Related papers: 12 Labours tools for developing Functional Tissue …
Partial differential equations are a convenient way to describe reaction- advection-diffusion processes of signalling models. If only one cell type is present, and tissue dynamics can be neglected, the equations can be solved directly.…
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…
A continuum model of epithelial tissue mechanics was formulated using cellular-level mechanical ingredients and cell morphogenetic processes, including cellular shape changes and cellular rearrangements. This model can include finite…
We describe a methodology for designing efficient parallel and distributed scientific software. This methodology utilizes sequences of mechanizable algebra--based optimizing transformations. In this study, we apply our methodology to the…
Before we proposed an algebraic technics for the Hamiltonian approach to the evolution systems of partial differential equations, including systems with constraints. Here we further develop this approach and present the defining system of…
This paper is placed at the intersection-point between the study of theoretical computational models aimed at capturing the essence of genetic regulatory networks and the field of Artificial Embryology (or Computational Development). A…
With this contribution, we give a complete and comprehensive framework for modeling the dynamics of complex mechanical structures as port-Hamiltonian systems. This is motivated by research on the potential of lightweight construction using…
To understand changes in physical systems and facilitate decisions, explaining how model predictions are made is crucial. We use model-based interpretability, where models of physical systems are constructed by composing basic constructs…
A new formulation for the modular construction of flexible multibody systems is presented. By rearranging the equations for a flexible floating body and introducing the appropriate canonical momenta, the model is recast into a coupled…
Fracton topological phases host fractionalized excitations that are either completely immobile or only mobile along certain lines or planes. We demonstrate how such phases can be understood in terms of two fundamentally different types of…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
We present functional forms allowing a broader range of analytic solutions to common economic equilibrium problems. These can increase the realism of pen-and-paper solutions or speed large-scale numerical solutions as computational…
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…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
Using functional equations, we define functors that generalize standard examples from calculus of one variable. Examples of such functors are discussed and their Taylor towers are computed. We also show that these functors factor through…
We introduce and develop a theory of fusion and statistical processes of gapped excitations in Abelian fracton phases. The key idea is to incorporate lattice translation symmetry via its action on superselection sectors, which results in a…
In this paper, a functional model of interactions in quantum theory (QT) is proposed. A functional model describes the dynamic evolution of a physical system in terms of process steps and intermediate states. That is, it describes how…
This article presents formalistic tool for description of structural and biochemical relations between cells in the course of development of the body of plants. This is flexible formalistic space, based on the Category theory and the Petri…
Cellular aggregates play a significant role in the evolution of biological systems such as tumor growth, tissue spreading, wound healing, and biofilm formation. Analysis of such biological systems, in principle, includes examining 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,…