Citation
J.L. Kaplan, A. Bonfanti and A. Kabla
Journal of Open Source Software 4(41):1700 (2020)
Abstract
Abstract
Rheology is the science of deformation and flow, with a focus on materials that do not exhibit simple linear elastic or viscous Newtonian behaviours. Rheology plays an important role in the characterisation of soft viscoelastic materials commonly found in the food and cosmetics industries, as well as in biology and bioengineering. Empirical and theoretical approaches are commonly used to identify and quantify material behaviours based on experimental data. RHEOS (RHEology, Open-Source) is a software package designed to make the analysis of rheological data simpler, faster, and more reproducible. RHEOS is currently limited to the broad family of linear viscoelastic models. A particular strength of the library is its ability to handle rheological models containing fractional derivatives, which have demonstrable utility for the modelling of biological materials (Aime, Cipelletti, & Ramos, 2018; Bonfanti, Fouchard, Khalilgharibi, Charras, & Kabla, 2019; Bouzid et al., 2018; Kaplan, Torode, Daher, & Braybrook, 2019), but have hitherto remained in relative obscurity – possibly due to their mathematical and computational complexity. RHEOS is written in Julia (Bezanson, Edelman, Karpinski, & Shah, 2017), which provides excellent computational efficiency and approachable syntax. RHEOS is fully documented and has extensive testing coverage. To our knowledge, there is to this date no other software package that offers RHEOS’ broad selection of rheology analysis tools and extensive library of both traditional and fractional models. It has been used to process data and validate a model in Bonfanti et al. (2019), and is currently in use for several ongoing projects. It should be noted that RHEOS is not an optimisation package. It builds on another optimisation package, NLopt (Johnson, n.d.), by adding a large number of abstractions and functionality specific to the exploration of viscoelastic data.
Figure sample
Fractional viscoelastic model for epithelial monolayers: constitutive model and stress relaxation behaviour. (a) Diagrammatic representation of the fractional rheological model and qualitative behaviour of its stress relaxation modulus. The three-element fractional model is fitted to the relaxation data for (b) untreated epithelial monolayers (black curves are the experimental data, while the red curves represent the fit) and (c) monolayers treated with an inhibitor of contractility, Y27632 (the black curves are the experimental data, while the blue curves are the fits). Note that the monolayers are loaded with the constant rate of strain 75%/s and that the time is set to zero at the beginnings of the loading ramp.
