An invariant in shock clustering and Burgers turbulence

1-D scalar conservation laws with convex flux and Markov initial data are now known to yield a completely integrable Hamiltonian system. In this article, we rederive the analogue of Loitsiansky's invariant in hydrodynamic turbulence from the perspective of integrable systems. Other relevant physical notions such as energy dissipation and spectrum are also discussed.Comment: 11 pages, no figures; v2: corrections mad

A boundary element regularised Stokeslet method applied to cilia and flagella-driven flow

A boundary element implementation of the regularised Stokeslet method of Cortez is applied to cilia and flagella-driven flows in biology. Previously-published approaches implicitly combine the force discretisation and the numerical quadrature used to evaluate boundary integrals. By contrast, a boundary element method can be implemented by discretising the force using basis functions, and calculating integrals using accurate numerical or analytic integration. This substantially weakens the coupling of the mesh size for the force and the regularisation parameter, and greatly reduces the number of degrees of freedom required. When modelling a cilium or flagellum as a one-dimensional filament, the regularisation parameter can be considered a proxy for the body radius, as opposed to being a parameter used to minimise numerical errors. Modelling a patch of cilia, it is found that: (1) For a fixed number of cilia, reducing cilia spacing reduces transport. (2) For fixed patch dimension, increasing cilia number increases the transport, up to a plateau at $9\times 9$ cilia. Modelling a choanoflagellate cell it is found that the presence of a lorica structure significantly affects transport and flow outside the lorica, but does not significantly alter the force experienced by the flagellum.Comment: 20 pages, 7 figures, postprin

Modelling bacterial behaviour close to a no-slip plane boundary: the influence of bacterial geometry

We describe a boundary-element method used to model the hydrodynamics of a bacterium propelled by a single helical flagellum. Using this model, we optimize the power efficiency of swimming with respect to cell body and flagellum geometrical parameters, and find that optima for swimming in unbounded fluid and near a no-slip plane boundary are nearly indistinguishable. We also consider the novel optimization objective of torque efficiency and find a very different optimal shape. Excluding effects such as Brownian motion and electrostatic interactions, it is demonstrated that hydrodynamic forces may trap the bacterium in a stable, circular orbit near the boundary, leading to the empirically observable surface accumulation of bacteria. Furthermore, the details and even the existence of this stable orbit depend on geometrical parameters of the bacterium, as described in this article. These results shed some light on the phenomenon of surface accumulation of micro-organisms and offer hydrodynamic explanations as to why some bacteria may accumulate more readily than others based on morphology

Pif1 Helicase Lengthens Some Okazaki Fragment Flaps Necessitating Dna2 Nuclease/Helicase Action in the Two-nuclease Processing Pathway

We have developed a system to reconstitute all of the proposed steps of Okazaki fragment processing using purified yeast proteins and model substrates. DNA polymerase δ was shown to extend an upstream fragment to displace a downstream fragment into a flap. In most cases, the flap was removed by flap endonuclease 1 (FEN1), in a reaction required to remove initiator RNA in vivo. The nick left after flap removal could be sealed by DNA ligase I to complete fragment joining. An alternative pathway involving FEN1 and the nuclease/helicase Dna2 has been proposed for flaps that become long enough to bind replication protein A (RPA). RPA binding can inhibit FEN1, but Dna2 can shorten RPA-bound flaps so that RPA dissociates. Recent reconstitution results indicated that Pif1 helicase, a known component of fragment processing, accelerated flap displacement, allowing the inhibitory action of RPA. In results presented here, Pif1 promoted DNA polymerase δ to displace strands that achieve a length to bind RPA, but also to be Dna2 substrates. Significantly, RPA binding to long flaps inhibited the formation of the final ligation products in the reconstituted system without Dna2. However, Dna2 reversed that inhibition to restore efficient ligation. These results suggest that the two-nuclease pathway is employed in cells to process long flap intermediates promoted by Pif1

Attempted Bethe ansatz solution for one-dimensional directed polymers in random media

We study the statistical properties of one-dimensional directed polymers in a short-range random potential by mapping the replicated problem to a many body quantum boson system with attractive interactions. We find the full set of eigenvalues and eigenfunctions of the many-body system and perform the summation over the entire spectrum of excited states. The analytic continuation of the obtained exact expression for the replica partition function from integer to non-integer replica parameter N turns out to be ambiguous. Performing the analytic continuation simply by assuming that the parameter N can take arbitrary complex values, and going to the thermodynamic limit of the original directed polymer problem, we obtain the explicit universal expression for the probability distribution function of free energy fluctuations.Comment: 32 pages, 1 figur

Exact probability function for bulk density and current in the asymmetric exclusion process

We examine the asymmetric simple exclusion process with open boundaries, a paradigm of driven diffusive systems, having a nonequilibrium steady state transition. We provide a full derivation and expanded discussion and digression on results previously reported briefly in M. Depken and R. Stinchcombe, Phys. Rev. Lett. {\bf 93}, 040602, (2004). In particular we derive an exact form for the joint probability function for the bulk density and current, both for finite systems, and also in the thermodynamic limit. The resulting distribution is non-Gaussian, and while the fluctuations in the current are continuous at the continuous phase transitions, the density fluctuations are discontinuous. The derivations are done by using the standard operator algebraic techniques, and by introducing a modified version of the original operator algebra. As a byproduct of these considerations we also arrive at a novel and very simple way of calculating the normalization constant appearing in the standard treatment with the operator algebra. Like the partition function in equilibrium systems, this normalization constant is shown to completely characterize the fluctuations, albeit in a very different manner.Comment: 10 pages, 4 figure

Clocked Atom Delivery to a Photonic Crystal Waveguide

Experiments and numerical simulations are described that develop quantitative understanding of atomic motion near the surfaces of nanoscopic photonic crystal waveguides (PCWs). Ultracold atoms are delivered from a moving optical lattice into the PCW. Synchronous with the moving lattice, transmission spectra for a guided-mode probe field are recorded as functions of lattice transport time and frequency detuning of the probe beam. By way of measurements such as these, we have been able to validate quantitatively our numerical simulations, which are based upon detailed understanding of atomic trajectories that pass around and through nanoscopic regions of the PCW under the influence of optical and surface forces. The resolution for mapping atomic motion is roughly 50 nm in space and 100 ns in time. By introducing auxiliary guided mode (GM) fields that provide spatially varying AC-Stark shifts, we have, to some degree, begun to control atomic trajectories, such as to enhance the flux into to the central vacuum gap of the PCW at predetermined times and with known AC-Stark shifts. Applications of these capabilities include enabling high fractional filling of optical trap sites within PCWs, calibration of optical fields within PCWs, and utilization of the time-dependent, optically dense atomic medium for novel nonlinear optical experiments

Orientation dynamics of weakly Brownian particles in periodic viscous flows

Evolution equations for the orientation distribution of axisymmetric particles in periodic flows are derived in the regime of small but non-zero Brownian rotations. The equations are based on a multiple time scale approach that allows fast computation of the relaxation processes leading to statistical equilibrium. The approach has been applied to the calculation of the effective viscosity of a thin disk suspension in gravity waves.Comment: 16 pages, 7 eps figures include

Exact joint density-current probability function for the asymmetric exclusion process

We study the asymmetric exclusion process with open boundaries and derive the exact form of the joint probability function for the occupation number and the current through the system. We further consider the thermodynamic limit, showing that the resulting distribution is non-Gaussian and that the density fluctuations have a discontinuity at the continuous phase transition, while the current fluctuations are continuous. The derivations are performed by using the standard operator algebraic approach, and by the introduction of new operators satisfying a modified version of the original algebra.Comment: 4 pages, 3 figure

Shocks in the asymmetric exclusion process with internal degree of freedom

We determine all families of Markovian three-states lattice gases with pair interaction and a single local conservation law. One such family of models is an asymmetric exclusion process where particles exist in two different nonconserved states. We derive conditions on the transition rates between the two states such that the shock has a particularly simple structure with minimal intrinsic shock width and random walk dynamics. We calculate the drift velocity and diffusion coefficient of the shock.Comment: 26 pages, 1 figur