相关论文: A Growth model for DNA evolution

Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…

Computer modelling for evolutionary systems consists in: 1) to store in the memory the individual features of each member of a large population; and 2) to update the whole system repeatedly, as time goes by, according to some prescribed…

This article gives a brief introduction to the mathematical modeling of large-scale biological evolution and extinction. We give three examples of simple models in this field: the coevolutionary avalanche model of Bak and Sneppen, the…

We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…

Genetic Algorithms have established their capability for solving many complex optimization problems. Even as good solutions are produced, the user's understanding of a problem is not necessarily improved, which can lead to a lack of…

This paper describes a methodology for analyzing the evolutionary dynamics of genetic programming (GP) using genealogical information, diversity measures and information about the fitness variation from parent to offspring. We introduce a…

Deep learning, a rebranding of deep neural network research works, has achieved a remarkable success in recent years. With multiple hidden layers, deep learning models aim at computing the hierarchical feature representations of the…

In this review, we discuss the applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described.…

The deterministic selection-recombination equation describes the evolution of the genetic type composition of a population under selection and recombination in a law of large numbers regime. So far, an explicit solution has seemed out of…

A simple model for the formation of a complex organism is introduced. Individuals can communicate and specialize, leading to an increase in productivity. If there are limits to the capacity of individuals to communicate with other…

This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…

We present a quantitative, multi-scale coarse-grained model of DNA coated colloids. The parameters of this model are transferable and are solely based on experimental data. As a test case, we focus on nano-sized colloids carrying…

In this paper, we consider a series of events observed at spaced time intervals and present a method of representation of the series. To explain an idea, by dealing with a set of gene expression data, which could be obtained from…

In a convergence of machine learning and biology, we reveal that diffusion models are evolutionary algorithms. By considering evolution as a denoising process and reversed evolution as diffusion, we mathematically demonstrate that diffusion…

DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…

We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…

This technical report deals with the concept of an artificial DNA which contains a blueprint of the structure and organization of an embedded system. This blueprint can be used to build up the embedded system in a self-organizing manner at…

We propose a simple cognitive model where qualitative and quantitative com- parisons enable animals to identify objects, associate them with their properties held in memory and make naive inference. Simple notions like equivalence re-…

We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…

Evolving networks with a constant number of edges may be modelled using a rewiring process. These models are used to describe many real-world processes including the evolution of cultural artifacts such as family names, the evolution of…