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Toward modeling a dynamic biological neural network

The organization of a mammalian macular endorgan is interpreted on physical and engineering principles. Having accomplished this task, it is possible to mathematically and symbolically model information processing by the macular neural network. A complex symbolic model is produced through use of mathematical notations that describe the functioning system. The model, consisting of six tiers, is constructed to mimic the neural system. On the basis of initial simulations, it is concluded that the network functions best when some of the detecting elements (i.e., type I hair cells) are weakly inhibitory. The simulations also illustrate the importance of disinhibition of receptors located in the third tier in shaping nerve discharge patterns at the sixth tier in the model system.

Ross, M. D.

From disorganized data to emergent dynamic models: Questionnaires to partial differential equations

Starting with sets of disorganized observations of spatially varying and temporally evolving systems, obtained at different (also disorganized) sets of parameters, we demonstrate the data-driven derivation of parameter dependent, evolutionary partial differential equation (PDE) models capable of generating the data. This tensor type of data is reminiscent of shuffled (multidimensional) puzzle tiles. The independent variables for the evolution equations (their “space” and “time”) as well as their effective parameters are all emergent , i.e. determined in a data-driven way from our disorganized observations of behavior in them. We use a diffusion map based questionnaire approach to build a smooth parametrization of our emergent space/time/parameter space for the data. This approach iteratively processes the data by successively observing them on the “space,” the “time” and the “parameter” axes of a tensor. Once the data become organized, we use machine learning (here, neural networks) to approximate the operators governing the evolution equations in this emergent space. Our illustrative examples are based (i) on a simple advection–diffusion model; (ii) on a previously developed vertex-plus-signaling model of Drosophila embryonic development; and (iii) on two complex dynamic network models (one neuronal and one coupled oscillator model) for which no obvious smooth embedding geometry is known a priori. This allows us to discuss features of the process like symmetry breaking, translational invariance, and autonomousness of the emergent PDE model, as well as its interpretability.

generative models

The chemical abundances of the Cassiopeia A fast-moving knots - Explosive nucleosynthesis on a minicomputer

A simplified nuclear reaction network for explosive nucleosynthesis calculations is described in which only the most abundant nuclear species and the most important reactions linking these species are considered. This scheme permits the exploration of many cases without excessive computational effort. Good agreement with previous calculations employing more complex reaction networks is obtained. This scheme is applied to the observed chemical abundances of the fast-moving knots in the supernova remnant Cassiopeia A and it is found that a wide range of initial conditions could yield the observed abundances. The abundances of four of the knots with significant and different amounts of elements heavier than oxygen are consistent with an origin in material of the same initial composition but processed at different peak temperatures and densities. Despite the observed high oxygen abundances and low abundances of light elements in the knots, they did not necessarily undergo incomplete oxygen burning; in fact, it is not even necessary that oxygen have been present in the initial composition. The agreement between the calculated and observed chemical abundances in Cas A and similar supernova remnants depends primarily upon the relevant nuclear physics and does not provide strong evidence in favor of any particular model of the supernova event.

Johnston, M. D.

Learning the factors controlling mineral dissolution in three-dimensional fracture networks: applications in geologic carbon sequestration

We perform a set of high-fidelity simulations of geochemical reactions within three-dimensional discrete fracture networks (DFN) and use various machine learning techniques to determine the primary factors controlling mineral dissolution. The DFN are partially filled with quartz that gradually dissolves until quasi-steady state conditions are reached. At this point, we measure the quartz remaining in each fracture within the domain as our primary quantity of interest. We observe that a primary sub-network of fractures exists, where the quartz has been fully dissolved out. This reduction in resistance to flow leads to increased flow channelization and reduced solute travel times. However, depending on the DFN topology and the rate of dissolution, we observe substantial variability in the volume of quartz remaining within fractures outside of the primary subnetwork. This variability indicates an interplay between the fracture network structure and geochemical reactions. We characterize the features controlling these processes by developing a machine learning framework to extract their relevant impact. Specifically, we use a combination of high-fidelity simulations with a graph-based approach to study geochemical reactive transport in a complex fracture network to determine the key features that control dissolution. We consider topological, geometric and hydrological features of the fracture network to predict the remaining quartz in quasi-steady state. We found that the dissolution reaction rate constant of quartz and the distance to the primary sub-network in the fracture network are the two most important features controlling the amount of quartz remaining. This study is a first step towards characterizing the parameters that control carbon mineralization using an approach with integrates computational physics and machine learning.

54 ENVIRONMENTAL SCIENCES

Identifying the Community Structure of the Food-Trade International Multi-Network

Achieving international food security requires improved understanding of how international trade networks connect countries around the world through the import-export flows of food commodities. The properties of international food trade networks are still poorly documented, especially from a multi-network perspective. In particular, nothing is known about the multi-network's community structure. Here we find that the individual crop-specific layers of the multi-network have densely connected trading groups, a consistent characteristic over the period 2001-2011. Further, the multi-network is characterized by low variability over this period but with substantial heterogeneity across layers in each year. In particular, the layers are mostly assortative: more-intensively connected countries tend to import from and export to countries that are themselves more connected. We also fit econometric models to identify social, economic and geographic factors explaining the probability that any two countries are co-present in the same community. Our estimates indicate that the probability of country pairs belonging to the same food trade community depends more on geopolitical and economic factors-such as geographical proximity and trade-agreement co-membership-than on country economic size and/or income. These community-structure findings of the multi-network are especially valuable for efforts to understand past and emerging dynamics in the global food system, especially those that examine potential 'shocks' to global food trade.

complex networks

PYSIMFRAC: A Python library for synthetic fracture generation and analysis

In this paper, we introduce PYSIMFRAC, an open-source python library for generating 3-D synthetic fracture realizations, integrating with fluid simulators, and performing analysis. PYSIMFRAC allows the user to specify one of three fracture generation techniques (Box, Gaussian, or Spectral) and perform statistical analysis including the autocorrelation, moments, and probability density functions of the fracture surfaces and aperture. This analysis and accessibility of a python library allows the user to create realistic fracture realizations and vary properties of interest. In addition, PYSIMFRAC includes integration examples to two different pore-scale simulators and the discrete fracture network simulator, dfnWorks. The capabilities developed in this work provides opportunity for quick and smooth adoption and implementation by the wider scientific community for accurate characterization of fluid transport in geologic media. We present PYSIMFRAC along with integration examples and discuss the ability to extend PYSIMFRAC from a single complex fracture to complex fracture networks.

58 GEOSCIENCES

Using G4FETs as a Data Router for In-Plane Crossing of Signal Paths

Theoretical analysis and some experiments have demonstrated that siliconon- insulator (SOI) 4-gate transistors the type known as G(exp 4)FETs could be efficiently used for in-plane crossing of signal paths. Much of the effort of designing very-large-scale integrated (VLSI) circuits is focused on area-efficient routing of signals. The main source of difficulty in VLSI signal routing is the requirement to prevent crossing, in the same plane, of wires that are meant to be kept electrically insulated from each other. Consequently, it often becomes necessary to design and build VLSI circuits in multiple layers with vias (connections between conductors in different layers at selected locations). Suitable devices that would prevent, or at least sufficiently suppress, undesired electrical coupling (cross-talk) between wires crossing in the same plane would enable compact, simpler implementation complex interconnection networks with in-plane crossings that, heretofore, have not been possible in VLSI circuitry. The use of G4FETs as in-plane signal-crossing devices or routers, in combination with the use of G(exp 4)FETs as universal programmable logic gates, would create opportunities for reducing complexity in VLSI design.

Fijany, Amir

Static and Dynamic Thermomechanical Properties of Phase-Separated Epoxy Networks with Tuned Microstructures

Here, polymerization-induced phase separation is a useful method for the construction of heterogeneous epoxy networks with properties exceeding their homogeneous counterparts. In this work, we examine the static and dynamic thermomechanical properties of phase-separated epoxy networks salient to their application as encapsulants. Three heterogeneous epoxy-amine networks with nano-, meso-, and macro-phase-separated morphologies comprised of hard and soft domains are compared to a rigid, unstructured network. The glass transition profiles of the heterogeneous networks are complex, spanning many decades in the frequency domain. The nanophase-separated morphology leads to higher coefficient of thermal expansion, yet surprisingly is characterized by reduced residual stress. Under both quasi-static and dynamic compression (strain rates of order 10 –3 and 10 3 s –1 , respectively), the nanophase-separated network also exhibits higher modulus and strength. In split-Hopkinson bar experiments, the energy dissipation characteristics of the epoxy networks were nearly identical. Curiously, however, the Hugoniot response of the macro-phase-separated network determined by ballistic shockwave analysis indicates a remarkable ability of this material to mitigate shockwave propagation in comparison to many homogeneous and heterogeneous polymer materials. Collectively, this work reveals several previously unreported phenomena with respect to structure–property relationships in phase-separated epoxy networks, illustrating the potential value of systematically tuned microstructures for optimization of application-specific physical properties.

36 MATERIALS SCIENCE

Distributed neural control of a hexapod walking vehicle

There has been a long standing interest in the design of controllers for multilegged vehicles. The approach is to apply distributed control to this problem, rather than using parallel computing of a centralized algorithm. Researchers describe a distributed neural network controller for hexapod locomotion which is based on the neural control of locomotion in insects. The model considers the simplified kinematics with two degrees of freedom per leg, but the model includes the static stability constraint. Through simulation, it is demonstrated that this controller can generate a continuous range of statically stable gaits at different speeds by varying a single control parameter. In addition, the controller is extremely robust, and can continue the function even after several of its elements have been disabled. Researchers are building a small hexapod robot whose locomotion will be controlled by this network. Researchers intend to extend their model to the dynamic control of legs with more than two degrees of freedom by using data on the control of multisegmented insect legs. Another immediate application of this neural control approach is also exhibited in biology: the escape reflex. Advanced robots are being equipped with tactile sensing and machine vision so that the sensory inputs to the robot controller are vast and complex. Neural networks are ideal for a lower level safety reflex controller because of their extremely fast response time. The combination of robotics, computer modeling, and neurobiology has been remarkably fruitful, and is likely to lead to deeper insights into the problems of real time sensorimotor control.

Beer, R. D.

WigglyRivers: A tool to characterize the multiscale nature of meandering channels

Channel sinuosity is ubiquitous along river networks, producing complex patterns that encapsulate and influence morphodynamic processes and ecosystem services. Accurately characterizing these patterns is challenging with traditional curvature-based algorithms. Here, in this study, we present WigglyRivers, a Python package that builds on existing wavelet-based methods to create an unsupervised meander identification and characterization tool. The package uses planimetric information the user provides or from the USGS’s High-Resolution National Hydrography Dataset to characterize individual reaches or entire river networks. WigglyRivers also includes a supervised river identification tool for manually selecting individual meandering features. Here, we provide examples of idealized river transects and show the capabilities of WigglyRivers. We also use the supervised identification tool to validate the unsupervised identification on river transects across the continental US. WigglyRivers is a tool to understand better the multiscale characteristics of river networks and the link between river geomorphology and river corridor connectivity.

54 ENVIRONMENTAL SCIENCES

Carbon Capture, Transport, And Storage (CTS) Cost Modeling Of The Onshore Gulf Coast

The onshore Gulf of Mexico region presents significant opportunities for CO2 capture, transport, and storage due to its numerous CO2 sources, such as power plants, refineries, and its substantial CO2 storage potential. However, operators face critical decisions in designing an efficient and cost-effective CO2 pipeline network. This study examines the economic implications of two primary strategies: constructing a trunkline with excess initial capacity versus developing dedicated pipelines incrementally as new CO2 sources come online. Building a trunkline first offers the advantage of future-proofing the network, allowing for the accommodation of increased CO2 volumes from various sources over time. However, this approach incurs higher upfront costs and risks underutilizing the transport capacity in the initial stages, potentially resulting in economic inefficiencies. Conversely, constructing dedicated pipelines for each new CO2 source as it becomes operational may avoid the initial overcapacity issue but fails to capitalize on the economies of scale. This could lead to higher overall costs due to the duplication of infrastructure and increased complexity in network management. This research employs a comprehensive cost-benefit analysis, integrating factors such as capital expenditure, operational costs, projected CO2 volumes, and potential economies of scale. Through this analysis, we aim to provide operators with insights into the most economically viable strategy for CO2 pipeline network design in the region. The findings underscore the importance of strategic planning and highlight the trade-offs between immediate capacity utilization and long-term cost savings, ultimately guiding stakeholders towards informed decision-making in the development of CO2 transport infrastructure. Presented at the 41st USAEE/IAEE North American Conference, 3-6 November 2024, Baton Rouge, LA, United States.

Shih, Chung Yan

RE-INTEGRATE EMT Simulation Software: Graph Convolutional Network for Sparse Matrix Pattern Detection

The increasing complexity of power networks, driven by proliferation of inverters, presents analytical challenges that simplified models often fail to capture, necessitating Electromagnetic Transient (EMT) simulations. EMT models are represented as discretized differential-algebraic equations (DAEs), forming a linear system Ax = b that is computationally intensive to solve. Due to inherent sparsity of adjacency matrix A, distinct patterns emerge that, when accurately identified, enable efficient solver selection to minimize computation time. However, identifying ideal pattern is complicated by numerous reordering algorithms and limited structural insights. To address this, we introduce a Graph Convolutional Network (GCN) model for classifying sparse matrix patterns common in power system analysis. The model, achieving 96% test accuracy, is validated using PV plant models of 125 MW capacities connected to New England 39-bus transmission system (TS), and further scaled to a 4,992-bus network with 384 PV plants, yielding 191, 616 × 191, 616 sized A matrix. For all cases, the GCN model accurately identifies the matrix’s intrinsic sparse pattern, demonstrating its potential to enhance solver performance in EMT analysis.

Hossain, Md Rifat [Florida International Universit

Spacecraft Antennas

Some of the various categories of issues that must be considered in the selection and design of spacecraft antennas for a Personal Access Satellite System (PASS) are addressed, and parametric studies for some of the antenna concepts to help the system designer in making the most appropriate antenna choice with regards to weight, size, and complexity, etc. are provided. The question of appropriate polarization for the spacecraft as well as for the User Terminal Antenna required particular attention and was studied in some depth. Circular polarization seems to be the favored outcome of this study. Another problem that has generally been a complicating factor in designing the multiple beam reflector antennas, is the type of feeds (single vs. multiple element and overlapping vs. non-overlapping clusters) needed for generating the beams. This choice is dependent on certain system design factors, such as the required frequency reuse, acceptable interbeam isolation, antenna efficiency, number of beams scanned, and beam-forming network (BFN) complexity. This issue is partially addressed, but is not completely resolved. Indications are that it may be possible to use relatively simple non-overlapping clusters of only a few elements, unless a large frequency reuse and very stringent isolation levels are required.

Jamnejad, Vahraz

An OSI Architecture for the Deep Space Network

The flexibility and robustness of a monitor and control system are a direct result of the underlying inter-processor communications architecture. A new architecture for monitor & control at the Deep Space Network Communications Complexes has been developed based on the Open System Interconnection (OSI) standards. The suitability of OSI standards for DSN M&C has been proven in the laboratory. The laboratory success has resulted in choosing an OSI-based architecture for DSS-13 M&C. DSS-13 is the DSN experimental station and is not part of the "operational" DSN; it's role is to provide an environment to test new communications concepts can be tested and conduct unique science experiments. Therefore, DSS-13 must be robust enough to support operational activities, while also being flexible enough to enable experimentation. This paper describes the M&C architecture developed for DSS-13 and the results from system and operational testing.

OSI

Multi‐Omics Analyses Reveal Divergent Molecular Mechanisms Underlying Plant Biomass Conversion by Five Fungi

Fungal plant biomass conversion (FPBC) is of great importance to the global carbon cycle and has been increasingly applied for the production of biofuel and biochemicals from lignocellulose. However, the comprehensive understanding of relevant molecular mechanisms in different fungi remains challenging. Here, we comparatively analyzed the transcriptome, proteome and metabolome profile of four ascomycetes and one basidiomycete fungi during their growth on two common agricultural feedstocks (soybean hulls and corn stover). We revealed strong time‐, substrate‐ and species‐specific responses at multi‐omics levels for the tested fungi, highlighting species‐specific carbon utilization approaches and evolutionary adaptation to environmental niches. Notably, a remarkable expressional diversity of lignocellulose degrading enzymes, sugar transporter and metabolic genes, as well as industrially relevant metabolites were identified across different fungi and cultivation conditions. The findings improves our understanding of complex molecular networks underlying FPBC and fungal ecological roles, offering novel insights that can guide future genetic engineering of fungi for valorization of agriculture waste into value‐added bioproducts.

CAZy

Clustering and Cliques in Preferential Attachment Random Graphs with Edge Insertion

In this paper, we investigate the global clustering coefficient (a.k.a transitivity) and clique number of graphs generated by a preferential attachment random graph model with an additional feature of allowing edge connections between existing vertices. Specifically, at each time step t, either a new vertex is added with probability f(t), or an edge is added between two existing vertices with probability 1 – f(t). We establish concentration inequalities for the global clustering and clique number of the resulting graphs under the assumption that f(t) is a regularly varying function at infinity with index of regular variation –$\gamma$, where $\gamma$ $\in$ [0, 1). Finally, we also demonstrate an inverse relation between these two statistics: the clique number is essentially the reciprocal of the global clustering coefficient.

97 MATHEMATICS AND COMPUTING

Degrees of rate control and AutoDiff-driven direct sensitivity analysis in heterogeneous catalysis

Despite the wide application and benefits of the degree of rate control (DRC) analysis, several details remain argued, particularly about the conservation of DRCs at transient (TR) and steady-state (SS) conditions, especially for complex reaction networks. This work argues that previous proofs about the conservation properties of DRCs have been incomplete, and we provide new mathematical proofs at TR and SS conditions. In addition, we use both analytical (automatic differentiation) and numerical (finite difference) approaches to compute DRCs for the case study of ethane hydrogenolysis (EH) over Pt(111). This work confirms that at both TR and SS conditions, the sum of all DRCs, i.e., sum of the degrees of kinetic (DKRC) and thermodynamic rate control (DTRC), is conserved at zero. At SS conditions, the sum of DKRC is conserved at 1 while the sum of DTRC is conserved at −1. In corroboration of previous works, we show that the DTRC for any adsorbate at SS is equal to the product of the species coverage and a constant. In contrast, at TR conditions, the individual sums of both DTRC and DKRC are not conserved and can be any real number, with potential implications for the novel field of dynamic catalysis. Finally, we show that the conventional finite difference (FD) approach, only useful at SS, is prone to inaccuracy and very sensitive to the value of the differential change applied. The optimal differential value also varies significantly with system and rate definition. Consequently, we describe and illustrate in this work the application of the automatic differentiation (AD) approach for the more accurate determination of DRCs at both TR and SS conditions.

Automatic differentiation

Effects of co-adsorbed water on different bond cleavages involved in acetic acid decomposition on Pt (111)

Acetic acid decomposition on Pt (111) in the presence of co-adsorbed water is a good model system for oxygenate decomposition on Pt (111) in aqueous phase, with application in hydrogen production and biomass conversion. Here, in this study, we present a density functional theory (DFT) theory calculation of how co-adsorbed water affects different bond cleavages of acetic acid decomposition on Pt (111). The presence of co-adsorbed water generally enhances O$-$H bond cleavage while inhibiting OC$-$O and OC$-$OH bond cleavage. The influence of co-adsorbed water on C$-$H bond cleavage varies the most and depends on the nature of the transition state and how co-adsorbed water stabilizes the initial and final state. Although these trends are useful as general guidance, they are not sufficient to predict the effect on a complex reaction network such as acetic acid decomposition on Pt (111) which has several parallel reaction paths with similar energies. In the absence of co-adsorbed water, the two lowest energy pathways are decarboxylation (DCX) and decarbonylation (DCN) pathways through a common CH 2 COO intermediate, in which the DCX pathway (C$-$H bond cleavage of CH 2 COO) is more favorable than DCN pathway (OC$-$O bond cleavage of CH 2 COO). In the presence of co-adsorbed water, the energy difference between Csingle bondH bond cleavage and OC$-$O bond cleavage of CH 2 COO increases, suggesting an increase in the favorability of acetic acid decarboxylation (formation of carbon dioxide) over acetic acid decarbonylation (formation of carbon monoxide) on Pt (111).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH