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Persistent motion of passive asymmetric bodies in non-equilibrium media has been experimentally observed in a variety of settings. However, fundamental constraints on the efficiency of such motion are not fully explored. Understanding such limits, and ways to circumvent them, is important for efficient utilization of energy stored in agitated surroundings for purposes of taxis and transport. Here, we examine such issues in the context of erratic movements of a passive asymmetric dumbbell driven by non-equilibrium noise. For uncorrelated (white) noise, we find a (non-Boltzmann) joint probability distribution for the velocity and orientation, which indicates that the dumbbell preferentially moves along its symmetry axis. The dumbbell thus behaves as an Ornstein–Uhlenbeck walker, a prototype of active matter. Exploring the efficiency of this active motion, we show that in the over-damped limit, the persistence length l of the dumbbell is bound from above by half its mean size, while the propulsion speed v∥ is proportional to its inverse size. The persistence length can be increased by exploiting inertial effects beyond the over-damped regime, but this improvement always comes at the price of smaller propulsion speeds. This limitation is explained by noting that the diffusivity of a dumbbell, related to the product v∥l, is always less than that of its components, thus severely constraining the usefulness of passive dumbbells as active particles. [ABSTRACT FROM AUTHOR]

Perturbations of fluid media can give rise to non-equilibrium dynamics, which may, in turn, cause motion of immersed inclusions or tracer particles. We consider perturbations ("activations") that are local in space and time, of a fluid density which is conserved, and study the resulting diffusiophoretic phenomena that emerge at a large distance. Specifically, we consider cases where the perturbations propagate diffusively, providing examples from passive and active matter for which this is expected to be the case. Activations can, for instance, be realized by sudden and local changes in interaction potentials of the medium or by local changes in its activity. Various analytical results are provided for the case of confinement by two parallel walls. We investigate the possibility of extracting work from inclusions, which are moving through the activated fluid. Furthermore, we show that a time-dependent density profile, created via suitable activation protocols, allows for the conveyance of inclusions along controlled and stable trajectories. In contrast, in states with a steady density, inclusions cannot be held at stable positions, reminiscent of Earnshaw's theorem of electrostatics. We expect these findings to be applicable in a range of experimental systems. The phenomena described here are argued to be distinct from other forms of phoresis such as thermophoresis. [ABSTRACT FROM AUTHOR]

Ensembles of biological and artificial microswimmers produce long-range velocity fields with strong nonequilibrium fluctuations, which result in a dramatic increase in diffusivity of embedded particles (tracers). While such enhanced diffusivity may point to enhanced mixing of the fluid, a rigorous quantification of the mixing efficiency requires analysis of pair dispersion of tracers, rather than simple one–particle diffusivity. Here, we calculate analytically the scale-dependent coefficient of relative diffusivity of passive tracers embedded in a dilute suspension of run-and-tumble microswimmers. Although each tracer is subject to strong fluctuations resulting in large absolute diffusivity, the small-scale relative dispersion is suppressed due to the correlations in fluid velocity which are relevant when the inter-tracer separation is below the persistence length of the swimmer's motion. Our results suggest that the reorientation of swimming direction plays an important role in biological mixing and should be accounted in the design of potential active matter devices capable of effective fluid mixing at microscale. [ABSTRACT FROM AUTHOR]

In many types of cells, binding of molecules to their receptors enables cascades of intracellular chemical reactions to take place (signaling). However, a low level of signaling also occurs in most unstimulated cells. Such basal signaling in resting cells can have many functions, one of which is that it is thought to be required for fast cellular responses to external stimuli. A mechanistic understanding of why this is true and which features of cellular signaling networks make basal signaling necessary for fast responses is unknown. We address this issue by obtaining the time required for activation of common types of cell signaling modules with and without basal signaling. Our results show that the absence of basal signaling does not have any dramatic effects on the response time for signaling modules that exhibit a graded response to increasing stimulus levels. In sharp contrast, signaling modules that exhibit sharp dose-response curves which discriminate sensitively between stimuli to which the cell needs to respond and low-grade inputs (or stochastic noise) require basal signaling for fast cellular responses. In such cases, we find that an optimal level of basal signaling balances the requirements for fast cellular responses while minimizing spurious activation without appropriate stimulation. [ABSTRACT FROM AUTHOR]

Positive feedback regulation is ubiquitous in cell signaling networks, often leading to binary outcomes in response to graded stimuli. However, the role of such feedbacks in clustering, and in spatial spreading of activated molecules, has come to be appreciated only recently. We focus on the latter, using a simple model developed in the context of Ras activation with competing negative and positive feedback mechanisms. We find that positive feedback, in the presence of slow diffusion, results in clustering of activated molecules on the plasma membrane, and rapid spatial spreading as the front of the cluster propagates with a constant velocity (dependent on the feedback strength). The advancing fronts of the clusters of the activated species are rough, with scaling consistent with the Kardar–Parisi–Zhang equation in one dimension. Our minimal model is general enough to describe signal transduction in a wide variety of biological networks where activity in the membrane-proximal region is subject to feedback regulation. [ABSTRACT FROM AUTHOR]

We study the space of all compact structures on a two-dimensional square lattice of size N=6×6. Each structure is mapped onto a vector in N-dimensions according to a hydrophobic model. Previous work has shown that the designabilities of structures are closely related to the distribution of the structure vectors in the N-dimensional space, with highly designable structures predominantly found in low density regions. We use principal component analysis to probe and characterize the distribution of structure vectors, and find a nonuniform density with a single peak. Interestingly, the principal axes of this peak are almost aligned with Fourier eigenvectors, and the corresponding Fourier eigenvalues go to zero continuously at the wave-number for alternating patterns (q=π). These observations provide a stepping stone for an analytic description of the distribution of structural points, and open the possibility of estimating designabilities of realistic structures by simply Fourier transforming the hydrophobicities of the corresponding sequences. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]