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ENGINEERING (1206 journals)                  1 2 3 4 5 6 7 | Last

Showing 1 - 200 of 1205 Journals sorted alphabetically
3 Biotech     Open Access   (Followers: 7)
3D Research     Hybrid Journal   (Followers: 19)
AAPG Bulletin     Hybrid Journal   (Followers: 6)
AASRI Procedia     Open Access   (Followers: 15)
Abstract and Applied Analysis     Open Access   (Followers: 3)
Aceh International Journal of Science and Technology     Open Access   (Followers: 2)
ACS Nano     Full-text available via subscription   (Followers: 234)
Acta Geotechnica     Hybrid Journal   (Followers: 7)
Acta Metallurgica Sinica (English Letters)     Hybrid Journal   (Followers: 5)
Acta Polytechnica : Journal of Advanced Engineering     Open Access   (Followers: 2)
Acta Scientiarum. Technology     Open Access   (Followers: 3)
Acta Universitatis Cibiniensis. Technical Series     Open Access  
Active and Passive Electronic Components     Open Access   (Followers: 7)
Adaptive Behavior     Hybrid Journal   (Followers: 11)
Adıyaman Üniversitesi Mühendislik Bilimleri Dergisi     Open Access  
Adsorption     Hybrid Journal   (Followers: 4)
Advanced Engineering Forum     Full-text available via subscription   (Followers: 6)
Advanced Science     Open Access   (Followers: 5)
Advanced Science Focus     Free   (Followers: 3)
Advanced Science Letters     Full-text available via subscription   (Followers: 7)
Advanced Science, Engineering and Medicine     Partially Free   (Followers: 7)
Advanced Synthesis & Catalysis     Hybrid Journal   (Followers: 17)
Advances in Calculus of Variations     Hybrid Journal   (Followers: 2)
Advances in Catalysis     Full-text available via subscription   (Followers: 5)
Advances in Complex Systems     Hybrid Journal   (Followers: 7)
Advances in Engineering Software     Hybrid Journal   (Followers: 25)
Advances in Fuel Cells     Full-text available via subscription   (Followers: 15)
Advances in Fuzzy Systems     Open Access   (Followers: 5)
Advances in Geosciences (ADGEO)     Open Access   (Followers: 10)
Advances in Heat Transfer     Full-text available via subscription   (Followers: 21)
Advances in Magnetic and Optical Resonance     Full-text available via subscription   (Followers: 9)
Advances in Natural Sciences: Nanoscience and Nanotechnology     Open Access   (Followers: 28)
Advances in Operations Research     Open Access   (Followers: 11)
Advances in OptoElectronics     Open Access   (Followers: 5)
Advances in Physics Theories and Applications     Open Access   (Followers: 12)
Advances in Polymer Science     Hybrid Journal   (Followers: 41)
Advances in Porous Media     Full-text available via subscription   (Followers: 4)
Advances in Remote Sensing     Open Access   (Followers: 37)
Advances in Science and Research (ASR)     Open Access   (Followers: 6)
Aerobiologia     Hybrid Journal   (Followers: 1)
African Journal of Science, Technology, Innovation and Development     Hybrid Journal   (Followers: 4)
AIChE Journal     Hybrid Journal   (Followers: 30)
Ain Shams Engineering Journal     Open Access   (Followers: 5)
Akademik Platform Mühendislik ve Fen Bilimleri Dergisi     Open Access  
Alexandria Engineering Journal     Open Access   (Followers: 1)
AMB Express     Open Access   (Followers: 1)
American Journal of Applied Sciences     Open Access   (Followers: 28)
American Journal of Engineering and Applied Sciences     Open Access   (Followers: 11)
American Journal of Engineering Education     Open Access   (Followers: 9)
American Journal of Environmental Engineering     Open Access   (Followers: 16)
American Journal of Industrial and Business Management     Open Access   (Followers: 23)
Analele Universitatii Ovidius Constanta - Seria Chimie     Open Access  
Annals of Combinatorics     Hybrid Journal   (Followers: 3)
Annals of Pure and Applied Logic     Open Access   (Followers: 2)
Annals of Regional Science     Hybrid Journal   (Followers: 7)
Annals of Science     Hybrid Journal   (Followers: 7)
Applicable Algebra in Engineering, Communication and Computing     Hybrid Journal   (Followers: 2)
Applicable Analysis: An International Journal     Hybrid Journal   (Followers: 1)
Applied Catalysis A: General     Hybrid Journal   (Followers: 6)
Applied Catalysis B: Environmental     Hybrid Journal   (Followers: 15)
Applied Clay Science     Hybrid Journal   (Followers: 5)
Applied Computational Intelligence and Soft Computing     Open Access   (Followers: 12)
Applied Magnetic Resonance     Hybrid Journal   (Followers: 4)
Applied Nanoscience     Open Access   (Followers: 8)
Applied Network Science     Open Access  
Applied Numerical Mathematics     Hybrid Journal   (Followers: 5)
Applied Physics Research     Open Access   (Followers: 3)
Applied Sciences     Open Access   (Followers: 2)
Applied Spatial Analysis and Policy     Hybrid Journal   (Followers: 4)
Arabian Journal for Science and Engineering     Hybrid Journal   (Followers: 5)
Archives of Computational Methods in Engineering     Hybrid Journal   (Followers: 4)
Archives of Foundry Engineering     Open Access  
Archives of Thermodynamics     Open Access   (Followers: 7)
Arkiv för Matematik     Hybrid Journal   (Followers: 1)
ASEE Prism     Full-text available via subscription   (Followers: 3)
Asian Engineering Review     Open Access  
Asian Journal of Applied Science and Engineering     Open Access   (Followers: 1)
Asian Journal of Applied Sciences     Open Access   (Followers: 2)
Asian Journal of Biotechnology     Open Access   (Followers: 8)
Asian Journal of Control     Hybrid Journal  
Asian Journal of Current Engineering & Maths     Open Access  
Asian Journal of Technology Innovation     Hybrid Journal   (Followers: 8)
Assembly Automation     Hybrid Journal   (Followers: 2)
at - Automatisierungstechnik     Hybrid Journal   (Followers: 1)
ATZagenda     Hybrid Journal  
ATZextra worldwide     Hybrid Journal  
Australasian Physical & Engineering Sciences in Medicine     Hybrid Journal   (Followers: 1)
Australian Journal of Multi-Disciplinary Engineering     Full-text available via subscription   (Followers: 2)
Autonomous Mental Development, IEEE Transactions on     Hybrid Journal   (Followers: 8)
Avances en Ciencias e Ingeniería     Open Access  
Balkan Region Conference on Engineering and Business Education     Open Access   (Followers: 1)
Bangladesh Journal of Scientific and Industrial Research     Open Access  
Basin Research     Hybrid Journal   (Followers: 5)
Batteries     Open Access   (Followers: 4)
Bautechnik     Hybrid Journal   (Followers: 1)
Bell Labs Technical Journal     Hybrid Journal   (Followers: 23)
Beni-Suef University Journal of Basic and Applied Sciences     Open Access   (Followers: 4)
BER : Manufacturing Survey : Full Survey     Full-text available via subscription   (Followers: 2)
BER : Motor Trade Survey     Full-text available via subscription   (Followers: 1)
BER : Retail Sector Survey     Full-text available via subscription   (Followers: 2)
BER : Retail Survey : Full Survey     Full-text available via subscription   (Followers: 2)
BER : Survey of Business Conditions in Manufacturing : An Executive Summary     Full-text available via subscription   (Followers: 3)
BER : Survey of Business Conditions in Retail : An Executive Summary     Full-text available via subscription   (Followers: 3)
Bharatiya Vaigyanik evam Audyogik Anusandhan Patrika (BVAAP)     Open Access   (Followers: 1)
Biofuels Engineering     Open Access  
Biointerphases     Open Access   (Followers: 1)
Biomaterials Science     Full-text available via subscription   (Followers: 10)
Biomedical Engineering     Hybrid Journal   (Followers: 16)
Biomedical Engineering and Computational Biology     Open Access   (Followers: 13)
Biomedical Engineering Letters     Hybrid Journal   (Followers: 5)
Biomedical Engineering, IEEE Reviews in     Full-text available via subscription   (Followers: 17)
Biomedical Engineering, IEEE Transactions on     Hybrid Journal   (Followers: 31)
Biomedical Engineering: Applications, Basis and Communications     Hybrid Journal   (Followers: 5)
Biomedical Microdevices     Hybrid Journal   (Followers: 9)
Biomedical Science and Engineering     Open Access   (Followers: 4)
Biomedizinische Technik - Biomedical Engineering     Hybrid Journal  
Biomicrofluidics     Open Access   (Followers: 4)
BioNanoMaterials     Hybrid Journal   (Followers: 2)
Biotechnology Progress     Hybrid Journal   (Followers: 39)
Boletin Cientifico Tecnico INIMET     Open Access  
Botswana Journal of Technology     Full-text available via subscription  
Boundary Value Problems     Open Access   (Followers: 1)
Brazilian Journal of Science and Technology     Open Access   (Followers: 2)
Broadcasting, IEEE Transactions on     Hybrid Journal   (Followers: 10)
Bulletin of Canadian Petroleum Geology     Full-text available via subscription   (Followers: 14)
Bulletin of Engineering Geology and the Environment     Hybrid Journal   (Followers: 3)
Bulletin of the Crimean Astrophysical Observatory     Hybrid Journal  
Cahiers, Droit, Sciences et Technologies     Open Access  
Calphad     Hybrid Journal  
Canadian Geotechnical Journal     Hybrid Journal   (Followers: 14)
Canadian Journal of Remote Sensing     Full-text available via subscription   (Followers: 41)
Case Studies in Engineering Failure Analysis     Open Access   (Followers: 8)
Case Studies in Thermal Engineering     Open Access   (Followers: 3)
Catalysis Communications     Hybrid Journal   (Followers: 6)
Catalysis Letters     Hybrid Journal   (Followers: 2)
Catalysis Reviews: Science and Engineering     Hybrid Journal   (Followers: 8)
Catalysis Science and Technology     Free   (Followers: 6)
Catalysis Surveys from Asia     Hybrid Journal   (Followers: 3)
Catalysis Today     Hybrid Journal   (Followers: 8)
CEAS Space Journal     Hybrid Journal  
Cellular and Molecular Neurobiology     Hybrid Journal   (Followers: 3)
Central European Journal of Engineering     Hybrid Journal   (Followers: 1)
CFD Letters     Open Access   (Followers: 6)
Chaos : An Interdisciplinary Journal of Nonlinear Science     Hybrid Journal   (Followers: 2)
Chaos, Solitons & Fractals     Hybrid Journal   (Followers: 3)
Chinese Journal of Catalysis     Full-text available via subscription   (Followers: 2)
Chinese Journal of Engineering     Open Access   (Followers: 2)
Chinese Science Bulletin     Open Access   (Followers: 1)
Ciencia e Ingenieria Neogranadina     Open Access  
Ciencia en su PC     Open Access   (Followers: 1)
Ciencias Holguin     Open Access   (Followers: 1)
CienciaUAT     Open Access  
Cientifica     Open Access  
CIRP Annals - Manufacturing Technology     Full-text available via subscription   (Followers: 11)
CIRP Journal of Manufacturing Science and Technology     Full-text available via subscription   (Followers: 14)
City, Culture and Society     Hybrid Journal   (Followers: 21)
Clay Minerals     Full-text available via subscription   (Followers: 10)
Clean Air Journal     Full-text available via subscription   (Followers: 2)
Coal Science and Technology     Full-text available via subscription   (Followers: 3)
Coastal Engineering     Hybrid Journal   (Followers: 11)
Coastal Engineering Journal     Hybrid Journal   (Followers: 5)
Coatings     Open Access   (Followers: 3)
Cogent Engineering     Open Access   (Followers: 2)
Cognitive Computation     Hybrid Journal   (Followers: 4)
Color Research & Application     Hybrid Journal   (Followers: 1)
COMBINATORICA     Hybrid Journal  
Combustion Theory and Modelling     Hybrid Journal   (Followers: 13)
Combustion, Explosion, and Shock Waves     Hybrid Journal   (Followers: 13)
Communications Engineer     Hybrid Journal   (Followers: 1)
Communications in Numerical Methods in Engineering     Hybrid Journal   (Followers: 2)
Components, Packaging and Manufacturing Technology, IEEE Transactions on     Hybrid Journal   (Followers: 26)
Composite Interfaces     Hybrid Journal   (Followers: 6)
Composite Structures     Hybrid Journal   (Followers: 259)
Composites Part A : Applied Science and Manufacturing     Hybrid Journal   (Followers: 181)
Composites Part B : Engineering     Hybrid Journal   (Followers: 236)
Composites Science and Technology     Hybrid Journal   (Followers: 216)
Comptes Rendus Mécanique     Full-text available via subscription   (Followers: 2)
Computation     Open Access  
Computational Geosciences     Hybrid Journal   (Followers: 14)
Computational Optimization and Applications     Hybrid Journal   (Followers: 7)
Computational Science and Discovery     Full-text available via subscription   (Followers: 2)
Computer Applications in Engineering Education     Hybrid Journal   (Followers: 6)
Computer Science and Engineering     Open Access   (Followers: 17)
Computers & Geosciences     Hybrid Journal   (Followers: 28)
Computers & Mathematics with Applications     Full-text available via subscription   (Followers: 5)
Computers and Electronics in Agriculture     Hybrid Journal   (Followers: 4)
Computers and Geotechnics     Hybrid Journal   (Followers: 10)
Computing and Visualization in Science     Hybrid Journal   (Followers: 5)
Computing in Science & Engineering     Full-text available via subscription   (Followers: 30)
Conciencia Tecnologica     Open Access  
Concurrent Engineering     Hybrid Journal   (Followers: 3)
Continuum Mechanics and Thermodynamics     Hybrid Journal   (Followers: 6)
Control and Dynamic Systems     Full-text available via subscription   (Followers: 9)
Control Engineering Practice     Hybrid Journal   (Followers: 42)
Control Theory and Informatics     Open Access   (Followers: 8)
Corrosion Science     Hybrid Journal   (Followers: 25)
CT&F Ciencia, Tecnologia y Futuro     Open Access  
CTheory     Open Access  
Current Applied Physics     Full-text available via subscription   (Followers: 4)
Current Science     Open Access   (Followers: 58)

        1 2 3 4 5 6 7 | Last

Journal Cover Communications in Numerical Methods in Engineering
  [2 followers]  Follow
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 1069-8299 - ISSN (Online) 1099-0887
   Published by John Wiley and Sons Homepage  [1577 journals]
  • Influence of Bronchial Diameter Change on the airflow dynamics Based on a
           Pressure-controlled Ventilation System
    • Authors: Shuai Ren; Maolin Cai, Yan Shi, Weiqing Xu, Xiaohua Douglas Zhang
      Abstract: Bronchial diameter is a key parameter that affects the respiratory treatment of mechanically ventilated patients. In this paper, to reveal the influence of bronchial diameter on the airflow dynamics of pressure-controlled mechanically ventilated patients, a new respiratory system model is presented which combines multi-generation airways with lungs. Furthermore, experiments and simulation studies to verify the model are performed. Finally, through the simulation study, it can be determined that in airway generations 2 to 7, when the diameter is reduced to half of the original value, the maximum air pressure (maximum air pressure in lungs) decreases by nearly 16%, the maximum flow decreases by nearly 30%, and the total airway pressure loss (sum of each generation pressure drop) is more than 5 times the original value. Moreover, in airway generations 8 to 16, with increasing diameter, the maximum air pressure, maximum flow and total airway pressure loss remain almost constant. When the diameter is reduced to half of the original value, the maximum air pressure decreases by 3%, the maximum flow decreases by nearly 5%, and the total airway pressure loss increases by 200%. The study creates a foundation for improvement in respiratory disease diagnosis and treatment.
      PubDate: 2017-09-14T07:40:35.205308-05:
      DOI: 10.1002/cnm.2929
  • Hybrid cell-centred/vertex model for multicellular systems with
           equilibrium-preserving remodelling
    • Authors: P. Mosaffa; A. Rodríguez-Ferran, J. J. Muñoz*
      Abstract: We present a hybrid vertex/cell-centred model for mechanically simulating planar cellular monolayers undergoing cell reorganisation. Cell centres are represented by a triangular nodal network, while the cell boundaries are formed by an associated vertex network. The two networks are coupled through a kinematic constraint which we allow to relax progressively. Special attention is paid to the change of cell-cell connectivity due to cell reorganisation or remodelling events. We handle these situations by using a variable resting length and applying an Equilibrium-Preserving Mapping (EPM) on the new connectivity, which computes a new set of resting lengths that preserve nodal and vertex equilibrium. We illustrate the properties of the model by simulating monolayers subjected to imposed extension and during a wound healing process. The evolution of forces and the EPM are analysed during the remodelling events. As a by-product, the proposed technique enables to recover fully vertex or fully cell-centred models in a seamless manner by modifying a numerical parameter of the model. This article is protected by copyright. All rights reserved.
      PubDate: 2017-09-12T16:50:31.860935-05:
      DOI: 10.1002/cnm.2928
  • Haptic simulation of tissue tearing during surgery
    • Authors: C. Quesada; I. Alfaro, D. González, F. Chinesta, E. Cueto
      Abstract: We present a method for the real-time, interactive simulation of tissue tearing during laparoscopic surgery. The method is designed to work at haptic feedback rates (i.e., around 1kHz). Tissue tearing is simulated under the general framework of continuum damage mechanics. The problem is stated as a general, multidimensional parametric problem, which is solved by means of Proper Generalized Decomposition (PGD) methods. One of the main novelties is the reduction of history-dependent problems, such as damage mechanics, by resorting to an approach in which a reduced-order field of initial damage values is considered as a parameter of the formulation. We focus on the laparoscopic cholecystectomy procedure as a general example of the performance of the method. This article is protected by copyright. All rights reserved.
      PubDate: 2017-09-12T15:05:30.252407-05:
      DOI: 10.1002/cnm.2926
  • Viscous effects in pelvic floor muscles during childbirth: a numerical
    • Authors: M.C.P. Vila Pouca; J.P.S. Ferreira, D.A. Oliveira, M.P.L. Parente, R.M. Natal Jorge
      Abstract: During vaginal delivery women sustain stretching of their pelvic floor, risking tissue injury and adverse outcomes. Realistic numerical simulations of childbirth can help in the understanding of the pelvic floor mechanics and on the prevention of related disorders.In previous studies, biomechanical finite element simulations of a vaginal delivery have been performed disregarding the viscous effects present on all biological soft tissues. The inclusion of the viscoelastic behaviour is fundamental, since it allows to investigate rate-dependent responses. The present work uses a visco-hyperelastic constitutive model to evaluate how the childbirth duration affects the efforts sustained by the pelvic floor during delivery.It was concluded that viscoelasticity adds a stiffness component that leads to higher forces comparing with the elastic response. Viscous solutions are rate-dependent and precipitous labours could be associated to higher efforts, while lower reaction forces were denoted for normal and prolonged labours, respectively. The existence of resting stages during labour demonstrated the capability of the tissue to relax and recover some of the initial properties, which helped to lower the forces and stresses involved.The present work represents a step further in achieving a robust non-invasive procedure, allowing to estimate how obstetrical factors influence labour and its outcomes.
      PubDate: 2017-09-08T16:50:24.626422-05:
      DOI: 10.1002/cnm.2927
  • Relative pressure estimation from velocity measurements in blood flows:
           state-of-the-art and new approaches
    • Authors: Cristóbal Bertoglio; Rodolfo Núñez, Felipe Galarce, David Nordsletten, Axel Osses
      Abstract: The relative pressure difference across stenotic blood vessels serves as an important clinical index for the diagnosis of many cardiovascular diseases. While the clinical gold standard for relative pressure difference measurements is invasive catheterization, Phase-Contrast Magnetic Resonance Imaging has emerged as a promising tool for enabling a non-invasive quantification, by linking highly spatially resolved velocity measurements with relative pressures via the incompressible Navier-Stokes equations. In this work we provide a review and analysis of current methods for relative pressure estimation and propose three additional techniques. Methods are compared using synthetic data from numerical examples and sensitivity to subsampling and noise was explored. Through our analysis, we verify that the newly proposed approaches are more robust with respect to spatial subsampling and less sensitive to noise, and therefore provide improved means for estimating relative pressure differences non-invasively. This article is protected by copyright. All rights reserved.
      PubDate: 2017-09-07T21:20:41.749902-05:
      DOI: 10.1002/cnm.2925
  • Issue Information
    • Abstract: No abstract is available for this article.
      PubDate: 2017-09-05T01:18:42.078985-05:
      DOI: 10.1002/cnm.2923
  • Flow Features and Device-Induced Blood Trauma in CF-VADs under a pulsatile
           blood flow condition: A CFD Comparative Study
    • Authors: Zengsheng Chen; Sofen K. Jena, Guruprasad A. Giridharan, Steven C. Koenig, Mark S. Slaughter, Bartley P. Griffith, Zhongjun J. Wu
      Abstract: In this study, the flow features and device-associated blood trauma in four clinical ventricular assist devices (VADs) (two implantable axial VADs, one implantable centrifugal VAD, and one extracorporeal VAD) were computationally analyzed under clinically relevant pulsatile flow conditions. The four VADs were operated at fixed pump speed at a mean rate of 4.5 L/min. Mean pressure difference, wall shear stress (WSS), volume distribution of scalar shear stress (SSS), and shear-induced hemolysis index (HI) were derived from the flow field of each VAD and were compared. The computationally predicted mean pressure difference across the three implantable VADs was ~ 70mm Hg and the extracorporeal VAD was ~ 345 mmHg, which matched well with their reported pressure-flow curves. The axial VADs had higher mean WSS and SSS compared to the centrifugal VADs. However, the residence time of the centrifugal VADs was much longer compared to the axial VADs because of the large volume of the centrifugal VADs. The highest SSS was observed in one axial VAD and the longest exposure time was observed in one centrifugal VAD. These two VADs generated the highest HI. The shear-induced HI varied as a function of flow rate within each cardiac cycle. At fixed pump speed, the HI was greatest at low flow rate due to longer exposure time to shear stress compared to at high flow rate. Subsequently, we hypothesize that in order to reduce the risk of blood trauma during VAD support, shear stress magnitude and exposure time need to be minimized.
      PubDate: 2017-08-31T17:00:38.953226-05:
      DOI: 10.1002/cnm.2924
  • The impact of personalized probabilistic wall thickness models on peak
           wall stress in abdominal aortic aneurysms
    • Authors: J. Biehler; W. A. Wall
      Abstract: If computational models are ever to be used in high stakes decision making in clinical practice, the use of personalized models and predictive simulation techniques is a must. This entails rigorous quantification of uncertainties as well as harnessing available patient-specific data to the greatest extent possible. Although researcher are beginning to realize that taking uncertainty in model input parameters into account is a necessity, the predominantly used probabilistic description for these uncertain parameters are based on elementary random variable models. In this work, we set out for a comparison of different probabilistic models for uncertain input parameters using the example of an uncertain wall thickness in finite element models of abdominal aortic aneurysms. We provide the first comparison between a random variable and a random field model for the aortic wall and investigate the impact on the probability distribution of the computed peak wall stress. Moreover, we show that the uncertainty about the prevailing peak wall stress can be reduced if non-invasively available, patient-specific data is harnessed for the construction of the probabilistic wall thickness model. This article is protected by copyright. All rights reserved.
      PubDate: 2017-08-10T10:49:35.686683-05:
      DOI: 10.1002/cnm.2922
  • A Comprehensive Pipeline for Multi-Resolution Modeling of the Mitral
           Valve: Validation, Computational Efficiency, and Predictive Capability
    • Authors: Andrew Drach; Amir H. Khalighi, Michael S. Sacks
      Abstract: Multiple studies have demonstrated that the pathological geometries unique to each patient can affect the durability of mitral valve (MV) repairs. While computational modeling of the MV is a promising approach to improve the surgical outcomes, the complex MV geometry precludes use of simplified models. Moreover, the lack of complete in-vivo geometric information presents significant challenges in the development of patient-specific computational models. There is thus a need to determine the level of detail necessary for predictive MV models. To address this issue, we have developed a novel pipeline for building attribute-rich computational models of MV with varying fidelity directly from the in-vitro imaging data. The approach combines high-resolution geometric information from loaded and unloaded states to achieve a high level of anatomic detail, followed by mapping and parametric embedding of tissue attributes to build a high resolution, attribute-rich computational models. Subsequent lower resolution models were then developed, and evaluated by comparing the displacements and surface strains to those extracted from the imaging data. We then identified the critical levels of fidelity for building predictive MV models in the dilated and repaired states. We demonstrated that a model with a feature size of ~5 mm and mesh size of ~1 mm was sufficient to predict the overall MV shape, stress, and strain distributions with high accuracy. However, we also noted that more detailed models were found to be needed to simulate microstructural events. We conclude that the developed pipeline enables sufficiently complex models for biomechanical simulations of MV in normal, dilated, repaired states.
      PubDate: 2017-08-03T20:25:28.324152-05:
      DOI: 10.1002/cnm.2921
  • Phase Contrast Cell Detection Using Multi-level Classification
    • Authors: Ehab Essa; Xianghua Xie
      Abstract: In this paper, we propose a fully automated learning based approach for detecting cells in time-lapse phase contrast images. The proposed system combines two machine learning approaches to achieve bottom-up image segmentation. We apply pixel-wise classification using random forests (RF) classifiers to determine the potential location of the cells. Each pixel is classified into four categories (cell, mitotic cell, halo effect, and background noise). Various image features are extracted at different scales to train the RF classifier. The resulting probability map is partitioned using the k-means algorithm to form potential cell regions. These regions are expanded into the neighboring areas to recover some missing or broken cell regions. In order to validate the cell regions, another machine learning method based on the bag-of-features and spatial pyramid encoding is proposed. The result of the second classifier can be a validated cell, a merged cell, or a non-cell. In the case that the cell region is classified as a merged cell, it is split by using the seeded watershed method. The proposed method is demonstrated on several phase contrast image datasets, i.e. U2OS, HeLa, and NIH 3T3. In comparison to state-of-the-art cell detection techniques, the proposed method shows improved performance, particularly in dealing with noise interference and drastic shape variations. This article is protected by copyright. All rights reserved.
      PubDate: 2017-07-28T20:00:48.851712-05:
      DOI: 10.1002/cnm.2916
  • A Novel Method for Rapid and Quantitative Mechanical Assessment of Soft
           Tissue for Diagnostic Purposes: A Computational Study
    • Authors: Javier Palacio-Torralba; Daniel W. Good, Grant D. Stewart, S. Alan McNeill, Robert L. Reuben, Yuhang Chen
      Abstract: Biological tissues often experience drastic changes in their microstructure due to their pathophysiological conditions. Such microstructural changes could result in variations in mechanical properties, which can be used in diagnosing or monitoring a wide range of diseases, most notably cancer. This paves the avenue for non-invasive diagnosis by instrumented palpation although challenges remain in quantitatively assessing the amount of diseased tissue by means of mechanical characterization. This paper presents a framework for tissue diagnosis using a quantitative and efficient estimation of the fractions of cancerous and non-cancerous tissue without a priori knowledge of tissue microstructure. First, the sample is tested in a creep or stress relaxation experiment and the behavior is characterized using a single term Prony series. A rule of mixtures, which relates tumor fraction to the apparent mechanical properties, is then obtained by minimizing the difference between strain energy of a heterogeneous system and an equivalent homogeneous one. Finally, the percentage of each tissue constituent is predicted by comparing the observed relaxation time with that calculated from the rule of mixtures. The proposed methodology is assessed using models reconstructed from histological samples and magnetic resonance imaging of prostate. Results show that estimation of cancerous tissue fraction can be obtained with a maximum error of 12% when samples of different sizes, geometries and tumor fractions are presented. The proposed framework has the potential to be applied to a wide range of diseases such as rectal polyps, cirrhosis or breast and prostate cancer whose current primary diagnosis remains qualitative.
      PubDate: 2017-07-28T08:30:48.509986-05:
      DOI: 10.1002/cnm.2917
  • A New Type of Neurons for Machine Learning
    • Authors: Fenglei Fan; Wenxiang Cong, Ge Wang
      Abstract: In machine learning, the use of an artificial neural network is the mainstream approach. Such a network consists of layers of neurons. These neurons are of the same type characterized by the two features: (1) an inner product of an input vector and a matching weighting vector of trainable parameters and (2) a nonlinear excitation function. Here we investigate the possibility of replacing the inner product with a quadratic function of the input vector, thereby upgrading the 1st order neuron to the 2nd order neuron, empowering individual neurons, and facilitating the optimization of neural networks. Also, numerical examples are provided to illustrate the feasibility and merits of the 2nd order neurons. Finally, further topics are discussed.
      PubDate: 2017-07-27T10:05:23.223874-05:
      DOI: 10.1002/cnm.2920
  • Inverse estimation of cardiac activation times via gradient-based
    • Authors: Siri Kallhovd; Mary M. Maleckar, Marie E. Rognes
      Abstract: Computational modeling may provide a quantitative framework for integrating multi-scale data to gain insight into mechanisms of heart disease, identify and test pharmacological and electrical therapy and interventions, and support clinical decisions. Patient-specific computational cardiac models can help guide such procedures, and cardiac inverse modelling is a promising alternative to adequately personalize these models. Indeed, full cardiac inverse modelling is currently becoming computationally feasible; however, fundamental work to assess the feasibility of emerging techniques is still needed. In this study, we use a PDE-constrained optimal control approach to numerically investigate the identifiability of an initial activation sequence from synthetic (partial) observations of the extracellular potential using the bidomain approximation and 2D representations of cardiac tissue. Our results demonstrate that activation times and duration of several stimuli can be recovered even with high levels of noise, that it is sufficient to sample the observations at the ECG-relevant sampling frequency of 1 kHz, and that spatial resolutions that are coarser than the standard in electrophysiological simulations can be used. The optimization of activation times is still effective when synthetic data are generated with a different cell membrane kinetics model than optimized for. The findings thus indicate that the presented approach has potential for finding activation sequences from clinical data modalities, as an extension to existing cardiac imaging approaches. This article is protected by copyright. All rights reserved.
      PubDate: 2017-07-25T21:55:32.161194-05:
      DOI: 10.1002/cnm.2919
  • Benchmark problems for numerical treatment of backflow at open boundaries
    • Authors: C. Bertoglio; A. Caiazzo, Y. Bazilevs, M. Braack, M. Esmaily, V. Gravemeier, A. Marsden, O. Pironneau, I. E. Vignon-Clementel, W. A. Wall
      Abstract: In computational fluid dynamics, incoming velocity at open boundaries, or backflow, often yields to unphysical instabilities already for moderate Reynolds numbers. Several treatments to overcome these backflow instabilities have been proposed in the literature. However, these approaches have not yet been compared in detail in terms of accuracy in different physiological regimes, in particular due to the difficulty to generate stable reference solutions apart from analytical forms. In this work, we present a set of benchmark problems in order to compare different methods in different backflow regimes (with a full reversal flow and with propagating vortices after a stenosis). The examples are implemented in FreeFem++ and the source code is openly available, making them a solid basis for future method developments. This article is protected by copyright. All rights reserved.
      PubDate: 2017-07-25T20:55:41.808253-05:
      DOI: 10.1002/cnm.2918
  • Integration of element specific persistent homology and machine learning
           for protein-ligand binding affinity prediction
    • Authors: Zixuan Cang; Guo Wei Wei
      Abstract: Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, gene expression, etc. Accurate prediction of protein-ligand binding affinities is vital to rational drug design and the understanding of protein-ligand binding and binding induced function. Existing binding affinity prediction methods are inundated with geometric detail and involve excessively high dimensions, which undermines their predictive power for massive binding data. Topology provides the ultimate level of abstraction and thus incurs too much reduction in geometric information. Persistent homology embeds geometric information into topological invariants and bridges the gap between complex geometry and abstract topology. However, it oversimplifies biological information. This work introduces element specific persistent homology (ESPH) or multicomponent persistent homology to retain crucial biological information during topological simplification. The combination of ESPH and machine learning gives rise to a powerful paradigm for macromolecular analysis. Tests on two large data sets indicate that the proposed topology based machine learning paradigm outperforms other existing methods in protein-ligand binding affinity predictions. ESPH reveals protein-ligand binding mechanism that can not be attained from other conventional techniques. The present approach reveals that protein-ligand hydrophobic interactions are extended to 40Å  away from the binding site, which has a significant ramification to drug and protein design. This article is protected by copyright. All rights reserved.
      PubDate: 2017-07-05T02:55:27.623639-05:
      DOI: 10.1002/cnm.2914
  • Performance evaluation of GPU parallelization, space-time adaptive
    • Authors: Rafael S. Oliveira; Bernardo M. Rocha, Denise Burgarelli, Wagner Meira Jr, Christakis Constantinides, Rodrigo Weber dos Santos
      Abstract: The use of computer models as a tool for the study and understanding of the complex phenomena of cardiac electrophysiology has attained increased importance nowadays. At the same time, the increased complexity of the biophysical processes translates into complex computational and mathematical models. In order to speed up cardiac simulations and to allow more precise and realistic uses, two different techniques have been traditionally exploited: parallel computing and sophisticated numerical methods. In this work, we combine a modern parallel computing technique based on multicore and graphics processing units (GPUs), and a sophisticated numerical method based on a new space-time adaptive algorithm. We evaluate each technique alone and in different combinations: multicore and GPU, multicore and GPU and space adaptivity, multicore and GPU and space adaptivity and time adaptivity. All the techniques and combinations were evaluated under different scenarios: 3D simulations on slabs, 3D simulations on a ventricular mouse mesh, i.e., complex geometry, sinus-rhythm, and arrhythmic conditions. Our results suggest that multicore and GPU accelerate the simulations by an approximate factor of 33×, whereas the speedups attained by the space-time adaptive algorithms were approximately 48. Nevertheless, by combining all the techniques we obtained speedups that ranged between 165-498. The tested methods were able to reduce the execution time of a simulation by more than 498× for a complex cellular model in a slab geometry and by 165× in a realistic heart geometry simulating spiral waves. The proposed methods will allow faster and more realistic simulations in a feasible time with no significant loss of accuracy. This article is protected by copyright. All rights reserved.
      PubDate: 2017-06-21T13:40:56.262362-05:
      DOI: 10.1002/cnm.2913
  • Gingival morphology-controlled design of the complete denture baseplate
    • Authors: Ning Dai; Xiaoling Yu, Yuchun Sun
      Abstract: A removable complete denture is still the main selection for edentulous patients. Over the last five years, digital technologies for producing complete dentures have rapidly developed. Nevertheless, the design method for the baseplate has become the bottleneck of digital complete denture technology development. In this study, we report a novel method for the generation of aesthetic gingiva and polished surfaces of complete dentures that are driven by the feature curve, which can be conveniently modified using the gingival shape factor. A solid modeling method based on Poisson's surface reconstruction is used to generate a high-quality baseplate solid. This method can aid dentists to realize the rapid design process of personalized aesthetic baseplace. Finally, the experimental results verify that the method of digital design for the baseplate proposed is efficient and accurate (standard deviation < 0.01 mm).
      PubDate: 2017-06-16T00:15:20.964917-05:
      DOI: 10.1002/cnm.2911
  • Physically consistent data assimilation method based on feedback control
           for patient-specific blood flow analysis
    • Authors: Satoshi Ii; Mohd Azrul Hisham Mohd Adib, Yoshiyuki Watanabe, Shigeo Wada
      Abstract: This paper presents a novel data assimilation method for patient-specific blood flow analysis based on feedback control theory called the physically consistent feedback control-based data assimilation (PFC-DA) method. In the PFC-DA method, the signal, which is the residual error term of the velocity when comparing the numerical and reference measurement data, is cast as a source term in a Poisson equation for the scalar potential field that induces flow in a closed system. The pressure values at the inlet and outlet boundaries are recursively calculated by this scalar potential field. Hence, the flow field is physically consistent because it is driven by the calculated inlet and outlet pressures, without any artificial body forces. As compared with existing variational approaches, although this PFC-DA method does not guarantee the optimal solution, only one additional Poisson equation for the scalar potential field is required, providing a remarkable improvement for such a small additional computational cost at every iteration. Through numerical examples for 2D and 3D exact flow fields, with both noise-free and noisy reference data as well as a blood flow analysis on a cerebral aneurysm using actual patient data, the robustness and accuracy of this approach is shown. Moreover, the feasibility of a patient-specific practical blood flow analysis is demonstrated. This article is protected by copyright. All rights reserved.
      PubDate: 2017-06-15T01:25:26.026643-05:
      DOI: 10.1002/cnm.2910
  • Computational method for estimating boundary of abdominal subcutaneous fat
           for absolute electrical impedance tomography
    • Authors: Tohru F. Yamaguchi; Yoshiwo Okamoto
      Abstract: Abdominal fat accumulation is considered an essential indicator of human health. Electrical impedance tomography has considerable potential for abdominal fat imaging because of the low specific conductivity of human body fat. In this paper, we propose a robust reconstruction method for high-fidelity conductivity imaging by abstraction of the abdominal cross section using a relatively small number of parameters. Toward this end, we assume homogeneous conductivity in the abdominal subcutaneous fat area, and characterize its geometrical shape by parameters defined as the ratio of the distance from the center to boundary of subcutaneous fat to the distance from the center to outer boundary in 64 equiangular directions. To estimate the shape parameters, the sensitivity of the non-invasively measured voltages with respect to the shape parameters is formulated for numerical optimization. Numerical simulations are conducted to demonstrate the validity of the proposed method. A three-dimensional finite element method is used to construct a computer model of the human abdomen. The inverse problems of shape parameters and conductivities are solved concurrently by iterative forward and inverse calculations. As a result, conductivity images are reconstructed with a small systemic error of less than 1% for the estimation of the subcutaneous fat area. A novel method is devised for estimating the boundary of the abdominal subcutaneous fat. The fidelity of the overall reconstructed image to the reference image is significantly improved. The results demonstrate the possibility of realization of an abdominal fat scanner as a low-cost, radiation-free medical device. This article is protected by copyright. All rights reserved.
      PubDate: 2017-06-14T18:20:27.510624-05:
      DOI: 10.1002/cnm.2909
  • Mesh Free based Variational Level Set Evolution for Breast Region
           Segmentation and Abnormality Detection using Mammograms
    • Authors: Kanchan L. Kashyap; Manish K. Bajpai, Pritee Khanna, George Giakos
      Abstract: Automatic segmentation of abnormal region is a crucial task in computer aided detection system using mammograms. In this work an automatic abnormality detection algorithm using mammographic images is proposed. In the preprocessing step, partial differential equation based variational level set method is employed for breast region extraction. The evolution of the level set method is done by applying mesh-free based radial basis function. The limitation of mesh-based approach is removed by using mesh-free based RBF method. The evolution of variational level set function is also done by mesh-based finite difference method for comparison purpose. Unsharp masking and median filtering is employed for mammogram enhancement. Suspicious abnormal regions are segmented by applying fuzzy c-means clustering. Texture features are extracted from the segmented suspicious regions by computing local binary pattern and dominated rotated local binary pattern (DRLBP). Finally, suspicious regions are classified as normal or abnormal regions by means of support vector machine with linear, multilayer Perceptron, radial basis, and polynomial kernel function. The algorithm is validated on 322 sample mammograms of mammographic image analysis society (MIAS) and 500 mammograms from digital database for screening mammography (DDSM) datasets. Proficiency of the algorithm is quantified by using sensitivity, specificity, and accuracy. The highest sensitivity, specificity and accuracy of 93.96%, 95.01%, and 94.48%, respectively, are obtained on MIAS dataset using DRLBP feature with RBF kernel function. Whereas, the highest 92.31% sensitivity, 98.45% specificity, and 96.21% accuracy are achieved on DDSM dataset using DRLBP feature with RBF kernel function.
      PubDate: 2017-06-11T22:45:25.61669-05:0
      DOI: 10.1002/cnm.2907
  • Estimating the accuracy of a reduced-order model for the calculation of
           fractional flow reserve (FFR)
    • Authors: Etienne Boileau; Sanjay Pant, Carl Roobottom, Igor Sazonov, Jingjing Deng, Xianghua Xie, Perumal Nithiarasu
      Abstract: Image-based non-invasive fractional flow reserve (FFR) is an emergent approach to determine the functional relevance of coronary stenoses. The present work aimed to determine the feasibility of using a method based on coronary computed tomography angiography (CCTA) and reduced-order models (0D-1D) for the evaluation of coronary stenoses. The reduced-order methodology (cFFRro) was kept as simple as possible and did not include pressure drop or stenosis models. The geometry definition was incorporated into the physical model used to solve coronary flow and pressure. cFFRro was assessed on a virtual cohort of 30 coronary artery stenoses in 25 vessels and compared with a standard approach based on 3D computational fluid dynamics (cFFR3D). In this proof-of-concept study, we sought to investigate the influence of geometry and boundary conditions on the agreement between both methods. Performance on a per-vessel level showed a good correlation between both methods (Pearson's product-moment R = 0.885, P < 0.01), when using cFFR3D as the reference standard. The 95% limits of agreement were -0.116 and 0.08, and the mean bias was -0.018 (SD =0.05). Our results suggest no appreciable difference between cFFRro and cFFR3D with respect to lesion length and/or aspect ratio. At a fixed aspect ratio, however, stenosis severity and shape appeared to be the most critical factors accounting for differences in both methods. Despite the assumptions inherent to the 1D formulation, asymmetry did not seem to affect the agreement. The choice of boundary conditions is critical in obtaining a functionally significant drop in pressure. Our initial data suggest that this approach may be part of a broader risk assessment strategy aimed at increasing the diagnostic yield of cardiac catheterisation for in-hospital evaluation of hæmodynamically significant stenoses. This article is protected by copyright. All rights reserved.
      PubDate: 2017-06-09T19:35:19.317247-05:
      DOI: 10.1002/cnm.2908
  • Robust non-dimensional estimators to assess the nasal airflow in health
           and disease
    • Authors: E. Sanmiguel-Rojas; M. A. Burgos, C. del Pino, M. A. Sevilla-García, F. Esteban-Ortega
      Abstract: There are significant variations of both human nose shapes and airflow patterns inside nasal cavities, so it is difficult to provide a comprehensive medical identification using a universal template for what otolaryngologists consider normal breathing at rest. In addition, airflow patterns present even more random characteristics in diseased nasal cavities. In order to give a medical assessment to differentiate the nasal cavities in health and disease, we propose two non-dimensional estimators obtained from both medical images and computational fluid dynamics (CFD). The first mathematical estimator ϕ is a function of geometric features and potential asymmetries between nasal passages, while the second estimator R represents in fluid mechanics terms the total nasal resistance that corresponds to the atmosphere-choana pressure drop. These estimators only require global information such as nasal geometry and magnitudes of flow determined by simulations under laminar conditions. We find that these estimators take low and high values for healthy and diseased nasal cavities, respectively. Our study based on 24 healthy and 25 diseased Caucasian subjects, reveals that there is an interval of values associated with healthy cavities which clusters in a small region of the plane ϕ − R. Therefore, these estimators can be seen as a first approximation to provide nasal airflow data to the clinician in a non-invasive method, as the CT scan that provides the required images is routinely obtained as a result of the preexisting naso-sinusal condition. This article is protected by copyright. All rights reserved.
      PubDate: 2017-06-02T09:00:25.356701-05:
      DOI: 10.1002/cnm.2906
  • On the Importance of Retaining Stresses and Strains in Repositioning
           Computational Biomechanical Models of the Cervical Spine
    • Authors: Solomon Boakye-Yiadom; Duane S. Cronin
      Abstract: Human body models are created in a specific posture and often repositioned and analyzed without retaining stresses that result from repositioning. For example, repositioning a human neck model within the physiological range of motion to a head-turned posture prior to an impact results in initial stresses within the tissues distracted from their neutral position. The aim of this study was to investigate the effect of repositioning on the subsequent kinetics, kinematics and failure modes of a lower cervical spine motion segment, to support future research at the full neck level.Repositioning was investigated for three modes (tension, flexion, extension) and three load cases. The model was repositioned and loaded to failure in one continuous load history (Case 1), or repositioned then restarted with retained stresses and loaded to failure (Case 2). In Case 3, the model was repositioned and then restarted in a stress-free state, representing current repositioning methods. It was found that not retaining the repositioning stresses and strains resulted in different kinetics, kinematics or failure modes, depending on the mode of loading. For the motion segment model, the differences were associated with the intervertebral disc fiber reorientation and load distribution, since the disc underwent the largest deformation during repositioning.This study demonstrated that repositioning led to altered response and tissue failure, which is critical for computational models intended to predict injury at the tissue level. It is recommended that stresses and strains be included and retained for subsequent analysis when repositioning a human computational neck model.
      PubDate: 2017-06-01T13:35:26.890013-05:
      DOI: 10.1002/cnm.2905
  • A numerical investigation and experimental verification of size effects in
           loaded bovine cortical bone
    • Authors: J.C. Frame; M.A. Wheel, P.E. Riches
      Abstract: In this paper we present two and three dimensional finite element based numerical models of loaded bovine cortical bone that explicitly incorporate the dominant microstructural feature: the vascular channel or Haversian canal system. The finite element models along with the representation of the microstructure within them are relatively simple: two dimensional models, consisting of a structured mesh of linear elastic planar elements punctuated by a periodic distribution of circular voids, are used to represent beam samples of cortical bone in which the channels are orientated perpendicular to the sample major axis, while three dimensional models, employing a corresponding mesh of equivalent solid elements, represent those samples in which the canals are aligned with the axis. However, these models are exploited in an entirely novel approach involving the representation of material samples of different sizes and surface morphology. The numerical results obtained for the virtual material samples when loaded in bending indicate that they exhibit size effects not forecast by either classical (Cauchy) or more generalized elasticity theories. However, these effects are qualitatively consistent with those that we observed in a series of carefully conducted experiments involving the flexural testing of bone samples of different sizes. Encouraged by this qualitative agreement we have identified appropriate model parameters, primarily void volume fraction but also void separation and matrix modulus by matching the computed size effects to those we observed experimentally. Interestingly, the parameter choices that provide the most suitable match of these effects broadly concur with those we actually observed in cortical bone.
      PubDate: 2017-05-30T14:15:26.610941-05:
      DOI: 10.1002/cnm.2903
  • Modeling Liver Electrical Conductivity during Hypertonic Injection
    • Authors: Quim Castellví; Patricia Sánchez-Velázquez, Xavier Moll, Enrique Berjano, Anna Andaluz, Fernando Burdío, Bart Bijnens, Antoni Ivorra
      Abstract: Metastases in the liver frequently grow as scattered tumor nodules which neither can be removed by surgical resection nor focally ablated. Previously, we have proposed a novel technique based on irreversible electroporation which may be able to simultaneously treat all nodules in the liver while sparing healthy tissue. The proposed technique requires increasing the electrical conductivity of healthy liver by injecting a hypersaline solution through the portal vein. Aiming to assess the capability of increasing the global conductivity of the liver by means of hypersaline fluids, here it is presented a mathematical model which estimates the NaCl distribution within the liver and the resulting conductivity change. The model fuses well-established compartmental pharmacokinetic models of the organ with saline injection models employed for resuscitation treatments and it considers changes in sinusoidal blood viscosity due to the hypertonicity of the solution. Here it is also described a pilot experimental study in pigs in which different volumes of NaCl 20% (from 100 to 200 ml) were injected through the portal vein at different flow rates (from 53 to 171 ml/min). The in vivo conductivity results fit those obtained by the model, both quantitatively and qualitatively, being able to predict the maximum conductivity with a 14.6% average relative error. The maximum conductivity value was 0.44 S/m which corresponds to increasing four times the mean basal conductivity (0.11 S/m). The results suggest that the presented model is well suited for predicting on liver conductivity changes during hypertonic saline injection. This article is protected by copyright. All rights reserved.
      PubDate: 2017-05-30T09:24:25.751746-05:
      DOI: 10.1002/cnm.2904
  • Simulation of non-linear transient elastography: finite element model for
           the propagation of shear waves in homogeneous soft tissues
    • Authors: W. Ye; A. Bel-Brunon, S. Catheline, A. Combescure, M. Rochette
      Abstract: In this study, visco-hyperelastic Landau's model which is widely used in acoustical physic field is introduced into a finite element formulation. It is designed to model the non-linear behaviour of finite amplitude shear waves in soft solids, typically, in biological tissues. This law is employed in finite element models based on elastography experiments reported in [1], the simulations results show a good agreement with the experimental studyred: it is observed in both that a plane shear wave generates only odd harmonics and a nonplane wave generates both odd and even harmonics in the spectral domain. In the second part, a parametric study is carried out to analyze the influence of different factors on the generation of odd harmonics of plane wave. A quantitative relation is fitted between the odd harmonic amplitudes and the non-linear elastic parameter of Landau's model, which provides a practical guideline to identify the nonlinearity of homogeneous tissues using elastography experiment. This article is protected by copyright. All rights reserved.
      PubDate: 2017-05-26T04:15:46.117565-05:
      DOI: 10.1002/cnm.2901
  • Viscoelastic computational modeling of the human head-neck system:
           eigenfrequencies and time-dependent analysis
    • Authors: E. Boccia; A. Gizzi, C. Cherubini, M. G. C. Nestola, S. Filippi
      Abstract: A subject-specific three-dimensional viscoelastic finite element model of the human head-neck system is presented and investigated based on Computed Tomography and Magnetic Resonance biomedical images. Ad hoc imaging processing tools are developed for the reconstruction of the simulation domain geometry and the internal distribution of bone and soft tissues. Materials viscoelastic properties are characterized point-wise through an image-based interpolating function used then for assigning the constitutive prescriptions of a heterogenous viscoelastic continuum model. The numerical study is conducted both for modal and time-dependent analyses, compared with similar studies and validated against experimental evidences. Spatio-temporal analyses are performed upon different exponential swept sine wave localized stimulations. The modeling approach proposes a generalized, patient-specific investigation of sound wave transmission and attenuation within the human head-neck system comprising skull and brain tissues. Model extensions and applications are finally discussed. This article is protected by copyright. All rights reserved.
      PubDate: 2017-05-26T04:10:26.136612-05:
      DOI: 10.1002/cnm.2900
  • A Novel Approach for Early Evaluation of Orthodontic Process by a
           Numerical Thermo-Mechanical Analysis
    • Authors: Z. Heidary; A. Mojra, M. Shirazi, M. Bazargan
      Abstract: The main objective of this paper is to propose a novel method that provides an opportunity to evaluate an orthodontic process at early phase of the treatment. This was accomplished by finding out a correlation between the applied orthodontic force and thermal variations in the tooth structure. To this end, geometry of the human tooth surrounded by the connective soft tissue called the periodontal ligament and the bone was constructed by employing dental CT scan images of a specific case. The periodontal ligament was modeled by finite strain viscoelastic model through a nonlinear stress-strain relation (hyperelasticity) and nonlinear stress-time relation (viscoelasticity). The tooth structure was loaded by a lateral force with fifteen different quantities applied to twenty different locations, along the mid-edge of the tooth crown. The resultant compressive stress in the periodontal ligament was considered as the cause of elevated cell activity that was modeled by a transient heat flux in the thermal analysis. The heat flux value was estimated by conducting an experiment on a pair of rats. The numerical results showed that by applying an orthodontic force to the tooth structure, a significant temperature rise was observed. By measuring the temperature rise, the orthodontic process can be evaluated.
      PubDate: 2017-05-21T21:15:44.655178-05:
      DOI: 10.1002/cnm.2899
  • The Prediction of Viscous Losses and Pressure Drop in Models of the Human
    • Authors: A.K. Wells; I.P. Jones, S. Hamill, R. Bordas
      Abstract: This paper examines the viscous flow resistance in branching tubes as applied to simplified models of the lungs, and compares the results of Computational Fluid Dynamics (CFD) simulations for a range of conditions with measurement data. The results are in good agreement with the available measurement data for both inspiration and expiration. A detailed sensitivity analysis of the dissipation and viscous resistance in a branch then examines the ratio of the viscous resistance to that for a fully developed Poiseuille flow, Z. As other researchers have noted, the calculated resistances give lower values than those from the standard correlation of Pedley et al. The results demonstrate that the resistance is sensitive to the velocity profile upstream of the bifurcations, and explain from fluid dynamical considerations the apparent sensitivity of the resistance to the generation number of the branch. The paper also suggests a revised value for the calibration constant in the expression for Z. Finally, a limited set of results are presented for junction losses, and for expiration.
      PubDate: 2017-05-18T19:45:22.534632-05:
      DOI: 10.1002/cnm.2898
  • Analysis of Tenodesis Techiques for treatment of Scapholunate Instability
           using the Finite Element method
    • Authors: Teresa Alonso Rasgado; Qinghang Zhang, David Jimenez Cruz, Colin Bailey, Elizabeth Pinder, Avanthi Mandaleson, Sumedh Talwalkar
      Abstract: Chronic Scapholunate ligament (SL) injuries are difficult to treat and can lead to wrist dysfunction. Whilst several tendon reconstruction techniques have been employed in the management of SL instability, SL gap reappearance after surgery has been reported. Using finite element model and cadaveric study data we investigated the performance of the Corella, schapolunate axis (SLAM) and modified Brunelli tenodesis (MBT) techniques. Virtual tenodesis surgery was undertaken in 3D finite element (FE) models to obtain the scapholunate (SL) gap and angle resulting from the three reconstruction techniques. The Corella technique was found to achieve the SL gap and angle closest to the intact, restoring SL gap and angle to within 5.6% and 0.6% respectively. The MBT method resulted in an SL gap least close to the intact. The results of our study indicate that the contribution of volar SLIL to scapholunate stability could be important.
      PubDate: 2017-05-18T18:50:24.082692-05:
      DOI: 10.1002/cnm.2897
  • The role of angled-tip microcatheter and microsphere injection velocity in
           liver radioembolization: a computational particle–hemodynamics study
    • Authors: Jorge Aramburu; Raúl Anton, Alejandro Rivas, Juan Carlos Ramos, Bruno Sangro, José Ignacio Bilbao
      Abstract: Liver radioembolization is a promising treatment option for combating liver tumors. It is performed by placing a microcatheter in the hepatic artery and administering radiation-emitting microspheres through the arterial bloodstream so that they get lodged in the tumoral bed. In avoiding nontarget radiation, the standard practice is to conduct a pretreatment, in which the microcatheter location and injection velocity are decided. However, between pretreatment and actual treatment some of the parameters that influence the particle distribution in the liver can vary, resulting in radiation-induced complications. The present study aims to analyze the influence of a commercially available microcatheter with an angled tip and particle injection velocity in terms of segment-to-segment particle distribution. Specifically, four tip orientations and two injection velocities are combined to yield a set of eight numerical simulations of the particle–hemodynamics in a patient-specific truncated hepatic artery. For each simulation, four cardiac pulses are simulated. Particles are injected during the first cycle, and the remaining pulses enable the majority of the injected particles to exit the computational domain. Results indicate that, in terms of injection velocity, particles are more spread out in the cross-sectional lumen areas as the injection velocity increases. The tip's orientation also plays a role because it influences the near-tip hemodynamics, therefore altering the particle travel through the hepatic artery. However, results suggest that particle distribution tries to match the blood flow split, therefore particle injection velocity and microcatheter tip orientation playing a minor role in segment-to-segment particle distribution.
      PubDate: 2017-05-04T22:35:26.612814-05:
      DOI: 10.1002/cnm.2895
  • Uncertainty quantification of two models of cardiac electromechanics
    • Authors: Daniel E. Hurtado; Sebastián Castro, Pedro Madrid
      Abstract: Computational models of the heart have reached a maturity level that render them useful for in-silico studies of arrhythmia and other cardiac diseases. However, the translation to the clinic of cardiac simulations critically depends on demonstrating the accuracy, robustness and reliability of the underlying computational models under the presence of uncertainties. In this work, we study for the first time the effect of parameter uncertainty on two state-of-the-art coupled models of excitation-contraction of cardiac tissue. To this end, we perform forward uncertainty propagation and sensitivity analyses to understand how variability in key maximal conductances affect selected quantities of interest, such as the action potential duration (APD90), maximum intracellular calcium concentration, cardiac stretch and stress. redOur results suggest a strong linear relationship between selected maximal conductances and quantities of interest for a variability in parameters up to 25%, which justifies the construction of linear response surfaces that are used to compute the empirical probability density functions of all the QOIs under study. For both electromechanical models analyzed, uncertainty in the material parameters associated to the passive mechanical response of cardiac tissue does not affect the duration of action potentials, neither the amplitude of intracellular calcium concentrations. Our results confirm the poor mechanoelectric feedback that classical models of cardiac electromechanics have, even under the presence of parameter uncertainty. This article is protected by copyright. All rights reserved.
      PubDate: 2017-05-04T20:35:28.268461-05:
      DOI: 10.1002/cnm.2894
  • Potential Biomechanical Roles of Risk Factors in the Evolution of
           Thrombus-Laden Abdominal Aortic Aneurysms
    • Authors: Lana Virag; John S. Wilson, Jay D. Humphrey, Igor Karšaj
      Abstract: Abdominal aortic aneurysms (AAAs) typically harbour an intraluminal thrombus (ILT), yet most prior computational models neglect biochemomechanical effects of thrombus on lesion evolution. We recently proposed a growth and remodelling model of thrombus-laden AAAs that introduced a number of new constitutive relations and associated model parameters. Because values of several of these parameters have yet to be elucidated by clinical data, and could vary significantly from patient to patient, the aim of this study was to investigate the possible extent to which these parameters influence AAA evolution. Given that some of these parameters model potential effects of factors that influence the risk of rupture, this study also provides insight into possible roles of common risk factors on the natural history of AAAs. Despite geometrical limitations of a cylindrical domain, findings support current thought that smoking, hypertension, and female sex likely increase the risk of rupture. Although thrombus thickness is not a reliable risk factor for rupture, the model suggests that the presence of ILT may have a destabilizing effect on AAA evolution, consistent with histological findings from human samples. Finally, simulations support two hypotheses that should be tested on patient-specific geometries in the future. First, ILT is a potential source of the staccato enlargement observed in many AAAs. Second, ILT can influence rupture risk, positively or negatively, via competing biomechanical (e.g., stress shielding) and biochemical (i.e., proteolytic) effects. Although further computational and experimental studies are needed, the present findings highlight the importance of considering ILT when predicting aneurysmal enlargement and rupture risk.
      PubDate: 2017-04-26T21:25:29.613877-05:
      DOI: 10.1002/cnm.2893
  • A holistic view of the effects of episiotomy on pelvic floor
    • Authors: Oliveira Dulce A; Parente Marco P. L, Calvo Begoña, Mascarenhas Teresa, Natal Jorge Renato M.
      Abstract: Vaginal delivery is commonly accepted as a risk factor in pelvic floor dysfunction (PFD), however, other obstetric procedures (episiotomy) are still controversial. In this work, to analyze the relationship between episiotomy and pelvic floor function, a finite element model (FEM) of the pelvic cavity is used considering the pelvic floor muscles (PFM) with damaged regions from spontaneous vaginal delivery, and from deliveries with episiotomy. Common features assessed at screening of PFD are evaluated during numerical simulations of both Valsalva maneuver and contraction.As stated in literature, a weakening of the PFM, represented by damaged regions in the FEM, would lead to a bladder neck hypermobility measured as a variation between the alpha angle (angle between the bladder neck and the symphysis pubis line and the midline of the symphysis) during straining and withholding.However, the present work does not associate bladder neck hypermobility to a more damaged muscle, suggesting that other supportive structures also play an important role in the stabilization of the pelvic organs. Furthermore, considering passive behavior of the PFM, independently of the amount of damage considered, the resultant displacements of the pelvic structures are the same.Regarding the PFM contraction, the less the muscle is damaged, the greater the movements of the pelvic organs. Furthermore, the internal organs of the female genital system are the most affected by the unhealthy of the PFM. Additionally, the present study shows that the muscle damage affects more the active muscle component than the passive.
      PubDate: 2017-04-26T08:55:33.372477-05:
      DOI: 10.1002/cnm.2892
  • A Multiscale Approach for Determining the Morphology of Endothelial Cells
           at a Coronary Artery
    • Authors: Hossein Ali Pakravan; Mohammad Said Saidi, Bahar Firoozabadi
      Abstract: The morphology of endothelial cells (ECs) may be an indication for determining the atheroprone sites. Until now, there is not any clinical imaging technique to visualize the morphology of ECs at the arteries. The present study, introduces a computational technique for determining the morphology of ECs. This technique is a multiscale simulation, consisting the artery-scale and the cell-scale. The artery-scale is a FSI simulation. The input for the artery-scale is the geometry of the coronary artery (CA), dynamic curvature of the artery due to the cardiac motion, blood flow, blood pressure, heart rate, and the mechanical properties of the blood and the arterial wall, which these quantities can be obtained for a specific patient. The results of the artery-scale are wall shear stress (WSS) and cyclic strains as the mechanical stimuli of ECs. The cell-scale is an inventive mass and spring model that is able to determine the morphological response of ECs to the any combination of mechanical stimuli. The results of the multiscale simulation show the morphology of ECs at different locations of the coronary artery. The results indicate that the atheroprone sites have at least one of the three factors: low time-averaged WSS, high angle of WSS and high longitudinal strain. The most probable sites for atherosclerosis are located at the bifurcation region and lie on the myocardial side of the artery. The results also indicated that, the higher dynamic curvature is a negative and the higher pulse pressure is a positive factor for protecting against atherosclerosis.
      PubDate: 2017-04-26T08:35:32.631709-05:
      DOI: 10.1002/cnm.2891
  • Hybrid finite difference/finite element immersed boundary method
    • Authors: Boyce E. Griffith; Xiaoyu Luo
      Abstract: The immersed boundary method is an approach to fluid-structure interaction that uses a Lagrangian description of the structural deformations, stresses, and forces along with an Eulerian description of the momentum, viscosity, and incompressibility of the fluid-structure system. The original immersed boundary methods described immersed elastic structures using systems of flexible fibers, and even now, most immersed boundary methods still require Lagrangian meshes that are finer than the Eulerian grid. This work introduces a coupling scheme for the immersed boundary method to link the Lagrangian and Eulerian variables that facilitates independent spatial discretizations for the structure and background grid. This approach employs a finite element discretization of the structure while retaining a finite difference scheme for the Eulerian variables.We apply this method to benchmark problems involving elastic, rigid, and actively contracting structures, including an idealized model of the left ventricle of the heart. Our tests include cases in which, for a fixed Eulerian grid spacing, coarser Lagrangian structural meshes yield discretization errors that are as much as several orders of magnitude smaller than errors obtained using finer structural meshes. The Lagrangian-Eulerian coupling approach developed in this work enables the effective use of these coarse structural meshes with the immersed boundary method. This work also contrasts two different weak forms of the equations, one of which is demonstrated to be more effective for the coarse structural discretizations facilitated by our coupling approach. This article is protected by copyright. All rights reserved.
      PubDate: 2017-04-20T05:37:33.019194-05:
      DOI: 10.1002/cnm.2888
  • Identification of Dynamic Load for Prosthetic Structures
    • Authors: Dequan Zhang; Xu Han, Zhongpu Zhang, Jie Liu, Chao Jiang, Nobuhiro Yoda, Xianghua Meng, Qing Li
      Abstract: Dynamic load exists in numerous biomechanical systems and its identification signifies a critical issue for characterizing dynamic behaviors and studying biomechanical consequence of the systems. This study aims to identify dynamic load in the dental prosthetic structures, namely three-unit implant-supported fixed partial denture (I-FPD) and teeth-supported fixed partial denture (T-FPD). The three-dimensional (3D) finite element (FE) models were constructed through patient's computerized tomography (CT) images. A forward algorithm and regularization technique were developed for identifying dynamic load. To verify the effectiveness of the identification method proposed, the I-FPD and T-FPD structures were investigated to determine the dynamic loads. For validating the results of inverse identification, an experimental force measuring system was developed by using a 3D piezoelectric transducer to measure the dynamic load in the I-FPD structure in vivo. The computationally identified loads were presented with different noise levels to determine their influence on the identification accuracy. The errors between the measured load and identified counterpart were calculated for evaluating the practical applicability of the proposed procedure in biomechanical engineering. This study is expected to serves as a demonstrative role in identifying dynamic loading in biomedical systems, where a direct in-vivo measurement may be rather demanding in some areas of interest clinically.
      PubDate: 2017-04-20T00:45:47.172064-05:
      DOI: 10.1002/cnm.2889
  • Numerical Analysis of Crimping and Inflation Process of Balloon Expandable
           Coronary Stent Using Implicit Solution
    • Authors: Jakub Bukala; Piotr Kwiatkowski, Jerzy Malachowski
      Abstract: The paper presents an applied methodology for numerical Finite Element analysis of coronary stent crimping and the free inflation process with the use of a folded non-compliant angioplasty balloon. The use of an implicit scheme is considered as the most original part of the work, as an explicit finite element procedure is very often preferred. Hitherto, when the implicit solution was used for the Finite Element solution, the simulated issue was largely simplified. Therefore, the authors focused on the modelling methodology with minimum possible simplification, i.e.: a full load path (compression and inflation in single analysis), solid element discretization and sophisticated contact models (bodies with highly different stiffness). The obtained results are partially compared with experimental data (radial force during the crimping procedure) and present satisfactory compliance. The authors believe that presented methodology allow for significant improvement of the obtained results, as well as potential extension of the research scope, compared to previous efforts performed using the explicit integration scheme. Moreover, the presented methodology is believed to be suitable for sensitivity and optimization studies.
      PubDate: 2017-04-20T00:45:41.320724-05:
      DOI: 10.1002/cnm.2890
  • Effective sparse representation of X-Ray medical images
    • Authors: Laura Rebollo-Neira
      Abstract: Effective sparse representation of X-Ray medical images within the context of data reduction is considered. The proposed framework is shown to render an enormous reduction in the cardinality of the data set required to represent this class of images at very good quality. The goal is achieved by a) creating a dictionary of suitable elements for the image decomposition in the wavelet domain and b) applying effective greedy strategies for selecting the particular elements which enable the sparse decomposition of the wavelet coefficients. The particularity of the approach is that it can be implemented at very competitive processing time and low memory requirements. This article is protected by copyright. All rights reserved.
      PubDate: 2017-04-07T16:35:39.522549-05:
      DOI: 10.1002/cnm.2886
  • Finite Element Modeling, Validation and Parametric Investigations of A
           Retinal Reattachment Stent
    • Authors: Razvan Rusovici; Dennis Dalli, Kunal Mitra, Gary Ganiban, Michael Grace, Rudy Mazzocchi, Michael Calhoun
      Abstract: A new retinal reattachment surgical procedure is based on a stent which is deployed to press the retina back in place. An eye-stent finite element model studied the strain induced by the stent on retina. FEM simulations were performed for several stent geometric configurations (number of loops, wire diameter, intraocular pressure). The FEM was validated against experiment. Parametric studies demonstrated that stents could be successfully designed so that the maximum strain would be below permanent damage strain threshold of 2%.
      PubDate: 2017-03-27T20:00:23.244963-05:
      DOI: 10.1002/cnm.2885
  • Bayesian sensitivity analysis of a 1D vascular model with Gaussian process
    • Authors: A. Melis; R. H. Clayton, A. Marzo
      Abstract: One-dimensional models of the cardiovascular system can capture the physics of pulse waves, but involve many parameters. Since these may vary among individuals, patient-specific models are difficult to construct. Sensitivity analysis can be used to rank model parameters by their effect on outputs, and to quantify how uncertainty in parameters influences output uncertainty. This type of analysis is often conducted with a Monte Carlo method, where large numbers of model runs are used to assess input-output relations. The aim of this study was to demonstrate the computational efficiency of variance based sensitivity analysis of 1D vascular models using Gaussian process emulators, compared to a standard Monte Carlo approach. The methodology was tested on four vascular networks of increasing complexity to analyse its scalability. The computational time needed to perform the sensitivity analysis with an emulator was reduced by the 99.96% compared to a Monte Carlo approach. Despite the reduced computational time, sensitivity indices obtained using the two approaches were comparable. The scalability study showed that the number of mechanistic simulations needed to train a Gaussian process for sensitivity analysis was of the order O(d), rather than O(d×103) needed for Monte Carlo analysis (where d is the number of parameters in the model). The efficiency of this approach, combined with capacity to estimate the impact of uncertain parameters on model outputs, will enable development of patient-specific models of the vascular system, and has the potential to produce results with clinical relevance. This article is protected by copyright. All rights reserved.
      PubDate: 2017-03-24T00:50:56.758272-05:
      DOI: 10.1002/cnm.2882
  • Face Shield Design against Blast-induced Head Injuries
    • Authors: Long Bin Tan; Kwong Ming Tse, Yuan Hong Tan, Mohamad Ali Bin Sapingi, Vincent Beng Chye Tan, Heow Pueh Lee
      Abstract: Blast-induced traumatic brain injury (TBI) has been on the rise in recent years due to the increasing use of improvised explosive devices (IEDs) in conflict zones. Our study investigates the response of a helmeted human head subjected to a blast of 1 atm peak overpressure, for cases with and without a standard polycarbonate (PC) face shield and for face shields comprising of composite PC and aerogel materials and with lateral edge extension. The novel introduction of aerogel into the laminate face shield is explored and its wave-structure interaction mechanics and performance in blast mitigation is analysed. Our numerical results show that the face shield prevented direct exposure of the blast wave to the face and help delays the transmission of the blast to reduce the intracranial pressures (ICPs) at the parietal lobe. However, the blast wave can diffract and enter the midface region at the bottom and side edges of the face shield, resulting in TBI. This suggests that the bottom and sides of the face shield are important regions to focus on to reduce wave ingress. The laminated PC/aerogel/PC face shield yielded higher peak positive and negative ICPs at the frontal lobe, than the original PC one. For the occipital and temporal brain regions, the laminated face shield performed better than the original. The composite face shield with extended edges reduced ICP at the temporal lobe but increases ICP significantly at the parietal lobe which suggests that a greater coverage may not lead to better mitigating effects.
      PubDate: 2017-03-22T11:17:51.724376-05:
      DOI: 10.1002/cnm.2884
  • Effect of Cerebrospinal Fluid Modelling on Spherically Convergent Shear
           Waves during Blunt Head Trauma
    • Authors: Amit Madhukar; Ying Chen, Martin Ostoja-Starzewski
      Abstract: The MRI-based computational model, previously validated by tagged MRI and HARP imaging analysis technique on in vivo human brain deformation, is employed to study transient wave dynamics during blunt head trauma. Three different constitutive models are used for the cerebrospinal fluid (CSF): incompressible solid elastic, viscoelastic and fluid-like elastic using an equation of state model. Three impact cases are simulated which indicate that the blunt impacts give rise not only to a fast pressure wave but also to a slow, and potentially much more damaging, shear (distortional) wave that converges spherically towards the brain center. The wave amplification due to spherical geometry is balanced by damping due to tissues’ viscoelasticity and the heterogeneous brain structure, suggesting a stochastic competition of these two opposite effects. It is observed that this convergent shear wave is dependent on the constitutive property of the CSF whereas the peak pressure is not as significantly affected.
      PubDate: 2017-03-14T03:30:46.116261-05:
      DOI: 10.1002/cnm.2881
  • Phase-field boundary conditions for the voxel finite cell method:
           surface-free stress analysis of CT-based bone structures
    • Authors: L. H. Nguyen; S. K. F. Stoter, T. Baum, J. S. Kirschke, M. Ruess, Z. Yosibash, D. Schillinger
      Abstract: The voxel finite cell method employs unfitted finite element meshes and voxel quadrature rules to seamlessly transfer CT data into patient-specific bone discretizations. The method, however, still requires the explicit parametrization of boundary surfaces to impose traction and displacement boundary conditions, which constitutes a potential roadblock to automation. We explore a phase-field based formulation for imposing traction and displacement constraints in a diffuse sense. Its essential component is a diffuse geometry model generated from metastable phase-field solutions of the Allen-Cahn problem that assumes the imaging data as initial condition. Phase-field approximations of the boundary and its gradient are then employed to transfer all boundary terms in the variational formulation into volumetric terms. We show that in the context of the voxel finite cell method, diffuse boundary conditions achieve the same accuracy as boundary conditions defined over explicit sharp surfaces, if the inherent length scales, i.e., the interface width of the phase-field, the voxel spacing and the mesh size, are properly related. We demonstrate the flexibility of the new method by analyzing stresses in a human femur and a vertebral body. This article is protected by copyright. All rights reserved.
      PubDate: 2017-03-11T05:25:39.273162-05:
      DOI: 10.1002/cnm.2880
  • Computational modeling of tracheal angioedema due to swelling of the
           submucous tissue layer
    • Authors: Kun Gou; Thomas J. Pence
      Abstract: Angioedema is a tissue-swelling pathology due to rapid change in soft tissue fluid content. Its occurrence in the trachea is predominantly localized to the soft mucous tissue that forms the innermost tracheal layer. The biomechanical consequences, such as airway constriction, are dependent upon the ensuing mechanical interactions between all of the various tissues that comprise the tracheal tube. We model the stress interactions by treating the trachea organ as a three-tissue system consisting of swellable mucous in conjunction with nonswelling cartilage and nonswelling trachealis musculature. Hyperelastic constitutive modeling is used by generalizing the standard anisotropic, incompressible soft tissue framework to incorporate the swelling effect. Finite element stress analysis then proceeds with swelling of the mucous layer providing the driving factor for the mechanical analysis. The amount of airway constriction is governed by the mechanical interaction between the three predominant tissue types. The detailed stress analysis indicates the presence of stress concentrations near the various tissue junctions. Because of the tissue's nonlinear mechanical behavior, this can lead to material stiffness fluctuations as a function of location on the trachea. Patient specific modeling is presented. The role of the modeling in the interpretation of diagnostic procedures and the assessment of therapies is discussed.This article models tracheal angioedema (swelling) using an advanced hyperelastic theory incorporated with swelling.The deformation is solely caused by internal swelling. We have various levels of modeling considering the trachea to be idealized symmetric, non-symmetric with trachealis on the back side, and patient-specific. All these different models help us understand tracheal angioedema more profoundly. The patient-specific modeling supplies a more realistic understanding of the tracheal angioedema, and assists corresponding clinical treatment.
      PubDate: 2017-03-09T05:11:02.554537-05:
      DOI: 10.1002/cnm.2861
  • Calculation of Cancellous Bone Elastic Properties with the
           Polarization-based FFT Iterative Scheme
    • Authors: Lucas Colabella; Ariel Alejandro Ibarra Pino, Josefina Ballarre, Piotr Kowalczyk, Adrián Pablo Cisilino
      Abstract: The FFT based method, originally introduced by Moulinec and Suquet in 1994 has gained popularity for computing homogenized properties of composites. In this work, the method is used for the computational homogenization of the elastic properties of cancellous bone. To the authors’ knowledge, this is the first study where the FFT scheme is applied to bone mechanics. The performance of the method is analyzed for artificial and natural bone samples of two species: bovine femoral heads and implanted femurs of Hokkaido rats. Model geometries are constructed using data from X-ray tomographies and the bone tissue elastic properties are measured using micro and nanoindentation tests. Computed results are in excellent agreement with those available in the literature. The study shows the suitability of the method to accurately estimate the fully anisotropic elastic response of cancellous bone. Guidelines are provided for the construction of the models and the setting of the algorithm.
      PubDate: 2017-03-07T19:25:28.518686-05:
      DOI: 10.1002/cnm.2879
  • Human body modeling method to simulate the biodynamic characteristics of
           spine in vivo with different sitting postures
    • Authors: Rui Chun Dong; Li Xin Guo
      Abstract: The aim of this study is to model the computational model of seated whole human body including skeleton, muscle, viscera, ligament, intervertebral disc and skin to predict effect of the factors (sitting postures, muscle and skin, buttocks, viscera, arms, gravity, and boundary conditions) on the biodynamic characteristics of spine. Two finite element (FE) models of seated whole body and a large number of FE models of different ligamentous motion segments were developed and validated. Static, modal and transient dynamic analyses were performed. The predicted vertical resonant frequency of seated body model was in the range of vertical natural frequency of 4-7Hz. Muscle, buttocks, viscera and the boundary conditions of buttocks have influence on the vertical resonant frequency of spine. Muscle played a very important role in biodynamic response of spine. Compared with the vertical posture, the posture of lean forward or backward led to an increase in stress on anterior or lateral posterior of lumbar intervertebral discs (LID). This indicated keeping correct posture could reduce the injury of vibration on LID under whole-body vibration. The driving posture not only reduced the load of spine, but also increased the resonant frequency of spine.
      PubDate: 2017-03-06T12:50:30.43009-05:0
      DOI: 10.1002/cnm.2876
  • Research and Primary Evaluation of an Automatic Fusion Method for
           Multi-source Tooth Crown Data
    • Authors: Ning Dai; Dawei Li, Xu Yang, Cheng Cheng, Yuchun Sun
      Abstract: BackgroundWith the development of 3D scanning technologies in dentistry, high accuracy optical scanning data from the crown and cone beam computed tomography (CBCT) data from the root can be acquired easily. In many dental fields, especially in digital orthodontics, it is useful to fuse the data from the crown and the root. However, the manual fusion method is complex and difficult. A novel automatic fusion method for two-source data from the crown and the root was researched and its accuracy was evaluated in this study.MethodsAn occlusal splint with several alumina ceramic spheres was fabricated using heat-curing resin. A multi-point (center of each sphere) alignment method was performed to achieve rapid registration of the crown data from optical scanning and the root data from CBCT. The segmentation algorithm based on heuristic search was adopted to perform extraction and segmentation of the crown from whole optical scanning data. The Level Set algorithm and the Marching Cubes algorithm were employed to reconstruct DICOM data into a 3D model. A novel multi-source data fusion algorithm, which is based on Iterative Laplacian Deformation (ILD), was researched and applied to achieve automatic fusion. Finally, the 3D errors of the method were evaluated.ResultsThe three groups of typical tooth data were automatically fused within 2 s. The mean standard deviation was less than 0.02 mm.ConclusionsThe novel method can aid the construction of a high-quality 3D model of complete teeth to enable orthodontists to safely, reliably, and visually plan tooth alignment programs.
      PubDate: 2017-03-03T18:05:29.183277-05:
      DOI: 10.1002/cnm.2878
  • Multiphoton microscope measurement–based biphasic multiscale analyses of
           knee joint articular cartilage and chondrocyte by using visco-anisotropic
           hyperelastic finite element method and smoothed particle hydrodynamics
    • Authors: Eiji Nakamachi; Tomohiro Noma, Kaito Nakahara, Yoshihiro Tomita, Yusuke Morita
      Abstract: The articular cartilage of a knee joint has a variety of functions including dispersing stress and absorbing shock in the tissue and lubricating the surface region of cartilage. The metabolic activity of chondrocytes under the cyclic mechanical stimulations regenerates the morphology and function of tissues. Hence, the stress evaluation of the chondrocyte is a vital subject to assess the regeneration cycle in the normal walking condition and predict the injury occurrence in the accidents. Further, the threshold determination of stress for the chondrocytes activation is valuable for development of regenerative bioreactor of articular cartilage. In this study, in both macroscale and microscale analyses, the dynamic explicit finite element (FE) method was used for the solid phase and the smoothed particle hydrodynamics (SPH) method was used for the fluid phase. In the homogenization procedure, the representative volume element for the microscale finite element model was derived by using the multiphoton microscope measured 3D structure comprising 3 different layers: surface, middle, and deep layers. The layers had different anisotropic structural and rigidity characteristics because of the collagen fiber orientation. In both macroscale and microscale FE analyses, the visco-anisotropic hyperelastic constitutive law was used. Material properties were identified by experimentally determined stress-strain relationships of 3 layers. With respect to the macroscale and microscale SPH models for non-Newtonian viscous fluid, the previous observation results of interstitial fluid and proteoglycan were used to perform parameter identifications. Biphasic multiscale FE and SPH analyses were conducted under normal walking conditions. Therefore, the hydrostatic and shear stresses occurring in the chondrocytes caused by the compressive load and shear viscous flow were evaluated. These stresses will be used to design an ex-vivo bioreactor to regenerate the damaged articular cartilage, where chondrocytes are seeded in the culture chamber. To know the stress occurred on and in the chondrocytes is vitally important not only to understand the normal metabolic activity of the chondrocyte but also to develop a bioreactor of articular cartilage regeneration as the knee joint disease treatment.We developed a biphasic multiscale analysis code to evaluate the stress occurred in the chondrocyte cell of articular cartilage to elucidate the metabolic activity for regeneration and the injury. We determined RVE for microscale FE models by using MPM measured results. We evaluated stresses in the chondrocyte caused by the normal compressive loading. Our numerical code can be applied for accurate stress evaluations by using more detail experimental results for material properties identification.
      PubDate: 2017-03-03T09:25:53.42354-05:0
      DOI: 10.1002/cnm.2864
  • A Hybrid Computational Model to Explore the Topological Characteristics of
           Epithelial Tissues
    • Authors: Ismael González-Valverde; José Manuel García Aznar
      Abstract: Epithelial tissues show a particular topology where cells resemble a polygon-like shape, but some biological processes can alter this tissue topology. During cell proliferation, mitotic cell dilation deforms the tissue and modifies the tissue topology. Additionally, cells are reorganized in the epithelial layer and these rearrangements also alter the polygon distribution.We present here a computer-based hybrid framework focused on the simulation of epithelial layer dynamics that combines discrete and continuum numerical models. In this framework, we consider topological and mechanical aspects of the epithelial tissue. Individual cells in the tissue are simulated by an off-lattice agent-based model, which keeps the information of each cell. In addition, we model the cell-cell interaction forces and the cell cycle. Otherwise, we simulate the passive mechanical behaviour of the cell monolayer using a material that approximates the mechanical properties of the cell. This continuum approach is solved by the finite element method, which uses a dynamic mesh generated by the triangulation of cell polygons. Forces generated by cell-cell interaction in the agent-based model are also applied on the finite element mesh. Cell movement in the agent-based model is driven by the displacements obtained from the deformed finite element mesh of the continuum mechanical approach.We successfully compare the results of our simulations with some experiments about the topology of proliferating epithelial tissues in Drosophila. Our framework is able to model the emergent behaviour of the cell monolayer that is due to local cell-cell interactions, which have a direct influence on the dynamics of the epithelial tissue.
      PubDate: 2017-03-01T15:00:55.9462-05:00
      DOI: 10.1002/cnm.2877
  • Aerosol transport throughout inspiration and expiration in the pulmonary
    • Authors: Jessica M. Oakes; Shawn C. Shadden, Céline Grandmont, Irene E. Vignon-Clementel
      Abstract: Little is known about transport throughout the respiration cycle in the conducting airways. It is challenging to appropriately describe the time-dependent number of particles entering back into the model during exhalation. Modeling the entire lung is not feasible; therefore, multidomain methods must be used. Here, we present a new framework that is designed to simulate particles throughout the respiration cycle, incorporating realistic airway geometry and respiration. This framework is applied for a healthy rat lung exposed to  ∼ 1μm diameter particles, chosen to facilitate parameterization and validation. The flow field is calculated in the conducting airways (3D domain) by solving the incompressible Navier-Stokes equations with experimentally derived boundary conditions. Particles are tracked throughout inspiration by solving a modified Maxey-Riley equation. Next, we pass the time-dependent particle concentrations exiting the 3D model to the 1D volume conservation and advection-diffusion models (1D domain). Once the 1D models are solved, we prescribe the time-dependent number of particles entering back into the 3D airways to again solve for 3D transport. The coupled simulations highlight that about twice as many particles deposit during inhalation compared to exhalation for the entire lung. In contrast to inhalation, where most particles deposit at the bifurcation zones, particles deposit relatively uniformly on the gravitationally dependent side of the 3D airways during exhalation. Strong agreement to previously collected regional experimental data is shown, as the 1D models account for lobe-dependent morphology. This framework may be applied to investigate dosimetry in other species and pathological lungs.Little is known about transport throughout the respiration cycle in the conducting airways. It is challenging to describe the time-dependent number of particles entering back into the airways during exhalation. Modeling the full lung is not feasible; hence, multi-domain methods must be employed. Here, we present a new framework that is designed to simulate particles throughout the respiration cycle. The in silico model was parametrized following rat exposure experiments and model predictions were compared to the experimental data.
      PubDate: 2017-02-24T05:00:41.044117-05:
      DOI: 10.1002/cnm.2847
  • Uncertainty quantification of inflow boundary condition and proximal
           arterial stiffness–coupled effect on pulse wave propagation in a
           vascular network
    • Authors: Antoine Brault; Laurent Dumas, Didier Lucor
      Abstract: This work aims at quantifying the effect of inherent uncertainties from cardiac output on the sensitivity of a human compliant arterial network response based on stochastic simulations of a reduced-order pulse wave propagation model. A simple pulsatile output form is used to reproduce the most relevant cardiac features with a minimum number of parameters associated with left ventricle dynamics. Another source of significant uncertainty is the spatial heterogeneity of the aortic compliance, which plays a key role in the propagation and damping of pulse waves generated at each cardiac cycle. A continuous representation of the aortic stiffness in the form of a generic random field of prescribed spatial correlation is then considered. Making use of a stochastic sparse pseudospectral method, we investigate the sensitivity of the pulse pressure and waves reflection magnitude over the arterial tree with respect to the different model uncertainties. Results indicate that uncertainties related to the shape and magnitude of the prescribed inlet flow in the proximal aorta can lead to potent variation of both the mean value and standard deviation of blood flow velocity and pressure dynamics due to the interaction of different wave propagation and reflection features. Lack of accurate knowledge in the stiffness properties of the aorta, resulting in uncertainty in the pulse wave velocity in that region, strongly modifies the statistical response, with a global increase in the variability of the quantities of interest and a spatial redistribution of the regions of higher sensitivity. These results will provide some guidance in clinical data acquisition and future coupling of arterial pulse wave propagation reduced-order model with more complex beating heart models.A stochastic sparse pseudospectral polynomial approximation is deployed to quantify the effect of cardiac output uncertainties on a human compliant arterial network response based on a reduced-order pulse wave propagation model. Natural spatial variability of the aortic wall stiffness properties is modeled with a continuous random field representation. The proposed numerical method accurately predicts the sensitivity of central and peripheral pulse pressure and pressure waves reflection to the considered parametric uncertainties.
      PubDate: 2017-02-24T04:55:36.380294-05:
      DOI: 10.1002/cnm.2859
  • Patient-specific computational modeling of Cortical Spreading Depression
           via Diffusion Tensor Imaging
    • Authors: Julia M. Kroos; Isabella Marinelli, Ibai Diez, Jesus M. Cortes, Sebastiano Stramaglia, Luca Gerardo-Giorda
      Abstract: Cortical Spreading Depression (CSD), a depolarization wave originating in the visual cortex and traveling towards the frontal lobe, is commonly accepted as a correlate of migraine visual aura. As of today, little is known about the mechanisms that can trigger or stop such phenomenon. However, the complex and highly individual characteristics of the brain cortex suggest that the geometry might have a significant impact in supporting or contrasting the propagation of CSD. Accurate patient-specific computational models are fundamental to cope with the high variability in cortical geometries among individuals, but also with the conduction anisotropy induced in a given cortex by the complex neuronal organisation in the grey matter. In this paper we integrate a distributed model for extracellular potassium concentration with patient-specific diffusivity tensors derived locally from Diffusion Tensor Imaging data. This article is protected by copyright. All rights reserved.
      PubDate: 2017-02-22T17:05:29.312808-05:
      DOI: 10.1002/cnm.2874
  • An efficient multi-stage algorithm for full calibration of the hemodynamic
           model from BOLD signal responses
    • Authors: Brian Zambri; Rabia Djellouli, Meriem Laleg-Kirati
      Abstract: We propose a computational strategy that falls into the category of prediction/correction iterative-type approaches, for calibrating the hemodynamic model introduced by Friston et al. (2000). The proposed method is employed to estimate consecutively the values of the biophysiological system parameters and the external stimulus characteristics of the model. Numerical results corresponding to both synthetic and real functional Magnetic Resonance Imaging (fMRI) measurements for a single stimulus as well as for multiple stimuli are reported to highlight the capability of this computational methodology to fully calibrate the considered hemodynamic model. This article is protected by copyright. All rights reserved.
      PubDate: 2017-02-22T17:05:24.502503-05:
      DOI: 10.1002/cnm.2875
  • A tree-parenchyma coupled model for lung ventilation simulation
    • Authors: N. Pozin; S. Montesantos, I. Katz, M. Pichelin, I. Vignon-Clementel, C. Grandmont
      Abstract: In this article we develop a lung-ventilation model. The parenchyma is described as an elastic homogenized media. It is irrigated by a space-filling dyadic resistive pipe network, which represents the tracheo-bronchial tree. In this model the tree and the parenchyma are strongly coupled. The tree induces an extra viscous term in the system constitutive relation, which leads, in the finite element framework, to a full matrix. We consider an efficient algorithm that takes advantage of the tree structure to enable a fast matrix-vector product computation. This framework can be used to model both free and mechanically induced respiration, in health and disease. Patient-specific lung geometries acquired from CT scans are considered. Realistic Dirichlet boundary conditions can be deduced from surface registration on CT images. The model is compared to a more classical exit-compartment approach. Results illustrate the coupling between the tree and the parenchyma, at global and regional levels, and how conditions for the purely 0D model can be inferred. Different types of boundary conditions are tested, including a nonlinear Robin model of the surrounding lung structures.
      PubDate: 2017-02-22T04:20:41.251928-05:
      DOI: 10.1002/cnm.2873
  • Fast left ventricle tracking using localized anatomical affine optical
    • Authors: Sandro Queirós; João L. Vilaça, Pedro Morais, Jaime C. Fonseca, Jan D'hooge, Daniel Barbosa
      Abstract: In daily clinical cardiology practice, left ventricle (LV) global and regional function assessment is crucial for disease diagnosis, therapy selection and patient follow-up. Currently, this is still a time-consuming task, spending valuable human resources. In this work, a novel fast methodology for automatic LV tracking is proposed based on localized anatomically constrained affine optical flow. This novel method can be combined to previously proposed segmentation frameworks or manually delineated surfaces at an initial frame to obtain fully delineated datasets and, thus, assess both global and regional myocardial function. Its feasibility and accuracy was investigated in three distinct public databases, namely in realistically simulated 3D ultrasound (US), clinical 3D echocardiography and clinical cine cardiac magnetic resonance (CMR) images. The method showed accurate tracking results in all databases, proving its applicability and accuracy for myocardial function assessment. Moreover, when combined to previous state-of-the-art segmentation frameworks, it outperformed previous tracking strategies in both 3D US and CMR data, automatically computing relevant cardiac indices with smaller biases and narrower limits of agreement compared to reference indices. Simultaneously, the proposed localized tracking method showed to be suitable for online processing, even for 3D motion assessment. Importantly, although here evaluated for LV tracking only, this novel methodology is applicable for tracking of other target structures with minimal adaptations. This article is protected by copyright. All rights reserved.
      PubDate: 2017-02-16T17:20:25.12805-05:0
      DOI: 10.1002/cnm.2871
  • Conditions of microvessel occlusion for blood coagulation in flow
    • Authors: A. Bouchnita; T. Galochkina, P. Kurbatova, P. Nony, V. Volpert
      Abstract: Vessel occlusion is a perturbation of blood flow inside a blood vessel because of the fibrin clot formation. As a result, blood circulation in the vessel can be slowed down or even stopped. This can provoke the risk of cardiovascular events. In order to explore this phenomenon, we used a previously developed mathematical model of blood clotting to describe the concentrations of blood factors with a reaction-diffusion system of equations. The Navier-Stokes equations were used to model blood flow, and we treated the clot as a porous medium. We identify the conditions of partial or complete occlusion in a small vessel depending on various physical and physiological parameters. In particular, we were interested in the conditions on blood flow and diameter of the wounded area. The existence of a critical flow velocity separating the regimes of partial and complete occlusion was demonstrated through the mathematical investigation of a simplified model of thrombin wave propagation in Poiseuille flow. We observed different regimes of vessel occlusion depending on the model parameters both for the numerical simulations and in the theoretical study. Then, we compared the rate of clot growth in flow obtained in the simulations with experimental data. Both of them showed the existence of different regimes of clot growth depending on the velocity of blood flow.Microvessel occlusion is the perturbation of blood flow inside a vein because of the formation of a fibrin clot. Mathematical model of clot growth was developed using a system of reaction-diffusion coupled with the Navier-Stokes equations for blood flow. Conditions of microvessel occlusion were identified using numerical simulations and mathematical investigation of simplified one-dimensional model. Experimental data and numerical simulations confirmed the existence of different regimes of clot growth velocity depending on the velocity of blood flow.
      PubDate: 2017-02-16T03:35:33.981459-05:
      DOI: 10.1002/cnm.2850
  • Modelling mitral valvular dynamics–current trend and future
    • Authors: Hao Gao; Nan Qi, Liuyang Feng, Xingshuang Ma, Mark Danton, Colin Berry, Xiaoyu Luo
      Abstract: Dysfunction of mitral valve causes morbidity and premature mortality and remains a leading medical problem worldwide. Computational modelling aims to understand the biomechanics of human mitral valve and could lead to the development of new treatment, prevention and diagnosis of mitral valve diseases. Compared with the aortic valve, the mitral valve has been much less studied owing to its highly complex structure and strong interaction with the blood flow and the ventricles. However, the interest in mitral valve modelling is growing, and the sophistication level is increasing with the advanced development of computational technology and imaging tools. This review summarises the state-of-the-art modelling of the mitral valve, including static and dynamics models, models with fluid-structure interaction, and models with the left ventricle interaction. Challenges and future directions are also discussed.We summarize the state-of-the-art modelling of the mitral valve, including static and dynamic models, mitral valve with fluid-structure interaction, and mitral valve with the left ventricle interaction. Challenges and future directions are also discussed.
      PubDate: 2017-02-16T03:26:26.554323-05:
      DOI: 10.1002/cnm.2858
  • A novel modelling approach to energy transport in a respiratory system
    • Authors: Perumal Nithiarasu; Igor Sazonov
      Abstract: In this paper, energy transport in a respiratory tract is modelled using the finite element method for the first time. The upper and lower respiratory tracts are approximated as a 1-dimensional domain with varying cross-sectional and surface areas, and the radial heat conduction in the tissue is approximated using the 1-dimensional cylindrical coordinate system. The governing equations are solved using 1-dimensional linear finite elements with convective and evaporative boundary conditions on the wall. The results obtained for the exhalation temperature of the respiratory system have been compared with the available animal experiments. The study of a full breathing cycle indicates that evaporation is the main mode of heat transfer, and convection plays almost negligible role in the energy transport. This is in-line with the results obtained from animal experiments.In this paper, energy transport in a respiratory tract is modelled using the finite element method for the first time. The upper and lower respiratory tracts are approximated as a one-dimensional domain with varying cross sectional and surface areas, and the radial heat conduction in the tissue is approximated using the one dimensional cylindrical coordinate system. The governing equations are solved using one-dimensional linear finite elements with convective and evaporative boundary conditions on the wall. The results obtained for the exhalation temperature of the respiratory system have been compared with the available animal experiments. The study of a full breathing cycle indicates that evaporation is the main mode of heat transfer, and convection plays almost negligible role in the energy transport. This is inline with the results obtained from animal experiments.
      PubDate: 2017-02-16T03:15:31.101832-05:
      DOI: 10.1002/cnm.2854
  • An Investigation of Dimensional Scaling Using Cervical Spine Motion
           Segment Finite Element Models
    • Authors: Dilaver Singh; Duane S. Cronin
      Abstract: The paucity of experimental data for validating computational models of different statures underscores the need for appropriate scaling methods so that models can be verified and validated using experimental data. Scaling was investigated using 50th percentile male (M50) and 5th percentile female (F05) cervical spine motion segment (C4-C5) finite element models subject to tension, flexion and extension loading. Two approaches were undertaken: geometric scaling of the models to investigate size effects (volumetric scaling) and scaling of the force-displacement or moment-angle model results (data scaling). Three sets of scale factors were considered: global (body mass), regional (neck dimensions) and local (segment tissue dimensions).Volumetric scaling of the segment models from M50 to F05, and vice-versa, produced correlations that were good or excellent in both tension and flexion (0.825-0.991); however, less agreement was found in extension (0.550-0.569). The reduced correlation in extension was attributed to variations in shape between the models leading to nonlinear effects such as different time to contact for the facet joints and posterior processes. Data scaling of the responses between the M50 and F05 models produced similar trends to volumetric scaling, with marginally greater correlations.Overall, the local tissue level and neck region level scale factors produced better correlations than the traditional global scaling. The scaling methods work well for a given subject, but are limited in applicability between subjects with different morphology, where nonlinear effects may dominate the response.
      PubDate: 2017-02-15T21:35:27.188101-05:
      DOI: 10.1002/cnm.2872
  • The role of the microvascular network structure on diffusion and
           consumption of anticancer drugs
    • Authors: Pietro Mascheroni; Raimondo Penta
      Abstract: We investigate the impact of microvascular geometry on the transport of drugs in solid tumors, focusing on the diffusion and consumption phenomena. We embrace recent advances in the asymptotic homogenization literature starting from a double Darcy—double advection-diffusion-reaction system of partial differential equations that is obtained exploiting the sharp length separation between the intercapillary distance and the average tumor size. The geometric information on the microvascular network is encoded into effective hydraulic conductivities and diffusivities, which are numerically computed by solving periodic cell problems on appropriate microscale representative cells. The coefficients are then injected into the macroscale equations, and these are solved for an isolated, vascularized spherical tumor. We consider the effect of vascular tortuosity on the transport of anticancer molecules, focusing on Vinblastine and Doxorubicin dynamics, which are considered as a tracer and as a highly interacting molecule, respectively. The computational model is able to quantify the treatment performance through the analysis of the interstitial drug concentration and the quantity of drug metabolized in the tumor. Our results show that both drug advection and diffusion are dramatically impaired by increasing geometrical complexity of the microvasculature, leading to nonoptimal absorption and delivery of therapeutic agents. However, this effect apparently has a minor role whenever the dynamics are mostly driven by metabolic reactions in the tumor interstitium, eg, for highly interacting molecules. In the latter case, anticancer therapies that aim at regularizing the microvasculature might not play a major role, and different strategies are to be developed.We numerically solve a double Darcy—double advection-diffusion-reaction model (derived via asymptotic homogenization) for fluid and drug transport in vascularized tumors, following a suitable algorithm to decouple microscale and macroscale spatial variations to reduce the computational cost.We consider for the first time variations of the diffusivity tensor (both in the vessel network and in the tumor interstitium) with respect to the microvascular structure, as well as its interplay with both weak and strong uptake mechanisms in the tumor and potential convective contributions across the vessels membrane.The numerical results show that geometrical tortuosity dramatically impairs diffusion and absorption of injected drugs, although the latter effect is apparently less significant for strongly interacting macromolecules.
      PubDate: 2017-02-14T02:30:33.16586-05:0
      DOI: 10.1002/cnm.2857
  • A velocity tracking approach for the data assimilation problem in blood
           flow simulations
    • Authors: J. Tiago; T. Guerra, A. Sequeira
      Abstract: Several advances have been made in data assimilation techniques applied to blood flow modeling. Typically, idealized boundary conditions, only verified in straight parts of the vessel, are assumed. We present a general approach, on the basis of a Dirichlet boundary control problem, that may potentially be used in different parts of the arterial system. The relevance of this method appears when computational reconstructions of the 3D domains, prone to be considered sufficiently extended, are either not possible, or desirable, because of computational costs. On the basis of taking a fully unknown velocity profile as the control, the approach uses a discretize then optimize methodology to solve the control problem numerically. The methodology is applied to a realistic 3D geometry representing a brain aneurysm. The results show that this data assimilation approach may be preferable to a pressure control strategy and that it can significantly improve the accuracy associated to typical solutions obtained using idealized velocity profiles.We present a general data assimilation approach, on the basis of a Dirichlet boundary control problem, that may potentially be used in different parts of the arterial system. The relevance of this method appears when computational reconstructions of the 3D domains, prone to be considered sufficiently extended to obtain reliable solutions, are not possible. The methodology is applied to a realistic 3D geometry representing a brain aneurysm.
      PubDate: 2017-02-14T02:25:41.478928-05:
      DOI: 10.1002/cnm.2856
  • Quantitative validation of anti-PTBP1 antibody for diagnostic
           neuropathology use: Image analysis approach
    • Authors: Evgin Goceri; Behiye Goksel, James B. Elder, Vinay K. Puduvalli, Jose J. Otero, Metin N. Gurcan
      Abstract: Traditional diagnostic neuropathology relies on subjective interpretation of visual data obtained from a brightfield microscopy. This approach causes high variability, unsatisfactory reproducibility, and inability for multiplexing even among experts. These problems may affect patient outcomes and confound clinical decision-making. Also, standard histological processing of pathological specimens leads to auto-fluorescence and other artifacts, a reason why fluorescent microscopy is not routinely implemented in diagnostic pathology. To overcome these problems, objective and quantitative methods are required to help neuropathologists in their clinical decision-making. Therefore, we propose a computerized image analysis method to validate anti-PTBP1 antibody for its potential use in diagnostic neuropathology. Images were obtained from standard neuropathological specimens stained with anti-PTBP1 antibody. First, the noise characteristics of the images were modeled and images are de-noised according to the noise model. Next, images are filtered with sigma-adaptive Gaussian filtering for normalization, and cell nuclei are detected and segmented with a k-means–based deterministic approach. Experiments on 29 data sets from 3 cases of brain tumor and reactive gliosis show statistically significant differences between the number of positively stained nuclei in images stained with and without anti-PTBP1 antibody. The experimental analysis of specimens from 3 different brain tumor groups and 1 reactive gliosis group indicates the feasibility of using anti-PTBP1 antibody in diagnostic neuropathology, and computerized image analysis provides a systematic and quantitative approach to explore feasibility.The experimental analysis of specimens from 3 different brain tumor groups and 1 reactive gliosis group indicates the feasibility of using anti-PTBP1 antibody in diagnostic neuropathology, and computerized image analysis provides a systematic and quantitative approach to explore feasibility.
      PubDate: 2017-02-10T06:11:08.256298-05:
      DOI: 10.1002/cnm.2862
  • How coagulation zone size is underestimated in computer modeling of RF
           ablation by ignoring the cooling phase just after RF power is switched off
    • Authors: Ramiro M. Irastorza; Macarena Trujillo, Enrique Berjano
      Abstract: All the numerical models developed for radiofrequency (RF) ablation so far have ignored the possible effect of the cooling phase (just after RF power is switched off) on the dimensions of the coagulation zone. Our objective was thus to quantify the differences in the minor radius of the coagulation zone computed by including and ignoring the cooling phase. We built models of RF tumor ablation with two needle-like electrodes: a dry electrode (5 mm long and 17G in diameter) with a constant temperature protocol (70 °C) and a cooled electrode (30 mm long and 17G in diameter) with a protocol of impedance control. We observed that the computed coagulation zone dimensions were always underestimated when the cooling phase was ignored. The mean values of the differences computed along the electrode axis were always lower than 0.15 mm for the dry electrode and 1.5 mm for the cooled electrode, which implied a value lower than 5% of the minor radius of the coagulation zone (which was 3 mm for the dry electrode, and 30 mm for the cooled electrode). The underestimation was found to be dependent on the tissue characteristics: being more marked for higher values of specific heat and blood perfusion and less marked for higher values of thermal conductivity.
      PubDate: 2017-02-01T10:40:58.299103-05:
      DOI: 10.1002/cnm.2869
  • Experiment for validation of fluid-structure interaction models and
    • Authors: A. Hessenthaler; N. R. Gaddum, O. Holub, R. Sinkus, O. Röhrle, D. Nordsletten
      Abstract: In this paper a fluid-structure interaction (FSI) experiment is presented. The aim of this experiment is to provide a challenging yet easy-to-setup FSI test case that addresses the need for rigorous testing of FSI algorithms and modeling frameworks. Steady-state and periodic steady-state test cases with constant and periodic inflow were established. Focus of the experiment is on biomedical engineering applications with flow being in the laminar regime with Reynolds numbers 1283 and 651. Flow and solid domains were defined using computer-aided design (CAD) tools. The experimental design aimed at providing a straightforward boundary condition definition. Material parameters and mechanical response of a moderately viscous Newtonian fluid and a nonlinear incompressible solid were experimentally determined. A comprehensive data set was acquired by using magnetic resonance imaging to record the interaction between the fluid and the solid, quantifying flow and solid motion.A fluid-structure interaction (FSI) experiment is presented with the aim to provide a challenging yet easy-to-setup FSI test case that addresses the need for rigorous testing of FSI algorithms and modeling frameworks. Focus of the experiment is on biomedical engineering applications. A comprehensive data set was acquired by employing magnetic resonance imaging to record the interaction between the fluid and the solid, quantifying flow and solid motion for steady-state and periodic steady-state test cases.
      PubDate: 2017-01-27T03:31:43.428518-05:
      DOI: 10.1002/cnm.2848
  • Large Eddy Simulations for blood dynamics in realistic stenotic carotids
    • Authors: Rocco Michele Lancellotti; Christian Vergara, Lorenzo Valdettaro, Sanjeeb Bose, Alfio Quarteroni
      Abstract: In this paper, we consider Large Eddy Simulations (LES) for human stenotic carotids in presence of atheromasic plaque, a pathological condition where transitional effects to turbulence may occur, with relevant clinical implications such as plaque rupture. We provide a reference numerical solution obtained at high resolution without any subgrid scale model, to be used to assess the accuracy of LES simulations. In the context we are considering, i.e. hemodynamics, we cannot refer to a statistically homogeneous, isotropic and stationary turbulent regime, hence the classical Kolmogorov theory cannot be used. For this reason, a mesh size and a time step are deemed fine enough if they allow to capture all the features of the velocity field in the shear layers developed after the bifurcation. To assess these requirements, we consider a simplified model of the evolution of a 2D shear layer, a relevant process in the formation of transitional effects in our case. Then, we compare the results of LES σ model (both static and dynamic) and of mixed LES models (where also a similarity contribution is considered). In particular, we consider a realistic scenario of a human carotid and we use the reference solution as gold standard. The results highlight the accuracy of the LES σ models, especially for the static model. This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-26T06:20:23.882565-05:
      DOI: 10.1002/cnm.2868
  • Three-dimensional assessment of impingement risk in geometrically
           parameterised hips compared with clinical measures
    • Authors: Robert J. Cooper; Marlène Mengoni, Dawn Groves, Sophie Williams, Marcus J. K. Bankes, Philip Robinson, Alison C. Jones
      Abstract: Abnormal bony morphology is a factor implicated in hip joint soft tissue damage and an increased lifetime risk of osteoarthritis. Standard two-dimensional radiographic measurements for diagnosis of hip deformities, such as cam deformities on the femoral neck, do not capture the full joint geometry and are not indicative of symptomatic damage.In this study, a three-dimensional geometric parameterisation system was developed to capture key variations in the femur and acetabulum of subjects with clinically diagnosed cam deformity. The parameterisation was performed for Computed Tomography scans of 20 patients (10 female, 10 male). Novel quantitative measures of cam deformity were taken and used to assess differences in morphological deformities between males and females.The parametric surfaces matched the more detailed, segmented hip bone geometry with low fitting error. The quantitative severity measures captured both the size and position of cams, and distinguished between cam and control femurs. The precision of the measures was sufficient to identify differences between subjects that could not be seen with the sole use of two-dimensional imaging. In particular, cams were found to be more superiorly located in males than in females.As well as providing a means to distinguish between subjects more clearly, the new geometric hip parameterisation facilitates the flexible and rapid generation of a range of realistic hip geometries including cams. When combined with material property models, these stratified cam shapes can be used for further assessment of the effect of the geometric variation under impingement conditions.
      PubDate: 2017-01-23T11:00:24.744388-05:
      DOI: 10.1002/cnm.2867
  • Method for the unique identification of hyperelastic material properties
           using full field measures. Application to the passive myocardium material
    • Authors: Luigi E. Perotti; Aditya V. Ponnaluri, Shankarjee Krishnamoorthi, Daniel Balzani, Daniel B. Ennis, William S. Klug
      Abstract: Quantitative measurement of the material properties (e.g., stiffness) of biological tissues is poised to become a powerful diagnostic tool. There are currently several methods in the literature to estimating material stiffness and we extend this work by formulating a framework that leads to uniquely identified material properties. We design an approach to work with full field displacement data — i.e., we assume the displacement field due to the applied forces is known both on the boundaries and also within the interior of the body of interest — and seek stiffness parameters that lead to balanced internal and external forces in a model. For in vivo applications, the displacement data can be acquired clinically using magnetic resonance imaging while the forces may be computed from pressure measurements, e.g., through catheterization. We outline a set of conditions under which the least-square force error objective function is convex, yielding uniquely identified material properties. An important component of our framework is a new numerical strategy to formulate polyconvex material energy laws that are linear in the material properties and provide one optimal description of the available experimental data. An outcome of our approach is the analysis of the reliability of the identified material properties, even for material laws that do not admit unique property identification. Lastly, we evaluate our approach using passive myocardium experimental data at the material point and show its application to identifying myocardial stiffness with an in silico experiment modeling the passive filling of the left ventricle. This article is protected by copyright. All rights reserved.
      PubDate: 2017-01-18T07:25:31.597019-05:
      DOI: 10.1002/cnm.2866
  • Direct numerical simulation of transitional hydrodynamics of the
           cerebrospinal fluid in Chiari I malformation: The role of cranio-vertebral
    • Authors: Kartik Jain; Geir Ringstad, Per-Kristian Eide, Kent-André Mardal
      Abstract: Obstruction to the cerebrospinal fluid (CSF) outflow caused by the herniation of cerebellar tonsils as a result of Chiari malformation type I leads to altered CSF hydrodynamics. This contribution explores the minutest characteristics of the CSF hydrodynamics in cervical subarachnoid space (SAS) of a healthy subject and 2 Chiari patients by performing highly resolved direct numerical simulation. The lattice Boltzmann method is used for the simulations because of its scalability on modern supercomputers that allow us to simulate up to approximately 109 cells while resolving the Kolmogorov microscales. The results depict that whereas the complex CSF flow remains largely laminar in the SAS of a healthy subject, constriction of the cranio-vertebral junction in Chiari I patients causes manifold fluctuations in the hydrodynamics of the CSF. These fluctuations resemble a flow that is in a transitional regime rather than laminar or fully developed turbulence. The fluctuations confine near the cranio-vertebral junction and are triggered due to the tonsillar herniation, which perturbs the flow as a result of altered anatomy of the SAS.Chiari malformation type I obstructs the outflow of the cerebrospinal fluid near the foramen magnum. We conducted direct numerical simulations with meshes containing up to 1 billion cells on case specific subarachnoid spaces of one control subject and 2 Chiari patients on a modern supercomputer. We found the onset of transitional-like hydrodynamics of CSF in 2 Chiari patients whereas the flow remained laminar in the control subject.
      PubDate: 2017-01-13T04:35:34.389861-05:
      DOI: 10.1002/cnm.2853
  • Multiphase fluid-solid coupled analysis of shock-bubble-stone interaction
           in shockwave lithotripsy
    • Authors: Kevin G. Wang
      Abstract: A novel multiphase fluid-solid–coupled computational framework is applied to investigate the interaction of a kidney stone immersed in liquid with a lithotripsy shock wave (LSW) and a gas bubble near the stone. The main objective is to elucidate the effects of a bubble in the shock path to the elastic and fracture behaviors of the stone. The computational framework couples a finite volume 2-phase computational fluid dynamics solver with a finite element computational solid dynamics solver. The surface of the stone is represented as a dynamic embedded boundary in the computational fluid dynamics solver. The evolution of the bubble surface is captured by solving the level set equation. The interface conditions at the surfaces of the stone and the bubble are enforced through the construction and solution of local fluid-solid and 2-fluid Riemann problems. This computational framework is first verified for 3 example problems including a 1D multimaterial Riemann problem, a 3D shock-stone interaction problem, and a 3D shock-bubble interaction problem. Next, a series of shock-bubble-stone–coupled simulations are presented. This study suggests that the dynamic response of a bubble to LSW varies dramatically depending on its initial size. Bubbles with an initial radius smaller than a threshold collapse within 1 μs after the passage of LSW, whereas larger bubbles do not. For a typical LSW generated by an electrohydraulic lithotripter (pmax = 35.0MPa, pmin =− 10.1MPa), this threshold is approximately 0.12mm. Moreover, this study suggests that a noncollapsing bubble imposes a negative effect on stone fracture as it shields part of the LSW from the stone. On the other hand, a collapsing bubble may promote fracture on the proximal surface of the stone, yet hinder fracture from stone interior.A 3D computational fluid dynamics (CFD)-computational solid dynamics (CSD) coupled computational framework is applied to investigate the interaction of model kidney stones immersed in liquid with a lithotripsy shock wave (LSW) and a gas bubble near the stone. The simulation results suggest that bubbles smaller than a certain threshold may collapse violently during the process, thereby promoting fracture on stone surface, yet hindering fracture in the interior.
      PubDate: 2017-01-13T04:05:46.50725-05:0
      DOI: 10.1002/cnm.2855
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