Reference : Nonequilibrium Thermodynamics in Biology: From Molecular Motors to Metabolic Pathways
Dissertations and theses : Doctoral thesis
Life sciences : Biochemistry, biophysics & molecular biology
Physical, chemical, mathematical & earth Sciences : Physics
Physics and Materials Science
Nonequilibrium Thermodynamics in Biology: From Molecular Motors to Metabolic Pathways
Wachtel, Artur mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit >]
University of Luxembourg, ​​Luxembourg
Docteur de l’Université du Luxembourg en Physique
xiv, 140 + 1
Esposito, Massimiliano mailto
Wirtz, Ludger mailto
Skupin, Alexander mailto
Wolpert, David mailto
Sollich, Peter mailto
[en] stochastic thermodynamics ; chemical reaction networks ; large deviation theory
[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.
Fonds National de la Recherche - FnR
Researchers ; Professionals ; Students
FnR ; FNR7865466 > Artur Wachtel > CNThermo > Thermodynamics of Chemical Networks > 01/07/2014 > 30/06/2018 > 2014

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