Citations to these works are tracked on the IBAMR Google Scholar page.
1. Acharya S, Halder S, Kou W, Kahrilas PJ, Pandolfino JE, Patankar NA. A
fully resolved multiphysics model of gastric peristalsis and bolus emptying in the upper gastrointestinal tract. Comput Biol Med. 2022;143:104948 (14 pages).
2. Acharya S, Kou W, Halder S, Carlson DA, Kahrilas PJ, Pandolfino JE, Patankar NA. Pumping
patterns and work done during peristalsis in finite-length elastic tubes. J Biomech Eng. 2021;143(7):071001 (13 pages).
3. Alben S, Miller LA, Peng J. Efficient kinematics for jet-propelled swimming. J
Fluid Mech. 2013;733:100–33.
4. Balboa Usabiaga F, Bell JB, Delgado-Buscalioni R, Donev A, Fai T, Griffith BE, Peskin CS. Staggered schemes for fluctuating hydrodynamics. Multiscale Model Simul. 2012;10(4):1369–408.
5. Balboa Usabiaga F, Kallemov B, Delmotte B, Bhalla APS, Griffith BE, Donev A. Hydrodynamics of suspensions of passive and active rigid particles: A rigid multiblob approach. Comm Appl Math Comput Sci. 2016;11(2):217–96.
6. Bale R, Bhalla APS, Griffith BE, Tsubokura M. A one-sided direct forcing
immersed boundary method using moving least squares. J Comput Phys. 2021;440:110359 (28 pages).
7. Bale R, Bhalla APS, Neveln ID, MacIver MA, Patankar NA. Convergent evolution
of mechanically optimal locomotion in aquatic invertebrates and vertebrates. PLOS Biol. 2015;3(4):e1002123 (22 pages).
8. Bale R, Hao M, Bhalla APS, Patankar NA. Energy efficiency and allometry of
movement of swimming and flying animals. Proc Natl Acad Sci U S A. 2014;111(21):7517–21.
9. Bale R, Hao M, Bhalla APS, Patel N, Patankar NA. On Gray’s paradox:
A fluid mechanical perspective. Sci Rep. 2014;4:5904 (5 pages).
10. Bale R, Shirgaonkar AA, Neveln ID, Bhalla APS, MacIver MA, Patankar NA. Separability of
drag and thrust in undulatory animals and machines. Sci Rep. 2014;4:7329 (11 pages).
11. Barrett A, Brown JA, Smith MA, Woodward A, Vavalle JP, Kheradvar A, Griffith BE, Fogelson AL. A model of fluid-structure and biochemical interactions for applications to subclinical leaflet thrombosis. Int J Numer Meth Biomed Eng. 2023;e3700 (19
pages).
12. Barrett A, Fogelson AL, Griffith BE. A hybrid semi-Lagrangian cut
cell method for advection-diffusion problems with Robin boundary conditions in moving domains. J Comput Phys. 2022;449:110805 (18 pages).
13. Battista NA, Douglas DR, Lane AN, Samsa LA, Liu J, Miller LA. Vortex dynamics in an
idealized embryonic ventricle with trabeculae. J Cardiovasc Dev Dis. 2019;6(1):6 (36 pages).
14. Battista N, Gaddam MG, Hamlet CL, Hoover AP, Miller LA, Santhanakrishnan A. The
presence of a substrate strengthens the jet generated by upside-down jellyfish. Front Mar Sci. 2022;9:847061 (16 pages).
15. Battista NA, Lane AN, Liu J, Miller LA. Fluid dynamics of heart development:
Effects of trabeculae and hematocrit. Math Med Biol. 2018;35(4):493–516.
16. Battista NA, Lane AN, Miller LA. On the dynamic suction pumping of blood
cells in tubular hearts. In: Layton A, Miller L, editors. Women in Mathematical Biology. Cham: Springer; 2017. p. 211–31. (Association for Women in
Mathematics Series; vol. 8).
17. Battista NA, Samson JE, Khatri S, Miller LA. Under the sea: Pulsing corals in
ambient flow. In: Anguelov R, Lachowicz M, editors. Mathematical Methods and Models in Biosciences. 2018. p. 22–35.
18. Bhalla APS, Bale R, Griffith BE, Patankar NA. A unified mathematical framework
and an adaptive numerical method for fluid-structure interaction with rigid, deforming, and elastic bodies. J Comput Phys. 2013;250:446–76.
19. Bhalla APS, Bale R, Griffith BE, Patankar NA. Fully resolved immersed
electrohydrodynamics for particle motion, electrolocation, and self-propulsion. J Comput Phys. 2014;256:88–108.
20. Bhalla APS, Griffith BE, Patankar NA. A forced damped oscillation framework
for undulatory swimming provides new insights into how propulsion arises in active and passive swimming. PLOS Comput Biol. 2013;9(6):e100309 (16 pages).
21. Bhalla APS, Griffith BE, Patankar NA, Donev A. A minimally-resolved immersed boundary
model for reaction-diffusion problems. J Chem Phys. 2013;139(21):214112 (15 pages).
22. Bhalla APS, Nangia N, Dafnakis P, Bracco G, Mattiazzo G. Simulating
water-entry/exit problems using Eulerian–Lagrangian and fully-Eulerian fictitious domain methods within the open-source IBAMR library. Appl
Ocean Res. 2020;94:101932 (20 pages).
23. Brown JA, Lee JH, Smith MA, Wells DR, Barrett A, Puelz C, Vavalle JP, Griffith BE. Patient-specific immersed finite element-difference model of transcatheter aortic valve replacement. Ann Biomed Eng. 2023;51:103–16.
24. Cai L, Hao Y, Ma P, Zhu G, Luo XY, Gao H. Fluid-structure interaction simulation of
calcified aortic valve stenosis. Math Biosci Eng. 2022;19(12):13172–92.
25. Cai L, Wang Y, Gao H, Li Y, Luo X. A mathematical model for active
contraction in healthy and failing myocytes and left ventricles. PLoS ONE. 2017;12(4):e0174834 (16 pages).
26. Cai L, Wang Y, Gao H, Ma XS, Zhu GY, Zhang RH, Shen X, Luo XY. Some effects of
different constitutive laws on FSI simulation for the mitral valve. Sci Rep. 2019;9:12753 (15 pages).
27. Cai L, Zhang R, Li Y, Zhu G, Ma X, Wang Y, Luo X, Gao H. The comparison of
different constitutive laws and fiber architectures for the aortic valve on fluid–structure interaction simulation. Front Physiol. 2021;12:682893 (17 pages).
28. Cai L, Zhao T, Wang Y, Luo XY, Gao H. Fluid–structure interaction simulation
of pathological mitral valve dynamics in a coupled mitral valve-left ventricle model. Intell Med. 2023;3(2):104–14.
29. Cerbino R, Sun Y, Donev A, Vailati A. Dynamic scaling for the growth of non-equilibrium
fluctuations during thermophoretic diffusion in microgravity. Sci Rep. 2015;5:14486 (11 pages).
30. Chao L-M, Bhalla APS, Li L. Vortex interactions of two burst-and-coast
swimmers in a side-by-side arrangement. Theor Comput Fluid Dyn. 2023;37:505–17.
31. Chao L-M, Couzin ID, Li L. On turning maneuverability in self-propelled burst-and-coast
swimming. Phys Fluids. 2024;36:111918 (11 pages).
32. Chao L-M, Jia L, Li L. Tailbeat perturbations improve swimming efficiency in
self-propelled flapping foils. J Fluid Mech. 2024;984:A46 (26 pages).
33. Chen WW, Gao H, Luo XY, Hill NA. Study of cardiovascular function using a
coupled left ventricle and systemic circulation model. J Biomech. 2016;49(12):2445–54.
34. Chao L-M, Li L. Hydrodynamic interactions in schooling fish: Prioritizing
real fish kinematics over travelling-wavy undulation. In: 2024 IEEE international conference on robotics and automation (ICRA). 2024. p. 16895–900.
35. Claus L, Ghysels P, Liu Y, Nhan TA, Thirumalaisamy R, Bhalla APS, Li S. Sparse
approximate multifrontal factorization with composite compression methods. ACM Trans Math Softw. 2023;9(3):24 (28 pages).
36. Dafnakis P, Bhalla APS, Sirigu SA, Bonfanti M, Bracco G, Mattiazzo G. Comparison of
wave–structure interaction dynamics of a submerged cylindrical point absorber with three degrees of freedom using potential flow and computational fluid dynamics models. Phys Fluid. 2020;32:093307
(20 pages).
38. Davis AL, Hoover AP, Miller LA. Lift and drag acting on the shell of the
American horseshoe crab (Limulus polyphemus). Bull Math Biol. 2019;81:3803–22.
39. Delong S, Balboa Usabiaga F, Delgado-Buscalioni R, Griffith BE, Donev A. Brownian dynamics without Green’s functions. J Chem Phys. 2014;140(13):134110 (23 pages).
40. Delong S, Griffith BE, Vanden-Eijnden E, Donev A. Temporal integrators for
fluctuating hydrodynamics. Phys Rev E. 2013;87(3):033302 (22 pages).
41. Delong S, Sun Y, Griffith BE, Vanden-Eijnden E, Donev A. Multiscale temporal
integrators for fluctuating hydrodynamics. Phys Rev E. 2014;90(6):063312 (23 pages).
42. Dombrowski T, Jones SK, Bhalla APS, Katsikis G, Griffith BE, Klotsa D. Transition in swimming direction in a model self-propelled inertial swimmer. Phys Rev Fluid. 2019;4:021101(R) (9 pages).
43. Dombrowski T, Klotsa D. Kinematics of a simple reciprocal model swimmer at
intermediate Reynolds numbers. Phys Rev Fluid. 2020;5:063103 (20 pages).
44. Feng L, Gao H, Griffith BE, Niederer SA, Luo XY. Analysis of a coupled fluid-structure
interaction model of the left atrium and mitral valve. Int J Numer Meth Biomed Eng. 2019;35(11):e3254 (23 pages).
45. Feng L, Gao H, Luo XY. Whole-heart modelling with valves in a fluid–structure
interaction framework. Comput Meth Appl Mech Eng. 2024;420:116724 (27 pages).
46. Feng L, Gao H, Qi N, Danton M, Hill NA, Luo XY. Fluid-structure interaction in
a fully coupled three-dimensional mitral–atrium–pulmonary model. Biomech Model Mechanobiol. 2021;20:1267–95.
47. Feng LY, Qi N, Gao H, Sun W, Vazquez M, Griffith BE, Luo XY. On the chordae
structure and dynamic behaviour of the mitral valve. IMA J Appl Math. 2018;83(6):1066–91.
48. Flamini V, DeAnda A, Griffith BE. Immersed boundary-finite element model of
fluid-structure interaction in the aortic root. Theor Comput Fluid Dynam. 2016;30(1):139–64.
49. Gao H, Aderhold A, Mangion K, Luo X, Husmeier D, Berry C. Changes and
classification in myocardial contractile function in the left ventricle following acute myocardial infarction. J R Soc Interface. 2017;14(132):20170203 (15 pages).
50. Gao H, Carrick D, Berry C, Griffith BE, Luo XY. Dynamic finite-strain modelling of
the human left ventricle in health and disease using an immersed boundary-finite element method. IMA J Appl Math. 2014;79(5):978–1010.
51. Gao H, Feng L, Qi N, Berry C, Griffith BE, Luo XY. A coupled mitral
valve-left ventricle model with fluid-structure interaction. Med Eng Phys. 2017;47:128–36.
52. Gao H, Ma XS, Qi N, Berry C, Griffith BE, Luo XY. A finite strain model of the human
mitral valve with fluid-structure interaction. Int J Numer Meth Biomed Eng. 2014;30(12):1597–613.
53. Gao H, Mangion K, Carrick D, Husmeier D, Luo XY, Berry C. Estimating prognosis
in patients with acute myocardial infarction using personalized computational heart models. Sci Rep. 2017;7:13527 (14 pages).
54. Gao H, Qi N, Feng LY, Ma SH, Danton M, Berry C, Luo XY. Modelling mitral valvular
dynamics: Current trend and future directions. Int J Numer Meth Biomed Eng. 2017;33(10):e2858 (15 pages).
55. Gao H, Qi N, Ma XS, Griffith BE, Berry C, Luo XY. Fluid-structure
interaction model of human mitral valve within left ventricle. In: van Assen H, Bovendeerd P, Delhaas T, editors. Functional Imaging and Modeling of the Heart. Cham:
Springer; 2015. p. 330–7. (Lecture Notes in Computer Science; vol. 9126).
56. Gao H, Wang HM, Berry C, Luo XY, Griffith BE. Quasi-static image-based immersed
boundary-finite element model of left ventricle under diastolic loading. Int J Numer Meth Biomed Eng. 2014;30(11):1199–222.
57. Giraudet C, Bataller H, Sun Y, Donev A, de Zárate JMO, Croccolo F. Confinement
effect on the dynamics of non-equilibrium concentration fluctuations far from the onset of convection. Eur Phys J E. 2016;39:120 (13 pages).
58. Giraudet C, Bataller H, Sun Y, Donev A, de Zárate JMO, Croccolo F. Slowing-down of non-equilibrium concentration fluctuations in confinement. Europhys Lett. 2015;111(6):60013 (6 pages).
59. Griffith BE. On the volume conservation of the immersed boundary method.
Comm Comput Phys. 2012;12(2):401–32.
60. Griffith BE. Immersed boundary model of aortic heart valve dynamics with physiological
driving and loading conditions. Int J Numer Meth Biomed Eng. 2012;28(3):317–45.
61. Griffith BE. An accurate and efficient method for the incompressible
Navier-Stokes equations using the projection method as a preconditioner. J Comput Phys. 2009;228(20):7565–95.
62. Griffith BE, Hornung RD, McQueen DM, Peskin CS. An adaptive, formally second
order accurate version of the immersed boundary method. J Comput Phys. 2007;223(1):10–49.
63. Griffith BE, Hornung RD, McQueen DM, Peskin CS. Parallel and adaptive
simulation of cardiac fluid dynamics. In: Parashar M, Li X, editors. Advanced computational infrastructures for parallel and distributed adaptive applications. Hoboken, NJ, USA: John Wiley; Sons;
2009. p. 105–30.
64. Griffith BE, Lim S. Simulating an elastic ring with bend and twist by an
adaptive generalized immersed boundary method. Comm Comput Phys. 2012;12(2):433–61.
65. Griffith BE, Luo XY. Hybrid finite difference/finite element version of the immersed
boundary method. Int J Numer Meth Biomed Eng. 2017;33(11):e2888 (31 pages).
66. Griffith BE, Luo XY, McQueen DM, Peskin CS. Simulating the fluid dynamics of
natural and prosthetic heart valves using the immersed boundary method. Int J Appl Mech. 2009;1(1):137–77.
67. Griffith BE, Patankar NA. Immersed methods for fluid-structure
interaction. Annu Rev Fluid Mech. 2020;52:421–48.
68. Griffith BE, Peskin CS. On the order of accuracy of the immersed boundary
method: Higher order convergence rates for sufficiently smooth problems. J Comput Phys. 2005;208(1):75–105.
69. Gruninger C, Barrett A, Fang F, Forest MG, Griffith BE. Benchmarking the
immersed boundary method for viscoelastic flows. J Comput Phys. 2024;506:112888 (23 pages).
70. Halder S, Acharya S, Kou W, Campagna RAJ, Triggs JR, Carlson DA, Aziz Aadam A, Hungness ES, Kahrilas PJ, Pandolfino JE, Patankar
NA. Myotomy technique and esophageal contractility impact blown-out myotomy formation in achalasia: An in silico investigation. Am J Physiol
Gastrointest Liver Physiol. 2022;322(5):G500–12.
71. Hamlet C, Fauci L, Morgan JR, Tytell ED. Proprioceptive feedback amplification
restores effective locomotion in a neuromechanical model of lampreys with spinal injuries. Proc Natl Acad Sci USA. 2023;120(11):e2213302120 (7 pages).
72. Hamlet C, Fauci LJ, Tytell ED. The effect of intrinsic muscular nonlinearities
on the energetics of locomotion in a computational model of an anguilliform swimmer. J Theor Biol. 2015;385:119–29.
73. Hamlet CL, Hoffman KA, Tytell ED, Fauci LJ. The role of curvature feedback
in the energetics and dynamics of lamprey swimming: A closed-loop model. PLOS Comput Biol. 2018;14(8):e1006324 (29 pages).
74. Hamlet C, Strychalski W, Miller L. Fluid dynamics of ballistic strategies in
nematocyst firing. Fluids. 2020;5(1):20 (18 pages).
75. Hasan A, Kolahdouz EM, Enquobahrie A, Caranasos TG, Vavalle JP, Griffith BE. Image-based immersed boundary model of the aortic root. Med Eng Phys. 2017;47:72–84.
76. Heath Richardson SI, Gao H, Cox J, Janiczek R, Griffith BE, Berry C, Luo XY. A
poroelastic immersed finite element framework for modeling cardiac perfusion and fluid-structure interaction. Int J Numer Meth Biomed Eng. 2021;37(5):e3446 (22 pages).
77. Heath Richardson S, Mackenzie J, Thekkethil N, Feng L, Lee J, Berry C, Hill NA, Luo XY, Gao H. Cardiac perfusion coupled with a structured coronary network tree. Comput Meth Appl Mech Eng. 2024;428:117083 (26 pages).
78. Heydari S, Hang H, Kanso E. Mapping spatial patterns to energetic benefits in
groups of flow-coupled swimmers. eLife. 2024;13:RP96129 (42 pages).
79. Hoover AP. Emergent metachronal waves using tension-driven, fluid–structure
interaction models of Tomopterid parapodia. Integr Comp Biol. 2021;icab088 (14 pages).
80. Hoover AP, Daniels J, Nawroth J, Katija K. A computational model for tail
undulation and fluid transport in the giant larvacean. Fluids. 2021;6:88 (17 pages).
81. Hoover AP, Griffith BE, Miller LA. Quantifying performance in the medusan mechanospace
with an actively swimming three-dimensional jellyfish model. J Fluid Mech. 2017;813:1112–55.
82. Hoover A, Miller L. A numerical study of the benefits of driving jellyfish
bells at their natural frequency. J Theor Biol. 2015;374:13–25.
83. Hoover AP, Porras AJ, Miller LA. Pump or coast: The role of resonance and passive
energy recapture in medusan swimming performance. J Fluid Mech. 2019;863:1031–61.
84. Hoover AP, Tytell ED. Decoding the relationships between body shape, tail beat
frequency, and stability for swimming fish. Fluids. 2020;5(4):215 (12 pages).
85. Hoover AP, Tytell ED, Cortez R, Fauci LJ. Swimming performance, resonance, and shape
evolution in heaving flexible panels. J Fluid Mech. 2018;847:386–416.
86. Hoover AP, Xu NW, Gemmell BJ, Colin SP, Costello JH, Dabiri JO, Miller LA. Neuromechanical wave resonance in jellyfish swimming. Proc Natl Acad Sci U S A. 2021;118(11):e2020025118 (8 pages).
87. Jones SK, Laurenza R, Hedrick TL, Griffith BE, Miller LA. Lift vs. Drag based
mechanisms for vertical force production in the smallest flying insects. J Theor Biol. 2015;384:105–20.
88. Jones SK, Yun YJ, Hedrick TL, Griffith BE, Miller LA. Bristles reduce the force
required to “fling” wings apart in the smallest insects. J Exp Biol. 2016;219:3759–72.
89. Kaiser AD, Haidar MA, Choi PS, Sharir A, Marsden AL, Ma MR. Simulation-based
design of bicuspidization of the aortic valve. J Thorac Cardiovasc Surg. 2024;168(3):923–32.
90. Kaiser AD, McQueen DM, Peskin CS. Modeling the mitral valve. Int J Numer Meth Biomed
Eng. 2020;35:e3240 (48 pages).
91. Kaiser AD, Schiavone NK, Elkins CJ, McElhinney DB, Eaton JK, Marsden AL. Comparison of immersed boundary simulations of heart valve hemodynamics against in vitro 4D flow MRI data. Ann Biomed
Eng. 2023;
92. Kaiser AD, Shad R, Hiesinger W, Marsden AL. A design-based model of the aortic
valve for fluid-structure interaction. Biomech Model Mechanobiol. 2021;20:2413–35.
93. Kaiser AD, Shad R, Schiavone N, Hiesinger W, Marsden AL. Controlled comparison
of simulated hemodynamics across tricuspid and bicuspid aortic valves. Ann Biomed Eng. 2022;50:1053–72.
94. Kallemov B, Bhalla APS, Griffith BE, Donev A. An immersed boundary method for
rigid bodies. Comm Appl Math Comput Sci. 2016;11(1):79–141.
95. Khedkar K, Bhalla APS. A model predictive control
(MPC)-integrated multiphase immersed boundary (IB) framework for simulating wave energy converters (WECs). Ocean Eng. 2022;260:111908 (25 pages).
96. Khedkar K, Nangia N, Thirumalaisamy R, Bhalla APS. The inertial sea wave
energy converter (ISWEC) technology: Device-physics, multiphase modeling and simulations. Ocean Eng. 2021;229:108879 (31 pages).
97. Kheradvar A, Groves EM, Falahatpisheh A, Mofrad MRK, Alavi SH, Tranquillo R, Dasi LP, Simmons CA, Grande-Allen KJ, Goergen CJ,
Baaijens F, Little SH, Canic S, Griffith B. Emerging trends in heart valve engineering: Part IV.
Computational modeling and experimental studies. Ann Biomed Eng. 2015;43(10):2314–33.
98. Kim KH, Bhalla APS, Griffith BE. An immersed peridynamics model of
fluid-structure interaction accounting for material damage and failure. J Comput Phys. 2023;493:112466 (24 pages).
99. Kolahdouz EM, Bhalla APS, Craven BA, Griffith BE. An immersed interface method
for discrete surfaces. J Comput Phys. 2020;400:108854 (37 pages).
100. Kolahdouz EM, Bhalla APS, Scotten LN, Craven BA, Griffith BE. A sharp
interface Lagrangian-Eulerian method for rigid-body fluid-structure interaction. J Comput Phys. 2021;443:110442 (33 pages).
101. Kolahdouz EM, Wells DR, Rossi S, Aycock KI, Craven BA, Griffith BE. A sharp
interface lagrangian-eulerian method for flexible-body fluid-structure interaction. 2023;488:112174 (28 pages).
102. Kou W, Bhalla APS, Griffith BE, Pandolfino JE, Kahrilas PJ, Patankar NA. A
fully resolved active musculo-mechanical model for esophageal transport. J Comput Phys. 2015;298:446–65.
103. Kou W, Griffith BE, Pandolfino JE, Kahrilas PJ, Patankar NA. A continuum
mechanics-based musculo-mechanical model for esophageal transport. J Comput Phys. 2017;348:433–59.
104. Kou W, Pandolfino JE, Kahrilas PJ, Patankar NA. Simulation studies of circular
muscle contraction, longitudinal muscle shortening, and their coordination in esophageal transport. Am J Physiol Gastrointest Liver Physiol. 2015;309(4):G238–47.
105. Kou W, Pandolfino JE, Kahrilas PJ, Patankar NA. Simulation studies of the role
of esophageal mucosa in bolus transport. Biomech Model Mechanobiol. 2017;16(3):1001–9.
106. Kou W, Pandolfino JE, Kahrilas PJ, Patankar NA. Studies of abnormalities of
the lower esophageal sphincter during esophageal emptying based on a fully-coupled bolus-esophageal-gastric model. Biomech Model Mechanobiol. 2018;17(4):1069–82.
107. Kou W, Pandolfino JE, Kahrilas PJ, Patankar NA. Could the peristaltic transition zone
be caused by non-uniform esophageal muscle fiber architecture? A simulation study. Neurogastroenterol Motil. 2017;29(6):e13022 (9 pages).
108. Land S, Gurev V, Arens S, Augustin CM, Baron L, Blake R, Bradley C, Castro S, Crozier A, Favino M, Fastl TE, Fritz T, Gao H, Gizzi
A, Griffith BE, Hurtado DE, Krause R, Luo XY, Nash MP, Pezzuto S, Plank G, Rossi S, Ruprecht D, Seemann G, Smith NP, Sundnes J, Rice JJ, Trayanova N, Wang D, Wang ZJ, Niederer SA. Verification of cardiac mechanics software: Benchmark problems and solutions for testing active and passive material behaviour. Proc R Soc A.
2015;471(2184):20150641 (20 pages).
109. Lee JH, Griffith BE. On the Lagrangian-Eulerian
coupling in the immersed finite element/difference method. J Comput Phys. 2022;457:111042 (23 pages).
110. Lee JH, Rygg AD, Kolahdouz EM, Rossi S, Retta SM, Duraiswamy N, Scotten LN, Craven BA, Griffith BE. Fluid–structure interaction models of bioprosthetic heart valve dynamics in an experimental pulse duplicator. Ann Biomed Eng. 2020;48(5):1475–90.
111. Lee JH, Scotten L, Hunt R, Caranasos TG, Vavalle JP, Griffith BE. Bioprosthetic aortic valve diameter and thickness are directly related to leaflet fluttering: Results from a combined experimental and computational
modeling study. JTCVS Open. 2021;6:60–81.
112. Li S, Liu S, Zhao D, Dong L, Jiao H. Drag reduction
characteristics of the placoid scale array skin supported by micro Stewart mechanism based on penalty immersed boundary method. Appl Ocean Res. 2024;149:104049 (12 pages).
113. Lin Z, Bhalla APS, Griffith BE, Seng Z, Li H, Liang D, Zhang Y. How
swimming style affects schooling of two fish-like wavy hydrofoils. Ocean Eng. 2023;268:113314 (25 pages).
114. Lin Z, Liang D, Bhalla APS, Al-Shabab AAS, Skote M, Zheng W, Zhang Y. How wavelength
affects hydrodynamic performance of two accelerating mirror-symmetric undulating hydrofoils. Phys Fluids. 2023;35:081901 (22 pages).
115. Lior D, Puelz C, Edwards C, Molossi S, Griffith BE, Birla RK, Rusin CG. Semi-automated construction of patient-specific aortic valves from computed tomography images. Ann Biomed Eng. 2023;51:189–99.
116. Liu Y, Gao M, Yu Y. Kinematics and hydrodynamic performance of zebrafish
C-type maneuvers: A comparison of two- and three-dimensional simulations. AIP Adv. 2024;14:105111 (20 pages).
117. Luo XY, Griffith BE, Ma XS, Yin M, Wang TJ, Liang CL, Watton PN, Bernacca GM. Effect of bending rigidity in a dynamic model of a polyurethane prosthetic mitral valve. Biomech Model Mechanobiol. 2012;11(6):815–27.
118. Ma XS, Gao H, Griffith BE, Berry C, Luo XY. Image-based fluid-structure
interaction model of the human mitral valve. Comput Fluid. 2013;71:417–25.
119. Nangia N, Bale R, Chen N, Hanna Y, Patankar NA. Optimal specific wavelength
for maximum thrust production in undulatory propulsion. PLoS ONE. 2017;12(6):e0179727 (23 pages).
120. Nangia N, Griffith BE, Patankar NA, Bhalla APS. A robust incompressible
Navier-Stokes solver for high density ratio multiphase flows. J Comput Phys. 2019;390:548–94.
121. Nangia N, Johansen H, Patankar NA, Bhalla APS. A moving control volume
approach to computing hydrodynamic forces and torques on immersed bodies. J Comput Phys. 2017;347:437–62.
122. Neveln ID, Bale R, Bhalla APS, Curet OM, Patankar NA, MacIver MA. Undulating fins
produce off-axis thrust and flow structures. J Exp Biol. 2014;217:201–13.
123. Nguyen H, Karp-Boss L, Jumars PA, Fauci L. Hydrodynamics of spines: A different
spin. Limnol Oceanogr Fluid Environ. 2011;1:110–9.
124. Nguyen H, Fauci L. Hydrodynamics of diatom chains and semiflexible fibres. J
R Soc Interface. 2014;11(96):20140314 (13 pages).
125. Olejnik DA, Muijres FT, Karásek M, Honfi Camilo L, De Wagter C, de Croon GCHE. Flying into the wind: Insects and bio-inspired micro-air-vehicles with a wing-stroke dihedral steer passively into wind-gusts. Front Robot AI.
2022;9:820363 (17 pages).
126. Patel NK, Bhalla APS, Patankar NA. A new constraint-based formulation for
hydrodynamically resolved computational neuromechanics of swimming animals. J Comput Phys. 2018;375:684–716.
127. Perl I, Maya R, Sabag O, Beatus T. Lateral instability in fruit flies is determined by
wing-wing interaction and wing elevation kinematics. Phys Fluid. 2023;35:041904 (14 pages).
128. Puelz C, Griffith BE. A sharp interface method for an immersed viscoelastic
solid. J Comput Phys. 2020;409:109217 (25 pages).
129. Samson JE, Battista NA, Khatri S, Miller LA. Pulsing corals: A story of
scale and mixing. Biomath. 2017;6(2):1712169 (14 pages).
130. Samson JE, Miller LA. Collective pulsing in xeniid corals: Part
II—using computational fluid dynamics to determine if there are benefits to coordinated pulsing. Bull Math Biol. 2020;82:67 (21 pages).
131. Samson JE, Miller LA, Roy D, Holzman R, Shavit U, Khatri S. A novel mechanism of
mixing by pulsing corals. J Exp Biol. 2019;222:jeb192518 (13 pages).
132. Santhanakrishnan A, Jones SK, Dickson WB, Peek M, Kasoju VT, Dickinson MH, Miller LA. Flow structure and force generation on flapping wings at low Reynolds numbers relevant to the flight of tiny insects. Fluids. 3(3):45 (22
pages).
133. Senter DM, Douglas DR, Strickland WC, Thomas SG, Talkington AM, Miller L, Battista NA. A semi-automated finite difference mesh creation method for use with immersed boundary software IB2d and IBAMR. Bioinspir
Biomim. 2021;16:016008 (18 pages).
134. Sharma G, Nangia N, Bhalla APS, Ray B. A coupled distributed
Lagrange multiplier (DLM) and discrete element method (DEM) approach to simulate particulate flow with collisions. Powder Technol. 2022;398:117091 (17
pages).
135. Sharma G, Ray B. Numerical simulation of square shaped particle
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136. Sharma G, Ray B. Resolved simulation of
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Citations to these works are tracked on the IBAMR Google Scholar page.
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Glasgow; 2016.
3. Bale R. Hydrodynamics and energetics of undulatory propulsion [PhD thesis]. Northwestern University; 2013.
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thesis]. University of North Carolina at Chapel Hill; 2019.
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the immersed finite element-difference method [PhD thesis]. University of North Carolina at Chapel Hill; 2023.
8. Chen WW. A coupled left ventricle and systemic arteries model [PhD thesis]. University of Glasgow; 2015.
9. Davey M. Construction of a four-chambered, fluid-structure interaction model of the heart with validation studies of physiologic
left heart performance [PhD thesis]. University of North Carolina at Chapel Hill; 2024.
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dynamics [PhD thesis]. Courant Institute of Mathematical Sciences, New York University; 2015.
11. Dombrowski TJ. From Single to Collective: Model Swimmers at Intermediate Reynolds Numbers [PhD thesis].
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14. Griffith BE. Simulating the blood-muscle-valve mechanics of the heart by an adaptive and parallel version of the immersed boundary
method [PhD thesis]. Courant Institute of Mathematical Sciences, New York University; 2005.
15. Halder S. Mechanics-informed diagnosis and treatment planning: Application to esophageal disorders [PhD thesis]. Northwestern
University; 2023.
16. Heydari S. Mechanical and flow interactions facilitate cooperative transport and collective locomotion in animal groups [PhD
thesis]. University of Southern California; 2023.
17. Hoover A. From pacemaker to vortex ring: Modeling jellyfish propulsion and turning [PhD thesis]. University of North Carolina at
Chapel Hill; 2015.
18. Hunt R. Part I: Diffusion-induced flows and particulate aggregation. Part II: Experiments and modeling of
replacement aortic valves. Part III: Enhanced diffusion in wall-driven shear flows [PhD thesis]. University of North Carolina at Chapel Hill; 2021.
19. Jiao Y. Evaluating sensing and control in underwater animal behaviors [PhD thesis]. University of Southern California; 2023.
20. Jones SK. A computational fluid dynamics study of the smallest flying insects [PhD thesis]. University of North Carolina at Chapel
Hill; 2016.
21. Kaiser AD. Modeling the mitral valve [PhD thesis]. Courant Institute of Mathematical Sciences, New York University; 2017.
22. Kim KH. Immersed peridynamics method [PhD thesis]. University of North Carolina at Chapel Hill; 2023.
23. Kou W. Studies of esophageal transport and emptying based on fully-resolved computational models [PhD thesis]. Northwestern
University; 2016.
24. Lee JH. Simulating in vitro models of cardiovascular fluid-structure interaction: Methods, models, and applications [PhD thesis].
University of North Carolina at Chapel Hill; 2020.
25. Ma XS. Dynamic simulation of the mitral valve [PhD thesis]. University of Glasgow; 2014.
26. Nagda BM. Modeling and simulation of ion-induced volume phase transitions in chemically-active polyelectrolyte gels [PhD thesis].
Florida Institute of Technology; 2023.
27. Nangia N. An adaptive constraint-based immersed body method for multiphase fluid-structure interaction [PhD thesis]. Northwestern
University; 2019.
28. Patel N. Computational investigation of the neuromechanical problem for swimming [PhD thesis]. Northwestern University; 2017.
29. Qi N. Modelling of soft tissue and fluid structure interaction with physiological applications [PhD thesis]. University of Glasgow;
2016.
30. Ruvalcaba CA. Numerical model of cilia-driven transport of inhaled particles in the periciliary layer of the human tracheobronchial
tree [PhD thesis]. University of California, Davis; 2022.
31. Samson JE. The fluid dynamics of collective pulsing behavior in xeniid corals [PhD thesis]. University of North Carolina at Chapel
Hill; 2018.
32. Santiago M. Numerical methods for modeling the fluid flow of pulsing soft corals and the photosynthesis of their symbiotic algae
[PhD thesis]. University of California, Merced; 2021.
33. Sprinkle BW. Development and use of high performance numerical methods to study fluid structure interaction phenomena at two
different scales [PhD thesis]. Northwestern University; 2018.
34. Vadala-Roth B. Stabilization of the hybrid immersed boundary method [PhD thesis]. University of North Carolina at Chapel Hill;
2020.
35. Braye M. Numerical and physical modeling of fluid flow through rigid structures [Undergraduate thesis]. University of North
Carolina at Chapel Hill; 2019.
36. DeLee E. Assessing the scalability of parallel programs: Case studies from IBAMR [Undergraduate thesis]. University of North
Carolina at Chapel Hill; 2018.
37. Hasan A. Patient specific hemodynamic modeling of the aortic root [Undergraduate thesis]. University of North Carolina at Chapel
Hill; 2017.
38. Lee J. A computational two-dimensional study of benthic suction feeding [Undergraduate thesis]. Cornell College; 2015.