Tools and applications of cybergenetics control of living cells
: taming complexity

Student thesis: Doctoral ThesisDoctor of Philosophy (PhD)

Abstract

Complexity is inherently tied to natural phenomena: in living organisms, complex patterns must arise for the organism itself to survive. Here, we will focus our efforts on unveiling complex behaviours that might arise in biological and synthetic biological systems. In particular, we will study the cellular interactions that result in nonlinear dynamics such as switches or oscillations, as these are often used for cellular regulation in gene expression. The thesis will cover different topics for the design of an experimental paradigm embedding segmentation methods for data analysis of cellular images, an algorithm for model-free experimental bifurcation analysis and bifurcation tracking for synthetic systems, and the concepts of optimal experimental design (OED) for model calibration.
The overall goal of the thesis is to link these three different topics and create a complete layout for model validation/calibration to reproduce a key dynamic feature - switching- for synthetic systems, starting from the collection of biochemical data via segmentation of microscopy-acquired images, and ending with the coupling of OED principles with the CBC algorithm, aiming to improve the application of CBC for the calibration of biochemical and synthetic models showing bistability.
Date of Award3 Oct 2023
Original languageEnglish
Awarding Institution
  • University of Bristol
SupervisorLucia Marucci (Supervisor), Ludovic Renson (Supervisor) & Martin E Homer (Supervisor)

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