Literature References

Please acknowledge the relevant publications from the following list if you are using SimVascular results in papers, presentations, and other publications.

SimVascular Review

H. Lan, A. Updegrove, N.M. Wilson, G.D. Maher, S.C. Shadden and A.L. Marsden, A Re-Engineered Software Interface and Workflow for the Open-Source SimVascular Cardiovascular Modeling Package, Journal of Biomechanical Engineering, online, 2018. Link

A. Updegrove, N.M. Wilson, J. Merkow, H. Lan, A.L. Marsden and S.C. Shadden, SimVascular: An Open Source Pipeline for Cardiovascular Simulation, Annals of Biomedical Engineering, online, 2016. Link

Finite Element Modeling Overview

C.A. Taylor, T.J.R. Hughes and C.K. Zarins, Finite element modeling of blood flow in arteries, Computer Methods in Applied Mechanics and Engineering, 158(1):155-196, 1998. Link

Marsden, A.L., and Esmaily Moghadam, M., Multiscale Modeling of Cardiovascular Flows for Clinical Decision Support, (invited), Applied Mechanics Reviews,67:030804-1-11, 2015. Link

Finite Element Solver Technology

C.H. Whiting and K.E. Jansen, A stabilized finite element method for the incompressible Navier-Stokes equations using a hierarchical basis, International Journal for Numerical Methods in Fluids, 35(1):93-116, 2001. Link

Patient Specific Model Construction:

N. Wilson, K. Wang, R. Dutton and C. A. Taylor, A Software Framework for Creating Patient Specific Geometric Models from Medical Imaging Data for Simulation Based Medical Planning of Vascular Surgery, Lecture Notes in Computer Science, 2208:449-456, 2001. Link

Resistance Boundary Conditions

I.E. Vignon-Clementel, C.A. Figueroa, K.E. Jansen and C.A. Taylor, Outflow boundary conditions for three-dimensional finite element modeling of blood flow and pressure in arteries, Computer Methods in Applied Mechanics and Engineering, 195(29):3776-3796, 2006. Link

RCR Boundary Conditions

I.E. Vignon-Clementel, C.A. Figueroa, K.E. Jansen and C.A. Taylor, Outflow boundary conditions for three-dimensional simulations of non-periodic blood flow and pressure fields in deformable arteries, Computer Methods in Biomechanics and Biomedical Engineering, 13(5):625-640, 2010. Link

Multiscale Coupling

M. Esmaily Moghadam, I.E. Vignon-Clementel, R. Figliola and A.L. Marsden, A modular numerical method for implicit 0D/3D coupling in cardiovascular finite element simulations, Journal of Computational Physics, 244:63-79, 2013. Link

Coronary Boundary Conditions

H.J. Kim, I.E. Vignon-Clementel, J.S. Coogan, C.A. Figueroa, K.E. Jansen and C.A. Taylor, Patient-specific modeling of blood flow and pressure in human coronary arteries, Annals of Biomedical Engineering, 38(10):3195-3209, 2010. Link

S. Sankaran, M. Esmaily Moghadam, A.M. Kahn, J. Guccione, E. Tseng and A.L. Marsden, Patient-specific multiscale modeling of blood flow for coronary artery bypass graft surgery, Annals of Biomedical Engineering, 40(1):2228-2242, 2012. Link

Backflow Stabilization

M. Esmaily Moghadam, Y. Bazilevs, T.Y. Hsia, I.E. Vignon-Clementel and A.L. Marsden, A comparison of outlet boundary treatments for prevention of backflow divergence with relevance to blood flow simulations, Computational Mechanics, 48(3):277-291, 2011. Link

Linear solver

M. Esmaily Moghadam, Y. Bazilevs and A.L. Marsden, A new preconditioning technique for implicitly coupled multidomain simulations with applications to hemodynamics, Computational Mechanics, 52(5):1141-1152, 2013. Link

M. Esmaily-Moghadam, Y. Bazilevs and A.L. Marsden., A bi-partitioned iterative algorithm for solving linear systems obtained from incompressible flow problems, Computer Methods in Applied Mechanics and Engineering, 286:40–62, 2015. Link

Fluid Structure Interaction

C.A. Figueroa, I.E. Vignon-Clementel, K.E. Jansen, T.J.R. Hughes and C.A. Taylor, A coupled momentum method for modeling blood flow in three-dimensional deformable arteries, Computer Methods in Applied Mechanics and Engineering, 195(41):5685-5706, 2006. Link

J.S. Tran, svFSI PDE and Discretization Documentation, 2018, link


A. Updegrove, N. M. Wilson, and S. C. Shadden, Boolean and smoothing of discrete polygonal surfaces, Advances in Engineering Software, 95, 16-27, 2016. Link


O. Sahni, K.E. Jansen, M.S. Shephard, C.A. Taylor and M.W. Beall, Adaptive boundary layer meshing for viscous flow simulations, Engineering with Computers, 24(3):267-285, 2008. Link


E.O. Kung, A.L. Les, C.A. Figueroa, F. Medina, K. Arcaute, R.B. Wicker, M.V. McConnell and C.A. Taylor, In vitro validation of finite element analysis of blood flow in deformable models, Annals of Biomedical Engineering, 39(7):1947-1960, 2011. Link

E.O. Kung, A.M. Kahn, J.C. Burns and A.L. Marsden, In-vitro validation of patient-specific hemodynamic simulations in coronary aneurysms caused by Kawasaki disease, Cardiovascular Engineering and Technology, 5(2):189-201, 2014. Link

Clinical Applications

J. M. Oakes, S. C. Shadden, C. Grandmont, and I. E. Vignon-Clemental, Aerosol transport throughout inspiration and expiration in the pulmonary airways, International Journal for Numerical Methods in Biomedical Engineering, DOI: 10.1002/cnm.2847, 2017. Link

A. Arzani, A. M. Gambaruto, G. Chen, and S. C. Shadden, Wall shear stress exposure time: A Lagrangian measure of near-wall stagnation and concentration in cardiovascular flows, Biomechanics and Modeling in Mechanobiology, DOI: 10.1007/s10237-016-0853-7, 2017. Link

D. Mukherjee, and S. C. Shadden, Inertial particle dynamics in large artery flows – Implications for modeling arterial embolisms, Journal of Biomechanics, 52, 155-164, 2016. Link

D. Mukherjee, N. Jani, K. Selvaganesan, C. L. Weng, and S. C. Shadden, Computational assessment of the relation between embolism source and embolus distribution to the circle of Willis for improved understanding of stroke etiology, Journal of Biomechanical Engineering, 138(8), 081008-1-13, 2016. Link

K. B. Hansen, and S. C. Shadden, A reduced-dimensional model for near-wall transport in cardiovascular flows, Biomechanics and Modeling in Mechanobiology, 15(3), 713-722, 2016. Link

A. Arzani, A. M. Gambaruto, G. Chen, and S. C. Shadden, Lagrangian wall shear stress structures and near wall transport in high Schmidt aneurysmal flows, Journal of Fluid Mechanics, 790, 158-172, 2016. Link

D. Mukherjee, J. Padilla, and S. C. Shadden, Numerical investigation of fluid–particle interactions for embolic stroke, Theoretical and Computational Fluid Dynamics, 30(1), 23-39, 2016. Link

S. C. Shadden, and A. Arzani, Lagrangian postprocessing of computational hemodynamics, Annals of Biomedical Engineering, 43(1), 41-58, 2015. Link

A. Arzani, A. S. Les, R. L. Dalman, and S. C. Shadden, Effect of exercise on patient specific abdominal aortic aneurysm flow topology and mixing, International Journal for Numerical Methods in Biomedical Engineering, 30(2), 280-295, 2014. Link

D. Sengupta, A.M. Kahn, J.C. Burns, S. Sankaran, S. Shadden and A.L. Marsden, Image-based modeling of hemodynamics and coronary artery aneurysms caused by Kawasaki disease, Biomechanics and Modeling in Mechanobiology, 11(6):915-932, 2012. Link

A.L. Marsden, A.J. Bernstein, V.M. Reddy, S. Shadden, R. Spilker, C.A. Taylor and J.A. Feinstein, Evaluation of a Novel Y-Shaped Extracardiac Fontan Baffle Using Computational Fluid Dynamics, Journal of Thoracic and Cardiovascular Surgery, 137(2):394-403, 2009. Link

A.L. Marsden, Simulation based planning of surgical interventions in pediatric cardiology, Physics of Fluids, 25(10):101303, 2013. Link

A.S. Les, S.C. Shadden, C.A. Figueroa, J.M. Park, M.M. Tedesco, R.J. Herfkens, R.L. Dalman and C.A. Taylor, Quantification of hemodynamics in abdominal aortic aneurysms during rest and exercise using magnetic resonance imaging and computational fluid dynamics, Annals of Biomedical Engineering, 38(4):1288-1313, 2010. Link

J. M. Oakes, A. L. Marsden, C. Grandmont, S. C. Shadden, C. Darquenne and I. E. Vignon-Clementel, Airflow and Particle Deposition Simulations in Health and Emphysema: From In Vivo to In Silico Animal Experiments, Annals of Biomedical Engineering, 42(4):899-914, 2014. Link

M. Esmaily-Moghadam, T-Y Hsia and A.L. Marsden, The Assisted Bidirectional Glenn: a novel surgical approach for first stage single ventricle heart palliation, Journal of Thoracic and Cardiovascular Surgery, 149(3):699-705, 2015. Link

A. B. Ramachandra, A. M. Kahn and A. L. Marsden, Patient specific simulations reveal significant differences in mechanical stimuli in venous and arterial coronary grafts, Journal of Cardiovascular Translational Research, 9(4):279–290, 2016. Link

D. Schiavazzi, E.O. Kung., A.L. Marsden, C. Baker, G. Pennati, T.-Y Hsia and A. Dorfman, Hemodynamic effects of left pulmonary artery stenosis following superior cavopulmonary connection: a patient-specific multiscale modeling study, Journal of Thoracic and Cardiovascular Surgery, 149(3):689–696.e3, 2015. Link


J.P. Schmidt, S.L. Delp, M.A. Sherman, C.A. Taylor, V.S. Pande, R.B. Altman, The Simbios National Center: Systems Biology in Motion, Proceedings of the IEEE, special issue on Computational System Biology, 96(8):1266-1280, 2008. Link

Optimization and Uncertainty Quantification

D. E. Schiavazzi, G. Arbia, C. Baker, A.M. Hlavacek, T. Y. Hsia, A. L. Marsden and I. E. Vignon-Clementel, Uncertainty quantification in virtual surgery hemodynamics predictions for single ventricle palliation, International Journal of Numerical Methods in Biomedical Engineering, 32(3):e02737, 2016. Link

J. S. Tran, D. E. Schiavazzi, A. B. Ramachandra, A. M. Kahn and A. L. Marsden, Automated Tuning for Parameter Identification in Multiscale Coronary Simulations, Computers and Fluids, 142(5):128–138, 2017 Link

D. E. Schiavazzi, A. Doostan, G. Iaccarino and A. L. Marsden, A Generalized Multi-resolution Expansion for Uncertainty Propagation with Application to Cardiovascular Modeling, Computer Methods in Applied Mechanics and Engineering, 314(1):196-221, 2017. Link

A.L. Marsden, Optimization in cardiovascular modeling, Annual Review of Fluid Mechanics, 46:519-546, 2014. Link

Other Contributors

C. Alberto Figueroa, Ph.D., Edward B. Diethrich Associate Professor of Surgery and Biomedical Engineering, University of Michigan

Kenneth Jansen, Ph.D., Professor of Aerospace Engineering, University of Colorado, Boulder

Gabriel Maher, Ph.D., Machine Learning Researcher, BlackRock, Palo Alto

Jameson Merkow, Ph.D., Computer Vision Laboratory, University of California, San Diego

Mahdi Esmaily Moghadam, Ph.D., Postdoctoral Fellow, CTR, Stanford University

Daniele E. Schiavazzi, Ph.D., Assistant Professor, Department of Applied and Computational Mathematics and Statistics, University of Notre Dame

Charles A. Taylor, Ph.D., Founder, CTO, and Member of the Board of Directors, HeartFlow Inc.

Irene Vignon-Clementel, Ph.D., Permanent Research Scientist, INRIA Paris Rocquencourt

Kenneth Wang, M.D., Ph.D., Department of Radiology, Johns Hopkins School of Medicine

Weiguang Yang, Ph.D., Research Scientist, Pediatrics, Stanford University