Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water-K+-TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT. (C) 2002 Elsevier Science B.V. All rights reserved.

The comparative analysis of the energies of conjugated triple base triplets and their applications

We built 64 sets of 3D models of DNA triplex base triplets (TBT) and minimized their energies. The TBTs were divided into 32 pairs of conjugated ones on the basis of their sequence characteristic, and the energies of each pair of them were compared and analyzed, the results showed: (i) The duplex DNA of which any strand contains at least a couple of A or T, has a preference for selecting the oligodeoxyribonucleic acid (ODN) strand containing abundant T to form TBT. (ii) The duplex DNA of which any strand contains at least a couple of G or C has a preference for selecting ODN containing abundant G to form symmetric antiparallel TBT, but selecting ODN containing abundant C to form asymmetric parallel TBT. (iii) The duplex DNA of which any strand contains only one of A, T, G or C has a preference for selecting ODN containing abundant pyrimidines (T or C) to form antiparallel TBT. Additionally, two examples of TBTs applications, in designing ODN to form triplex with duplex were presented. The energy calculation result revealed that 15-TCG is the best ligand of the HIV PPT duplex. The comparative analysis of energies of the conjugated TBTs provides directive significance for designing ODN strand that is easy to form triplex in theory. (C) 2002 Elsevier Science B.V. All rights reserved.

1310 nm GaInNAs triple quantum well laser with 13 GHz modulation bandwidth

The emission wavelength of a GaInNAs quantum well (QW) laser was adjusted to 1310 nm, the zero dispersion wavelength of optical fibre, by an appropriate choice of QW composition and thickness and N concentration in the barriers. A triple QW design was employed to enable the use of a short cavity with a small photon lifetime while having sufficient differential gain for a large modulation bandwidth. High speed, ridge waveguide lasers fabricated from high quality material grown by molecular beam epitaxy exhibited a damped modulation response with a bandwidth of 13 GHz.

Transmission electron microscopy study of triple-ribbon contrast features in a ZnTe epitaxial layer

A transmission electron microscopy study of triple-ribbon contrast features in a ZnTe layer grown epitaxially on a vicinal GaAs (001) substrate is reported. The ribbons go through the layer as threading dislocations near the [<(11)over bar 2>](111) or [112](<(11)over bar 1>) directions. Each of these (with a 40 nm width) has two narrow parts enclosed by three partial dislocations (with a 20 nm spacing). By contrast analysis and contrast simulation, the ribbons have been shown to be composed of two partially overlapping stacking faults. Their origin is attributed to a forced reaction between two crossing perfect misfit dislocations.

Kondo effect in a triangular triple quantum dots ring with three terminals

For a triangular triple quantum dots (TTQDs) ring with three terminals, when lowering one of the dot-lead coupling to realize the left-right (L-R) reflection symmetry coupling, the internal C-upsilon of the TTQDs is well preserved in the absence of many-body effect for the symmetric distribution of the dot-lead coupling on the molecular orbits. In the presence of Kondo effect, the decrement of one of the dot-lead couplings suppresses the inter-dot hopping. This happens especially for the coupled quantum dot (QD), which decouples with the other two ones gradually to form a localized state near the Fermi level As a result, the internal dynamic symmetry of the TTQDs ring is reduced to L-R reflection symmetry, and simultaneously, the linear conductance is lifted for the new forming molecular orbit near the Fermi level

Multi-channel effect of condensation flow in a micro triple-channel condenser

Multi-channel effect is important to understand transport phenomenon in phase change systems with parallel channels. In this paper, visualization studies were performed to study the multi-channel effect in a silicon triple-channel condenser with an aspect ratio of 0.04. Saturated water vapor was pumped into the microcondenser, which was horizontally positioned. The condenser was cooled by the air natural convention heat transfer in the air environment. Flow patterns are either the annular flow at high inlet vapor pressures, or a quasi-stable elongated bubble at the microchannel upstream followed by a detaching or detached miniature bubble at smaller inlet vapor pressures. The downstream miniature bubble was detached from the elongated bubble tip induced by the maximum Weber number there. It is observed that either a single vapor thread or dual vapor threads are at the front of the elongated bubble. A miniature bubble is fully formed by breaking up the vapor thread or threads. The transient vapor thread formation and breakup process is exactly symmetry against the centerline of the center channel. In side channels, the Marangoni effect induced by the small temperature variation over the channel width direction causes the vapor thread formation and breakup process deviating from the side channel centerline and approaching the center channel. The Marangoni effect further forces the detached bubble to rotate and approach the center channel, because the center channel always has higher temperatures, indicating the multi-channel effect. 

Compact and efficient triple-pass optical parametric chirped pulse amplification

Compact and efficient triple-pass optical parametric chirped pulse amplification in a single crystal has been demonstrated. The signal was triple-pass amplified in a single nonlinear crystal by a nanosecond pump pulse. The first-pass optical parametric amplification is completely phase matched in the plane of the maximum effective nonlinearity, and the other two passes work symmetrically near to the first-pass optical parametric amplification plane. This architecture efficiently increases the overall gain, overcomes the optical parametric fluorescence, and clearly simplifies the amplification scheme.

A High-Performance Silicon Electro-Optic Phase Modulator with a Triple MOS Capacitor

We propose and analyze a novel Si-based electro-optic modulator with an improved metal-oxide-semiconductor (MOS) capacitor configuration integrated into silicon-on-insulator (SOI).Three gate-oxide layers embedded in the silicon waveguide constitute a triple MOS capacitor structure,which boosts the modulation efficiency compared with a single MOS capacitor.The simulation results demonstrate that the VπLπ product is 2.4V·cm.The rise time and fall time of the proposed device are calculated to be 80 and 40ps from the transient response curve,respectively,indicating a bandwidth of 8GHz.The phase shift efficiency and bandwidth can be enhanced by rib width scaling.

A single-strand conformation polymorphism method by capillary electrophoresis with laser-induced fluorescence for detection of the T1151A mutation in hMLH1 gene

Mutation of hMLH1 gene plays an important role in human tumorigenesis. A highly sensitive single-strand conformation polymorphism (SSCP) method for detection of the T1151A mutation in exon 12 of the hMLH1 gene was for the first time developed employing laser-induced fluorescence capillary electrophoresis (LIF-CE). Effects of the concentration of linear polyacrylamide solution, running temperature, running voltage and the addition of glycerol on SSCP analysis were investigated, and the optimum separation conditions were defined. Thirty colorectal cancer patients and eight lung cancer patients were screened and the T1151A mutation was found in four of them. Based on CE-sequencing the mutation was further confirmed. To our knowledge, this is for the first time that the T1151A mutation is found in lung cancer. Our method is simple, rapid, and highly sensitive and is well suited to the analysis of large numbers of clinical samples.

Effects of pH on the Interactions and Conformation of Bovine Serum Albumin: Comparison between Chemical Force Microscopy and Small-Angle Neutron Scattering

The conformation of bovine serum albumin (BSA), as well as its interactions with negatively charged mica surfaces in saline solutions of different pH values, have been studied by small-angle neutron scattering (SANS) and chemical force microscopy (CFM), respectively. A new approach to extract the contribution of elementary interactions from the statistically averaged force-extension curves through self-consistent fitting was proposed and used to understand the effects of pH on the interactions and conformation of BSA in saline solutions. When pH increases, the SANS results reveal that the sizes of BSA molecules increase slightly, while the statistical analysis of the CFM results shows that the averaged pull-off force for the elongation monotonously decreases. The decrease of pull-off force with the increase of pH results from the decrease in the strength of hydrogen bonding and the number of interaction pairs, as well as the slight increase of the strength of van der Waals interaction. When pH approaches the isoelectric point (pI) of BSA, results from both SANS and CFM suggest a loss of long-range interactions in BSA molecules. Our results also suggest that the force-extension curve is mainly contributed by the van der Waals interaction. The combination of SANS and CFM provides new insight to understand the interactions and conformation of BSA molecules