Computational Bio-Engineering : Scipedia

From medical images to anatomically accurate finite element grids
J. Cebral, R. Lohner

Int. J. Numer. Meth. Engng. (2001). Vol. 51 (8), pp. 985-1008
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Blood Flow Modeling in Carotid Arteries with Computational Fluid Dynamics and MR Imaging
J. Cebral, P. Yim, R. Lohner, O. Soto, P. Choyke

Academic Radiology (2002). Vol. 9 (11), pp. 1286-1299

Abstract
The authors' goal was to develop a noninvasive method for detailed assessment of blood flow patterns from direct in vivo measurements of vessel anatomy and flow rates. The authors developed a method to construct realistic patient-specific finite element models of blood flow in carotid arteries. Anatomic models are reconstructed from contrast material-enhanced magnetic resonance (MR) angiographic images with a tubular deformable model along each arterial branch. A surface-merging algorithm is used to create a watertight model of the carotid bifurcation for subsequent finite element grid generation, and a fully implicit scheme is used to solve the incompressible Navier-Stokes equations on unstructured grids. Physiologic boundary conditions are derived from cine phase-contrast MR flow velocity measurements at two locations below and above the bifurcation. Vessel wall compliance is incorporated by means of fluid-solid interaction algorithms. The method was tested on imaging data from a healthy subject and a patient with mild stenosis. Finite element grids were successfully generated, and pulsatile blood flow calculations were performed. Computed and measured velocity profiles show good agreement. Flow patterns and wall shear stress distributions were visualized. Patient-specific computational fluid dynamics modeling based on MR images can be performed robustly and efficiently. Preliminary validation studies in a physical flow-through model suggest that the model is accurate. This method can be used to characterize blood flow patterns in healthy and diseased arteries and may eventually help physicians to supplement imaging-based diagnosis and predict and evaluate the outcome of interventional procedures.
Abstract
The authors' goal was to develop a noninvasive method for detailed assessment of blood flow patterns from direct in vivo measurements of vessel anatomy and flow rates. [...]
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Applications of patient-specific CFD in medicine and life science
R. Lohner, J. Cebral, O. Soto, P. Yim, J. Burgess

Int. J. Numer. Meth. Fluids (2003). Vol. 43 (6-7), pp. 637-650

Abstract
Recent advances in medical image segmentation, grid generation, flow solvers, realistic boundary conditions, fluid–structure interaction, data reduction and visualization arc reviewed with special emphasis on patient‐specific flow prediction. At the same time, present shortcomings in each one of these areas are identified. Several examples are given that show that this methodology is maturing rapidly, and may soon find widespread use in medicine.
Abstract
Recent advances in medical image segmentation, grid generation, flow solvers, realistic boundary conditions, fluid–structure interaction, data reduction and visualization [...]
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Blood-flow models of the circle of Willis from magnetic resonance data
J. Cebral, M. Castro, O. Soto, R. Lohner, N. Alperin

Journal of Engineering Mathematics (2003). Vol. 47, pp. 369-386

Abstract
Detailed knowledge of the cerebral hemodynamics is important for a variety of clinical applications. Cerebral perfusion depends not only on the status of the diseased vessels but also on the patency of collateral pathways provided by the circle of Willis. Due to the large anatomical and physiologic variability among individuals, realistic patient-specific models can provide new insights into the cerebral hemodynamics. This paper presents an image-based methodology for constructing patient-specific models of the cerebral circulation. This methodology combines anatomical and physiologic imaging techniques with computer simulation technology. The methodology is illustrated with a finite element model constructed from magnetic resonance image data of a normal volunteer. Several of the remaining challenging problems are identified. This work represents a starting point in the development of realistic models that can be applied to the study of cerebrovascular diseases and their treatment.
Abstract
Detailed knowledge of the cerebral hemodynamics is important for a variety of clinical applications. Cerebral perfusion depends not only on the status of the diseased vessels [...]
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Efficient simulation of blood flow past complex endovascular devices using an adaptive embedding technique
J. Cebral, R. Lohner

IEEE Transactions on Intelligent Transportation Systems (2005). Vol. 24 (4), pp. 468-476

Abstract
The simulation of blood flow past endovascular devices such as coils and stents is a challenging problem due to the complex geometry of the devices. Traditional unstructured grid computational fluid dynamics relies on the generation of finite element grids that conform to the boundary of the computational domain. However, the generation of such grids for patient-specific modeling of cerebral aneurysm treatment with coils or stents is extremely difficult and time consuming. This paper describes the application of an adaptive grid embedding technique previously developed for complex fluid structure interaction problems to the simulation of endovascular devices. A hybrid approach is used: the vessel walls are treated with body conforming grids and the endovascular devices with an adaptive mesh embedding technique. This methodology fits naturally in the framework of image-based computational fluid dynamics and opens the door for exploration of different therapeutic options and personalization of endovascular procedures.
Abstract
The simulation of blood flow past endovascular devices such as coils and stents is a challenging problem due to the complex geometry of the devices. Traditional unstructured [...]
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Computational fluid dynamics of stented intracranial aneurysms using adaptive embedded unstructured grids
S. Appanaboyina, F. Mut, R. Lohner, C. Putman, J. Cebral

Int. J. Numer. Meth. Fluids (2008). Vol. 57 (5), pp. 475-493

Abstract
Recently, there has been increased interest in the use of stents as flow diverters in the endovascular treatment of cerebral aneurysms as an alternative to surgical clipping or endovascular embolization with coils. The aim of aneurysm stenting is to block the flow into the aneurysm in order to clot the blood inside the aneurysm and effectively isolate it from the circulation and prevent bleeding from the aneurysm. A hybrid meshing approach that combines body‐fitted grids for the vessels and adaptive embedded grids for the stents is proposed and analyzed. This strategy simplifies considerably the geometry modeling problem and allows accurate patient‐specific hemodynamic simulations with endovascular devices. This approach is compared with the traditional body‐fitted approach in the case of the flow around a circular cylinder at representative Reynolds number and an idealized aneurysm model with a stent. A novel technique to map different stent designs to a given patient‐specific anatomical model is presented. The methodology is demonstrated on a patient‐specific hemodynamic model of an aneurysm of the internal carotid artery constructed from a 3D rotational angiogram and stented with two different stent designs. The results show that the methodology can be successfully used to model patient‐specific anatomies with different stents thereby making it possible to explore different stent designs
Abstract
Recently, there has been increased interest in the use of stents as flow diverters in the endovascular treatment of cerebral aneurysms as an alternative to surgical clipping [...]
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Simulation of intracranial aneurysm stenting: Techniques and challenges
S. Appanaboyina, F. Mut, R. Lohner, C. Putman, J. Cebral

Comput. Methods Appl. Mech. Engrg., (2009). Vol. 198 (45-46), pp. 3567-3582

Abstract
Recently, there has been considerable interest in the use of stents as endovascular flow diverters for the treatment of intracranial aneurysms. Simulating this novel method of treatment is essential for understanding the intra-aneurysmal hemodynamics in order to design better stents and to personalize and optimize the endovascular stenting procedures. This paper describes a methodology based on unstructured embedded grids for patient-specific modeling of stented cerebral aneurysms, demonstrates how the methodology can be used to address specific clinical questions, and discusses remaining technical issues. In particular, simulations are presented on a number of patient-specific models constructed from medical images and using different stent designs and treatment alternatives. Preliminary sensitivity analyses with respect to stent positioning and truncation of the stent model are presented. The results show that these simulations provide useful and valuable information that can be used during the planning phase of endovascular stenting interventions for the treatment of intracranial aneurysms.
Abstract
Recently, there has been considerable interest in the use of stents as endovascular flow diverters for the treatment of intracranial aneurysms. Simulating this novel method [...]
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The journal Communications in Numerical Methods in Engineering with Biomedical Applications becomes the International Journal for Numerical Methods in Biomedical Engineering (IJNMBE) from 1st January 2010
P. Nithiarasu, R. Lohner

Int. J. Numer. Meth. Fluids (2009). Vol. 61 (10), pp. 1179-1180

Abstract
Communications in Numerical Methods in Engineering , founded by Roland W. Lewis in 1985, will change its title to the ‘International Journal for Numerical Methods in Biomedical Engineering ’ and has a revised Aims and Scope.
Abstract
Communications in Numerical Methods in Engineering , founded by Roland W. Lewis in 1985, will change its title to the ‘International Journal for Numerical Methods [...]
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Fast numerical solutions of patient‐specific blood flows in 3D arterial systems
F. Mut, R. Aubry, R. Lohner, J. Cebral

Int. J. Numer. Meth. Bio. Engng. (2010). Vol. 26 (1), pp. 73-86

Abstract
The study of hemodynamics in arterial models constructed from patient‐specific medical images requires the solution of the incompressible flow equations in geometries characterized by complex branching tubular structures. The main challenge with this kind of geometries is that the convergence rate of the pressure Poisson solver is dominated by the graph depth of the computational grid. This paper presents a deflated preconditioned conjugate gradients (DPCG) algorithm for accelerating the pressure Poisson solver. A subspace deflation technique is used to approximate the lowest eigenvalues along the tubular domains. This methodology was tested with an idealized cylindrical model and three patient‐specific models of cerebral arteries and aneurysms constructed from medical images. For these cases, the number of iterations decreased by up to a factor of 16, while the total CPU time was reduced by up to 4 times when compared with the standard PCG solver.
Abstract
The study of hemodynamics in arterial models constructed from patient‐specific medical images requires the solution of the incompressible flow equations in geometries characterized [...]
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Hemodynamic Analysis of Intracranial Aneurysms with Moving Parent Arteries: Basilar Tip Aneurysms
D. Sforza, R. Lohner, C. Putman, J. Cebral

Int. J. Numer. Meth. Bio. Engng. (2010). Vol. 26 (10), pp. 1219-1227

Abstract
The effects of parent artery motion on the hemodynamics of basilar tip saccular aneurysms and its potential effect on aneurysm rupture were studied. The aneurysm and parent artery motions in two patients were determined from cine loops of dynamic angiographies. The oscillatory motion amplitude was quantified by registering the frames. Patient‐specific computational fluid dynamics (CFD) models of both aneurysms were constructed from 3D rotational angiography images. Two CFD calculations were performed for each patient, corresponding to static and moving models. The motion estimated from the dynamic images was used to move the surface grid points in the moving model. Visualizations from the simulations were compared for wall shear stress (WSS), velocity profiles, and streamlines. In both patients, a rigid oscillation of the aneurysm and basilar artery in the anterio‐posterior direction was observed and measured. The distribution of WSS was nearly identical between the models of each patient, as well as major intra‐aneurysmal flow structures, inflow jets, and regions of impingement. The motion observed in pulsating intracranial vasculature does not have a major impact on intra‐aneurysmal hemodynamic variables. Parent artery motion is unlikely to be a risk factor for increased risk of aneurysmal rupture.
Abstract
The effects of parent artery motion on the hemodynamics of basilar tip saccular aneurysms and its potential effect on aneurysm rupture were studied. The aneurysm and parent [...]
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Computational Hemodynamics Framework for the Analysis of Cerebral Aneurysms
F. Mut, R. Lohner, A. Chien, S. Tateshima, F. Viñuela, C. Putman, J. Cebral

Int. J. Numer. Meth. Bio. Engng. (2010). Vol. 27 (6), pp. 822-839

Abstract
Assessing the risk of rupture of intracranial aneurysms is important for clinicians because the natural rupture risk can be exceeded by the small but significant risk carried by current treatments. To this end numerous investigators have used image‐based computational fluid dynamics models to extract patient‐specific hemodynamics information, but there is no consensus on which variables or hemodynamic characteristics are the most important. This paper describes a computational framework to study and characterize the hemodynamic environment of cerebral aneurysms in order to relate it to clinical events, such as growth or rupture. In particular, a number of hemodynamic quantities are proposed to describe the most salient features of these hemodynamic environments. Application to a patient population indicates that ruptured aneurysms tend to have concentrated inflows, concentrated wall shear stress distributions, high maximal wall shear stress, and smaller viscous dissipation ratios than unruptured aneurysms. Furthermore, these statistical associations are largely unaffected by the choice of physiologic flow conditions. This confirms the notion that hemodynamic information derived from image‐based computational models can be used to assess aneurysm rupture risk, to test hypotheses about the mechanisms responsible for aneurysm formation, progression, and rupture, and to answer specific clinical questions.
Abstract
Assessing the risk of rupture of intracranial aneurysms is important for clinicians because the natural rupture risk can be exceeded by the small but significant risk carried [...]
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Mechanisms Involved in the Formation of Biocompatible Lipid Polymeric Hollow Patchy Particles
N. Rasheed, A. Khorasani, J. Cebral, C. Salvador-Morales, F. Mut, R. Lohner

Langmuir (2015). Vol. 31 (24), pp. 6639-6648

Abstract
Patchy polymeric particles have anisotropic surface domains that can be remarkably useful in diverse medical and industrial fields because of their ability to simultaneously present two different surface chemistries on the same construct. In this article, we report the mechanisms involved in the formation of novel lipid–polymeric hollow patchy particles during their synthesis. By cross-sectioning the patchy particles, we found that a phase segregation phenomenon occurs between the core, shell, and patch. Importantly, we found that the shear stress that the polymer blend undergoes during the particle synthesis is the most important parameter for the formation of these patchy particles. In addition, we found that the interplay of solvent–solvent, polymer–solvent, and polymer–polymer–solvent interactions generates particles with different surface morphologies. Understanding the mechanisms involved in the formation of patchy particles allows us to have a better control on their physicochemical properties. Therefore, these fundamental studies are critical to achieve batch control and scalability, which are essential aspects that must be addressed in any type of particle synthesis to be safely used in medicine.
Abstract
Patchy polymeric particles have anisotropic surface domains that can be remarkably useful in diverse medical and industrial fields because of their ability to simultaneously [...]
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Mechanistic studies on the self-assembly of PLGA patchy particles and their potential applications in biomedical imaging
C. Salvador-Morales, B. Brahmbhatt, V. Márquez-Miranda, I. Araya-Dura, J. Canan, F. González-Nilo, C. Vilos, J. Cebral, F. Mut, R. Lohner, B. Leong, G. Sundaresan, J. Zweit

Langmuir (2016). Vol. 32 (31), pp. 7929-7949

Abstract
Currently, several challenges prevent poly(lactic-co-glycolic acid) (PLGA) particles from reaching clinical settings. Among these is a lack of understanding of the molecular mechanisms involved in the formation of these particles. We have been studying in depth the formation of patchy polymeric particles. These particles are made of PLGA and lipid–polymer functional groups. They have unique patch–core–shell structural features: hollow or solid hydrophobic cores and a patchy surface. Previously, we identified the shear stress as the most important parameter in a patchy particle’s formation. Here, we investigated in detail the role of shear stress in the patchy particle’s internal and external structure using an integrative experimental and computational approach. By cross-sectioning the multipatch particles, we found lipid-based structures embedded in the entire PLGA matrix, which represents a unique finding in the PLGA field. By developing novel computational fluid dynamics and molecular dynamics simulations, we found that the shear stress determines the internal structure of the patchy particles. Equally important, we discovered that these particles emit a photoacoustic (PA) signal in the optical clinical imaging window. Our results show that particles with multiple patches emit a higher PA signal than single-patch particles. This phenomenon most likely is due to the fact that multipatchy particles absorb more heat than single-patchy particles as shown by differential scanning calorimetry analysis. Furthermore, we demonstrated the use of patchy polymeric particles as photoacoustic molecular probes both in vitro and in vivo studies. The fundamental studies described here will help us to design more effective PLGA carriers for a number of medical applications as well as to accelerate their medical translation.
Abstract
Currently, several challenges prevent poly(lactic-co-glycolic acid) (PLGA) particles from reaching clinical settings. Among these is a lack of understanding of the [...]
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Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research
A. Erdemir, P. Hunter, G. Holzapfel, L. Loew, J. Middleton, C. Jacobs, P. Nithiarasu, R. Lohner, G. Wei, B. Winkelstein, V. Barocas, F. Guilak, J. Ku, J. Hicks, S. Delp, M. Sacks, J. Weiss, G. Ateshian, S. Mass, A. McCulloch, G. Peng

Journal of Biomechanics Engineering (2018). Vol. 140 (2), pp. 1-11

Abstract
The role of computational modeling for biomechanics will be increasingly prominent. In computational biomechanics, model sharing can facilitate assessment of reproducibility, and can provide an opportunity for repurposing and reuse, and a venue for medical training. The community's desire to investigate biological and biomechanical phenomena crossing multiple systems, scales, and physical domains, also motivates sharing of modeling resources as blending of models developed by domain experts is anticipated. The goal of this article is to understand current perspectives in the biomechanics community for the sharing of computational models and related resources. Opinions on opportunities, challenges, and pathways to model sharing, particularly as part of the scholarly publishing workflow, were sought. A synthesis of these opinion pieces indicates that the community recognizes the necessity and usefulness of model sharing. There is a strong will to facilitate model sharing and there are corresponding initiatives by the scientific journals. Outside the publishing enterprise, infrastructure to facilitate model sharing in biomechanics exists and simulation software developers are interested in accommodating the community's needs for sharing of modeling resources. Encouragement for the use of standardized markups, concerns related to quality assurance, acknowledgement of increased burden, and importance of stewardship of resources are noted. In the short-term, it is advisable that the community builds upon recent strategies and experiments with new pathways for continued demonstration of model sharing, its promotion, and its utility. Nonetheless, the need for a long term strategy to unify approaches in sharing computational models and related resources is acknowledged.
Abstract
The role of computational modeling for biomechanics will be increasingly prominent. In computational biomechanics, model sharing can facilitate assessment of reproducibility, [...]
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Planar differential growth rates initiate precise fold positions in complex epithelia
M. Tozlouglu, M. Duda, N. Kirkland, R. Barrientos, J. Burden, J. Muñoz, Y. Mao

Developmental cell (2019). Vol. 51 (3), pp. 299-312

Abstract
Tissue folding is a fundamental process that shapes epithelia into complex 3D organs. The initial positioning of folds is the foundation for the emergence of correct tissue morphology. Mechanisms forming individual folds have been studied, but the precise positioning of folds in complex, multi-folded epithelia is less well-understood. We present a computational model of morphogenesis, encompassing local differential growth and tissue mechanics, to investigate tissue fold positioning. We use the Drosophila wing disc as our model system and show that there is spatial-temporal heterogeneity in its planar growth rates. This differential growth, especially at the early stages of development, is the main driver for fold positioning. Increased apical layer stiffness and confinement by the basement membrane drive fold formation but influence positioning to a lesser degree. The model successfully predicts the in vivo morphology of overgrowth clones and wingless mutants via perturbations solely on planar differential growth in silico.
Abstract
Tissue folding is a fundamental process that shapes epithelia into complex 3D organs. The initial positioning of folds is the foundation for the emergence of correct tissue [...]
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Computational modeling of epithelial wound healing: Short and long term chemo-mechanical mechanisms
L. Roldán, J. Muñoz, P. Sáez

Comput. Methods Appl. Mech. Engrg., (2019). Vol. 350, pp. 28-56

Abstract
During the lifetime of all living multicellular organisms, wounds in their tissues are frequently observed. The capability of closing those gaps is fundamental for a healthy development. If done deficiently, many diseases may occur from simple inflammation to tumor formation. The wound healing process in epithelial tissue occurs in three different stages. The first one is the assembly of a supra-cellular actomyosin cable and its migration towards the wound edge, triggered by biochemical processes in which calcium plays a distinctive role. How this process is orchestrated following damage remains unclear. Later, after its positioning, the cable contracts driving the tissue towards the gap and reducing the wound area. Finally, cell migration towards the interior of the wound ends up sealing the tissue. In this work, we make use of a mechanical continuum model for the first two stages in order to developed and 2D finite element simulations within a monolithically fully implicit implementation. The model for the actomyosin cable formation involves the coupling of transient calcium ions transport, with actin fibers and myosin motors recruitment and non-linear mechanical response of the tissue. The contraction stage, the active deformation of the previously formed actomyosin cable is taken into account. The relative motion of the myosin motors over the actin filaments is modeled so there exists an active tissue contraction in the direction of those fibers. Upon implementation, the model is capable of performing a wide range of biophysical situations reported experimentally, as we demonstrate in our numerical results. We have been able to rationalize through computational mechanics the firing of calcium in the wound right after damage infliction as well as the consequent formation of actin ring, reproducing nicely what has been reported in biological literature. Thereafter, the numerical model of acto-myosin contraction, fully integrated with the non-linear mechanics of the problem, correlates with the mechanics of wound closure at the actin-ring contraction stage. More importantly, the approach is the first of its kind in the modeling of epithelial and embryonic cell layers, where a wide number of complex mechanics has been integrated and solved though computational methods in engineering. We believe that the simulations will help to unravel new insights in open questions of developmental biology.
Abstract
During the lifetime of all living multicellular organisms, wounds in their tissues are frequently observed. The capability of closing those gaps is fundamental [...]
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Stress relaxation in epithelial monolayers is controlled by the actomyosin cortex
N. Khalilgharibi, J. Fouchard, N. Asadipour, R. Barrientos, M. Duda, A. Bonfanti, A. Yonis, A. Harris, P. Mosaffa, Y. Fujita, A. Kabla, Y. Mao, B. Baum, J. Muñoz, M. Miodownik, G. Charras

Nature Physics (2019). Vol. 15, pp. 839-847 (Preprint)

Abstract
Epithelial monolayers are one-cell-thick tissue sheets that line most of the body surfaces, separating internal and external environments. As part of their function, they must withstand extrinsic mechanical stresses applied at high strain rates. However, little is known about how monolayers respond to mechanical deformations. Here, by subjecting suspended epithelial monolayers to stretch, we find that they dissipate stresses on a minute timescale and that relaxation can be described by a power law with an exponential cut-off at timescales larger than about 10 s. This process involves an increase in monolayer length, pointing to active remodelling of cellular biopolymers at the molecular scale during relaxation. Strikingly, monolayers consisting of tens of thousands of cells relax stress with similar dynamics to single rounded cells, and both respond similarly to perturbations of the actomyosin cytoskeleton. By contrast, cell–cell junctional complexes and intermediate filaments do not relax tissue stress, but form stable connections between cells, allowing monolayers to behave rheologically as single cells. Taken together, our data show that actomyosin dynamics governs the rheological properties of epithelial monolayers, dissipating applied stresses and enabling changes in monolayer length.
Abstract
Epithelial monolayers are one-cell-thick tissue sheets that line most of the body surfaces, separating internal and external environments. As part of their function, they [...]
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Mechanical oscillations in biological tissues as a result of delayed rest-length changes
J. Muñoz, M. Dingle, M. Wenzel

Physical review E: statistical, nonlinear and soft matter physics (2018). Vol. 98 (5), pp. 1-15 (Preprint)

Abstract
Oscillatory behavior in tissue biology is ubiquitous and may be observed in the form of either chemical or mechanical signals. We present here and solve a mechanical cell model that exhibits oscillations emerging from delayed viscoelastic rheological laws. These include a time delay between the mechanical response and the rest-length changes, which evolve proportionally to the delayed cell deformation and use a remodeling rate parameter. We show that different regimes (no oscillatory response, sustained oscillations, and unstable oscillations) are obtained for different values of the delay or the remodeling rate. The results are analytically demonstrated in a one-dimensional problem with one and two cells that are represented by simple line elements. Oscillations of the cell deformations are obtained whenever different delays coexist, or when the delay is size-dependent. We also extend our results to a multicellular two-dimensional vertex model that includes the same rheological law, and which inherits the presence of critical values of the delay or remodeling rate. We numerically show that indeed the size-dependent rest-length changes induce oscillations in the cell shapes and areas.
Abstract
Oscillatory behavior in tissue biology is ubiquitous and may be observed in the form of either chemical or mechanical signals. We present here and solve a mechanical cell [...]
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Computation of forces from deformed visco-elastic biological tissues
J. Muñoz, D. Amat, V. Conte

Inverse Problems (2018). Vol. 34 (4), pp. 1-27 (Preprint)

Abstract
We present a least-squares based inverse analysis of visco-elastic biological tissues. The proposed method computes the set of contractile forces (dipoles) at the cell boundaries that induce the observed and quantified deformations. We show that the computation of these forces requires the regularisation of the problem functional for some load configurations that we study here. The functional measures the error of the dynamic problem being discretised in time with a second-order implicit time-stepping and in space with standard finite elements. We analyse the uniqueness of the inverse problem and estimate the regularisation parameter by means of an L-curved criterion. We apply the methodology to a simple toy problem and to an in vivo set of morphogenetic deformations of the Drosophila embryo.
Abstract
We present a least-squares based inverse analysis of visco-elastic biological tissues. The proposed method computes the set of contractile forces (dipoles) at the cell boundaries [...]
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Hybrid cell-centred/vertex model for multicellular systems with equilibrium-preserving remodelling
P. Mosaffa, A. Rodríguez-Ferran, J. Muñoz

Int. J. Numer. Meth. Bio. Engng. (2018). Vol. 34 (3), pp. 1-33 (Preprint)

Abstract
We present a hybrid cell‐centred/vertex model for mechanically simulating planar cellular monolayers undergoing cell reorganisation. Cell centres are represented by a triangular nodal network, while the cell boundaries are formed by an associated vertex network. The two networks are coupled through a kinematic constraint which we allow to relax progressively. Special attention is paid to the change of cell‐cell connectivity due to cell reorganisation or remodelling events. We handle these situations by using a variable resting length and applying an Equilibrium‐Preserving Mapping on the new connectivity, which computes a new set of resting lengths that preserve nodal and vertex equilibrium. We illustrate the properties of the model by simulating monolayers subjected to imposed extension and during a wound healing process. The evolution of forces and the Equilibrium‐Preserving Mapping are analysed during the remodelling events. As a by‐product, the proposed technique enables to recover fully vertex or fully cell‐centred models in a seamless manner by modifying a numerical parameter of the model.
Abstract
We present a hybrid cell‐centred/vertex model for mechanically simulating planar cellular monolayers undergoing cell reorganisation. Cell centres are represented by a triangular [...]
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From medical images to anatomically accurate finite element grids

Blood Flow Modeling in Carotid Arteries with Computational Fluid Dynamics and MR Imaging

Applications of patient-specific CFD in medicine and life science

Blood-flow models of the circle of Willis from magnetic resonance data

Efficient simulation of blood flow past complex endovascular devices using an adaptive embedding technique

Computational fluid dynamics of stented intracranial aneurysms using adaptive embedded unstructured grids

Simulation of intracranial aneurysm stenting: Techniques and challenges

The journal Communications in Numerical Methods in Engineering with Biomedical Applications becomes the International Journal for Numerical Methods in Biomedical Engineering (IJNMBE) from 1st January 2010

Fast numerical solutions of patient‐specific blood flows in 3D arterial systems

Hemodynamic Analysis of Intracranial Aneurysms with Moving Parent Arteries: Basilar Tip Aneurysms

Computational Hemodynamics Framework for the Analysis of Cerebral Aneurysms

Mechanisms Involved in the Formation of Biocompatible Lipid Polymeric Hollow Patchy Particles

Mechanistic studies on the self-assembly of PLGA patchy particles and their potential applications in biomedical imaging

Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research

Planar differential growth rates initiate precise fold positions in complex epithelia

Computational modeling of epithelial wound healing: Short and long term chemo-mechanical mechanisms

Stress relaxation in epithelial monolayers is controlled by the actomyosin cortex

Mechanical oscillations in biological tissues as a result of delayed rest-length changes

Computation of forces from deformed visco-elastic biological tissues

Hybrid cell-centred/vertex model for multicellular systems with equilibrium-preserving remodelling

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