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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Applying molecular dynamics simulations to the study of micro cold spray of yttria

Micro cold spray (MCS) is a novel manufacturing process with proven success depositing dense, thick films of technical ceramics without the need for elevated processing temperatures or chemical precursors. The process transforms a loose sub-micrometer powder into an adherent film with mechanical properties approaching that of the bulk material through a phenomenon known as room temperature impact consolidation. While this phenomenon has been demonstrated for a wide variety of ceramic materials and film substrates, yttria stands out as a material that is both well-characterized in experiments and of significant interest for industrial applications due to its excellent refractory properties. This dissertation seeks to investigate the fundamental mechanisms that enable room temperature impact consolidation by using molecular dynamics (MD) simulations of yttria particle impacts and characterizing the deformation behavior of the system.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Computational Fluid Dynamics Simulations to Predict Oxidation in Heat Recovery Steam Generator Tubes

Heat Recovery Steam Generators (HRSGs) are widely used across United States in combined cycle power plants to recover waste heat from the gas turbine (GT). HRSGs are used either to generate electricity or to produce process steam for industrial applications. The primary components of HRSG consists of a duct and a heat exchanger (HX). It is known across the power industry that the high temperature oxidation and ensuing exfoliation problem is a major cause for the damage of HX materials of HRSG. Alloys and/or coatings that can prevent or mitigate oxidation are very expensive, therefore they must be used or applied on the select regions of the HX tubes where the tendency of oxide formation is the highest. The main goal of this project is to identify such regions through Computational Fluid Dynamics (CFD) simulations. Therefore, in this work, we developed a CFD framework using commercial code StarCCM+ for the prediction of the fluid flow and heat transfer in a HRSG and associated oxidation inside the tubes of the HX. The developed CFD framework was verified and validated with experimental data before deployment. We also developed an innovative method to model the effect of the fins on the heat transfer and the pressure drop using a porous media model (PMM) approach to keep the mesh size within reasonable limits. After validation, we performed high-fidelity CFD simulations of a real-scale HRSG using the PMM, with High Performance Computing (HPC) resources of ORNL. From the simulation results, we acquired oxide thickness maps for all the tubes of the select HX sections of HRSG prone to oxidation. These oxide maps can inform regions of the HX tubes that requires oxide-resistant coatings, thereby guiding engineers for cost-efficient manufacturing of the HX that can combat oxidation in HRSGs.

36 MATERIALS SCIENCE↗
DOE OSTI2021

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, the capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Evaluation of 6-OxP-CD, an Oxime-based cyclodextrin as a viable medical countermeasure against nerve agent poisoning: Experimental and molecular dynamic simulation studies on its inclusion complexes with cyclosarin, soman and VX

The ability of the cyclodextrin-oxime construct 6-OxP-CD to bind and degrade the nerve agents Cyclosarin (GF), Soman (GD) and S -[2-[Di(propan-2-yl)amino]ethyl] O -ethyl methylphosphonothioate (VX) has been studied using 31 P-nuclear magnetic resonance (NMR) under physiological conditions. While 6-OxP-CD was found to degrade GF instantaneously under these conditions, it was found to form an inclusion complex with GD and significantly improve its degradation (t 1/2 ~ 2 hrs) relative over background (t 1/2 ~ 22 hrs). Consequently, effective formation of the 6-OxP-CD:GD inclusion complex results in the immediate neutralization of GD and thus preventing it from inhibiting its biological target. In contrast, NMR experiments did not find evidence for an inclusion complex between 6-OxP-CD and VX, and the agent’s degradation profile was identical to that of background degradation (t 1/2 ~ 24 hrs). As a complement to this experimental work, molecular dynamics (MD) simulations coupled with Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) calculations have been applied to the study of inclusion complexes between 6-OxP-CD and the three nerve agents. These studies provide data that informs the understanding of the different degradative interactions exhibited by 6-OxP-CD with each nerve agent as it is introduced in the CD cavity in two different orientations (up and down). For its complex with GF, it was found that the oxime in 6-OxP-CD lies in very close proximity (P GF …O Oxime ~ 4–5 Å) to the phosphorus center of GF in the ‘down GF ’ orientation for most of the simulation accurately describing the ability of 6-OxP-CD to degrade this nerve agent rapidly and efficiently. Further computational studies involving the center of masses (COMs) for both components (GF and 6-OxP-CD) also provided some insight on the nature of this inclusion complex. Distances between the COMs (ΔCOM) lie closer in space in the ‘down GF ’ orientation than in the ‘up GF ’ orientation; a correlation that seems to hold true not only for GF but also for its congener, GD. In the case of GD, calculations for the ‘down GD ’ orientation showed that the oxime functional group in 6-OxP-CD although lying in close proximity (P GD …O Oxime ~ 4–5 Å) to the phosphorus center of the nerve agent for most of the simulation, adopts another stable conformation that increase this distance to ~ 12–14 Å, thus explaining the ability of 6-OxP-CD to bind and degrade GD but with less efficiency as observed experimentally (t 1/2 ~ 4 hr. vs. immediate). Lastly, studies on the VX:6-OxP-CD system demonstrated that VX does not form a stable inclusion complex with the oxime-bearing cyclodextrin and as such does not interact in a way that is conducive to an accelerated degradation scenario. Collectively, these studies serve as a basic platform from which the development of new cyclodextrin scaffolds based on 6-OxP-CD can be designed in the development of medical countermeasures against these highly toxic chemical warfare agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Machine learning enabled quantification of the hydrogen bonds inside the polyelectrolyte brush layer probed using all-atom molecular dynamics simulations

The configuration of densely grafted charged polyelectrolyte (PE) brushes is strongly dictated by the properties and behavior of the counterions that screen the PE brush charges and the solvent molecules (typically water) that solvate the brush molecules and these screening counterions. Only recently, efforts have been made to study the PE brushes atomistically, thereby shedding light on the properties of brush-supported ions and water molecules. However, even for such efforts, there are limitations associated with using a generic definition to estimate certain properties of water and ions inside the brush layer. For example, water–water hydrogen bonds (HBs) will behave differently for locations outside and inside the brush layer, given the fact that the densely closely grafted PE brush molecules create a soft nanoconfinement where the water connectivity becomes highly disrupted: therefore, using the same definition to quantify the HBs inside and outside the brush layer will be unwise. In this paper, we address this limitation by employing an unsupervised machine learning (ML) approach to predict the water–water hydrogen bonding inside a cationic PE brush layer modeled using all-atom molecular dynamics (MD) simulations. Here, the ML method, which relies on a clustering approach and uses the equilibrium coordinates of the water molecules (obtained from the all-atom MD simulations) as the input, is capable of identifying the structural modification of water–water HBs (revealed through appropriate clustering of the data) inside the PE brush layer induced soft nanoconfinement. Such capabilities would not have been possible by using a generic definition of the HBs. Our calculations lead to four key findings: (1) the clusters formed inside and outside the brush layer are structurally similar; (2) the margin of the cluster is shorter inside the PE brush layer confirming the possible disruption of the HBs inside the PE brush layer; (3) the average “hydrogen–acceptor-oxygen–donor-oxygen” angle that defines the HB is reduced for the HBs formed inside the brush layer; (4) the use of the generic definition (definition usable for characterizing the HBs in brush-free bulk) leads to an overprediction of the number of HBs formed inside the PE brush layer.

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

Local structure analysis of low-temperature neutron pair distribution function coupled with molecular dynamics simulations of CH 4 and CO 2 hydrates from 2 to 210 K

CH 4 hydrates occur naturally and are an abundant potential fuel source with a corresponding risk of potent greenhouse gas release, due to their stability conditions at low temperature and high pressure. Byproduct CO 2 can be exchanged with CH 4 in these natural deposits and can potentially stabilize the hydrates at higher temperatures. CH 4 , CO 2 , and mixed CH 4 -CO 2 hydrates are studied with in situ neutron pair distribution function experiments from 2 to 210 K to investigate the impact of varying the CH 4 -CO 2 guest composition in the gas hydrate structure. These experiments combined with Reverse Monte Carlo analysis allow for the characterization of intermolecular CH 4 and CO 2 interactions with the water molecules which form the hydrate lattice and how they impact the local structure of the lattice itself. Results indicate that when CH 4 and CO 2 co-occupy the hydrate, the host is more strongly distorted than in the pure CH 4 and CO 2 hydrates, but this becomes less defined with increasing temperature. The presence of CO 2 in mixed hydrate increases the stability range and creates a barrier for CH 4 to completely leave the structure.

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

Towards computational polar-topotronics: Multiscale neural-network quantum molecular dynamics simulations of polar vortex states in SrTiO3/PbTiO3 nanowires

Recent discoveries of polar topological structures ( e.g ., skyrmions and merons) in ferroelectric/paraelectric heterostructures have opened a new field of polar topotronics. However, how complex interplay of photoexcitation, electric field and mechanical strain controls these topological structures remains elusive. To address this challenge, we have developed a computational approach at the nexus of machine learning and first-principles simulations. Our multiscale neural-network quantum molecular dynamics molecular mechanics approach achieves orders-of-magnitude faster computation, while maintaining quantum-mechanical accuracy for atoms within the region of interest. This approach has enabled us to investigate the dynamics of vortex states formed in PbTiO 3 nanowires embedded in SrTiO 3 . We find topological switching of these vortex states to topologically trivial, uniformly polarized states using electric field and trivial domain-wall states using shear strain. These results, along with our earlier results on optical control of polar topology, suggest an exciting new avenue toward opto-electro-mechanical control of ultrafast, ultralow-power polar topotronic devices.

Linker, Thomas↗
DOE OSTI2021

Accelerated molecular dynamics simulations of dislocation climb in nickel

We report the mechanical behavior of materials operating under high temperatures is strongly influenced by creep mechanisms such as dislocation climb, which is controlled by the diffusion of vacancies. However, atomistic simulations of these mechanisms have traditionally been impractical due to the long time scales required. To overcome these time scale challenges, we use Parallel Trajectory Splicing (ParSplice), an accelerated molecular dynamics method, to simulate dislocation climb in nickel. We focus on modeling the activity of a vacancy near a jog on an edge dislocation in order to observe vacancy pipe diffusion and vacancy absorption at the jog. From rigorously constructed trajectories encompassing more than 2000 vacancy absorption events over a simulation time of more than 4μs at 900 K, a comprehensive sampling of available atomistic mechanisms is collated and analyzed further with molecular statics calculations. We estimate average rates for pipe diffusion and vacancy absorption into the jog using data from the dynamic and static calculations, finding very good agreement. Our results strongly suggest that the dominant mechanism for vacancy absorption by jogs is via biased diffusion to the dislocation core followed by fast pipe diffusion to the jog.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Modification of a force field for molecular dynamics simulations of silicon etching by chlorine atoms

Here, a modified classical molecular dynamics (MD) force field is presented for the interaction between silicon (Si) and chlorine (Cl). The original version of the force field is shown to significantly overestimate the probability of Si etching by thermal Cl atoms. However, the modified force field corrects this problem and results in generally good agreement with experimental data. Further, it is shown that while the modification of the force field improves the prediction of Si spontaneous etching with Cl atoms, it does not degrade predictions of atomic-layer etching of Si with Cl[Formula: see text] molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Beam Dynamics Simulations of Transient Beam Loading Effects in the 10GeV EIC Electron Storage Ring

We report on beam dynamics studies of transient beam loading effects in the 10 GeV EIC electron storage ring [1]. The studies are carried out with time-dependent Vlasov-Fokker-Planck simulations performed with the parallel, particle tracking code SPACE [2], which allows to follow self-consistently the dynamics of h bunches, where h in the number of RF buckets, in arbitrary multi-bunch configurations. The specific goal of the numerical simulations is to determine stable RF cavity settings under heavy beam loading. We also study the option to operate with a passive, third-harmonic cavity (3HC) system for bunch lengthening, addressing both stability and the performance limitation due to a gap in the uniform filling pattern for ion clearing.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

First Principles Molecular Dynamics Simulations of Ammonia Adsorption onto MFI Zeolite Nanosheets

MFI zeolite nanosheets membranes are promising candidates for ammonia separation from nitrogen and hydrogen, yet questions remain on the origin of their high selectivity. Silanols, Si-OH, are present in high concentration at the surface of zeolite nanosheets, and force-field-based simulations indicate that surface adsorption at the silanols contributes to selectivity. Silanols can chemically react with ammonia, which may further contribute to the ability of zeolite nanosheet membranes to separate it from other gases. In this work, we use first-principles molecular dynamics techniques to simulate ammonia’s behavior within stacked MFI zeolite nanosheets. We find that at 523 K and a loading corresponding to 35 bar, conditions desired for the ammonia separation, about 30% of ammonia reacts with surface silanols. Our work explores H-bonding and proton transfer within this system.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Orientational Pair Correlations and Local Structure of Benzonitrile from Molecular Dynamics Simulations with Comparisons to Experiments [plus supplemental information]

Here, we present an experimentally parametrized molecular dynamics study of single-molecule and collective orientational relaxation in neat benzonitrile through the analysis of the reorientational anisotropy and polarizability anisotropy time-correlation function (PA-TCF). The simulations show that the PA-TCF is dominated by collective reorientation after 20 ps. Collective reorientation is found to be slower than single-molecule reorientation by a factor of 1.67, consistent with recent experiments. The simulations provide direct evidence of local antiparallel benzonitrile configurations. These structures, which have been the center of some debate, are responsible for the slower rate of collective vs. single-molecule reorientation in the liquid. Further structural analysis indicates that significant Coulombic interactions between the nitrile group and hydrogen atoms on adjacent molecules play a role in the formation of the antiparallel structures. The single-molecule dynamics reflected in the anisotropy are complex and consist of a ballistic regime, restricted angular diffusion, and spatially anisotropic free diffusion. The principal components of the rotational diffusion tensor are independently obtained and shown to reproduce the free diffusion regime of the anisotropy for each principal axis according to the predictions of a previous theory.

14 SOLAR ENERGY↗
DOE OSTI2025

First-Principles Molecular Dynamics Simulations of Ammonia Adsorption onto MFI Zeolite Nanosheets

MFI zeolite nanosheet membranes are promising candidates for ammonia separation from nitrogen and hydrogen gases, yet questions remain on the origin of their high selectivity. Silanols, Si–OH, are present in high concentration at the surface of zeolite nanosheets, and force-field-based simulations indicate that surface adsorption at the silanols contributes to selectivity. Acidic silanol groups can chemically react with ammonia via transfer of a proton to form ammonium ions, which may further contribute to the ability of zeolite nanosheet membranes to separate ammonia from other gases. In this work, we used first-principles molecular dynamics techniques to simulate ammonia’s behavior within stacked MFI zeolite nanosheets. We found that at 523 K and a loading corresponding to 35 bar, conditions desired for the ammonia separation, about 30% of ammonia reacts with surface silanols. Our work explored H-bonding and proton transfer within this system.

ammonia↗
DOE OSTI2020

Nonadiabatic Dynamics Simulation of the Wavelength-Dependent Photochemistry of Azobenzene Excited to the nπ* and ππ* Excited States

Azobenzene is one of the most ubiquitous photoswitches in photochemistry and a prototypical model for photoisomerizing systems. Despite this, its wavelength-dependent photochemistry has puzzled researchers for decades. Upon excitation to the higher energy ππ* excited state instead of the dipole-forbidden nπ* state, the quantum yield of isomerization from trans- to cis-azobenzene is halved. The difficulties associated with unambiguously resolving this effect both experimentally and theoretically have contributed to lasting controversies regarding the photochemistry of azobenzene. Here, we systematically characterize the dynamic photoreaction pathways of azobenzene by performing first-principles simulations of the nonadiabatic dynamics following excitation to both the ππ* and the nπ* states. In this work, we demonstrate that ground-state recovery is mediated by two distinct S1 decay pathways: a reactive twisting pathway and an unreactive planar pathway. Increased preference for the unreactive pathway upon ππ* excitation largely accounts for the wavelength-dependent behavior observed in azobenzene.

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

Efficacy of the radial pair potential approximation for molecular dynamics simulations of dense plasmas

Macroscopic simulations of dense plasmas rely on detailed microscopic information that can be computationally expensive and is difficult to verify experimentally. In this work, we delineate the accuracy boundary between microscale simulation methods by comparing Kohn–Sham density functional theory molecular dynamics (KS-MD) and radial pair potential molecular dynamics (RPP-MD) for a range of elements, temperature, and density. By extracting the optimal RPP from KS-MD data using force matching, we constrain its functional form and dismiss classes of potentials that assume a constant power law for small interparticle distances. Our results show excellent agreement between RPP-MD and KS-MD for multiple metrics of accuracy at temperatures of only a few electron volts. The use of RPPs offers orders of magnitude decrease in computational cost and indicates that three-body potentials are not required beyond temperatures of a few eV. Due to its efficiency, the validated RPP-MD provides an avenue for reducing errors due to finite-size effects that can be on the order of ∼20%.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

AENET–LAMMPS and AENET–TINKER : Interfaces for accurate and efficient molecular dynamics simulations with machine learning potentials

Machine-learning potentials (MLPs) trained on data from quantum-mechanics based first-principles methods can approach the accuracy of the reference method at a fraction of the computational cost. To facilitate efficient MLP-based molecular dynamics and Monte Carlo simulations, an integration of the MLPs with sampling software is needed. Here, we develop two interfaces that link the atomic energy network (ænet) MLP package with the popular sampling packages TINKER and LAMMPS. The three packages, ænet, TINKER, and LAMMPS, are free and open-source software that enable, in combination, accurate simulations of large and complex systems with low computational cost that scales linearly with the number of atoms. Scaling tests show that the parallel efficiency of the ænet–TINKER interface is nearly optimal but is limited to shared-memory systems. The ænet–LAMMPS interface achieves excellent parallel efficiency on highly parallel distributed memory systems and benefits from the highly optimized neighbor list implemented in LAMMPS. We demonstrate the utility of the two MLP interfaces for two relevant example applications: the investigation of diffusion phenomena in liquid water and the equilibration of nanostructured amorphous battery materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Micro-beam bending of FCC bicrystals: A comparison between defect dynamics simulations and experiments

To understand the role of the grain boundary (GB) in plasticity at small scale, a concurrently coupled mesoscale plasticity model was developed to simulate micro-bending of bicrystalline micron-sized beams. By coupling dislocation dynamics (DD) with a finite element model (FEM), a novel defect dynamics model provides the means to investigate intricate interactions between dislocations and GBs under various loading conditions. Our simulations of micro-bending agree well with corresponding micro-bending experiments, and they show that mechanical response of bicrystals could have not only hardening but also softening depending on the characters of the GB. In addition, changing the location of the GB in the microbeams results in different mechanical responses; GBs located at the neutral plane show softening compared to single crystals, while inclined GBs located halfway along the length of the beam show little effect. In conclusion, simulation results could provide a clear picture on detailed dislocation-GB interactions, and quantitative resolved shear stress analysis supplemented by dislocation density distribution is used to analyze the mechanical response of bicrystalline samples.

36 MATERIALS SCIENCE↗