Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Experimental evaluation of thermodynamic cost and speed limit in living cells via information geometry

View ORCID ProfileKeita Ashida, View ORCID ProfileKazuhiro Aoki, Sosuke Ito
doi: https://doi.org/10.1101/2020.11.29.403097
Keita Ashida
1Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0031, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Keita Ashida
Kazuhiro Aoki
2Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
3Division of Quantitative Biolny, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
4Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kazuhiro Aoki
Sosuke Ito
1Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0031, Japan
5Department of Physics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0031, Japan
6JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: sosuke.ito@ubi.s.u-tokyo.ac.jp
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Chemical reactions are responsible for information processing in living cells, and their accuracy and speed have been discussed from a thermodynamic viewpoint [1–5]. The recent development in stochastic thermodynamics enables evaluating the thermodynamic cost of information processing [6–8]. However, because experimental estimation of the thermodynamic cost based on stochastic thermodynamics requires a sufficient number of samples [9], it is only estimated in simple living systems such as RNA folding [10] and F1-ATPase [11]. Therefore, it is challenging to estimate the thermodynamic cost of information processing by chemical reactions in living cells. Here, we evaluated the thermodynamic cost and its efficiency of information processing in living systems at the singlecell level for the first time by establishing an informationgeometric method to estimate them with a relatively small number of samples. We evaluated the thermodynamic cost of the extracellular signal-regulated kinase (ERK) phosphorylation from the time series of the fluorescence imaging data by calculating the intrinsic speed in information geometry. We also evaluated a thermodynamic efficiency based on the thermodynamic speed limit [8, 12, 13], and thus this paper reports the first experimental test of thermodynamic uncertainty relations in living systems. Our evaluation revealed the change of the efficiency under the conditions of different cell densities and its robustness to the upstream pathway perturbation. Because our approach is widely applicable to other signal transduction pathways such as the G-protein coupled receptor pathways for sensation [14], it would clarify efficient mechanisms of information processing in such a living system.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted November 30, 2020.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Experimental evaluation of thermodynamic cost and speed limit in living cells via information geometry
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Experimental evaluation of thermodynamic cost and speed limit in living cells via information geometry
Keita Ashida, Kazuhiro Aoki, Sosuke Ito
bioRxiv 2020.11.29.403097; doi: https://doi.org/10.1101/2020.11.29.403097
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Experimental evaluation of thermodynamic cost and speed limit in living cells via information geometry
Keita Ashida, Kazuhiro Aoki, Sosuke Ito
bioRxiv 2020.11.29.403097; doi: https://doi.org/10.1101/2020.11.29.403097

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Biophysics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4682)
  • Biochemistry (10357)
  • Bioengineering (7670)
  • Bioinformatics (26330)
  • Biophysics (13523)
  • Cancer Biology (10683)
  • Cell Biology (15438)
  • Clinical Trials (138)
  • Developmental Biology (8497)
  • Ecology (12820)
  • Epidemiology (2067)
  • Evolutionary Biology (16851)
  • Genetics (11399)
  • Genomics (15478)
  • Immunology (10616)
  • Microbiology (25207)
  • Molecular Biology (10220)
  • Neuroscience (54463)
  • Paleontology (401)
  • Pathology (1668)
  • Pharmacology and Toxicology (2897)
  • Physiology (4342)
  • Plant Biology (9243)
  • Scientific Communication and Education (1586)
  • Synthetic Biology (2557)
  • Systems Biology (6780)
  • Zoology (1466)