Molecular dynamics simulation on dislocation emission process

A correlative reference model for a computer simulation of molecular dynamics is proposed in this paper. Based on this model, a flexible displacement boundary scheme is naturally introduced and the dislocations emitted from a crack tip are presumed to continuously pass through the border of an inner discrete atomic region to pile up at an outer continuum region. The simulations for a Mo crystal show that the interaction between a crack and emitted dislocations results in the decrease in local stress intensity factor gradually.

Molecular Dynamics Simulation of Microstructure of Nanocrystalline Copper

The microstructure of computer generated nanocrystalline coppers is simulated by using molecular dynamics with the Finnis-Sinclair potential, analysed by means of radial distribution functions, coordination number, atomic energy and local crystalline order. The influence of the grain size on the nanocrystalline structure is studied. The results reveal that as the grain size is reduced, the grain boundary shows no significant structural difference, but the grain interior becomes more disordered, and their structural difference diminishes gradually; however, the density and the atomic average energy of the grain boundary present different tendencies from those of the grain interior.

Measurement and simulation of surface roughness noise using phased microphone arrays

A turbulent boundary-layer flow over a rough wall generates a dipole sound field as the near-field hydrodynamic disturbances in the turbulent boundary-layer scatter into radiated sound at small surface irregularities. In this paper, phased microphone arrays are applied to the measurement and simulation of surface roughness noise. The radiated sound from two rough plates and one smooth plate in an open jet is measured at three streamwise locations, and the beamforming source maps demonstrate the dipole directivity. Higher source strengths can be observed on the rough plates which also enhance the trailing-edge noise. A prediction scheme in previous theoretical work is used to describe the strength of a distribution of incoherent dipoles and to simulate the sound detected by the microphone array. Source maps of measurement and simulation exhibit satisfactory similarities in both source pattern and source strength, which confirms the dipole nature and the predicted magnitude of roughness noise. However, the simulations underestimate the streamwise gradient of the source strengths and overestimate the source strengths at the highest frequency. © 2008 Elsevier Ltd. All rights reserved.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

Modeling and Simulation of Liquid Pulsed Particulate Fluidized Beds

Pulsed fluidization is of considerable interest in process engineering for improving fluidization quality. Quantitative understanding of the pulsed two-phase flow behaviors is very important for proper design and optimum operation of such contactors. The

Numerical Simulation of 3D-Thermal Field with Phase Transformation

以激光熔凝表面强韧化处理为背景,应用空间的弹塑性有限单元和高精度的数值算法、同时考虑材料组织性能的变化来模拟材料的温度场。主要研究激光熔凝加工中瞬时温度场数值模拟,同时考虑相变潜热的影响,为第二步热应力场及残余应力的数值模拟做准备。最后用算例验证了模型的正确性,并给出了不同时刻温度场的分布。

Theoretical simulation studies of pulsed field magnetisation of (RE)BCO bulk superconductors

The magnetisation of bulk high temperature superconductors (HTS), such as RE-Ba-Cu-O [(RE)BCO, where RE is a rare earth element or Y], by a practical technique is essential for their application in high field, permanent magnet-like devices. Research to-date into the pulsed field magnetisation (PFM) of these materials, however, has been limited generally to experimental techniques, with relatively little progress in the development of theoretical models. This is because not only is a multi-physics approach needed to take account of the heating of the samples but also the high electric fields generated are well above the regime in which there are reliable experimental results. This paper describes a framework of theoretical simulation using the finite element method (FEM) that is applicable to both single- and multi-pulse magnetisation processes of (RE)BCO bulk superconductors. The model incorporates the heat equation and provides a convenient way of determining the distribution of trapped field, current density and temperature change within a bulk superconductor at each stage of the magnetisation process. An example of the single-pulse magnetisation of a (RE)BCO bulk is described. Potentially, the model may serve as a cost-effective tool for the optimisation of the bulk geometry and the magnetisation profile in multi-pulse magnetisation processes. © 2010 IOP Publishing Ltd.

Forced Dissociation of Selectin-ligand Complexes Using Steered Molecular Dynamics Simulation

Selectin-ligand interactions are crucial to such biological processes as inflammatory cascade or tumor metastasis. How transient formation and dissociation of selectin-ligand bonds in blood flow are coupled to molecular conformation at atomic level, however, has not been well understood. In this study, steered molecular dynamics (SMD) simulations were used to elucidate the intramolecular and intermolecular conformational evolutions involved in forced dissociation of three selectin-ligand systems: the construct consisting of P-selectin lectin (Lec) and epidermal growth factor (EGF)-like domains (P-LE) interacting with synthesized sulfoglycopeptide or SGP-3, P-LE with sialyl Lewis X (sLeX), and E-LE with sLeX. SMD simulations were based on newly built-up force field parameters including carbohydrate units and sulfated tyrosine(s) using an analogy approach. The simulations demonstrated that the complex dissociation was coupled to the molecular extension. While the intramolecular unraveling in P-LESGP-3 system mainly resulted from the destroy of the two anti-parallel sheets of EGF domain and the breakage of hydrogen-bond cluster at the Lec-EGF interface, the intermolecular dissociation was mainly determined by separation of fucose (FUC) from Ca2+ ion in all three systems. Conformational changes during forced dissociations depended on pulling velocities and forces, as well as on how the force was applied. This work provides an insight into better understanding of conformational changes and adhesive functionality of selectin-ligand interactions under external forces.

Numerical Simulation of Transient Thermal Field in Laser Melting Process

Numerical simulation of thermal field was studied in laser processing. The 3-D finite element model of transient thermal calculation is given by thermal conductive equation. The effects of phase transformation latent are considered. Numerical example is given to verify the model. Finally the real example of transient thermal field is given.

Molecular Dynamics Simulation of Thermal and Mechanical Properties of Polyimide-Carbon-Nanotube Composites

An aromatic polyimide and its mixture with randomly distributed carbon nanotubes (NTs) are simulated by using molecular dynamics, repeated energy minimization and cooling processes. The glass transition temperatures are identified through volume-temperature curves. Stress-strain curves, Young's moduli, densities and Poisson ratios are computed at different temperatures. It is demonstrated that the carbon NT reduces the softening effects of temperature on mechanical properties and increases the ability to resist deformation.

A detailed chemistry multi-cycle simulation of a gasoline fueled HCCI engine operated with NVO

A previously developed Stochastic Reactor Model (SRM) is used to simulate combustion in a four cylinder in-line four-stroke naturally aspirated direct injection Spark Ignition (SI) engine modified to run in Homogeneous Charge Compression Ignition (HCCI) mode with a Negative Valve Overlap (NVO). A portion of the fuel is injected during NVO to increase the cylinder temperature and enable HCCI combustion at a compression ratio of 12:1. The model is coupled with GT-Power, a one-dimensional engine simulation tool used for the open valve portion of the engine cycle. The SRM is used to model in-cylinder mixing, heat transfer and chemistry during the NVO and main combustion. Direct injection is simulated during NVO in order to predict heat release and internal Exhaust Gas Recycle (EGR) composition and mass. The NOx emissions and simulated pressure profiles match experimental data well, including the cyclic fluctuations. The model predicts combustion characteristics at different fuel split ratios and injection timings. The effect of fuel reforming on ignition timing is investigated along with the causes of cycle to cycle variations and unstable operation. A detailed flux analysis during NVO unearths interesting results regarding the effect of NOx on ignition timing compared with its effect during the main combustion. © 2009 SAE International.

Numerical Simulation of Pulsed Liquid Fluidized Bed and Its Experimental Validation

The pulsed liquid fluidized bed was studied using numerical simulation and experimental methods, The area-averaged two-fluid model (TFM) was used to simulate the pulsed fluidization. The bed expansion and collapse processes were simulated first and the phenomena obtained from the calculation were consistent with our previous experiments and observations. In the pulsed fluidization, the variation of bed height, the variations of particle velocity and concentration distribution were obtained and analyzed. Experiments were carried out to validate the simulation results. The pressure variation with time at different locations was measured using pressure transducers and compared with the simulated results. The variations of bed height and particle concentration distribution were recorded using a digital video camera recorder. The results were consistent with the simulation results as a whole.

Numerical Simulation on the Micro-Scale Bending Induced by Pulsed Laser Beam

利用自行研制的含热传导、冲击动力学大、变形有限元程序,模拟了小尺寸梁在脉冲激光加热条件下的变形过程。在此基础上,利用商用程序模拟了冷却及残余应力的产生,研究了激光参数（强度及分布）等对于微弯曲的影响。数值模拟结果与文献中的实验观察相吻合。

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated.We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard–Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.