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Results for “computational structural dynamics”

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 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Visualizing group II intron dynamics between the first and second steps of splicing

Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5’-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.

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

Spectroscopic and computational investigations of organometallic complexation of group 12 transition metals by methanobactins from Methylocystis sp. SB2

Methanotrophic bacteria catalyze the aerobic oxidation of methane to methanol using Cu-containing enzymes, thereby exerting a modulating influence on the global methane cycle. To facilitate the acquisition of Cu ions, some methanotrophic bacteria secrete small modified peptides known as “methanobactins,” which strongly bind Cu and function as an extracellular Cu recruitment relay, analogous to siderophores and Fe. In addition to Cu, methanobactins form complexes with other late transition metals, including the Group 12 transition metals Zn, Cd, and Hg, although the interplay among solution-phase configurations, metal interactions, and the spectroscopic signatures of methanobactin-metal complexes remains ambiguous. In this study, the complexation of Zn, Cd, and Hg by methanobactin from Methylocystis sp. strain SB2 was studied using a combination of absorbance, fluorescence, extended x-ray absorption fine structure (EXAFS) spectroscopy, and time-dependent density functional theory (TD-DFT) calculations. We report changes in sample absorbance and fluorescence spectral dynamics, which occur on a wide range of experimental timescales and characterize a clear stoichiometric complexation dependence. Mercury L3-edge EXAFS and TD-DFT calculations suggest a linear model for Hg--S coordination, and TD-DFT suggests a tetrahedral model for Zn 2+ and Cd 2+ . We observed an enhancement in the fluorescence of methanobactin upon interaction with transition metals and propose a mechanism of complexation-hindered isomerization drawing inspiration from the wild-type Green Fluorescent Protein active site. Collectively, our results represent the first combined computational and experimental spectroscopy study of methanobactins and shed new light on molecular interactions and dynamics that characterize complexes of methanobactins with Group 12 transition metals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data-driven Distributed Learning of Multi-agent Systems: A Koopman Operator Approach

Koopman operator theory provides a model-free technique for studying nonlinear dynamical systems purely from data. Since the Koopman operator is infinite-dimensional, researchers have developed several methods that provide a finite-dimensional approximation of the Koopman operator so that it can be applied for practical use cases. One common thing with most of the methods is that their solutions are obtained by solving a centralized minimization problem. In this work, we treat the dynamical system to be a multi-agent system and propose an algorithm to compute the finite-dimensional approximation of the Koopman operator in a distributed manner using the knowledge of the topology of the underlying multi-agent system. The proposed distributed approach is shown to be equivalent to the centralized learning problem and results in a sparse Koopman whose block structure mimics the Laplacian of the multi-agent system. Extensive simulation studies illustrate the proposed framework on the network of oscillators and the IEEE 68 bus system.

Nandanoori, Sai Pushpak↗
DOE OSTI2022

Precision QCD, Hadronic Structure & Forward QCD, Heavy Ions: Report of Energy Frontier Topical Groups 5, 6, 7 submitted to Snowmass 2021

This report was prepared on behalf of three Energy Frontier Topical Groups of the Snowmass 2021 Community Planning Exercise. It summarizes the status and implications of studies of strong interactions in high-energy experiments and QCD theory. We emphasize the rich landscape and broad impact of these studies in the decade ahead. Hadronic interactions play a central role in the high-luminosity Large Hadron Collider (LHC) physics program, and strong synergies exist between the (HL-)LHC and planned or proposed experiments at the U.S. Electron-Ion Collider, CERN forward physics experiments, high-intensity facilities, and future TeV-range lepton and hadron colliders. Prospects for precision determinations of the strong coupling and a variety of nonperturbative distribution and fragmentation functions are examined. We also review the potential of envisioned tests of new dynamical regimes of QCD in high-energy and high-density scattering processes with nucleon, ion, and photon initial states. The important role of the high-energy heavy-ion program in studies of nuclear structure and the nuclear medium, and its connections with QCD involving nucleons are summarized. We address ongoing and future theoretical advancements in multi-loop QCD computations, lattice QCD, jet substructure, and event generators. Cross-cutting connections between experimental measurements, theoretical predictions, large-scale data analysis, and high-performance computing are emphasized.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Scalable edge clustering of dynamic graphs via weighted line graphs

Timestamped relational datasets consisting of records (or connections) between pairs of entities are ubiquitous in network science. For applications like peer-to-peer communication, email, various social network interactions, and computer network security, it is useful to organize these records into groups based on how and when they are occurring. Weighted line graphs offer a natural way to model how records are related in such datasets but for large real-world graph topologies, building and utilizing the line graph is prohibitively expensive. Here, we present the framework to cluster the edges of a dynamic graph via the associated line graph that contains two major contributions. The first is a method to work with the line graph implicitly and the second is a distributed scale implementation of an agglomerative hierarchical graph clustering algorithm. We outline a novel hierarchical dynamic graph edge clustering approach that efficiently breaks massive relational datasets into small sets of edges containing events at various timescales. This is in stark contrast to traditional graph clustering algorithms that prioritize highly connected (clique-like) community structures. Our approach relies on constructing a sufficient subgraph of a weighted line graph and applying a hierarchical agglomerative clustering. This approach is related to scalable techniques from spatial clustering, nonlinear-dimension reduction, topological data analysis, and draws particular inspiration from HDBSCAN. As an edge clustering, this method yields an overlapping node clustering. Our algorithm is parallelizable and we demonstrate efficient clustering of a billion-scale, real-world dynamic graph into small edge sets that correlate in topology and time. The entire clustering process for a graph with tens of billions of edges takes just a few minutes of run time on 256 nodes of a distributed compute environment. We argue how the output of the edge clustering is useful for a multitude of data visualization and powerful machine learning tasks, both involving the original massive dynamic graph data and metadata associated with the nodes and edges. Finally, we describe how this approach can be extended to dynamic hypergraphs and dynamic graphs/hypergraphs with unstructured data living on vertices and edges.

Data Analysis↗
DOE OSTI2023

Towards a predictive, physics-based friction model for the dynamics of jointed structures

Bolted connections are ubiquitous in mechanical designs and pose a significant challenge to understanding and predicting the vibration response of assembled structures. The present paper develops a physics-based rough contact model of the frictional interactions within a joint. This model sums over the probable interactions of asperities – defined as locally maximum surface features – to determine the contact forces. Here, the tangential contact forces vary smoothly between sticking and slipping and allow the model to better capture the qualitative trends of experimental amplitude dependent frequency and damping than previous studies. Furthermore, the novel model is generalized to allow for arbitrarily varying normal pressure including potential separation to better represent the interfacial dynamics. This includes developing a new, computationally tractable approximation to the analytical Mindlin partial slip solution for tangential loading of contacting spheres. Further, the results highlight the importance of accurately characterizing the as-built topology of the interface, the plastic behavior of the contacting asperities, the relevant length scale of asperities, and the eccentricity of asperities. A predictive friction coefficient based on plasticity provides a poor match to experiments, so fitting the friction coefficient is also considered. Numerical results are compared to experiments on the Brake-Reuß Beam to assess the predictive potential of the models. While blind predictions over-predict the slip limit, the current model presents a significant improvement in physics-based modeling and highlights areas for ongoing research.

42 ENGINEERING↗
DOE OSTI2021

Neural-network model for force prediction in multi-principal-element alloys

Atomistic simulations can provide useful insights into the physical properties of multi-principal-element alloys. However, classical potentials mostly fail to capture key quantum (electronic-structure) effects. Here we present a deep 3D convolutional neural network (3D CNN) based framework combined with a voxelization technique to design interatomic potentials for chemically complex alloys. We highlight the performance of the 3D CNN model and its efficacy in computing potentials using the medium-entropy alloy TaNbMo. In order to provide insights into the effect of voxel resolution, we implemented two approaches based on the inner and outer bounding boxes. An efficient 3D CNN model, which is as accurate as the density-functional theory (DFT) approach, for calculating potentials will provide a promising schema for accurate atomistic simulations of structure and dynamics of general multi-principle element alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Simulation studies of the interaction of laser radiation with additively manufactured foams

The interaction of laser radiation with foams of various porosities and low densities has been the subject of several numerical and experimental studies. In all cases, the modeling of low-Z under-dense foams as uniform gases of equivalent average density using standard radiation-hydrodynamics codes has resulted in heat-front velocities that are considerably faster than those observed experimentally. It has been theoretically conjectured that this difference may be attributed to the breakdown of the foam’s morphology, leading to a dynamics of filament expansion where the ion and electron energy partitions are significantly different from those calculated using the uniform gas model. We found that 3D computer simulations employing a disconnected representation of the foam’s microstructure which allowed for the dynamics of foam element heating, expansion, and stagnation largely supported the theoretical picture. Simulations using this model for laser experiments on under-dense 2 mg cc -1 SiO 2 aerogel foams reproduced the experimental data fairly well. We used the validated model in simulations of low-density structured foam-like materials (produced via additive manufacturing) with a variety of morphologies. We found that the log-pile configurations were consistent with the analytical propagation model of Gus’kov et al. Further validation of the model was obtained by simulating experiments performed at the Jupiter Laser Facility using the log-pile and octet-truss foam morphologies. Simulations of the foam-laser interaction using a wave propagation code showed that the microstructure was able to enhance stimulated Brillouin scattering (SBS) by concentrating the light energy into density holes. In turn, this promotes laser filamentation, reducing SBS and bringing the predicted values closer to the experimental data.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Challenging Common Assumptions of Thick-Wall Chamber Dynamics in Inertial Fusion Systems using MOOSE

As an increasing number of companies look toward commercial Inertial Fusion Energy (IFE) designs, there is a pressing need to understand the physics of thick-wall chamber gas dynamics. The thick liquid wall approach implements a renewable wall to mitigate the fusion target emissions, thereby reducing the radiation damage rate and significantly extending the lifetime of chamber structures, leading to increased plant availability and reduced waste streams in comparison to dry wall chamber designs. It is necessary, however, to assess the critical performance and safety aspects of these systems. For example, it is crucial to predict (1) where the mass ablated from the liquid walls will vent, which determines the placement of condensing surfaces; (2) debris propagation up the beam lines, which provides essential information for design and protection requirements; (3) peak pressures and impulse on chamber walls, which affect chamber structural design; and (4) momentum transfer to the liquid jets, which constrains the shape and positioning of the jets. In turn, the chamber design and its liquid walls affect shielding requirements, material activation, and tritium fuel cycle. Currently available simulation tools, however, are unable to accurately capture key thick-wall chamber dynamics. Significant assumptions are often made to simplify the system and reduce computational cost and modeling capability needs, but the impact of these assumptions on simulation predictions has not been evaluated. For example, no three-dimensional simulations can be found in the open literature to evaluate gas venting and momentum transfer to the jets with simulations using two-dimensional domains to represent complex three-dimensional geometries. Moreover, limited studies have been dedicated to jet breakup due to both turbulence and neutron heating, and no studies have been found that evaluate how jet breakup can impact shock-jet interaction. Furthermore, effects of radiative heat transfer have rarely been included for the hydrodynamic phase of shock propagation, and integration of proper equations of state in shock dynamics codes has been mostly exploratory. In this study, we use the flexible, high-fidelity Multiphysics Object-Oriented Simulation Environment (MOOSE) to model these complex phenomena and inform design and safety studies. Capabilities to model thick-wall chamber gas dynamics are being developed, and the impact of the assumptions listed above (i.e., two-dimensional vs three-dimensional, absence of jet breakout, no radiative heat transfer, and ideal gas behavior) are being quantified.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Challenging Common Assumptions of Thick-Wall Chamber Dynamics in Inertial Fusion Systems Using MOOSE-based Multiphysics Simulations

As an increasing number of companies look toward commercial Inertial Fusion Energy (IFE) designs, there is a pressing need to understand the physics of thick-wall chamber gas dynamics. The thick liquid wall approach implements a renewable wall to mitigate the fusion target emissions, thereby reducing the radiation damage rate and significantly extending the lifetime of chamber structures, leading to increased plant availability and reduced waste streams in comparison to dry wall chamber designs. It is necessary, however, to assess the critical performance and safety aspects of these systems. For example, it is crucial to predict (1) where the mass ablated from the liquid walls will vent, which determines the placement of condensing surfaces; (2) debris propagation up the beam lines, which provides essential information for design and protection requirements; (3) peak pressures and impulse on chamber walls, which affect chamber structural design; and (4) momentum transfer to the liquid jets, which constrains the shape and positioning of the jets. In turn, the chamber design and its liquid walls affect shielding requirements, material activation, and tritium fuel cycle. Currently available simulation tools, however, are unable to accurately capture key thick-wall chamber dynamics. Significant assumptions are often made to simplify the system and reduce computational cost and modeling capability needs, but the impact of these assumptions on simulation predictions has not been evaluated. For example, no three-dimensional simulations can be found in the open literature to evaluate gas venting and momentum transfer to the jets with simulations using two-dimensional domains to represent complex three-dimensional geometries. Moreover, limited studies have been dedicated to jet breakup due to both turbulence and neutron heating, and no studies have been found that evaluate how jet breakup can impact shock-jet interaction. Furthermore, effects of radiative heat transfer have rarely been included for the hydrodynamic phase of shock propagation, and integration of proper equations of state in shock dynamics codes has been mostly exploratory. In this study, we use the flexible, high-fidelity Multiphysics Object-Oriented Simulation Environment (MOOSE) to model these complex phenomena and inform design and safety studies. Capabilities to model thick-wall chamber gas dynamics are being developed, and the impact of the assumptions listed above (i.e., two-dimensional vs three-dimensional, absence of jet breakout, no radiative heat transfer, and ideal gas behavior) are being quantified.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Robust Implicit Adaptive Low Rank Time-Stepping Methods for Matrix Differential Equations

In this work, we develop implicit rank-adaptive schemes for time-dependent matrix differential equations. The dynamic low rank approximation (DLRA) is a well-known technique to capture the dynamic low rank structure based on Dirac–Frenkel time-dependent variational principle. In recent years, it has attracted a lot of attention due to its wide applicability. Our schemes are inspired by the three-step procedure used in the rank adaptive version of the unconventional robust integrator (the so called BUG integrator) (Ceruti et al. in BIT Numer Math 62(4):1149–1174, 2022) for DLRA. First, a prediction (basis update) step is made computing the approximate column and row spaces at the next time level. Second, a Galerkin evolution step is invoked using an implicit solves for the small core matrix. Finally, a truncation is made according to a prescribed error threshold. Since the DLRA is evolving the differential equation projected on to the tangent space of the low rank manifold, the error estimate of the BUG integrator contains the tangent projection (modeling) error which cannot be easily controlled by mesh refinement. This can cause convergence issue for equations with cross terms. To address this issue, we propose a simple modification, consisting of merging the row and column spaces from the explicit step truncation method together with the BUG spaces in the prediction step. In addition, we propose an adaptive strategy where the BUG spaces are only computed if the residual for the solution obtained from the prediction space by explicit step truncation method, is too large. Here, we prove stability and estimate the local truncation error of the schemes under assumptions. We benchmark the schemes in several tests, such as anisotropic diffusion, solid body rotation and the combination of the two, to show robust convergence properties.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Reduced‐Order Modeling of Energetic Materials Using Physics‐Aware Recurrent Convolutional Neural Networks in a Latent Space (LatentPARC)

Physics-aware deep learning (PADL) has gained popularity for use in spatiotemporal dynamics simulations, such as those in computational modeling of energetic materials (EM). We show that the challenge PADL methods face while learning complex field evolution problems can be simplified and accelerated by decoupling it into two tasks: learning complex geometric features in evolving fields and modeling dynamics over these features in a lower-dimensional feature space. We build upon our previous work on physics-aware recurrent convolutional neural networks (PARC). PARC embeds knowledge of underlying physics into its neural network architecture for more robust and accurate prediction of evolving physical fields. PARC was shown to effectively learn complex nonlinear features such as the formation of hotspots and coupled shock fronts in various initiation scenarios of EMs, as a function of microstructures, serving effectively as a microstructure-aware burn model. Here, we further accelerate PARC and reduce its computational cost by projecting the original dynamics onto a lower-dimensional invariant manifold, or “latent space.” The projected latent representation encodes the complex geometry of evolving fields (e.g., temperature and pressure) in a set of data-driven features. The reduced dimension of this latent space allows us to learn the dynamics during the initiation of EM with a lighter and more efficient model. We observe a significant decrease in training and inference time while maintaining results comparable to PARC at inference. This work takes steps towards enabling rapid prediction of EM thermomechanics at larger scales and characterization of EM structure–property–performance linkages at a full application scale.

Mathematics and Computing↗
DOE OSTI2024

Universality of Collective Density Fluctuations in Liquids at and away from Equilibrium – An Integrated Neutron Scattering, Theoretical, and Computational Study (Final Technical Report)

Liquids, ubiquitous on earth, are prototypical disordered condensed matter. As the mediate phase between non-structured gases and ordered solids, liquids p ossess intriguing complexities that are absent on either extreme counter phase, especially when they are driven away from equilibrium. Despite decades of studies, the physics of liquids still keeps surprising us and challenges our understanding of condensed matter, emergent phenomena, and complex systems. Among the many interesting properties, the nature of collective dynamics in liquids remains elusive because of both the presence of strong interactions and the absence of translational invariance. This project studied the universal features of collective density fluctuations (or collective modes), which include both phonon-like excitations and collective relaxations, in the Q-dependent generalized hydrodynamic regime in liquids and liquid-like matter both at and away from equilibrium. We performed systematic studies of the fast collective dynamics (including both phonon-like excitations and collective relaxations) of four classes of liquids characterized by different fragilities and interactions using synergistically integrated coherent neutron scattering experiments (Inelastic Neutron Scattering (INS), Quasi-Elastic Neutron Scattering (QENS), and Neutron Spin Echo (NSE)), a ViscoElastic Hydrodynamics theory we have been developing, andMolecular Dynamics (MD) simulations and our analysis package LiquidLib. The transformative knowledge of the collective dynamics in liquids is important to understand and ultimately control the transport of mass, energy, and charge in liquids, both at and away from thermal equilibrium, which may will likely impact a wide range of disciplines.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Uncertainty quantification of bank vegetation impacts on the flood flow field in the American River, California, using large‐eddy simulations

Bank vegetation plays a key role in both hydrodynamics and morphodynamics of natural rivers; however, these effects are often unaccounted for in the computational flow dynamics of natural waterways. Recent studies using the large‐eddy simulation (LES), however, have attempted to gain insights into the impacts of bank vegetation on the mean flow field of the natural rivers using a vegetation model, which applies a sink term to the momentum equations of motion. This approach accounts for the effects of the vegetation and provides a practical approach to account for the complex patches of bank vegetation in large‐scale rivers. To implement the vegetation model, a drag coefficient reflecting the overall resistance of vegetal structures to the flow is needed, but due to the lack of calibrated data and range of size, density and type of vegetation, this parameter can be a significant source of uncertainty in the model results. Here, in this study, we use uncertainty quantification (UQ) to investigate the hydrodynamics and bed shear results when a bank vegetation is incorporated in an LES model. To this end, we used the polynomial chaos expansion and Monte Carlo sampling techniques to determine the uncertainties associated with the drag coefficient in the vegetation model and from uncertainties in the bed roughness and inflow discharge. The UQ analysis provided spatially varying confidence levels for the spanwise and vertical distribution of velocity magnitude and for the bed shear stress distributions. In addition, Sobol indices were computed to indicate the relative influence that each parameter had on the overall uncertainty. In general, it was found that uncertainty in flow discharge was the dominant source of uncertainty; however, the drag coefficient in the vegetation model and the bed roughness parameter also made significant contribution to the uncertainty near the banks and bed, respectively.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

AIMD‐Based Protocols for Modeling Exciplex Fluorescence Spectra and Inter‐System Crossing in Photocatalytic Chromophores

ABSTRACT This study introduces a computational protocol for modeling the emission spectra of exciplexes using excited‐state ab initio molecular dynamics (AIMD) simulations. The protocol is applied to a model exciplex formed by oligo‐p‐phenylenes (OPPs) and triethylamine (TEA), which is of interest in the context of photocatalytic reduction of . AIMD facilitates efficient sampling of the conformational space of OPP3 and OPP4 exciplexes with TEA, offering a dynamic alternative to previously employed static methods. The AIMD‐based protocol successfully reproduces experimental emission spectra for OPP‐TEA exciplexes, agreeing with previous computational and experimental findings. The results show that AIMD simulations provide an efficient means of sampling the conformational space of these exciplexes, requiring less user input and, in some instances, fewer computational resources than multiple excited‐state optimizations initiated from user‐specified initial structures. The study also evaluates the yield of intersystem crossing (ISC) using AIMD and Landau‐Zener probability. The results suggest that ISC is a minor decay channel for OPP3 and OPP4. This work provides new insights into the structural flexibility and emission characteristics of OPP‐TEA photoredox catalyst systems, potentially contributing to improved design strategies for organic chromophores in reduction applications.

Giudetti, Goran [Department of Chemistry Universit↗
DOE OSTI2020

Order-disorder behavior at thin film oxide interfaces

Order-disorder processes fundamentally determine the structure and properties of many important oxide systems for energy and computing applications. While these processes have been intensively studied in bulk materials, they are less investigated and understood for nanostructured oxides in highly non-equilibrium conditions. These systems can now be realized through a range of deposition techniques and probed at exceptional spatial and chemical resolution, leading to a greater focus on interface dynamics. In this work, we survey a selection of recent studies of order-disorder behavior at thin film oxide interfaces, with a particular emphasis on the emergence of order during synthesis and disorder in extreme irradiation environments. We summarize key trends and identify directions for future study in this growing research area.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Multi-level optimization with the koopman operator for data-driven, domain-aware, and dynamic system security

Cyber-Physical Systems (CPSs) like the power grid are critically important but also increasingly vulnerable; ensuring reliable system operation in the face of disruptions is becoming more and more challenging. Multi-Level Optimization (MLO) is a powerful way to model adversarial interactions, which naturally makes it applicable to studying CPS security. However, MLO typically does not address underlying system dynamics, and incorporating nonlinear dynamics is generally infeasible. In this paper, we show how to combine MLO with the Koopman Operator (KO) to remedy this. The KO maps nonlinear dynamics to a lifted space in which those dynamics are linear, thus making it ideal for use with MLO. Moreover, the structure of the KO also provides convenient ways to incorporate domain knowledge into the data-driven process of learning the KO representation of a given system. Here we then demonstrate the use of MLO-KO on a small example problem taken from the power grid domain, discuss the scalability and computational cost of MLO-KO, and identify future research directions for this work.

42 ENGINEERING↗