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

Kinetic Regimes and Cross-Over Times in Many-Particle Reacting Systems

We study kinetics of single species reactions ("A+A -> 0") for general local reactivity Q and dynamical exponent z (rms displacement x_t ~ t^{1/z}.) For small molecules z=2, whilst z=4,8 for certain polymer systems. For dimensions d above the critical value d_c=z, kinetics are always mean field (MF). Below d_c, the density n_t initially follows MF decay, n_0 - n_t ~ n_0^2 Q t. A 2-body diffusion-controlled regime follows for strongly reactive systems (Q>Qstar ~ n_0^{(z-d)/d}) with n_0 - n_t ~ n_0^2 x_t^d. For Q<Qstar, MF kinetics persist, with n_t ~ 1/Qt. In all cases n_t ~ 1/x_t^d at the longest times. Our analysis avoids decoupling approximations by instead postulating weak physically motivated bounds on correlation functions.Comment: 10 pages, 1 figure, uses bulk2.sty, minor changes, submitted to Europhysics Letter

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

On the origin of the unusual behavior in the stretching of single-stranded DNA

Force extension curves (FECs), which quantify the response of a variety of biomolecules subject to mechanical force ($f$), are often quantitatively fit using worm-like chain (WLC) or freely-jointed chain (FJC) models. These models predict that the chain extension, $x$, normalized by the contour length increases linearly at small $f$ and at high forces scale as $x \sim (1 - f^{-\alpha})$ where $\alpha$= 0.5 for WLC and unity for FJC. In contrast, experiments on ssDNA show that over a range of $f$ and ionic concentration, $x$ scales as $x\sim\ln f$, which cannot be explained using WLC or FJC models. Using theory and simulations we show that this unusual behavior in FEC in ssDNA is due to sequence-independent polyelectrolyte effects. We show that the $x\sim \ln f$ arises because in the absence of force the tangent correlation function, quantifying chain persistence, decays algebraically on length scales on the order of the Debye length. Our theory, which is most appropriate for monovalent salts, quantitatively fits the experimental data and further predicts that such a regime is not discernible in double stranded DNA.Comment: Accepted for publication in JC

Directional motion of forced polymer chains with hydrodynamic interaction

We study the propulsion of a one-dimensional (1D) polymer chain under sinusoidal external forces in the overdamped (low Reynolds number) regime. We show that, when hydrodynamical interactions are included, the polymer presents directional motion which depends on the phase differences of the external force applied along the chain. Moreover, the velocity shows a maximum as a function of the frequency. We discuss the relevance of all these results in light of recent nanotechnology experiments.Comment: 5 pages, 6 figure

Boundary Condition of Polyelectrolyte Adsorption

The modification of the boundary condition for polyelectrolyte adsorption on charged surface with short-ranged interaction is investigated under two regimes. For weakly charged Gaussian polymer in which the short-ranged attraction dominates, the boundary condition is the same as that of the neutral polymer adsorption. For highly charged polymer (compressed state) in which the electrostatic interaction dominates, the linear relationship (electrostatic boundary condition) between the surface monomer density and the surface charge density needs to be modified.Comment: 4 page

The A+B -> 0 annihilation reaction in a quenched random velocity field

Using field-theoretic renormalization group methods the long-time behaviour of the A+B -> 0 annihilation reaction with equal initial densities n_A(0) = n_B(0) = n_0 in a quenched random velocity field is studied. At every point (x, y) of a d-dimensional system the velocity v is parallel or antiparallel to the x-axis and depends on the coordinates perpendicular to the flow. Assuming that v(y) have zero mean and short-range correlations in the y-direction we show that the densities decay asymptotically as n(t) ~ A n_0^(1/2) t^(-(d+3)/8) for d<3. The universal amplitude A is calculated at first order in \epsilon = 3-d.Comment: 19 pages, LaTeX using IOP-macros, 5 eps-figures. It is shown that the amplitude of the density is universal, i.e. independent of the reaction rat

Path integrals for stiff polymers applied to membrane physics

Path integrals similar to those describing stiff polymers arise in the Helfrich model for membranes. We show how these types of path integrals can be evaluated and apply our results to study the thermodynamics of a minority stripe phase in a bulk membrane. The fluctuation induced contribution to the line tension between the stripe and the bulk phase is computed, as well as the effective interaction between the two phases in the tensionless case where the two phases have differing bending rigidities.Comment: 11 pages RevTex, 4 figure

A Laplace Transform Method for Molecular Mass Distribution Calculation from Rheometric Data

Polydisperse linear polymer melts can be microscopically described by the tube model and fractal reptation dynamics, while on the macroscopic side the generalized Maxwell model is capable of correctly displaying most of the rheological behavior. In this paper, a Laplace transform method is derived and different macroscopic starting points for molecular mass distribution calculation are compared to a classical light scattering evaluation. The underlying assumptions comprise the modern understanding on polymer dynamics in entangled systems but can be stated in a mathematically generalized way. The resulting method is very easy to use due to its mathematical structure and it is capable of calculating multimodal molecular mass distributions of linear polymer melts

Classification of graph C*-algebras with no more than four primitive ideals

We describe the status quo of the classification problem of graph C*-algebras with four primitive ideals or less