Splitting the fast and slow motions in molecular dynamics simulations based on the change of cold potential well bottom

Abstract. The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

Splitting the Fast and Slow Motions in Molecular Dynamics Simulations Based on the Change of Cold Potential Well Bottom

The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

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.

Formation of Fivefold Deformation Twins in Nanocrystalline Face-Centered-Cubic Copper Based on Molecular Dynamics Simulations

Fivefold deformation twins were reported recently to be observed in the experiment of the nanocrystalline face-centered-cubic metals and alloys. However, they were not predicted previously based on the molecular dynamics (MD) simulations and the reason was thought to be a uniaxial tension considered in the simulations. In the present investigation, through introducing pretwins in grain regions, using the MD simulations, the authors predict out the fivefold deformation twins in the grain regions of the nanocrystal grain cell, which undergoes a uniaxial tension. It is shown in their simulation results that series of Shockley partial dislocations emitted from grain boundaries provide sequential twining mechanism, which results in fivefold deformation twins. (c) 2006 American Institute of Physics.

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.

Correlative reference model and molecular dynamics simulation of dislocation emission process

A correlative reference model for computer molecular dynamics simulations is proposed. Based on this model, a flexible displacement boundary scheme is introduced and the dislocations emitted from a crack tip can continuously pass through the border of the inner discrete atomic region and pile up at the outer continuum region. The effect of the emitted dislocations within the plastic zone on the inner atomistic region can be clearly demonstrated. The simulations for a molybdinum crystal show that a full dislocation in a bcc crystal is dissociated into three partial dislocations and interaction between the crack and the emitted dislocations results in gradual decrease of the local stress intensity factor.

Molecular dynamics simulation of hydrogen enhancing dislocation emission

The interactive pair potential between Al and H is obtained based on the ab initio calculation and the Chen-Mobius 3D lattice inversion formula. By utilizing the pair potentials calculated, the effects of hydrogen on the dislocation emission from crack tip have been studied. The simulated result shows that hydrogen can reduce the cohesive strength for Al single crystal, and then the critical stress intensity factor for partial dislocation emission decreases from 0.11 MPa root m (C-H = 0) to 0.075 MPa root m (C-H=0.72%) and 0.06 MPa root m (C-H = 1.44%). This indicates thar hydrogen can enhance the dislocation emission. The simulation also shows that atoms of hydrogen can gather and turn into small bubbles, resulting in enhancement of the equilibrium vacancy concentration.

Molecular Dynamics Modeling of Diffusion Bonding

Molecular dynamics simulations on diffusion bonding of Cu-Ag showed that the thickness of the interfacial region depended on the stress. The interfacial region became amorphous during diffusion bonding, and it would normally transform from amorphous into crystalline structure when the structure was cooled to the room temperature.

Molecular Dynamics Simulation of the Uniaxial Tensile Deformation of Nanocrystalline Copper

纳米材料是由尺度在1～100 nm的微小颗粒组成的体系,由于它具有独特的性能而备受关注.本文简要地回顾了分子动力学在纳米材料研究中的应用,并运用它模拟了平均晶粒尺寸从1.79～5.38nm的纳米晶体的力学性质.模拟结果显示:随着晶粒尺寸的减小,系统与晶粒内部的原子平均能量升高,而晶界上则有所下降;纳米晶体的弹性模量要小于普通多晶体,并随着晶粒尺寸的减小而减小;纳米晶铜的强度随着晶粒的减小而减小,显示了反常的Hall-Petch效应;纳米晶体的塑性变形主要是通过晶界滑移与运动,以及晶粒的转动来实现的;位错运动起着次要的、有限的作用;在较大的应变下(约大于5%),位错运动开始起作用;这种作用随着晶粒尺寸的增加而愈加明显.

The Influence of Grain Size and Temperature on the mechanical Deformation of Nanocrystalline Materials: Molecular Dynamics Simulation

Nanocrystalline (nc) materials are characterized by a typical grain size of 1-100nm. The uniaxial tensile deformation of computer-generated nc samples, with several average grain sizes ranging from 5.38 to 1.79nm, is simulated by using molecular dynamics with the Finnis-Sinclair potential. The influence of grain size and temperature on the mechanical deformation is studied in this paper. The simulated nc samples show a reverse Hall-Petch effect. Grain boundary sliding and motion, as well as grain rotation are mainly responsible for the plastic deformation. At low temperatures, partial dislocation activities play a minor role during the deformation. This role begins to occur at the strain of 5%, and is progressively remarkable with increasing average grain size. However, at elevated temperatures no dislocation activity is detected, and the diffusion of grain boundaries may come into play.

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.

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.

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.