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Register a new userHydrogenation and defect formation control the strength and ductility of MoS2 nanosheets: Reactive molecular dynamics simulation
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Two-dimensional (2D) molybdenum disulfide (MoS2) has attracted significant attention because of its outstanding properties, suitable for application in several critical technologies like, solar cells, photocatalysis, lithium-ion batteries, nanoelectronics, and electrocatalysis. Similar to graphene and other 2D materials, the physical and chemical properties of MoS2 can be tuned by the chemical functionalization and defects. In this investigation, our objective is to explore the mechanical properties of single-layer MoS2 functionalized by the hydrogen atoms. We moreover analyze the effects of different types of defects on the mechanical response of MoS2 at the room temperature. To investigate these systems, we conducted reactive molecular dynamics simulations using the ReaxFF forcefield. We demonstrate that an increase in the hydrogen adatoms or defects contents significantly affects the critical mechanical characteristics of MoS2, elastic modulus, tensile strength, stretchability and failure behavior. Our reactive molecular dynamics results provide useful information concerning the mechanical response of hydrogenated and defective MoS2 and the design of nanodevices.
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Hydrogenated diamond has been regarded as a promising material in electronic device applications, especially in field-effect transistors (FETs). However, the quality of diamond hydrogenation has not yet been established, nor has the specific orientation that would provide the optimum hydrogen coverage. In addition, most theoretical work in the literature use models with 100% hydrogenated diamond surfaces to study electronic properties, which is far from the experimentally observed hydrogen coverage. In this work, we have carried out a detailed study using fully atomistic reactive molecular dynamics (MD) simulations on low indices diamond surfaces i.e. (001), (013), (110), (113) and (111) to evaluate the quality and hydrogenation thresholds on different diamond surfaces and their possible effects on electronic properties. Our simulation results indicate that the 100% surface hydrogenation in these surfaces is hard to achieve because of the steric repulsion between the terminated hydrogen atoms. Among all the considered surfaces, the (001), (110), and (113) surfaces incorporate a larger number of hydrogen atoms and passivate the surface dangling bonds. Our results on hydrogen stability also suggest that these surfaces with optimum hydrogen coverage are robust under extreme conditions and could provide homogeneous p-type surface conductivity in the diamond surfaces, a key requirement for high-field, high-frequency device applications.
Curved fluid interfaces are investigated on the nanometre length scale by molecular dynamics simulation. Thereby, droplets surrounded by a metastable vapour phase are stabilized in the canonical ensemble. Analogous simulations are conducted for cylindrical menisci separating vapour and liquid phases under confinement in planar nanopores. Regarding the emergence of nanodroplets during nucleation, a non-equilibrium phenomenon, both the non-steady dynamics of condensation processes and stationary quantities related to supersaturated vapours are considered. Results for the truncated and shifted Lennard-Jones fluid and for mixtures of quadrupolar fluids confirm the applicability of the capillarity approximation and the classical nucleation theory.
Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine.
Ab initio molecular dynamics simulations using VASP was employed to calculate threshold displacement energies and defect formation energies of Y4Zr3O12 {delta}-phase, which is the most commonly found phase in newly developed Zr and Al-containing ODS steels. The Threshold displacement energy (Ed) values are determined to be 28 eV for Zr3a primary knock-on atom along [111] direction, 40 eV for Zr18f atoms along [111] direction and 50 eV for Y recoils along [110] direction. Minimum Ed values for O and O atoms are 13 eV and 16 eV respectively. The displacement energies of anions are much smaller compared to cations, thus suggesting that anion disorder is more probable than cation disorder. All directions except the direction in which inherent structural vacancies are aligned, cations tend to occupy another cation site. The threshold displacement energies are larger than that of Y2Ti2O7, the conventional precipitates in Ti containing ODS steels. Due to the partial occupancy of Y and Zr in the 18f position, the antisite formation energy is negligibly small, and it may help the structure to withstand more disorder upon irradiation. These results convey that Zr/Al ODS alloys, which have better corrosion resistance properties compared to the conventional Ti-ODS alloys, may also possess superior radiation resistance.
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further speedup the computations.
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