arXiv subjects

J. S. Sa Martins

Publications and source records attributed to J. S. Sa Martins.

13 recordsLinked to original sources

arXiv2009

Modelling survival and allele complementation in the evolution of genomes with polymorphic loci

We have simulated the evolution of sexually reproducing populations composed of individuals represented by diploid genomes. A series of eight bits formed an allele occupying one of 128 loci of one haploid genome (chromosome). The environment required a specific activity of each locus, this being the sum of the activities of both alleles located at the corresponding loci on two chromosomes. This activity is represented by the number of bits set to zero. In a constant environment the best fitted individuals were homozygous with alleles' activities corresponding to half of the environment requirement for a locus (in diploid genome two alleles at corresponding loci produced a proper activity). Changing the environment under a relatively low recombination rate promotes generation of more polymorphic alleles. In the heterozygous loci, alleles of different activities complement each other fulfilling the environment requirements. Nevertheless, the genetic pool of populations evolves in the direction of a very restricted number of complementing haplotypes and a fast changing environment kills the population. If simulations start with all loci heterozygous, they stay heterozygous for a long time.

q-bio.GN↗

arXiv2008

Simulated self-organisation of death by inherited mutations

An agent-based computer simulation of death by inheritable mutations in a changing environment shows a maximal population, or avoids extinction, at so intermediate mutation rate of the individuals. Thus death seems needed to al for evolution of the fittest, as required by a changing environment.

q-bio.PE↗

arXiv2007

Computer simulations on the sympatric speciation modes for the Midas cichlid species complex

Cichlid fishes are one of the best model system for the study of evolution of the species. Inspired by them, in this paper we simulated the splitting of a single species into two separate ones via random mutations, with both populations living together in sympatry, sharing the same habitat. We study the ecological, mating and genetic conditions needed to reproduce the polychromatism and polymorphism of three species of the Midas Cichlid species complex. Our results show two scenarios for the A. Citrinellus speciation process, one with and the other without disruptive natural selection. In the first scenario, the ecological and genetic conditions are sufficient to create two new species, while in the second the mating and genetic conditions must be synchronized in order to control the velocity of genetic drift.

q-bio.PE↗

arXiv2006

Ergodicity in Natural Earthquake Fault Networks

Numerical simulations have shown that certain driven nonlinear systems can be characterized by mean-field statistical properties often associated with ergodic dynamics [C.D. Ferguson, W. Klein, and J.B. Rundle, Phys. Rev. E 60, 1359 (1999); D. Egolf, Science 287, 101 (2000)]. These driven mean-field threshold systems feature long-range interactions and can be treated as equilibrium-like systems with dynamics that are statistically stationary over long time intervals. Recently the equilibrium property of ergodicity was identified in an earthquake fault system, a natural driven threshold system, by means of the Thirumalai-Mountain (TM) fluctuation metric developed in the study of diffusive systems [K.F. Tiampo, J.B. Rundle, W. Klein, J.S. Sa Martins, and C. D. Ferguson, Phys. Rev. Lett. 91, 238501 (2003)]. In this work we analyze the seismicity of three naturally-occurring earthquake faults networks from a variety of tectonic settings in an attempt to investigate the range of applicability of effective ergodicity, using the TM metric and other, related statistics. Results suggest that, once variations in the catalog data resulting from technical and network issues are accounted for, all of these natural earthquake systems display stationary periods of metastable equilibrium and effective ergodicity that are disrupted by large events. We conclude that a constant rate of events is an important prerequisite for these periods of punctuated ergodicity, and that while the level of temporal variability in the spatial statistics is the controlling factor in the ergodic behavior of seismic networks, no single statistic is sufficient to ensure quantification of ergodicity. Specifically, we demonstrate that stationarity, while a necessary condition, is not sufficient to ensure ergodicity in fault systems.

physics.geo-ph↗

arXiv2005

The Coester Line in Relativistic Mean Field Nuclear Matter

The Walecka model contains essentially two parameters that are associated with the Lorentz scalar (S) and vector (V) interactions. These parameters are related to a two-body interaction consisting of S and V, imposing the condition that the two-body binding energy is fixed. We have obtained a set of different values for the nuclear matter binding energies at equilibrium densities. We investigated the existence of a linear correlation between $B_N$ and $ρ_0$, claimed to be universal for nonrelativistic systems and usually known as the Coester line, and found an approximate linear correlation only if $V?S$ remains constant. It is shown that the relativistic content of the model, which is related to the strength of $V?S$, is responsible for the shift of the Coester line to the empirical region of nuclear matter saturation.

nucl-th↗

arXiv2003

Penna bit-string model with constant population

We removed from the Penna model for biological ageing any random killing Verhulst factor. Deaths are due only to genetic diseases and the population size is fixed, instead of fluctuating around some constant value. We show that these modifications give qualitatively the same results obtained in an earlier paper, where the random killings (used to avoid an exponential increase of the population) were applied only to newborns.

cond-mat.stat-mech↗

arXiv2003

Positive mutations and mutation-dependent Verhulst factor in Penna ageing model

We twice modify the Penna model for biological ageing. First we introduce back (good) mutations and a memory for them into the model. It allows us to observe an improvement of the species fitness over long time scales as well as punctuated equilibrium. Second we adopt a food/space competition factor that depends on the number of accumulated mutations in the individuals genomes, and get rid of the fixed limiting number of allowed mutations. Besides reproducing the main results of the standard model, we also observe a mortality maximum for the oldest old.

cond-mat.stat-mech↗

arXiv2003

Asymmetry in hierarchy model of Bonabeau et al

The 1995 model of Bonabeau et al. explains the emergence of social hierarchies through randomness, but gives as many leaders as followers. A simple modification allows a more realistic asymmetry with much less leaders.

cond-mat.stat-mech↗

arXiv2003

Simulation of Galam's contrarian opinions

Galam's model of people voting always against the majority is shown to give for the quenched case different results than the original annealed model. For people diffusing on a lattice, Galam's phase transitions happen only at higher concentrations of people.

cond-mat.stat-mech↗

arXiv2003

Should retirement age be coupled to life expectancy ?

Increasing every year the retirement age by the same amount as the increase of the life expectancy gives roughly stable ratios of the number of retired to working-age people in industrialized countries. Continuous influx of immigrants, below one percent per year of the total population, is needed for this stabilization.

cond-mat.stat-mech↗

arXiv2002

The evolutionary advantage of diploid sex

We modify the Penna Model for biological aging, which is based on the mutation-accumulation theory, in order to verify if there would be any evolutionary advantage of triploid over diploid organisms. We show that this is not the case, and that usual sex is always better than that involving three individuals.

cond-mat.stat-mech↗

arXiv2001

Emergence of Hierarchy on a Network of Complementary Agents

Complementarity is one of the main features underlying the interactions in biological and biochemical systems. Inspired by those systems we propose a model for the dynamical evolution of a system composed by agents that interact due to their complementary attributes rather than their similarities. Each agent is represented by a bit-string and has an activity associated to it; the coupling among complementary peers depends on their activity. The connectivity of the system changes in time respecting the constraint of complementarity. We observe the formation of a network of active agents whose stability depends on the rate at which activity diffuses in the system. The model exhibits a non-equilibrium phase transition between the ordered phase, where a stable network is generated, and a disordered phase characterized by the absence of correlation among the agents. The ordered phase exhibits multi-modal distributions of connectivity and activity, indicating a hierarchy of interaction among different populations characterized by different degrees of activity. This model may be used to study the hierarchy observed in social organizations as well as in business and other networks.

cond-mat.dis-nn↗

arXiv2000

Evolution and Ageing

The idea of this review is to connect the different models of evolution to those of biological ageing through Darwin's theory. We start with the Eigen model of quasispecies for microevolution, then introduce the Bak-Sneppen model for macroevolution and, finally, present the Penna model for biological ageing and some of its most important results. We also explore the concept of coevolution using this model.

cond-mat.stat-mech↗