Related papers: Information-Theoretical Measures for Developmental…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
One of the fundamental problems in biology concerns the method by which a cluster of organisms can regulate the proportion of individuals that perform various roles or modes as if each individual knows a whole situation without a leader. A…
Recent experimental results for covalent glasses suggest the existence of an intermediate phase attributed to the self-organization of the glass network resulting from the tendency to minimize its internal stress. However, the exact nature…
What role does phenotypic complexity play in the systems-level function of an embodied agent? The organismal phenotype is a topologically complex structure that interacts with a genotype, developmental physics, and an informational…
Cyclic cellular automata (CCA) are models of excitable media. Started from random initial conditions, they produce several different kinds of spatial structure, depending on their control parameters. We introduce new tools from information…
This paper concerns the modeling and numerical simulation of the process of speciation. In particular, given conditions for which one or more speciation events within an ecosystem occur, our aim is to develop the necessary modeling and…
Advances in cellular imaging technologies, especially those based on fluorescence in situ hybridization (FISH) now allow detailed visualization of the spatial organization of human or bacterial cells. Quantifying this spatial organization…
A steadily growing computational power is employed to perform molecular dynamics simulations of biological macromolecules, which represents at the same time an immense opportunity and a formidable challenge. In fact, large amounts of data…
Luminogenesis, the formation of a fluid-filled cavity (lumen), is an essential process in early mammalian embryonic development, coinciding with the second cell-fate decision that differentiates the inner-cell-mass (ICM) into epiblast (EPI)…
Predicting the fate of ecologies is a daunting, albeit extremely important, task. As part of this task one needs to develop an understanding of the organization, hierarchies, and correlations among the species forming the ecology. Focusing…
Despite being optimized, the information processing of biological organisms exhibits significant variability in its complexity and capability. One potential source of this diversity is the limitation of resources required for information…
Assembly theory predicts that a distinguishing signature of life is its ability to produce complex molecules in abundance, opening new possibilities for life detection. Experimental validation of this approach has so far relied on abiotic…
Long ago, life obtained nucleotides in the course of evolution and became a vehicle for them. Before assembly with nucleotides, in the pre-RNA era, what system dominated heredity? What was the subject of survival competition? Is it still a…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
In a developing embryo, information about the position of cells is encoded in the concentrations of "morphogen" molecules. In the fruit fly, the local concentrations of just a handful of proteins encoded by the gap genes are sufficient to…
Biological information processing manifests a huge variety in its complexity and capability among different organisms, which presumably stems from the evolutionary optimization under limited computational resources. Starting from the…
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…
Understanding the pattern formation in communities has been at the center of attention in various fields. Here we introduce a novel model, called an "information-particle model," which is based on the reaction-diffusion model and the…