noisy and incomplete matrix representations of phylogenetic trees. Sempervirens uses an iterative maximum-likelihood approach to determine the topology tree represented by the corrupted data. We show that Sempervirens is at least three orders of magnitude faster than other methods on thousand by thousand matrices, with the speed gap widening with larger matrices. We also show that Sempervirens matches state-of-the-art methods in reconstruction accuracy. The speed of Sempervirens enables it to be tractably applied to reconstructing much larger matrices than those that other methods can reconstruct. In addition to experimental results, we justify the algorithm with a mathematical treatment of its subprocedures.

algorithms↗
DOE OSTI2020

Data for Training and Testing Radiation Detection Algorithms in an Urban Environment

The US government routinely performs radiological response deployments to search for the presence of illicit nuclear materials (e.g., highly enriched uranium and weapons-grade plutonium) in a specified area. The deployments can be intelligence driven, in support of law enforcement, and for planned events such as WrestleMania, presidential inaugurations, or political conventions. In a typical deployment, radiation detection systems carried by human operators or mounted on vehicles move in a clearing pattern through the search area. Search teams rely on radiation detection algorithms running on these systems in real time to alert them to the presence of an illicit threat source. The detection and identification of sources is complicated by large variation of natural radiation background throughout a search area and the potential presence of localized non-threat sources such as patients undergoing treatment with medical isotopes. As a result, detection algorithms must be carefully balanced between missing real sources (false negatives) and reporting too many false alarms (false positives).The purpose of this data set is to spur innovations in detecting, identifying, and localizing nuclear materials inurban search missions.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2022

Controlled precision QUBO-based algorithm to compute eigenvectors of symmetric matrices

We describe an algorithm to compute the extremal eigenvalues and corresponding eigenvectors of a symmetric matrix which is based on solving a sequence of Quadratic Binary Optimization problems. This algorithm is robust across many different classes of symmetric matrices; It can compute the eigenvector/eigenvalue pair to essentially any arbitrary precision, and with minor modifications, can also solve the generalized eigenvalue problem. Performance is analyzed on small random matrices and selected larger matrices from practical applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Code Coupling via Jacobian-Free Newton-Krylov Algorithms with Application to Magnetized Fluid Plasma and Kinetic Neutral Models

Jacobian-free Newton-Krylov (JFNK) algorithms are a potentially powerful class of methods for solving the problem of coupling codes that address dfferent physics models. As communication capability between individual submodules varies, different choices of coupling algorithms are required. The more communication that is available, the more possible it becomes to exploit the simple sparsity pattern of the Jacobian, albeit of a large system. The less communication that is available, the more dense the Jacobian matrices become and new types of preconditioners must be sought to efficiently take large time steps. In general, methods that use constrained or reduced subsystems can offer a compromise in complexity. The specific problem of coupling a fluid plasma code to a kinetic neutrals code is discussed as an example.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

X-ray simulation algorithms used in ISP

ISP is a simulation code which is sometimes used in the USNDS program. ISP is maintained by Sandia National Lab. However, the X-ray simulation algorithm used by ISP was written by scientists at LANL – mainly by Ed Fenimore with some contributions from John Sullivan and George Neuschaefer and probably others. In email to John Sullivan on July 25, 2016, Jill Rivera, ISP project lead, said “ISP uses the function xdosemeters_sim from the xgen library.” The is a fortran subroutine which is also used to simulate the X-ray response in consim (a descendant of xgen). Therefore, no separate documentation of the X-ray simulation algorithms in ISP have been written – the documentation for the consim simulation can be used.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Final Technical Report: Sparse Grid Scenario Generation and Interior Algorithms for Stochastic Optimization in a Parallel Computing Environment

The support from this grant resulted in seven published papers and a technical report. Two papers are published in SIAM J. on Optimization [87, 88]; two papers are published in IEEE Transactions on Power Systems [77, 78]; one paper is published in Smart Grid [79]; one paper is published in Computational Optimization and Applications [44] and one in INFORMS J. on Computing [67]). The works in [44, 67, 87, 88] were funded primarily by this DOE grant. The applied papers in [77, 78, 79] were also supported through a subcontract from the Argonne National Lab. We start by presenting our main research results on the scenario generation problem in Sections 1–2. We present our algorithmic results on interior point methods for convex optimization problems in Section 3. We describe a new ‘central’ cutting surface algorithm developed for solving large scale convex programming problems (as is the case with our proposed research) with semi-infinite number of constraints in Section 4. In Sections 5–6 we present our work on two application problems of interest to DOE.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Parallel Algorithms for the Exascale Era

New parallel algorithms are needed to reach the Exascale level of parallelism with millions of cores. We look at some of the research developed by students in projects at LANL. The research blends ideas from the early days of computing while weaving in the fresh approach brought by students new to the field of high performance computing. We look at reproducibility of global sums and why it is important to parallel computing. Next we look at how the concept of hashing has led to the development of more scalable algorithms suitable for next-generation parallel computers. Nearly all of this work has been done by undergraduates and published in leading scientific journals.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Extreme-scale Algorithms and Solver Resilience

A widening gap exists between the peak performance of high-performance computers and the performance achieved by complex applications running on these platforms. Over the next decade, extreme-scale systems will present major new challenges to algorithm development that could amplify this mismatch in such a way that it prevents the productive use of future DOE Leadership computers due to the following; Extreme levels of parallelism due to multicore processors; An increase in system fault rates requiring algorithms to be resilient beyond just checkpoint/restart; Complex memory hierarchies and costly data movement in both energy and performance; Heterogeneous system architectures (mixing CPUs, GPUs, etc.); and Conflicting goals of performance, resilience, and power requirements.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Performance of Advanced Signal Processing and Pattern Recognition Algorithms Using Raw Data from Ultrasonic Guided Waves and Fiber Optics Transducers

The Light Water Reactor Sustainability Program was initiated to evaluate technologies that could be used to perform online monitoring of piping and other secondary system structural components in commercial nuclear power plants. These online monitoring systems have the potential to identify when a more detailed inspection is needed using real-time measurements, rather than at a pre-determined inspection interval. This transition to condition-based, risk-informed automated maintenance will contribute to a significant reduction of operations and maintenance costs that account for most nuclear power generation costs. This report describes the current state of research related to ultrasonic guided wave testing and its application to detecting defects in commercial nuclear power plants. The report analyzes the applicability of the guided wave technology to secondary piping systems, as well as studying the potential for expanding the range of guided wave technology to include bent piping and other piping components. The ultrasonic guided waves can inspect long stretches of straight piping; however, more complex geometries such as elbows, welds, and tees are causing spurious reflections and coherent noise, which significantly decreases the sensitivity of the technique. To deal with these limitations, high-definition fiber optic sensors are applied to complex piping geometries, and advanced machine learning algorithms are used to detect deviations from healthy states. This report also analyzes the performance of advanced signal processing and machine learning-based pattern recognition algorithms in detecting defects in secondary structures. It is demonstrated on guided wave data collected at nuclear power plants that the independent component analysis can separate different coherent noise components and segregate them from useful signals. It also demonstrates that advanced machine learning techniques, such as neural networks, support vector machines, and deep learning networks, can detect minor defects present in inspected structures. Recommendation about the applicability of advanced machine learning techniques to online piping monitoring are also given.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2019

Algorithm for Nonlinear Optimization of Finishing Operations

A model is proposed for nonlinear optimization of final turning. On that basis, an automated computational algorithm is developed. The algorithm maximizes the productivity, while maintaining specified quality of the machined surface.

42 ENGINEERING↗
DOE OSTI2022

Scaling and Benchmarking an Evolutionary Algorithm for Constructing Biophysical Neuronal Models

Single neuron models are fundamental for computational modeling of the brain's neuronal networks, and understanding how ion channel dynamics mediate neural function. A challenge in defining such models is determining biophysically realistic channel distributions. Here, we present an efficient, highly parallel evolutionary algorithm for developing such models, named NeuroGPU-EA. NeuroGPU-EA uses CPUs and GPUs concurrently to simulate and evaluate neuron membrane potentials with respect to multiple stimuli. We demonstrate a logarithmic cost for scaling the stimuli used in the fitting procedure. NeuroGPU-EA outperforms the typically used CPU based evolutionary algorithm by a factor of 10 on a series of scaling benchmarks. We report observed performance bottlenecks and propose mitigation strategies. Finally, we also discuss the potential of this method for efficient simulation and evaluation of electrophysiological waveforms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Biomass Grinding Process Optimization Using Response Surface Methodology and a Hybrid Genetic Algorithm

Biomass could be a key source of renewable energy. Agricultural waste products, such as corn stover, provide a convenient means to replace fossil fuels, such as coal, and a large amount of feedstock is currently available for energy consumption in the U.S. This study has two main objectives: (1) to understand the impact of corn stover moisture content and grinder speed on grind physical properties; and (2) develop response surface models and optimize these models using a hybrid genetic algorithm. The response surface models developed were used to draw surface plots to understand the interaction effects of the corn stover grind moisture content and grinder speed on the grind physical properties and specific energy consumption. The surface plots indicated that a higher corn stover grind moisture content and grinder speed had a positive effect on the bulk and tapped density. The final grind moisture content was highly influenced by the initial moisture content of the corn stover grind. Optimization of the response surface models using the hybrid genetic algorithm indicated that moisture content in the range of 17 to 19% (w.b.) and a grinder speed of 47 to 49 Hz maximized the bulk and tapped density and minimized the geomantic mean particle length. The specific energy consumption was minimized when the grinder speed was about 20 Hz and the corn stover grind moisture content was about 10% (w.b.).

09 BIOMASS FUELS↗
DOE OSTI2022

A Novel Method for Controlling Crud Deposition in Nuclear Reactors Using Optimization Algorithms and Deep Neural Network Based Surrogate Models

This work presents the use of a high-fidelity neural network surrogate model within a Modular Optimization Framework for treatment of crud deposition as a constraint within light-water reactor core loading pattern optimization. The neural network was utilized for the treatment of crud constraints within the context of an advanced genetic algorithm applied to the core design problem. This proof-of-concept study shows that loading pattern optimization aided by a neural network surrogate model can optimize the manner in which crud distributes within a nuclear reactor without impacting operational parameters such as enrichment or cycle length. Several analysis methods were investigated. Analysis found that the surrogate model and genetic algorithm successfully minimized the deviation from a uniform crud distribution against a population of solutions from a reference optimization in which the crud distribution was not optimized. Strong evidence is presented that shows boron deposition in crud can be optimized through the loading pattern. This proof-of-concept study shows that the methods employed provide a powerful tool for mitigating the effects of crud deposition in nuclear reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Enhancing Camera Calibration for Traffic Surveillance with an Integrated Approach of Genetic Algorithm and Particle Swarm Optimization

Recent advancements in sensor technologies, coupled with signal processing and machine learning, have enabled real-time traffic control systems to effectively adapt to changing traffic conditions. Cameras, as sensors, offer a cost-effective means to determine the number, location, type, and speed of vehicles, aiding decision-making at traffic intersections. However, the effective use of cameras for traffic surveillance requires proper calibration. This paper proposes a new optimization-based method for camera calibration. In this approach, initial calibration parameters are established using the Direct Linear Transformation (DLT) method. Then, optimization algorithms are applied to further refine the calibration parameters for the correction of nonlinear lens distortions. A significant enhancement in the optimization process is achieved through the integration of the Genetic Algorithm (GA) and Particle Swarm Optimization (PSO) into a combined Integrated GA and PSO (IGAPSO) technique. The effectiveness of this method is demonstrated through the calibration of eleven roadside cameras at three different intersections. The experimental results show that when compared to the baseline DLT method, the vehicle localization error is reduced by 22.30% with GA, 22.31% with PSO, and 25.51% with IGAPSO.

47 OTHER INSTRUMENTATION↗
DOE OSTI2016

ELM: AN ALGORITHM TO ESTIMATE THE ALPHA ABUNDANCE FROM LOW-RESOLUTION SPECTRA

We have investigated a novel methodology using the extreme learning machine (ELM) algorithm to determine the α abundance of stars. Applying two methods based on the ELM algorithm—ELM+spectra and ELM+Lick indices—to the stellar spectra from the ELODIE database, we measured the α abundance with a precision better than 0.065 dex. By applying these two methods to the spectra with different signal-to-noise ratios (S/Ns) and different resolutions, we found that ELM+spectra is more robust against degraded resolution and ELM+Lick indices is more robust against variation in S/N. To further validate the performance of ELM, we applied ELM+spectra and ELM+Lick indices to SDSS spectra and estimated α abundances with a precision around 0.10 dex, which is comparable to the results given by the SEGUE Stellar Parameter Pipeline. We further applied ELM to the spectra of stars in Galactic globular clusters (M15, M13, M71) and open clusters (NGC 2420, M67, NGC 6791), and results show good agreement with previous studies (within 1σ). A comparison of the ELM with other widely used methods including support vector machine, Gaussian process regression, artificial neural networks, and linear least-squares regression shows that ELM is efficient with computational resources and more accurate than other methods.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Modeling the Swift BAT trigger algorithm with machine learning

To draw inferences about gamma-ray burst (GRB) source populations based on Swift observations, it is essential to understand the detection efficiency of the Swift burst alert telescope (BAT). This study considers the problem of modeling the Swift/BAT triggering algorithm for long GRBs, a computationally expensive procedure, and models it using machine learning algorithms. A large sample of simulated GRBs from Lien et al. is used to train various models: random forests, boosted decision trees (with AdaBoost), support vector machines, and artificial neural networks. The best models have accuracies of ≳97% (≲3% error), which is a significant improvement on a cut in GRB flux, which has an accuracy of 89.6% (10.4% error). These models are then used to measure the detection efficiency of Swift as a function of redshift z, which is used to perform Bayesian parameter estimation on the GRB rate distribution. We find a local GRB rate density of n{sub 0}∼0.48{sub −0.23}{sup +0.41} Gpc{sup −3} yr{sup −1} with power-law indices of n{sub 1}∼1.7{sub −0.5}{sup +0.6} and n{sub 2}∼−5.9{sub −0.1}{sup +5.7} for GRBs above and below a break point of z{sub 1}∼6.8{sub −3.2}{sup +2.8}. This methodology is able to improve upon earlier studies by more accurately modeling Swift detection and using this for fully Bayesian model fitting.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Qubit Lattice Algorithms Based on the Schrödinger-Dirac Representation of Maxwell Equations and Their Extensions

It is well known that Maxwell equations can be expressed in a unitary Schrodinger-Dirac representation for homogeneous media. However, difficulties arise when considering inhomogeneous media. A Dyson map points to a unitary field qubit basis, but the standard qubit lattice algorithm of interleaved unitary collision-stream operators must be augmented by some sparse non-unitary potential operators that recover the derivatives on the refractive indices. Here, the effect of the steepness of these derivatives on two-dimensional scattering is examined with simulations showing quite complex wavefronts emitted due to transmissions/reflections within the dielectric objects. Maxwell equations are extended to handle dissipation using Kraus operators. Then, our theoretical algorithms are extended to these open quantum systems. A quantum circuit diagram is presented as well as estimates on the required number of quantum gates for implementation on a quantum computer.

2D electromagnetic scattering↗