Learning from reproducing computational results: introducing three principles and the Reproduction Package.

We carry out efforts to reproduce computational results for seven published articles and identify barriers to computational reproducibility. We then derive three principles to guide the practice and dissemination of reproducible computational research: (i) Provide transparency regarding how computational results are produced; (ii) When writing and releasing research software, aim for ease of (re-)executability; (iii) Make any code upon which the results rely as deterministic as possible. We then exemplify these three principles with 12 specific guidelines for their implementation in practice. We illustrate the three principles of reproducible research with a series of vignettes from our experimental reproducibility work. We define a novel Reproduction Package, a formalism that specifies a structured way to share computational research artifacts that implements the guidelines generated from our reproduction efforts to allow others to build, reproduce and extend computational science. We make our reproduction efforts in this paper publicly available as exemplar Reproduction Packages. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.

Spatial Characteristics of Roughness Sublayer Mean Flow and Turbulence Over a Realistic Urban Surface.

Single-point measurements from towers in cities cannot properly quantify the impact of all terms in the turbulent kinetic energy (TKE) budget and are often not representative of horizontally-averaged quantities over the entire urban domain. A series of large-eddy simulations (LES) is here performed to quantify the relevance of non-measurable terms, and to explore the spatial variability of the flow field over and within an urban geometry in the city of Basel, Switzerland. The domain has been chosen to be centered around a tower where single-point turbulence measurements at six heights are available. Buildings are represented through a discrete-forcing immersed boundary method and are based on detailed real geometries from a surveying dataset. The local model results at the tower location compare well against measurements under near-neutral stability conditions and for the two prevailing wind directions chosen for the analysis. This confirms that LES in conjunction with the immersed boundary condition is a valuable model to study turbulence and dispersion within a real urban roughness sublayer (RSL). The simulations confirm that mean velocity profiles in the RSL are characterized by an inflection point z γ located above the average building height z h . TKE in the RSL is primarily produced above z γ , and turbulence is transported down into the urban canopy layer. Pressure transport is found to be significant in the very-near-wall regions. Further, spatial variations of time-averaged variables and non-measurable dispersive terms are important in the RSL above a real urban surface and should therefore be considered in future urban canopy parametrization developments.

The application of multiscale modelling to the process of development and prevention of stenosis in a stented coronary artery.

The inherent complexity of biomedical systems is well recognized; they are multiscale, multiscience systems, bridging a wide range of temporal and spatial scales. While the importance of multiscale modelling in this context is increasingly recognized, there is little underpinning literature on the methodology and generic description of the process. The COAST (complex autonoma simulation technique) project aims to address this by developing a multiscale, multiscience framework, coined complex autonoma (CxA), based on a hierarchical aggregation of coupled cellular automata (CA) and agent-based models (ABMs). The key tenet of COAST is that a multiscale system can be decomposed into N single-scale CA or ABMs that mutually interact across the scales. Decomposition is facilitated by building a scale separation map on which each single-scale system is represented according to its spatial and temporal characteristics. Processes having well-separated scales are thus easily identified as the components of the multiscale model. This paper focuses on methodology, introduces the concept of the CxA and demonstrates its use in the generation of a multiscale model of the physical and biological processes implicated in a challenging and clinically relevant problem, namely coronary artery in-stent restenosis.

Analysis of 3D transient blood flow passing through an artificial aortic valve by Lattice-Boltzmann methods.

The development of flow instabilities due to high Reynolds number flow in artificial heart valve geometries inducing high strain rates and stresses often leads to hemolysis and related highly undesired effects. Geometric and functional optimization of artificial heart valves is therefore mandatory. In addition to experimental work in this field it is meanwhile possible to obtain increasing insight into flow dynamics by computer simulation of refined model problems. After giving an introductory overview we report the results of the simulation of three-dimensional transient physiological flows in fixed geometries similar to a CarboMedics bileaflet heart valve at different opening angles. The visualization of emerging complicated flow patterns gives detailed information about the transient history of the systems dynamical stability. Stress analysis indicates temporal shear stress peaks even far away from walls. The mathematical approach used is the Lattice Boltzmann method. We obtained reasonable results for velocity and shear stress fields. The code is implemented on parallel hardware in order to decrease computation time. Finally, we discuss problems, shortcomings and possible extensions of our approach.