University of Illinois Urbana-Champaign

Simulating the cell cycle of the minimal cell in 4D

Thornburg, Zane R

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https://hdl.handle.net/2142/122226

Description

Title
Simulating the cell cycle of the minimal cell in 4D
Author(s)
Thornburg, Zane R
Issue Date
2023-11-22
Director of Research (if dissertation) or Advisor (if thesis)
Luthey-Schulten, Zaida
Doctoral Committee Chair(s)
  • Luthey-Schulten, Zaida
  • Gruebele, Martin
Committee Member(s)
  • Chemla, Yann
  • Peters, Baron
Department of Study
Chemistry
Discipline
Chemistry
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
  • Whole Cell Modeling
  • Minimal Cell
  • Simulations
  • Biophysics
  • Kinetics
Abstract
To understand the fundamentals of cellular life, Whole-Cell Models (WCMs) aim to simulate the time-evolution of cellular states to explain cell behavior. To make the most powerful predictions, WCMs should simulate the dynamics of all cellular processes and their correlations simultaneously. As an effort to simulate the most complete cell state possible over time scales of an entire cell cycle (hours), we have chosen to work with the genetically minimal cell, JCVI-syn3A. As a minimal cell, it has the fewest number of processes that need to be modeled, minimizing the complexity of our simulations. Here, we present the model construction of the near-complete reaction system and physical properties of Syn3A using both well-stirred and spatially-resolved hybrid stochastic-deterministic simulations. To model the wide range of length- and time-scales involved in simulating a complete cell cycle, we hybridize multiple methods into a single model to simulate the complete cell cycle of Syn3A. Time-dependent behaviors of concentrations and reaction fluxes over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth and offer insight into the principles of life for this minimal cell.
Graduation Semester
2023-12
Type of Resource
Thesis
Copyright and License Information
Copyright 2023 Zane R. Thornburg

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