1,495 research outputs found
Work and heat probability distributions in out-of-equilibrium systems
We review and discuss the equations governing the distribution of work done
on a system which is driven out of equilibrium by external manipulation, as
well as those governing the entropy flow to a reservoir in a nonequilibrium
system. We take advantage of these equations to investigate the path phase
transition in a manipulated mean-field Ising model and the large-deviation
function for the heat flow in the asymmetric exclusion process with
periodically varying transition probabilities.Comment: Contribution to Proceedings of "Work, Dissipation, and Fluctuations
in Nonequilibrium Physics", Brussels, 200
Maximum power operation of interacting molecular motors
We study the mechanical and thermodynamic properties of different traffic
models for kinesin which are relevant in biological and experimental contexts.
We find that motor-motor interactions play a fundamental role by enhancing the
thermodynamic efficiency at maximum power of the motors, as compared to the
non-interacting system, in a wide range of biologically compatible scenarios.
We furthermore consider the case where the motor-motor interaction directly
affects the internal chemical cycle and investigate the effect on the system
dynamics and thermodynamics.Comment: 19 pages, 22 figure
Evaluation of free energy landscapes from manipulation experiments
A fluctuation relation, which is an extended form of the Jarzynski equality,
is introduced and discussed. We show how to apply this relation in order to
evaluate the free energy landscape of simple systems. These systems are
manipulated by varying the external field coupled with a systems' internal
characteristic variable. Two different manipulation protocols are here
considered: in the first case the external field is a linear function of time,
in the second case it is a periodic function of time. While for simple mean
field systems both the linear protocol and the oscillatory protocol provide a
reliable estimate of the free energy landscape, for a simple model
ofhomopolymer the oscillatory protocol turns out to be not reliable for this
purpose. We then discuss the possibility of application of the method here
presented to evaluate the free energy landscape of real systems, and the
practical limitations that one can face in the realization of an experimental
set-up
Work probability distribution in systems driven out of equilibrium
We derive the differential equation describing the time evolution of the work
probability distribution function of a stochastic system which is driven out of
equilibrium by the manipulation of a parameter. We consider both systems
described by their microscopic state or by a collective variable which
identifies a quasiequilibrium state. We show that the work probability
distribution can be represented by a path integral, which is dominated by
``classical'' paths in the large system size limit. We compare these results
with simulated manipulation of mean-field systems. We discuss the range of
applicability of the Jarzynski equality for evaluating the system free energy
using these out-of-equilibrium manipulations. Large fluctuations in the work
and the shape of the work distribution tails are also discussed
Mechanical unfolding and refolding pathways of ubiquitin
Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo
simulations of a Go model with binary variables. The exponential dependence of
the time constants on the force is verified, and folding and unfolding lengths
are computed, with good agreement with experimental results. Furthermore, the
model exhibits intermediate kinetic states, as observed in experiments.
Unfolding and refolding pathways and intermediate states, obtained by tracing
single secondary structure elements, are consistent with simulations of
previous all-atom models and with the experimentally observed step sizes
Efficiency at maximum power of motor traffic on networks
We study motor traffic on Bethe networks subject to hard-core exclusion for
both tightly coupled one-state machines and loosely coupled two-state machines
that perform work against a constant load. In both cases we find an
interaction-induced enhancement of the efficiency at maximum power (EMP) as
compared to non-interacting motors. The EMP enhancement occurs for a wide range
of network and single motor parameters and is due to a change in the
characteristic load-velocity relation caused by phase transitions in the
system. Using a quantitative measure of the trade-off between the EMP
enhancement and the corresponding loss in the maximum output power we identify
parameter regimes where motor traffic systems operate efficiently at maximum
power without a significant decrease in the maximum power output due to jamming
effects.Comment: 9 pages, 9 figures, submitted to Phys. Rev.
The distribution function of entropy flow in stochastic systems
We obtain a simple direct derivation of the differential equation governing
the entropy flow probability distribution function of a stochastic system first
obtained by Lebowitz and Spohn. Its solution agrees well with the experimental
results of Tietz et al [2006 {\it Phys. Rev. Lett.} {\bf 97} 050602]. A
trajectory-sampling algorithm allowing to evaluate the entropy flow
distribution function is introduced and discussed. This algorithm turns out to
be effective at finite times and in the case of time-dependent transition
rates, and is successfully applied to an asymmetric simple exclusion process
Heat flow in chains driven by thermal noise
We consider the large deviation function for a classical harmonic chain
composed of N particles driven at the end points by heat reservoirs, first
derived in the quantum regime by Saito and Dhar and in the classical regime by
Saito and Dhar and Kundu et al. Within a Langevin description we perform this
calculation on the basis of a standard path integral calculation in Fourier
space. The cumulant generating function yielding the large deviation function
is given in terms of a transmission Green's function and is consistent with the
fluctuation theorem. We find a simple expression for the tails of the heat
distribution which turn out to decay exponentially. We, moreover, consider an
extension of a single particle model suggested by Derrida and Brunet and
discuss the two-particle case. We also discuss the limit for large N and
present a closed expression for the cumulant generating function. Finally, we
present a derivation of the fluctuation theorem on the basis of a Fokker-Planck
description. This result is not restricted to the harmonic case but is valid
for a general interaction potential between the particles.Comment: Latex: 26 pages and 9 figures, appeared in J. Stat. Mech. P04005
(2012
Heat fluctuations and fluctuation theorems in the case of multiple reservoirs
We consider heat fluctuations and fluctuation theorems for systems driven by
multiple reservoirs. We establish a fundamental symmetry obeyed by the joint
probability distribution for the heat transfers and system coordinates. The
symmetry leads to a generalisation of the asymptotic fluctuation theorem for
large deviations at large times. As a result the presence of multiple
reservoirs influence the tails in the heat distribution. The symmetry,
moreover, allows for a simple derivation of a recent exact fluctuation theorem
valid at all times. Including a time dependent work protocol we also present a
derivation of the integral fluctuation theorem.Comment: 27 pages, 1 figure, new extended version, to appear in J. Stat. Mech,
(2014
- …