Stabilized lowest order finite element approximation for linear three-field poroelasticity

A stabilized conforming mixed finite element method for the three-field (displacement, fluid flux and pressure) poroelasticity problem is developed and analyzed. We use the lowest possible approximation order, namely piecewise constant approximation for the pressure and piecewise linear continuous elements for the displacements and fluid flux. By applying a local pressure jump stabilization term to the mass conservation equation we ensure stability and avoid pressure oscillations. Importantly, the discretization leads to a symmetric linear system. For the fully discretized problem we prove existence and uniqueness, an energy estimate and an optimal a-priori error estimate, including an error estimate for the divergence of the fluid flux. Numerical experiments in 2D and 3D illustrate the convergence of the method, show the effectiveness of the method to overcome spurious pressure oscillations, and evaluate the added mass effect of the stabilization term.Comment: 25 page

A poroelastic model coupled to a fluid network with applications in lung modelling

Here we develop a lung ventilation model, based a continuum poroelastic representation of lung parenchyma and a 0D airway tree flow model. For the poroelastic approximation we design and implement a lowest order stabilised finite element method. This component is strongly coupled to the 0D airway tree model. The framework is applied to a realistic lung anatomical model derived from computed tomography data and an artificially generated airway tree to model the conducting airway region. Numerical simulations produce physiologically realistic solutions, and demonstrate the effect of airway constriction and reduced tissue elasticity on ventilation, tissue stress and alveolar pressure distribution. The key advantage of the model is the ability to provide insight into the mutual dependence between ventilation and deformation. This is essential when studying lung diseases, such as chronic obstructive pulmonary disease and pulmonary fibrosis. Thus the model can be used to form a better understanding of integrated lung mechanics in both the healthy and diseased states

Chaste: an open source C++ library for computational physiology and biology

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to "re-invent the wheel" with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials

Chaste : Cancer, Heart and Soft Tissue Environment

Funding: UK Engineering and Physical Sciences Research Council [grant number EP/N509711/1 (J.K.)].Chaste (Cancer, Heart And Soft Tissue Environment) is an open source simulation package for the numerical solution of mathematical models arising in physiology and biology. To date, Chaste development has been driven primarily by applications that include continuum modelling of cardiac electrophysiology (‘Cardiac Chaste’), discrete cell-based modelling of soft tissues (‘Cell-based Chaste’), and modelling of ventilation in lungs (‘Lung Chaste’). Cardiac Chaste addresses the need for a high-performance, generic, and verified simulation framewor kfor cardiac electrophysiology that is freely available to the scientific community. Cardiac chaste provides a software package capable of realistic heart simulations that is efficient, rigorously tested, and runs on HPC platforms. Cell-based Chaste addresses the need for efficient and verified implementations of cell-based modelling frameworks, providing a set of extensible tools for simulating biological tissues. Computational modelling, along with live imaging techniques, plays an important role in understanding the processes of tissue growth and repair. A wide range of cell-based modelling frameworks have been developed that have each been successfully applied in a range of biological applications. Cell-based Chaste includes implementations of the cellular automaton model, the cellular Potts model, cell-centre models with cell representations as overlapping spheres or Voronoi tessellations, and the vertex model. Lung Chaste addresses the need for a novel, generic and efficient lung modelling software package that is both tested and verified. It aims to couple biophysically-detailed models of airway mechanics with organ-scale ventilation models in a package that is freely available to the scientific community.Publisher PDFPeer reviewe

Diez reglas sencillas para una exitosa colaboración transdisciplinar

El presente artículo es la versión en castellano de la publicación: KNAPP, B.; BARDENET, R.; BERNABEU, M.O.; BORDAS, R.; BRUNA, M.; CALDERHEAD, B. ET AL. (2015) “Ten Simple Rules for a Successful Cross-Disciplinary Collaboration”. PLoS Comput Biol 11(4): e1004214, disponible en: https://doi.org/10.1371/journal.pcbi.1004214. La traducción, autorizada por la entidad editora, ha sido llevada a cabo por Ona Lorda Roure y Leila Adim, colaboradoras del Instituto de Investigación TransJus y supervisada por el Dr. Juli Ponce Solé, Director del TransJus. En la misma se han incluido algunas notas aclaratorias para el lector en español, así como bibliografía complementaria en español.[spa] En el auge de las colaboraciones interdisciplinarias entre los distintos campos científicos, la transdisciplinariedad se presenta como la clave para encontrar soluciones a una variedad de problemas globales. Este trabajo, situado en el marco de la biología informática, se centra en exponer una lista extensa de reglas y consejos útiles para lograr una exitosa sinergia entre los varios colaboradores de un proyecto transdisciplinar. Se trata, de hecho, de una guía que pretende dirigirse tanto a investigadores noveles como a aquellos investigadores consolidados que se adentran en un espacio transdisciplinar por primera vez. En particular, este trabajo expone los beneficios principales de establecer una colaboración transdisciplinar, así como los problemas que de ella puedan surgir.[cat] En l'auge de les col·laboracions interdisciplinàries entre els diferents camps científics, la transdisciplinarietat es presenta com la clau per trobar solucions a una varietat de problemes globals. Aquest treball, situat en el marc de la biologia informàtica, es centra en exposar una llista extensa de regles i consells útils per aconseguir una reeixida sinergia entre els varis col·laboradors d'un projecte transdisciplinar. Es tracta, de fet, d'una guia que pretén dirigir-se tant a recercadors novells com a aquells recercadors consolidats que s'endinsen en un espai transdisciplinar per primera vegada. En particular, aquest treball exposa els beneficis principals d'establir una col·laboració transdisciplinar, així com els problemes que d'ella puguin sorgir.[eng] At a time of increasing interdisciplinary collaboration between different scientific fields, cross-disciplinarity represents a key for finding solutions to a variety of global problems. This work, located within the framework of computer biology, focuses on exposing an extensive list of rules and useful tips to achieve a successful synergy among the various collaborators of a transdisciplinary project. It is, in fact, a guide aimed at addressing both first-time researchers and consolidated researchers who enter a transdisciplinary space for the first time. In particular, this work exposes the main benefits of establishing a cross-disciplinary collaboration, as well as the problems that may arise from it

Ten Simple Rules for a Successful Cross-Disciplinary Collaboration

Cross-disciplinary collaborations have become an increasingly important part of science. They are seen as key if we are to find solutions to pressing, global-scale societal challenges, including green technologies, sustainable food production, and drug development. Regulators and policy- makers have realized the power of such collaborations, for example, in the 80 billion Euro "Horizon 2020" EU Framework Programme for Research and Innovation. This programme puts special emphasis on “breaking down barriers to create a genuine single market for knowledge, research and innovation

Impact of tissue microstructure on a model of cardiac electromechanics based on MRI data

Cardiac motion is a highly complex and integrated process of vital importance as it sustains the primary function of the heart, that is pumping blood. Cardiac tissue microstructure, in particular the alignment of myocytes (also referred to as fibre direction) and their lateral organisation into laminae (or sheets), has been shown by both experimental and computational research to play an important role in the determination of cardiac motion patterns. However, current models of cardiac electromechanics, although already embedding structural information in the models equations, are not yet able to fully reproduce the connection between structural dynamics and cardiac deformation. The aim of this thesis was to develop an electromechanical modelling framework to investigate the impact of tissue structure on cardiac motion, focussing on left ventricular contraction in rat. The computational studies carried out were complemented with a preliminary validation study based on experimental data of tissue structure rearrangement during contraction from diffusion tensor MRI.This thesis is not currently available in OR