Computational simulation methodologies for mechanobiological modelling: a cell-centred approach to neointima development in stents

The design of medical devices could be very much improved if robust tools were available for computational simulation of tissue response to the presence of the implant. Such tools require algorithms to simulate the response of tissues to mechanical and chemical stimuli. Available methodologies include those based on the principle of mechanical homeostasis, those which use continuum models to simulate biological constituents, and the cell-centred approach, which models cells as autonomous agents. In the latter approach, cell behaviour is governed by rules based on the state of the local environment around the cell; and informed by experiment. Tissue growth and differentiation requires simulating many of these cells together. In this paper, the methodology and applications of cell-centred techniques-with particular application to mechanobiology-are reviewed, and a cell-centred model of tissue formation in the lumen of an artery in response to the deployment of a stent is presented. The method is capable of capturing some of the most important aspects of restenosis, including nonlinear lesion growth with time. The approach taken in this paper provides a framework for simulating restenosis; the next step will be to couple it with more patient-specific geometries and quantitative parameter data.

Computational simulation of the early stage of bone healing under different configurations of locking compression plates

Flexible fixation or the so-called ‘biological fixation’ has been shown to encourage the formation of fracture callus, leading to better healing outcomes. However, the nature of the relationship between the degree of mechanical stability provided by a flexible fixation and the optimal healing outcomes has not been fully understood. In this study, we have developed a validated quantitative model to predict how cells in fracture callus might respond to change in their mechanical microenvironment due to different configurations of locking compression plate (LCP) in clinical practice, particularly in the early stage of healing. The model predicts that increasing flexibility of the LCP by changing the bone–plate distance (BPD) or the plate working length (WL) could enhance interfragmentary strain in the presence of a relatively large gap size (.3 mm). Furthermore, conventional LCP normally results in asymmetric tissue development during early stage of callus formation, and the increase of BPD or WL is insufficient to alleviate this problem.

A study on the usefulness of Support Vector Machines for the realtime computational simulation of soft biological organs

Realistic and realtime computational simulation of soft biological organs (e.g., liver, kidney) is necessary when one tries to build a quality surgical simulator that can simulate surgical procedures involving these organs. Since the realistic simulation of these soft biological organs should account for both nonlinear material behavior and large deformation, achieving realistic simulations in realtime using continuum mechanics based numerical techniques necessitates the use of a supercomputer or a high end computer cluster which are costly. Hence there is a need to employ soft computing techniques like Support Vector Machines (SVMs) which can do function approximation, and hence could achieve physically realistic simulations in realtime by making use of just a desktop computer. Present work tries to simulate a pig liver in realtime. Liver is assumed to be homogeneous, isotropic, and hyperelastic. Hyperelastic material constants are taken from the literature. An SVM is employed to achieve realistic simulations in realtime, using just a desktop computer. The code for the SVM is obtained from [1]. The SVM is trained using the dataset generated by performing hyperelastic analyses on the liver geometry, using the commercial finite element software package ANSYS. The methodology followed in the present work closely follows the one followed in [2] except that [2] uses Artificial Neural Networks (ANNs) while the present work uses SVMs to achieve realistic simulations in realtime. Results indicate the speed and accuracy that is obtained by employing the SVM for the targeted realistic and realtime simulation of the liver.

A study of the speed and the accuracy of the Boundary Element Method as applied to the computational simulation of biological organs

In this work, first a Fortran code is developed for three dimensional linear elastostatics using constant boundary elements; the code is based on a MATLAB code developed by the author earlier. Next, the code is parallelized using BLACS, MPI, and ScaLAPACK. Later, the parallelized code is used to demonstrate the usefulness of the Boundary Element Method (BEM) as applied to the realtime computational simulation of biological organs, while focusing on the speed and accuracy offered by BEM. A computer cluster is used in this part of the work. The commercial software package ANSYS is used to obtain the `exact' solution against which the solution from BEM is compared; analytical solutions, wherever available, are also used to establish the accuracy of BEM. A pig liver is the biological organ considered. Next, instead of the computer cluster, a Graphics Processing Unit (GPU) is used as the parallel hardware. Results indicate that BEM is an interesting choice for the simulation of biological organs. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature. Also, a serial MATLAB code, and both serial and parallel versions of a Fortran code, which can solve three dimensional (3D) linear elastostatic problems using constant boundary elements, are provided as supplementary files that can be freely downloaded.

A study of the speed and the accuracy of the Boundary Element Method as applied to the computational simulation of biological organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated, with specific reference to the speed and the accuracy offered by BEM. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. A pig liver is the biological organ considered. Results indicate that BEM is an interesting choice for the simulation of biological organs. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.

A Study of Speed of the Boundary Element Method as applied to the Realtime Computational Simulation of Biological Organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is the element type used. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. Results indicate that BEM is fast enough to provide for realtime graphics if biological organs are assumed to follow linear elastostatic material behavior. Although the present work does not conduct any simulation using nonlinear material models, results from using the linear elastostatic material model imply that it would be difficult to obtain realtime performance if highly nonlinear material models that properly characterize biological organs are used. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.

A literature survey on the real-time computational simulation of biological organs

This paper lists some references that could in some way be relevant in the context of the real-time computational simulation of biological organs, the research area being defined in a very broad sense. This paper contains 198 references.

Computational simulation of the flow-induced vibration of a circular cylinder subjected to wake interference

In this work, we considered the flow around two circular cylinders of equal diameter placed in tandem with respect to the incident uniform flow. The upstream cylinder was fixed and the downstream cylinder was completely free to move in the cross-stream direction, with no spring or damper attached to it. The centre-to-centre distance between the cylinders was four diameters, and the Reynolds number was varied from 100 to 645. We performed two- and three-dimensional simulations of this flow using a Spectral/hp element method to discretise the flow equations, coupled to a simple Newmark integration routine that solves the equation of the dynamics of the cylinder. The differences of the behaviours observed in the two- and three-dimensional simulations are highlighted and the data is analysed under the light of previously published experimental results obtained for higher Reynolds numbers.

Comparing the economic impacts of Asian integration by computational simulation analysis

The Geographical Simulation Model developed by IDE-JETRO (IDE-GSM) is a computer simulation model based on spatial economics. IDE-GSM enables us to predict the economic impacts of various trade and transport facilitation measures. Here, we mainly compare the prioritized projects of the Master Plan on ASEAN Connectivity (MPAC) and the Comprehensive Asia Development Plan (CADP). MPAC focus on specific hard or soft infrastructure projects that connect one ASEAN member state to another while the CADP emphasizes the importance of economic corridors or linkages between a large cluster and another cluster. As compared with MPAC projects, the simulation analysis shows that CADP projects have much larger positive impacts on ASEAN countries.

Impact of coronary tortuosity on coronary pressure: Numerical simulation study

Background: Coronary tortuosity (CT) is a common coronary angiographic finding. Whether CT leads to an apparent reduction in coronary pressure distal to the tortuous segment of the coronary artery is still unknown. The purpose of this study is to determine the impact of CT on coronary pressure distribution by numerical simulation. Methods: 21 idealized models were created to investigate the influence of coronary tortuosity angle (CTA) and coronary tortuosity number (CTN) on coronary pressure distribution. A 2D incompressible Newtonian flow was assumed and the computational simulation was performed using finite volume method. CTA of 30°, 60°, 90°, 120° and CTN of 0, 1, 2, 3, 4, 5 were discussed under both steady and pulsatile conditions, and the changes of outlet pressure and inlet velocity during the cardiac cycle were considered. Results: Coronary pressure distribution was affected both by CTA and CTN. We found that the pressure drop between the start and the end of the CT segment decreased with CTA, and the length of the CT segment also declined with CTA. An increase in CTN resulted in an increase in the pressure drop. Conclusions: Compared to no-CT, CT can results in more decrease of coronary blood pressure in dependence on the severity of tortuosity and severe CT may cause myocardial ischemia.

Correlation of solder paste rheology with computational simulations of the stencil printing process

Soldering technologies continue to evolve to meet the demands of the continuous miniaturisation of electronic products, particularly in the area of solder paste formulations used in the reflow soldering of surface mount devices. Stencil printing continues to be a leading process used for the deposition of solder paste onto printed circuit boards (PCBs) in the volume production of electronic assemblies, despite problems in achieving a consistent print quality at an ultra-fine pitch. In order to eliminate these defects a good understanding of the processes involved in printing is important. Computational simulations may complement experimental print trials and paste characterisation studies, and provide an extra dimension to the understanding of the process. The characteristics and flow properties of solder pastes depend primarily on their chemical and physical composition and good material property data is essential for meaningful results to be obtained by computational simulation.This paper describes paste characterisation and computational simulation studies that have been undertaken through the collaboration of the School of Aeronautical, Mechanical and Manufacturing Engineering at Salford University and the Centre for Numerical Modelling and Process Analysis at the University of Greenwich. The rheological profile of two different paste formulations (lead and lead-free) for sub 100 micron flip-chip devices are tested and applied to computational simulations of their flow behaviour during the printing process.

Investigação das características I x V e C x V de NCPS puro, com nitrogênio substitucional carregado (-1 e +1) e com grupos doador (NO2)-aceitador (NH2) através de métodos derivados de hartree-fock

Neste trabalho, fizemos uma investigação sobre o estudo teórico das características I x V e C x V de Nanotubo Carbono de Parede Simples (NCPS) puro, com Nitrogênio substitucional carregado com cargas -1 (caracterizando um indicativo de dopagem tipo n) e +1 (caracterizando um indicativo de dopagem tipo p) e na presença de grupos doador (NO₂)-aceitador (NH₂), através da simulação computacional do estado fundamental de NCPS, bem como de sua estrutura eletrônica e propriedades ópticas, utilizando parametrizações semi-empíricas AM1 (Austin Mudel 1) e ZINDO/S-ClS (Zerner´s lntermediate Neglect of Differential Orbital/Spectroscopic - Cunfiguration lnteraction Single) derivadas da Teoria de Hartree-Fock baseada em técnicas de química quântica. Por meio deste modelo teórico analisamos as propriedades ópticas e eletrônicas, de maior interesse para esses materiais, a fim de se entender a melhor forma de interação desses materiais na fabricação de dispositivos eletrônicos, tais como TECs (Transistores de Efeito de Campo) ou em aplicações em optoeletrônica tais como DEL (Dispositivo Emissor de Luz). Observamos que NCPS com Nitrogênio substitucional apresentam defeitos conformacionais do tipo polarônico. Fizemos as curvas dos espectros UV-visível de Absorção para NCPS armchair e zigzag puro, com Nitrogênio substitucional carregado com cargas (-1 e +1) e na presença de grupos doador (NO₂)-aceitador (NH₂), quando perturbados por intensidades diferentes de campo elétrico. Verificamos que em NCPS zigzag ao aumentarmos a intensidade do campo elétrico, suas curvas sofrem grandes perturbações. Obtivemos as curvas p x E, I x V e C x V para esses NCPS, concluímos que NCPS armchair possui comportamento resistor, pois suas curvas são lineares e zigzag possui comportamento semelhante ao dos dispositivos eletrônicos importantes para o avanço tecnológico. Assim, nossos resultados estão de bom acordo com os resultados experimentais e teóricos de NCPS puro e com Nitrogênio encontrados na literatura.