447 research outputs found
Dynamics of Molecular Motors and Polymer Translocation with Sequence Heterogeneity
The effect of sequence heterogeneity on polynucleotide translocation across a
pore and on simple models of molecular motors such as helicases, DNA
polymerase/exonuclease and RNA polymerase is studied in detail. Pore
translocation of RNA or DNA is biased due to the different chemical
environments on the two sides of the membrane, while the molecular motor motion
is biased through a coupling to chemical energy. An externally applied force
can oppose these biases. For both systems we solve lattice models exactly both
with and without disorder. The models incorporate explicitly the coupling to
the different chemical environments for polymer translocation and the coupling
to the chemical energy (as well as nucleotide pairing energies) for molecular
motors. Using the exact solutions and general arguments we show that the
heterogeneity leads to anomalous dynamics. Most notably, over a range of forces
around the stall force (or stall tension for DNA polymerase/exonuclease
systems) the displacement grows sublinearly as t^\mu with \mu<1. The range over
which this behavior can be observed experimentally is estimated for several
systems and argued to be detectable for appropriate forces and buffers. Similar
sequence heterogeneity effects may arise in the packing of viral DNA.Comment: 42 pages, 12 figure
Unzipping flux lines from extended defects in type-II superconductors
With magnetic force microscopy in mind, we study the unbinding transition of
individual flux lines from extended defects like columnar pins and twin planes
in type II superconductors. In the presence of point disorder, the transition
is universal with an exponent which depends only on the dimensionality of the
extended defect. We also consider the unbinding transition of a single vortex
line from a twin plane occupied by other vortices. We show that the critical
properties of this transition depend strongly on the Luttinger liquid parameter
which describes the long distance physics of the two-dimensional flux line
array.Comment: 5 pages, 4 figure
Coarsening of a Class of Driven Striped Structures
The coarsening process in a class of driven systems exhibiting striped
structures is studied. The dynamics is governed by the motion of the driven
interfaces between the stripes. When two interfaces meet they coalesce thus
giving rise to a coarsening process in which l(t), the average width of a
stripe, grows with time. This is a generalization of the reaction-diffusion
process A + A -> A to the case of extended coalescing objects, namely, the
interfaces. Scaling arguments which relate the coarsening process to the
evolution of a single driven interface are given, yielding growth laws for
l(t), for both short and long time. We introduce a simple microscopic model for
this process. Numerical simulations of the model confirm the scaling picture
and growth laws. The results are compared to the case where the stripes are not
driven and different growth laws arise
Slow Coarsening in a Class of Driven Systems
The coarsening process in a class of driven systems is studied. These systems
have previously been shown to exhibit phase separation and slow coarsening in
one dimension. We consider generalizations of this class of models to higher
dimensions. In particular we study a system of three types of particles that
diffuse under local conserving dynamics in two dimensions. Arguments and
numerical studies are presented indicating that the coarsening process in any
number of dimensions is logarithmically slow in time. A key feature of this
behavior is that the interfaces separating the various growing domains are
smooth (well approximated by a Fermi function). This implies that the
coarsening mechanism in one dimension is readily extendible to higher
dimensions.Comment: submitted to EPJB, 13 page
Phase transition in a non-conserving driven diffusive system
An asymmetric exclusion process comprising positive particles, negative
particles and vacancies is introduced. The model is defined on a ring and the
dynamics does not conserve the number of particles. We solve the steady state
exactly and show that it can exhibit a continuous phase transition in which the
density of vacancies decreases to zero. The model has no absorbing state and
furnishes an example of a one-dimensional phase transition in a homogeneous
non-conserving system which does not belong to the absorbing state universality
classes
Solitons in the Yakushevich model of DNA beyond the contact approximation
The Yakushevich model of DNA torsion dynamics supports soliton solutions,
which are supposed to be of special interest for DNA transcription. In the
discussion of the model, one usually adopts the approximation ,
where is a parameter related to the equilibrium distance between bases
in a Watson-Crick pair. Here we analyze the Yakushevich model without . The model still supports soliton solutions indexed by two winding
numbers ; we discuss in detail the fundamental solitons, corresponding
to winding numbers (1,0) and (0,1) respectively
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