LJ团簇和H2O团簇的局域优化计算

将传统分子动力学方法中时间积分步长定义成粒子的最大加速度、最大速度和变化的最大允许空间步长的函数,并给出了空间步长的确定方法.作为对这个算法有效性的检验,计算了较小Lennard-Jones团簇和H₂O团簇的稳定结构,发现了新的(H₂O)₁₃的最小能结构.     

单壁碳纳米管储氢研究

摘要 利用Gaussian03程序计算出C-H键的键能是1.88eV，键长是0.113nm。已知H-H键能是4.748eV，键长是0.074nm。显然， H-H键能大于C-H键的键能，所以在常温常压下碳纳米管储氢时，以物理吸附H2分子为主，化学形式的C-H键吸附为辅。另外，利用LJ势能函数，计算了H2分子在碳纳米管中C原子所成的六边形中心正上方、C原子正上方以及相邻两C原子中间正上方时H2分子与碳纳米管之间的势能。得到无论管内、管外或者两端，都是H2分子在C原子所成的六边形中心正上方时能量最低。且在管内时H2分子距离管壁的距离是0.320nm，在管外时距离管壁的距离是0.309nm；在两端的管内时距离管壁的距离是0.324nm，在两端的管外时距离管壁的距离是0.313nm。     

Orientations of special water dipoles that accelerate water molecules exiting from carbon nanotube

One-dimensional ordered water molecules entering and exiting from a carbon nanotube with an appropriate radius are studied with molecular dynamics simulations.It can be found that a water molecule near the nanotube end is more likely to be expelled from the nanotube if its dipole is almost perpendicular to the nanotube axis.The key to this observation is that those water molecules axe closer to the wall of the nanotube away from the equilibrium position of the Lennar-Jones (LJ) potential.Thus,the interaction energy for those water molecules is relatively high.There are two particular structures of the perpendicular water molecule depending on the dipole direction of the adjacent water molecule in the nanotube.Although the probabilities of these structures are quite small,their contributions to the net flux across the nanotube end are approximately equal to the predominant structures.The present findings further show the possibility of controlling the water flow by regulating the dipole directions of the water molecules inside the nanochannels.     

Orientations of special water dipoles that accelerate water molecules exiting from carbon nanotube

One-dimensional ordered water molecules entering and exiting from a carbon nanotube with an appropriate radius are studied with molecular dynamics simulations. It can be found that a water molecule near the nanotube end is more likely to be expelled from the nanotube if its dipole is almost perpendicular to the nanotube axis. The key to this observation is that those water molecules are closer to the wall of the nanotube away from the equilibrium position of the Lennar-Jones (LJ) potential. Thus, the interaction energy for those water molecules is relatively high. There are two particular structures of the perpendicular water molecule depending on the dipole direction of the adjacent water molecule in the nanotube. Although the probabilities of these structures are quite small, their contributions to the net flux across the nanotube end are approximately equal to the predominant structures. The present findings further show the possibility of controlling the water flow by regulating the dipole directions of the water molecules inside the nanochannels.     

论VLW状态方程

 论述了VLW状态方程中爆轰产物分子势参数的确定；根据不同类型炸药爆轰性能参数计算结果对炸药爆轰产物碳在CJ态的相进行了分析讨论，认为不同的炸药，产物碳有石墨和金刚石两种相存在；将VLW状态方程和BKW状态方程进行了比较分析，指出了BKW状态方程与VLW状态方程的区别及其产生的原因，并给出了VLW状态方程计算含能材料（包括高能炸药、燃料空气炸药、民用炸药）的爆轰性能参数计算结果。结果表明，计算值与实验值符合较好。     

Adsorption of DNA onto anionic lipid surfaces

Currently self-assembled DNA delivery systems composed of DNA multivalent cations and anionic lipids are considered to be promising tools for gene therapy. These systems become an alternative to traditional cationic lipid–DNA complexes because of their low cytotoxicity lipids. However, currently these nonviral gene delivery methods exhibit low transfection efficiencies. This feature is in large part due to the poorly understood DNA complexation mechanisms at the molecular level. It is well-known that the adsorption of DNA onto like charged lipid surfaces requires the presence of multivalent cations that act as bridges between DNA and anionic lipids. Unfortunately, the molecular mechanisms behind such adsorption phenomenon still remain unclear. Accordingly a historical background of experimental evidence related to adsorption and complexation of DNA onto anionic lipid surfaces mediated by different multivalent cations is firstly reviewed. Next, recent experiments aimed to characterise the interfacial adsorption of DNA onto a model anionic phospholipid monolayer mediated by Ca^2 + (including AFM images) are discussed. Afterwards, modelling studies of DNA adsorption onto charged surfaces are summarised before presenting preliminary results obtained from both CG and all-atomic MD computer simulations. Our results allow us to establish the optimal conditions for cation-mediated adsorption of DNA onto negatively charged surfaces. Moreover, atomistic simulations provide an excellent framework to understand the interaction between DNA and anionic lipids in the presence of divalent cations. Accordingly,our simulation results in conjunction go beyond the macroscopic picture in which DNA is stuck to anionic membranes by using multivalent cations that form glue layers between them. Structural aspects of the DNA adsorption and molecular binding between the different charged groups from DNA and lipids in the presenceof divalent cations are reported in the last part of the study. Although this research work is far from biomedical applications, we truly believe that scientific advances in this line will assist, at least in part, in the rationaldesign and development of optimal carrier systems for genes and applicable to other drugs.     

提高水分子流出纳米碳管速度的特殊水分子偶极排布研究

使用分子动力学的方法,研究了水分子进出狭窄碳纳米管的过程．发现管口处水分子的偶极垂直于碳管时容易流出碳管．根据碳管中与之相邻的水分子的偶极方向可以把这种特殊构型分为2类．虽然,这2类特殊结构的出现概率非常小,但是它们对净流过碳管水分子的贡献与其它结构的贡献基本相同．这2种偶极排布中水分子比较接近管壁、远离Lennard-Jones势的平衡位置,导致这2种偶极排布中水分子能量升高,处于相对不稳定的状态,容易流出碳管．这个发现表明可以通过调控碳纳米管内的水分偶极方向控制管内的水分子流动．     

Determination of the structure factor for the rare gas fluids based on the ORPA theory and LIR equation of state

Linear isotherm regularity is applied to generate an expression for the direct correlation function (DCF), based on the optimized random-phase approximation theory. We use the Lennard-Jones potential in the modelling of real fluids, in which its molecular parameters are state-dependent. Based on the perturbation theory, we assume that the core contribution of the DCF is related to the geometric effect via a linear form, which arises from the excluded volume, and the tail contribution is related to the long-range intermolecular interactions of the system via a non-linear form. We use this model to predict the behaviour of the structure factor, S(k), in a wide range of k values for the xenon and krypton liquids. Finally, we compare our results with the experimental and theoretical data available in literature. The model is also successful in the presentation of the Ornstein–Zernike behaviour of S(k) at the low-k region.