相关论文: Fold or die: experimental evolution in vitro

We present a number of new contributions to the topic of constructing efficient higher-order splitting methods for the numerical integration of evolution equations. Particular schemes are constructed via setup and solution of polynomial…

Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…

In addressing the origins of Darwinian evolution, recent experimental work has been focussed on the discovery of simple physical effects which would provide a relevant selective advantage to protocells competing with each other for a…

Character evolution that affects ecological community interactions often occurs contemporaneously with temporal changes in population size, potentially altering the very nature of those dynamics. Such eco-evolutionary processes may be most…

We propose a model for evolution aiming to reproduce statistical features of fossil data, in particular the distributions of extinction events, the distribution of species per genus and the distribution of lifetimes, all of which are known…

As Evolutionary Dynamics moves from the realm of theory into application, algorithms are needed to move beyond simple models. Yet few such methods exist in the literature. Ecological and physiological factors are known to be central to…

We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…

We introduce a framework to model the evolution of a class of open quantum systems whose environments periodically undergo an instantaneous non-unitary evolution stage. For the special case of quadratic models, we show how this approach can…

We study the stochastic evolution of four species in cyclic competition in a well mixed environment. In systems composed of a finite number $N$ of particles these simple interaction rules result in a rich variety of extinction scenarios,…

In this paper we explore the eco-evolutionary dynamics of a predator-prey model, where the prey population is structured according to a certain life history trait. The trait distribution within the prey population is the result of interplay…

Particle-mesh simulations trade small-scale accuracy for speed compared to traditional, computationally expensive N-body codes in cosmological simulations. In this work, we show how a data-driven model could be used to learn an effective…

Evolutionary algorithms, inspired by natural evolution, aim to optimize difficult objective functions without computing derivatives. Here we detail the relationship between population genetics and evolutionary optimization and formulate a…

Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and…

Using information theory, we propose an estimation method for traits parameters in a Darwinian evolution model for species with on trait or multiple traits. We use the Fisher's information to obtain the errors on the estimation for one…

The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…

Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time…

Design of experiments and model selection, though essential steps in data science, are usually viewed as unrelated processes in the study and analysis of biological networks. Not accounting for their inter-relatedness has the potential to…

Recently, evolutionary reinforcement learning has obtained much attention in various domains. Maintaining a population of actors, evolutionary reinforcement learning utilises the collected experiences to improve the behaviour policy through…

We study a class of evolution models, where the breeding process involves an arbitrary exchangeable process, allowing for mutations to appear. The population size $n$ is fixed, hence after breeding, selection is applied. Individuals are…

Purpose: This study aimed to enhance protein sequence classification using natural language processing (NLP) techniques while addressing the impact of sequence similarity on model performance. We compared various machine learning and deep…