Cloning and characterization of squalene synthase (SQS) gene from Ganoderma lucidum.

This report provides the complete nucleotide sequences of the full-length cDNA encoding squalene synthase (SQS) and its genomic DNA sequence from a triterpene-producing fungus, Ganoderma lucidum. The cDNA of the squalene synthase (SQS) (GenBank Accession Number: DQ494674) was found to contain an open reading frame (ORF) of 1,404 bp encoding a 468-amino-acid polypeptide, whereas the SQS genomic DNA sequence (GenBank Accession Number: DQ494675) consisted of 1,984 bp and contained four exons and three introns. Only one gene copy was present in the G lucidum genome.

Tuning the electronic structures of semiconducting SiC nanotubes by N and NHx (x=1,2) groups.

We investigate the stable configurations and electronic structures of silicon carbide nanotubes (SiCNTs) decorated by N and NHx (x=1,2) groups by using first-principles calculations. We find that these groups can be chemically incorporated into the network of SiCNTs in different ways, accompanied with the formation of N-C and N-Si bonds. The adsorbing energy of N and NHx (x=1,2) groups on (5,5) and (8,0) SiCNTs ranges from -1.

Electron stopping power and inelastic mean free path in amino acids and protein over the energy range of 20-20,000 eV.

Systematic calculations of stopping power (SPs) and inelastic mean free path (IMFP) values for 20-20,000 eV electrons in a group of 15 amino acids and a simple protein have been performed. The calculations are based on the dielectric response model and take into account the exchange effect between the incident electron and target electrons. The optical energy-loss functions for the 15 investigated amino acids and the protein are evaluated by using an empirical approach, because of the lack of experimental optical data.

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).

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.

Manipulating the electronic structures of silicon carbide nanotubes by selected hydrogenation.

We show that the electronic and atomic structures of silicon carbide nanotubes (SiCNTs) undergo dramatic changes with hydrogenation from first-principles calculations based on density-functional theory. The exo-hydrogenation of a single C atom results in acceptor states close to the highest occupied valence band of pristine SiCNT, whereas donor states close to the lowest unoccupied conduction band appear as a Si atom being hydrogenated. Upon fully hydrogenating Si atoms, (8,0) and (6,6) SiCNTs become metallic with very high density of states at the Fermi level.

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.

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.