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Mathematical modelling allows us to concisely describe fundamental principles in biology. Analysis of models can help to both explain known phenomena, and predict the existence of new, unseen behaviours. Model analysis is often a complex…
This document is meant to be a practical introduction to the analytical and numerical manipulation of Fermionic Gaussian systems. Starting from the basics, we move to relevant modern results and techniques, presenting numerical examples and…
Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cell interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on…
Physiological whole-body models are valuable tools for the development of novel drugs where understanding the system aspects is important. This paper presents a generalized model that encapsulates the structure and flow of whole-body human…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
The many-body states in an extended Fermionic Molecular Dynamics approach are flexible enough to allow the description of nuclei with shell model nature as well as nuclei with cluster and halo structures. Different many-body configurations…
Cellular automata are a discrete dynamical system which models massively parallel computation. Much attention is devoted to computations with small time complexity for which the parallelism may provide further possibilities. In this paper,…
BondGraphTools is a Python library for scripted modelling of complex multi-physics systems. In contrast to existing modelling solutions, BondGraphTools is based upon the well established bond graph methodology, provides a programming…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
This case for the Transformation Tool Contest 2013 is about evaluating the scope and usability of transformation languages and tools for a set of four tasks requiring very different capabilities. One task deals with typical model-to-model…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
This paper proposes the use of notebooks for the design documentation and tool interaction in the rigorous design of embedded systems. Conventionally, a notebook is a sequence of cells alternating between (textual) code and prose to form a…
Duality transformations are very important in both classical and quantum physics. They allow one to relate two seemingly different formulations of the same physical realm through clever mathematical manipulations, and offer numerous…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
Transient gas network simulations can significantly assist in design and operational aspects of gas networks. Models used in these simulations require a detailed framework integrating various models of the network constituents - pipes and…
Navigating topological transitions in cellular mechanical systems is a significant challenge for existing simulation methods. While abstract models lack predictive capabilities at the cellular level, explicit network representations…
Distributed software engineering is widely recognized as a complex task. Among the inherent complexities is the process of obtaining a system design from its global requirement specification. This paper deals with such transformation…
MatchingTools is a Python library for doing symbolic calculations in effective field theory. It provides the tools to construct general models by defining their field content and their interaction Lagrangian. Once a model is given, the…
Operator splitting methods allow to split the operator describing a complex dynamical system into a sequence of simpler subsystems and treat each part independently. In the modeling of dynamical problems, systems of (possibly coupled)…