M.S. Thesis Defense: Sehee Sun
Friday, June 6, 2025
10:00
Zoom: https://unl.zoom.us/j/91090289025
"Biocomputing Approach to Modeling and Modulating Calcium Signaling"
Biocomputing leverages biological systems for computation, offering energy-efficient and parallel alternatives to traditional electronic computing. Among various cellular mechanisms, calcium signaling plays a central role in regulating essential biological functions, making it a promising substrate for programmable logic in living systems. This thesis introduces a novel framework for modeling and modulating calcium dynamics using biologically inspired Boolean logic circuits.
First, the thesis will present the Calcium Boolean Logic (CaBL) model, which abstracts calcium fluxes and interactions into logic gates constructed based on the kinetic processes underlying calcium signaling. These gates are composed into sub-circuits that replicate physiological signaling behaviors. Next, to modulate the cytoplasmic calcium level, the thesis will propose the Biosignal Modulation Engine (BME), a search-based algorithm that reconfigures the CaBL circuit by identifying effective gate placements and parameter values to produce a desired digital output. Simulation results demonstrate that the BME successfully identifies circuit configurations that can either increase or decrease the cytoplasmic calcium concentration.
Lastly, a case study on GPCR-mediated calcium suppression will illustrate how the reconfigured CaBL circuit can reproduce the downstream effects of GPCR signaling. This alignment between logic-based circuit output and biological behavior highlights the potential of this framework for future applications in therapeutic biocomputing and synthetic biology.
Committee:
Dr. Sasitharan Balasubramaniam, Advisor
Dr. Massimiliano Pierobon
Dr. Ashok Samal