Zigzag transitions and nonequilibrium pattern formation in colloidal chains

Paramagnetic colloidal particles that are optically trapped in a linear array can form a zigzag pattern when an external magnetic field induces repulsive interparticle interactions. When the traps are abruptly turned off, the particles form a nonequilibrium expanding pattern with a zigzag symmetry, even when the strength of the magnetic interaction is weaker than that required to break the linear symmetry of the equilibrium state. We show that the transition to the equilibrium zigzag state is always potentially possible for purely harmonic traps. For anharmonic traps that have a finite height, the equilibrium zigzag state becomes unstable above a critical anharmonicity. A normal mode analysis of the equilibrium line configuration demonstrates that increasing the magnetic field leads to a hardening and softening of the spring constants in the longitudinal and transverse directions, respectively. The mode that first becomes unstable is the mode with the zigzag symmetry, which explains the symmetry of nonequilibrium patterns. Our analytically tractable models help to give further insight into the way that the interplay of such factors as the length of the chain, hydrodynamic interactions, thermal fluctuations affect the formation and evolution of the experimentally observed nonequilibrium patterns.Comment: 16 pages, 8 figures; to appear in the Journal of Chemical Physic

Hydrodynamically enforced entropic trapping of Brownian particles

We study the transport of Brownian particles through a corrugated channel caused by a force field containing curl-free (scalar potential) and divergence-free (vector potential) parts. We develop a generalized Fick-Jacobs approach leading to an effective one-dimensional description involving the potential of mean force. As an application, the interplay of a pressure-driven flow and an oppositely oriented constant bias is considered. We show that for certain parameters, the particle diffusion is significantly suppressed via the property of hyrodynamically enforced entropic particle trapping.Comment: 5 pages, 4 figures, in press with Physical Review Letter

Pattern formation in colloidal explosions

We study the non-equilibrium pattern formation that emerges when magnetically repelling colloids, trapped by optical tweezers, are abruptly released, forming colloidal explosions. For multiple colloids in a single trap we observe a pattern of expanding concentric rings. For colloids individually trapped in a line, we observe explosions with a zigzag pattern that persists even when magnetic interactions are much weaker than those that break the linear symmetry in equilibrium. Theory and computer simulations quantitatively describe these phenomena both in and out of equilibrium. An analysis of the mode spectrum allows us to accurately quantify the non-harmonic nature of the optical traps. Colloidal explosions provide a new way to generate well-characterized non-equilibrium behaviour in colloidal systems.Comment: New restructured version (supplementary material goes into main text, no change of content), added journal reference and DOI information; 6 pages, 6 figures, published in Europhysics Letters (EPL

Giant enhancement of hydrodynamically enforced entropic trapping in thin channels

Using our generalized Fick-Jacobs approach [Martens et al., PRL 110, 010601 (2013); Martens et al., Eur. Phys. J. Spec. Topics 222, 2453-2463 (2013)] and extensive Brownian dynamics simulations, we study particle transport through three-dimensional periodic channels of different height. Directed motion is caused by the interplay of constant bias acting along the channel axis and a pressure-driven flow. The tremendous change of the flow profile shape in channel direction with the channel height is reflected in a crucial dependence of the mean particle velocity and the effective diffusion coefficient on the channel height. In particular, we observe a giant suppression of the effective diffusivity in thin channels; four orders of magnitude compared to the bulk value.Comment: 16 pages, 8 figure

Transport of a colloidal particle driven across a temporally oscillating optical potential energy landscape

A colloidal particle is driven across a temporally oscillating one-dimensional optical potential energy landscape and its particle motion is analysed. Different modes of dynamic mode locking are observed and are confirmed with the use of phase portraits. The effect of the oscillation frequency on the mode locked step width is addressed and the results are discussed in light of a high-frequency theory and compared to simulations. Furthermore, the influence of the coupling between the particle and the optical landscape on mode locking is probed by increasing the maximum depth of the optical landscape. Stronger coupling is seen to increase the width of mode locked steps. Finally, transport across the temporally oscillating landscape is studied by measuring the effective diffusion coefficient of a mobile particle, which is seen to be highly sensitive to the driving velocity and mode locking

Pattern Formation Induced by Time-Dependent Advection

We study pattern-forming instabilities in reaction-advection-diffusion systems. We develop an approach based on Lyapunov-Bloch exponents to figure out the impact of a spatially periodic mixing flow on the stability of a spatially homogeneous state. We deal with the flows periodic in space that may have arbitrary time dependence. We propose a discrete in time model, where reaction, advection, and diffusion act as successive operators, and show that a mixing advection can lead to a pattern-forming instability in a two-component system where only one of the species is advected. Physically, this can be explained as crossing a threshold of Turing instability due to effective increase of one of the diffusion constants

Mixing-induced activity in open flows

We develop a theory describing how a convectively unstable active field in an open flow is transformed into absolutely unstable by local mixing. Presenting the mixing region as one with a locally enhanced effective diffusion allows us to find the linear transition point to an unstable global mode analytically. We derive the critical exponent that characterizes weakly nonlinear regimes beyond the instability threshold and compare it with numerical simulations of a full two-dimensional flow problem. The obtained scaling law turns out to be universal as it depends neither on geometry nor on the nature of the mixing region.Comment: 11 pages, 7 figures, published in Physica Scripta; see also Phys. Rev. Lett. 99, 184503 (2007

Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate equation models

Chemical reactions inside cells occur in compartment volumes in the range of atto- to femtolitres. Physiological concentrations realized in such small volumes imply low copy numbers of interacting molecules with the consequence of considerable fluctuations in the concentrations. In contrast, rate equation models are based on the implicit assumption of infinitely large numbers of interacting molecules, or equivalently, that reactions occur in infinite volumes at constant macroscopic concentrations. In this article we compute the finite-volume corrections (or equivalently the finite copy number corrections) to the solutions of the rate equations for chemical reaction networks composed of arbitrarily large numbers of enzyme-catalyzed reactions which are confined inside a small sub-cellular compartment. This is achieved by applying a mesoscopic version of the quasi-steady state assumption to the exact Fokker-Planck equation associated with the Poisson Representation of the chemical master equation. The procedure yields impressively simple and compact expressions for the finite-volume corrections. We prove that the predictions of the rate equations will always underestimate the actual steady-state substrate concentrations for an enzyme-reaction network confined in a small volume. In particular we show that the finite-volume corrections increase with decreasing sub-cellular volume, decreasing Michaelis-Menten constants and increasing enzyme saturation. The magnitude of the corrections depends sensitively on the topology of the network. The predictions of the theory are shown to be in excellent agreement with stochastic simulations for two types of networks typically associated with protein methylation and metabolism.Comment: 13 pages, 4 figures; published in The Journal of Chemical Physic