Related papers: Evolutionary timeline of a modeled cell
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
Aspects of cell metabolism are modeled by ordinary differential equations describing the change of intracellular chemical concentrations. There is a correspondence between this dynamical system and a complex network. As in the classic…
The basic principles underlying galactic chemical evolution and the most important results of chemical evolution models are discussed. In particular, the chemical evolution of the Milky Way galaxy, for which we possess the majority of…
Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing "replicator-first" and "metabolism-first"…
Using data from gene expression databases on various organisms and tissues, including yeast, nematodes, human normal and cancer tissues, and embryonic stem cells, we found that the abundances of expressed genes exhibit a power-law…
Isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and cell division process following consumption of some chemicals. According to the simulations of…
During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular…
All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which…
Ecology and evolution are inseparable. Motivated by some recent experiments, we have developed models of evolutionary ecology from the perspective of dynamic networks. In these models, in addition to the intra-node dynamics, which…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…
How multicellular life forms evolved out from unicellular ones constitutes a major problem in our understanding of the evolution of our biosphere. A recent set of experiments involving yeast cell populations has shown that selection for…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
A general theory is developed for the evolution of the cell order (CO) distribution in planar granular systems. Dynamic equations are constructed and solved in closed form for several examples: systems under compression; dilation of very…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate…
One of the great challenges in science is determining when, where, why, and how life first arose as well as the form taken by this life. In the present study, life was assumed to be (1) bounded, (2) replicating, (3) able to inherit…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…