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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 OSTI2017

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

We report that an increasingly important endeavor is to develop computational strategies that enable molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in protonation states under conditions of constant pH. The present work describes our efforts to implement the powerful constant-pH MD simulation method, based on a hybrid nonequilibrium MD/Monte Carlo (neMD/MC) technique within the highly scalable program NAMD. The constant-pH hybrid neMD/MC method has several appealing features; it samples the correct semigrand canonical ensemble rigorously, the computational cost increases linearly with the number of titratable sites, and it is applicable to explicit solvent simulations. The present implementation of the constant-pH hybrid neMD/MC in NAMD is designed to handle a wide range of biomolecular systems with no constraints on the choice of force field. Furthermore, the sampling efficiency can be adaptively improved on-the-fly by adjusting algorithmic parameters during the simulation. Finally, illustrative examples emphasizing medium- and large-scale applications on next-generation supercomputing architectures are provided.

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

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

CLOSE STELLAR ENCOUNTERS IN YOUNG, SUBSTRUCTURED, DISSOLVING STAR CLUSTERS: STATISTICS AND EFFECTS ON PLANETARY SYSTEMS

Both simulations and observations indicate that stars form in filamentary, hierarchically clustered associations, most of which disperse into their galactic field once feedback destroys their parent clouds. However, during their early evolution in these substructured environments, stars can undergo close encounters with one another that might have significant impacts on their protoplanetary disks or young planetary systems. We perform N-body simulations of the early evolution of dissolving, substructured clusters with a wide range of properties, with the aim of quantifying the expected number and orbital element distributions of encounters as a function of cluster properties. We show that the presence of substructure both boosts the encounter rate and modifies the distribution of encounter velocities compared to what would be expected for a dynamically relaxed cluster. However, the boost only lasts for a dynamical time, and as a result the overall number of encounters expected remains low enough that gravitational stripping is unlikely to be a significant effect for the vast majority of star-forming environments in the Galaxy. We briefly discuss the implications of this result for models of the origin of the solar system, and of free-floating planets. We also provide tabulated encounter rates and orbital element distributions suitable for inclusion in population synthesis models of planet formation in a clustered environment.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Dirac open-quantum-system dynamics: Formulations and simulations

In this work, we present an open-system interaction formalism for the Dirac equation. Overcoming a complexity bottleneck of alternative formulations, our framework enables efficient numerical simulations (utilizing a typical desktop) of relativistic dynamics within the von Neumann density matrix and Wigner phase-space descriptions. Employing these instruments, we gain important insights into the effect of quantum dephasing for relativistic systems in many branches of physics. In particular, the conditions for robustness of Majorana spinors against dephasing are established. Using the Klein paradox and tunneling as examples, we show that quantum dephasing does not suppress negative energy particle generation. Hence, the Klein dynamics is also robust to dephasing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Initial position optimization in molecular dynamics simulations for a Coulomb system

A new algorithm for molecular dynamics (MD) simulations is developed to optimize plasma particle distributions at given initial temperatures. By combining velocity scaling and reassignment, the method effectively eliminates the initial rise and oscillation in temperatures observed with randomly distributed positions. These rises and oscillations are undesired numerical artifacts observed in conventional plasma MD simulations, arising from unoptimized particle positions. The algorithm demonstrates temperature relaxation without initial rises or oscillations, as well as precise flow velocity relaxation, enabling accurate measurement of relaxation times. The code is accelerated using graphics processing units for parallel processing, enhancing the study of plasma dynamics. The proposed method for distributing physically valid particles in MD simulations enables accurate studies of intrinsic collision processes in plasmas, including the dynamics of strongly coupled plasmas, plasma–wave interactions, and transport phenomena in magnetized plasmas. The paper concludes with a discussion of potential applications and future enhancements to the algorithm.

Jo, Jawon (ORCID:0009000924193285)↗
DOE OSTI2025

SCALE Non-LWR Models for NRC Volume 3

This dataset contains input and result files of computational simulations with the SCALE code system. The simulations cover radionuclide inventory and reactivity analyses of various advanced reactors. Users wanting to reproduce results from this dataset are required to obtain a license to the SCALE code system for which details on the distribution can be found here: https://www.ornl.gov/scale/releases

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2025

SCALE Non-LWR Models for NRC Volume 5

This dataset contains input and result files of computational simulations with the SCALE code system. The simulations cover radionuclide inventory generation, criticality calculations, and dose rate/shielding analyses of various advanced reactors. Users wanting to reproduce results from this dataset are required to obtain a license to the SCALE code system for which details on the distribution can be found here: https://www.ornl.gov/scale/releases

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2026

Physics-aware adaptive checkpointing with shadow systems for nonlinear PDE simulations

Large-scale simulations of nonlinear partial differential equations (PDEs) that exhibit strongly transient behavior and pattern-forming dynamics produce enormous amounts of data, which, even with modern storage systems, cannot be stored for later curation. Current I/O strategies either write dense time series of snapshots, which is often prohibitive in I/O and storage, or store a few checkpoints that enable restart but incur expensive recomputation cost and provide no control over post-restart error growth, especially when lossy compression is used. Moreover, most, if not all, existing strategies take no account of the actual physical state of the system. Here, we present a simple physics-aware I/O framework in which a low-cost shadow system adaptively triggers lossy checkpoints when the shadow system deviates from the fine-scale simulation. The shadow system can be a coarsened replica of the fine-scale simulation that evolves concurrently. This means that checkpoints are taken based on the physical state of the system: fewer checkpoints are triggered when the system is quiescent while more are taken when the system undergoes a rapid change. This type of behavior is observed in many systems such as Brusselator and FitzHugh–Nagumo. We illustrate that our framework maintains stable restarts, keeps fine-scale restart errors bounded by shadow errors, and reconstructs the time history with significantly lower error and storage than interpolating fixed-interval snapshots, with low-cost shadow replay and modest online synchronization overhead.

Gong, Qian [ORNL] (ORCID:0000000235704142)↗
DOE OSTI2023

Simulating the Impact of Dynamic Rerouting on Metropolitan-scale Traffic Systems

The rapid introduction of mobile navigation aides that use real-time road network information to suggest alternate routes to drivers is making it more difficult for researchers and government transportation agencies to understand and predict the dynamics of congested transportation systems. Computer simulation is a key capability for these organizations to analyze hypothetical scenarios; however, the complexity of transportation systems makes it challenging for them to simulate very large geographical regions, such as multi-city metropolitan areas. In this article, we describe enhancements to the Mobiliti parallel traffic simulator to model dynamic rerouting behavior with the addition of vehicle controller actors and vehicle-to-controller reroute requests. The simulator is designed to support distributed-memory parallel execution using discrete event simulation and be scalable on high-performance computing platforms. We demonstrate the potential of the simulator by analyzing the impact of varying the population penetration rate of dynamic rerouting on the San Francisco Bay Area road network. Using high-performance parallel computing, we can simulate a day in the San Francisco Bay Area with 19 million vehicle trips with 50 percent dynamic rerouting penetration over a road network with 0.5 million nodes and 1 million links in less than three minutes. We present a sensitivity study on the dynamic rerouting parameters, discuss the simulator’s parallel scalability, and analyze system-level impacts of changing the dynamic rerouting penetration. Furthermore, we examine the varying effects on different functional classes and geographical regions and present a validation of the simulation results compared to real-world data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

ReaxFF molecular dynamics simulations of electrolyte–water systems at supercritical temperature

We have performed ReaxFF molecular dynamics simulations of alkali metal–chlorine pairs in different water densities at supercritical temperature (700 K) to elucidate the structural and dynamical properties of the system. The radial distribution function and the angular distribution function explain the inter-ionic structural and orientational arrangements of atoms during the simulation. The coordination number of water molecules in the solvation shell of ions increases with an increase in the radius of ions. We find that the self-diffusion coefficient of metal ions increases with a decrease in density under supercritical conditions due to the formation of voids within the system. The hydrogen bond dynamics has been interpreted by the residence time distribution of various ions, which shows Li+ having the highest water retaining capability. The void distribution within the system has been analyzed by using the Voronoi polyhedra algorithm providing an estimation of void formation within the system at high temperatures. We observe the formation of salt clusters of Na+ and K+ at low densities due to the loss of dielectric constants of ions. The diffusion of ions gets altered dramatically due to the formation of voids and nucleation of ions in the system.

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

Dynamic-Phasor Model of Transformer Inrush Simulation for Unbalanced Distribution System

Abstract— Power system stability is a critical concern, with respect to the increasing distributed energy resources, microgrids, and emphasis on enhancing resiliency. For stability analysis and evaluation, modeling and simulation capabilities are important. In this paper, the authors’ previous work on modeling transformer inrush dynamics is improved with a new formulation of the key equation that converts the dynamic-phasor into real-time value. Simulation results in an electromechanical time-scale are compared with PSCAD results in an electromagnetic time-scale to demonstrate the improvement. The impact of simulation step size is discussed. A bug in PSCAD transformer setting that leads to incorrect magnetizing flux and current under Delta winding type is identified and reported. In addition, explanations and analysis are provided on two modeling techniques utilized since the previous work. This work is being incorporated into the next release of GridLAB-D. The improved transformer inrush calculation enables more accurate predictions of current amplitudes for analyzing the dynamics of distribution operation and control.

power transformers, power system simulation, satur↗
DOE OSTI2016

Conservative tightly-coupled simulations of stochastic multiscale systems

Multiphysics problems often involve components whose macroscopic dynamics is driven by microscopic random fluctuations. The fidelity of simulations of such systems depends on their ability to propagate these random fluctuations throughout a computational domain, including subdomains represented by deterministic solvers. When the constituent processes take place in nonoverlapping subdomains, system behavior can be modeled via a domain-decomposition approach that couples separate components at the interfaces between these subdomains. Its coupling algorithm has to maintain a stable and efficient numerical time integration even at high noise strength. We propose a conservative domain-decomposition algorithm in which tight coupling is achieved by employing either Picard's or Newton's iterative method. Coupled diffusion equations, one of which has a Gaussian white-noise source term, provide a computational testbed for analysis of these two coupling strategies. Fully-converged (“implicit”) coupling with Newton's method typically outperforms its Picard counterpart, especially at high noise levels. This is because the number of Newton iterations scales linearly with the amplitude of the Gaussian noise, while the number of Picard iterations can scale superlinearly. At large time intervals between two subsequent inter-solver communications, the solution error for single-iteration (“explicit”) Picard's coupling can be several orders of magnitude higher than that for implicit coupling. Increasing the explicit coupling's communication frequency reduces this difference, but the resulting increase in computational cost can make it less efficient than implicit coupling at similar levels of solution error, depending on the communication frequency of the latter and the noise strength. This trend carries over into higher dimensions, although at high noise strength explicit coupling may be the only computationally viable option.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

A One System Integrated Approach to Simulant Selection for Hanford High Level Waste Mixing and Sampling Tests - 13342

The Hanford Tank Operations Contractor (TOC) and the Hanford Waste Treatment and Immobilization Plant (WTP) contractor are both engaged in demonstrating mixing, sampling, and transfer system capabilities using simulated Hanford High-Level Waste (HLW) formulations. This represents one of the largest remaining technical issues with the high-level waste treatment mission at Hanford. Previous testing has focused on very specific TOC or WTP test objectives and consequently the simulants were narrowly focused on those test needs. A key attribute in the Defense Nuclear Facilities Safety Board (DNFSB) Recommendation 2010-2 is to ensure testing is performed with a simulant that represents the broad spectrum of Hanford waste. The One System Integrated Project Team is a new joint TOC and WTP organization intended to ensure technical integration of specific TOC and WTP systems and testing. A new approach to simulant definition has been mutually developed that will meet both TOC and WTP test objectives for the delivery and receipt of HLW. The process used to identify critical simulant characteristics, incorporate lessons learned from previous testing, and identify specific simulant targets that ensure TOC and WTP testing addresses the broad spectrum of Hanford waste characteristics that are important to mixing, sampling, and transfer performance are described. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2016

Numerical simulation of break flows occurring in the reactor cavity cooling system of a very high temperature reactor using a system CFD approach - 18437

To avoid accidents due to human error or the failure of components, the reactor cavity cooling system (RCCS) of a high temperature reactor must be able to operate naturally or passively safe. The system under consideration in this investigation is an air-cooled system which consists of an annular downcomer which is connected via a bottom-header to riser tubes. The downcomer and riser tubes are connected to the atmosphere via inlet and outlet manifold systems respectively. In this study the entire system is simulated using the 1D network codes GAMMA+ and Flownex. The study investigates the effect that breaks, causing a short circuit between one half of the inlet manifold and the corresponding half of the outlet manifold, will have on the performance of the cooling system. The agreement between the results obtained with the two codes is good. When the break size exceeds a certain value the flow may reverse in the relevant half of the outlet manifold. The critical break size is dependent on the elevation at which the break occurs. The reversal in the flow results in a drop of 10% in the heat removal capacity of the RCCS. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2026

Prediction of dynamic behavior of a system undergoing an exchange of components using a transmission simulator method

In systems with modular design, it is of interest to perform component exchanges to upgrade components and explore new system configurations. If the dynamics of the components are known, then dynamic substructuring can be used to obtain a prediction of system performance for the new configuration. The transmission simulator method is a substructuring technique that utilizes an additional fixture to apply an elastic boundary condition to a test article such that an appropriate dynamic response can be obtained for a given substructuring application, and the technique has been used widely for performing coupling and decoupling operations. Here, in this work, a modified transmission simulator method is proposed that allows a direct exchange of components to be performed. In a numerical demonstration, the proposed method is shown to accurately predict the dynamics of an assembly that has undergone a component exchange in which the exchanged components have different material properties and different geometric properties. This approach can be applied to dynamic qualification frameworks in which structures undergo modifications or upgrades rather than complete redesigns.

Component exchange↗
DOE OSTI2014

Parameter estimation for chaotic systems using a hybrid adaptive cuckoo search with simulated annealing algorithm

This paper introduces a novel hybrid optimization algorithm to establish the parameters of chaotic systems. In order to deal with the weaknesses of the traditional cuckoo search algorithm, the proposed adaptive cuckoo search with simulated annealing algorithm is presented, which incorporates the adaptive parameters adjusting operation and the simulated annealing operation in the cuckoo search algorithm. Normally, the parameters of the cuckoo search algorithm are kept constant that may result in decreasing the efficiency of the algorithm. For the purpose of balancing and enhancing the accuracy and convergence rate of the cuckoo search algorithm, the adaptive operation is presented to tune the parameters properly. Besides, the local search capability of cuckoo search algorithm is relatively weak that may decrease the quality of optimization. So the simulated annealing operation is merged into the cuckoo search algorithm to enhance the local search ability and improve the accuracy and reliability of the results. The functionality of the proposed hybrid algorithm is investigated through the Lorenz chaotic system under the noiseless and noise condition, respectively. The numerical results demonstrate that the method can estimate parameters efficiently and accurately in the noiseless and noise condition. Finally, the results are compared with the traditional cuckoo search algorithm, genetic algorithm, and particle swarm optimization algorithm. Simulation results demonstrate the effectiveness and superior performance of the proposed algorithm.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

A time-domain electromechanical co-simulation framework for power system transient analysis with retainment of user defined models

This paper proposes a time-domain electromechanical co-simulation framework to accomplish concurrent running of multiple simulators in order to preserve user-defined models and allow maximum simulation accuracy for power system transient analysis. Here, a middleware interface is developed to manage the interaction and synchronization of the multiple simulators via boundary model. Consequently, it eliminates the requirement of model conversion of each subsystem and thus ensure the user-defined models in each specific software are retained for entire system situational awareness. Preliminary testing results on 140-bus Northeastern Power Coordinating Council (NPCC) model validate the effectiveness and accuracy of the proposed framework for PSS/E and PSLF co-simulation.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2019

Heterogeneous CPU+GPU-Enabled Simulations for DFTB Molecular Dynamics of Large Chemical and Biological Systems

We introduce a new heterogeneous CPU+GPU-enhanced DFTB approach for the routine and efficient simulation of large chemical and biological systems. Here, compared to homogenous computing with conventional CPUs, heterogeneous computing approaches exhibit substantial performance with only a modest increase in power consumption, both of which are essential to upcoming exascale computing initiatives. We show that DFTB-based molecular dynamics is a natural candidate for heterogeneous computing since the computational bottleneck in these simulations is the diagonalization of the Hamiltonian matrix, which is performed several times during a single molecular dynamics trajectory. To thoroughly test and understand the performance of our heterogeneous CPU+GPU approach, we examine a variety of algorithmic implementations, benchmarks of different hardware configurations, and applications of this methodology on several large chemical and biological systems. Finally, to demonstrate the capability of our implementation, we conclude with a large-scale DFTB MD simulation of explicitly solvated HIV protease (3,974 atoms total) as a proof-of-concept example of an extremely large/complex system which, to the best of our knowledge, is the first time that an entire explicitly-solvated protein has been treated at a quantum-based MD level of detail.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗