Non-equilibrium Thermodynamics in Biology: from Chemical Reaction Networks to Natural Selection

Monday, June 14 at 09:30am (PDT)
Monday, June 14 at 05:30pm (BST)
Tuesday, June 15 01:30am (KST)

SMB2021 SMB2021 Follow Monday (Tuesday) during the "MS01" time block.
Note: this minisymposia has multiple sessions. The second session is MS02-EVOP (click here).

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John Baez (University of California, Riverside, USA), William Cannon (Pacific Northwest National Laboratory, USA), Larry Li (University of California, Riverside, USA)


Since Lotka, physical scientists have argued that living things belong to a class of complex and orderly systems that exist not despite the second law of thermodynamics, but because of it. Life and evolution, through natural selection of dissipative structures, are based on non-equilibrium thermodynamics. The challenge is to develop an understanding of what the respective physical laws can tell us about flows of energy and matter in living systems, and about growth, death and selection. This session will address current challenges including understanding emergence, regulation and control across scales, and entropy production, from metabolism in microbes to evolving ecosystems.

John Harte

(University of California, Berkeley, USA)
"Nonequilibrium dynamics of disturbed ecosystems"
The Maximum Entropy Theory of Ecology (METE) predicts the shapes of macroecological metrics in relatively static ecosystems, across spatial scales, taxonomic categories, and habitats, using constraints imposed by static state variables. In disturbed ecosystems, however, with time-varying state variables, its predictions often fail. We extend macroecological theory from static to dynamic, by combining the MaxEnt inference procedure with explicit mechanisms governing disturbance. In the static limit, the resulting theory, DynaMETE, reduces to METE but also predicts a new scaling relationship among static state variables. Under disturbances, expressed as shifts in demographic, ontogenic growth, or migration rates, DynaMETE predicts the time trajectories of the state variables as well as the time-varying shapes of macroecological metrics such as the species abundance distribution and the distribution of metabolic rates over individuals. An iterative procedure for solving the dynamic theory is presented. Characteristic signatures of the deviation from static predictions of macroecological patterns are shown to result from different kinds of disturbance. By combining MaxEnt inference with explicit dynamical mechanisms of disturbance, DynaMETE is a candidate theory of macroecology for ecosystems responding to anthropogenic or natural disturbances.

Hong Qian

(University of Washington, USA)
"Large deviations theory and emergent landscapes in biological dynamics"
The mathematical theory of large deviations provides a nonequilibrium thermodynamic description of complex biological systems that consist of heterogeneous individuals. In terms of the notions of stochastic elementary reactions and pure kinetic species, the continuous-time, integer-valued Markov process dictates a thermodynamic structure that generalizes (i) Gibbs’ macroscopic chemical thermodynamics of equilibrium matters to nonequilibrium small systems such as living cells and tissues; and (ii) Gibbs’ potential function to the landscapes for biological dynamics, such as that of C. H. Waddington’s and S. Wright’s.

Pierre Gaspard

(Université libre de Bruxelles, Belgium)
"Nonequilibrium biomolecular information processes"
Nearly 70 years have passed since the discovery of DNA structure and its role in coding genetic information. Yet, the kinetics and thermodynamics of genetic information processing in DNA replication, transcription, and translation remain poorly understood. These template-directed copolymerization processes are running away from equilibrium, being powered by extracellular energy sources. Recent advances show that their kinetic equations can be exactly solved in terms of so-called iterated function systems. Remarkably, iterated function systems can determine the effects of genome sequence on replication errors, up to a million times faster than kinetic Monte Carlo algorithms. With these new methods, fundamental links can be established between molecular information processing and the second law of thermodynamics, shedding a new light on genetic drift, mutations, and evolution.

Carsten Wiuf

(University of Copenhagen, Denmark)
"Reduction and the Quasi-Steady State Approximation"
Chemical reactions often occur at different time-scales. In applications of chemical reaction network theory it is often desirable to reduce a reaction network to a smaller reaction network by elimination of fast species or fast reactions. There exist various techniques for doing so, e.g. the Quasi-Steady-State Approximation or the Rapid Equilibrium Approximation. However, these methods are not always mathematically justifiable. Here, a method is presented for which (so-called) non-interacting species are eliminated by means of QSSA. It is argued that this method is mathematically sound. Various examples are given (Michaelis-Menten mechanism, two-substrate mechanism, ...) and older related techniques from the 50-60ies are briefly discussed.

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Virtual conference of the Society for Mathematical Biology, 2021.