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.     

Concentration of nitrogen molecules needed by nitrogen nanobubbles existing in bulk water

This paper investigates the stability of nitrogen nanobubbles under dif~ ferent concentrations of nitrogen molecules by molecular dynamics simulations. It is found that the stability of nanobubbles is very sensitive to the concentration of nitrogen molecules in water. A sharp transition between disperse states and assemble states of nitrogen molecules is observed when the concentration of nitrogen molecules is changed. The relevant critical concentration of nitrogen molecules needed by the existing nitrogen nanobubbles is analyzed.     

液态水微观结构研究的新进展

液态水有很多奇异特性.近年来,对液态水以何种微观结构形式存在的问题争议激烈.文章介绍了当前对水的微观结构的一些研究及其进展,讨论了液态水中的氢键模式与水的结构关系,进而用一个简化模型探讨了氢键的取向性与强弱性对水的异常行为的作用.     

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.     

有限时间尺度内分子指向相关的不对称扩散研究

传统的经典扩散理论常常将分子和物体假设为球形,这些分子和物体的扩散是无偏移各向同性的。然而,当我们在纳米尺度去看分子和物体时,这些分子和物体呈现出各种不对称的结构。进一步,当我们观察的时间有限到小于几十纳秒时,我们会看到这些分子和物体的自由扩散表现出与它们的初始方位相关的特性。对于像甲醇分子这样的小分子,在约100 ps的有限时间内,常温下,不对称扩散能占到总扩散的10%左右。这样的不对称扩散丰富了分子的扩散理论,对生命和其他自然界现象的理解具有重要的意义,同时也可能提供一种通过控制分子的方向来驱动分子的方法。     

Determination of the vapor–liquid transition of square-well particles using a novel generalized-canonical-ensemble-based method

The square-well(SW) potential is one of the simplest pair potential models and its phase behavior has been clearly revealed, therefore it has become a benchmark for checking new theories or numerical methods. We introduce the generalized canonical ensemble(GCE) into the isobaric replica exchange Monte Carlo(REMC) algorithm to form a novel isobaric GCE-REMC method, and apply it to the study of vapor–liquid transition of SW particles. It is validated that this method can reproduce the vapor–liquid diagram of SW particles by comparing the estimated vapor–liquid binodals and the critical point with those from the literature. The notable advantage of this method is that the unstable vapor–liquid coexisting states,which cannot be detected using conventional sampling techniques, are accessed with a high sampling efficiency. Besides,the isobaric GCE-REMC method can visit all the possible states, including stable, metastable or unstable states during the phase transition over a wide pressure range, providing an effective pathway to understand complex phase transitions during the nucleation or crystallization process in physical or biological systems.     

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．     

Influence of atomic force microscope (AFM) probe shape on adhesion force measured in humidity environment

In micro-manipulation, the adhesion force has very important influence on behaviors of micro-objects. Here, a theoretical study on the effects of humidity on the adhesion force is presented between atomic force microscope （AFM） tips and substrate. The analysis shows that the precise tip geometry plays a critical role on humidity depen- dence of the adhesion force, which is the dominant factor in manipulating micro-objects in AFM experiments. For a blunt （paraboloid） tip, the adhesion force versus humidity curves tends to the apparent contrast （peak-to-valley corrugation） with a broad range. This paper demonstrates that the abrupt change of the adhesion force has high correla- tion with probe curvatures, which is mediated by coordinates of solid-liquid-vapor contact lines （triple point） on the probe profiles. The study provides insights for further under- standing nanoscale adhesion forces and the way to choose probe shapes in manipulating micro-objects in AFM experiments.     

Effect of interaction between loop bases and ions on stability of G-quadruplex DNA

G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics(MD), and steered MD(SMD)simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions(K⁺/Na⁺)is about the base stacking free energies indicates that there will be a competition among the binding of M⁺-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt.     

Gating of Water Flow Induced by Bending of a Carbon Nanotube

The ON-OFF state transition of the water transport induced by the structural bending of a carbon nanotube is studied by molecule dynamics simulation. The water permeation through a bent carbon nanotube shows excellent gating property with a threshold bending angle of about 14.6°. We also investigate the water density distribution inside the nanochannel to illustrate the mechanism.