Modeling the crystallization of a Ti–Al nanoparticle by the molecular dynamics method

Crystallization of the Ti–Al intermetallide in the process of cooling from a melt at a constant volume has been simulated numerically using the molecular dynamics method.     

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.     

Research on pyrolysis of toluene under microwave heating by using ReaxFF molecular dynamics simulations

ReaxFF molecular dynamics (MD) simulations are performed to study high-temperature pyrolysis of toluene under microwave heating. It is observed that the temperature of the reaction system under microwave heating has a rapidly rising stage, which is similar to the phenomenon of thermal runaway often appeared in reactions under microwave heating. Simulations indicate that the consumption rate of toluene and generating rates of H₂ and CH₄ obtained under microwave heating are always lower than those obtained under conventional heating at the early stage. Analyses of the pyrolysis of toluene show that ReaxFF MD simulations can provide an efficient way to study chemical reactions under microwave heating.     

Maxwell-Jüttner distributions in relativistic molecular dynamics

In relativistic kinetic theory, which underlies relativistic hydrodynamics, the molecular chaos hypothesis stands at the basis of the equilibrium Maxwell-J ttner probability distribution for the four-momentum p^α. We investigate the possibility of validating this hypothesis by means of microscopic relativistic dynamics. We do this by introducing a model of relativistic colliding particles, and studying its dynamics. We verify the validity of the molecular chaos hypothesis, and of the Maxwell-J ttner distributions for our model. Two linear relations between temperature and average kinetic energy are obtained in classical and ultrarelativistic regimes.     

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.     

Computational mechanics of molecular systems: Quantifying high-dimensional dynamics by distribution of Poincaré recurrence times

A framework that connects computational mechanics and molecular dynamics has been developed and described. As the key parts of the framework, the problem of symbolising molecular trajectory and the associated interrelation between microscopic phase space variables and macroscopic observables of the molecular system are considered. Following Shalizi and Moore, it is shown that causal states, the constituent parts of the main construct of computational mechanics, the ε-machine, define areas of the phase space that are optimal in the sense of transferring information from the micro-variables to the macro-observables. We have demonstrated that, based on the decay of their Poincare? return times, these areas can be divided into two classes that characterise the separation of the phase space into resonant and chaotic areas. The first class is characterised by predominantly short time returns, typical to quasi-periodic or periodic trajectories. This class includes a countable number of areas corresponding to resonances. The second class includes trajectories with chaotic behaviour characterised by the exponential decay of return times in accordance with the Poincare? theorem.     

How to identify dislocations in molecular dynamics simulations?

Dislocations are of great importance in revealing the underlying mechanisms of deformed solid crystals.With the development of computational facilities and technologies,the observations of dislocations at atomic level through numerical simulations are permitted.Molecular dynamics(MD)simulation suggests itself as a powerful tool for understanding and visualizing the creation of dislocations as well as the evolution of crystal defects.However,the numerical results from the large-scale MD simulations are not very illuminating by themselves and there exist various techniques for analyzing dislocations and the deformed crystal structures.Thus,it is a big challenge for the beginners in this community to choose a proper method to start their investigations.In this review,we summarized and discussed up to twelve existing structure characterization methods in MD simulations of deformed crystal solids.A comprehensive comparison was made between the advantages and disadvantages of these typical techniques.We also examined some of the recent advances in the dynamics of dislocations related to the hydraulic fracturing.It was found that the dislocation emission has a significant effect on the propagation and bifurcation of the crack tip in the hydraulic fracturing.     

Thermodynamic properties of gold–water nanofluids using molecular dynamics

Conflicts and discrepancies around nanoparticle (NP) size effect on the optical properties of metal NPs of sizes below the mean free path of electron can be traced to the internal damping effect of the hybrid resonance of the inner band (IB) and the conduction band (CB) electrons of the noble metals. We present a scheme to show how alternative mathematical formulation of the physics of interaction between the CB and the IB electrons of NP sizes <50?nm justifies this and resolves the conflicts. While a number of controversies exist between classical and quantum theories over the phenomenological factors to attribute to the NP size effect on the absorption bandwidth, this article shows that the bandwidth behavior can be well predicted from a different treatment of the IB damping effect, without invoking any of the controversial phenomenological factors. It finds that the IB damping effect is mainly frequency dependent and only partly size dependent and shows how its influence on the surface plasmon resonance can be modeled to show the influence of NP size on the absorption properties. Through the model, it is revealed that strong coupling of IB and CB electrons drastically alters the absorption spectra, splitting it into distinctive dipole and quadrupole modes and even introduce a behavioral switch. It finds a strong overlap between the IB and the CB absorptions for Au and Cu but not Ag, which is sensitive to the NP environment. The CB modes shift with the changing refractive index of the medium in a way that can allow their independent excitation, free of influence of the IB electrons. Through a hybrid of parameters, the model further finds that metal NP sizes can be established not only by their spectral absorption peak locations but also from a proper correlation of the peak location and the bandwidth (FWHM).     

Thermal transport property of investigated by molecular Ge34 and d-Ge dynamics and the Slack＇s equation

In this study, we evaluate the values of lattice thermal conductivity κL of type Ⅱ Ge clathrate （Ge34） and diamond phase Ge crystal （d-Ce） with the equilibrium molecular dynamics （EMD） method and the Slack＇s equation. The key parameters of the Slack＇s equation are derived from the thermodynamic properties obtained from the lattice dynamics （LD） calculations. The empirical Tersoff＇s potential is used in both EMD and LD simulations. The thermal conductivities of d-Ge calculated by both methods are in accordance with the experimental values. The predictions of the Slack＇s equation are consistent with the EMD results above 250 K for both Ge34 and d-Ge. In a temperature range of 200-1000 K, the κL value of d-Ge is about several times larger than that of Ge34.     

Study of mechanical properties of amorphous copper with molecular dynamics simulation

The formation and mechanical properties of amorphous copper are studied using molecular dynamics simulation. The simulations of tension and shearing show that more pronounced plasticity is found under shearing, compared to tension. Apparent strain hardening and strain rate effect are observed. Interestingly, the variations of number density of atoms during deformation indicate free volume creation, especially under higher strain rate. In particular, it is found that shear induced dilatation does appear in the amorphous metal.     

Investigation of molecular dynamics in β-carotene using femtosecond pump-FWM spectroscopy

We have carried out two different pump four-wave mixing experiments, combining an initial pump excitation and a subsequent four-wave mixing probe process, on the photosynthetic pigment β-carotene to reveal different aspects of its molecular dynamics after photoexcitation. Firstly, the pump degenerate four-wave mixing (pump -DFWM) technique, in which the DFWM is resonant with the S₁- to S _n -transition of β-carotene, is used to monitor the events following excitation of the system. The transient shows a peculiar shape and is seen to depend on the energy of the initial pump pulse as well as on the concentration of the solute in the solvent. Secondly, pump coherent anti-Stokes Raman scattering (pump-CARS) is used to elucidate the excited state vibrational dynamics of β-carotene. This technique gives access to the dynamics of both ground and excited electronic states with vibrational selectivity.     

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.     

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.     

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.     

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.     

Phonon relaxation and heat conduction in one-dimensional Fermiben Pastaben 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.     

Magnetic properties and relaxation dynamics of a frustrated Ni? molecular nanomagnet

The Ni? nanomagnet represents an ideal model system for investigating the effects of geometrical frustration in magnetic interactions. The Ni ions in the magnetic core are arranged on two corner-sharing tetrahedra and interact through antiferromagnetic exchange couplings. We show that the high degree of frustration leads to a magnetic energy spectrum with large degeneracies which result in unusual static and dynamical magnetic properties. In particular, the relaxation dynamics of the magnetization is characterized by several distinct characteristic times. We also discuss the possible interest of Ni? for magnetocaloric refrigeration.     

A novel fluid–wall heat transfer model for molecular dynamics simulations

The ‘fluid–wall thermal equilibrium model’, to numerically simulate heating/cooling of fluid atoms by wall atoms, is used to compare molecular dynamics simulation results to the analytical solution of 1-D heat equation. Liquid argon atoms are placed between two platinum walls and simultaneous heating and cooling is simulated at the walls. Temperature gradient in liquid argon is evaluated and the results are found to match well with the analytical solution showing the physical soundness of the proposed model. Additional simulations are done where liquid argon atoms are heated by both the walls for two different channel heights and it is shown that in such cases, heat transfer occurs at a faster rate than predicted by heat equation with decreasing channel heights.