Related papers: Evolutionary timeline of a modeled cell
The process of evolutionary emergence of purposeful adaptive behavior is investigated by means of computer simulations. The model proposed implies that there is an evolving population of simple agents, which have two natural needs: energy…
A phenomenological model of self-organization explaining the emergence of a complexity with features that apparently satisfy the specific criteria usually required for recognizing the appearance of life in laboratory is presented. The…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. By adopting a simple theoretical framework for intra-cellular chemical reaction dynamics with…
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…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
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,…
This study explores the emergence of life through a simulation model approach. The model "Multi-set chemical lattice model" is a model that allows virtual molecules of multiple types to be placed in each lattice cell on a two-dimensional…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species…
Stem cells, through their ability to produce daughter stem cells and differentiate into specialized cells, are essential in the growth, maintenance, and repair of biological tissues. Understanding the dynamics of cell populations in the…
Darwin's hypothesis that all extant life forms are descendants of a last common ancestor cell and diversification of life forms results from gradual mutation plus natural selection represents a mainstream view that has influenced biology…
A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers…
A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process…
The periods after the end of the "primary" nucleation are considered. The approximate analytical description is given. The process is split into several periods which form the loop of evolution.
Apparent biodiversity on earth exists only if we compare different species separated from their environments. Meanwhile coexisting species have to be identical in terms of energetic interactions. Consider the biosphere as a network of…
An adult human body is made up of some 30 to 40 trillion cells, all of which stem from a single fertilized egg cell. The process by which the right cells appear to arrive in their right numbers at the right time at the right place --…
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to…
A fundamental issue discussed in evolutionary biology is the transition from unicellular to multicellular organisms. Here we develop non-robust models provided in [1] and attempt to get robust models investigated how differentiation of…