Biomedical subjects

Alexandre Rosas

Publications and source records attributed to Alexandre Rosas.

9 recordsLinked to original sources

PubMed2005

Scaling, genetic drift, and clonal interference in the extinction pattern of asexual population.

We investigate the dynamics of loss of favorable mutations in an asexual haploid population. In the current work, we consider homogeneous as well as spatially structured population models. We focus our analysis on statistical measurements of the probability distribution of the maximum population size N(sb) achieved by those mutations that have not reached fixation. Our results show a crossover behavior which demonstrates the occurrence of two evolutionary regimes. In the first regime, which takes place for small N(sb) , the probability distribution is described by a power law with characteristic exponent theta(d) =1.8 +/- 0.01. This power law is not influenced by the rate of beneficial mutations. The second regime, which occurs for intermediate to large values of N(sb), has a characteristic exponent theta(c) which increases as the rate of beneficial mutations grows. These results establish where genetic drift and clonal interference become the main underlying mechanism in the extinction of advantageous mutations.

Demography↗

PubMed2005

Velocity distribution in a viscous granular gas.

We investigate the velocity relaxation of a viscous one-dimensional granular gas in which neither energy nor momentum is conserved in a collision. Of interest is the distribution of velocities in the gas as it cools, and the time dependence of the relaxation behavior. A Boltzmann equation of instantaneous binary collisions leads to a two-peaked distribution, as do numerical simulations of grains on a line. Of particular note is that in the presence of friction there is no inelastic collapse, so there is no need to invoke additional assumptions such as the quasielastic limit.

Journal Article↗

PubMed2004

Pulse velocity in a granular chain.

We discuss the applicability of two very different analytic approaches to the study of pulse propagation in a chain of particles interacting via a Hertz potential, namely, a continuum model and a binary collision approximation. While both methods capture some qualitative features equally well, the first is quantitatively good for softer potentials and the latter is better for harder potentials.

Journal Article↗

PubMed2004

Pulse propagation in chains with nonlinear interactions.

Pulse propagation in nonlinear arrays continues to be of interest because it provides a possible mechanism for energy transfer with little dispersion. Here we show that common measures of pulse dispersion might be misleading; in strongly anharmonic systems they tend to reflect a succession of extremely narrow pulses traveling at decreasing velocities rather than the actual width of a single pulse. We present analytic estimates for the fraction of the initial energy that travels in the leading pulses. We also provide analytic predictions for the leading pulse velocity in a Fermi-Pasta-Ulam beta chain.

Journal Article↗

PubMed2003

Self-similarity in random collision processes.

Kinetics of collision processes with linear mixing rules are investigated analytically. The velocity distribution becomes self-similar in the long-time limit and the similarity functions have algebraic or stretched exponential tails. The characteristic exponents are roots of transcendental equations and vary continuously with the mixing parameters. In the presence of conservation laws, the velocity distributions become universal.

Journal Article↗

PubMed2003

Pulse dynamics in a chain of granules with friction.

We study the dynamics of a pulse in a chain of granules with friction. We present theories for chains of cylindrical granules (Hertz potential with exponent n=2) and of granules with other geometries (n>2). Our results are supported via numerical simulations for cylindrical and for spherical granules (n=5/2).

Journal Article↗

PubMed2003

Dynamics of two granules.

We study the dynamics of two particles that interact only when in contact. In this sense, although not in every particular, the interactions mimic those in granular materials. The detailed solution of the dynamics allows an analysis of the backscattering behavior of the first particle and of the energy dissipation in the system as a function of various parameters.

Journal Article↗

PubMed2003

Spatial dynamics and the evolution of enzyme production.

We re-examine the problem of the evolution of protein synthesis or enzyme production using a stochastic cellular automaton model, where the replicators are fixed in the sites of a two-dimensional square lattice. In contrast with the classical chemical kinetics or mean-field predictions, we show that a small colony of mutant, protein-mediated (enzymatic) replicators has an appreciable probability to take over a resident population of simpler, direct-template replicators. In addition, we argue that the threshold phenomenon corresponding to the onset of invasion can be described quantitatively within the physics framework of nonequilibrium phase transitions. We study also the invasion of a resident population of enzymatic replicators by more efficient replicators of the same kind, and show that although slightly more efficient mutants cannot invade, invasion is a likely event if the productivity advantage of the mutants is large. In this sense, the establishment of a population of enzymatic replicators is not a 'once-forever' evolutionary decision.

Animals↗

PubMed2002

Multifractal analysis of DNA walks and trails.

The characterization of the long-range order and fractal properties of DNA sequences has proved a difficult though rewarding task mainly due to the mosaic character of DNA consisting of many interwoven patches of various lengths with different nucleotide constitutions. We apply here a recently proposed generalization of the detrended fluctuation analysis method to show that the DNA walk construction, in which the DNA sequence is viewed as a time series, exhibits a monofractal structure regardless of the existence of local trends in the series. In addition, we point out that the monofractal structure of the DNA walks carries over to an apparently alternative graphical construction given by the projection of the DNA walk into the d spatial coordinates, termed DNA trails. In particular, we calculate the fractal dimension D(t) of the DNA trails using a well-known result of fractal theory linking D(t) to the Hurst exponent H of the corresponding DNA walk. Comparison with estimates obtained by the standard box-counting method allows the evaluation of both finite-length and local trends effects.

Biophysical Phenomena↗