相关论文: A Growth model for DNA evolution

Vital to primary visual processing, retinal circuitry shows many similar structures across a very broad array of species, both vertebrate and non-vertebrate, especially functional components such as lateral inhibition. This surprisingly…

Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…

The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally…

Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…

We propose a novel approach for learning the evolution that employs differentiable neural networks to approximate the full GENERIC structure. Instead of manually choosing the fitted parameters, we learn the whole model together with the…

This paper presents a simple model to measure the relative economic growth of economic systems. The model considers S-Shaped patterns of economic growth that, represented with a linear model, measure how an economic system grows in…

The whole complex process to obtain a protein encoded by a gene is difficult to include in a mathematical model. There are many models for describing different aspects of a genetic network. Finding a better model is one of the most…

"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…

We introduce an encoder-only approach to learn the evolution operators of large-scale non-linear dynamical systems, such as those describing complex natural phenomena. Evolution operators are particularly well-suited for analyzing systems…

A list of open problems on global behavior in time of some evolution systems, mainly governed by P.D.E, is given together with some background information explaining the context in which these problems appeared. The common characteristic of…

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…

Complex systems' modeling and simulation are powerful ways to investigate a multitude of natural phenomena providing extended knowledge on their structure and behavior. However, enhanced modeling and simulation require integration of…

It has recently been suggested that evolution exploits a form of fitness landscape smoothing within eukaryotic sex due to the haploid-diploid cycle. This short paper presents a simple modification to the standard evolutionary computing…

Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…

This paper is concerned with a reaction-diffusion single species model with harvesting on $n$-dimensional isotropically growing domain. The model on growing domain is derived and the corresponding comparison principle is proved. The…

In this study, we construct an evolutionary model of a population of DNA sequences interacting with the surrounding environment on the topological monoid A* of strings on the alphabet A = { a, c, g, t }. A partial differential equation…

Based on a model first studied in [Physical Review A, vol. 43, 5240-5260,1991] properties of correlation function for expansion-modification systems are developed. The existence of several characteristic exponents is proved. The…

There is a growing body of work considering the use of representations based upon genetic regulatory networks. This paper uses a recently presented abstract, tunable Boolean regulatory network model to explore aspects of mobile DNA, such as…

The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…

The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…