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Currently Active Research Projects
Currently Active Research Projects
Jellyfish Swimming and Neuromechanics
Jellyfish have been the focus of many recent studies due to the discovery of their highly efficient swimming mechanism. Their propulsive cycle is initiated by pacemakers, located at the rim of the jellyfish bell, that signal for the contraction of coronally-oriented muscles, located in the subumbrellar cavity of the bell, to push fluid out of the bell cavity and generate forward thrust. Following the release of muscular tension, the elastic bell passively expands until it has reached its resting state. Momentum generated by the bell during the contraction and expansion phases leads to the formation of two oppositely-spinning vortex rings, the starting and stopping vortex rings. The interaction between the two vortex rings and the bell yields a sustained secondary thrust at no additional metabolic cost, in a process known as passive energy recapture. Due to this swimming mechanism, jellyfish reach sizes larger than phylogenetic constraints would allow.
I am particularly interested in modeling jellyfish biomechanics from to vantage point of neuromechanics, where considerations of the medusan nervous system is taken into account or modeled explicitly using electrophysiology models. Understand the neuromechanical mechanisms for maneuverability are essential for the development of soft body and biohybrid robotics with distributed control.
Publications:
A numerical study of the benefits of driving jellyfish bells at their natural frequency. Alexander P Hoover and Laura A Miller. Journal of theoretical biology 374, 13-25. (2015)
Quantifying performance in the medusan mechanospace with an actively swimming three-dimensional jellyfish model. Alexander P Hoover, Boyce E Griffith, and Laura A Miller. Journal of Fluid Mechanics 813, 1112-1155. (2017)
Pump or coast: the role of resonance and passive energy recapture in medusan swimming performance. Alexander P Hoover, Antonio J Porras, Laura A Miller. Journal of Fluid Mechanics 863, 1031-1061. (2019)
Neuromechanical wave resonance in jellyfish swimming. Alexander P Hoover, Nicole W Xu, Bradford J Gemmell, Sean P Colin, John H Costello, JO Dabiri, and Laura Miller. Proceedings of the National Academy of Sciences 118 (11), e2020025118. (2021)
Flexible Panels and Undulatory Locomotion
A fundamental question in the biomechanics of swimming and flying is whether or not flexibility can be advantageous for performance. Much work has been geared towards the development of vehicles that are propelled with the actuation of flexible propulsors. Here, understanding the limitations and constraints that shapes the locomotion of biological organisms can yield insight into design of the vehicle and an optimized pattern of actuation. Recently it was found that the flexible appendages of swimming and flying animals that move using undulatory motions exhibit similar bending patterns across a wide range of sizes and animal taxa, and in both air and water, though the reason is unknown. Other experimental studies measured the thrust and power of tethered, flexible panels and found that a non-monotonic relationship between the actuation frequency and the swimming performance of the panel. There are many open questions present in this field and careful mathematical modeling of actuated, elastic bodies in a fluid can provide a great deal of insight.
In my research, I have been focussed on decoding the nature of undulatory swimmers. This focus has been two-fold, with both a research focus on the role passive elastic properties play in swimming performance and stability as well as understanding the active-passive dynamics that internally-actuated tension and musculature plays.
Publications:
Swimming performance, resonance and shape evolution in heaving flexible panels. Alexander P Hoover, Ricardo Cortez, Eric D Tytell, Lisa J Fauci. Journal of Fluid Mechanics 847, 386-416. (2018)
Decoding the relationships between body shape, tail beat frequency, and stability for swimming fish. AP Hoover, E Tytell. Fluids 5 (4), 215. (2021)
A computational model for tail undulation and fluid transport in the giant larvacean. Alexander P Hoover, J Daniels, JC Nawroth, K Katija. Fluids 6 (2), 88. (2021)
Metachronal Motion in Fluid Pumping
Metachronal motion, or the coordinated motion of multiple appendages with an attenuated phase lag, is ubiquitous throughout the biological world, from terrestrial locomotion of centipedes to the fluid pumping of ciliary carpets. It is also found as a propulsive mechanism for many marine organisms, from the pleopods of crustacean to the ctene combs of ctenophores. In collaboration with the Monterey Bay Aquarium Research Institute (MBARI), I started to examine the metachronal motion of the soft flexible paddles of the gossamer worm Tomopteris. Gossamer worms have two sets of fleshy paddles, known as parapodia, that line the sides of their body. Working with Kakani Katija (MBARI), Joost Daniels (MBARI), and Karen Osborn (Smithsonian Institute), we developed an FSI model that incorporates the musculature found in individual parapodia to drive the oscillations of the individual parapodia, as well as the phase lag of multiple parapodia with a phase lag to account for the metachronal motion. The control of this phase lag allows us an to modulate asymmetrical jet that form as a result of metachrony.
Collaborators:
Publications:
Alexander P Hoover. Emergent metachronal waves using tension-driven, fluid-structure interaction models of tomopterid parapodia. Integrative and Comparative Biology 61 (5), 1594-1607 (2021)
Margaret L Byron, David W Murphy, Kakani Katija, Alexander P Hoover, Joost Daniels, Kuvvat Garayev, Daisuke Takagi, Eva Kanso, Bradford J Gemmell, Melissa Ruszczyk, and Arvind Santhanakrishnan. Metachronal motion across scales: current challenges and future directions. Integrative and Comparative Biology 61 (5), 1674-1688. (2021)
Bacterial Swimming and Collective Dynamics at Low Reynolds Numbers
At microscopic scales, bacterial swimmers are influenced by the flows generated by other microswimmers, leading to complex collective dynamics. The use of high fidelity models to describe the fine features of each swimmer becomes computationally intractable, leading to the development of reduced models that capture the cycle averaged flow fields of swimmers. Many of the methods I employ in this area take advantage of the negligible inertial contributions of microorganisms, allowing us to employ the method of regularized Stokeslets to find fundamental (regularized) solutions to the Stokes equation.
In collaboration with Shilpa Boindala (Georgia Gwinett College, Mathematics) and Ricardo Cortez (Tulane University, Mathematics), we have developed a one-point model by taking a limit of two-point, force dipole pusher-puller model to arrive at a single-point formulation, known as the force doublet model, that is able to capture the transition from anomalous to normal diffusive behavior observed experimentally in higher concentrations at a certain critical time, as well as a decrease in velocity correlation with increase in pairwise distances for pushers compared to pullers.
Collaborators:
Publications:
A regularised force-doublet framework for self-propelled microswimmers. Alexander P Hoover, Priya S Boindala, Ricardo Cortez. Journal of Fluid Mechanics 1009, A1 (2025)
Benthic Organisms and Nutrient Cycles
From corals to clams, benthic organisms, whose life is predominantly on the seafloor, have developed fluid transport mechanisms to ensure the nutrient transport necessary for life. This can range from the microscopic cilia that adorn the hard coral of the Great Barrier Reef, to the pulsing bells of upside jellyfish that live in nutrient-dense mangroves. These processes in turn aid the symbionts present on the organism that provide energy for the host organism. When examining these processes, we are particularly interested in mixing processes that the organisms takes part in and their potential impact on the oceanic carbon cycle, with biogenic oceanic mixing being an important component in nutrient cycle.
Collaborators:
Nicholas Battista
Publications:
Lift and Drag Acting on the Shell of the American Horseshoe Crab (Limulus polyphemus). Alexander L Davis, Alexander P Hoover, Laura A Miller. Bulletin of Mathematical Biology 81 (10), 3803-3822. (2019)
The presence of a substrate strengthens the jet generated by upside-down jellyfish. Nicholas Battista, Manikantam G Gaddam, Christina L Hamlet, Alexander P Hoover, Laura A Miller, and Arvind Santhanakrishnan. Frontiers in Marine Science 9, 847061. (2022)
Emergent Kinematics and Flow Structure of Tension Driven Pulsing Xeniid Corals. Matea Santiago, Alexander P Hoover, Laura A Miller. Bulletin of Mathematical Biology 87 (9), 133. (2025)
Uncertainty Quantification and Machine Learning in Mathematical Biology
As a mathematical biologist, uncertainty is ubiquitous, whether it be the noise from experimental recordings or the intrinsically stochastic nature of biological processes. I began to delve into the world of uncertainty quantification and Bayesian scientific computing. COVID-19 and the subsequent shutdown allowed me to further my experience in these methodologies for infection forecasting. Since then I have begun a number of research projects that engage with these methodologies, from the muscular synergies of terrestrial biomechanics to the inflammatory response to pathogens in human lungs. Additionally, in collaboration with Nicholas Battista and Matea Santiago, we have begun applying machine learning frameworks to examine the energetics of undulatory swimmers.
Collaborators:
Daniela Calvetti
Erkki Somersalo
Andrea Arnold
Nicholas Battista
Giorgio Davico
Marissa Renardy
Nick Cogan
Isaac Klapper
Ivan Ramirez-Zuniga
Publications:
Daniela Calvetti, Alexander P Hoover, Johnnie Rose, Erkki Somersalo. Metapopulation network models for understanding, predicting, and managing the coronavirus disease COVID-19. Frontiers in Physics 8, 261. (2020)
Daniela Calvetti, Alexander P Hoover, Johnnie Rose, Erkki Somersalo. Bayesian particle filter algorithm for learning epidemic dynamics. Inverse Problems 37 (11), 115008. (2021)
Daniela Calvetti, Alexander P Hoover, Johnnie Rose, Erkki Somersalo. Modeling epidemic spread among a commuting population using transport schemes. Mathematics 9 (16), 1861. (2021)
Daniela Calvetti, Andrea N Arnold, Alexander P Hoover, Giorgio Davico, Erkki Somersalo. Separable hierarchical priors applied to analysis of synergies in human locomotion. Philosophical Transactions A 383 (2305), 20240055. (2025)
Nicholas Battista, Alexander P Hoover, Matea Santiago. Using machine-learning and CFD to understand biomechanics of marine organisms. (accepted as a book chapter for Foundations for Undergraduate Research in Mathematics.) (2025)
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