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.

Investigation of periodicity fluctuations in strained (GaNAs)(1)(GaAs)(m) superlattices by the kinematical simulation of x-ray diffraction

Periodicity fluctuations of layer thickness and composition in a superlattice not only decrease the intensity, they also broaden the width of the satellite peaks in the x-ray diffraction pattern. In this letter, we develop a method that is dependent on the width of satellite peaks to assess periodicity fluctuations of a superlattice quickly. A linear relation of the magnitude of fluctuations, peak width and peak order has been derived from x-ray diffraction kinematical theory. By means of this method, periodicity fluctuations in strained (GaNAs)(1)(GaAs)(m) superlattices grown on GaAs substrates by molecular beam epitaxy have been studied. Distinct satellite peaks indicate that the superlattices are of high quality. The N composition of 0.25 and its fluctuation of 20% in a strained GaNxAs1-x monolayer are obtained from simulations of the measured diffraction pattern. The x-ray simulations and in situ observation results of reflection high-energy electron diffraction are in good agreement. (C) 1999 American Institute of Physics. [S0003-6951(99)00828-1].

delegation model for periodicity constraints-based dac

Xidian University

Lateral periodicity in highly-strained (GaIn)As/Ga(PAs) superlattices investigated by X-ray scattering techniques

In this work we investigate the lateral periodicity of symmetrically strained (GaIn)As/GaAs/Ga(PAs)/GaAs superlattices by means of X-ray scattering techniques. The multilayers were grown by metalorganic Vapour phase epitaxy on (001)GaAs substrates, which were intentionally off-oriented towards the [011]-direction. The substrate off-orientation and the strain distribution was found to affect the structural properties of the superlattices inducing the generation of laterally ordered macrosteps. Several high-resolution triple-crystal reciprocal space maps, which were recorded for different azimuth angles in the vicinity of the (004) Bragg diffraction and contour maps of the specular reflected beam collected in the vicinity of the (000) reciprocal lattice point, are reported and discussed. The reciprocal space maps clearly show a two-dimensional periodicity of the X-ray peak intensity distribution which can be ascribed to the superlattice periodicity in the direction of the surface normal and to a lateral periodicity in a crystallographic direction coinciding with the miscut orientation. The distribution and correlation of the vertical as well as of the lateral interface roughness was investigated by specular reflectivity and diffuse scattering measurements. Our results show that the morphology of the roughness is influenced by the off-orientation angle and can be described by a 2-dimensional waviness.

Asymptotic periodicity of the Volterra equation with infinite delay

For some species, hereditary factors have great effects on their population evolution, which can be described by the well-known Volterra model. A model developed is investigated in this article, considering the seasonal variation of the environment, where the diffusive effect of the population is also considered. The main approaches employed here are the upper-lower solution method and the monotone iteration technique. The results show that whether the species dies out or not depends on the relations among the birth rate, the death rate, the competition rate, the diffusivity and the hereditary effects. The evolution of the population may show asymptotic periodicity, provided a certain condition is satisfied for the above factors. (c) 2006 Elsevier Ltd. All rights reserved.

Asymptotic weighted-periodicity of the impulsive parabolic equation with time delay

The main aim of this paper is to investigate the effects of the impulse and time delay on a type of parabolic equations. In view of the characteristics of the equation, a particular iteration scheme is adopted. The results show that Under certain conditions on the coefficients of the equation and the impulse, the solution oscillates in a particular manner-called "asymptotic weighted-periodicity".

Magnetic properties and magnetic domain structure of bulk glass forming Nd60Al10Fe20Co10 alloy

The transition from hard to soft magnetic behaviour with increasing quenching rate is shown for Nd60WAl10Fe20Co10 melt-spun ribbons with different thickness. Microstructure and magnetic domain structure of ribbons were studied by magnetic force microscopy (MFM). Particle sizes < 5 nm decreasing gradually with increasing quenching rate were deduced from topographic images which differ from large-scale magnetic domains with a periodicity of about 350 nm in all ribbons irrespective the coercivity. This indicates that the magnetic properties of the alloy are governed by interaction of small magnetic particles. It is concluded that the presence of short-range-ordered structures with a local ordering similar to the Al metastable Nd-Fe binary phase is responsible for the hard magnetic properties in samples subjected to relatively low quenching rate.

Mechanisms of ultrafast laser-induced deep-subwavelength gratings on graphite and diamond

Deep-subwavelength gratings with periodicities of 170, 120, and 70 nm can be observed on highly oriented pyrolytic graphite irradiated by a femtosecond (fs) laser at 800 nm. Under picosecond laser irradiation, such gratings likewise can be produced. Interestingly, the 170-nm grating is also observed on single-crystal diamond irradiated by the 800-nm fs laser. In our opinion, the optical properties of the high-excited state of material surface play a key role for the formation of the deep-subwavelength gratings. The numerical simulations of the graphite deep-subwavelength grating at normal and high-excited states confirm that in the groove the light intensity can be extraordinarily enhanced via cavity-mode excitation in the condition of transverse-magnetic wave irradiation with near-ablation-threshold fluences. This field enhancement of polarization sensitiveness in deep-subwavelength apertures acts as an important feedback mechanism for the growth and polarization dependence of the deep-subwavelength gratings. In addition, we suggest that surface plasmons are responsible for the formation of seed deep-subwavelength apertures with a particular periodicity and the initial polarization dependence. Finally, we propose that the nanoscale Coulomb explosion occurring in the groove is responsible for the ultrafast nonthermal ablation mechanism.

A uniform 290 nm periodic square structure on ZnO fabricated by two-beam femtosecond laser ablation

A uniform submicron periodic square structure was fabricated on the surface of ZnO by a technique of two linearly polarized femtosecond laser beams with orthogonal polarizations ablating material alternately. The formed two-dimensional ordering submicron structure consists of close-packed submicron squares with a spacial periodicity of 290 nm, which arises from the intercrossing of two orthogonal submicron ripple structures induced by the two beams respectively. The result demonstrates a noninterference effect of two-beam ablation based on the alternate technique, which should come from the polarization-dependent enhancement of the subwavelength ripple structure and the large interval of two alternate pulses. This two-beam alternate ablation technique is expected to open up prospects for the submicron fabrication of wide-bandgap materials.

不具有3-碱基周期性的编码序列初探

对 12 0个较短编码序列 (<12 0 0bp)的Fourier频谱进行分析表明 ,3 碱基周期性在短编码序列中并不是绝对存在的 .统计分析提示 ,编码序列有无 3 碱基周期性与序列的碱基组成和分布、所编码蛋白质氨基酸的选用和顺序以及同义密码子的使用都有一定的关系 .一般地 ,非周期 3序列中A +U含量高于G +C含量 ,周期 3序列的情况则相反 ;非周期 3序列中碱基在密码子三个位点上的分布比周期 3序列中的分布均匀 ;非周期 3序列密码子和氨基酸的使用偏向没有周期 3序列的大 .在利用Fourier分析方法预测DNA序列中的基因和外显子时 ,应充分考虑到这些现象

Otolith microstructure of Oxygymnocypris stewartii (Cypriniformes, Cyprinidae, Schizothoracinae) in the Lhasa River in Tibet, China

Otolith microstructure of Oxygymnocypris stewartii collected from the Lhasa River was examined and described with regards to the early life history events. The monthly changes in the number of microincrements on the margin of the otolith were examined to validate the approximately daily periodicity of otolith increment formation. The microstructure of otoliths was used to detect changes in microincrement deposition patterns corresponding with events during early life. The annuli, microincrements and checks including the hatch check, yolk absorption check and several recurrent patterns in the otolith were described. Periodicity of the recurrent patterns was weekly, fortnightly and monthly. Through counting the number of the microincrements, it was confirmed that the primary growth of O. stewartii was in a period of 7 or 8 months from late March to October; it was estimated that O. stewartii might hatch between April and May.

The reproductive traits of brown trout (Salmo trutta fario L.) from the Yadong River, Tibet

Some key aspects of the reproductive strategy of the brown trout (Salmo trutta fario L.) in the Yadong River, Tibet, including spawning season, age at sexual maturity, fecundity and egg size, have been studied. The majority of the samples were less than 215 mm and age ranged from 1 to 4 in both sexes, indicating that the majority of the fish were younger and the pressure by overfishing was high. The spawning periodicity was determined to be between the end of October and January, mainly in November and December. The ratio of male to female brown trout population (1.29:1 with P > 0.05) suggested no sex significant differences, although males were significantly more abundant than females in October (P < 0.0001) on monthly basis. Age and size of males and females at maturity was different and males matured earlier than females. Fecundity was markedly correlated with their body weight (P < 0.001, r = 0.9255), standard length (P < 0.01, r = 0.8879), and gonad weight (P < 0.001, r = 0.9366). The mean size of mature eggs in the spawning season was: 4.0 +/- 0.45 mm and tended to increase along with the female spawners size (P < 0.001, r = 0.9641). Further researches about the brown trout population in the Yadong River should be conducted on issues such as artificial reproduction, culture, conservation, management, and restocking.

Validation of a method of estimating age, modelling growth, and describing the age composition of Coilia mystus from the Yangtze Estuary, China

A collection of 577 Coilia mystus was made during April 2006 and 2007 from China's Yangtze Estuary to estimate the age structure and growth patterns of the population. Examination of sectioned sagittal otoliths revealed a periodic straight/curved growth pattern. The straight zone was from April to November, and the curved zone from October to May, indicating annual periodicity. Annual periodicity was also verified by margin zone analysis. The shift from a curved-zone to the next straight-zone stanza was defined as an annulus. The fish from which the otoliths were taken were 0-5 years old. The von Bertalanffy growth function was fitted to standard length (LS)-at-age data as L-S = 215.16 (1 - e(-0.53(t+0.30))) (n = 577, r(2) = 0.81, p < 0.05). The mature females included five age classes, ages 1 and 2 accounting for 74.3% of the population. The mature males included fish aged 1 and 2, those at age 1 accounting for 86.4% of the population. Mean length was smaller, and annual growth less, for mature males than for females of comparable age. The study demonstrated that the Yangtze population of C. mystus consists of more age classes than previously thought and that the age structure of the population needs to be considered in management decisions.

An in situ estimate of food consumption by icefish in Lake Chaohu, China

The icefish (Neosalanx taihuensis) of Lake Chaohu, China, foraged almost exclusively on crustacean zooplankton in both spring and summer. The icefish showed diurnal feeding periodicity, with peak feeding in the morning. No food was observed in icefish guts collected at night. Our results indicate that that the icefish was a particulate feeder and light intensity greatly affected its foraging on zooplankton. Daily consumption of zooplankton by icefish varied significantly both diurnally and among seasons, which ranged from 0.22 to 2.23 g (wet weight) per 100 g wet fish weight at temperatures between 16.3 degrees C (spring) and 28.8 degrees C (summer).