First-principles calculations of AlN nanowires and nanotubes: atomic structures, energetics, and surface states.

We explore the atomic and electronic structures of single-crystalline aluminum nitride nanowires (AlNNWs) and thick-walled aluminum nitride nanotubes (AlNNTs) with the diameters ranging from 0.7 to 2.2 nm by using first-principles calculations and molecular dynamics simulations based on density functional theory (DFT). We find that the preferable lateral facets of AlNNWs and thick-walled AlNNTs are {1010} surfaces, giving rise to hexagonal cross sections. Quite different from the cylindrical network of hexagons revealed in single-walled AlNNTs, the wall of thick-walled AlNNTs displays a wurtzite structure. The strain energies per atom in AlNNWs are proportional to the inverse of the wire diameter, whereas those in thick-walled AlNNTs are independent of tube diameter but proportional to the inverse of the wall thickness. Thick-walled AlNNTs are energetically comparable to AlNNWs of similar diameter, and both of them are energetically more favorable than single-walled AlNNTs. Both AlNNWs and AlNNTs are wide band gap semiconductors accompanied with surface states located in the band gap of bulk wurtzite AlN.

The effect of salt concentration on DNA conformation transition: a molecular-dynamics study.

We performed three 3-ns molecular dynamics simulations of d(CGCGAATTCGCG)2 using the AMBER 8 package to determine the effect of salt concentration on DNA conformational transitions. All the simulations were started with A-DNA, with different salt concentrations, and converged with B-DNA with similar conformational parameters. However, the dynamic processes of the three MD simulations were very different. We found that the conformation transition was slow in the solution with higher salt concentration. To determine the cause of this retardation, we performed three additional 1.5-ns simulations starting with B-DNA and with the salt concentrations corresponding to the simulations mentioned above. However, astonishingly, there was no delayed conformation evolution found in any of the three simulations. Thus, our simulation conclusion is that higher salt concentrations slows the A --> B conformation transition, but have no effect on the final stable structure. [Figure: see text].

Distribution patterns and controllable transport of water inside and outside charged single-walled carbon nanotubes.

The density distribution patterns of water inside and outside neutral and charged single-walled carbon nanotubes (SWNTs) soaked in water have been studied using molecular dynamics simulations based on TIP3P potential and Lennard-Jones parameters of CHARMM force field, in conjunction with ab initio calculations to provide the electron density distributions of the systems. Water molecules show different electropism near positively and negatively charged SWNTs. Different density distribution patterns of water, depending on the diameter and chirality of the SWNTs, are observed inside and outside the tube wall. These special distribution patterns formed can be explained in terms of the van der Waals and electrostatic interactions between the water molecules and the carbon atoms on the hexagonal network of carbon nanotubes. The electric field produced by the highly charged SWNTs leads to high filling speed of water molecules, while it prevents them from flowing out of the nanotube. Water molecules enter the neutral SWNTs slowly and can flow out of the nanotube in a fluctuating manner. It indicates that by adjusting the electric charge on the SWNTs, one can control the adsorption and transport behavior of polar molecules in SWNTs to be used as stable storage medium with template effect or transport channels. The transport rate can be tailored by changing the charge on the SWNTs.

Cross sections of electron inelastic interactions in DNA.

The cross sections of electron inelastic interaction in DNA are calculated using the dielectric response theory and Penn statistical approximation, with the exchange correction included. An empirical approach to obtain optical energy loss function is given for the organic compounds without available optical data. Comparisons of the calculated data with available experimental and theoretical results have been done to show the reliability of the approach proposed in this work. Using this approach, the total inelastic cross sections for five bases: guanine, adenine, thymine, cytosine and uracil have been calculated in the energy range of E< or =10 keV and compared with those recently obtained with the Deutsch-Mark formalism and the Binary-Encounter-Bethe model, respectively. An equivalent unit of the DNA molecule is constructed according to the contents of A-T and G-C base pairs in DNA, and is divided into five constituents, i.e. sugar-phosphate and four bases. The total inelastic cross sections for the constructed unit of the DNA molecule and its constituents have also been calculated.