Molecular dynamics simulations of nanopore processing in a graphene sheet by using gas cluster ion beam

The formation of a nanopore in a graphene sheet by collision with an argon cluster is simulated using molecular dynamics method. The number of removed carbon atoms and the size of the nanopore are obtained as a function of the kinetic energy of the cluster. In contrast to nanosculpting with a monomer ion beam, the size of the nanopore that is created by one shot of the cluster varies because of the variety of atom configuration. However, the mean size of the nanopore can be controlled over a wide range only by changing the kinetic energy of the cluster. This implies that the cleaning and processing of the graphene sheet may be realized simultaneously by changing the acceleration energy of the cluster.     

Thermal decomposition of the solid phase of nitromethane: ab initio molecular dynamics simulations

The Car-Parrinello molecular dynamics simulations were employed to investigate thermal decomposition of the solid nitromethane. It is found that it undergoes chemical decomposition at about 2200?K under ambient pressure. The initiation of reactions involves both proton transfer and commonly known C-N bond cleavage. About 75 species and 100 elementary reactions were observed with the final products being H2O, CO2, N2, and CNCNC. It represents the first complete simulation of solid-phase explosive reactions reported to date, which is of far-reaching implication for design and development of new energetic materials.     

Molecular dynamics simulations of laser-induced damage of nanostructures and solids

A theoretical approach to treat laser induced femtosecond structural changes in covalently bonded nanostructures and solids is described. Our approach consists in molecular dynamic simulations performed on the basis of time-dependent, many-body potential energy surfaces derived from tight-binding Hamiltonians. The shape and spectral composition of the laser pulse is explicitly taking into account in a non-perturbative way. We show a few examples of the application of this approach to describe the laser damage and healing of defects in carbon nanotubes with different chiralities and the ultrafast nonequilibrium melting of bulk germanium, initiated by the laser-induced softening and destabilization of transversal acoustic phonon modes.     

Simulation of α-Zr structural stability under pressure using the molecular dynamics method

The structural stability of α-Zr was studied using the molecular dynamics method in wide temperature and pressure ranges. The interatomic interaction was described by a pair potential calculated within the Animalu pseudopotential model. The potential parameters were selected using α-Zr phonon spectra. The features in the dynamics of the α-β and α-ω phase transitions at various temperatures and pressures were considered. The calculated hysteresis of forward and backward phase transitions and its pressure and temperature dependences are discussed. The data obtained were used to plot phase equilibrium lines in the P-T phase diagram.     

A molecular dynamics study of phase transformations in mono-crystalline Si under nanoindentation

A molecular dynamics (MD) simulation is adopted to examine the deformation behavior and phase transformation of mono-crystalline Si in nanoindentation with a spherical indenter. The techniques of coordination number and radial distribution function are used to monitor and elucidate the detailed mechanism of the phase transformation throughout the whole process in which the evolution of structural phase change and the relevant distributions of bonding length can be traced and exhibited. In this article, the phases of BC8 and R8, which have the same coordinate number as the phase Si-I and were difficult to distinguish from each other in previous studies, are successfully identified and extracted from the deformed region during unloading. Moreover, the effect of the indenter-radius size on the structural phase transformation of mono-crystalline Si for three different crystallographically oriented surfaces is investigated. It is found that the onset of the plastic deformation tends to take place only as the ratio of the indentation depth to the tip radius is larger than 0.7. Under this condition the structural phase transformation can be easily observed in the residual deformed region after unloading.     

Desolvation of polymers by ultrafast heating: Influence of hydrophilicity

Using molecular-dynamics simulation, we investigate the consequences of ultrafast laser-induced heating of a small water droplet containing a solvated polymer. Two polymers are studied: polyethylene as an example of a hydrophobic, and polyketone as an example of a hydrophilic polymer. In both cases, when the droplet is heated below the critical temperature of water, strong water evaporation is started, but the polymer remains in contact with a central water cluster. However, upon heating beyond the critical temperature, the hydrophilic polyethylene becomes completely desolvated, while polyketone still remains solvated. We analyze this behavior in terms of the intermolecular interactions and of the expansion dynamics of the heated droplet.     

Brittle and ductile fracture of semiconductor nanowires – molecular dynamics simulations

Fracture of silicon and germanium nanowires in tension at room temperature is studied by molecular dynamics simulations using several interatomic potential models. While some potentials predict brittle fracture initiated by crack nucleation from the surface, most potentials predict ductile fracture initiated by dislocation nucleation and slip. A simple parameter based on the ratio between the ideal tensile strength and the ideal shear strength is found to correlate very well with the observed brittle versus ductile behaviours for all the potentials used in this study. This parameter is then computed by ab initio methods, which predict brittle fracture at room temperature. A brittle-to-ductile transition (BDT) is observed in MD simulations at higher temperature. The BDT mechanism in semiconductor nanowires is different from that in the bulk, due to the lack of a pre-existing macrocrack that is always assumed in bulk BDT models.     

Processes of DNA condensation induced by multivalent cations： Approximate annealing experiments and molecular dynamics simulations

The condensation of DNA induced by spermine is studied by atomic force microscopy （AFM） and molecular dynamics （MD） simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics （SMD） simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA--cation complexes.     

Phonon relaxation and heat conduction in one-dimensional Fermi-Pasta-Ulam β lattices by molecular dynamics simulations

The phonon relaxation and heat conduction in one-dimensional Fermi-Pasta-Ulam (FPU) β lattices are studied by using molecular dynamics simulations.The phonon relaxation rate,which dominates the length dependence of the FPU β lattice,is first calculated from the energy autocorrelation function for different modes at various temperatures through equilibrium molecular dynamics simulations.We find that the relaxation rate as a function of wave number k is proportional to k 1.688,which leads to a N 0.41 divergence of the thermal conductivity in the framework of Green-Kubo relation.This is also in good agreement with the data obtained by non-equilibrium molecular dynamics simulations which estimate the length dependence exponent of the thermal conductivity as 0.415.Our results confirm the N 2/5 divergence in one-dimensional FPU β lattices.The effects of the heat flux on the thermal conductivity are also studied by imposing different temperature differences on the two ends of the lattices.We find that the thermal conductivity is insensitive to the heat flux under our simulation conditions.It implies that the linear response theory is applicable towards the heat conduction in one-dimensional FPU β lattices.     

Thermodynamic properties of gold–water nanolayer mixtures using molecular dynamics

The physical behavior of a fluid in contact with solid layers is still not fully understood. The present work focuses on the study and understanding of thermodynamic and structural properties of gold–water nanolayer mixtures using molecular dynamics simulations. Two different systems are considered, where approximately 1,700 water molecules are confined between gold nanolayers with separations of 7.4 and 6.2 nm, respectively. Novelties of the present work are in the use of accurate force fields for modeling the inter- and intra-molecular interactions of the components, and providing comprehensive thermodynamic properties of the mixtures. The results are validated by examination of the pure fluid and pure solid properties. Results indicate that the thermodynamics of the system does not behave as an ideal mixture. The structure of the pure fluid is also analyzed and compared against the structure of the confined fluid in the mixture. Anisotropicity is observed in the fluid structure close to the surface of the nanolayer. Higher ordering and higher flux are detected in the fluid molecules close to the fluid–solid interface. Unusual thermodynamic behavior, anisotropicity, liquid layering, and higher interfacial fluid flux could be just some of the factors leading to the enhanced energy transport observed in mixtures involving at least one nanoscale component, such as nanofluids.     

Comprehensive investigations of interaction properties of polylactic Acid‒Attapulgite composite by reactive molecular dynamics simulations and dispersion corrected DFT calculations

We have evaluated the interactive nature of attapulgite (ATB) and PLA (Poly (lactic acid)) by dispersion corrected density functional theory (DFT‒D2) calculations and reactive molecular dynamic (MD) simulations. Our DFT‒D2 findings revealed that PLA interacted strongly with pristine and calcined ATB surface with interaction energies of -4.706 and -10.101 eV, respectively. The accuracy of obtained interaction energies has been validated against the advanced second order Møller–Plesset level. Atom‒in‒molecule (AIM) analysis illustrated that the interactive nature was typical for the chemisorption (high polar and partially covalent) in PLA/calcined ATB and strong physisorption (hydrogen bonding) in PLA/pristine ATB system. Finally, reactive MD simulations at room temperature showed that as result of strong attraction between PLA and ATB surface a clear approaching and bonding procedure between O atom from PLA and H/Al atom of ATB was observed in pristine/calcined crystal.     

Measurements of cavitation bubble dynamics based on a beam-deflection probe

We present an optodynamic measurement of a laser-induced cavitation bubble and its oscillations based on a scanning technique using a laser beam-deflection probe. The deflection of the beam was detected with a fast quadrant photodiode which was built into the optical probe. The applied experimental setup enabled us to carry out one- or two-dimensional scanning of the cavitation bubble, automatic control of the experiment, data acquisition and data processing. Shadow photography was used as a comparative method during the experiments.     

Hardening of smooth pulsed laser deposited PMMA films by heating

Smooth poly(methyl methacrylate) (PMMA) films without any droplets were pulsed laser deposited at a wavelength of 248 nm and a laser fluence of 125 mJ/cm². After deposition at room temperature, the films possess low universal hardness of only 3 N/mm². Thermal treatments up to 200°C, either during deposition or afterwards, lead to film hardening up to values of 200 N/mm². Using a combination of complementary methods, two main mechanisms could be made responsible for this temperature induced hardening effect well above the glass transition temperature of 102°C. The first process is induced by the evaporation of chain fragments and low molecular mass material, which are present in the film due to the ablation process, leading to an increase of the average molecular mass and thus to hardening. The second mechanism can be seen in partial cross-linking of the polymer film as soon as chain scission occurs at higher temperatures and the mobility and reactivity of the polymer material is high enough.     

The characterisation of atomic structure and glass-forming ability of the Zr–Cu–Co metallic glasses studied by molecular dynamics simulations

In the present work, the glass formation process and structural properties of Zr₅₀Cu_50-xCo_x (0 ≤ x ≤ 50) bulk metallic glasses were investigated by a molecular dynamics simulation with the many body tight-binding potentials. The evolution of structure and glass formation process with temperature were discussed using the coordination number, the radial distribution functions, the volume–temperature curve, icosahedral short-range order, glass transition temperature, Voronoi analysis, Honeycutt–Andersen pair analysis technique and the distribution of bond–angles. Results indicate that adding Co causes similar responses on the nature of the Zr₅₀Cu_50-xCo_x (0 ≤ x ≤ 50) alloys except for higher glass transition temperature and ideal icosahedral type ordered local atomic environment. Also, the differences of the atomic radii play the key role in influencing the atomic structure of these alloys. Both Cu and Co atoms play a significant role in deciding the chemical and topological short-range orders of the Zr₅₀Cu_50-xCo_x ternary liquids and amorphous alloys. The glass-forming ability of these alloys is supported by the experimental observations reported in the literature up to now.     

Investigation of the superionic behaviour of BaF 2 ( x mol% LaF 3 ) by raman and brillouin scattering and molecular dynamics simulations

High temperature Raman and Brillouin light scattering experiments have been combined with molecular dynamics simulations to provide a comprehensive study of the superionic state of BaF 2 ( x v mol% LaF 3 ) over a particularly wide range of LaF 3 dopant concentrations from x =0 to 50. Room temperature Raman spectra for x =0, 5 and 10 show the usual T 2g symmetry mode at 241 v cm m 1 , but for samples with x =20, 30 and 50 the dominant Raman mode is at higher frequencies and of E g symmetry. The temperature dependence of the Raman line-widths show initial near linear increases followed by substantial increases above temperatures ( T c ) at 1200, 850, 800, 975, 950 and 920 v K for x =0, 5, 10, 20, 30 and 50. In the Brillouin scattering experiments, the acoustic modes respectively related to elastic constants C 11 and C 44 initially showed a quasi-linear decrease in frequency with increasing temperature. Above the same characteristic values of T c , where the Raman line-widths show marked increases, there are substantial decreases in the elastic constant C 11 for all samples with x =0 to 50. Only the doped samples showed significant decreases in C 44 at corresponding values of T c . Molecular dynamics (MD) simulations have been carried out on the same systems. From the calculated mean square displacements, the diffusion coefficients ( D ) of the mobile fluorine ions were calculated as a function of temperature for each of the samples. Substantial increases in the values of D occur above the respective values of T c determined in the light scattering experiments. The MD simulations also provide details of the mechanisms of diffusion of the mobile fluorine ions. The results emphasize the role of motional effects as an explanation of the mechanisms responsible and provide a self-consistent explanation of the dominant processes in the superionic phase of doped fluorites.     

Study of the effect of varying core diameter,shell thickness and strain velocity on the tensile properties of single crystals of Cu–Ag core–shell nanowire using molecular dynamics simulations

Core–shell type nanostructures show exceptional properties due to their unique structure having a central solid core of one type and an outer thin shell of another type which draw immense attention among researchers. In this study, molecular dynamics simulations are carried out on single crystals of copper–silver core–shell nanowires having wire diameter ranging from 9 to 30 nm with varying core diameter, shell thickness, and strain velocity. The tensile properties like yield strength, ultimate tensile strength, and Young’s modulus are studied and correlated by varying one parameter at a time and keeping the other two parameters constant. The results obtained for a fixed wire size and different strain velocities were extrapolated to calculate the tensile properties like yield strength and Young’s modulus at standard strain rate of 1 mm/min. The results show ultra-high tensile properties of copper–silver core–shell nanowires, several times than that of bulk copper and silver. These copper–silver core–shell nanowires can be used as a reinforcing agent in bulk metal matrix for developing ultra-high strength nanocomposites.     

Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6

In aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate how competing mechanisms can explain the seemingly contradictory statements about the structure and dynamics of ion-coordinated solvent in aqueous solutions of two interesting and technologically important electrolytes, NaBF₄ and NaPF₆. While the static structural data (i.e. radial, radial-angular and spatial distribution functions, as well as hydrogen bonding statistics) unequivocally point at very weak anion–water hydrogen bonding in both salts, dynamic analyses (in particular, orientational anisotropy decay and solvent residence times) reveal quite significant retardation of water rotation and mobility due to solute coordination. Additionally, rotational immobilisation of coordinated solvent molecules is clearly unrelated to the hydrogen bond strength between them, as demonstrated by the interatomic oxygen–oxygen distance distributions for coordinated and bulk water.     

Single-pulse drilling study on Au,Al and Ti alloy by using a picosecond laser

Picosecond laser single pulse ablation of Au, Al and Ti alloy (Ti6Al4V) was experimentally investigated with a laser pulse width of 10 ps at a wavelength of 1064 nm for potential industrial micromachining applications. The diameters, depths and morphologies of the drilled craters were studied. Two novel phenomena were found: as hole diameters decreased with fluence, a change of slope of the trend line indicated a change in ablation mechanism for Al and Ti alloy, metallic materials with short electron-phonon coupling times (<10 ps), while Au showed no such transition: an isolated island structure was also observed on Au due to significant melt expulsion. A one-dimensional two-temperature model has been used to discriminate different ablation phenomena. It is shown that metallic materials with different electron–phonon coupling constant have different ablation characteristics in the ps regime. This study could be very helpful for metallic material micromachining with high repetition rate ps lasers pulses which indicates that high throughput may be achieved as well as good machining quality.     

The investigation of solid–solid phase transformation at CuAlNi alloy using molecular dynamics simulation

In this study the thermodynamic and structural properties of a CuAlNi model alloy (3A) system were investigated using a molecular dynamics (MD) simulation method. The interactions between atoms were modelled by the Sutton-Chen embedded atom method (SCEAM) based on many-body interactions. It was observed that at the end of thermal process the thermo-elastic phase transformation occurred in the model alloy system. In order to analyse the structures obtained from MD simulation, techniques such as thermodynamic parameters and radial distribution function (RDF) were used. The local atomic order in the model alloy was analysed using Honeycutt–Andersen (HA) method.