Doctoral thesis (Dissertations and theses)
Nonequilibrium Thermodynamics in Biology: From Molecular Motors to Metabolic Pathways
Wachtel, Artur
2018
 

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Keywords :
stochastic thermodynamics; chemical reaction networks; large deviation theory
Abstract :
[en] Biological systems need to exchange energy and matter with their environment in order to stay functional or “alive”. This exchange has to obey the laws of thermodynamics: energy cannot be created and exchange comes at the cost of dissipation, which limits the efficiency of biological function. Additionally, subcellular processes that involve only few molecules are stochastic in their dynamics and a consistent theoretical modeling has to account for that. This dissertation connects recent development in nonequilibrium thermodynamics with approaches taken in biochemical modeling. I start by a short introduction to thermodynamics and statistical mechanics, with a special emphasis on large deviation theory and stochastic thermodynamics. Building on that, I present a general theory for the thermodynamic analysis of networks of chemical reactions that are open to the exchange of matter. As a particularly insightful concrete example I discuss the mechanochemical energy conversion in stochastic models of a molecular motor protein, and show how a similar analysis can be performed for more general models. Furthermore, I compare the dissipation in stochastically and deterministically modeled open chemical networks, and present a class of chemical networks that displays exact agreement for arbitrary abundance of chemical species and arbitrary distance from thermodynamic equilibrium. My major achievement is a thermodynamically consistent coarse-graining procedure for biocatalysts, which are ubiquitous in molecular cell biology. Finally, I discuss the thermodynamics of unbranched enzymatic chains.
Disciplines :
Physics
Biochemistry, biophysics & molecular biology
Author, co-author :
Wachtel, Artur ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit
Language :
English
Title :
Nonequilibrium Thermodynamics in Biology: From Molecular Motors to Metabolic Pathways
Defense date :
17 May 2018
Number of pages :
xiv, 140 + 1
Institution :
Unilu - University of Luxembourg, Luxembourg
Degree :
Docteur de l’Université du Luxembourg en Physique
President :
Jury member :
Skupin, Alexander  
Wolpert, David
Sollich, Peter
Focus Area :
Physics and Materials Science
FnR Project :
FNR7865466 - Thermodynamics Of Chemical Networks, 2014 (01/07/2014-30/06/2018) - Artur Wachtel
Funders :
FNR - Fonds National de la Recherche [LU]
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since 13 November 2018

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