The diversity and scope of understanding biological processes is a highly difficult task. We can simplify them and turn the complexity of these systems into reliable and predictive mathematical models, through which these complexities can be delineated systematically. One such complex system is the natural oscillatory network of genes that have evolved to reliably regulate metabolic and developmental activities over the 24 hours, tracking a solar day. These biological networks that give rise to oscillators have been identified ranging from a simple regulatory network controlled exclusively by photoreceptor activities, which take advantage of the rhythmic day-night cycle, to a complex network of gene regulations that is self-sufficient and highly adaptable through entrainment. The first is an example of the simplest photoperiodic response, and the latter is called the circadian clock. Due to their ubiquity, studies on circadian rhythms have a wide scope in industrial, agricultural, and health sectors. Since many of the circadian clocks integrate aspects of photoperiodic rhythm through photoreceptors (directly or indirectly), photoreceptors present a unique way to build a mathematical model and rapidly test them as their functions can be modulated through light availability as an input. In this work, the functions of three photoreceptors are discussed in the context of the circadian or photoperiodic responses. First, photoactive cryptochromes (CRY) which are found in most organisms, where they impart photoperiodic response to the systems, are discussed as a putative protein for magnetoreception, required for navigation during their migration. Specifically, the photochemistry of CRY4 from Colombia livia is studied and a mathematical model is generated to investigate the novel role of photoactive CRYs as a magnetoreceptor. Second, the Light-Oxygen-Voltage (LOV) domain of a DNA binding protein, Aureochromes, from a brown alga, Nannochloropsis oceanica (No), which is valuable for human health as well as industrial feedstocks, are discussed for their role in maintaining a photoperiodic rhythm. Specifically, the photochemistry of NoAureo2, NoAureo3, and NoAureo4 is delineated, and their combined function postulated through a mathematical model. Lastly, Zeitlupe, a LOV domain containing protein, is discussed in the context of its role as a light integrator into the circadian clock of plants. Specifically, the rate of light activation of the LOV domain is delineated with a prospect of incorporating these rates along with the rate of deactivation in the dark into the mathematical model used to describe the plant circadian clock. These three systems, although very different in both their host organisms and the system architecture, are three different strategies organisms employ to respond to the rhythm of our planet.

Degree Date

Winter 12-16-2023

Document Type


Degree Name





Brian Zoltowski

Second Advisor

Nicolay Vasilev Tsarevsky

Third Advisor

Devin Matthews

Fourth Advisor

Alexander Lippert

Fifth Advisor

Thomas Carr

Sixth Advisor

Peng Tao

Subject Area

Agricultural Sciences, Biochemistry, Biological Sciences, General, Biophysics, Bioengineering and Biomedical Engineering, Chemistry, Life Sciences, Life Sciences, General/Other, Mathematics, Applied, Molecular Biology

Number of Pages




Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

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