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At least 109 records · Page 6

Ab initio molecular dynamics simulations of low energy recoil events in ceramics

The recent progress in the use of large-scale ab initio molecular dynamics (AIMD) to investigate low energy recoil events and determine threshold displacement energies, Ed, in ceramics is reviewed. In general, Ed shows a significant dependence on recoil direction and atom. In 3C-SiC, the minimum Ed for both C and Si atoms is found along the <100> direction, with a value of 20 and 49 eV, respectively. The results demonstrate that significant charge transfer occurs during the dynamics process, and defects can enhance charge transfer to surrounding atoms, which provides important insights into the formation of charged defects. It is found that the C vacancy is a positively charged defect, whereas the Si vacancy is in its neutral state. The minimum Ed in GaN is determined to be 17 and 39 eV for N and Ga atoms, respectively, both along the direction. The average Ed for N atoms (32.4 eV) is smaller than that for Ga atoms (73.2 eV). It is of interest to note that the N defects created along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed. In Y2Ti2O7 prochlore, the minimum Ed for Y atoms is determined to be 27 eV for a recoil along the <100> direction, 31.5 eV for Ti atoms along the <100> direction, 14.5 eV for O48f atoms along the <110> direction and 13 eV for O8b atoms along the <111> direction. The average Ed values determined are 32.7, 34.2, 14.2 and 16.1 eV for yttrium, titanium, O48f and O8b atoms, respectively. Cation interstitials at vacant 8a sites, which are generally occupied by oxygen anions, and at the bridge sites between two neighboring cations along the <010> direction are observed after low energy recoil events.

Ab initio MD↗

Insights into Spontaneous Solid Electrolyte Interphase Formation at Magnesium Metal Anode Surface from Ab Initio Molecular Dynamics Simulations

Spontaneous chemical reactivity at multivalent (Mg, Ca, Zn, Al) electrode surfaces is critical to solid electrolyte interphase (SEI) formation, and hence, directly affects the longevity of batteries. Here, we report an investigation of the reactivity of 0.5 M Mg(TFSI)2 in 1,2-dimethoxyethane (DME) solvent at a Mg(0001) surface using ab initio molecular dynamics (AIMD) simulations and detailed Bader charge analysis. Based on the simulations, the initial degradation reactions of the electrolyte strongly depend on the structure of the Mg(TFSI)2 species near the anode surface. At the surface, the dissociation of Mg(TFSI)2 species occurs via cleavage of the N-S bond for the solvent separated ion pair (SSIP) and via cleavage of the C-S bond for the contact ion pair (CIP) configuration. In the case of the CIP, both TFSI anions undergo spontaneous bond dissociation reactions to form atomic O, C, S, F, and N species adsorbed on the surface of the Mg anode. These products indicate that the initial SEI layer formed on the surface of the pristine Mg anode consists of a complex mixture of multiple components such as oxides, carbides, sulfides, fluorides, and nitrides. We believe that the atomic level insights gained from these simulations will lay the groundwork for the rational design of tailored and functional interphases that are critical for the success of multivalent battery technology.

Agarwal, Garvit↗

Nanoparticle generation and transport resulting from femtosecond laser ablation of ultrathin metal films: Time-resolved measurements and molecular dynamics simulations

The synthesis of metal nanoparticles by ultrafast laser ablation of nanometers-thick metal films has been studied experimentally and computationally. Near-threshold backside laser ablation of 2–20 nm-thick Pt films deposited on fused silica substrates was found to produce nanoparticles with size distributions that were bimodal for the thicker films, but collapsed into a single mode distribution for the thinnest film. Time-resolved imaging of blackbody emission from the Pt nanoparticles was used to reveal the nanoparticle propagation dynamics and estimate their temperatures. The observed nanoparticle plume was compact and highly forward-directed with a well-defined collective velocity that permitted multiple rebounds with substrates to be revealed. Large-scale molecular dynamics simulations were used to understand the evolution of compressive and tensile stresses in the thicker melted liquid films that lead to their breakup and ejection of two groups of nanoparticles with different velocity and size distributions. Ultrafast laser irradiation of ultrathin (few nm) metal films avoids the splitting of the film and appears to be a method well-suited to cleanly synthesize and deposit nanoparticles from semitransparent thin film targets in highly directed beams.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

System-size corrections for self-diffusion coefficients calculated from molecular dynamics simulations: The case of CO{sub 2}, n-alkanes, and poly(ethylene glycol) dimethyl ethers

Molecular dynamics simulations were carried out to study the self-diffusion coefficients of CO{sub 2}, methane, propane, n-hexane, n-hexadecane, and various poly(ethylene glycol) dimethyl ethers (glymes in short, CH{sub 3}O–(CH{sub 2}CH{sub 2}O){sub n}–CH{sub 3} with n = 1, 2, 3, and 4, labeled as G1, G2, G3, and G4, respectively) at different conditions. Various system sizes were examined. The widely used Yeh and Hummer [J. Phys. Chem. B 108, 15873 (2004)] correction for the prediction of diffusion coefficient at the thermodynamic limit was applied and shown to be accurate in all cases compared to extrapolated values at infinite system size. The magnitude of correction, in all cases examined, is significant, with the smallest systems examined giving for some cases a self-diffusion coefficient approximately 15% lower than the infinite system-size extrapolated value. The results suggest that finite size corrections to computed self-diffusivities must be used in order to obtain accurate results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however, the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight into understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular dynamics simulations of zinc oxide solubility: From bulk down to nanoparticles

The solubility of metal oxides is one of the key descriptors for the evaluation of their potential toxic effects, both in the bulk form and in nanoparticulated aggregates. Current work presents a new methodology for the in silico assessment of the solubility of metal oxides, which is demonstrated using a well-studied system, ZnO. The calculation of the solubility is based on statistical thermodynamics tools combined with Density Functional Tight Binding theory for the evaluation of the free energy exchange during the dissolution process. Models of small ZnO clusters are used for describing the final dissolved material, since the complete ionic dissolution of ZnO is hindered by the formation of O2- anions in solution, which are highly unstable. Results show very good agreement between the computed solubility values and experimental data for ZnO bulk, up to 0.5 mg·L-1 and equivalents of 50 g·L-1 for the free Zn2+ cation in solution. However, the reference model for solid nanoparticles formed by free space nanoparticles can only give a limited quantitative solubility evaluation for ZnO nanoparticles.

DFTB modelling↗

A coupled ordinates method for solution acceleration of rarefied gas dynamics simulations

Non-equilibrium rarefied flows are frequently encountered in a wide range of applications, including atmospheric re-entry vehicles, vacuum technology, and microscale devices. Rarefied flows at the microscale can be effectively modeled using the ellipsoidal statistical Bhatnagar–Gross–Krook (ESBGK) form of the Boltzmann kinetic equation. Numerical solutions of these equations are often based on the finite volume method (FVM) in physical space and the discrete ordinates method in velocity space. However, existing solvers use a sequential solution procedure wherein the velocity distribution functions are implicitly coupled in physical space, but are solved sequentially in velocity space. This leads to explicit coupling of the distribution function values in velocity space and slows down convergence in systems with low Knudsen numbers. Furthermore, this also makes it difficult to solve multiscale problems or problems in which there is a large range of Knudsen numbers. In this paper, we extend the coupled ordinates method (COMET), previously developed to study participating radiative heat transfer, to solve the ESBGK equations. In this method, at each cell in the physical domain, distribution function values for all velocity ordinates are solved simultaneously. This coupled solution is used as a relaxation sweep in a geometric multigrid method in the spatial domain. Enhancements to COMET to account for the non-linearity of the ESBGK equations, as well as the coupled implementation of boundary conditions, are presented. The methodology works well with arbitrary convex polyhedral meshes, and is shown to give significantly faster solutions than the conventional sequential solution procedure. Acceleration factors of 5–9 are obtained for low to moderate Knudsen numbers on single processor platforms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Molecular Dynamics Simulations of Water Structure and Diffusion in a 1 nm Diameter Silica Nanopore as a Function of Surface Charge and Alkali Metal Counterion Identity

Water confined in nanopores-particularly in pores narrower than 2 nm-displays distinct physicochemical properties that remain incompletely examined despite their importance in nanofluidics, molecular biology, geology, and materials sciences. In this study, we use molecular dynamics simulations to investigate the coordination structure and mobility of water and alkali metals (Li, Na, K, Cs) inside a 1 nm diameter cylindrical silica nanopore as a function of surface charge density, a model system particularly relevant to the alteration kinetics of silicate glasses and minerals in geologic formations. We find that the presence of a negative surface charge and adsorbed counterions within the pore strongly impacts water structure and dynamics. In particular, it significantly orients water O-H bonds toward the surface and slows water diffusion by almost 1 order of magnitude. Ion crowding in the charged nanopore enhances the tendency of counterions to coordinate closely with the silica surface, which moderates the impact of ions on water dynamics. Co-ions are strongly excluded from the nanopore at all surface charges, suggesting that the 1 nm diameter cylindrical silica nanopores likely exhibit nearly ideal semipermeable membrane transport properties.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Visual Analytics for Deep Embeddings of Large Scale Molecular Dynamics Simulations

Molecular Dynamics (MD) simulation have been emerging as an excellent candidate for understanding complex atomic and molecular scale mechanism of bio-molecules that control essential bio-physical phenomenon in a living organism. But this MD technique produces large-size and long-timescale data that are inherently high-dimensional and occupies many terabytes of data. Processing this immense amount of data in a meaningful way is becoming increasingly difficult. Therefore, specific dimensionality reduction algorithm using deep learning technique has been employed here to embed the high-dimensional data in a lower-dimension latent space that still preserves the inherent molecular characteristics i.e. retains biologically meaningful information. Subsequently, the results of the embedding models are visualized for model evaluation and analysis of the extracted underlying features. However, most of the existing visualizations for embeddings have limitations in evaluating the embedding models and understanding the complex simulation data. We propose an interactive visual analytics system for embeddings of MD simulations to not only evaluate and explain an embedding model but also analyze various characteristics of the simulations. Our system enables exploration and discovery of meaningful and semantic embedding results and supports the understanding and evaluation of results by the quantitatively described features of the MD simulations (even without specific labels).

Chae, Junghoon↗