CRIMSON is based on state of the art scientific advancements on parallel computing, computational mechanics, cardiovascular physiology, and medical image processing. The following is a list of the main publications related to methods and techniques available in CRIMSON.
Main CRIMSON paper
CRIMSON: An open-source Software Framework for Cardiovascular Integrated Modelling and Simulation (2021). C.J. Arthurs, R. Khlebnikov, A. Melville, A. Gomez, D. Dillon-Murphy, F. Cuomo, M. Silva Vieira, J. Schollenberger, S.R. Lynch, C. Tossas-Betancourt, K. Iyer, S. Hopper, E. Livingston, P. Youssefi, A. Noorani, S. Ben Ahmed, F.J.H. Nauta, T.M.J. van Bakel, Y. Ahmed, P.A.J. van Bakel, J. Mynard, P. Di Achille, H. Gharahi, K.D. Lau, V. Filonova, M. Aguirre, N. Nama, N. Xiao, S. Baek, K. Garikipati, O. Sahni, D. Nordsletten, C.A. Figueroa. PLOS: Computational Biology. DOI: 10.1371/journal.pcbi.1008881
Clinical Applications (first author is an M.D.)
Computational Study of Anatomical Risk Factors in Idealized Models of Type B Aortic Dissection (2016). S. Ben Ahmed, D. Dillon-Murphy, C.A. Figueroa. European Journal of Vascular and Endovascular Surgery. DOI: 10.1016/j.ejvs.2016.07.025
Functional Assessment of Thoracic Aortic Aneurysms – The Future of Risk Prediction? (2017). P. Youssefi, R. Sharma, C.A. Figueroa, M. Jahangiri. British Medical Bulletin. DOI: 10.1093/bmb/ldw049
Computational Fluid Dynamics and Aortic Thrombus Formation Following Thoracic Endovascular Aortic Repair (2017). F.J.H. Nauta, K.D. Lau, C.J. Arthurs, K.A. Eagle, D.M. Williams, S. Trimarchi, H.J. Patel, C.A. Figueroa. Annals of Thoracic Surgery. DOI: 10.1016/j.athoracsur.2016.09.067
Patient-specific Computational Fluid Dynamics – Assessment of Aortic Hemodynamics in a Spectrum of Aortic Valve Pathologies (2017). P. Youssefi, A. Gomez, T. He, L. Anderson, N. Bunce, R. Sharma, C.A. Figueroa, M. Jahangiri. Journal of Thoracic and Cardiovascular Surgery. DOI: 10.1016/j.jtcvs.2016.09.040
Impact of Patient-specific Inflow Velocity Profiles on Haemodynamics of the Thoracic Aorta (2017). P. Youssefi, A. Gomez, C.J. Arthurs, R. Sharma, M. Jahangiri, C.A. Figueroa. Journal of Biomechanical Engineering. DOI: 10.1115/1.4037857
Patient-Specific Modeling of Hemodynamics: Optimizing a Fontan Circulation Correction (2018). T.M.J. van Bakel, K.D. Lau, J. Hirsch-Romano, S. Trimarchi, A.L. Dorfman, C.A. Figueroa. Journal of Cardiovascular Translational Research. DOI: 10.1007/s12265-017-9781-x
Hemodynamic Performance of Different Endograft Designs for Zone 0 Aortic Arch Repair: A Computational Study (2018). T.M.J. van Bakel, C.J. Arthurs, J.A. Herwaarden, F.L. Moll, K.A. Eagle, H.J. Patel, S. Trimarchi, C.A. Figueroa. European Journal of Cardio-Thoracic Surgery. DOI: 10.1093/ejcts/ezy068
Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in Alagille’s syndrome (2018). M.S. Vieira, C.J. Arthurs, T. Hussain, R. Razavi, C.A. Figueroa. PLOS ONE. DOI: 10.1371/journal.pone.0205829
Cardiac Remodeling following Thoracic Endovascular Aortic Repair for Descending Aortic Aneurysms (2018). T.M.J. van Bakel, C.J. Arthurs, F.J.H. Nauta, K.A. Eagle, J.A. Herwaarden, F.L. Moll, S. Trimarchi, H.J. Patel, C.A. Figueroa. European Journal of Cardiothoracic Surgery. DOI: 10.1093/ejcts/ezy399
Ascending Aortic Rupture after Zone 2 Endovascular Repair: A Multi-Parametric Computational Study (2019). T.M.J. van Bakel, N. Burris, H.J. Patel, C.A. Figueroa. European Journal of Cardiothoracic Surgery. DOI: 10.1093/ejcts/ezy458
Mapping pre-dissection aortic wall abnormalities: a multiparametric assessment (2020). I. Houben, N. Nama, F.L. Moll, J.A. Herwaarden, D. Nordsletten, D.M. Williams, H.J. Patel, C.A. Figueroa, N. Burris. European Journal of Cardiothoracic Surgery. DOI: 10.1093/ejcts/ezz381
Interventional planning for endovascular revision of a Lateral Tunnel Fontan: a patient-specific computational analysis (2021). Y. Ahmed, C, Tossas-Betancourt, P. van Bakel, J. Primeaux, W.J. Weadock, J.C. Lu, J.D. Zampi, A. Salavitabar, C. Alberto Figueroa. Frontiers in Physiology, Computational Physiology and Medicine. DOI: 10.3389/fphys.2021.718254
Stabilized Finite Element Formulation
A stabilized finite element method for the incompressible Navier–Stokes equations using a hierarchical basis (2001). C.H. Whiting, K.E. Jansen. International Journal for Numerical Methods in Fluids. DOI: 10.1002/1097-0363(20010115)35:1<93::AID-FLD85>3.0.CO;2-G
Fluid-structure Interaction
A coupled momentum method for modeling blood flow in three-dimensional deformable arteries (2006). C.A. Figueroa, I.E. Vignon-Clementel, K.E. Jansen, T.J.R. Hughes, C.A. Taylor. Computer Methods in Applied Mechanics and Engineering. DOI: 10.1016/j.cma.2005.11.011
External Tissue Support and Fluid-Structure Simulation in Blood Flows (2012). P. Moireau, N. Xiao, M. Astorino, C.A. Figueroa, D. Chapelle, C.A. Taylor, J.F. Gerbeau. Biomechanics and Modeling in Mechanobiology. DOI: 10.1007/s10237-011-0289-z
A Nonlinear Rotation-free Shell Formulation with Pre-stressing for Vascular Biomechanics (2020). N. Nama, M. Aguirre, J.D. Humphrey, C.A. Figueroa. Nature Scientific Reports. DOI: 10.1038/s41598-020-74277-5
Boundary Conditions
Outflow boundary conditions for three-dimensional finite element modeling of blood flow and pressure in arteries (2006). I.E. Vignon-Clementel, C.A. Figueroa, K.E. Jansen, C.A. Taylor. Computer Methods in Applied Mechanics and Engineering. DOI: 10.1016/j.cma.2005.04.014
On Coupling a Lumped Parameter Heart Model and a Three-Dimensional Finite Element Aorta Model (2009). H.J. Kim, I.E. Vignon-Clementel, C.A. Figueroa, J.F. LaDisa, K.E. Jansen, J.A. Feinstein, C.A. Taylor. Annals of Biomedical Engineering. DOI: 10.1007/s10439-009-9760-8
Patient-Specific Modeling of Blood Flow and Pressure in Human Coronary Arteries (2010). H.J. Kim, I.E. Vignon-Clementel, J.S. Coogan, C.A. Figueroa, K.E. Jansen, C.A. Taylor. Annals of Biomedical Engineering. DOI: 10.1007/s10439-010-0083-6
Optimal B-Spline Mapping of Flow Imaging Data for Imposing Patient-Specific Velocity Profiles in Computational Haemodynamics (2018). A. Gomez, M. Marčan, C.J. Arthurs, R. Wright, P. Youssefi, M. Jahangiri, C.A. Figueroa. IEEE Transactions on Biomedical Engineering. DOI: 10.1109/TBME.2018.2880606
Parameter Estimation
Sequential Identification of Boundary Support Parameters in a Fluid-Structure Vascular Model using Patient Data. (2013). P. Moireau, C. Bertoglio, N. Xiao, C.A. Figueroa, C.A. Taylor, D. Chapelle, J.F. Gerbeau. Biomechanics and Modeling in Mechanobiology. DOI: 10.1007/s10237-012-0418-3
A flexible framework for sequential estimation of model parameters in computational hemodynamics. (2020). C.J. Arthurs, N. Xiao, P. Moireau, T. Schaeffter, C. A. Figueroa. Advanced Modeling & Simulation in Engineering Sciences. DOI: 10.1186/s40323-020-00186-x
Transitional CV Physiology
Simulation of short-term pressure regulation during the tilt test in a coupled 3D–0D closed-loop model of the circulation (2015). K.D. Lau, C.A. Figueroa. Biomechanics and Modeling in Mechanobiology. DOI: 10.1007/s10237-014-0645-x
A Mathematical Model of Coronary Blood Flow Control: Simulation of Patient-Specific Three-Dimensional Haemodynamics during Exercise (2016). C.J. Arthurs, K.D. Lau, K.N. Asrress, S.R. Redwood, C.A. Figueroa. American Journal of Physiology - Heart and Circulatory Physiology. DOI: 10.1152/ajpheart.00517.2015
CRIMSON: An open-source Software Framework for Cardiovascular Integrated Modelling and Simulation (2021). C.J. Arthurs, R. Khlebnikov, A. Melville, A. Gomez, D. Dillon-Murphy, F. Cuomo, M. Silva Vieira, J. Schollenberger, S.R. Lynch, C. Tossas-Betancourt, K. Iyer, S. Hopper, E. Livingston, P. Youssefi, A. Noorani, S. Ben Ahmed, F.J.H. Nauta, T.M.J. van Bakel, Y. Ahmed, P.A.J. van Bakel, J. Mynard, P. Di Achille, H. Gharahi, K.D. Lau, V. Filonova, M. Aguirre, N. Nama, N. Xiao, S. Baek, K. Garikipati, O. Sahni, D. Nordsletten, C.A. Figueroa. PLOS: Computational Biology. DOI: 10.1371/journal.pcbi.1008881
Clinical Applications (first author is an M.D.)
Computational Study of Anatomical Risk Factors in Idealized Models of Type B Aortic Dissection (2016). S. Ben Ahmed, D. Dillon-Murphy, C.A. Figueroa. European Journal of Vascular and Endovascular Surgery. DOI: 10.1016/j.ejvs.2016.07.025
Functional Assessment of Thoracic Aortic Aneurysms – The Future of Risk Prediction? (2017). P. Youssefi, R. Sharma, C.A. Figueroa, M. Jahangiri. British Medical Bulletin. DOI: 10.1093/bmb/ldw049
Computational Fluid Dynamics and Aortic Thrombus Formation Following Thoracic Endovascular Aortic Repair (2017). F.J.H. Nauta, K.D. Lau, C.J. Arthurs, K.A. Eagle, D.M. Williams, S. Trimarchi, H.J. Patel, C.A. Figueroa. Annals of Thoracic Surgery. DOI: 10.1016/j.athoracsur.2016.09.067
Patient-specific Computational Fluid Dynamics – Assessment of Aortic Hemodynamics in a Spectrum of Aortic Valve Pathologies (2017). P. Youssefi, A. Gomez, T. He, L. Anderson, N. Bunce, R. Sharma, C.A. Figueroa, M. Jahangiri. Journal of Thoracic and Cardiovascular Surgery. DOI: 10.1016/j.jtcvs.2016.09.040
Impact of Patient-specific Inflow Velocity Profiles on Haemodynamics of the Thoracic Aorta (2017). P. Youssefi, A. Gomez, C.J. Arthurs, R. Sharma, M. Jahangiri, C.A. Figueroa. Journal of Biomechanical Engineering. DOI: 10.1115/1.4037857
Patient-Specific Modeling of Hemodynamics: Optimizing a Fontan Circulation Correction (2018). T.M.J. van Bakel, K.D. Lau, J. Hirsch-Romano, S. Trimarchi, A.L. Dorfman, C.A. Figueroa. Journal of Cardiovascular Translational Research. DOI: 10.1007/s12265-017-9781-x
Hemodynamic Performance of Different Endograft Designs for Zone 0 Aortic Arch Repair: A Computational Study (2018). T.M.J. van Bakel, C.J. Arthurs, J.A. Herwaarden, F.L. Moll, K.A. Eagle, H.J. Patel, S. Trimarchi, C.A. Figueroa. European Journal of Cardio-Thoracic Surgery. DOI: 10.1093/ejcts/ezy068
Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in Alagille’s syndrome (2018). M.S. Vieira, C.J. Arthurs, T. Hussain, R. Razavi, C.A. Figueroa. PLOS ONE. DOI: 10.1371/journal.pone.0205829
Cardiac Remodeling following Thoracic Endovascular Aortic Repair for Descending Aortic Aneurysms (2018). T.M.J. van Bakel, C.J. Arthurs, F.J.H. Nauta, K.A. Eagle, J.A. Herwaarden, F.L. Moll, S. Trimarchi, H.J. Patel, C.A. Figueroa. European Journal of Cardiothoracic Surgery. DOI: 10.1093/ejcts/ezy399
Ascending Aortic Rupture after Zone 2 Endovascular Repair: A Multi-Parametric Computational Study (2019). T.M.J. van Bakel, N. Burris, H.J. Patel, C.A. Figueroa. European Journal of Cardiothoracic Surgery. DOI: 10.1093/ejcts/ezy458
Mapping pre-dissection aortic wall abnormalities: a multiparametric assessment (2020). I. Houben, N. Nama, F.L. Moll, J.A. Herwaarden, D. Nordsletten, D.M. Williams, H.J. Patel, C.A. Figueroa, N. Burris. European Journal of Cardiothoracic Surgery. DOI: 10.1093/ejcts/ezz381
Interventional planning for endovascular revision of a Lateral Tunnel Fontan: a patient-specific computational analysis (2021). Y. Ahmed, C, Tossas-Betancourt, P. van Bakel, J. Primeaux, W.J. Weadock, J.C. Lu, J.D. Zampi, A. Salavitabar, C. Alberto Figueroa. Frontiers in Physiology, Computational Physiology and Medicine. DOI: 10.3389/fphys.2021.718254
Stabilized Finite Element Formulation
A stabilized finite element method for the incompressible Navier–Stokes equations using a hierarchical basis (2001). C.H. Whiting, K.E. Jansen. International Journal for Numerical Methods in Fluids. DOI: 10.1002/1097-0363(20010115)35:1<93::AID-FLD85>3.0.CO;2-G
Fluid-structure Interaction
A coupled momentum method for modeling blood flow in three-dimensional deformable arteries (2006). C.A. Figueroa, I.E. Vignon-Clementel, K.E. Jansen, T.J.R. Hughes, C.A. Taylor. Computer Methods in Applied Mechanics and Engineering. DOI: 10.1016/j.cma.2005.11.011
External Tissue Support and Fluid-Structure Simulation in Blood Flows (2012). P. Moireau, N. Xiao, M. Astorino, C.A. Figueroa, D. Chapelle, C.A. Taylor, J.F. Gerbeau. Biomechanics and Modeling in Mechanobiology. DOI: 10.1007/s10237-011-0289-z
A Nonlinear Rotation-free Shell Formulation with Pre-stressing for Vascular Biomechanics (2020). N. Nama, M. Aguirre, J.D. Humphrey, C.A. Figueroa. Nature Scientific Reports. DOI: 10.1038/s41598-020-74277-5
Boundary Conditions
Outflow boundary conditions for three-dimensional finite element modeling of blood flow and pressure in arteries (2006). I.E. Vignon-Clementel, C.A. Figueroa, K.E. Jansen, C.A. Taylor. Computer Methods in Applied Mechanics and Engineering. DOI: 10.1016/j.cma.2005.04.014
On Coupling a Lumped Parameter Heart Model and a Three-Dimensional Finite Element Aorta Model (2009). H.J. Kim, I.E. Vignon-Clementel, C.A. Figueroa, J.F. LaDisa, K.E. Jansen, J.A. Feinstein, C.A. Taylor. Annals of Biomedical Engineering. DOI: 10.1007/s10439-009-9760-8
Patient-Specific Modeling of Blood Flow and Pressure in Human Coronary Arteries (2010). H.J. Kim, I.E. Vignon-Clementel, J.S. Coogan, C.A. Figueroa, K.E. Jansen, C.A. Taylor. Annals of Biomedical Engineering. DOI: 10.1007/s10439-010-0083-6
Optimal B-Spline Mapping of Flow Imaging Data for Imposing Patient-Specific Velocity Profiles in Computational Haemodynamics (2018). A. Gomez, M. Marčan, C.J. Arthurs, R. Wright, P. Youssefi, M. Jahangiri, C.A. Figueroa. IEEE Transactions on Biomedical Engineering. DOI: 10.1109/TBME.2018.2880606
Parameter Estimation
Sequential Identification of Boundary Support Parameters in a Fluid-Structure Vascular Model using Patient Data. (2013). P. Moireau, C. Bertoglio, N. Xiao, C.A. Figueroa, C.A. Taylor, D. Chapelle, J.F. Gerbeau. Biomechanics and Modeling in Mechanobiology. DOI: 10.1007/s10237-012-0418-3
A flexible framework for sequential estimation of model parameters in computational hemodynamics. (2020). C.J. Arthurs, N. Xiao, P. Moireau, T. Schaeffter, C. A. Figueroa. Advanced Modeling & Simulation in Engineering Sciences. DOI: 10.1186/s40323-020-00186-x
Transitional CV Physiology
Simulation of short-term pressure regulation during the tilt test in a coupled 3D–0D closed-loop model of the circulation (2015). K.D. Lau, C.A. Figueroa. Biomechanics and Modeling in Mechanobiology. DOI: 10.1007/s10237-014-0645-x
A Mathematical Model of Coronary Blood Flow Control: Simulation of Patient-Specific Three-Dimensional Haemodynamics during Exercise (2016). C.J. Arthurs, K.D. Lau, K.N. Asrress, S.R. Redwood, C.A. Figueroa. American Journal of Physiology - Heart and Circulatory Physiology. DOI: 10.1152/ajpheart.00517.2015
