Book Chapters

  1. Shadden, S. C., Lagrangian Coherent Structures, Transport and Mixing in Laminar Flows: From Microfluidics to Oceanic Currents, Roman Grigoriev, Ed., Wiley-VCH, 2011.Shadden Lab publication
  2. Ameli, S., Desai, Y. and Shadden, S. C., Development of an efficient and flexible pipeline for Lagrangian coherent structure computation, Topological Methods in Data Analysis and Visualization III, Mathematics and Visualization, P.-T. Bremer et al. (eds.). Springer, 2014. Shadden Lab publication
  3. Shadden, S. C., Multi-scale/physics Image-Based Hemodynamics Modeling, Research Trends in Biological Fluid Dynamics, S. Jung, A. E. Staples, et al., Ed., USNCTAM, 2016.Shadden Lab publication
  4. Chen, M., Hart, J. C. and Shadden, S. C., Hierarchical Watershed Ridges for Visualizing Lagrangian Coherent Structures, Topological Methods in Data Analysis and Visualization IV, Mathematics and Visualization, H. Carr et al. (eds.). Springer, 2017. Shadden Lab publication

Journal Publications

  1. Oakes, J. M., Shadden, S. C., Grandmont, C. and Vignon-Clemental, I. E., Aerosol transport throughout inspiration and expiration in the pulmonary airways, International Journal for Numerical Methods in Biomedical Engineering, in press. DOI: 10.1002/cnm.2847
  2. Arzani, A., Gambaruto, A. M., Chen, G. and Shadden, S. C., Wall shear stress exposure time: A Lagrangian measure of near-wall stagnation and concentration in cardiovascular flows, Biomechanics and Modeling in Mechanobiology, 16(3), 787–803. Shadden Lab publication
  3. Ryu, J., Ko, N., Hu, X. and Shadden, S. C., Numerical investigation of vasospasm detection by extracranial blood velocity ratios, Cerebrovascular Diseases, 43(5-6), 214-222, 2017. Shadden Lab publication
  4. Updegrove, A., Wilson, N., Merkow, J., Lan, H., Marsden, A. L. and Shadden, S. C., SimVascular - An open source pipeline for cardiovascular simulation, Annals of Biomedical Engineering, 45(3), 525–541, 2017. Shadden Lab publication
  5. Mukherjee, D. and Shadden, S. C., Inertial particle dynamics in large artery flows – Implications for modeling arterial embolisms, Journal of Biomechanics, 52, 155-164, 2017.Shadden Lab publication
  6. Rossini, L., Martinez-Legazpi, P., Benito, Y., Perez del Villar, C., Gonzalez-Mansilla, A., Barrio, A., Borja, M.-G., Yotti, R., Kahn, A. M., Shadden, S. C., Fernandez-Aviles, F., Bermejo, J. and del Alamo, J. C., Clinical assessment of intraventricular blood transport in patients undergoing cardiac resynchronization therapy, Meccanica, 52(3), 563–576, 2017.
  7. Wu, J. and Shadden, S. C., Stability analysis of a continuum-based constrained mixture model for vascular growth and remodeling, Biomechanics and Modeling in Mechanobiology, 15(6), 1669–1684, 2016.Shadden Lab publication
  8. Chen, M., Shadden, S. C. and Hart, J. C., Fast coherent particle advection through time-varying unstructured flow datasets, Transactions on Visualization and Computer Graphics, 22(8), 1959-1972, 2016.Shadden Lab publication
  9. Mukherjee, D., Jani, N., Selvaganesan, K., Weng, C. L. and Shadden, S. C., 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.Shadden Lab publication
  10. Hansen, K. B. and Shadden, S. C., A reduced-dimensional model for near-wall transport in cardiovascular flows, Biomechanics and Modeling in Mechanobiology, 15(3), 713-722, 2016.Shadden Lab publication
  11. Updegrove, A., Wilson, N. M. and Shadden, S. C., Boolean and smoothing of discrete polygonal surfaces, Advances in Engineering Software, 95, 16-27, 2016.Shadden Lab publication
  12. Arzani, A., Gambaruto, A. M., Chen, G. and Shadden, S. C., Lagrangian wall shear stress structures and near wall transport in high Schmidt aneurysmal flows, Journal of Fluid Mechanics, 790, 158-172, 2016.Shadden Lab publication
  13. Mukherjee, D., Padilla, J. and Shadden, S. C., Numerical investigation of fluid–particle interactions for embolic stroke, Theoretical and Computational Fluid Dynamics, 30(1), 23-39, 2016.Shadden Lab publication
  14. Arzani, A. and Shadden, S. C. Characterizations and correlations of wall shear stress in aneurysmal flow, Journal of Biomechanical Engineering 138(1), 014503-1-10, 2015.Shadden Lab publication
  15. Ryu, J., Hu, X. and Shadden, S. C., A coupled lumped-parameter and distributed network model for cerebral pulse-wave hemodynamics, Journal of Biomechanical Engineering, 137(10), 101009-1-13, 2015.Shadden Lab publication
  16. Wu, J. and Shadden, S. C., Coupled simulation of hemodynamics and vascular growth and remodeling in a subject-specific geometry, Annals of Biomedical Engineering, 43(7), 1543-1554, 2015.Shadden Lab publication
  17. Hansen, K. B., Arzani, A. and Shadden, S. C., Mechanical platelet activation potential in abdominal aortic aneurysms, Journal of Biomechanical Engineering, 137(4), 041005-1-8, 2015.Shadden Lab publication
  18. Shadden, S. C. and Arzani, A., Lagrangian postprocessing of computational hemodynamics, Annals of Biomedical Engineering, 43(1), 41-58, 2015. Shadden Lab publication
  19. Arzani, A., Suh, G. Y., Dalman, R. L. and Shadden, S. C., A longitudinal comparison of hemodynamics and intraluminal thrombus deposition in abdominal aortic aneurysms, American Journal of Physiology- Heart and Circulatory Physiology, 307(12), H1786-H1795, 2014.Shadden Lab publication
  20. Chian, A. C.-L., Rempel, E. L., Aulanier, G., Schmieder, B., Shadden, S. C., Welsch, B. T. and Yeates A. R., Detection of coherent structures in photospheric turbulent flows, The Astrophysical Journal, 786(1), 51(13pp), 2014.Shadden Lab publication
  21. Oakes, J. M., Marsden, A. L., Grandmont, C., Shadden, S. C., Darquenne, C. and 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, 42(4), 899-914, 2014. Shadden Lab publication
  22. Arzani, A., Les, A. S., Dalman, R. L. and Shadden, S. C., 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. Shadden Lab publication
  23. Carr, I. A., Nemoto, N., Schwartz, R. S. and Shadden, S. C., Size-dependent predilections of cardiogenic embolic transport, American Journal of Physiology- Heart and Circulatory Physiology, 305(5), 732–739, 2013. Shadden Lab publication
  24. Hendabadi, S., Bermejo, J., Benito, Y., Yotti, R., Fernandez-Aviles, F., del Alamo, J. C. and Shadden, S. C., Topology of blood transport in the human left ventricle assessed by Doppler echocardiography and Lagrangian coherent structures, Annals of Biomedical Engineering, 41(12), 2603–2616, 2013. Shadden Lab publication
  25. Rempel, E. L., Chian, A. C.-L., Brandenburg, A., Munuz, P. R. and Shadden, S. C., Coherent structures and the saturation of a nonlinear dynamo, Journal of Fluid Mechanics, 729, 309-329, 2013.Shadden Lab publication
  26. Steinman, D. A., Hoi, Y., Fahy, P., Morris, L., Walsh, M. T., Aristokleous, N., Anayiotos, A. S., Papaharilaou, Y., Arzani, A., Shadden, S. C., et al., Variability of computational fluid dynamics solutions for pressure and flow in a giant aneurysm: The ASME 2012 Summer Bioengineering Conference CFD Challenge, Journal of Biomechanical Engineering, 135(2), 021016-1-13, 2013.Shadden Lab publication
  27. Shadden, S. C., Carr, I. A., Nemoto, N. and Schwartz, R. S., Embolic stroke hemispheric location is highly dependent of aortic arch and cerebral vessel configuration, Circulation, 128(22), A14079 (abstract), 2013.
  28. Shadden, S. C. and Hendabadi, S., Potential fluid mechanic pathways of platelet activation, Biomechanics and Modeling in Mechanobiology, 12(3), 467-474, 2013.Shadden Lab publication
  29. 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), 445-461, 2013.Shadden Lab publication
  30. Wendell, D. C., Samyn, M. M., Cava, J. R., Ellwein, L. M., Krolikowski, M. M. Gandy, K. L., Pelech, A. N., Shadden, S. C. and LaDisa, J. F. Jr., Including aortic valve morphology in computational fluid dynamics simulations: Initial findings and application to aortic coarctation, Medical Engineering and Physics, 35(6), 723-35, 2013.Shadden Lab publication
  31. 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, Journal of Biomechanical Engineering, 135(1), 011002-1-12, 2013.Shadden Lab publication
  32. Shadden, S. C., Nemoto, N., Pedersen, W. R., Lesser, J. R. and Schwartz, R. S., Embolic Particles Show Surprising Size Dependent Predilection for Cerebral versus Peripheral Arteries: Results from Computational Fluid Dynamic Modeling, Circulation, 126(21), A19053 (abstract), 2012.
  33. Bockman, M. D., Kansagra, A. P., Shadden, S. C., Wong, E. C. and Marsden, A. L., Fluid mechanics of mixing in the vertebrobasilar system: Comparison of simulation and MRI, Cardiovascular Engineering and Technology, 3(4), 450-461, 2012.Shadden Lab publication
  34. Arzani, A. and Shadden, S. C., Characterization of the transport topology in patient-specific abdominal aortic aneurysm models, Physics of Fluids, 24(8), 081901-1-16, 2012.Shadden Lab publication
  35. Astorino, M., Hamers, J., Shadden, S. C. and Gerbeau, J.-F., A robust and efficient valve model based on resistive immersed surfaces, International Journal for Numerical Methods in Biomedical Engineering, 28(9), 937-959, 2012.Shadden Lab publication
  36. Shadden, S. C., Nemoto, N., Pedersen, W. R., Lesser, J. R. and Schwartz, R. S., Embolic Particles Show Surprising Size Dependent Predilection for Cerebral versus Peripheral Arteries: Results from Computational Fluid Dynamic Modeling, Journal of the American College of Cardiology, 60(17), B244 (abstract), 2012.
  37. Sengupta, D., Kahn, A. M., Burns, J. C., Sankaran, S., Shadden, S. C. and Marsden, A. L., Image-based modeling of hemodynamics in coronary artery aneurysms caused by Kawasaki disease, Biomechanics and Modeling in Mechanobiology, 11(6), 915-932, 2012.Shadden Lab publication
  38. Arzani, A., Dyverfeldt, P., Ebbers, T. and Shadden, S. C., In vivo validation of numerical prediction for turbulence intensity in an aortic coarctation, Annals of Biomedical Engineering, 40(4), 860-870, 2012.Shadden Lab publication
  39. Suh, G. Y., Les, A. S., Tenforde, A. S., Shadden, S. C., Spilker, R. L., Yeung, J. J., Cheng, C. P., Herfkens, R. J., Dalman, R. L. and Taylor, C. A., Hemodynamic changes quantified in abdominal aortic aneurysms with increasing exercise intensity using MR exercise imaging and image-based computational fluid dynamics, Annals of Biomedical Engineering, 39(8), 2186-2202, 2011.Shadden Lab publication
  40. Gundert, T. J., Shadden, S. C., Williams, A. R., Koo, B. K., Feinstein, J. A. and LaDisa, J. F. Jr., A rapid and computationally inexpensive way to quantify altered hemodynamics for current and next-generation stents, Annals of Biomedical Engineering, 39(5), 1423-1437, 2011.Shadden Lab publication
  41. Suh, G. Y., Les, A. S., Tenforde, A. S., Shadden, S. C., Spilker, R. L., Yeung, J. J., Cheng, C. P., Herfkens, R. J., Dalman, R. L. and Taylor, C. A., Quantification of particle residence time in abdominal aortic aneurysms using magnetic resonance imaging and computational fluid dynamics, Annals of Biomedical Engineering, 39(2), 864-883, 2011.Shadden Lab publication
  42. Lonyai, A., Dubin, A. M., Feinstein, J. A., Taylor, C. A. and Shadden, S. C., New insights into pacemaker lead-induced venous occlusion: Simulation-based investigation of alterations in venous biomechanics, Cardiovascular Engineering, 10(2), 84-90, 2010.Shadden Lab publication
  43. Marsden, A. L., Reddy, V. M., Shadden, S. C., Chan, F. P., Taylor, C. A. and Feinstein, J. A., A new multiparameter approach to computational simulation for Fontan assessment and redesign, Congenital Heart Disease, 5(2), 104-117, 2010.Shadden Lab publication
  44. Les, A. S., Shadden, S. C., Figueroa, C. A., Park, J. M., Tedesco, M. M., Herfkens, R. J., Dalman, R. L. and Taylor, C. A., 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.Shadden Lab publication
  45. Shadden, S. C., Astorino, M. and Gerbeau, J. F., Computational analysis of an aortic valve jet with Lagrangian coherent structures, Chaos, 20(1), 017512-1-10, 2010.Shadden Lab publication
  46. Shadden, S. C., Lekien, F., Paduan, J. D., Chavez, F. and Marsden, J.E., The correlation between surface drifters and coherent structures based on HF radar in Monterey Bay, Deep-Sea Research Part II: Topical Studies in Oceanography, 56(3-5), 161-172, 2009.Shadden Lab publication
  47. Xu, Z., Chen, N., Shadden, S. C., Marsden, J. E., Kamocka, M. M., Rosen, E. D. and Alber, M., Study of blood flow impact on growth of thrombi using a multiscale model, Soft Matter, 5(4), 769-779, 2009.Shadden Lab publication
  48. Marsden, A. L., Bernstein, A., Reddy, V. M., Shadden, S. C., Spilker, R. L., Chan, F. P., 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, 137(2), 394-403, 2009.Shadden Lab publication
  49. Shadden, S. C. and Taylor, C. A., Characterization of coherent structures in the cardiovascular system, Annals of Biomedical Engineering, 36(7), 1152-1162, 2008.Shadden Lab publication
  50. Shadden, S. C., Katija, K., Rosenfeld, M., Marsden, J. E. and Dabiri, J. O., Transport and stirring induced by vortex formation, Journal of Fluid Mechanics, 593, 315-331, 2007.Shadden Lab publication
  51. Lekien, F., Shadden, S. C. and Marsden, J. E., Lagrangian coherent structures in n-dimensional systems, Journal of Mathematical Physics, 48(6), 065404-1-19, 2007.Shadden Lab publication
  52. Shadden, S. C., Dabiri, J. O. and Marsden, J. E., Lagrangian analysis of fluid transport in empirical vortex ring flows, Physics of Fluids, 18(4), 047105-1-11, 2006.Shadden Lab publication
  53. Shadden, S. C., Lekien, F. and Marsden, J. E., Definition and properties of Lagrangian coherent structures from finite-time Lyapunov exponents in two-dimensional aperiodic flows, Physica D, 212(3-4), 271-304, 2005.Shadden Lab publication

Conference Publications

  1. Inanc, T., Shadden, S. C. and Marsden, J. E., Optimal trajectory generation in ocean flows, Proc. of the American Control Conference, June 2005, Portland, OR.Shadden Lab publication
  2. Chang, D.E, Shadden, S.C., Marsden, J.E. and Olfati-Saber, R., Collision avoidance for multiple agent systems, Proc. Conference on Decision and Control, December 2003, Maui, HI.Shadden Lab publication