Related papers: Categorical Description Of Plant Morphogenesis
The present study is aimed at analysing the benefits of an ontological approach in Functional Structural Plant Modelling. The ontological approach has been used at two levels, to refine the conceptual modelling approach, and to define the…
The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…
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,…
The formalism of the models with Petri networks provides a sound theoretical base, supported by powerful mathematical methods able to extract information necessary for the formalism and simulation of the real system that provides features…
The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes…
How morphogenesis depends on cell properties is an active direction of research. Here, we focus on mechanical models of growing plant tissues, where microscopic (sub)cellular structure is taken into account. In order to establish links…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
The growth of plants is a hydromechanical phenomenon in which cells enlarge by absorbing water, while their walls expand and remodel under turgor-induced tension. In multicellular tissues, where cells are mechanically interconnected,…
Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…
In this paper homogenization of a mathematical model for biomechanics of a plant tissue with randomly distributed cells is considered. Mechanical properties of a plant tissue are modelled by a strongly coupled system of…
In silico, cell based approaches for modeling biological morphogenesis are used to test and validate our understanding of the biological and mechanical process that are at work during the growth and the organization of multi-cell tissues.…
Morphogenesis, the process by which an adult organism emerges from a single cell, has fascinated humans for a long time. Modelling this process can provide novel insights into development and the principles that orchestrate the…
We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…
We introduce the concept of a morphism between coloured nets. Our definition generalizes Petris definition for ordinary nets. A morphism of coloured nets maps the topological space of the underlying undirected net as well as the kernel and…
We develop a rigorous, equation-free category-theoretic foundation for fungal organisation. A fungal organism is formalised as a functor from a category $\Env$ of structured environmental states and admissible transformations to a category…
Petri networks and network models are two frameworks for the compositional design of systems of interacting entities. Here we show how to combine them using the concept of a "catalyst": an entity that is neither destroyed nor created by any…
The complexity of a neuronal cell shape is known to be related to its function. Specifically, among other indicators, a decreased complexity in the dendritic trees of cortical pyramidal neurons has been associated with mental retardation.…
Spatial distributions of morphogens provide positional information in developing systems, but how the distributions are established and maintained remains an open problem. Transport by diffusion has been the traditional mechanism, but…
In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped…
Urban systems are composed by complex couplings of several components, and more particularly between the built environment and transportation networks. Their interaction is involved in the emergence of the urban form. We propose in this…