Modal fields and bending loss analyses of three-layer large flattened mode fibers

Theoretical method to analyze three-layer large flattened mode (LFM) fibers is presented. The modal fields, including the fundamental and higher order modes, and bending loss of the fiber are analyzed. The reason forming the different modal fields is explained and the feasibility to filter out the higher order modes via bending to realize high power, high beam quality fiber laser is given. Comparisons are made with the standard step-index fiber. (c) 2006 Elsevier B.V. All rights reserved.

Electric and magnetic losses and gains in determining the sign of refractive index

Within the framework of classic electromagnetic theories, we have studied the sign of refractive index of optical medias with the emphases on the roles of the electric and magnetic losses and gains. Starting from the Maxwell equations for an isotropic and homogeneous media, we have derived the general form of the complex refractive index and its relation with the complex electric permittivity and magnetic permeability, i.e. n = root epsilon mu, in which the intrinsic electric and magnetic losses and gains are included as the imaginary parts of the complex permittivity and permeability, respectively, as epsilon = epsilon(r) + i(epsilon i) and mu = mu(r) + i mu(i). The electric and magnetic losses are present in all passive materials, which correspond, respectively, to the positive imaginary permittivity and permeability epsilon(i) > 0 and mu(i) > 0. The electric and magnetic gains are present in materials where external pumping sources enable the light to be amplified instead of attenuated, which correspond, respectively, to the negative imaginary permittivity and permeability epsilon(i) < 0 and mu(i) < 0. We have analyzed and determined uniquely the sign of the refractive index, for all possible combinations of the four parameters epsilon(r), mu(r), epsilon(i), and mu(i), in light of the relativistic causality. A causal solution requires that the wave impedance be positive Re {Z} > 0. We illustrate the results for all cases in tables of the sign of refractive index. One of the most important messages from the sign tables is that, apart from the well-known case where simultaneously epsilon < 0 and mu < 0, there are other possibilities for the refractive index to be negative n < 0, for example, for epsilon(r) < 0, mu(r) > 0, epsilon(i) > 0, and mu(i) > 0, the refractive index is negative n < 0 provided mu(i)/epsilon(i) > mu(r)/vertical bar epsilon(r)vertical bar. (c) 2006 Elsevier B.V. All rights reserved.

Comparison of quantum chemistry calculation methods of nucleic acid base-quartets

Nine base-quartets were calculated by six semi-empirical methods and ab initio Hartree-Fork method using STO-3G basis set. The results showed that PM3 method can be use to calculate base quartets, the results of PM3 calculations are close to the ab initio

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

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.

Tentative study of the coding sequences without 3-base periodicity

Fourier spectra of 120 short coding sequences (<1 200 bp) show that not all coding sequences are characterized by 3-base periodicity. Statistical analysis suggests that whether a coding sequence has 3-base periodicity may be related to the composition and distribution of bases, the usage and the order of the amino acids of the encoded protein as well as the synonymous codon usage. Generally, the content of A+U is higher than that of G+C in non-period-3 sequences, inversely in period-3 sequences. In the three codon positions, the base distribution in the non-periodic-3 sequences is more uniform than in the periodic-3 sequences. The usage biases of the amino acids and the codons in non-period-3 sequences are weaker than that in period-3 sequences. All of these phenomena should be considered sufficiently in predicting the genes and exons of DNA sequences by Fourier analysis method.

PNA(T).DNA(AT) triplexes with Hoogsteen base pairing are more favorable

Peptide nucleic acids (PNAs) are nucleic acid analogs with the deoxyribose phosphate backbone replaced by pseudo-peptide polymers to which the nucleobases are linked. The achiral, uncharged and rather flexible properties of the peptide backbone permit peptide nucleic acids more potential than oligonucleotides in application to antisence and antigenic reagents. The process of PNA binding to DNA duplex and forming triplex is the first step of PNA interacting with PNA. But there are no PNA.2DNA triplex crystal data up to date and little has been reported on the structure features and the force of the PNA.2DNA triplex. In this work, PNA(T).DNA(AT) triplexes are successfully built and the structures and forces to stabilize the triplex after optimizations and molecule dynamics are systematically examined, which are expected to aid in the application of PNAs as anticense and antigene agents.

Moisture content in Dall's porpoise (Phocoenoides dalli) tissues: a reference base for conversion factors between dry and wet weight trace element concentrations in cetaceans

Concentration of trace elements measured by dry weight basis has become more commonly used in recent studies on cetaceans than wet weight basis, which was used more in earlier studies. Because few authors present moisture content data in their papers, it is difficult to compare the concentrations of trace elements between various studies. Therefore, we felt that it would be useful if a reference conversion factor (CF) for tissue types could be found to convert between wet weight and dry weight data on trace element concentrations. We determined the moisture contents of 14 tissues of Dall's porpoise (Phocoenoides dalli), and then, calculated the CF values for those tissues. Because the moisture content of each tissue differs from other tissues, it is necessary to use a specific CIF for each tissue rather than a general CF for several tissues. We have also found that CIF values for Dall's porpoise tissues are similar to the same tissues in other cetaceans. Therefore CF values from Dall's porpoise can be reliably used to convert between wet and dry weight concentrations for other cetacean tissues as reference data. (C) 2002 Elsevier Science Ltd. All rights reserved.

A base-emitter self-aligned multi-finger Si1-xGex/Si power heterojunction bipolar transistor

With a crystal orientation dependent on the etch rate of Si in KOH-based solution, a base-emitter self-aligned large-area multi-linger configuration power SiGe heterojunction bipolar transistor (HBT) device (with an emitter area of about 880 mu m(2)) is fabricated with 2 mu m double-mesa technology. The maximum dc current gain is 226.1. The collector-emitter junction breakdown voltage BVCEO is 10 V and the collector-base junction breakdown voltage BVCBO is 16 V with collector doping concentration of 1 x 10(17) cm(-3) and thickness of 400 nm. The device exhibited a maximum oscillation frequency f(max) of 35.5 GHz and a cut-off frequency f(T) of 24.9 GHz at a dc bias point of I-C = 70 mA and the voltage between collector and emitter is V-CE = 3 V. Load pull measurements in class-A operation of the SiGe HBT are performed at 1.9 GHz with input power ranging from 0 dBm to 21 dBm. A maximum output power of 29.9 dBm (about 977 mW) is obtained at an input power of 18.5 dBm with a gain of 11.47 dB. Compared to a non-self-aligned SiGe HBT with the same heterostructure and process, f(max) and f(T) are improved by about 83.9% and 38.3%, respectively.

WG-like modes selectivity in a square cavity with posts

We investigate the characteristics of Whispering-Gallery(WG)-like modes in a square cavity with posts by employing the two-dimentional (2D) finite-difference time-domain (FDTD) technique combined with the effective index method. The results indicate that the posts can result in mode selection in the WG-like modes. The WG-like modes with odd mode numbers are not much sensitive to the sizes of the posts. However, the quality factor (i.e. Q-factor) of the WG-like modes with even mode numbers decreases sharply with the increasing size of the posts. The decreasing Q-factor is attributed to mode leakage and scattering loss due to the presence of the post. The mode selection increases with the mode spacing of square cavity twice in an optimized strucure.

On the performance analysis and design of a novel shared-layer integrated devices using RCE-p-i-n-PD/SHBT - art. no. 67820J

We have explored the shared-layer integration fabrication of an resonant-cavity-enhanced p-i-n photodector (RCE- p-i-n-PD) and a single heterojunction bipolar transistor (SHBT) with the same epitaxy grown layer structure. MOCVD growth of the different layer structure for the GaAs based RCE- p-i-n-PD/SHBT require compromises to obtain the best performance of the integrated devices. The SHBT is proposed with super-lattice in the collector, and the structure of the base and the collector of the SHBT is used for the RCE. Up to now, the DC characteristics of the integrated device have been obtained.

High speed silicon optical switches based on carrier depletion - art. no. 67812D

The novel design of a silicon optical switch on the mechanism of a reverse p-n junction is proposed. The figuration of contact regions at slab waveguides and the ion implantation technology for creation of junctions are employed in the new design. The two-layer rib structure is helpful for reduction of optical absorption losses induced by metal and heavily-doped contact. And more, simulation results show that the index modulation efficiency of Mach-Zehnder interferometer enhances as the concentrations of dopants in junctions increase, while the trade-off of absorption loss is less than 3 dB/mu m. The phase shift reaches about 5 x 10(-4) pi/mu m at a reverse bias of 10V with the response time of about 0.2ns. The preliminary experimental results are presented. The frequency bandwidth of modulation operation can arrive in the range of GHz. However, heavily-doped contacts have an important effect on pulse response of these switches. While the contact region is not heavily-doped, that means metal electrodes have schottky contacts with p-n junctions, the operation bandwidth of the switch is limited to about 1GHz. For faster response, the heavily-doped contacts must be considered in the design.