Structural Transitions and Soft Modes in Frustrated DNA Crystals

Relying on symmetry considerations appropriate for helical biopolymers such as DNA and filamentous actin, we argue that crystalline packings of mutually repulsive helical macromolecules fall principally into two categories: unfrustrated (hexagonal) and frustrated (rhombohedral). For both cases, we construct the Landau-Ginzburg free energy for the 2D columnar-hexagonal to 3D crystalline phase transition, including the coupling between molecular displacements {\it along} biopolymer backbone to displacements in the plane of hexagonal order. We focus on the distinct elastic properties that emerge upon crystallization of helical arrays due to this coupling. Specifically, we demonstrate that frustrated states universally exhibit a highly anisotropic in-plane elastic response, characterized by an especially soft compliance to simple-shear deformations and a comparatively large resistance to those deformations that carry the array from the low- to high-density crystalline states of DNA.Comment: 7 pages, 3 figures (revised version

Self-organized criticality in an interface-growth model with quenched randomness

We study a modified model of the Kardar-Parisi-Zhang equation with quenched disorder, in which the driving force decreases as the interface rises up. A critical state is self-organized, and the anomalous scaling law with roughness exponent alpha=0.63 is numerically obtained.Comment: 4 pages, 4 figure

Identification of a polymer growth process with an equilibrium multi-critical collapse phase transition: the meeting point of swollen, collapsed and crystalline polymers

We have investigated a polymer growth process on the triangular lattice where the configurations produced are self-avoiding trails. We show that the scaling behaviour of this process is similar to the analogous process on the square lattice. However, while the square lattice process maps to the collapse transition of the canonical interacting self-avoiding trail model (ISAT) on that lattice, the process on the triangular lattice model does not map to the canonical equilibrium model. On the other hand, we show that the collapse transition of the canonical ISAT model on the triangular lattice behaves in a way reminiscent of the $\theta$-point of the interacting self-avoiding walk model (ISAW), which is the standard model of polymer collapse. This implies an unusual lattice dependency of the ISAT collapse transition in two dimensions. By studying an extended ISAT model, we demonstrate that the growth process maps to a multi-critical point in a larger parameter space. In this extended parameter space the collapse phase transition may be either $\theta$-point-like (second-order) or first-order, and these two are separated by a multi-critical point. It is this multi-critical point to which the growth process maps. Furthermore, we provide evidence that in addition to the high-temperature gas-like swollen polymer phase (coil) and the low-temperature liquid drop-like collapse phase (globule) there is also a maximally dense crystal-like phase (crystal) at low temperatures dependent on the parameter values. The multi-critical point is the meeting point of these three phases. Our hypothesised phase diagram resolves the mystery of the seemingly differing behaviours of the ISAW and ISAT models in two dimensions as well as the behaviour of the trail growth process

First-order scaling near a second-order phase transition: Tricritical polymer collapse

The coil-globule transition of an isolated polymer has been well established to be a second-order phase transition described by a standard tricritical O(0) field theory. We provide compelling evidence from Monte Carlo simulations in four dimensions, where mean-field theory should apply, that the approach to this (tri)critical point is dominated by the build-up of first-order-like singularities masking the second-order nature of the coil-globule transition: the distribution of the internal energy having two clear peaks that become more distinct and sharp as the tricritical point is approached. However, the distance between the peaks slowly decays to zero. The evidence shows that the position of this (pseudo) first-order transition is shifted by an amount from the tricritical point that is asymptotically much larger than the width of the transition region. We suggest an explanation for the apparently contradictory scaling predictions in the literature.Comment: 4 pages, 2 figures included in tex

Chirality transfer and stereo-selectivity of imprinted cholesteric networks

Imprinting of cholesteric textures in a polymer network is a method of preserving a macroscopically chiral phase in a system with no molecular chirality. By modifying the elastics properties of the network, the resulting stored helical twist can be manipulated within a wide range since the imprinting efficiency depends on the balance between the elastics constants and twisting power at network formation. One spectacular property of phase chirality imprinting is the created ability of the network to adsorb preferentially one stereo-component from a racemic mixture. In this paper we explore this property of chirality transfer from a macroscopic to the molecular scale. In particular, we focus on the competition between the phase chirality and the local nematic order. We demonstrate that it is possible to control the subsequent release of chiral solvent component from the imprinting network and the reversibility of the stereo-selective swelling by racemic solvents

Hamiltonian dynamics of homopolymer chain models

The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of observables numerically computed along dynamical trajectories are found to reproduce results given by the statistical mechanics of homopolymer models. The dynamical treatment, however, indicates a nontrivial transition between regimes of slow and fast phase space mixing. Such a transition is inaccessible to a statistical mechanical treatment and reflects a bimodality in the relaxation of time averages to corresponding ensemble averages. It is also found that a change in the energy dependence of the largest Lyapunov exponent indicates the theta-transition between filamentary and globular polymer configurations, clearly detecting the transition even for a finite number of particles.Comment: 11 pages, 8 figures, accepted for publication in Physical Review

On the orientational ordering of long rods on a lattice

We argue that a system of straight rigid rods of length k on square lattice with only hard-core interactions shows two phase transitions as a function of density, rho, for k >= 7. The system undergoes a phase transition from the low-density disordered phase to a nematic phase as rho is increased from 0, at rho = rho_c1, and then again undergoes a reentrant phase transition from the nematic phase to a disordered phase at rho = rho_c2 < 1.Comment: epl.cl

Unbiased sampling of globular lattice proteins in three dimensions

We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular proteins, upon adding suitable local interactions. Our algorithm can easily be equipped with such interactions, but we study here mainly the flexible homopolymer case where each conformation is generated with uniform probability. We argue that the algorithm is ergodic and has dynamical exponent z=0. We then use it to study polymers of size up to 64^3 = 262144 monomers. Results are presented for the effective interaction between end points, and the interaction with the boundaries of the system

Superfluid pairing in a mixture of a spin-polarized Fermi gas and a dipolar condensate

We consider a mixture of a spin-polarized Fermi gas and a dipolar Bose-Einstein condensate in which s-wave scattering between fermions and the quasiparticles of the dipolar condensate can result in an effective attractive Fermi-Fermi interaction anisotropic in nature and tunable by the dipolar interaction. We show that such an interaction can significantly increase the prospect of realizing a superfluid with a gap parameter characterized with a coherent superposition of all odd partial waves. We formulate, in the spirit of the Hartree-Fock-Bogoliubov mean-field approach, a theory which allows us to estimate the critical temperature when the anisotropic Fock potential is taken into consideration and to determine the system parameters that optimize the critical temperature at which such a superfluid emerges before the system begins to phase separate.Comment: 10 pages, 3 figure

Swimmers in thin films: from swarming to hydrodynamic instabilities

We investigate theoretically the collective dynamics of a suspension of low Reynolds number swimmers that are confined to two dimensions by a thin fluid film. Our model swimmer is characterized by internal degrees of freedom which locally exert active stresses (force dipoles or quadrupoles) on the fluid. We find that hydrodynamic interactions mediated by the film can give rise to spontaneous continuous symmetry breaking (swarming), to states with either polar or nematic homogeneous order. For dipolar swimmers, the stroke averaged dynamics are enough to determine the leading contributions to the collective behaviour. In contrast, for quadrupolar swimmers, our analysis shows that detailed features of the internal dynamics play an important role in determining the bulk behaviour. In the broken symmetry phases, we investigate fluctuations of hydrodynamic variables of the system and find that these destabilize order. Interestingly, this instability is not generic and depends on length-scale.Comment: 4 pages, 2 figures, references added, typos corrected, new introductio