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Elucidation of Reaction Mechanisms Far from Thermodynamic Equilibrium.

ABSTRACT: Far from equilibrium: This thesis provides a deep mechanistic analysis of the electrooxidation of methanol when the system is kept far from the thermodynamic equilibrium. Under an oscillatory regime, interesting characteristics between the elementary reaction steps were observed. We were able to elucidate the effect of the intrinsic drift in a potential time-series responsible for spontaneous transition of temporal patterns and the carbon dioxide decoupling from direct and indirect pathways.

SUBMITTER: Nagao R

PROVIDER: S-EPMC4906474 | biostudies-other | 2016 Apr

REPOSITORIES: biostudies-other

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Elucidation of Reaction Mechanisms Far from Thermodynamic Equilibrium.

Nagao Raphael R

ChemistryOpen 20151220 2

Far from equilibrium: This thesis provides a deep mechanistic analysis of the electrooxidation of methanol when the system is kept far from the thermodynamic equilibrium. Under an oscillatory regime, interesting characteristics between the elementary reaction steps were observed. We were able to elucidate the effect of the intrinsic drift in a potential time-series responsible for spontaneous transition of temporal patterns and the carbon dioxide decoupling from direct and indirect pathways. ...[more]

PMID: 27308227

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Project description:Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. However, most of this interest has focused on developing coarse ecosystem-level maximisation principles, providing little insight into underlying mechanisms that lead to such emergent constraints. Microbial communities are a natural system to decipher this mechanistic basis because their interactions in the form of substrate consumption, metabolite production, and cross-feeding can be described explicitly in thermodynamic terms. Previous work has considered how thermodynamic constraints impact competition between pairs of species, but restrained from analysing how this manifests in complex dynamical systems. To address this gap, we develop a thermodynamic microbial community model with fully reversible reaction kinetics, which allows direct consideration of free-energy dissipation. This also allows species to interact via products rather than just substrates, increasing the dynamical complexity, and allowing a more nuanced classification of interaction types to emerge. Using this model, we find that community diversity increases with substrate lability, because greater free-energy availability allows for faster generation of niches. Thus, more niches are generated in the time frame of community establishment, leading to higher final species diversity. We also find that allowing species to make use of near-to-equilibrium reactions increases diversity in a low free-energy regime. In such a regime, two new thermodynamic interaction types that we identify here reach comparable strengths to the conventional (competition and facilitation) types, emphasising the key role that thermodynamics plays in community dynamics. Our results suggest that accounting for realistic thermodynamic constraints is vital for understanding the dynamics of real-world microbial communities.

Dataset Information

Elucidation of Reaction Mechanisms Far from Thermodynamic Equilibrium.

Publications

Elucidation of Reaction Mechanisms Far from Thermodynamic Equilibrium.

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