Related papers: Accessibility Percolation on Cartesian Power Graph…
The exploration of vast genotype spaces poses fundamental challenges for evolving populations. As the number of genotypes encoding viable phenotypes grows exponentially with genome length, populations can only explore a tiny fraction of…
Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…
Complex networks are characterized by several topological properties: degree distribution, clustering coefficient, average shortest path length, etc. Using a simple model to generate scale-free networks embedded on geographical space, we…
Nodes are randomly distributed within an annulus (and then a shell) to form a point pattern of communication terminals which are linked stochastically according to the Rayleigh fading of radio-frequency data signals. We then present…
A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
It has recently been noted that the relative prevalence of the various kinds of epistasis varies along an adaptive walk. This has been explained as a result of mean regression in NK model fitness landscapes. Here we show that this…
Machine learning models increasingly map biological sequence-fitness landscapes to predict mutational effects. Effective evaluation of these models requires benchmarks curated from empirical data. Despite their impressive scales, existing…
In this paper we explore the features of a graph generated by random walkers with nodes that have evolutionary attractiveness and Boltzmann-like transition probabilities that depend both on the euclidean distance between the nodes and on…
Percolation is a model for random damage to a network. It is one of the simplest models that displays a phase transition: when the network is severely damaged, it falls apart in many small connected components, while if the damage is light,…
We consider a stochastic model of population dynamics where each individual is characterised by a trait in {0,1,...,L} and has a natural reproduction rate, a logistic death rate due to age or competition and a probability of mutation…
Energy landscape theory describes how a full-length protein can attain its native fold by sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome,…
Graph-structured data is central to many scientific and industrial domains, where the goal is often to optimize objectives defined over graph structures. Given the combinatorial complexity of graph spaces, such optimization problems are…
Within the framework of population genetics we consider the evolution of an asexual haploid population under the effect of a rapidly varying natural selection (microevolution). We focus on the case in which the environment exerting…
Biological systems must be robust for stable function against perturbations, but robustness alone is not sufficient. The ability to switch between appropriate states (phenotypes) in response to different conditions is essential for…
We study the nature of fitness landscapes of 'quenched' Kauffman's Boolean model with a scale-free network. We have numerically calculated the rugged fitness landscapes, the distributions, its tails, and the correlation between the fitness…
Mutational neighbourhoods in genotype-phenotype (GP) maps are widely believed to be more likely to share characteristics than expected from random chance. Such genetic correlations should, as John Maynard Smith famously pointed out,…
Connectomes are spatially embedded networks whose architecture has been shaped by physical constraints and communication needs throughout evolution. Using a decentralized navigation protocol, we investigate the relationship between the…
In this paper we present two modifications of traditional $NK$ fitness landscapes, the $\theta NK$ and $HNK$ models, and explore these modifications via accessibility and ruggedness. The $\theta NK$ model introduces a parameter $\theta$ to…
In this paper, we consider accessibility percolation on hypercubes, i.e., we place i.i.d. uniform [0,1] random variables on vertices of a hypercube, and study whether there is a path connecting two vertices such that the values of these…