201 research outputs found
Interfaces of Modulated Phases
Numerically minimizing a continuous free-energy functional which yields
several modulated phases, we obtain the order-parameter profiles and
interfacial free energies of symmetric and non-symmetric tilt boundaries within
the lamellar phase, and of interfaces between coexisting lamellar, hexagonal,
and disordered phases. Our findings agree well with chevron, omega, and
T-junction tilt-boundary morphologies observed in diblock copolymers and
magnetic garnet films.Comment: 4 page
Fluctuation spectrum of fluid membranes coupled to an elastic meshwork: jump of the effective surface tension at the mesh size
We identify a class of composite membranes: fluid bilayers coupled to an
elastic meshwork, that are such that the meshwork's energy is a function
\textit{not} of the real microscopic membrane area ,
but of a \textit{smoothed} membrane's area , which corresponds to the
area of the membrane coarse-grained at the mesh size . We show that the
meshwork modifies the membrane tension both below and above the scale
, inducing a tension-jump . The
predictions of our model account for the fluctuation spectrum of red blood
cells membranes coupled to their cytoskeleton. Our results indicate that the
cytoskeleton might be under extensional stress, which would provide a means to
regulate available membrane area. We also predict an observable tension jump
for membranes decorated with polymer "brushes"
A twist in chiral interaction between biological helices
Using an exact solution for the pair interaction potential, we show that
long, rigid, chiral molecules with helical surface charge patterns have a
preferential interaxial angle ~((RH)^1/2)/L, where L is the length of the
molecules, R is the closest distance between their axes, and H is the helical
pitch. Estimates based on this formula suggest a solution for the puzzle of
small interaxial angles in a-helix bundles and in cholesteric phases of DNA.Comment: 7 pages, 2 figures, PDF file onl
Metastable liquid lamellar structures in binary and ternary mixtures of Lennard-Jones fluids
We have carried out extensive equilibrium molecular dynamics (MD) simulations
to investigate the Liquid-Vapor coexistence in partially miscible binary and
ternary mixtures of Lennard-Jones (LJ) fluids. We have studied in detail the
time evolution of the density profiles and the interfacial properties in a
temperature region of the phase diagram where the condensed phase is demixed.
The composition of the mixtures are fixed, 50% for the binary mixture and
33.33% for the ternary mixture. The results of the simulations clearly indicate
that in the range of temperatures K, --in the scale of
argon-- the system evolves towards a metastable alternated liquid-liquid
lamellar state in coexistence with its vapor phase. These states can be
achieved if the initial configuration is fully disordered, that is, when the
particles of the fluids are randomly placed on the sites of an FCC crystal or
the system is completely mixed. As temperature decreases these states become
very well defined and more stables in time. We find that below K,
the alternated liquid-liquid lamellar state remains alive for 80 ns, in the
scale of argon, the longest simulation we have carried out. Nonetheless, we
believe that in this temperature region these states will be alive for even
much longer times.Comment: 18 Latex-RevTex pages including 12 encapsulated postscript figures.
Figures with better resolution available upon request. Accepted for
publication in Phys. Rev. E Dec. 1st issu
Phase Behavior of Columnar DNA Assemblies
The pair interaction between two stiff parallel linear DNA molecules depends
not only on the distance between their axes but on their azimuthal orientation.
The positional and orientational order in columnar B-DNA assemblies in solution
is investigated, based on the DNA-DNA electrostatic pair potential that takes
into account DNA helical symmetry and the amount and distribution of adsorbed
counterions. A phase diagram obtained by lattice sum calculations predicts a
variety of positionally and azimuthally ordered phases and bundling transitions
strongly depending on the counterion adsorption patterns.Comment: 4 pages, 3 figures, submitted to PR
Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties
Advanced Monte Carlo simulations are used to study the effect of nano-slit
confinement on metric and topological properties of model DNA chains. We
consider both linear and circularised chains with contour lengths in the
1.2--4.8 m range and slits widths spanning continuously the 50--1250nm
range. The metric scaling predicted by de Gennes' blob model is shown to hold
for both linear and circularised DNA up to the strongest levels of confinement.
More notably, the topological properties of the circularised DNA molecules have
two major differences compared to three-dimensional confinement. First, the
overall knotting probability is non-monotonic for increasing confinement and
can be largely enhanced or suppressed compared to the bulk case by simply
varying the slit width. Secondly, the knot population consists of knots that
are far simpler than for three-dimensional confinement. The results suggest
that nano-slits could be used in nano-fluidic setups to produce DNA rings
having simple topologies (including the unknot) or to separate heterogeneous
ensembles of DNA rings by knot type.Comment: 12 pages, 10 figure
Homogeneous Bubble Nucleation driven by local hot spots: a Molecular Dynamics Study
We report a Molecular Dynamics study of homogenous bubble nucleation in a
Lennard-Jones fluid. The rate of bubble nucleation is estimated using
forward-flux sampling (FFS). We find that cavitation starts with compact
bubbles rather than with ramified structures as had been suggested by Shen and
Debenedetti (J. Chem. Phys. 111:3581, 1999). Our estimate of the
bubble-nucleation rate is higher than predicted on the basis of Classical
Nucleation Theory (CNT). Our simulations show that local temperature
fluctuations correlate strongly with subsequent bubble formation - this
mechanism is not taken into account in CNT
Thermodynamics and structure of self-assembled networks
We study a generic model of self-assembling chains which can branch and form
networks with branching points (junctions) of arbitrary functionality. The
physical realizations include physical gels, wormlike micells, dipolar fluids
and microemulsions. The model maps the partition function of a solution of
branched, self-assembling, mutually avoiding clusters onto that of a Heisenberg
magnet in the mathematical limit of zero spin components. The model is solved
in the mean field approximation. It is found that despite the absence of any
specific interaction between the chains, the entropy of the junctions induces
an effective attraction between the monomers, which in the case of three-fold
junctions leads to a first order reentrant phase separation between a dilute
phase consisting mainly of single chains, and a dense network, or two network
phases. Independent of the phase separation, we predict the percolation
(connectivity) transition at which an infinite network is formed that partially
overlaps with the first-order transition. The percolation transition is a
continuous, non thermodynamic transition that describes a change in the
topology of the system. Our treatment which predicts both the thermodynamic
phase equilibria as well as the spatial correlations in the system allows us to
treat both the phase separation and the percolation threshold within the same
framework. The density-density correlation correlation has a usual
Ornstein-Zernicke form at low monomer densities. At higher densities, a peak
emerges in the structure factor, signifying an onset of medium-range order in
the system. Implications of the results for different physical systems are
discussed.Comment: Submitted to Phys. Rev.
Equation of state for polymer liquid crystals: theory and experiment
The first part of this paper develops a theory for the free energy of
lyotropic polymer nematic liquid crystals. We use a continuum model with
macroscopic elastic moduli for a polymer nematic phase. By evaluating the
partition function, considering only harmonic fluctuations, we derive an
expression for the free energy of the system. We find that the configurational
entropic part of the free energy enhances the effective repulsive interactions
between the chains. This configurational contribution goes as the fourth root
of the direct interactions. Enhancement originates from the coupling between
bending fluctuations and the compressibility of the nematic array normal to the
average director. In the second part of the paper we use osmotic stress to
measure the equation of state for DNA liquid crystals in 0.1M to 1M NaCl
solutions. These measurements cover 5 orders of magnitude in DNA osmotic
pressure. At high osmotic pressures the equation of state, dominated by
exponentially decaying hydration repulsion, is independent of the ionic
strength. At lower pressures the equation of state is dominated by fluctuation
enhanced electrostatic double layer repulsion. The measured equation of state
for DNA fits well with our theory for all salt concentrations. We are able to
extract the strength of the direct electrostatic double layer repulsion. This
is a new and alternative way of measuring effective charge densities along
semiflexible polyelectrolytes.Comment: text + 5 figures. Submitted to PR
Effective interaction between helical bio-molecules
The effective interaction between two parallel strands of helical
bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using
computer simulations of the "primitive" model of electrolytes. In particular we
study a simple model for B-DNA incorporating explicitly its charge pattern as a
double-helix structure. The effective force and the effective torque exerted
onto the molecules depend on the central distance and on the relative
orientation. The contributions of nonlinear screening by monovalent counterions
to these forces and torques are analyzed and calculated for different salt
concentrations. As a result, we find that the sign of the force depends
sensitively on the relative orientation. For intermolecular distances smaller
than it can be both attractive and repulsive. Furthermore we report a
nonmonotonic behaviour of the effective force for increasing salt
concentration. Both features cannot be described within linear screening
theories. For large distances, on the other hand, the results agree with linear
screening theories provided the charge of the bio-molecules is suitably
renormalized.Comment: 18 pages, 18 figures included in text, 100 bibliog
- …