PHYSICA: A multiphysics computational framework and its application to casting simulations

Metal casting is a process governed by the interaction of a range of physical phenomena. Most computational models of this process address only what are conventionally regarded as the primary phenomena – heat conduction and solidification. However, to predict other phenomena, such as porosity formation, requires modelling the interaction of the fluid flow, heat transfer, solidification and the development of stressdeformation in the solidified part of the casting. This paper will describe a modelling framework called PHYSICA[1] which has the capability to stimulate such multiphysical phenomena.

Effects of fibrosis morphology on reentrant ventricular tachycardia inducibility and simulation fidelity in patient-derived models

Myocardial fibrosis detected via delayed-enhanced magnetic resonance imaging (MRI) has been shown to be a strong indicator for ventricular tachycardia (VT) inducibility. However, little is known regarding how inducibility is affected by the details of the fibrosis extent, morphology, and border zone configuration. The objective of this article is to systematically study the arrhythmogenic effects of fibrosis geometry and extent, specifically on VT inducibility and maintenance. We present a set of methods for constructing patient-specific computational models of human ventricles using in vivo MRI data for patients suffering from hypertension, hypercholesterolemia, and chronic myocardial infarction. Additional synthesized models with morphologically varied extents of fibrosis and gray zone (GZ) distribution were derived to study the alterations in the arrhythmia induction and reentry patterns. Detailed electrophysiological simulations demonstrated that (1) VT morphology was highly dependent on the extent of fibrosis, which acts as a structural substrate, (2) reentry tended to be anchored to the fibrosis edges and showed transmural conduction of activations through narrow channels formed within fibrosis, and (3) increasing the extent of GZ within fibrosis tended to destabilize the structural reentry sites and aggravate the VT as compared to fibrotic regions of the same size and shape but with lower or no GZ. The approach and findings represent a significant step toward patient-specific cardiac modeling as a reliable tool for VT prediction and management of the patient. Sensitivities to approximation nuances in the modeling of structural pathology by image-based reconstruction techniques are also implicated.

Modelling the effects of bone fragment contact in fracture healing

The fracture healing process is modulated by the mechanical environment created by imposed loads and motion between the bone fragments. Contact between the fragments obviously results in a significantly different stress and strain environment to a uniform fracture gap containing only soft tissue (e.g. haematoma). The assumption of the latter in existing computational models of the healing process will hence exaggerate the inter-fragmentary strain in many clinically-relevant cases. To address this issue, we introduce the concept of a contact zone that represents a variable degree of contact between cortices by the relative proportions of bone and soft tissue present. This is introduced as an initial condition in a two-dimensional iterative finite element model of a healing tibial fracture, in which material properties are defined by the volume fractions of each tissue present. The algorithm governing the formation of cartilage and bone in the fracture callus uses fuzzy logic rules based on strain energy density resulting from axial compression. The model predicts that increasing the degree of initial bone contact reduces the amount of callus formed (periosteal callus thickness 3.1mm without contact, down to 0.5mm with 10% bone in contact zone). This is consistent with the greater effective stiffness in the contact zone and hence, a smaller inter-fragmentary strain. These results demonstrate that the contact zone strategy reasonably simulates the differences in the healing sequence resulting from the closeness of reduction.

Personalised ontology learning and mining for web information gathering

Over the last decade, the rapid growth and adoption of the World Wide Web has further exacerbated user needs for e±cient mechanisms for information and knowledge location, selection, and retrieval. How to gather useful and meaningful information from the Web becomes challenging to users. The capture of user information needs is key to delivering users' desired information, and user pro¯les can help to capture information needs. However, e®ectively acquiring user pro¯les is di±cult. It is argued that if user background knowledge can be speci¯ed by ontolo- gies, more accurate user pro¯les can be acquired and thus information needs can be captured e®ectively. Web users implicitly possess concept models that are obtained from their experience and education, and use the concept models in information gathering. Prior to this work, much research has attempted to use ontologies to specify user background knowledge and user concept models. However, these works have a drawback in that they cannot move beyond the subsumption of super - and sub-class structure to emphasising the speci¯c se- mantic relations in a single computational model. This has also been a challenge for years in the knowledge engineering community. Thus, using ontologies to represent user concept models and to acquire user pro¯les remains an unsolved problem in personalised Web information gathering and knowledge engineering. In this thesis, an ontology learning and mining model is proposed to acquire user pro¯les for personalised Web information gathering. The proposed compu- tational model emphasises the speci¯c is-a and part-of semantic relations in one computational model. The world knowledge and users' Local Instance Reposito- ries are used to attempt to discover and specify user background knowledge. From a world knowledge base, personalised ontologies are constructed by adopting au- tomatic or semi-automatic techniques to extract user interest concepts, focusing on user information needs. A multidimensional ontology mining method, Speci- ¯city and Exhaustivity, is also introduced in this thesis for analysing the user background knowledge discovered and speci¯ed in user personalised ontologies. The ontology learning and mining model is evaluated by comparing with human- based and state-of-the-art computational models in experiments, using a large, standard data set. The experimental results are promising for evaluation. The proposed ontology learning and mining model in this thesis helps to develop a better understanding of user pro¯le acquisition, thus providing better design of personalised Web information gathering systems. The contributions are increasingly signi¯cant, given both the rapid explosion of Web information in recent years and today's accessibility to the Internet and the full text world.

The mechanical response of the ovine lumbar anulus fibrosus to uniaxial, biaxial and shear loads

Analytical and computational models of the intervertebral disc (IVD) are commonly employed to enhance understanding of the biomechanics of the human spine and spinal motion segments. The accuracy of these models in predicting physiological behaviour of the spine is intrinsically reliant on the accuracy of the material constitutive representations employed to represent the spinal tissues. There is a paucity of detailed mechanical data describing the material response of the reinforced­ground matrix in the anulus fibrosus of the IVD. In the present study, the ‘reinforced­ground matrix’ was defined as the matrix with the collagen fibres embedded but not actively bearing axial load, thus incorporating the contribution of the fibre-fibre and fibre-matrix interactions. To determine mechanical parameters for the anulus ground matrix, mechanical tests were carried out on specimens of ovine anulus, under unconfined uniaxial compression, simple shear and biaxial compression. Test specimens of ovine anulus fibrosus were obtained with an adjacent layer of vertebral bone/cartilage on the superior and inferior specimen surface. Specimen geometry was such that there were no continuous collagen fibres coupling the two endplates. Samples were subdivided according to disc region - anterior, lateral and posterior - to determine the regional inhomogeneity in the anulus mechanical response. Specimens were loaded at a strain rate sufficient to avoid fluid outflow from the tissue and typical stress-strain responses under the initial load application and under repeated loading were determined for each of the three loading types. The response of the anulus tissue to the initial and repeated load cycles was significantly different for all load types, except biaxial compression in the anterior anulus. Since the maximum applied strain exceeded the damage strain for the tissue, experimental results for repeated loading reflected the mechanical ability of the tissue to carry load, subsequent to the initiation of damage. To our knowledge, this is the first study to provide experimental data describing the response of the ‘reinforced­ground matrix’ to biaxial compression. Additionally, it is novel in defining a study objective to determine the regionally inhomogeneous response of the ‘reinforced­ground matrix’ under an extensive range of loading conditions suitable for mechanical characterisation of the tissue. The results presented facilitate the development of more detailed and comprehensive constitutive descriptions for the large strain nonlinear elastic or hyperelastic response of the anulus ground matrix.

Mapping a suburb with a single camera using a biologically inspired SLAM system

This paper describes a biologically inspired approach to vision-only simultaneous localization and mapping (SLAM) on ground-based platforms. The core SLAM system, dubbed RatSLAM, is based on computational models of the rodent hippocampus, and is coupled with a lightweight vision system that provides odometry and appearance information. RatSLAM builds a map in an online manner, driving loop closure and relocalization through sequences of familiar visual scenes. Visual ambiguity is managed by maintaining multiple competing vehicle pose estimates, while cumulative errors in odometry are corrected after loop closure by a map correction algorithm. We demonstrate the mapping performance of the system on a 66 km car journey through a complex suburban road network. Using only a web camera operating at 10 Hz, RatSLAM generates a coherent map of the entire environment at real-time speed, correctly closing more than 51 loops of up to 5 km in length.

RatSLAM : a hippocampal model for simultaneous localization and mapping

The work presents a new approach to the problem of simultaneous localization and mapping - SLAM - inspired by computational models of the hippocampus of rodents. The rodent hippocampus has been extensively studied with respect to navigation tasks, and displays many of the properties of a desirable SLAM solution. RatSLAM is an implementation of a hippocampal model that can perform SLAM in real time on a real robot. It uses a competitive attractor network to integrate odometric information with landmark sensing to form a consistent representation of the environment. Experimental results show that RatSLAM can operate with ambiguous landmark information and recover from both minor and major path integration errors.

The feasibility of vibration analysis as a technique to detect osseointegration of transfemoral implants

One of the main causes of above knee or transfemoral amputation (TFA) in the developed world is trauma to the limb. The number of people undergoing TFA due to limb trauma, particularly due to war injuries, has been increasing. Typically the trauma amputee population, including war-related amputees, are otherwise healthy, active and desire to return to employment and their usual lifestyle. Consequently there is a growing need to restore long-term mobility and limb function to this population. Traditionally transfemoral amputees are provided with an artificial or prosthetic leg that consists of a fabricated socket, knee joint mechanism and a prosthetic foot. Amputees have reported several problems related to the socket of their prosthetic limb. These include pain in the residual limb, poor socket fit, discomfort and poor mobility. Removing the socket from the prosthetic limb could eliminate or reduce these problems. A solution to this is the direct attachment of the prosthesis to the residual bone (femur) inside the residual limb. This technique has been used on a small population of transfemoral amputees since 1990. A threaded titanium implant is screwed in to the shaft of the femur and a second component connects between the implant and the prosthesis. A period of time is required to allow the implant to become fully attached to the bone, called osseointegration (OI), and be able to withstand applied load; then the prosthesis can be attached. The advantages of transfemoral osseointegration (TFOI) over conventional prosthetic sockets include better hip mobility, sitting comfort and prosthetic retention and fewer skin problems on the residual limb. However, due to the length of time required for OI to progress and to complete the rehabilitation exercises, it can take up to twelve months after implant insertion for an amputee to be able to load bear and to walk unaided. The long rehabilitation time is a significant disadvantage of TFOI and may be impeding the wider adoption of the technique. There is a need for a non-invasive method of assessing the degree of osseointegration between the bone and the implant. If such a method was capable of determining the progression of TFOI and assessing when the implant was able to withstand physiological load it could reduce the overall rehabilitation time. Vibration analysis has been suggested as a potential technique: it is a non destructive method of assessing the dynamic properties of a structure. Changes in the physical properties of a structure can be identified from changes in its dynamic properties. Consequently vibration analysis, both experimental and computational, has been used to assess bone fracture healing, prosthetic hip loosening and dental implant OI with varying degrees of success. More recently experimental vibration analysis has been used in TFOI. However further work is needed to assess the potential of the technique and fully characterise the femur-implant system. The overall aim of this study was to develop physical and computational models of the TFOI femur-implant system and use these models to investigate the feasibility of vibration analysis to detect the process of OI. Femur-implant physical models were developed and manufactured using synthetic materials to represent four key stages of OI development (identified from a physiological model), simulated using different interface conditions between the implant and femur. Experimental vibration analysis (modal analysis) was then conducted using the physical models. The femur-implant models, representing stage one to stage four of OI development, were excited and the modal parameters obtained over the range 0-5kHz. The results indicated the technique had limited capability in distinguishing between different interface conditions. The fundamental bending mode did not alter with interfacial changes. However higher modes were able to track chronological changes in interface condition by the change in natural frequency, although no one modal parameter could uniquely distinguish between each interface condition. The importance of the model boundary condition (how the model is constrained) was the key finding; variations in the boundary condition altered the modal parameters obtained. Therefore the boundary conditions need to be held constant between tests in order for the detected modal parameter changes to be attributed to interface condition changes. A three dimensional Finite Element (FE) model of the femur-implant model was then developed and used to explore the sensitivity of the modal parameters to more subtle interfacial and boundary condition changes. The FE model was created using the synthetic femur geometry and an approximation of the implant geometry. The natural frequencies of the FE model were found to match the experimental frequencies within 20% and the FE and experimental mode shapes were similar. Therefore the FE model was shown to successfully capture the dynamic response of the physical system. As was found with the experimental modal analysis, the fundamental bending mode of the FE model did not alter due to changes in interface elastic modulus. Axial and torsional modes were identified by the FE model that were not detected experimentally; the torsional mode exhibited the largest frequency change due to interfacial changes (103% between the lower and upper limits of the interface modulus range). Therefore the FE model provided additional information on the dynamic response of the system and was complementary to the experimental model. The small changes in natural frequency over a large range of interface region elastic moduli indicated the method may only be able to distinguish between early and late OI progression. The boundary conditions applied to the FE model influenced the modal parameters to a far greater extent than the interface condition variations. Therefore the FE model, as well as the experimental modal analysis, indicated that the boundary conditions need to be held constant between tests in order for the detected changes in modal parameters to be attributed to interface condition changes alone. The results of this study suggest that in a clinical setting it is unlikely that the in vivo boundary conditions of the amputated femur could be adequately controlled or replicated over time and consequently it is unlikely that any longitudinal change in frequency detected by the modal analysis technique could be attributed exclusively to changes at the femur-implant interface. Therefore further development of the modal analysis technique would require significant consideration of the clinical boundary conditions and investigation of modes other than the bending modes.

Perfusion model system to generate engineered grafts with controlled cellular distributions

Engineered tissue grafts, which mimic the spatial variations of cell density and extracellular matrix present in native tissues, could facilitate more efficient tissue regeneration and integration. We previously demonstrated that cells could be uniformly seeded throughout a 3D scaffold having a random pore architecture using a perfusion bioreactor2. In this work, we aimed to generate 3D constructs with defined cell distributions based on rapid prototyped scaffolds manufactured with a controlled gradient in porosity. Computational models were developed to assess the influence of fluid flow, associated with pore architecture and perfusion regime, on the resulting cell distribution.

Exploring the parameter space of a rabbit ventricular action potential model to investigate the effect of variation on action potential and calcium transients

Computational models for cardiomyocyte action potentials (AP) often make use of a large parameter set. This parameter set can contain some elements that are fitted to experimental data independently of any other element, some elements that are derived concurrently with other elements to match experimental data, and some elements that are derived purely from phenomenological fitting to produce the desired AP output. Furthermore, models can make use of several different data sets, not always derived for the same conditions or even the same species. It is consequently uncertain whether the parameter set for a given model is physiologically accurate. Furthermore, it is only recently that the possibility of degeneracy in parameter values in producing a given simulation output has started to be addressed. In this study, we examine the effects of varying two parameters (the L-type calcium current (I(CaL)) and the delayed rectifier potassium current (I(Ks))) in a computational model of a rabbit ventricular cardiomyocyte AP on both the membrane potential (V(m)) and calcium (Ca(2+)) transient. It will subsequently be determined if there is degeneracy in this model to these parameter values, which will have important implications on the stability of these models to cell-to-cell parameter variation, and also whether the current methodology for generating parameter values is flawed. The accuracy of AP duration (APD) as an indicator of AP shape will also be assessed.

Stochastic analysis of the VEGF receptor response curve

Recently, an analysis of the response curve of the vascular endothelial growth factor (VEGF) receptor and its application to cancer therapy was described in [T. Alarcón, and K. Page, J. R. Soc. Lond. Interface 4, 283–304 (2007)]. The analysis is significantly extended here by demonstrating that an alternative computational strategy, namely the Krylov FSP algorithm for the direct solution of the chemical master equation, is feasible for the study of the receptor model. The new method allows us to further investigate the hypothesis of symmetry in the stochastic fluctuations of the response. Also, by augmenting the original model with a single reversible reaction we formulate a plausible mechanism capable of realizing a bimodal response, which is reported experimentally but which is not exhibited by the original model. The significance of these findings for mechanisms of tumour resistance to antiangiogenic therapy is discussed.

Outdoor simultaneous localisation and mapping using RatSLAM

In this paper an existing method for indoor Simultaneous Localisation and Mapping (SLAM) is extended to operate in large outdoor environments using an omnidirectional camera as its principal external sensor. The method, RatSLAM, is based upon computational models of the area in the rat brain that maintains the rodent’s idea of its position in the world. The system uses the visual appearance of different locations to build hybrid spatial-topological maps of places it has experienced that facilitate relocalisation and path planning. A large dataset was acquired from a dynamic campus environment and used to verify the system’s ability to construct representations of the world and simultaneously use these representations to maintain localisation.

Patient-Specific Modeling of Scoliosis

Current complication rates for adolescent spinal deformity surgery are unacceptably high and in order to improve patient outcomes, the development of a simulation tool which enables the surgical strategy for an individual patient to be optimized is necessary. In this chapter we will present our work to date in developing and validating patient-specific modeling techniques to simulate and predict patient outcomes for surgery to correct adolescent scoliosis deformity. While these simulation tools are currently being developed to simulate adolescent idiopathic scoliosis patients, they will have broader applications in simulating spinal disorders and optimizing surgical planning for other types of spine surgery. Our studies to date have highlighted the need for not only patient-specific anatomical data, but also patient-specific tissue parameters and biomechanical loading data, in order to accurately predict the physiological behaviour of the spine. Even so, patient-specific computational models are the state-of-the art in computational biomechanics and offer much potential as a pre-operative surgical planning tool.

Text mining and probabilistic language modeling for online review spam detecting

In the era of Web 2.0, huge volumes of consumer reviews are posted to the Internet every day. Manual approaches to detecting and analyzing fake reviews (i.e., spam) are not practical due to the problem of information overload. However, the design and development of automated methods of detecting fake reviews is a challenging research problem. The main reason is that fake reviews are specifically composed to mislead readers, so they may appear the same as legitimate reviews (i.e., ham). As a result, discriminatory features that would enable individual reviews to be classified as spam or ham may not be available. Guided by the design science research methodology, the main contribution of this study is the design and instantiation of novel computational models for detecting fake reviews. In particular, a novel text mining model is developed and integrated into a semantic language model for the detection of untruthful reviews. The models are then evaluated based on a real-world dataset collected from amazon.com. The results of our experiments confirm that the proposed models outperform other well-known baseline models in detecting fake reviews. To the best of our knowledge, the work discussed in this article represents the first successful attempt to apply text mining methods and semantic language models to the detection of fake consumer reviews. A managerial implication of our research is that firms can apply our design artifacts to monitor online consumer reviews to develop effective marketing or product design strategies based on genuine consumer feedback posted to the Internet.

Concept combination and the origins of complex cognition

At the core of our uniquely human cognitive abilities is the capacity to see things from different perspectives, or to place them in a new context. We propose that this was made possible by two cognitive transitions. First, the large brain of Homo erectus facilitated the onset of recursive recall: the ability to string thoughts together into a stream of potentially abstract or imaginative thought. This hypothesis is sup-ported by a set of computational models where an artificial society of agents evolved to generate more diverse and valuable cultural outputs under conditions of recursive recall. We propose that the capacity to see things in context arose much later, following the appearance of anatomically modern humans. This second transition was brought on by the onset of contextual focus: the capacity to shift between a minimally contextual analytic mode of thought, and a highly contextual associative mode of thought, conducive to combining concepts in new ways and ‘breaking out of a rut’. When contextual focus is implemented in an art-generating computer program, the resulting artworks are seen as more creative and appealing. We summarize how both transitions can be modeled using a theory of concepts which high-lights the manner in which different contexts can lead to modern humans attributing very different meanings to the interpretation of one concept.