F等离子体刻蚀Si中Lag效应的分子动力学模拟

通过分子动力学模拟的方法对感应耦合等离子体刻蚀中Lag效应的产生机理进行了研究. 研究结果表明,在刻蚀过程中普遍存在Lag效应,宽槽的刻蚀率明显比窄槽的刻蚀率要高,这是由于宽槽更有利于产物从槽中的逸出;窄槽中产物从槽中逸出的速率较低,较多的产物拥挤在窄槽中降低了入射的F等离子体入射的速度,从而降低了F等离子体到达Si表面的能量,而相同条件下,刻蚀率随能量的降低而降低;另一方面,窄槽中入射的等离子体与槽壁的距离较近,使得入射的F更容易与槽壁表面的Si的悬挂键结合沉积在槽壁表面,使刻蚀出的槽宽度变窄,进一步影响到后继粒子的入射;Lag 效应随槽宽的减小而增强,随温度的升高而减弱,随入射粒子能量的升高而增强. 关键词： 分子动力学 Lag效应 刻蚀 刻蚀率     

分子动力学模拟压水反应堆中氢气对水的影响

通过分子动力学方法模拟了在常温常压下(1 atm, 298 K)和在压水堆环境下(155 atm, 626 K), 水分子数为256, 氢分子数为0, 25, 50, 75和100等不同数目时, 粒子系统的动力学性质和微观结构, 分析了不同氢气对水中溶解氧的影响. 从模拟结果可知, 在常温常压和压水堆环境下, 当氢粒子数分别为0, 25, 50, 75和100时, 粒子系统的均方位移会随氢分子数增加而增加, 并且常温常压下的增长幅度远小于压水堆环境下的增长幅度, 如压水堆环境下氢分子数为75时系统的均方位移约是常温常压下氢分子数为75时系统的均方位移的6.02倍, 比压水堆环境下氢分子数0时系统的均方位移增加了131.88%. 此外, 粒子系统的微观结构, 从径向分布函数看, 在常温常压下随着氢分子数目的增加而小幅度增加, 这与常温常压下因氢气溶解在水中增大了氧离子周围的粒子密度相符合. 而在压水堆环境下, 氢分子数为75, 50, 25与为0时的水比较, 其径向分布均不会有太大的变化, 而分子数为100时会出现明显增加, 与为0时的水比较其径向分布增加了22.00%. 模拟结果表明, 往压水堆中的水加入氢气能明显地抑制水中的溶解氧.     

Intermittency at critical transitions and aging dynamics at the onset of chaos

We recall that at both the intermittency transitions and the Feigenbaum attractor, in unimodal maps of non-linearity of order ζ > 1, the dynamics rigorously obeys the Tsallis statistics. We account for theq-indices and the generalized Lyapunov coefficients λ^q that characterize the universality classes of the pitchfork and tangent bifurcations. We identify the Mori singularities in the Lyapunov spectrum at the onset of chaos with the appearance of a special value for the entropic indexq. The physical area of the Tsallis statistics is further probed by considering the dynamics near criticality and glass formation in thermal systems. In both cases a close connection is made with states in unimodal maps with vanishing Lyapunov coefficients.     

高压作用下相分离液体玻璃转变的分子动力学研究

采用分子动力学模拟方法,研究了二元混合液体在不同外压作用下的相分离与玻璃转变过程,计算了相分离液体在玻璃转变过程中的结构和动力学特征.研究发现,外压会促进相分离的产生,并提高玻璃转变温度,会使β弛豫出现的温度更高、存在的时间更长,导致系统扩散性降低.同时还发现,相分离液体的玻璃转变过程存在微观不均匀现象. 关键词： 相分离 玻璃转变 分子动力学模拟 外压影响     

Electronic localization at mesoscopic length scales: different definitions of localization and contact effects in a heuristic DNA model

In this work we investigate the electronic transport along model disordered DNA molecules using an effective tight-binding approach, addressing the localization properties. Different tools to investigate the degree of localization are examined as a function of system length, energy dependence and DNA to electrode coupling: localization length, participation number and sensitivity to boundary conditions. Combining the results obtained from these different tools, a thermodynamic limit for the model DNA molecule, within the mesoscopic length scale, can be established. Furthermore, three aspects are investigated: (i) the influence of strongly localized resonances on the localization length is discussed as an important mechanism defining the degree of localization for sizes below the thermodynamic limit; (ii) the dependence on the Hamiltonian parameters on a possible diffusive regime for short systems; and, finally, (iii) possible length dependent origins for the large discrepancies among experimental results for the electronic transport in DNA samples.     

几何构型不同的Na团簇碰撞动力学研究

采用距离相关紧密束缚的分子动力学模型,在不同碰撞能量以及不同的碰撞参数下,研究了两种构型的Na6(2D),Na6(3D)与Na8团簇间的碰撞.讨论了反应机制的变化,即全融合、深度非弹、非弹性碰撞过程.结果表明:构型不同的团簇与相同的靶碰撞显示了不同的特征.低能时Na6(3D)易融合;DIC反应时,易于形成大的团簇 关键词： Na团簇 原子团簇碰撞 紧束缚模型     

Modelling transient heat conduction in solids at multiple length and time scales: A coupled non-equilibrium molecular dynamics/continuum approach

A method for controlling the thermal boundary conditions of non-equilibrium molecular dynamics simulations is presented. The method is simple to implement into a conventional molecular dynamics code and independent of the atomistic model employed. It works by regulating the temperature in a thermostatted boundary region by feedback control to achieve the desired temperature at the edge of an inner region where the true atomistic dynamics are retained. This is necessary to avoid intrinsic boundary effects in non-equilibrium molecular dynamics simulations. Three thermostats are investigated: the global deterministic Nosé–Hoover thermostat and two local stochastic thermostats, Langevin and stadium damping. The latter thermostat is introduced to avoid the adverse reflection of phonons that occurs at an abrupt interface. The method is then extended to allow atomistic/continuum models to be thermally coupled concurrently for the analysis of large steady state and transient heat conduction problems. The effectiveness of the algorithm is demonstrated for the example of heat flow down a three-dimensional atomistic rod of uniform cross-section subjected to a variety of boundary conditions.     

Molecular dynamics and quantum chemical approaches in the study of the hydration of protonated cyclohexyldiamines

Explicit hydration of the neutral and charged cyclohexylamine and of the cyclohexyldiamine isomers in their mono- or diprotonated forms is investigated through classical molecular dynamics (MD) simulations in aqueous solutions combined with DFT calculations in amine–water complexes. The MD studies performed in the monoamines reveal that the structure of the hydration shell around the neutral amino group (NH₂) is quite distinct from that around the charged one (NH₃⁺). On average, the number of water molecules surrounding the two groups is calculated to be ～2 and 3–4, respectively. The variation of the hydration structure prompted by the groups’ proximity is discussed based on the data found for the mono- and diprotonated diamines. To have a more detailed picture of the water molecules’ arrangement around the amino groups and of the amine–water hydrogen bonds, geometry optimisations in hydrates with up to six water molecules are carried out at the B3LYP/aug-cc-pVDZ level. Complexation energies are also computed. The main findings emerging from these calculations are found to be very helpful to rationalise the mutual influence of the amino groups and therefore to better elucidate the MD findings. The complementary nature of the two research methods is emphasised as an excellent tool in order to closely examine the hydration of polyamines, as exemplified for the cyclohexyldiamines.     

BaTiO3铁电体中辐射位移效应的分子动力学模拟

运用基于壳模型的分子动力学方法研究了BaTiO₃铁电体中的辐射位移效应.采用O原子作为初级击出原子,模拟了当初级击出原子能量为1 keV时体系内缺陷的产生和演化.模拟结果表明,当入射方向为[001]时,体系内产生的缺陷最多.在所有缺陷中,以O缺陷的含量为最高,达80%以上.同时,这些缺陷的产生并不显著改变体系的自发极化强度,对体系的极化翻转过程也基本没有影响.在外电场作用下,观察到了显著的缺陷迁移. 关键词： 分子动力学 3铁电体')" href="#">BaTiO₃铁电体 辐射位移效应     

Hydration of the chloride ion in concentrated aqueous solutions using neutron scattering and molecular dynamics

Neutron scattering experiments were performed on 6 m LiCl solutions in order to obtain the solvation structure around the chloride ion. Molecular dynamics simulations on systems mirroring the concentrated electrolyte conditions of the experiment were carried out with a variety of chloride force-fields. In each case the simulations were run with both full ionic charges and employing the electronic continuum correction (implemented through charge scaling) to account effectively for electronic polarisation. The experimental data were then used to assess the successes and shortcomings of the investigated force-fields. We found that due to the very good signal-to-noise ratio in the experimental data, they provide a very narrow window for the position of the first hydration shell of the chloride ion. This allowed us to establish the importance of effectively accounting for electronic polarisation, as well as adjusting the ionic size, for obtaining a force-field which compares quantitatively to the experimental data. The present results emphasise the utility of performing neutron diffraction with isotopic substitution as a powerful tool in gaining insight and examining the validity of force-fields in concentrated electrolyte solutions.     

A molecular dynamics simulation study on the cavitation inception of water with dissolved gases

The promotion/prevention mechanism of dissolved gases on cavitation inception is essential for many high-tech industries and research. In the present study, large-scale molecular dynamics simulations are performed to investigate the effects of water cavitation caused by different gas types by using nitrogen and oxygen gases with TIP4P/2005 water. The cavitation inception behaviour is analyzed via Mean First Passage Time method. Water with dissolved gases has a higher nucleation rate and is easier to cavitate than pure water. At the same gas concentration, the cavitation of water with nitrogen is promoted to a greater extent than that with oxygen. The number and energy of hydrogen bond (HB) are further calculated by the Acceptor-Hydrogen-Donor method to explain this promotion mechanism. The number and energy of HB in water with gases decrease compared with those in pure water. The introduction of gases weakens the HB network and promotes cavitation inception because of weaker interactions between gas and water molecules. A model is developed to describe the relationship between nucleation rate and HB energy. Gas molecules assemble on the surface of bubbles during water cavitation, which may decrease the free energy of bubble surface, maintain the existing bubble, and contribute to the growth process.     

Effect of alkyl chain length in protic ionic liquids: an AIMD perspective

In this study we have explored, by means of ab initio molecular dynamics, a subset of three different protic ionic liquids (ILs). We present both structural and dynamical information of the liquid state of these compounds as revealed by accurate ab initio computations of the interactions. Our analysis figures out the presence of a strong hydrogen bond network in the bulk state, that is more stable in those ILs characterised by a longer alkyl side chain. Indeed it becomes more long-lasting passing from ethyl ammonium to butyl ammonium, owing to the hydrophobic effects stemming from alkyl chain contacts. Furthermore, the relative free energy landscape of the cation–anion interaction exhibits a progressively deeper well as the side chain of the cation gets longer. The hydrogen bond interaction, as already mentioned in previous works, leads to loss of degeneracy of the asymmetric stretching vibrations of the nitrate anions. The resulting frequency splitting between the two normal modes is about 90 cm^?1.     

异质原子对液体气泡成核影响的分子动力学模拟

采用分子动力学方法模拟了池沸腾中液体层加入异质原子对气泡成核的影响.分析了异质原子能量参数对液体起始气泡成核时间和温度的影响及其机理.结果表明,当异质原子能量参数小于液氩能量参数时,液体起始气泡成核时间缩短,起始温度降低.当异质原子剂能量参数大于液氩能量参数时,液体起始气泡成核时间增加,起始温度升高.异质原子在壁面上的吸附及在液体中的扩散行为影响固液界面性质,较大能量参数的异质原子扩散系数较小,更多能量参数较大的原子吸附在固体表面上使得壁面势能壁垒增加,导致沸腾时间延迟,液体需要吸收更多的热量克服势能壁垒,进而提高沸腾起始温度.能量参数较小的异质原子扩散系数较大,异质原子更容易分散到液体中,使得壁面附近液体层势能减小,液体层更容易气泡成核行为.     

微液滴在不同能量表面上润湿状态的分子动力学模拟

微小液滴在不同能量表面上的润湿状态对于准确预测非均相核化速率和揭示界面效应影响液滴增长微观机理具有重要意义. 通过分子动力学模拟, 研究了纳米级液滴在不同能量表面上的铺展过程和润湿形态. 结果表明, 固液界面自由能随固液作用强度增加而增加, 并呈现不同液滴铺展速率和润湿特性. 固液作用强度小于1.6的低能表面呈现疏水特征, 继续增强固液作用强度时表面变为亲水, 而固液作用强度大于3.5的高能表面上液体呈完全润湿特征. 受微尺度条件下非连续、非对称作用力影响, 微液滴气液界面存在明显波动, 呈现与宏观液滴不同的界面特征. 统计意义下, 微小液滴在不同能量表面上铺展后仍可以形成特定接触角, 该接触角随固液作用强度增加而线性减小, 模拟结果与经典润湿理论计算获得的结果呈现相似变化趋势. 模拟结果从分子尺度为核化理论中的毛细假设提供了理论支持, 揭示了液滴气液界面和接触角的波动现象, 为核化速率理论预测结果和实验测定结果之间的差异提供了定性解释.     

Molecular dynamics study of water in contact with the TiO2 rutile-110, 100, 101, 001 and anatase-101, 001 surface

We have carried out classical molecular dynamics of various surfaces of TiO₂ with its interface with water. We report the geometrical features of the first and second monolayers of water using a Matsui Akaogi (MA) force field for the TiO₂ surface and a flexible single point charge model for the water molecules. We show that the MA force field can be applied to surfaces other than rutile (110). It was found that water OH bond lengths, H–O–H bond angles and dipole moments do not vary due to the nature of the surface. However, their orientation within the first and second monolayers suggest that planar rutile (001) and anatase (001) surfaces may play an important role in not hindering removal of the products formed on these surfaces. Also, we discuss the effect of surface termination in order to explain the layering of water molecules throughout the simulation box.     

MD simulation of the effect of contact area and tip radius on nanoindentation

Nanoindentation,namelydepth-sensingindentation(DSI),involvesforcingarigidindenterwithknowngeometryintothesurfaceofamaterialwhilecontinuouslymonitoringtheloadontheindenter,thedisplacementoftheindenterintothesurface,andthetimeoftheexperiment.Thedepthisthenusedtocalculatetheprojectedareaofcontactforthepurposeofcalculatingthehardnessandelasticmodulus.Infact,variouserrorsareassociatedwiththisprocedure.Oneofthemcomesfromthemeasurementofthepenetrationdepth.Ideally,thepenetrationdepthshouldbecalcula…     

Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution

A-form DNA is one of the biologically active double helical structure. The study of A-DNA structure has an extensive application for developing the field of DNA packaging in biotechnology. In aqueous solution, the A-DNA structure will have a free transformation, the A-DNA structure will be translated into B-form structure with the evolution of time, and eventually stabilized in the B-DNA structure. To explore the stability function of the bivalent metal ions on the A-DNA structure, a series of molecular dynamics simulations have been performed on the A-DNA of sequence (CCCGGCCGGG). The results show that bivalent metal ions (Mg²⁺, Zn²⁺, Ca²⁺) generate a great effect on the structural stability of A-DNA in the environment of high concentration. As the interaction between metal ions and electronegative DNA chains, the stability of A-DNA in solution is gradually improved with the increasing solution concentration of ions. In metal salt solution with high concentration, metal ions can be easily distributed in the solvation shells around the phosphate groups and further lead to the formation of shorter and more compact DNA structure. Also, under the condition of the same concentration and valency of the metal ions, the stability of A-DNA structure is different. The calculations indicate that the structure of A-DNA in CaCl₂ solution is less stable than in MgCl₂ and ZnCl₂ solution.     

The structure,dynamics and solvation mechanisms of ions in water from long time molecular dynamics simulations: a case study of CaCl2 (aq) aqueous solutions

Systematic long time (5–20 ns) molecular dynamics (MD) simulations have been carried out to study the structural and dynamical properties of CaCl₂ aqueous solutions over a wide range of concentrations (≤9.26 m) in this study. Our simulations reveal totally different structural characteristics of those yielded from short time (≤1 ns) MD simulations [A.A. Chialvo and J.M. Simonson, J. Chem. Phys. 119, 8052 (2003); T. Megyes, I. Bako, S. Balint, T. Grosz, and T. Radnai, J. Mol. Liq. 129, 63 (2006)]. An apparent discontinuity was found at 4–5 m of CaCl₂ in various properties including ion–water coordination number and self-diffusion coefficient of ions, which were first noticed by Phutela and Pitzer in their thermodynamic modelling [R.C. Phutela and K.S. Pitzer, J. Sol. Chem. 12, 201 (1983)]. In this study, residence time was first taken into consideration in the study of Ca²⁺–Cl^? ion pairing, and it was found that contact ion pair and solvent-sharing ion pair start to form at the CaCl₂(aq) concentrations of about 4.5 and 4 m, respectively, which may be responsible for the apparent discontinuity. In addition, the residence time of water molecules around Ca²⁺ or Cl^? showed that the hydration structures of Ca²⁺ and Cl^? are flexible with short residence time (<1 ns). It needs to be pointed out that it takes much longer simulation time for the CaCl₂–H₂O system to reach equilibrium than what was assumed in previous studies.     

Applicability of molecular dynamics method to the pressure-driven gas flow in finite length nano-scale slit pores

This study investigates the applicability of the molecular dynamics (MD) method to the pressure-driven gas flow in finite length nano-scale slit pores. The reflecting particle membrane is introduced to induce a pressure difference between the inlet and outlet. The flow properties are compared with those of the Burnett equations. The inlet and outlet pressures, as well as the mass flow rate in these two simulations are maintained the same by adjusting the tangential momentum accommodation coefficient in the Burnett simulation, which is found to be between 0.4 and 0.5. Qualitative and quantitative agreements are observed between the MD and Burnett simulation results in the bulk of the pore for both streamwise distributions and cross-section profiles. The MD simulation shows an advantage in the near-wall region, in which the wall force field dominates flow behaviour. This study indicates that MD simulation can be used to describe the pressure-driven gas flow characteristics in finite length nano-scale slit pores.