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.     

First-principles study on the doping effects of Al in α-MnO2

In this paper, first-principles calculations have been implemented to study the structural relaxation, formation energies and electronic structure of Al doped α-MnO₂. Both Al insertion and Al substitution reactions in the α-MnO₂ were considered. Calculated formation energies indicate that Mn atom is easier to be displaced by Al atom under the O-rich growth condition compared with Al insertion reaction. Besides, it can be found that Al doping can afford acceptor impurity level which can accommodate electrons, thus contributing to the improvement of conductivity of α-MnO₂. The conductivity of α-MnO₂ is gradually improved with the increasing doping concentration of Al, and Al_0.0417Mn_0.9583O₂ exhibits the best conductivity. Lastly, the electronic structure of Al_0.0417Mn_0.9583O₂ was further investigated by analysis of total charge density and Bader charge. It is clear that Al doping can afford more electrons for α-MnO₂, which also contributes to improvement of its conductivity.     

Interaction of point defects with twin boundaries in Au： A molecular dynamics study

The molecular dynamics simulation technique with many-body and semi-empirical potentials （based on the embedded atom method potentials） has been used to calculate the interactions of point defects with （1 1 1）, （1 1 3）, and （1 2 0） twin boundaries in Au at different temperatures. The interactions of single-, di-, and tri-vacancies （at on- and off-mirror sites） with the twin interfaces at 300 K are calculated. All vacancy clusters are favorable at the on-mirror arrangement near the （1 1 3） twin boundary. Single- and di-vacancies are more favorable at the on-mirror sites near the （1 1 l） twin boundary, while they are favorable at the oft-mirror sites near the （1 2 0） twin boundary. Almost all vacancy clusters energetically prefer to lie in planes closest to the interface rather than away from it, except for tri-vacancies near the （1 2 0） interface at the off-mirror site and for 3.3 and 3.4 vacancy clusters at both sites near the （1 1 1） interface, which are favorable away from the interface. The interaction energy is high at high temperatures.     

Effect of electrolyte concentration on DNA A—B conformational transition:An unrestrained molecular dynamics simulation study

<正>The DNA conformational transition depends on both the DNA sequences and environment such as solvent as well as electrolyte in the solution.This paper uses the AMBER8 package to investigate the electrolyte concentration influence on the dynamics of the A→B conformational transition of DNA duplex d(CGCGAATTCGCG)_2.The results from the restrained molecular dynamics(MD) simulations indicate that the total energies of the systems for A-DNA are always higher than those for B-DNA,and that the A→B conformational transition in aqueous NaCl solution is a downhill process.The results from the unrestrained MD simulations,as judged by the average distance between the C5' atoms(average helical rise per ten base pair),show that the concentrated NaCl solution slows down the A→B conformational transition.This observation can be well understood by analyses of the difference between the counterion distributions around A-DNA and B-DNA.     

Lowest energy structures of self-interstitial atom clusters in α-iron from a combination of Langevin molecular dynamics and the basin-hopping technique

A combination of simulated annealing with Langevin molecular dynamics and the basin-hopping with occasional jumping (BHOJ) technique was used to systematically determine the most stable configurations of self-interstitial atom (SIA) clusters I _n (n = 1–38) in α-iron. In addition to the original BHOJ technique, we introduced an additional long jumping process in which a randomly selected less-bounded atom is moved to a neighbouring site of another SIA in the cluster to enhance the probability of locating the global minimum structure. With the obtained putative lowest energy structures, the binding energies as a function of cluster size were estimated. We also determined the sizes of particular stable clusters based on their geometrical symmetry. Furthermore, the values were extrapolated based on accurately determined formation energies, and are available for immediate use in kinetic Monte Carlo or rate theory models.     

Lattice thermal conductivity of δ-graphyne — A molecular dynamics study

Thermal conductivity of δ-graphyne was investigated using reverse non-equilibrium molecular dynamics simulations. The dependence of the thermal conductivities with the temperature, acetylenic linkages, and external strain were explained by the phonon density of states. Our simulations revealed that as the temperature increased, the thermal conductivity of graphene first increased and then decreased, whereas that of δ-graphyne monotonically decreased. Owing to the presence of the acetylenic linkages, a significant reduction was found in the thermal conductivity of δ-graphyne, which resulted in a phonon vibration mismatch or weakened coupling. Moreover, the temperature profile changed from mono linear to the ladder the number of acetylenic linkages increased. These results play a guidance role in the design and application of thermoelectrics devices using 2D carbon materials.     

Experimental study on terahertz radiation

In this letter, we describe a coherent subpicosecond terahertz (THz) spectroscopy system based on non-resonant optical rectification for the generation of THz radiation. We studied the two-photon absorption (TPA) of ZnTe induced by femtosecond laser pulses via THz generation, and its influence on the generation of THz radiation. Experimental results demonstrated that the intensity of pump beam against TPA must be traded off to get an optimum generation of THz radiation. As an example, we measured absorption spectrum of water vapor by time-domain spectroscopy (TDS) in the frequency range from 0.5 to 2.5 THz with a high overall accuracy.     

Coil-to-globule transition of thermo-responsive γ-substituted poly (ɛ-caprolactone) in water: A molecular dynamics simulation study

The coil-to-globule behavior of poly{γ-2-[2-(2methoxyethoxy)ethoxy]ethoxy-3-caprolactone} (PMEEECL) as a γ-substituted poly (ɛ-caprolactone) was investigated via atomistic molecular dynamics (MD) simulation. For this purpose, radius of gyration, end-to-end distance and radial distribution function of the chain in the presence of water were calculated. Consequently, the lower critical solution temperature (LCST) of PMEEECL chain at which the coil-to-globule transition takes place, was determined in each calculated parameter curve. The simulation results indicated that the LCST of PMEEECL was occurred at close to 320 K, which is in a good agreement with previous experimental results. Additionally, the appearance of sudden change in both Flory-Huggins interaction parameter (χ) and interaction energy between the PMEEECL chain and water molecules at about 320 K confirmed the calculated LCST result. The radial distribution function (RDF) results showed that the affinity of the PMEEECL side chain to water molecules is lower than its backbone.     

Diffusion activation energy versus the favourable energy in two-order-parameter model:A molecular dynamics study of liquid Al

In the present work, we find that both diffusion activation energy E_a(D) and E_a(S^ex) increase linearly with pressure and have the same slope (0.022±0.001 eV/GPa) for liquid Al. The temperature and pressure dependence of excess entropy is well fitted by the expression -S^ex(T,P)/k_B=a(P)+b(P)T+c(P)exp(E_f/k_BT), which together with the small ratio of E_f/k_BT leads to the relationship of excess entropy to temperature and pressure, i.e. S^ex≈-cE_f/T, where c is about 12 and E_f (=Δ E-PΔV) is the favourable energy. Therefore, there exists a simple relation between E_a(S^ex) and E_f, i.e. E_a(S^ex)≈cE_f.     

Femtosecond laser ablation of metals:a molecular dynamics simulation study

Using molecular dynamics (MD) methods combining with two-step radiation heating model, the mechanisms of ablation and the thermodynamic states at Ni surface under femtosecond laser irradiation are investigated. Simulation results show that the main mechanisms of ablation are evaporation and tensile stresses generated inside the target. The velocity of stress wave is predicted to be nearly equal to sound velocity. The rates of ablation at different fluences obtained from simulations are in good agreement with experimental data.     

Lattice dynamics and ordering effects in high-concentrated α′-NbD x -alloys

The phonon dispersion of NbD _x (0.57≦x≦0.77) in [110]-direction has been determined by inelastic neutron scattering after in situ loading of the sample. Two quasioptical excitations with Γ-point frequencies of ν=3.8 THz and ν=4.2 THz, respectively, are observed along with a threefold splitting of the longitudinal acoustic branch. At the zone boundary two of these branches are getting soft when increasing the deuterium concentration. The elastic constants extracted from the initial slopes of acoustic phonon branches exhibit an anomalous behavior in the concentration range under consideration.     

Influence of ion–ion correlation on Na+ transport in Na2Ni2TeO6: molecular dynamics study

Molecular dynamics (MD) study of Na⁺ transport in Na₂Ni₂TeO₆ is performed systematically with varying strength of Na⁺–Na⁺ short range repulsions to understand the physical principle governing ion transport mechanism. Na⁺ diffusion is enhanced by nearly an order of magnitude with reduced Na⁺–Na⁺ short range repulsion within the studied range. A similar behavior is also observed in other systems, e.g., AgI and Na₂Zn₂TeO₆, where mobile ions are located closely. The Na⁺ ion occupancy in Na₂Ni₂TeO₆ shows a significant shift from Na1 to Na2 sites gaining some degree of correlation. The study also emphasizes how mobile ion size influences the ionic diffusion. The fresh insight such as microscopic migration pathways, energy barriers, and jumping mechanism of Na⁺ are derived from the study.     

Effect of water–methanol content on the structure of Nafion in the sandwich model and solvent dynamics in nano-channels; a molecular dynamics study

Continuing an ongoing study, molecular dynamics (MD) simulations were performed to investigate the effects of methanol concentration on Nafion morphology, such as the size of solvent cluster, solvent location, and polymer structure via the sandwich model. Our survey shows that high methanol concentrations resulted in increment of solvent cluster size in Nafion membrane. The sulfonic acid clusters also befall much in order as subsequent layers of such ionic clusters are formed. The number of neighbouring hydronium ions around a sulfur atom is independent of methanol concentration, but the first shell of hydronium and water around sulfonic acid clusters is broader. Although methanol would prefer to interact with water molecules rather than sulfonic acid groups, gathering of methanol molecules via hydrophobic self-aggregation is preferred. Methanol is located closer to the hydrophobic part of the polymer than water, while water is located closer to the hydrophilic part of the polymer. It was found that methanol distributes specifically more than water in nano-channels. Investigation of solvent dynamics in nano-channels shows that diffusion coefficients (D) of water, methanol, and hydronium decrease with increasing methanol concentration and they may be ordered as follows: D _Water?>?D _Methanol?>?D _Hydronium (D _Water?≈?1.6–2.0D _Methanol and D _Methanol?≈?2.1–3.0D _Hydronium).     

A VQ study on diatone in Putonghua

1IntroductionIthasbeenbelievedthatthetonemodelofwordisthebasisoftheintonationmodel,thoughtherearestillsomeargumentsontheintonationmodelsinPutonghua.Inaddition,mostoftheChinesewordsaredisyllables,whichisabout80%ofthetotalChineselexiconstatistically,andmostofwhicharederivativeandcompoundwords.Fromthepointofviewofphonetics,thereare15diatones,exceptthosewithaneutralizedtone.ThebasicphoneticmodelsofdiatonesaregivenbyWu[1]andthepitChvariationmodels,thloughtheacousticandstatisticstudyoffundamentalf…     

A theoretical study of substitution effects on halogen–π interactions

Ab initio calculations are performed to analyse the existence of intermolecular halogen···π interactions in NCX complexes with YC≡CY, where X = Cl, Br and Y = H, CN, F, Cl, OH, NH₂, and CH₃. Molecular geometries and interaction energies of the complexes are investigated at the MP2/aug-cc-pVTZ level of theory. Our results indicate that the interaction energies for the NCX···YC≡CY complexes lie in the range between ?0.5 and ?5.9 kcal/mol. The physical nature of the interactions is studied using symmetry-adapted perturbation theory (SAPT). The stability of the X···π interactions is predicted to be attributable mainly to electrostatic and dispersion effects.