Molecular Mechanism of the Early Stage of Amyloidogenic Hexapeptides(NFGAIL) Aggregation

Peptides/proteins aggregation can give rise to pathological conditions of many human diseases.Small partially ordered oligomers formed in the early stage of aggregation,rather than mature fibrils,are thought to be the main toxicity agent for the living cell.Thus,understanding the pathway and the underlying physical mechanism in the early stage of aggregation is very important for prevention and treatment of these protein functional diseases.Herein we use all-atom molecular dynamics simulations to study the aggregation of four NFGAIL hexapeptides(NFGAIL peptide is a core segment of human islet amyloid polypeptide and exhibits similar aggregation kinetics as the full-length polypeptide).We observe that the peptide monomers in water mainly adopt non-structural coil configurations;the four peptides which are randomly placed in water aggregate spontaneously to partially ordered oligomer(β-sheets)through dimerization or trimerization,with the dimerization predominated.Both parallel and anti-parallelβ-sheets are observed.The hydrophobic interactions drive the initial peptides associations,and the subsequent conformational fluctuations promote the formation of more hydrogen bonds between the dangling hydrogen sites in the main chains of peptides.     

Aggregation of fullerene (C_(60)) nanoparticle:A molecular-dynamic study

We present the results of molecular dynamics simulations of net positively charged fullerene nanoparticles in salt- free and salt-added solution. The aggregation of fullerene （C60）-like nanoparticle and counterion are studied in detail as a function of temperatures and a finite salt concentration. Our simulations show that the strong conformation changes as temperature changes. The net positively-charged nanoparticles do not repel each other but are condensed under proper temperatures. If salts are added, the aggregated nanoparticles will be disaggregated due to the Debye screening effect.     

C36团簇自组装的分子动力学研究

提出了利用C36团簇在气相条件下自组装制备新纳米团簇的设想，并利用分子动力学方法模 拟了包括真实氦气氛作用的碳团簇生长过程，发现环境气体温度是影响最后所生成的团簇结 构的关键因素：C36团簇在1000?K到2000?K的温度范围内，自组装形成保持C36线径特征的 蚕茧状新纳米团簇；在高于2000?K的温度下，最后形成的团簇趋于球状. 关键词： 分子动力学模拟 纳米碳团簇     

纳米尺度下毛细流动的分子动力学模拟

采用分子动力学模拟研究纳米尺度下壁面润湿性对毛细流动的影响,主要考虑纳米通道两侧壁面润湿性相同与不同两种情况。研究表明：两侧壁面润湿性相同条件下,毛细流动随着壁面润湿性增强而加快, 毛细高度随时间的变化早期偏离Lucas-Washburn理论,但后期与其预测符合。在纳米通道两侧壁面润湿性不同的情况下,液面会发生振荡,两侧壁面毛细高度也不相等,且液面振荡的幅度和两侧壁面毛细高度差都随着两侧壁面润湿性差异的增大而增大。基于能量转化分析,提出两侧壁面湿润性不同情况下纳米通道中毛细流动发生的条件以及毛细流动快慢的判别依据。研究结果加深了对纳米尺度下毛细流动机理的认识,并为相关工程应用提供理论参考。     

High density gas state at water/graphite interface studied by molecular dynamics simulation

In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results： gas films （pancake-like） for a larger ratio and nanobubbles for a smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film （pancake-like） and nanobubbles.     

Molecular Properties and Aggregation of Porphyrin-modified Polysiloxane in Solutions

Molecular properties and aggregation behavior of a polysiloxane with grafted side chain groups consisting of asymmetrical hydroxy-functionalized porphyrin were studied in dilute solutions. In order to understand the mechanism of aggregation of the polymeric porphyrin derivatives, several analyses of chloroform solutions were performed permitting comparison of the data obtained by means of different techniques. Molar mass and hydrodynamic size of the macromolecules were obtained using the methods of analytical ultracentrifugation, isothermal translational diffusion, and viscometry. Long distance interactions between macromolecules in dilute solutions were detected with static light scattering. With increasing the concentration of the solutions, the electronic and fluorescence spectra bands assigned to generation of H and J aggregates became apparent. The organization of aggregates, which seemed to be favored by chloroform, was visualized by atomic force microscopy images that displayed sponge-like morphology, small triangular particles, characteristic of H aggregates, and nano or micro-structured ring geometries obtained by the side-by-side J-process, coexisting together.     

Molecular dynamics simulations of the nano-droplet impact process on hydrophobic surfaces

Large-scale molecular dynamics simulations are used to study the dynamic processes of a nano-droplet impacting on hydrophobic surfaces at a microscopic level. Both the impact phenomena and the velocity distributions are recorded and analyzed. According to the simulation results, similar phenomena are obtained to those in macro-experiments. Impact velocity affects the spread process to a greater degree than at a level of contact angle when the velocity is relatively high. The velocity distribution along the X axis during spread is wave-like, either W- or M-shaped, and the velocity at each point is oscillatory; while the edges have the highest spread velocity and there are crests in the distribution curve which shift toward the edges over time. The distribution along the Y axis is 〈- or 〉-shaped, and the segments above the middle have the lowest decrease rate in the spreading process and the highest increase rate in the retraction process.     

The influence of changes in the framework on the diffusion in zeolites. Molecular dynamics simulations

Some less known methods are described for the analysis of trajectories of guest molecules in porous solids. Such trajectories can be calculated by Molecular Dynamics (MD) computer simulations in order to analyze the interrelations between the structure and the particle behaviour including collective phenomena. Some results obtained with these methods for diffusing methane in zeolites of type LTA are presented. An analytical potential model for LTA type zeolites is given that make extremely long runs or simulations of large lattice regions for systems with rigid lattice possible. Such runs are necessary e.g. to examine questions as the influence of extented lattice defects or the fractal behaviour of the partical trajectories.     

CF interaction with Si(1 0 0)-(2 × 1): Molecular dynamics simulation

In this study, the interaction of CF with the clean Si(1 0 0)-(2 × 1) surface at normal incidence and room temperature was investigated using molecular dynamics simulation. Incident energies of 2, 12 and 50 eV were simulated. C atoms, arising from dissociation, preferentially react with Si to form Si-C bonds. A Si_xC_yF_z interfacial layer is formed, but no etching is observed. The interfacial layer thickness increases with increasing incident energy, mainly through enhanced penetration of the silicon lattice. Silicon carbide and fluorosilyl species are formed at 50 eV, which is in good agreement with available experimental data. The level of agreement between the simulated and experimental results is discussed.     

Molecular dynamics simulations of compressed hydrogen

Abstract

Molecular dynamics simulations have been performed for highly compressed fluid hydrogen in the density and temperature regime of recent shock-compression experiments. Both density functional and tight-binding electronic structure techniques have been used to describe interatomic forces. Two tight-binding models of hydrogen have been developed with a single s-type orbital on each atom that reproduce properties of the dimer, of various crystalline structures, and of the fluid. The simulations indicate that the rapid rise in the electrical conductivity observed in the gas-gun experiments depends critically on the dissociated atoms (monomers). We find that the internal structure of warm, dense hydrogen has a pronounced time-dependent nature with the continual dissociation of molecules (dimers) and association of atoms (monomers). Finally, Hugoniots derived from the equations-of-state of these models do not exhibit the large compressions predicted by the recent laser experiments.     

Molecular dynamics study of self-diffusion in Zr

We employed a recently developed semi-empirical Zr potential to determine the diffusivities in hcp and bcc Zr via molecular dynamics simulation. The point defect concentration was determined directly from molecular dynamics (MD) simulation rather than from theoretical methods using T = 0 calculations. Our MD simulation indicates that the diffusion proceeds via the interstitial mechanism in hcp Zr, and both vacancy and interstitial mechanisms contribute to diffusivity in bcc Zr. The agreement with the experimental data is excellent for hcp Zr and rather good for bcc Zr at high temperatures, but there is considerable disagreement at low temperatures.     

Ti3Al合金短程序和中程序的分子动力学模拟

本文利用分子动力学模拟方法, 研究了非晶态Ti3Al合金在300 K时的短程序和中程序。利用对相关函数分布函数、配位数和Voronoi多面体方法研究了微观局域结构短程序和中程序。 研究发现：在Ti3Al合金非晶体中,短、中程序具有二十面体或缺陷二十面体的壳层结构。     

纳米流体分散稳定性的分子动力学研究初探

纳米流体的制备和分散稳定性是纳米流体研究工作的前提。本文利用平衡分子动力学模拟方法,尝试从微观角度研究纳米流体的分散稳定性。以纳米颗粒Cu在液态CO_2中的分散稳定为算例,通过跟踪每个固体分子和液体分子的位置,分别观察了颗粒周围的液体吸附现象和颗粒的团聚现象。通过改变固液分子间的引力和斥力,观察其对颗粒周围液体分子的密...     

双酚A在氧化石墨烯表面吸附的分子动力学模拟

双酚A(bisphenol A,BPA)是一种内分泌干扰物,会对机体多方面产生不良影响,包括生殖系统、神经系统、胚胎发育等.因此,在水环境中如何检测和去除BPA显得尤为重要.实验研究表明,氧化石墨烯(graphene oxide,GO)对BPA具有优异的吸附去除性能,但在分子层面的吸附机制尚不清楚.分子动力学模拟,能提供BPA在GO表面的动态吸附过程以及吸附构象等详细信息,可以弥补实验的不足.本文利用GROMACS分子动力学模拟软件,系统模拟了BPA在含GO的水溶液中的吸附过程,并计算了吸附自由能.结果显示:所有的BPA均被吸附在GO两侧,通过分析BPA的吸附构象以及与GO的相互作用,发现π-π疏水作用对吸附起主导作用,且显示出很好的稳定性,而静电和氢键作用增加了GO的吸附能力.通过自由能计算,BPA在GO表面的结合能达30 k J/mol,远大于水分子的5 k J/mol.这些结果进一步证实GO对BPA具有很强的吸附能力以及GO作为吸附剂在水溶液中去除BPA的可行性.     

液滴在润湿梯度表面运动的分子动力学模拟

本文进行了液滴在不同润湿梯度表面运动的分子动力学模拟,通过改变Lennard-Jones(LJ)势参数来实现表面的不同润湿性。模拟结果表明在润湿梯度差为10°的界面上,疏水表面的液滴运动更快,达到最终界面所需时间最短,并且液滴运动方向距离最远。当润湿梯度差为20°和30°时,液滴在疏水表面工况的运动速度与从疏水跨越到亲水的工况之间的差距越来越小,并且液滴在从疏水跨越到亲水的工况达到了最远的运动距离。同时,润湿梯度差的增加也引起了液滴运动速度的增大。     

低能Cl原子刻蚀Si(100)表面的分子动力学模拟

使用分子动力学模拟方法研究了不同能量(0.3—10 eV)的Cl原子对表面温度为300 K的Si(100)表面的刻蚀过程.模拟中采用了Tersoff-Brenner势能函数来描述Cl-Si体系的相互作用.模拟结果显示,随着入射Cl原子在表面的吸附达到饱和,Si表面形成一层富Cl反应层.这和实验结果是一致的.反应层厚度随入射能量增加而增加.反应层中主要化合物类型为SiCl,且主要分布于反应层底部.模拟结果发现随初始入射能量的增加,Si的刻蚀率增大.在入射能量为0.3,1和5 eV时,主要的Si刻蚀产物为Si 关键词： 分子动力学 Cl刻蚀Si 分子动力学模拟 微电子机械系统     

Molecular kinetic theory of boundary slip on textured surfaces by molecular dynamics simulations

A theoretical model extended from the Frenkel-Eyring molecular kinetic theory (MKT) was applied to describe the boundary slip on textured surfaces. The concept of the equivalent depth of potential well was adopted to characterize the solid-liquid interactions on the textured surfaces. The slip behaviors on both chemically and topographically textured surfaces were investigated using molecular dynamics (MD) simulations. The extended MKT slip model is validated by our MD simulations under various situations, by constructing different complex surfaces and varying the surface wettability as well as the shear stress exerted on the liquid. This slip model can provide more comprehensive understanding of the liquid flow on atomic scale by considering the influence of the solid-liquid interactions and the applied shear stress on the nano-flow. Moreover, the slip velocity shear-rate dependence can be predicted using this slip model, since the nonlinear increase of the slip velocity under high shear stress can be approximated by a hyperbolic sine function.     

Notch fatigue of Cu_(50)Zr_(50) metallic glasses under cyclic loading: molecular dynamics simulations

Molecular dynamics simulation is performed to simulate the tension–compression fatigue of notched metallic glasses(MGs), and the notch effect of MGs is explored. The notches will accelerate the accumulation of shear transition zones, leading to faster shear banding around the notches' root causing it to undergo severe plastic deformation. Furthermore, a qualitative investigation of the notched MGs demonstrates that fatigue life gradually becomes shorter with the increase in sharpness until it reaches a critical scale. The fatigue performance of blunt notches is stronger than that of sharp notches. Making the notches blunter can improve the fatigue life of MGs.     

单壁碳纳米管在石墨基底上运动的分子动力学模拟

采用分子动力学模拟方法研究单壁碳纳米管在石墨基底上的运动.首先碳纳米管在基底弛豫至平衡状态，然后对其施加一固定外力，撤去外力后，碳纳米管在基底上逐渐减速至停止.为了研究管径、手性角对运动方式的影响，本文选择了C(10,10)，C(10,9)，C(10,8)，C(10,5)，C(10,0)，C(8,8)六种单壁碳纳米管进行模拟.结果表明，碳纳米管在石墨基底上的运动方式由手性角决定，与管径无关.手性角等于30°时，碳纳米管与石墨基底之间为公度结构，碳纳米管的运动出现周期性的滑动和翻滚现象；手性角大于28.3°小于30°时，碳纳米管一边向前滑动一边滚动；手性角小于26.3°时，碳纳米管在基底上滑动.碳纳米管的手性角决定了它与石墨基底接触界面的微观构型，从而决定了碳纳米管的运动方式. 关键词： 分子动力学模拟 碳纳米管 动能 结构公度性     

Molecular dynamics simulations of the effects of sodium dodecyl sulfate on lipid bilayer

Molecular dynamics simulations have been performed on the fully hydrated lipid bilayer with different concentrations of sodium dodecyl sulfate(SDS). SDS can readily penetrate into the membrane. The insertion of SDS causes a decrease in the bilayer area and increases in the bilayer thickness and lipid tail order, when the fraction of SDS is less than 28%.Through calculating the binding energy, we confirm that the presence of SDS strengthens the interactions among the DPPC lipids, while SDS molecules act as intermedia. Both the strong hydrophilic interactions between sulfate and phosphocholine groups and the hydrophobic interactions between SDS and DPPC hydrocarbon chains contribute to the tight packing and ordered alignment of the lipids. These results are in good agreement with the experimental observations and provide atomic level information that complements the experiments.