A model for the emergence of cooperation, interdependence and structure in evolving networks

Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of cooperative molecular species arises and evolves to become more complex and structured. The network is modeled by a directed weighted graph whose positive and negative links represent `catalytic' and `inhibitory' interactions among the molecular species, and which evolves as the least populated species (typically those that go extinct) are replaced by new ones. A small autocatalytic set (ACS), appearing by chance, provides the seed for the spontaneous growth of connectivity and cooperation in the graph. A highly structured chemical organization arises inevitably as the ACS enlarges and percolates through the network in a short, analytically determined time scale. This self-organization does not require the presence of self-replicating species. The network also exhibits catastrophes over long time scales triggered by the chance elimination of `keystone' species, followed by recoveries.Comment: 8 pages, 4 figure

Simulating Brownian suspensions with fluctuating hydrodynamics

Fluctuating hydrodynamics has been successfully combined with several computational methods to rapidly compute the correlated random velocities of Brownian particles. In the overdamped limit where both particle and fluid inertia are ignored, one must also account for a Brownian drift term in order to successfully update the particle positions. In this paper, we present an efficient computational method for the dynamic simulation of Brownian suspensions with fluctuating hydrodynamics that handles both computations and provides a similar approximation as Stokesian Dynamics for dilute and semidilute suspensions. This advancement relies on combining the fluctuating force-coupling method (FCM) with a new midpoint time-integration scheme we refer to as the drifter-corrector (DC). The DC resolves the drift term for fluctuating hydrodynamics-based methods at a minimal computational cost when constraints are imposed on the fluid flow to obtain the stresslet corrections to the particle hydrodynamic interactions. With the DC, this constraint need only be imposed once per time step, reducing the simulation cost to nearly that of a completely deterministic simulation. By performing a series of simulations, we show that the DC with fluctuating FCM is an effective and versatile approach as it reproduces both the equilibrium distribution and the evolution of particulate suspensions in periodic as well as bounded domains. In addition, we demonstrate that fluctuating FCM coupled with the DC provides an efficient and accurate method for large-scale dynamic simulation of colloidal dispersions and the study of processes such as colloidal gelation

Lubrication approximation for micro-particles moving along parallel walls

Lubrication expressions for the friction coefficients of a spherical particle moving in a fluid between and along two parallel solid walls are explicitly evaluated in the low-Reynolds-number regime. They are used to determine lubrication expression for the particle free motion under an ambient Poiseuille flow. The range of validity and the accuracy of the lubrication approximation is determined by comparing with the corresponding results of the accurate multipole procedure. The results are applicable for thin, wide and long microchannels, or quasi-two-dimensional systems.Comment: 4 pages, 5 figure

Lattice-Boltzmann simulations of the drag force on a sphere approaching a superhydrophobic striped plane

By means of lattice-Boltzmann simulations the drag force on a sphere of radius R approaching a superhydrophobic striped wall has been investigated as a function of arbitrary separation h. Superhydrophobic (perfect-slip vs. no-slip) stripes are characterized by a texture period L and a fraction of the gas area $\phi$. For very large values of h/R we recover the macroscopic formulae for a sphere moving towards a hydrophilic no-slip plane. For h/R=O(1) and smaller the drag force is smaller than predicted by classical theories for hydrophilic no-slip surfaces, but larger than expected for a sphere interacting with a uniform perfectly slipping wall. At a thinner gap, $h\ll R$ the force reduction compared to a classical result becomes more pronounced, and is maximized by increasing $\phi$. In the limit of very small separations our simulation data are in quantitative agreement with an asymptotic equation, which relates a correction to a force for superhydrophobic slip to texture parameters. In addition, we examine the flow and pressure field and observe their oscillatory character in the transverse direction in the vicinity of the wall, which reflects the influence of the heterogeneity and anisotropy of the striped texture. Finally, we investigate the lateral force on the sphere, which is detectable in case of very small separations and is maximized by stripes with $\phi=0.5$.Comment: 9 pages, 7 figure

Tilted algebras and short chains of modules

We provide an affirmative answer for the question raised almost twenty years ago concerning the characterization of tilted artin algebras by the existence of a sincere finitely generated module which is not the middle of a short chain

Hydrodynamic orienting of asymmetric microobjects under gravity

It is shown that nonsymmetric microobjects orient while settling under gravity in a viscous fluid. To analyze this process, a simple shape is chosen: a non-deformable `chain'. The chain consists of two straight arms, made of touching solid spheres. In the absence of external torques, the spheres are free to spin along the arms. The motion of the chain is evaluated by solving the Stokes equations with the use of the multipole method. It is demonstrated that the spinning beads speed up sedimentation by a small amount, and increase the orientation rate significantly in comparison to the corresponding rigid chain. It is shown that chains orient towards the V-shaped stable stationary configuration. In contrast, rods and star-shaped microobjects do not rotate. The hydrodynamic orienting is relevant for efficient swimming of non-symmetric microobjects, and for sedimenting suspensions.Comment: 9 page

Symmetric three-particle motion in Stokes flow: equilibrium for heavy spheres in contrast to "end-of-world" for point forces

A stationary stable solution of the Stokes equations for three identical heavy solid spheres falling in a vertical plane is found. It has no analog in the point-particle approximation. Three spheres aligned horizontally at equal distances evolve towards the equilibrium relative configuration while the point particles collapse onto a single point in a finite time.Comment: 4 pages, 7 figure

Jet propulsion without inertia

A body immersed in a highly viscous fluid can locomote by drawing in and expelling fluid through pores at its surface. We consider this mechanism of jet propulsion without inertia in the case of spheroidal bodies, and derive both the swimming velocity and the hydrodynamic efficiency. Elementary examples are presented, and exact axisymmetric solutions for spherical, prolate spheroidal, and oblate spheroidal body shapes are provided. In each case, entirely and partially porous (i.e. jetting) surfaces are considered, and the optimal jetting flow profiles at the surface for maximizing the hydrodynamic efficiency are determined computationally. The maximal efficiency which may be achieved by a sphere using such jet propulsion is 12.5%, a significant improvement upon traditional flagella-based means of locomotion at zero Reynolds number. Unlike other swimming mechanisms which rely on the presentation of a small cross section in the direction of motion, the efficiency of a jetting body at low Reynolds number increases as the body becomes more oblate, and limits to approximately 162% in the case of a flat plate swimming along its axis of symmetry. Our results are discussed in the light of slime extrusion mechanisms occurring in many cyanobacteria