{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/125602"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/125602","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Information theory and mereology with applications to biology","abstract":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-02-04 without embargo terms","abstract_html":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-02-04 without embargo terms","abstract_has_math":false,"creators":["Inafuku, Daniel A"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Physics","degree_department":null,"school":null,"contributors":["Kirkpatrick, Kay L","Song, Jun S","Rapti, Zoi","Cooper, S Lance"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024-07-10","date_published":"2024-07-10","updated_at":"2026-07-22T22:25:02Z","subjects":["Biological Information Theory","Mathematical Biology","Shannon Capacity","Channel Capacity","Biophysics","Mereology","Measure Theory"],"languages":["en","eng"],"rights":["Copyright 2024 Daniel A. 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Inafuku"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/125602"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-02-04 without embargo terms","The student, Daniel Inafuku, accepted the attached license on 2024-07-10 at 02:32.","The student, Daniel Inafuku, submitted this Dissertation for approval on 2024-07-10 at 02:42.","This Dissertation was approved for publication on 2024-07-10 at 16:23.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21034 on 2025-02-04 at 21:04:51","Molecular machines carry out many important biological processes in the cell, such as replication, transcription, and translation. In this thesis, we calculate information-theoretic quantities of several biomolecules using tools from classical Shannon information theory. In particular, we introduce models of the ribosome, DNA polymerase, and RNA polymerase as information-transmitting communication channels. We perform analytic calculations of bounds on the ribosome's channel capacity and an explicit formula for the capacity of DNA polymerase and RNA polymerase. We demonstrate that these enzymes safely operate at speeds below their capacity by comparing our calculations to experimentally observed rates. Finally, we conclude this thesis by presenting results on a model of mereological parthood and propose ways this model may be applied to knowledge representation in biomedical informatics."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Information theory and mereology with applications to biology"]}]}],"canonical_facts":{"dc:contributor":["Kirkpatrick, Kay L","Song, Jun S","Rapti, Zoi","Cooper, S Lance"],"dc:creator":["Inafuku, Daniel A"],"dc:date":["2024-07-10","2024-08"],"dc:description":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-02-04 without embargo terms","The student, Daniel Inafuku, accepted the attached license on 2024-07-10 at 02:32.","The student, Daniel Inafuku, submitted this Dissertation for approval on 2024-07-10 at 02:42.","This Dissertation was approved for publication on 2024-07-10 at 16:23.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21034 on 2025-02-04 at 21:04:51","Molecular machines carry out many important biological processes in the cell, such as replication, transcription, and translation. In this thesis, we calculate information-theoretic quantities of several biomolecules using tools from classical Shannon information theory. In particular, we introduce models of the ribosome, DNA polymerase, and RNA polymerase as information-transmitting communication channels. We perform analytic calculations of bounds on the ribosome's channel capacity and an explicit formula for the capacity of DNA polymerase and RNA polymerase. We demonstrate that these enzymes safely operate at speeds below their capacity by comparing our calculations to experimentally observed rates. Finally, we conclude this thesis by presenting results on a model of mereological parthood and propose ways this model may be applied to knowledge representation in biomedical informatics."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/125602"],"dc:language":["en","eng"],"dc:rights":["Copyright 2024 Daniel A. 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