Phase Separation by Entanglement of Active Polymerlike Worms

We investigate the aggregation and phase separation of thin, living T. tubifex worms that behave as active polymers. Randomly dispersed active worms spontaneously aggregate to form compact, highly entangled blobs, a process similar to polymer phase separation, and for which we observe power-law growth kinetics. We find that the phase separation of active polymerlike worms does not occur through Ostwald ripening, but through active motion and coalescence of the phase domains. Interestingly, the growth mechanism differs from conventional growth by droplet coalescence: the diffusion constant characterizing the random motion of a worm blob is independent of its size, a phenomenon that can be explained from the fact that the active random motion arises from the worms at the surface of the blob. This leads to a fundamentally different phase-separation mechanism that may be unique to active polymers.Comment: 4 pages, 4 figure

Boundary conditions in local electrostatics algorithms

We study the simulation of charged systems in the presence of general boundary conditions in a local Monte Carlo algorithm based on a constrained electric field. We firstly show how to implement constant-potential, Dirichlet, boundary conditions by introducing extra Monte Carlo moves to the algorithm. Secondly, we show the interest of the algorithm for studying systems which require anisotropic electrostatic boundary conditions for simulating planar geometries such as membranes.Comment: 8 pages, 6 figures, accepted in JC

Local Molecular Dynamics with Coulombic Interaction

We propose a local, O(N) molecular dynamics algorithm for the simulation of charged systems. The long ranged Coulomb potential is generated by a propagating electric field that obeys modified Maxwell equations. On coupling the electrodynamic equations to an external thermostat we show that the algorithm produces an effective Coulomb potential between particles. On annealing the electrodynamic degrees of freedom the field configuration converges to a solution of the Poisson equation much like the electronic degrees of freedom approach the ground state in ab-initio molecular dynamics.Comment: 4 pages with 3 figure

Modification of turbulent transport with continuous variation of flow shear in the Large Plasma Device

Continuous control over azimuthal flow and shear in the edge of the Large Plasma Device (LAPD) has been achieved using a biasable limiter which has allowed a careful study of the effect of flow shear on pressure-gradient-driven turbulence and transport in LAPD. LAPD rotates spontaneously in the ion diamagnetic direction (IDD); positive limiter bias first reduces, then minimizes (producing a near-zero shear state), and finally reverses the flow into the electron diamagnetic direction (EDD). Degradation of particle confinement is observed in the minimum shearing state and reduction in turbulent particle flux is observed with increasing shearing in both flow directions. Near-complete suppression of turbulent particle flux is observed for shearing rates comparable to the turbulent autocorrelation rate measured in the minimum shear state. Turbulent flux suppression is dominated by amplitude reduction in low-frequency ($<10$kHz) density fluctuations. An increase in fluctuations for the highest shearing states is observed with the emergence of a coherent mode which does not lead to net particle transport. The variations of density fluctuations are fit well with power-laws and compare favorably to simple models of shear suppression of transport.Comment: 10 pages, 5 figures; Submitted to Phys. Rev. Let

Simulating nanoscale dielectric response

We introduce a constrained energy functional to describe dielectric response. We demonstrate that the local functional is a generalization of the long ranged Marcus energy. Our re-formulation is used to implement a cluster Monte Carlo algorithm for the simulation of dielectric media. The algorithm avoids solving the Poisson equation and remains efficient in the presence of spatial heterogeneity, nonlinearity and scale dependent dielectric properties.Comment: 4 pages, 2 figures. Revtex

Coulomb Interactions via Local Dynamics: A Molecular--Dynamics Algorithm

We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the Molecular Dynamics version of the method and show that it is intimately related to the Car--Parrinello approach, while being equivalent to solving Maxwell's equations with freely adjustable speed of light. Unphysical self--energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green's function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented.Comment: 8 figure

Adhesion Induced DNA Naturation

DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface, the entropy gain is smaller than in the bulk, leading to a stronger binding and, upon neglecting self-avoidance, absence of a denatured phase. Now consider conditions where the binding potentials are too weak for naturation, and the surface potential too weak to adsorb single strands. In a variational approach it is shown that their combined action may lead to a naturated adsorbed phase. Conditions for the absence of naturation and adsorption are derived too. The phase diagram is constructed qualitatively.Comment: 4 pages, 1 figur

Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers

In this paper, we have studied, within a discrete WLC model, the spatial constraints in magnetic tweezers used in single molecule experiments. Two elements are involved: first, the fixed plastic slab on which is stuck the initial strand, second, the magnetic bead which pulls (or twists) the attached molecule free end. We have shown that the bead surface can be replaced by its tangent plane at the anchoring point, when it is close to the bead south pole relative to the force. We are led to a model with two parallel repulsive plates: the fixed anchoring plate and a fluctuating plate, simulating the bead, in thermal equilibrium with the system. The bead effect is a slight upper shift of the elongation, about four times smaller than the similar effect induced by the fixed plate. This rather unexpected result, has been qualitatively confirmed within the soluble Gaussian model. A study of the molecule elongation versus the countour length exhibits a significant non-extensive behaviour. The curve for short molecules (with less than 2 kbp) is well fitted by a straight line, with a slope given by the WLC model, but it does not go through the origin. The non-extensive offset gives a 15% upward shift to the elongation of a 2 kbp molecule stretched by a 0.3 pN force.Comment: 28 pages, 6 figures An explanatory figure has been added. The physical interpretation of the results has been made somewhat more transparen