International Journal for Numerical Methods in Biomedical Engineering

Cover image for Vol. 33 Issue 7

Early View (Online Version of Record published before inclusion in an issue)

Edited By: Perumal Nithiarasu, Rainald Löhner, Guowei Wei

Impact Factor: 2.192

ISI Journal Citation Reports © Ranking: 2016: 12/57 (Mathematical & Computational Biology); 21/100 (Mathematics Interdisciplinary Applications); 34/77 (Engineering Biomedical)

Online ISSN: 2040-7947

Associated Title(s): International Journal for Numerical Methods in Engineering, International Journal for Numerical Methods in Fluids, International Journal of Numerical Modelling: Electronic Networks, Devices and Fields, Numerical Linear Algebra with Applications


  1. 1 - 52

    1. A numerical investigation and experimental verification of size effects in loaded bovine cortical bone

      J. C. Frame, M. A. Wheel and P. E. Riches

      Version of Record online: 19 JUL 2017 | DOI: 10.1002/cnm.2903

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      A, An idealized representation of cortical bone incorporating the major microstructural feature, the vascular channel or Haversian canal system, has been used to generate B, finite element models of different sizes that are loaded in bending. The surface morphology of the models reflects that of C, bone samples where the exposed channels are evident. Samples (C) and FE models (B) both exhibit increasing compliance with D, decreasing beam depth, a paradoxical size effect not forecast by more generalized continuum theories.

    2. Viscoelastic computational modeling of the human head-neck system: Eigenfrequencies and time-dependent analysis

      E. Boccia, A. Gizzi, C. Cherubini, M. G. C. Nestola and S. Filippi

      Version of Record online: 19 JUL 2017 | DOI: 10.1002/cnm.2900

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      A subject-specific human head-neck system is studied based on computed tomography and magnetic resonance dataset. Eigenfrequencies and time-dependent analysis are performed via finite element method. Pixel-based mechanical and viscoelastic properties are assigned.

    3. The prediction of viscous losses and pressure drop in models of the human airways

      Andrew K. Wells, Ian P. Jones, Ian S. Hamill and Rafel Bordas

      Version of Record online: 19 JUL 2017 | DOI: 10.1002/cnm.2898

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      • Airway resistance key indicator of progression of asthma disease.
      • Pedley et al proposed simple model for airway resistance. Calibrated using measured data.
      • Parametric survey and sensitivity analysis using CFD applied to Pedley configuration.
      • Results show complex flow structures.
      • Very good quantitative validation.
      • Confirm scaling analysis of Pedley model.
      • Results explain sensitivity to inflow conditions and lung topology.
      • Propose revised calibration for Pedley model.
      • Confirm Pedley conclusion that upper airways contribute most to airway resistance.

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    1. Uncertainty quantification of 2 models of cardiac electromechanics

      Daniel E. Hurtado, Sebastián Castro and Pedro Madrid

      Version of Record online: 4 JUL 2017 | DOI: 10.1002/cnm.2894

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      • We study the effect of parameter uncertainty on 2 state-of-the-art finite-element models of excitation-contraction of cardiac tissue.
      • Forward uncertainty propagation and sensitivity analyses are performed to study how variability in input variables, such as key maximal conductances and elastic parameters, affect output variables, such as the action potential duration, intracellular calcium, and tissue deformation and stress.
      • We confirm a strong linear relationship between input and output variables for a variability up to 25%, which supports the use of linear response surfaces that are used to compute the empirical probability density functions.
    2. A tree-parenchyma coupled model for lung ventilation simulation

      Nicolas Pozin, Spyridon Montesantos, Ira Katz, Marine Pichelin, Irene Vignon-Clementel and Céline Grandmont

      Version of Record online: 20 JUN 2017 | DOI: 10.1002/cnm.2873

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      A strongly coupled tree-parenchyma ventilation model is developed. The tree induces an extra viscous term in the constitutive law, leading, in the finite element framework, to a full matrix. We propose an efficient iterative method taking advantage of the tree dyadic structure. Relevance of various boundary conditions is investigated. A comparison with a model in which terminal compartments are mechanically independent demonstrates the need to consider the parenchyma as a continuum, in particular in pathological situations.

    3. A multiscale approach for determining the morphology of endothelial cells at a coronary artery

      Hossein Ali Pakravan, Mohammad Said Saidi and Bahar Firoozabadi

      Version of Record online: 14 JUN 2017 | DOI: 10.1002/cnm.2891

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      The present study introduces a computational technique for visualizing the morphology of ECs at the arteries of a specific patient. This technique is a multiscale simulation, consisting of the artery scale and the cell scale. The artery scale is an FSI simulation. The cell scale is an inventive model that is able to determine the morphological response of ECs to any combination of mechanical stimuli. The results of the multiscale simulation show the morphology of ECs at different locations of the coronary artery.

    4. A holistic view of the effects of episiotomy on pelvic floor

      Dulce A. Oliveira, Marco P.L. Parente, Begoña Calvo, Teresa Mascarenhas and Renato M. Natal Jorge

      Version of Record online: 14 JUN 2017 | DOI: 10.1002/cnm.2892

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      A biocomputational model is used to analyze the relationship between episiotomy and pelvic floor function, analyzing the damage in the pelvic floor muscles from such obstetric procedures. Common features assessed at screening of pelvic floor dysfunction are evaluated during numerical simulations of both Valsalva maneuver and contraction. Weakened muscles do not lead to bladder neck hypermobility indicating that other supportive structures also have an important role in the pelvic organs stabilization. However, weakened muscles have a reduced contraction ability.

    5. Identification of dynamic load for prosthetic structures

      Dequan Zhang, Xu Han, Zhongpu Zhang, Jie Liu, Chao Jiang, Nobuhiro Yoda, Xianghua Meng and Qing Li

      Version of Record online: 9 JUN 2017 | DOI: 10.1002/cnm.2889

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      This study aimed to identify dynamic load in the dental prosthetic structures, which is expected to serve as a demonstrative tool in estimating unmeasurable forces in biomedical systems. For validating the proposed inverse identification approach, an experimental force measurement system was developed by using a 3D piezoelectric transducer in the implant-supported fixed partial denture (I-FPD) structure in vivo. The numerically identified loads are exceedingly accurate in comparison with the actual load.

    6. Calculation of cancellous bone elastic properties with the polarization-based FFT iterative scheme

      Lucas Colabella, Ariel Alejandro Ibarra Pino, Josefina Ballarre, Piotr Kowalczyk and Adrián Pablo Cisilino

      Version of Record online: 5 JUN 2017 | DOI: 10.1002/cnm.2879

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      A polarization-based FFT iterative scheme is used for the computational homogenization of the elastic properties of cancellous bone. The performance of the method is analyzed for artificial and natural bone samples of 2 species: bovine femoral heads and implanted femurs of Hokkaido rats. The study shows the suitability of the method to accurately estimate the fully anisotropic elastic response of cancellous bone. There are provided guidelines for the construction of the models and the setting of the algorithm.

    7. Potential biomechanical roles of risk factors in the evolution of thrombus-laden abdominal aortic aneurysms

      Lana Virag, John S. Wilson, Jay D. Humphrey and Igor Karšaj

      Version of Record online: 2 JUN 2017 | DOI: 10.1002/cnm.2893

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      Abdominal aortic aneurysms (AAAs) typically harbour an intraluminal thrombus (ILT), yet most prior computational models neglect biochemomechanical effects of thrombus on lesion evolution. This comprehensive thrombus-laden AAA model provides insight into potential effects of commonly proposed rupture 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 but also suggest that the presence of ILT may be a potential source of the staccato enlargement observed in many AAAs.

    8. Effective sparse representation of X-ray medical images

      Laura Rebollo-Neira

      Version of Record online: 31 MAY 2017 | DOI: 10.1002/cnm.2886

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      The proposed dictionary-based framework for sparse representation of X-ray medical images achieves an enormous reduction of the significant data points required to represent an image at high quality. Comparisons with the results produced by the discrete cosine transform and the discrete wavelet transform approximations demonstrates a huge improvement in sparsity. Certainly, on a standard set of test images of average size 1943×1364 pixels, the mean value improvement in the reduction of data points is of 148%, which is attained in 11.4 seconds per image using a small laptop and Matlab environment.

    9. Numerical analysis of crimping and inflation process of balloon-expandable coronary stent using implicit solution

      Jakub Bukala, Piotr Kwiatkowski and Jerzy Malachowski

      Version of Record online: 31 MAY 2017 | DOI: 10.1002/cnm.2890

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      This paper presents an applied methodology for numerical finite element analysis of coronary stent crimping and the free inflation process with the use of an implicit scheme for numerical finite element analysis. Presented methodology is focused on modelling with minimum possible simplification, ie, a full load path, solid element discretization, and sophisticated contact models. The authors believe that presented methodology allows for significant improvement of the obtained results compared to previous efforts.

    10. Face shield design against blast-induced head injuries

      Long Bin Tan, Kwong Ming Tse, Yuan Hong Tan, Mohamad Ali Bin Sapingi, Vincent Beng Chye Tan and Heow Pueh Lee

      Version of Record online: 31 MAY 2017 | DOI: 10.1002/cnm.2884

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      • The novel inclusion of aerogel into the laminated face shield and its effectiveness against blast was explored due to its transparency and excellent shock-absorbing capability.
      • In general, a face shield gives better protection against blast, with a laminated face shield performing better than the conventional polycarbonate face shield.
      • A face shield with extended side edges may not lead to better mitigating effects due to wave ingress effect at the edges.
      • All face shields reduced air pressures significantly at the eyes.
    11. Method for the unique identification of hyperelastic material properties using full-field measures. Application to the passive myocardium material response

      Luigi E. Perotti, Aditya V. S. Ponnaluri, Shankarjee Krishnamoorthi, Daniel Balzani, Daniel B. Ennis and William S. Klug

      Version of Record online: 30 MAY 2017 | DOI: 10.1002/cnm.2866

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      We present an approach to identify uniquely biomechanics material properties in finite kinematics. This approach requires knowledge of loading conditions and corresponding full field displacements. Our method EMS is based on (1) an equilibrium-based objective function; (2) material energy function optimization; and (3) stability and uniqueness analysis of the identified material properties. We evaluate EMS using passive myocardium experimental data and demonstrate its applicability at the ventricular level with an in silico experiment modeling cardiac passive filling.

    12. Finite element modeling, validation, and parametric investigations of a retinal reattachment stent

      R. Rusovici, D. Dalli, K. Mitra, G. Ganiban, M. Grace, R. Mazzocchi and M. Calhoun

      Version of Record online: 24 MAY 2017 | DOI: 10.1002/cnm.2885

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      A new retinal reattachment surgical procedure is based on a stent that 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%.

    13. Phase-field boundary conditions for the voxel finite cell method: Surface-free stress analysis of CT-based bone structures

      Lam Nguyen, Stein Stoter, Thomas Baum, Jan Kirschke, Martin Ruess, Zohar Yosibash and Dominik Schillinger

      Version of Record online: 11 MAY 2017 | DOI: 10.1002/cnm.2880

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      We explore a phase field-based formulation for imposing traction and displacement boundary conditions in a diffuse sense. 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. We demonstrate the flexibility of the new method by analyzing stresses in a human femur and a vertebral body.


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      Bayesian sensitivity analysis of a 1D vascular model with Gaussian process emulators

      Alessandro Melis, Richard H. Clayton and Alberto Marzo

      Version of Record online: 11 MAY 2017 | DOI: 10.1002/cnm.2882

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      A statistical emulator based on Gaussian process regression is used to predict 1D vascular model outcomes needed to perform the sensitivity analysis. Four vascular models of increasing size and complexity are used to test this methodology. The number of training samples needed to train the Gaussian process emulator is proved to be 3 order of magnitudes smaller than the number of 1D simulation runs needed for a traditional Monte Carlo analysis. The scored mean average prediction error is maintained below 1%.


    1. Research and primary evaluation of an automatic fusion method for multisource tooth crown data

      Ning Dai, Dawei Li, Xu Yang, Cheng Cheng and Yuchun Sun

      Version of Record online: 11 MAY 2017 | DOI: 10.1002/cnm.2878

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      We propose a novel method for automatic data fusion using high-precision tooth crown data from optical scanning and root data from CBCT. The proposed method can help to construct a rapid, high-quality 3D model of complete teeth, which can visually enable orthodontists to safely, reliably, and comprehensively plan tooth alignment programs during the tooth alignment simulation process.

    2. Effect of cerebrospinal fluid modeling on spherically convergent shear waves during blunt head trauma

      Amit Madhukar, Ying Chen and Martin Ostoja-Starzewski

      Version of Record online: 11 MAY 2017 | DOI: 10.1002/cnm.2881

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      Our magnetic resonance imaging-based computational model is used to investigate the effect of cerebrospinal fluid modelling on shear wave propagation during blunt head trauma. We find that the blunt impacts give rise not only to a fast pressure wave but also to a slow, and potentially much more damaging, shear wave that converges spherically towards the brain center. This convergent shear wave is dependent on the constitutive property of the cerebrospinal fluid, whereas the peak pressure is not as significantly affected.

    3. Patient-specific computational modeling of cortical spreading depression via diffusion tensor imaging

      Julia M. Kroos, Isabella Marinelli, Ibai Diez, Jesus M. Cortes, Sebastiano Stramaglia and Luca Gerardo-Giorda

      Version of Record online: 11 APR 2017 | DOI: 10.1002/cnm.2874

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      Cortical spreading depression, a depolarisation wave propagating from the visual cortex to the frontal lobe, is commonly accepted as a correlate of migraine aura. Although CSD is not fully understood yet, the highly individual geometry of the cortex is expected to have an impact on its propagation. We introduce a patient-specific model that combines individual geometries, obtained from MRI imaging, with personalized coefficients, derived from diffusion tensor imaging to account for the anisotropy of the cortical tissue.

    4. Fast left ventricle tracking using localized anatomical affine optical flow

      Sandro Queirós, João L. Vilaça, Pedro Morais, Jaime C. Fonseca, Jan D'hooge and Daniel Barbosa

      Version of Record online: 11 APR 2017 | DOI: 10.1002/cnm.2871

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      A left ventricle tracking framework is proposed on the basis of a novel fast localized anatomically constrained affine optical flow strategy. Its applicability for global and regional myocardial function assessment in multiple imaging modalities was investigated in 3 distinct public databases, namely in realistically simulated 3D ultrasound, clinical 3D echocardiography, and clinical cine magnetic resonance images. The method showed accurate tracking results in all databases, outperforming previous state-of-the-art strategies with respect to the extracted clinical cardiac indices.

    5. An efficient multistage algorithm for full calibration of the hemodynamic model from BOLD signal responses

      Brian Zambri, Rabia Djellouli and Taous-Meriem Laleg-Kirati

      Version of Record online: 11 APR 2017 | DOI: 10.1002/cnm.2875

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      We propose a computational strategy that falls into the category of prediction/correction iterative-type approaches, for calibrating the hemodynamic model. The proposed method is used to estimate consecutively the values of the two sets of model parameters. Numerical results corresponding to both synthetic and real functional magnetic resonance imaging 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.

    6. Large eddy simulations for blood dynamics in realistic stenotic carotids

      Rocco Michele Lancellotti, Christian Vergara, Lorenzo Valdettaro, Sanjeeb Bose and Alfio Quarteroni

      Version of Record online: 11 APR 2017 | DOI: 10.1002/cnm.2868

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      We propose and validate large eddy simulations in realistic carotids.


    1. Adaptive unified continuum FEM modeling of a 3D FSI benchmark problem

      Johan Jansson, Niyazi Cem Degirmenci and Johan Hoffman

      Version of Record online: 11 APR 2017 | DOI: 10.1002/cnm.2851

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      We address a 3D fluid-structure interaction benchmark problem representing important characteristics of biomedical modeling. We present a goal-oriented adaptive finite element methodology for incompressible fluid-structure interaction based on a stabilization of the balance equations for the entire continuum in the domain, with a discontinuous phase marker selecting constitutive law tracked by the mesh, which is implemented in the Unicorn/FEniCS framework. We present detailed results for the benchmark problem compared with experiments, together with a mesh convergence study.


    1. A hybrid computational model to explore the topological characteristics of epithelial tissues

      Ismael González-Valverde and José Manuel García-Aznar

      Version of Record online: 11 APR 2017 | DOI: 10.1002/cnm.2877

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      We model the topology of epithelial monolayers using a hybrid framework that not only represents cells as discrete entities but also epithelial tissue as a continuum material. We demonstrate that this novel approach can simulate the topology and other emergent tissue properties from the interaction of cells in the monolayer. We observe on the results of the simulations that proliferation and mechanical properties are fundamental to describe the topology in epithelial tissues.

    2. Human body modeling method to simulate the biodynamic characteristics of spine in vivo with different sitting postures

      Rui-Chun Dong and Li-Xin Guo

      Version of Record online: 7 APR 2017 | DOI: 10.1002/cnm.2876

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      1. The finite element model of the seated whole body modeled using new human body–modeling methods in this study could be used to study the biodynamic characteristics of spine in vivo more precisely and comprehensively.

      2. Effect of different factors on biodynamic characteristics of spine was analyzed.

      3. The stress distributions of lumbar intervertebral disc in different sitting postures under vibration investigated in this paper could offer potential references for spinal injury protection and orthopedics.

    3. An investigation of dimensional scaling using cervical spine motion segment finite element models

      Dilaver Singh and Duane S. Cronin

      Version of Record online: 7 APR 2017 | DOI: 10.1002/cnm.2872

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      Stature scaling of loading responses was investigated using 50th percentile male and 5th percentile female cervical spine motion segment finite element models subject to tension, flexion, and extension loading. Two approaches were undertaken using global, regional, and local scale factors: geometric scaling of the models to investigate size effects (volumetric scaling) and scaling of the model response such as the force-displacement data in tension (data scaling).

    4. How coagulation zone size is underestimated in computer modeling of RF ablation by ignoring the cooling phase just after RF power is switched off

      Ramiro M. Irastorza, Macarena Trujillo and Enrique Berjano

      Version of Record online: 7 APR 2017 | DOI: 10.1002/cnm.2869

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      Ignoring the cooling phase that occurs just after power has been switched off always involves underestimating the computed coagulation zone dimensions in radiofrequency ablation of tumors.

      The underestimation was found to be dependent on the tissue thermal characteristics, it was marked for higher values of specific heat and blood perfusion and less marked for higher values of conductivity.

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      Three-dimensional assessment of impingement risk in geometrically parameterised hips compared with clinical measures

      Robert J. Cooper, Marlène Mengoni, Dawn Groves, Sophie Williams, Marcus J.K. Bankes, Philip Robinson and Alison C. Jones

      Version of Record online: 5 APR 2017 | DOI: 10.1002/cnm.2867

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      This work generated a geometric parameterisation system for the capture cam deformity of the hip joint and quantification of impingement risk. Parametric surfaces and novel 3-dimensional deformity measures were generated for 20 patients clinically diagnosed with cam impingement. The method was precise enough to demonstrate that cams in males were more superiorly located than in females, a finding that could not be derived from standard clinical 2-dimensional imaging.

    6. High-resolution data assimilation of cardiac mechanics applied to a dyssynchronous ventricle

      Gabriel Balaban, Henrik Finsberg, Hans Henrik  Odland, Marie E. Rognes, Stian Ross, Joakim Sundnes and Samuel Wall

      Version of Record online: 2 APR 2017 | DOI: 10.1002/cnm.2863

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      We propose an efficient adjoint gradient–based data assimilation method for high-dimensional parameters in cardiac mechanics. We test this procedure on a synthetic data set and then fit a computational model to a clinical example of a dyssynchronous left ventricle with highly irregular motion.

    7. Computational modeling of tracheal angioedema due to swelling of the submucous tissue layer

      Kun Gou and Thomas J. Pence

      Version of Record online: 9 MAR 2017 | DOI: 10.1002/cnm.2861

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      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.

    8. 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 method

      Eiji Nakamachi, Tomohiro Noma, Kaito Nakahara, Yoshihiro Tomita and Yusuke Morita

      Version of Record online: 3 MAR 2017 | DOI: 10.1002/cnm.2864

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      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.


    1. Aerosol transport throughout inspiration and expiration in the pulmonary airways

      Jessica M. Oakes, Shawn C. Shadden, Céline Grandmont and Irene E. Vignon-Clementel

      Version of Record online: 24 FEB 2017 | DOI: 10.1002/cnm.2847

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      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.


    1. Uncertainty quantification of inflow boundary condition and proximal arterial stiffness–coupled effect on pulse wave propagation in a vascular network

      Antoine Brault, Laurent Dumas and Didier Lucor

      Version of Record online: 24 FEB 2017 | DOI: 10.1002/cnm.2859

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      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.


    1. A monolithic 3D-0D coupled closed-loop model of the heart and the vascular system: Experiment-based parameter estimation for patient-specific cardiac mechanics

      Marc Hirschvogel, Marina Bassilious, Lasse Jagschies, Stephen M. Wildhirt and Michael W. Gee

      Version of Record online: 16 FEB 2017 | DOI: 10.1002/cnm.2842

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      We present a model for patient-specific cardiac mechanics, incorporating a 3D finite element ventricular model coupled to a reduced-order 0D closed-loop vascular system, heart valve, and atrial chamber model. The coupled problem is consistently linearized with respect to 3D structural and 0D vascular unknowns and iteratively solved in one monolithic Newton iteration using physics-based block preconditioning. Efficient strategies for calibrating active contractile and vascular resistance parameters to experimental data gained in porcine experiments are presented, proposing a novel 2-level nonlinear optimization procedure.


    1. Conditions of microvessel occlusion for blood coagulation in flow

      A. Bouchnita, T. Galochkina, P. Kurbatova, P. Nony and V. Volpert

      Version of Record online: 16 FEB 2017 | DOI: 10.1002/cnm.2850

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      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.


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      Modelling mitral valvular dynamics–current trend and future directions

      Hao Gao, Nan Qi, Liuyang Feng, Xingshuang Ma, Mark Danton, Colin Berry and Xiaoyu Luo

      Version of Record online: 16 FEB 2017 | DOI: 10.1002/cnm.2858

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      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.


    1. A novel modelling approach to energy transport in a respiratory system

      Perumal Nithiarasu and Igor Sazonov

      Version of Record online: 16 FEB 2017 | DOI: 10.1002/cnm.2854

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      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.


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      Validation of a non-conforming monolithic fluid-structure interaction method using phase-contrast MRI

      Andreas Hessenthaler, Oliver Röhrle and David Nordsletten

      Version of Record online: 16 FEB 2017 | DOI: 10.1002/cnm.2845

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      A non-conforming arbitrary Lagrangian-Eulerian fluid-structure interaction (FSI) technique is validated using PC MRI data from a 3D FSI experiment with flow in the laminar regime. Performance of the method, spatial refinement, and time to (periodic) steady-state are studied. Very good overall agreement between numerical results and experimental data is found.


    1. The role of the microvascular network structure on diffusion and consumption of anticancer drugs

      Pietro Mascheroni and Raimondo Penta

      Version of Record online: 14 FEB 2017 | DOI: 10.1002/cnm.2857

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      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.


    1. A velocity tracking approach for the data assimilation problem in blood flow simulations

      J. Tiago, T. Guerra and A. Sequeira

      Version of Record online: 14 FEB 2017 | DOI: 10.1002/cnm.2856

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      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.


    1. Quantitative validation of anti-PTBP1 antibody for diagnostic neuropathology use: Image analysis approach

      Evgin Goceri, Behiye Goksel, James B. Elder, Vinay K. Puduvalli, Jose J. Otero and Metin N. Gurcan

      Version of Record online: 10 FEB 2017 | DOI: 10.1002/cnm.2862

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      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.


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      Experiment for validation of fluid-structure interaction models and algorithms

      A. Hessenthaler, N. R. Gaddum, O. Holub, R. Sinkus, O. Röhrle and D. Nordsletten

      Version of Record online: 27 JAN 2017 | DOI: 10.1002/cnm.2848

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      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.


    1. Direct numerical simulation of transitional hydrodynamics of the cerebrospinal fluid in Chiari I malformation: The role of cranio-vertebral junction

      Kartik Jain, Geir Ringstad, Per-Kristian Eide and Kent-André Mardal

      Version of Record online: 13 JAN 2017 | DOI: 10.1002/cnm.2853

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      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.

    2. Assessment of reduced-order unscented Kalman filter for parameter identification in 1-dimensional blood flow models using experimental data

      A. Caiazzo, Federica Caforio, Gino Montecinos, Lucas O. Muller, Pablo J. Blanco and Eluterio F. Toro

      Version of Record online: 13 JAN 2017 | DOI: 10.1002/cnm.2843

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      This work considers a parameter estimation approach on the basis of the reduced-order unscented Kalman filter in the context of one-dimensional blood flow models, investigating the effects of using real measurements versus synthetic data for the estimation procedure. The filter is assessed considering the results of an in vitro model of the human arterial network and the available experimental measurements, comparing the estimation results with an identifiability analysis on the basis of the generalized sensitivity function and considering flow and pressure observations.

    3. Multiphase fluid-solid coupled analysis of shock-bubble-stone interaction in shockwave lithotripsy

      Kevin G. Wang

      Version of Record online: 13 JAN 2017 | DOI: 10.1002/cnm.2855

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      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.

    4. Numerical simulation of volume-controlled mechanical ventilated respiratory system with 2 different lungs

      Yan Shi, Bolun Zhang, Maolin Cai and Xiaohua Douglas Zhang

      Version of Record online: 29 DEC 2016 | DOI: 10.1002/cnm.2852

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      Because coupling effects of 2 lungs has a significant influence on safety and efficiency of mechanical ventilation, a pneumatic model with 2 lungs has been built in this paper to study the coupling effects of 2 lungs in volume-controlled ventilation. It can be concluded that a change of compliance or air resistance of one lung can affect both lungs and an unbalance of 2 lungs may result in overly high pressure in the trachea and overventilation.


    1. A novel approach to the quantification of aortic root in vivo structural mechanics

      E. Votta, M. Presicce, A. Della Corte, S. Dellegrottaglie, C. Bancone, F. Sturla and A. Redaelli

      Version of Record online: 28 DEC 2016 | DOI: 10.1002/cnm.2849

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      We simulated aortic root (AR) dynamics combining subject-specific anatomical reconstructions, based on in vivo medical imaging, with a realistic modeling of AR loading conditions. This novel approach aimed for the consistency between AR geometry and pressure loads loading it, and hence at a reliable computation of tissues strains and stresses. The proposed strategy was successfully applied to 4 subject-specific AR models; simulations highlighted the key role of both geometrical features and tissues prestresses and suggested the potential of our method.


    1. Automated femoral landmark extraction for optimal prosthesis placement in total hip arthroplasty

      Diogo F. de Almeida, Rui B. Ruben, João Folgado, Paulo R. Fernandes, João Gamelas, Benedict Verhegghe and Matthieu De Beule

      Version of Record online: 25 NOV 2016 | DOI: 10.1002/cnm.2844

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      The presented method provides an automated presurgical guidance for prosthesis sizing and placement. In a first stage, it is able to accurately locate key anchor points in the 3D femoral mesh volume. Moreover, optimal prosthesis alignment and sizing estimation can be achieved based on the patient-specific femoral and medullary canal dimensions in an accurate, repeatable, and reliable way. The positional and orientation errors are significantly reduced, and therefore, the risk of implant failure and consequent revision surgery are minimized.

    2. An atlas- and data-driven approach to initializing reaction-diffusion systems in computer cardiac electrophysiology

      Corné Hoogendoorn, Rafael Sebastian, José Félix Rodriguez, Karim Lekadir and Alejandro F. Frangi

      Version of Record online: 23 NOV 2016 | DOI: 10.1002/cnm.2846

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      In cardiac electrophysiology modeling and simulation, the nonlinearity associated with the cell models requires a stabilization process in the entire 3D domain. This work develops a novel procedure for the initialization of reaction-diffusion systems for simulations of cardiac electrophysiology from steady-state conditions. Obtained prediction error was typically less than 10% for all model variables. Simulation times could be cut by at least two-thirds and potentially more, which saves hours or days of high-performance computing.

    3. Computational design and engineering of polymeric orthodontic aligners

      S. Barone, A. Paoli, A. V. Razionale and R. Savignano

      Version of Record online: 21 OCT 2016 | DOI: 10.1002/cnm.2839

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      This article presents a digital methodology to study patient-specific orthodontic treatments based on the use of polymeric aligners. The approach integrates computer-aided technologies, from tomographic imaging to optical scanning, from parametric modeling to finite element analyses. Numerical analyses proved to be a powerful tool to study different aligner's configurations evidencing how auxiliary elements features might affect the loading system delivered by the aligner. For instance, results pointed out that the loads elicited by divot geometries are higher than those provided by using attachment geometries.


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