Finite element implementation of a new model of slight compressibility for transversely isotropic materials

Modelling transversely isotropic materials in finite strain problems is a complex task in biomechanics, and is usually addressed by using finite element (FE) simulations. The standard method developed to account for the quasi-incompressible nature of soft tissues is to decompose the strain energy function (SEF) into volumetric and deviatoric parts. However, this decomposition is only valid for fully incompressible materials, and its use for slightly compressible materials yields an unphysical response during the simulation of hydrostatic tension/compression of a transversely isotropic material. This paper presents the FE implementation as subroutines of a new volumetric model solving this deficiency in two FE codes: Abaqus and FEBio. This model also has the specificity of restoring the compatibility with small strain theory. The stress and elasticity tensors are first derived for a general SEF. This is followed by a successful convergence check using a particular SEF and a suite of single-element tests showing that this new model does not only correct the hydrostatic deficiency but may also affect stresses during shear tests (Poynting effect) and lateral stretches during uniaxial tests (Poisson's effect). These FE subroutines have numerous applications including the modelling of tendons, ligaments, heart tissue, etc. The biomechanics community should be aware of specificities of the standard model, and the new model should be used when accurate FE results are desired in the case of compressible materials.     

Verification, validation and sensitivity studies in computational biomechanics

Computational techniques and software for the analysis of problems in mechanics have naturally moved from their origins in the traditional engineering disciplines to the study of cell, tissue and organ biomechanics. Increasingly complex models have been developed to describe and predict the mechanical behavior of such biological systems. While the availability of advanced computational tools has led to exciting research advances in the field, the utility of these models is often the subject of criticism due to inadequate model verification and validation (V&V). The objective of this review is to present the concepts of verification, validation and sensitivity studies with regard to the construction, analysis and interpretation of models in computational biomechanics. Specific examples from the field are discussed. It is hoped that this review will serve as a guide to the use of V&V principles in the field of computational biomechanics, thereby improving the peer acceptance of studies that use computational modeling techniques.     

Finite element implementation of a generalized Fung-elastic constitutive model for planar soft tissues

Numerical simulations of the anisotropic mechanical properties of soft tissues and tissue-derived biomaterials using accurate constitutive models remain an important and challenging research area in biomechanics. While most constitutive modeling efforts have focused on the characterization of experimental data, only limited studies are available on the feasibility of utilizing those models in complex computational applications. An example is the widely utilized exponential constitutive model proposed by Fung. Although present in the biomechanics literature for several decades, implementation of this model into finite element (FE) simulations has been limited. A major reason for limited numerical implementations are problems associated with inherent numerical instability and convergence. To address this issue, we developed and applied two restrictions for a generalized Fung-elastic constitutive model necessary to achieve numerical stability. These are (1) convexity of the strain energy function, and (2) the condition number of material stiffness matrix set lower than a prescribed value. These constraints were implemented in the nonlinear regression used for constitutive model parameter estimation to the experimental biaxial mechanical data. We then implemented the generalized Fung-elastic model into a commercial FE code (ABAQUS, Pawtucket, RI, USA). Single element and multi-element planar biaxial test simulations were conducted to verify the accuracy and robustness of the implementation. Results indicated that numerical convergence and accurate FE implementation were consistently obtained. The present study thus presents an integrated framework for accurate and robust implementation of pseudo-elastic constitutive models for planar soft tissues. Moreover, since our approach is formulated within a general FE code, it can be straightforwardly adopted across multiple software platforms.     

Growing multiblock structures: a semi-automated approach to block placement for multiblock hexahedral meshing

Finite element (FE) analysis is a cornerstone of orthopaedic biomechanics research. Three-dimensional medical imaging provides sufficient resolution for the subject-specific FE models to be generated from these data-sets. FE model development requires discretisation of a three-dimensional domain, which can be the most time-consuming component of a FE study. Hexahedral meshing tools based on the multiblock method currently rely on the manual placement of building blocks for mesh generation. We hypothesise that angular analysis of the geometric centreline for a three-dimensional surface could be used to automatically generate building block structures for the multiblock hexahedral mesh generation. Our algorithm uses a set of user-defined points and parameters to automatically generate a multiblock structure based on a surface's geometric centreline. This significantly reduces the time required for model development. We have applied this algorithm to 47 bones of varying geometries and successfully generated a FE mesh in all cases. This work represents significant advancement in automatically generating multiblock structures for a wide range of geometries.     

Statistical methods in finite element analysis

Finite element analysis (FEA) is a commonly used tool within many areas of engineering and can provide useful information in structural analysis of mechanical systems. However, most analyses within the field of biomechanics usually take no account either of the wide variation in material properties and geometry that may occur in natural tissues or manufacturing imperfections in synthetic materials. This paper discusses two different methods of incorporating uncertainty in FE models. The first, Taguchi's robust parameter design, uses orthogonal matrices to determine how to vary the parameters in a series of FE models, and provides information on the sensitivity of a model to input parameters. The second, probabilistic analysis, enables the distribution of a response variable to be determined from the distributions of the input variables. The methods are demonstrated using a simple example of an FE model of a beam that is assigned material properties and geometry over a range similar to an orthopaedic fixation plate. In addition to showing how each method may be used on its own, we also show how computational effort may be minimised by first identifying the most important input variables before determining the effects of imprecision.     

Growing multiblock structures: a semi-automated approach to block placement for multiblock hexahedral meshing

Finite element (FE) analysis is a cornerstone of orthopaedic biomechanics research. Three-dimensional medical imaging provides sufficient resolution for the subject-specific FE models to be generated from these data-sets. FE model development requires discretisation of a three-dimensional domain, which can be the most time-consuming component of a FE study. Hexahedral meshing tools based on the multiblock method currently rely on the manual placement of building blocks for mesh generation. We hypothesise that angular analysis of the geometric centreline for a three-dimensional surface could be used to automatically generate building block structures for the multiblock hexahedral mesh generation. Our algorithm uses a set of user-defined points and parameters to automatically generate a multiblock structure based on a surface's geometric centreline. This significantly reduces the time required for model development. We have applied this algorithm to 47 bones of varying geometries and successfully generated a FE mesh in all cases. This work represents significant advancement in automatically generating multiblock structures for a wide range of geometries.     

Lumbar spine finite element model for healthy subjects: development and validation

Finite element (FE) method is a proven powerful and efficient tool to study the biomechanics of the human lumbar spine. However, due to the large inter-subject variability of geometries and material properties in human lumbar spines, concerns existed on the accuracy and predictive power of one single deterministic FE model with one set of spinal geometry and material properties. It was confirmed that the combined predictions (median or mean value) of several distinct FE models can be used as an improved prediction of behavior of human lumbar spine under identical loading and boundary conditions. In light of this improved prediction, five FE models (L1-L5 spinal levels) of the human lumbar spine were developed based on five healthy living subjects with identical modeling method. The five models were extensively validated through experimental and computational results in the literature. Mesh convergence and material sensitivity analysis were also conducted. We have shown that the results from the five FE models developed in this paper were consistent with the experimental data and simulation results from the existing literature. The validated modeling method introduced in this study can be used in modeling dysfunctional lumber spines such as disc degeneration and scoliosis in future work.     

Finite element modelling approaches for well-ordered porous metallic materials for orthopaedic applications: cost effectiveness and geometrical considerations

The mechanical properties of well-ordered porous materials are related to their geometrical parameters at the mesoscale. Finite element (FE) analysis is a powerful tool to design well-ordered porous materials by analysing the mechanical behaviour. However, FE models are often computationally expensive. This article aims to develop a cost-effective FE model to simulate well-ordered porous metallic materials for orthopaedic applications. Solid and beam FE modelling approaches are compared, using finite size and infinite media models considering cubic unit cell geometry. The model is then applied to compare two unit cell geometries: cubic and diamond. Models having finite size provide similar results than the infinite media model approach for large sample sizes. In addition, these finite size models also capture the influence of the boundary conditions on the mechanical response for small sample sizes. The beam FE modelling approach showed little computational cost and similar results to the solid FE modelling approach. Diamond unit cell geometry appeared to be more suitable for orthopaedic applications than the cubic unit cell geometry.     

Dynamic Modelling of Tooth Deformation Using Occlusal Kinematics and Finite Element Analysis

Background

Dental biomechanics based on finite element (FE) analysis is attracting enormous interest in dentistry, biology, anthropology and palaeontology. Nonetheless, several shortcomings in FE modeling exist, mainly due to unrealistic loading conditions. In this contribution we used kinematics information recorded in a virtual environment derived from occlusal contact detection between high resolution models of an upper and lower human first molar pair (M¹ and M₁, respectively) to run a non-linear dynamic FE crash colliding test.

Methodology

MicroCT image data of a modern human skull were segmented to reconstruct digital models of the antagonistic right M¹ and M₁ and the dental supporting structures. We used the Occlusal Fingerprint Analyser software to reconstruct the individual occlusal pathway trajectory during the power stroke of the chewing cycle, which was applied in a FE simulation to guide the M₁ 3D-path for the crash colliding test.

Results

FE analysis results showed that the stress pattern changes considerably during the power stroke, demonstrating that knowledge about chewing kinematics in conjunction with a morphologically detailed FE model is crucial for understanding tooth form and function under physiological conditions.

Conclusions/Significance

Results from such advanced dynamic approaches will be applicable to evaluate and avoid mechanical failure in prosthodontics/endodontic treatments, and to test material behavior for modern tooth restoration in dentistry. This approach will also allow us to improve our knowledge in chewing-related biomechanics for functional diagnosis and therapy, and it will help paleoanthropologists to illuminate dental adaptive processes and morphological modifications in human evolution.     

FEBio finite element models of the human lumbar spine

Finite element analysis has proven to be a viable method for assessing many structure-function relationships in the human lumbar spine. Several validated models of the spine have been published, but they typically rely on commercial packages and are difficult to share between labs. The goal of this study is to present the development of the first open-access models of the human lumbar spine in FEBio. This modeling framework currently targets three deficient areas in the field of lumbar spine modeling: 1) open-access models, 2) accessibility for multiple meshing schemes, and 3) options to include advanced hyperelastic and biphasic constitutive models.     

Subject-specific finite element model of the pelvis: development, validation and sensitivity studies

A better understanding of the three-dimensional mechanics of the pelvis, at the patient-specific level, may lead to improved treatment modalities. Although finite element (FE) models of the pelvis have been developed, validation by direct comparison with subject-specific strains has not been performed, and previous models used simplifying assumptions regarding geometry and material properties. The objectives of this study were to develop and validate a realistic FE model of the pelvis using subject-specific estimates of bone geometry, location-dependent cortical thickness and trabecular bone elastic modulus, and to assess the sensitivity of FE strain predictions to assumptions regarding cortical bone thickness as well as bone and cartilage material properties. A FE model of a cadaveric pelvis was created using subject-specific computed tomography image data. Acetabular loading was applied to the same pelvis using a prosthetic femoral stem in a fashion that could be easily duplicated in the computational model. Cortical bone strains were monitored with rosette strain gauges in ten locations on the left hemipelvis. FE strain predictions were compared directly with experimental results for validation. Overall, baseline FE predictions were strongly correlated with experimental results (r2=0.824), with a best-fit line that was not statistically different than the line y=x (experimental strains = FE predicted strains). Changes to cortical bone thickness and elastic modulus had the largest effect on cortical bone strains. The FE model was less sensitive to changes in all other parameters. The methods developed and validated in this study will be useful for creating and analyzing patient-specific FE models to better understand the biomechanics of the pelvis.     

DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results

Background  

Systems biology research and applications require creation, validation, extensive usage of mathematical models and visualization of simulation results by end-users. Our goal is to develop novel method for visualization of simulation results and implement it in simulation software package equipped with the sophisticated mathematical and computational techniques for model development, verification and parameter fitting.     

An In Vivo Experimental Validation of a Computational Model of Human Foot

Reliable computational foot models offer an alternative means to enhance knowledge on the biomechanics of human foot.Model validation is one of the most critical aspects of the entire foot modeling and analysis process.This paper presents an invivo experiment combining motion capture system and plantar pressure measure platform to validate a three-dimensional finiteelement model of human foot.The Magnetic Resonance Imaging(MRI)slices for the foot modeling and the experimental datafor validation were both collected from the same volunteer subject.The validated components included the comparison of staticmodel predictions of plantar force,plantar pressure and foot surface deformation during six loading conditions,to equivalentmeasured data.During the whole experiment,foot surface deformation,plantar force and plantar pressure were recorded simultaneouslyduring six different loaded standing conditions.The predictions of the current FE model were in good agreementwith these experimental results.     

A phase-contrast microscopy-based method for modeling the mechanical behavior of mesenchymal stem cells

We present three-dimensional (3D) finite element (FE) models of single, mesenchymal stem cells (MSCs), generated from images obtained by optical phase-contrast microscopy and used to quantify the structural responses of the studied cells to externally applied mechanical loads. Mechanical loading has been shown to affect cell morphology and structure, phenotype, motility and other biological functions. Cells experience mechanical loads naturally, yet under prolonged or sizable loading, damage and cell death may occur, which motivates research regarding the structural behavior of loaded cells. For example, near the weight-bearing boney prominences of the buttocks of immobile persons, tissues may become highly loaded, eventually leading to massive cell death that manifests as pressure ulcers. Cell-specific computational models have previously been developed by our group, allowing simulations of cell deformations under compressive or stretching loads. These models were obtained by reconstructing specific cell structures from series of 2D fluorescence, confocal image-slices, requiring cell-specific fluorescent-staining protocols and costly (confocal) microscopy equipment. Alternative modeling approaches represent cells simply as half-spheres or half-ellipsoids (i.e. idealized geometries), which neglects the curvature details of the cell surfaces associated with changes in concentrations of strains and stresses. Thus, we introduce here for the first time an optical image-based FE modeling, where loads are simulated on reconstructed 3D geometrical cell models from a single 2D, phase-contrast image. Our novel modeling method eliminates the need for confocal imaging and fluorescent staining preparations (both expensive), and makes cell-specific FE modeling affordable and accessible to the biomechanics community. We demonstrate the utility of this cost-effective modeling method by performing simulations of compression of MSCs embedded in a gel.     

计算系统生物学:理论、方法及在药物研发中的应用

计算系统生物学是一个多学科交叉的新兴领域,旨在通过整合海量数据建立其生物系统相互作用的复杂网络。数据的整合和模型的建立需要发展合适的数学方法和软件工具,这也是计算系统生物学的主要任务。生物系统模型有助于从整体上理解生物体的内在功能和特性。同时,生物网络模型在药物研发中的应用也越来越受到制药企业以及新药研发机构的重视,如用于特异性药物作用靶点的预测和药物毒性评估等。该文简要介绍计算系统生物学的常见网络和计算模型,以及建立模型所用的研究方法,并阐述其在建模和分析中的作用及面临的问题和挑战。     

TOM software toolbox: acquisition and analysis for electron tomography

Automated data acquisition procedures have changed the perspectives of electron tomography (ET) in a profound manner. Elaborate data acquisition schemes with autotuning functions minimize exposure of the specimen to the electron beam and sophisticated image analysis routines retrieve a maximum of information from noisy data sets. "TOM software toolbox" integrates established algorithms and new concepts tailored to the special needs of low dose ET. It provides a user-friendly unified platform for all processing steps: acquisition, alignment, reconstruction, and analysis. Designed as a collection of computational procedures it is a complete software solution within a highly flexible framework. TOM represents a new way of working with the electron microscope and can serve as the basis for future high-throughput applications.     

Finite element simulation of the behavior of the periodontal ligament: A validated nonlinear contact model

Due to its significance in tooth movement, the stress/deformation field of periodontium and the alveolar bone remodeling process, periodontal ligament (PDL) cannot be excluded from the studies investigating dental biomechanics regarding its excessive deformability. Therefore, many analytical and numerical researches are carried out to simulate its response and to create a constitutive model via experiments intending to discover the material properties of PDL. The aim of this study is to formulate a user specified contact model that can be used in conjunction with finite element (FE) software and reflects PDL’s influence on neighboring structures based on the currently available information, without requiring an actual volumetric finite element mesh of ligament. The results show good agreement with available experimental tooth mobility data. Smooth stress fields are obtained on the tooth root and alveolar bone, which is a significant aspect in bone-remodeling studies. The advantage of simulating PDL as a contact model at the interface of tooth root and the alveolar process instead of a solid-meshed FE model with poor geometric morphology and/or very dense mesh is expected to save pre/post-processing workforce, to increase the accuracy and to contribute to the smoothness of interface stress distributions.     

Estimation of in vivo inter-vertebral loading during motion using fluoroscopic and magnetic resonance image informed finite element models

Finite element (FE) models driven by medical image data can be used to estimate subject-specific spinal biomechanics. This study aimed to combine magnetic resonance (MR) imaging and quantitative fluoroscopy (QF) in subject-specific FE models of upright standing, flexion and extension. Supine MR images of the lumbar spine were acquired from healthy participants using a 0.5 T MR scanner. Nine 3D quasi-static linear FE models of L3 to L5 were created with an elastic nucleus and orthotropic annulus. QF data was acquired from the same participants who performed trunk flexion to 60° and trunk extension to 20°. The displacements and rotations of the vertebrae were calculated and applied to the FE model. Stresses were averaged across the nucleus region and transformed to the disc co-ordinate system (S1 = mediolateral, S2 = anteroposterior, S3 = axial). In upright standing S3 was predicted to be −0.7 ± 0.6 MPa (L3L4) and −0.6 ± 0.5 MPa (L4L5). S3 increased to −2.0 ± 1.3 MPa (L3L4) and −1.2 ± 0.6 MPa (L4L5) in full flexion and to −1.1 ± 0.8 MPa (L3L4) and −0.7 ± 0.5 MPa (L4L5) in full extension. S1 and S2 followed similar patterns; shear was small apart from S23. Disc stresses correlated to disc orientation and wedging. The results demonstrate that MR and QF data can be combined in a participant-specific FE model to investigate spinal biomechanics in vivo and that predicted stresses are within ranges reported in the literature.