Goriely, Alain; Moulton, Derek(New Trends in the Physics and Mechanics of Biological Systems, Oxford University Press (OUP), 2011-10-11)[Book Chapter]
This chapter is concerned with the modelling of growth processes in the framework of continuum mechanics and nonlinear elasticity. It begins by considering growth and deformation in a one-dimensional setting, illustrating the key relationship between growth, the elastic response of the material, and the generation of residual stresses. The general three-dimensional theory of morphoelasticity is then developed from conservation of mass and momentum balance equations. In the formulation, the multiplicative decomposition of the deformation tensor, the standard approach in morphoelasticity, is derived in a new way. A discussion of continuous growth is also included. The chapter concludes by working through a sample problem of a growing cylindrical tube. A stability analysis is formulated, and the effect of growth on mucosal folding, a commonly seen instability in biological tubes, is demonstrated.
MacLean, Adam L.; Harrington, Heather A.; Stumpf, Michael P. H.; Byrne, Helen M.(Methods in Molecular Biology, Springer Nature, 2015-12-16)[Book Chapter]
The last decade has seen an explosion in models that describe phenomena in systems medicine. Such models are especially useful for studying signaling pathways, such as the Wnt pathway. In this chapter we use the Wnt pathway to showcase current mathematical and statistical techniques that enable modelers to gain insight into (models of) gene regulation and generate testable predictions. We introduce a range of modeling frameworks, but focus on ordinary differential equation (ODE) models since they remain the most widely used approach in systems biology and medicine and continue to offer great potential. We present methods for the analysis of a single model, comprising applications of standard dynamical systems approaches such as nondimensionalization, steady state, asymptotic and sensitivity analysis, and more recent statistical and algebraic approaches to compare models with data. We present parameter estimation and model comparison techniques, focusing on Bayesian analysis and coplanarity via algebraic geometry. Our intention is that this (non-exhaustive) review may serve as a useful starting point for the analysis of models in systems medicine.
Woolley, Thomas E.; Baker, Ruth E.; Maini, Philip K.(Theory and Applications of Computability, Springer Nature, 2017-05-06)[Book Chapter]
Over 60 years have passed since Alan Turing first postulated a mechanism for biological pattern formation. Although Turing did not have the chance to extend his theories before his unfortunate death two years later, his work has not gone unnoticed. Indeed, many researchers have since taken up the gauntlet and extended his revolutionary and counter-intuitive ideas. Here, we reproduce the basics of his theory as well as review some of the recent generalisations and applications that have led our mathematical models to be closer representations of the biology than ever before. Finally, we take a look to the future and discuss open questions that not only show that there is still much life in the theory, but also that the best may be yet to come.
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