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Journal Papers

  1. Marsden, A.L., Vasilyev, O.V. and Moin, P., "Construction of commutative filters for LES on unstructured meshes." Journal of Computational Physics, Vol. 175 No. 2, pp. 584--603, 2002.
  2. Marsden, A.L., Wang, M., Dennis, J.E., Jr., and Moin, P., "Optimal aeroacoustic shape design using the surrogate management framework," Optimization and Engineering, Vol. 5, No. 2, pp. 235-262, 2004.  Special Issue on "Surrogate Optimization."
  3. Marsden, A.L., Wang, M., Dennis, J.E., Jr., and Moin, P., "Suppression of vortex-shedding noise via derivative-free shape optimization," Physics of Fluids, Vol. 16, No. 10, pp. L83-L86, 2004.
  4. Marsden, A.L., Wang, M., Dennis, J.E., Jr., and Moin, P., "Trailing-edge noise reduction using derivative-free optimization and large-eddy simulation" Journal of Fluid Mechanics, Vol. 572, pp. 13-36, 2007.
  5. Marsden, A.L., Vignon-Clementel, I.E., Chan, F., Feinstein, J.A., and Taylor, C.A., "Effects of exercise and respiration on hemodynamic efficiency in CFD simulations of the total cavopulmonary connection," Annals of Biomedical Engineering, Vol. 35, No. 2, pp. 250-263, 2007.
  6. Ihme, M., Marsden, A.L., and Pitsch, H., "Generation of optimal artificial neural networks using a pattern search algorithm: application to approximation of chemical systems," Neural Computation, 20:2, 2008.
  7. Marsden, A.L., Feinstein, J.A., and Taylor, C.A., "A computational framework for derivative-free optimization of cardiovascular geometries," Computer Methods in Applied Mechanics and Engineering, Vol. 197 No. 21-24, pp.1890-1905, 2008.
  8. Marsden, A.L., Bernstein, A.J., Reddy, V.M., Shadden, S., Spilker, R., Taylor, C.A. and Feinstein, J.A.,  "Evaluation of a Novel Y-Shaped Extracardiac Fontan Baffle Using Computational Fluid Dynamics," Journal of Thoracic and Cardiovascular Surgery, Vol. 137, pp. 394-403, 2009.
  9. del Alamo, J.C., Marsden, A.L. and Lasheras, J., “Recent Advances in Computational Mechanics for the Diagnosis and Treatment of Cardiovascular Disease”, Revista Espanola de Cardiología, Vol 62, No. 7, pp. 781-805, 2009.
  10. Bazilevs, Y., Hsu, M.-C., Benson, D.J., Sankaran, S. and Marsden, A.L., “Computational Fluid-Structure Interaction: Methods and Application to a Total Cavopulmonary Connection,” Computational Mechanics, Vol 45 (1), pp. 77-89, (2009).
  11. Marsden, A.L., Reddy, V.M., Shadden, S.C., Chan, F.P., Taylor, C.A. and Feinstein, J.A., “A new multi-parameter approach to computational simulation for Fontan assessment and redesign,” Congenital Heart Disease, 5(2), 2010, 104-117.
  12. Sankaran, S., Audet, C. and Marsden A. L. “A method for stochastic constrained optimization using derivative-free surrogate pattern search and collocation'” Journal of Computational Physics, 229(12), 2010, pp. 4664-4682.
  13. Yang, W., Feinstein, J.A. and Marsden, A.L., “Constrained Optimization of an idealized Y-shaped baffle for the Fontan surgery at rest and exercise,” Computer Methods in Applied Mechanics and Engineering, 199, pp. 2135-2149 (2010).
  14. Sankaran, S. and Marsden, A. L., “The impact of uncertainty on shape optimization of idealized bypass graft models in unsteady flow,” Physics of Fluids, Vol 22 (12), 121902, (2010).
  15. de Zélicourt, D.A., Marsden, A.L., Fogel, M.A., Yoganathan, A.P., “Imaging and patient-specific simulations for the Fontan surgery: current methodologies and clinical applications,” Progress in Pediatric Cardiology Vol 30 (1-2), pp. 31-44 (2010).
  16. Vignon-Clementel, I.E., Marsden, A.L., Feinstein, J.A., “A Primer on Computational Simulation in Congenital Heart Disease for the Clinician,” Progress in Pediatric Cardiology, Vol 30 (1-2) 2010, pp. 3-13.
  17. Lesshafft, L., Meiburg, E., Kneller, B., and Marsden, A. L., “Towards inverse modeling of turbidity currents: the inverse lock-exchange problem” Computers & Geosciences, Vol 37, No. 4, pp. 521-529 (2011).
  18. Sankaran, S. and Marsden, A.L., “A stochastic collocation method for uncertainty quantification in cardiovascular simulations,” J. Biomech. Eng., Vol 133, No. 3, pp. 031001, 2011.
  19. Baretta A., Corsini C., Yang W., Vignon-Clementel I.E., Marsden A.L., Feinstein J.A., Hsia T.-Y., Dubini G., Migliavacca F., Pennati G. “Virtual surgeries in patients with congenital heart disease: a multiscale modelling test case,'' Phil. Trans. R. Soc. A, Vol. 369(1954), pp. 4316-4330 (2011).
  20. Esmaily Moghadam, M., Bazilevs, Y., Hsia, T.-Y., Vignon-Clementel, I. and Marsden, A.L., “A comparison of outlet boundary treatments for prevention of backflow divergence with relevance to blood flow simulations,” Computational Mechanics, Vol 48, pp. 277-291, (2011).
  21. Yang, W., Vignon-Clementel, I.E., Troianowski, G., Reddy, V.M., Feinstein, J.A., Marsden, A.L., “Hepatic blood flow distribution and performance in traditional and Y-graft Fontan Geometries: A Case Series Computational Fluid Dynamics Study,” Journal of Thoracic and Cardiovascular Surgery, 143(5), 1086-1097, (2012).
  22. Feinstein JA, Benson DW, Dubin AM, Cohen MS, Maxey DM, Mahle WT, Pahl E, Villafañe J, Bhatt AB, Peng LF, Johnson BA, Marsden AL, Daniels CJ, Rudd NA, Caldarone CA, Mussatto KA, Morales DL, Ivy DD, Gaynor JW, Tweddell JS, Deal BJ, Furck AK, Rosenthal GL, Ohye RG, Ghanayem NS, Cheatham JP, Tworetzky W, Martin GR:  Hypoplastic Left Heart Syndrome: Current Considerations and Expectations: A JACC White Paper. J Am Coll Cardiol. Vol. 59 (1, Suppl. S), S1-S42, (2012).
  23. Sengupta, D., Kahn, AM, Burns, JC, Sankaran, S., Shadden, S. and Marsden, AL, “Image-based modeling of hemodynamics and coronary artery aneurysms caused by Kawasaki disease,” Biomechanics and Modeling in Mechanobiology, Vol. 11(6), pp. 915-932, 2012.
  24. Esmaily Moghadam, M., Migliavacca, F., Vignon-Clementel, I.E., Hsia, T.-Y., and Marsden, A.L., “Optimization of shunt placement for the Norwood surgery using multi-domain modeling,” J. Biomech. Eng. Vol. 134(5), (2012).
  25. Long, C.C., Hsu, M.-C., Bazilevs, Y., Feinstein, J.A., Marsden, A.L., “Fluid-structure interaction simulations of the Fontan procedure using variable wall properties,” International Journal of Numerical Methods in Biomedical Engineering, Vol. 28(5), pp. 513-527, (2012).
  26. Sankaran, S., Esmaily Moghadam, M., Kahn, A.M., Guccione, J., Tseng, E., and Marsden, A.L., “Patient-specific multiscale modeling of blood flow for coronary artery bypass graft surgery,” Annals of Biomedical Engineering, Vol. 40(1)), pp. 2228-2242, (2012).  
  27. Gundert, T.J., Marsden, A.L., Yang, W., Marks, D.S., and LaDisa, Jr., J.F., “Identification of Hemodynamically Optimal Coronary Stent Designs Based on Vessel Caliber,” IEEE Transactions in Biomedical Engineering, Vol. 59(11), pp. 1992-2002, (2012).
  28. Gundert, T.J., Marsden, A.L., Yang, W., and LaDisa, Jr., J.F., “Optimization of Cardiovascular Stent Design Using Computational Fluid Dynamics,” J. Biomech. Eng., Vol 134(1), (2012).
  29. Oakes, J.M., Scadeng, M., Breen, E., Marsden, A.L., Darquenne, C. “Rat airway morphometry measured from 3D geometric models derived from in-situ magnetic resonance imaging.’’ Journal of Applied Physiology, Vol. 112(11), pp. 1921-1931, (2012).
  30. Baretta, A., Corsini, C., Marsden, A.L., Vignon-Clementel, I.E., Hsia, T.-Y. Dubini G.,  Migliavacca, F., Pennati, G., “Respiratory effects on hemodynamics in patient-specific CFD models of the Fontan circulation under exercise conditions”  European Journal of Mechanics B/Fluids, Vol. 35 pp. 61-69, (2012).
  31. Bockman, M.D., Kansagra, A.P., Shadden, S.C., Wong, E.C., Marsden, A.L., “Fluid mechanics of mixing in the vertebrobasilar system: Comparison of Simulation and MRI,'' Cardiovascular Engineering and Technology, 3(4), pp. 450-461, (2012).
  32. Esmaily Moghadam, M., Vignon-Clementel, I.E., Figliola, R., and Marsden, A.L., “A modular numerical method for implicit 0D/3D coupling in cardiovascular finite element simulations,” Journal of Computational Physics, 244, pp. 63-79, (2013).
  33. Yang, W., Feinstein, J.A., Shadden, S.C., Vignon-Clementel, I.E., and Marsden, A.L., “Optimization of a Y-graft design for improved hepatic flow distribution in the Fontan circulation,” J. Biomech. Eng. 135(1), (2013).
  34. Duvernois, V., Marsden, A.L. and Shadden, S.C., “Lagrangian analysis of hemodynamics data from FSI simulation,” International Journal for Numerical Methods in Biomedical Engineering, 29(4), pp. 445-461, (2013).
  35. Sankaran, S., Humphrey, J.D., Marsden, A.L., “Optimization and parameter sensitivity analysis for arterial growth and remodeling computations,” CMAME, 256, pp. 200-210 (2013).
  36. Kung, E.O., Baretta, A., Baker, C., Arbia, G., Biglino, G., Corsini, C., Schievano, S., Vignon-Clementel, I.E., Dubini, G., Pennati, G., Taylor, A., Dorfman, A., Hlavacek, A.M., Marsden, A.L., Hsia, T.-Y.  Migliavacca, F. “Predictive modeling of the virtual Hemi-Fontan operation for second stage single ventricle palliation: two patient-specific cases,” Journal of Biomechanics, 46(2), pp. 423-429 (2013).
  37. Esmaily Moghadam, M. Hsia, T.Y., Marsden, A.L., “A non-discrete method for computation of residence time in fluid mechanics simulations,” Physics of Fluids. 25, 110802, (2013).
  38. Steinman, D. et al. “Variability of CFD Solutions for Pressure and Flow in a Giant Aneurysm: The SBC2012 CFD Challenge,” Journal of Biomechanical Engineering, 135, (2013).
  39. Lee, J., Esmaily Moghadam, M., Kung, E., Cao, H., Beebe, T., Miller, Y., Roman, B.L., Lien, C., N.C. Chi, Marsden, A.L., Hsiai, T.K., “Moving Domain Computational Fluid Dynamics to Interface with an Embryonic Model of Cardiac Morphogenesis,” PLOS one, 8(8), (2013). 
  40. Marsden, A.L., “Simulation based planning of surgical interventions in pediatric cardiology,'' Physics of Fluids (invited paper), Vol. 25, 101303 (2013). 
  41. Long, C.C., Esmaily Moghadam, M., Marsden, A.L., Bazilevs, Y., “Computation of Residence Time in the Simulation of Pulsatile Ventricular Assist Devices,” Computational Mechanics, Vol. 54(4), pp. 911-919, (2013).
  42. Esmaily Moghadam, M., Bazilevs, Y., Marsden, A.L., “A new preconditioning technique for implicitly coupled multidomain simulations with applications to hemodynamics,” Computational Mechanics, Vol. 52(5), pp. 1141-1152, (2013). 
  43. Long, C. C., Marsden, A. L., Bazilevs, Y., “Fluid-Structure Interaction Simulation of Pulsatile Ventricular Assist Devices,” Computational Mechanics, Vol. 52(5), pp. 971-981, (2013). 
  44. Oakes, J.M., Marsden, A.L., Grandmont, C., Shadden, S.C., Darquenne, C., Vignon-Clementel, I.E., “Airflow and Particle Deposition Simulations in Health and Emphysema: From In Vivo to In Silico Animal Experiments,” Annals of Biomedical Engineering, Vol. 42(4), pp. 899-914, (2013).
  45.  Arbia, G., Corsini, C., Esmaily Moghadam, M., Marsden, A.L., Migliavacca, F., Pennati, G., Hsia, T-Y, Vignon-Clementel, I.E., ``Numerical blood flow simulation in surgical corrections: what do we need for an accurate analysis?'' Journal of Surgical Research, Vol. 186(1), pp. 44-55, (2014).  
  46. Corsini, C., Baker, C., Kung, E.O., Schievano, S., Arbia, G., Baretta, A., Biglino, G., Migliavacca, F., Dubini, G., Pennati, G., Marsden, A., Vignon-Clementel, I., Taylor, A, Hsia, T.-Y., and Dorfman, A., “An Integrated Approach to Patient-specific Predictive Modeling for Single Ventricle Heart Palliation,” Computer Methods  in Biomechanics and Biomedical Engineering, Vol. 17(14), pp. 1572-1589, (2014).
  47. Sengupta, D., Kahn, A.M., Shirinsky, O., Lyskina, G., Burns, J.C., Marsden, A.L., “Thrombotic risk stratification using computational modeling in patients with coronary artery aneurysms following Kawasaki disease,” Biomechanics and Modeling in Mechanobiology, Vol. 13(6), pp. 1261-1276, (2014).
  48. Marsden, A.L., “Optimization in cardiovascular modeling,” Annual Review of Fluid Mechanics, Vol. 46 pp. 519-546, (2014). 
  49. Marsden, A.L., Bazilevs, Y., Long, C.C., Behr, M., “Recent advances in computational methodology for simulation of mechanical circulatory assist devices,” WIREs Systems Biology & Medicine (invited paper), Vol 6(2), pp. 169-188, (2014).
  50. Kung E.O., Pennati G., Migliavacca F., Hsia T.Y., Marsden, A.L., Giardini A., MOCHA Investigators.  “A simulation protocol for exercise physiology in Fontan patients using a closed-loop lumped-parameter model,” Journal of Biomechanical Engineering, Vol. 136(8), pp. 081007, (2014).
  51. Kung E.O., Kahn A.M., Burns J.C., Marsden, A.L., “In-vitro Validation of Patient-Specific Hemodynamic Simulations in Coronary Aneurysms Caused by Kawasaki Disease.” Cardiovascular Engineering and Technology, Vol. 5(2), pp. 189–201, (2014)
  52. Esmaily Moghadam, M. Bazilevs, Y., Marsden, A.L., “Impact of data distribution on the parallel performance of iterative linear solvers with emphasis on CFD of incompressible flows,'' Computational Mechanics, Vol. 55(1), pp. 93-103, (2015).
  53. Esmaily-Moghadam, M., Murtuza, B., Hsia, T.Y., Marsden, A.L., “Simulations reveal adverse hemodynamics in single ventricle patients with multiple systemic to pulmonary shunts,” Journal of Biomechanical Engineering, Vol. 137(3), 031001, (2015). 
  54. Corsini, C., Baker, C., Baretta, A., Biglino, G., Hlavacek, A. M., Hsia, T.-Y., Kung E., Marsden, A.L., Migliavacca, F., Vignon-Clementel, I., Pennati, G., “Collateral vessel occlusion in a patient-specific model of single ventricle circulation for hemodynamics prediction,” in revision.
  55. Long, C.C., Bazilevs, Y., Marsden, A.L., “Shape Optimization of Pulsatile Ventricular Assist Devices Using FSI to Minimize Thrombotic Risk,” Computational Mechanics, Vol. 54(4), pp. 921-932, (2014).
  56. Ramachandra, A. B., Sankaran, S., Humphrey, J.D., Marsden, A.L., “Computational simulation of the adaptive capacity of vein grafts in response to increased pressure,” Journal of Biomechanical Engineering, Vol. 137, pp. 031009-1, (2015). PMCID: PMC4321118
  57. Bao, G., Bazilevs, Y., Chung, J.H., Decuzzi, P. Espinosa, H.D., Ferrari, M., Gao, H., Hossain, S., Hughes, T.J.R., Kamm, R., Liu, W.K., Marsden, A.L., “USNCTAM Perspectives on Mechanics in medicine,” Journal of the Royal Society Interface, Vol. 11(97), pp. 20140301, (2014).
  58. Kung, E.O., Perry, J.C., Davis, C.K., Migliavacca, F., Pennati, G., Hsia, T-Y, Giardini, A., Marsden, A.L., “Computational Modeling of Pathophysiologic Responses to Exercise in Fontan Patients,” Annals of Biomedical Engineering, Vol. 43(6), pp. 1335-1347, (2015).
  59. Esmaily-Moghadam, M., Bazilevs, Y., Marsden, A.L., “A bi-partitioned iterative algorithm for solving linear systems obtained from incompressible flow problems,” Computer Methods in Applied Mechanics and Engineering, Vol. 286, pp. 40–62, (2015).
  60. Schiavazzi, D., Kung, E.O., Marsden, A.L., Baker, C., Pennati, G., Hsia, T.-Y., Dorfman, A., “Hemodynamic effects of left pulmonary artery stenosis following superior cavopulmonary connection: a patient-specific multiscale modeling study,” Journal of Thoracic and Cardiovascular Surgery, Vol. 149(3), pp. 689–696.e3, (2015).
  61. Esmaily-Moghadam, M., Hsia, T-Y, Marsden, A.L., “The Assisted Bidirectional Glenn: a novel surgical approach for first stage single ventricle heart palliation,” Journal of Thoracic and Cardiovascular Surgery, 149(3), pp. 699-705, (2015). 
  62. Takizawa, K., Tezduyar, T.E., Long, C. C., Marsden, A. L., Schjodt, K., “ST and ALE-VMS methods for patient-specific cardiovascular fluid mechanics modeling,” Mathematical Models and Methods in Applied Sciences, Vol 24(12), pp. 2437–2486, (2014).
  63. Oakes, J.M., Marsden, A.L., Grandmont, C., Darquenne, C., Vignon-Clementel, I.E., “Distribution of Aerosolized Particles in Healthy and Emphysematous Rat Lungs: Comparison Between Experimental and Numerical Studies,” Journal of Biomechanics, Vol. 48(6), pp. 1147–1157, (2015).
  64. Martin, M.H., Feinstein, J.A., Chan, F.P., Marsden, A.L., Yang, W., Reddy, V.M., “Technical Feasibility and Intermediate Outcomes of a Hand-Crafted, Area-Preserving, Bifurcated “Y-Graft” Fontan,” Journal of Thoracic and Cardiovascular Surgery, Vol. 149(1), pp. 247–255, (2015).
  65. Yang, W., Chan, F.P., Reddy, V.M., Marsden, A.L., Feinstein, J.A., “Flow Simulations and Validation for the First Cohort of Y-graft Fontan Patients,” Journal of Thoracic and Cardiovascular Surgery, Vol. 149(1), pp. 247–255, (2015).
  66. Corsini, C., Baker, C.E., Baretta, A., Biglino, G., Hlavacek, A.M., Hsia, T.Y., Kung, E.O., Marsden, A.L., Migliavacca, F., Vignon-Clementel, I.E., Pennati, G., “Integration of clinical data collected at different times for virtual surgery in single ventricle patients: a case study,” Annals of Biomedical Engineering, Vol. 43 (6), pp. 1310-1320, (2015).
  67. Marsden, A.L., and Esmaily Moghadam, M., “Multiscale Modeling of Cardiovascular Flows for Clinical Decision Support,” (invited), Applied Mechanics Reviews, Vol. 67, pp. 030804-1-11 (2015).
  68. Zhou, J., Esmaily-Moghadam, M., Conover, T., Hsia, T.-Y., Marsden, A.L., Figliola, R., “In vitro experimental assessment of the assisted bidirectional Glenn procedure for stage one single ventricle repair” Cardiovascular Engineering and Technology, Vol 6 (3), pp. 256-267, (2015). 
  69. Marsden, A.L., Feinstein, J.A., “Computational modeling and engineering in pediatric and congenital heart disease,” (invited), Current Opinion in Pediatrics, Vol. 27 (5), pp. 587-596, (2015).
  70. Van De Bruaene, A., Claessen, G, La Gerche, A., Kung E., Marsden, A., De Meester, P., Devroe, S., Bogaert, J., Claus, P., Heidbuchel, H., Budts, W., Gewillig, M., “Effect of respiration on cardiac filling at rest and during exercise in Fontan patients: A clinical and computational modeling study,” IJC Heart & Vasculature 9, pp. 100-108, (2015).
  71. Farrar, G., Suinesiaputra, A., Gilbert, K., Perry, J., Hegde, S., Marsden, A., Young, A., Omens, J., McCulloch, A., “Atlas-Based Patient-Specific Ventricular Shape Analysis for Understanding Congenital Heart Disease,” Progress in Pediatric Cardiology, Vol. 43, pp. 61-69, (2016).  
  72. Schiavazzi, D. E., Arbia, G., Baker, C., Hlavacek, A.M., Hsia, T.Y., Marsden, A.L., Vignon-Clementel, I.E., “Uncertainty quantification in virtual surgery hemodynamics predictions for single ventricle palliation,” International Journal of Numerical Methods in Biomedical Engineering, Vol. 32 (3) (2016).
  73. Schiavazzi, D.E., Hsia, T.Y., Marsden, A.L., “On a sparse pressure-flow rate condensation of rigid circulation models,” Journal of Biomechanics, Vol. 49(11) (Special Issue) pp. 2174-2186, (2016).
  74. Ramachandra, A. B., Kahn, A. M., Marsden, A.L., “Patient specific simulations reveal significant differences in mechanical stimuli in venous and arterial coronary grafts,” Journal of Cardiovascular Translational Research, Vol. 9 (4), pp 279–290, (2016). PMCID: PMC5533611
  75. Jung, S., Staples, A., Dabiri, J.O., Marsden, A.L., Prakash, M., Davis, K.A., Shadden, S.C., Savin, T., Bourouiba, L., Sznitman, J., “Research trends in biological fluid dynamics,” A USNCTAM Report on Recent Trends in Mechanics, 2016.
  76. Schiavazzi, D.E., Baretta, A., Pennati, G., Hsia, T.-Y., Marsden, A.L., “Patient-specific parameter estimation in single-ventricle lumped circulation models under uncertainty,” International Journal for Numerical Methods in Biomedical Engineering, Vol 33 (3), e02799, (2017).
  77. Schmidt, T., Rosenthal, D., Reinhartz, O., Riemer, R., He, F., Hsia, T.-Y., Marsden, A.L., Kung, E.,  “Superior Performance of Continuous Over Pulsatile Flow Ventricular Assist Devices in the Single Ventricle Circulation: A Computational Study," Vol 52, pp. 48-54, Journal of Biomechanics, (2017).
  78. Ward, E.P., Shiavazzi, D., Sood, D., Marsden, A., Lane, J., Owens, E., Barleben, A., ``Computed Tomography Fractional Flow Reserve Can Identify Culprit Lesions in Aortoiliac Occlusive Disease Using Minimally Invasive Techniques,'' Annals of Vascular Surgery, Vol. 38, pp. 151-157, (2017).
  79. Tran, J. S., Schiavazzi, D. E., Ramachandra, A. B., Kahn, A. M., Marsden, A. L., “Automated Tuning for Parameter Identification in Multiscale Coronary Simulations,” Computers and Fluids, Vol. 142(5), pp. 128–138, (2017). PMCID: PMC5287494
  80. Schiavazzi, D. E., Doostan, A., Iaccarino, G., Marsden, A. L., “A Generalized Multi-resolution Expansion for Uncertainty Propagation with Application to Cardiovascular Modeling,” Computer Methods in Applied Mechanics and Engineering, Vol. 314, Special Issue (SI), pp. 196-221, (2017).
  81. Updegrove, A., Wilson, N.M., Merkow, J., Lan, H., Marsden, A.L., Shadden, S. C., “SimVascular - An Open Source Pipeline for Cardiovascular Simulation,” Annals of Biomedical Engineering, Vol 45 (3), pp. 525-541, (2017). 
  82. Wu, M. C.H., Kamensky, D., Wang, C., Herrema, A.J., Xu, F., Pigazzini, M.S., Marsden, A.L., Bazilevs, Y., Hsu, M.C., “Optimizing fluid-structure interaction systems with immersogeometric analysis and surrogate modeling: Application to a hydraulic arresting gear,” Computer Methods in Applied Mechanics and Engineering, Vol 316 (Special Issue), pp. 668–693 (2017).
  83. Ramachandra, A. B., Humphrey, J. D., Marsden, A. L., “Gradual loading ameliorates maladaptation in computational simulations of vein graft growth and remodeling,” Journal of the Royal Society Interface, Vol. 14 (130), 2017. PMCID: PMC5454282
  84. Grande Gutierrez, N., Shirinsky, O., Gagarina, N.V., Lyskina, G.A., Fukazawa, R., Ogawa, S., Burns, J.C., Marsden, A.L., Kahn, A.M., “Assessment of Coronary Artery Aneurysms Caused by Kawasaki Disease Using Transluminal Attenuation Gradient Analysis of Computerized Tomography Angiograms,” American Journal of Cardiology, Vol. 120 (4), pp. 556-562, (2017). PMCID: PMC6046216
  85. Grande-Gutierrez, N., Kahn, A., Burns, J.C., Alison, A. L., “Computational blood flow simulations in Kawasaki disease patients: Insight into coronary artery aneurysm hemodynamics,” Global Cardiology Science & Practice, 2017. PMCID: PMC5856960
  86. Vedula, V., Lee, J., Xu, H., Kuo, J.C.-C., Hsiai, T.K., Marsden, A.L., “A Method to Quantify Mechanobiologic Forces during Zebrafish Cardiac Development using 4-D Light Sheet Imaging and Computational Modeling,” PLOS Computational Biology, Vol. 13 (10), e1005828, (2017).
  87. Bertoglio, C., Caiazzo, A., Bazilevs, Y., Braack, M., Esmaily-Moghadam, M., Gravemeier, V., Marsden, A.L., Pironneau, O., Vignon-Clementel, I.E., Wall, W.A., “Benchmark problems for numerical treatment of backflow at open boundaries,” Int. J. Numer. Meth. Biomed. Eng. Vol. 34 (2) (2018).
  88. Lan, H., Updegrove, A., Wilson, N.M., Maher, G.D., Shadden, S.C., Marsden, A.L., “A re-engineered interface and workflow for the open source SimVascular cardiovascular modeling package,” Journal of Biomechanical Engineering, Vol. 140(2), 024501 (2018). PMCID: PMC5816252
  89. Verma, A., Esmaily, M., Shang, J.K., Figliola, R.S., Feinstein, J.A., Hsia, T.Y., Marsden, A.L., “Optimization of the Assisted Bidirectional Glenn Procedure for First Stage Single Ventricle Repair”, World Journal for Pediatric and Congenital Heart Surgery, Vol. 9(2), pp. 157-170, (2018).
  90. Yang, W., Hanley, F.L., Chan, F.P., Marsden, A.L., Vignon-Clementel, I.E., Feinstein, J.A., “Computational simulation of post-operative pulmonary flow distribution in Alagille patients with peripheral pulmonary artery stenosis,” Congenital Heart Disease, Vol. 13 (2), pp. 241-250 (2018).
  91. Yang, W., Marsden, A.L., Ogawa, M.T., Sakarovitch,C., Phillips, K. K., Rabinovitch, M., Feinstein, J.A., “Right Ventricular Stroke Work Correlates with Outcomes in Pediatric Pulmonary Arterial Hypertension,” Pulmonary Circulation, Vol. 8(3) (2018).
  92. Lee, J., Vedula, V., Baek, K., Chen, J., Hsu, J.J., Ding, Y., Chang, C.-C., Kang, H., Small, A., Fei, P., Chuong, C.-M., Li, R., Demer, L., Sevag Packard, R.R., Marsden, A. L., Hsiai, T. K., “Spatial and temporal variations in hemodynamic forces initiate cardiac trabeculation,” JCI Insight, Vol. 3(13), (2018).
  93. Liu, J., Marsden, A.L., “A unified continuum and variational multiscale formulation for fluids, solids, and fluid-structure interaction,” Computer Methods for Applied Mechanics and Engineering, Vol. 337 (1), pp. 549-597 (2018).
  94. Abiri, A., Ding, Y., Abiri, P., Packard, R.R.S., Vedula, V., Marsden, A., Kuo, C.J., Hsiai, T.K., “Simulating Developmental Cardiac Morphology in Virtual Reality Using a Deformable Image Registration Approach,” Annals of Biomedical Engineering, Vol. 46 (12), pp. 2177-2188 (2018).
  95. Berg, P., Voß, S., Saalfeld, S., Janiga, G., Bergersen, A. W., Valen-Sendstad, K., Bruening, J., Goubergrits, L., Spuler, A., Cancelliere, N. M., Steinman, D. A., Pereira, V. M., Chiu, T. L., Tsang, A. C. O., Chung, B. J., Cebral, J. R., Salvatore, C., Pallarès, J., Copelli, G., Csippa, B., Paál, G., Fujimura, S., Takao, H., Hodis, S., Hille, G., Karmonik, C., Elias, S., Kellermann, K., Khan, M. O., Marsden, A. L., Morales, H. G., Piskin, S., Finol, E. A., Pravdivtseva, M., Rajabzadeh-Oghaz, H., Paliwal, N., Meng, H., Seshadhri, S., Howard, M., Shojima, M., Sugiyama, S., Niizuma, K., Sindeev, S., Frolov, S., Wagner, T., Brawanski, A., Qian, Y., Wu, Y.-A., Carlson, K. D., Dragomir-Daescu, D., Beuing, O., "Multiple Aneurysms AnaTomy CHallenge 2018 (MATCH): Phase I: Segmentation," Cardiovascular Engineering and Technology, pp. 1-17 (2018).
  96. Yang, W., Dong, M., Rabinovitch, M., Chan, F. P., Marsden, A. L., Feinstein, J. A., “Evolution of hemodynamic forces in the pulmonary tree with progressively worsening pulmonary arterial hypertension in pediatric patients,” Biomechanics and Modeling in Mechanobiology, pp. 1-18 (2019).
  97. Tran, J. S., Schiavazzi, D. E., Kahn, A. M., and Marsden, A.L., “Uncertainty quantification of simulated biomechanical stimuli in coronary bypass grafts,” Computer Methods in Applied Mechanics and Engineering, Vol. 345 (1), pp.402-428 (2019).
  98. Grande Gutierrez, N., Mathew, M., McCrindle, B.W., Tran, J.S., Kahn, A.M., Burns, J.C., Marsden, A.L., “Hemodynamic Variables in Aneurysms are Associated with Thrombotic Risk in Children with Kawasaki Disease,” International Journal of Cardiology, Vol. 281, pp.15-21, (2019).
  99. Shang, J., Esmaily, M., Verma, A., Reinhartz, O., Figliola, R.S., Hsia, T.-Y., Feinstein, J.A., Marsden, A.L., “Patient-specific multiscale modeling of the Assisted Bidirectional Glenn,” Annals of Thoracic Surgery, Vol. 107, Issue 4, Pages 1232–1239, (2019).
  100. Liu, J., Marsden A.L., “A robust and efficient iterative method for hyper-elastodynamics with nested block preconditioning,” Journal of Computational Physics, Vol. 383, pp. 72-93 (2019).
  101. Hsiai, T. K., Abiri, A., Ding, Y., Abiri, P., Packard, R. R. S., Vedula, V., Marsden, A. L., Kuo, C.-C.J., to appear in Annals of Biomedical Engineering.
  102. Seo, J., Schiavazzi, D.E., Marsden, A.L., “Performance of preconditioned iterative linear solvers for cardiovascular simulations in rigid and deformable vessels,” Computational Mechanics, in press (2019).
  103. Hsu, J.J., Vedula, V.,  Baek, K.I.,  Chen, C.,  Chen, J., Chou, M.I., Lam, J., Subhedar, S., Wang, J., Ding, Y., Chang, C.-C., Lee, J., Demer, L.L.,  Tintut, Y., Marsden, A.L.,  Hsiai, T.K., "Contractile and Hemodynamic Forces Coordinate Notch1b-Mediated Outflow tract valve formation'', Journal of Clinical Investigation Insight, (2019) in press. 
  104. Gijsen, F.,  Katagiri, Y.,  Barlis, P.,  Bourantas, C., Collet, C., Coskun, U., Daemen, J., Dijkstra, J.,  Edelman, E., Evans, P., van der Heiden, K., Hose, R.,  Ko, B., Krams, R., Marsden, A.L.,, Migliavacca, F.,  Onuma, Y., Ooi, A.,  Poon, E., Samady, H.,  Stone, P., Takahashi, K., Tang, D., Thondapu, V., Tenekecioglu, E., Timmins, L., Torii, R., Wentzel, J., Serruys, P., "Expert consensus on the assessment of wall shear stress in human coronary arteries: existing methodologies, technical considerations, and clinical applications,'' European Heart Journal, to appear.   
  105. Eslami, P., Tran, J., Jin, Z., Karady, J., Sotoodeh, R., Lu, M.T., Hoffmann, U., Marsden, A., "Effect of Wall Elasticity on Hemodynamics and Wall Shear Stress in Patient-Specific Simulations in the Coronary Arteries'', Journal of Biomechanical Engineering, (2019) in press.
  106. Rodefeld, M.D., Marsden, A.L., Figliola, R., Jonas, T., Nearye, M., Giridharan, G.A., Cavopulmonary assist: long-term reversal of the Fontan paradox,'' Journal of Thoracic and Cardiovascular Surgery, to appear.
  107. Szafron, J., Ramachandra, A. B., Breuer, C., Marsden, A., Humphrey, J., "Optimization of Tissue Engineered Vascular Graft Design Using Computational Modeling,'' Tissue Engineering, Part C, to appear. 
  108. Liu, J., Marsden, A.L., and Tao, Z., "An energy-stable mixed formulation for isogeometric analysis of incompressible hyper-elastodynamics,'' International Journal for Numerical Methods in Engineering, to appear.
  109. Zhong, L., Scharuben, E.M., Garcia, J., Uribe, S., Grieve, S.M., Elbaz, M.S.M, Barker, A.J., Geiger, J., Nordmeyer, S., Marsden, A.L., Carlsson, M., Tan, R-S., Garg, P., Westenberg, J.J.M., Markl, M., Ebbers, T., "Intracardiac 4D Flow MRI in Congenital Heart Disease: Recommendations on Behalf of the ISMRM Flow and Motion Study Group," Journal of Magnetic Resonance Imaging, in press.

Book Chapters

  1. Marsden, A. and Kung, E.O., “Multiscale Modeling of Cardiovascular Flows,” Computational Bioengineering, CRC Press Taylor & Francis Group, edited by Guigen Zhang.
  2. Alberto Figueroa, Charles A. Taylor, Alison L. Marsden, ``Blood Flow," Encyclopedia of Computational Mechanics," 2nd Edition, Wiley, (2018).

Refereed Conference Papers

  1. Bazilevs, Y., Marsden, A.L., Lanza di Scalea, F., Majumdar, A., Tatineni, M., “Toward a Computational Steering Framework for Large-Scale Composite Structures Based on Continually and Dynamically Injected Sensor Data,” Pro- cedia Computer Science 9, pp. 1149-1158, (2012)
  2. Xie, J., Frazier, P.I., Sankaran, S., Marsden, A.L., Elmohamed, S. “Optimization of Computationally Expensive Simu- lations with Gaussian Processes and Parameter Uncertainty: Application to Cardiovascular Surgery,” Acccepted as an invited paper at the 50th Annual Allerton Conference on Communication, Control, and Computing, (2012).
  3. Esmaily-Moghadam, M., Bazilevs, Y., Marsden, A.L., “Low entropy data mapping for sparse iterative linear solvers”, Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, ACM, p. 2., (2013).​ 
  4. Gilbert, K., Farrar, G., Cowan, B., Suinesiaputra, A., Occleshaw, C., Perry, J., Hegde, S., Marsden A., Omens, J., McCulloch, A., Young, A., “Creating Shape Templates for Patient Specific Biventricular Modeling in Congenital Heart Disease,” Conf Proc IEEE Eng Med Biol Soc. pp. 679-82, (2015). 
  5. Merkow, J., Tu, Z., Kriegman, D.,  Marsden, A., ``Structural edge detection for cardiovascular modeling,'' International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 735-742, (2015).
  6. Goergen, C., Shadden, S.C., Marsden, A.L., “SimVascualr as an instructional tool in the classroom,” Frontiers in Education, Indiannapolis, Indiana, Oct. 2017. 
  7. Merkow, J., Marsden, A.L., Kriegman, D., Tu, Z., ``Dense volume-to-volume vascular boundary detection,'' International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 371-379, (2016).
  8. Goergen, C., Shadden, S.C., Marsden, A.L., ``SimVascualr as an instructional tool in the classroom,'' Frontiers in Education, Indiannapolis, Indiana, (2017).
  9. Wilson, N.M.,  Marru, S.,  Abeysinghe, E.,  Christie, M.A.,  Maher, G.D.,  Updegrove, A.R.,  Pierce, M.,  Marsden, A.L.,``Using a Science Gateway to Deliver SimVascular Software as a Service for Classroom Instruction'' Proceedings of the Practice and Experience on Advanced Research Computing, 102, (2018).


  1. Marsden, A.L. and Feinstein, J.A., “Will computational simulation in congenital heart disease ever make it out of the lab and into the clinic?” (editorial) Therapy, 6(4) pp. 541-543, (2009).
  2. Marsden, A.L. “Cardiovascular blood flow simulation: from computation to clinic,” SIAM News (invited article), in press, (2015). 

  3. Marsden, A.L. ``Clinically Useful Computational Models for Personalized Treatment Planning in Cardiovascular Disease,'' SIAM News (invited article), (2018).