Related papers: Evolutionary timeline of a modeled cell
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
The conceptual landscape of convection has two simple gateways: optimal function and random form. Optimal convection adjusts toward a univariate ideal called neutrality. Convection form involves elements (parcels, bubbles, drafts) whose…
We introduce a simple physical picture to explain the process of molecular sorting, whereby specific proteins are concentrated and distilled into submicrometric lipid vesicles in eukaryotic cells. To this purpose, we formulate a model based…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other…
Competing strategies in an evolutionary game model, or species in a biosystem, can easily form a larger unit which protects them from the invasion of an external actor. Such a defensive alliance may have two, three, four or even more…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
A number of biological processes, such as embryo development, cancer metastasis or wound healing, rely on cells moving in concert. The mechanisms leading to the emergence of coordinated motion remain however largely unexplored. Although…
According to the universally accepted concept of the development of life on the Earth, multicellular organisms initially emerged as a result of either the union of identical unicellular organisms with the following functional…
Life is a complex biological phenomenon represented by numerous chemical, physical and biological processes performed by a biothermodynamic system/cell/organism. Both living organisms and inanimate objects are subject to aging, a biological…
An explanatory model for the emergence of evolvable units must display emerging structures that (1) preserve themselves in time (2) self-reproduce and (3) tolerate a certain amount of variation when reproducing. To tackle this challenge,…
We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…
We present a novel mathematical model of heterogeneous cell proliferation where the total population consists of a subpopulation of slow-proliferating cells and a subpopulation of fast-proliferating cells. The model incorporates two…
We study the evolution of networks when the creation and decay of links are based on the position of nodes in the network measured by their centrality. We show that the same network dynamics arises under various centrality measures, and…
Many mechanisms, functions and structures of life have been unraveled. However, the fundamental driving force that propelled chemical evolution and led to life has remained obscure. The 2nd law of thermodynamics, written as an equation of…
Formation and competition of associations are studied in a six-species ecological model where each species has two predators and two prey. Each site of a square lattice is occupied by an individual belonging to one of the six species. The…