Simulating the cell cycle of the minimal cell in 4D

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2023

Author dc:creator

• Thornburg, Zane R

Contributors dc:contributor

• Luthey-Schulten, Zaida
• Gruebele, Martin
• Chemla, Yann
• Peters, Baron

• Whole Cell Modeling
• Minimal Cell
• Simulations
• Biophysics
• Kinetics

Statement dc:rights

• Copyright 2023 Zane R. Thornburg

Language dc:language

en, eng

Handle dc:identifier

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

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F122226