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The low- and infralow-frequency (ε[sup *]) spectra have been studied for the polar phase of diglycine nitrate crystals of different history (slowly cooled and heated above the Curie point T[sub c]). The specific features of the spectra are discussed in terms of point defect "freezing" and interaction with domain walls. [ABSTRACT FROM AUTHOR]

scanning electron microscopy was used to study of the initial stages of the formation of a semipolar GaN(11 2) layer during Metalorganic Chemical Vapor Deposition on Si(113) substrates, on the surface of which U-shaped grooves with element sizes <100 nm (NP-Si(113)) were formed. It was found that NP-Si(113) substrates with a buffer AlN layer stimulate the formation of islands faceted by the planes m-GaN, c‑GaN. It is shown that there is a predominant growth of the m-GaN facet in comparison with c-GaN. The experimental results correspond to the Gibbs-Curie-Wolff selection principle, but taking into account elastic stresses in the c-GaN plane. [ABSTRACT FROM AUTHOR]

We have studied epitaxial layers of gallium nitride (GaN) in a template composition grown by surfactant-mediated hydride-chloride vapor phase epitaxy. The surfactant component was provided by 5 mass % additives of antimony and indium to the source of gallium. Comparative analysis of the obtained results shows evidence of the positive influence of surfactants on the morphology of epitaxial GaN layers. [ABSTRACT FROM AUTHOR]

A new method of synthesis of semipolar gallium nitride on a silicon substrate using the technology of solid-phase epitaxy of 3C-SiC nanocrystals has been suggested. It has been demonstrated that application of buffer layers of 3C-SiC and AlN enables one to form epitaxial layers of semipolar gallium nitride with layer deviation from the polar position of the c axis of a wurtzite crystal by an angle of 48°-51° at the minimal half-width of the X-ray diffraction rocking curve (ω) ∼ 24′. The observed bend of a cylindrical character in the structure of GaN/AlN/3C-SiC(001) is explained by the anisotropic deformation of semipolar GaN on silicon. [ABSTRACT FROM AUTHOR]

The effect of annealing temperature and time on the luminescence intensity of the InGaN/GaN heterostructure subjected to ion beam etching was studied. We show that annealing at a temperature of 1100°C makes it possible to eliminate the radiation defects in the GaN layers that arise in the etching process with a focused Ga+ ion beam (30 keV). [ABSTRACT FROM AUTHOR]

It has been studied the morphology of the surface of the semipolar gallium nitride layers synthesized on nano-pattemed Si(100) or Si(113) substrates with a V-shaped or U-shaped surface profile, respectively. The morphology of the surface of the semipolar layers indicates that the different height-to-width ratio of the GaN(11-22) and GaN(10-11) blocks is associated with a higher growth rate of the GAN(11-22) face than GaN(10-11) and with different growth rates of the semipolar and polar crystal faces during the nucleation of the layer on a nano-patterned substrate. [ABSTRACT FROM AUTHOR]

Abstract Background Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1) the fundamental veto on "foresight evolution", 2) modular structures of tRNAs and aminoacyl-tRNA synthetases, and 3) the updated library of aa-binding sites in RNA aptamers successfully selected in vitro for eight amino acids. Results The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. We have noticed that these cases might be associated with palindrome-dinucleotides. For example, one-base shift to the left brings arginine codons CGN, with CG at 1-2 positions, to the respective anticodons NCG, with CG at 2-3 positions. Formally, the concomitant presence of codons and anticodons is also expected in the reverse situation, with codons containing palindrome-dinucleotides at their 2-3 positions, and anticodons exhibiting them at 1-2 positions. A closer analysis reveals that, surprisingly, RNA binding sites for Arg, Ile and Tyr "prefer" (exactly as in the actual genetic code) the anticodon(2-3)/codon(1-2) tetramers to their anticodon(1-2)/codon(2-3) counterparts, despite the seemingly perfect symmetry of the latter. However, since in vitro selection of aa-specific RNA aptamers apparently had nothing to do with translation, this striking preference provides a new strong support to the notion of the genetic code emerging before translation, in response to catalytic (and possibly other) needs of ancient RNA life. Consistently with the pre-translation origin of the code, we propose here a new model of tRNA origin by the gradual, Fibonacci process-like, elongation of a tRNA molecule from a primordial coding triplet and 5'DCCA3' quadruplet (D is a base-determinator) to the eventual 76 base-long cloverleaf-shaped molecule. Conclusion Taken together, our findings necessarily imply that primordial tRNAs, tRNA aminoacylating ribozymes, and (later) the translation machinery in general have been co-evolving to ''fit'' the (likely already defined) genetic code, rather than the opposite way around. Coding triplets in this primal pre-translational code were likely similar to the anticodons, with second and third nucleotides being more important than the less specific first one. Later, when the code was expanding in co-evolution with the translation apparatus, the importance of 2-3 nucleotides of coding triplets "transferred" to the 1-2 nucleotides of their complements, thus distinguishing anticodons from codons. This evolutionary primacy of anticodons in genetic coding makes the hypothesis of primal stereo-chemical affinity between amino acids and cognate triplets, the hypothesis of coding coenzyme handles for amino acids, the hypothesis of tRNA-like genomic 3' tags suggesting that tRNAs originated in replication, and the hypothesis of ancient ribozymes-mediated operational code of tRNA aminoacylation not mutually contradicting but rather co-existing in harmony. Reviewers This article was reviewed by Eugene V. Koonin, Wentao Ma (nominated by Juergen Brosius) and Anthony Poole.

Abstract Background The genetic code is brought into action by 20 aminoacyl-tRNA synthetases. These enzymes are evenly divided into two classes (I and II) that recognize tRNAs from the minor and major groove sides of the acceptor stem, respectively. We have reported recently that: (1) ribozymic precursors of the synthetases seem to have used the same two sterically mirror modes of tRNA recognition, (2) having these two modes might have helped in preventing erroneous aminoacylation of ancestral tRNAs with complementary anticodons, yet (3) the risk of confusion for the presumably earliest pairs of complementarily encoded amino acids had little to do with anticodons. Accordingly, in this communication we focus on the acceptor stem. Results Our main result is the emergence of a palindrome structure for the acceptor stem's common ancestor, reconstructed from the phylogenetic trees of Bacteria, Archaea and Eukarya. In parallel, for pairs of ancestral tRNAs with complementary anticodons, we present updated evidence of concerted complementarity of the second bases in the acceptor stems. These two results suggest that the first pairs of "complementary" amino acids that were engaged in primordial coding, such as Gly and Ala, could have avoided erroneous aminoacylation if and only if the acceptor stems of their adaptors were recognized from the same, major groove, side. The class II protein synthetases then inherited this "primary preference" from isofunctional ribozymes. Conclusion Taken together, our results support the hypothesis that the genetic code per se (the one associated with the anticodons) and the operational code of aminoacylation (associated with the acceptor) diverged from a common ancestor that probably began developing before translation. The primordial advantage of linking some amino acids (most likely glycine and alanine) to the ancestral acceptor stem may have been selective retention in a protocell surrounded by a leaky membrane for use in nucleotide and coenzyme synthesis. Such acceptor stems (as cofactors) thus transferred amino acids as groups for biosynthesis. Later, with the advent of an anticodon loop, some amino acids (such as aspartic acid, histidine, arginine) assumed a catalytic role while bound to such extended adaptors, in line with the original coding coenzyme handle (CCH) hypothesis. Reviewers This article was reviewed by Rob Knight, Juergen Brosius and Anthony Poole.

A new approach for calculating the ion dose spatial distribution of the focused ion beam is proposed. The approach is based on the analysis of the secondary electron microscopy image of the area irradiated by the focused ion beam. [ABSTRACT FROM AUTHOR]