Stereochemical restrictions on the occurrence of amino acid residues in the collagen structure

The primary structure of collagen is characterized by the repeating tripeptide sequence (Gly-R2-R3)n. The results of theoretical studies, carried out using contact criteria to compute the stereochemically allowed orientations for various side chains at locations 2 and 3, are reported here. It is found that side chains with only γ-atoms, as in valine, serine and threonine, or with only one δ-methyl group, as in isoleucine, can occur equally well at locations 2 and 3, as is actually the case in collagen. Side chains with two Cδ-atoms, as in leucine and phenyl-alanine, can also be accommodated at both positions. However, if they occur as R3 their freedom of orientation is severely restricted in the presence of a proline residue as R2 in a neighbouring chain. If water molecules bound to the chains of the triple helix are assumed to be present, then location 3 is virtually impossible for leucine and phenylalanine residues. Location 2 is, however, unaffected, and their presence as R2 can help to shield the water molecules from disturbance by the solvent medium. This may be the reason for the preferential occurrence of Leu and Phe residues in location 2 in the collagen triplets, although the polypeptides (Gly-Pro-Leu)n and (Gly-Pro-Phe)n form collagen-like structures.

Positional Preferences of Polypurine/Polypyrimidine Tracts in Saccharomyces cerevisiae Genome: Implications for cis Regulation of Gene Expression

The complete genome of the baker's yeast S. cerevisiae was analyzed for the presence of polypurine/polypyrimidine (poly[pu/py]) repeats and their occurrences were classified on the basis of their location within and outside open reading frames (ORFs). The analysis reveals that such sequence motifs are present abundantly both in coding as well as noncoding regions. Clear positional preferences are seen when these tracts occur in noncoding regions. These motifs appear to occur predominantly at a unit nucleosomal length both upstream and downstream of ORFs. Moreover, there is a biased distribution of polypurines in the coding strands when these motifs occur within open reading frames. The significance of the biased distribution is discussed with reference to the occurrence of these motifs in other known mRNA sequences and expressed sequence tags. A model for cis regulation of gene expression is proposed based on the ability of these motifs to form an intermolecular triple helix structure when present within the coding region and/or to modulate nucleosome positioning via enhanced histone affinity when present outside coding regions.

Diffusion and Creep in Silica-Doped Tetragonal Zirconia

Silica segregation at two grain junctions or in amorphous triple junction pockets can influence creep by altering the grain-boundary diffusion coefficient. Although the addition of silica to superplastic yttria-stabilized tetragonal zirconia enhances ductility, differences in reported creep parameters have limited critical identification of rate controlling mechanisms. The present study on a pure 3 mol% yttria-stabilized tetragonal zirconia (3YTZ) and 3YTZ with 0.39 or 3.9 wt% silica involved a detailed characterization of creep over a wide range of experimental conditions and also tracer diffusion measurements. The data broadly show transitions in creep stress exponents from n∼1 to ∼2 to ∼3 with a decrease in the stress. The data at high stresses are consistent with Coble diffusion creep, and creep at lower stresses is attributed to interface-controlled diffusion creep. Measurements indicated that silica does not have any significant influence on grain boundary or lattice diffusion, and this is consistent with the observation that 3YTZ and 3YTZ with 0.39% or 3.9% silica exhibit essentially identical creep behavior in the Coble creep regime. Silica influences the interface control process so that the transitions in stress exponents are pushed to lower stresses with an increase in silica content.

False Error Study of On-line Soft Error Detection Mechanisms

With technology scaling, vulnerability to soft errors in random logic is increasing. There is a need for on-line error detection and protection for logic gates even at sea level. The error checker is the key element for an on-line detection mechanism. We compare three different checkers for error detection from the point of view of area, power and false error detection rates. We find that the double sampling checker (used in Razor), is the simplest and most area and power efficient, but suffers from very high false detection rates of 1.15 times the actual error rates. We also find that the alternate approaches of triple sampling and integrate and sample method (I&S) can be designed to have zero false detection rates, but at an increased area, power and implementation complexity. The triple sampling method has about 1.74 times the area and twice the power as compared to the Double Sampling method and also needs a complex clock generation scheme. The I&S method needs about 16% more power with 0.58 times the area as double sampling, but comes with more stringent implementation constraints as it requires detection of small voltage swings.

Microstructural stability and creep in nanocrystals

Microstructural stability is an important consideration during high temperature deformation and processing of nanomaterials. We will address issues relating to triple junctions in limiting grain growth during creep as well as densification. Although early studies on deformation have considered diffusion creep as a possible rate controlling deformation mechanism in nanocrystals, a critical inspection of available data indicates that there is no strong evidence for conventional diffusion creep in such materials. The possibility of diffusion creep by rapid diffusion along triple junctions will be analyzed, and interface controlled diffusion creep will also be discussed critically. It is shown that the critical grain size for dislocation activity is similar to that for occurrence of conventional diffusion creep.