14 research outputs found
Fluctuation Theorems for Entropy Production and Heat Dissipation in Periodically Driven Markov Chains
Asymptotic fluctuation theorems are statements of a Gallavotti-Cohen symmetry
in the rate function of either the time-averaged entropy production or heat
dissipation of a process. Such theorems have been proved for various general
classes of continuous-time deterministic and stochastic processes, but always
under the assumption that the forces driving the system are time independent,
and often relying on the existence of a limiting ergodic distribution. In this
paper we extend the asymptotic fluctuation theorem for the first time to
inhomogeneous continuous-time processes without a stationary distribution,
considering specifically a finite state Markov chain driven by periodic
transition rates. We find that for both entropy production and heat
dissipation, the usual Gallavotti-Cohen symmetry of the rate function is
generalized to an analogous relation between the rate functions of the original
process and its corresponding backward process, in which the trajectory and the
driving protocol have been time-reversed. The effect is that spontaneous
positive fluctuations in the long time average of each quantity in the forward
process are exponentially more likely than spontaneous negative fluctuations in
the backward process, and vice-versa, revealing that the distributions of
fluctuations in universes in which time moves forward and backward are related.
As an additional result, the asymptotic time-averaged entropy production is
obtained as the integral of a periodic entropy production rate that generalizes
the constant rate pertaining to homogeneous dynamics
A review of Monte Carlo simulations of polymers with PERM
In this review, we describe applications of the pruned-enriched Rosenbluth
method (PERM), a sequential Monte Carlo algorithm with resampling, to various
problems in polymer physics. PERM produces samples according to any given
prescribed weight distribution, by growing configurations step by step with
controlled bias, and correcting "bad" configurations by "population control".
The latter is implemented, in contrast to other population based algorithms
like e.g. genetic algorithms, by depth-first recursion which avoids storing all
members of the population at the same time in computer memory. The problems we
discuss all concern single polymers (with one exception), but under various
conditions: Homopolymers in good solvents and at the point, semi-stiff
polymers, polymers in confining geometries, stretched polymers undergoing a
forced globule-linear transition, star polymers, bottle brushes, lattice
animals as a model for randomly branched polymers, DNA melting, and finally --
as the only system at low temperatures, lattice heteropolymers as simple models
for protein folding. PERM is for some of these problems the method of choice,
but it can also fail. We discuss how to recognize when a result is reliable,
and we discuss also some types of bias that can be crucial in guiding the
growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011
Piston rotaxane monolayers: shear swelling and nanovalve behavior
A piston-rotaxane is a rotaxane molecule where one of the free rings is attached to a rod-like polymer (the piston). We examine the behavior of a system of piston rotaxanes grafted by one end to a surface in the presence of a fluid flow. At a critical shear rate the rotaxane layer will extend perpendicular to the surface, i.e. the system undergoes shear-induced swelling. When the inside surface of a narrow tube is coated with these rotaxanes a nanovalve can be created which has a highly nonlinear flow-rate versus pressure curve. In particular a valve can be created which limits the maximum discharge over a wide range of pressures
Nonequilibrium umbrella sampling and the functional crooks fluctuation theorem
We review the theoretical underpinning of nonequilibrium umbrella sampling. We provide its historical context and show how it relates to other important results in nonequilibrium statistical mechanics. Its relationships to the generalised Yamada-Kawasaki distribution function is explored. A new functional version of the Crooks Fluctuation Theorem is also presented