Reduced Persistence Length and Fluctuation-Induced Interactions of Directed Semiflexible Polymers on Fluctuating surfaces

We consider directed semiflexible polymers embedded in a fluctuating surface which is governed by either surface tension or bending rigidity. The attractive interactions induced by the fluctuations of the surface reduce the rigidity of the polymers. In particular, it is shown that for arbitrarily stiff parallel polymers, there is a characteristic separation below which they prefer to bend rather than stay linear. The out-of plane fluctuations of the polymer, screen out the long-range fluctuation-induced forces, resulting in only a short-ranged effective attraction.Comment: REVTEX, one postscript figur

Three-Sphere Low Reynolds Number Swimmer with a Cargo Container

A recently introduced model for an autonomous swimmer at low Reynolds number that is comprised of three spheres connected by two arms is considered when one of the spheres has a large radius. The Stokes hydrodynamic flow associated with the swimming strokes and net motion of this system can be studied analytically using the Stokes Green's function of a point force in front of a sphere of arbitrary radius $R$ provided by Oseen. The swimming velocity is calculated, and shown to scale as $1/R^3$ with the radius of the sphere.Comment: 4 pages, 1 figur

Enhanced Diffusion of Enzymes that Catalyze Exothermic Reactions

Enzymes have been recently found to exhibit enhanced diffusion due to their catalytic activities. A recent experiment [C. Riedel et al., Nature 517, 227 (2015)] has found evidence that suggests this phenomenon might be controlled by the degree of exothermicity of the catalytic reaction involved. Four mechanisms that can lead to this effect, namely, self-thermophoresis, boost in kinetic energy, stochastic swimming, and collective heating, are critically discussed, and it is shown that only the last two could be strong enough to account for the observations. The resulting quantitative description is used to examine the biological significance of the effect.Comment: To appear in PR

Casimir-Lifshitz Interaction between Dielectrics of Arbitrary Geometry: A Dielectric Contrast Perturbation Theory

The general theory of electromagnetic--fluctuation--induced interactions in dielectric bodies as formulated by Dzyaloshinskii, Lifshitz, and Pitaevskii is rewritten as a perturbation theory in terms of the spatial contrast in (imaginary) frequency dependent dielectric function. The formulation can be used to calculate the Casimir-Lifshitz forces for dielectric objects of arbitrary geometry, as a perturbative expansion in the dielectric contrast, and could thus complement the existing theories that use perturbation in geometrical features. We find that expansion in dielectric contrast recasts the resulting Lifshitz energy into a sum of the different many-body contributions. The limit of validity and convergence properties of the perturbation theory is discussed using the example of parallel semi-infinite objects for which the exact result is known.Comment: 9 pages, 5 (combined) figures; to appear in Phys. Rev.

Bose-Einstein Condensation in Scalar Active Matter with Diffusivity Edge

Due to their remarkable properties, systems that exhibit self-organization of their components resulting from intrinsic microscopic activity have been extensively studied in the last two decades. In a generic class of active matter, the interactions between the active components are represented via an effective density-dependent diffusivity in a mean-field single-particle description. Here, a new class of scalar active matter is proposed by incorporating a diffusivity edge into the dynamics: when the local density of the system surpasses a critical threshold, the diffusivity vanishes. The effect of the diffusivity edge is studied under the influence of an external potential, which introduces the ability to control the behaviour of the system by changing an effective temperature, which is defined in terms of the single-particle diffusivity and mobility. At a critical effective temperature, a system that is trapped by a harmonic potential is found to undergo a condensation transition, which manifests formal similarities to Bose-Einstein condensation

Distribution of Interacting Ionic Particles in Disordered Media

Equilibrium distribution of interacting ionic particles in a charged disordered background is studied using the nonlinear Poisson-Boltzmann equation. For an arbitrarily given realization of the disorder, an exact solution of the equation is obtained in one dimension using a mapping of the nonlinear Poisson-Boltzmann equation to a self-consistent Schrodinger equation. The resulting density profile shows that the ions are delocalized, despite what the equivalent Schrodinger formulation in one dimension would suggest. It is shown that the ions are not distributed so as to locally neutralize the background, presumably due to their mutual interactions

Exact axisymmetric interaction of phoretically active Janus particles

We study the axisymmetric interaction of two chemically active Janus particles. By relying on the linearity of the field equations and symmetry arguments, we derive a generic solution for the relative velocity of the particles. We show that regardless of the chemical properties of the system, the relative velocity can be written as a linear summation of geometrical functions which only depend on the gap size between the particles. We evaluate these functions via an exact approach which accounts for the full chemical and hydrodynamic interactions. Using the obtained solution, we expose the role of each compartment in the relative motion, and also discuss the contribution of different interactions. We then show that the dynamical system describing the relative motion of two Janus particles can have up to three fixed points. These fixed points can be stable or unstable, indicating that a system of two Janus particles can exhibit a variety of nontrivial behaviour depending on their initial gap size, and their chemical properties. We also look at the specific case of Janus particles in which one compartment is inert, and present regime diagrams for their relative behaviour in the activity-mobility parameter space

Run-and-tumble in a crowded environment: persistent exclusion process for swimmers

The effect of crowding on the run-and-tumble dynamics of swimmers such as bacteria is studied using a discrete lattice model of mutually excluding particles that move with constant velocity along a direction that is randomized at a rate $\alpha$. In stationary state, the system is found to break into dense clusters in which particles are trapped or stopped from moving. The characteristic size of these clusters predominantly scales as $\alpha^{-0.5}$ both in 1D and 2D. For a range of densities, due to cooperative effects, the stopping time scales as ${\cal T}_{1d}^{0.85}$ and as ${\cal T}_{2d}^{0.8}$, where ${\cal T}_d$ is the diffusive time associated with the motion of cluster boundaries. Our findings might be helpful in understanding the early stages of biofilm formation.Comment: 7 pages, 5 figures, accepted in PR

Length scale dependence of DNA mechanical properties

Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for cellular processes such as DNA packaging and gene regulation. Here, we perform a systematic study of the effective elastic properties of DNA at different length scales by probing the conformation and fluctuations of DNA from single base-pair level up to four helical turns, using trajectories from atomistic simulation. We find evidence that supports cooperative softening of the stretch modulus and identify the essential modes that give rise to this effect. The bend correlation exhibits modulations that reflect the helical periodicity, while it yields a reasonable value for the effective persistence length, and the twist modulus undergoes a smooth crossover---from a relatively smaller value at the single base-pair level to the bulk value---over half a DNA-turn.Comment: 5 pages, 4 figures, accepted for publication in Phys. Rev. Let

Self-assembly of Active Colloidal Molecules with Dynamic Function

Catalytically active colloids maintain non-equilibrium conditions in which they produce and deplete chemicals and hence effectively act as sources and sinks of molecules. While individual colloids that are symmetrically coated do not exhibit any form of dynamical activity, the concentration fields resulting from their chemical activity decay as $1/r$ and produce gradients that attract or repel other colloids depending on their surface chemistry and ambient variables. This results in a non-equilibrium analogue of ionic systems, but with the remarkable novel feature of action-reaction symmetry breaking. We study solutions of such chemically active colloids in dilute conditions when they join up to form molecules via generalized ionic bonds, and discuss how we can achieve structures with time dependent functionality. In particular, we study a molecule that adopts a spontaneous oscillatory pattern of conformations, and another that exhibits a run-and-tumble dynamics similar to bacteria. Our study shows that catalytically active colloids could be used for designing self-assembled structures that posses dynamical functionalities that are determined by their prescribed 3D structures, a strategy that follows the design principle of proteins