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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 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Attention for Causal Relationship Discovery from Biological Neural Dynamics

This paper explores the potential of the transformer models for learning Granger causality in networks with complex nonlinear dynamics at every node, as in neurobiological and biophysical networks. Our study primarily focuses on a proof-of-concept investigation based on simulated neural dynamics, for which the ground-truth causality is known through the underlying connectivity matrix. For transformer models trained to forecast neuronal population dynamics, we show that the cross-attention module effectively captures the causal relationship among neurons, with an accuracy equal to or superior to that of the most popular Granger causality discovery method. While we acknowledge that real-world neurobiology data will bring further challenges, including dynamic connectivity and unobserved variability, this research offers an encouraging preliminary glimpse into the utility of the transformer model for causal representation learning in neuroscience.

Lu, Ziyu↗
DOE OSTI2018

Sparse Hardware Embedding of Spiking Neuron Systems for Community Detection

We study the applicability of spiking neural networks and neuromorphic hardware for solving general optimization problems without the use of adaptive training or learning algorithms. We leverage the dynamics of Hopfield networks and spin-glass systems to construct a fully connected spiking neural system to generate synchronous spike responses indicative of the underlying community structure in an undirected, unweighted graph. Mapping this fully connected system to current generation neuromorphic hardware is done by embedding sparse tree graphs to generate only the leading-order spiking dynamics. Here, we demonstrate that for a chosen set of benchmark graphs, the spike responses generated on a current generation neuromorphic processor can improve the stability of graph partitions and non-overlapping communities can be identified even with the loss of higher-order spiking behavior if the graphs are sufficiently dense. For sparse graphs, the loss of higher-order spiking behavior improves the stability of certain graph partitions but does not retrieve the known community memberships.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Theory of kinetic arrest, elasticity, and yielding in dense binary mixtures of rods and spheres

We extend the quiescent and stressed versions of naïve mode coupling theory to treat the dynamical arrest, shear modulus, and absolute yielding of particle mixtures where one or more species is a nonrotating nonspherical object. The theory is applied in detail to dense isotropic “chemically matched” mixtures of variable aspect ratio rods and spheres that interact via repulsive and short range attractive site-site pair potentials. A remarkably rich ideal kinetic arrest behavior is predicted with up to eight “dynamical phases” emerging: an ergodic fluid, partially localized states where the spheres remain fluid but the rods can be a gel, repulsive glass or attractive glass, doubly localized glasses and gels, a porous rod gel plus sphere glass, and a narrow window where a type of rod glass and gel localization coexist. Dynamical complexity increases with rod length and the introduction of attractive forces between all species which both enhance gel network formation. Multiple dynamic reentrant features and triple points are predicted, and each dynamic phase has unique particle localization characteristics and mechanical properties. Orders of magnitude variation of the linear shear modulus and absolute yield stress are found as rod length, mixture composition and the detailed nature of interparticle attractions are varied. The interplay of total (high) mixture packing fraction and composition at fixed temperature is also briefly studied. The present work provides a foundation to study more complex rod-sphere mixtures of both biological and synthetic interest that include physical features such as interaction site size asymmetry, rod-sphere specific attractions, and/or Coulomb repulsion.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

Deep Neural Network Based Convergence Classification for Computational Fluid Dynamics

A supervised deep learning approach is coupled with heuristic convergence criteria to construct a classification model for detecting the completion (convergence) of computational fluid dynamics (CFD) simulations. Heuristic convergence criteria alone are not always sufficient and more complex decisions are often left to a human analyst. The proposed approach leverages heuristic convergence criteria as well as two deep neural network (DNN) models, one binary and one multi-class, to improve the efficiency and consistency of convergence classification across a wide range of flight regimes. The DNN models presented are each trained on a subset of ascent aerodynamic CFD simulations for NASA’s Space Launch System and were produced using NASA’s unstructured Navier-Stokes solver FUN3D. Individual solutions are analyzed intermittently and are classified as sufficiently converged, further iterations required, or switch from steady Reynolds Averaged Navier-Stokes (RANS) to unsteady RANS CFD based on the iterative histories of four aerodynamic coefficients. The implemented classification model is shown to produce solutions that closely correlate to solutions produced by a human analyst. This work lays groundwork for expanding the capabilities of DNNs for automating and improving more of the CFD process.

SLS↗
NASA NTRS1977

Coupled dynamics analysis of wind energy systems

A qualitative description of all key elements of a complete wind energy system computer analysis code is presented. The analysis system addresses the coupled dynamics characteristics of wind energy systems, including the interactions of the rotor, tower, nacelle, power train, control system, and electrical network. The coupled dynamics are analyzed in both the frequency and time domain to provide the basic motions and loads data required for design, performance verification and operations analysis activities. Elements of the coupled analysis code were used to design and analyze candidate rotor articulation concepts. Fundamental results and conclusions derived from these studies are presented.

Hoffman, J. A.↗
NASA NTRS2012

Cognitive Network Modeling as a Basis for Characterizing Human Communication Dynamics and Belief Contagion in Technology Adoption

Societal level macro models of social behavior do not sufficiently capture nuances needed to adequately represent the dynamics of person-to-person interactions. Likewise, individual agent level micro models have limited scalability - even minute parameter changes can drastically affect a model's response characteristics. This work presents an approach that uses agent-based modeling to represent detailed intra- and inter-personal interactions, as well as a system dynamics model to integrate societal-level influences via reciprocating functions. A Cognitive Network Model (CNM) is proposed as a method of quantitatively characterizing cognitive mechanisms at the intra-individual level. To capture the rich dynamics of interpersonal communication for the propagation of beliefs and attitudes, a Socio-Cognitive Network Model (SCNM) is presented. The SCNM uses socio-cognitive tie strength to regulate how agents influence--and are influenced by--one another's beliefs during social interactions. We then present experimental results which support the use of this network analytical approach, and we discuss its applicability towards characterizing and understanding human information processing.

Hutto, Clayton↗
DOE OSTI2020

GRANT: Ground-Roaming Autonomous Neuromorphic Targeter

In this work we describe the design, implementation, and testing of the first neuromorphic robot capable of obstacle avoidance, grid coverage, and targeting controlled by the second generation Dynamic Adaptive Neural Network Array (DANNA2) digital spiking neuromorphic processor. The simplicity of the DANNA2 processor along with the TENNLab hardware/software co-design framework allows for compact spiking networks that can run efficiently on a small, resource-constrained, platform such as a Xilinx Artix-7 field-programmable gate array. Additionally, we present the dynamic reconfigurability of DANNA2 arrays as a method of realizing complex, multi-objective tasks on hardware that is restricted to relatively small networks.

Ambrose, Jonathan↗
DOE OSTI2019

Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps

Sliding clamp proteins encircle duplex DNA and are involved in processive DNA replication and the DNA damage response. Clamp proteins are ring-shaped oligomers (dimers or trimers) and are loaded onto DNA by an ATP-dependent clamp loader complex that ruptures the interface between two adjacent subunits. Here we measured the solution dynamics of the human clamp protein, proliferating cell nuclear antigen, by monitoring the change in the fluorescence of a site-specifically labeled. To unravel the origins of clamp subunit interface stability, we carried out comprehensive comparative analysis of the interfaces of seven sliding clamps. Here, we used computational modeling (molecular dynamic simulations and MM/GBSA binding energy decomposition analyses) to identify conserved networks of hydrophobic residues critical for clamp stability and ring-opening dynamics. The hydrophobic network is shared among clamp proteins and exhibits a “key in a keyhole” pattern where a bulky aromatic residue from one clamp subunit is anchored into a hydrophobic pocket of the opposing subunit. Bioinformatics and dynamic network analyses showed that this oligomeric latch is conserved across DNA sliding clamps from all domains of life and dictates the dynamics of clamp opening and closing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Hindered segmental dynamics in associative protein hydrogels studied by neutron spin-echo spectroscopy

Transient binding between associating macromolecules can cause qualitative changes to chain dynamics, including modes of conformational relaxation and diffusion, through tethering effects imparted by long-range connectivity. Here, in this work, the role of binding on short-time segmental dynamics in associative polymer gels is investigated by neutron spin-echo (NSE) measurements on a class of model artificial coiled-coil proteins with a systematically varied architecture, probing timescales of 0.1–130 ns, and length scales close to the molecular radius of gyration. The results illustrate effects of transient cross-linking on chain dynamics on different timescales, manifested in changes in segmental relaxation behavior with variations in strand length, chain concentration, and sticker distribution (endblock- vs midblock-functionalized). In all gels, a short-time cooperative diffusion mode is seen over all wave vectors, analogous to a semidilute solution, with no transitions seen at any known structural length scale. However, the diffusion coefficients are found to decrease with increasing junction density across all gels, with the strand length and number of stickers per chain in each gel appearing to play a relatively minor role. The slowing of cooperative diffusion with junction density contrasts with classical predictions of a greater restoring force for fluctuation dissipation due to the increased elasticity, suggesting additional effects of the coiled-coil junctions such as an enhancement in local viscosity that slows dynamics. Notably, the relaxation rates for all gels can be rescaled by the interjunction spacing inferred from small-angle neutron scattering, where they collapse onto a master curve suggestive of self-similar dynamics even in networks with different strand lengths and chain architectures. On long timescales (but shorter than the junction exchange time), a slowing of network relaxation is observed, resulting in a nondecaying plateau in the spin-echo amplitude attributed to a freezing of chain dynamics due to tethering. A characteristic length scale corresponding to the extent of dynamic fluctuations is estimated for each gel, which appears to be smaller than the interjunction spacing but similar to the correlation blob size of the overlapping strands. The results indicate an important role of transient binding on molecular-scale dynamics in associative polymer gels, even on timescales shorter than the junction exchange time, in addition to its effects on long-range self-diffusion previously observed.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Neural network representation of electronic structure from ab initio molecular dynamics

Despite their rich information content, electronic structure data amassed at high volumes in ab initio molecular dynamics simulations are generally under-utilized. Here we introduce a transferable high-fidelity neural network representation of such data in the form of tight-binding Hamiltonians for crystalline materials. This predictive representation of ab initio electronic structure, combined with machine-learning boosted molecular dynamics, enables efficient and accurate electronic evolution and sampling. When it is applied to a one-dimension charge-density wave material, carbyne, we are able to compute the spectral function and optical conductivity in the canonical ensemble. The spectral functions evaluated during soliton-antisoliton pair annihilation process reveal significant renormalization of low-energy edge modes due to retarded electron-lattice coupling beyond the Born–Oppenheimer limit. The availability of an efficient and reusable surrogate model for the electronic structure dynamical system will enable calculating many interesting physical properties, paving the way to previously inaccessible or challenging avenues in materials modeling.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Efficient learning of power grid voltage control strategies via model-based deep reinforcement learning

Here this article proposes a model-based deep reinforcement learning (DRL) method to design emergency control strategies for short-term voltage stability problems in power systems. Recent advances show promising results for model-free DRL-based methods in power systems control problems. But in power systems applications, these model-free methods have certain issues related to training time (clock time) and sample efficiency; both are critical for making state-of-the-art DRL algorithms practically applicable. DRL-agent learns an optimal policy via a trial-and-error method while interacting with the real-world environment. It is also desirable to minimize the direct interaction of the DRL agent with the real-world power grid due to its safety-critical nature. Additionally, the state-of-the-art DRL-based policies are mostly trained using a physics-based grid simulator where dynamic simulation is computationally intensive, lowering the training efficiency. We propose a novel model-based DRL framework where a deep neural network (DNN)-based dynamic surrogate model (SM), instead of a real-world power grid or physics-based simulation, is utilized within the policy learning framework, making the process faster and more sample efficient. However, having stable training in model-based DRL is challenging because of the complex system dynamics of large-scale power systems. We addressed these issues by incorporating imitation learning to have a warm start in policy learning, reward-shaping, and multi-step loss in surrogate model training. Finally, we achieved 97.5% reduction in samples and 87.7% reduction in training time for an application to the IEEE 300-bus test system.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2015

A framework for stochastic simulations and visualization of biological electron-transfer dynamics

Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr–Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. Finally, VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr–Omc complex due to electron–electron interactions.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Assessing electrogenetic activation via a network model of biological signal propagation

Introduction: Molecular communication is the transfer of information encoded by molecular structure and activity. We examine molecular communication within bacterial consortia as cells with diverse biosynthetic capabilities can be assembled for enhanced function. Their coordination, both in terms of engineered genetic circuits within individual cells as well as their population-scale functions, is needed to ensure robust performance. We have suggested that “electrogenetics,” the use of electronics to activate specific genetic circuits, is a means by which electronic devices can mediate molecular communication, ultimately enabling programmable control. Methods: Here, we have developed a graphical network model for dynamically assessing electronic and molecular signal propagation schemes wherein nodes represent individual cells, and their edges represent communication channels by which signaling molecules are transferred. We utilize graph properties such as edge dynamics and graph topology to interrogate the signaling dynamics of specific engineered bacterial consortia. Results: We were able to recapitulate previous experimental systems with our model. In addition, we found that networks with more distinct subpopulations (high network modularity) propagated signals more slowly than randomized networks, while strategic arrangement of subpopulations with respect to the inducer source (an electrode) can increase signal output and outperform otherwise homogeneous networks. Discussion: We developed this model to better understand our previous experimental results, but also to enable future designs wherein subpopulation composition, genetic circuits, and spatial configurations can be varied to tune performance. We suggest that this work may provide insight into the signaling which occurs in synthetically assembled systems as well as native microbial communities.

Chun, Kayla↗
DOE OSTI2023

Eco-PiNN: A Physics-informed Neural Network for Eco-toll Estimation

The eco-toll estimation problem quantifies the expected environmental cost (e.g., energy consumption, exhaust emissions) for a vehicle to travel along a path. This problem is important for societal applications such as eco-routing, which aims to find paths with the lowest exhaust emissions or energy need. The challenges of this problem are threefold: (1) the dependence of a vehicle's eco-toll on its physical parameters; (2) the lack of access to data with eco-toll information; and (3) the influence of contextual information (i.e. the connections of adjacent segments in the path) on the eco-toll of road segments. Prior work on eco-toll estimation has mostly relied on pure data-driven approaches and has high estimation errors given the limited training data. To address these limitations, we propose a novel Eco-toll estimation Physics-informed Neural Network framework (Eco-PiNN) using three novel ideas, namely, (1) a physics-informed decoder that integrates the physical laws governing vehicle dynamics into the network, (2) an attention-based contextual information encoder, and (3) a physics-informed regularization to reduce overfitting. Experiments on real-world heavy-duty truck data show that the proposed method can greatly improve the accuracy of eco-toll estimation compared with state-of-the-art methods.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1998

Dynamic Load Balancing for Adaptive Meshes using Symmetric Broadcast Networks

Many scientific applications involve grids that lack a uniform underlying structure. These applications are often dynamic in the sense that the grid structure significantly changes between successive phases of execution. In parallel computing environments, mesh adaptation of grids through selective refinement/coarsening has proven to be an effective approach. However, achieving load balance while minimizing inter-processor communication and redistribution costs is a difficult problem. Traditional dynamic load balancers are mostly inadequate because they lack a global view across processors. In this paper, we compare a novel load balancer that utilizes symmetric broadcast networks (SBN) to a successful global load balancing environment (PLUM) created to handle adaptive unstructured applications. Our experimental results on the IBM SP2 demonstrate that performance of the proposed SBN load balancer is comparable to results achieved under PLUM.

Das, Sajal K.↗
DOE OSTI2021

Dynamical Large Deviations of Two-Dimensional Kinetically Constrained Models Using a Neural-Network State Ansatz

We use a neural-network ansatz originally designed for the variational optimization of quantum systems to study dynamical large deviations in classical ones. We use recurrent neural networks to describe the large deviations of the dynamical activity of model glasses, kinetically constrained models in two dimensions. We present the first finite size-scaling analysis of the large-deviation functions of the two-dimensional Fredrickson-Andersen model, and explore the spatial structure of the high-activity sector of the South-or-East model. These results provide a new route to the study of dynamical large-deviation functions, and highlight the broad applicability of the neural-network state ansatz across domains in physics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗