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.
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.
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 MV dynamics in a coupled MV-LV 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. 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.
32. 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).
34. 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.
35. 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).
36. Delong S, Griffith BE, Vanden-Eijnden E, Donev A. Temporal integrators for fluctuating hydrodynamics. Phys Rev E. 2013;87(3):033302 (22 pages).
37. 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).
38. 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).
39. Dombrowski T, Klotsa D. Kinematics of a simple reciprocal model swimmer at intermediate Reynolds numbers. Phys Rev Fluid. 2020;5:063103 (20 pages).
40. 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).
41. 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.
42. 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.
43. 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.
44. 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).
45. 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.
46. 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.
47. 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.
48. 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).
49. 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).
50. 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).
51. 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.
52. 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).
53. 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).
54. Griffith BE. On the volume conservation of the immersed boundary method. Comm Comput Phys. 2012;12(2):401–32.
57. 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.
58. 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.
60. 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).
61. 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.
62. Griffith BE, Patankar NA. Immersed methods for fluid-structure interaction. Annu Rev Fluid Mech. 2020;52:421–48.
64. 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.
65. 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).
67. 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).
68. Hamlet C, Strychalski W, Miller L. Fluid dynamics of ballistic strategies in nematocyst firing. Fluids. 2020;5(1):20 (18 pages).
69. 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.
70. 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).
72. 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).
73. 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.
74. 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.
75. 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.
77. 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.
78. 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).
79. 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.
80. 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.
81. Kaiser AD, McQueen DM, Peskin CS. Modeling the mitral valve. Int J Numer Meth Biomed Eng. 2020;35:e3240 (48 pages).
82. 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;
83. 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.
84. 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.
85. 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.
87. 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).
88. 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.
89. 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).
90. Kolahdouz EM, Bhalla APS, Craven BA, Griffith BE. An immersed interface method for discrete surfaces. J Comput Phys. 2020;400:108854 (37 pages).
91. 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).
92. 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).
93. 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.
94. 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.
95. 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.
96. 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.
97. 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.
98. 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).
99. 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).
100. Lee JH, Griffith BE. On the Lagrangian-Eulerian coupling in the immersed finite element/difference method. J Comput Phys. 2022;457:111042 (23 pages).
101. 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.
103. 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).
104. 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).
105. 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.
106. 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.
107. 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.
108. 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).
109. 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.
110. 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.
111. 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.
112. Nguyen H, Karp-Boss L, Jumars PA, Fauci L. Hydrodynamics of spines: A different spin. Limnol Oceanogr Fluid Environ. 2011;1:110–9.
113. Nguyen H, Fauci L. Hydrodynamics of diatom chains and semiflexible fibres. J R Soc Interface. 2014;11(96):20140314 (13 pages).
114. 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).
115. 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.
116. 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).
117. Puelz C, Griffith BE. A sharp interface method for an immersed viscoelastic solid. J Comput Phys. 2020;409:109217 (25 pages).
118. Samson JE, Battista NA, Khatri S, Miller LA. Pulsing corals: A story of scale and mixing. Biomath. 2017;6(2):1712169 (14 pages).
120. 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).
121. 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).
122. 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).
123. 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).
124. Sharma G, Ray B. Numerical simulation of square shaped particle sedimentation. Particuology. 2024;107–16.
125. Sheldon KS, Zhao L, Chuang A, Panayotova IN, Miller LA, Bourouiba L. Revisiting the physics of spider ballooning. In: Layton A, Miller L, editors. Women in Mathematical Biology. Cham: Springer; 2017. p. 163–78. (Association for Women in Mathematics Series; vol. 8).
127. Skorczewski T, Griffith BE, Fogelson AL. Multi-bond models for platelet adhesion and cohesion. In: Olson SD, Layton AT, editors. Biological Fluid Dynamics: Modeling, Computation, and Applications. Providence, RI, USA: American Mathematical Society; 2014. p. 149–72. (Contemporary Mathematics).
128. Sprinkle B, Balboa Usabiaga F, Patankar NA, Donev A. Large scale Brownian dynamics of confined suspensions of rigid particles. J Chem Phys. 2017;147:244103.
129. Sprinkle B, Bale R, Bhalla APS, MacIver MA, Patankar NA. Hydrodynamic optimality of balistiform and gymnotiform locomotion. Eur J Comput Mech. 2017;26(1–2):31–43.
130. Strickland WC, Miller LA, Santhanakrishnan A, Hamlet C, Battista NA, Pasour V. Three-dimensional low reynolds number flows near biological filtering and protective layers. Fluids. 2017;2(4):62 (24 pages).
131. Strychalski W, Bryant S, Jadamba B, Kilkian E, Lai X, Shahriyari L, Segal R, Wei N, Miller LA. Fluid dynamics of nematocyst prey capture. In: Radunskaya A, Segal R, Shtylla B, editors. Understanding Complex Biological Systems with Mathematics. Cham: Springer; 2018. (Association for Women in Mathematics Series; vol. 14).
132. Sun W, Mao W, Griffith BE. Computer modeling and simulation of heart valve function and intervention. In: Kheradvar A, editor. Principles of heart valve engineering. Cambridge, MA, USA: Academic Press; 2019. p. 177–211.
133. Thirumalaisamy R, Khedkar K, Ghysels P, Bhalla APS. An effective preconditioning strategy for volume penalized incompressible/low Mach multiphase flow solvers. J Comput Phys. 2023;490:112325 (36 pages).
134. Thirumalaisamy R, Nangia N, Bhalla APS. Critique on Volume penalization for inhomogeneous Neumann boundary conditions modeling scalar flux in complicated geometry”. J Comput Phys. 2021;433:110163 (11 pages).
135. Thirumalaisamy R, Patankar NA, Bhalla APS. Handling Neumann and Robin boundary conditions in a fictitious domain volume penalization framework. J Comput Phys. 2022;448:110726 (28 pages).
136. Tytell ED, Hsu C-Y, Fauci LJ. The role of mechanical resonance in the neural control of swimming in fishes. Zoology. 2014;117(1):48–56.
137. Tytell ED, Hsu C-Y, Williams TL, Cohen AH, Fauci LJ. Interactions between internal forces, body stiffness, and fluid environment in a neuromechanical model of lamprey swimming. Proc Natl Acad Sci U S A. 2010;107(46):19832–7.
138. Tytell ED, Leftwich MC, Hsu C-Y, Griffith BE, Cohen AH, Smits AJ, Hamlet C, Fauci LJ. The role of body stiffness in undulatory swimming: Insights from robotic and computational models. Phys Rev Fluids. 2016;1:073202 (17 pages).
139. Vadala-Roth B, Acharya S, Patankar NA, Rossi S, Griffith BE. Stabilization approaches for the hyperelastic immersed boundary method for problems of large-deformation incompressible elasticity. Comput Meth Appl Mech Eng. 2020;365:112978 (48 pages).
140. Van Hirtum A, Wu B, Gao H, Luo XY. Constricted channel flow with different cross-section shapes. Eur J Mech B Fluid. 2017;63:1–8.
141. van Veen WG, van Leeuwen JL, Muijres FT. Malaria mosquitoes use leg push‐off forces to control body pitch during take‐off. J Exp Zool A Ecol Integr Physiol. 2020;333(1):38–49.
142. van Veen WG, van Leeuwen JL, Muijres FT. A chordwise offset of the wing-pitch axis enhances rotational aerodynamic forces on insect wings: A numerical study. J R Soc Interface. 2019;16(155):20190118 (13 pages).
143. van Veen WG, van Leeuwen JL, van Oudheusden BW, Muijres FT. The unsteady aerodynamics of insect wings with rotational stroke accelerations, a systematic numerical study. J Fluid Mech. 2022;936:A3 (45 pages).
144. Vo GD, Heys J. Biofilm deformation in response to fluid flow in capillaries. Biotechnol Bioeng. 2011;108(8):1893–9.
146. Waldrop LD, He Y, Battista NA, Neary Peterman T, Miller LA. Uncertainty quantification reveals the physical constraints on pumping by peristaltic hearts. J R Soc Interface. 2020;17:20200232 (14 pages).
147. Waldrop L, Miller L. Large-amplitude, short-wave peristalsis and its implications for transport. Biomechan Model Mechanobiol. 2016;15(3):629–42.
148. Wang W, Song S, Hu W. Concurrent actuation and sensing in fluid by cilia-like transducers. Adv Intell Syst. 2023;230004 (13 pages).
149. Wei C, Hu Q, Li S, Shi X. Hydrodynamic interactions and wake dynamics of fish schooling in rectangle and diamond formations. Ocean Eng. 2023;267:113258 (19 pages).
150. Wells DR, Vadala-Roth B, Lee JH, Griffith BE. A nodal immersed finite element-finite difference method. J Comput Phys. 2023;477:111890 (29 pages).
151. Wei C, Hu Q, Li S, Zhang T, Shi X. Hydrodynamic performance analysis of undulating fin propulsion. Phys Fluids. 2023;35:091906 (17 pages).
153. Zhang D, Chao L, Pan G. Ground effect on a self-propelled undulatory foil. Mod Phys Lett B. 2018;32(11):1850135 (9 pages).
154. Zhang D, Pan G, Chao L, Yan G. Mechanisms influencing the efficiency of aquatic locomotion. Mod Phys Lett B. 2018;32(25):1850229 (11 pages).
155. Zhang D, Pan G, Chao L, Zhang Y. Effects of Reynolds number and thickness on an undulatory self-propelled foil. Phys Fluids. 2018;30(7):071902 (12 pages).
156. Zhao L, Panayotova IN, Chuang A, Sheldon KS, Bourouiba L, Miller LA. Flying spiders: Simulating and modeling the dynamics of ballooning. In: Layton A, Miller L, editors. Women in Mathematical Biology. Cham: Springer; 2017. p. 179–201. (Association for Women in Mathematics Series; vol. 8).

Citations to these works are tracked on the IBAMR Google Scholar page.

1. Acharya S. Investigating Gastroesophageal Motility: Mechanical Work Done During Esophageal Contractility and Fully Resolved Multiphysics Modeling of Gastric Peristalsis [PhD thesis]. Northwestern University; 2021.
2. Allan A. Examination of myocardial electrophysiology using novel panoramic optical mapping techniques [PhD thesis]. University of Glasgow; 2016.
3. Bale R. Hydrodynamics and energetics of undulatory propulsion [PhD thesis]. Northwestern University; 2013.
4. Battista NA. The fluid dynamics of heart development: The effect of morphology on flow at several stages [PhD thesis]. University of North Carolina at Chapel Hill; 2017.
5. Barrett A. An adaptive viscoelastic fluid solver: Formulation, verification, and applications to fluid-structure interaction [PhD thesis]. University of North Carolina at Chapel Hill; 2019.
6. Bhalla APS. Constraint-based adaptive immersed body technique for multiphysics problems [PhD thesis]. Northwestern University; 2013.
7. Brown JA. Modeling transcatheter aortic valve replacement in patient-specific anatomies: Fluid-structure interaction models using 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. Delong S. Temporal integrators for Langevin equations with applications to fluctuating hydrodynamics and brownian dynamics [PhD thesis]. Courant Institute of Mathematical Sciences, New York University; 2015.
10. Dombrowski TJ. From Single to Collective: Model Swimmers at Intermediate Reynolds Numbers [PhD thesis]. University of North Carolina at Chapel Hill; 2021.
11. Fang F. Numerical advances for fluid-structure interactions in entangled polymer solutions with applications to active microbead rheology [PhD thesis]. University of North Carolina at Chapel Hill; 2020.
12. 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.
13. Halder S. Mechanics-informed diagnosis and treatment planning: Application to esophageal disorders [PhD thesis]. Northwestern University; 2023.
14. Hoover A. From pacemaker to vortex ring: Modeling jellyfish propulsion and turning [PhD thesis]. University of North Carolina at Chapel Hill; 2015.
15. 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.
16. Jones SK. A computational fluid dynamics study of the smallest flying insects [PhD thesis]. University of North Carolina at Chapel Hill; 2016.
17. Kaiser AD. Modeling the mitral valve [PhD thesis]. Courant Institute of Mathematical Sciences, New York University; 2017.
18. Kim KH. Immersed peridynamics method [PhD thesis]. University of North Carolina at Chapel Hill; 2023.
19. Kou W. Studies of esophageal transport and emptying based on fully-resolved computational models [PhD thesis]. Northwestern University; 2016.
20. 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.
21. Ma XS. Dynamic simulation of the mitral valve [PhD thesis]. University of Glasgow; 2014.
22. Nagda BM. Modeling and simulation of ion-induced volume phase transitions in chemically-active polyelectrolyte gels [PhD thesis]. Florida Institute of Technology; 2023.
23. Nangia N. An adaptive constraint-based immersed body method for multiphase fluid-structure interaction [PhD thesis]. Northwestern University; 2019.
24. Patel N. Computational investigation of the neuromechanical problem for swimming [PhD thesis]. Northwestern University; 2017.
25. Qi N. Modelling of soft tissue and fluid structure interaction with physiological applications [PhD thesis]. University of Glasgow; 2016.
26. 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.
27. Samson JE. The fluid dynamics of collective pulsing behavior in xeniid corals [PhD thesis]. University of North Carolina at Chapel Hill; 2018.
28. 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.
29. 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.
30. Vadala-Roth B. Stabilization of the hybrid immersed boundary method [PhD thesis]. University of North Carolina at Chapel Hill; 2020.
31. Braye M. Numerical and physical modeling of fluid flow through rigid structures [Undergraduate thesis]. University of North Carolina at Chapel Hill; 2019.
32. DeLee E. Assessing the scalability of parallel programs: Case studies from IBAMR [Undergraduate thesis]. University of North Carolina at Chapel Hill; 2018.
33. Hasan A. Patient specific hemodynamic modeling of the aortic root [Undergraduate thesis]. University of North Carolina at Chapel Hill; 2017.
34. Lee J. A computational two-dimensional study of benthic suction feeding [Undergraduate thesis]. Cornell College; 2015.