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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MDSAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2011

Strategies for Fault Tolerance in Multicomponent Applications

This paper discusses on-going work with the Integrated Plasma Simulator (IPS), a framework for coupled multiphysics simulations of plasmas, to allow simulations to run through the loss of nodes on which the simulation is executing. While many different techniques are available to improve the fault tolerance of computational science applications on high-performance computer systems, checkpoint/restart (C/R) remains virtually the only one that see widespread use in practice. Our focus here is to augment the traditional C/R approach with additional techniques that can provide a more localized and tailored response to faults based on the ability to restart failed tasks on an individual basis, and the use of information external to the application itself in order to guide decision-making, in many cases avoiding the need to stop and restart the entire simulation. This capability involves several features within the IPS framework, and leverages the Fault Tolerance Backplane, a publish/subscribe event service to disseminate fault-related information throughout HPC systems, to obtain information from the Reliability, Availability and Serviceability (RAS) subsystem of the HPC system. This work is described in the context of Cray XT-series computer systems for concreteness, but is applicable to other environments as well. As part of the analysis of this work, we discuss the requirements to generalize this approach to other complex simulation applications beyond the Integrated Plasma Simulator.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2017

Path integral Monte Carlo simulations of dense carbon-hydrogen plasmas

Carbon-hydrogen plasmas and hydrocarbon materials are of broad interest to laser shock experimentalists, high energy density physicists, and astrophysicists. Accurate equations of state (EOSs) of hydrocarbons are valuable for various studies from inertial confinement fusion to planetary science. By combining path integral Monte Carlo (PIMC) results at high temperatures and density functional theory molecular dynamics results at lower temperatures, we compute the EOSs for hydrocarbons from simulations performed at 1473 separate (ρ, T)-points distributed over a range of compositions. These methods accurately treat electronic excitation effects with neither adjustable parameter nor experimental input. PIMC is also an accurate simulation method that is capable of treating many-body interaction and nuclear quantum effects at finite temperatures. These methods therefore provide a benchmark-quality EOS that surpasses that of semi-empirical and Thomas-Fermi-based methods in the warm dense matter regime. By comparing our first-principles EOS to the LEOS 5112 model for CH, we validate the specific heat assumptions in this model but suggest that the Grüneisen parameter is too large at low temperatures. Based on our first-principles EOSs, we predict the principal Hugoniot curve of polystyrene to be 2%-5% softer at maximum shock compression than that predicted by orbital-free density functional theory and SESAME 7593. By investigating the atomic structure and chemical bonding of hydrocarbons, we show a drastic decrease in the lifetime of chemical bonds in the pressure interval from 0.4 to 4 megabar. We find the assumption of linear mixing to be valid for describing the EOS and the shock Hugoniot curve of hydrocarbons in the regime of partially ionized atomic liquids. We make predictions of the shock compression of glow-discharge polymers and investigate the effects of oxygen content and C:H ratio on its Hugoniot curve. In conclusion, our full suite of first-principles simulation results may be used to benchmark future theoretical investigations pertaining to hydrocarbon EOSs and should be helpful in guiding the design of future experiments on hydrocarbons in the gigabar regime.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2011

Integrated EM & Thermal Simulations with Upgraded VORPAL Software

Nuclear physics accelerators are powered by microwaves which must travel in waveguides between room-temperature sources and the cryogenic accelerator structures. The ohmic heat load from the microwaves is affected by the temperature-dependent surface resistance and in turn affects the cryogenic thermal conduction problem. Integrated EM & thermal analysis of this difficult non-linear problem is now possible with the VORPAL finite-difference time-domain simulation tool. We highlight thermal benchmarking work with a complex HOM feed-through geometry, done in collaboration with researchers at the Thomas Jefferson National Accelerator Laboratory, and discuss upcoming design studies with this emerging tool. This work is part of an effort to generalize the VORPAL framework to include generalized PDE capabilities, for wider multi-physics capabilities in the accelerator, vacuum electronics, plasma processing and fusion R&D fields, and we will also discuss user interface and algorithmic upgrades which facilitate this emerging multiphysics capability.

43 PARTICLE ACCELERATORS↗
DOE OSTI2014

A novel adaptive time stepping variant of the Boris–Buneman integrator for the simulation of particle accelerators with space charge

We show that adaptive time stepping in particle accelerator simulation is an enhancement for certain problems. The new algorithm has been implemented in the OPAL (Object Oriented Parallel Accelerator Library) framework. The idea is to adjust the frequency of costly self-field calculations, which are needed to model Coulomb interaction (space charge) effects. In analogy to a Kepler orbit simulation that requires a higher time step resolution at the close encounter, we propose to choose the time step based on the magnitude of the space charge forces. Inspired by geometric integration techniques, our algorithm chooses the time step proportional to a function of the current phase space state instead of calculating a local error estimate like a conventional adaptive procedure. Building on recent work, a more profound argument is given on how exactly the time step should be chosen. An intermediate algorithm, initially built to allow a clearer analysis by introducing separate time steps for external field and self-field integration, turned out to be useful by its own, for a large class of problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Integrating Ab Initio Simulations and X-ray Photoelectron Spectroscopy: Toward A Realistic Description of Oxidized Solid/Liquid Interfaces

Many energy storage and conversion devices rely on processes that take place at complex interfaces, where structural and chemical properties are often difficult to probe under operating conditions. A primary example is solar water splitting using high-performance photoelectrochemical cells, where surface chemistry, including native oxide formation, affects hydrogen generation. In this Perspective, we discuss some of the challenges associated with interrogating interface chemistry, and how they may be overcome by integrating high-level first-principles calculations of explicit interfaces with ambient pressure X-ray photoelectron spectroscopy and direct spectroscopic simulations. We illustrate the benefit of this combined approach toward insights into native oxide chemistry at prototypical InP/water and GaP/water interfaces. Lastly, this example suggests a more general roadmap for obtaining a realistic and reliable description of the chemistry of complex interfaces by combining state-of-the-art computational and experimental techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

High Performance Equilibrium Solvers for Integrated Magnetic Fusion Simulations

With the funding provided by this award, we developed numerical codes for the study of magnetically confined plasmas for fusion applications. Accordingly, our work can be divided into two separate categories: 1) the design and analysis of novel numerical methods providing high accuracy and high efficiency; 2) the study of the equilibrium and stability of magnetically confined plasmas with some of these numerical codes, as well as the study of the nature of the turbulent behavior which may arise in the presence of instabilities. We first developed new numerical schemes based on integral equation methods for the computation of steady-state magnetic configurations in fusion experiments, providing high accuracy for the magnetic field and its derivatives, which are required for stability and turbulence calculations. We employed different integral formulations depending on the application of interest: axisymmetric or non-axisymmetric equilibria, force-free or magnetohydrodynamic equilibria, fixed-boundary equilibria or free-boundary equilibria. While efficient, these methods do not yet apply to plasma boundaries which are not smooth, a situation which is fairly common in magnetic confinement experiments. To address this temporary weakness, we also constructed a new steady-state solver based on the Hybridizable Discontinuous Galerkin (HDG) method, which provides full geometric flexibility. In addition to these numerical tools focused on steady-states, we also contributed to the improvement of the speed and accuracy of codes simulating the plasma dynamics of fusion plasmas, by developing a novel velocity space representation for the efficient solution of kinetic equations, which most accurately describe the time evolution of hot plasmas in fusion experiments. Using the tools discussed above, we studied several questions pertaining to the equilibrium and stability of magnetically confined plasmas. In particular, we derived a new simple model for axisymmetric devices called tokamaks, to predict how elongated a fusion plasma can be before it becomes unstable and collapses. We also looked at the effect of the shape of the outer plasma surface on key properties of the steady-state magnetic configurations, and how these properties impact turbulence in fusion plasmas, and the corresponding transport of momentum. Likewise, we studied the role of large localized flows on the steady-state magnetic configurations, and how they may influence plasma stability and turbulence. Non-axisymmetric steady-state magnetic configurations are inherently more complex than axisymmetric steady-state configurations, and the subject of ongoing controversies regarding the regularity of the equations determining such steady-states, and their solutions. Implementing an existing NYU code in a new geometry, we studied the nature of the singularity of the solutions observed in the code, and methods to eliminate them. Our main conclusion is that by appropriately tailoring the plasma boundary, it is possible to eliminate the singularities otherwise appearing in our simulations, and to obtain steady-states which appear to be smooth. To gain further insights on incompletely understood turbulence phenomena, we proposed a new reduced model capturing most of these phenomena, which is simple enough to not require expensive numerical simulations on massive supercomputers to investigate them. We demonstrated the strong similarity between our simulations and published results obtained from computationally expensive simulations, and plan to rely on our reduced model to identify the key mechanisms determining the evolution and strength turbulent driven transport in fusion plasmas. Finally, we proposed a new framework for tokamak reactor design studies, enabling us to consider the relative merits of steady-state versus pulsed fusion reactors. We found that pulsed fusion reactors may benefit most from recent advances in magnet technology, and the availability of very high field magnets. As such, they may become more desirable than steady-state tokamak reactors for cost efficient electricity generation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

Used Nuclear Fuel Loading and Structural Performance Under Normal Conditions of Transport - Modeling, Simulation and Experimental Integration RD&D Plan

Under current U.S. Nuclear Regulatory Commission regulation, it is not sufficient for used nuclear fuel (UNF) to simply maintain its integrity during the storage period, it must maintain its integrity in such a way that it can withstand the physical forces of handling and transportation associated with restaging the fuel and moving it to treatment or recycling facilities, or a geologic repository. Hence it is necessary to understand the performance characteristics of aged UNF cladding and ancillary components under loadings stemming from transport initiatives. Researchers would like to demonstrate that enough information, including experimental support and modeling and simulation capabilities, exists to establish a preliminary determination of UNF structural performance under normal conditions of transport (NCT). This research, development and demonstration (RD&D) plan describes a methodology, including development and use of analytical models, to evaluate loading and associated mechanical responses of UNF rods and key structural components. This methodology will be used to provide a preliminary assessment of the performance characteristics of UNF cladding and ancillary components under rail-related NCT loading. The methodology couples modeling and simulation and experimental efforts currently under way within the Used Fuel Disposition Campaign (UFDC). The methodology will involve limited uncertainty quantification in the form of sensitivity evaluations focused around available fuel and ancillary fuel structure properties exclusively. The work includes collecting information via literature review, soliciting input/guidance from subject matter experts, performing computational analyses, planning experimental measurement and possible execution (depending on timing), and preparing a variety of supporting documents that will feed into and provide the basis for future initiatives. The methodology demonstration will focus on structural performance evaluation of Westinghouse WE 17×17 pressurized water reactor fuel assemblies with a discharge burnup range of 30-58 GWd/MTU (assembly average), loaded in a representative high-capacity (≥32 fuel rod assemblies) transportation package. Evaluations will be performed for representative normal conditions of rail transport involving a rail conveyance capable of meeting the Association of American Railroads (AAR) S-2043 specification. UNF modeling is anticipated to be defined to the pellet-cladding level and take in to account influences associated with spacer grids, intermediate fluid mixers, and control components. The influence of common degradation issues such as ductile-to-brittle-transition will also be accounted for. All model development and analysis will be performed with commercially available software packages exclusively. Inputs and analyses will be completely documented, all supporting information will be traceable, and bases will be defendable so as to be most useful to the U.S. Department of Energy community and mission. The expected completion date is the end of fiscal year (FY) 2013.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2014

Thermodynamics and structure of a two-dimensional electrolyte by integral equation theory

Monte Carlo simulations and integral equation theory were used to predict the thermodynamics and structure of a two-dimensional Coulomb fluid. We checked the possibility that integral equations reproduce Kosterlitz-Thouless and vapor-liquid phase transitions of the electrolyte and critical points. Integral equation theory results were compared to Monte Carlo data and the correctness of selected closure relations was assessed. Among selected closures hypernetted-chain approximation results matched computer simulation data best, but these equations unfortunately break down at temperatures well above the Kosterlitz-Thouless transition. The Kovalenko-Hirata closure produces results even at very low temperatures and densities, but no sign of phase transition was detected.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Simulation games that integrate research, entertainment, and learning around ecosystem services

Humans currently spend over 3 billion person-hours per week playing computer games. Most of these games are purely for entertainment, but use of computer games for education has also expanded dramatically. At the same time, experimental games have become a staple of social science research but have depended on relatively small sample sizes and simple, abstract situations, limiting their range and applicability. If only a fraction of the time spent playing computer games could be harnessed for research, it would open up a huge range of new opportunities. We review the use of games in research, education, and entertainment and develop ideas for integrating these three functions around the idea of ecosystem services valuation. This approach to valuation can be seen as a version of choice modeling that allows players to generate their own scenarios taking account of the trade-offs embedded in the game, rather than simply ranking pre-formed scenarios. We outline a prototype game called Lagom Island to test the proposition that gaming can be used to reveal the value of ecosystem services. Ultimately, our prototype provides a potential pathway and functional building blocks for approaching the relatively untapped potential of games in the context of ecosystem services research.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Antiviral discovery using sparse datasets by integrating experiments, molecular simulations, and machine learning

Computational methods have demonstrated success in identifying virucidal agents, effectively contributing to the discovery of novel virucidal molecules. In this study, we developed a machine learning (ML) model, trained on a small dataset, to predict inhibitors of human enterovirus 71 (EV71), a pathological agent that causes severe disease in children and immunocompromised adults. Despite the dataset’s limitation, comprising of only 36 compounds tested, our ML framework demonstrated significant predictive capability. Notably, experimental validation revealed that five out of the eight compounds predicted by our model from the Chinese cosmetic material list exhibited virucidal activity. The inhibitor effects displayed by the main active compounds were further confirmed by molecular dynamics simulation. This underscores the potential of our AI-driven approach to bypass data constraints in identifying active molecules against viral pathogens.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Elucidating the Atomic Structures of the Gel Layer Formed during Aluminoborosilicate Glass Dissolution: An Integrated Experimental and Simulation Study

The altered glasses produced during aqueous dissolution of silicate and borosilicate glasses are among the most complex structures to understand at the atomic level due to their amorphous nature, random porosity and various levels of hydration. In this study, we gained insights of the complex atomic structures of altered aluminoborosilicate glasses by combining a range of experimental and computational approaches. The altered glasses were prepared by dissolution of three glasses with varying level of alumina in acid for 7 days. A comprehensive set of experimental [elemental analysis, high-energy X-ray diffraction, 29 Si and 27 Al solid-state nuclear magnetic resonance (NMR), and O 1s X-ray photoelectron spectroscopy (XPS)] and modeling (molecular dynamics (MD) simulations using non-reactive and reactive force fields) were used to study the atomic structures of these altered glasses. Elemental analysis showed that most of the B in the pristine glasses was leached into the solution and was not contained in the altered glass. The 29 Si and 27 Al solid-state NMR spectra revealed that the altered glasses have more polymerized silicate network as compared to those in the pristine glasses due to the reformation of linkages among Si and Al oxygen polyhedral in the altered glasses. The bridging and non-bridging (or hydroxyl O) atoms in the altered glasses were also quantified from their O 1s XPS spectra. Atomic structure models of the altered glasses were constructed by using MD simulations using the reactive force field based on the compositional information obtained from experiments. Various pore structures were generated using the charge-scaling (CS) method by using different initial densities and CS temperatures; the best CS parameters of each alternated glass were then determined by comparing with the experimental structure factors obtained from high energy X-ray diffraction. Pore and the atomic structures and vibrational properties around these pore surfaces were analyzed. Furthermore, these results from this comprehensive study thus provides a realistic insight into the pore morphology, atomic structure, and vibrational properties of altered glasses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Orientation and Conformation of Proteins at the Air–Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy

Understanding the assembly of proteins at the air-water interface (AWI) informs the formation of protein films, emulsion properties, and protein aggregation. Determination of protein conformation and orientation at an interface is difficult to resolve with a single experimental or simulation technique alone. To date, the interfacial structure of even one of the most widely studied proteins, lysozyme, at the AWI remains unresolved. Here in this study, molecular dynamics (MD) simulations are used to determine if the protein adopts a side-on, head-on, or axial orientation at the AWI with two different forcefields, GROMOS-53a6 + SPC/E and a99SB-disp + TIP4P-D. Vibrational sum frequency generation (SFG) spectroscopy experiments and spectral SFG calculations validate consistency between the structure determined from MD and experiments. Overall, we show with strong agreement that lysozyme adopts an axial conformation at pH 7. Further, we provide molecular-level insight as to how pH influences the binding domains of lysozyme resulting in side-on adsorption near the isoelectric point of the lysozyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗