{"id":{"repo_id":"houston","oai_identifier":"oai:uh-ir.tdl.org:10657/20685"},"canonical_url":"https://search.dev.ndltd.org/etd/houston/oai:uh-ir.tdl.org:10657/20685","repository":{"repo_id":"houston","name":"University of Houston","base_url":"https://uh-ir.tdl.org/server/oai/request"},"display":{"title":"Distributed Delay Improves the Dynamics of Gene Regulation","abstract":"Gene Regulatory Networks (GRNs) are the principal decision-making apparatuses of cells. GRNs play a critical role in a diverse array of biological processes; cell-fate determination in embryonic development, the induction of labor at the end of pregnancy, maintenance of circadian rhythms, the onset of puberty, quorum sensing in bacteria, and preventing cells from becoming cancerous are some examples of what GRNs do. A critical feature that governs the dynamics of GRNs is the delay between the start of transcription of a gene and the formation of a functional protein. Indeed, any model of Gene Regulation must account for this delay in some way in order to be useful. But the molecular mechanisms in a cell are subject to stochasticity, making this delay inherently random. Through a combination of computer simulation and explanatory modeling, this dissertation demonstrates the counterintuitive advantages that arise from the presence of stochasticity in transcriptional delay. In particular, for negative feedback architectures, genetic oscillators, distributed delay increases the signal-to-noise ratio of the oscillatory signal and reduces resource utilization to maintain stable oscillations, and for positive feedback architectures, bistable toggles, distributed delay increases mean residency times.","abstract_html":"Gene Regulatory Networks (GRNs) are the principal decision-making apparatuses of cells. GRNs play a critical role in a diverse array of biological processes; cell-fate determination in embryonic development, the induction of labor at the end of pregnancy, maintenance of circadian rhythms, the onset of puberty, quorum sensing in bacteria, and preventing cells from becoming cancerous are some examples of what GRNs do. A critical feature that governs the dynamics of GRNs is the delay between the start of transcription of a gene and the formation of a functional protein. Indeed, any model of Gene Regulation must account for this delay in some way in order to be useful. But the molecular mechanisms in a cell are subject to stochasticity, making this delay inherently random. Through a combination of computer simulation and explanatory modeling, this dissertation demonstrates the counterintuitive advantages that arise from the presence of stochasticity in transcriptional delay. In particular, for negative feedback architectures, genetic oscillators, distributed delay increases the signal-to-noise ratio of the oscillatory signal and reduces resource utilization to maintain stable oscillations, and for positive feedback architectures, bistable toggles, distributed delay increases mean residency times.","abstract_has_math":false,"creators":["Campbell, Sean Paul 1994-"],"institution":"University of Houston","degree_name":"Doctor of Philosophy","degree_level":null,"degree_discipline":"Mathematics","degree_department":null,"school":null,"contributors":[],"advisors":["Ott, William"],"committee_chairs":[],"committee_members":["Timofeyev, Ilya","Azevedo, Ricardo","Perepelitsa, Mikhail"],"year":2025,"date_issued":"2025-08","date_published":"2025-08","updated_at":"2026-07-24T02:31:42Z","subjects":["Molecular biology","Mathematics"],"languages":["English"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/10657/20685","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Ott, William"]},{"key":"dc:contributor.committeemember","label":"Committee Member","values":["Timofeyev, Ilya","Azevedo, Ricardo","Perepelitsa, Mikhail"]},{"key":"dc:creator","label":"Author","values":["Campbell, Sean Paul 1994-"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2025-10-06T18:36:34Z"]},{"key":"dc:date.issued","label":"Date","values":["2025-08"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Mathematics"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy"]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Houston"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Molecular biology","Mathematics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["English"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/10657/20685"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Gene Regulatory Networks (GRNs) are the principal decision-making apparatuses of cells. GRNs play a critical role in a diverse array of biological processes; cell-fate determination in embryonic development, the induction of labor at the end of pregnancy, maintenance of circadian rhythms, the onset of puberty, quorum sensing in bacteria, and preventing cells from becoming cancerous are some examples of what GRNs do. A critical feature that governs the dynamics of GRNs is the delay between the start of transcription of a gene and the formation of a functional protein. Indeed, any model of Gene Regulation must account for this delay in some way in order to be useful. But the molecular mechanisms in a cell are subject to stochasticity, making this delay inherently random. Through a combination of computer simulation and explanatory modeling, this dissertation demonstrates the counterintuitive advantages that arise from the presence of stochasticity in transcriptional delay. In particular, for negative feedback architectures, genetic oscillators, distributed delay increases the signal-to-noise ratio of the oscillatory signal and reduces resource utilization to maintain stable oscillations, and for positive feedback architectures, bistable toggles, distributed delay increases mean residency times."]},{"key":"dc:format.mimetype","label":"Dc Format Mimetype","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Distributed Delay Improves the Dynamics of Gene Regulation"]}]}],"canonical_facts":{"dc:contributor.advisor":["Ott, William"],"dc:contributor.committeemember":["Timofeyev, Ilya","Azevedo, Ricardo","Perepelitsa, Mikhail"],"dc:creator":["Campbell, Sean Paul 1994-"],"dc:date.accessioned":["2025-10-06T18:36:34Z"],"dc:date.issued":["2025-08"],"dc:description.abstract":["Gene Regulatory Networks (GRNs) are the principal decision-making apparatuses of cells. GRNs play a critical role in a diverse array of biological processes; cell-fate determination in embryonic development, the induction of labor at the end of pregnancy, maintenance of circadian rhythms, the onset of puberty, quorum sensing in bacteria, and preventing cells from becoming cancerous are some examples of what GRNs do. A critical feature that governs the dynamics of GRNs is the delay between the start of transcription of a gene and the formation of a functional protein. Indeed, any model of Gene Regulation must account for this delay in some way in order to be useful. But the molecular mechanisms in a cell are subject to stochasticity, making this delay inherently random. Through a combination of computer simulation and explanatory modeling, this dissertation demonstrates the counterintuitive advantages that arise from the presence of stochasticity in transcriptional delay. In particular, for negative feedback architectures, genetic oscillators, distributed delay increases the signal-to-noise ratio of the oscillatory signal and reduces resource utilization to maintain stable oscillations, and for positive feedback architectures, bistable toggles, distributed delay increases mean residency times."],"dc:format.mimetype":["application/pdf"],"dc:identifier.uri":["https://hdl.handle.net/10657/20685"],"dc:language.iso":["English"],"dc:subject":["Molecular biology","Mathematics"],"dc:title":["Distributed Delay Improves the Dynamics of Gene Regulation"],"dc:type":["Thesis"],"thesis:degree_discipline":["Mathematics"],"thesis:degree_name":["Doctor of Philosophy"],"thesis:institution_name":["University of Houston"]},"updated_at":"2026-07-24T02:31:42Z"}