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At least 1,027 records · Page 57Linked to original sources

arXiv2001

Dynamics of a simple evolutionary process

We study the simple evolutionary process in which we repeatedly find the least fit agent in a population of agents and give it a new fitness which is chosen independently at random from a specified distribution. We show that many of the average properties of this process can be calculated exactly using analytic methods. In particular we find the distribution of fitnesses at arbitrary time, and the distribution of the lengths of runs of hits on the same agent, the latter being found to follow a power law with exponent -1, similar to the distribution of times between evolutionary events in the Bak-Sneppen model and models based on the so-called record dynamics. We confirm our analytic results with extensive numerical simulations.

nlin.AO↗

arXiv2001

Applications and Sexual Version of a Simple Model for Biological Ageing

We use a simple model for biological ageing to study the mortality of the population, obtaining a good agreement with the Gompertz law. We also simulate the same model on a square lattice, considering different strategies of parental care. The results are in agreement with those obtained earlier with the more complicated Penna model for biological ageing. Finally, we present the sexual version of this simple model.

cond-mat.stat-mech↗

arXiv2001

An Epidemic Model on Small-World Networks and Ring Vaccination

A modified version of susceptible-infected-recovered-susceptible (SIRS) model for the outbreaks of foot-and-mouth disease (FMD) is introduced. The model is defined on small-world networks, and a ring vaccination programme is included. This model can be a theoretical explanation for the nonlocal interactions in epidemic spreading. Ring vaccination is capable of eradicating FMD provided that the probability of infection is high enough. Also an analytical approximation for this model is studied.

nlin.CG↗

arXiv2002

The range of the contact interactions and the kinetics of the Go models of proteins

We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$, between the C$_α$ atoms. The folding times depend on the value of $R_c$ strongly and non-monotonically due to the interplay between frustration and the free energy barrier for folding. This indicates a need for a physically determined set of native contacts that takes into account all the residual atoms. %%. One may accomplish it This can be accomplished by considering the van der Waals radii of the atoms and checking if %%the atoms overlap. they are found within a proper range of the van der Waals attraction. In the second model, non-native attractive contacts are added to the system. This leads to bad foldability. However, for a small number of such extra contacts there is a slight acceleration in the kinetics of folding.

cond-mat↗

arXiv2002

Structure of the Energy Landscape of Short Peptides

We have simulated, as a showcase, the pentapeptide Met-enkephalin (Tyr-Gly-Gly-Phe-Met) to visualize the energy landscape and investigate the conformational coverage by the multicanonical method. We have obtained a three-dimensional topographic picture of the whole energy landscape by plotting the histogram with respect to energy(temperature) and the order parameter, which gives the degree of resemblance of any created conformation with the global energy minimum (GEM).

cond-mat.stat-mech↗

arXiv2002

Hamiltonian model for multidimensional epistasis

We propose and solve a Hamiltonian model for multidimensional epistastatic interactions between beneficial mutations. The model is able to give rise either to a phase transition between two equilibrium states, without any coexistence, or exhibits a state where hybrid species can coexist, with gradual passage from one wild type to another. The transition takes place as a function of the "tolerance" of the environment, which we define as the amount of noise in the system.

physics.bio-ph↗

arXiv2002

Simulating Male Selfish Strategy in Reproduction Dispute

We introduce into the Penna Model for biological ageing one of the possible male mechanisms used to maximize the ability of their sperm to compete with sperm from other males. Such a selfish mechanism increases the male reproduction success but may decrease the survival probability of the whole female population, depending on how it acts. We also find a dynamic phase transition induced by the existence of an absorbing state where no selfish males survive.

cond-mat↗

arXiv2003

Phase transitions in some epidemic models defined on small-world networks

Some modified versions of susceptible-infected-recovered-susceptible (SIRS) model are defined on small-world networks. Latency, incubation and variable susceptibility are included, separately. Phase transitions in these models are studied. Then inhomogeneous models are introduced. In some cases, the application of the models to small-world networks is shown to increase the epidemic region.

cond-mat.stat-mech↗

arXiv1995

Efficient Monte Carlo Simulation of Biological Aging

A bit-string model of biological life-histories is parallelized, with hundreds of millions of individuals. It gives the desired drastic decay of survival probabilities with increasing age for 32 age intervals.

cond-mat↗

arXiv1995

Influence of Refractory Periods in the Hopfield model

We study both analytically and numerically the effects of including refractory periods in the Hopfield model for associative memory. These periods are introduced in the dynamics of the network as thresholds that depend on the state of the neuron at the previous time. Both the retrieval properties and the dynamical behaviour are analyzed.

cond-mat↗

arXiv1997

A simple ansatz to describe thermodynamic quantities of peptides and proteins at low temperatures

We describe a simple ansatz to approximate the low temperature behavior of proteins and peptides by a mean-field-like model which is analytically solvable. For a small peptide some thermodynamic quantities are calculated and compared with numerical results of an all-atoms simulation. Our approach can be used to determine the weights for a multicanonical simulation of the molecule under consideration.

cond-mat↗

arXiv1998

Species Formation in Simple Ecosystems

In this paper we consider a microscopic model of a simple ecosystem. The basic ingredients of this model are individuals, and both the phenotypic and genotypic levels are taken in account. The model is based on a long range cellular automaton (CA); introducing simple interactions between the individuals, we get some of the complex collective behaviors observed in a real ecosystem. Since our fitness function is smooth, the model does not exhibit the error threshold transition; on the other hand the size of total population is not kept constant, and the mutational meltdown transition is present. We study the effects of competition between genetically similar individuals and how it can lead to species formation. This speciation transition does not depend on the mutation rate. We present also an analytical approximation of the model.

cond-mat.stat-mech↗

arXiv1999

Eigen's Error Threshold and Mutational Meltdown in a Quasispecies Model

We introduce a toy model for interacting populations connected by mutations and limited by a shared resource. We study the presence of Eigen's error threshold and mutational meltdown. The phase diagram of the system shows that the extinction of the whole population due to mutational meltdown can occur well before an eventual error threshold transition.

cond-mat.stat-mech↗

arXiv1999

Lattice three-species models of the spatial spread of rabies among foxes

Lattice models describing the spatial spread of rabies among foxes are studied. In these models, the fox population is divided into three-species: susceptible, infected or incubating, and infectious or rabid. They are based on the fact that susceptible and incubating foxes are territorial while rabid foxes have lost their sense of direction and move erratically. Two different models are investigated: a one-dimensional coupled-map lattice model, and a two-dimensional automata network model. Both models take into account the short-range character of the infection process and the diffusive motion of rabid foxes. Numerical simulations show how the spatial distribution of rabies, and the speed of propagation of the epizootic front depend upon the carrying capacity of the environment and diffusion of rabid foxes out of their territory.

adap-org↗

arXiv2000

Condensed Matter Physics - Biology Resonance

The field of condensed matter physics had its genesis this century and it has had a remarkable evolution. A closer look at its growth reveals a hidden aim in the collective consciousness of the field - a part of the development this century is a kind of warm up exercise to understand the nature of living condensed matter, namely the field of biology, by a growing new breed of scientists in the coming century. Through some examples the vitality of this interaction will be pointed out.

cond-mat↗

arXiv1998

Diversity, Stability, Recursivity, and Rule Generation in Biological System: Intra-inter Dynamics Approach

Basic problems for the construction of a scenario for the Life are discussed. To study the problems in terms of dynamical systems theory, a scheme of intra-inter dynamics is presented. It consists of internal dynamics of a unit, interaction among the units, and the dynamics to change the dynamics itself, for example by replication (and death) of units according to their internal states. Applying the dynamics to cell differentiation, isologous diversification theory is proposed. According to it, orbital instability leads to diversified cell behaviors first. At the next stage, several cell types are formed, first triggered by clustering of oscillations, and then as attracting states of internal dynamics stabilized by the cell-to-cell interaction. At the third stage, the differentiation is determined as a recursive state by cell division. At the last stage, hierarchical differentiation proceeds, with the emergence of stochastic rule for the differentiation to sub-groups, where regulation of the probability for the differentiation provides the diversity and stability of cell society. Relevance of the theory to cell biology is discussed.

adap-org↗

arXiv1997

Evolution and extinction dynamics in rugged fitness landscapes

Macroevolution is considered as a problem of stochastic dynamics in a system with many competing agents. Evolutionary events (speciations and extinctions) are triggered by fitness records found by random exploration of the agents' fitness landscapes. As a consequence, the average fitness in the system increases logarithmically with time, while the rate of extinction steadily decreases. This dynamics is studied by numerical simulations and, in a simpler mean field version, analytically. We also study the effect of externally added `mass' extinctions. The predictions for various quantities of paleontological interest (life-time distributions, distribution of event sizes and behavior of the rate of extinction) are robust and in good agreement with available data. Brief version of parts of this work have been published as Letters. (PRL 75, 2055, (1995) and PRL, 79, 1413, (1997))

adap-org↗

arXiv1997

Kinetics, Hydrodynamics and Stochastodynamics of Cellular Structure Coarsening

For the first time the phenomenon of cellular structure coarsening are consistently analysed from the positions of kinetic, hydrodynamic and stochastodynamic theories of nonequilibrium statistical systems. Thereby micro-, meso- and macroscopic levels of approach are distinguished. At the microscopic level the cellular structure is describe by a probability distribution function in a phase space of cell coordinates and of cell sizes. A kinetic equation for the function is written and a development to a hydrodynamic equation of a mesoscopic cell medium is realised. It has the form of a diffusion-reaction equation with a negative "diffusion" coefficient and with a cell interface density playing the role of concentration. Its analysis reveals a new effect of macroscopic patterning in the cell medium: existence of space-correlated stochastic fluctuations of the cell interface density.

cond-mat↗