2,225 research outputs found
DNA Spools under Tension
DNA-spools, structures in which DNA is wrapped and helically coiled onto
itself or onto a protein core are ubiquitous in nature. We develop a general
theory describing the non-equilibrium behavior of DNA-spools under linear
tension. Two puzzling and seemingly unrelated recent experimental findings, the
sudden quantized unwrapping of nucleosomes and that of DNA toroidal condensates
under tension are theoretically explained and shown to be of the same origin.
The study provides new insights into nucleosome and chromatin fiber stability
and dynamics
Facet Formation in the Negative Quenched Kardar-Parisi-Zhang Equation
The quenched Kardar-Parisi-Zhang (QKPZ) equation with negative non-linear
term shows a first order pinning-depinning (PD) transition as the driving force
is varied. We study the substrate-tilt dependence of the dynamic transition
properties in 1+1 dimensions. At the PD transition, the pinned surfaces form a
facet with a characteristic slope as long as the substrate-tilt is
less than . When , the transition is discontinuous and the critical
value of the driving force is independent of , while the transition
is continuous and increases with when . We explain these
features from a pinning mechanism involving a localized pinning center and the
self-organized facet formation.Comment: 4 pages, source TeX file and 7 PS figures are tarred and compressed
via uufile
Molecular Weight Dependence of Spreading Rates of Ultrathin Polymeric Films
We study experimentally the molecular weight dependence of spreading
rates of molecularly thin precursor films, growing at the bottom of droplets of
polymer liquids. In accord with previous observations, we find that the radial
extension R(t) of the film grows with time as R(t) = (D_{exp} t)^{1/2}. Our
data substantiate the M-dependence of D_{exp}; we show that it follows D_{exp}
\sim M^{-\gamma}, where the exponent \gamma is dependent on the chemical
composition of the solid surface, determining its frictional properties with
respect to the molecular transport. In the specific case of hydrophilic
substrates, the frictional properties can be modified by the change of the
relative humidity (RH). We find that \gamma \approx 1 at low RH and tends to
zero when RH gets progressively increased. We propose simple theoretical
arguments which explain the observed behavior in the limits of low and high RH.Comment: 4 pages, 2 figures, to appear in PR
Angles from Decays with Charm
Proceedings of the CKM 2005 Workshop (WG5), UC San Diego, 15-18 March 2005.Comment: 62 pages, 55 figures. Proceedings of the CKM 2005 Workshop (WG5), UC
San Diego, 15-18 March 200
Fluctuation-Facilitated Charge Migration along DNA
We propose a model Hamiltonian for charge transfer along the DNA double helix
with temperature driven fluctuations in the base pair positions acting as the
rate limiting factor for charge transfer between neighboring base pairs. We
compare the predictions of the model with the recent work of J.K. Barton and
A.H. Zewail (Proc.Natl.Acad.Sci.USA, {\bf 96}, 6014 (1999)) on the unusual
two-stage charge transfer of DNA.Comment: 4 pages, 2 figure
Nonequilibrium dynamics of random field Ising spin chains: exact results via real space RG
Non-equilibrium dynamics of classical random Ising spin chains are studied
using asymptotically exact real space renormalization group. Specifically the
random field Ising model with and without an applied field (and the Ising spin
glass (SG) in a field), in the universal regime of a large Imry Ma length so
that coarsening of domains after a quench occurs over large scales. Two types
of domain walls diffuse in opposite Sinai random potentials and mutually
annihilate. The domain walls converge rapidly to a set of system-specific
time-dependent positions {\it independent of the initial conditions}. We obtain
the time dependent energy, magnetization and domain size distribution
(statistically independent). The equilibrium limits agree with known exact
results. We obtain exact scaling forms for two-point equal time correlation and
two-time autocorrelations. We also compute the persistence properties of a
single spin, of local magnetization, and of domains. The analogous quantities
for the spin glass are obtained. We compute the two-point two-time correlation
which can be measured by experiments on spin-glass like systems. Thermal
fluctuations are found to be dominated by rare events; all moments of truncated
correlations are computed. The response to a small field applied after waiting
time , as measured in aging experiments, and the fluctuation-dissipation
ratio are computed. For ,
, it equals its equilibrium value X=1, though time
translational invariance fails. It exhibits for aging regime
with non-trivial , different from mean field.Comment: 55 pages, 9 figures, revte
Vibrational Enhancement of the Effective Donor - Acceptor Coupling
The paper deals with a simple three sites model for charge transfer phenomena
in an one-dimensional donor (D) - bridge (B) - acceptor (A) system coupled with
vibrational dynamics of the B site. It is found that in a certain range of
parameters the vibrational coupling leads to an enhancement of the effective
donor - acceptor electronic coupling as a result of the formation of the
polaron on the B site. This enhancement of the charge transfer efficiency is
maximum at the resonance, where the effective energy of the fluctuating B site
coincides with the donor (acceptor) energy.Comment: 5 pages, 3 figure
The depinning transition of a driven interface in the random-field Ising model around the upper critical dimension
We investigate the depinning transition for driven interfaces in the
random-field Ising model for various dimensions. We consider the order
parameter as a function of the control parameter (driving field) and examine
the effect of thermal fluctuations. Although thermal fluctuations drive the
system away from criticality the order parameter obeys a certain scaling law
for sufficiently low temperatures and the corresponding exponents are
determined. Our results suggest that the so-called upper critical dimension of
the depinning transition is five and that the systems belongs to the
universality class of the quenched Edward-Wilkinson equation.Comment: accepted for publication in Phys. Rev.
Dynamic Scaling of Ion-Sputtered Surfaces
We derive a stochastic nonlinear equation to describe the evolution and
scaling properties of surfaces eroded by ion bombardment. The coefficients
appearing in the equation can be calculated explicitly in terms of the physical
parameters characterizing the sputtering process. We find that transitions may
take place between various scaling behaviors when experimental parameters such
as the angle of incidence of the incoming ions or their average penetration
depth, are varied.Comment: 13 pages, Revtex, 2 figure
Intermittency in Dynamics of Two-Dimensional Vortex-like Defects
We examine high-order dynamical correlations of defects (vortices,
disclinations etc) in thin films starting from the Langevin equation for the
defect motion. We demonstrate that dynamical correlation functions of
vorticity and disclinicity behave as where is the
characteristic scale and is the fugacity. As a consequence, below the
Berezinskii-Kosterlitz-Thouless transition temperature are
characterized by anomalous scaling exponents. The behavior strongly differs
from the normal law occurring for simultaneous correlation
functions, the non-simultaneous correlation functions appear to be much larger.
The phenomenon resembles intermittency in turbulence.Comment: 30 pages, 11 figure
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