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 $g_0$ to some maximum value $g_m$ that lies above the phase boundary and then decreased back again to $g_{0}$. 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 $\sigma^2$ of the tube length follows in the early-time regime a simple universal power law $\sigma^2 = A \sqrt{t}$ originating in the diffusive motion of the polymer segments. The amplitude $A$ 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 $P(t)$ that a given site remains unvisited by any of a set of random walkers in $d$ dimensions undergoing the reaction $A+A\to0$ when they meet. We find that asymptotically $P(t)\sim t^{-\theta}$ with a universal exponent \theta=\ffrac12-O(\epsilon) for $d=2-\epsilon$, while, for $d>2$, $\theta$ is non-universal and depends on the reaction rate. The analysis, which uses field-theoretic renormalisation group methods, is also applied to the reaction $kA\to0$ with $k>2$. In this case, a stretched exponential behaviour is found for all $d\geq1$, except in the case $k=3$, $d=1$, where P(t)\sim {\rm e}^{-\const (\ln t)^{3/2}}.Comment: 10 pages, (revised version with abstract included) OUTP-94-35