Kumar Mithraratne

OpenCMISS: A multi-physics & multi-scale computational infrastructure for the VPH/Physiome project

The VPH/Physiome Project is developing the model encoding standards CellML (cellml.org) and FieldML (fieldml.org) as well as web-accessible model repositories based on these standards (models.physiome.org). Freely available open source computational modelling software is also being developed to solve the partial differential equations described by the models and to visualise results. The OpenCMISS code (opencmiss.org), described here, has been developed by the authors over the last six years to replace the CMISS code that has supported a number of organ system Physiome projects. OpenCMISS is designed to encompass multiple sets of physical equations and to link subcellular and tissue-level biophysical processes into organ-level processes. In the Heart Physiome project, for example, the large deformation mechanics of the myocardial wall need to be coupled to both ventricular flow and embedded coronary flow, and the reaction-diffusion equations that govern the propagation of electrical waves through myocardial tissue need to be coupled with equations that describe the ion channel currents that flow through the cardiac cell membranes. In this paper we discuss the design principles and distributed memory architecture behind the OpenCMISS code. We also discuss the design of the interfaces that link the sets of physical equations across common boundaries (such as fluid-structure coupling), or between spatial fields over the same domain (such as coupled electromechanics), and the concepts behind CellML and FieldML that are embodied in the OpenCMISS data structures. We show how all of these provide a flexible infrastructure for combining models developed across the VPH/Physiome community.

Subject-specific modelling of lower limb muscles in children with cerebral palsy

BACKGROUND Recent studies suggest that the architecture of spastic muscles in children with cerebral palsy is considerably altered; however, only little is known about the structural changes that occur other than in the gastrocnemius muscle. In the present study, Magnetic Resonance Imaging (MRI) and subject-specific modelling techniques were used to compare the lengths and volumes of six lower limb muscles between children with cerebral palsy and typically developing children. METHODS MRI scans of the lower limbs of two children with spastic hemiplegia cerebral palsy, four children with spastic diplegia cerebral palsy (mean age 9.6 years) and a group of typically developing children (mean age 10.2 years) were acquired. Subject-specific models of six lower limb muscles were developed from the MRI data using a technique called Face Fitting. Muscle volumes and muscle lengths were derived from the models and normalised to body mass and segmental lengths, respectively. FINDINGS Normalised muscle volumes in the children with cerebral palsy were smaller than in the control group with the difference being 22% in the calf muscles, 26% in the hamstrings and 22% in the quadriceps, respectively. Only the differences in the hamstrings and the quadriceps were statistically significant (P=0.036, P=0.038). Normalised muscle lengths in the children with cerebral palsy were significantly shorter (P<0.05), except for soleus and biceps femoris. No significant relationship was found between normalised lengths and volumes of any muscle in either group. INTERPRETATION The present results show that lower limb muscles in ambulatory children with cerebral palsy are significantly altered, suggesting an overall mechanical deficit due to predominant muscle atrophy. Further investigations of the underlying causes of the muscle atrophy are required to better define management and treatment strategies for children with cerebral palsy.

Mechanics of the foot Part 1: a continuum framework for evaluating soft tissue stiffening in the pathologic foot.

Soft tissue stiffening is a common mechanical observation reported in foot pathologies including diabetes mellitus and gout. These material changes influence the spatial distribution of stress and affect blood flow, which is essential to nutrient entry and waste removal. An anatomically-based subject-specific foot model was developed to explore the influence of tissue stiffening on plantar pressure and internal von Mises stress at heel-strike, midstance and toe-off. This work draws on the model database developed for the Physiome project consisting of muscles, bones, soft tissue and other structures such as sensory nerves. The anisotropic structure of soft tissue was embedded in a single continuum as an efficient model for finite soft tissue deformation, and customisation methods were used to capture the unique foot profile. The model was informed by kinetics from an instrumented treadmill and kinematics from motion capture, synchronised together. Foot sole pressure predictions were evaluated against a commercial pressure platform. Key outcomes showed that internal stress can be up to 1.6 times the surface pressure with implications for internal soft tissue damage not observed at the surface. The main nerve branch stimulated during gait was the lateral plantar nerve. This subject-specific modelling framework can play an integral part in therapeutic treatments by informing assistive strategies such as mechanical noise stimulation and orthotics.

Characterizing facial tissue sliding using ultrasonography

An integrated structure of gliding spaces and ligament attachments in the facial anatomy provides a fine balance between mobility and stability. In order to understand the sliding kinematics between facial muscular layers, an experimental program was undertaken to infer the way underlying soft tissue motion takes place in the human face in vivo. The motion data of the facial soft tissue structures were acquired using ultrasonography. An optical flow algorithm was implemented to visualize the deformation field and to segment out the region of discontinuity. Finite-element tracking meshes with cubic-Hermite bases were used to measure the displacement and strain at the discontinuous interface. To improve the convergence properties of the tracking mesh, a multi-resolution scheme was adapted. The tracking results from our method have been shown to give better correlation compared to optical flow algorithm at interface region.

Anatomically-based musculoskeletal modeling: prediction and validation of muscle deformation during walking

Accurate modeling of the musculoskeletal system during motion is a challenging task that has not yet been solved. In this paper, we outline and validate a free-form deformation method called the Host Mesh Fitting (HMF) technique for predicting muscle deformation during walking of a subject-specific musculoskeletal model. 20 lower limb muscles were deformed according to the HMF solution of a surrounding host mesh that resembled the skin boundary, resulting in a realistic walking simulation of the anatomically-based model. The shape changes of five muscles were further validated by comparing the predicted deformations with magnetic resonance image data in two lower limb positions.

Generating Facial Expressions Using an Anatomically Accurate Biomechanical Model

This paper presents a computational framework for modelling the biomechanics of human facial expressions. A detailed high-order (Cubic-Hermite) finite element model of the human head was constructed using anatomical data segmented from magnetic resonance images. The model includes a superficial soft-tissue continuum consisting of skin, the subcutaneous layer and the superficial Musculo-Aponeurotic system. Embedded within this continuum mesh, are 20 pairs of facial muscles which drive facial expressions. These muscles were treated as transversely-isotropic and their anatomical geometries and fibre orientations were accurately depicted. In order to capture the relative composition of muscles and fat, material heterogeneity was also introduced into the model. Complex contact interactions between the lips, eyelids, and between superficial soft tissue continuum and deep rigid skeletal bones were also computed. In addition, this paper investigates the impact of incorporating material heterogeneity and contact interactions, which are often neglected in similar studies. Four facial expressions were simulated using the developed model and the results were compared with surface data obtained from a 3D structured-light scanner. Predicted expressions showed good agreement with the experimental data.

Mechanics of the foot Part 2: A coupled solid-fluid model to investigate blood transport in the pathologic foot.

A coupled computational model of the foot consisting of a three-dimensional soft tissue continuum and a one-dimensional (1D) transient blood flow network is presented in this article. The primary aim of the model is to investigate the blood flow in major arteries of the pathologic foot where the soft tissue stiffening occurs. It has been reported in the literature that there could be up to about five-fold increase in the mechanical stiffness of the plantar soft tissues in pathologic (e.g. diabetic) feet compared with healthy ones. The increased stiffness results in higher tissue hydrostatic pressure within the plantar area of the foot when loaded. The hydrostatic pressure acts on the external surface of blood vessels and tend to reduce the flow cross-section area and hence the blood supply. The soft tissue continuum model of the foot was modelled as a tricubic Hermite finite element mesh representing all the muscles, skin and fat of the foot and treated as incompressible with transversely isotropic properties. The details of the mechanical model of soft tissue are presented in the companion paper, Part 1. The deformed state of the soft tissue continuum because of the applied ground reaction force at three foot positions (heel-strike, midstance and toe-off) was obtained by solving the Cauchy equations based on the theory of finite elasticity using the Galerkin finite element method. The geometry of the main arterial network in the foot was represented using a 1D Hermite cubic finite element mesh. The flow model consists of 1D Navier-Stokes equations and a nonlinear constitutive equation to describe vessel radius-transmural pressure relation. The latter was defined as the difference between the fluid and soft tissue hydrostatic pressure. Transient flow governing equations were numerically solved using the two-step Lax-Wendroff finite difference method. The geometry of both the soft tissue continuum and arterial network is anatomically-based and was developed using the data derived from visible human images and magnetic resonance images of a healthy male volunteer. Simulation results reveal that a two-fold increase in tissue stiffness leads to about 28% reduction in blood flow to the affected region.

A framework for generating anatomically detailed subject-specific human facial models for biomechanical simulations

Realistic biomechanical simulations of the human face rely on detailed and accurate anatomical models. A recent study involving ultrasound imaging revealed that tissue structures in the human face can be separated into two major strata that move independent of each other. Based on this observation, anatomically accurate finite element models representing soft tissues in both layers of the human face were developed using 3D segmented data derived from the high-resolution US Visible Human cryosection images. The three-dimensional geometry of these tissue structures was described using Cubic Hermite finite elements. The use of Hermite family elements ensures the continuity of displacement gradient across element boundaries and hence maintains the moment balance throughout the computational domain in mechanical simulations. This in turn leads to more accurate predictions of soft tissue deformations. Creating subject-specific detailed model of the face suitable for biomechanical analysis is, however, a time-consuming task. This paper proposes a fast semi-automated framework for generating detailed subject-specific facial models including internal muscles using techniques that involve landmark-based affine transformation, iterative surface-fitting and free-form deformation. Generated models for three individuals are presented to demonstrate the efficacy of the proposed methodology.

Adaptive bill morphology for enhanced tool manipulation in New Caledonian crows

Early increased sophistication of human tools is thought to be underpinned by adaptive morphology for efficient tool manipulation. Such adaptive specialisation is unknown in nonhuman primates but may have evolved in the New Caledonian crow, which has sophisticated tool manufacture. The straightness of its bill, for example, may be adaptive for enhanced visually-directed use of tools. Here, we examine in detail the shape and internal structure of the New Caledonian crow’s bill using Principal Components Analysis and Computed Tomography within a comparative framework. We found that the bill has a combination of interrelated shape and structural features unique within Corvus, and possibly birds generally. The upper mandible is relatively deep and short with a straight cutting edge, and the lower mandible is strengthened and upturned. These novel combined attributes would be functional for (i) counteracting the unique loading patterns acting on the bill when manipulating tools, (ii) a strong precision grip to hold tools securely, and (iii) enhanced visually-guided tool use. Our findings indicate that the New Caledonian crow’s innovative bill has been adapted for tool manipulation to at least some degree. Early increased sophistication of tools may require the co-evolution of morphology that provides improved manipulatory skills.

The influence and biomechanical role of cartilage split line pattern on tibiofemoral cartilage stress distribution during the stance phase of gait

This study presents an evaluation of the role that cartilage fibre ‘split line’ orientation plays in informing femoral cartilage stress patterns. A two-stage model is presented consisting of a whole knee joint coupled to a tissue-level cartilage model for computational efficiency. The whole joint model may be easily customised to any MRI or CT geometry using free-form deformation. Three ‘split line’ patterns (medial–lateral, anterior–posterior and random) were implemented in a finite element model with constitutive properties referring to this ‘split line’ orientation as a finite element fibre field. The medial–lateral orientation was similar to anatomy and was derived from imaging studies. Model predictions showed that ‘split lines’ are formed along the line of maximum principal strains and may have a biomechanical role of protecting the cartilage by limiting the cartilage deformation to the area of higher cartilage thickness.