Sequences close to periodic

The paper is a survey of notions and results related to classical and new generalizations of the notion of a periodic sequence. The topics related to almost periodicity in combinatorics on words, symbolic dynamics, expressibility in logical theories, algorithmic computability, Kolmogorov complexity, number theory, are discussed.Comment: In Russian. 76 pages, 6 figure

COORDINATION THROUGH DE BRUIJN SEQUENCES

Let µ be a rational distribution over a finite alphabet, and ( ) be a n-periodic sequences which first n elements are drawn i.i.d. according to µ. We consider automata of bounded size that input and output at stage t. We prove the existence of a constant C such that, whenever , with probability close to 1 there exists an automaton of size m such that the empirical frequency of stages such that is close to 1. In particular, one can take , where and .Coordination, complexity, De Bruijn sequences, automata

Velocity and distance of neighbourhood sequences

Das et al. [2] defined the notion of periodic neighbourhood sequences. They also introduced a natural ordering relation for such sequences. Fazekas et al. [4] generalized the concept of neighbourhood sequences, by dropping periodicity. They also extended the ordering to these generalized neighbourhood sequences. The relation has some unpleasant properties (e.g., it is not a complete ordering). In certain applications it can be useful to compare any two neighbourhood sequences. For this purpose, in the present paper we introduce a norm-like concept, called velocity, for neighbourhood sequences. This concept is in very close connection with the natural ordering relation. We also define a metric for neighbourhood sequences, and investigate its properties

Symbolic dynamics and periodic orbits of the Lorenz attractor*

The butterfly-like Lorenz attractor is one of the best known images of chaos. The computations in this paper exploit symbolic dynamics and other basic notions of hyperbolicity theory to take apart the Lorenz attractor using periodic orbits. We compute all 111011 periodic orbits corresponding to symbol sequences of length 20 or less, periodic orbits whose symbol sequences have hundreds of symbols, the Cantor leaves of the Lorenz attractor, and periodic orbits close to the saddle at the origin. We derive a method for computing periodic orbits as close as machine precision allows to a given point on the Lorenz attractor. This method gives an algorithmic realization of a basic hypothesis of hyperbolicity theory—namely, the density of periodic orbits in hyperbolic invariant sets. All periodic orbits are computed with 14 accurate digits.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/49072/2/no3314.pd

Incoherent Exciton Trapping in Self-Similar Aperiodic Lattices

Incoherent exciton dynamics in one-dimensional perfect lattices with traps at sites arranged according to aperiodic deterministic sequences is studied. We focus our attention on Thue-Morse and Fibonacci systems as canonical examples of self-similar aperiodic systems. Excitons progressively extend over the lattice on increasing time and, in this sense, they act as a probe of the particular arrangements of traps in each system considered. The analysis of the characteristic features of their time decay indicates that exciton dynamics in self-similar aperiodic arrangements of traps is quite close to that observed in periodic ones, but differs significatively from that corresponding to random lattices. We also report on characteristic features of exciton motion suggesting that Fibonacci and Thue-Morse orderings might be clearly observed by appropriate experimental measurements. In the conclusions we comment on the implications of our work on the way towards a unified theory of the orderings of matter.Comment: REVTeX 3.0, 10 pages, 2 figures on request from FD-A ([email protected]). Submitted to Phys Rev B. MA/UC3M/11/9

Patterns of nucleotides that flank substitutions in human orthologous genes

<p>Abstract</p> <p>Background</p> <p>Sequence context is an important aspect of base mutagenesis, and three-base periodicity is an intrinsic property of coding sequences. However, how three-base periodicity is influenced in the vicinity of substitutions is still unclear. The effect of context on mutagenesis should be revealed in the usage of nucleotides that flank substitutions. Relative entropy (also known as Kullback-Leibler divergence) is useful for finding unusual patterns in biological sequences.</p> <p>Results</p> <p>Using relative entropy, we visualized the periodic patterns in the context of substitutions in human orthologous genes. Neighbouring patterns differed both among substitution categories and within a category that occurred at three codon positions. Transition tended to occur in periodic sequences relative to transversion. Periodic signals were stronger in a set of flanking sequences of substitutions that occurred at the third-codon positions than in those that occurred at the first- or second-codon positions. To determine how the three-base periodicity was affected near the substitution sites, we fitted a sine model to the values of the relative entropy. A sine of period equal to 3 is a good approximation for the three-base periodicity at sites not in close vicinity to some substitutions. These periods were interrupted near the substitution site and then reappeared away from substitutions. A comparative analysis between the native and codon-shuffled datasets suggested that the codon usage frequency was not the sole origin of the three-base periodicity, implying that the native order of codons also played an important role in this periodicity. Synonymous codon shuffling revealed that synonymous codon usage bias was one of the factors responsible for the observed three-base periodicity.</p> <p>Conclusions</p> <p>Our results offer an efficient way to illustrate unusual periodic patterns in the context of substitutions and provide further insight into the origin of three-base periodicity. This periodicity is a result of the native codon order in the reading frame. The length of the period equal to 3 is caused by the usage bias of nucleotides in synonymous codons. The periodic features in nucleotides surrounding substitutions aid in further understanding genetic variation and nucleotide mutagenesis.</p