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At least 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
NASA NTRS2016

Using NASA's GeneLab for VESGEN Systems Analysis of Vascular Phenotypes from Stress and Other Signaling Pathways

One fundamental requirement shared by humans with all higher terrestrial life forms, including other vertebrates, insects, and higher land plants, is a complex, fractally branching vascular system. NASA's VESsel GENeration Analysis (VESGEN) software maps and quantifies vascular trees, networks, and tree-network composites according to weighted physiological rules such as vessel connectivity, tapering and bifurcational branching. According to fluid dynamics, successful vascular transport requires a complex distributed system of highly regulated laminar flow. Microvascular branching rules within vertebrates, dicot leaves and the other organisms therefore display many similarities. A unifying perspective is that vascular patterning offers a useful readout of molecular signaling that necessarily integrates these complex pathways. VESGEN has elucidated changes in vascular pattern resulting from inflammatory, developmental and other signaling within numerous tissues and major model organisms studied for Space Biology. For a new VESGEN systems approach, we analyzed differential gene expression in leaves of Arabidopsis thaliana reported by GeneLab (GLDS-7) for spaceflight. Vascularrelated changes in leaf gene expression were identified that can potentially be phenocopied by mutants in ground-based experiments. To link transcriptional, protein and other molecular change with phenotype, alterations in the spatial and dynamic dimensions of vascular patterns for Arabidopsis leaves and other model species are being co-localized with signaling patterns of single molecular expression analyzed as information dimensions. Previously, Drosophila microarray data returned from space suggested significant changes in genes related to wing venation development that include EGF, Notch, Hedghog, Wingless and Dpp signaling. Phenotypes of increasingly abnormal ectopic wing venation in the (non-spaceflight) Drosophila wing generated by overexpression of a Notch antagonist were analyzed by VESGEN. Other VESGEN research applications include the mouse retina, GI and coronary vessels, avian placental analogs and translational studies in the astronaut retina related to health challenges for long-duration missions.

Venation↗
DOE OSTI2020

Quantitative assessment of eddy viscosity rans models for turbulent mixed convection in a differentially heated plane channel

Turbulent mixed convection between two vertical, infinite parallel plates at different temperatures is studied using various two-equation turbulence models. The numerical simulations are performed at a turbulent Reynolds number of Re τ = 150 and a Grashof number of Gr = 9.6 × 10 5 . Comparisons are made against the highly trusted DNS results. Consistent with the DNS approach, the current simulations are performed using constant properties and the Boussinesq approximation to predict the influence of buoyancy. Previous studies have provided assessments of two-equation turbulence models for various scenarios, but often rely on a qualitative “eye” test in order to determine the most appropriate model to predict a given flow. This study aims to provide a new form of quantitative assessment that accounts for both the physics captured by the turbulence model as well as the magnitude of the system response quantities (SRQ) using a modified symmetric mean absolute percent error (SMAPE) method. This method is designed to be approachable to researchers at any level and can be applied to system response quantities from multiple research fields. Uncertainty quantification is also performed to determine the discretization error for each turbulence model. Recommendations are made as to which turbulence models best capture the physics – hydrodynamically and thermally – using both local and global validation metrics. Lastly, a sensitivity analysis is performed on the damping functions used in the most accurate models. This underpins the potential of model developments and adjustments most worth pursuing for buoyant flows. Finally, this framework provides a more physics-based comparative analysis of the selected turbulence models.

42 ENGINEERING↗
NASA NTRS1996

Further Development of a New, Flux-Conserving Newton Scheme for the Navier-Stokes Equations

This paper is one of a series of papers describing the development of a new numerical approach for solving the steady Navier-Stokes equations. The key features in the current development are (1) the discrete representation of the dependent variables by way of high order polynomial expansions, (2) the retention of all derivatives in the expansions as unknowns to be explicitly solved for, (3) the automatic balancing of fluxes at cell interfaces, and (4) the discrete simulation of both the integral and differential forms of the governing equations. The main purpose of this paper is, first, to provide a systematic and rigorous derivation of the conditions that are used to simulate the differential form of the Navier-Stokes equations, and second, to extend our previously-presented internal flow scheme to external flows and nonuniform grids. Numerical results are presented for high Reynolds number flow (Re = 100,000) around a finite flat plate, and detailed comparisons are made with the Blasius flat plate solution and Goldstein wake solution. It is shown that the error in the streamwise velocity decreases like r(sup alpha)(Delta)y(exp 2), where alpha approx. 0.25 and r = delta(y)/delta(x) is the grid aspect ratio.

Scott, James R.↗
NASA NTRS2018

Increasing the Statistical Rigor of Cross-Species Differential Expression Analysis

Microgravity inflicts substantial, but undercharacterized, pressure on organisms that induces metabolic responses such as increased microbial virulence and antibiotic resistance, altered organ weights in developing rats, and loss of bone tissue in astronauts. Numerous studies have analyzed the effects of microgravity on specific organisms, tissues, or test conditions, but these projects are necessarily limited by the small sample size of space research. Increasing the sample size of spaceflight studies is non-trivial; however, pooling data from numerous studies can greatly increase the statistical rigor of comparative analyses. The GeneLab houses datasets from 73 spaceflight studies that performed transcription profiling assays. These data encompass a diverse array of organisms ranging from Escherichia coli to Mus musculus to Homo sapiens and comprise studies analyzing ionizing radiation, mammalian pregnancy, etc. Collectively, the GeneLab database contains a large quantity of transcription assays and RNA sequence data analyzing Differential Gene Expression (DGE) between microand normogravity. Xspecies, a cross-species analysis method for DGE developed by Kristiansson, et al. in 2012, identifies homologous genes between species that are universally up- or downregulated in response to test conditions. Previous work by an intern at GeneLab applied Xspecies to 19 datasets containing seven different species and identified 14 homologous groups differentially expressed under spaceflight conditions including several heat shock proteins and cytoskeletal components. Unfortunately, these results may be biased by the disproportionate number of studies on Arabidopsis thaliana (5) and Mus musculus (6) and the results are not normalized by evolutionary distances. Here, we present modifications to the Xspecies algorithm that permits incorporation of multi-omic data and normalizes data for effect size, directionality, and evolutionary distances. We then apply this algorithm to all currently available GeneLab studies

Xspecies↗
NASA NTRS1991

The asymptotic spectra of banded Toeplitz and quasi-Toeplitz matrices

Toeplitz matrices occur in many mathematical, as well as, scientific and engineering investigations. This paper considers the spectra of banded Toeplitz and quasi-Toeplitz matrices with emphasis on non-normal matrices of arbitrarily large order and relatively small bandwidth. These are the type of matrices that appear in the investigation of stability and convergence of difference approximations to partial differential equations. Quasi-Toeplitz matrices are the result of non-Dirichlet boundary conditions for the difference approximations. The eigenvalue problem for a banded Toeplitz or quasi-Toeplitz matrix of large order is, in general, analytically intractable and (for non-normal matrices) numerically unreliable. An asymptotic (matrix order approaches infinity) approach partitions the eigenvalue analysis of a quasi-Toeplitz matrix into two parts, namely the analysis for the boundary condition independent spectrum and the analysis for the boundary condition dependent spectrum. The boundary condition independent spectrum is the same as the pure Toeplitz matrix spectrum. Algorithms for computing both parts of the spectrum are presented. Examples are used to demonstrate the utility of the algorithms, to present some interesting spectra, and to point out some of the numerical difficulties encountered when conventional matrix eigenvalue routines are employed for non-normal matrices of large order. The analysis for the Toeplitz spectrum also leads to a diagonal similarity transformation that improves conventional numerical eigenvalue computations. Finally, the algorithm for the asymptotic spectrum is extended to the Toeplitz generalized eigenvalue problem which occurs, for example, in the stability of Pade type difference approximations to differential equations.

Beam, Richard M.↗
DOE OSTI2022

The effect of differential mineral shrinkage on crack formation and network geometry

Rock, concrete, and other engineered materials are often composed of several minerals that change volumetrically in response to variations in the moisture content of the local environment. Such differential shrinkage is caused by varying shrinkage rates between mineral compositions during dehydration. Using both 3D X-ray imaging of geo-architected samples and peridynamic (PD) numerical simulations, we show that the spatial distribution of the clay affects the crack network geometry with distributed clay particles yielding the most complex crack networks and percent damage (99.56%), along with a 60% reduction in material strength. We also demonstrate that crack formation, growth, coalescence, and distribution during dehydration, are controlled by the differential shrinkage rates between a highly shrinkable clay and a homogeneous mortar matrix. Sensitivity tests performed with the PD models show a clay shrinkage parameter of 0.4 yields considerable damage, and reductions in the parameter can result in a significant reduction in fracturing and an increase in material strength. Additionally, isolated clay inclusions induced localized fracturing predominantly due to debonding between the clay and matrix. These insights indicate differential shrinkage is a source of potential failure in natural and engineered barriers used to sequester anthropogenic waste.

58 GEOSCIENCES↗
DOE OSTI2025

Nyström type exponential integrators for strongly magnetized charged particle dynamics

Solving for charged particle motion in electromagnetic fields (i.e. the particle pushing problem) is a computationally intensive component of particle-in-cell (PIC) methods for plasma physics simulations. This task is especially challenging when the plasma is strongly magnetized due numerical stiffness arising from the wide range of time scales between highly oscillatory gyromotion and long term macroscopic behavior. A promising approach to solve these problems is by a class of methods known as exponential integrators that can solve linear problems exactly and are A-stable. This work extends the standard exponential integration framework to derive Nyström-type exponential integrators that integrates the Newtonian equations of motion as a second-order differential equation directly. In particular, we derive second-order and third-order Nyström-type exponential integrators for strongly magnetized particle pushing problems. Numerical experiments show that the Nyström-type exponential integrators exhibit significant improvement in computation speed over the standard exponential integrators.

general physics↗
DOE OSTI2021

Large-eddy simulation of a multi-injection flame in a diesel engine environment using an unsteady flamelet/progress variable approach

In this work, large-eddy simulations (LESs) are conducted for a multiple-injection flame in a diesel engine environment using an unsteady flamelet/progress variable (UFPV) approach in which differential diffusion is considered. The suitability of the UFPV tabulation approach is first evaluated through a priori analyses using the state-of-the-art direct numerical simulation (DNS) dataset. Both the instantaneous data and the conditional values for the major and minor species' mass fractions are compared between the UFPV and the DNS. The comparisons show that the proposed UFPV tabulation approach can give good predictions for the multiple-injection flame at different injection phases. While the gas temperature and major species mass fractions can be accurately predicted with or without differential diffusion being considered in the UFPV flamelet library, the prediction accuracy for the highly diffusive species (e.g., hydrogen) in the main injection phase can be noticeably improved when differential diffusion is taken into account. The fully coupled LES/UFPV simulations show that the overall structure of the multiple-injection flame can be predicted, and the conditional thermo-chemical values are close to the filtered DNS dataset. The reasons for the remaining discrepancies found in the a priori analyses and the a posteriori simulations using the UFPV approach are analyzed.

Wen, Xu (ORCID:0000000331334292)↗
DOE OSTI2022

State elimination for mixed‐integer optimal control of partial differential equations by semigroup theory

Abstract Mixed‐integer optimal control problems governed by partial differential equations (MIPDECOs) are powerful modeling tools but also challenging in terms of theory and computation. We propose a highly efficient state elimination approach for MIPDECOs that are governed by partial differential equations that have the structure of an abstract ordinary differential equation in function space. This allows us to avoid repeated calculations of the states for all time steps, and our approach is applied only once before starting the optimization. The presentation of theoretical results is complemented by numerical experiments.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1986

Optimization methods and silicon solar cell numerical models

An optimization algorithm for use with numerical silicon solar cell models was developed. By coupling an optimization algorithm with a solar cell model, it is possible to simultaneously vary design variables such as impurity concentrations, front junction depth, back junction depth, and cell thickness to maximize the predicted cell efficiency. An optimization algorithm was developed and interfaced with the Solar Cell Analysis Program in 1 Dimension (SCAP1D). SCAP1D uses finite difference methods to solve the differential equations which, along with several relations from the physics of semiconductors, describe mathematically the performance of a solar cell. A major obstacle is that the numerical methods used in SCAP1D require a significant amount of computer time, and during an optimization the model is called iteratively until the design variables converge to the values associated with the maximum efficiency. This problem was alleviated by designing an optimization code specifically for use with numerically intensive simulations, to reduce the number of times the efficiency has to be calculated to achieve convergence to the optimal solution.

Girardini, K.↗
NASA NTRS1994

Numerical Simulation Of Cutting Of Gear Teeth

Shapes of gear teeth produced by gear cutters of specified shape simulated computationally, according to approach based on principles of differential geometry. Results of computer simulation displayed as computer graphics and/or used in analyses of design, manufacturing, and performance of gears. Applicable to both standard and non-standard gear-tooth forms. Accelerates and facilitates analysis of alternative designs of gears and cutters. Simulation extended to study generation of surfaces other than gears. Applied to cams, bearings, and surfaces of arbitrary rolling elements as well as to gears. Possible to develop analogous procedures for simulating manufacture of skin surfaces like automobile fenders, airfoils, and ship hulls.

Oswald, Fred B.↗
NASA NTRS2007

Transient Numerical Modeling of Catalytic Channels

This paper presents a transient model of catalytic combustion suitable for isolated channels and monolith reactors. The model is a lumped two-phase (gas and solid) model where the gas phase is quasi-steady relative to the transient solid. Axial diffusion is neglected in the gas phase; lateral diffusion, however, is accounted for using transfer coefficients. The solid phase includes axial heat conduction and external heat loss due to convection and radiation. The combustion process utilizes detailed gas and surface reaction models. The gas-phase model becomes a system of stiff ordinary differential equations while the solid phase reduces, after discretization, into a system of stiff ordinary differential-algebraic equations. The time evolution of the system came from alternating integrations of the quasi-steady gas and transient solid. This work outlines the numerical model and presents some sensitivity studies on important parameters including internal transfer coefficients, catalytic surface site density, and external heat-loss (if applicable). The model is compared to two experiments using CO fuel: (1) steady-state conversion through an isothermal platinum (Pt) tube and (2) transient propagation of a catalytic reaction inside a small Pt tube. The model requires internal mass-transfer resistance to match the experiments at lower residence times. Under mass-transport limited conditions, the model reasonably predicted exit conversion using global mass-transfer coefficients. Near light-off, the model results did not match the experiment precisely even after adjustment of mass-transfer coefficients. Agreement improved for the first case after adjusting the surface kinetics such that the net rate of CO adsorption increased compared to O2. The CO / O2 surface mechanism came from a sub-set of reactions in a popular CH4 / O2 mechanism. For the second case, predictions improved for lean conditions with increased external heat loss or adjustment of the kinetics as in the first case. Finally, the results show that different initial surface-species distribution leads to different steady-states under certain conditions. These results demonstrate the utility of a lumped two-phase model of a transient catalytic combustor with detailed chemistry.

Struk, Peter M.↗
DOE OSTI2023

A guide to diagnosing colored resonances at hadron colliders

We present a comprehensive study on how to distinguish the properties of heavy dijet resonances at hadron colliders. A variety of spins, chiral couplings, charges, and QCD color representations are considered. Distinguishing the different color representations is particularly difficult at hadron colliders. To determine the QCD color structure, we consider a third jet radiated in a resonant dijet event. We show that the relative rates of three-jet versus two-jet processes are sensitive to the color representation of the resonance. We also show analytically that the antennae radiation pattern of soft radiation depends on the color structure of dijet events and develops an observable that is sensitive to the antennae patterns. Finally, we exploit a Convolutional Neural Network with Machine Learning techniques to differentiate the radiation patterns from different colored resonances and find encouraging results to discriminate them. We demonstrate our results numerically at a 14 TeV LHC, and the methodology presented here should be applicable to other future hadron colliders.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Tackling the curse of dimensionality in fractional and tempered fractional PDEs with physics-informed neural networks

Fractional and tempered fractional partial differential equations (PDEs) are effective models of long-range interactions, anomalous diffusion, and non-local effects. Traditional numerical methods for these problems are mesh-based, thus struggling with the curse of dimensionality (CoD). Physics-informed neural networks (PINNs) offer a promising solution due to their universal approximation, generalization ability, and mesh-free training. In principle, Monte Carlo fractional PINN (MC-fPINN) estimates fractional derivatives using Monte Carlo methods and thus could lift CoD. However, this may cause significant variance and errors, hence affecting convergence; in addition, MC-fPINN is sensitive to hyperparameters. In general, numerical methods and specifically PINNs for tempered fractional PDEs are under-developed. Herein, we extend MC-fPINN to tempered fractional PDEs to address these issues, resulting in the Monte Carlo tempered fractional PINN (MC-tfPINN). To reduce possible high variance and errors from Monte Carlo sampling, we replace the one-dimensional (1D) Monte Carlo with 1D Gaussian quadrature, applicable to both MC-fPINN and MC-tfPINN. We validate our methods on various forward and inverse problems of fractional and tempered fractional PDEs, scaling up to 100,000 dimensions. Our improved MC-fPINN/MC-tfPINN using quadrature consistently outperforms the original versions in accuracy and convergence speed in very high dimensions.

42 ENGINEERING↗
DOE OSTI2024

Machine learning for the identification of phase transitions in interacting agent-based systems: A Desai-Zwanzig example

Deriving closed-form analytical expressions for reduced-order models, and judiciously choosing the closures leading to them, has long been the strategy of choice for studying phase- and noise-induced transitions for agent-based models (ABMs). In this paper, we propose a data-driven framework that pinpoints phase transitions for an ABM—the Desai-Zwanzig model—in its mean-field limit, using a smaller number of variables than traditional closed-form models. To this end, we use the manifold learning algorithm Diffusion Maps to identify a parsimonious set of data-driven latent variables, and we show that they are in one-to-one correspondence with the expected theoretical order parameter of the ABM. We then utilize a deep learning framework to obtain a conformal reparametrization of the data-driven coordinates that facilitates, in our example, the identification of a single parameter-dependent ordinary differential equation (ODE) in these coordinates. Additionally, we identify this ODE through a residual neural network inspired by a numerical integration scheme (forward Euler). We then use the identified ODE—enabled through an odd symmetry transformation—to construct the bifurcation diagram exhibiting the phase transition.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Fluctuations in Hill’s equation parameters and application to cosmic reheating

Cosmic inflation provides a compelling framework for explaining several observed features of our Universe, but its viability depends on an efficient reheating phase that converts the inflaton’s energy into Standard Model particles. This conversion often proceeds through nonperturbative mechanisms such as parametric resonance, which is described by Hill’s equation. In this work, we investigate how stochastic fluctuations in the parameters of Hill’s equation can influence particle production during reheating. We show that such fluctuations can arise from couplings to light scalar fields and can significantly alter the stability bands in the resonance structure, thereby enhancing the growth of fluctuations and broadening the region of efficient energy transfer. Using random matrix theory and stochastic differential equations, we decompose the particle growth rate into deterministic and noise-induced components and demonstrate analytically and numerically that even modest noise leads to substantial particle production in otherwise stable regimes. Furthermore, these results suggest that stochastic effects can robustly enhance the efficacy of reheating across a wide swath of parameter space, with implications for early Universe cosmology, UV completions involving multiple scalar fields, and the resolution of the cosmological moduli problem.

Cosmology↗
DOE OSTI2020

Neuromorphic scaling advantages for energy-efficient random walk computations

Computing stands to be radically improved by neuromorphic computing (NMC) approaches inspired by the brain's incredible efficiency and capabilities. Most NMC research, which aims to replicate the brain's computational structure and architecture in man-made hardware, has focused on artificial intelligence; however, less explored is whether this brain-inspired hardware can provide value beyond cognitive tasks. We demonstrate that high-degree parallelism and configurability of spiking neuromorphic architectures makes them well-suited to implement random walks via discrete time Markov chains. Such random walks are useful in Monte Carlo methods, which represent a fundamental computational tool for solving a wide range of numerical computing tasks. Additionally, we show how the mathematical basis for a probabilistic solution involving a class of stochastic differential equations can leverage those simulations to provide solutions for a range of broadly applicable computational tasks. Despite being in an early development stage, we find that NMC platforms, at a sufficient scale, can drastically reduce the energy demands of high-performance computing platforms.

59 BASIC BIOLOGICAL SCIENCES↗