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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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints

Abstract Background Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cycles (TICs) causing unbounded metabolic flux ranges are often encountered. TICs satisfy the mass balance and directionality constraints but violate the second law of thermodynamics. Current practices involve implementing additional constraints to ensure not only optimal but also loopless flux distributions. However, the mixed integer linear programming problems required to solve become computationally intractable for genome-scale metabolic models. Results We aimed to identify the fewest needed constraints sufficient for optimality under the loopless requirement. We found that loopless constraints are required only for the reactions that share elementary flux modes representing TICs with reactions that are part of the objective function. We put forth the concept of localized loopless constraints (LLCs) to enforce this minimal required set of loopless constraints. By combining with a novel procedure for minimal null-space calculation, the computational time for loopless flux variability analysis (ll-FVA) is reduced by a factor of 10–150 compared to the original loopless constraints and by 4–20 times compared to the current fastest method Fast-SNP with the percent improvement increasing with model size. Importantly, LLCs offer a scalable strategy for loopless flux calculations for multi-compartment/multi-organism models of large sizes, for example, shortening the CPU time for ll-FVA from 35 h to less than 2 h for a model with more than104 reactions. Availability and implementation Matlab functions are available in the Supplementary Material or at https://github.com/maranasgroup/lll-FVA Supplementary information Supplementary data are available at Bioinformatics online.

Chan, Siu H. J. (ORCID:000000027707656X)↗
DOE OSTI2018

Clusterdv: a simple density-based clustering method that is robust, general and automatic

Abstract Motivation How to partition a dataset into a set of distinct clusters is a ubiquitous and challenging problem. The fact that data vary widely in features such as cluster shape, cluster number, density distribution, background noise, outliers and degree of overlap, makes it difficult to find a single algorithm that can be broadly applied. One recent method, clusterdp, based on search of density peaks, can be applied successfully to cluster many kinds of data, but it is not fully automatic, and fails on some simple data distributions. Results We propose an alternative approach, clusterdv, which estimates density dips between points, and allows robust determination of cluster number and distribution across a wide range of data, without any manual parameter adjustment. We show that this method is able to solve a range of synthetic and experimental datasets, where the underlying structure is known, and identifies consistent and meaningful clusters in new behavioral data. Availability and implementation The clusterdv is implemented in Matlab. Its source code, together with example datasets are available on: https://github.com/jcbmarques/clusterdv. Supplementary information Supplementary data are available at Bioinformatics online.

Marques, João C.↗
DOE OSTI2011

Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites

Finding conserved motifs in genomic sequences represents one of essential bioinformatic problems. However, achieving high discovery performance without imposing substantial auxiliary constraints on possible motif features remains a key algorithmic challenge. This work describes BAMBI—a sequential Monte Carlo motifidentification algorithm, which is based on a position weight matrix model that does not require additional constraints and is able to estimate such motif properties as length, logo, number of instances and their locations solely on the basis of primary nucleotide sequence data. Furthermore, should biologically meaningful information about motif attributes be available, BAMBI takes advantage of this knowledge to further refine the discovery results. In practical applications, we show that the proposed approach can be used to find sites of such diverse DNA-binding molecules as the cAMP receptor protein (CRP) and Din-family site-specific serine recombinases. Results obtained by BAMBI in these and other settings demonstrate better statistical performance than any of the four widely-used profile-based motif discovery methods: MEME, BioProspector with BioOptimizer, SeSiMCMC and Motif Sampler as measured by the nucleotide-level correlation coefficient. Additionally, in the case of Din-family recombinase target site discovery, the BAMBI-inferred motif is found to be the only one functionally accurate from the underlying biochemical mechanism standpoint. C++and Matlab code is available at http://www.ee.columbia.edu/guido/ BAMBI or http://genomics.lbl.gov/BAMBI/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2010

Numerical estimation of the relative entropy of entanglement

We propose a practical algorithm for the calculation of the relative entropy of entanglement (REE), defined as the minimum relative entropy between a state and the set of states with positive partial transpose. Our algorithm is based on a practical semidefinite cutting plane approach. In low dimensions the implementation of the algorithm in matlab provides an estimation for the REE with an absolute error smaller than 10{sup -3}.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Comparing, optimizing, and benchmarking quantum-control algorithms in a unifying programming framework

For paving the way to novel applications in quantum simulation, computation, and technology, increasingly large quantum systems have to be steered with high precision. It is a typical task amenable to numerical optimal control to turn the time course of pulses, i.e., piecewise constant control amplitudes, iteratively into an optimized shape. Here, we present a comparative study of optimal-control algorithms for a wide range of finite-dimensional applications. We focus on the most commonly used algorithms: GRAPE methods which update all controls concurrently, and Krotov-type methods which do so sequentially. Guidelines for their use are given and open research questions are pointed out. Moreover, we introduce a unifying algorithmic framework, DYNAMO (dynamic optimization platform), designed to provide the quantum-technology community with a convenient matlab-based tool set for optimal control. In addition, it gives researchers in optimal-control techniques a framework for benchmarking and comparing newly proposed algorithms with the state of the art. It allows a mix-and-match approach with various types of gradients, update and step-size methods as well as subspace choices. Open-source code including examples is made available at http://qlib.info.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2011

Relativistic distorted-wave analysis of quasielastic proton-nucleus scattering

A relativistic distorted-wave impulse approximation formalism is presented for the calculation of quasielastic proton-nucleus scattering. It is shown that the double differential cross section may be written as a contraction between the hadronic tensor (describing the projectile and ejectile) and the polarization tensor (describing the nuclear target) and that this mathematical structure also holds for the case where distortions are included. The eikonal approximation is used to introduce distortions in the wave functions, and the nuclear response is described using a Fermi gas model. The highly oscillatory nine-dimensional integrand contained in the expression for the double differential cross section is computed using a novel technique based on combining traditional Gaussian integration methods with the powerful fitting functions in the matlab programming language. This work has successfully calculated the distorted-wave quasielastic differential cross section for proton-nucleus scattering within a fully relativistic framework. It is found that the distortions lead to a reduction in the double differential cross section and have a negligible effect on the computed spin observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

GIWAXS-SIIRkit: scattering intensity, indexing and refraction calculation toolkit for grazing-incidence wide-angle X-ray scattering of organic materials

Grazing-incidence wide-angle X-ray scattering (GIWAXS) has become an increasingly popular technique for quantitative structural characterization and comparison of thin films. For this purpose, accurate intensity normalization and peak position determination are crucial. At present, few tools exist to estimate the uncertainties of these measurements. Here, a simulation package is introduced called GIWAXS-SIIRkit , where SIIR stands for scattering intensity, indexing and refraction. Furthermore, the package contains several tools that are freely available for download and can be executed in MATLAB. The package includes three functionalities: estimation of the relative scattering intensity and the corresponding uncertainty based on experimental setup and sample dimensions; extraction and indexing of peak positions to approximate the crystal structure of organic materials starting from calibrated GIWAXS patterns; and analysis of the effects of refraction on peak positions. Additionally, each tool is based on a graphical user interface and designed to have a short learning curve. A user guide is provided with detailed usage instruction, tips for adding functionality and customization, and exemplary files.

36 MATERIALS SCIENCE↗
DOE OSTI2020

XtalCAMP: a comprehensive program for the analysis and visualization of scanning Laue X-ray micro-/nanodiffraction data

XtalCAMP is a software package based on the MATLAB platform, which is suitable for, but not limited to, the analysis and visualization of scanning Laue X-ray micro-/nanodiffraction data. The main objective of the software is to provide complementary functionalities to the Laue indexing software packages used at several synchrotron beamlines. Here, the graphical user interfaces allow the easy analysis of characteristic microstructure features, including real-time intensity mapping for a quick examination of phase, grain and defect distribution, 2D color-coded mapping of microstructural properties from the output of other Laue indexing software, crystal orientation visualization, grain boundary characterization based on orientation/misorientation calculation, principal strain/stress analysis, and strain ellipsoid representation, as well as a series of additional toolkits. As an example, XtalCAMP is applied to the microstructural investigation of a solution-heat-treated Ni-based superalloy manufactured using a laser 3D-printing technique, and a deformed natural quartzite from Val Bregaglia in the Central Alps.

36 MATERIALS SCIENCE↗
DOE OSTI2016

HiSPoD : a program for high-speed polychromatic X-ray diffraction experiments and data analysis on polycrystalline samples

Here, a high-speed X-ray diffraction technique was recently developed at the 32-ID-B beamline of the Advanced Photon Source for studying highly dynamic, yet non-repeatable and irreversible, materials processes. In experiments, the microstructure evolution in a single material event is probed by recording a series of diffraction patterns with extremely short exposure time and high frame rate. Owing to the limited flux in a short pulse and the polychromatic nature of the incident X-rays, analysis of the diffraction data is challenging. Here, HiSPoD , a stand-alone Matlab-based software for analyzing the polychromatic X-ray diffraction data from polycrystalline samples, is described. With HiSPoD , researchers are able to perform diffraction peak indexing, extraction of one-dimensional intensity profiles by integrating a two-dimensional diffraction pattern, and, more importantly, quantitative numerical simulations to obtain precise sample structure information.

36 MATERIALS SCIENCE↗
DOE OSTI2022

AXEAP : a software package for X-ray emission data analysis using unsupervised machine learning

The Argonne X-ray Emission Analysis Package ( AXEAP ) has been developed to calibrate and process X-ray emission spectroscopy (XES) data collected with a two-dimensional (2D) position-sensitive detector. AXEAP is designed to convert a 2D XES image into an XES spectrum in real time using both calculations and unsupervised machine learning. AXEAP is capable of making this transformation at a rate similar to data collection, allowing real-time comparisons during data collection, reducing the amount of data stored from gigabyte-sized image files to kilobyte-sized text files. With a user-friendly interface, AXEAP includes data processing for non-resonant and resonant XES images from multiple edges and elements. AXEAP is written in MATLAB and can run on common operating systems, including Linux, Windows, and MacOS.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Framework for X-ray mirror surface shape fitting

For accurate characterization of grazing-incidence X-ray mirrors, we present a comprehensive framework to fit measured surface shapes (either slope or height) of X-ray mirrors used in synchrotron radiation and free-electron laser facilities. We summarize the closed-form expressions of some typical surface shapes of X-ray mirrors including elliptic cylinders, hyperbolic cylinders, ellipsoids, hyperboloids, and diaboloids. This framework is composed of four layers: definition of standard shapes with closed-form expressions, generation of theoretical surface with pose parameters (six degrees of freedom defining an object's position and orientation relative to a coordinate system), parameter optimization with the ability to select which parameters are fit and which are held constant, and the development of user-friendly fitting function wrappers for particular fitting tasks. A few practical fitting examples are demonstrated to verify the effectiveness of the proposed fitting framework. We discuss the physical meanings of the fitting parameters, and provide several examples using the elliptic cylinder and ellipsoid shapes to highlight some features of the framework. Moreover, we provide the presented framework as open-source codes (MATLAB and Python codes available at https://github.com/nsls2omf/xmf) to the community to encourage academic collaboration and further improvements.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Genetic Algorithm-Based Commutation Angle Control for Torque Ripple Mitigation in Switched Reluctance Motor Drives

This work addresses the application of the Genetic Algorithm (GA) technique to optimize the commutation angles of a 2 kW 8/6 switched reluctance machine (SRM). The primary goal is to reduce the well-known drawback of SRMs: the torque ripple. Firstly, the machine was modeled in Matlab /Simulink ® using lookup tables obtained via finite element method (FEM) simulations. Subsequently, the model was used to perform the GA routine aiming to find the optimal phase commutation angles that minimize the torque ripple factor. Notably, the torque performance of the SRM was significantly affected by the commutation angles during the search for the optimal solution. Afterwards, the GA results for four different operation points were verified experimentally through a developed drive platform with digital signal processor-based (DSP) control and an asymmetric bridge converter. As showed by the experiments, the proposed approach was suitable to reduce the torque ripple by more than 50% for one of the evaluated operating points. Furthermore, it was confirmed that the torque ripple mitigation led to acoustic noise improvement.

42 ENGINEERING↗
DOE OSTI2018

Radioisotope power source dose estimation tool (RPS-DET)

The purpose of this work is to develop a radioisotope power source dose estimation tool (RPS-DET) capable of rapidly predicting accurate neutron and gamma-ray flux/dose implications from various radioisotope power sources (RPSs). RPS-DET can use this information to calculate the flux/dose incident on or absorbed by nearby humans, materials, and electronics over a complex mission lifetime. This simulation tool uses a Matlab user interface to combine common geometry scenarios for traditional and new RPS design configurations to write a particle-transport simulation using Monte Carlo N-Particle (MCNP) 6, which provides results that are automatically post-processed for interactive analysis. The user defines the average age of the PuO2fuel, which determines the appropriate time-dependent gamma-ray and neutron spectra, along with the desired RPS and local environment for the simulation. Results for a given simulation are gamma-ray, neutron, and combined flux spectra, whole-body effective dose for humans, and absorbed dose in silicon for electronics. This work has been benchmarked against measurements of existing RPS units and has been determined to predict neutron and gamma flux, absorbed dose, and dose equivalent within 50% of simulation uncertainties.

Smith, Michael↗
DOE OSTI2011

Investigations of laser plasmas dynamics by means of real and virtual Langmuir probes

In this paper we propose a novel technique for LPP-Laser Produced Plasmas investigation, combining high time resolved measurements using compact Langmuir Probes with the output of a theoretical model called HYBLAS developed on purpose, which is able to simulate the charged particles collected by a so-called virtual probe. It will be shown that with an appropriate experimental set-up and with the use of a Matlab software able to accurately analyze the experimental I-V curves, laser plasmas can be investigated properly even if the probe is placed very close to the target surface. This permits not only to study the plume expansion with a high temporal resolution, but also to estimate correctly the self-generated coulomb electric field inside the plume and to detect the inner structure of the the first upcoming expanding plasma. HYBLAS is able to predict and describe the plume expansion at relatively low power densities and is a powerful method to compare directly the experimental current signals with the numerical results if the initial conditions are settled properly. A direct comparison of the theoretical data with the experimental ones realized on different metal targets shows that our method is able to predict properly the overall plasma expansion in the nanosecond laser pulse duration regime. The virtual probe method was moreover tested by comparing the numerical results with another numerical code called MULTI, which simulate the expansion by combining the hydrodynamics equations to a multigroup method in order to include the radiation transport. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

50-kW 1kV DC bus air-cooled inverter with 1.7 kV SiC MOSFETs and 3D-printed novel power module packaging structure for grid applications

The traditional heatsink design technologies for forced air-cooling and power semiconductors with low junction temperatures have constrained the converters to be designed with massive heatsinks. The low power losses of WBG device technology and higher junction temperature operation over a wide operating range of power have not been fully utilized with liquid-cooled systems. The other major limitation has also been the traditional power module packaging “stack” approach with baseplate. This paper presents a novel power stage design which involves 1.7 kV silicon carbide (SiC) MOSFETs, a heatsink design with Genetic Algorithm (GA) and built using 3D printing technology, and a novel integrated modular power module for high power density. The air-cooled module assembly has a SiC MOSFET phase leg module with split high-side and low-side switches and a gate driver with cross-talk and short circuit protection functions. The heatsink design was modeled using a co-simulation environment with finite element analysis software and GA in MATLAB and COMSOL. The proposed concepts were verified and validated through experiments at each stage of development. The power stage was evaluated at 800V, 900 V, and 1kV for 20 kHz switching frequency and 50-kW load. The experimental results show that the CEC efficiency is 98.4 %. In addition to the efficiency, a power density of 75 W/in 3 was also achieved.

Chinthavali, Madhu Sudhan↗
DOE OSTI2019

Single-Submodule Open-Circuit Fault Diagnosis for a Modular Multi-level Converter Using Artificial Intelligent-based Techniques

Modular multi-level converters (MMCs) are one of the promising topologies in recent years for medium or high voltage applications. They are considered as the next generation DC/AC converters for medium/high voltage (MV/HV) motor drive applications due to their transform-less structures, high efficiency and modularity. Reliability is one of the most important challenges in MMCs, since a large number of power switching devices are used and each of these devices can be considered as a potential failure point. It is significant to detect and locate the fault accurately and apply appropriate protections in a timely manner. This paper investigates the behavior of the failure submodules and healthy submodules and use artificial neural network (ANN) classification algorithms for singlesubmodule open-circuit fault diagnosis. The ANN algorithm is implemented in field programmable gate array (FPGA) and the ANN parameters training is completed offline in Matlab. Experimental results of the proposed fault diagnosis for a singlemodule open-circuit fault are presented in this paper.

artificial intelligent↗
DOE OSTI2022

A Comprehensive Approach towards Multi-Objective EMI Filter Design Optimization in High-Frequency SiC-Based Motor Drives

With rapid penetration of high-frequency, highdensity power electronics into the industry, controlling the system generated EMI becomes one of the major design challenges. Designing practical optimized EMI filters require simultaneous consideration of multiple aspects - including electromagnetic couplings, magnetic materials, practical component parasitics and their impacts at high-frequencies, and also the overall manufacturing costs. The multi-dimensional nature of the problem often results in overcompensated designs that hurt the system efficiency and power density. This paper focuses on a comprehensive design platform (developed in MATLAB) towards designing high-density, optimized, highly efficient EMI filters by analyzing the generated noise spectrum and evaluating a vast array of potential solutions before outputting an optimized filter solution. The proposed tool includes database-based component selection, optimal topology selection, multistage filter design, overall optimization for volume, mass, cost and total loss. The proposed filter has been thoroughly evaluated in a PSIM simulation environment emulating the hardware in CRD300DA12EXM3, a 300kW three-phase inverter from Wolfspeed with an RL load representing a motor drive application. Furthermore, a 20kHz switching frequency is chosen and impacts of the motor high-frequency characteristics on the generated EMI noise spectrum of the overall system have been analyzed.

42 ENGINEERING↗