Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Atomistic models”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

2023 Roadmap on molecular modelling of electrochemical energy materials

New materials for electrochemical energy storage and conversion are the key to the electrification and sustainable development of our modern societies. Molecular modelling based on the principles of quantum mechanics and statistical mechanics as well as empowered by machine learning techniques can help us to understand, control and design electrochemical energy materials at atomistic precision. Therefore, this roadmap, which is a collection of authoritative opinions, serves as a gateway for both the experts and the beginners to have a quick overview of the current status and corresponding challenges in molecular modelling of electrochemical energy materials for batteries, supercapacitors, CO 2 reduction reaction, and fuel cell applications.

25 ENERGY STORAGE↗
NASA NTRS2023

Thermomechanical Property Prediction of Amorphous and Crystal PEKK via Molecular Dynamics

Traditionally, advanced aerospace composites have been manufactured using thermoset resins. However, recently, thermoplastics have been investigated for use in the manufacturing of composite materials due to their unique manufacturing characteristics. Thermoplastic resins can be reshaped and formed, along with the added benefit of being recyclable, which thermoset resin cannot. Thermoplastic materials undergo a crystallization process during manufacturing which affects the percent crystallinity of the material. The crystallization needs to be understood better to maximize the potential of thermoplastic resins. PEKK is a thermoplastic material with good chemical, thermal, and mechanical loading resistance. PEKK is also a material NASA is interested in for developing new bonded joint technology. The crystalline microstructure of PEKK is at the micrometer length scale, and it is of interest to model the effects of the crystallinity structure on PEKK’s bulk properties. Molecular dynamics (MD) is a simulation tool that allows for property-structure relationships between atomistic structure and nanometer-length portions of a material. This makes MD a useful tool for developing the structure-property relationship of PEKK. However, the micrometer length scale of PEKK’s crystal structure is too large for MD. Thus, a hybrid approach to modeling PEKK’s microstructure is proposed in this work where MD models are built of both the amorphous and crystalline phases of PEKK. The engineering material properties can be obtained using MD at the nanometer length scale. A micromechanics approach can then generate the micrometer length scale of the crystallinity and the effective properties can be homogenized. The objective of this paper is to show the MD model workflow and the MD-predicted properties of PEKK. The properties can then be homogenized with different crystalline percentages to build design graphs that can be used to tailor PEKK for specific composite applications.

poly ether ketone ketone↗
DOE OSTI2021

Size-dependent radiation damage mechanisms in nanowires and nanoporous structures

Nanostructures with a high density of interfaces, such as in nanoporous materials and nanowires, resist radiation damage by promoting the annihilation and migration of defects. This study details the size effect and origins of the radiation damage mechanisms in nanowires and nanoporous structures in model face-centered (gold) and body-centered (niobium) cubic nanostructures using accelerated multi-cascade atomistic simulations and in-situ ion irradiation experiments. Our results reveal three different size-dependent mechanisms of damage accumulation in irradiated nanowires and nanoporous structures: sputtering for very small nanowires and ligaments, the formation and accumulation of point defects and dislocation loops in larger nanowires, and a face-centered-cubic to hexagonal-close-packed phase transformation for a narrow range of wire diameters in the case of gold nanowires. Smaller nanowires and ligaments have a net effect of lowering the radiation damage as compared to larger wires that can be traced back to the fact that smaller nanowires transition from a rapid accumulation of defects to a saturation and annihilation mechanism at a lower dose than larger nanowires. These irradiation damage mechanisms are accompanied with radiation-induced surface roughening resulting from defect-surface interactions. Comparisons between nanowires and nanoporous structures show that the various mechanisms seen in nanowires provide adequate bounds for the defect accumulation mechanisms in nanoporous structures with the difference attributed to the role of nodes connecting ligaments in nanoporous structures. Altogether, our results shed light on the compounded, size-dependent mechanisms leading to the radiation resistance of nanowires and nanoporous structures.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Point defect evolution under irradiation: Finite size effects and spatio-temporal correlations

The evolution of point defect concentrations under irradiation is controlled by their diffusion properties, and by their formation and elimination mechanisms. The latter includes the mutual recombination of vacancies and interstitials, and the elimination of point defects at sinks. Two models are traditionally used to predict the defect concentration evolution, the standard rate theory (SRT) and the atomistic kinetic Monte Carlo (AKMC). We show in this work a large discrepancy in the defect concentrations between both methods when the average number of defects in the AKMC simulation box is close or lower than one. The reason is that AKMC naturally captures strong space and time correlations between vacancies and interstitials generated by the finite size of the periodic simulation box. These correlations strongly affect the recombination rate and the point defect concentrations. SRT fails to predict such correlations, and the corresponding solution deviates from the more accurate solution given by the AKMC simulation under similar conditions. These finite size correlation effects are strong when the elimination of point defects occurs by recombination only, but can still be significant in the presence of sinks. In order to account for the spacio-temporal correlation in a continuum framework, we introduce a Correlated Pair Theory (CPT). This theory fully takes into account the correlations between vacancy and interstitial pairs and predicts point defect concentrations in good agreement with AKMC simulations. Inversely, if the goal is for the AKMC to reproduce defect concentrations in bulk using small simulation boxes, the naturally occurring correlations need to be corrected. We show here that the CPT can be used to modify the elimination rates in the AKMC simulations, so as to yield point defect concentrations in agreement with SRT.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

PLAT domain protein 1 (PLAT1/PLAFP) binds to the Arabidopsis thaliana plasma membrane and inserts a lipid

Robust agricultural yields depend on the plant's ability to fix carbon amid variable environmental conditions. Over seasonal and diurnal cycles, the plant must constantly adjust its metabolism according to available resources or external stressors. The metabolic changes that a plant undergoes in response to stress are well understood, but the long-distance signaling mechanisms that facilitate communication throughout the plant are less studied. The phloem is considered the predominant conduit for the bidirectional transport of these signals in the form of metabolites, nucleic acids, proteins, and lipids. Lipid trafficking through the phloem in particular attracted our attention due to its reliance on soluble lipid-binding proteins (LBP) that generate and solubilize otherwise membrane-associated lipids. The Phloem Lipid-Associated Family Protein (PLAFP) from Arabidopsis thaliana is generated in response to abiotic stress as is its lipid-ligand phosphatidic acid (PA). PLAFP is proposed to transport PA through the phloem in response to drought stress. To understand the interactions between PLAFP and PA, nearly 100 independent systems comprised of the protein and one PA, or a plasma membrane containing varying amounts of PA, were simulated using atomistic classical molecular dynamics methods. In these simulations, PLAFP is found to bind to plant plasma membrane models independent of the PA concentration. When bound to the membrane, PLAFP adopts a binding pose where W41 and R82 penetrate the membrane surface and anchor PLAFP. This triggers a separation of the two loop regions containing W41 and R82. Subsequent simulations indicate that PA insert into the β -sandwich of PLAFP, driven by interactions with multiple amino acids besides the W41 and R82 identified during the insertion process. Finally, fine-tuning the protein-membrane and protein-PA interface by mutating a selection of these amino acids may facilitate engineering plant signaling processes by modulating the binding response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structure-dependent clustering-to-declustering solute segregation transitions near disconnections

Grain-boundary disconnections, characterized by a step and a dislocation, are pervasive interfacial line defects that play a critical role in governing the properties and performance of nanocrystalline alloys. Although segregation of alloying elements is frequently observed at GB disconnections, the underlying mechanisms remain poorly understood, particularly at elevated temperatures and non-dilute conditions. In this study, we employ atomistic simulations to study the segregation behavior of Ag at various faulted disconnections in Cu as a model material system. Our results demonstrate a pronounced size and compactness effect on the segregation behavior: more compact faulted disconnection structures promote the formation of Ag segregation clusters due to a highly localized tensile field, whereas more spread faulted disconnection structures (i.e., with wider partial dislocation spacing) exhibit much weaker clustering tendencies. Furthermore, with increasing temperature, Ag clustering in small disconnections initially intensifies and then disappears, indicating a thermally driven transition from clustering to declustering segregation behavior.

Disconnections↗
DOE OSTI2024

Effect of Solvent Composition on Non-DLVO Forces and Oriented Attachment of Zinc Oxide Nanoparticles

Oriented attachment (OA) occurs when nanoparticles in solution align their crystallographic axes prior to colliding and subsequently fuse into single crystals. Traditional colloidal theories such as DLVO provide a framework for evaluating OA but fail to capture key particle interactions due to the atomistic details of both the crystal structure and the interfacial solution structure. Using zinc oxide as a model system, we investigated the effect of the solvent on short-ranged and long-ranged particle interactions and the resulting OA mechanism. In situ TEM imaging showed that ZnO nanocrystals in toluene undergo long-range attraction comparable to 1kT at separations of 10 nm and 3kT near particle contact. These observations were rationalized by considering non-DLVO interactions, namely dipole-dipole forces and torques between the polar ZnO nanocrystals. Langevin dynamics simulations showed stronger interactions in toluene compared to methanol solvents, consistent with the experimental results. Concurrently, we performed atomic force microscopy measurements using ZnO-coated probes for the short-ranged interaction. Our data provided valuable insights into another type of non-DLVO interaction, namely the repulsive solvation force. Specifically, the solvation force was stronger in water compared to ethanol and methanol, due to the stronger hydrogen bonding and denser packing of water molecules at the interface. In conclusion, our results highlight the importance of non-DLVO forces in a general framework for understanding and predicting particle aggregation and attachment.

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

Topological energy barrier for skyrmion lattice formation in MnSi

We report the direct measurement of the topological skyrmion energy barrier through a hysteresis of the skyrmion lattice in the chiral magnet MnSi. Measurements were made using small-angle neutron scattering with a custom-built resistive coil to allow for high-precision minor hysteresis loops. The experimental data were analyzed using an adapted Preisach model to quantify the energy barrier for skyrmion formation and corroborated by the minimum-energy path analysis based on atomistic spin simulations. Here, we reveal that the skyrmion lattice in MnSi forms from the conical phase progressively in small domains, each of which consisting of hundreds of skyrmions, and with an activation barrier of several eV.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

A Modeling and Neutron Diffraction Study of the High Temperature Properties of Sub-Stoichiometric Yttrium Hydride for Novel Moderator Applications

Low-enriched-uranium (LEU) reactor systems utilize moderators to improve neutron economy. Solid yttrium hydride is one of the primary moderator candidates for high-temperature (>700 °C) nuclear reactor applications. This is due to its ability to retain hydrogen at elevated temperatures compared to other metal hydrides. For reactor modeling purposes, both neutronic and thermos-mechanical modeling, several high-temperature properties for sub-stoichiometric yttrium hydride (YH2−x) are needed. In this paper, we present an atomistics and a neutron diffraction study of the high-temperature properties of Y and YH2−x. Specifically, we focus on the thermal lattice expansion effects in yttrium metal and yttrium hydride, which also govern bulk thermal expansion. Previously reported physical and mechanical properties for sub-stoichiometric yttrium hydride at ambient conditions are expanded using lattice dynamics to take into account high-temperature effects. Accordingly, an array of newly generated properties is presented that enables high-fidelity neutronics, and thermomechanical modeling. These properties include various elastic moduli, thermal expansion parameters for yttrium and yttrium hydride, and single-phase (YH2−x) and two-phase (Y + YH2−x) density as a function of stoichiometry and density.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Quantum bath augmented stochastic nonequilibrium atomistic simulations for molecular heat conduction

Classical molecular dynamics (MD) has been shown to be effective in simulating heat conduction in certain molecular junctions since it inherently takes into account some essential methodological components which are lacking in the quantum Landauer-type transport model, such as many-body full force-field interactions, anharmonicity effects and nonlinear responses for large temperature biases. However, the classical MD reaches its limit in the environments where the quantum effects are significant (e.g. with low-temperatures substrates, presence of extremely high frequency molecular modes). Here, we present an atomistic simulation methodology for molecular heat conduction that incorporates the quantum Bose–Einstein statistics into an “effective temperature” in the form of a modified Langevin equation. We show that the results from such a quasi-classical effective temperature MD method deviates drastically when the baths temperature approaches zero from classical MD simulations and the results converge to the classical ones when the bath approaches the high-temperature limit, which makes the method suitable for full temperature range. In addition, we show that our quasi-classical thermal transport method can be used to model the conducting substrate layout and molecular composition (e.g. anharmonicities, high-frequency modes). Anharmonic models are explicitly simulated via the Morse potential and compared to pure harmonic interactions to show the effects of anharmonicities under quantum colored bath setups. Finally, the chain length dependence of heat conduction is examined for one-dimensional polymer chains placed in between quantum augmented baths.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2008

New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation

A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain has been enhanced. The concurrent MD-FEM coupling methodology uses statistical averaging of the deformation of the atomistic MD domain to provide interface displacement boundary conditions to the surrounding continuum FEM region, which, in turn, generates interface reaction forces that are applied as piecewise constant traction boundary conditions to the MD domain. The enhancement is based on the addition of molecular dynamics-based cohesive zone model (CZM) elements near the MD-FEM interface. The CZM elements are a continuum interpretation of the traction-displacement relationships taken from MD simulations using Cohesive Zone Volume Elements (CZVE). The addition of CZM elements to the concurrent MD-FEM analysis provides a consistent set of atomistically-based cohesive properties within the finite element region near the growing crack. Another set of CZVEs are then used to extract revised CZM relationships from the enhanced embedded statistical coupling method (ESCM) simulation of an edge crack under uniaxial loading.

Saether, E.↗
DOE OSTI2020

A density-functional theory study of the Al/AlOx/Al tunnel junction

The aluminum oxide tunnel junction is a key component of the majority of superconducting quantum devices. For high-quality, reproducible, and scalably manufacturable qubits, the ability to fabricate Josephson junctions (JJs) with a targeted critical current and high uniformity is essential. In this study, we use first-principles modeling to assess fundamental aspects of the atomic structure of both amorphous and crystalline aluminum oxide tunnel junctions and relate the structure to predicted performance metrics. We use modified ab initio molecular dynamics to develop realistic models of the tunnel junction, from which interface roughness and local thickness fluctuations are analyzed in an unbiased manner by training a neural network to identify the boundary between metal and oxide. We show that the effective thickness of the insulating part of the junction can be different from the apparent physical thickness. We calculate the rate of Cooper pair tunneling for the atomically resolved electrostatic potential using direct numerical solution in 3D, which shows a channeling effect that impacts the junction critical current. The predicted critical current is a useful JJ design parameter that can be accessed from the ab initio calculations without fitting parameters. To assess the limits of uniformity and fabrication choices (e.g., oxidation vs epitaxy), we compare the amorphous junctions to crystalline models, which show order of magnitude more efficient tunneling compared to the amorphous case, underlining the connection between atomistic structure and Cooper pair tunneling efficiency. Further, this work provides a foundation for ab initio materials design and evaluation to help accelerate future development of improved tunnel junctions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Nuclear–Electronic Orbital QM/MM Approach: Geometry Optimizations and Molecular Dynamics

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods allow simulations of chemical reactions in atomistic solvent and heterogeneous environments such as proteins. Herein, the nuclear–electronic orbital (NEO) QM/MM approach is introduced to enable the quantization of specified nuclei, typically protons, in the QM region using a method such as NEO-density functional theory (NEO-DFT). This approach includes proton delocalization, polarization, anharmonicity, and zero-point energy in geometry optimizations and dynamics. Expressions for the energies and analytical gradients associated with the NEO-QM/MM method, as well as the previously developed polarizable continuum model (NEO-PCM), are provided. Geometry optimizations of small organic molecules hydrogen bonded to water in either dielectric continuum solvent or explicit atomistic solvent illustrate that aqueous solvation can strengthen hydrogen-bonding interactions for the systems studied, as indicated by shorter intermolecular distances at the hydrogen-bond interface. We then performed a real-time direct dynamics simulation of a phenol molecule in explicit water using the NEO-QM/MM method. Furthermore, these developments and initial examples provide the foundation for future studies of nuclear–electronic quantum dynamics in complex chemical and biological environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2007

A Statistical Approach for the Concurrent Coupling of Molecular Dynamics and Finite Element Methods

Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, increasing the size of the MD domain quickly presents intractable computational demands. A robust approach to surmount this computational limitation has been to unite continuum modeling procedures such as the finite element method (FEM) with MD analyses thereby reducing the region of atomic scale refinement. The challenging problem is to seamlessly connect the two inherently different simulation techniques at their interface. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the typical boundary value problem used to define a coupled domain. The method uses statistical averaging of the atomistic MD domain to provide displacement interface boundary conditions to the surrounding continuum FEM region, which, in return, generates interface reaction forces applied as piecewise constant traction boundary conditions to the MD domain. The two systems are computationally disconnected and communicate only through a continuous update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM) as opposed to a direct coupling method where interface atoms and FEM nodes are individually related. The methodology is inherently applicable to three-dimensional domains, avoids discretization of the continuum model down to atomic scales, and permits arbitrary temperatures to be applied.

Saether, E.↗
DOE OSTI2021

Machine learning in materials science: From explainable predictions to autonomous design

The advent of big data and algorithmic developments in the field of machine learning (and artificial intelligence, in general) have greatly impacted the entire spectrum of physical sciences, including materials science. Materials data, measured or computed, combined with various techniques of machine learning have been employed to address a myriad of challenging problems, such as, development of efficient and predictive surrogate models for a range of materials properties, screening and down-selection of novel candidate materials for targeted applications, new methodologies to improve and further expedite molecular and atomistic simulations, with likely many more important developments to come in the foreseeable future. While the applications thus far have provided a glimpse of the true potential data-enabled routes have to offer, it has also become clear that further progress in this direction hinges on our ability to understand, explain and rationalize findings of a machine learning model in light of the domain-knowledge. This focused review provides an overview of the main areas where machine learning has been widely and successfully used in materials science. Subsequently, a brief discussion of several techniques that have been helpful in extracting physically-meaningful insights, causal relationships and design-centric knowledge from materials data is provided. Finally, we identify some of the imminent opportunities and challenges that materials community faces in this exciting and rapidly growing field.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Data-Efficient Generation of Protein Conformational Ensembles with Backbone-to-Side-Chain Transformers

Excitement at the prospect of using data-driven generative models to sample configurational ensembles of biomolecular systems stems from the extraordinary success of these models on a diverse set of high-dimensional sampling tasks. Unlike image generation or even the closely related problem of protein structure prediction, there are currently no data sources with sufficient breadth to parametrize generative models for conformational ensembles. To enable discovery, a fundamentally different approach to building generative models is required: models should be able to propose rare, albeit physical, conformations that may not arise in even the largest data sets. Here, in this work, we introduce a modular strategy to generate conformations based on “backmapping” from a fixed protein backbone that (1) maintains conformational diversity of the side chains and (2) couples the side-chain fluctuations using global information about the protein conformation. Our model combines simple statistical models of side-chain conformations based on rotamer libraries with the now ubiquitous transformer architecture to sample with atomistic accuracy. Together, these ingredients provide a strategy for rapid data acquisition and hence a crucial ingredient for scalable physical simulation with generative neural networks.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Grazing Incidence Wide-Angle X-ray Scattering of Water Adsorption in Polyamide Barrier Layers of Reverse Osmosis Membranes

To understand the relationship between the intermolecular structure of aromatic polyamide (PA) scaffold and the water molecules in the barrier layers of reverse osmosis (RO) membranes, a grazing incidence wide-angle X-ray scattering (GIWAXS) study was carried out on freestanding PA thin films at varying relative humidity (RH) conditions. The scattering results were analyzed by an interference scattering model, containing a phase factor between a PA chain and an adsorbed water molecule. This model yielded good fits to the GIWAXS profiles where the water adsorption was found to vary linearly with RH. Atomistic molecular dynamics (MD) simulations were also performed to complement the experimental study. Furthermore, the simulations revealed that a rapid condensation layer initially formed on the PA film surface, followed by the slow water molecule diffusion inside the PA membrane. Sparse adsorbed water, isolated in subnanopores of the PA film adjacent to the polar atoms, even in very low quantities, modifies the X-ray scattering. Atomistic simulations at the microscopic scale provide partial support for several X-ray scattering findings.

36 MATERIALS SCIENCE↗
DOE OSTI2023

An interplay between a hydrogen atmosphere and dislocation characteristics in BCC Fe from time-averaged molecular dynamics

The interplay between hydrogen and dislocations (e.g., core and elastic energies, and dislocation–dislocation interactions) has implications on hydrogen embrittlement but is poorly understood. Continuum models of hydrogen enhanced local plasticity have not considered the effect of hydrogen on dislocation core energies. Energy minimization atomistic simulations can only resolve dislocation core energies in hydrogen-free systems because hydrogen motion is omitted so hydrogen atmosphere formation can’t occur. Additionally, previous studies focused more on face-centered-cubic than body-centered-cubic metals. Discrete dislocation dynamics studies of hydrogen–dislocation interactions assume isotropic elasticity, but the validity of this assumption isn’t understood. Here, we perform time-averaged molecular dynamics simulations to study the effect of hydrogen on dislocation energies in body-centered-cubic iron for several dislocation character angles. We see atmosphere formation and highly converged dislocation energies. We find that hydrogen reduces dislocation core energies but can increase or decrease elastic energies of isolated dislocations and dislocation–dislocation interaction energies depending on character angle. We also find that isotropic elasticity can be well fitted to dislocation energies obtained from simulations if the isotropic elastic constants are not constrained to their anisotropic counterparts. These results are relevant to ongoing efforts in understanding hydrogen embrittlement and provide a foundation for future work in this field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗