66 research outputs found
Statistical mechanics of base stacking and pairing in DNA melting
We propose a statistical mechanics model for DNA melting in which base
stacking and pairing are explicitly introduced as distinct degrees of freedom.
Unlike previous approaches, this model describes thermal denaturation of DNA
secondary structure in the whole experimentally accessible temperature range.
Base pairing is described through a zipper model, base stacking through an
Ising model. We present experimental data on the unstacking transition,
obtained exploiting the observation that at moderately low pH this transition
is moved down to experimentally accessible temperatures. These measurements
confirm that the Ising model approach is indeed a good description of base
stacking. On the other hand, comparison with the experiments points to the
limitations of the simple zipper model description of base pairing.Comment: 13 pages with figure
Attractive Interactions Between Rod-like Polyelectrolytes: Polarization, Crystallization, and Packing
We study the attractive interactions between rod-like charged polymers in
solution that appear in the presence of multi-valence counterions. The
counterions condensed to the rods exhibit both a strong transversal
polarization and a longitudinal crystalline arrangement. At short distances
between the rods, the fraction of condensed counterions increases, and the
majority of these occupy the region between the rods, where they minimize their
repulsive interactions by arranging themselves into packing structures. The
attractive interaction is strongest for multivalent counterions. Our model
takes into account the hard-core volume of the condensed counterions and their
angular distribution around the rods. The hard core constraint strongly
suppresses longitudinal charge fluctuations.Comment: 4 figures, uses revtex, psfig and epsf. The new version contains a
different introduction, and the bibliography has been expande
Collapse of a semiflexible polymer in poor solvent
We investigate the dynamics and the pathways of the collapse of a single,
semiflexible polymer in a poor solvent via 3-D Brownian Dynamics simulations.
Earlier work indicates that the condensation of semiflexible polymers
generically proceeds via a cascade through metastable racquet-shaped,
long-lived intermediates towards the stable torus state. We investigate the
rate of decay of uncollapsed states, analyze the preferential pathways of
condensation, and describe likelihood and lifespan of the different metastable
states. The simulation are performed with a bead-stiff spring model with
excluded volume interaction and exponentially decaying attractive potential.
The semiflexible chain collapse is studied as functions of the three relevant
length scales of the phenomenon, i.e., the total chain length , the
persistence length and the condensation length , where is a measure of the attractive potential per unit
length. Two dimensionless ratios, and , suffice to describe
the decay rate of uncollapsed states, which appears to scale as . The condensation sequence is described in terms of the time series
of the well separated energy levels associated with each metastable collapsed
state. The collapsed states are described quantitatively through the spatial
correlation of tangent vectors along the chain. We also compare the results
obtained with a locally inextensible bead-rod chain and with a phantom
bead-spring model. Finally, we show preliminary results on the effects of
steady shear flow on the kinetics of collapse.Comment: 9 pages, 8 figure
The Persistence Length of a Strongly Charged, Rod-like, Polyelectrolyte in the Presence of Salt
The persistence length of a single, intrinsically rigid polyelectrolyte
chain, above the Manning condensation threshold is investigated theoretically
in presence of added salt. Using a loop expansion method, the partition
function is consistently calculated, taking into account corrections to
mean-field theory. Within a mean-field approximation, the well-known results of
Odijk, Skolnick and Fixman are reproduced. Beyond mean-field, it is found that
density correlations between counterions and thermal fluctuations reduce the
stiffness of the chain, indicating an effective attraction between monomers for
highly charged chains and multivalent counterions. This attraction results in a
possible mechanical instability (collapse), alluding to the phenomenon of DNA
condensation. In addition, we find that more counterions condense on slightly
bent conformations of the chain than predicted by the Manning model for the
case of an infinite cylinder. Finally, our results are compared with previous
models and experiments.Comment: 13 pages, 2 ps figure
Charge Fluctuations and Counterion Condensation
We predict a condensation phenomenon in an overall neutral system, consisting
of a single charged plate and its oppositely charged counterions. Based on the
``two-fluid'' model, in which the counterions are divided into a ``free'' and a
``condensed'' fraction, we argue that for high surface charge, fluctuations can
lead to a phase transition in which a large fraction of counterions is
condensed. Furthermore, we show that depending on the valence, the condensation
is either a first-order or a smooth transition.Comment: 16 pages, 1 figure, accepted to be published in PR
Counterion Condensation and Fluctuation-Induced Attraction
We consider an overall neutral system consisting of two similarly charged
plates and their oppositely charged counterions and analyze the electrostatic
interaction between the two surfaces beyond the mean-field Poisson-Boltzmann
approximation. Our physical picture is based on the fluctuation-driven
counterion condensation model, in which a fraction of the counterions is
allowed to ``condense'' onto the charged plates. In addition, an expression for
the pressure is derived, which includes fluctuation contributions of the whole
system. We find that for sufficiently high surface charges, the distance at
which the attraction, arising from charge fluctuations, starts to dominate can
be large compared to the Gouy-Chapmann length. We also demonstrate that
depending on the valency, the system may exhibit a novel first-order binding
transition at short distances.Comment: 15 pages, 8 figures, to appear in PR
Adsorption of mono- and multivalent cat- and anions on DNA molecules
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose
nucleic acid (DNA) molecule from a salt solution is investigated by computer
simulation. The ions are modelled as charged hard spheres, the DNA molecule as
a point charge pattern following the double-helical phosphate strands. The
geometrical shape of the DNA molecules is modelled on different levels ranging
from a simple cylindrical shape to structured models which include the major
and minor grooves between the phosphate strands. The densities of the ions
adsorbed on the phosphate strands, in the major and in the minor grooves are
calculated. First, we find that the adsorption pattern on the DNA surface
depends strongly on its geometrical shape: counterions adsorb preferentially
along the phosphate strands for a cylindrical model shape, but in the minor
groove for a geometrically structured model. Second, we find that an addition
of monovalent salt ions results in an increase of the charge density in the
minor groove while the total charge density of ions adsorbed in the major
groove stays unchanged. The adsorbed ion densities are highly structured along
the minor groove while they are almost smeared along the major groove.
Furthermore, for a fixed amount of added salt, the major groove cationic charge
is independent on the counterion valency. For increasing salt concentration the
major groove is neutralized while the total charge adsorbed in the minor groove
is constant. DNA overcharging is detected for multivalent salt. Simulations for
a larger ion radii, which mimic the effect of the ion hydration, indicate an
increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure
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
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