154 results for The University of Auckland Library, Hunter, Peter

  • Using CellML in Computational Models of Multiscale Physiology

    Nickerson, David; Hunter, Peter (2005)

    Conference paper
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. A computational modeling framework is presented which enables the integration of multiple physics and spatial scales in models of physiological systems. A novel aspect of the framework is the use of CellML to specify all model and simulation specific mathematical equations including cellular models and material constitutive relationships. Models of cardiac electromechanics at cellular, tissue, and organ spatial scales are used to illustrate the developed and implemented framework and other applications are discussed.

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  • Internet Applications for Computational Biology, the CMISS Web Browser Extension and and Use in Education

    Stevens, Carey; Blackett, Shane; LeGrice, Ian; Hunter, Peter (2005)

    Conference paper
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. The internet is becoming increasingly accessable and new technologies are enabling the delivery of more features to end users. It is therefore increasingly compelling to develop technology to facilitate the delivery of educational content and computational tools via the internet. Here we report on the internet enabling of the CMISS package as a web browser extension, and its use in a custom online teaching application for medical students.

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  • High Resolution 3D Imaging of Lung Tissue using Structured Light Microscopy

    Kvistedal, Yme; Tawhai, Merryn; Hunter, Peter; Nielsen, Poul (2005)

    Conference paper
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. A 3D reconstruction microscope has been built in order to investigate the structural details of the airway tree and the vasculature of mouse lungs. The objective is to create an anatomically correct finite element model of a mouse lung in order to validate results from simulations obtained using an existing model of the human lung. The 3D reconstruction microscope consists of a fully automated scanning stage, a vibratome and a structured light optical microscope. Structured light microscopy is a new approach to optical sectioning of tissue and offers several advantages over confocal microscopy.

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  • Evaluation of the effect of postural and gravitational variations on the distribution of pulmonary blood flow via an image-based computational model

    Burrowes, Kelly; Hunter, Peter; Tawhai, Merryn (2005)

    Conference paper
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. We have developed an image-based computational model of blood flow within the human pulmonary circulation in order to investigate the distribution of flow under various conditions of posture and gravity. Geometric models of the lobar surfaces and largest arterial and venous vessels were derived from multi-detector row x-ray computed tomography. The remaining blood vessels were generated using a volume-filling branching algorithm. Equations representing conservation of mass and momentum are solved within the vascular geometry to calculate pressure, radius, and velocity distributions. Flow solutions are obtained within the model in the upright, inverted, prone, and supine postures and in the upright posture with and without gravity. Additional equations representing large deformation mechanics are used to calculate the change in lung geometry and pressure distributions within the lung in the various postures - creating a coupled, co-dependent model of mechanics and flow. The embedded vascular meshes deform in accordance with the lung geometry. Results illustrate a persistent flow gradient from the top to the bottom of the lung even in the absence of gravity and in all postures, indicating that vascular branching structure is largely responsible for the distribution of flow.

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  • Insight from modelling can address controversial observations

    Ramsey, Glenn; Hunter, Peter; Nash, Martyn (2012-07)

    Journal article
    The University of Auckland Library

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  • The influence of loading conditions on equine hoof capsule deflections and stored energy assessed by finite element analysis

    Ramsey, Glenn; Hunter, Peter; Nash, Martyn (2013-07)

    Journal article
    The University of Auckland Library

    The biomechanical effects on the hoof capsule of the location of the centre of pressure of the ground reaction force may be important to understand the functioning of the hoof capsule. This study investigated the effect of changes in loading and contact friction on hoof deflections and elastic energy storage by varying the boundary conditions applied to finite element models. For all cases a load of 10 N kg???1, typical of the peak load in the trot gait, was used. In one scenario the coefficient of contact friction was varied from 0 (frictionless) to 1, at a constant non-zero joint moment, to simulate the effects of restriction of the hoof at the ground surface. In the other scenario a varying joint moment, with contact friction set at 0, was used to move the centre of pressure (COP) forward. Both increasing the ground surface friction and moving the COP forward caused the hoof capsule deflections and stored elastic energy to decrease. Peak strain energy in the capsule occurred when the frictional coefficient was 0 and when the COP was below the centre of rotation of the distal interphalangeal joint. Minimum strain energy occurred when the frictional coefficient was 1.0 and when the COP location was 30 mm forward of the joint centre. Hoof expansion and elastic energy storage are considerably influenced by ground surface friction and centre of pressure location. Therefore model validation studies should account for these parameters. Maximising the energy absorption may explain why heel first landing is preferred.

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  • The influence of tissue hydration on equine hoof capsule deformation and energy storage assessed using finite element methods

    Ramsey, Glenn; Hunter, Peter; Nash, Martyn (2012-02)

    Journal article
    The University of Auckland Library

    The mechanical properties of equine hoof horn are known to vary with moisture content and this property is sometimes utilised for interventions that attempt to reshape the hoof capsule. However, the relationship of moisture content modulation to the mechanics of the whole hoof is unknown. This study explores the effect of moisture variation on hoof capsule mechanics and, in particular, deflections and stored elastic energy variations in the hoof. A finite element model of the hoof was used. The hoof capsule tissue was modelled using finite elasticity with a heterogeneous transversely isotropic material relation, in which the elastic parameters were varied according to the moisture content of the tissue. The laminar junction and sole corium were modelled using an exponential Fung-type constitutive relation fitted to published data. The distal phalanx bone was modelled as a homogeneous isotropic material. Substrate interaction was modelled by contact with a rigid plate and loads typical of a trot were applied. Different scenarios were modelled where the moisture content of the hoof wall was varied from 40% to 100% of the fully hydrated case. Results demonstrated that hoof capsule deflections and stored elastic energy in the capsule increased monotonically with increasing moisture content. Stored energy in the laminar junction and sole corium remained constant. The mechanical behaviour of the hoof capsule is sensitive to variation in moisture content and this mechanism may provide a way to modulate impact energy transmission. Experimental validations of hoof models should control for moisture content to improve reliability.

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  • Detailed hoof morphometry is sparsely documented

    Ramsey, Glenn; Hunter, Peter; Nash, Martyn (2012-07)

    Journal article
    The University of Auckland Library

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  • 3D finite element modeling of avascular circulation in the ocular lens

    Vaghefi Rezaei, Seyed; Hunter, Peter; Jacobs, Marc (2008)

    Conference item
    The University of Auckland Library

    The ability to see is dependent on the actions of several structures in and around the eyeball. By looking at an object, light rays are reflected from the object to the cornea. Light rays are refracted and focused by the cornea, lens, and "vitreous". The lens function is to ensure that the light rays come to a sharp focus point on the retina.A comprehensive, quantitative model of lens functionality would be of great utility for the development of any anti-cataract medicine. Yet most of the research to date has focused on isolated and specific features of the crystalline lens. Thus a full integrated 3D model of the lens is needed in order to facilitate development of therapies and prevention procedures for cataracts.Here we developed an initial 3D model of the lens circulation using a finite element modeling approach based on the CMISS simulation environment created at the Auckland Bioengineering Institute. This work represents the first multiscale integrative numerical model of the avascular circulation system. The model we have developed correctly simulates and predicts the available empirical data on lens physiology.

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  • Conservative and non-conservative arbitrary Lagrangian-Eulerian forms for ventricular flows

    Nordsletten, DA; Hunter, Peter; Smith, Nicolas (2008-03-20)

    Conference item
    The University of Auckland Library

    Blood flow through the heart is driven by a complex motion of the endocardial heart wall, where dilation or contraction results in filling and ejection. Boundary-driven flows of this type are inherently sensitive to conservation principles. Considering the finite element approach to the arbitrary Lagrangian???Eulerian (ALE) form of the Navier???Stokes equations, we present analysis addressing critical assumptions concerning conservation and numerical approximation which affect the accuracy and stability of ALE schemes for boundary-driven flows.

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  • Multilayer soft tissue continuum model: Towards realistic simulation of facial expression

    Hung, APL; Mithraratne, Premakumar; Hunter, Peter (2009)

    Conference item
    The University of Auckland Library

    A biophysically based multilayer continuum model of the facial soft tissue composite has been developed for simulating wrinkle formation. The deformed state of the soft tissue block was determined by solving large deformation mechanics equations using the Galerkin finite element method. The proposed soft tissue model is composed of four layers with distinct mechanical properties. These include stratum corneum, epidermal-dermal layer (living epidermis and dermis), subcutaneous tissue and the underlying muscle. All the layers were treated as non-linear, isotropic Mooney Rivlin materials. Contraction of muscle fibres was approximated using a steady-state relationship between the fibre extension ratio, intracellular calcium concentration and active stress in the fibre direction. Several variations of the model parameters (stiffness and thickness of epidermal-dermal layer, thickness of subcutaneous tissue layer) have been considered.

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  • Developing a Realistic 3D Model of the Ventricular Cardiomyocyte

    Rajagopal, Vijayaraghavan; Theakston, Elizabeth; Jayasinghe, Isuru; Walker, CG; O'Sullivan, Michael; Crampin, Edmund; Soeller, Christian; Hunter, Peter (2009-07-27)

    Conference item
    The University of Auckland Library

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  • Coupled mechanics and airflow of a human lung

    Hedges, Kerry; Hunter, Peter; Tawhai, Merryn (2006)

    Conference item
    The University of Auckland Library

    To study the ventilation distribution within a human lung a model has been produced that couples soft tissue mechanics and a simplified airflow solution. The model takes account of the regional changes in the material properties of the lung which affect the pressures developed by the lung tissue during ventilation and determine the patency of the airways. The lung geometry was constructed using CT scanned data as far as the 9 th generation. Further airways are grown within the CT-based tissue lobes using a volume filling algorithm. Equations for large deformation elasticity are used to compute regional tissue pressures and a pseudo-elastic strain energy function defines the stress-strain behavior of the lung tissue. These pressures are used in the relationship between pressure and airway radius and as regional alveolar pressures that act as boundary conditions for the flow solution. Initial studies compared the flow component of the model with symmetrical, Horsfield and anatomical (physically realistic) airway geometries to investigate the influence that branching geometry and dimensional asymmetry has on the air flow distribution. The coupled model is used to compare flow distribution and flow-volume loops in a normal human lung undergoing quiet breathing while exposed to different gravities and in different orientations. Results from the isolated flow model and the fully coupled system demonstrate consistency with earlier symmetrical models and with physiological measurements. However, the accuracy of the predictions is sensitive to the accuracy of the strain energy function used for the lung tissue elasticity.

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  • Quantifying the Contributions of Anatomical Structure and Posture-Dependent Tissue Deformation to Regional Distributions of V, Q, and V/Q

    Swan, Annalisa; Burrowes, Kelly; Hunter, Peter; Tawhai, Merryn (2009)

    Conference item
    The University of Auckland Library

    Rationale Efficient gas exchange depends on the close matching of blood and air delivered to the parenchymal tissue. Ventilation (V) and perfusion (Q) distributions are influenced by airway/vasculature geometry, by pressures to which the conduits are exposed, and by tissue deformation. We have developed computational models of V and Q, coupled to soft???tissue mechanical deformation. This modeling approach allows us to predict distributions in any posture, and provides quantification of gradients and heterogeneity. Method Computational models for airflow and blood flow through the airways and pulmonary arteries, respectively, are used to predict regional V and Q. Local tethering pressure and tissue compliance are obtained from a model that describes lung tissue deformation under gravity. Fluid flow is governed by conservation of mass and a modified 1D Poiseuille flow equation that includes a gravitational term, energy losses at bifurcations, and empirical pressure???area relationships describing conduit distensibility. Results Both V and Q are distributed preferentially to the gravitationally???dependent regions in all postures. There is a larger flow gradient in the gravitational direction in the supine posture compared to the prone posture, and significant isogravitational heterogeneity in V, Q, and V/Q matching. Whole lung heterogeneity compares well with measurements from imaging studies. Conclusions The difference in supine and prone flow gradients is due to the effect of the tree branching structures and a noticeable difference in regional tissue compliance in the two postures. Heterogeneity of results in isogravitational slices results from variability in path resistance in the asymmetric trees and heterogeneity in regional tissue compliance.

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  • Optimisation of property enhancement of polypropylene/organoclay nanocomposites

    Dong, Yu; Bhattacharyya, Debes; Hunter, Peter (2007)

    Conference item
    The University of Auckland Library

    Three grades of polypropylene (PP) with different melt viscosities and three types of organomodified montmorillonite (MMT) clays with varied interlayer spacings were used to prepare PP/organoclay nanocomposites in the presence of maleated PP(MAPP). Taguchi design of experiments (DoE) was employed as an effective engineering statistical method to investigate the enhancement of mechanical properties of nanocomposites in relation to the selected materials. Individual optimum factors to promote each of tensile, flexural and impact properties were then determined using a Pareto analysis of variance (ANOVA). PP grade was found to be the most significant factor to improve the overall mechanical properties with the lowest PP viscosity demonstrating the best performance. Clay content appeared to play the second important role for the enhancement of tensile and flexural properties. Although clay type and MAPP content were determined as two non-significant factors for the tensile and flexural properties, MAPP content greatly influenced the impact strengths of nanocomposites.

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  • Modelling NFAT Cycling Sensitivity in the Cardiac Myocyte

    Cooling, Michael; Hunter, Peter; Crampin, Edmund (2007-10-01)

    Conference poster
    The University of Auckland Library

    The transcription factor NFAT acts as a signal integrator for a number of signal transduction pathways in cardiac myocytes that initiates gene expression in the disease Pathological Cardiac Hypertrophy[1]. Here we develop a quantitative mathematical model of the cytoplasmicnuclear-cytoplasmic cycling of NFAT in response to calcium signals in the cardiac myocyte

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  • Multi-Scale and Multi-Physics Visualization

    Blackett, Shane; Bullivant, D; Nickerson, David; Hunter, Peter (2005-07-31)

    Conference poster
    The University of Auckland Library

    Accurate computational models of physiology require the coupling of different physical processes that occur across a wide range of spatial scales. The interpretation and analysis of the calculated results of these models require the integrated visualization of these multi-scale and multi-physics processes. A number of different strategies for doing this are presented for a model of the heart left ventricle.

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  • Stereoscopic Particle Image Velocimetry Measurement of Articulatory Airflow for Validation of a Computer Model of Speech

    Spence, CJT; Geoghegan, PH; Lu, XB; Jermy, MC; Hunter, Peter; Cater, John (2010)

    Conference item
    The University of Auckland Library

    The interaction of the airflow and the vocal articulators while speaking is not completely understood. The regions of articulation in the airway are flow obstructions that convert aerodynamic energy into acoustic energy and can be passive (stationary) such as the teeth and hard palette, or active (moving) in the case of the lower lip and tongue. By modifying the positions of the vocal articulators and the various sounds that make up speech can be generated. Models of the articulators have been constructed from Magnetic Resonance Imaging (MRI) scans taken during quiet breathing, and articulatory kinematics were obtained from Electromagnetic Articulography (EMA) and a video of the face. A three-dimensional computer model that can represent the motion of vocal articulators and simulate the airflow during vowels and consonants has also been developed. A fricative is a hissing or buzzing consonant that is produced when a steady air stream is forced through a constriction in the oral cavity and the flow state becomes transitional or even turbulent. In the current paper Stereoscopic Particle Image Velocimetry (SPIV) measurements of the airflow through the modelled vocal tract geometries for the production of "s" and "sh" fricatives are presented.

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  • Multi-scale modelling of aneurysm formation - linking continuum mechanics and adaptation to signalling events

    Schmid, H; Cooling, Michael; Watton, P; Hunter, Peter; Itskov, M (2010)

    Conference item
    The University of Auckland Library

    Contents (1) Aneurysms, forms and location (2) Arterial micro-structure (3) Remodelling framework (4) Some basic concepts (5) Subsequent steps (6) Challenge

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  • Visualizing multiscale models of the nephron

    Nickerson, David; Terkildsen, J; Hamilton, K; Hunter, Peter (2010-04)

    Conference poster
    The University of Auckland Library

    We present the development of a tool which provides users with the ability to visualize and interact with multiscale models of the nephron ??? from the scale of models of membrane bound proteins, to that of an individual nephron. A 1-D finite element model of the nephron has been created and is used for both visualization and modeling of the tubule transport. Mathematical models of nephron segments (for example, Weinstein et al., Am. J. Physiol. 292:F1164-F1181, 2007 for the proximal tubule) are embedded in the finite element model. At the cellular level these segment models utilize models encoded in CellML (www.cellml.org) to describe cellular transport kinetics. A user interface has been developed which allows the visualization and interaction with the multiscale nephron models and simulation results. The zinc extension to Firefox (http://www.cmiss.org/cmgui/zinc/) is used to provide an interactive 3-D view of the model(s). This model viewer is embedded in a web page which dynamically presents content based on user input. For example, when viewing the whole nephron model the user might be presented with information on the various embedded segment models as they select them in the 3-D model view. Similarly, the user might choose to focus the model viewer on a cellular model in a particular segment in order to view the various membrane transport proteins. Selecting a specific protein might present the user with a full reference description of the mathematical model governing the behavior of that protein (Nickerson et al., Bioinformatics 24:1112-1114, 2008).

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