Facilitated diffusion on confined DNA

In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA. The confining geometry and DNA elasticity are key parameters: we find that facilitated diffusion is most efficient inside an isotropic volume, and on a flexible polymer. By considering the typical copy numbers of proteins in vivo, we show that the speedup due to sliding becomes insensitive to fine tuning of parameters, rendering facilitated diffusion a robust mechanism to speed up intracellular diffusion-limited reactions. The parameter range we focus on is relevant for in vitro systems and for facilitated diffusion on yeast chromatin

Spinodal decomposition to a lamellar phase: effects of hydrodynamic flow

Results are presented for the kinetics of domain growth of a two-dimensional fluid quenched from a disordered to a lamellar phase. At early times when a Lifshitz-Slyozov mechanism is operative the growth process proceeds logarithmically in time to a frozen state with locked-in defects. However when hydrodynamic modes become important, or the fluid is subjected to shear, the frustration of the system is alleviated and the size and orientation of the lamellae attain their equilibrium values.Comment: 4 Revtex pages, 4 figures, to appear in Physical Review Letter

Switching dynamics in cholesteric blue phases

Blue phases are networks of disclination lines, which occur in cholesteric liquid crystals near the transition to the isotropic phase. They have recently been used for the new generation of fast switching liquid crystal displays. Here we study numerically the steady states and switching hydrodynamics of blue phase I (BPI) and blue phase II (BPII) cells subjected to an electric field. When the field is on, there are three regimes: for very weak fields (and strong anchoring at the boundaries) the blue phases are almost unaffected, for intermediate fields the disclinations twist (for BPI) and unzip (for BPII), whereas for very large voltages the network dissolves in the bulk of the cell. Interestingly, we find that a BPII cell can recover its original structure when the field is switched off, whereas a BPI cell is found to be trapped more easily into metastable configurations. The kinetic pathways followed during switching on and off entails dramatic reorganisation of the disclination networks. We also discuss the effect of changing the director field anchoring at the boundary planes and of varying the direction of the applied field.Comment: 17 pages, 11 figure

Bistable defect structures in blue phase devices

Blue phases (BPs) are liquid crystals made up by networks of defects, or disclination lines. While existing phase diagrams show a striking variety of competing metastable topologies for these networks, very little is known as to how to kinetically reach a target structure, or how to switch from one to the other, which is of paramount importance for devices. We theoretically identify two confined blue phase I systems in which by applying an appropriate series of electric field it is possible to select one of two bistable defect patterns. Our results may be used to realise new generation and fast switching energy-saving bistable devices in ultrathin surface treated BPI wafers.Comment: 4 pages, 3 figures. Accepted for publication in Phys. Rev. Let

Lattice Boltzmann simulations of lamellar and droplet phases

Lattice Boltzmann simulations are used to investigate spinodal decomposition in a two-dimensional binary fluid with equilibrium lamellar and droplet phases. We emphasise the importance of hydrodynamic flow to the phase separation kinetics. For mixtures slightly asymmetric in composition the fluid phase separates into bulk and lamellar phases with the lamellae forming distinctive spiral structures to minimise their elastic energy.Comment: 19 pages, 5 figure

Universal properties of knotted polymer rings

By performing Monte Carlo sampling of $N$-steps self-avoiding polygons embedded on different Bravais lattices we explore the robustness of universality in the entropic, metric and geometrical properties of knotted polymer rings. In particular, by simulating polygons with $N$ up to $10^5$ we furnish a sharp estimate of the asymptotic values of the knot probability ratios and show their independence on the lattice type. This universal feature was previously suggested although with different estimates of the asymptotic values. In addition we show that the scaling behavior of the mean squared radius of gyration of polygons depends on their knot type only through its correction to scaling. Finally, as a measure of the geometrical self-entanglement of the SAPs we consider the standard deviation of the writhe distribution and estimate its power-law behavior in the large $N$ limit. The estimates of the power exponent do depend neither on the lattice nor on the knot type, strongly supporting an extension of the universality property to some features of the geometrical entanglement.Comment: submitted to Phys.Rev.

Topological Friction and Relaxation Dynamics of Spatially Confined Catenated Polymers

We study catenated ring polymers confined inside channels and slits with Langevin dynamics simulations and address how the contour position and size of the interlocked or physically linked region evolve with time. We show that the catenation constraints generate a drag, or topological friction, that couples the contour motion of the interlocked regions. Notably, the coupling strength decreases as the interlocking is made tighter, but also shorter, by confinement. Though the coupling strength differs for channel and slit confinement, the data outline a single universal curve when plotted against the size of the linked region. Finally, we study how the relaxation kinetics changes after one of the rings is cut open and conclude that considering interlocked circular polymers is key for isolating the manifestations of topological friction. The results ought to be relevant for linked biomolecules in experimental or biological confining conditions

Application of the Lorentz-Transform Technique to Meson Photoproduction

We show that the Lorentz integral transform (LIT) technique which has been successfully applied to photoreactions in light nuclei can also be applied to photoreactions involving particle production. A simple model where results are easily calculable in the traditional fashion is used to test the technique. Specifically we compute inclusive $\pi^+$ photoproduction from deuterium for photon energies less than 200 MeV using a Yamaguchi model for the NN interaction. It is demonstrated that although the response functions for inclusive meson production do not have favourable asymptotic behavior one can nontheless extract them by inversion of the transform. The implication is that one can treat realistic problems of photo-meson production including all final state interactions by means of the LIT technique

Topological Constraints at the Theta Point: Closed Loops at Two Loops

We map the problem of self-avoiding random walks in a Theta solvent with a chemical potential for writhe to the three-dimensional symmetric U(N)-Chern-Simons theory as N goes to 0. We find a new scaling regime of topologically constrained polymers, with critical exponents that depend on the chemical potential for writhe, which gives way to a fluctuation-induced first-order transition.Comment: 5 pages, RevTeX, typo