arXiv subjects

J. F. Fontanari

Publications and source records attributed to J. F. Fontanari.

17 recordsLinked to original sources

arXiv2013

Solvable model for template coexistence in protocells

Compartmentalization of self-replicating molecules (templates) in protocells is a necessary step towards the evolution of modern cells. However, coexistence between distinct template types inside a protocell can be achieved only if there is a selective pressure favoring protocells with a mixed template composition. Here we study analytically a group selection model for the coexistence between two template types using the diffusion approximation of population genetics. The model combines competition at the template and protocell levels as well as genetic drift inside protocells. At the steady state, we find a continuous phase transition separating the coexistence and segregation regimes, with the order parameter vanishing linearly with the distance to the critical point. In addition, we derive explicit analytical expressions for the critical steady-state probability density of protocell compositions.

physics.bio-ph↗

arXiv2012

Critical behavior in a cross-situational lexicon learning scenario

The associationist account for early word-learning is based on the co-occurrence between objects and words. Here we examine the performance of a simple associative learning algorithm for acquiring the referents of words in a cross-situational scenario affected by noise produced by out-of-context words. We find a critical value of the noise parameter $γ_c$ above which learning is impossible. We use finite-size scaling to show that the sharpness of the transition persists across a region of order $τ^{-1/2}$ about $γ_c$, where $τ$ is the number of learning trials, as well as to obtain the learning error (scaling function) in the critical region. In addition, we show that the distribution of durations of periods when the learning error is zero is a power law with exponent -3/2 at the critical point.

physics.soc-ph↗

arXiv2002

Complementarity and diversity in a soluble model ecosystem

Complementarity among species with different traits is one of the basic processes affecting biodiversity, defined as the number of species in the ecosystem. We present here a soluble model ecosystem in which the species are characterized by binary traits and their pairwise interactions follow a complementarity principle. Manipulation of the species composition, and so the study of its effects on the species diversity is achieved through the introduction of a bias parameter favoring one of the traits. Using statistical mechanics tools we find explicit expressions for the allowed values of the equilibrium species concentrations in terms of the control parameters of the model.

cond-mat.dis-nn↗

arXiv2001

Fractal geometry of spin-glass models

Stability and diversity are two key properties that living entities share with spin glasses, where they are manifested through the breaking of the phase space into many valleys or local minima connected by saddle points. The topology of the phase space can be conveniently condensed into a tree structure, akin to the biological phylogenetic trees, whose tips are the local minima and internal nodes are the lowest-energy saddles connecting those minima. For the infinite-range Ising spin glass with p-spin interactions, we show that the average size-frequency distribution of saddles obeys a power law $<ψ(w) > \sim w^{-D}$, where w=w(s) is the number of minima that can be connected through saddle s, and D is the fractal dimension of the phase space.

cond-mat.dis-nn↗

arXiv2001

Extinctions in the random replicator model

The statistical properties of an ecosystem composed of species interacting via pairwise, random interactions and deterministic, concentration limiting self-interaction are studied analytically with tools of equilibrium statistical mechanics of disordered systems. Emphasis is given to the effects of externally induced extinction of a fixed fraction of species at the outset of the evolutionary process. The manner the ecosystem copes with the initial extinction event depends on the degree of competition among the species as well as on the strength of that event. For instance, in the regime of high competition the ecosystem diversity, given by the fraction of surviving species, is practically insensitive to the strengt of the initial extinction provided it is not too large, while in the less competitive regime the diversity decreases linearly with the size of the event. In the case of large extinction events we find that no further biotic extinctions take place and, furthermore, that rare species become very unlikely to be found in the ecosystem at equilibrium. In addition, we show that the reciprocal of the Edwards-Anderson order parameter yields a good measure of the diversity of the model ecosystem.

cond-mat.dis-nn↗

arXiv2001

Nonequilibrium phase transitions in a model for the origin of life

The requisites for the persistence of small colonies of self-replicating molecules living in a two-dimensional lattice are investigated analytically in the infinite diffusion or mean-field limit and through Monte Carlo simulations in the position-fixed or contact process limit. The molecules are modeled by hipercyclic replicators A which are capable of replicating via binary fission A + E --2A with production rates s as well as via catalytically assisted replication 2A + E --3A with rate c. In addition, a molecule can degrade into its source materials E with rate $γ$. In the asymptotic regime the population can be characterized by the presence (active phase) and the absence (empty phase) of replicators in the lattice. In both diffusion regimes, we find that for small values of the ratio c/$γ$ these phases are separated by a second-order phase transition which is in the universality class of the directed percolation, while for small values s/$gamma$ the phase transition is of first order. Furthermore, we illustrate the suitability of the dynamic Monte Carlo method, which is based on the analysis of the spreading behaviour of a few active cells in the center of an otherwise infinite empty lattice, to adress the problem of emergence of replicators. Rather surprisingly, we show that this method allows an unambiguous identification of the order of the nonequilibrium phase transition.

physics.bio-ph↗

arXiv2000

Group selection models in prebiotic evolution

The evolution of enzyme production is studied analytically using ideas of the group selection theory for the evolution of altruistic behavior. In particular, we argue that the mathematical formulation of Wilson's structured deme model ({\it The Evolution of Populations and Communities}, Benjamin/Cumings, Menlo Park, 1980) is a mean-field approach in which the actual environment that a particular individual experiences is replaced by an {\it average} environment. That formalism is further developed so as to avoid the mean-field approximation and then applied to the problem of enzyme production in the prebiotic context, where the enzyme producer molecules play the altruists role while the molecules that benefit from the catalyst without paying its production cost play the non-altruists role. The effects of synergism (i.e., division of labor) as well as of mutations are also considered and the results of the equilibrium analysis are summarized in phase diagrams showing the regions of the space of parameters where the altruistic, non-altruistic and the coexistence regimes are stable. In general, those regions are delimitated by discontinuous transition lines which end at critical points.

cond-mat.stat-mech↗

arXiv2000

Random replicators with high-order interactions

We use tools of the equilibrium statistical mechanics of disordered systems to study analytically the statistical properties of an ecosystem composed of N species interacting via random, Gaussian interactions of order p >= 2, and deterministic self-interactions u <= 0. We show that for nonzero u the effect of increasing the order of the interactions is to make the system more cooperative, in the sense that the fraction of extinct species is greatly reduced. Furthermore, we find that for p > 2 there is a threshold value which gives a lower bound to the concentration of the surviving species, preventing then the existence of rare species and, consequently, increasing the robustness of the ecosystem to external perturbations.

cond-mat.stat-mech↗

arXiv1999

On the structure pf genealogical trees in the presence of selection

We investigate through numerical simulations the effect of selection on two summary statistics for nucleotide variation in a sample of two genes from a population of N asexually reproducing haploid individuals. One is the mean time since two individuals had their most recent common ancestor ($\bar{T_s}$), and the other is the mean number of nucleotide differences between two genes in the sample ($\bar{d_s}$). In the case of diminishing epistasis, in which the deleterious effect of a new mutation is attenuated, we find that the scale of $\bar{d_s}$ with the population size depends on the mutation rate, leading then to the onset of a sharp threshold phenomenon as N becomes large.

cond-mat.stat-mech↗

arXiv1999

Instance Space of the Number Partitioning Problem

Within the replica framework we study analytically the instance space of the number partitioning problem. This classic integer programming problem consists of partitioning a sequence of N positive real numbers $\{a_1, a_2,..., a_N}$ (the instance) into two sets such that the absolute value of the difference of the sums of $a_j$ over the two sets is minimized. We show that there is an upper bound $α_c N$ to the number of perfect partitions (i.e. partitions for which that difference is zero) and characterize the statistical properties of the instances for which those partitions exist. In particular, in the case that the two sets have the same cardinality (balanced partitions) we find $α_c=1/2$. Moreover, we show that the disordered model resulting from hte instance space approach can be viewed as a model of replicators where the random interactions are given by the Hebb rule.

cond-mat↗

arXiv1999

Metastable States in High Order Short-Range Spin Glasses

The mean number of metastable states in higher order short-range spin glasses is estimated analytically using a variational method introduced by Tanaka and Edwards for very large coordination numbers. For lattices with small connectivities, numerical simulations do not show any significant dependence on the relative positions of the interacting spins on the lattice, indicating thus that these systems can be described by a few macroscopic parameters. As an extremely anisotropic model we consider the low autocorrelated binary spin model and we show through numerical simulations that its landscape has an exceptionally large number of local optima.

cond-mat.stat-mech↗

arXiv1999

Error Propagation in the Hypercycle

We study analytically the steady-state regime of a network of n error-prone self-replicating templates forming an asymmetric hypercycle and its error tail. We show that the existence of a master template with a higher non-catalyzed self-replicative productivity, a, than the error tail ensures the stability of chains in which m<n-1 templates coexist with the master species. The stability of these chains against the error tail is guaranteed for catalytic coupling strengths (K) of order of a. We find that the hypercycle becomes more stable than the chains only for K of order of a2. Furthermore, we show that the minimal replication accuracy per template needed to maintain the hypercycle, the so-called error threshold, vanishes like sqrt(n/K) for large K and n<=4.

physics.bio-ph↗

arXiv1999

Stochastic group selection model for the evolution of altruism

We study numerically and analytically a stochastic group selection model in which a population of asexually reproducing individuals, each of which can be either altruist or non-altruist, is subdivided into $M$ reproductively isolated groups (demes) of size $N$. The cost associated with being altruistic is modelled by assigning the fitness $1- τ$, with $τ\in [0,1]$, to the altruists and the fitness 1 to the non-altruists. In the case that the altruistic disadvantage $τ$ is not too large, we show that the finite $M$ fluctuations are small and practically do not alter the deterministic results obtained for $M \to \infty$. However, for large $τ$ these fluctuations greatly increase the instability of the altruistic demes to mutations. These results may be relevant to the dynamics of parasite-host systems and, in particular, to explain the importance of mutation in the evolution of parasite virulence.

adap-org↗

arXiv1998

Statistical Mechanics Analysis of the Continuous Number Partitioning Problem

The number partitioning problem consists of partitioning a sequence of positive numbers ${a_1,a_2,..., a_N}$ into two disjoint sets, ${\cal A}$ and ${\cal B}$, such that the absolute value of the difference of the sums of $a_j$ over the two sets is minimized. We use statistical mechanics tools to study analytically the Linear Programming relaxation of this NP-complete integer programming. In particular, we calculate the probability distribution of the difference between the cardinalities of ${\cal A}$ and ${\cal B}$ and show that this difference is not self-averaging.

cond-mat.stat-mech↗

arXiv1998

Finite-size scaling of the error threshold transition in finite population

The error threshold transition in a stochastic (i.e. finite population) version of the quasispecies model of molecular evolution is studied using finite-size scaling. For the single-sharp-peak replication landscape, the deterministic model exhibits a first-order transition at $Q=Q_c=1/a$, where $% Q$ is the probability of exact replication of a molecule of length $L \to \infty$, and $a$ is the selective advantage of the master string. For sufficiently large population size, $N$, we show that in the critical region the characteristic time for the vanishing of the master strings from the population is described very well by the scaling assumption $τ= N^{1/2} f_a \left [ \left (Q - Q_c) N^{1/2} \right ] $, where $f_a$ is an $a$-dependent scaling function.

cond-mat.stat-mech↗

arXiv1998

Error threshold in finite populations

A simple analytical framework to study the molecular quasispecies evolution of finite populations is proposed, in which the population is assumed to be a random combination of the constiyuent molecules in each generation,i.e., linkage disequilibrium at the population level is neglected. In particular, for the single-sharp-peak replication landscape we investigate the dependence of the error threshold on the population size and find that the replication accuracy at threshold increases linearly with the reciprocal of the population size for sufficiently large populations. Furthermore, in the deterministic limit our formulation yields the exact steady-state of the quasispecies model, indicating then the population composition is a random combination of the molecules.

cond-mat.stat-mech↗

arXiv1996

Error threshold in the evolution of diploid organisms

The effects of error propagation in the reproduction of diploid organisms are studied within the populational genetics framework of the quasispecies model. The dependence of the error threshold on the dominance parameter is fully investigated. In particular, it is shown that dominance can protect the wild-type alleles from the error catastrophe. The analysis is restricted to a diploid analogue of the single-peaked landscape.

cond-mat.dis-nn↗