Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random mutation but primarily grows by random segmental duplication. That genomes grew mostly by duplication is consistent with the observation that repeat sequences in all genomes are widespread and intragenomic and intergenomic homologous genes are preponderant across all life forms.
Dust particles effectively charged by plasma recently have been optically observed to exhibit crystalline phases not expected of Wigner or Yukawa crystals. Under varying conditions the crystal sometimes appears as deformed and oriented three-dimensional close-packed lattices of bcc, fcc, or hcp type, but mostly as a triangular array of vertical chains of particles. The unusual phases are shown to be caused by dipole-dipole interactions. The dipole moments are induced on the dust particles by gravity and by drag forces generated by ion stream. We describe in detail stable lattice structures and present the highly complex phase diagram of the dusty plasma. It turns out that in large parts of the phase diagram the stable phases indeed correspond to chains, but particles in neighboring chains belong to different sublattices. The stability of the lattices against excitations due to compression ͑i.e., aspect ratio variations͒ and vibration ͑i.e., phonons or charge density waves͒ is established. ͓S1063-651X͑97͒07409-6͔
Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.PACS number: 87.10.+e, 87.15.By The three-dimensional structure of proteins is a complex physical and mathematical problem of prime importance in molecular biology, medicine and pharmacology [1]. It is believed that the folding instruction of a protein is encoded in its amino acid sequence [2] and from model studies much has been learned about protein structure and folding kinetics [3][4][5][6]. Yet much still remains to be understood. This simple fact is already intriguing: the number of possible globular structures for a peptide of typical length -about 300 amino acids -is practically infinite; the number of proteins whose structures are known empirically or hypothetically is more than a hundred thousand and is growing rapidly with time; the number of classes of native protein structures is about five hundred and is believed unlikely to exceed a thousand in the long run [1,7]. Numerical simulations based on lattice models have shown that structures of exceptionally high designability -those that attract a large number of protein sequences to conform to it -do exist [5,6,8]. Why such structures would emerge is however not well understood. Protein folding also has an outstanding temporal feature: the initial collapse to globular shape and the formation of α-helices are completed in less than 10 −7 seconds [10], while the rest of the folding takes up to ten seconds to complete.In this report, based on results from a mean-field lattice model we observe that structures with high designability are preponderant in a type of substructure that suggests α-helices in real proteins and we explain the reason for this phenomenon. This notion is supported by global comparisons of model structural sequences with (binary) sequences constructed from sets of proteins of known structure: the Protein Data Bank (PDB) [9] and the Dali Domain Dictionary (DDD) [7]. Since the meanfield in the model represents the hydrophobic potential that is known to cause the initial collapse of a peptide to a globular shape, the results may explain why the initial collapse and the formation of α-helices occur essentially simultaneously and rapidly, and are temporally separated from other slower folding processes that are driven by far-neighbor inter-residual interactions.In the minimal model for protein folding, the HP model of Dill et al. [3], the 20 kinds of amino acids are divided into two types, hydrophobic and polar. This reduces a peptide chain of length N to a binary "pepti...
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