A variable charge molecular dynamics study of the initial stage of nickel oxidation

The oxidation of nickel single crystals is investigated by using variable charge molecular dynamics. The simulations are performed on three nickel low-index surfaces ((1 0 0), (1 1 0) and (1 1 1)) at temperatures between 300 K and 950 K. The results show that the shape of the oxidation kinetics is independent of the crystallographic orientation and the temperature under the present conditions. The oxide thin film grows according to an island growth mode, this initial stage of oxidation can be divided in three steps: (i) the dissociative chemisorption step (ii) the oxide island nucleation and (iii) the lateral growth of the island. The first step is slowdown/speedup by the surface orientation and temperature. Finally, the simulations show the onset of an oxide layer.     

Oxidation of nanocrystalline aluminum by variable charge molecular dynamics

We investigate the oxidation of nanocrystalline aluminum surfaces using molecular dynamics (MD) simulations with the variable charge model that allows charge dynamically transfer among atoms. The interaction potential between atoms is described by the electrostatic plus (Es+) potential model, which is composed of an embedded atom method potential and an electrostatic term. The simulations were performed from 300 to 750 K on polycrystalline samples with a mean grain size of 5 nanometers. We mainly focused on the effect of the temperature parameter on the oxidation kinetic. The results show that, beyond a first linear regime, the kinetics follows a direct logarithmic law (governed by diffusion process) and tends to a limiting value corresponding to a thickness of ∼3 nm. We also characterized at 600 K the effects of an external applied strain on the microstructure and the chemical composition of oxide films formed at the surface. In particular, we obtained a partially crystalline oxide films for all temperatures and we noticed a strong correlation between the degree of crystallinity of the oxide film and the oxidation temperature.     

Diffusion of adatoms and vacancies on otherwise perfect surfaces: A molecular dynamics study

Using computer simulation by the technique of molecular dynamics, we have investigated the influence of the terrace structure on the type and the dynamical aspects of atomic mechanisms for surface diffusion in fcc structure crystals. On the (100) terraces, vacancies are much more mobile than adatoms, while the opposite is true for (111) terraces. On the latter, vacancies migrate through the creation in their vicinity of paired, adatom-vacancy, defects. On the (100) face, the adatom jump length incrases with increasing temperature and reaches a value equal to several times the nearest neighbour distance. Adatoms are also fully delocalized on the (111) face and spend much more time in flight over the surface than by vibrations in the equilibrium sites. Large dynamical correlations are present in the vacancy movement on the (100) face and have been identified as new mechanisms of the defect migration by multiple jumps. On the (110) terrace, despite its anisotropic structure, two-dimensional diffusion takes place by an original atomic exchange mechanism. This mechanism has been identified to be the same as the one proposed by Halicioglu to explain two-dimensional diffusion on (110) Pt terraces, and recently corroborated by the FIM experiments of Wrigley and Ehrlich.     

Diffusion and growth of nickel,iron and magnesium adatoms on the aluminum truncated octahedron: A molecular dynamics simulation

The structure of nickel (Ni), iron (Fe), and magnesium (Mg) adatoms on the aluminum (Al) truncated octahedron is studied using molecular dynamics and the analytic embedded atom method. First, the energy barriers of several typical diffusion processes of Ni, Fe, and Mg adatoms on the Al truncated octahedral cluster were calculated using the nudged elastic band method. The calculated energy barriers were found to be related to the surface energy and atomic radius of the adatom and substrate atom. The result shows that the incorporation of Ni and Fe atoms into Al core easily occurs, and the Mg atom should segregate at the surface of the Al cluster. Thus, the growth of Ni, Fe and Mg on the Al truncated octahedron with 1289 atoms was simulated at several temperatures. In the Ni–Al and Fe–Al cases, the core-shell structure was not obtained. For the Mg–Al system, a good Mg shell on the Al core was found at lower temperatures, and an almost perfect truncated octahedron with more Al shells emerged with an increase in temperature.     

Diffusion of gases across lipid membranes with OmpA channel: a molecular dynamics study

Molecular transport across biological membranes occurs in a range of important chemical and biological processes. The biological membrane can usually be modelled as a phospholipid bilayer, but to correctly represent biological transport, the embedded transmembrane proteins must also be included. In previous molecular simulation studies on transport of small gas molecules in dipalmitoylphosphatidylcholine (DPPC) bilayer membrane, a coarse-grained model was used to provide direct insight into collective phenomena in biological membranes. Coarse graining allowed investigation of longer time and length scales by reducing the degrees of freedom and employing suitable potentials. In this work, membranes that include transmembrane proteins are modelled. This allows one to compare the molecular transport across a lipid membrane with and without the assistance of transmembrane channels. Outer membrane protein A (OmpA) – a porin from Escherichia coli with a small pore size – was chosen in this study because its detailed structure is known, it has high stability and is known to form a nonspecific diffusion channel that permits the penetration of various solutes. In this work the pore characteristics and interaction between lipid and protein were investigated and transport of water and other small gas molecules within the channel were studied. The MD simulation results obtained are compared with previous simulation results and available experimental data. The results obtained from this study will lead to better understanding of protein functionality and advance the development of biochips and drug delivery systems.     

Manipulation of biomolecules: A molecular dynamics study

With the rapid progression of bionanorobotics, manipulation of nano-scale biosamples is becoming increasingly attractive for different biological purposes. Nevertheless, the interaction between a robotic probe and a biological sample is poorly understood and the conditions for appropriate handling is not well-known. Here, we use the molecular dynamics (MD) simulation method to investigate the manipulation process when a nanoprobe tries to move a biosample on a substrate. For this purpose, we have used Ubiquitin (UBQ) as the biomolecule, a single-walled carbon nanotube (SWCNT) as the manipulation probe, and a double-layered graphene sheets as the substrate. A series of simulations were conducted to study the effects of different conditions on the success of the manipulation process. These conditions include the tip diameter, the vertical gap between the tip and substrate, and the initial orientation of the protein. Also we have studied two strategies for the manipulation of the protein by a nano-scale probe that we have named pushing and pulling. Interaction force between carbon nanotube (CNT) tips and the biomolecule, the root-mean-square deviation (RMSD), and the radius of gyration of the protein are monitored for different conditions. We found that larger tip diameters, smaller gaps between tip and substrate, and a pulling strategy increase the chance of a successful manipulation.     

Dielectrophoresis of nanocolloids: A molecular dynamics study

Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In this article we present, to our knowledge, the first molecular dynamics simulations of DEP of nanometer-sized colloidal particles. We introduce a simplified model for a polarizable nanoparticle, consisting of a large charged macroion and oppositely charged microions, in an explicit solvent. The model is then used to study DEP motion of the particle at different combinations of temperature and electric field strength. In accord with linear response theory, the particle drift velocities are shown to be proportional to the DEP force. Analysis of the colloid DEP mobility shows a clear time dependence, demonstrating the variation of friction under non-equilibrium. The time dependence of the mobility further results in an apparent weak variation of the DEP displacements with temperature.     

Twisting carbon nanotubes: A molecular dynamics study

We simulate the twist of carbon nanotubes using atomic molecular dynamic simulations. The ultimate twist angle per unit length and the deformation energy are calculated for nanotubes of different geometries. It is found that the thick tube is harder to be twisted while the thin tube exhibits higher ultimate twisting ratio. For multi-walled nanotubes, the zigzag tube is found to be able to stand more deformation than the armchair one. We observed the surface transformation during twisting. Formation of structural defects is observed prior to fracture.     

Growth of taylor vortices: A molecular dynamics study

Molecular dynamics methods have been used in a quantitative study of the growth and decay of Taylor vortices in a fluid confined between concentric cylinders when the rotation of the inner cylinder is instantaneously started or stopped. Analysis of the temporal evolution of the vortex flow fields shows that the behavior of this microscopic system agrees with experiment. In order to make the analysis entirely self-contained, torque measurements have been used to determine the effective viscosity of the fluid.     

非晶态石英的变电荷分子动力学模拟

基于迭代变电荷方法,用分子动力学模拟了非晶态石英的结构与振动特征.首先利用熔化-猝火方法得到了非晶石英的平衡结构.在此基础上获得了体系不同原子对之间的对关联函数、键角分布函数和振动频谱等,结果与实验数据均符合较好.变电荷方法的计算结果表明,非晶石英体系内粒子的电荷与石英晶体内粒子电荷显著不同,并且出现了较大的涨落. 关键词： 分子动力学 变电荷 非晶石英     

A molecular dynamics study on iridium

In this study, molecular dynamics simulations are performed by using a modified form of Morse potential function in the framework of the Embedded Atom Method (EAM). Temperature-and pressure-dependent behaviours of bulk modulus, second-order elastic constants (SOEC), and the linear-thermal expansion coefficient is calculated and compared with the available experimental data. The melting temperature is estimated from 3 different plots. The obtained results are in agreement with the available experimental findings for iridium.      

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.     

A molecular dynamics study of uranyl hydration

Molecular dynamics calculations were carried out in order to investigate the hydration structure of uranyl in aqueous solution. The CF1 model of flexible water molecules is used. This model allows one to investigate a hydrolysis reaction for water molecules in the first uranyl hydration shell. Charge redistribution effects on hydrolysis products are also taken into account. We found five ligands in uranyl hydration shell, which is of bipyramidal pentacoordinated structure. The charge redistribution effects resulted in ligands of four water molecules and one hydroxyl, which was found closer to uranium than the other ligands.     

Diffusion mechanism of hydrogen in amorphous silicon: ab initio molecular dynamics simulation

The mechanism of H migration in amorphous Si has remained an unresolved problem. The main issue is the small activation energy (1.5 eV) relative to the known strength of Si-H bonds (2-3.5 eV). We report first-principles finite-temperature simulations which demonstrate vividly that H is not released spontaneously, as proposed by most models, but awaits the arrival of a floating bond (FB). The "migrating species" is an FB-H complex, with H jumping from Si to Si and the FB literally floating around it. Migration stops when the FB veers away.