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Nonequilibrium Thermodynamics in Biology: From Molecular Motors to Metabolic Pathways Wachtel, Artur Doctoral thesis (2018) 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 ... [more ▼] 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. [less ▲] Detailed reference viewed: 197 (16 UL)Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten Wachtel, Artur ; Rao, Riccardo ; Esposito, Massimiliano in New Journal of Physics (2018), 20(4), 042002 Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries ... [more ▼] Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicability of ideas that originated in enzyme kinetics. Our results lay the foundations for systematic studies of the thermodynamics of large-scale biochemical reaction networks. Moreover, we identify the conditions under which a relation between one-way fluxes and forces holds at the coarse-grained level as it holds at the detailed level. In doing so, we clarify the speculations and broad claims made in the literature about such a general flux–force relation. As a further consequence we show that, in contrast to common belief, the second law of thermodynamics does not require the currents and the forces of biochemical reaction networks to be always aligned. [less ▲] Detailed reference viewed: 273 (10 UL)Fluctuating currents in stochastic thermodynamics. I. Gauge invariance of asymptotic statistics Wachtel, Artur ; ; in Physical Review. E. (2015), 92(4), 042132 Stochastic thermodynamics uses Markovian jump processes to model random transitions between observable mesoscopic states. Physical currents are obtained from antisymmetric jump observables defined on the ... [more ▼] Stochastic thermodynamics uses Markovian jump processes to model random transitions between observable mesoscopic states. Physical currents are obtained from antisymmetric jump observables defined on the edges of the graph representing the network of states. The asymptotic statistics of such currents are characterized by scaled cumulants. In the present work, we use the algebraic and topological structure of Markovian models to prove a gauge invariance of the scaled cumulant-generating function. Exploiting this invariance yields an efficient algorithm for practical calculations of asymptotic averages and correlation integrals. We discuss how our approach generalizes the Schnakenberg decomposition of the average entropy-production rate, and how it unifies previous work. The application of our results to concrete models is presented in an accompanying publication. [less ▲] Detailed reference viewed: 115 (3 UL)Fluctuating currents in stochastic thermodynamics. II. Energy conversion and nonequilibrium response in kinesin models ; Wachtel, Artur ; in Physical Review. E. (2015), 92(4), 042133 Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic thermodynamics uses Markovian jump processes to model the random transitions between ... [more ▼] Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational states of these biological macromolecules. A recently developed theoretical framework [A. Wachtel, J. Vollmer, and B. Altaner, Phys. Rev. E 92, 042132 (2015)] provides a simple algorithm for the determination of macroscopic currents and correlation integrals of arbitrary fluctuating currents. Here we use it to discuss energy conversion and nonequilibrium response in different models for the molecular motor kinesin. Methodologically, our results demonstrate the effectiveness of the algorithm in dealing with parameter-dependent stochastic models. For the concrete biophysical problem our results reveal two interesting features in experimentally accessible parameter regions: the validity of a nonequilibrium Green-Kubo relation at mechanical stalling as well as a negative differential mobility for superstalling forces. [less ▲] Detailed reference viewed: 135 (3 UL)Dissipation in noisy chemical networks: The role of deficiency Esposito, Massimiliano ; Polettini, Matteo ; Wachtel, Artur in Journal of Chemical Physics (2015), 145(18), 184103 We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known ... [more ▼] We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known to determine the possibility of complex behavior such as multistability and oscillations, is shown to also characterize the entropic balance. In particular, when deficiency is zero the average stochastic dissipation rate equals that of the corresponding deterministic model, where correlations are disregarded. In fact, dissipation can be reduced by the effect of noise, as occurs in a toy model of metabolism that we employ to illustrate our findings. This phenomenon highlights that there is a close interplay between deficiency and the activation of new dissipative pathways at low molecule numbers [less ▲] Detailed reference viewed: 288 (22 UL) |
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