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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Linking structural and transport properties in three-dimensional fracture networks

Here, we investigate large scale particle motion and solute breakthrough in sparse three-dimensional discrete fracture networks (DFN) characterized by power-law distributed fracture lengths. The three networks we consider have the same fracture intensity values but exhibit different percolation densities, geometric properties and topological structures. We considered two different average transport models to predict solute breakthrough, a streamtube model and a Bernoulli CTRW model, both of which provide insights into the flow fields within the networks. The streamtube model provides acceptable predictions at short distances in two of the networks, but fails in all cases to predict breakthrough times at the outlet plane, which indicates that particle motion in such fracture networks cannot be characterized by a constant velocity between the inlet and control plane at which the breakthrough curve is detected. Rather the structure of the network requires that frequent velocity transitions be made as particles move through the system. Despite the relatively broad distribution of fracture radii and relatively small number of independent velocity transitions, the CTRW approach conditioned on the initial velocity distribution provides reasonable predictions for the breakthrough curves at different distances from the inlet. The application of these averaged transport models provides a richer understanding of the link from the fracture network structure to ow and transport properties.

58 GEOSCIENCES↗
DOE OSTI2022

Detection of Forced Change Within Combined Climate Fields Using Explainable Neural Networks

Abstract Assessing forced climate change requires the extraction of the forced signal from the background of climate noise. Traditionally, tools for extracting forced climate change signals have focused on one atmospheric variable at a time, however, using multiple variables can reduce noise and allow for easier detection of the forced response. Following previous work, we train artificial neural networks to predict the year of single‐ and multi‐variable maps from forced climate model simulations. To perform this task, the neural networks learn patterns that allow them to discriminate between maps from different years—that is, the neural networks learn the patterns of the forced signal amidst the shroud of internal variability and climate model disagreement. When presented with combined input fields (multiple seasons, variables, or both), the neural networks are able to detect the signal of forced change earlier than when given single fields alone by utilizing complex, nonlinear relationships between multiple variables and seasons. We use layer‐wise relevance propagation, a neural network explainability tool, to identify the multivariate patterns learned by the neural networks that serve as reliable indicators of the forced response. These “indicator patterns” vary in time and between climate models, providing a template for investigating inter‐model differences in the time evolution of the forced response. This work demonstrates how neural networks and their explainability tools can be harnessed to identify patterns of the forced signal within combined fields.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Deep reaction network exploration at a heterogeneous catalytic interface

Characterizing the reaction energies and barriers of reaction networks is central to catalyst development. However, heterogeneous catalytic surfaces pose several unique challenges to automatic reaction network characterization, including large sizes and open-ended reactant sets, that make ad hoc network construction the current state-of-the-art. Here, we show how automated network exploration algorithms can be adapted to the constraints of heterogeneous systems using ethylene oligomerization on silica-supported single-site Ga 3+ as a model system. Using only graph-based rules for exploring the network and elementary constraints based on activation energy and size for identifying network terminations, a comprehensive reaction network is generated and validated against standard methods. The algorithm (re)discovers the Ga-alkyl-centered Cossee-Arlman mechanism that is hypothesized to drive major product formation while also predicting several new pathways for producing alkanes and coke precursors. These results demonstrate that automated reaction exploration algorithms are rapidly maturing towards general purpose capability for exploratory catalytic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Controllable growth of interpenetrating or random copolymer networks

Interpenetrating and random copolymer networks are vital in a number of industrial applications, including the fabrication of automotive parts, damping materials, and tissue engineering scaffolds. We develop a theoretical model for a process that enables the controlled growth of interpenetrating network (IPNs), or a random copolymer network (RCN) of specified size and mechanical properties. In this process, a primary gel “seed” is immersed into a solution containing the secondary monomer and crosslinkers. After the latter species are absorbed into the primary network, the absorbed monomers are polymerized to form the secondary polymer chains, which then can undergo further crosslinking to form an IPN, or undergo inter-chain exchange with the existing network to form a RCN. The swelling and elastic properties of the IPN and RCN networks can be tailored by modifying the monomer and crosslinker concentrations in the surrounding solution, or by tuning the enthalpic interactions between the primary polymer, secondary monomer and solvent through a proper choice of chemistry. This process can be used repeatedly to fabricate gels with a range of mechanical properties from stiff, rigid materials to soft, flexible networks, allowing the method to meet the materials requirements of a variety of applications.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Cooperative effect of local active stresses on the macroscopic contractility of elastic fiber networks

The collective action of actively contractile units embedded in elastic biopolymer networks plays a crucial role in regulating the network's macroscopic mechanical response. Here, in this study, we investigate how the macroscopic boundary stress in model elastic fiber networks depends on the number and nature of embedded contractile units, each exerting an isotropic force dipole, as well as on the bending stiffness of fibers. We find that the macroscopic stress increases nonlinearly with the number of dipoles due to mutual stiffening of initially soft, bending-dominated networks. Using effective medium theory, we relate this enhanced contractility to an increase in the effective average network coordination number due to constraints imposed by the force dipoles. By comparing three distinct force dipole models that differ in their local structures, we demonstrate that the specific manner in which an active unit constrains the network strongly influences the onset and nature of the stiffening transition. Our results highlight that not only the quantity but also the local geometry of force-generating units critically determines the macroscopic mechanical behavior. This framework provides a physical basis for understanding how biological systems—such as molecular motors in the cytoskeleton, or adherent cells in the extracellular matrix—can modulate network-scale nonlinear elastic properties through local tuning of active force-generating units.

Biological and medical sciences↗
DOE OSTI2013

Generative model selection using a scalable and size-independent complex network classifier

Real networks exhibit nontrivial topological features, such as heavy-tailed degree distribution, high clustering, and small-worldness. Researchers have developed several generative models for synthesizing artificial networks that are structurally similar to real networks. An important research problem is to identify the generative model that best fits to a target network. In this paper, we investigate this problem and our goal is to select the model that is able to generate graphs similar to a given network instance. By the means of generating synthetic networks with seven outstanding generative models, we have utilized machine learning methods to develop a decision tree for model selection. Our proposed method, which is named “Generative Model Selection for Complex Networks,” outperforms existing methods with respect to accuracy, scalability, and size-independence.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Characterizing system dynamics with a weighted and directed network constructed from time series data

In this work, we propose a novel method to transform a time series into a weighted and directed network. For a given time series, we first generate a set of segments via a sliding window, and then use a doubly symbolic scheme to characterize every windowed segment by combining absolute amplitude information with an ordinal pattern characterization. Based on this construction, a network can be directly constructed from the given time series: segments corresponding to different symbol-pairs are mapped to network nodes and the temporal succession between nodes is represented by directed links. With this conversion, dynamics underlying the time series has been encoded into the network structure. We illustrate the potential of our networks with a well-studied dynamical model as a benchmark example. Results show that network measures for characterizing global properties can detect the dynamical transitions in the underlying system. Moreover, we employ a random walk algorithm to sample loops in our networks, and find that time series with different dynamics exhibits distinct cycle structure. That is, the relative prevalence of loops with different lengths can be used to identify the underlying dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Pinning impulsive control algorithms for complex network

In this paper, we further investigate the synchronization of complex dynamical network via pinning control in which a selection of nodes are controlled at discrete times. Different from most existing work, the pinning control algorithms utilize only the impulsive signals at discrete time instants, which may greatly improve the communication channel efficiency and reduce control cost. Two classes of algorithms are designed, one for strongly connected complex network and another for non-strongly connected complex network. It is suggested that in the strongly connected network with suitable coupling strength, a single controller at any one of the network's nodes can always pin the network to its homogeneous solution. In the non-strongly connected case, the location and minimum number of nodes needed to pin the network are determined by the Frobenius normal form of the coupling matrix. In addition, the coupling matrix is not necessarily symmetric or irreducible. Illustrative examples are then given to validate the proposed pinning impulsive control algorithms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws

In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks “in a box”, whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = s{sup Y} between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats s{sup Y}. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Forced synchronization of autonomous dynamical Boolean networks

We present the design of an autonomous time-delay Boolean network realized with readily available electronic components. Through simulations and experiments that account for the detailed nonlinear response of each circuit element, we demonstrate that a network with five Boolean nodes displays complex behavior. Furthermore, we show that the dynamics of two identical networks display near-instantaneous synchronization to a periodic state when forced by a common periodic Boolean signal. A theoretical analysis of the network reveals the conditions under which complex behavior is expected in an individual network and the occurrence of synchronization in the forced networks. This research will enable future experiments on autonomous time-delay networks using readily available electronic components with dynamics on a slow enough time-scale so that inexpensive data collection systems can faithfully record the dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Functional network inference of the suprachiasmatic nucleus

In the mammalian suprachiasmatic nucleus (SCN), noisy cellular oscillators communicate within a neuronal network to generate precise system-wide circadian rhythms. Although the intracellular genetic oscillator and intercellular biochemical coupling mechanisms have been examined previously, the network topology driving synchronization of the SCN has not been elucidated. This network has been particularly challenging to probe, due to its oscillatory components and slow coupling timescale. In this work, we investigated the SCN network at a single-cell resolution through a chemically induced desynchronization. We then inferred functional connections in the SCN by applying the maximal information coefficient statistic to bioluminescence reporter data from individual neurons while they resynchronized their circadian cycling. Our results demonstrate that the functional network of circadian cells associated with resynchronization has small-world characteristics, with a node degree distribution that is exponential. We show that hubs of this small-world network are preferentially located in the central SCN, with sparsely connected shells surrounding these cores. Lastly, we used two computational models of circadian neurons to validate our predictions of network structure.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Auxetic metamaterials from disordered networks

Recent theoretical work suggests that systematic pruning of disordered networks consisting of nodes connected by springs can lead to materials that exhibit a host of unusual mechanical properties. In particular, global properties such as Poisson's ratio or local responses related to deformation can be precisely altered. Tunable mechanical responses would be useful in areas ranging from impact mitigation to robotics and, more generally, for creation of metamaterials with engineered properties. However, experimental attempts to create auxetic materials based on pruningbased theoretical ideas have not been successful. In this study, we introduce a more realistic model of the networks, which incorporates angle-bending forces and the appropriate experimental boundary conditions. A sequential pruning strategy of select bonds in this model is then devised and implemented that enables engineering of specific mechanical behaviors upon deformation, both in the linear and in the nonlinear regimes. In particular, it is shown that Poisson's ratio can be tuned to arbitrary values. The model and concepts discussed here are validated by preparing physical realizations of the networks designed in this manner, which are produced by laser cutting 2D sheets and are found to behave as predicted. Furthermore, by relying on optimization algorithms, we exploit the networks' susceptibility to tuning to design networks that possess a distribution of stiffer and more compliant bonds and whose auxetic behavior is even greater than that of homogeneous networks. Finally, taken together, the findings reported here serve to establish that pruned networks represent a promising platform for the creation of unique mechanical metamaterials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Xylem-dwelling pathogen unaffected by local xylem vessel network properties in grapevines ( Vitis spp.)

Abstract Background and aims Xylella fastidiosa (Xf) is the xylem-dwelling bacterium associated with Pierce’s disease (PD), which causes mortality in agriculturally important species, such as grapevine (Vitis vinifera). The development of PD symptoms in grapevines depends on the ability of Xf to produce cell-wall-degrading enzymes to break up intervessel pit membranes and systematically spread through the xylem vessel network. Our objective here was to investigate whether PD resistance could be mechanistically linked to xylem vessel network local connectivity. Methods We used high-resolution X-ray micro-computed tomography (microCT) imaging to identify and describe the type, area and spatial distribution of intervessel connections for six different grapevine genotypes from three genetic backgrounds, with varying resistance to PD (four PD resistant and two PD susceptible). Key results Our results suggest that PD resistance is unlikely to derive from local xylem network connectivity. The intervessel pit area (Ai) varied from 0.07 ± 0.01 mm2 mm−3 in Lenoir to 0.17 ± 0.03 mm2 mm−3 in Blanc do Bois, both PD resistant. Intervessel contact fraction (Cp) was not statically significant, but the two PD-susceptible genotypes, Syrah (0.056 ± 0.015) and Chardonnay (0.041 ± 0.013), were among the most highly connected vessel networks. Neither Ai nor Cp explained differences in PD resistance among the six genotypes. Bayesian re-analysis of our data shows moderate evidence against the effects of the traits analysed: Ai (BF01 = 4.88), mean vessel density (4.86), relay diameter (4.30), relay density (3.31) and solitary vessel proportion (3.19). Conclusions Our results show that radial and tangential xylem network connectivity is highly conserved within the six different Vitis genotypes we sampled. The way that Xf traverses the vessel network may limit the importance of local network properties to its spread and may confer greater importance on host biochemical responses.

Plant Sciences↗
DOE OSTI2012

Inference of gene regulatory networks from genome-wide knockout fitness data

Motivation: Genome-wide fitness is an emerging type of highthroughput biological data generated for individual organisms by creating libraries of knockouts, subjecting them to broad ranges of environmental conditions, and measuring the resulting clone-specific fitnesses. Since fitness is an organism-scale measure of gene regulatory network behaviour, it may offer certain advantages when insights into such phenotypical and functional features are of primary interest over individual gene expression. Previous works have shown that genome-wide fitness data can be used to uncover novel gene regulatory interactions, when compared with results of more conventional gene expression analysis. Yet, to date, few algorithms have been proposed for systematically using genome-wide mutant fitness data for gene regulatory network inference. Results: In this article, we describe a model and propose an inference algorithm for using fitness data from knockout libraries to identify underlying gene regulatory networks. Unlike most prior methods, the presented approach captures not only structural, but also dynamical and non-linear nature of biomolecular systems involved. A state– space model with non-linear basis is used for dynamically describing gene regulatory networks. Network structure is then elucidated by estimating unknown model parameters. Unscented Kalman filter is used to cope with the non-linearities introduced in the model, which also enables the algorithm to run in on-line mode for practical use. Here, we demonstrate that the algorithm provides satisfying results for both synthetic data as well as empirical measurements of GAL network in yeast Saccharomyces cerevisiae and TyrR–LiuR network in bacteria Shewanella oneidensis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Syntgen: a system to generate temporal networks with user-specified topology

Abstract In the last few years, the study of temporal networks has progressed markedly. The evolution of clusters of nodes (or communities) is one of the major focus of these studies. However, the time dimension increases complexity, introducing new constructs and requiring novel and enhanced algorithms. In spite of recent improvements, the relative scarcity of timestamped representations of empiric networks, with known ground truth, hinders algorithm validation. A few approaches have been proposed to generate synthetic temporal networks that conform to static topological specifications while in general adopting an ad hoc approach to temporal evolution. We believe there is still a need for a principled synthetic network generator that conforms to problem domain topological specifications from a static as well as temporal perspective. Here, we present such a system. The unique attributes of our system include accepting arbitrary node degree and cluster size distributions and temporal evolution under user control, while supporting tunable joint distribution and temporal correlation of node degrees. Theoretical contributions include the analysis of conditions for graphic sequences of inter- and intracluster node degrees and cluster sizes and the development of a heuristic to search for the cluster membership of nodes that minimizes the shared information distance between clusterings. Our work shows that this system is capable of generating networks under user controlled topology with up to thousands of nodes and hundreds of clusters with strong topology adherence. Much larger networks are possible with relaxed requirements. The generated networks support algorithm validation as well as problem domain analysis.

Pereira, Luis Ramada↗
DOE OSTI2024

Abiotic Stress Reorganizes Rhizosphere and Endosphere Network Structure of Sorghum bicolor

Sorghum bicolor is a promising bioenergy feedstock with high biomass production and unusual tolerance for stresses, such as water and nutrient limitation. Although the membership of the sorghum microbiome in response to stress has been explored, relatively little is known about how microbe–microbe networks change under water- or nutrient-limited conditions. This is important because network changes can indicate impacts on the functionality and stability of microbial communities. We performed network-based analysis on the core bacterial and archaeal community of an agronomically promising high biomass bioenergy genotype, Grassl, grown under nitrogen and water stress. Stress caused relatively minor changes in bacterial abundances within soil, rhizosphere, and endosphere communities but led to significant changes in bacterial network structure and modularity. We found a complete reorganization of network roles in all plant compartments, as well as an increase in the modularity and proportion of positive associations, which potentially could represent coexistence and cooperation in the sorghum bacterial/archaeal community under stress. Although stressors are often believed to be destabilizing, we found stressed networks were as or more stable than non-stressed networks, likely due to their redundancy and compartmentalization. Together, these findings support the idea that both sorghum and its bacterial/archaeal community can be resilient to future environmental stressors.

09 BIOMASS FUELS↗
DOE OSTI2022

Galaxy deblending using residual dense neural networks

We present a new neural network approach for deblending galaxy images in astronomical data using Residual Dense Neural network (RDN) architecture. We train the network on synthetic galaxy images similar to the typical arrangements of field galaxies with a finite point spread function (PSF) and realistic noise levels. The main novelty of our approach is the usage of two distinct neural networks: i) a deblending network which isolates a single galaxy postage stamp from the composite and, ii) a classifier network which counts the remaining number of galaxies. The deblending proceeds by iteratively peeling one galaxy at a time from the composite until the image contains no further objects as determined by the classifier, or by other stopping criteria. By looking at the consistency in the outputs of the two networks, we can assess the quality of the deblending. Further, we characterize the flux and shape reconstructions in different quality bins and compare our deblender with the industry standard, SExtractor. We also discuss possible future extensions for the project with variable PSFs and noise levels.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Characterizing the impact of particle behavior at fracture intersections in three-dimensional discrete fracture networks

We characterize the influence of different intersection mixing rules for particle tracking simulations on transport properties through three-dimensional discrete fracture networks. It is too computationally burdensome to explicitly resolve all fluid dynamics within a large three-dimensional fracture network. In discrete fracture network (DFN) models, mass transport at fracture intersections is modeled as a subgrid scale process based on a local Péclet number. The two most common mass transfer mixing rules are (1) complete mixing, where diffusion dominates mass transfer, and (2) streamline routing, where mass follows pathlines through an intersection. Although it is accepted that mixing rules impact local mass transfer through single intersections, the effect of the mixing rule on transport at the fracture network scale is still unresolved. Through the use of explicit particle tracking simulations, we study transport through a quasi-two-dimensional lattice network and a three-dimensional network whose fracture radii follow a truncated power-law distribution. We find that the impact of the mixing rule is a function of the initial particle injection condition, the heterogeneity of the velocity field, and the geometry of the network. Furthermore, our particle tracking simulations show that the mixing rule can particularly impact concentrations on secondary flow pathways. As a result, we relate these local differences in concentration to reactive transport and show that streamline routing increases the average mixing rate in DFN simulations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗