Related papers: Accessibility Percolation on Cartesian Power Graph…
Complex systems of interacting components often can be modeled by a simple graph $\mathcal{G}$ that consists of a set of $n$ nodes and a set of $m$ edges. Such a graph can be represented by an adjacency matrix $A\in\R^{n\times n}$, whose…
We propose a network characterization of combinatorial fitness landscapes by adapting the notion of inherent networks proposed for energy surfaces. We use the well-known family of NK landscapes as an example. In our case the inherent…
We study the evolution of large but finite asexual populations evolving in fitness landscapes in which all mutations are either neutral or strongly deleterious. We demonstrate that despite the absence of higher fitness genotypes, adaptation…
We investigate the properties of a deterministic walk, whose locomotion rule is always to travel to the nearest site. Initially the sites are randomly distributed in a closed rectangular ($A/L \times L)$ landscape and, once reached, they…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
We study transition paths in energy landscapes over multi-categorical Potts configurations using the mean-field approach introduced by Mauri et al., {\em Phys Rev Lett 130, 158402 (2023)}. Paths interpolate between two fixed configurations…
The rapid growth in feature dimension may introduce implicit associations between features and labels in multi-label datasets, making the relationships between features and labels increasingly complex. Moreover, existing methods often adopt…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Molecular evolution is often conceptualised as adaptive walks on rugged fitness landscapes, driven by mutations and constrained by incremental fitness selection. It is well known that epistasis shapes the ruggedness of the landscape's…
Epistatic interactions between mutations add substantial complexity to adaptive landscapes, and are often thought of as detrimental to our ability to predict evolution. Yet, patterns of global epistasis, in which the fitness effect of a…
This is an introductory review of deterministic mutation-selection models for asexual populations (i.e., quasispecies theory) and related topics. First, the basic concepts of fitness, mutations, and sequence space are introduced. Different…
The connective constant $\mu(G)$ of an infinite transitive graph $G$ is the exponential growth rate of the number of self-avoiding walks from a given origin. The relationship between connective constants and amenability is explored in the…
Bootstrap percolation is a well-known activation process in a graph, in which a node becomes active when it has at least $r$ active neighbors. Such process, originally studied on regular structures, has been recently investigated also in…
It has previously been shown that the network of connected minima on a potential energy landscape is scale-free, and that this reflects a power-law distribution for the areas of the basins of attraction surrounding the minima. Here, we set…
Access to healthy food is key to maintaining a healthy lifestyle and can be quantified by the distance to the nearest grocery store. However, calculating this distance forces a trade-off between cost and correctness. Accurate route-based…
Complex systems are made up of many interacting components. Network science provides the tools to analyze and understand these interactions. Community detection is a key technique in network science for uncovering the structures that shape…
We consider the $n$-dimensional random temporal hypercube, i.e., the $n$-dimensional hypercube graph with its edges endowed with i.i.d. continuous random weights. We say that a vertex $w$ is accessible from another vertex $v$ if and only if…
We relativise the Thomassen--Woess definition of accessibility in graphs, defining what it means for a graph to be accessible relative to a peripheral system. In the case of locally finite, quasi-transitive graphs, we characterise relative…
Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness…