LaCàN - Laboratori de Càlcul Numèric
http://hdl.handle.net/2117/2072
2017-01-17T09:06:53ZNon-regularised inverse finite element analysis for 3D traction force microscopy
http://hdl.handle.net/2117/99311
Non-regularised inverse finite element analysis for 3D traction force microscopy
Muñoz Romero, José
The tractions that cells exert on a gel substrate from the observed
displacements is an increasingly attractive and valuable information in
biomedical experiments. The computation of these tractions requires in
general the solution of an inverse problem. Here, we resort to the discretisation
with finite elements of the associated direct variational formulation,
and solve the inverse analysis using a least square approach.
This strategy requires the minimisation of an error functional, which is
usually regularised in order to obtain a stable system of equations with
a unique solution. In this paper we show that for many common threedimensional
geometries, meshes and loading conditions, this regularisation
is unnecessary. In these cases, the computational cost of the inverse
problem becomes equivalent to a direct finite element problem. For the
non-regularised functional, we deduce the necessary and sufficient conditions
that the dimensions of the interpolated displacement and traction
fields must preserve in order to exactly satisfy or yield a unique solution
of the discrete equilibrium equations. We apply the theoretical results to
some illustrative examples and to real experimental data. Due to the relevance
of the results for biologists and modellers, the article concludes with
some practical rules that the finite element discretisation must satisfy.
2017-01-16T12:38:07ZMuñoz Romero, JoséThe tractions that cells exert on a gel substrate from the observed
displacements is an increasingly attractive and valuable information in
biomedical experiments. The computation of these tractions requires in
general the solution of an inverse problem. Here, we resort to the discretisation
with finite elements of the associated direct variational formulation,
and solve the inverse analysis using a least square approach.
This strategy requires the minimisation of an error functional, which is
usually regularised in order to obtain a stable system of equations with
a unique solution. In this paper we show that for many common threedimensional
geometries, meshes and loading conditions, this regularisation
is unnecessary. In these cases, the computational cost of the inverse
problem becomes equivalent to a direct finite element problem. For the
non-regularised functional, we deduce the necessary and sufficient conditions
that the dimensions of the interpolated displacement and traction
fields must preserve in order to exactly satisfy or yield a unique solution
of the discrete equilibrium equations. We apply the theoretical results to
some illustrative examples and to real experimental data. Due to the relevance
of the results for biologists and modellers, the article concludes with
some practical rules that the finite element discretisation must satisfy.Charting molecular free-energy landscapes with an atlas of collective variables
http://hdl.handle.net/2117/98674
Charting molecular free-energy landscapes with an atlas of collective variables
Hashemian, B.; Millán, Raúl Daniel; Arroyo Balaguer, Marino
Collective variables (CVs) are a fundamental tool to understand molecular flexibility, to compute free energy landscapes, and to enhance sampling in molecular dynamics simulations. However, identifying suitable CVs is challenging, and is increasingly addressed with systematic data-driven manifold learning techniques. Here, we provide a flexible framework to model molecular systems in terms of a collection of locally valid and partially overlapping CVs: an atlas of CVs. The specific motivation for such a framework is to enhance the applicability and robustness of CVs based on manifold learning methods, which fail in the presence of periodicities in the underlying conformational manifold. More generally, using an atlas of CVs rather than a single chart may help us better describe different regions of conformational space. We develop the statistical mechanics foundation for our multi-chart description and propose an algorithmic implementation. The resulting atlas of data-based CVs are then used to enhance sampling and compute free energy surfaces in two model systems, alanine dipeptide and ß-D-glucopyranose, whose conformational manifolds have toroidal and spherical topologies.
2016-12-20T19:26:33ZHashemian, B.Millán, Raúl DanielArroyo Balaguer, MarinoCollective variables (CVs) are a fundamental tool to understand molecular flexibility, to compute free energy landscapes, and to enhance sampling in molecular dynamics simulations. However, identifying suitable CVs is challenging, and is increasingly addressed with systematic data-driven manifold learning techniques. Here, we provide a flexible framework to model molecular systems in terms of a collection of locally valid and partially overlapping CVs: an atlas of CVs. The specific motivation for such a framework is to enhance the applicability and robustness of CVs based on manifold learning methods, which fail in the presence of periodicities in the underlying conformational manifold. More generally, using an atlas of CVs rather than a single chart may help us better describe different regions of conformational space. We develop the statistical mechanics foundation for our multi-chart description and propose an algorithmic implementation. The resulting atlas of data-based CVs are then used to enhance sampling and compute free energy surfaces in two model systems, alanine dipeptide and ß-D-glucopyranose, whose conformational manifolds have toroidal and spherical topologies.Un estimador de error residual semiexplícito en cantidades de interés para un problema mecánico lineal
http://hdl.handle.net/2117/98648
Un estimador de error residual semiexplícito en cantidades de interés para un problema mecánico lineal
Rosales, R.; Díez, Pedro
We aim at defining a semi-explicit approach to estimate the error in quantities of interest associated with the Finite Element solution of a linear elasticity problem. The advocated procedure is split in two parts, an implicit error estimate for the adjoint problem and an explicit estimate assessing the error in the direct (primal) problem. The implicit part of the estimate (on the adjoint problem) embraces two phases, each consisting in projecting the error on
2016-12-20T16:27:14ZRosales, R.Díez, PedroWe aim at defining a semi-explicit approach to estimate the error in quantities of interest associated with the Finite Element solution of a linear elasticity problem. The advocated procedure is split in two parts, an implicit error estimate for the adjoint problem and an explicit estimate assessing the error in the direct (primal) problem. The implicit part of the estimate (on the adjoint problem) embraces two phases, each consisting in projecting the error onVademecum-based GFEM (V-GFEM): optimal enrichment for transient problems
http://hdl.handle.net/2117/98640
Vademecum-based GFEM (V-GFEM): optimal enrichment for transient problems
Canales, Diego; Leygue, Adrien; Chinesta Soria, Francisco; González Ibáñez, David; Cueto Prendes, Elias; Feulvarch, Eric; Bergheau, Jean-Michel; Huerta, Antonio
This paper proposes a generalized finite element method based on the use of parametric solutions as enrichment functions. These parametric solutions are precomputed off-line and stored in memory in the form of a computational vademecum so that they can be used on-line with negligible cost. This renders a more efficient computational method than traditional finite element methods at performing simulations of processes. One key issue of the proposed method is the efficient computation of the parametric enrichments. These are computed and efficiently stored in memory by employing proper generalized decompositions. Although the presented method can be broadly applied, it is particularly well suited in manufacturing processes involving localized physics that depend on many parameters, such as welding. After introducing the vademecum-generalized finite element method formulation, we present some numerical examples related to the simulation of thermal models encountered in welding processes.
This is the accepted version of the following article: [Canales, D., Leygue, A., Chinesta, F., González, D., Cueto, E., Feulvarch, E., Bergheau, J. -M., and Huerta, A. (2016) Vademecum-based GFEM (V-GFEM): optimal enrichment for transient problems. Int. J. Numer. Meth. Engng, 108: 971–989. doi: 10.1002/nme.5240.], which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/nme.5240/full
2016-12-20T15:41:21ZCanales, DiegoLeygue, AdrienChinesta Soria, FranciscoGonzález Ibáñez, DavidCueto Prendes, EliasFeulvarch, EricBergheau, Jean-MichelHuerta, AntonioThis paper proposes a generalized finite element method based on the use of parametric solutions as enrichment functions. These parametric solutions are precomputed off-line and stored in memory in the form of a computational vademecum so that they can be used on-line with negligible cost. This renders a more efficient computational method than traditional finite element methods at performing simulations of processes. One key issue of the proposed method is the efficient computation of the parametric enrichments. These are computed and efficiently stored in memory by employing proper generalized decompositions. Although the presented method can be broadly applied, it is particularly well suited in manufacturing processes involving localized physics that depend on many parameters, such as welding. After introducing the vademecum-generalized finite element method formulation, we present some numerical examples related to the simulation of thermal models encountered in welding processes.Real-time simulation techniques for augmented learning in science and engineering
http://hdl.handle.net/2117/97463
Real-time simulation techniques for augmented learning in science and engineering
Quesada, C.; González, D.; Alfaro, Icíar; Cueto Prendes, Elias; Huerta, Antonio; Chinesta, Francisco
In this paper we present the basics of a novel methodology for the development of simulation-based and augmented learning tools in the context of applied science and engineering. It is based on the extensive use of model order reduction, and particularly, of the so-called Proper Generalized Decomposition (PGD) method. This method provides a sort of meta-modeling tool without the need for prior computer experiments that allows the user to obtain real-time response in the solution of complex engineering or physical problems. This real-time capability also allows for its implementation in deployed, touch-screen, handheld devices or even to be immersed into electronic textbooks. We explore here the basics of the proposed methodology and give examples on a few challenging applications never until now explored, up to our knowledge.
2016-11-29T17:42:46ZQuesada, C.González, D.Alfaro, IcíarCueto Prendes, EliasHuerta, AntonioChinesta, FranciscoIn this paper we present the basics of a novel methodology for the development of simulation-based and augmented learning tools in the context of applied science and engineering. It is based on the extensive use of model order reduction, and particularly, of the so-called Proper Generalized Decomposition (PGD) method. This method provides a sort of meta-modeling tool without the need for prior computer experiments that allows the user to obtain real-time response in the solution of complex engineering or physical problems. This real-time capability also allows for its implementation in deployed, touch-screen, handheld devices or even to be immersed into electronic textbooks. We explore here the basics of the proposed methodology and give examples on a few challenging applications never until now explored, up to our knowledge.Internet-based tutorial providing mathematical complements for technical master students: TIMEMathCom
http://hdl.handle.net/2117/97026
Internet-based tutorial providing mathematical complements for technical master students: TIMEMathCom
Estela Carbonell, M. Rosa; Díez, Pedro
The mathematical background of international students in Technical Master programs is pretty heterogeneous. They often lack of a sound basis in specific topics, which are necessary to follow the Master. Filling this gap is often stressing because it requires these students to make an additional effort reviewing basic references. The goal of this initiative is to produce a tailored learning tool for these students. Previous experiences of the proposing teams suggest that using a Moodle environment is a suitable choice to develop the tool. The idea is to cover synthetically the topics and to allow getting acquainted
with the knowledge in a straight-to-the point approach. T.I.M.E. is a network assembling more than 50 Higher Education Institutions (mostly in Europe) with a focus in Scientific and Technical training. T.I.M.E. provides an ideal framework for developing and testing the tool. This is because the contents are enriched by the feedback of the experience of the members involved. Moreover, T.I.M.E. community is a perfect test bench for the tool.
2016-11-22T14:22:27ZEstela Carbonell, M. RosaDíez, PedroThe mathematical background of international students in Technical Master programs is pretty heterogeneous. They often lack of a sound basis in specific topics, which are necessary to follow the Master. Filling this gap is often stressing because it requires these students to make an additional effort reviewing basic references. The goal of this initiative is to produce a tailored learning tool for these students. Previous experiences of the proposing teams suggest that using a Moodle environment is a suitable choice to develop the tool. The idea is to cover synthetically the topics and to allow getting acquainted
with the knowledge in a straight-to-the point approach. T.I.M.E. is a network assembling more than 50 Higher Education Institutions (mostly in Europe) with a focus in Scientific and Technical training. T.I.M.E. provides an ideal framework for developing and testing the tool. This is because the contents are enriched by the feedback of the experience of the members involved. Moreover, T.I.M.E. community is a perfect test bench for the tool.Towards the STEM knowledge homogenization of pre-university students in 21st century MOOC: The Language for Engineering
http://hdl.handle.net/2117/97023
Towards the STEM knowledge homogenization of pre-university students in 21st century MOOC: The Language for Engineering
Estela Carbonell, M. Rosa; Codina Mendoza, Andreu; Poblet-Puig, Jordi; Pardo Tràfach, Patricia; Puigví Burniol, Maria Àngels; Pujadas Gispert, Ester; Valls del Barrio, Susanna; Álvarez del Castillo, María Dolores; Guaus Guerrero, Ester; Hervada Sala, Carme; Macanás de Benito, Jorge; Masip Álvarez, Albert; Morillo Cazorla, Margarita; Nejjari Akhi-Elarab, Fatiha
For the past five years, Engineering students from Barcelona School of Civil Engineer in UPC BarcelonaTech have shown that educational intervention in first-year engineering programs can positively affect students’ awareness of Science, Technology, Engineering and Mathematics (STEM) concepts by introducing students to basics concepts and motivating them to follow next ones. At Terrassa School of Industrial, Aerospace and Audiovisual Engineering, also belonging to UPC BarcelonaTech, STEM concepts are strengthen to high school students by means of the Mercat de Tecnologia, (a science fair among schools) and by some recommended but not compulsory propaedeutic courses of basic subjects, carried out the week prior to the official start of university studies. Still, many students entering university show
some lacks on theoretical items, particularly those who do not follow the usual way to access to tertiary studies after obligatory secondary education but a parallel and more practical one. In fact, there is a large heterogeneity in terms of the average previous knowledge of every subject as well as in the individual curriculum of each student, since they might have enrolled different courses before entering the university. Due to those lacks, some professors at both aforementioned
schools have developed a MOOC oriented to new university students. The designed MOOC is useful in order to improve the basic knowledge of new students regarding these sciences.
2016-11-22T14:16:28ZEstela Carbonell, M. RosaCodina Mendoza, AndreuPoblet-Puig, JordiPardo Tràfach, PatriciaPuigví Burniol, Maria ÀngelsPujadas Gispert, EsterValls del Barrio, SusannaÁlvarez del Castillo, María DoloresGuaus Guerrero, EsterHervada Sala, CarmeMacanás de Benito, JorgeMasip Álvarez, AlbertMorillo Cazorla, MargaritaNejjari Akhi-Elarab, FatihaFor the past five years, Engineering students from Barcelona School of Civil Engineer in UPC BarcelonaTech have shown that educational intervention in first-year engineering programs can positively affect students’ awareness of Science, Technology, Engineering and Mathematics (STEM) concepts by introducing students to basics concepts and motivating them to follow next ones. At Terrassa School of Industrial, Aerospace and Audiovisual Engineering, also belonging to UPC BarcelonaTech, STEM concepts are strengthen to high school students by means of the Mercat de Tecnologia, (a science fair among schools) and by some recommended but not compulsory propaedeutic courses of basic subjects, carried out the week prior to the official start of university studies. Still, many students entering university show
some lacks on theoretical items, particularly those who do not follow the usual way to access to tertiary studies after obligatory secondary education but a parallel and more practical one. In fact, there is a large heterogeneity in terms of the average previous knowledge of every subject as well as in the individual curriculum of each student, since they might have enrolled different courses before entering the university. Due to those lacks, some professors at both aforementioned
schools have developed a MOOC oriented to new university students. The designed MOOC is useful in order to improve the basic knowledge of new students regarding these sciences.La formació doctoral en la societat del coneixement: situació actual i nous reptes de futur
http://hdl.handle.net/2117/96500
La formació doctoral en la societat del coneixement: situació actual i nous reptes de futur
Alba, Jordi; Córdoba, Francesc; Huerta, Antonio
L’Anuari 2015 de la Fundació Jaume Bofill analitza un seguit de reptes clau de l’educació a Catalunya i planteja algunes de les qüestions prioritàries en matèria de política educativa per tal d’aconseguir un sistema de qualitat i amb equitat.
Estructurat en sis grans blocs i dotze capítols, l’Anuari aprofundeix en temes claus com, entre d’altres, el de la cultura de la innovació educativa, la personalització de l’educació, el multilingüisme i la internacionalització de les aules, l’abandonament escolar prematur, l’equitat i l’eficiència del sistema, les polítiques de professorat, el finançament de l’educació a Catalunya i els efectes de l’austeritat i la crisi actual, els reptes de l’educació secundària obligatòria i de l’ensenyament superior.
L’Anuari inclou un seguit de propostes d’acció en els diversos reptes estudiats que configuren una agenda per a la transformació educativa del nostre país. Reptes de l’educació a Catalunya està dirigit per Josep M. Vilalta, i compta amb la col·laboració de vint experts en les distintes matèries i àmbits del sistema educatiu.
2016-11-10T16:17:15ZAlba, JordiCórdoba, FrancescHuerta, AntonioL’Anuari 2015 de la Fundació Jaume Bofill analitza un seguit de reptes clau de l’educació a Catalunya i planteja algunes de les qüestions prioritàries en matèria de política educativa per tal d’aconseguir un sistema de qualitat i amb equitat.
Estructurat en sis grans blocs i dotze capítols, l’Anuari aprofundeix en temes claus com, entre d’altres, el de la cultura de la innovació educativa, la personalització de l’educació, el multilingüisme i la internacionalització de les aules, l’abandonament escolar prematur, l’equitat i l’eficiència del sistema, les polítiques de professorat, el finançament de l’educació a Catalunya i els efectes de l’austeritat i la crisi actual, els reptes de l’educació secundària obligatòria i de l’ensenyament superior.
L’Anuari inclou un seguit de propostes d’acció en els diversos reptes estudiats que configuren una agenda per a la transformació educativa del nostre país. Reptes de l’educació a Catalunya està dirigit per Josep M. Vilalta, i compta amb la col·laboració de vint experts en les distintes matèries i àmbits del sistema educatiu.eXtended Hybridizable Discontinuous Galerkin (X-HDG) for void and bimaterial problems
http://hdl.handle.net/2117/91042
eXtended Hybridizable Discontinuous Galerkin (X-HDG) for void and bimaterial problems
Gurkan, Ceren; Sala Lardies, Esther; Kronbichler, Martin; Fernandez Mendez, Sonia
This book gathers selected contributions on emerging research work presented at the International Conference eXtended Discretization MethodS (X-DMS), held in Ferrara in September 2015. It highlights the most relevant advances made at the international level in the context of expanding classical discretization methods, like finite elements, to the numerical analysis of a variety of physical problems. The improvements are intended to achieve higher computational efficiency and to account for special features of the solution directly in the approximation space and/or in the discretization procedure. The methods described include, among others, partition of unity methods (meshfree, XFEM, GFEM), virtual element methods, fictitious domain methods, and special techniques for static and evolving interfaces. The uniting feature of all contributions is the direct link between computational methodologies and their application to different engineering areas.
2016-10-25T08:22:56ZGurkan, CerenSala Lardies, EstherKronbichler, MartinFernandez Mendez, SoniaThis book gathers selected contributions on emerging research work presented at the International Conference eXtended Discretization MethodS (X-DMS), held in Ferrara in September 2015. It highlights the most relevant advances made at the international level in the context of expanding classical discretization methods, like finite elements, to the numerical analysis of a variety of physical problems. The improvements are intended to achieve higher computational efficiency and to account for special features of the solution directly in the approximation space and/or in the discretization procedure. The methods described include, among others, partition of unity methods (meshfree, XFEM, GFEM), virtual element methods, fictitious domain methods, and special techniques for static and evolving interfaces. The uniting feature of all contributions is the direct link between computational methodologies and their application to different engineering areas.Hybrid cell centred/vertex model for large tissue deformations
http://hdl.handle.net/2117/90839
Hybrid cell centred/vertex model for large tissue deformations
Muñoz Romero, José; Mosafa, Payman; Mao, Yanlan; Tetley, Rob; Asadipour, Nina; Rodríguez Ferran, Antonio
Macroscopic deformations in embryonic soft tissues are due to the intra-cellular remodelling
and cell intercalation. We here present a computational approach that can handle the
two types of deformations, and also take into account the active cell response. The model resorts
to cell-centred techniques, where particles represent cell nuclei, and to vertex models, where the
vertices represent cell boundaries. This hybrid approach allows to consider separately intracellular
and inter-cellular forces, and at the same time impose cell incompressibility.
In the proposed model, the cell boundaries (defined by vertices) and cell nuclei (or cellcentres)
networks are coupled through an interpolation scheme, which is eventually relaxed in
order to smooth the cell boundaries. We show that this coupling between the two networks
modifies the equilibrium equations and stabilises the vertex network. Incompressibility is implemented
through a penalty method. The resulting model can be implemented in two- and
three-dimensions, and is complemented with active rheological models.
We apply the model to simulate the stretching and relaxation of cell monolayers, and to
simulate wound healing process in the wing disc of Drosophila fly embryo. We show that the
numerical results agree with the experimental measurements.
2016-10-18T10:43:30ZMuñoz Romero, JoséMosafa, PaymanMao, YanlanTetley, RobAsadipour, NinaRodríguez Ferran, AntonioMacroscopic deformations in embryonic soft tissues are due to the intra-cellular remodelling
and cell intercalation. We here present a computational approach that can handle the
two types of deformations, and also take into account the active cell response. The model resorts
to cell-centred techniques, where particles represent cell nuclei, and to vertex models, where the
vertices represent cell boundaries. This hybrid approach allows to consider separately intracellular
and inter-cellular forces, and at the same time impose cell incompressibility.
In the proposed model, the cell boundaries (defined by vertices) and cell nuclei (or cellcentres)
networks are coupled through an interpolation scheme, which is eventually relaxed in
order to smooth the cell boundaries. We show that this coupling between the two networks
modifies the equilibrium equations and stabilises the vertex network. Incompressibility is implemented
through a penalty method. The resulting model can be implemented in two- and
three-dimensions, and is complemented with active rheological models.
We apply the model to simulate the stretching and relaxation of cell monolayers, and to
simulate wound healing process in the wing disc of Drosophila fly embryo. We show that the
numerical results agree with the experimental measurements.