Doctor of Philosophy (PhD)


Chemical Engineering

Document Type



This aim of this research project is to probe the activation process of zebrafish spermatozoa. Zebrafish are a model species for biological engineering applications, and the cryopreservation of their reproductive cells allows for inexpensive cataloging and maintenance of valuable biological material. Evaluation of cryopreservation protocols for aquatic sperm cells is typically accomplished by motility analysis after subjecting cells to a cryopreservation treatment. In zebrafish sperm cells, motility is initiated when cells come into contact with a hypo-osmotic environment. Subsequent activation analysis is currently done manually and brings with it an inherent difficulty and error. This process is slow and not ideal for high-throughput sample processing and analysis. As such, there is a critical need for an influx of enabling technologies to improve the throughput and optimization of these procedures. Microfluidics offers an intriguing solution to this problem. These devices, the size of a single 1-inch by 3-inch glass slide, offer automated, high-throughput, highly reproducible results. Additionally they utilize small sample volumes, which is important in minimizing valuable sample loss. Cells can be input into a micromixer which can rapidly dilute the extracellular environment, and then sent to an analysis chamber that acn determine the efficacy of a cryopreservation treatment. Despite its popularity in other fields, computational modeling of sperm cell activation has been nearly non-existent in literature. In this work, we model both the macroscopic aspects of particulate flow in a microchannel, and the microscopic mass transport across the cellular membrane. By tracking cells as they move throughout a simulated microdevice, we can find a history for each particle and predict cell outcomes. We are the first to introduce this combinatory model to the problem of cryoprotectant loading, where numerical modeling has well-established presence, and to the problem of zebrafish sperm cell activation. I envision the combination of microfluidics, with their controllable and reproducible flow patterns, and computational methods capturing both macro- and micro-transport, as two examples of the very enabling technologies that cryopreservation needs. While we apply these methods primarily to sperm cell analysis, the framework can be widely applied to a variety of cells and tissues.



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Committee Chair

Nandakumar, Krishnaswamy