Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Molecular dynamics (MD) simulations are performed to study the interaction of His-tagged peptide with three different metal surfaces in explicit water. The equilibrium properties are analyzed by using pair correlation functions (PCF) to give an insight into the behavior of the peptide adsorption to metal surfaces in water solvent. The intermolecular interactions between peptide residues and the metal surfaces are evaluated. By pulling the peptide away from the peptide in the presence of solvent water, peeling forces are obtained and reveal the binding strength of peptide adsorption on nickel, copper and gold. From the analysis of the dynamics properties of the peptide interaction with the metal surfaces, it is shown that the affinity of peptide to Ni surface is the strongest, while on Cu and An the affinity is a little weaker. In MD simulations including metals, the His-tagged region interacts with the substrate to an extent greater than the other regions. The work presented here reveals various interactions between His-tagged peptide and Ni/Cu/Au surfaces. The interesting affinities and dynamical properties of the peptide are also derived. The results give predictions for the structure of His-tagged peptide adsorbing on three different metal surfaces and show the different affinities between them, which assist the understanding of how peptides behave on metal surfaces and of how designers select amino sequences in molecule devices design. (c) 2007 Elsevier Ltd. All rights reserved.

Computer simulation on the collision-sticking dynamics of two colloidal particles in an optical trap

Collisions of a particle pair induced by optical tweezers have been employed to study colloidal stability. In order to deepen insights regarding the collision-sticking dynamics of a particle pair in the optical trap that were observed in experimental approaches at the particle level, the authors carry out a Brownian dynamics simulation. In the simulation, various contributing factors, including the Derjaguin-Landau-Verwey-Overbeek interaction of particles, hydrodynamic interactions, optical trapping forces on the two particles, and the Brownian motion, were all taken into account. The simulation reproduces the tendencies of the accumulated sticking probability during the trapping duration for the trapped particle pair described in our previous study and provides an explanation for why the two entangled particles in the trap experience two different statuses. (c) 2007 American Institute of Physics.

A coupled model for multiphase fluid flow and sedimentation deformation in oil reservoir and its numerical simulation

A mathematical model for coupled multiphase fluid flow and sedimentation deformation is developed based on fluid-solid interaction mechanism. A finite difference-finite element numerical approach is presented. The results of an example show that the fluid-solid coupled effect has great influence on multiphase fluid flow and reservoir recovery performances, and the coupled model has practical significance for oilfield development.

Collective evolution characteristics and computer simulation of short fatigue cracks

Fatigue testing was conducted using a kind of triangular isostress specimen to obtain the short-fatigue-crack behaviour of a weld low-carbon steel. The experimental results show that short cracks continuously initiate at slip bands within ferrite grain domains and the crack number per unit area gradually increases with increasing number of fatigue cycles. The dispersed short cracks possess an orientation preference, which is associated with the crystalline orientation of the relevant slip system. Based on the observed collective characteristics, computer modelling was carried out to simulate the evolution process of initiation, propagation and coalescence of short cracks. The simulation provides progressive displays which imitate the appearance of experimental observations. The results of simulation indicate that the crack path possesses a stable value of fractal dimension whereas the critical value of percolation covers a wide datum band, suggesting that the collective evolution process of short cracks is sensitive to the pattern of crack site distribution.

Investigation on a simulation model of floating half zone convection .2. Experiment

A simulation model of floating half zone with non-uniform temperature distribution at the upper rod and uniform temperature distribution at lower rod was discussed by numerical investigation in a previous paper. In the present paper, the experimental investigation of the simulation model is given generally. The results of the present model show that the temperature profile is quite different and the critical applied temperature difference is lower than the one of usual model with same geometrical parameters in most cases. The features of critical Marangoni number depending on the liquid bridge volume are also different from the ones of usual model.

Two-dimensional fluid model simulation of bell jar top inductively coupled plasma

In the present paper, argon (Ar) plasmas in a bell jar inductively coupled plasma (ICP) source are systematically studied over pressures from 5 to 20 mtorr and power inputs from 0.2 to 0.5 kW. In this study, both a two-dimensional (2-D) fluid model simulation and global model calculation are compared, The 2-D fluid model simulation with a self-consistent power deposition is developed to describe the Ar plasma behavior as well as predict the plasma parameter distributions, Finally, a quantitative comparison between the global model and the fluid model is made to test their validity.

Numerical simulation of coherent structure in two-dimensional compressible mixing layers

The coherent structure in two-dimensional mixing layers is simulated numerically with the compressible Navier-Stokes equations. The Navier-Stokes equations are discretized with high-order accurate upwind compact schemes. The process of development of flow structure is presented: loss of stability, development of Kelvin-Helmholtz instability, rolling up and pairing. The time and space development of the plane mixing layer and influence of the compressibility are investigated.

Numerical investigation on a simulation model of floating zone convection

A simulation model with adiabatic condition at the upper rod and constant temperature at the lower rod is studied numerically in this paper. The temperature distribution in a simulation model is closer to the one in the half part of a floating full zone in comparison with the one in a usual floating half zone model with constant temperature at both rods, because the temperature distribution of a floating full zone is symmetric for the middle plane in a microgravity environment. The results of the simulation model show that the temperature profiles and the how patterns are different from those of the usual floating half zone model. Another type of half zone model, with a special non-uniform temperature distribution at the upper rod and constant temperature at the lower rod, has been suggested by recent experiments. The temperature boundary condition of the upper rod has a maximum value in the center and a lower value near the free surface. This modified simulation model is also simulated numerically in the present paper. Copyright (C)1996 Elsevier Science Ltd.

Numerical simulation of g-jitter effects on half floating zone convection under microgravity environment

The g-jitter effects on the thermocapillary convection in liquid bridge of floating half zone were studied by numerical simulation for unsteady and axi-symmetric model in the cylindrical coordinate system. The g-jitter field was given by a steady microgravity field in addition to an oscillatory low-gravity field, and the effects on the flow field, temperature distribution and free surface deformation were analyzed numerically.

Molecular dynamics simulation of interaction of a dislocation array from a crack tip with grain boundaries

The interaction of a dislocation array emitted from a crack tip under mode II loading with asymmetric tilt grain boundaries (GBs) is analysed by the molecular dynamics method. The GBs can generally be described by planar and linear matching zones and unmatching zones. All GBs are observed to emit dislocations. The GBs migrated easily due to their planar and linear matching structure and asymmetrical type. The diffusion induced by stress concentration is found to promote the GB migration. The transmissions of dislocations are either along the matched plane or along another plane depending on tilt angle theta. Alternate processes of stress concentration and stress relaxation take place ahead of the pileup. The stress concentration can be released either by transmission of dislocations, by atom diffusion along GBs, or by migration of GBs by formation of twinning bands. The simulated results also unequivocally demonstrate two processes, i.e. asymmetrical GBs evolving into symmetrical ones and unmatching zones evolving into matching ones during the loading process.

Two-dimensional simulation of inductive plasma sources with self-consistent power deposition

A time averaged two-dimensional fluid model including an electromagnetic module with self-consistent power deposition was developed to simulate the transport of a low pressure radio frequency inductively coupled plasma source. Comparsions with experiment and previous simulation results show, that the fluid model is feasible in a certain range of gas pressure. In addition, the effects of gas pressure and power input have been discussed.

Numerical simulation of axisymmetric unsteady incompressible flow by a vorticity-velocity method

A new numerical method for solving the axisymmetric unsteady incompressible Navier-Stokes equations using vorticity-velocity variables and a staggered grid is presented. The solution is advanced in time with an explicit two-stage Runge-Kutta method. At each stage a vector Poisson equation for velocity is solved. Some important aspects of staggering of the variable location, divergence-free correction to the velocity held by means of a suitably chosen scalar potential and numerical treatment of the vorticity boundary condition are examined. The axisymmetric spherical Couette flow between two concentric differentially rotating spheres is computed as an initial value problem. Comparison of the computational results using a staggered grid with those using a non-staggered grid shows that the staggered grid is superior to the non-staggered grid. The computed scenario of the transition from zero-vortex to two-vortex flow at moderate Reynolds number agrees with that simulated using a pseudospectral method, thus validating the temporal accuracy of our method.

Molecular dynamics simulation of crack-tip processes in copper

The crack tip processes in copper under mode II loading have been simulated by a molecular dynamics method. The nucleation, emission, dislocation free zone (DFZ) and pile-up of the dislocations are analyzed by using a suitable atom lattice configuration and Finnis & Sinclair potential. The simulated results show that the dislocation emitted always exhibits a dissociated fashion. The stress intensity factor for dislocation nucleation, DFZ and dissociated width of partial dislocations are strongly dependent on the loading rate. The stress distributions are in agreement with the elasticity solution before the dislocation emission, but are not in agreement after the emission. The dislocation can move at subsonic wave speed (less than the shear wave speed) or at transonic speed (greater than the shear wave speed but less than the longitudinal wave speed), but at the longitudinal wave speed the atom lattice breaks down.

Numerical simulation of evolution-induced catastrophe

A numerical simulation of damage evolution in a two-dimensional system of micocracks is presented. It reveals that the failure is induced by a cascade of coalescences of microcracks, and the fracture surface appears fractal. A model of evolution-induced catastrophe is introduced. The fractal dimension is found to be a function of evolution rule only. This result could qualitatively explain the correlation of fractal dimension and fracture toughness discovered in experiments.