Thermodynamics of accuracy in kinetic proofreading: Dissipation and efficiency trade-offs

The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide a consistent thermodynamic description of enzyme-assisted assembly processes involving competing substrates, in a Master Equation framework. We introduce and evaluate a measure of the efficiency based on rigorous non-equilibrium inequalities. The performance of several proofreading models are thus analyzed and the related time, dissipation and efficiency vs. error trade-offs exhibited for different discrimination regimes. We finally introduce and analyze in the same framework a simple model which takes into account correlations between consecutive enzyme-assisted assembly steps. This work highlights the relevance of the distinction between energetic and kinetic discrimination regimes in enzyme-substrate interactions.Comment: IOP Class, 20 pages, 9 figure

Aging in a simple model of a structural glass

We consider a simple model of a structural glass, represented by a lattice gas with kinetic constraints in contact with a particle reservoir. Quench below the glass transition is represented by the jump of the chemical potential above a threshold. After a quench, the density approaches the critical density-where the diffusion coefficient of the particles vanishes-following a power law in time. In this regime, the two-time self-correlation functions exhibit aging. The behavior of the model can be understood in terms of simple mean-field arguments.Comment: LaTeX, 8 pages, 4 figures. Contribution to the Conference "Disorder and Chaos", Rome, September 1997. A few misprints corrected, and references update

A simple system with two temperatures

We study the stationary nonequilibrium regime which settles in when two single-spin paramagnets each in contact with its own thermal bath are coupled. The response vs. correlation plot exhibits some features of aging systems, in particular the existence, in some regimes, of effective temperatures.Comment: 7 pages, 3 figure

Emergent cooperative behavior in transient compartments

We introduce a minimal model of multilevel selection on structured populations, considering the interplay between game theory and population dynamics. Through a bottleneck process, finite groups are formed with cooperators and defectors sampled from an infinite pool. After the fragmentation, these transient compartments grow until the carrying capacity is attained. Eventually, all compartments are merged, well mixed and the whole process is repeated. We show that cooperators, even if interacting only through mean-field intra-group interactions that favor defectors, may perform well because of the inter-group competition and the size diversity among the compartments. These cycles of isolation and coalescence may therefore be important in maintaining diversity among different species or strategies and may help to understand the underlying mechanisms of the scaffolding processes in the transition to multicellularity.Comment: 7 pages, 5 figure