相关论文: Neutral evolution of model proteins: diffusion in …
Latent space models for network data characterize each node through a vector of latent features whose pairwise similarities define the edge probabilities among the pairs of nodes. Although this formulation has led to successful…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
We consider a propagation of transition fronts in one-dimensional chains with bi-stable nondegenerate on-site potential. If one adopts linear coupling in the chain and piecewise linear on-site force, then it is possible to develop…
We consider the overdamped dynamics of a paradigmatic long-range system of particles residing on the sites of a one-dimensional lattice, in the presence of thermal noise. The internal degree of freedom of each particle is a periodic…
We review models of biological evolution in which the population frequency changes deterministically with time. If the population is self-replicating, although the equations for simple prototypes can be linearised, nonlinear equations arise…
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…
Various genome evolutionary models have been proposed these last decades to predict the evolution of a DNA sequence over time, essentially described using a mutation matrix. By essence, all of these models relate the evolution of DNA…
We introduce a minimalistic model based on dynamic node deletion and node duplication with heterodimerisation. The model is intended to capture the essential features of the evolution of protein interaction networks. We derive an exact…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
We investigate the evolutionary dynamics of a finite population of RNA sequences adapting to a neutral fitness landscape. Despite the lack of differential fitness between viable sequences, we observe typical properties of adaptive…
We investigate the evolution of populations of random Boolean networks under selection for robustness of the dynamics with respect to the perturbation of the state of a node. The fitness landscape contains a huge plateau of maximum fitness…
The study of real-life network modeling has become very popular in recent years. An attractive model is the scale-free percolation model on the lattice $\mathbb{Z}^d$, $d\ge1$, because it fulfills several stylized facts observed in large…
Robustness to mutations and noise has been shown to evolve through stabilizing selection for optimal phenotypes in model gene regulatory networks. The ability to evolve robust mutants is known to depend on the network architecture. How do…
Nowadays, software has become a complex piece of work that may be beyond our control. Understanding how software evolves over time plays an important role in controlling software development processes. Recently, a few researchers found the…
The spread in time of a mutation through a population is studied analytically and computationally in fully-connected networks and on spatial lattices. The time, t_*, for a favourable mutation to dominate scales with population size N as…
We are interested in the study of models describing the evolution of a polymorphic population with mutation and selection in the specific scales of the biological framework of adaptive dynamics. The population size is assumed to be large…
The predominant success of diffusion models in generative modeling has spurred significant interest in understanding their theoretical foundations. In this work, we propose a feature learning framework aimed at analyzing and comparing the…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
We consider a class of mass transfer models on a one-dimensional lattice with nearest-neighbour interactions. The evolution is given by the discrete backward fast diffusion equation, with exponent $\beta$ in the regime $(-\infty,0) \cup…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…