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TaTi_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution binary alloys tantalum-titanium (Ta-Ti). The electronic structures of alloys have been calculated using Vienna Ab initio Simulation Package (VASP). Within this package the DFT approach is used to reduce many-body Schrodinger equation to set of single particle Kohn-Sham (KS) equations. The generalized electronic exchange-correlation functional is described by generalized gradient approximation with the Perdew-Burke-Ernzerhof parametrization. The electron-ion interactions is described by pseudopotentials developed within the plane-wave basis projector augmented-wave (PAW) approach. These pseudopotentials are available at the VASP portal (http://cms.mpi.univie.ac.at/vasp/). Our calculations have been run with the pseudopotentials treating s and p semi-core states as valence in case for the elements Hf and Nb. The electronic densities and potentials are expanded over plane-waves with energy cutoff of 350 eV. 2x2x2 k-mesh and normal precision were used. The alloys were modeled by supercell containing 128 randomly distributed atoms. At initial step the atoms occupy perfect bcc lattice cites. This initial structure was optimized until energy changes less than 1e-6 eV, while forces acting on atoms don't exceed 1e-2 eV/angstrom. The electron-ion interaction is described by PAW pseudopotentials. The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 4. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 3,100 randomized atomic structures over 31 chemical compositions. The calculations have been collected on Air Force HPC11 cluster using the VASP 6.5.1. Additional methodology and file structure information is available in the dataset README.txt file.

36 MATERIALS SCIENCE

HfNb_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution binary alloys hafnium-niobium (Hf-Nb). The electronic structures of alloys have been calculated using Vienna Ab initio Simulation Package (VASP). Within this package the DFT approach is used to reduce many-body Schrodinger equation to set of single particle Kohn-Sham (KS) equations. The generalized electronic exchange-correlation functional is described by generalized gradient approximation with the Perdew-Burke-Ernzerhof parametrization. The electron-ion interactions is described by pseudopotentials developed within the plane-wave basis projector augmented-wave (PAW) approach. These pseudopotentials are available at the VASP portal (http://cms.mpi.univie.ac.at/vasp/). Our calculations have been run with the pseudopotentials treating s and p semi-core states as valence in case for the elements Hf and Nb. The electronic densities and potentials are expanded over plane-waves with energy cutoff of 350 eV. 2x2x2 k-mesh and normal precision were used. The alloys were modeled by supercell containing 128 randomly distributed atoms. At initial step the atoms occupy perfect BCC lattice cites. This initial structure was optimized until energy changes less than 1e-6 eV, while forces acting on atoms don't exceed 1e-2 eV/angstrom. The electron-ion interaction is described by PAW pseudopotentials. The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 4. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 3,029 randomized atomic structures over 31 chemical compositions. Further methodological and structural information is contained in the dataset README.txt file.

36 MATERIALS SCIENCE

Effect of Solvents on Lignin–Surface Interactions via Molecular Dynamics Simulations

Lignin, an essential building block of lignocellulosic biomass, is a potential abundant source of aromatic monomers for the polymer and chemical industry. Reductive catalytic fractionation (RCF) is one promising process that can produce high yields of phenolic monomers and oligomers from lignin under different catalytic conditions. An important choice in optimizing RCF is the selection of solvent; however, detailed insights into solvent effects on lignin behaviors and interactions remain limited. Here, in this work, we perform all-atom molecular dynamics simulations to study the solvation of lignin, solvent-mediated conformational changes, and the interaction of solvated lignin oligomers with model surfaces. We focus on the behavior of an oligomeric lignin model compound in methanol, ethanol, a binary mixture of ethanol and water, and water at both the RCF reaction temperature (473 K) and room temperature. Analysis of structural features of lignin suggests that these three organic solvent systems favorably solvate lignin, resulting in a more extended conformation suitable for catalytic conversion to valuable chemicals. We further introduce model palladium (Pd) and carbon (C) surfaces to understand how solvent choice impacts adsorption onto a representative catalytic surface and support, and to quantify the competition among the reactant and solvent molecules for the surface. Unbiased simulations suggest strong adsorption of lignin on both Pd and C surfaces at 473 K, with notable solvent-mediated differences in adsorption energies. Additionally, our findings indicate that lignin adsorption is promoted by the entropy change resulting from the displacement of solvent molecules from the surface. This study provides a molecular perspective of adsorption of lignin onto varying surfaces, which is a step towards understanding and optimizing the catalytic conversion of lignin into valuable chemicals.

adsorption

VZr_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution binary alloys vanadium-zirconium (V-Zr). The electronic structures of alloys have been calculated using Vienna Ab initio Simulation Package (VASP). Within this package the DFT approach is used to reduce many-body Schrodinger equation to set of single particle Kohn-Sham (KS) equations. The generalized electronic exchange-correlation functional is described by generalized gradient approximation with the Perdew-Burke-Ernzerhof parametrization. The electron-ion interactions is described by pseudopotentials developed within the plane-wave basis projector augmented-wave (PAW) approach \cite{PAW}. These pseudopotentials are available at the VASP portal (http://cms.mpi.univie.ac.at/vasp/). Our calculations have been run with the pseudopotentials treating s and p semi-core states as valence in case for the elements V and Zr. The electronic densities and potentials are expanded over plane-waves with energy cutoff of 350 eV. 2x2x2 k-mesh and normal precision were used. The alloys were modeled by supercell containing 128 randomly distributed atoms. At initial step the atoms occupy perfect bcc lattice cites. This initial structure was optimized until energy changes less than 1e-6 eV, while forces acting on atoms don't exceed 1e-2 eV/angstrom. The electron-ion interaction is described by PAW pseudopotentials. The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 4. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 3,100 randomized atomic structures over 31 chemical compositions.

36 MATERIALS SCIENCE

A Simulator for Neyer Tests of Explosives

Explosives and explosive devices such as detonators are typically tested by applying a range of stimuli such as voltage or mechanical shock, and recording binary “detonated/did not detonate” responses. These are analyzed using maximum likelihood or generalized linear models to provide estimates of quantities such as the all-fire and no-fire points. Given that the true threshold for detonation is unknown a priori , sequential design methods are typically used to optimize the set of test points. One popular method, implemented in commercial software, is Neyer’s algorithm. To support simulation and experimental design, we have developed code in the R programming language to duplicate the functions of the Neyer software. We provide code for the simulator along with a description and examples of usage.

42 ENGINEERING

A partitioning strategy for nonuniform problems on multiprocessors

The partitioning of a problem on a domain with unequal work estimates in different subddomains is considered in a way that balances the work load across multiple processors. Such a problem arises for example in solving partial differential equations using an adaptive method that places extra grid points in certain subregions of the domain. A binary decomposition of the domain is used to partition it into rectangles requiring equal computational effort. The communication costs of mapping this partitioning onto different microprocessors: a mesh-connected array, a tree machine and a hypercube is then studied. The communication cost expressions can be used to determine the optimal depth of the above partitioning.

Berger, M. J.

A partitioning strategy for nonuniform problems on multiprocessors

The partitioning of a problem on a domain with unequal work estimates in different subdomains is considered in a way that balances the work load across multiple processors. Such a problem arises for example in solving partial differential equations using an adaptive method that places extra grid points in certain subregions of the domain. A binary decomposition of the domain is used to partition it into rectangles requiring equal computational effort. The communication costs of mapping this partitioning onto different microprocessors: a mesh-connected array, a tree machine and a hypercube is then studied. The communication cost expressions can be used to determine the optimal depth of the above partitioning.

Berger, Marsha J.

Design of Ternary Correlation Filters to Reduce Probability of Error

The problem of designing ternary phase and amplitude filters (TPAF's) that reduce the probability of image misclassification for a two-class image set is studied. The Fisher ratio is used as a measure of the correct classification rate, and an attempt is made to maximize this quantity in the filter designs. Given the nonanalytical nature of the design problem, a simulated annealing optimization technique is employed. Computer simulation results are presented for several cases including single in-class and out-of-class image sets and multiple image sets corresponding to the design of synthetic discriminant function filters. Significant improvements are found in expected rates of correct classification in comparison to binary phase-only filters and other TPAF designs. Approaches to accelerate the filter design process are also discussed.

Downie, John D.

Automated Pneumothorax Diagnosis using Deep Neural Networks

Thoracic ultrasound can provide information leading to rapid diagnosis of pneumothorax with improved accuracy over the standard physical examination and with higher sensitivity than anteroposterior chest radiography. However, the clinical We have Furthermore, remote environments, such as the battlefield or deep-space exploration, may lack expertise for diagnosing developed an automated image interpretation pipeline for the analysis of thoracic ultrasound data and the classification of pneumothorax events to provide decision support in such situations. Our pipeline consists of image preprocessing, data augmentation, and deep learning architectures for medical diagnosis. In this work, we demonstrate that robust, accurate interpretation of chest images and video can be achieved using deep neural networks. A number of novel image processing techniques were employed to achieve this result. Affine transformations were applied for data augmentation. Hyperparameters were optimized for learning rate, dropout regularization, batch size, and epoch iteration by a sequential model-based Bayesian approach. In addition, we utilized pretrained architecturesinterpretation of a patient medical image is highly operator dependent. certain pathologies., applying transfer learning and fine-tuning techniques to fully connected layers. Our pipeline yielded binary classification validation accuracies of 98.3% for M-mode images and 99.8% with B-mode video frames.

US Army collaboration

Towards large-scale quantum optimization solvers with few qubits

Quantum computers hold the promise of more efficient combinatorial optimization solvers, which could be game-changing for a broad range of applications. However, a bottleneck for materializing such advantages is that, in order to challenge classical algorithms in practice, mainstream approaches require a number of qubits prohibitively large for near-term hardware. Here we introduce a variational solver for MaxCut problems over $m={{\mathcal{O}}}({n}^{k})$ binary variables using only n qubits, with tunable k > 1. The number of parameters and circuit depth display mild linear and sublinear scalings in m , respectively. Moreover, we analytically prove that the specific qubit-efficient encoding brings in a super-polynomial mitigation of barren plateaus as a built-in feature. Altogether, this leads to high quantum-solver performances. For instance, for m = 7000, numerical simulations produce solutions competitive in quality with state-of-the-art classical solvers. In turn, for m = 2000, experiments with n = 17 trapped-ion qubits feature MaxCut approximation ratios estimated to be beyond the hardness threshold 0.941. Our findings offer an interesting heuristics for quantum-inspired solvers as well as a promising route towards solving commercially-relevant problems on near-term quantum devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

Enhancing Electron Microscopy Image Classification Using Data Augmentation

Manual labeling for machine learning tasks such as image classification is tedious and labor-intensive; as a result, scientific datasets suitable for deep learning applications are scarce and limited. While data augmentation techniques have shown promise for extending image datasets, very little work has been done to understand the impact of combining multiple augmentation methods sequentially or the limits of their effectiveness when combined. Our work addresses this gap by examining how standard and combinatorial data augmentation affects the performance of machine learning models when trained on small datasets for label classification tasks. For our analysis, we generate single, double and quadruple-augmented datasets for a microscopy image classification task using six standard augmentation methods, and compare the resultant improvements observed in binary classification accuracy with three standard image classification models (DenseNet169, MobileNetV2, ResNet101V2). Our experiments show a non-monotonic relationship between the number of simultaneous augmentation methods and classification accuracy, indicating that there is a trade-off between the degree of augmentation and the model performance. These findings suggest that the optimal number of augmentation methods will vary by domain and use case. We also find that the order in which augmentation methods are applied to a limited dataset matters when combining augmentation schemes, with our use case showing performance differences up to 2.6% when the augmentation order is reversed for double-augmented datasets. Our work offers insights to the limits of data augmentation when working on image classification tasks with limited datasets.

Welsman, Jordan A

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format

Advances in mass spectrometry (MS) instrumentation, such as higher resolution, faster scan speeds, and improved sensitivity, have significantly increased the volume and complexity of data. The growing adoption of imaging and ion mobility further amplifies these challenges across MS-based omics fields, including proteomics, metabolomics, and lipidomics. While these technologies unlock new possibilities, they also present significant challenges in data management, storage, and accessibility. Existing open formats, such as the XML-based community standards mzML and imzML, struggle to meet the demands of modern MS workflows due to their large file sizes, slow data access, and limited metadata support. Vendor-specific formats, while optimized for proprietary instruments, lack interoperability, comprehensive metadata support and long-term archival reliability. This white paper lays the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multi-dimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will enable enhanced interoperability across platforms, seamless support for complex workflows including ion mobility and MS imaging, and faster data access compared to existing community formats such as mzML. Its design will ensure data is managed in compliance with regulatory standards, essential for applications such as precision medicine and chemical safety, where long-term data integrity and accessibility are critical. For vendors, mzPeak provides a streamlined, open alternative to proprietary formats, reducing the burden of regulatory compliance while aligning with the industry's push for transparency and standardization. By offering a high-performance, interoperable solution, mzPeak positions vendors to meet customer demands for sustainable data management tools which will be able to handle emerging and future data types and workflows. mzPeak aspires to become the cornerstone of MS data management, empowering researchers, vendors, and developers to innovate and collaborate more effectively.

data formats

Reducing the Parameter Dependency of Phase-Picking Neural Networks with Dice Loss

Training a neural network for picking seismic phase arrivals has been commonly posed as a segmentation problem. It is a highly imbalanced segmentation problem in the sense that the background vastly dominates the foreground because we are trying to pick the optimal single sample point that represents the arrival of a seismic phase in a many seconds long time window. Here, we test the Dice loss, which is a preferred loss function for highly imbalanced image segmentation problems. We show that phase-picking neural networks trained on the Dice loss behave in a binary fashion for which the prediction output is almost always either nearly 1 or nearly 0. This feature removes the strong dependence of data processing workflows on the prediction score threshold, which is an otherwise critical parameter to determine when using neural networks trained on the cross-entropy loss. When strategically used, models trained on the Dice loss can reduce the parameter dependency of machine learning-based seismic monitoring.

58 GEOSCIENCES

A Novel Gene Stacking Method in Plant Transformation Utilizing Split Selectable Markers

Gene stacking, the process of introducing multiple genes into a single plant to enhance desired traits, is essential for plant genetic improvement through both conventional breeding and genetic transformation. In general, transformation-based gene stacking can be achieved through either co-transformation to simultaneously introduce multiple genes or sequential multi-round transformation. While co-transformation is generally faster and more efficient than sequential multi-round transformation, it often requires two selectable marker genes, which confer resistance to antibiotics, for selecting transgenic events. However, in most cases, there is only one best selectable marker gene for a specific plant species or genotype. Also, it is harder to optimize the concentrations of two antibiotics for co-transformation than using one antibiotic for selecting transgenic events. To overcome this challenge, we recently developed an innovative split selectable marker system for plant co-transformation, allowing the use of one selectable marker gene to select transgenic events. This method involves constructing two binary vectors, each carrying a subset of genes of interest and a partial fragment of the selectable marker gene, which is connected to a partial intein fragment. Following Agrobacterium -mediated co-transformation, plants harboring both binary vectors are selected using a single antibiotic, such as kanamycin. This split-marker system can be used to co-transform multiple genes into both herbaceous and woody plants, accelerating genetic improvement of polygenic traits or integrative improvement of multiple traits to simultaneously increase crop yield and quality.

59 BASIC BIOLOGICAL SCIENCES

Asymmetric three-beam binary optic grating

Binary and diffractive optical components are finding many applications in optical systems and integrated optical devices. A recent application required the development of a two-dimensional diffraction grating to perform an asymmetric, three-beam fanout. In this paper, techniques are presented for the design of arbitrary fanout grating devices. Modeling and optimization processes are demonstrated for the three-beam grating. The counter-intuitive results of the initial design are discussed, and experimental data verifying performance are presented.

Kathman, Alan D.

The First Diffraction-Limited Images from the W. M. Keck Telescope

The first diffraction limited, 0.05s resolution, images on the W. M. Keck Telescope have been obtained at a wavelength of 2.2 micrometers. These images were part of an experiment to test the suitability of the Keck Telescope for speckle imaging. In order to conduct this test, it was necessary to modify the pixel scale of the Keck facility Near Infrared Camera (NIRC) to optimally sample the spatial frequencies made available by the Keck telescope. The design and implementation of the external reimaging optics, which convert the standard fl25 beam from the secondary mirror to fl182, are described here. Techniques for reducing speckle data with field rotation on an alt-az telescope are also described. Three binary stars were observed in this experiment with separations as small as 0.05s. With only 100 frames of data on each, a dynamic range of at least 3.5 mag was achieved in all cases. These observations imply that a companion as faint as 14.5 mag at 2.2 micrometers could be detected around an 11th magnitude point source.

Matthews, K.

Synergistic CuWO 4 /NiS 2 Binary Nanostructures for Efficient Photocatalytic Hydrogen Production

A viable and ecologically safe method for producing green hydrogen is photocatalytic hydrogen (H 2 ) production. However, the development of effective semiconductor materials with improved activity and long-term stability is still a major obstacle. Here, in this work, we report the development of a broadband-gap, UV light-responsive CuWO 4 /NiS 2 nanocomposite using simple hydrothermal and wet impregnation techniques. The hybrid systems, with photocatalytic presentation, were thoroughly assessed using spectroscopic, photophysical, and microscopic characterization methods. The optimized CuWO 4 /NiS 2 nanostructure demonstrated an impressive H 2 generation rate of 28.2 mmol h –1 g –1 under light irradiation, which is roughly 2.71 and 3.28 times greater than those of pristine CuWO 4 (10.4) and NiS 2 (8.6 mmol h -1 g (cat) -1 ), respectively. The enhanced presentation is ascribed to the synergetic interface between the coupled semiconductors, which facilitates the formation of a nanostructure. This arrangement inhibits electron–hole recombination and encourages effective charge carrier parting. Additionally, compared with pristine CuWO 4 and NiS 2 , respectively, the CuWO 4 /NiS 2 composite showed a noticeably greater photocurrent density. The developed nanostructured CuWO 4 /NiS 2 displayed a 28.6% quantum efficiency at 450 nm. These outcomes validate CuWO 4 /NiS 2 ’s significant aptitude as a non-noble-metal photocatalyst for the production of sustainable hydrogen.

CuWO4/NiS2

On Approaching the Ultimate Limits of Communication Using a Photon-Counting Detector

Coherent states achieve the Holevo capacity of a pure-loss channel when paired with an optimal measurement, but a physical realization of this measurement scheme is as of yet unknown, and it is also likely to be of high complexity. In this paper, we focus on the photon-counting measurement and study the photon and dimensional efficiencies attainable with modulations over classical- and nonclassical-state alphabets. We analyze two binary modulation architectures that improve upon the dimensional versus photon efficiency tradeoff achievable with the state-of-the-art coherent-state on-off keying modulation. We show that at high photon efficiency these architectures achieve an efficiency tradeoff that differs from the best possible tradeoff--determined by the Holevo capacity--by only a constant factor. The first architecture we analyze is a coherent-state transmitter that relies on feedback from the receiver to control the transmitted energy. The second architecture uses a single-photon number-state source.

photon-counting measurement