450 research outputs found
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
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