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At least 73 records · Page 4

Atomistic Simulations of Thermal and Chemical Expansions of PrNi x Co 1‐x O 3‐δ Accelerated by Machine Learning Potentials

The electrodes and solid-state electrolytes in protonic ceramic electrochemical cells (PCECs) experience significant lattice expansions when exposed to high steam concentrations at elevated temperatures. In this paper, phonon calculations based on a new machine learning potential (MLP) are employed to elucidate the volume expansions of the proton-conducting PrNi x Co 1-x O 3-δ (PNC) lattices, manifested under a combined influence of oxygen vacancies (V$^{\cdot\cdot}_O$ ) and proton uptake (OH$^{\cdot}_O$ ) in the bulk at varying Ni/Co occupancies. It is revealed that the Ni/Co occupancy contributes to thermal and chemical expansions differently, where thermal expansions are related to Co occupancy. In contrast, chemical expansions are more closely associated with the Ni occupancy. Both V$^{\cdot\cdot}_O$ and OH$^{\cdot}_O$ lead to higher thermal expansions when compared to the pristine PNC. The temperature increase will negatively impact the hydration-induced chemical expansions. For combined thermal and chemical expansions, it is predicted that the strategies that boost the PCEC's electrochemical performance may harm the electrode–electrolyte interfacial stability, when the Ni occupancy is high, due to severe chemical expansions. Mitigating chemical expansions of the Ni-abundant PNC will benefit the interfacial stability. Finally, the presented computational methods for phonon calculations, based on emerging machine learning interatomic potential techniques are anticipated to have a lasting impact on future PCEC development.

computational prediction↗

Assessment of mechanical, thermal properties and crystal shapes of monoclinic tricalcium silicate from atomistic simulations

The two most common polymorphs in industrial alite, M1 and M3, were characterized at the molecular scale. Different methods were employed and discussed to assess mechanical properties and specific heat of both polymorphs. The calculated homogenized elastic moduli and specific heat were found in good agreement with experimental measurements. A comparative analysis of spacial Youngs modulus reveal isotropic and anisotropic spacial distribution for M{sub 1} and M{sub 3} respectively. A more isotropic compressive strength is also reported for M{sub 1} when compared to M{sub 3} polymorph. Cleavage energies computation allowed to proposed equilibrium shapes for both polymorph, with significant differences. While the lowest cleavage energies were found along (100) and (001) for both polymorphs, the constructed M1 crystal possesses 3 independent facets, against seven for the M3 polymorph.

36 MATERIALS SCIENCE↗

Atomistic simulations of nanoindentation on nanoglasses: Effects of grain size and gradient microstructure on the mechanical properties

The use of nanoglass (NG) microstructures has been shown as an effective strategy to improve the ductility of rather brittle metallic glass alloys. To evaluate the effects of grain size and gradient design on the mechanical properties of NGs, we perform molecular dynamics simulations of nanoindentation on Cu 64 Zr 36 NGs. We consider samples with uniform 3 and 7 nm grain sizes as well as gradient microstructures with gradient grain sizes varying from 3 to 7 nm. Here, the results show that the deformation mechanism in NGs with small grain sizes is dominated by the activation and evolution of multiple shear transformation zones. Increasing grain sizes enhances the elastic modulus and hardness at the cost of reduced abrasion resistance. Though the average grain size at the indentation surface plays a crucial role in the deformation behavior of gradient NG models, their strain localization and plastic deformation states are affected by the grain sizes far from the indenter. Desired combinations of mechanical properties can be realized by different NG microstructure designs.

36 MATERIALS SCIENCE↗

Stability and mobility of tungsten clusters on tungsten (110) surface: Ab initio and atomistic simulations

Quantifying the surface transport properties of tungsten (W) is of prime importance to understand the formation of nano-fuzz in fusion plasma-facing conditions. The stability and mobility of W adatom clusters (W n , n = 2-9) on the W(110) surface has been investigated by computer simulations, including ab initio calculations using density functional theory (DFT) and molecular statics (MS) simulations with multiple W interatomic potentials. The DFT results demonstrate that the sequential binding energy generally increases with number of W adatoms, except for the 5 th and 7 th W adatoms. The most common elemental migration steps of W n (n>2) clusters are observed to consist of monomer and dimer hops, while larger W n clusters can also diffuse by dissociation and recombination of smaller clusters. The threshold migration energy of W 9 is the highest, then followed by W 8 , W 4 , and W 6 , while W 3 , W 5 , and W 7 have similar migration energies. Compared to DFT, each interatomic potential evaluated overestimates the binding energies of W n clusters. Additionally, the embedded-atom potential developed by Juslin and Wirth adequately predicts the threshold migration energy of W n (n>2) clusters, although it predicts different underlying migration mechanisms. The results show that interaction mechanism between W adatoms controls the stability and mobility of W n clusters on the W(110) surface.

36 MATERIALS SCIENCE↗

Atomistic Simulations of Polydisperse Lignin Melts Using Simple Polydisperse Residue Input Generator

Understanding the physics of lignin will help rationalize its function in plant cell walls as well as aiding practical applications such as deriving biofuels and bioproducts. Here, in this work, we present SPRIG (Simple Polydisperse Residue Input Generator), a program for generating atomic-detail models of random polydisperse lignin copolymer melts i.e., the state most commonly found in nature. Using these models, we use all-atom molecular dynamics (MD) simulations to investigate the conformational and dynamic properties of polydisperse melts representative of switchgrass (Panicum virgatum L.) lignin. Polydispersity, branching and monolignol sequence are found to not affect the calculated glass transition temperature, T g . The Flory–Huggins scaling parameter for the segmental radius of gyration is 0.42 ± 0.02, indicating that the chains exhibit statistics that lie between a globular chain and an ideal Gaussian chain. Below T g the atomic mean squared displacements are independent of molecular weight. In contrast, above T g , they decrease with increasing molecular weight. Therefore, a monodisperse lignin melt is a good approximation to this polydisperse lignin when only static properties are probed, whereas the molecular weight distribution needs to be considered while analyzing lignin dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomistic simulations of dislocation mobility in refractory high-entropy alloys and the effect of chemical short-range order

Abstract Refractory high-entropy alloys (RHEAs) are designed for high elevated-temperature strength, with both edge and screw dislocations playing an important role for plastic deformation. However, they can also display a significant energetic driving force for chemical short-range ordering (SRO). Here, we investigate mechanisms underlying the mobilities of screw and edge dislocations in the body-centered cubic MoNbTaW RHEA over a wide temperature range using extensive molecular dynamics simulations based on a highly-accurate machine-learning interatomic potential. Further, we specifically evaluate how these mechanisms are affected by the presence of SRO. The mobility of edge dislocations is found to be enhanced by the presence of SRO, whereas the rate of double-kink nucleation in the motion of screw dislocations is reduced, although this influence of SRO appears to be attenuated at increasing temperature. Independent of the presence of SRO, a cross-slip locking mechanism is observed for the motion of screws, which provides for extra strengthening for refractory high-entropy alloy system.

36 MATERIALS SCIENCE↗

Thermodynamics of high-pressure ice phases explored with atomistic simulations

Most experimentally known high-pressure ice phases have a body-centred cubic (bcc) oxygen lattice. Our large-scale molecular-dynamics simulations with a machine-learning potential indicate that, amongst these bcc ice phases, ices VII, VII' and X are the same thermodynamic phase under different conditions, whereas superionic ice VII" has a first-order phase boundary with ice VII'. Moreover, at about 300 GPa, the transformation between ice X and the Pbcm phase has a sharp structural change but no apparent activation barrier, whilst at higher pressures the barrier gradually increases. Our study thus clarifies the phase behaviour of the high-pressure ices and reveals peculiar solid–solid transition mechanisms not known in other systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates

As genetic code expansion advances beyond l-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-l-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi–Dunitz angle of 76–115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.

59 BASIC BIOLOGICAL SCIENCES↗

Atomistic simulation of brittle-to-ductile transition in silicon carbide embedded with nano-sized helium bubbles

In this study, the tensile response of cubic silicon carbide (SiC) bulk containing cavities (voids and He bubbles) has been investigated using molecular dynamic simulations. The formation of cavities in SiC leads to a significant degradation in the mechanical properties of SiC with more influence on material fracture than initial elastic deformation. The brittle-to-ductile transition occurs in cavity-embedded SiC as the pressure in He bubbles increases. This is associated with the deformation mechanism that bond breaking at a low He bubble pressure transfers to extensive dislocation activities at a higher He bubble pressure. The cavities can effectively concentrate stress around them in the direction perpendicular to the tension, which leads to preferred cracking in the region with a higher tensile stress. The failure mechanism as revealed by this study improves understanding of property degradation in SiC that may be useful for applications of SiC in advanced nuclear energy systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A methodology to generate crystal-based molecular structures for atomistic simulations

Abstract We propose a systematic method to construct crystal-based molecular structures often needed as input for computational chemistry studies. These structures include crystal ‘slabs’ with periodic boundary conditions (PBCs) and non-periodic solids such as Wulff structures. We also introduce a method to build crystal slabs with orthogonal PBC vectors. These methods are integrated into our code, Los Alamos Crystal Cut ( LCC ), which is open source and thus fully available to the community. Examples showing the use of these methods are given throughout the manuscript.

42 ENGINEERING↗