Information theory and mereology with applications to biology

Inafuku, Daniel A

Permalink

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

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

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.

Graduation Semester

2024-08

Type of Resource

Thesis

Handle URL

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

Copyright and License Information

Copyright 2024 Daniel A. Inafuku

Owning Collections