Parameterizing a Simple Potential Energy Function Appropriate for Vibrational Frequencies Using Molecular Dynamics

A Maple scheme for quickly parameterizing vibrational potential energy functions is presented. As an example, the potential energy function's parameters for the vibrational motions in H_2O_2 are obtained assuming the simplest potential energy function. This paper was originally written as a research paper, but rejected by the referees. It is therefore being edited into an ``educational'' paper for student usage.

Molecular dynamics study of dynamic buckling properties of nanowires with defects

Based on the embedded atom method (EAM) and molecular dynamics (MD) method, the deformation properties of Cu nanowires with different single defects under dynamic compression have been studied. The mechanical behaviours of the perfect nanowire are first studied, and the critical stress decreases with the increase of the nanowire’s length, which is well agreed with the modified Euler theory. We then consider the effects to the buckling phenomenon resulted from different defects. It is found that obvious decrease of the critical stress is resulted from different defects, and the largest decrease is found in nanowire with the surface vertical defect. Surface defects are found exerting larger influence than internal defects. The buckling duration is found shortened due to different defects except the nanowire with surface horizon defect, which is also found possessing the largest deflection. Different deflections are also observed for different defected nanowires. It is find that due to surface defects, only deflection in one direction is happened, but for internal defects, more complex deflection circumstances are observed.

Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.

Subquadratic quantum number dependence and other anomalies of vibrational dephasing in liquid nitrogen: Molecular dynamics simulation study from the triple point to the critical point and beyond

Vibrational phase relaxation near gas-liquid and liquid-solid phase coexistence has been studied by molecular dynamics simulations of N-N stretch in N-2. Experimentally observed pronounced insensitivity of phase relaxation from the triple point to beyond the boiling point is found to originate from a competition between density relaxation and resonant-energy transfer terms. The sharp rise in relaxation rate near the critical point (CP) can be attributed at least partly to the sharp, rise in vibration-rotation coupling contribution. Substantial subquadratic quantum number dependence of overtone dephasing rate is found near the CP and in supercritical fluids. [S0031-9007 (99)09318-7].

Splitting the fast and slow motions in molecular dynamics simulations based on the change of cold potential well bottom

Abstract. The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

Splitting the Fast and Slow Motions in Molecular Dynamics Simulations Based on the Change of Cold Potential Well Bottom

The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

Mode-specific chemisorption of CH4 on Pt{110}-(1 x 2) explored by first-principles molecular dynamics

The chemisorption of CH4 on Pt{110}-(1 x 2) has been studied by vibrational analysis of the reaction pathway defined by the potential energy surface and, in time reversal, by first-principles molecular dynamics simulations of CH4 associative desorption, with the electronic structure treated explicitly using density functional theory. We find that the symmetric stretch vibration ν1 is strongly coupled to the reaction coordinate; our results therefore provide a firm theoretical basis for recently reported state-resolved reactivity measurements, which show that excitation of the ν1 normal mode is the most efficient way to enhance the reaction probability

Molecular Dynamics and the Diatomic Molecule as Harmonic Oscillator and Rigid Rotor

The HCl molecule is simulated (using Maple) in its dynamics, for both vibrational (and implied) rotational motions. A discussion of the center of mass transformations involved is part of the total presentation.

A coupled meshless technique/molecular dynamics approach for deformation characterization of monocrystalline metal

This paper presents a multiscale study using the coupled Meshless technique/Molecular Dynamics (M2) for exploring the deformation mechanism of mono-crystalline metal (focus on copper) under uniaxial tension. In M2, an advanced transition algorithm using transition particles is employed to ensure the compatibility of both displacements and their gradients, and an effective local quasi-continuum approach is also applied to obtain the equivalent continuum strain energy density based on the atomistic poentials and Cauchy-Born rule. The key parameters used in M2 are firstly investigated using a benchmark problem. Then M2 is applied to the multiscale simulation for a mono-crystalline copper bar. It has found that the mono-crystalline copper has very good elongation property, and the ultimate strength and Young's modulus are much higher than those obtained in macro-scale.

Molecular dynamics studies of the effects of branching characteristics on the crystalline structure of polyethylene

Molecular dynamics simulations were carried out on single chain models of linear low-density polyethylene in vacuum to study the effects of branch length, branch content, and branch distribution on the polymer’s crystalline structure at 300 K. The trans/gauche (t/g) ratios of the backbones of the modeled molecules were calculated and utilized to characterize their degree of crystallinity. The results show that the t/g ratio decreases with increasing branch content regardless of branch length and branch distribution, indicating that branch content is the key molecular parameter that controls the degree of crystallinity. Although t/g ratios of the models with the same branch content vary, they are of secondary importance. However, our data suggests that branch distribution (regular or random) has a significant effect on the degree of crystallinity for models containing 10 hexyl branches/1,000 backbone carbons. The fractions of branches that resided in the equilibrium crystalline structures of the models were also calculated. On average, 9.8% and 2.5% of the branches were found in the crystallites of the molecules with ethyl and hexyl branches while C13 NMR experiments showed that the respective probabilities of branch inclusion for ethyl and hexyl branches are 10% and 6% [Hosoda et al., Polymer 1990, 31, 1999–2005]. However, the degree of branch inclusion seems to be insensitive to the branch content and branch distribution.

Molecular dynamics investigation on edge stress and shape transition in graphene nanoribbons

Graphene nanoribbon (GNR) with free edges demonstrates unique pre-existing edge energy and edge stress, leading to non-flat morphologies. Using molecular dynamics (MD) methods, we evaluated edge energies as well as edge stresses for four different edge types, including regular edges (armchair and zigzag), armchair edge terminated with hydrogen and reconstructed armchair. The results showed that compressive stress exists in the regular and hydrogen-terminated edges along the edge direction. In contrast, the reconstructed armchair edge is generally subject to tension. Furthermore, we also investigated shape transition between flat and rippled configurations of GNRs with different free edges. It was found that the pre-existing stress at free edges can greatly influence the initial energy state and the shape transition.

Molecular dynamics simulation of fracture strength and morphology of defective graphene

Different types of defects can be introduced into graphene during material synthesis, and significantly influence the properties of graphene. In this work, we investigated the effects of structural defects, edge functionalisation and reconstruction on the fracture strength and morphology of graphene by molecular dynamics simulations. The minimum energy path analysis was conducted to investigate the formation of Stone-Wales defects. We also employed out-of-plane perturbation and energy minimization principle to study the possi-ble morphology of graphene nanoribbons with edge-termination. Our numerical results show that the fracture strength of graphene is dependent on defects and environmental temperature. However, pre-existing defects may be healed, resulting in strength recovery. Edge functionalization can induce compressive stress and ripples in the edge areas of gra-phene nanoribbons. On the other hand, edge reconstruction contributed to the tensile stress and curved shape in the graphene nanoribbons.

Insights into the nature of the coupling interactions between uracil corrosion inhibitors and copper : a DFT and molecular dynamics study

In this study, the nature of the coupling interactions between copper and uracil as well as its several derivatives has been systematically investigated employing the atoms in molecules (AIM) theory and energy decomposition analyses. The whole interaction process has been investigated through the analyses of the radial distribution functions of the Cu⋯X (X = S and O) contact on the basis of the ab initio molecular dynamics. No direct relationship between the adsorption strengths and inhibition efficiencies of the inhibitors has been observed. Additionally, the possibility of the methyl-substituted dithiouracil species to act as copper corrosion inhibitors has been tested.

Growth of C36-films on diamond surface through molecular dynamics simulation

In this paper, the initial stage of films assembled by energetic C36 fullerenes on diamond (001)–(2 × 1) surface at low-temperature was investigated by molecular dynamics simulation using the Brenner potential. The incident energy was first uniformly distributed within an energy interval 20–50 eV, which was known to be the optimum energy range for chemisorption of single C36 on diamond (001) surface. More than one hundred C36 cages were impacted one after the other onto the diamond surface by randomly selecting their orientation as well as the impact position relative to the surface. The growth of films was found to be in three-dimensional island mode, where the deposited C36 acted as building blocks. The study of film morphology shows that it retains the structure of a free C36 cage, which is consistent with Low Energy Cluster Beam Deposition (LECBD) experiments. The adlayer is composed of many C36-monomers as well as the covalently bonded C36 dimers and trimers which is quite different from that of C20 fullerene-assembled film, where a big polymerlike chain was observed due to the stronger interaction between C20 cages. In addition, the chemisorption probability of C36 fullerenes is decreased with increasing coverage because the interaction between these clusters is weaker than that between the cluster and the surface. When the incident energy is increased to 40–65 eV, the chemisorption probability is found to increased and more dimers and trimers as well as polymerlike-C36 were observed on the deposited films. Furthermore, C36 film also showed high thermal stability even when the temperature was raised to 1500 K.

Molecular dynamics simulation of structural characteristics in metal cluster deposition on surfaces

The deposition of small metal clusters (Cu, Au and Al) on f.c.c. metals (Cu, Au and Ni) has been studied by molecular dynamics simulation using Finnis–Sinclair (FS) potential. The impact energy varied from 0.01 to 10 eV/atom. First, the deposition of single cluster was simulated. We observed that, even at much lower energy, a small cluster with (Ih) icosahedral symmetry was reconstructed to match the substrate structure (f.c.c.) after deposition. Next, clusters were modeled to drop, one after the other, on the surface. The nanostructure was found by soft landing of Au clusters on Cu with increasing coverage, where interfacial energy dominates. While at relatively higher deposition energy (a few eV), the ordered f.c.c.-like structure was observed in the first adlayer of the film formed by Al clusters depositing on Ni substrate. This characteristic is mainly attributive to the ballistic collision. Our results indicate that the surface morphology synthesized by cluster deposition could be controlled by experimental parameters, which will be helpful for controlled design of nanostructure.