Information theory and mereology with applications to biology

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Physics

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2024

Author dc:creator

• Inafuku, Daniel A

Contributors dc:contributor

• Kirkpatrick, Kay L
• Song, Jun S
• Rapti, Zoi
• Cooper, S Lance

• Biological Information Theory
• Mathematical Biology
• Shannon Capacity
• Channel Capacity
• Biophysics
• Mereology
• Measure Theory

Statement dc:rights

• Copyright 2024 Daniel A. Inafuku

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/125602

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F125602