Kakani Katija

Principal Engineer

Monterey Bay Aquarium Research Institute

7700 Sandholdt Road

Moss Landing, CA 95039

Phone: (831) 775-1952

email: kakani@mbari.org

Curriculum Vitae

Google Scholar Profile


  • PhD Bioengineering, California Institute of Technology, 2010
  • MSc Aeronautics, California Institute of Technology, 2005
  • BSc Aeronautics and Astronautics, University of Washington, 2004

Research Description

The science theme that drives my research is: As organisms live and develop in a turbulent and changing fluid environment, how do fluid interactions impact their ecology, swimming ability, and behavior, and how can we learn from these strategies for application to bio-inspired design? To address this science theme, my research strives to answer the following questions: What are the tools that we need to study marine organisms and processes in their natural environment? How can we use these tools to inform how systems function, their optimizations (e.g., ecological niches), and how do changes in this system (e.g., morphological and environmental perturbations) impact their ability to function? From the lessons learned, how can we apply these ideas to technology that furthers exploration and discovery of the oceans? I hope to address these questions by using an integrated design, ecological, and engineering approach: (1) bringing the laboratory into the ocean by developing tools and techniques that provide insight on how the marine organism or process functions within its natural environment (e.g., ecological context); (2) bringing the ocean into the laboratory by conducting advanced imaging experiments on live specimens and/or developing mechanical mimics (e.g., models, robotics) to further delineate function and investigate how the system is optimized during controlled experiments; and (3) applying the lessons learned to technology that advance marine research and engineering missions. I address these questions by:

  1. Bringing the laboratory into the ocean

    To bring the laboratory into the ocean, I develop less-invasive techniques to understand biological-physical interactions by furthering fine-scale measurements of organismal behavior and their physical and chemical environments. DeepPIV is an instrument that allows for high temporal and spatial resolution measurements of fluid motion that serves as a proxy for energetics, forces generated, transport, and performance (with Alana Sherman and Bruce Robison, MBARI). DeepPIV has been used in novel ways to reconstruct 3D gelatinous structures using structured light. Additional instrumentation developments in the short- and long-term involve coupling behavioral and environmental sensors (e.g., accelerometers, magnetometers, temperature, depth, salinity, light, dissolved oxygen) on minimally invasive platforms [ITAG: tagging package, collaboration with Aran Mooney (WHOI) and Alex Shorter (Univ. of Michigan), funded by NSF-IDBR; Mesobot: stereo tracking underwater vehicle, collaboration with Dana Yoerger (WHOI) and Steve Rock (Stanford), funded by NSF-OTIC] to allow for quantification of organismal behaviors (e.g., swimming, feeding, reproduction) in response to the environment (e.g., thermoclines, oxygen minimum zones) to understand when organismal behaviors are selected in specific environmental conditions, and to predict organismal response to a changing ocean.

    Relevant publications:

    • Katija K, Troni G, Daniels J, Lance K, Sherlock RE, Sherman AD, Robison BH (2020). “DeepPIV reveals the 3D structure of giant larvacean mucus houses in the Ocean Twilight Zone.” Nature, 583, 78-82.
    • Flaspohler G, Mooney TA, Katija K, Fontes J, Afonso P, Shorter KA (2019). “Quantifying the swimming gaits of veined squid (Loligo forbesii) using bio-logging tags. J. Exp. Biol., 222: jeb198226.
    • Fannjiang C, Mooney TA, Shorter KA, Mann D, Katija K (2019). “Augmenting biologging with supervised machine learning to study in situ behavior of the medusa Chrysaora fuscescens.” J. Exp. Biol., 22: 16.
    • Choy CA, Robison BH, Gagne TO, Erwin B, Firl E, Halden RU, Hamilton JA, Katija K, Lisin SE, Rolsky C, Van Houtan KS (2019). The vertical distribution and biological transport of marine microplastics across the epipelagic and mesopelagic water column. Nature Sci. Rep., 9: 7843.
    • Katija K*, Choy CA*, Sherlock RE, Sherman AD, Robison BH (2017). “From the surface to the seafloor: How giant larvaceans transport microplastics into the deep sea.” Science Advances, e1700715.
    • Katija K, Sherlock RE, Sherman AD, Robison BH (2017). “New technology reveals role of giant larvaceans in oceanic carbon cycling.” Science Advances, e1602374.
    • Fossette S, Katija K, Goldbogen JA, Bograd S, Patry W, Howard MJ, Knowles T, Haddock SHD, Bedell L, Hazen EL, Robison BH, Mooney TA, Shorter KA, Bastian T, Gleiss AC (2016). “How to tag a jellyfish? A methodological review and guidelines to successful jellyfish tagging.” Journal of Plankton Research, in press.
    • Mooney, T.A.*, K. Katija*, K.A. Shorter*, T. Hurst, J. Fontes, and P. Afonso (2015). “ITAG: An eco-sensor for fine-scale behavioral measurements of soft-bodied marine invertebrates.” Animal Biotelemetry, 3: 31. [manuscript]
    • Katija K, Colin SP, Dabiri JO, Costello JH (2011). “Quantitatively measuring in situ flows using a self-contained underwater velocimetry apparatus (SCUVA).” Journal of Visualized Experiments, vol. 56, e2615. [manuscript]
    • Dabiri JO, Young KK, Costello JH, Colin SP (2011) “Self-contained underwater velocimetry apparatus.” US Patent, No. 7864305. [patent]
    • Katija K, Colin SP, Dabiri JO, Costello JH (2011). “Comparison of flows generated by Aequorea victoria: A coherent structure analysis.” Marine Ecological Progress Series, vol. 435, pp. 111-123. [manuscript]
    • Katija K, Dabiri JO (2009). “A viscosity-enhanced mechanism for biogenic ocean mixing.” Nature, vol. 460, pp. 624-626. [manuscript]
    • Katija K, Dabiri JO (2008) “Real-time field measurements of aquatic animal-fluid interactions using a self-contained underwater velocimetry apparatus (SCUVA).” Limnology and Oceanography: Methods, vol. 6, pp. 162-171. [manuscript]
  2. Bringing the ocean into the laboratory

    To bring the ocean into the laboratory, I employ both cutting edge and commonly used diagnostic techniques in engineering to study biological and physical processes in more detail. We collect organisms using SCUBA and ROVs and transport them into the laboratory to further investigate features that cannot be adequately understood using in situ methods. This is an active area of research with collaborative efforts on understanding giant larvacean ecology (with Bruce Robison, MBARI), tomopterid fluid interactions to enable agile swimming and maneuvering (with Karen Osborn, Smithsonian), the mechanisms behind swimming by prayiid siphonophores (with Jack Costello and Sean Colin), arguably the largest organisms on our planet, and fluid interactions with benthic filter feeders (with James Barry, MBARI). In addition, using small-scale robotics, rapid prototyping, and advanced, optically clear and soft materials, we can design and build mechanical mimics to investigate how marine systems function in detail, and evaluate optimization and performance. Not only do these mechanical mimics contribute to the understanding of systems being studied, they will also streamline the technological pipeline to apply these lessons learned more rapidly to underwater technology.

    Relevant publications:

    • Hoover A, Daniels J, Nawroth J, Katija K (2021). “Bending modes for effective fluid transport: The case of the giant larvacean.” Submitted to J. Fluids.
    • Katija K (2015). “Morphology alters fluid transport and the ability of organisms to mix oceanic waters.” Journal of Integrative and Comparative Biology, 55(4): 698-705. [manuscript]
    • Katija K, S.P. Colin, J.H. Costello, and H. Jiang (2015). “Ontogenetic propulsive transitions by medusae Sarsia tubulosa.Journal of Experimental Biology, 218: 2333-2343. [manuscript]
    • Lucas K, Colin SP, Costello JH, Katija K, Klos E (2013). “Fluid interactions that enable stealth predation by the upstream foraging hydromedusa Craspedacusta sowerbyi.” Biological Bulletin, vol. 225(1), pp. 60-70. [manuscript]
    • Katija K, Jiang H (2013). “Swimming by medusae Sarsia tubulosa in the viscous vortex ring limit.” Limnology and Oceanography: Fluids and Environments, vol. 3, pp. 103-118. [manuscript]
    • Colin SP, Costello JH, Katija K, Seymour J, Kiefer K (2013). “Propulsion in Cubomedusae: Mechanisms and Utility.” PlOs One, vol. 8(2), e56393. [manuscript]
    • Katija K (2012). “Biogenic inputs to ocean mixing.” Journal of Experimental Biology, vol. 215, pp. 1040-1049. [manuscript]
    • Dabiri JO, Colin SP, Katija K, Costello JH (2010). “A wake-based correlate of swimming performance and foraging behavior in seven co-occurring jellyfish species.” Journal of Experimental Biology, vol. 213(8), pp. 1217-1225. [manuscript]
  3. Advancing marine technology for research and engineering missions

    The lessons that we learn during in situ and laboratory studies can be used to improve ocean technology that advances exploration and discovery. Some of these improvements can be achieved by enhancing the maneuverability of AUVs and improving the sampling and sorting capability of in situ instrumentation. Research has shown that by manipulating the exit conditions of a propulsor, the resultant thrust can be modified and improved. Investigations based on ROV observations of escaping Humboldt squid and DeepPIV measurements of larvacean in-house flows provide novel methods of fluid transport that could be applied to improve AUV thrust capability while minimizing energy expenditure. In addition, enhanced maneuverability of AUVs can be achieved by introducing thrust vectoring similar to the function of nectophores along the stem of a physonect siphonophore. To improve the sampling capabilities of instrumentation, we need to understand the limits to hydromechanical sensing in invertebrates, fish larvae, and forage species, and design sampling systems so as to not exceed these limits. Finally, by continuing to study the function of larvacean houses and the mechanisms behind their ability to sort particles by size and composition, we can apply these findings to improve the sorting capabilities of in situ instrumentation.

    Relevant publications:

    • Yoerger DR, Govindarajan AF, Howland JC, Llopiz JK, Wiebe PH, Curran M, Fujii J, Gomez-Ibanez D, Katija K, Robison BH, Hobson BW, Risi M, Rock SM (2020). “Mesobot: A hybrid underwater robot for multidisciplinary investigation of the Ocean Twilight Zone.” To appear in Science Robotics.
    • Katija K, Roberts PLD, Daniels J, Lapides A, Barnard K, Risi M, Ranaan BY, Takahashi J, Woodward BG (2021). “Visual tracking of deepwater animals using machine learning-controlled robotic underwater vehicles.” Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 860-869.
    • Boulais O, B Woodward, L Lundsten, K Barnard, B Schlining, KC Bell, K Katija (2020). “FathomNet: An underwater image training database for ocean exploration and discovery.” arXiv: 2007.00114.
    • Masmitja I, J Navarro, S Gomariz, J Aguzzi, B Kieft, T O’Reilly, K Katija, PJ Bouvet, C Fannjiang, M Vigo, P Puig, A Alcocer, G Vallicrosa, N Palomeras, M Carreras, J Del-Rio, JB Company (2020). “Mobile robotic platforms for the acoustic tracking of deep-sea demersal fishery resources.” Science Robotics, 5:48, eabc3701.
    • Rosenfeld M, Katija K, Dabiri JO (2009) “Circulation generation and vortex ring formation by static conic nozzles.” Journal of Fluids Engineering, vol. 131(9). [manuscript]
    • Shadden SC, Katija K, Rosenfeld M, Marsden JE, Dabiri JO (2007) “Transport and stirring induced by vortex formation.” Journal of Fluid Mechanics, vol. 593, pp. 315-331. [manuscript]