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Balboa Usabiaga, F., J. B. Bell, R. Delgado-Buscalioni, A. Donev, T. Fai, B. E. Griffith, and C. S. Peskin. 2012. “Staggered Schemes for Fluctuating Hydrodynamics.” Multiscale Model Simul 10 (4): 1369–1408.

Bale, R., A. P. S. Bhalla, I. D. Neveln, M. A. MacIver, and N. A. Patankar. 2015. “Convergent Evolution of Mechanically Optimal Locomotion in Aquatic Invertebrates and Vertebrates.” PLOS Biol 3 (4): e1002123.

Bale, R., M. Hao, A. P. S. Bhalla, and N. A. Patankar. 2014. “Energy Efficiency and Allometry of Movement of Swimming and Flying Animals.” Proc Natl Acad Sci U S A 111 (21): 7517–21.

Bale, R., M. Hao, A. P. S. Bhalla, N. Patel, and N. A. Patankar. 2014. “On Gray’s Paradox: A Fluid Mechanical Prespective.” Sci Rep 4: 5904 (5 pages).

Bale, R., A. A. Shirgaonkar, I. D. Neveln, A. P. S. Bhalla, M. A. MacIver, and N. A. Patankar. 2014. “Separability of Drag and Thrust in Undulatory Animals and Machines.” Sci Rep 4 (7329).

Battista, N. A., A. N. Lane, J. Liu, and L. A. Miller. n.d. “Fluid Dynamics of Heart Development: Effects of Trabeculae and Hematocrit.” Math Med Biol.

Battista, N. A., A. N. Lane, and L. A. Miller. 2017. “On the Dynamic Suction Pumping of Blood Cells in Tubular Hearts.” In Women in Mathematical Biology: Research Collaboration, 211–31.

Battista, N. A., J. E. Samson, S. Khatri, and L. A. Miller. 2018. “Under the Sea: Pulsing Corals in Ambient Flow.” In Mathematical Methods and Models in Biosciences, edited by R. Anguelov and M. Lachowicz, 22–35.

Bhalla, A. P. S., R. Bale, B. E. Griffith, and N. A. Patankar. 2013. “A Unified Mathematical Framework and an Adaptive Numerical Method for Fluid-Structure Interaction with Rigid, Deforming, and Elastic Bodies.” J Comput Phys 250: 446–76.

———. 2014. “Fully Resolved Immersed Electrohydrodynamics for Particle Motion, Electrolocation, and Self-Propulsion.” J Comput Phys 256: 88–108.

Bhalla, A. P. S., B. E. Griffith, and N. A. Patankar. 2013. “A Forced Damped Oscillation Framework for Undulatory Swimming Provides New Insights into How Propulsion Arises in Active and Passive Swimming.” PLOS Comput Biol 9 (6): e100309 (16 pages).

Bhalla, A. P. S., B. E. Griffith, N. A. Patankar, and A. Donev. 2013. “A Minimally-Resolved Immersed Boundary Model for Reaction-Diffusion Problems.” J Chem Phys 139 (21): 214112 (15 pages).

Cai, L., Y. Wang, H. Gao, Y. Li, and X. Luo. 2017. “A Mathematical Model for Active Contraction in Healthy and Failing Myocytes and Left Ventricles.” PLOS ONE 12 (4): e0174834.

Cerbino, R., Y. Sun, A. Donev, and A. Vailati. 2015. “Dynamic Scaling for the Growth of Non-Equilibrium Fluctuations During Thermophoretic Diffusion in Microgravity.” Sci Rep 5: 14486.

Chen, W. W., H. Gao, X. Y. Luo, and N. A. Hill. 2016. “Study of Cardiovascular Function Using a Coupled Left Ventricle and Systemic Circulation Model.” J Biomech 49 (12): 2445–54.

Delong, S., F. Balboa Usabiaga, R. Delgado-Buscalioni, B. E. Griffith, and A. Donev. 2014. “Brownian Dynamics Without Green’s Functions.” J Chem Phys 140 (13): 134110 (23 pages).

Delong, S., B. E. Griffith, E. Vanden-Eijnden, and A. Donev. 2013. “Temporal Integrators for Fluctuating Hydrodynamics.” Phys Rev E 87 (3): 033302 (22 pages).

Delong, S., Y. Sun, B. E. Griffith, E. Vanden-Eijnden, and A. Donev. 2014. “Multiscale Temporal Integrators for Fluctuating Hydrodynamics.” Phys Rev E 90 (6): 063312 (23 pages).

Flamini, V., A. DeAnda, and B. E. Griffith. 2016. “Immersed Boundary-Finite Element Model of Fluid-Structure Interaction in the Aortic Root.” Theor Comput Fluid Dynam 30 (1): 139–64.

Gao, H., A. Aderhold, K. Mangion, X. Luo, D. Husmeier, and C. Berry. 2017. “Changes and Classification in Myocardial Contractile Function in the Left Ventricle Following Acute Myocardial Infarction.” J R Soc Interface 14 (132): 20170203.

Gao, H., D. Carrick, C. Berry, B. E. Griffith, and X. Y. Luo. 2014. “Dynamic Finite-Strain Modelling of the Human Left Ventricle in Health and Disease Using an Immersed Boundary-Finite Element Method.” IMA J Appl Math 79 (5): 978–1010.

Gao, H., L. Feng, N. Qi, C. Berry, B. E. Griffith, and X. Y. Luo. 2017. “A Coupled Mitral Valve-Left Ventricle Model with Fluid-Structure Interaction.” Med Eng Phys 47: 128–36.

Gao, H., X. S. Ma, N. Qi, C. Berry, B. E. Griffith, and X. Y. Luo. 2014. “A Finite Strain Model of the Human Mitral Valve with Fluid-Structure Interaction.” Int J Numer Meth Biomed Eng 30 (12): 1597–1613.

Gao, H., H. M. Wang, C. Berry, X. Y. Luo, and B. E. Griffith. 2014. “Quasi-Static Image-Based Immersed Boundary-Finite Element Model of Left Ventricle Under Diastolic Loading.” Int J Numer Meth Biomed Eng 30 (11): 1199–1222.

Giraudet, C., H. Bataller, Y. Sun, A. Donev, J. M. O. de Zárate, and F. Croccolo. 2015. “Slowing-down of Non-Equilibrium Concentration Fluctuations in Confinement.” Europhysics Letters 111 (6): 60013.

———. 2016. “Confinement Effect on the Dynamics of Non-Equilibrium Concentration Fluctuations Far from the Onset of Convection.” Eur Phys J E 39: 120.

Griffith, B. E. 2012a. “Immersed Boundary Model of Aortic Heart Valve Dynamics with Physiological Driving and Loading Conditions.” Int J Numer Meth Biomed Eng 28 (3): 317–45.

———. 2012b. “On the Volume Conservation of the Immersed Boundary Method.” Comm Comput Phys 12 (2): 401–32.

Griffith, B. E., R. D. Hornung, D. M. McQueen, and C. S. Peskin. 2007. “An Adaptive, Formally Second Order Accurate Version of the Immersed Boundary Method.” J Comput Phys 223 (1): 10–49.

———. 2009. “Parallel and Adaptive Simulation of Cardiac Fluid Dynamics.” In Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications, edited by M. Parashar and X. Li, 105–30. Hoboken, NJ, USA: John Wiley; Sons.

Griffith, B. E., and S. Lim. 2012. “Simulating an Elastic Ring with Bend and Twist by an Adaptive Generalized Immersed Boundary Method.” Comm Comput Phys 12 (2): 433–61.

Griffith, B. E., and X. Y. Luo. 2017. “Hybrid Finite Difference/Finite Element Version of the Immersed Boundary Method.” Int J Numer Meth Biomed Eng 33 (11): e2888 (31 pages).

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Hamlet, C., L. J. Fauci, and E. D. Tytell. 2015. “The Effect of Intrinsic Muscular Nonlinearities on the Energetics of Locomotion in a Computational Model of an Anguilliform Swimmer.” J Theor Biol 385: 119–29.

Hasan, A., E. M. Kolahdouz, A. Enquobahrie, T. G. Caranasos, J. P. Vavalle, and B. E. Griffith. 2017. “Image-Based Immersed Boundary Model of the Aortic Root.” Med Eng Phys 47: 72–84.

Hoover, A., and L. Miller. 2015. “A Numerical Study of the Benefits of Driving Jellyfish Bells at Their Natural Frequency.” J Theor Biol 374: 13–25.

Hoover, A. P., B. E. Griffith, and L. A. Miller. 2017. “Quantifying Performance in the Medusan Mechanospace with an Actively Swimming Three-Dimensional Jellyfish Model.” J Fluid Mech 813: 1112–55.

Hoover, A. P., E. D. Tytell, R. Cortez, and L. J. Fauci. n.d. “Swimming Performance, Resonance, and Shape Evolution in Heaving Flexible Panels.” J Fluid Mech.

Jones, S. K., R. Laurenza, T. L. Hedrick, B. E. Griffith, and L. A. Miller. 2015. “Lift Vs. drag Based Mechanisms for Vertical Force Production in the Smallest Flying Insects.” J Theor Biol 384: 105–20.

Jones, S. K., Y. J. Yun, T. L. Hedrick, B. E. Griffith, and L. A. Miller. 2016. “Bristles Reduce the Force Required to ‘Fling’ Wings Apart in the Smallest Insects.” J Exp Biol 219: 3759–72.

Kallemov, B., A. P. S. Bhalla, B. E. Griffith, and A. Donev. 2016. “An Immersed Boundary Method for Rigid Bodies.” Comm Appl Math Comput Sci 11 (1): 79–141.

Kou, W., A. P. S. Bhalla, B. E. Griffith, J. E. Pandolfino, P. J. Kahrilas, and N. A. Patankar. 2015. “A Fully Resolved Active Musculo-Mechanical Model for Esophageal Transport.” J Comput Phys 298: 446–65.

Kou, W., B. E. Griffith, J. E. Pandolfino, P. J. Kahrilas, and N. A. Patankar. 2017. “A Continuum Mechanics-Based Musculo-Mechanical Model for Esophageal Transport.” J Comput Phys 348: 433–59.

Kou, W., J. E. Pandolfino, P. J. Kahrilas, and N. A. Patankar. 2015. “Simulation Studies of Circular Muscle Contraction, Longitudinal Muscle Shortening, and Their Coordination in Esophageal Transport.” Am J Physiol Gastrointest Liver Physiol 309 (4): G238–G247.

———. 2017a. “Could the Peristaltic Transition Zone Be Caused by Non-Uniform Esophageal Muscle Fiber Architecture? A Simulation Study.” Neurogastroenterol Motil 29 (6): e13022.

———. 2017b. “Simulation Studies of the Role of Esophageal Mucosa in Bolus Transport.” Biomech Model Mechanobiol 16 (3): 1001–9.

———. n.d. “Studies of Abnormalities of the Lower Esophageal Sphincter During Esophageal Emptying Based on a Fully-Coupled Bolus-Esophageal-Gastric Model.” Biomech Model Mechanobiol.

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Luo, X. Y., B. E. Griffith, X. S. Ma, M. Yin, T. J. Wang, C. L. Liang, P. N. Watton, and G. M. Bernacca. 2012. “Effect of Bending Rigidity in a Dynamic Model of a Polyurethane Prosthetic Mitral Valve.” Biomech Model Mechanobiol 11 (6): 815–27.

Ma, X. S., H. Gao, B. E. Griffith, C. Berry, and X. Y. Luo. 2013. “Image-Based Fluid-Structure Interaction Model of the Human Mitral Valve.” Comput Fluid 71: 417–25.

Nangia, N., R. Bale, N. Chen, Y. Hanna, and N. A. Patankar. 2017. “Optimal Specific Wavelength for Maximum Thrust Production in Undulatory Propulsion.” PLoS ONE 12 (6): e0179727.

Nangia, N., H. Johansen, N. A. Patankar, and A. P. S. Bhalla. 2017. “A Moving Control Volume Approach to Computing Hydrodynamic Forces and Torques on Immersed Bodies.” J Comput Phys 347: 437–62.

Neveln, I. D., R. Bale, A. P. S. Bhalla, O. M. Curet, N. A. Patankar, and M.A. MacIver. 2014. “Undulating Fins Produce Off-Axis Thrust and Flow Structures.” J Exp Biol 217: 201–13.

Nguyen, H., and L. Fauci. 2014. “Hydrodynamics of Diatom Chains and Semiflexible Fibres.” J R Soc Interface 11 (96): 20140314.

Nguyen, H., L. Karp-Boss, P. A. Jumars, and L. Fauci. 2011. “Hydrodynamics of Spines: A Different Spin.” Limnol Oceanogr Fluid Environ 1: 110–19.

Samson, J. E., N. A. Battista, S. Khatri, and L. A. Miller. 2017. “Pulsing Corals: A Story of Scale and Mixing.” BIOMATH 6 (2): 1712169.

Skorczewski, T., B. E. Griffith, and A. L. Fogelson. 2014. “Multi-Bond Models for Platelet Adhesion and Cohesion.” In Biological Fluid Dynamics: Modeling, Computation, and Applications, edited by S. D. Olson and A. T. Layton, 149–72. Contemporary Mathematics. Providence, RI, USA: American Mathematical Society.

Sprinkle, B., R. Bale, A. P. S. Bhalla, M. A. MacIver, and N. A. Patankar. 2017. “Hydrodynamic Optimality of Balistiform and Gymnotiform Locomotion.” Eur J Comput Mech 26 (1–2): 31–43.

Strickland, W. C., L. A. Miller, A. Santhanakrishnan, C. Hamlet, N. A. Battista, and V. Pasour. 2017. “Three-Dimensional Low Reynolds Number Flows Near Biological Filtering and Protective Layers.” Fluids 2 (4): 62.

Tytell, E. D., C.-Y. Hsu, and L. J. Fauci. 2014. “The Role of Mechanical Resonance in the Neural Control of Swimming in Fishes.” Zoology 117 (1): 48–56.

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Tytell, E. D., M. C. Leftwich, C.-Y. Hsu, B. E. Griffith, A. H. Cohen, A. J. Smits, C. Hamlet, and L. J. Fauci. 2016. “The role of body stiffness in undulatory swimming: Insights from robotic and computational models.” Phys Rev Fluids 1: 073202 (17 pages).

Van Hirtum, Annemie, B Wu, H Gao, and XY Luo. 2017. “Constricted Channel Flow with Different Cross-Section Shapes.” European Journal of Mechanics-B/Fluids 63. Elsevier Masson: 1–8.

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Vo, G. D., and J. Heys. 2011. “Biofilm Deformation in Response to Fluid Flow in Capillaries.” Biotechnol Bioeng 108 (8): 1893–9.

Waldrop, L., and L. Miller. 2016. “Large-Amplitude, Short-Wave Peristalsis and Its Implications for Transport.” Biomechan Model Mechanobiol 15 (3): 629–42.

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Battista, N. A. 2017. “The Fluid Dynamics of Heart Development: The Effect of Morphology on Flow at Several Stages.” PhD thesis, University of North Carolina at Chapel Hill.

Bhalla, A. P. S. 2013. “Constraint-Based Adaptive Immersed Body Technique for Multiphysics Problems.” PhD thesis, Northwestern University.

Chen, W. W. 2015. “A Coupled Left Ventricle and Systemicarteries Model.” PhD thesis, University of Glasgow.

DeLee, E. 2018. “Assessing the Scalability of Parallel Programs: Case Studies from Ibamr.” Undergraduate thesis, University of North Carolina at Chapel Hill.

Delong, S. 2015. “Temporal Integrators for Langevin Equations with Applications to Fluctuating Hydrodynamics and Brownian Dynamics.” PhD thesis, Courant Institute of Mathematical Sciences, New York University.

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Hasan, A. 2017. “Patient Specific Hemodynamic Modeling of the Aortic Root.” Undergraduate thesis, University of North Carolina at Chapel Hill.

Hoover, A. 2015. “From Pacemaker to Vortex Ring: Modeling Jellyfish Propulsion and Turning.” PhD thesis, University of North Carolina at Chapel Hill.

Jones, S. K. 2016. “A Computational Fluid Dynamics Study of the Smallest Flying Insects.” PhD thesis, University of North Carolina at Chapel Hill.

Kaiser, A. D. 2017. “Modeling the Mitral Valve.” PhD thesis, Courant Institute of Mathematical Sciences, New York University.

Kou, W. 2016. “Computational Modeling of Fluid-Structure-Muscle Activation for Esophageal Transport.” PhD thesis, Northwestern University.

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Qi, N. 2016. “Modelling of Soft Tissue and Fluid Structure Interaction with Physiological Applications.” PhD thesis, University of Glasgow.

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