arXiv subjects

Arthur V. Straube

Publications and source records attributed to Arthur V. Straube.

At least 37 records · Page 2Linked to original sources

arXiv2016

Functional colloidal micro-sieves assembled and guided above a channel-free magnetic striped film

Colloidal inclusions in lab-on-a-chip devices can be used to perform analytic operations in a non-invasive fashion. We demonstrate here a novel approach to realize fast and reversible micro-sieving operations by manipulating and transporting colloidal chains via mobile domain walls in a magnetic structured substrate. We show that this technique allows to precisely move and sieve non-magnetic particles, to tweeze microscopic cargos or to mechanically compress highly dense colloidal monolayers.

cond-mat.soft↗

arXiv2015

Colloidal particles driven across periodic optical potential energy landscapes

We study the motion of colloidal particles driven by a constant force over a periodic optical potential energy landscape. Firstly, the average particle velocity is found as a function of the driving velocity and the wavelength of the optical potential energy landscape. The relationship between average particle velocity and driving velocity is found to be well described by a theoretical model treating the landscape as sinusoidal, but only at small trap spacings. At larger trap spacings, a non-sinusoidal model for the landscape must be used. Subsequently, the critical velocity required for a particle to move across the landscape is determined as a function of the wavelength of the landscape. Finally, the velocity of a particle driven at a velocity far exceeding the critical driving velocity is examined. Both of these results are again well described by the two theoretical routes, for small and large trap spacings respectively. Brownian motion is found to have a significant effect on the critical driving velocity, but a negligible effect when the driving velocity is high.

cond-mat.soft↗

arXiv2014

Tunable interactions between paramagnetic colloidal particles driven in a modulated ratchet potential

We study experimentally and theoretically the interactions between paramagnetic particles dispersed in water and driven above the surface of a stripe patterned magnetic garnet film. An external rotating magnetic field modulates the stray field of the garnet film and generates a translating potential landscape which induces directed particle motion. By varying the ellipticity of the rotating field, we tune the inter-particle interactions from net attractive to net repulsive. For attractive interactions, we show that pairs of particles can approach each other and form stable doublets which afterwards travel along the modulated landscape at a constant mean speed. We measure the strength of the attractive force between the moving particles and propose an analytically tractable model that explains the observations and is in quantitative agreement with experiment.

cond-mat.soft↗

arXiv2013

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.

cond-mat.stat-mech↗

arXiv2013

Synchronous versus asynchronous transport of a paramagnetic particle in a modulated ratchet potential

We present a combined experimental and theoretical study describing the dynamical regimes displayed by a paramagnetic colloidal particle externally driven above a stripe-patterned magnetic garnet film. A circularly polarized rotating magnetic field modulates the stray field of the garnet film and generates a translating periodic potential which induces particle motion. Increasing the driving frequency, we observe a transition from a phase-locked motion with constant speed to a sliding dynamics characterized by a lower speed due to the loss of synchronization with the traveling potential. We explain the experimental findings with an analytically tractable theoretical model and interpret the particle dynamics in the presence of thermal noise. The model is in good quantitative agreement with the experiments.

cond-mat.stat-mech↗

arXiv2012

Rigorous elimination of fast stochastic variables from the linear noise approximation using projection operators

The linear noise approximation (LNA) offers a simple means by which one can study intrinsic noise in monostable biochemical networks. Using simple physical arguments, we have recently introduced the slow-scale LNA (ssLNA) which is a reduced version of the LNA under conditions of timescale separation. In this paper, we present the first rigorous derivation of the ssLNA using the projection operator technique and show that the ssLNA follows uniquely from the standard LNA under the same conditions of timescale separation as those required for the deterministic quasi-steady state approximation. We also show that the large molecule number limit of several common stochastic model reduction techniques under timescale separation conditions constitutes a special case of the ssLNA.

cond-mat.stat-mech↗

arXiv2011

Limitations of the stochastic quasi-steady-state approximation in open biochemical reaction networks

The application of the quasi-steady-state approximation to the Michaelis-Menten reaction embedded in large open chemical reaction networks is a popular model reduction technique in deterministic and stochastic simulations of biochemical reactions inside cells. It is frequently assumed that the predictions of the reduced master equations obtained using the stochastic quasi-steady-state approach are in very good agreement with the predictions of the full master equations, provided the conditions for the validity of the deterministic quasi-steady-state approximation are fulfilled. We here use the linear-noise approximation to show that this assumption is not generally justified for the Michaelis-Menten reaction with substrate input, the simplest example of an open embedded enzyme reaction. The reduced master equation approach is found to considerably overestimate the size of intrinsic noise at low copy numbers of molecules. A simple formula is obtained for the relative error between the predictions of the reduced and full master equations for the variance of the substrate concentration fluctuations. The maximum error is reached when modeling moderately or highly efficient enzymes, in which case the error is approximately 30%. The theoretical predictions are validated by stochastic simulations using experimental parameter values for enzymes involved in proteolysis, gluconeogenesis and fermentation.

cond-mat.stat-mech↗

arXiv2011

How accurate are the non-linear chemical Fokker-Planck and chemical Langevin equations?

The chemical Fokker-Planck equation and the corresponding chemical Langevin equation are commonly used approximations of the chemical master equation. These equations are derived from an uncontrolled, second-order truncation of the Kramers-Moyal expansion of the chemical master equation and hence their accuracy remains to be clarified. We use the system-size expansion to show that chemical Fokker-Planck estimates of the mean concentrations and of the variance of the concentration fluctuations about the mean are accurate to order $Ω^{-3/2}$ for reaction systems which do not obey detailed balance and at least accurate to order $Ω^{-2}$ for systems obeying detailed balance, where $Ω$ is the characteristic size of the system. Hence the chemical Fokker-Planck equation turns out to be more accurate than the linear-noise approximation of the chemical master equation (the linear Fokker-Planck equation) which leads to mean concentration estimates accurate to order $Ω^{-1/2}$ and variance estimates accurate to order $Ω^{-3/2}$. This higher accuracy is particularly conspicuous for chemical systems realized in small volumes such as biochemical reactions inside cells. A formula is also obtained for the approximate size of the relative errors in the concentration and variance predictions of the chemical Fokker-Planck equation, where the relative error is defined as the difference between the predictions of the chemical Fokker-Planck equation and the master equation divided by the prediction of the master equation. For dimerization and enzyme-catalyzed reactions, the errors are typically less than few percent even when the steady-state is characterized by merely few tens of molecules.

q-bio.QM↗

arXiv2011

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.

cond-mat.stat-mech↗

arXiv2011

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.

cond-mat.soft↗

arXiv2010

Superexponential droplet fractalization as a hierarchical formation of dissipative compactons

We study the dynamics of a thin film over a substrate heated from below in a framework of a strongly nonlinear one-dimensional Cahn-Hillard equation. The evolution leads to a fractalization into smaller and smaller scales. We demonstrate that a primitive element in the appearing hierarchical structure is a dissipative compacton. Both direct simulations and the analysis of a self-similar solution show that the compactons appear at superexponentially decreasing scales, what means vanishing dimension of the fractal.

nlin.PS↗

arXiv2009

Stick-slip dynamics of an oscillated sessile drop

The dynamics of an oscillated sessile drop of incompressible liquid with the focus on the contact line hysteresis is under theoretical consideration. The solid substrate is subject to transverse oscillations, which are assumed small amplitude and high frequency. The dynamic boundary condition that involves an ambiguous dependence of the contact angle on the contact line velocity is applied: the contact line starts to move only when the deviation of the contact angle exceeds a certain critical value. As a result, the stick-slip dynamics can be observed. The frequency response of surface oscillations on the substrate and at the pole of the drop are analyzed. It is shown that novel features such as the emergence of antiresonant frequency bands and nontrivial competition of different resonances are caused by contact line hysteresis.

physics.flu-dyn↗

arXiv2008

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.

nlin.PS↗

arXiv2008

The impact of diffusion on confined oscillated bubbly fluid

We consider the dynamics of monodisperse bubbly fluid confined by two plane solid walls and subjected to small-amplitude high-frequency transversal oscillations. The frequency these oscillations is assumed to be high in comparison with typical relaxation times for a single bubble, but comparable with the eigenfrequency of volume oscillations. A time-averaged description accounting for mutual coupling of the phases and the diffusivity of bubbles is applied. We find nonuniform steady states with the liquid quiescent on average. At relatively low frequencies accumulation of bubbles either at the walls or in planes oriented parallel to the walls is detected. These one-dimensional states are shown to be unstable. At relatively high frequencies the bubbles accumulate at the central plane and the solution is stable.

physics.flu-dyn↗

arXiv2008

Linear oscillations of a compressible hemispherical bubble on a solid substrate

The linear natural and forced oscillations of a hemispherical bubble on a solid substrate are under theoretical consideration. The contact line dynamics is taken into account with the Hocking condition, which eventually leads to interaction of the shape and volume oscillations. Resonant phenomena, mostly pronounced for the bubble with the fixed contact line or with the fixed contact angle, are found out. The limiting case of weakly compressible bubble is studied. The general criterion identifying whether the compressibility of a bubble can be neglected is obtained.

physics.flu-dyn↗

arXiv2008

Mixing-induced global modes in open active flow

We describe how a convectively unstable active field in an open flow configuration becomes absolutely unstable due to local mixing. A representation of the mixing region as those with locally enhanced effective diffusion allows us to find the linear transition point to unstable global mode analytically. We derive the critical exponent characterizing weakly nonlinear regimes beyond instability and compare it with numerical simulations of a full two-dimensional flow problem.

nlin.PS↗

arXiv2007

Particle entrapment as a feedback effect

We consider a suspension of polarizable particles under the action of traveling wave dielectrophoresis (DEP) and focus on particle induced effects. In a situation where the particles are driven by the DEP force, but no external forces are exerted on the fluid, the joint motion of the particles can induce a steady fluid flow, which leads to particle entrapment. This feedback effect is proven to be non-negligible even for small volume concentration of particles.

physics.flu-dyn↗

arXiv2006

Steady Stokes flow with long-range correlations, fractal Fourier spectrum, and anomalous transport

We consider viscous two-dimensional steady flows of incompressible fluids past doubly periodic arrays of solid obstacles. In a class of such flows, the autocorrelations for the Lagrangian observables decay in accordance with the power law, and the Fourier spectrum is neither discrete nor absolutely continuous. We demonstrate that spreading of the droplet of tracers in such flows is anomalously fast. Since the flow is equivalent to the integrable Hamiltonian system with 1 degree of freedom, this provides an example of integrable dynamics with long-range correlations, fractal power spectrum, and anomalous transport properties.

cond-mat.stat-mech↗