664 research outputs found
Denaturation of Heterogeneous DNA
The effect of heterogeneous sequence composition on the denaturation of
double stranded DNA is investigated. The resulting pair-binding energy
variation is found to have a negligible effect on the critical properties of
the smooth second order melting transition in the simplest (Peyrard-Bishop)
model. However, sequence heterogeneity is dramatically amplified upon adopting
a more realistic treatment of the backbone stiffness. The model yields features
of ``multi-step melting'' similar to those observed in experiments.Comment: 4 pages, LaTeX, text and figures also available at
http://matisse.ucsd.edu/~hw
Dynamics of Counterion Condensation
Using a generalization of the Poisson-Boltzmann equation, dynamics of
counterion condensation is studied. For a single charged plate in the presence
of counterions, it is shown that the approach to equilibrium is diffusive. In
the far from equilibrium case of a moving charged plate, a dynamical counterion
condensation transition occurs at a critical velocity. The complex dynamic
behavior of the counterion cloud is shown to lead to a novel nonlinear
force-velocity relation for the moving plate.Comment: 5 pages, 1 ps figure included using eps
A new bond fluctuation method for a polymer undergoing gel electrophoresis
We present a new computational methodology for the investigation of gel
electrophoresis of polyelectrolytes. We have developed the method initially to
incorporate sliding motion of tight parts of a polymer pulled by an electric
field into the bond fluctuation method (BFM). Such motion due to tensile force
over distances much larger than the persistent length is realized by non-local
movement of a slack monomer at an either end of the tight part. The latter
movement is introduced stochastically. This new BFM overcomes the well-known
difficulty in the conventional BFM that polymers are trapped by gel fibers in
relatively large fields. At the same time it also reproduces properly
equilibrium properties of a polymer in a vanishing filed limit. The new BFM
thus turns out an efficient computational method to study gel electrophoresis
in a wide range of the electric field strength.Comment: 15 pages, 11 figure
Formation of helical states in wormlike polymer chains
We propose a potential for wormlike polymer chains which can be used to model
the low-temperature conformational structures. We successfully reproduced helix
ground states up to 6.5 helical loops, using the multicanonical Monte Carlo
simulation method. We demonstrate that the coil-helix transition involves four
distinct phases: coil(gaslike), collapsed globular(liquidlike), and two helical
phases I and II (both solidlike). The helix I phase is characterized by a
helical structure with dangling loose ends, and the helix II phase corresponds
to a near perfect helix ordering in the entire crystallized chain.Comment: 5 pages, 2 figures, Submitted to PR
Scaling and Universality in the Counterion-Condensation Transition at Charged Cylinders
We address the critical and universal aspects of counterion-condensation
transition at a single charged cylinder in both two and three spatial
dimensions using numerical and analytical methods. By introducing a novel
Monte-Carlo sampling method in logarithmic radial scale, we are able to
numerically simulate the critical limit of infinite system size (corresponding
to infinite-dilution limit) within tractable equilibration times. The critical
exponents are determined for the inverse moments of the counterionic density
profile (which play the role of the order parameters and represent the inverse
localization length of counterions) both within mean-field theory and within
Monte-Carlo simulations. In three dimensions (3D), correlation effects
(neglected within mean-field theory) lead to an excessive accumulation of
counterions near the charged cylinder below the critical temperature
(condensation phase), while surprisingly, the critical region exhibits
universal critical exponents in accord with the mean-field theory. In two
dimensions (2D), we demonstrate, using both numerical and analytical
approaches, that the mean-field theory becomes exact at all temperatures
(Manning parameters), when number of counterions tends to infinity. For finite
particle number, however, the 2D problem displays a series of peculiar singular
points (with diverging heat capacity), which reflect successive de-localization
events of individual counterions from the central cylinder. In both 2D and 3D,
the heat capacity shows a universal jump at the critical point, and the energy
develops a pronounced peak. The asymptotic behavior of the energy peak location
is used to locate the critical temperature, which is also found to be universal
and in accordance with the mean-field prediction.Comment: 31 pages, 16 figure
Polymer Induced Bundling of F-actin and the Depletion Force
The inert polymer polyethylene glycol (PEG) induces a "bundling" phenomenon
in F-actin solutions when its concentration exceeds a critical onset value C_o.
Over a limited range of PEG molecular weight and ionic strength, C_o can be
expressed as a function of these two variables. The process is reversible, but
hysteresis is also observed in the dissolution of the bundles, with ionic
strength having a large influence. Additional actin filaments are able to join
previously formed bundles. Little, if any, polymer is associated with the
bundle structure.
Continuum estimates of the Asakura-Oosawa depletion force, Coulomb repulsion,
and van der Waals potential are combined for a partial explanation of the
bundling effect and hysteresis. Conjectures are presented concerning the
apparent limit in bundle size
Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation
The paper uses mesoscopic, non-linear lattice dynamics based
(Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA
below and near the denaturation temperature. Computationally efficient notation
is introduced for the relevant statistical mechanics. Computed melting profiles
of long and short heterogeneous sequences are presented, using a recently
introduced reparametrization of the PBD model, and critically discussed. The
statistics of extended open bubbles and bound clusters is formulated and
results are presented for selected examples.Comment: to appear in a special issue of the Journal of Nonlinear Mathematical
Physics (ed. G. Gaeta
Reconstruction of a first-order phase transition from computer simulations of individual phases and subphases
We present a new method for investigating first-order phase transitions using
Monte Carlo simulations. It relies on the multiple-histogram method and uses
solely histograms of individual phases. In addition, we extend the method to
include histograms of subphases. The free energy difference between phases,
necessary for attributing the correct statistical weights to the histograms, is
determined by a detour in control parameter space via auxiliary systems with
short relaxation times. We apply this method to a recently introduced model for
structure formation in polypeptides for which other methods fail.Comment: 13 pages in preprint mode, REVTeX, 2 Figures available from the
authors ([email protected], [email protected]
Lateral Separation of Macromolecules and Polyelectrolytes in Microlithographic Arrays
A new approach to separation of a variety of microscopic and mesoscopic
objects in dilute solution is presented. The approach takes advantage of unique
properties of a specially designed separation device (sieve), which can be
readily built using already developed microlithographic techniques. Due to the
broken reflection symmetry in its design, the direction of motion of an object
in the sieve varies as a function of its self-diffusion constant, causing
separation transverse to its direction of motion. This gives the device some
significant and unique advantages over existing fractionation methods based on
centrifugation and electrophoresis.Comment: 4 pages with 3 eps figures, needs RevTeX 3.0 and epsf, also available
in postscript form http://cmtw.harvard.edu/~deniz
Gel-Electrophoresis and Diffusion of Ring-Shaped DNA
A model for the motion of ring-shaped DNA in a gel is introduced and studied
by numerical simulations and a mean-field approximation. The ring motion is
mediated by finger-shaped loops (hernias) that move in an amoeba-like fashion
around the gel obstructions. This constitutes an extension of previous
reptation tube treatments. It is shown that tension is essential for describing
the dynamics in the presence of hernias. It is included in the model as long
range interactions over stretched DNA regions. The mobility of ring-shaped DNA
is found to saturate much as in the well-studied case of linear DNA.
Experiments in polymer gels, however, show that the mobility drops
exponentially with the DNA ring size. This is commonly attributed to
dangling-ends in the gel that can impale the ring. The predictions of the
present model are expected to apply to artificial 2D obstacle arrays (W.D.
Volkmuth, R.H. Austin, Nature 358,600 (1992)) which have no dangling-ends. In
the zero-field case an exact solution of the model steady-state is obtained,
and quantities such as the average ring size are calculated. An approximate
treatment of the ring dynamics is given, and the diffusion coefficient is
derived. The model is also discussed in the context of spontaneous symmetry
breaking in one dimension.Comment: 8 figures, LaTeX, Phys. Rev. E - in pres
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