2,280 research outputs found
Coexistence between fluid and crystalline phases of proteins in photosynthetic membranes
Photosystem II (PSII) and its associated light-harvesting complex II (LHCII)
are highly concentrated in the stacked grana regions of photosynthetic
thylakoid membranes. Within the membrane, PSII-LHCII supercomplexes can be
arranged in disordered packings, ordered arrays, or mixtures thereof. The
physical driving forces underlying array formation are unknown, complicating
attempts to determine a possible functional role for arrays in regulating light
harvesting or energy conversion efficiency. Here we introduce a coarse-grained
model of protein interactions in coupled photosynthetic membranes, focusing on
just two particle types that feature simple shapes and potential energies
motivated by structural studies. Reporting on computer simulations of the
model's equilibrium fluctuations, we demonstrate its success in reproducing
diverse structural features observed in experiments, including extended
PSII-LHCII arrays. Free energy calculations reveal that the appearance of
arrays marks a phase transition from the disordered fluid state to a
system-spanning crystal, which can easily be arrested by thermodynamic
constraints or slow dynamics. The region of fluid-crystal coexistence is broad,
encompassing much of the physiologically relevant parameter regime. Our results
suggest that grana membranes lie at or near phase coexistence, conferring
significant structural and functional flexibility to this densely packed
membrane protein system.Comment: 11 pages, 5 figure
Efficiency and Large Deviations in Time-Asymmetric Stochastic Heat Engines
In a stochastic heat engine driven by a cyclic non-equilibrium protocol,
fluctuations in work and heat give rise to a fluctuating efficiency. Using
computer simulations and tools from large deviation theory, we have examined
these fluctuations in detail for a model two-state engine. We find in general
that the form of efficiency probability distributions is similar to those
described by Verley et al. [2014 Nat Comm, 5 4721], in particular featuring a
local minimum in the long-time limit. In contrast to the time-symmetric engine
protocols studied previously, however, this minimum need not occur at the value
characteristic of a reversible Carnot engine. Furthermore, while the local
minimum may reside at the global minimum of a large deviation rate function, it
does not generally correspond to the least likely efficiency measured over
finite time. We introduce a general approximation for the finite-time
efficiency distribution, , based on large deviation statistics of work
and heat, that remains very accurate even when deviates significantly
from its large deviation form.Comment: 10 pages, 3 figure
Editorial: Popular concerns about medical research projects in sub-Saharan Africa--a critical voice in debates about medical research ethics.
Near-optimal protocols in complex nonequilibrium transformations
The development of sophisticated experimental means to control nanoscale
systems has motivated efforts to design driving protocols which minimize the
energy dissipated to the environment. Computational models are a crucial tool
in this practical challenge. We describe a general method for sampling an
ensemble of finite-time, nonequilibrium protocols biased towards a low average
dissipation. We show that this scheme can be carried out very efficiently in
several limiting cases. As an application, we sample the ensemble of
low-dissipation protocols that invert the magnetization of a 2D Ising model and
explore how the diversity of the protocols varies in response to constraints on
the average dissipation. In this example, we find that there is a large set of
protocols with average dissipation close to the optimal value, which we argue
is a general phenomenon.Comment: 6 pages and 3 figures plus 4 pages and 5 figures of supplemental
materia
Equilibrium free energies from fast-switching trajectories with large time steps
Jarzynski's identity for the free energy difference between two equilibrium
states can be viewed as a special case of a more general procedure based on
phase space mappings. Solving a system's equation of motion by approximate
means generates a mapping that is perfectly valid for this purpose, regardless
of how closely the solution mimics true time evolution. We exploit this fact,
using crudely dynamical trajectories to compute free energy differences that
are in principle exact. Numerical simulations show that Newton's equation can
be discretized to low order over very large time steps (limited only by the
computer's ability to represent resulting values of dynamical variables)
without sacrificing thermodynamic accuracy. For computing the reversible work
required to move a particle through a dense liquid, these calculations are more
efficient than conventional fast switching simulations by more than an order of
magnitude. We also explore consequences of the phase space mapping perspective
for systems at equilibrium, deriving an exact expression for the statistics of
energy fluctuations in simulated conservative systems
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