9,676 research outputs found
Hysteresis and nonequilibrium work theorem for DNA unzipping
We study by using Monte Carlo simulations the hysteresis in unzipping and
rezipping of a double stranded DNA (dsDNA) by pulling its strands in opposite
directions in the fixed force ensemble. The force is increased, at a constant
rate from an initial value to some maximum value that lies above
the phase boundary and then decreased back again to . We observed
hysteresis during a complete cycle of unzipping and rezipping. We obtained
probability distributions of work performed over a cycle of unzipping and
rezipping for various pulling rates. The mean of the distribution is found to
be close (the difference being within 10%, except for very fast pulling) to the
area of the hysteresis loop. We extract the equilibrium force versus separation
isotherm by using the work theorem on repeated non-equilibrium force
measurements. Our method is capable of reproducing the equilibrium and the
non-equilibrium force-separation isotherms for the spontaneous rezipping of
dsDNA.Comment: 8 figures, Final version to appear in Physical Review
Monoidal Hom-Hopf algebras
Hom-structures (Lie algebras, algebras, coalgebras, Hopf algebras) have been
investigated in the literature recently. We study Hom-structures from the point
of view of monoidal categories; in particular, we introduce a symmetric
monoidal category such that Hom-algebras coincide with algebras in this
monoidal category, and similar properties for coalgebras, Hopf algebras and Lie
algebras.Comment: 25 pages; extended version: compared to the version that appeared in
Comm. Algebra, the Section Preliminary Results and Remarks 5.1 and 6.1 have
been adde
Non-equilibrium tube length fluctuations of entangled polymers
We investigate the nonequilibrium tube length fluctuations during the
relaxation of an initially stretched, entangled polymer chain. The
time-dependent variance of the tube length follows in the early-time
regime a simple universal power law originating in the
diffusive motion of the polymer segments. The amplitude is calculated
analytically both from standard reptation theory and from an exactly solvable
lattice gas model for reptation and its dependence on the initial and
equilibrium tube length respectively is discussed. The non-universality
suggests the measurement of the fluctuations (e.g. using flourescence
microscopy) as a test for reptation models.Comment: 12 pages, 2 figures. Minor typos correcte
A non-monotonic constitutive model is not necessary to obtain shear banding phenomena in entangled polymer solutions
In 1975 Doi and Edwards predicted that entangled polymer melts and solutions
can have a constitutive instability, signified by a decreasing stress for shear
rates greater than the inverse of the reptation time. Experiments did not
support this, and more sophisticated theories incorporated Marrucci's idea
(1996) of removing constraints by advection; this produced a monotonically
increasing stress and thus stable constitutive behavior. Recent experiments
have suggested that entangled polymer solutions may possess a constitutive
instability after all, and have led some workers to question the validity of
existing constitutive models. In this Letter we use a simple modern
constitutive model for entangled polymers, the non-stretching Rolie-Poly model
with an added solvent viscosity, and show that (1) instability and shear
banding is captured within this simple class of models; (2) shear banding
phenomena is observable for weakly stable fluids in flow geometries that impose
a sufficiently inhomogeneous total shear stress; (3) transient phenomena can
possess inhomogeneities that resemble shear banding, even for weakly stable
fluids. Many of these results are model-independent.Comment: 5 figure
Proportion of Unaffected Sites in a Reaction-Diffusion Process
We consider the probability that a given site remains unvisited by any
of a set of random walkers in dimensions undergoing the reaction
when they meet. We find that asymptotically with a
universal exponent \theta=\ffrac12-O(\epsilon) for , while, for
, is non-universal and depends on the reaction rate. The
analysis, which uses field-theoretic renormalisation group methods, is also
applied to the reaction with . In this case, a stretched
exponential behaviour is found for all , except in the case ,
, where P(t)\sim {\rm e}^{-\const (\ln t)^{3/2}}.Comment: 10 pages, (revised version with abstract included) OUTP-94-35
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