Spontaneous periodic travelling waves in oscillatory systems with cross-diffusion

We identify a new type of pattern formation in spatially distributed active systems. We simulate one-dimensional two-component systems with predator-prey local interaction and pursuit-evasion taxis between the components. In a sufficiently large domain, spatially uniform oscillations in such systems are unstable with respect to small perturbations. This instability, through a transient regime appearing as spontanous focal sources, leads to establishment of periodic traveling waves. The traveling waves regime is established even if boundary conditions do not favor such solutions. The stable wavelength are within a range bounded both from above and from below, and this range does not coincide with instability bands of the spatially uniform oscillations.Comment: 7 pages, 4 figures, as accepted to Phys Rev E 2009/10/2

The Viscous Nonlinear Dynamics of Twist and Writhe

Exploiting the "natural" frame of space curves, we formulate an intrinsic dynamics of twisted elastic filaments in viscous fluids. A pair of coupled nonlinear equations describing the temporal evolution of the filament's complex curvature and twist density embodies the dynamic interplay of twist and writhe. These are used to illustrate a novel nonlinear phenomenon: ``geometric untwisting" of open filaments, whereby twisting strains relax through a transient writhing instability without performing axial rotation. This may explain certain experimentally observed motions of fibers of the bacterium B. subtilis [N.H. Mendelson, et al., J. Bacteriol. 177, 7060 (1995)].Comment: 9 pages, 4 figure

Twirling Elastica: Kinks, Viscous Drag, and Torsional Stress

Biological filaments such as DNA or bacterial flagella are typically curved in their natural states. To elucidate the interplay of viscous drag, twisting, and bending in the overdamped dynamics of such filaments, we compute the steady-state torsional stress and shape of a rotating rod with a kink. Drag deforms the rod, ultimately extending or folding it depending on the kink angle. For certain kink angles and kink locations, both states are possible at high rotation rates. The agreement between our macroscopic experiments and the theory is good, with no adjustable parameters.Comment: 4 pages, 4 figure

Effective viscosity of microswimmer suspensions

The measurement of a quantitative and macroscopic parameter to estimate the global motility of a large population of swimming biological cells is a challenge Experiments on the rheology of active suspensions have been performed. Effective viscosity of sheared suspensions of live unicellular motile micro-algae (\textit{Chlamydomonas Reinhardtii}) is far greater than for suspensions containing the same volume fraction of dead cells and suspensions show shear thinning behaviour. We relate these macroscopic measurements to the orientation of individual swimming cells under flow and discuss our results in the light of several existing models

Molecular elasticity and the geometric phase

We present a method for solving the Worm Like Chain (WLC) model for twisting semiflexible polymers to any desired accuracy. We show that the WLC free energy is a periodic function of the applied twist with period 4 pi. We develop an analogy between WLC elasticity and the geometric phase of a spin half system. These analogies are used to predict elastic properties of twist-storing polymers. We graphically display the elastic response of a single molecule to an applied torque. This study is relevant to mechanical properties of biopolymers like DNA.Comment: five pages, one figure, revtex, revised in the light of referee's comments, to appear in PR

Labels for non-individuals

Quasi-set theory is a first order theory without identity, which allows us to cope with non-individuals in a sense. A weaker equivalence relation called ``indistinguishability'' is an extension of identity in the sense that if $x$ is identical to $y$ then $x$ and $y$ are indistinguishable, although the reciprocal is not always valid. The interesting point is that quasi-set theory provides us a useful mathematical background for dealing with collections of indistinguishable elementary quantum particles. In the present paper, however, we show that even in quasi-set theory it is possible to label objects that are considered as non-individuals. We intend to prove that individuality has nothing to do with any labelling process at all, as suggested by some authors. We discuss the physical interpretation of our results.Comment: 11 pages, no figure

Effective Viscosity of Dilute Bacterial Suspensions: A Two-Dimensional Model

Suspensions of self-propelled particles are studied in the framework of two-dimensional (2D) Stokesean hydrodynamics. A formula is obtained for the effective viscosity of such suspensions in the limit of small concentrations. This formula includes the two terms that are found in the 2D version of Einstein's classical result for passive suspensions. To this, the main result of the paper is added, an additional term due to self-propulsion which depends on the physical and geometric properties of the active suspension. This term explains the experimental observation of a decrease in effective viscosity in active suspensions.Comment: 15 pages, 3 figures, submitted to Physical Biolog

The universal Glivenko-Cantelli property

Let F be a separable uniformly bounded family of measurable functions on a standard measurable space, and let N_{[]}(F,\epsilon,\mu) be the smallest number of \epsilon-brackets in L^1(\mu) needed to cover F. The following are equivalent: 1. F is a universal Glivenko-Cantelli class. 2. N_{[]}(F,\epsilon,\mu)0 and every probability measure \mu. 3. F is totally bounded in L^1(\mu) for every probability measure \mu. 4. F does not contain a Boolean \sigma-independent sequence. It follows that universal Glivenko-Cantelli classes are uniformity classes for general sequences of almost surely convergent random measures.Comment: 26 page

Twirling and Whirling: Viscous Dynamics of Rotating Elastica

Motivated by diverse phenomena in cellular biophysics, including bacterial flagellar motion and DNA transcription and replication, we study the overdamped nonlinear dynamics of a rotationally forced filament with twist and bend elasticity. Competition between twist injection, twist diffusion, and writhing instabilities is described by a novel pair of coupled PDEs for twist and bend evolution. Analytical and numerical methods elucidate the twist/bend coupling and reveal two dynamical regimes separated by a Hopf bifurcation: (i) diffusion-dominated axial rotation, or twirling, and (ii) steady-state crankshafting motion, or whirling. The consequences of these phenomena for self-propulsion are investigated, and experimental tests proposed.Comment: To be published in Physical Review Letter

Diffusion and spatial correlations in suspensions of swimming particles

Populations of swimming microorganisms produce fluid motions that lead to dramatically enhanced diffusion of tracer particles. Using simulations of suspensions of swimming particles in a periodic domain, we capture this effect and show that it depends qualitatively on the mode of swimming: swimmers ``pushed'' from behind by their flagella show greater enhancement than swimmers that are ``pulled'' from the front. The difference is manifested by an increase, that only occurs for pushers, of the diffusivity of passive tracers and the velocity correlation length with the size of the periodic domain. A physical argument supported by a mean field theory sheds light on the origin of these effects.Comment: 10 pages, 3 figures, to be published in Phys. Rev. Let