Description: This article discusses a dynamical model for DNA sequences. Abstract: We address the problem of DNA sequences, developing a "dynamical" method based on the assumption that the statistical properties of DNA paths are determined by the joint action of two processes, one deterministic with long-range correlations and the other random and δ-function correlated. The generator of the deterministic evolution is a nonlinear map belonging to a class of maps recently tailored to mimic the processes of weak chaos responsible for the birth of anomalous diffusion. It is assumed that the deterministic process corresponds to unknown biological rules that determine the DNA path, whereas the noise mimics the influence of an infinite-dimensional environment on the biological process under study. We prove that the resulting diffusion process, if the effect of the random process is determined by the joint action of the deterministic and the random process, the correlation effects of the "deterministic dynamics" are canceled on the short-range scale, but show up in the long-range one. We denote their prescription to generate statistical sequences as the copying mistake map (CMM). We carry out their analysis of several DNA sequences and their CMM realizations with a variety of techniques and the authors ...

Description: This article discusses fractional Brownian motion as a nonstationary process. Abstract: The long-range correlations in DNA sequences are currently interpreted as an example of stationary fractional Brownian motion (FBM). First the authors show that the dynamics of a dichotomous stationary process with long-range correlations such as that used to model DNA sequences should correspond to Lévy statistics and not to FBM. To explain why, in spite of this, the statistical analysis of the data seems to be compatible with FBM, the authors notice that an initial Gaussian condition, generated by a process foreign to the mechanism establishing the long-range correlations and consequently implying a departure from the stationary condition is maintained approximately unchanged for very long times. This is so because due to the nature itself of the long-range correlation process, it takes virtually an infinite time for the system to reach the genuine stationary state. Then the authors discuss a possible generator of initial Gaussian conditions, based on a folding mechanism of the nucleic acid in the cell nucleus. The model adopted is compatible with the known biological and physical constraints, namely, it is shown to be consistent with the information of current biological literature on folding as well ...

Description: This article discusses a dynamical approach to Lévy processes.Abstract: We derive the diffusion process generated by a correlated dichotomous fluctuating variable y starting from a Liouville-like equation by means of a projection procedure. This approach makes it possible to derive all statistical properties of the diffusion process from the correlation function of the dichotomous fluctuating variable Φy(t). Of special interest is that the distribution of the times of sojourn in the two states of the fluctuating process is proportional to d²Φy(t)/dt². Furthermore, in the special case where Φy(t) has an inverse power law, with the index β ranging from 0 to 1, thus making it nonintegrable, the authors show analytically that the statistics of the diffusing variable approximate in the long-time limit the α-stable Lévy distributions. The departure of the diffusion process of dynamical origin from the ideal condition of the Lévy statistics is established by means of a simple analytical expression. We note, first of all, that the characteristic function of a genuine Lévy process should be an exponential in time. We evaluate the correction to this exponential and show it to be expressed by a harmonic time oscillation modulated by the correlation function Φy(t). Since the characteristic function ...

Description: This article discusses Z1 oscillations of the mean charge for isotachic ions in carbon foils. Oscillations in the mean-charge state of swift ions as a function of the atomic number Z1 are reported for a wide range of ions of identical velocity (isotachic ions). A previously suggested mechanism for the enhancement of the mean charge for certain ion-charge combinations that involves closed shells is shown to be an inadequate explanation. Post-foil-Auger processes, however, are demonstrated to be a more plausible explanation for the observed behavior of the mean charge of the ions.

Description: This article discusses the design of highly specific cytotoxins by using trans-splicing ribozymes. Abstract: We have designed ribozymes based on a self-splicing group I intron that can trans-splice exon sequences into a chosen RNA target to create a functional chimeric mRNA and provide a highly specific trigger for gene expression. We have targeted ribozymes against the coat protein mRNA of a widespread plant pathogen, cucumber mosaic virus. The ribozymes were designed to trans-splice the coding sequence of the diphtheria toxin A chain in frame with the viral initiation codon of the target sequence. Diphtheria toxin A chain catalyzes the ADP ribosylation of elongation factor 2 and can cause the cessation of protein translation. In a Saccharomyces cerevisiae model system, ribozyme expression was shown to specifically inhibit the growth of cells expressing the virus mRNA. A point mutation at the target splice site alleviated this ribozyme-mediated toxicity. Increasing the extent of base pairing between the ribozyme and target dramatically increased specific expression of the cytotoxin and reduced illegitimate toxicity in vivo. Trans-splicing ribozymes may provide a new class of agents for engineering virus resistance and therapeutic cytotoxins.