Information theory and mereology with applications to biology
Inafuku, Daniel A
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https://hdl.handle.net/2142/125602
Description
Title
Information theory and mereology with applications to biology
Author(s)
Inafuku, Daniel A
Issue Date
2024-07-10
Director of Research (if dissertation) or Advisor (if thesis)
Kirkpatrick, Kay L
Doctoral Committee Chair(s)
Song, Jun S
Committee Member(s)
Rapti, Zoi
Cooper, S Lance
Department of Study
Physics
Discipline
Physics
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biological Information Theory
Mathematical Biology
Shannon Capacity
Channel Capacity
Biophysics
Mereology
Measure Theory
Language
eng
Abstract
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.
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