N P Smith's research while affiliated with University of Auckland and other places

Publications (53)

Article
From basic science to translation, modern biomedical research demands computational models which integrate several interacting physical systems. This paper describes the infrastructural framework for generic multiphysics integration implemented in the software CHeart, a finite-element code for biomedical research. To generalize the coupling of phys...
Article
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Article
Key points: Hypokalaemia is a risk factor for development of ventricular arrhythmias. In rat ventricular myocytes, low extracellular K(+) (corresponding to clinical moderate hypokalaemia) increased Ca(2+) wave probability, Ca(2+) transient amplitude, sarcoplasmic reticulum (SR) Ca(2+) load and induced SR Ca(2+) leak. Low extracellular K(+) reduced...
Article
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This manuscript describes our recent developments towards better understanding of the mechanisms amenable to cardiac resynchronization therapy response. We report the results from a full multimodal dataset corresponding to eight patients from the euHeart project. The datasets include echocardiography, MRI and electrophysiological studies. We invest...
Article
We present a method to efficiently simulate coronary perfusion in subject-specific models of the heart within clinically relevant time frames. Perfusion is modelled as a Darcy porous-media flow, where the permeability tensor is derived from homogenization of an explicit anatomical representation of the vasculature. To account for the disparity in l...
Article
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Cardiac diseases represent one of the primary causes of mortality and result in a substantial decrease in quality of life. Optimal surgical planning and long-term treatment are crucial for a successful and cost-effective patient care. Recently developed state-of-the-art imaging techniques supply a wealth of detailed data to support diagnosis. This...
Article
Response to cardiac resynchronization therapy (CRT) is reduced in patients with posterolateral scar. Multipolar pacing leads offer the ability to select desirable pacing sites and/or stimulate from multiple pacing sites concurrently using a single lead position. Despite this potential, the clinical evaluation and identification of metrics for optim...
Article
The link between experimental data and biophysically based mathematical models is key to computational simulation meeting its potential to provide physiological insight. However, despite the importance of this link, scrutiny and analysis of the processes by which models are parameterised from data are currently lacking. While this situation is comm...
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The strong coupling between the flow in coronary vessels and the mechanical deformation of the myocardial tissue is a central feature of cardiac physiology and must therefore be accounted for by models of coronary perfusion. Currently available geometrically explicit vascular models fail to capture this interaction satisfactorily, are numerically i...
Article
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Computational models of the heart at various scales and levels of complexity have been independently developed, parameterised and validated using a wide range of experimental data for over four decades. However, despite remarkable progress, the lack of coordinated efforts to compare and combine these computational models has limited their impact on...
Article
Understanding the underlying feedback mechanisms of fluid/solid coupling and the role it plays in heart function is crucial for characterizing normal heart function and its behavior in disease. To improve this understanding, an anatomically accurate computational model of fluid–solid mechanics in the left ventricle is presented which assesses both...
Article
We describe a simulation study of Ca²(+) dynamics in mice with cardiomyocyte-specific conditional excision of the sarco(endo)plasmic reticulum calcium ATPase (SERCA) gene, using an experimental data-driven biophysically-based modeling framework. Previously, we reported a moderately impaired heart function measured in mice at 4 weeks after SERCA2 ge...
Article
Full-text available
Mathematical modeling of Ca(2+) dynamics in the heart has the potential to provide an integrated understanding of Ca(2+)-handling mechanisms. However, many previous published models used heterogeneous experimental data sources from a variety of animals and temperatures to characterize model parameters and motivate model equations. This methodology...
Chapter
LVAD implantation is often used to assist patients suffering heart failure. These devices profoundly alter ventricular behaviour, however, the precise impact on the myocardium and on ventricular blood flow remains unknown. We have developed an anatomically accurate coupled fluidmechanical model of the left ventricle under LVAD support to enhance un...
Article
We outline and review the mathematical framework for representing mechanical deformation and contraction of the cardiac ventricles, and how this behaviour integrates with other processes crucial for understanding and modelling heart function. Building on general conservation principles of space, mass and momentum, we introduce an arbitrary Eulerian...
Article
In this study, we introduced a biophysically based, mathematical model that represented whole-cell small intestinal ICC slow wave activity generated from a discrete unitary potential basis. This model expanded on the recently developed pacemaker unit modeling framework of Faville et al. ( 14 • Faville R. • Pullan A. • Sanders K. • Smith N. A bioph...
Article
Tension-dependent binding of Ca(2+) to troponin C in the cardiac myocyte has been shown to play an important role in the regulation of Ca(2+) and the activation of tension development. The significance of this regulatory mechanism is quantified experimentally by the quantity of Ca(2+) released following a rapid change in the muscle length. Using a...
Article
Computational models of cardiac electrophysiology are exemplar demonstrations of the integration of multiple data sets into a consistent biophysical framework. These models encapsulate physiological understanding to provide quantitative predictions of function. The combination or extension of existing models within a common framework allows integra...
Article
Unitary potential (UP) depolarizations are the basic intracellular events responsible for pacemaker activity in interstitial cells of Cajal (ICCs), and are generated at intracellular sites termed "pacemaker units". In this study, we present a mathematical model of the transmembrane ion flows and intracellular Ca(2+) dynamics from a single ICC pacem...
Article
In this brief review, we have focussed largely on the well-established, but essentially phenomenological, linear relationship between the energy expenditure of the heart (commonly assessed as the oxygen consumed per beat, oxygen consumption (VO2)) and the pressure-volume-area (PVA, the sum of pressure-volume work and a specified 'potential energy'...
Article
Protons are powerful modulators of cardiac function. Their intracellular concentration is regulated by sarcolemmal ion transporters that export or import H+-ions (or their ionic equivalent: HCO3-, OH-). One such transporter, which imports H+-equivalents, is a putative Cl-/OH- exchanger (CHE). A strong candidate for CHE is SLC26A6 protein, a product...
Article
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...
Article
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The generation of triangulations on p-order parametric surfaces is a fundamental first step to numerical solutions for multidomain problems involving complex geometries such as those encountered in biological fluid dynamics and other applications. In this study we develop a novel, computationally efficient method for generating triangulations in co...
Article
Many functional pathologies of the small intestine are difficult to diagnose clinically without an invasive surgical intervention. Often such conditions are associated with a disruption of the normal electrical activity occurring within the musculature of the small intestine. The far field electrical signals on the torso surface arising from the el...
Article
The determinants of relaxation in cardiac muscle are poorly understood, yet compromised relaxation accompanies various pathologies and impaired pump function. In this study, we develop a model of active contraction to elucidate the relative importance of the [Ca2+]i transient magnitude, the unbinding of Ca2+ from troponin C (TnC), and the length-de...
Article
Compared to cardiac ischemia, relatively little is known about ischemia that develops within the gastrointestinal system. The work presented here is a first step towards developing a detailed anatomically and biophysically based model of the mesenteric arterial system of the human intestine to be used to simulate normal and compromised blood flows....
Article
The mechanical motion of the heart plays a role in determining the waveforms observed in an ECG. This study is designed to ascertain, from a theoretical perspective, the influence of this motion. This is achieved through an analysis of a detailed forward model including a full bidomain description and a strongly coupled model of cardiac electromech...
Chapter
Acta Numerica surveys annually the most important developments in numerical mathematics and scientific computing. The subjects and authors of the substantive survey articles are chosen by a distinguished international editorial board so as to report the most important and timely developments in a manner accessible to the wider community of professi...
Article
This study presents a method for the reduction of biophysically-based kinetic models for the active transport of ions. A lumping scheme is presented which exploits the differences in timescales associated with fast and slow transitions between model states, while maintaining the thermodynamic properties of the model. The goal of this approach is to...
Article
A computational framework is presented for integrating the electrical, mechanical and biochemical functions of the heart. Finite element techniques are used to solve the large-deformation soft tissue mechanics using orthotropic constitutive laws based in the measured fibre-sheet structure of myocardial (heart muscle) tissue. The reaction-diffusion...
Article
Electrical and magnetic fields are generated by the smooth muscle's electrical activity in the walls of the gastrointestinal system. These fields can be measured on the torso surface. We present a computational model that is capable of simulating the electrical activity occurring within the small intestine. Finite elements were used to represent th...
Article
This study analyzes the effect of a poorly perfused (ischemic) region on active tension and strain at a point in a model of the cardiac ventricles. The cellular active mechanics and electrophysiology were calculated using a coupled electromechanical cell model. The deformation of the heart was calculated combining an anisotropic constitutive law wi...
Article
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In this study the construction of an initial three-dimensional anatomically based mathematical model of the esophagus is presented. The aim of this model is to provide a framework with which to examine the functional behavior of the esophagus and the lower esophageal sphincter during swallowing. Anatomical data from the Visible Human Project was us...
Article
Detailed existing studies on microvessels are combined within a biophysically-based modeling framework to construct a mathematical and computational model of the coronary microcirculation. Morphometric data of porcine coronary arteries, veins and capillaries are used to build a network structure of a capillary bed. The Poiseuille flow steady state...
Article
Results from recent experiments undertaken on tissue from the gastrointestinal (GI) tract suggests that the interstitial cells of cajal (ICC) are the pacemaker cells responsible for slow wave propagation. The pace-making mechanism of ICC networks is strongly dependant on intracellular spatial dynamics of Ca/sup 2+/. A modeling framework has being d...
Article
Full-text available
An anatomically accurate model of the forearm and hand musculo-skeletal system using finite element geometries is presented. Anatomical data has been digitized from the male Visible Human dataset to create meshes which accurately approximate each bone and muscle volume. Each muscle's anatomical structure has been accounted for via the topology of t...
Article
Single cell and whole organ mathematical models of cardiac electrophysiology, mechanics and metabolism are presented. The important elements of each model are outlined and, in particular, the methods, techniques and con-siderations for coupling each element together to create an integrated cardiac model are discussed. Results for both individual ti...
Conference Paper
Presented here are the initial stages in an effort to create an anatomically based model of the human digestive system from a bioelectrical perspective. The activation of the smooth muscle in the walls of the gastrointestinal tract gives rise to electrical and magnetic fields at the torso surface that can be measured experimentally. The model prese...
Article
An efficient finite difference model of blood flowthrough the coronary vessels is de- veloped and applied to a geometric model of the largest six generations of the coronary arterial net- work. By constraining the form of the velocity profile across the vessel radius, the three-dimensional Navier-Stokes equations are reduced to one-dimensional equa...
Article
Recent advances in high performance computing combined with increasing knowledge of them kinetics of biochemical reactions and transport processes have allowed us to develop mathematical models that describe various aspects of cardiac physiology. These models include both single cell and three-dimensional tissue models that simulate important featu...
Article
A coupled electromechanics model of a single cardiac cell is used to interpret a wide variety of experimental tests and i compared to a limited extent (since no other cardiac model dealing with the full range of mechanical tests is available) wit other models of myofilament mechanics. We consider the passive elasticity of the cell, troponin–C–calci...
Article
A discrete anatomically accurate finite element model of the largest six generations of the coronary arterial network is developed. Using a previously developed anatomically accurate model of ventricular geometry the boundaries of the coronary mesh are defined from measured epicardial coronaries. Network topology is then generated stochastically fr...

Citations

... 7,11,27 All these mathematical models, which describe different physical processes, interact one another, leading to a highly coupled system. 3,6,16,54,55,59,61 Computational strategies for the resulting cardiac EM models have made significant developments in recent years. 3,12,28,33,63 However, as mentioned above for EP models, the computational costs typically remain still very large. ...
... Cardiac clinical imaging data was leveraged to derive models of the LA and LV prescribed with patient-specific myocardial motion. Each component of Virchow's triad was assessed through biophysical modelling using the finite-element solver, CHeart [16]. ...
... where w ¼ {w i } is the velocity of the moving ALE frame. Through this relation, the rate of change in momentum may be considered in an ALE frame of reference by substitution, yielding the ALE form of Cauchy's first law (Nordsletten et al., 2007), ...
... Moreover, the inverse association between the blood [K + ] and ARI duration was observed. It can be explained by the suppression of K + channels conductance at lowering the extracellular [K + ], specifically IK1 inhibition (Bouchard et al. 2004) and reduced Na + /K + -ATPase currents (Aronsen et al. 2015) resulting in the prolongation of the repolarization phase. As it has been already mentioned above, the ARI shortening in the ischemic zone might be expected to be determined not by the blood [K + ] level but by the local rise of extracellular [K + ]. ...
... Surgery and interventions aim to restore this to the greatest extent possible. Computational Fluid Dynamics (CFD) simulation enables the flow of blood in the heart to be computed before being visualised and analysed [23], and so aids treatment planning. CFD data are fundamentally 3D and often complex, so VR could provide an aid in their understanding by improving visualisation and interaction. ...
... More recently, ref. [4] proposed a framework for the simulation of cardiac perfusion using Darcy's law using the idea of multicompartments to represent the different blood vessels' spatial scale. In medical image analysis, ref. [5] proposed quantifying the behavior of contrast agents in MR perfusion imaging. The work used a simplified model of contrast agent transport and provided interesting insights on the design and selection of the appropriate CA for specific imaging protocols and postprocessing methods. ...
... Simulations of both continuous [25] and pulsatile flow pumps [26,27] have been performed to assess the impact of circulatory devices in HFpEF and optimize their design. Furthermore, advanced LVAD models that use realistic geometries [28][29][30] have also been developed to study their effect on ventricular pressure. Granegger et al. [31] have recently used lumped parameter models to compare several device-based methodologies for HFpEF, including various pacemaker-like devices and an interatrial shunt. ...
... Bioengineering Institute of the University of Auckland (Hunter & Pullan 2002). The animated model is integrated into a web site using the ZINC plug-in and adapts to user input such as heart rate, state of the arteries (e.g., no plaque), and structure and number of capillaries. ...
... where σf along the fiber and σcf across fiber. In some three-dimensional simulation works, directions of sheet of fiber and cross-sheet of fiber are treated differently [22, 30]. ...
... Stretch-induced changes in the Ca 2ϩ affinity of TnC have been studied extensively, using computational simulations to understand effects on cardiac electrical activity (617). In the context of MEC, simulations have shown that with constant stretch, changes in TnC-Ca 2ϩ affinity would be expected to delay repolarization, due to elevated Ca 2ϩ buffering by TnC causing an increase in total SR Ca 2ϩ release and a delay in reuptake that leads to an increase and prolongation of I NCX (312,429,598). These stretch-induced AP changes differ from those predicted to arise from SAC activation, which, as described above, tends to cause AP shortening or crossover of the repolarization curve. ...