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<p><h3>References</h3></p>
<li><a href="#refSec1">Overview</a></li>
<li><a href="#refSec2">Boundary Conditions</a></li>
<li><a href="#refSec3">Linear Solver</a></li>
<li><a href="#FSI">Fluid Structure Interaction</a></li>
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<div class="manRefs"> <section id="refSec1" class="group"><h3>Literature References</h3>
<p>Please acknowledge the relevant publications from the following list if you are using <strong>SimVascular</strong> results in papers, presentations, and other publications.</p>
<p><br></p>
<h4>SimVascular Review</h4>
<p>H. Lan, A. Updegrove, N.M. Wilson, G.D. Maher, S.C. Shadden and A.L. Marsden, <strong>A Re-Engineered Software Interface and Workflow for the Open-Source SimVascular Cardiovascular Modeling Package</strong>, <em>Journal of Biomechanical Engineering</em>, online, 2018. <a href="http://biomechanical.asmedigitalcollection.asme.org/article.aspx?articleid=2666622">Link</a></p>
<p>A. Updegrove, N.M. Wilson, J. Merkow, H. Lan, A.L. Marsden and S.C. Shadden, <strong>SimVascular: An Open Source Pipeline for Cardiovascular Simulation</strong>, <em>Annals of Biomedical Engineering</em>, online, 2016. <a href="http://link.springer.com/article/10.1007/s10439-016-1762-8">Link</a></p>
<h4>Finite Element Modeling Overview</h4>
<p>C.A. Taylor, T.J.R. Hughes and C.K. Zarins, <strong>Finite element modeling of blood flow in arteries</strong>, <em>Computer Methods in Applied Mechanics and Engineering</em>, 158(1):155-196, 1998. <a href="http://www.sciencedirect.com/science/article/pii/S004578259880008X">Link</a></p>
<p>Marsden, A.L., and Esmaily Moghadam, M., <strong>Multiscale Modeling of Cardiovascular Flows for Clinical Decision Support</strong>, (invited), <em>Applied Mechanics Reviews</em>,67:030804-1-11, 2015. <a href="http://appliedmechanicsreviews.asmedigitalcollection.asme.org/article.aspx?articleid=2174058">Link</a></p>
<h4>Finite Element Solver Technology</h4>
<p>C.H. Whiting and K.E. Jansen, <strong>A stabilized finite element method for the incompressible Navier-Stokes equations using a hierarchical basis</strong>, <em>International Journal for Numerical Methods in Fluids</em>, 35(1):93-116, 2001. <a href="http://onlinelibrary.wiley.com/doi/10.1002/1097-0363(20010115)35:1%3C93::AID-FLD85%3E3.0.CO;2-G/abstract">Link</a></p>
<h4>Patient Specific Model Construction:</h4>
<p>N. Wilson, K. Wang, R. Dutton and C. A. Taylor, <strong>A Software Framework for Creating Patient Specific Geometric Models from Medical Imaging Data for Simulation Based Medical Planning of Vascular Surgery</strong>, Lecture Notes in Computer Science, 2208:449-456, 2001. <a href="http://link.springer.com/chapter/10.1007/3-540-45468-3_54#page-1">Link</a></p>
</section>
<section id="refSec2" class="group"><h4>Resistance Boundary Conditions</h4>
<p>I.E. Vignon-Clementel, C.A. Figueroa, K.E. Jansen and C.A. Taylor, <strong>Outflow boundary conditions for three-dimensional finite element modeling of blood flow and pressure in arteries</strong>, <em>Computer Methods in Applied Mechanics and Engineering</em>, 195(29):3776-3796, 2006. <a href="http://www.sciencedirect.com/science/article/pii/S0045782505002586">Link</a></p>
<h4>RCR Boundary Conditions</h4>
<p>I.E. Vignon-Clementel, C.A. Figueroa, K.E. Jansen and C.A. Taylor, <strong>Outflow boundary conditions for three-dimensional simulations of non-periodic blood flow and pressure fields in deformable arteries</strong>, <em>Computer Methods in Biomechanics and Biomedical Engineering</em>, 13(5):625-640, 2010. <a href="http://www.tandfonline.com/doi/abs/10.1080/10255840903413565#.VCdsQ3Wx3UY">Link</a></p>
<h4>Multiscale Coupling</h4>
<p>M. Esmaily Moghadam, I.E. Vignon-Clementel, R. Figliola and A.L. Marsden, <strong>A modular numerical method for implicit 0D/3D coupling in cardiovascular finite element simulations</strong>, <em>Journal of Computational Physics</em>, 244:63-79, 2013. <a href="http://www.sciencedirect.com/science/article/pii/S0021999112004202">Link</a></p>
<h4>Coronary Boundary Conditions</h4>
<p>H.J. Kim, I.E. Vignon-Clementel, J.S. Coogan, C.A. Figueroa, K.E. Jansen and C.A. Taylor, <strong>Patient-specific modeling of blood flow and pressure in human coronary arteries</strong>, <em>Annals of Biomedical Engineering</em>, 38(10):3195-3209, 2010. <a href="http://link.springer.com/article/10.1007/s10439-010-0083-6#page-1">Link</a></p>
<p>S. Sankaran, M. Esmaily Moghadam, A.M. Kahn, J. Guccione, E. Tseng and A.L. Marsden, <strong>Patient-specific multiscale modeling of blood flow for coronary artery bypass graft surgery</strong>, <em>Annals of Biomedical Engineering</em>, 40(1):2228-2242, 2012. <a href="http://link.springer.com/article/10.1007/s10439-012-0579-3#page-1">Link</a></p>
<h4>Backflow Stabilization</h4>
<p>M. Esmaily Moghadam, Y. Bazilevs, T.Y. Hsia, I.E. Vignon-Clementel and A.L. Marsden, <strong>A comparison of outlet boundary treatments for prevention of backflow divergence with relevance to blood flow simulations</strong>, <em>Computational Mechanics</em>, 48(3):277-291, 2011. <a href="http://link.springer.com/article/10.1007/s00466-011-0599-0#page-1">Link</a></p>
</section>
<section id="refSec3" class="group"><h4>Linear solver</h4>
<p>M. Esmaily Moghadam, Y. Bazilevs and A.L. Marsden, <strong>A new preconditioning technique for implicitly coupled multidomain simulations with applications to hemodynamics</strong>, <em>Computational Mechanics</em>, 52(5):1141-1152, 2013. <a href="http://link.springer.com/article/10.1007/s00466-013-0868-1#page-1">Link</a></p>
<p>M. Esmaily-Moghadam, Y. Bazilevs and A.L. Marsden., <strong>A bi-partitioned iterative algorithm for solving linear systems obtained from incompressible flow problems</strong>, <em>Computer Methods in Applied Mechanics and Engineering</em>, 286:40–62, 2015. <a href="http://www.sciencedirect.com/science/article/pii/S0045782514004666">Link</a></p>
</section>
<section id="FSI" class="group"><h4>Fluid Structure Interaction</h4>
<p>C.A. Figueroa, I.E. Vignon-Clementel, K.E. Jansen, T.J.R. Hughes and C.A. Taylor, <strong>A coupled momentum method for modeling blood flow in three-dimensional deformable arteries</strong>, <em>Computer Methods in Applied Mechanics and Engineering</em>, 195(41):5685-5706, 2006. <a href="http://www.sciencedirect.com/science/article/pii/S004578250500513X">Link</a></p>
<p>J.S. Tran, <strong>svFSI PDE and Discretization Documentation</strong>, 2018, <a href="https://simtk.org/frs/download_confirm.php/file/5485/fsi_pde_documentation.pdf?group_id=188">link</a></p>
</section>
<section id="refSec4" class="group"><h4>Modeling</h4>
<p>A. Updegrove, N. M. Wilson, and S. C. Shadden, <strong>Boolean and smoothing of discrete polygonal surfaces</strong>, <em>Advances in Engineering Software</em>, 95, 16-27, 2016. <a href="http://www.sciencedirect.com/science/article/pii/S0965997816300230">Link</a></p>
</section>
<section id="refSec5" class="group"><h4>Meshing</h4>
<p>O. Sahni, K.E. Jansen, M.S. Shephard, C.A. Taylor and M.W. Beall, <strong>Adaptive boundary layer meshing for viscous flow simulations</strong>, <em>Engineering with Computers</em>, 24(3):267-285, 2008. <a href="http://link.springer.com/article/10.1007/s00366-008-0095-0#page-1">Link</a></p>
</section>
<section id="refSec6" class="group"><h4>Validation</h4>
<p>E.O. Kung, A.L. Les, C.A. Figueroa, F. Medina, K. Arcaute, R.B. Wicker, M.V. McConnell and C.A. Taylor, <strong>In vitro validation of finite element analysis of blood flow in deformable models</strong>, <em>Annals of Biomedical Engineering</em>, 39(7):1947-1960, 2011. <a href="http://link.springer.com/article/10.1007/s10439-011-0284-7">Link</a></p>
<p>E.O. Kung, A.M. Kahn, J.C. Burns and A.L. Marsden, <strong>In-vitro validation of patient-specific hemodynamic simulations in coronary aneurysms caused by Kawasaki disease</strong>, <em>Cardiovascular Engineering and Technology</em>, 5(2):189-201, 2014. <a href="http://link.springer.com/article/10.1007/s13239-014-0184-8#page-1">Link</a></p>
</section>
<section id="refSec7" class="group"><h4>Clinical Applications</h4>
<p>J. M. Oakes, S. C. Shadden, C. Grandmont, and I. E. Vignon-Clemental, <strong>Aerosol transport throughout inspiration and expiration in the pulmonary airways</strong>, <em>International Journal for Numerical Methods in Biomedical Engineering</em>, DOI: 10.1002/cnm.2847, 2017. <a href="http://onlinelibrary.wiley.com/doi/10.1002/cnm.2847/full">Link</a></p>
<p>A. Arzani, A. M. Gambaruto, G. Chen, and S. C. Shadden, <strong>Wall shear stress exposure time: A Lagrangian measure of near-wall stagnation and concentration in cardiovascular flows</strong>, <em>Biomechanics and Modeling in Mechanobiology</em>, DOI: 10.1007/s10237-016-0853-7, 2017. <a href="https://link.springer.com/article/10.1007/s10237-016-0853-7">Link</a></p>
<p>D. Mukherjee, and S. C. Shadden, <strong>Inertial particle dynamics in large artery flows – Implications for modeling arterial embolisms</strong>, <em>Journal of Biomechanics</em>, 52, 155-164, 2016. <a href="http://www.sciencedirect.com/science/article/pii/S0021929016313215">Link</a></p>
<p>D. Mukherjee, N. Jani, K. Selvaganesan, C. L. Weng, and S. C. Shadden, <strong>Computational assessment of the relation between embolism source and embolus distribution to the circle of Willis for improved understanding of stroke etiology</strong>, <em>Journal of Biomechanical Engineering</em>, 138(8), 081008-1-13, 2016. <a href="http://biomechanical.asmedigitalcollection.asme.org/article.aspx?articleID=2531719">Link</a></p>
<p>K. B. Hansen, and S. C. Shadden, <strong>A reduced-dimensional model for near-wall transport in cardiovascular flows</strong>, <em>Biomechanics and Modeling in Mechanobiology</em>, 15(3), 713-722, 2016. <a href="https://link.springer.com/article/10.1007/s10237-015-0719-4">Link</a></p>
<p>A. Arzani, A. M. Gambaruto, G. Chen, and S. C. Shadden, <strong>Lagrangian wall shear stress structures and near wall transport in high Schmidt aneurysmal flows</strong>, <em>Journal of Fluid Mechanics</em>, 790, 158-172, 2016. <a href="https://www.cambridge.org/core/journals/journal-of-fluid-mechanics/article/lagrangian-wall-shear-stress-structures-and-nearwall-transport-in-highschmidtnumber-aneurysmal-flows/0826EE0545D5E1FC47A3BBB5637E0C0B">Link</a></p>
<p>D. Mukherjee, J. Padilla, and S. C. Shadden, <strong>Numerical investigation of fluid–particle interactions for embolic stroke</strong>, <em>Theoretical and Computational Fluid Dynamics</em>, 30(1), 23-39, 2016. <a href="https://link.springer.com/article/10.1007/s00162-015-0359-4">Link</a></p>
<p>S. C. Shadden, and A. Arzani, <strong>Lagrangian postprocessing of computational hemodynamics</strong>, <em>Annals of Biomedical Engineering</em>, 43(1), 41-58, 2015. <a href="https://link.springer.com/article/10.1007%2Fs10439-014-1070-0">Link</a></p>
<p>A. Arzani, A. S. Les, R. L. Dalman, and S. C. Shadden, <strong>Effect of exercise on patient specific abdominal aortic aneurysm flow topology and mixing</strong>, <em>International Journal for Numerical Methods in Biomedical Engineering</em>, 30(2), 280-295, 2014. <a href="http://onlinelibrary.wiley.com/doi/10.1002/cnm.2601/abstract">Link</a></p>
<p>D. Sengupta, A.M. Kahn, J.C. Burns, S. Sankaran, S. Shadden and A.L. Marsden, <strong>Image-based modeling of hemodynamics and coronary artery aneurysms caused by Kawasaki disease</strong>, <em>Biomechanics and Modeling in Mechanobiology</em>, 11(6):915-932, 2012. <a href="http://link.springer.com/article/10.1007/s10237-011-0361-8#page-1">Link</a></p>
<p>A.L. Marsden, A.J. Bernstein, V.M. Reddy, S. Shadden, R. Spilker, C.A. Taylor and J.A. Feinstein, <strong>Evaluation of a Novel Y-Shaped Extracardiac Fontan Baffle Using Computational Fluid Dynamics</strong>, <em>Journal of Thoracic and Cardiovascular Surgery</em>, 137(2):394-403, 2009. <a href="http://www.sciencedirect.com/science/article/pii/S0022522308016681">Link</a></p>
<p>A.L. Marsden, <strong>Simulation based planning of surgical interventions in pediatric cardiology</strong>, <em>Physics of Fluids</em>, 25(10):101303, 2013. <a href="http://scitation.aip.org/content/aip/journal/pof2/25/10/10.1063/1.4825031">Link</a></p>
<p>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, <strong>Quantification of hemodynamics in abdominal aortic aneurysms during rest and exercise using magnetic resonance imaging and computational fluid dynamics</strong>, <em>Annals of Biomedical Engineering</em>, 38(4):1288-1313, 2010. <a href="http://link.springer.com/article/10.1007/s10439-010-9949-x#page-1">Link</a></p>
<p>J. M. Oakes, A. L. Marsden, C. Grandmont, S. C. Shadden, C. Darquenne and I. E. Vignon-Clementel, <strong>Airflow and Particle Deposition Simulations in Health and Emphysema: From In Vivo to In Silico Animal Experiments</strong>, <em>Annals of Biomedical Engineering</em>, 42(4):899-914, 2014. <a href="http://link.springer.com/article/10.1007/s10439-013-0954-8#page-1">Link</a></p>
<p>M. Esmaily-Moghadam, T-Y Hsia and A.L. Marsden, <strong>The Assisted Bidirectional Glenn: a novel surgical approach for first stage single ventricle heart palliation</strong>, <em>Journal of Thoracic and Cardiovascular Surgery</em>, 149(3):699-705, 2015. <a href="http://www.sciencedirect.com/science/article/pii/S0022522314015402">Link</a></p>
<p>A. B. Ramachandra, A. M. Kahn and A. L. Marsden, <strong>Patient specific simulations reveal significant differences in mechanical stimuli in venous and arterial coronary grafts</strong>, <em>Journal of Cardiovascular Translational Research</em>, 9(4):279–290, 2016. <a href="https://link.springer.com/article/10.1007%2Fs12265-016-9706-0">Link</a></p>
<p>D. Schiavazzi, E.O. Kung., A.L. Marsden, C. Baker, G. Pennati, T.-Y Hsia and A. Dorfman, <strong>Hemodynamic effects of left pulmonary artery stenosis following superior cavopulmonary connection: a patient-specific multiscale modeling study</strong>, <em>Journal of Thoracic and Cardiovascular Surgery</em>, 149(3):689–696.e3, 2015. <a href="http://www.sciencedirect.com/science/article/pii/S0022522314021849">Link</a></p>
<h4>Simbios</h4>
<p>J.P. Schmidt, S.L. Delp, M.A. Sherman, C.A. Taylor, V.S. Pande, R.B. Altman, <strong>The Simbios National Center: Systems Biology in Motion</strong>, <em>Proceedings of the IEEE, special issue on Computational System Biology</em>, 96(8):1266-1280, 2008. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811325/">Link</a></p>
</section>
<section id="UQ" class="group"><h4>Optimization and Uncertainty Quantification</h4>
<p>D. E. Schiavazzi, G. Arbia, C. Baker, A.M. Hlavacek, T. Y. Hsia, A. L. Marsden and I. E. Vignon-Clementel, <strong>Uncertainty quantification in virtual surgery hemodynamics predictions for single ventricle palliation</strong>, <em>International Journal of Numerical Methods in Biomedical Engineering</em>, 32(3):e02737, 2016. <a href="http://onlinelibrary.wiley.com/doi/10.1002/cnm.2737/abstract;jsessionid=EA23F66BAD33FE10108F0F5AE8F2C636.f03t04">Link</a></p>
<p>J. S. Tran, D. E. Schiavazzi, A. B. Ramachandra, A. M. Kahn and A. L. Marsden, <strong>Automated Tuning for Parameter Identification in Multiscale Coronary Simulations</strong>, <em>Computers and Fluids</em>, 142(5):128–138, 2017 <a href="http://www.sciencedirect.com/science/article/pii/S004579301630161X">Link</a></p>
<p>D. E. Schiavazzi, A. Doostan, G. Iaccarino and A. L. Marsden, <strong>A Generalized Multi-resolution Expansion for Uncertainty Propagation with Application to Cardiovascular Modeling</strong>, <em>Computer Methods in Applied Mechanics and Engineering</em>, 314(1):196-221, 2017. <a href="http://www.sciencedirect.com/science/article/pii/S0045782516311951">Link</a></p>
<p>A.L. Marsden, <strong>Optimization in cardiovascular modeling</strong>, <em>Annual Review of Fluid Mechanics</em>, 46:519-546, 2014. <a href="http://www.annualreviews.org/doi/abs/10.1146/annurev-fluid-010313-141341">Link</a></p>
</section>
<section id="refSec8" class="group bottom-buffer"><h4>Other Contributors</h4>
<p>Charles A. Taylor, Ph.D., Founder, CTO, and Member of the Board of Directors, HeartFlow Inc.</p>
<p>Mahdi Esmaily Moghadam, Ph.D., Postdoctoral Fellow, CTR, Stanford University</p>
<p>C. Alberto Figueroa, Ph.D., Edward B. Diethrich Associate Professor of Surgery and Biomedical Engineering, University of Michigan</p>
<p>Kenneth Jansen, Ph.D., Professor of Aerospace Engineering, University of Colorado, Boulder</p>
<p>Weiguang Yang, Ph.D., Research Scientist, Pediatrics, Stanford University</p>
<p>Irene Vignon-Clementel, Ph.D., Permanent Research Scientist, INRIA Paris Rocquencourt</p>
<p>Kenneth Wang, M.D., Ph.D., Department of Radiology, Johns Hopkins School of Medicine</p>
<p>Daniele E. Schiavazzi, Ph.D., Assistant Professor, Department of Applied and Computational Mathematics and Statistics, University of Notre Dame </p>
<p>Jameson Merkow, Ph.D., Computer Vision Laboratory, University of California, San Diego</p>
<p><br></p>
</section>
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