159 research outputs found
Dominance of extreme statistics in a prototype many-body Brownian ratchet
Many forms of cell motility rely on Brownian ratchet mechanisms that involve
multiple stochastic processes. We present a computational and theoretical study
of the nonequilibrium statistical dynamics of such a many-body ratchet, in the
specific form of a growing polymer gel that pushes a diffusing obstacle. We
find that oft-neglected correlations among constituent filaments impact
steady-state kinetics and significantly deplete the gel's density within
molecular distances of its leading edge. These behaviors are captured
quantitatively by a self-consistent theory for extreme fluctuations in
filaments' spatial distribution.Comment: 5 pages with 3 figures + 20 pages of Supplementary Material with 2
figures. Updated to agree with published version; published as a
Communication in J. Chem. Phy
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
Symmetrized Drude Oscillator Force Fields Improve Numerical Performance of Polarizable Molecular Dynamics
Drude oscillator potentials are a popular and computationally efficient class
of polarizable models that represent each polarizable atom as a positively
charged Drude core harmonically bound to a negatively charged Drude shell. We
show that existing force fields that place all non-Coulomb forces on the Drude
core and none on the shell inadvertently couple the dipole to non-Coulombic
forces. This introduces errors where interactions with neutral particles can
erroneously induce atomic polarization, leading to spurious polarizations in
the absence of an electric field and exacerbating violations of equipartition
in the employed Carr-Parinello scheme. A suitable symmetrization of the
interaction potential that correctly splits the force between the Drude core
and shell can correct this shortcoming, improving the stability and numerical
performance of Drude oscillator based simulations. The symmetrization procedure
is straightforward and only requires the rescaling of a few force field
parameters
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