Related papers: Quantifying Slow Evolutionary Dynamics in RNA Fitn…
A model for the evolution of a finite population in a rugged fitness landscape is introduced and solved. The population is trapped in an evolutionary loop, alternating periods of stasis to periods in which it performs adaptive walks. The…
We propose a stochastic model for evolution. Births and deaths of species occur with constant probabilities. Each new species is associated with a fitness sampled from the uniform distribution on [0,1]. Every time there is a death event…
Epochal dynamics, in which long periods of stasis in population fitness are punctuated by sudden innovations, is a common behavior in both natural and artificial evolutionary processes. We use a recent quantitative mathematical analysis of…
We consider the evolution of large but finite populations on arbitrary fitness landscapes. We describe the evolutionary process by a Markov, Moran process. We show that to $\mathcal O(1/N)$, the time-averaged fitness is lower for the finite…
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic…
We study competitive DNA sequence evolution directed by {\it in vitro} protein binding. The steady-state dynamics of this process is well described by a shape-preserving pulse which decelerates and eventually reaches equilibrium. We explain…
The functioning of animal as well as human societies fundamentally relies on cooperation. Yet, defection is often favorable for the selfish individual, and social dilemmas arise. Selection by individuals' fitness, usually the basic driving…
We present a study by linear stability analysis and large-scale Monte Carlo simulations of a simple model of biological coevolution. Selection is provided through a reproduction probability that contains quenched, random interspecies…
Efficient dynamic spectrum access mechanism is crucial for improving the spectrum utilization. In this paper, we consider the dynamic spectrum access mechanism design with both complete and incomplete network information. When the network…
Darwinian evolution can be modeled in general terms as a flow in the space of fitness (i.e. reproductive rate) distributions. In the diffusion approximation, Tsimring et al. have showed that this flow admits "fitness wave" solutions:…
In this paper, we show that different types of evolutionary game dynamics are, in principle, special cases of a dynamical system model based on our previously reported framework of generalized growth transforms. The framework shows that…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
Boolean networks may be viewed as idealizations of biological genetic networks, where each node is represented by an on-off switch which is a function of the binary output from some other nodes. We evolve connectivity in a single Boolean…
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…
Species sharing a habitat will co-evolve to make use of the available resources, as consumption is modulated by competition and negative feedback loops between consumers and resources. The dietary range of a given species determines the…
The concept of fitness as a measure for a species's success in natural selection is central to the theory of evolution. We here investigate how reproduction rates which are not constant but vary in response to environmental fluctuations,…
Evolution on neutral networks of genotypes has been found in models to concentrate on genotypes with high mutational robustness, to a degree determined by the topology of the network. Here analysis is generalized beyond neutral networks to…
One essential ingredient of evolutionary theory is the concept of fitness as a measure for a species' success in its living conditions. Here, we quantify the effect of environmental fluctuations onto fitness by analytical calculations on a…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…