One important problem in computational structural biology is protein designability, that is, why protein sequences are not random strings of amino acids but instead show regular patterns that encode protein structures. Many previous studies that have attempted to solve the problem have relied upon reduced models of proteins. In particular, the 2D square and the 3D cubic lattices together with reduced amino acid alphabet models have been examined extensively and have led to interesting results that shed some light on the evolutionary relationship among proteins. Here we perform designability studies on the 2D square lattice and explore the effects of variable overall shapes on protein designability using a binary hydrophobic-polar (HP) amino acid alphabet. Because we rely on a simple energy function that counts the total number of H-H interactions between non-sequential residues, we restrict our studies to protein shapes that have the same number of residues and also a constant number of non-bonded contacts. We have found that there is a marked difference in the designability between various protein shapes, with some of them accounting for a significantly larger share of the total foldable sequences.
Si Plasma-enhanced chemical vapor deposition (PECVD) at a near-atmospheric pressure (NAP) of 500 Torr has been conducted by using a pulsed-electric-field based NAP-PECVD system. At a growth temperature of 180°C, poly-Si films with a high Raman ratio of 7.4 were obtained on glass substrates, while epitaxial-like growth occurred when Si(100) substrates were employed, as confirmed by Raman-scattering spectroscopy, X-ray diffraction, and a cross-sectional transmission-electron microscopy.
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