Generalized finite element solution to one-dimensional flux problems

A finite element numerical solution to the general one-dimensional flow equation is derived in a form that provides a convenient and general means to simulate a wide variety of one-dimensional flow techniques of interest to biological scientists, e.g., ultracentrifugation, electrophoresis, chromatography, etc. Diverse physical models defined in terms of column geometry, solute interactions, and the dependence of transport parameters on column position, time, or concentrations of one or more solutes, can be accommodated. A particularly useful aspect of the formulation is that a wide variety of boundary conditions can be simply applied to the end result, without rederivation of the solution for each new case. The numerical solution is expressed as matrix equations that are sufficiently general so that incorporation of particular models can be effected by substitution of appropriate quantities into the final result.     

A new method for finite element simulation of orthodontic appliance-teeth-periodontium-alveolus system

This paper describes a new simulation method to analyze the initial behavior of the total system comprising orthodontic appliance, teeth, and their supporting structures. It is based on a finite element method which additionally takes account of a rotational degree of freedom. Beam and rod elements are used for finite element idealization of orthodontic appliance. Through spring elements it is connected with the teeth supported by the alveolar structures. The technique of 'initial strain' is introduced so as to analyze the effects of a gable bend and activation on the force system which is delivered by the orthodontic appliance. As compared with the photoelastic technique hitherto used, this method serves to investigate systematically and quantitatively the initial aspect of orthodontic tooth movement.     

A penetration-based finite element method for hyperelastic 3D biphasic tissues in contact. Part II: finite element simulations

The penetration method allows for the efficient finite element simulation of contact between soft hydrated biphasic tissues in diarthrodial joints. Efficiency of the method is achieved by separating the intrinsically nonlinear contact problem into a pair of linked biphasic finite element analyses, in which an approximate, spatially and temporally varying contact traction is applied to each of the contacting tissues. In Part I of this study, we extended the penetration method to contact involving nonlinear biphasic tissue layers, and demonstrated how to derive the approximate contact traction boundary conditions. The traction derivation involves time and space dependent natural boundary conditions, and requires special numerical treatment. This paper (Part II) describes how we obtain an efficient nonlinear finite element procedure to solve for the biphasic response of the individual contacting layers. In particular, alternate linearization of the nonlinear weak form, as well as both velocity-pressure, v-p, and displacement-pressure, u-p, mixed formulations are considered. We conclude that the u-p approach, with linearization of both the material law and the deformation gradients, performs best for the problem at hand. The nonlinear biphasic contact solution will be demonstrated for the motion of the glenohumeral joint of the human shoulder joint.     

A finite element method for mechanical response of hair cell ciliary bundles

This paper describes the development of a methodology for performing a mechanical analysis of hair cell ciliary bundles. The cilia were modeled as shear deformable beams, and interconnections were modeled as two-force members. These models were incorporated into software, which performs a finite element analysis of a user-defined bundle. The algorithm incorporates aspects of the bundle such as geometric realignment and buckling of compressed side links. A sample bundle is introduced and results of modeling it are presented.     

A fully implicit finite element method for bidomain models of cardiac electrophysiology

This work introduces a novel, unconditionally stable and fully coupled finite element method for the bidomain system of equations of cardiac electrophysiology. The transmembrane potential Φ(i)-Φ(e) and the extracellular potential Φ(e) are treated as independent variables. To this end, the respective reaction-diffusion equations are recast into weak forms via a conventional isoparametric Galerkin approach. The resultant nonlinear set of residual equations is consistently linearised. The method results in a symmetric set of equations, which reduces the computational time significantly compared to the conventional solution algorithms. The proposed method is inherently modular and can be combined with phenomenological or ionic models across the cell membrane. The efficiency of the method and the comparison of its computational cost with respect to the simplified monodomain models are demonstrated through representative numerical examples.     

Anisotropic adaptive finite element method for modelling blood flow

In this study, we present an adaptive anisotropic finite element method (FEM) and demonstrate how computational efficiency can be increased when applying the method to the simulation of blood flow in the cardiovascular system. We use the SUPG formulation for the transient 3D incompressible Navier-Stokes equations which are discretised by linear finite elements for both the pressure and the velocity field. Given the pulsatile nature of the flow in blood vessels we have pursued adaptivity based on the average flow over a cardiac cycle. Error indicators are derived to define an anisotropic mesh metric field. Mesh modification algorithms are used to anisotropically adapt the mesh according to the desired size field. We demonstrate the efficiency of the method by first applying it to pulsatile flow in a straight cylindrical vessel and then to a porcine aorta with a stenosis bypassed by a graft. We demonstrate that the use of an anisotropic adaptive FEM can result in an order of magnitude reduction in computing time with no loss of accuracy compared to analyses obtained with uniform meshes.     

Statistical finite element method for real-time tissue mechanics analysis

The finite element (FE) method can accurately calculate tissue deformation. However, its low speed renders it ineffective for many biomedical applications involving real-time data processing. To accelerate FE analysis, we introduce a novel tissue mechanics simulation technique. This technique is suitable for real-time estimation of tissue deformation of specific organs, which is required in computer-aided diagnostic or therapeutic procedures. In this method, principal component analysis is used to describe each organ shape and its corresponding FE field for a pool of patients by a small number of weight factors. A mapping function is developed to relate the parameters of organ shape to their FE field counterpart. We show that irrespective of the complexity of the tissue's constitutive law or its loading conditions, the proposed technique is highly accurate and fast in estimating the FE field. Average deformation errors of less than 2% demonstrate the accuracy of the proposed technique.     

A three-dimensional finite element model for arterial clamping

Clamp induced injuries of the arterial wall may determine the outcome of surgical procedures. Thus, it is important to investigate the underlying mechanical effects. We present a three-dimensional finite element model, which allows the study of the mechanical response of an artery-treated as a two-layer tube-during arterial clamping. The important residual stresses, which are associated with the load-free configuration of the artery, are also considered. In particular, the finite element analysis of the deformation process of a clamped artery and the associated stress distribution is presented. Within the clamping area a zone of axial tensile peak-stresses was identified, which (may) cause intimal and medial injury. This is an additional injury mechanism, which clearly differs from the commonly assumed wall damage occurring due to compression between the jaws of the clamp. The proposed numerical model provides essential insights into the mechanics of the clamping procedure and the associated injury mechanisms. It allows detailed parameter studies on a virtual clamped artery, which can not be performed with other methodologies. This approach has the potential to identify the most appropriate clamps for certain types of arteries and to guide optimal clamp design.     

Tissue-fluid interface analysis using biphasic finite element method

Numerical studies on fluid-structure interaction have primarily relied on decoupling the solid and fluid sub-domains with the interactions treated as external boundary conditions on the individual sub-domains. The finite element applications for the fluid-structure interactions can be divided into iterative algorithms and sequential algorithms. In this paper, a new computational methodology for the analysis of tissue-fluid interaction problems is presented. The whole computational domain is treated as a single biphasic continuum, and the same space and time discretisation is carried out for the sub-domains using a penalty-based finite element model. This procedure does not require the explicit modelling of additional boundary conditions or interface elements. The developed biphasic interface finite element model is used in analysing blood flow through normal and stenotic arteries. The increase in fluid flow velocity when passing through a stenosed artery and the drop in pressure at the region are captured using this method.     

A comparative analysis of different treatments for distal femur fractures using the finite element method

The main objective of this work is the evaluation, by means of the finite element method (FEM) of the mechanical stability and long-term microstructural modifications in bone induced to three different kinds of fractures of the distal femur by three types of implants: the Condyle Plate, the less invasive stabilization system plate (LISS) and the distal femur nail (DFN). The displacement and the stress distributions both in bone and implants and the internal bone remodelling process after fracture and fixation are obtained and analysed by computational simulation. The main conclusions of this work are that distal femoral fractures can be treated correctly with the Condyle Plate, the LISS plate and the DFN. The stresses both in LISS and DFN implant are high especially around the screws. When respect to remodelling, the LISS produces an important resorption in the fractured region, while the other two implants do not strongly modify bone tissue microstructure.     

A simulation-based marginal method for longitudinal data with dropout and mismeasured covariates

Longitudinal data often contain missing observations and error-prone covariates. Extensive attention has been directed to analysis methods to adjust for the bias induced by missing observations. There is relatively little work on investigating the effects of covariate measurement error on estimation of the response parameters, especially on simultaneously accounting for the biases induced by both missing values and mismeasured covariates. It is not clear what the impact of ignoring measurement error is when analyzing longitudinal data with both missing observations and error-prone covariates. In this article, we study the effects of covariate measurement error on estimation of the response parameters for longitudinal studies. We develop an inference method that adjusts for the biases induced by measurement error as well as by missingness. The proposed method does not require the full specification of the distribution of the response vector but only requires modeling its mean and variance structures. Furthermore, the proposed method employs the so-called functional modeling strategy to handle the covariate process, with the distribution of covariates left unspecified. These features, plus the simplicity of implementation, make the proposed method very attractive. In this paper, we establish the asymptotic properties for the resulting estimators. With the proposed method, we conduct sensitivity analyses on a cohort data set arising from the Framingham Heart Study. Simulation studies are carried out to evaluate the impact of ignoring covariate measurement error and to assess the performance of the proposed method.     

A finite element model for protein transport in vivo

Background  

Biological mass transport processes determine the behavior and function of cells, regulate interactions between synthetic agents and recipient targets, and are key elements in the design and use of biosensors. Accurately predicting the outcomes of such processes is crucial to both enhancing our understanding of how these systems function, enabling the design of effective strategies to control their function, and verifying that engineered solutions perform according to plan.     

A finite element simulation scheme for biological muscular hydrostats

An explicit finite element scheme is developed for biological muscular hydrostats such as squid tentacles, octopus arms and elephant trunks. The scheme is implemented by embedding muscle fibers in finite elements. In any given element, the fiber orientation can be assigned arbitrarily and multiple muscle directions can be simulated. The mechanical stress in each muscle fiber is the sum of active and passive parts. The active stress is taken to be a function of activation state, muscle fiber shortening velocity and fiber strain; while the passive stress depends only on the strain. This scheme is tested by simulating extension of a squid tentacle during prey capture; our numerical predictions are in close correspondence with existing experimental results. It is shown that the present finite element scheme can successfully simulate more complex behaviors such as torsion of a squid tentacle and the bending behavior of octopus arms or elephant trunks.     

Mechanics of cranial sutures using the finite element method

To investigate how cranial suture morphology and the arrangement of sutural collagen fibres respond to compressive and tensile loads, an idealised bone–suture–bone complex was analysed using a two-dimensional finite element model. Three suture morphologies were simulated with an increasing interdigitation index (I.I.): butt-ended, moderate interdigitated, and complex interdigitated. The collagen matrix within all sutures was modelled as an isotropic material, and as an orthotropic material in the interdigitated sutures with fibre alignment as reported in studies of miniature pigs. Static uniform compressive or tensile loading was applied to the complex. In interdigitated sutures with isotropic material properties, the orientation of the maximum (tensile) principal stresses within the suture matched the collagen fibre orientation observed in compressed and tensed sutures of miniature pigs. This suggests that randomly arranged sutural collagen fibres could optimise to an orientation most appropriate to withstand the predominant type of loading. A compression-resistant fibre arrangement imparted the highest suture strain energy relative to the isotropic and tension-resistant arrangements, indicating that this configuration maximises energy storage. A comparison across the different suture morphologies indicated that bone strain energy generally decreased with a decrease in I.I., irrespective of the sutural fibre arrangement. However, high bone stress at the interdigitation apices shifted to the limbs of the suture with an increase in I.I. These combined findings highlight the importance of suture morphology and anisotropy as properties having a significant influence on sutural mechanics.     

Characterization of craniofacial sutures using the finite element method

Characterizing the biomechanical behavior of sutures in the human craniofacial skeleton (CFS) is essential to understand the global impact of these articulations on load transmission, but is challenging due to the complexity of their interdigitated morphology, the multidirectional loading they are exposed to and the lack of well-defined suture material properties. This study aimed to quantify the impact of morphological features, direction of loading and suture material properties on the mechanical behavior of sutures and surrounding bone in the CFS. Thirty-six idealized finite element (FE) models were developed. One additional specimen-specific FE model was developed based on the morphology obtained from a µCT scan to represent the morphological complexity inherent in CFS sutures. Outcome variables of strain energy (SE) and von Mises stress (σ_vm) were evaluated to characterize the sutures’ biomechanical behavior. Loading direction was found to impact the relationship between SE and interdigitation index and yielded varied patterns of σ_vm in both the suture and surrounding bone. Adding bone connectivity reduced suture strain energy and altered the σ_vm distribution. Incorporating transversely isotropic material properties was found to reduce SE, but had little impact on stress patterns. High-resolution µCT scanning of the suture revealed a complex morphology with areas of high and low interdigitations. The specimen specific suture model results were reflective of SE absorption and σ_vm distribution patterns consistent with the simplified FE results. Suture mechanical behavior is impacted by morphologic factors (interdigitation and connectivity), which may be optimized for regional loading within the CFS.     

A real time finite element based tissue simulation method incorporating nonlinear elastic behavior

This paper presents a new finite element simulation approach for surgical simulators. Based on the solution of the algebraic equations derived from a nonlinear elastic model, we propose a real time simulation rule based on the implicit relation between the displacements of contacted and free nodes. This rule is an analytic expression in the linear case, and an approximation of the implicit relation in the non-linear case. We also remove some of the restrictions on flexibility exhibited by previous linear and nonlinear approaches. In the linear case, real time reconfiguration of the contacted nodes and the boundary constraints is realized using the simulation rule, while in the nonlinear case, a similar result is obtained by employing affine mapping. These methods allow nonlinear material properties to be applied to real time tissue simulation, with an efficiency comparable to that of the tensor matrix method for linear elastic models.     

A power-law rheology-based finite element model for single cell deformation

Physical forces can elicit complex time- and space-dependent deformations in living cells. These deformations at the subcellular level are difficult to measure but can be estimated using computational approaches such as finite element (FE) simulation. Existing FE models predominantly treat cells as spring-dashpot viscoelastic materials, while broad experimental data are now lending support to the power-law rheology (PLR) model. Here, we developed a large deformation FE model that incorporated PLR and experimentally verified this model by performing micropipette aspiration on fibroblasts under various mechanical loadings. With a single set of rheological properties, this model recapitulated the diverse micropipette aspiration data obtained using three protocols and with a range of micropipette sizes. More intriguingly, our analysis revealed that decreased pipette size leads to increased pressure gradient, potentially explaining our previous counterintuitive finding that decreased pipette size leads to increased incidence of cell blebbing and injury. Taken together, our work leads to more accurate rheological interpretation of micropipette aspiration experiments than previous models and suggests pressure gradient as a potential determinant of cell injury.     

An inverse finite element method for determining the anisotropic properties of the cornea

An inverse finite element method was developed to determine the anisotropic properties of bovine cornea from an in vitro inflation experiment. The experiment used digital image correlation (DIC) to measure the three-dimensional surface geometry and displacement field of the cornea at multiple pressures. A finite element model of a bovine cornea was developed using the DIC measured surface geometry of the undeformed specimen. The model was applied to determine five parameters of an anisotropic hyperelastic model that minimized the error between the measured and computed surface displacement field and to investigate the sensitivity of the measured bovine inflation response to variations in the anisotropic properties of the cornea. The results of the parameter optimization revealed that the collagen structure of bovine cornea exhibited a high degree of anisotropy in the limbus region, which agreed with recent histological findings, and a transversely isotropic central region. The parameter study showed that the bovine corneal response to the inflation experiment was sensitive to the shear modulus of the matrix at pressures below the intraocular pressure, the properties of the collagen lamella at higher pressures, and the degree of anisotropy in the limbus region. It was not sensitive to a weak collagen anisotropy in the central region.     

A finite element based method to determine the properties of planar soft tissue.

A finite element based method to determine the incremental elastic material properties of planar membranes was developed and evaluated. The method is applicable to tissues that exhibit inhomogeneity, geometric and material nonlinearity, and anisotropy. Markers are placed on the tissue to form a four-node quadrilateral element. The specimen is loaded to an initial reference state, then three incremental loading sets are applied and the nodal displacements recorded. One of these loadings must include shear. These data are used to solve an over-determined system of equations for the tangent stiffness matrix. The method was first verified using analytical data. Next, data obtained from a latex rubber sheet were used to evaluate experimental procedures. Finally, experiments conducted on preconditioned rat skin revealed nonlinear orthotropic behavior. The vector norm comparing the applied and calculated nodal force vectors was used to evaluate the accuracy of the solutions.