Multiple time step molecular dynamics simulation for interaction between dislocations and grain boundaries

A multiple time step algorithm, called reversible reference system propagator algorithm, is introduced for the long time molecular dynamics simulation. In contrast to the conventional algorithms, the multiple time method has better convergence, stability and efficiency. The method is validated by simulating free relaxation and the hypervelocity impact of nano-clusters. The time efficiency of the multiple time step method enables us to investigate the long time interaction between lattice dislocations and low-angle grain boundaries.The project supported by the National Natural Science Foundation of China (the 973 Project 2004CB619304).     

Coarse grained molecular dynamics and theoretical studies of carbon nanotubes entering cell membrane

Motivated by recent experimental observations that carbon nanotubes （CNT） can enter animal cells, here we conduct coarse grained molecular dynamics and theoretical studies of the intrinsic interaction mechanisms between CNT＇s and lipid bilayer. The results indicate that CNT-cell interaction is dominated by van der Waals and hydrophobic forces, and that CNT＇s with sufficiently small radii can directly pierce through cell membrane while larger tubes tend to enter cell via a wrapping mechanism. Theoretical models are proposed to explain the observed size effect in transition of entry mechanisms.     

Multiscale coupling of molecular dynamics and peridynamics

We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the “supercell” developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy–Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.     

Carbopol gels: Elastoviscoplastic and slippery glasses made of individual swollen sponges: Meso- and macroscopic properties,constitutive equations and scaling laws

This paper gives details of new data on neutralized Carbopol 940 dispersions. Appropriate techniques have been used to characterize the physical properties of the bulk gel and inter-phase slip at the wall. Previously published data are analysed and used wherever possible. Terminology and measurement difficulties are also addressed.     

Amorphous and crystalline states of ultrasoft colloids: a molecular dynamics study

In this work, we study the temperature-induced development of “dynamically arrested” states in dense suspensions of “soft colloids” (multi-arm star polymers and/or block-copolymers micelles) by means of molecular dynamics (MD) simulations. Temperature increase in marginal solvents results in “soft sphere” swelling, dynamical arrest, and eventually crystallization. However, two distinct “dynamically arrested” states were found, one almost amorphous (“glassy”) and one with a considerable degree of crystallinity, yet lower than that of the fully equilibrated crystal. It is remarkable that even that latter state permitted self-diffusion in the timescale of the simulations, an effect that underlies the importance of the “ultra-soft” nature of inter-particle potential. The “number of connections” criterion for crystallinity proved to be very successful in identifying the ultimate thermodynamic trend from the very early stages of the α-relaxation. This paper was presented at the Third Annual Rheology Conference, AERC 2006, April 27–29, 2006, Crete, Greece.     

Size effects in indentation response of thin films at the nanoscale: A molecular dynamics study

The indentation response of Ni thin films of thicknesses in the nanoscale was studied using molecular dynamics simulations with embedded atom method (EAM) interatomic potentials. A series of simulations were performed in films in the [1 1 1] orientation with thicknesses varying from 4 to 12.8 nm. The study included both single crystal films and films containing low angle grain boundaries perpendicular to the film surface. The simulation results for single crystal films show that as film thickness decreases larger forces are required for similar indentation depths but the contact stress necessary to emit the first dislocation under the indenter is nearly independent of film thickness. The low angle grain boundaries can act as dislocation sources under indentation. The mechanism of preferred dislocation emission from these boundaries operates at stresses that are lower as the film thickness increases and is not active for the thinnest films tested. These results are interpreted in terms of a simple model.     

Coarse-grained simulation of molecular mechanisms of recovery in thermally activated shape-memory polymers

Thermally actuated shape-memory polymers (SMPs) are capable of being programmed into a temporary shape and then recovering their permanent reference shape upon exposure to heat, which facilitates a phase transition that allows dramatic increase in molecular mobility. Experimental, analytical, and computational studies have established empirical relations of the thermomechanical behavior of SMPs that have been instrumental in device design. However, the underlying mechanisms of the recovery behavior and dependence on polymer microstructure remain to be fully understood for copolymer systems. This presents an opportunity for bottom-up studies through molecular modeling; however, the limited time-scales of atomistic simulations prohibit the study of key performance metrics pertaining to recovery. In order to elucidate the effects of phase fraction, recovery temperature, and deformation temperature on shape recovery, here we investigate the shape-memory behavior in a copolymer model with coarse-grained potentials using a two-phase molecular model that reproduces physical crosslinking. Our simulation protocol allows observation of upwards of 90% strain recovery in some cases, at time-scales that are on the order of the timescale of the relevant relaxation mechanism (stress relaxation in the unentangled soft-phase). Partial disintegration of the glassy phase during mechanical deformation is found to contribute to irrecoverable strain. Temperature dependence of the recovery indicates nearly full elastic recovery above the trigger temperature, which is near the glass-transition temperature of the rubbery switching matrix. We find that the trigger temperature is also directly correlated with the deformation temperature, indicating that deformation temperature influences the recovery temperatures required to obtain a given amount of shape recovery, until the plateau regions overlap above the transition region. Increasing the fraction of glassy phase results in higher strain recovery at low to intermediate temperatures, a widening of the transition region, and an eventual crossover at high temperatures. Our results corroborate experimental findings on shape-memory behavior and provide new insight into factors governing deformation recovery that can be leveraged in biomaterials design. The established computational methodology can be extended in straightforward ways to investigate the effects of monomer chemistry, low-molecular-weight solvents, physical and chemical crosslinking, different phase-separation morphologies, and more complicated mechanical deformation toward predictive modeling capabilities for stimuli-responsive polymers.     

纳米镍板裂纹扩展的分子动力学模拟和宏微观分析

建立了半无限弹性纳米镍板Ⅰ型裂纹扩展的二维分子动力学计算模型。采用镶嵌原子法描述原子间作用,模拟了纳观裂纹区在远场常应变率作用下变化直至起始扩展的过程。同时基于原子势函数和二维正三角形晶格常数计算材料弹性参数,进行连续介质力学断裂分析。分子动力学模拟和宏微观分析均得到裂纹起始扩展的临界时刻、裂尖应力场和原子平均能量。二者的结果比较表明本文的二维简化模型和模拟方法可以准确地描述Ⅰ型裂纹扩展的物理本质,基于原子势函数和晶格常数的连续介质力学分析也是一种可行的研究纳米材料断裂的方法。     

Analysis of semi-classical potentials for molecular dynamics and Monte Carlo simulations of warm dense matter

Effective, semi-classical potentials may present a powerful tool for the determination of properties of warm dense matter, systems characterized by both moderate coupling and moderate degeneracy. However, this requires the use of these potentials in a regime where the approximations employed in their derivation begin to break down. This work presents a careful analysis of the methodology and approximations used to derive semi-classical potentials for Coulomb systems. Particular attention is paid to the appearance of many-body effects and the techniques that may be used to model them. Analytical arguments and simple examples indicate that the role of many-body effects cannot be ignored in the warm dense matter regime, and those semi-classical Coulomb potentials that focus on the pair interaction do not adequately treat many-body effects.     

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.     

固体塑性实验室时间尺度的分子动力学模拟概述

随着超级计算机软硬件的飞速提升,基于经验势函数的分子动力学模拟在解析固体塑性的微观机制方面发挥着关键作用.但是,由于传统分子动力学基于牛顿运动方程数值积分,积分时间步长通常为飞秒量级,其模拟的时间尺度通常限于纳秒量级,从而为模拟长时间尺度固体塑性机制带来了巨大的挑战.本文从分子动力学模拟的时间尺度限制切入,介绍目前国际...     

Size and temperature effects on the fracture mechanisms of silicon nanowires: Molecular dynamics simulations

We present molecular dynamics simulations of [1 1 0]-oriented Si nanowires (NWs) under a constant strain rate in tension until failure, using the modified embedded-atom-method (MEAM) potential. The fracture behavior of the NWs depends on both temperature and NW diameter. For NWs of diameter larger than 4 nm, cleavage fracture on the transverse (1 1 0) plane are predominantly observed at temperatures below 1000 K. At higher temperatures, the same NWs shear extensively on inclined {1 1 1} planes prior to fracture, analogous to the brittle-to-ductile transition (BDT) in bulk Si. Surprisingly, NWs with diameter less than 4 nm fail by shear regardless of temperature. Detailed analysis reveals that cleavage fracture is initiated by the nucleation of a crack, while shear failure is initiated by the nucleation of a dislocation, both from the surface. While dislocation mobility is believed to be the controlling factor of BDT in bulk Si, our analysis showed that the change of failure mechanism in Si NWs with decreasing diameters is nucleation controlled. Our results are compared with a recent in situ tensile experiment of Si NWs showing ductile failure at room temperature.     

基于粗粒化分子动力学的自由水与水化硅酸钙孔隙水冻结模拟

水化硅酸钙是水泥基材料的主要水化产物,其孔隙内的水分是影响水泥基材料抗冻性的主要因素。本文基于粗粒化分子动力学方法研究水化硅酸钙孔隙水的冻结机制,针对水的粗粒化P₄粒子和水化硅酸钙胶体颗粒,建立了水化硅酸钙孔隙水的冻结模型。根据此模型计算了不同孔径孔隙水冰点,分析了水泥基材料孔径孔隙在冻融破坏中的危害程度;模拟得到了水化硅酸钙孔隙内水的冻结分布特征和密度分布特征。研究工作表明,本文建立的模型有效提高了分子动力学模拟水化硅酸钙孔隙水冻结问题的规模,为后续进行水泥基材料的冻融破坏分析提供了研究基础。     

聚合物粘结剂PVP、PAM和PVA结构与性能的分子动力学研究

在粉末打印骨支架的工艺中,粘结剂的性质是影响骨支架质量的关键因素。采用分子动力学的模拟方法对三种常用高分子粘结剂的体系进行了构建和模拟,从微观分子层面研究了聚合物粘结剂PVP,PAM和PVA的部分性质,比如密度、内聚能及力学性能,并对三种粘结剂的性能参数进行了比较,对其内在关系进行了揭示。此外,还通过建立粘结剂与羟基磷灰石的界面相互作用模型,对三种粘结剂与羟基磷灰石的界面结合能进行了计算和比较,分析了影响高聚物粘结特性的根本原因。这一工作不仅对常用粘结剂的基本性质进行了预估,而且对骨支架粉末粘结工艺中粘结剂的选择提供了理论依据。     

Coupling the finite element method and molecular dynamics in the framework of the heterogeneous multiscale method for quasi-static isothermal problems

Multiscale models are designed to handle problems with different length scales and time scales in a suitable and efficient manner. Such problems include inelastic deformation or failure of materials. In particular, hierarchical multiscale methods are computationally powerful as no direct coupling between the scales is given. This paper proposes a hierarchical two-scale setting appropriate for isothermal quasi-static problems: a macroscale treated by continuum mechanics and the finite element method and a microscale modelled by a canonical ensemble of statistical mechanics solved with molecular dynamics. This model will be implemented into the framework of the heterogeneous multiscale method. The focus is laid on an efficient coupling of the macro- and micro-solvers. An iterative solution algorithm presents the macroscopic solver, which invokes for each iteration an atomistic computation. As the microscopic computation is considered to be very time consuming, two optimisation strategies are proposed. Firstly, the macroscopic solver is chosen to reduce the number of required iterations to a minimum. Secondly, the number of time steps used for the time average on the microscale will be increased with each iteration. As a result, the molecular dynamics cell will be allowed to reach its state of thermodynamic equilibrium only in the last macroscopic iteration step. In the preceding iteration steps, the molecular dynamics cell will reach a state close to equilibrium by using considerably fewer microscopic time steps. This adapted number of microsteps will result in an accelerated algorithm (aFE-MD-HMM) obtaining the same accuracy of results at significantly reduced computational cost. Numerical examples demonstrate the performance of the proposed scheme.     

分子模拟在非常规油气开发中的应用

非常规油气资源储量丰富,具有广阔的开发前景.我国低渗/特低渗油藏以陆相沉积为主,储层特征差异性大,孔喉细小,孔隙度低,可动原油气大量储集于亚微米孔隙中,开采难度大,采收率低.岩油界面微观力学作用和限域传质力学机理是其中的关键科学问题.近年来,分子模拟技术在非常规油气开采的研究领域已经成为一种重要的研究手段.本文介绍了分...     

Flow of linear molecules through a 4:1:4 contraction–expansion using non-equilibrium molecular dynamics: Extensional rheology and pressure drop

In this work, non-equilibrium molecular dynamics simulations are used to generate the flow of linear polymer chains (monomer-springs with FENE potential) and a Lennard–Jones fluid (Newtonian fluid) through a contraction–expansion (4:1:4) geometry. An external force field simulating a constant pressure gradient upstream the contraction region induces the flow, where the confining action of the walls is represented by a Lennard–Jones potential. The equations of motion are solved through a multiple-step integration algorithm coupled to a Nosé-Hoover dynamics [S. Nose, A unified formulation of the constant temperature molecular dynamics methods, J. Chem. Phys. 81 (1984) 511–519], i.e., to simulate a thermostat, which maintains a constant temperature. In this investigation, we assume that the energy removed by the thermostat is related to the viscous dissipation along the contraction–expansion geometry. A non-linear increasing function between the pressure drop and the mean velocity along the contraction for the linear molecules is found, being an order of magnitude larger than that predicted for the Lennard–Jones fluid. The pressure drop of both systems (the linear molecules and Lennard–Jones fluid) is related to the dissipated energy at the contraction entry. The large deformation that the linear molecules experience and the evolution of the normal stress at the contraction entry follow a different trajectory in the relaxation process past the contraction, generating large hysteresis loops. The area enclosed by these cycles is related to the dissipated energy. Large shear stresses developed near the re-entrant corners as well as the vortex formation, dependent on the Deborah number, are also predicted at the exit of the contraction. To our knowledge, for the first time, the excessive pressure losses found in experimental contraction flows can be explained theoretically.     

A study on the measurement of mean velocity and its convergence in molecular dynamics simulations

In many particle‐based simulations, measurement of local mean flow velocity and other continuum‐based properties are of utmost importance. Macroscopic quantities, such as mean flow velocity, temperature, and density, can be estimated by averaging the corresponding microscopic behavior of the particles. The two main subjects that should be considered in the averaging over the particles in a specific problem are spatial and temporal behaviors of them. In this paper, we study the latter. Because of the chaotic nature of the collisions among the molecules and consequently their random path, extracted macroscopic values fluctuate about their average values causing statistical errors. In this paper, an averaging method called SAM‐Modified‐CAM (SMC) will be proposed for the measurement of mean velocity that reduces statistical errors in its calculation. This proposal is based on the study conducted here on the implementations of two common averaging methods, sample‐averaged measurement (SAM) and cumulative average measurement (CAM) in molecular dynamics. In addition, convergence of mean flow velocity measurement is thoroughly discussed, and a convergence criterion is proposed for this purpose. Implementation of the proposed method in different test cases has approved its reliable performance. Copyright © 2010 John Wiley & Sons, Ltd.     

Molecular dynamics studies on the local disordering of Σ3 and Σ11 grain boundaries in aluminium bicrystal

Molecular dynamics (MD) simulations using Morse interaction potential are performed in studies of [110] symmetrical tilt grain boundary (GB) structures with mis-orientation angles 50.5°(Σ11), 129.5°(Σ11), 70.5°(Σ3) and 109.5°(Σ3) at various tempratures. The GB structures are found to start local disordering at about 0.5T _m (T _m is the melting point of aluminium) for 50.5°(Σ11), 0.32T _m for 129.5° (Σ11) and 0.38T _m for 70.5°(Σ3), respectively. These results agree with conclusions deduced from the anelastic measurements. But, for twin-boundary structure 109.5°(Σ3), this disordering has not been found even when temperature increases up to 0.9T _m . The project supported by the National Natural Science Foundation of China and Laboratory for Non-linear Mechanics of Continuous Media, Institute of Mechanics, Academia Sinica.