Related papers: Cellular Development Follows the Path of Minimum A…
Self-organization is the autonomous assembly of a network of interacting components into a stable, organized pattern. This article shows that the process of self-assembly can be encoded in terms of evolutionary entropy, a statistical…
Understanding the evolution of cellular microenvironments in spatiotemporal data is essential for deciphering tissue development and disease progression. While experimental techniques like spatial transcriptomics now enable high-resolution…
A dynamical systems scenario for developmental cell biology is proposed, based on numerical studies of a system with interacting units with internal dynamics and reproduction. Diversification, formation of discrete and recursive types, and…
We study the average asymptotic growth rate of cells in randomly fluctuating environments, with multiple viable phenotypes per environment. We show that any information processing strategy has an asymptotic growth rate, which is the sum of:…
A path information is defined in connection with different possible paths of irregular dynamic systems moving in its phase space between two points. On the basis of the assumption that the paths are physically differentiated by their…
Organisms have evolved a variety of mechanisms to cope with the unpredictability of environmental conditions, and yet mainstream models of metabolic regulation are typically based on strict optimality principles that do not account for…
The development of multicellular organisms entails a deep connection between time-dependent biochemical processes taking place at the subcellular level, and the resulting macroscopic phenotypes that arise in populations of up to trillions…
Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is competency, as cells are not a passive material but…
Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial…
This piece serves two purposes. Firstly, it aims at elucidating the role of epistasis in shaping, at a molecular level, the evolutionary paths of proteins, as well as the extent to which these epistatic effects are the outcome of an…
There is now growing evidence of the emergence and biological functionality of liquid crystal features, including nematic order and topological defects, in cellular tissues. However, how such features that intrinsically rely on particle…
Living systems maintain or increase local order by working against the Second Law of Thermodynamics. Thermodynamic consistency is restored as they dissipate heat, thereby increasing the net entropy of their environment. Recently introduced…
How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells whose gene expression is under stochastic fluctuations,…
A number of factors, such as, cell-cell interactions and self-propulsion of cells driven by cytoskeletal forces determine tissue morphologies and dynamics. To explore the interplay between these factors in controlling the dynamics at the…
The minimal requirements for life are autopoiesis and cognition. We propose autopoietic models with cognition and perform three classes of evolutionary simulation. In our models the plasticity of the metabolic cycle and the regulation…
Cell competition is a quality control mechanism in tissues that results in the elimination of less fit cells. Over the past decade, the phenomenon of cell competition has been identified in many physiological and pathological contexts,…
This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…
Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the…
The rate at which individual bacterial cells grow depends on the concentrations of cellular components such as ribosomes and proteins. These concentrations continuously fluctuate over time and are inherited from mother to daughter cells,…
We show that a rate of conditional Shannon entropy reduction, characterizing the learning of an internal process about an external process, is bounded by the thermodynamic entropy production. This approach allows for the definition of an…