Slow nucleic acid unzipping kinetics from sequence-defined barriers

Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al., Science 297, 733-737 (2001)]. Using a simple dynamical model, we show that these phenomena result from the slow kinetics of crossing large free energy barriers which separate the open and closed conformations. The dependence of barriers on sequence along the helix, and on the size of the loop(s) is analyzed. Some DNAs and RNAs sequences that could show dynamics on different time scales, or three(or more)-state unzipping, are proposed.Comment: 8 pages Revtex, including 4 figure

Elasticity model of a supercoiled DNA molecule

Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral representation for a quantum charged particle in the field of a magnetic monopole with unquantized charge. We show that the theory is singular in the continuum limit and must be regularised at an intermediate length scale. We find good agreement with existing experimental data, and point out how to measure the twist rigidity accurately.Comment: Latex, 4 pages. The figure contains new experimental data, giving a new determination of the twist rigidit

Continuum model for polymers with finite thickness

We consider the continuum limit of a recently-introduced model for discretized thick polymers, or tubes. We address both analytically and numerically how the polymer thickness influences the decay of tangent-tangent correlations and find how the persistence length scales with the thickness and the torsional rigidity of the tube centerline. At variance with the worm-like chain model, the phase diagram that we obtain for a continuous tube is richer; in particular, for a given polymer thickness there exists a threshold value for the centerline torsional rigidity separating a simple exponential decay of the tangent-tangent correlation from an oscillatory one.Comment: 8 pages, 4 figures. Accepted for publication in J. Phys.

In-flight dissipation as a mechanism to suppress Fermi acceleration

Some dynamical properties of time-dependent driven elliptical-shaped billiard are studied. It was shown that for the conservative time-dependent dynamics the model exhibits the Fermi acceleration [Phys. Rev. Lett. 100, 014103 (2008)]. On the other hand, it was observed that damping coefficients upon collisions suppress such phenomenon [Phys. Rev. Lett. 104, 224101 (2010)]. Here, we consider a dissipative model under the presence of in-flight dissipation due to a drag force which is assumed to be proportional to the square of the particle's velocity. Our results reinforce that dissipation leads to a phase transition from unlimited to limited energy growth. The behaviour of the average velocity is described using scaling arguments.Comment: 4 pages, 5 figure

Rotator and extender ferroelectrics: Importance of the shear coefficient to the piezoelectric properties of domain-engineered crystals and ceramics

The importance of a high shear coefficient d15 (or d24) to the piezoelectric properties of domain-engineered and polycrystalline ferroelectrics is discussed. The extent of polarization rotation, as a mechanism of piezoelectric response, is directly correlated to the shear coefficient. The terms "rotator" and "extender" are introduced to distinguish the contrasting behaviors of crystals such as 4mm BaTiO3 and PbTiO3. In "rotator" ferroelectrics, where d15 is high relative to the longitudinal coefficient d33, polarization rotation is the dominant mechanism of piezoelectric response; the maximum longitudinal piezoelectric response is found away from the polar axis. In "extender" ferroelectrics, d15 is low and the collinear effect dominates; the maximum piezoelectric response is found along the polar axis. A variety of 3m, mm2 and 4mm ferroelectrics, with various crystal structures based on oxygen octahedra, are classified in this way. It is shown that the largest piezoelectric anisotropies d15/d33 are always found in 3m crystals; this is a result of the intrinsic electrostrictive anisotropy of the constituent oxygen octahedra. Finally, for a given symmetry, the piezoelectric anisotropy increases close to ferroelectric-ferroelectric phase transitions; this includes morphotropic phase boundaries and temperature induced polymorphic transitions.Comment: accepted in J. Appl. Phy

Bending and Base-Stacking Interactions in Double-Stranded Semiflexible Polymer

Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a Schr\"{o}dinger equation variationally. Theoretical results based on this model on the extension versus force and extension versus degree of supercoiling relations of DNA chain are in good agreement with the experimental observations of Cluzel {\it et al.} [Science {\bf 271}, 792 (1996)], Smith {\it et al.} [{\it ibid.} {\bf 271}, 795 (1996)], and Strick {\it et al.} [{\it ibid.} {\bf 271}, 1835 (1996)].Comment: 8 pages in Revtex format, with 4 EPS figure

Hamiltonians for curves

We examine the equilibrium conditions of a curve in space when a local energy penalty is associated with its extrinsic geometrical state characterized by its curvature and torsion. To do this we tailor the theory of deformations to the Frenet-Serret frame of the curve. The Euler-Lagrange equations describing equilibrium are obtained; Noether's theorem is exploited to identify the constants of integration of these equations as the Casimirs of the euclidean group in three dimensions. While this system appears not to be integrable in general, it {\it is} in various limits of interest. Let the energy density be given as some function of the curvature and torsion, $f(\kappa,\tau)$. If $f$ is a linear function of either of its arguments but otherwise arbitrary, we claim that the first integral associated with rotational invariance permits the torsion $\tau$ to be expressed as the solution of an algebraic equation in terms of the bending curvature, $\kappa$. The first integral associated with translational invariance can then be cast as a quadrature for $\kappa$ or for $\tau$.Comment: 17 page

Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers

When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension curves (FECs). A characteristic plateau force (around 10 pN) and hysteresis between the pulling and relaxation cycles are observed for different dendrimer sizes, indicating the existence of a first-order transition between two phases (condensed and extended) of the fiber. The fact that we can reproduce the same FECs in the absence of additional dendrimers in the buffer medium indicates that dendrimers remain irreversibly bound to the DNA backbone. Upon salt variation FECs change noticeably confirming that electrostatic forces drive the condensation transition. Finally, we propose a simple model for the decondensing transition that qualitatively reproduces the FECs and which is confirmed by AFM images.Comment: Latex version, 4 pages+3 color figure

Topological interactions in systems of mutually interlinked polymer rings

The topological interaction arising in interlinked polymeric rings such as DNA catenanes is considered. More specifically, the free energy for a pair of linked random walk rings is derived where the distance $R$ between two segments each of which is part of a different ring is kept constant. The topology conservation is imposed by the Gauss invariant. A previous approach (M.Otto, T.A. Vilgis, Phys.Rev.Lett. {\bf 80}, 881 (1998)) to the problem is refined in several ways. It is confirmed, that asymptotically, i.e. for large $R\gg R_G$ where $R_G$ is average size of single random walk ring, the effective topological interaction (free energy) scales $\propto R^4$.Comment: 16 pages, 3 figur

A length-dynamic Tonks gas theory of histone isotherms

We find exact solutions to a new one-dimensional (1D) interacting particle theory and apply the results to the adsorption and wrapping of polymers (such as DNA) around protein particles (such as histones). Each adsorbed protein is represented by a Tonks gas particle. The length of each particle is a degree of freedom that represents the degree of DNA wrapping around each histone. Thermodynamic quantities are computed as functions of wrapping energy, adsorbed histone density, and bulk histone concentration (or chemical potential); their experimental signatures are also discussed. Histone density is found to undergo a two-stage adsorption process as a function of chemical potential, while the mean coverage by high affinity proteins exhibits a maximum as a function of the chemical potential. However, {\it fluctuations} in the coverage are concurrently maximal. Histone-histone correlation functions are also computed and exhibit rich two length scale behavior.Comment: 5 pp, 3 fig