62,603 research outputs found
Periodic correlation structures in bacterial and archaeal complete genomes
The periodic transference of nucleotide strings in bacterial and archaeal
complete genomes is investigated by using the metric representation and the
recurrence plot method. The generated periodic correlation structures exhibit
four kinds of fundamental transferring characteristics: a single increasing
period, several increasing periods, an increasing quasi-period and almost
noincreasing period. The mechanism of the periodic transference is further
analyzed by determining all long periodic nucleotide strings in the bacterial
and archaeal complete genomes and is explained as follows: both the repetition
of basic periodic nucleotide strings and the transference of non-periodic
nucleotide strings would form the periodic correlation structures with
approximately the same increasing periods.Comment: 23 pages, 6 figures, 2 table
Order in glassy systems
A directly measurable correlation length may be defined for systems having a
two-step relaxation, based on the geometric properties of density profile that
remains after averaging out the fast motion. We argue that the length diverges
if and when the slow timescale diverges, whatever the microscopic mechanism at
the origin of the slowing down. Measuring the length amounts to determining
explicitly the complexity from the observed particle configurations. One may
compute in the same way the Renyi complexities K_q, their relative behavior for
different q characterizes the mechanism underlying the transition. In
particular, the 'Random First Order' scenario predicts that in the glass phase
K_q=0 for q>x, and K_q>0 for q<x, with x the Parisi parameter. The hypothesis
of a nonequilibrium effective temperature may also be directly tested directly
from configurations.Comment: Typos corrected, clarifications adde
Electronic transport in DNA
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localization lengths (crudely speaking, the length over
which electrons travel). Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations on poly(dG)-poly(dC), telomeric-DNA, random-ATGC DNA, and l-DNA. We find that random and l-DNA have localization lengths allowing for electron motion among a few dozen basepairs only. A novel enhancement of localization lengths is observed at particular energies for an increasing binary backbone disorder. We comment on the possible biological relevance of sequence-dependent charge transfer in DNA
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