1,748 research outputs found
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
Free-energy distribution of the directed polymer at high temperature
We study the directed polymer of length in a random potential with fixed
endpoints in dimension 1+1 in the continuum and on the square lattice, by
analytical and numerical methods. The universal regime of high temperature
is described, upon scaling 'time' and space (with for the discrete model) by a continuum model with
-function disorder correlation. Using the Bethe Ansatz solution for the
attractive boson problem, we obtain all positive integer moments of the
partition function. The lowest cumulants of the free energy are predicted at
small time and found in agreement with numerics. We then obtain the exact
expression at any time for the generating function of the free energy
distribution, in terms of a Fredholm determinant. At large time we find that it
crosses over to the Tracy Widom distribution (TW) which describes the fixed
infinite limit. The exact free energy distribution is obtained for any time
and compared with very recent results on growth and exclusion models.Comment: 6 pages, 3 figures large time limit corrected and convergence to
Tracy Widom established, 1 figure changed
Fluctuation induced interactions between domains in membranes
We study a model lipid bilayer composed of a mixture of two incompatible
lipid types which have a natural tendency to segregate in the absence of
membrane fluctuations. The membrane is mechanically characterized by a local
bending rigidity which varies with the average local lipid
composition . We show, in the case where varies weakly with
, that the effective interaction between lipids of the same type can
either be everywhere attractive or can have a repulsive component at
intermediate distances greater than the typical lipid size. When this
interaction has a repulsive component, it can prevent macro-phase separation
and lead to separation in mesophases with a finite domain size. This effect
could be relevant to certain experimental and numerical observations of
mesoscopic domains in such systems.Comment: 9 pages RevTex, 1 eps figur
Spicules and the effect of rigid rods on enclosing membrane tubes
Membrane tubes (spicules) arise in cells, or artificial membranes, in the
nonlinear deformation regime due to, e.g. the growth of microtubules, actin
filaments or sickle hemoglobin fibers towards a membrane. We calculate the
axial force exerted by the cylindrical membrane tube, and its average radius,
by taking into account steric interactions between the fluctuating membrane and
the enclosed rod. The force required to confine a fluctuating membrane near the
surface of the enclosed rod diverges as the separation approaches zero. This
results in a smooth crossover of the axial force between a square root and a
linear dependence on the membrane tension as the tension increases and the tube
radius shrinks. This crossover can occur at the most physiologically relevant
membrane tensions. Our work may be important in (i) interpreting experiments in
which axial force is related to the tube radius or membrane tension (ii)
dynamical theories for biopolymer growth in narrow tubes where these
fluctuation effects control the tube radius.Comment: 10 pages, 1 figur
Diffusion-controlled generation of a proton-motive force across a biomembrane
Respiration in bacteria involves a sequence of energetically-coupled electron
and proton transfers creating an electrochemical gradient of protons (a
proton-motive force) across the inner bacterial membrane. With a simple kinetic
model we analyze a redox loop mechanism of proton-motive force generation
mediated by a molecular shuttle diffusing inside the membrane. This model,
which includes six electron-binding and two proton-binding sites, reflects the
main features of nitrate respiration in E. coli bacteria. We describe the time
evolution of the proton translocation process. We find that the electron-proton
electrostatic coupling on the shuttle plays a significant role in the process
of energy conversion between electron and proton components. We determine the
conditions where the redox loop mechanism is able to translocate protons
against the transmembrane voltage gradient above 200 mV with a thermodynamic
efficiency of about 37%, in the physiologically important range of temperatures
from 250 to 350 K.Comment: 26 pages, 4 figures. A similar model is used in arXiv:0806.3233 for a
different biological system. Minor changes in the Acknowledgements sectio
Competition for hydrogen bond formation in the helix-coil transition and protein folding
The problem of the helix-coil transition of biopolymers in explicit solvents,
like water, with the ability for hydrogen bonding with solvent is addressed
analytically using a suitably modified version of the Generalized Model of
Polypeptide Chains. Besides the regular helix-coil transition, an additional
coil-helix or reentrant transition is also found at lower temperatures. The
reentrant transition arises due to competition between polymer-polymer and
polymer-water hydrogen bonds. The balance between the two types of hydrogen
bonding can be shifted to either direction through changes not only in
temperature, but also by pressure, mechanical force, osmotic stress or other
external influences. Both polypeptides and polynucleotides are considered
within a unified formalism. Our approach provides an explanation of the
experimental difficulty of observing the reentrant transition with pressure;
and underscores the advantage of pulling experiments for studies of DNA.
Results are discussed and compared with those reported in a number of recent
publications with which a significant level of agreement is obtained.Comment: 21 pages, 3 figures, submitted to Phys Rev
Universal features of cell polarization processes
Cell polarization plays a central role in the development of complex
organisms. It has been recently shown that cell polarization may follow from
the proximity to a phase separation instability in a bistable network of
chemical reactions. An example which has been thoroughly studied is the
formation of signaling domains during eukaryotic chemotaxis. In this case, the
process of domain growth may be described by the use of a constrained
time-dependent Landau-Ginzburg equation, admitting scale-invariant solutions
{\textit{\`a la}} Lifshitz and Slyozov. The constraint results here from a
mechanism of fast cycling of molecules between a cytosolic, inactive state and
a membrane-bound, active state, which dynamically tunes the chemical potential
for membrane binding to a value corresponding to the coexistence of different
phases on the cell membrane. We provide here a universal description of this
process both in the presence and absence of a gradient in the external
activation field. Universal power laws are derived for the time needed for the
cell to polarize in a chemotactic gradient, and for the value of the smallest
detectable gradient. We also describe a concrete realization of our scheme
based on the analysis of available biochemical and biophysical data.Comment: Submitted to Journal of Statistical Mechanics -Theory and Experiment
Analytical Solution of a Stochastic Content Based Network Model
We define and completely solve a content-based directed network whose nodes
consist of random words and an adjacency rule involving perfect or approximate
matches, for an alphabet with an arbitrary number of letters. The analytic
expression for the out-degree distribution shows a crossover from a leading
power law behavior to a log-periodic regime bounded by a different power law
decay. The leading exponents in the two regions have a weak dependence on the
mean word length, and an even weaker dependence on the alphabet size. The
in-degree distribution, on the other hand, is much narrower and does not show
scaling behavior. The results might be of interest for understanding the
emergence of genomic interaction networks, which rely, to a large extent, on
mechanisms based on sequence matching, and exhibit similar global features to
those found here.Comment: 13 pages, 5 figures. Rewrote conclusions regarding the relevance to
gene regulation networks, fixed minor errors and replaced fig. 4. Main body
of paper (model and calculations) remains unchanged. Submitted for
publicatio
Rheology of Active-Particle Suspensions
We study the interplay of activity, order and flow through a set of
coarse-grained equations governing the hydrodynamic velocity, concentration and
stress fields in a suspension of active, energy-dissipating particles. We make
several predictions for the rheology of such systems, which can be tested on
bacterial suspensions, cell extracts with motors and filaments, or artificial
machines in a fluid. The phenomena of cytoplasmic streaming, elastotaxis and
active mechanosensing find natural explanations within our model.Comment: 3 eps figures, submitted to Phys Rev Let
Fission of a multiphase membrane tube
A common mechanism for intracellular transport is the use of controlled
deformations of the membrane to create spherical or tubular buds. While the
basic physical properties of homogeneous membranes are relatively well-known,
the effects of inhomogeneities within membranes are very much an active field
of study. Membrane domains enriched in certain lipids in particular are
attracting much attention, and in this Letter we investigate the effect of such
domains on the shape and fate of membrane tubes. Recent experiments have
demonstrated that forced lipid phase separation can trigger tube fission, and
we demonstrate how this can be understood purely from the difference in elastic
constants between the domains. Moreover, the proposed model predicts timescales
for fission that agree well with experimental findings
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