98 research outputs found
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
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