模拟聚乙烯块体相变和导热的粗粒化模型和势场建立EI北大核心CSCD

建立适用于介观尺度聚乙烯块体相变和导热分子模拟的粗粒化模型及势场,并对其进行验证。基于全原子分子动力学模拟结果,采用多态-迭代玻尔兹曼变换法进行粗粒化分子动力学模拟来获得粗粒化势场。结果表明:粗粒化势场采用函数形式的势能描述,易于使用;对比全原子模拟结果,粗粒化势场能够较准确地模拟聚乙烯块体的静态结构性质;聚乙烯块体在300 K和500 K下密度的模拟值与实验值误差小于3%,玻璃化转变温度和熔化温度的模拟值与实验值相符较好;单链聚乙烯导热系数的粗粒化势场模拟值与全原子模拟值较一致,无序聚乙烯块体导热系数的模拟值与实验值吻合较好。研究结果为介观尺度聚乙烯的导热研究提供了一种更高效的模拟方法。     

Engineering molecular mechanics: an efficient static high temperature molecular simulation technique

Inspired by the need for an efficient molecular simulation technique, we have developed engineering molecular mechanics (EMM) as an alternative molecular simulation technique to model high temperature (T>0?K) phenomena. EMM simulations are significantly more computationally efficient than conventional techniques such as molecular dynamics simulations. The advantage of EMM is achieved by converting the dynamic atomistic system at high temperature (T>0?K) into an equivalent static system. Fundamentals of the EMM methodology are derived using thermal expansion to modify the interatomic potential. Temperature dependent interatomic potentials are developed to account for the temperature effect. The efficiency of EMM simulations is demonstrated by simulating the temperature dependence of elastic constants of copper and nickel and the thermal stress developed in a confined copper system.     

Ab initio studies of single-height Si(001) steps

We have studied the Si(001) surface with single-height steps by ab initio molecular dynamics simulations. Surface dimers were found to be unstable with respect to buckling for all geometries considered. However, the ground state reconstruction depends on the type of step. For the SA step, the c(2 × 4) geometry is induced by the step edge, while, for the SB step, the p(2 × 2) reconstruction is more stable. The binding sites and diffusion barriers for a single Si adatom were investigated via the adiabatic trajectory method. In agreement with other studies of the flat surface, fast diffusion takes place along the dimer rows. The local changes to buckling induced by the adatom are sizable and lead to changes in the activation barriers for diffusion, in particular for the path perpendicular to the dimer rows. We also investigated the diffusion of the adatom over the rebonded SB step. The calculations show that there is no additional barrier for the arrival of the adatom at the edge from the upper terrace, while a barrier of at least 1 eV exists for the arrival of the adatom from the lower edge. In step flow growth involving the rebonded SB step, most of the adatoms will thus arrive from the upper terrace.     

Catalytic Nanomotors: Self‐Propelled Sphere Dimers

Experimental and theoretical studies of the self‐propelled motional dynamics of a new genre of catalytic sphere dimer, which comprises a non‐catalytic silica sphere connected to a catalytic platinum sphere, are reported for the first time. Using aqueous hydrogen peroxide as the fuel to effect catalytic propulsion of the sphere dimers, both quasi‐linear and quasi‐circular trajectories are observed in the solution phase and analyzed for different dimensions of the platinum component. In addition, well‐defined rotational motion of these sphere dimers is observed at the solution–substrate interface. The nature of the interaction between the sphere dimer and the substrate in the aqueous hydrogen peroxide phase is discussed. In computer simulations of the sphere dimer in solution and the solution–substrate interface, sphere‐dimer dynamics are simulated using molecular‐dynamics methods and solvent dynamics are modeled by mesoscopic multiparticle collision methods taking hydrodynamic interactions into account. The rotational and translational dynamics of the sphere dimer are found to be in good accord with the predictions of computer simulations.     

Prediction of Young’s modulus of graphene sheets and carbon nanotubes using nanoscale continuum mechanics approach

Analytical formulations are presented to predict the elastic moduli of graphene sheets and carbon nanotubes using a linkage between lattice molecular structure and equivalent discrete frame structure. The obtained results for a graphene sheet show an isotropic behavior, in contrast to limited molecular dynamic simulations. Young’s modulus of CNT represents a high dependency of stiffness on tube thickness, while dependency on tube diameter is more tangible for smaller tube diameters. The presented closed-form solution provides an insight to evaluate finite element models constructed by beam elements. The results are in a good agreement with published data and experimental results.     

Anharmonic effects on Be(0 0 0 1): A molecular dynamics study

Using molecular dynamics simulations and a modified analytic embedded atom method (MAEAM), the anharmonic effects of Be(0 0 0 1) surface have been studied in the temperature range from 0 K to 1400 K. The temperature dependence of the interlayer separation, mean square vibrational displacement, phonon frequencies and phonon line width, and layer structure factor are calculated. The obtained results for temperature dependence of interlayer separation and mean square displacement show that the anharmonic effects are small in the temperature range from 0 K to 1100 K. The calculated layer order parameters indicate that Be(0 0 0 1) surface loses its long-range translational order, but do not premelt up to 50 K below the bulk melting point. The surface disordering may result from strongly contracted c/a ratio of Be.     

Enhanced Liposomal Drug Delivery Via Membrane Fusion Triggered by Dimeric Coiled-Coil Peptides

An ideal nanomedicine system improves the therapeutic efficacy of drugs. However, most nanomedicines enter cells via endosomal/lysosomal pathways and only a small fraction of the cargo enters the cytosol inducing therapeutic effects. To circumvent this inefficiency, alternative approaches are desired. Inspired by fusion machinery found in nature, synthetic lipidated peptide pair E4/K4 is used to induce membrane fusion previously. Peptide K4 interacts specifically with E4, and it has a lipid membrane affinity and resulting in membrane remodeling. To design efficient fusogens with multiple interactions, dimeric K4 variants are synthesized to improve fusion with E4-modified liposomes and cells. The secondary structure and self-assembly of dimers are studied; the parallel PK4 dimer forms temperature-dependent higher-order assemblies, while linear K4 dimers form tetramer-like homodimers. The structures and membrane interactions of PK4 are supported by molecular dynamics simulations. Upon addition of E4, PK4 induced the strongest coiled-coil interaction resulting in a higher liposomal delivery compared to linear dimers and monomer. Using a wide spectrum of endocytosis inhibitors, membrane fusion is found to be the main cellular uptake pathway. Doxorubicin delivery results in efficient cellular uptake and concomitant antitumor efficacy. These findings aid the development of efficient delivery systems of drugs into cells using liposome-cell fusion strategies.     

Molecular dynamics simulations of ion bombardment processes

Abstract

An improved molecular dynamics technique that allows reduction of the computation time required in ion bombardment simulations is presented. This technique has been used to study the influence of the target temperature and structure on the argon sputtering of silicon. Molecular dynamics simulations of l keV Ar+ ion bombardment of silicon were carried out for several types of sample: (100) crystalline at 0 K, (100) crystalline at 300 K, and amorphous at 300 K. The yield of the sputtering process and the energy distribution of the sputtered atoms have been obtained. These results show that the sputtering process depends on the target surface binding energy which, in turn, is very sensitive to the structure of the sample surface.     

Application of molecular dynamics simulations for structural studies of carbon nanotubes

Molecular dynamics studies based on the Brenner-Tersoff second-generation reactive empirical bond order potential and the Lennard-Jones carbon-carbon potential for intra- and inter-layer interactions have been performed for carbon nanotubes. These potentials reproduce reasonably the carbon-carbon distances and inter-layer spacing. The structure factors and the reduced radial distribution functions computed from the cartesian coordinates, resulting from energy minimisation and molecular dynamics simulations at 2 K and 300 K have been obtained for two models of two- and five-wall carbon nanotubes containing defects in the form of five and seven membered carbon rings. The results of computations have been compared with experimental data obtained from neutron and X-ray diffraction. The energy relaxation and the molecular dynamics simulations at 2 K and 300 K with appropriate values of the Debye-Waller factor lead practically to the same results which are in a good agreement with the experimental data indicating that molecular dynamics reproduce all structure features of the investigated carbon nanotubes together with thermal oscillations. Possible applications of this approach for other carbon nanotubes and related materials have been also discussed.     

A 'first principles' potential energy surface for liquid water from VRT spectroscopy of water clusters

We present results of gas phase cluster and liquid water simulations from the recently determined VRT(ASP-W)III water dimer potential energy surface (the third fitting of the Anisotropic Site Potential with Woermer dispersion to vibration-rotation-tunnelling data). VRT(ASP-W)III is shown to not only be a model of high 'spectroscopic' accuracy for the water dimer, but also makes accurate predictions of vibrational ground-state properties for clusters up through the hexamer. Results of ambient liquid water simulations from VRT(ASP-W)III are compared with those from ab initio molecular dynamics, other potentials of 'spectroscopic' accuracy and with experiment. The results herein represent the first time to the authors' knowledge that a 'spectroscopic' potential surface is able to correctly model condensed phase properties of water.     

Temperature and composition dependent structural evolution of AgPd bimetallic nanoparticle: phase diagram of (AgPd)151 nanoparticle

We study the structural evolution of a 151 atom Ag-Pd bimetallic nanoparticle with composition and temperature. The solid-to-liquid transition region was investigated using molecular dynamics simulations with an improved collision method, and the solid-state structure of the nanoparticle was explored with a combination of molecular dynamics and density functional theory. Results show that an fcc-to-icosahedron transformation occurs at high temperature in all composition range and that a composition of nanoparticles concerns the atomic distribution of the (AgPd)151 nanoparticle. As a result, we constructed a phase diagram of the (AgPd)151 nanoparticle. Our phase diagram offers guidance on the application of Ag-Pd nanoparticles.     

Determination of Temperature-Dependent Elasto-Plastic Properties of Thin-Film by MD Nanoindentation Simulations and an Inverse GA/FEM Computational Scheme

This study presents a novel numerical method for extracting the tempe -rature-dependent mechanical properties of the gold and aluminum thin-films. In the proposed approach, molecular dynamics (MD) simulations are performed to establish the load-displacement response of the thin substrate nanoindented at temperatures ranging from 300-900 K. A simple but effective procedure involving genetic algorithm (GA) and finite element method (FEM) is implemented to extract the material constants of the gold and aluminum substrates. The material constants are then used to construct the corresponding stress-strain curve, from which the elastic modulus, yield stress and the tangent modulus of the thin film are subsequently derived. Results from high-temperature (900 K) nanoindentation MD simulation show that the value of elastic modulus of the gold and aluminum thin-films could decrease by 63.9% and 73.1%, respectively, as compared with the room temperature values. The resulting temperature-dependent stress-strain curves presented in this paper provide the crucial requirement for quantitative computer simulation of nanofabrication process.     

Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function

Molecular modeling and simulations enable extrapolation for the structure of bacterial potassium channels to the function of their mammalian homologues. Molecular dynamics simulations have revealed the concerted single-file motion of potassium ions and water molecules through the selectivity filter of K channels and the role of filter flexibility in ion permeation and in "fast gating." Principal components analysis of extended K channel simulations suggests that hinge-bending of pore-lining M2 (or S6) helices plays a key role in K channel gating. Based on these and other simulations, a molecular model for gating of inward rectifier K channel gating is presented.     

Atomistic simulations of electrowetting in carbon nanotubes

Electrowetting of carbon nanotubes by mercury was studied using classical molecular dynamics simulations in conjunction with a macroscopic electrocapillarity model. A scaled ab initio mercury dimer potential, optimized to reproduce the mercury liquid density (at 300 K), melting point, and wetting angle on graphite, was selected for the simulations. Wetting of (20,20) single-walled carbon nanotubes by mercury occurs above a threshold voltage of 2.5 V applied across the interface. Both the electrocapillary pressure and imbibition velocity increase quadratically with voltage and can acquire large values, for example, 2.4 kbar and 28 m/s at 4 V, indicating a notable driving force. The observed voltage scaling can be captured by the Lucas-Washburn equation modified to include a wetting-line friction term.     

Healing mechanism of multi-vacancy defective graphene under carbon irradiation

The irradiation healing process of defective graphene was studied by reactive molecular dynamics simulation of injecting C atoms on a multi-vacancy graphene sheet. We studied the effect of environment temperature and incident energy of injected atoms on healing process of defective graphene. Our simulations show that a relatively high temperature (about 1600?K) is prerequisite for perfect healing of defective graphene. Moreover, an appropriate incident energy for injected atoms (0.16?eV/atom for ～1800?K) is also necessary for perfect healing, even under a suitable temperature for perfect healing. Defect structures, such as carbon chains and blister-like structures, will occur and hinder the healing process, if the adsorption process (determined basically by incident energy) is faster than the reorganization process (dominated by temperature). In addition, the temperature dependence of reorganization capability of graphene was further studied by molecular dynamics simulation of relaxing an intact graphene sheet with adsorbed atoms. The analysis of the evolution of various micro-structures, emerged during the reorganization simulations, is helpful for deeply understanding the healing mechanism of defective graphene sheet under carbon irradiation.     

Stability of single-wall silicon carbide nanotubes – molecular dynamics simulations

One-dimensional silicon carbide (SiC) nanotubes and nanowires are both realizable and may co-exist. The stability of SiC nanotubes relative to nanowires and against heating is still unknown. Using classical molecular dynamics simulations, the authors investigate the stabilities of SiC nanotubes; as a first step, the study focuses on single-wall nanotubes (SWNTs). The results show that SiC nanotubes are more stable than nanowires below a critical diameter of about 1.6 nm, while SiC nanowires are more stable than nanotubes beyond that. As temperature increases, melting takes place at about 1620 K in SiC nanotubes by heterogeneous nucleation from the non-hexagonal defects due to reconstruction at a free end, and at about 1820 K in nanotubes without free ends by homogeneous nucleation within the wall from thermally activated 5-7-7-5 defects. In both cases formation of Si–Si and C–C bonds proceeds melting.     

Self-assembling peptides: A combined XPS and NEXAFS investigation on the structure of two dipeptides Ala–Glu,Ala–Lys

The two dipeptides AE (Lalanine–Lglutamic acid) and AK (Lalanine–Llysine), that constitute the “building blocks” of the 16-unit self-complementary amphiphilic oligopeptide EAK16, have been investigated by XPS (X-ray photoelectron spectroscopy) and NEXAFS (near-edge X-ray absorption fine structure) spectroscopy. Thin films of both dipeptides on TiO₂, a distinguished biocompatible surface, were prepared by incubation from aqueous solutions. Thick films of dipeptides on inert Au substrates were also studied for comparison. The chemical structure and composition were investigated by XPS spectroscopy; furthermore, molecular orientation of dipeptides on TiO₂ was checked by angular dependent NEXAFS measurements at both C–K and N–K edges. In order to yield some insight on adsorption geometry and molecular orientation MD (molecular dynamic) simulations were also carried out.The performed molecular and electronic characterization of AE and AK provides an excellent model for the interpretation of more complex peptide spectra.     

Reversible bistable switching in nanoscale thiol-substituted oligoaniline molecular junctions

Single molecular monolayers of oligoaniline dimers were integrated into sub-40-nm-diameter metal nanowires to form in-wire molecular junctions. These junctions exhibited reproducible room temperature bistable switching with zero-bias high- to low-current state conductance ratios of up to 50, switching threshold voltages of approximately +/-1.5 V, and no measurable decay in the high-state current over 22 h. Such switching was not observed in similarly fabricated saturated dodecane (C12) or conjugated oligo(phenylene ethynylene) (OPE) molecular junctions. The low- and high-state current versus voltage was independent of temperature (10-300 K), suggesting that the dominant transport mechanism in these junctions is coherent tunneling. Inelastic electron tunneling spectra collected at 10 K show a change in the vibrational modes of the oligoaniline dimers when the junctions are switched from the low- to the high-current state. The results of these measurements suggest that the switching behavior is an inherent molecular feature that can be attributed to the oligoaniline dimer molecules that form the junction.     

Comparison of experimental AA6063 extrusion trials to 3D numerical simulations, using a general solute-dependent constitutive model

In this paper, laboratory scale extrusion experiments carried out on AA6063 billets are compared to numerical simulations. The numerical simulations are performed with a general solute-dependent elasto-viscoplastic constitutive model based on a hyperbolic sine law, allowing for the quantification of pressure levels, strain rates and stresses. The parameters for the material model were determined with compression tests. The extrusion trials were performed isothermally at temperatures of 623 and 723 K and with two distinct material conditions. The results of the numerical simulations show good agreement with the experimental results. It turns out that local high strain rates (>40 s⁻¹) have a significant influence on the extrusion pressure. However adequate test methods to provide constitutive data at these strain rates are very limited. At high temperatures the difference between material conditions had a considerably smaller influence on the extrusion experiments compared to the simulations. It is argued that this effect can be attributed to dynamic precipitation that occurred during the experiments under high temperature, high strain rate conditions.