Molecular Dynamics Simulation Code Research Articles

Layer-by-layer heteroepitaxial growth process of a BaO layer on SrTiO3(001) as investigated by molecular dynamics

Layer-by-layer heteroepitaxial growth processes of a BaO layer on SrTiO3(001) were simulated in order to predict an appropriate buffer layer for a YBa2Cu3O7−x(YBCO)/SrTiO3(001) heterojunction by using our crystal growth molecular dynamics (MD) simulation code. The SrTiO3(001) terminated by a TiO2 atomic plane was employed as the substrate in the present simulations. BaO molecules were continuously deposited on the SrTiO3(001) one by one, and finally a two-dimensional and epitaxial growth of a BaO layer was observed at 700 K. Moreover, the constructed BaO layer was atomically flat and smooth without defects, retaining a NaCl-type structure and (001) oriented configuration. However, the stress of the BaO/SrTiO3(001) heterojunction gradually increased and finally reached to approximately 1.2 GPa during the epitaxial growth process. It is expected that the large stress disturbs the subsequent fabrication of the uniform YBCO/SrTiO3(001) heterojunction. We also simulated the epitaxial growth process of a BaO layer on a [single SrO layer/SrTiO3(001)]. An atomically flat and smooth BaO layer without defects was also obtained at 700 K. Surprisingly, the stress of the BaO/[single SrO layer/SrTiO3(001)] heterojunction was almost 0.0 GPa after epitaxial growth. We have already suggested that [BaO layers/single SrO layer] are suitable buffer layers for the YBCO/SrTiO3(001) heterojunction on the basis of regular MD simulations [M. Kubo et al., Phys. Rev. B 56, 13535 (1997)]. From the present crystal growth simulations, we confirmed that the above atomically uniform and smooth BaO/SrO/SrTiO3(001) can be fabricated and almost no heterointerface stress was induced after the epitaxial growth. Moreover, the effect of substrate temperature on the heteroepitaxial growth process of the BaO layer on the SrO/SrTiO3(001) was discussed.

Molecular dynamics simulation on a layer-by-layer homoepitaxial growth process of SrTiO3(001)

The effect of substrate temperature on the homoepitaxial growth process of a SrTiO3(001) surface has been investigated using our crystal growth molecular dynamics simulation code. SrO molecules were continuously deposited one by one on the SrTiO3(001) surface terminated by TiO2 atomic plane at 300 K. Two-dimensional and epitaxial growth of a SrO thin layer was observed on the SrTiO3(001) surface retaining perovskite type structure and (001) oriented configuration. However, some defects were constructed in the grown film at a low temperature of 300 K, which is in significant contrast to that at 713 K. In the latter case, a single flat and smooth SrO layer was formed without any defects, which is in good agreement with the experimental results. The self-diffusion coefficient, activation energy for surface migration, and adsorption energy of the deposited SrO molecules on the SrTiO3(001) surface were discussed. A higher migration ability of the deposited SrO molecules at high temperature was found to lead to complete layer-by-layer homoepitaxial growth.

Characterization of Formation and Resolution Processes of Bone Collagen Microfibril by Molecular Structure Analysis.

The static and dynamic molecular structure analyses of the collagen microfibril were carried out by using the molecular mechanics (MM) and molecular dynamics (MD) simulation code, AMBER, which has been developed by Kollman et al. In this study, the characterization of collagen microfibril was performed by studying the difference between the formation process collagen (bonding model) and resolution process collagen (off-bonding model). The collagen microfibril was modeled by assembling collagen monomers, named Smith-Collagen. The formation and resolution mechanism is studied by MM and MD analyses in cases of peptide bonding and off-bonding between GLY 226-PRO 227 (Atom 1622 Atom 1623) of collagen molecule. The molecular mechanics analysis demonstrates that bonding model might be more stable as a whole and more active locally than off-bonding model. Further, the isothermal compressibility of off-bonding model is lower than bonding one. It means that the resolution of collagen molecule, which corresponds to the off-bonding, cause the higher rigidity and lose the activation ability. The molecular dynamics analysis reveals that the bonding model has the higher possibility of large scale structure change, especially at the biding part- the terminates between collagen units-. The microscale evaluations of static and dynamic micromechanical properties shows the stable and high dynamical function of the native bone structure.

Ab initio model potentials and their application to the thermal stability of metal clusters

A procedure is presented for finding a model potential for metal clusters with parameters fitted to ab initio energetic surfaces. The potential includes two-body, three-body and four-body interaction energies, each one consisting of exponential exchange and dispersion terms taken from perturbation theory up to the fourth order. The proposed potential and its first derivatives are incorporated in the molecular dynamics simulation code. The present approach is illustrated by constructing an ab initio model potential for the Ag 6 cluster and applying it in a thermal stability study of the pentagonal pyramid ( C 5 v ) isomer form of Ag 6.

A parallel molecular dynamics simulation code for dialkyl cationic surfactants

We have developed a new simulation code, COMFORT, for the study of assemblies of flexible surfactant molecules, structured for parallel execution and specialised to surfactants with dialkyl chain geometry. The approach is a hybrid domain-decomposition and systolic-loop algorithm which is suitable for systems composed of long chain molecules and with tens of thousands of atoms in total. The algorithm uses a modified Ewald technique for two dimensionally periodic systems which has been successfully parallelized. The code was designed to be highly portable between machines of different architectures. The code has been tested on a number of platforms including the Intel iPSC/860, the IBM SP1, the CRAY T3D, a SGI Power Challenge and a number of workstation clusters. We demonstrate that scalable parallel computing technology, combined with appropriate software, can provide a commercially viable simulation system for use in the exploration and development of surfactant assemblies.

Molecular Dynamics Simulations of a Siloxane-Based Liquid Crystal Using an Improved Fast Multipole Algorithm Implementation

AbstractIn our continuing efforts towards designing materials with controlled optical properties, largescale molecular dynamics simulations of a molecular cluster of a liquid crystalline cyclic siloxane are still limited by the size of the molecular system. Such simulations enable evaluation of the orientation order parameter of the system, as well as modelling the behavior of the material in bulk. This study summarizes improvements in the implementation of the fast multipole algorithm for computing electrostatic interactions which is included in the molecular dynamics program PMD[7, 8], such as the elimination of computations for empty cells and the use of optimal interaction lists. Moreover, an improved implementation of a 3-D Fast Multipole Method (FMM3D) based on the algorithm previously proposed[1, 2] is described in detail. The structure of the module, details of the expansions, parallelization, and its integration with the molecular dynamics simulation code are explained in detail. Finally, the utility of this approach in the study of liquid crystalline materials is briefly illustrated.

Low energy cluster impact simulated by molecular dynamics; angular distribution of sputtering yield and impact under various impact angles

The collision process of low energetic gold atoms and solid targets has been simulated using our molecular dynamics simulation code CLIMPACT II. The used algorithm is a third-order predictor Verlet algorithm [L. Verlet, Phys. Rev. 159 (1967) 98; W.F. van Gusteren and H.J.C. Berendsen, in: Molecular Liquids — Dynamics and Interfaces, A.J. Barnes et al., eds. (Reidel, 1984) p. 475.]. The iteration time step is continuously optimized by the program. About 50% of the total computer time is spent to integrate the motions during the first 100 fs of simulation time [B. Nitzschmann, Diploma thesis, Univ. of Oldenburg, Germany, 1992)]. When the crater formation ends and the motions in the target are slower, the step increases up to 20 times the start step size. Using this algorithm we are able to simulate a target of up to 10 5 particles. We use new nonreflecting boundary conditions. Only mechanical interactions are considered. The projectile can be chosen as a cluster with variable impact angle. Specifically the output yield under different impact angles and the distribution of the desorbed particles are presented and discussed. The temporal development of the desorption shows three distinct processes: an early explosive process, a surface ablation by an apparent surface shock wave, a final thermal evaporation.