A nonlinear viscoelastic finite element model of polyethylene

A nonlinear viscoelastic finite element model of ultra-high molecular weight polyethylene (UHMWPE) was developed in this study. Eight cylindrical specimens were machined from ram extruded UHMWPE bar stock (GUR 1020) and tested under constant compression at 7% strain for 100 sec. The stress strain data during the initial ramp up to 7% strain was utilized to model the instantaneous stress-strain response using a Mooney-Rivlin material model. The viscoelastic behavior was modeled using the time-dependent relaxation in stress seen after the initial maximum stress was achieved using a stored energy formulation. A cylindrical model of similar dimensions was created using a finite element analysis software program. The cylinder was made up of hexahedral elements, which were given the material properties utilizing the instantaneous stress-strain curve and the energy-relaxation curve obtained from the experimental data. The cylinder was compressed between two flat rigid bodies that simulated the fixtures of the testing machine. Experimental stress-relaxation, creep and dynamic testing data were then used to validate the model. The mean error for predicted versus experimental data for stress relaxation at different strain levels was 4.2%. The mean error for the creep test was 7% and for dynamic test was 5.4%. Finally, dynamic loading in a hip arthroplasty was modeled and validated experimentally with an error of 8%. This study establishes a working finite element material model of UHMWPE that can be utilized to simulate a variety of postoperative arthroplasty conditions.     

Evaluation of a fast implicit solvent model for molecular dynamics simulations.

A solvation term based on the solvent accessible surface area (SASA) is combined with the CHARMM polar hydrogen force field for the efficient simulation of peptides and small proteins in aqueous solution. Only two atomic solvation parameters are used: one is negative for favoring the direct solvation of polar groups and the other positive for taking into account the hydrophobic effect on apolar groups. To approximate the water screening effects on the intrasolute electrostatic interactions, a distance-dependent dielectric function is used and ionic side chains are neutralized. The use of an analytical approximation of the SASA renders the model extremely efficient (i.e., only about 50% slower than in vacuo simulations). The limitations and range of applicability of the SASA model are assessed by simulations of proteins and structured peptides. For the latter, the present study and results reported elsewhere show that with the SASA model it is possible to sample a significant amount of folding/unfolding transitions, which permit the study of the thermodynamics and kinetics of folding at an atomic level of detail.     

Modified Bilston nonlinear viscoelastic model for finite element head injury studies

This paper proposes a modified nonlinear viscoelastic Bilston model (Bilston et al., 2001, Biorheol., 38, pp. 335-345). for the modeling of brain tissue constitutive properties. The modified model can be readily implemented in a commercial explicit finite element (FE) code, PamCrash. Critical parameters of the model have been determined through a series of rheological tests on porcine brain tissue samples and the time-temperature superposition (TTS) principle has been used to extend the frequency to a high region. Simulations by using PamCrash are compared with the test results. Through the use of the TTS principle, the mechanical and rheological behavior at high frequencies up to 10(4) rads may be obtained. This is important because the properties of the brain tissue at high frequencies and impact rates are especially relevant to studies of traumatic head injury. The averaged dynamic modulus ranges from 130 Pa to 1500 Pa and loss modulus ranges from 35 Pa to 800 Pa in the frequency regime studied (0.01 rads to 3700 rads). The errors between theoretical predictions and averaged relaxation test results are within 20% for strains up to 20%. The FEM simulation results are in good agreement with experimental results. The proposed model will be especially useful for application to FE analysis of the head under impact loads. More realistic analysis of head injury can be carried out by incorporating the nonlinear viscoelastic constitutive law for brain tissue into a commercial FE code.     

A new implicit solvent model for protein-ligand docking

Peroxisomes are small subcellular compartments responsible for a range of essential metabolic processes. Efforts in predicting peroxisomal protein import are challenged by species variation and sparse sequence data sets with experimentally confirmed localization. We present a predictor of peroxisomal import based on the presence of the dominant peroxisomal targeting signal one (PTS1), a seemingly wellconserved but highly unspecific motif. The signal appears to rely on subtle dependencies with the preceding residues. We evaluate prediction accuracies against two alternative predictor services, PEROXIP and the PTS1 PREDICTOR. We test the integrity of prediction on a range of prokaryotic and eukaryotic proteomes lacking peroxisomes. Similarly we test the accuracy on peroxisomal proteins known to not overlap with training data. The model identified a number of proteins within the RIKEN IPS7 mouse protein dataset as potentially novel peroxisomal proteins. Three were confirmed in vitro using immunofluorescent detection of myc-epitope-tagged proteins in transiently transfected BHK-21 cells (Dhrs2, Serhl, and Ehhadh). The final model has a superior specificity to both alternatives, and an accuracy better than PEROXIP and on par with PTS1 PREDICTOR. Thus, the model we present should prove invaluable for labeling PTS1 targeted proteins with high confidence. We use the predictor to screen several additional eukaryotic genomes to revise previously estimated numbers of peroxisomal proteins. Available at http://pprowler.itee.uq.edu.au.     

A chimaeric animal model for confined placental mosaicism

The reason for chromosome mosaicism being sometimes confined to only part of the conceptus is unknown. To address this problem, we produced tetraploid diploid chimaeric mouse conceptuses. At 12 1/2 days, no tetraploid cells were detected in the fetus. They rarely contributed to other derivatives of the primitive ectoderm lineage but were commonly found in the primitive endoderm and trophectoderm lineages. This provides a useful animal model of human confined placental mosaicism and suggests that the primitive endoderm (hypoblast) lineage should be included in future studies of human mosaic conceptuses.     

A transversely isotropic viscoelastic constitutive equation for brainstem undergoing finite deformation

The objective of this study was to define the constitutive response of brainstem undergoing finite shear deformation. Brainstem was characterized as a transversely isotropic viscoelastic material and the material model was formulated for numerical implementation. Model parameters were fit to shear data obtained in porcine brainstem specimens undergoing finite shear deformation in three directions: parallel, perpendicular, and cross sectional to axonal fiber orientation and determined using a combined approach of finite element analysis (FEA) and a genetic algorithm (GA) optimizing method. The average initial shear modulus of brainstem matrix of 4-week old pigs was 12.7 Pa, and therefore the brainstem offers little resistance to large shear deformations in the parallel or perpendicular directions, due to the dominant contribution of the matrix in these directions. The fiber reinforcement stiffness was 121.2 Pa, indicating that brainstem is anisotropic and that axonal fibers have an important role in the cross-sectional direction. The first two leading relative shear relaxation moduli were 0.8973 and 0.0741, respectively, with corresponding characteristic times of 0.0047 and 1.4538 s, respectively, implying rapid relaxation of shear stresses. The developed material model and parameter estimation technique are likely to find broad applications in neural and orthopaedic tissues.     

A second-order high resolution finite difference scheme for a structured erythropoiesis model subject to malaria infection

We develop a second-order high-resolution finite difference scheme to approximate the solution of a mathematical model describing the within-host dynamics of malaria infection. The model consists of two nonlinear partial differential equations coupled with three nonlinear ordinary differential equations. Convergence of the numerical method to the unique weak solution with bounded total variation is proved. Numerical simulations demonstrating the achievement of the designed accuracy 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.     

Stability of an ion channel in lipid bilayers: implicit solvent model calculations with gramicidin

Gramicidin is a helical peptide, 15 residues in length, which dimerizes to form ion-conducting channels in lipid bilayers. Here we report calculations of its free energy of transfer from the aqueous phase into bilayers of different widths. The electrostatic and nonpolar contributions to the desolvation free energy were calculated using implicit solvent models, in which gramicidin was described in atomic detail and the hydrocarbon region of the membrane was described as a slab of hydrophobic medium embedded in water. The free energy penalties from the lipid perturbation and membrane deformation effects, and the entropy loss associated with gramicidin immobilization in the bilayer, were estimated from a statistical thermodynamic model of the bilayer. The calculations were carried out using two classes of experimentally observed conformations: a head-to-head dimer of two single-stranded (SS) beta-helices and a double-stranded (DS) intertwined double helix. The calculations showed that gramicidin is likely to partition into the bilayer in all of these conformations. However, the SS conformation was found to be significantly more stable than the DS in the bilayer, in agreement with most of the experimental data. We tested numerous transmembrane and surface orientations of gramicidin in bilayers of various widths. Our calculations indicate that the most favorable orientation is transmembrane, which is indeed to be expected from a channel-forming peptide. The calculations demonstrate that gramicidin insertion into the membrane is likely to involve a significant deformation of the bilayer to match the hydrophobic width of the peptide (22 A), again in good agreement with experimental data. Interestingly, deformation of the bilayer was induced by all of the gramicidin conformations.     

A finite difference model of O2 transport in aortic valve cusps: importance of intrinsic microcirculation

Recent studies have reported the presence of a microcirculation within the tissue of aortic valves. To test the hypothesis that this vascular bed is needed to satisfy the oxygen demands of the cusp tissue, a two-dimensional (2D) finite difference model of oxygen diffusion was developed. The in vivo environment was modeled for vascular and avascular cusps using thickness data from precise radiographic measurements of fresh porcine valves, and O2 diffusivity (DO2) and O2 consumption (VO2) values from experimental data. The location and density of the cusp vasculature were determined by the model to prevent oxygen levels from falling to zero. Validation of the model was performed by simulation of the experimental measurements of cusp DO2 and VO2. For a test cusp with uniform thickness, the model returned simulated DO2 and VO2 measurements within 1.43% and 0.18% difference of the true parameter values, respectively. For native cusps, the simulated DO2 measurements were sensitive to thickness variations (-38 to +21% difference), whereas the VO2 measurements were minimally affected (8% difference). An improved DO2 measurement technique was found to reduce these errors to <5% and is recommended for analysis of experimental data. In the avascular case, the model predicted large regions of hypoxic tissue, whereas in the vascular case, the model predicted vessel locations and densities similar to what was experimentally observed in porcine cusps. Overall, the in vivo model developed in this study confirmed the need for an intrinsic microcirculation in the thicker basal regions of aortic cusps.     

A rivet model for channel formation by aerolysin-like pore-forming toxins

The bacterial toxin aerolysin kills cells by forming heptameric channels, of unknown structure, in the plasma membrane. Using disulfide trapping and cysteine scanning mutagenesis coupled to thiol-specific labeling on lipid bilayers, we identify a loop that lines the channel. This loop has an alternating pattern of charged and uncharged residues, suggesting that the transmembrane region has a beta-barrel configuration, as observed for Staphylococcal alpha-toxin. Surprisingly, we found that the turn of the beta-hairpin is composed of a stretch of five hydrophobic residues. We show that this hydrophobic turn drives membrane insertion of the developing channel and propose that, once the lipid bilayer has been crossed, it folds back parallel to the plane of the membrane in a rivet-like fashion. This rivet-like conformation was modeled and sequence alignments suggest that such channel riveting may operate for many other pore-forming toxins.     

Developing initial conditions for simulations of asymmetric membranes: a practical recommendation

It has been proposed that the surface tension difference between leaflets (or differential stress) in asymmetric bilayers is generally nonvanishing. This implies that there is no unique approach to generate initial conditions for simulations of asymmetric bilayers in the absence of experimentally derived constraints. Current generation methods include individual area per lipid (APL) based, leaflet surface area (SA) matching, and zero leaflet tension based (0-DS). This work adds a bilayer-based approach that aims for achieving partial chemical equilibrium by interleaflet switching of selected lipids via P2₁ periodic boundary conditions. Based on a recently proposed theoretical framework, we obtained expressions for tensions in asymmetric bilayers from both the bending and area strains. We also developed a quantitative measure for the energetic penalty from the differential stress. The impacts of APL-, SA-, and 0-DS-based approaches on mechanical properties are assessed for two different asymmetric bilayers. The lateral pressure profile and its moments differ significantly for each method, whereas the area compressibility modulus is relatively insensitive. Application of P2₁ periodic boundary conditions (APL/P2₁, SA/P2₁, and 0-DS/P2₁) results in better agreement in mechanical properties between asymmetric bilayers generated by APL-, SA-, and 0-DS-based approaches, in which changes are the smallest for bilayers from the SA-based method. The estimated differential stress from the theory shows good agreement with that from the simulations. These simulation results and the good agreement between the predicted and observed differential stress further support the theoretical framework in which bilayer mechanical properties are outcomes of the interplay between intrinsic bending and asymmetric lipid packing. Based on the simulation results and theoretical predictions, the SA/P2₁-based, or at least the SA-based (when the differential stress is small), approach is recommended as a practical method for developing initial conditions for asymmetric bilayer simulations.     

A correct formulation for a spatially implicit predator-prey metacommunity model

In order to mitigate the problem of increasing model complexity with increasing number of occupation states in spatially implicit metacommunity models, the assumption of independency among species distributions is often required. In the present paper, we show that this approach only works correctly if set relations among patch occupancy states are considered adequately. This is illustrated by means of a well-known, although incorrectly formulated, predator-prey metacommunity model devised by Bascompte and Solé [1]. We demonstrate that this model shows anomalous dynamical behavior caused by inconsistence between the model formulation and its assumptions. In order to formalize our finding we develop a corrected model formulation that accounts for the principles of set theory so that the sum of the system compartments change rate is nulled. Applying this method successfully rules out the occurrence of anomalous dynamical behavior found in the original model. Finally we discuss the implications of our findings for the accuracy of model predictions.     

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.     

The finite cell method for bone simulations: verification and validation

Standard methods for predicting bone’s mechanical response from quantitative computer tomography (qCT) scans are mainly based on classical h-version finite element methods (FEMs). Due to the low-order polynomial approximation, the need for segmentation and the simplified approach to assign a constant material property to each element in h-FE models, these often compromise the accuracy and efficiency of h-FE solutions. Herein, a non-standard method, the finite cell method (FCM), is proposed for predicting the mechanical response of the human femur. The FCM is free of the above limitations associated with h-FEMs and is orders of magnitude more efficient, allowing its use in the setting of computational steering. This non-standard method applies a fictitious domain approach to simplify the modeling of a complex bone geometry obtained directly from a qCT scan and takes into consideration easily the heterogeneous material distribution of the various bone regions of the femur. The fundamental principles and properties of the FCM are briefly described in relation to bone analysis, providing a theoretical basis for the comparison with the p-FEM as a reference analysis and simulation method of high quality. Both p-FEM and FCM results are validated by comparison with an in vitro experiment on a fresh-frozen femur.     

A constituent-based model for the nonlinear viscoelastic behavior of ligaments

This paper presents a constitutive model for predicting the nonlinear viscoelastic behavior of soft biological tissues and in particular of ligaments. The constitutive law is a generalization of the well-known quasi-linear viscoelastic theory (QLV) in which the elastic response of the tissue and the time-dependent properties are independently modeled and combined into a convolution time integral. The elastic behavior, based on the definition of anisotropic strain energy function, is extended to the time-dependent regime by means of a suitably developed time discretization scheme. The time-dependent constitutive law is based on the postulate that a constituent-based relaxation behavior may be defined through two different stress relaxation functions: one for the isotropic matrix and one for the reinforcing (collagen) fibers. The constitutive parameters of the viscoelastic model have been estimated by curve fitting the stress relaxation experiments conducted on medial collateral ligaments (MCLs) taken from the literature, whereas the predictive capability of the model was assessed by simulating experimental tests different from those used for the parameter estimation. In particular, creep tests at different maximum stresses have been successfully simulated. The proposed nonlinear viscoelastic model is able to predict the time-dependent response of ligaments described in experimental works (Bonifasi-Lista et al., 2005, J. Orthopaed. Res., 23, pp. 67-76; Hingorani et al., 2004, Ann. Biomed. Eng., 32, pp. 306-312; Provenzano et al., 2001, Ann. Biomed. Eng., 29, pp. 908-214; Weiss et al., 2002, J. Biomech., 35, pp. 943-950). In particular, the nonlinear viscoelastic response which implies different relaxation rates for different applied strains, as well as different creep rates for different applied stresses and direction-dependent relaxation behavior, can be described.     

A thick walled viscoelastic model for the mechanics of arteries

A knowledge of the mechanics of arteries is of importance in the determination of vessel rheological properties and in the studies of blood flow and certain arterial diseases. Most existing arterial models treat only wave motions; however, other types of motion, in particular those associated with flow development and other end effects, occur in the vascular system. Thus, a model is needed which can be applied to a variety of possible types of motion.

An arterial model is described which includes the effects of thick walls, linear viscoelasticity, and wall tethering. The forms of the displacements and stresses are found independently of the exact form of the applied fluid stresses; thus, the results are applicable to a range of possible dynamical conditions. Displacements and stress states can then be found from experimental or theoretical knowledge of the blood pressure and flow. The results are applied to flow development and wave propagation regions in the arteries.