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A. A. Louis

Publications and source records attributed to A. A. Louis.

At least 19 recordsLinked to original sources

How Peclet number affects microstructure and transient cluster aggregation in sedimenting colloidal suspensions

We study how varying the P éclet number (Pe) affects the steady state sedimentation of colloidal particles that interact through short-ranged attractions. By employing a hybrid molecular dynamics simulation method we demonstrate that the average sedimentation velocity changes from a non- monotonic dependence on packing fraction ϕ at low Pe numbers, to a monotonic decrease with ϕ at higher Pe numbers. At low Pe number the pair correlation functions are close to their equilibrium values, but as the Pe number increases, important deviations from equilibrium forms are observed. Although the attractive forces we employ are not strong enough to form permanent clusters, they do induce transient clusters whose behaviour is also affected by Pe number. In particular, clusters are more likely to fragment and less likely to aggregate at larger Pe numbers, and the probability of finding larger clusters decreases with increasing Pe number. Interestingly, the life-time of the clusters is more or less independent of Pe number in the range we study. Instead, the change in cluster distribution occurs because larger clusters are less likely to form with increasing Pe number. These results illustrate some of the subtleties that occur in the crossover from equilibrium like to purely non-equilibrium behaviour as the balance between convective and thermal forces changes.

cond-mat.stat-mech

Complex dynamics of knotted filaments in shear flow

Coarse-grained simulations are used to demonstrate that knotted filaments in shear flow at zero Reynolds number exhibit remarkably rich dynamic behaviour. For stiff filaments that are weakly deformed by the shear forces, the knotted filaments rotate like rigid objects in the flow. But away from this regime the interplay between between shear forces and the flexibility of the filament leads to intricate regular and chaotic modes of motion that can be divided into distinct families. The set of accessible mode families depends to first order on a dimensionless number that relates the filament length, the elastic modulus, the friction per unit length and the shear rate.

cond-mat.soft

Confinement of knotted polymers in a slit

We investigate the effect of knot type on the properties of a ring polymer confined to a slit. For relatively wide slits, the more complex the knot, the more the force exerted by the polymer on the walls is decreased compared to an unknotted polymer of the same length. For more narrow slits the opposite is true. The crossover between these two regimes is, to first order, at smaller slit width for more complex knots. However, knot topology can affect these trends in subtle ways. Besides the force exerted by the polymers, we also study other quantities such as the monomer-density distribution across the slit and the anisotropic radius of gyration.

cond-mat.soft

Effect of topology on dynamics of knots in polymers under tension

We use computer simulations to compare the dynamical behaviour of torus and even-twist knots in polymers under tension. The knots diffuse through a mechanism similar to reptation. Their friction coefficients grow linearly with average knot length for both knot types. For similar complexity, however, the torus knots diffuse faster than the even twist knots. The knot-length auto-correlation function exhibits a slow relaxation time that can be linked to a breathing mode. Its timescale depends on knot type, being typically longer for torus than for even-twist knots. These differences in dynamical behaviour are interpreted in terms of topological features of the knots.

cond-mat.soft

Self-assembly, modularity and physical complexity

We present a quantitative measure of physical complexity, based on the amount of information required to build a given physical structure through self-assembly. Our procedure can be adapted to any given geometry, and thus to any given type of physical system. We illustrate our approach using self-assembling polyominoes, and demonstrate the breadth of its potential applications by quantifying the physical complexity of molecules and protein complexes. This measure is particularly well suited for the detection of symmetry and modularity in the underlying structure, and allows for a quantitative definition of structural modularity. Furthermore we use our approach to show that symmetric and modular structures are favoured in biological self-assembly, for example of protein complexes. Lastly, we also introduce the notions of joint, mutual and conditional complexity, which provide a useful distance measure between physical structures.

cond-mat.stat-mech

The Effects of Inter-particle Attractions on Colloidal Sedimentation

We use a mesoscopic simulation technique to study the effect of short-ranged inter-particle attraction on the steady-state sedimentation of colloidal suspensions. Attractions increase the average sedimentation velocity $v_s$ compared to the pure hard-sphere case, and for strong enough attractions, a non-monotonic dependence on the packing fraction $ϕ$ with a maximum velocity at intermediate $ϕ$ is observed. Attractions also strongly enhance hydrodynamic velocity fluctuations, which show a pronounced maximum size as a function of $ϕ$. These results are linked to a complex interplay between hydrodynamics and the formation and break-up of transient many-particle clusters.

cond-mat.soft

The crossover from single file to Fickian diffusion

The crossover from single-file diffusion, where the mean-square displacement scales as ~t^(1/2), to normal Fickian diffusion, where ~t$, is studied as a function of channel width for colloidal particles. By comparing Brownian dynamics to a hybrid molecular dynamics and mesoscopic simulation technique, we can study the effect of hydrodynamic interactions on the single file mobility and on the crossover to Fickian diffusion for wider channel widths. For disc-like particles with a steep interparticle repulsion, the single file mobilities for different particle densities are well described by the exactly solvable hard-rod model. This holds both for simulations that include hydrodynamics, as well as for those that don't. When the single file constraint is lifted, then for particles of diameter σand pipe of width $L$ such that (L- 2 σ)/σ= δ_c << 1 the particles can be described as hopping past one-another in an average time t_{hop}. For shorter times t << t_{hop} the particles still exhibit sub-diffusive behaviour, but at longer times t > t_{hop}, normal Fickian diffusion sets in with an effective diffusion constant D_{hop} ~ t_{hop}^(1/2). For the Brownian particles, t_{hop} ~ 1/δ_c^(2) when δ<< 1, but when hydrodynamic interactions are included, we find a stronger dependence than δ_c^{-2}. We attribute this difference to short-range lubrication forces that make it more difficult for particles to hop past each other in very narrow channels.

cond-mat.soft

Knot-controlled ejection of a polymer from a virus capsid

We present a numerical study of the effect of knotting on the ejection of flexible and semiflexible polymers from a spherical, virus-like capsid. The polymer ejection rate is primarily controlled by the knot, which moves to the hole in the capsid and then acts as a ratchet. Polymers with more complex knots eject more slowly and, for large knots, the knot type, and not the flexibility of the polymer, determines the rate of ejection. We discuss the relation of our results to the ejection of DNA from viral capsids and conjecture that this process has the biological advantage of unknotting the DNA before it enters a cell.

q-bio.BM

The interplay between hydrodynamic and Brownian fluctuations in sedimenting colloidal suspensions

We apply a hybrid Molecular Dynamics and mesoscopic simulation technique to study the steady-state sedimentation of hard sphere particles for Peclet numbers (Pe) ranging from 0.08 to 12. Hydrodynamic back-flow causes a reduction of the average sedimentation velocity relative to the Stokes velocity. We find that this effect is independent of Pe number. Velocity fluctuations show the expected effects of thermal fluctuations at short correlation times. At longer times, non-equilibrium hydrodynamic fluctuations are visible, and their character appears to be independent of the thermal fluctuations. The hydrodynamic fluctuations dominate the diffusive behavior even for modest Pe number, while conversely the short-time fluctuations are dominated by thermal effects for a surprisingly large Pe numbers. Inspired by recent experiments, we also study finite sedimentation in a horizontal planar slit. In our simulations distinct lateral patterns emerge, in agreement with observations in the experiments.

cond-mat.soft

Phase diagram of model anisotropic particles with octahedral symmetry

We computed the phase diagram for a system of model anisotropic particles with six attractive patches in an octahedral arrangement. We chose to study this model for a relatively narrow value of the patch width where the lowest-energy configuration of the system is a simple cubic crystal. At this value of the patch width, there is no stable vapour-liquid phase separation, and there are three other crystalline phases in addition to the simple cubic crystal that is most stable at low pressure. Firstly, at moderate pressures, it is more favourable to form a body-centred cubic crystal, which can be viewed as two interpenetrating, and almost non-interacting, simple cubic lattices.Secondly, at high pressures and low temperatures, an orientationally ordered face-centred cubic structure becomes favourable. Finally, at high temperatures a face-centred cubic plastic crystal is the most stable solid phase.

cond-mat.soft

Hydrodynamic interactions and Brownian forces in colloidal suspensions: Coarse-graining over time and length-scales

We describe in detail how to implement a coarse-grained hybrid Molecular Dynamics and Stochastic Rotation Dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The importance of carefully tuning the simulation parameters to correctly resolve the multiple time and length-scales of this problem is emphasized. We systematically analyze how our coarse-graining scheme resolves dimensionless hydrodynamic numbers such as the Reynolds number, the Schmidt number, the Mach number, the Knudsen number, and the Peclet number. The many Brownian and hydrodynamic time-scales can be telescoped together to maximize computational efficiency while still correctly resolving the physically relevant physical processes. We also show how to control a number of numerical artifacts, such as finite size effects and solvent induced attractive depletion interactions. When all these considerations are properly taken into account, the measured colloidal velocity auto-correlation functions and related self diffusion and friction coefficients compare quantitatively with theoretical calculations. By contrast, these calculations demonstrate that, notwithstanding its seductive simplicity, the basic Langevin equation does a remarkably poor job of capturing the decay rate of the velocity auto-correlation function in the colloidal regime, strongly underestimating it at short times and strongly overestimating it at long times. Finally, we discuss in detail how to map the parameters of our method onto physical systems, and from this extract more general lessons that may be relevant for other coarse-graining schemes such as Lattice Boltzmann or Dissipative Particle Dynamics.

cond-mat.soft

Stick boundary conditions and rotational velocity auto-correlation functions for colloidal particles in a coarse-grained representation of the solvent

We show how to implement stick boundary conditions for a spherical colloid in a solvent that is coarse-grained by the method of stochastic rotation dynamics. This allows us to measure colloidal rotational velocity auto-correlation functions by direct computer simulation. We find quantitative agreement with Enskog theory for short times and with hydrodynamic mode-coupling theory for longer times. For aqueous colloidal suspensions, the Enskog contribution to the rotational friction is larger than the hydrodynamic one when the colloidal radius drops below 35nm.

cond-mat.soft

Coarse-graining diblock copolymer solutions: a macromolecular version of the Widom-Rowlinson model

We propose a systematic coarse-grained representation of block copolymers, whereby each block is reduced to a single ``soft blob'' and effective intra- as well as intermolecular interactions act between centres of mass of the blocks. The coarse-graining approach is applied to simple athermal lattice models of symmetric AB diblock copolymers, in particular to a Widom-Rowlinson-like model where blocks of the same species behave as ideal polymers (i.e. freely interpenetrate), while blocks of opposite species are mutually avoiding walks. This incompatibility drives microphase separation for copolymer solutions in the semi-dilute regime. An appropriate, consistent inversion procedure is used to extract effective inter- and intramolecular potentials from Monte Carlo results for the pair distribution functions of the block centres of mass in the infinite dilution limit.

cond-mat.soft

Polymer solutions: from hard monomers to soft polymers

A coarse-graining strategy for dilute and semi-dilute solutions of interacting polymers, and of colloid polymer mixtures is briefly described. Monomer degrees of freedom are traced out to derive an effective, state dependent pair potential between the polymer centres of mass. The cross-over between good and poor solvent conditions is discussed within a scaling analysis. The method is extended to block copolymers represented as "necklaces" of soft "blobs", and its success is illustrated here in the case of a symmetric diblock copolymer which exhibits microphase separation.

cond-mat.soft

From concentration profiles to polymer osmotic equations of state

We show that equilibrium monomer and centre-of-mass concentration profiles of lattice polymers in a gravitational field, computed by Monte-Carlo simulations, provide an accurate and efficient road to the osmotic equation-of-state of polymer solutions, via a straightforward application of the hydrostatic equilibrium condition. The method yields the full equation of state over a wide range of concentrations from a single simulation, and does not suffer from significant finite size effects. It has been applied to self-avoiding walk polymer chains with nearest neighbour monomer attractions, from the good solvent to the theta solvent regimes. The consistency of the method has been carefully checked by varying the strength of the gravitational field.

cond-mat.soft

Hydrodynamic and Brownian Fluctuations in Sedimenting Suspensions

We use a mesoscopic computer simulation method to study the interplay between hydrodynamic and Brownian fluctuations during steady-state sedimentation of hard sphere particles for Peclet numbers (Pe) ranging from 0.1 to 15. Even when the hydrodynamic interactions are an order of magnitude weaker than Brownian forces, they still induce backflow effects that dominate the reduction of the average sedimentation velocity with increasing particle packing fraction. Velocity fluctuations, on the other hand, begin to show nonequilibrium hydrodynamic character for Pe > 1

cond-mat.soft

A density--functional study of interfacial properties of colloid--polymer mixtures

Interfacial properties of colloid--polymer mixtures are examined within an effective one--component representation, where the polymer degrees of freedom are traced out, leaving a fluid of colloidal particles interacting via polymer--induced depletion forces. Restriction is made to zero, one and two--body effective potentials, and a free energy functional is used which treats colloid excluded volume correlations within Rosenfeld's Fundamental Measure Theory, and depletion--induced attraction within first--order perturbation theory. This functional allows a consistent treatment of both ideal and interacting polymers. The theory is applied to surface properties near a hard wall, to the depletion interaction between two walls, and to the fluid--fluid interface of demixed colloid--polymer mixtures. The results of the present theory compare well with predictions of a fully two--component representation of mixtures of colloids and ideal polymers (the Asakura--Oosawa model), and allow a systematic investigation of the effects of polymer--polymer interactions on interfacial properties. In particular, the wall surface tension is found to be significantly larger for interacting than for ideal polymers, while the opposite trend is predicted for the fluid--fluid interfacial tension.

cond-mat.soft

Dynamic Colloidal Stabilization by Nanoparticle Halos

We explore the conditions under which colloids can be stabilized by the addition of smaller particles. The largest repulsive barriers between colloids occur when the added particles repel each other with soft interactions, leading to an accumulation near the colloid surfaces. At lower densities these layers of mobile particles (nanoparticle halos) result in stabilization, but when too many are added, the interactions become attractive again. We systematically study these effects --accumulation repulsion, re-entrant attraction, and bridging -- by accurate integral equation techniques.

cond-mat.soft