3,996 research outputs found
Domain Growth, Budding, and Fission in Phase Separating Self-Assembled Fluid Bilayers
A systematic investigation of the phase separation dynamics in self-assembled
multi-component bilayer fluid vesicles and open membranes is presented. We use
large-scale dissipative particle dynamics to explicitly account for solvent,
thereby allowing for numerical investigation of the effects of hydrodynamics
and area-to-volume constraints. In the case of asymmetric lipid composition, we
observed regimes corresponding to coalescence of flat patches, budding,
vesiculation and coalescence of caps. The area-to-volume constraint and
hydrodynamics have a strong influence on these regimes and the crossovers
between them. In the case of symmetric mixtures, irrespective of the
area-to-volume ratio, we observed a growth regime with an exponent of 1/2. The
same exponent is also found in the case of open membranes with symmetric
composition
Phase Transitions in Multicomponent String Model
We propose a one-dimensional model of a string decorated with adhesion
molecules (stickers) to mimic multicomponent membranes in restricted
geometries. The string is bounded by two parallel walls and it interacts with
one of them by short range attractive forces while the stickers are attracted
by the other wall. The exact solution of the model in the case of infinite wall
separation predicts both continuous and discontinuous transitions between
phases characterised by low and high concentration of stickers on the string.
Our model exhibits also coexistence of these two phases, similarly to models of
multicomponent membranes.Comment: letter, 8 pages, 3 figure
A Classical Density-Functional Theory for Describing Water Interfaces
We develop a classical density functional for water which combines the White
Bear fundamental-measure theory (FMT) functional for the hard sphere fluid with
attractive interactions based on the Statistical Associating Fluid Theory
(SAFT-VR). This functional reproduces the properties of water at both long and
short length scales over a wide range of temperatures, and is computationally
efficient, comparable to the cost of FMT itself. We demonstrate our functional
by applying it to systems composed of two hard rods, four hard rods arranged in
a square and hard spheres in water
Equilibrium Chemical Engines
An equilibrium reversible cycle with a certain engine to transduce the energy
of any chemical reaction into mechanical energy is proposed. The efficiency for
chemical energy transduction is also defined so as to be compared with Carnot
efficiency. Relevance to the study of protein motors is discussed. KEYWORDS:
Chemical thermodynamics, Engine, Efficiency, Molecular machine.Comment: 5 pages, late
Fluctuation spectrum of quasispherical membranes with force-dipole activity
The fluctuation spectrum of a quasi-spherical vesicle with active membrane
proteins is calculated. The activity of the proteins is modeled as the proteins
pushing on their surroundings giving rise to non-local force distributions.
Both the contributions from the thermal fluctuations of the active protein
densities and the temporal noise in the individual active force distributions
of the proteins are taken into account. The noise in the individual force
distributions is found to become significant at short wavelengths.Comment: 9 pages, 2 figures, minor changes and addition
Fluctuation-Driven Molecular Transport in an Asymmetric Membrane Channel
Channel proteins, that selectively conduct molecules across cell membranes,
often exhibit an asymmetric structure. By means of a stochastic model, we argue
that channel asymmetry in the presence of non-equilibrium fluctuations, fueled
by the cell's metabolism as observed recently, can dramatically influence the
transport through such channels by a ratchet-like mechanism. For an
aquaglyceroporin that conducts water and glycerol we show that a previously
determined asymmetric glycerol potential leads to enhanced inward transport of
glycerol, but for unfavorably high glycerol concentrations also to enhanced
outward transport that protects a cell against poisoning.Comment: REVTeX4, 4 pages, 3 figures; Accepted for publication in Phys. Rev.
Let
Anomalous lateral diffusion in a viscous membrane surrounded by viscoelastic media
We investigate the lateral dynamics in a purely viscous lipid membrane
surrounded by viscoelastic media such as polymeric solutions. We first obtain
the generalized frequency-dependent mobility tensor and focus on the case when
the solvent is sandwiched by hard walls. Due to the viscoelasticity of the
solvent, the mean square displacement of a disk embedded in the membrane
exhibits an anomalous diffusion. An useful relation which connects the mean
square displacement and the solvent modulus is provided. We also calculate the
cross-correlation of the particle displacements which can be applied for
two-particle tracking experiments.Comment: 6 pages, 2 figure
Modeling of solvent flow effects in enzyme catalysis under physiological conditions
A stochastic model for the dynamics of enzymatic catalysis in explicit,
effective solvents under physiological conditions is presented.
Analytically-computed first passage time densities of a diffusing particle in a
spherical shell with absorbing boundaries are combined with densities obtained
from explicit simulation to obtain the overall probability density for the
total reaction cycle time of the enzymatic system. The method is used to
investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate
kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The
direct simulation of the enzyme-substrate binding and reaction is carried out
using an elastic network model for the protein, and the solvent motions are
described by multiparticle collision dynamics, which incorporates hydrodynamic
flow effects. Systems where solvent-enzyme coupling occurs through explicit
intermolecular interactions, as well as systems where this coupling is taken
into account by including the protein and substrate in the multiparticle
collision step, are investigated and compared with simulations where
hydrodynamic coupling is absent. It is demonstrated that the flow of solvent
particles around the enzyme facilitates the large-scale hinge motion of the
enzyme with bound substrates, and has a significant impact on the shape of the
probability densities and average time scales of substrate binding for
substrates near the enzyme, the closure of the enzyme after binding, and the
overall time of completion of the cycle.Comment: 15 pages in double column forma
Discreteness-induced Transition in Catalytic Reaction Networks
Drastic change in dynamics and statistics in a chemical reaction system,
induced by smallness in the molecule number, is reported. Through stochastic
simulations for random catalytic reaction networks, transition to a novel state
is observed with the decrease in the total molecule number N, characterized by:
i) large fluctuations in chemical concentrations as a result of intermittent
switching over several states with extinction of some molecule species and ii)
strong deviation of time averaged distribution of chemical concentrations from
that expected in the continuum limit, i.e., . The origin of
transition is explained by the deficiency of molecule leading to termination of
some reactions. The critical number of molecules for the transition is obtained
as a function of the number of molecules species M and that of reaction paths
K, while total reaction rates, scaled properly, are shown to follow a universal
form as a function of NK/M
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