Molecular dynamics simulation of peeling a DNA molecule on substrate

Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.The project supported by the Distinguished Young Scholar Fund of NSFC (10225209) and key project from the Chinese Academy of Sciences (KJCX2-SW-L2)     

Burnett simulations of gas flow in microchannels

The Burnett equations with slip boundary conditions are used to model the gas flow in microchannels in transition flow regime. As the Navier-Stokes equations are not appropriate to model the gas flow in this regime, the higher-order Burnett equations are adopted in the present study. In earlier studies, convergent solutions of the Burnett equations of microPoiseuille flow could only be obtained when Knudsen number is less than 0.2. By using a relaxation method on the boundary values, convergent solutions of the Burnett equations can be obtained even when Knudsen number reaches 0.4. The solutions of Burnett equations agree very well with experimental data and direct simulation Monte Carlo (DSMC) results. The pressure distributions and velocity profiles are then discussed in detail.     

Molecular dynamics simulation of deformation and failure of nanocrystals of bcc metals

Simulations of uniaxial and hydrostatic tension of Fe and Mo nanocrystal are made by molecular dynamics method. Stress versus strain are obtained while regularities of lattice rearrangement during nanocrystal plastic deformation are considered. Local instability of nanocrystal lattice, which is the cause for transition from elastic to plastic deformation of nanocrystal, is found. It is shown that local shear stresses is a driving force of nanocrystal lattice rearrangements under the conditions of both uniaxial and hydrostatic tension, so, local instability of nanocrystal of bcc metals should be considered as shear instability. Realization of “orthorhombic” path of deformation at 1 0 0 tension of Mo nanocrystal is specific case of above effect. It is demonstrated that unlike covalent nanocrystal, metallic nanocrystals display “heterogeneous” mechanism of crack nucleation, which essence is that cracks nucleate not in homogeneous elastically deformed lattice but in shear bands or near their boundaries, i.e., after non-homogeneous plastic deformation of nanocrystal.     

Molecular dynamics study on mechanics of metal nanowire

The new concept of using nanowires as building blocks for logic and memory circuits makes it very necessary to fully understand the mechanical behaviors of these nanowires. Embedded-atom method is employed to carry out three-dimensional molecular dynamics simulations of the mechanical properties of rectangular cross-section copper nanowire. A stable free-relaxation state and the stress–strain relation of nanowire under extension are obtained. The elastic modulus, yielding strength and deformation are studied. The surface effect, size effect, and temperature effect on the extension property of metal nanowire are discussed in detail. The simulation results from our present work show that at nanoscale surface atoms play an important role on the mechanical behaviors of nano-structures. This study of mechanical properties of metal nanowires will be helpful to the design, manufacture and manipulation of nano-devices.     

Brownian dynamics simulation of rodlike polymers under shear flow

The highly nonlinear behaviors of rodlike polymers in nematic phase under shear flow are studied with Brownian dynamics simulation. The LebwohlLasher nematogen model is taken as the prototype of the simulation and the mean-field approximation is avoided. By considering the nearest-neighbor intermolecular interaction, the spatial orientational correlation is introduced and therefore the spatial inhomogeneity such as the multiple-domain effect can automatically be incorporated. The transient order parameters, birefringence axes, shear stresses and first normal stress differences are calculated. The important finding of this work is that the director wagging and damped oscillation share the same molecular origin as director tumbling. The only difference is that the system is split into micro-domains which tumble with different phase angles in the wagging and damped oscillation regimes. The tumbling of the director of the whole system is suppressed due to the spatial inhomogeneity of director fields and then the damped oscillation of macroscopic stresses becomes predominant. The negative first normal stress difference exists at moderate shear rates, where both elasticity and viscosity play important role. Our simulation results including some dimensionless scaling parameters find good agreement with experimental observations in literature.     

Squeeze flow of soft solids between rough surfaces

Newtonian liquids and non-Newtonian soft solids were squeezed between parallel glass plates by a constant force F applied at time t=0. The plate separation h(t) and the squeeze-rate were measured for different amplitudes of plate roughness in the range 0.3–31 m. Newtonian liquids obeyed the relation Vh ³ of Stephan (1874) for large plate separations. Departures from this relation that occurred when h approached the roughness amplitude were attributed to radial liquid permeation through the rough region. Most non-Newtonian materials showed boundary-slip that varied with roughness amplitude. Some showed slip that varied strongly during the squeezing process. Perfect slip (zero boundary shear stress) was not approached by any material, even when squeezed by optically-polished plates. If the plates had sufficient roughness amplitude (e.g. about 30 m), boundary slip was practically absent, and the dependence of V on h was close to that predicted by no-slip theory of a Herschel-Bulkley fluid in squeeze flow (Covey and Stanmore 1981, Adams et al. 1994).     

Molecular dynamics simulation of the role of dislocations in microcrack healing

The molecular dynamics method is used to simulate microcrack healing during heating or/and under compressive stress. A centre microcrack in Cu crystal would be sealed under compressive stress or by heating. The role of compressive stress and heating in crack healing was additive. During microcrack healing, dislocation generation and motion occurred. When there were pre-existing dislocations around the microcrack, the critical temperature or compressive stress necessary for microcrack healing would decrease, and, the higher the number of dislocations, the lower the critical temperature or compressive stress. The critical temperature necessary for microcrack healing depended upon the orientation of the crack plane. For example, the critical temperature for the crack along the (001) plane was the lowest, i.e. 770K. The project supported by the Special Fund for the Major State Basic Research Projects (No. G19990650) and by the National Natural Science Foundation of China (No. 19891180, 59871010)     

Molecular dynamics simulations of DFZ

Dislocation emission from the crack tip in copper under mode II loading is simulated with molecular dynamics method. After 26 partial dislocations are emitted and then relaxed to reach the equilibrium under the constant displacement, the double pile-ups (including an inverse pile-up and a pile-up) are formed. i.e., the first dislocation is piled up before the obstruction, and the last dislocation is piled up ahead of the crack tip. These results conform to the TEM observations. The project supported by the National Natural Science Foundation of China     

Direct simulation of fluid flow with cellular automata and the lattice-Boltzmann equation

With the invention of the Hexagonal Lattice Gas it was hoped that this new technique would facilitate direct simulation of turbulent flow. In the past years, however, we have learned about its barriers on numerical accuracy and computational efficiency, which cannot easily be taken. The work on lattice gases has evolved in the introduction of the lattice-Boltzmann scheme. With the appropriate refinements this scheme provides the essential balance between robustness and numerical accuracy and enables us to simulate three-dimensional time-dependent flows at Reynolds numbers up to 50000.     

Effect of random longitudinal vibrations on the Poiseuille flow of a complex liquid

In this work, the rectilinear Poiseuille flow of a complex liquid flowing in a vibrating pipe is analyzed. The pipe wall performs oscillations of small amplitude that can be adequately represented by a weakly stochastic process, for which a quasi-static perturbation solution scheme is suggested. The flow is analyzed using the Bautista–Manero–Puig constitutive equation, consisting on the upper-convected Maxwell equation coupled to a kinetic equation to account for the breakdown and reformation of the fluid structure. A drastic enhancement of the volumetric flow is predicted in the region where the fluid experiences pronounced shear-thinning. Finally, flow enhancement is predicted using experimental data reported elsewhere for wormlike micellar solutions of cetyl trimethyl ammonium tosilate.     

Determination of statistically reliable transport diffusivities from molecular dynamics simulation

Using molecular dynamics simulations we determine the composition dependence of the self-diffusivity and transport diffusivity of a methane/ethane mixture at high pressure. We compute the transport diffusivity in two ways. First, the transport diffusivity is generated from the simulated self-diffusivities using an approximation known as the Darken equation. Second, the transport diffusivity is generated from the simulated phenomenological coefficients, based upon linear irreversible thermodynamics (LIT). We discuss the relative advantages of the two methods in terms of: (i) accuracy and (ii) computational demands of the approach. We find that the Darken equation gives values of the transport diffusivity within 6% of the more rigorous approach and is subject to substantially less statistical error with less computational effort. We find that the mean and standard deviation of the transport diffusivity obtained from linear irreversible thermodynamics are strong functions of the implementation of the infinite-time limit required in the evaluation. We suggest and implement an algorithm for statistically reliable transport diffusivities from molecular dynamics simulations.     

Slip and no-slip squeezing flow of liquid food in a wedge

Squeezing flow in a wedge simulates a number of practical processes, e.g. lubrication, coating and the sensory evaluation of liquid foods. This paper reports analytical approximate solutions for both slip (or lubricated) and no-slip squeezing flow of liquid food in a wedge, in which the power law fluid model was used. The solutions do not seem to be more complex than that for squeezing flow between two parallel disks and may be used as a variation of the psycho-physical models of in-mouth viscosity and food spreadability. Alternatively, a rheometer for testing liquid foods may be developed according to the equations described in this paper.     

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. The project supported by the National Natural Science Foundation of China     

Near-wall measurements of turbulence statistics in a fully developed channel flow with a novel laser Doppler velocity profile sensor

This paper reports on the measurements of the near-wall turbulence statistics in a fully developed channel flow. The flow measurements were carried out with a novel laser Doppler velocity profile sensor with a high spatial resolution. The sensor provides both the information of velocity and position of individual tracer particles inside the measurement volume. Hence, it yields the velocity profile inside the measurement volume, in principle, without the sensor being mechanically traversed. Two sensor systems were realized with different techniques. Typically the sensor has a relative accuracy of velocity measurement of 10⁻³ and the spatial resolution of a few micrometers inside the measurement volume of about 500 μm long. The streamwise velocity was measured with two independent sensor systems at three different Reynolds number conditions. The resulting turbulence statistics show a good agreement with available data of direct numerical simulations up to fourth order moment. This demonstrates the velocity profile sensor to be one of the promising techniques for turbulent flow research with the advantage of a spatial resolution more than one magnitude higher than a conventional laser Doppler technique.     

Molecular dynamics investigation of patterning via cold welding

We perform a series of molecular dynamics simulations of a subtractive cold-welding patterning process. The effects of film thickness and work of adhesion between the thin film and substrate are examined. For small works of adhesion, the film elastically debonds from the substrate before the onset of plastic deformation inside the film during stamp retraction. A simple model is proposed to describe the debonding and deformation of the film. The model provides an analytical framework that describes the playoff between adhesion, yield strength, and film thickness in determining the debond length of the film induced by stamp retraction.     

Numerical simulation of pore-scale flow in chemical flooding process

Chemical flooding is one of the effective technologies to increase oil recovery of petroleum reservoirs after water flooding. Above the scale of representative elementary volume (REV), phenomenological modeling and numerical simulations of chemical flooding have been reported in literatures, but the studies alike are rarely conducted at the pore-scale, at which the effects of physicochemical hydrodynamics are hardly resolved either by experimental observations or by traditional continuum-based simulations. In this paper, dissipative particle dynamics (DPD), one of mesoscopic fluid particle methods, is introduced to simulate the pore-scale flow in chemical flooding processes. The theoretical background, mathematical formulation and numerical approach of DPD are presented. The plane Poiseuille flow is used to illustrate the accuracy of the DPD simulation, and then the processes of polymer flooding through an oil-wet throat and a water-wet throat are studies, respectively. The selected parameters of those simulations are given in details. These preliminary results show the potential of this novel method for modeling the physicochemical hydrodynamics at the pore scale in the area of chemical enhanced oil recovery.     

原子尺度摩擦行为的分子动力学模拟

应用大规模分子动力学方法,模拟了具有原子级光滑和原子级粗糙形貌的刚性球形探头与弹性平面基体的干摩擦行为,研究了无/有粘附条件下的载荷与摩擦力、载荷与真实接触面积,以及摩擦力与真实接触面积之间的关系,对纳米尺度下的摩擦行为规律进行了分析.几种系统的真实接触面积-载荷关系都与相应的连续力学接触模型定性的一致,它们分别是Hertz光滑表面接触模型、Greenwood-Williamson粗糙表面接触模型和Mau-gis Dugdale粘着接触模型.无论是由光滑表面还是粗糙表面构成的摩擦系统,在无粘附条件下摩擦力与载荷成正比,而摩擦力与真实接触面积之间没有一个简单的关系;在粘附条件下摩擦力与真实接触面积成正比,而摩擦力与载荷之间表现为Maugis Dugdale模型预测的亚线性关系.研究表明,当表面作用从无粘附到粘附时,控制摩擦力的决定因素从载荷转变为接触面积,摩擦行为从载荷控制摩擦转变为粘着控制摩擦.