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.

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。

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.

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.

可压剪切层线性稳定性特征直接数值模拟=Direct Simulation of the Linear Instabilities in Compressible Shear Layers

基于伪随机数生成技术促生白噪声扰动,以高精度迎风/对称紧致混合差分算法求解二维/三维非定常可压Navier-Stokes方程,揭示了可压自由剪切层初始剪切过程中扰动的线性演化特征,以及该过程对扰动波数和方向的内在选择性.验证了所用算法的有效性,表明线性理论同数值模拟相结合是可压剪切层研究的合理途径之一.

Simulation of Coal Combustion by AUSM Turbulence-Chemistry Char Combustion Model and a Full Two-Fluid Model

An algebraic unified second-order moment (AUSM) turbulence-chemistry model of char combustion is introduced in this paper, to calculate the effect of particle temperature fluctuation on char combustion. The AUSM model is used to simulate gas-particle flows, in coal combustion in a pulverized coal combustor, together with a full two-fluid model for reacting gas-particle flows and coal combustion, including the sub-models as the k-epsilon-k(p) two-phase turbulence niodel, the EBU-Arrhenius volatile and CO combustion model, and the six-flux radiation model. A new method for calculating particle mass flow rate is also used in this model to correct particle outflow rate and mass flow rate for inside sections, which can obey the principle of mass conservation for the particle phase and can also speed up the iterating convergence of the computation procedure effectively. The simulation results indicate that, the AUSM char combustion model is more preferable to the old char combustion model, since the later totally eliminate the influence of particle temperature fluctuation on char combustion rate.

Numerical simulation of temperature field evolution of metallic alloy surface due to pulsed laser treatment

This paper performed a numerical simulation on temperature field evolution for the surface layer of a metallic alloy subjected to pulsed Nd:YAG laser treatment. The enthalpy method was adopted to solve the moving boundary problem, I.e. Stefan problem. Computational results were obtained to show the temperature field evolution. Effects of latent heat and mushy zone width on the temperature field were investigated. The results also show very high values of temperature gradient and cooling rate, which are typical characteristics during the solidification process.