Articles de revista
http://hdl.handle.net/2117/6145
2017-02-20T22:43:03ZCollective cell durotaxis emerges from long-range intercellular force transmission
http://hdl.handle.net/2117/100437
Collective cell durotaxis emerges from long-range intercellular force transmission
Sunyer, Raimon; Conte, Vito; Escribano, Jorge; Elosegui Artola, Alberto; Labernadie, Anna; Valon, Leo; Navajas Navarro, Daniel; Garcia Aznar, José Manuel; Muñoz Romero, José; Trepat, Xavier
The ability of cells to follow gradients of extracellular matrix stiffness—durotaxis—has been implicated in development, fibrosis, and cancer. Here, we found multicellular clusters that exhibited durotaxis even if isolated constituent cells did not. This emergent mode of directed collective cell migration applied to a variety of epithelial cell types, required the action of myosin motors, and originated from supracellular transmission of contractile physical forces. To explain the observed phenomenology, we developed a generalized clutch model in which local stick-slip dynamics of cell-matrix adhesions was integrated to the tissue level through cell-cell junctions. Collective durotaxis is far more efficient than single-cell durotaxis; it thus emerges as a robust mechanism to direct cell migration during development, wound healing, and collective cancer cell invasion.
2017-02-01T10:48:46ZSunyer, RaimonConte, VitoEscribano, JorgeElosegui Artola, AlbertoLabernadie, AnnaValon, LeoNavajas Navarro, DanielGarcia Aznar, José ManuelMuñoz Romero, JoséTrepat, XavierThe ability of cells to follow gradients of extracellular matrix stiffness—durotaxis—has been implicated in development, fibrosis, and cancer. Here, we found multicellular clusters that exhibited durotaxis even if isolated constituent cells did not. This emergent mode of directed collective cell migration applied to a variety of epithelial cell types, required the action of myosin motors, and originated from supracellular transmission of contractile physical forces. To explain the observed phenomenology, we developed a generalized clutch model in which local stick-slip dynamics of cell-matrix adhesions was integrated to the tissue level through cell-cell junctions. Collective durotaxis is far more efficient than single-cell durotaxis; it thus emerges as a robust mechanism to direct cell migration during development, wound healing, and collective cancer cell invasion.Fourth order phase-field model for local max-ent approximants applied to crack propagation
http://hdl.handle.net/2117/100372
Fourth order phase-field model for local max-ent approximants applied to crack propagation
Amiri, Fatemeh; Millán, Daniel; Arroyo Balaguer, Marino; Silani, Mohammad; Rabczuk, Timon
We apply a fourth order phase-field model for fracture based on local maximum entropy (LME) approximants. The higher order continuity of the meshfree LME approximants allows to directly solve the fourth order phase-field equations without splitting the fourth order differential equation into two second order differential equations. We will first show that the crack surface can be captured more accurately in the fourth order model. Furthermore, less nodes are needed for the fourth order model to resolve the crack path. Finally, we demonstrate the performance of the proposed meshfree fourth order phase-field formulation for 5 representative numerical examples. Computational results will be compared to analytical solutions within linear elastic fracture mechanics and experimental data for three-dimensional crack propagation.
2017-01-31T11:50:05ZAmiri, FatemehMillán, DanielArroyo Balaguer, MarinoSilani, MohammadRabczuk, TimonWe apply a fourth order phase-field model for fracture based on local maximum entropy (LME) approximants. The higher order continuity of the meshfree LME approximants allows to directly solve the fourth order phase-field equations without splitting the fourth order differential equation into two second order differential equations. We will first show that the crack surface can be captured more accurately in the fourth order model. Furthermore, less nodes are needed for the fourth order model to resolve the crack path. Finally, we demonstrate the performance of the proposed meshfree fourth order phase-field formulation for 5 representative numerical examples. Computational results will be compared to analytical solutions within linear elastic fracture mechanics and experimental data for three-dimensional crack propagation.Computational modeling of acute myocardial infarction
http://hdl.handle.net/2117/100078
Computational modeling of acute myocardial infarction
Sáez Viñas, Pablo; Kuhl, E.
Myocardial infarction, commonly known as heart attack, is caused by reduced blood supply and damages the heart muscle because of a lack of oxygen. Myocardial infarction initiates a cascade of biochemical and mechanical events. In the early stages, cardiomyocytes death, wall thinning, collagen degradation, and ventricular dilation are the immediate consequences of myocardial infarction. In the later stages, collagenous scar formation in the infarcted zone and hypertrophy of the non-infarcted zone are auto-regulatory mechanisms to partly correct for these events. Here we propose a computational model for the short-term adaptation after myocardial infarction using the continuum theory of multiplicative growth. Our model captures the effects of cell death initiating wall thinning, and collagen degradation initiating ventricular dilation. Our simulations agree well with clinical observations in early myocardial infarction. They represent a first step toward simulating the progression of myocardial infarction with the ultimate goal to predict the propensity toward heart failure as a function of infarct intensity, location, and size.
This is an Accepted Manuscript of an article published by Taylor & Francis Group in Computer Methods in Biomechanics and Biomedical Engineering on October, 2016, available online at: http://www.tandfonline.com/10.1080/10255842.2015.1105965
2017-01-25T18:46:40ZSáez Viñas, PabloKuhl, E.Myocardial infarction, commonly known as heart attack, is caused by reduced blood supply and damages the heart muscle because of a lack of oxygen. Myocardial infarction initiates a cascade of biochemical and mechanical events. In the early stages, cardiomyocytes death, wall thinning, collagen degradation, and ventricular dilation are the immediate consequences of myocardial infarction. In the later stages, collagenous scar formation in the infarcted zone and hypertrophy of the non-infarcted zone are auto-regulatory mechanisms to partly correct for these events. Here we propose a computational model for the short-term adaptation after myocardial infarction using the continuum theory of multiplicative growth. Our model captures the effects of cell death initiating wall thinning, and collagen degradation initiating ventricular dilation. Our simulations agree well with clinical observations in early myocardial infarction. They represent a first step toward simulating the progression of myocardial infarction with the ultimate goal to predict the propensity toward heart failure as a function of infarct intensity, location, and size.Elliptic harbor wave model with perfectly matched layer and exterior bathymetry effects
http://hdl.handle.net/2117/99974
Elliptic harbor wave model with perfectly matched layer and exterior bathymetry effects
Modesto Galende, David; Fernandez Mendez, Sonia; Huerta, Antonio
Standard strategies for dealing with the Sommerfeld condition in elliptic mild-slope models require strong assumptions on the wave field in the region exterior to the computational domain. More precisely, constant bathymetry along (and beyond) the open boundary, and parabolic approximations–based boundary conditions are usually imposed. Generally, these restrictions require large computational domains, implying higher costs for the numerical solver. An alternative method for coastal/harbor applications is proposed here. This approach is based on a perfectly matched layer (PML) that incorporates the effects of the exterior bathymetry. The model only requires constant exterior depth in the alongshore direction, a common approach used for idealizing the exterior bathymetry in elliptic models. In opposition to standard open boundary conditions for mild-slope models, the features of the proposed PML approach include (1) completely noncollinear coastlines, (2) better representation of the real unbounded domain using two different lateral sections to define the exterior bathymetry, and (3) the generation of reliable solutions for any incoming wave direction in a small computational domain. Numerical results of synthetic tests demonstrate that solutions are not significantly perturbed when open boundaries are placed close to the area of interest. In more complex problems, this provides important performance improvements in computational time, as shown for a real application of harbor agitation.
2017-01-24T18:45:56ZModesto Galende, DavidFernandez Mendez, SoniaHuerta, AntonioStandard strategies for dealing with the Sommerfeld condition in elliptic mild-slope models require strong assumptions on the wave field in the region exterior to the computational domain. More precisely, constant bathymetry along (and beyond) the open boundary, and parabolic approximations–based boundary conditions are usually imposed. Generally, these restrictions require large computational domains, implying higher costs for the numerical solver. An alternative method for coastal/harbor applications is proposed here. This approach is based on a perfectly matched layer (PML) that incorporates the effects of the exterior bathymetry. The model only requires constant exterior depth in the alongshore direction, a common approach used for idealizing the exterior bathymetry in elliptic models. In opposition to standard open boundary conditions for mild-slope models, the features of the proposed PML approach include (1) completely noncollinear coastlines, (2) better representation of the real unbounded domain using two different lateral sections to define the exterior bathymetry, and (3) the generation of reliable solutions for any incoming wave direction in a small computational domain. Numerical results of synthetic tests demonstrate that solutions are not significantly perturbed when open boundaries are placed close to the area of interest. In more complex problems, this provides important performance improvements in computational time, as shown for a real application of harbor agitation.A new equilibrated residual method improving accuracy and efficiency of flux-free error estimates
http://hdl.handle.net/2117/99967
A new equilibrated residual method improving accuracy and efficiency of flux-free error estimates
Parés Mariné, Núria; Díez, Pedro
This paper presents a new methodology to compute guaranteed upper bounds for the energy norm of the error in the context of linear finite element approximations of the reaction–diffusion equation. The new approach revisits the ideas in Parés et al. (2009) [6, 4], with the goal of substantially reducing the computational cost of the flux-free method while retaining the good quality of the bounds. The new methodology provides also a technique to compute equilibrated boundary tractions improving the quality of standard equilibration strategies. The zeroth-order equilibration conditions are imposed using an alternative less restrictive form of the first-order equilibration conditions, along with a new efficient minimization criterion. This new equilibration strategy provides much more accurate upper bounds for the energy and requires only doubling the dimension of the local linear systems of equations to be solved.
2017-01-24T17:24:44ZParés Mariné, NúriaDíez, PedroThis paper presents a new methodology to compute guaranteed upper bounds for the energy norm of the error in the context of linear finite element approximations of the reaction–diffusion equation. The new approach revisits the ideas in Parés et al. (2009) [6, 4], with the goal of substantially reducing the computational cost of the flux-free method while retaining the good quality of the bounds. The new methodology provides also a technique to compute equilibrated boundary tractions improving the quality of standard equilibration strategies. The zeroth-order equilibration conditions are imposed using an alternative less restrictive form of the first-order equilibration conditions, along with a new efficient minimization criterion. This new equilibration strategy provides much more accurate upper bounds for the energy and requires only doubling the dimension of the local linear systems of equations to be solved.A distortion measure to validate and generate curved high-order meshes on CAD surfaces with independence of parameterization
http://hdl.handle.net/2117/99966
A distortion measure to validate and generate curved high-order meshes on CAD surfaces with independence of parameterization
Gargallo Peiró, Abel; Roca Navarro, Xevi; Peraire Guitart, Jaume; Sarrate Ramos, Josep
A framework to validate and generate curved nodal high-order meshes on Computer-Aided Design (CAD) surfaces is presented. The proposed framework is of major interest to generate meshes suitable for thin-shell and 3D finite element analysis with unstructured high-order methods. First, we define a distortion (quality) measure for high-order meshes on parameterized surfaces that we prove to be independent of the surface parameterization. Second, we derive a smoothing and untangling procedure based on the minimization of a regularization of the proposed distortion measure. The minimization is performed in terms of the parametric coordinates of the nodes to enforce that the nodes slide on the surfaces. Moreover, the proposed algorithm repairs invalid curved meshes (untangling), deals with arbitrary polynomial degrees (high-order), and handles with low-quality CAD parameterizations (independence of parameterization). Third, we use the optimization procedure to generate curved nodal high-order surface meshes by means of an a posteriori approach. Given a linear mesh, we increase the polynomial degree of the elements, curve them to match the geometry, and optimize the location of the nodes to ensure mesh validity. Finally, we present several examples to demonstrate the features of the optimization procedure, and to illustrate the surface mesh generation process.
This is the accepted version of the following article: [Gargallo-Peiró, A., Roca, X., Peraire, J., and Sarrate, J. (2016) A distortion measure to validate and generate curved high-order meshes on CAD surfaces with independence of parameterization. Int. J. Numer. Meth. Engng, 106: 1100–1130. doi: 10.1002/nme.5162], which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/nme.5162/abstract
2017-01-24T17:02:08ZGargallo Peiró, AbelRoca Navarro, XeviPeraire Guitart, JaumeSarrate Ramos, JosepA framework to validate and generate curved nodal high-order meshes on Computer-Aided Design (CAD) surfaces is presented. The proposed framework is of major interest to generate meshes suitable for thin-shell and 3D finite element analysis with unstructured high-order methods. First, we define a distortion (quality) measure for high-order meshes on parameterized surfaces that we prove to be independent of the surface parameterization. Second, we derive a smoothing and untangling procedure based on the minimization of a regularization of the proposed distortion measure. The minimization is performed in terms of the parametric coordinates of the nodes to enforce that the nodes slide on the surfaces. Moreover, the proposed algorithm repairs invalid curved meshes (untangling), deals with arbitrary polynomial degrees (high-order), and handles with low-quality CAD parameterizations (independence of parameterization). Third, we use the optimization procedure to generate curved nodal high-order surface meshes by means of an a posteriori approach. Given a linear mesh, we increase the polynomial degree of the elements, curve them to match the geometry, and optimize the location of the nodes to ensure mesh validity. Finally, we present several examples to demonstrate the features of the optimization procedure, and to illustrate the surface mesh generation process.A Lagrangian–Eulerian finite element algorithm for advection–diffusion–reaction problems with phase change
http://hdl.handle.net/2117/99876
A Lagrangian–Eulerian finite element algorithm for advection–diffusion–reaction problems with phase change
Oliveira, Beñat; Afonso, Juan Carlos; Zlotnik, Sergio
This paper presents a particle-based Lagrangian–Eulerian algorithm for the solution of the unsteady advection–diffusion–reaction heat transfer equation with phase change. The algorithm combines a Lagrangian formulation for the advection + reaction problem with the Eulerian-based heat source method for the diffusion + phase change problem. The coupling between the Lagrangian and Eulerian subproblems is achieved with a phase change detector scheme based on a local latent heat balance and a consistent/conservative interpolation technique between Lagrangian particles and the Eulerian grid. This technique makes use of an auxiliary (finer) Eulerian grid that provides a simple and efficient method of tracking internal heterogeneities (e.g. phase boundaries), allows the use of higher order integration quadratures, and facilitates the implementation of multiscale techniques. The performance of the proposed algorithm is compared against one- and two-dimensional benchmark problems, i.e. pure rigid-body advection, isothermal and non-isothermal phase change, two-phase advective heat transfer and chemical reactions coupled with diffusion and advection. The numerical results confirm that the proposed solution method is accurate, oscillation-free and useful for and applicable to a wide range of fully coupled problems in science and engineering.
2017-01-23T15:28:21ZOliveira, BeñatAfonso, Juan CarlosZlotnik, SergioThis paper presents a particle-based Lagrangian–Eulerian algorithm for the solution of the unsteady advection–diffusion–reaction heat transfer equation with phase change. The algorithm combines a Lagrangian formulation for the advection + reaction problem with the Eulerian-based heat source method for the diffusion + phase change problem. The coupling between the Lagrangian and Eulerian subproblems is achieved with a phase change detector scheme based on a local latent heat balance and a consistent/conservative interpolation technique between Lagrangian particles and the Eulerian grid. This technique makes use of an auxiliary (finer) Eulerian grid that provides a simple and efficient method of tracking internal heterogeneities (e.g. phase boundaries), allows the use of higher order integration quadratures, and facilitates the implementation of multiscale techniques. The performance of the proposed algorithm is compared against one- and two-dimensional benchmark problems, i.e. pure rigid-body advection, isothermal and non-isothermal phase change, two-phase advective heat transfer and chemical reactions coupled with diffusion and advection. The numerical results confirm that the proposed solution method is accurate, oscillation-free and useful for and applicable to a wide range of fully coupled problems in science and engineering.Proper generalized decomposition solution of the parameterized Helmholtz problem: application to inverse geophysical problems
http://hdl.handle.net/2117/99875
Proper generalized decomposition solution of the parameterized Helmholtz problem: application to inverse geophysical problems
Signorini, Marianna; Zlotnik, Sergio; Díez, Pedro
The identification of the geological structure from seismic data is formulated as an inverse problem. The properties and the shape of the rock formations in the subsoil are described by material and geometric parameters, which are taken as input data for a predictive model. Here, the model is based on the Helmholtz equation, describing the acoustic response of the system for a given wave length. Thus, the inverse problem consists in identifying the values of these parameters such that the output of the model agrees the best with observations. This optimization algorithm requires multiple queries to the model with different values of the parameters. Reduced order models are especially well suited to significantly reduce the computational overhead of the multiple evaluations of the model.
In particular, the proper generalized decomposition produces a solution explicitly stating the parametric dependence, where the parameters play the same role as the physical coordinates. A proper generalized decomposition solver is devised to inexpensively explore the parametric space along the iterative process. This exploration of the parametric space is in fact seen as a post-process of the generalized solution. The approach adopted demonstrates its viability when tested in two illustrative examples.
This is the peer reviewed version of the following article: [Signorini, M., Zlotnik, S., and Díez, P. (2017) Proper generalized decomposition solution of the parameterized Helmholtz problem: application to inverse geophysical problems. Int. J. Numer. Meth. Engng, 109: 1085–1102. doi: 10.1002/nme.5313], which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/nme.5313/full. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
2017-01-23T15:19:36ZSignorini, MariannaZlotnik, SergioDíez, PedroThe identification of the geological structure from seismic data is formulated as an inverse problem. The properties and the shape of the rock formations in the subsoil are described by material and geometric parameters, which are taken as input data for a predictive model. Here, the model is based on the Helmholtz equation, describing the acoustic response of the system for a given wave length. Thus, the inverse problem consists in identifying the values of these parameters such that the output of the model agrees the best with observations. This optimization algorithm requires multiple queries to the model with different values of the parameters. Reduced order models are especially well suited to significantly reduce the computational overhead of the multiple evaluations of the model.
In particular, the proper generalized decomposition produces a solution explicitly stating the parametric dependence, where the parameters play the same role as the physical coordinates. A proper generalized decomposition solver is devised to inexpensively explore the parametric space along the iterative process. This exploration of the parametric space is in fact seen as a post-process of the generalized solution. The approach adopted demonstrates its viability when tested in two illustrative examples.Unified formulation of a family of iterative solvers for power systems analysis
http://hdl.handle.net/2117/99557
Unified formulation of a family of iterative solvers for power systems analysis
Borzacchiello, Domenico; Chinesta, Francisco; Malik, Muhammad H.; García Blanco, Raquel; Díez, Pedro
This paper illustrates the construction of a new class of iterative solvers for power flow calculations based on the method of Alternating Search Directions. This method is fit to the particular algebraic structure of the power flow problem resulting from the combination of a globally linear set of equations and nonlinear local relations imposed by power conversion devices, such as loads and generators. The choice of the search directions is shown to be crucial for improving the overall robustness of the solver. A noteworthy advantage is that constant search directions yield stationary methods that, in contrast with Newton or Quasi-Newton methods, do not require the evaluation of the Jacobian matrix. Such directions can be elected to enforce the convergence to the high voltage operative solution. The method is explained through an intuitive example illustrating how the proposed generalized formulation is able to include other nonlinear solvers that are classically used for power flow analysis, thus offering a unified view on the topic. Numerical experiments are performed on publicly available benchmarks for large distribution and transmission systems.
2017-01-17T19:26:06ZBorzacchiello, DomenicoChinesta, FranciscoMalik, Muhammad H.García Blanco, RaquelDíez, PedroThis paper illustrates the construction of a new class of iterative solvers for power flow calculations based on the method of Alternating Search Directions. This method is fit to the particular algebraic structure of the power flow problem resulting from the combination of a globally linear set of equations and nonlinear local relations imposed by power conversion devices, such as loads and generators. The choice of the search directions is shown to be crucial for improving the overall robustness of the solver. A noteworthy advantage is that constant search directions yield stationary methods that, in contrast with Newton or Quasi-Newton methods, do not require the evaluation of the Jacobian matrix. Such directions can be elected to enforce the convergence to the high voltage operative solution. The method is explained through an intuitive example illustrating how the proposed generalized formulation is able to include other nonlinear solvers that are classically used for power flow analysis, thus offering a unified view on the topic. Numerical experiments are performed on publicly available benchmarks for large distribution and transmission systems.Sticking and sliding of lipid bilayers on deformable substrates
http://hdl.handle.net/2117/99478
Sticking and sliding of lipid bilayers on deformable substrates
Stubbington, L; Arroyo Balaguer, Marino; Staykova, M
We examine here the properties of lipid bilayers coupled to deformable substrates. We show that by changing the extent of the substrate hydrophilicity, we can control the membrane–substrate coupling and the response of the bilayer to strain deformation. Our results demonstrate that lipid bilayers coupled to flexible substrates can easily accommodate large strains, form stable protrusions and open reversibly pores. These properties, which differ significantly from those of free standing membranes, can extend the applications of the current lipid technologies. Moreover, such systems better capture the mechanical architecture of the cell interface and can provide insights into the capacity of cells to reshape and respond to mechanical perturbations.
2017-01-17T13:23:54ZStubbington, LArroyo Balaguer, MarinoStaykova, MWe examine here the properties of lipid bilayers coupled to deformable substrates. We show that by changing the extent of the substrate hydrophilicity, we can control the membrane–substrate coupling and the response of the bilayer to strain deformation. Our results demonstrate that lipid bilayers coupled to flexible substrates can easily accommodate large strains, form stable protrusions and open reversibly pores. These properties, which differ significantly from those of free standing membranes, can extend the applications of the current lipid technologies. Moreover, such systems better capture the mechanical architecture of the cell interface and can provide insights into the capacity of cells to reshape and respond to mechanical perturbations.