Related papers: Complexity and self-organization in Turing
The process of morphogenesis is an evolution of the shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such…
A model to describe the arising of new structures in an initial homogeneous biological system is proposed. The essay is motivated by the intention to work on a non-equilibrium situation grouping together several mechanisms and processes as:…
Interactions between the components in many-body systems can give rise to spontaneous formation of complex structures. Usually very little is known about the connection between the interactions and the resulting structure. Here we present a…
This manuscript has been written to address questions related to our recent publication (Science 347:78-81, 2015). We appreciate the many reactions to this paper that have been communicated to us, either privately or publicly. The following…
DNA, RNA and proteins are among the most important macromolecules in a living cell. These molecules are polymerized by molecular machines. These natural nano-machines polymerize such macromolecules, adding one monomer at a time, using…
So far, following the works of A.M. Turing, the algorithms were considered as the mathematical abstraction from which we could write programs for computers whose principle was based on the theoretical concept of Turing machine. We start…
From the point of view of a programmer, the robopsychology is a synonym for the activity is done by developers to implement their machine learning applications. This robopsychological approach raises some fundamental theoretical questions…
Plant morphogenesis relies on dynamic growth deformations at the cell and tissue scales driven by osmotic fluxes. A mechanistic understanding of this phenomenon demands a physical framework that integrates cell imbibition, tissue mechanics,…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
Although Turing pattern is one of the most universal mechanisms for pattern formation, in its standard model the number of stripes changes with the system size, since the wavelength of the pattern is invariant: It fails to preserve the…
The question how complex systems become more organized and efficient with time is open. Examples are, the formation of elementary particles from pure energy, the formation of atoms from particles, the formation of stars and galaxies, the…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
This two-part review examines how automation has contributed to different aspects of discovery in the chemical sciences. In this first part, we describe a classification for discoveries of physical matter (molecules, materials, devices),…
The reproduction of a living cell requires a repeatable set of chemical events to be properly coordinated. Such events define a replication cycle, coupling the growth and shape change of the cell membrane with internal metabolic reactions.…
This is the unedited authors' version of Chapter 3 appearing in the following book: Self-Assembly Systems: Theory and Simulations Ed. Li-Tang Yan John Wiley & Sons, Ltd, Chichester, pp. 53-84 (2017)
The morphometric approach is a powerful ansatz for decomposing the chemical potential for a complex solute into purely geometrical terms. This method has proven accuracy in hard spheres, presenting an alternative to comparatively expensive…
Chemical systems are traditionally described by lists of species, reactions, and externally imposed kinetic laws, a framework that lacks an intrinsic algebraic structure governing how transformations compose. We propose an axiomatic…
Research in cell biology is steadily contributing new knowledge about many different aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function.…
We present chemlambda (or the chemical concrete machine), an artificial chemistry with the following properties: (a) is Turing complete, (b) has a model of decentralized, distributed computing associated to it, (c) works at the level of…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…