747 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
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
Deprivations and Inequities in Cities Viewed Through a Pandemic Lens
The COVID-19 pandemic brought a halt to life as we knew it in our cities. It has also put a magnifying glass on existing inequalities and poverty. While everyone has been facing the pandemic's risks, the lived challenges of the lockdowns have been felt most acutely by the poor, the vulnerable, those in the informal sector, and without savings and safety nets. Here, we identify three ways that the COVID-19 pandemic and related containment measures have exacerbated urban inequalities and how subsequent recovery measures and policy responses have tried to redress these. First, lockdowns amplified urban energy poverty, while recovery measures and policies offer an opportunity to address entrenched inequalities in shelter and energy access. Second, preexisting digital divides even within well-connected cities have translated into inequalities in preparedness for living through the lockdown, but digitalization strategies can enhance equity in access to e-services, online work and education for all in the future. Third, slum dwellers in the world's cities have been particularly hard hit by the pandemic and lockdown measures, but the spotlight on them provides further impetus for slum upgradation efforts that through improved access to infrastructure can improve living conditions and provide more secure livelihoods
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
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
Why is the DNA Denaturation Transition First Order?
We study a model for the denaturation transition of DNA in which the
molecules are considered as composed of a sequence of alternating bound
segments and denaturated loops. We take into account the excluded-volume
interactions between denaturated loops and the rest of the chain by exploiting
recent results on scaling properties of polymer networks of arbitrary topology.
The phase transition is found to be first order in d=2 dimensions and above, in
agreement with experiments and at variance with previous theoretical results,
in which only excluded-volume interactions within denaturated loops were taken
into account. Our results agree with recent numerical simulations.Comment: Revised version. To appear in Phys. Rev. Let
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
A Simple Model for the DNA Denaturation Transition
We study pairs of interacting self-avoiding walks on the 3d simple cubic
lattice. They have a common origin and are allowed to overlap only at the same
monomer position along the chain. The latter overlaps are indeed favored by an
energetic gain.
This is inspired by a model introduced long ago by Poland and Sheraga [J.
Chem. Phys. {\bf 45}, 1464 (1966)] for the denaturation transition in DNA
where, however, self avoidance was not fully taken into account. For both
models, there exists a temperature T_m above which the entropic advantage to
open up overcomes the energy gained by forming tightly bound two-stranded
structures.
Numerical simulations of our model indicate that the transition is of first
order (the energy density is discontinuous), but the analog of the surface
tension vanishes and the scaling laws near the transition point are exactly
those of a second order transition with crossover exponent \phi=1. Numerical
and exact analytic results show that the transition is second order in modified
models where the self-avoidance is partially or completely neglected.Comment: 29 pages, LaTeX, 20 postscript figure
Screening by symmetry of long-range hydrodynamic interactions of polymers confined in sheets
Hydrodynamic forces may significantly affect the motion of polymers. In
sheet-like cavities, such as the cell's cytoplasm and microfluidic channels,
the hydrodynamic forces are long-range. It is therefore expected that that
hydrodynamic interactions will dominate the motion of polymers in sheets and
will be manifested by Zimm-like scaling. Quite the opposite, we note here that
although the hydrodynamic forces are long-range their overall effect on the
motion of polymers vanishes due to the symmetry of the two-dimensional flow. As
a result, the predicted scaling of experimental observables such as the
diffusion coefficient or the rotational diffusion time is Rouse-like, in accord
with recent experiments. The effective screening validates the use of the
non-interacting blobs picture for polymers confined in a sheet.Comment: http://www.weizmann.ac.il/complex/tlusty/papers/Macromolecules2006.pdf
http://pubs.acs.org/doi/abs/10.1021/ma060251
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