Forcing reversibility in the no strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons

Because of the base pairing rules in DNA, some mutations experienced by a portion of DNA during its evolution result in the same substitution, as we can only observe differences in coupled nucleotides. Then, in the absence of a bias between the two DNA strands, a model with at most 6 different parameters instead of 12 is sufficient to study the evolutionary relationship between homologous sequences derived from a common ancestor. On the other hand the same symmetry reduces the number of independent observations which can be made. Such a reduction can in some cases invalidate the calculation of the parameters. A compromise between biologically acceptable hypotheses and tractability is introduced and a five parameter reversible no-strand-bias condition (RNSB) is presented. The identifiability of the parameters under this model is shown by examples.Comment: 12 pages, 4 figures, corrected typo

Food-chain competition influences gene's size

We have analysed an effect of the Bak-Sneppen predator-prey food-chain self-organization on nucleotide content of evolving species. In our model, genomes of the species under consideration have been represented by their nucleotide genomic fraction and we have applied two-parameter Kimura model of substitutions to include the changes of the fraction in time. The initial nucleotide fraction and substitution rates were decided with the help of random number generator. Deviation of the genomic nucleotide fraction from its equilibrium value was playing the role of the fitness parameter, $B$, in Bak-Sneppen model. Our finding is, that the higher is the value of the threshold fitness, during the evolution course, the more frequent are large fluctuations in number of species with strongly differentiated nucleotide content; and it is more often the case that the oldest species, which survive the food-chain competition, might have specific nucleotide fraction making possible generating long genesComment: 11 pages including 7 figure

Drift without flux: Brownian walker with a space dependent diffusion coefficient

Space dependent diffusion of micrometer sized particles has been directly observed using digital video microscopy. The particles were trapped between two nearly parallel walls making their confinement position dependent. Consequently, not only did we measure a diffusion coefficient which depended on the particles' position, but also report and explain a new effect: a drift of the particles' individual positions in the direction of the diffusion coefficient gradient, in the absence of any external force or concentration gradient.Comment: 4 pages, 4 ps figures, include

The peaking Phenomenon and Singular Perturbations : An Extension of Tikhonov's Theorem

We study the asymptotic behaviour, when the parameter $\gamma$ tends to infinity, of a class of singularly perturbed triangular systems $\dot x=f(x,y)$, $\dot y=G(y,\gamma)$. The first equation may be considered as a control system recieving the inputs from the states of the second equation. With zero input, the origin of the first equation is globally asymptotically stable. We assume that all solutions of the second equation tend to zero arbitrarily fast when $\gamma$ tends to infinity. Some states of the second equation may peak to very large values, before they rapidly decay to zero. Such peaking states can destabilize the first equation. The paper introduces the concept of \em instantaneous stability, to measure the fast decay to zero of the solutions of the second equation, and the concept of uniform infinitesimal boundedness to measure the effects of peaking on the first equation. Whe show that all the solutions of the triangular system tend to zero when $\gamma$ and $t$ tend to infinity. Our results are a generalization of the classical Tikhonov's theorem of singular perturbation theory, concerning the asymptotic behaviour of the solutions in the particular case where the second equation is of the form $\dot y=\gamma G(y)$. Our results are formulated in both classical mathematics and nonstandard analysis

Effect of population size in a Prey-Predator model

We consider a stochastic version of the basic predator-prey differential equation model. The model, which contains a parameter \omega which represents the number of individuals for one unit of prey -- If x denotes the quantity of prey in the differential equation model x = 1 means that there are \omega individuals in the discontinuous one -- is derived from the classical birth and death process. It is shown by the mean of simulations and explained by a mathematical analysis based on results in singular perturbation theory (the so called theory of Canards) that qualitative properties of the model like persistence or extinction are dramatically sensitive to \omega. For instance, in our example, if \omega = 107 we have extinction and if \omega = 108 we have persistence. This means that we must be very cautious when we use continuous variables in place of jump processes in dynamic population modeling even when we use stochastic differential equations in place of deterministic ones

Turbulent liquid–liquid dispersion in SMV static mixer at high dispersed phase concentration

The aim of this paper is to investigate the influence of physico-chemical parameters on liquid–liquid dispersion at high dispersed phase concentration in Sulzer SMV™ mixer. Four different oil-in-water systems involving two different surfactants are used in order to evaluate the effect of interfacial tension, densities and viscosities ratio on mean droplets size diameters. Moreover the influence of the dispersed phase concentration on the pressure drop as well as on the droplet size distribution is investigated. Two different droplets size distribution analysis techniques are used in order to compare the resulting Sauter mean diameters. The comparison between residence time in the mixer and surfactants adsorption kinetics leads to take into account the evolution of the interfacial tension between both phases at short times. Finally experimental results are correlated as a function of dimensionless Reynolds and Weber numbers

The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007

In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial genomes available in Genbank in April 2007, belong to these lines with high accuracy. The main challenge now is to explain the observed high accuracy. The new phenomenon of complementary symmetry for codon position--specific nucleotide frequencies is observed. The results of analysis of several codon usage models are presented. We demonstrate that the mean--field approximation, which is also known as context--free, or complete independence model, or Segre variety, can serve as a reasonable approximation to the real codon usage. The first two principal components of codon usage correlate strongly with genomic G+C content and the optimal growth temperature respectively. The variation of codon usage along the third component is related to the curvature of the mean-field approximation. First three eigenvalues in codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and archaeal genomes codon usage is clearly distributed along two third order curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct bacterial genomes available in Genbank in April 200

Conspiracy in bacterial genomes

The rank ordered distribution of the codon usage frequencies for 123 bacteriae is best fitted by a three parameters function that is the sum of a constant, an exponential and a linear term in the rank n. The parameters depend (two parabolically) from the total GC content. The rank ordered distribution of the amino acids is fitted by a straight line. The Shannon entropy computed over all the codons is well fitted by a parabola in the GC content, while the partial entropies computed over subsets of the codons show peculiar different behavior, exhibiting therefore a first conspiracy effect. Moreover the sum of the codon usage frequencies over particular sets, e.g. with C and A (respectively G and U) as i-th nucleotide, shows a clear linear dependence from the GC content, exhibiting another conspiracy effect.Comment: revised version: introduction and conclusion enhanced, references added, figures added, some tables remove