VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations.

We present the VECMA toolkit (VECMAtk), a flexible software environment for single and multiscale simulations that introduces directly applicable and reusable procedures for verification, validation (V&V), sensitivity analysis (SA) and uncertainty quantication (UQ). It enables users to verify key aspects of their applications, systematically compare and validate the simulation outputs against observational or benchmark data, and run simulations conveniently on any platform from the desktop to current multi-petascale computers. In this sequel to our paper on VECMAtk which we presented last year [1] we focus on a range of functional and performance improvements that we have introduced, cover newly introduced components, and applications examples from seven different domains such as conflict modelling and environmental sciences. We also present several implemented patterns for UQ/SA and V&V, and guide the reader through one example concerning COVID-19 modelling in detail. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.

The heterogeneous multiscale method applied to inelastic polymer mechanics.

Mechanisms emerging across multiple scales are ubiquitous in physics and methods designed to investigate them are becoming essential. The heterogeneous multiscale method (HMM) is one of these, concurrently simulating the different scales while keeping them separate. Owing to the significant computational expense, developments of HMM remain mostly theoretical and applications to physical problems are scarce. However, HMM is highly scalable and is well suited for high performance computing. With the wide availability of multi-petaflop infrastructures, HMM applications are becoming practical. Rare applications to mechanics of materials at low loading amplitudes exist, but are generally confined to the elastic regime. Beyond that, where history-dependent, irreversible or nonlinear mechanisms occur, not only computational cost but also data management issues arise. The micro-scale description loses generality, developing a specific microstructure based on the deformation history, which implies inter alia that as many microscopic models as discrete locations in the macroscopic description must be simulated and stored. Here, we present a detailed description of the application of HMM to inelastic mechanics of materials, with emphasis on the efficiency and accuracy of the scale-bridging methodology. The method is well suited to the estimation of macroscopic properties of polymers (and derived nanocomposites) starting from knowledge of their atomistic chemical structure. Through application of the resulting workflow to polymer fracture mechanics, we demonstrate deviation in the predicted fracture toughness relative to a single-scale molecular dynamics approach, thus illustrating the need for such concurrent multiscale methods in the predictive estimation of macroscopic properties. This article is part of the theme issue 'Multiscale modelling, simulation and computing: from the desktop to the exascale'.

Stem cell mechanical behaviour modelling: substrate's curvature influence during adhesion.

Recent experiments hint that adherent cells are sensitive to their substrate curvature. It is already well known that cells behaviour can be regulated by the mechanical properties of their environment. However, no mechanisms have been established regarding the influence of cell-scale curvature of the substrate. Using a numerical cell model, based on tensegrity structures theory and the non-smooth contact dynamics method, we propose to investigate the mechanical state of adherent cells on concave and convex hemispheres. Our mechanical cell model features a geometrical description of intracellular components, including the cell membrane, the focal adhesions, the cytoskeleton filament networks, the stress fibres, the microtubules, the nucleus membrane and the nucleoskeleton. The cell model has enabled us to analyse the evolution of the mechanical behaviour of intracellular components with varying curvature radii and with the removal of part of these components. We have observed the influence of the convexity of the substrate on the cell shape, the cytoskeletal force networks as well as on the nucleus strains. The more convex the substrate, the more tensed the stress fibres and the cell membrane, the more compressed the cytosol and the microtubules, leading to a stiffer cell. Furthermore, the more concave the substrate, the more stable and rounder the nucleus. These findings achieved using a verified virtual testing methodology, in particular regarding the nucleus stability, might be of significant importance with respect to the division and differentiation of mesenchymal stem cells. These results can also bring some hindsights on cell migration on curved substrates.