A Gibbs approach to Chargaff's second parity rule

Chargaff's second parity rule (CSPR) asserts that the frequencies of short polynucleotide chains are the same as those of the complementary reversed chains. Up to now, this hypothesis has only been observed empirically and there is currently no explanation for its presence in DNA strands. Here we argue that CSPR is a probabilistic consequence of the reverse complementarity between paired strands, because the Gibbs distribution associated with the chemical energy between the bonds satisfies CSPR. We develop a statistical test to study the validity of CSPR under the Gibbsian assumption and we apply it to a large set of bacterial genomes taken from the GenBank repository.Comment: 16 page

Flutter mechanism of sheet

Basic study has been conducted on sheet flutter which becomes an obstacle to the operation of printing machines and paper making machines in higher speed. Following three topics are presented in this paper.(1) Fluctuating pressure causes sheet flutter. This fluctuation occurs as the vortex separates at the leading edge of the sheet and grows toward the downstream corresponding to the sheet movement.(2) Characteristics of sheet flutter were clarified with respect to the following points.(a) Flutter mode, (b) Flutter amplitude, (c) Flutter frequency, (d) Influence of damping factor(3) The critical velocity of sheet flutter is determined by the following three parameters.(a) Aspect ratio (b/c), (b) Rigidity parameter (Eh3/12pAc 3), (c) Mass ratio (pph/pAc)(where b = sheet width, c = sheet length, h = sheet thickness, E = Young's modulus, pp= Sheet density, pA= Air density

Eustatic change modulates exhumation in the Japanese Alps

The exhumation of bedrock is controlled by the interplay between tectonics, surface processes, and climate. The highest exhumation rates of centimeters per year are recorded in zones of highly active tectonic convergence such as the Southern Alps of New Zealand or the Himalayan syntaxes, where high rock uplift rates combine with very active surface processes. Using a combination of different thermochronometric systems including trapped-charge thermochronometry, we show that such rates also occur in the Hida Mountain Range, Japanese Alps. Our results imply that centimeter per year rates of exhumation are more common than previously thought. Our thermochronometry data allow the development of time series of exhumation rate changes at the time scale of glacial-interglacial cycles, which show a fourfold increase in baseline rates to rates of ~10 mm/yr within the past ~65 k.y. This increase in exhumation rate is likely explained by knickpoint propagation due to a combination of very high precipitation rates, climatic change, sea-level fall, range-front faulting, and moderate rock uplift. Our data resolve centimeter-scale sub-Quaternary exhumation rate changes, which show that in regions with horizontal convergence, coupling between climate, surface processes, and tectonics can exert a significant and rapid effect on rates of exhumatio

Does codon bias have an evolutionary origin?

<p>Abstract</p> <p>Background</p> <p>There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information about the origin and evolution of this bias.</p> <p>Results</p> <p>Codon Usage Bias (CUB, defined here as deviation from equal usage of synonymous codons) was studied in 113 species. The average CUB was 29.3 ± 1.1% (S.E.M, n = 113) of the theoretical maximum and declined progressively with evolution and increasing genome complexity. A Pan-Genomic Codon Usage Frequency (CUF) Table was constructed to describe genome-wide relationships among codons. Significant correlations were found between the number of synonymous codons and (i) the frequency of the respective amino acids (ii) the size of CUB. Numerous, statistically highly significant, internal correlations were found among codons and the nucleic acids they comprise. These strong correlations made it possible to predict missing synonymous codons (wobble bases) reliably from the remaining codons or codon residues.</p> <p>Conclusion</p> <p>The results put the concept of "codon bias" into a novel perspective. The internal connectivity of codons indicates that all synonymous codons might be integrated parts of the Genetic Code with equal importance in maintaining its functional integrity.</p

Short communication: Inverse correlation between radiation damage and fission-track etching time on monazite

In this study, we explored the impacts of radiation damage and chemical composition on the etching time of fission tracks in monazite. Despite the potential of monazite fission-track (MFT) dating as an ultralow-temperature thermochronology, the comprehensive effects of radiation damage and non-formula elements, especially on the etching rate of MFTs, remain unexplored, and established analytical procedures are lacking. We quantified the degree of radiation damage (ΔFHWM) in Cretaceous to Quaternary monazites distributed in the Japan arc through Raman spectroscopy and chemical composition analyses. Subsequently, MFT etching was performed to examine the correlation between these parameters and the etching time. Estimation of the degree of radiation damage showed an increase in radiation damage corresponding to the cooling age of each geological unit. For example, the Toya ignimbrite (ca. 0.1 Ma) and the Kurobegawa granodiorite (&lt; 0.8 Ma), both of which are types of monazite from Quaternary geological units, have ΔFHWM values of 0.27 and 0.55 cm−1, respectively. In contrast, the Muro ignimbrite (ca. 15 Ma) has a ΔFHWM value of 4.01 cm−1, while the Kibe granite and the Sagawa granite, both of which are Cretaceous granitoids, yielded 7.35 and 6.31 cm−1, respectively. MFT etching of these samples according to the existing recipe (6 M HCl at 90 °C for 60–90 min) was completed at 1200, 860, 210, 120, and 90 min for the Toya ignimbrite, Kurobegawa granodiorite, Muro ignimbrite, Sagawa granite, and Kibe granite, respectively. These outcomes highlight an inverse relationship between MFT etching time and the degree of radiation damage in monazite, while the correlation between MFT etching time and chemical composition was unclear. The results affirm earlier considerations that the etching rate of MFTs is strongly influenced by radiation damage. Conversely, young samples with lower levels of radiation damage exhibit higher chemical resistance, suggesting that existing etching recipes may not adequately etch MFTs.</p

An observation of spin-valve effects in a semiconductor field effect transistor: a novel spintronic device

We present the first spintronic semiconductor field effect transistor. The injector and collector contacts of this device were made from magnetic permalloy thin films with different coercive fields so that they could be magnetized either parallel or antiparallel to each other in different applied magnetic fields. The conducting medium was a two dimensional electron gas (2DEG) formed in an AlSb/InAs quantum well. Data from this device suggest that its resistance is controlled by two different types of spin-valve effect: the first occurring at the ferromagnet-2DEG interfaces; and the second occuring in direct propagation between contacts.Comment: 4 pages, 2 figure

Optical limiting in solid-core photonic crystal fibers

Optical limiting in solid-core photonic crystal fibers filled with reverse-saturable absorbers has been observed. A sharp change in limiting threshold was found for materials in the fiber holes with refractive indices near n = 1.44