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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

High Fidelity Dynamic Simulation of Cycling in a Natural Gas Combined Cycle Power Plant

The CRADA objective is to use a high-fidelity natural gas combined cycle (NGCC) dynamic simulator deployed at the National Energy Technology Laboratory (NETL) to produce practical engineering ideas that would either reduce the impact on equipment resulting from cycling, or improve certain plant operational modes. The goal is to demonstrate to National Rural Electric Cooperative Association (NRECA) that a high-fidelity dynamic simulator offers a relatively low-cost option for investigation and testing without direct plant experimentation. Initial operation of the simulator revealed the potential for saturation conditions in the final high pressure superheater as the attemperator tried to control temperature at the superheater outlet during gas turbine loading and unloading. Subsequent plant operational data confirmed simulation results. Thus, this particular area was chosen for further investigation. Multiple simulations were performed during loading and unloading of the gas turbine in order to determine operational strategies that prevented saturation and increased the approach to saturation temperature. The results of these simulations are presented in this report. The summary at the end of this report suggests trials that could be performed at the plant to confirm the benefits seen by simulator investigations, such as changes to the attemperator temperature control setpoints and strategic control of the steam turbine inlet pressure control valve.

03 NATURAL GAS↗
DOE OSTI2020

Identification of preferred multimodal ligand‐binding regions on IgG1 F C using nuclear magnetic resonance and molecular dynamics simulations

Abstract In this study, the binding of multimodal chromatographic ligands to the IgG1 F C domain were studied using nuclear magnetic resonance and molecular dynamics simulations. Nuclear magnetic resonance experiments carried out with chromatographic ligands and a perdeuterated 15 N‐labeled F C domain indicated that while single‐mode ion exchange ligands interacted very weakly throughout the F C surface, multimodal ligands containing negatively charged and aromatic moieties interacted with specific clusters of residues with relatively high affinity, forming distinct binding regions on the F C . The multimodal ligand‐binding sites on the F C were concentrated in the hinge region and near the interface of the C H 2 and C H 3 domains. Furthermore, the multimodal binding sites were primarily composed of positively charged, polar, and aliphatic residues in these regions, with histidine residues exhibiting some of the strongest binding affinities with the multimodal ligand. Interestingly, comparison of protein surface property data with ligand interaction sites indicated that the patch analysis on F C corroborated molecular‐level binding information obtained from the nuclear magnetic resonance experiments. Finally, molecular dynamics simulation results were shown to be qualitatively consistent with the nuclear magnetic resonance results and to provide further insights into the binding mechanisms. An important contribution to multimodal ligand‐F C binding in these preferred regions was shown to be electrostatic interactions and π–π stacking of surface‐exposed histidines with the ligands. This combined biophysical and simulation approach has provided a deeper molecular‐level understanding of multimodal ligand–F C interactions and sets the stage for future analyses of even more complex biotherapeutics.

Gudhka, Ronak B.↗
DOE OSTI2024

Extended dynamic mode decomposition for model reduction in fluid dynamics simulations

High computational cost and storage/memory requirements of fluid dynamics simulations constrain their usefulness as a predictive tool. Reduced-order models (ROMs) provide a viable solution to this challenge by extracting the key underlying dynamics of a complex system directly from data. We investigate the efficacy and robustness of an extended dynamic mode decomposition (xDMD) algorithm in constructing ROMs of three-dimensional cardiovascular computations. Focusing on the ROMs' accuracy in representation and interpolation, we relate these metrics to the truncation rank of singular value decomposition, which underpins xDMD and other approaches to ROM construction. Our key innovation is to relate the truncation rank to the singular values of the original flow problem. This result establishes a priori guidelines for the xDMD deployment and its likely success as a means of data compression and reconstruction of the system's dynamics from dominant spatiotemporal structures present in the data.

Mechanics↗
DOE OSTI2023

Molecular dynamics simulation of Fe-Si alloys using a neural network machine learning potential

Interatomic potential development using machine learning (ML) approaches has attracted a lot of attention in recent years because these potentials can effectively describe the structural and dynamical properties of complex materials at the atomistic level. Here, in this work, we present the development of a neural network (NN) deep ML interatomic potential for Fe-Si alloys, and we demonstrate the effectiveness of the NN-ML potential in predicting the structures and energies of liquid and crystalline phases of Fe-Si alloys in comparison with the results from ab initio molecular dynamics simulations or experimental data. The developed NN-ML potential is also used to perform molecular dynamics simulations to study the structures of Fe-Si alloys with various compositions under rapid solidification conditions. The short-ranged orders in the rapidly solidified Fe-Si alloys are also analyzed by a cluster alignment method.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Molecular dynamics simulations of Na{sup +} and leucine transport by LeuT

Molecular dynamics simulations are used to gain insight into the binding of Na{sup +} and leucine substrate to the bacterial amino acid transporter LeuT, focusing on the crystal structures of LeuT in the outward-open and inward-open states. For both conformations of LeuT, a third Na{sup +} binding site involving Glu290 in addition to the two sites identified from the crystal structures is observed. Once the negative charge from Glu290 in the inward-open LeuT is removed, the ion bound to the third site is ejected from LeuT rapidly, suggesting that the protonation state of Glu290 regulates Na{sup +} binding and release. In Cl{sup −}-dependent transporters where Glu290 is replaced by a neutral serine, a Cl{sup −} ion would be required to replace the role of Glu290. Thus, the simulations provide insights into understanding Na{sup +} and substrate transport as well as Cl{sup −}-independence of LeuT. - Highlights: • Ion binding site involving Glu290 is identified in the outward- and inward-open LeuT. • Sodium is released from inward-open LeuT once the side chain of Glu290 is protonated. • Protonation state of Glu290 regulates sodium binding and transport in LeuT.

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

Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results

Herein, we present a novel method to incorporate structural results from surface-sensitive scattering, such as X-ray or neutron reflectometry, into molecular dynamics simulations. While reflectometry techniques generally provide a means to determine the molecular-scale structures of organized interfacial films, they were recently shown to offer the capability to characterize the structures of protein-membrane complexes supported by a solid substrate. One-dimensional information inherent in the experimental results is used in the form of component volume occupancy (CVO) profiles, which describe the distribution of molecular components within an interfacial architecture, to construct real-space constraints in the form of a biasing potential for the simulation that vanishes when the simulated and experimental profiles agree. This approach improves the correspondence between simulation and experiment, as shown in the re-evaluation of an neutron-reflection-derived structure which was approximated by an independent molecular dynamics simulation in earlier work, and it also leads to faster equilibration of ensemble structures. We further show that time averaging the CVO profile that develops in the simulation while biasing with this approach permits fluctuations about the average that are necessary for conformational exploration of the system. This method is particularly valuable for studies of proteins at interfaces that contain disordered regions since the conformation of such regions is difficult to judge from the analysis of one-dimensional experimental profiles and may take prohibitively long to equilibrate in simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Testing thermal conductivity models with equilibrium molecular dynamics simulations of the one-component plasma

Equilibrium molecular dynamics simulations are used to calculate the thermal conductivity of the onecomponent plasma via the Green-Kubo formalism over a broad range of Coulomb coupling strength, 0.1 ≤ Γ ≤180. These simulations address previous discrepancies between computations using equilibrium versus nonequilibrium methods. Analysis of heat flux autocorrelation functions show that very long (6×10 5 $ω^{-1}_{p}$) time series are needed to reduce the noise level to allow ≲2% accuracy. The simulations provide accurate data for Γ ≲ 1. Furthermore, this enables a test of the traditional Landau-Spitzer theory, which is found to agree with the simulations for Γ ≲ 0.3. It also enables tests of theories to address moderate and strong Coulomb coupling. Two are found to provide accurate extensions to the moderate coupling regime of Γ ≲ 10, but none are accurate in the Γ ≳ 10 regime where potential energy transport and coupling between mass flow and stress dominate thermal conduction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Accelerators for Classical Molecular Dynamics Simulations of Biomolecules

Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model biomolecular structures such as proteins and their interactions with drug-like small molecules with greater spatiotemporal resolution than is otherwise possible using experimental methods. MD simulations are notoriously expensive computational endeavors that have traditionally required massive investment in specialized hardware to access biologically relevant spatiotemporal scales. Our goal is to summarize the fundamental algorithms that are employed in the literature to then highlight the challenges that have affected accelerator implementations in practice. We consider three broad categories of accelerators: Graphics Processing Units (GPUs), Field-Programmable Gate Arrays (FPGAs), and Application Specific Integrated Circuits (ASICs). These categories are comparatively studied to facilitate discussion of their relative trade-offs and to gain context for the current state of the art. We conclude by providing insights into the potential of emerging hardware platforms and algorithms for MD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

The Impact of Protonation on Early Translocation of Anthrax Lethal Factor: Kinetics from Molecular Dynamics Simulations and Milestoning Theory

We report atomically detailed molecular dynamics simulations of the permeation of the lethal factor (LF) N-terminal segment through the anthrax channel. The N-terminal chain is unstructured and leads the permeation process for the LF protein. The simulations were conducted in explicit solvent with milestoning theory, making it possible to extract kinetic information from nanosecond to millisecond time scales. Here, we illustrate that the initial event is strongly influenced by the protonation states of the permeating amino acids. While the N-terminal segment passes easily at high protonation state through the anthrax channel (and the Φ clamp), the initial permeation represents a critical step, which can be irreversible and establishes a hook in the channel mouth.

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

Dynamic simulation of 10 kW Brayton cryocooler for HTS cable

Dynamic simulation of a Brayton cryocooler is presented as a partial effort of a Korean governmental project to develop 1∼3 km HTS cable systems at transmission level in Jeju Island. Thermodynamic design of a 10 kW Brayton cryocooler was completed, and a prototype construction is underway with a basis of steady-state operation. This study is the next step to investigate the transient behavior of cryocooler for two purposes. The first is to simulate and design the cool-down process after scheduled or unscheduled stoppage. The second is to predict the transient behavior following the variation of external conditions such as cryogenic load or outdoor temperature. The detailed specifications of key components, including plate-fin heat exchangers and cryogenic turbo-expanders are incorporated into a commercial software (Aspen HYSYS) to estimate the temporal change of temperature and flow rate over the cryocooler. An initial cool-down scenario and some examples on daily variation of cryocooler are presented and discussed, aiming at stable control schemes of a long cable system.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Molecular Dynamics Simulations of a Liquid Metal Wetting Zirconia Suboxides

Molecular dynamics simulations were performed of a liquid metal (Ag) interacting with various zirconia suboxides to calculate the work of adhesion between the liquid metal and the suboxides. These simulations were then used to assess the impact of oxygen content on wetting. The results of this work show a wetting transition as oxygen content is reduced.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Molecular dynamics simulation of the solid-liquid interface migration in terbium

In this work, we developed a Tb embedded atom method potential which properly reproduces the liquid structure obtained from the ab initio molecular dynamics simulation, the hexagonal close packed (hcp)-body-centered cubic (bcc) phase transformation, and melting temperatures. At least three crystal phases [hcp, face-centered cubic (fcc), and bcc] described by this potential can coexist with the liquid phase. Thus, the developed potential provides an excellent test bed for studies of the completive phase nucleation and growth in a single component system. The molecular dynamics simulation showed that all crystal phases can grow from the liquid phase close to their melting temperatures. However, in the cases of the hcp and fcc growth from the liquid phase at very large supercoolings, the bcc phase forms at the solid-liquid interface in the close packed orientations in spite of the fact that both hcp and fcc phases are more stable than the bcc phase at these temperatures. Finally, this bcc phase closes the hcp and fcc phase from the liquid such that the remaining liquid solidifies into the bcc phase. The initial hcp phase then slowly continues growing in expense of the bcc phase.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Impact of Molecular Dynamics Simulations on Research and Development of Semiconductor Materials

Atomic scale defects critically limit performance of semiconductor materials. To improve materials, defect effects and defect formation mechanisms must be understood. In this paper, we demonstrate multiple examples where molecular dynamics simulations have effectively addressed these issues that were not well addressed in prior experiments. In the first case, we report our recent progress on modelling graphene growth, where we found that defects in graphene are created around periphery of islands throughout graphene growth, not just in regions where graphene islands impinge as believed previously. In the second case, we report our recent progress on modelling TlBr, where we discovered that under an electric field, edge dislocations in TlBr migrate in both slip and climb directions. The climb motion ejects extensive vacancies that can cause the rapid aging of the material seen in experiments. In the third case, we discovered that the growth of InGaN films on (0001) surfaces suffers from a serious polymorphism problem that creates enormous amounts of defects. Growth on ( $11\bar{2}0$ ) surfaces, on the other hand, results in single crystalline wurtzite films without any of these defects. In the fourth case, we first used simulations to derive dislocation energies that do not possess any noticeable statistical errors, and then used these error-free methods to discover possible misuse of misfit dislocation theory in past thin film studies. Lastly, we highlight the significance of molecular dynamics simulations in reducing defects in the design space of nanostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Fast predictions of liquid-phase acid-catalyzed reaction rates using molecular dynamics simulations and convolutional neural networks

The rates of liquid-phase, acid-catalyzed reactions relevant to the upgrading of biomass into high-value chemicals are highly sensitive to solvent composition and identifying suitable solvent mixtures is theoretically and experimentally challenging. We show that the complex atomistic configurations of reactant–solvent environments generated by classical molecular dynamics simulations can be exploited by 3D convolutional neural networks to enable accurate predictions of Brønsted acid-catalyzed reaction rates for model biomass compounds. We develop a 3D convolutional neural network, which we call SolventNet, and train it to predict acid-catalyzed reaction rates using experimental reaction data and corresponding molecular dynamics simulation data for seven biomass-derived oxygenates in water–cosolvent mixtures. We show that SolventNet can predict reaction rates for additional reactants and solvent systems an order of magnitude faster than prior simulation methods. This combination of machine learning with molecular dynamics enables the rapid, high-throughput screening of solvent systems and identification of improved biomass conversion conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Large-scale molecular dynamics simulations of TiN/TiN(001) epitaxial film growth

Large-scale classical molecular dynamics simulations of epitaxial TiN/TiN(001) thin film growth at 1200 K are carried out using incident flux ratios N/Ti = 1, 2, and 4. The films are analyzed as a function of composition, island size distribution, island edge orientation, and vacancy formation. Results show that N/Ti = 1 films are globally understoichiometric with dispersed Ti-rich surface regions which serve as traps to nucleate 111-oriented islands, leading to local epitaxial breakdown. Films grown with N/Ti = 2 are approximately stoichiometric and the growth mode is closer to layer-by-layer, while N/Ti = 4 films are stoichiometric with N-rich surfaces. As N/Ti is increased from 1 to 4, island edges are increasingly polar, i.e., 110-oriented, and N-terminated to accommodate the excess N flux, some of which is lost by reflection of incident N atoms. N vacancies are produced in the surface layer during film deposition with N/Ti = 1 due to the formation and subsequent desorption of N{sub 2} molecules composed of a N adatom and a N surface atom, as well as itinerant Ti adatoms pulling up N surface atoms. The N vacancy concentration is significantly reduced as N/Ti is increased to 2; with N/Ti = 4, Ti vacancies dominate. Overall, our results show that an insufficient N/Ti ratio leads to surface roughening via nucleation of small dispersed 111 islands, whereas high N/Ti ratios result in surface roughening due to more rapid upper-layer nucleation and mound formation. The growth mode of N/Ti = 2 films, which have smoother surfaces, is closer to layer-by-layer.

42 ENGINEERING↗
DOE OSTI2021

Molecular dynamics simulation of metallic Al–Ce liquids using a neural network machine learning interatomic potential

Al-rich Al-Ce alloys have the possibility of replacing heavier steel and cast-irons for use in high-temperature applications. Knowledge about the structures and properties of Al-Ce alloys at liquid state is vital for optimizing the manufacture process to produce desired allows. However, reliable molecular dynamics simulation of Al-Ce alloy systems remains a great challenge due to the lack of accurate Al-Ce interatomic potential. In this work, an artificial neural network (ANN) deep machine learning (ML) method is used to develop a reliable interatomic potential for Al-Ce alloy. Ab initio molecular dynamics (AIMD) simulation data on Al-Ce liquid with small unit cell (~200 atoms) and on the known Al-Ce crystalline compounds are collected to train the interatomic potential using ANN-ML. The obtained ANN-ML model reproduces well the energies, forces, and atomic structure of Al 90 Ce 10 liquid and crystalline phases of Al-Ce compounds in comparison with ab initio results. The developed ANN-ML potential is applied in molecular dynamics simulations to study the structures and properties of metallic Al 90 Ce 10 liquid, which would provide useful insight for guiding experimental process to produce desired Al-Ce allows.

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

Calculating adsorption isotherms using the two-phase thermodynamic method and molecular dynamics simulations

We describe the calculation of adsorption isotherms from molecular dynamics simulations based on the two-phase thermodynamic (2PT) model. The 2PT model developed for bulk fluid phases treats the gas-like components as hard spheres (HSs), which correctly recovers the limiting behaviors of unconfined fluids. We showed that this treatment, however, does not always lead to the correct zero-loading behavior in strongly confining systems. For methane adsorption into zeolite MFI, the HS reference state underestimates entropy by up to 20% at low loadings and leads to an order-of-magnitude increase in the adsorption onset pressure. To fix these issues, we propose the use of ideal adsorbed gas (IAG) as the gas reference model, the properties of which can be computed using the Widom insertion method on an empty adsorbent. We further describe three routes to compute adsorption isotherms from the Helmholtz free energy at different loadings. Comparing against established Monte Carlo (MC) methods, we found that the adsorption isotherms obtained using the IAG reference state agrees to within 40%, which corresponds to deviations of <5% in adsorption free energy. The isotherms calculated using the HS reference state underestimate the adsorption uptake at low to medium loadings in strongly confining systems, but its accuracy improves at higher loadings and as the pore size increases relative to the sorbate diameter. The methods described here provide an alternative approach for computing adsorption isotherms when MC simulations in an open ensemble are undesirable and enable a direct comparison of computed adsorption thermodynamics with experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Crystallographic structure and molecular dynamics simulations of the major endoglucanase from Xanthomonas campestris pv. campestris shed light on its oligosaccharide products release pattern

Cellulases are critical enzymatic components for the transformation of plant biomass into fuels, renewable materials and green chemicals. In this work, we determined the crystal structure, pattern of hydrolysis products release, and conducted molecular dynamics simulations of the major endoglucanase from the Xanthomonas campestris pv. campestris (XccCel5A). XccCel5A has a TIM barrel fold with the catalytic site centrally placed in a binding groove surrounded by aromatic side chains. Molecular dynamics simulations show that productive position of the substrate is secured by a network of hydrogen bonds in the four main subsites, which differ in details from homologous structures. Capillary zone electrophoresis and computational studies reveal XccCel5A can act both as endoglucanase and licheninase, but there are preferable arrangements of substrate regarding β-1,3 and β-1,4 bonds within the binding cleft which are related to the enzymatic efficiency.

59 BASIC BIOLOGICAL SCIENCES↗