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At least 145 records · Page 8

Machine-Learned Manifold-Based Models for Large Eddy Simulation of Turbulent Combustion

Reduced-order manifold combustion models are commonly used to lower the cost of reacting Large Eddy Simulations (LES) and may be derived either from physical principles as in flamelet models or from data-driven methods like Principal Component Analysis (PCA). In either case, neural networks are increasingly used as part of these models to provide a nonlinear mapping between a small set of pre-defined variables that parameterize the manifold and outputs of interest, such as reaction rates. In this work, we propose a new manifold-based modeling approach that combines the definition of the manifold-parameterizing variables (linear combinations of species), the nonlinear mapping to the outputs, and closure of filtered quantities for LES into the structure of a single neural network. This allows the process used to train the neural network to simultaneously optimize both the functional form of the model and the identities of the inputs to the model. The new approach can flexibly incorporate thermochemical data from any combustion system; if trained on data from 1D flames it can be interpreted as an optimized flamelet model, but it can also be used to learn models from data from more complex configurations. This work presents a priori evaluations of the new approach in both contexts. Evaluation using data from 1D premixed flames demonstrates the physical interpretability of the manifold variables generated by the new approach. Evaluation using data from direct numerical simulations of turbulent flames shows improved predictions relative to either flamelet or PCA-based models in a more complex configuration.

47 OTHER INSTRUMENTATION↗

Representation of Probability Density Functions from Orbit Determination using the Particle Filter

Statistical orbit determination enables us to obtain estimates of the state and the statistical information of its region of uncertainty. In order to obtain an accurate representation of the probability density function (PDF) that incorporates higher order statistical information, we propose the use of nonlinear estimation methods such as the Particle Filter. The Particle Filter (PF) is capable of providing a PDF representation of the state estimates whose accuracy is dependent on the number of particles or samples used. For this method to be applicable to real case scenarios, we need a way of accurately representing the PDF in a compressed manner with little information loss. Hence we propose using the Independent Component Analysis (ICA) as a non-Gaussian dimensional reduction method that is capable of maintaining higher order statistical information obtained using the PF. Methods such as the Principal Component Analysis (PCA) are based on utilizing up to second order statistics, hence will not suffice in maintaining maximum information content. Both the PCA and the ICA are applied to two scenarios that involve a highly eccentric orbit with a lower apriori uncertainty covariance and a less eccentric orbit with a higher a priori uncertainty covariance, to illustrate the capability of the ICA in relation to the PCA.

Mashiku, Alinda K.↗

Short-term time variability of Cygnus X-1. II

A complete theory for shot-noise analysis is presented. The theory takes into account the effects of counting statistics, time resolution, and finite observing times on the autocorrelation function and on the moments of data assumed to consist of shot noise plus a steady component. When applied to X-ray observations of Cyg X-1 in the high and low states, the results provide evidence that both the typical correlation time (about 0.5 s) and the fraction of flux in shots (about 30%) are constant, independent of the state. The rate of occurrence of the shots may also be constant at approximately one shot per second, a possibility which, if verified, would imply that the principal difference in time variability in the two states is the amplitude of the shots. We also suggest that the occasionally observed large flares may possibly be just the rare superposition of several shots.

Sutherland, P. G.↗

A cluster analysis method for identification of subpopulations of cells in flow cytometric list-mode arrays

A specialized program was developed for flow cytometric list-mode data using an heirarchical tree method for identifying and enumerating individual subpopulations, the method of principal components for a two-dimensional display of 6-parameter data array, and a standard sorting algorithm for characterizing subpopulations. The program was tested against a published data set subjected to cluster analysis and experimental data sets from controlled flow cytometry experiments using a Coulter Electronics EPICS V Cell Sorter. A version of the program in compiled BASIC is usable on a 16-bit microcomputer with the MS-DOS operating system. It is specialized for 6 parameters and up to 20,000 cells. Its two-dimensional display of Euclidean distances reveals clusters clearly, as does its 1-dimensional display. The identified subpopulations can, in suitable experiments, be related to functional subpopulations of cells.

Li, Z. K.↗

Global Monitoring of Terrestrial Chlorophyll Fluorescence from Moderate-Spectral-Resolution Near-Infrared Satellite Measurements: Methodology, Simulations, and Application to GOME-2

Globally mapped terrestrial chlorophyll fluorescence retrievals are of high interest because they can provide information on the functional status of vegetation including light-use efficiency and global primary productivity that can be used for global carbon cycle modeling and agricultural applications. Previous satellite retrievals of fluorescence have relied solely upon the filling-in of solar Fraunhofer lines that are not significantly affected by atmospheric absorption. Although these measurements provide near-global coverage on a monthly basis, they suffer from relatively low precision and sparse spatial sampling. Here, we describe a new methodology to retrieve global far-red fluorescence information; we use hyperspectral data with a simplified radiative transfer model to disentangle the spectral signatures of three basic components: atmospheric absorption, surface reflectance, and fluorescence radiance. An empirically based principal component analysis approach is employed, primarily using cloudy data over ocean, to model and solve for the atmospheric absorption. Through detailed simulations, we demonstrate the feasibility of the approach and show that moderate-spectral-resolution measurements with a relatively high signal-to-noise ratio can be used to retrieve far-red fluorescence information with good precision and accuracy. The method is then applied to data from the Global Ozone Monitoring Instrument 2 (GOME-2). The GOME-2 fluorescence retrievals display similar spatial structure as compared with those from a simpler technique applied to the Greenhouse gases Observing SATellite (GOSAT). GOME-2 enables global mapping of far-red fluorescence with higher precision over smaller spatial and temporal scales than is possible with GOSAT. Near-global coverage is provided within a few days. We are able to show clearly for the first time physically plausible variations in fluorescence over the course of a single month at a spatial resolution of 0.5 0.5. We also show some significant differences between fluorescence and coincident normalized difference vegetation indices (NDVI) retrievals.

Fluorescence↗

Global Monitoring of Terrestrial Chlorophyll Fluorescence from Moderate-spectral-resolution Near-infrared Satellite Measurements: Methodology, Simulations, and Application to GOME-2

Globally mapped terrestrial chlorophyll fluorescence retrievals are of high interest because they can provide information on the functional status of vegetation including light-use efficiency and global primary productivity that can be used for global carbon cycle modeling and agricultural applications. Previous satellite retrievals of fluorescence have relied solely upon the filling-in of solar Fraunhofer lines that are not significantly affected by atmospheric absorption. Although these measurements provide near-global coverage on a monthly basis, they suffer from relatively low precision and sparse spatial sampling. Here, we describe a new methodology to retrieve global far-red fluorescence information; we use hyperspectral data with a simplified radiative transfer model to disentangle the spectral signatures of three basic components: atmospheric absorption, surface reflectance, and fluorescence radiance. An empirically based principal component analysis approach is employed, primarily using cloudy data over ocean, to model and solve for the atmospheric absorption. Through detailed simulations, we demonstrate the feasibility of the approach and show that moderate-spectral-resolution measurements with a relatively high signal-to-noise ratio can be used to retrieve far-red fluorescence information with good precision and accuracy. The method is then applied to data from the Global Ozone Monitoring Instrument 2 (GOME-2). The GOME-2 fluorescence retrievals display similar spatial structure as compared with those from a simpler technique applied to the Greenhouse gases Observing SATellite (GOSAT). GOME-2 enables global mapping of far-red fluorescence with higher precision over smaller spatial and temporal scales than is possible with GOSAT. Near-global coverage is provided within a few days. We are able to show clearly for the first time physically plausible variations in fluorescence over the course of a single month at a spatial resolution of 0.5 deg × 0.5 deg. We also show some significant differences between fluorescence and coincident normalized difference vegetation indices (NDVI) retrievals.

remote sensing↗

Reducing the matrix effect in mass spectral imaging of biofilms using flow-cell culture

The interactions between soil microorganisms and soil minerals play a crucial role in the formation and evolution of minerals and the stability of soil aggregates. Due to the heterogeneity and diversity of the soil environment, the under-standing of the functions of bacterial biofilms in soil minerals at the microscale is limited. A soil mineral-bacterial biofilm system was used as a model in this study, and it was analyzed by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to acquire molecular level information. Static culture in multi-wells and dynamic flow-cell culture in microfluidics of biofilms were investigated. Our results show that more characteristic molecules of biofilms can be observed in SIMS spectra of the flow-cell culture. In contrast, biofilm signature peaks are buried under the mineral components in SIMS spectra in the static culture case. Spectral overlay was used in peak selection prior to performing Principal component analysis (PCA). Comparisons of the PCA results between the static and flow-cell culture show more pronounced molecular features and higher loadings of organic peaks of the dynamic cultured specimens. For example, fatty acids secreted from bacterial biofilm extracellular polymeric substance are likely to be responsible for biofilm dispersal due to mineral treatment up to 48 h. Such findings suggest that the use of microfluidic cells to dynamically culture biofilms be a more suitable method for reducing the matrix effect arisen from the growth medium and minerals as a perturbation fac-tor for improved spectral and multivariate analysis of complex mass spectral data in ToF-SIMS. These results show that the interaction mechanism between biofilms and soil minerals at the molecular level can be better studied using the flow-cell culture and advanced mass spectral imaging techniques like ToF-SIMS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗

Orientational Pair Correlations and Local Structure of Benzonitrile from Molecular Dynamics Simulations with Comparisons to Experiments [plus supplemental information]

Here, we present an experimentally parametrized molecular dynamics study of single-molecule and collective orientational relaxation in neat benzonitrile through the analysis of the reorientational anisotropy and polarizability anisotropy time-correlation function (PA-TCF). The simulations show that the PA-TCF is dominated by collective reorientation after 20 ps. Collective reorientation is found to be slower than single-molecule reorientation by a factor of 1.67, consistent with recent experiments. The simulations provide direct evidence of local antiparallel benzonitrile configurations. These structures, which have been the center of some debate, are responsible for the slower rate of collective vs. single-molecule reorientation in the liquid. Further structural analysis indicates that significant Coulombic interactions between the nitrile group and hydrogen atoms on adjacent molecules play a role in the formation of the antiparallel structures. The single-molecule dynamics reflected in the anisotropy are complex and consist of a ballistic regime, restricted angular diffusion, and spatially anisotropic free diffusion. The principal components of the rotational diffusion tensor are independently obtained and shown to reproduce the free diffusion regime of the anisotropy for each principal axis according to the predictions of a previous theory.

14 SOLAR ENERGY↗

Galactic plane gamma-radiation

Analysis of the SAS 2 data together with the COS B results shows that the distribution of galactic gamma-radiation has several similarities to that of other large-scale tracers of galactic structure. The radiation is primarily confined to a thin disc which exhibits offsets from b = 0 degrees similar to warping at radio frequencies. The principal distinction of the gamma-radiation is a stronger contrast in intensity between the region from 310 to 45 degrees in longitude and the regions away from the center that can be attributed to a variation in cosmic-ray density as a function of position in Galaxy. The diffuse galactic gamma-ray energy spectrum shows no significant variation in direction, and the spectrum seen along the plane is the same as that for the galactic component of the gamma-radiation at high altitudes. The uniformity of the galactic gamma-ray spectrum, the smooth decrease in intensity as a function of altitude, and the absence of any galactic gamma-ray sources at high altitudes indicate a diffuse origin for bulk of the galactic gamma-radiation rather than a collection of localized sources.

Hartman, R. C.↗

Identification of blood protein biomarkers associated with prostate cancer risk using genetic prediction models: analysis of over 140,000 subjects

Prostate cancer (PCa) brings huge public health burden in men. A growing number of conventional observational studies report associations of multiple circulating proteins with PCa risk. However, the existing findings may be subject to incoherent biases of conventional epidemiologic studies. To better characterize their associations, herein, we evaluated associations of genetically predicted concentrations of plasma proteins with PCa risk. In this study, we developed comprehensive genetic prediction models for protein levels in plasma. After testing 1308 proteins in 79 194 cases and 61 112 controls of European ancestry included in the consortia of BPC3, CAPS, CRUK, PEGASUS, and PRACTICAL, 24 proteins showed significant associations with PCa risk, including 16 previously reported proteins and eight novel proteins. Of them, 14 proteins showed negative associations and 10 showed positive associations with PCa risk. For 18 of the identified proteins, potential functional somatic changes of encoding genes were detected in PCa patients in The Cancer Genome Atlas (TCGA). Genes encoding these proteins were significantly involved in cancer-related pathways. We further identified drugs targeting the identified proteins, which may serve as candidates for drug repurposing for treating PCa. In conclusion, this study identifies novel protein biomarker candidates for PCa risk, which may provide new perspectives on the etiology of PCa and improve its therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗

Manifold projection image segmentation for nano-XANES imaging

As spectral imaging techniques are becoming more prominent in science, advanced image segmentation algorithms are required to identify appropriate domains in these images. We present a version of image segmentation called manifold projection image segmentation (MPIS) that is generally applicable to a broad range of systems without the need for training because MPIS uses unsupervised machine learning with a few physically motivated hyperparameters. We apply MPIS to nanoscale x-ray absorption near edge structure (XANES) imaging, where XANES spectra are collected with nanometer spatial resolution. We show the superiority of manifold projection over linear transformations, such as the commonly used principal component analysis (PCA). Moreover, MPIS maintains accuracy while reducing computation time and sensitivity to noise compared to the standard nano-XANES imaging analysis procedure. Finally, we demonstrate how multimodal information, such as x-ray fluorescence data and spatial location of pixels, can be incorporated into the MPIS framework. We propose that MPIS is adaptable for any spectral imaging technique, including scanning transmission x-ray microscopy, where the length scale of domains is larger than the resolution of the experiment.

36 MATERIALS SCIENCE↗

Mass spectral imaging showing the plant growth-promoting rhizobacteria's effect on the Brachypodium awn

The plant growth-promoting rhizobacteria (PGPR) on the host plant surface play a key role in biological control and pathogenic response in plant functions and growth. However, it is difficult to elucidate the PGPR effect on plants. Such information is important in biomass production and conversion. Brachypodium distachyon (Brachypodium), a genomics model for bioenergy and native grasses, was selected as a C3 plant model; and the Gram-negative Pseudomonas fluorescens SBW25 ( P.) and Gram-positive Arthrobacter chlorophenolicus A6 ( A.) were chosen as representative PGPR strains. The PGPRs were introduced to the Brachypodium seed's awn prior to germination, and their possible effects on the seeding and growth were studied using different modes of time-of-flight secondary ion mass spectrometry (ToF-SIMS) measurements, including a high mass-resolution spectral collection and delayed image extraction. We observed key plant metabolic products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and auxin indole-3-acetic acid in the Brachypodium awns. Furthermore, principal component analysis and two-dimensional imaging analysis reveal that the Brachypodium awns are sensitive to the PGPR, leading to chemical composition and morphology changes on the awn surface. Our results show that ToF-SIMS can be an effective tool to probe cell-to-cell interactions at the biointerface. This work provides a new approach to studying the PGPR effects on awn and shows its potential for the research of plant growth in the future.

metabolite↗

A protein scaffold enables hydrogen evolution for a Ni-bisdiphosphine complex

We find that an artificial metalloenzyme acting as a functional biomimic of hydrogenase enzymes was activated by assembly via covalent attachment of the molecular complex, [Ni(PN glycine P) 2 ] 2- , within a structured protein scaffold. Electrocatalytic H2 production was observed from pH 3.0 to 10.0 for the artificial enzyme, while no electrocatalytic activity was observed for similar [Ni(PNP) 2 ] 2+ systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamics Questions Associated with the AERCam Sprint Free-Flyer

The International Space Station will require the development of small robotic vehicles for such tasks as external inspection, monitoring of extravehicular activities (EVA's) and station build-up, and providing additional lighting at EVA worksites. The Autonomous EVA Robotic Camera (AERCam) family of free-flyers is currently being developed at NASA Johnson Space Center to perform these functions; the first member of the family is the AERCam Sprint vehicle. Many interesting dynamical questions are associated with the Sprint free-flyer. For instance, the reaction of a vehicle which is nearly spherically symmetric (such as Sprint) to a stuck-on thruster is significantly more complicated than that obtained for an idealized, perfectly spherical, spacecraft model. In particular, the real spacecraft will experience a form of forced nutation, with convergence towards either its major or minor principal axis, depending on both the applied torque and the mass properties of the vehicle. Furthermore, the body-fixed jet force vector may have a significant component along this principal axis, so giving rise to a considerable net linear acceleration of the spacecraft. The large velocity that can result is very important, as it may lead to collision with the nearby Orbiter, and is completely overlooked in the idealized analysis. This report will firstly briefly describe the stuck-on thruster dynamics of the real vehicle, and outline how the small products of inertia of the spacecraft determine the time constants of the motion. Secondly, the dynamical effects of a failed-off jet on the Sprint free-flyer will be described in more detail, and compared with the stuck-on thruster case. This will help to show whether the two malfunctions should be dealt with differently in flight. Finally, the stuck-on thruster detection software (known as the uncommanded motion algorithm) that is proposed to be flown on the Sprint vehicle will be analyzed, and all possible perturbation sources that may tend to give rise to false stuck-on thruster alarms quantified. It will be shown that false alarms can be triggered by discrete events such as a failed-off thruster, a glancing collision with Orbiter structure, or thruster saturation. They can also be triggered by a combination of errors introduced by constantly present sources such as thrust level errors, thruster misalignment, inertial cross-coupling, angular rate sensor noise, and structural vibrations induced by thruster firings. Based on this fact, the original plan to have the spacecraft enter safe mode whenever the uncommanded motion algorithm is triggered does not appear to be advisable. A better approach seems to be to provide the Sprint pilot with a warning whenever uncommanded motion is detected, and then allow the crew to determine whether safing the vehicle is appropriate.

Williams, Trevor↗

CELCAP: A Computer Model for Cogeneration System Analysis

A description of the CELCAP cogeneration analysis program is presented. A detailed description of the methodology used by the Naval Civil Engineering Laboratory in developing the CELCAP code and the procedures for analyzing cogeneration systems for a given user are given. The four engines modeled in CELCAP are: gas turbine with exhaust heat boiler, diesel engine with waste heat boiler, single automatic-extraction steam turbine, and back-pressure steam turbine. Both the design point and part-load performances are taken into account in the engine models. The load model describes how the hourly electric and steam demand of the user is represented by 24 hourly profiles. The economic model describes how the annual and life-cycle operating costs that include the costs of fuel, purchased electricity, and operation and maintenance of engines and boilers are calculated. The CELCAP code structure and principal functions of the code are described to how the various components of the code are related to each other. Three examples of the application of the CELCAP code are given to illustrate the versatility of the code. The examples shown represent cases of system selection, system modification, and system optimization.

Source record↗

Non-intrusive reduced order modeling of natural convection in porous media using convolutional autoencoders: Comparison with linear subspace techniques

Natural convection in porous media is a highly nonlinear multiphysical problem relevant to many engineering applications (e.g., the process of CO 2 sequestration). Here, we extend and present a non-intrusive reduced order model of natural convection in porous media employing deep convolutional autoencoders for the compression and reconstruction and either radial basis function (RBF) interpolation or artificial neural networks (ANNs) for mapping parameters of partial differential equations (PDEs) on the corresponding nonlinear manifolds. To benchmark our approach, we also describe linear compression and reconstruction processes relying on proper orthogonal decomposition (POD) and ANNs. Further, we present comprehensive comparisons among different models through three benchmark problems. The reduced order models, linear and nonlinear approaches, are much faster than the finite element model, obtaining a maximum speed-up of 7 × 10 6 because our framework is not bound by the Courant–Friedrichs–Lewy condition; hence, it could deliver quantities of interest at any given time contrary to the finite element model. Our model’s accuracy still lies within a relative error of 7% in the worst-case scenario. We illustrate that, in specific settings, the nonlinear approach outperforms its linear counterpart and vice versa. We hypothesize that a visual comparison between principal component analysis (PCA) and t-Distributed Stochastic Neighbor Embedding (t-SNE) could indicate which method will perform better prior to employing any specific compression strategy.

97 MATHEMATICS AND COMPUTING↗

Model-based quantification of image quality

In 1982, Park and Schowengerdt published an end-to-end analysis of a digital imaging system quantifying three principal degradation components: (1) image blur - blurring caused by the acquisition system, (2) aliasing - caused by insufficient sampling, and (3) reconstruction blur - blurring caused by the imperfect interpolative reconstruction. This analysis, which measures degradation as the square of the radiometric error, includes the sample-scene phase as an explicit random parameter and characterizes the image degradation caused by imperfect acquisition and reconstruction together with the effects of undersampling and random sample-scene phases. In a recent paper Mitchell and Netravelli displayed the visual effects of the above mentioned degradations and presented subjective analysis about their relative importance in determining image quality. The primary aim of the research is to use the analysis of Park and Schowengerdt to correlate their mathematical criteria for measuring image degradations with subjective visual criteria. Insight gained from this research can be exploited in the end-to-end design of optical systems, so that system parameters (transfer functions of the acquisition and display systems) can be designed relative to each other, to obtain the best possible results using quantitative measurements.

Hazra, Rajeeb↗