{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/122226"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/122226","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Simulating the cell cycle of the minimal cell in 4D","abstract":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-12-01","abstract_html":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-12-01","abstract_has_math":false,"creators":["Thornburg, Zane R"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Chemistry","degree_department":null,"school":null,"contributors":["Luthey-Schulten, Zaida","Gruebele, Martin","Chemla, Yann","Peters, Baron"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023-12","date_published":"2023-12","updated_at":"2026-07-22T22:25:00Z","subjects":["Whole Cell Modeling","Minimal Cell","Simulations","Biophysics","Kinetics"],"languages":["en","eng"],"rights":["Copyright 2023 Zane R. Thornburg"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/122226","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Luthey-Schulten, Zaida","Gruebele, Martin","Chemla, Yann","Peters, Baron"]},{"key":"dc:creator","label":"Author","values":["Thornburg, Zane R"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2023-12","2023-11-22"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Chemistry"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Whole Cell Modeling","Minimal Cell","Simulations","Biophysics","Kinetics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2023 Zane R. Thornburg"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/122226"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-12-01","The student, Zane Thornburg, accepted the attached license on 2023-11-17 at 09:20.","The student, Zane Thornburg, submitted this Dissertation for approval on 2023-11-17 at 09:36.","This Dissertation was approved for publication on 2023-11-22 at 11:11.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19949 on 2024-03-01 at 13:49:05","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."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Simulating the cell cycle of the minimal cell in 4D"]}]}],"canonical_facts":{"dc:contributor":["Luthey-Schulten, Zaida","Gruebele, Martin","Chemla, Yann","Peters, Baron"],"dc:creator":["Thornburg, Zane R"],"dc:date":["2023-12","2023-11-22"],"dc:description":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-12-01","The student, Zane Thornburg, accepted the attached license on 2023-11-17 at 09:20.","The student, Zane Thornburg, submitted this Dissertation for approval on 2023-11-17 at 09:36.","This Dissertation was approved for publication on 2023-11-22 at 11:11.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19949 on 2024-03-01 at 13:49:05","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."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/122226"],"dc:language":["en","eng"],"dc:rights":["Copyright 2023 Zane R. Thornburg"],"dc:subject":["Whole Cell Modeling","Minimal Cell","Simulations","Biophysics","Kinetics"],"dc:title":["Simulating the cell cycle of the minimal cell in 4D"],"dc:type":["text"],"thesis:degree_discipline":["Chemistry"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:00Z"}