In many natural and artificial devices diffusive transport takes place in confined geometries with corrugated boundaries. Such boundaries cause both entropic and hydrodynamic effects, which have been studied only for the case of spherical particles. Here we experimentally investigate diffusion of particles of elongated shape confined into a corrugated quasi-two-dimensional channel. Elongated shape causes complex excluded-volume interactions between particle and channel walls which reduce the accessible configuration space and lead to novel entropic free energy effects. The extra rotational degree of freedom also gives rise to a complex diffusivity matrix that depends on both the particle location and its orientation. We further show how to extend the standard Fick-Jacobs theory to incorporate combined hydrodynamic and entropic effects, so as, for instance, to accurately predict experimentally measured mean first passage times along the channel. Our approach can be used as a generic method to describe translational diffusion of anisotropic particles in corrugated channels.
We investigate - with Monte Carlo computer simulations - the phase behaviour of dimeric colloidal molecules on periodic substrates with square symmetry. The molecules are formed in a two-dimensional suspension of like charged colloids subject to periodic external confinement, which can be experimentally realized by optical methods. We study the evolution of positional and orientational order by varying the temperature across the melting transition. We propose and evaluate appropriate order parameters as well as the specific heat capacity and show that the decay of positional correlations belon…
Cellulose nanocrystals (CNC) can be considered as model colloidal rods and have practical applications in the formation of soft materials with tailored anisotropy. Here, we employ two contrasting microfluidic devices to quantitatively elucidate the role of shearing and extensional flows on the alignment of a dilute CNC dispersion. Characterization of the flow field by micro-particle image velocimetry is coupled to flow-induced birefringence analysis to quantify the deformation rate--alignment relationship. The deformation rate required for CNC alignment is 4$\times$ smaller in extension than i…
Inclusions dissolved in an anisotropic quasi-2D membrane acquire new types of interactions that can drive assembly of complex structures and patterns. We study colloidal membranes composed of a binary mixture of long and short rods, such that the length ratio of the long to short rods is approximately two. At very low volume fractions, short rods dissolve in the membrane of long rods by strongly anchoring to the membrane polymer interface. At higher fractions, the dissolved short rods phase separate from the background membrane, creating a composite structure comprised of bilayer droplets enri…
Complex fluids containing low concentrations of slender colloidal rods can display a high viscosity, while little flow is needed to thin the fluid. This feature makes slender rods essential constituents in industrial applications and biology. Though this behaviour strongly depends on the rod-length, so far no direct relation could be identified. We employ a library of filamentous viruses to study the effect of rod size and flexibility on the zero-shear viscosity and shear-thinning behaviour. Rheology and small angle neutron scattering data are compared to a revised version of the standard theo…
Shear history plays an important role in determining the linear and nonlinear rheological response of colloidal gels and can be used for tuning their structure and flow properties. Increasing colloidal particle aspect ratio lowers the critical volume fraction for gelation due to an increase of the particle excluded volume. Using a combination of rheology and confocal microscopy we investigate the effect of steady and oscillatory pre-shear history on the structure and rheology of colloidal gels formed by silica spheres and rods of length L and diameter D (L/D = 10) dispersed in 11 M CsCl soluti…
We report on the identification and quantitative characterization of elementary edge and screw dislocations in a colloidal smectic phase of tip-labeled rods. Thanks to the micrometer layer spacing, direct visualization of dislocations has been performed at the \textit{smectic periodicity scale} by optical fluorescence microscopy. As a result, the displacement field around an edge dislocation has been experimentally established and compared with the profile predicted by elastic theory. Elementary screw dislocations have been also evidenced, for which the core size as well as the \textit{in situ…
Understanding the hydrodynamic alignment of colloidal rods in polymer solutions is pivotal for manufacturing structurally ordered materials. How polymer crowding influences the flow-induced alignment of suspended colloidal rods remains unclear when rods and polymers share similar length-scales. We tackle this problem by analyzing the alignment of colloidal rods suspended in crowded polymer solutions, and comparing against the case where crowding is provided by additional colloidal rods in a pure solvent. We find that the polymer dynamics govern the onset of shear-induced alignment of colloidal…
We study the layer-to-layer diffusion in smectic-A liquid crystals of colloidal hard rods with different length-to-diameter ratios using computer simulations. The layered arrangement of the smectic phase yields a hopping-type diffusion due to the presence of permanent barriers and transient cages. Remarkably, we detect stringlike clusters composed of inter-layer rods moving cooperatively along the nematic director. Furthermore, we find that the structural relaxation in equilibrium smectic phases shows interesting similarities with that of out-of-equilibrium supercooled liquids, although there …
Self-diffusion in isotropic and liquid crystalline phases of fd virus colloidal rods: a combined single particle tracking and differential dynamic microscopy study
Understanding the relaxation dynamics of colloidal suspensions is crucial to identify the elements that influence the mobility of their constituents, assess their macroscopic response across the relevant time and length scales, and thus disclose the fundamentals underpinning their exploitation in formulation engineering. In this work, we specifically assess the impact of long-ranged ordering on the relaxation dynamics of suspensions of soft-repulsive rod-like particles, which are able to self-organise into nematic and smectic liquid-crystalline phases. By performing Dynamic Monte Carlo simulat…
We assess the possibility of shear banding of semidilute rod-like colloidal suspensions under steady shear ow very close to the isotropic-nematic spinodal, using a combination of rheology, small angle neutron scattering, and laser Doppler velocimetry. Model systems are employed which allow for a length and stiffness variation of the particles. The rheological signature reveals that these systems are strongly shear thinning at moderate shear rates. It is shown that the longest and most flexible rods undergo the strongest shear thinning and have the greatest potential to form shear bands. Althou…
In the absence of advection, confined diffusion characterizes transport in many natural and artificial devices, such as ionic channels, zeolites, and nanopores. While extensive theoretical and numerical studies on this subject have produced many important predictions, experimental verifications of the predictions are rare. Here, we experimentally measure colloidal diffusion times in microchannels with periodically varying width and contrast results with predictions from the Fick-Jacobs theory and Brownian dynamics simulation. While the theory and simulation correctly predict the entropic effec…
Using a combination of theory and experiments we study the interface between two immiscible domains in a colloidal membrane composed of rigid rods of different lengths. Geometric considerations of rigid rod packing imply that a domain of sufficiently short rods in a background membrane of long rods is more susceptible to twist than the inverse structure, a long-rod domain in a short-rod membrane background. The tilt at the inter-domain edge forces splay, which in turn manifests as a spontaneous edge curvature whose energetics are controlled by the length asymmetry of constituent rods. A thermo…
In order to investigate the coupling between the degrees of alignment of elongated particles in binary nematic dispersions, surfactant stabilized single-wall carbon nanotubes (CNTs) have been added to nematic suspensions of colloidal rodlike viruses in aqueous solution.We have independently measured the orientational order parameter of both components of the guest-host system by means of polarized Raman spectroscopy and by optical birefringence, respectively. Our system allows us therefore to probe the regime where the guest particles (CNTs) are shorter and thinner than the fd virus host parti…
We study suspensions of semi-flexible colloidal rods and biopolymers using an Onsager-type second-virial functional for a segmented-chain model. For suspensions of thin and thick fd virus particles we calculate phase diagrams in quantitative agreement with experimental observations, and we find their effective state-point dependent shape to be much shorter and thicker than the actual shape. We also calculate the stretching of worm-like micelles in a host fd virus solution, again finding agreement with experiments. For both systems, our results show that the fd virus stiffness can play a key ro…
Detailed control over the motion of colloidal particles is relevant in many applications in colloidal science such as lab-on-a-chip devices. Here, we use an external magnetic field to assemble paramagnetic colloidal spheres into colloidal rods of several lengths. The rods reside above a square magnetic pattern and are transported via modulation of the direction of the external magnetic field. The rods behave like bipeds walking above the pattern. Depending on their length, the bipeds perform topologically distinct classes of protected walks above the pattern. We demonstrate that it is possible…
We study theoretically the effect of a gravitational field on the equilibrium behaviour of a colloidal suspension of rods with different length-to-width aspect ratios. The bulk phases of the system are described with analytical equations of state. The gravitational field is then incorporated via sedimentation path theory, which assumes a local equilibrium condition at each altitude of the sample. The bulk phenomenology is significantly enriched by the presence of the gravitational field. In a suspension of elongated rods with five stable phases in bulk, the gravitational field stabilizes up to…
We formulate a density functional theory that describes the phase behavior of hard rods and depleting polymers, as realized in recent experiments on suspensions of \emph{fd} virus and non-adsorbing polymer. The theory predicts the relative stability of nematic droplets, stacked smectic columns, and a recently discovered phase of isolated monolayers of rods, or colloidal membranes. We find that a minimum rod aspect ratio is required for stability of colloidal membranes and that collective protrusion undulations are the dominant effect that stabilizes this phase. The theoretical predictions are …
In the presence of a non-adsorbing polymer, monodisperse rod-like colloids assemble into one-rod-length thick liquid-like monolayers, called colloidal membranes. The density of the rods within a colloidal membrane is determined by a balance between the osmotic pressure exerted by the enveloping polymer suspension and the repulsion between the colloidal rods. We developed a microfluidic device for continuously observing an isolated membrane while dynamically controlling the osmotic pressure of the polymer suspension. Using this technology we measured the membrane rod density over a range of osm…
Using computer simulations, we explore how thermal noise-induced randomness in a self-assembled photonic crystal affects its photonic band gaps (PBGs). We consider a two-dimensional photonic crystal comprised of a self-assembled array of parallel dielectric hard rods of infinite length with circular or square cross section. We find the PBGs can exist over a large range of intermediate packing densities. Counterintuitively, the largest band gap does not always appear at the packing density where the crystal is most ordered, despite the randomness inherent in any self-assembled structure. For ro…
The dynamics of colloidal suspension confined within porous materials strongly differs from that in the bulk. In particular, within porous materials, the presence of boundaries with complex shapes entangles the longitudinal and transverse degrees of freedom inducing a coupling between the transport of the suspension and the density inhomogeneities induced by the walls. Colloidal suspension confined within model porous media are characterized by means of active microrheology where a net force is applied on a single colloid (tracer particle) whose transport properties are then studied. The traje…
There is now convincing evidence that inter-particle frictional contacts are essential for observing shear-thickening in concentrated suspensions of compact particles. While this has inspired many strategies to tailor the rheology in these systems, in the more general case, viz-a-viz suspensions of anisotropic particles, the mechanism of shear-thickening remains unclear. Here through simultaneous measurements of the bulk viscosity and the first Normal stress difference, we show that strong shear thickening in suspensions of colloidal rods is accompanied by large positive normal stresses, indic…
In modern transformation optics, one explores metamaterials with properties that vary from point to point in space and time, suitable for applications in devices such as an "optical invisibility cloak" and an "optical black hole". We propose an approach to construct spatially varying and switchable metamaterials that are based on colloidal dispersions of metal nano-rods (NRs) in dielectric fluids, in which dielectrophoretic forces, originating in the electric field gradients, create spatially varying configurations of aligned NRs. The electric field controls orientation and concentration of NR…
We construct a phenomenological Landau-de Gennes theory for hard colloidal rods by performing an order parameter expansion of the chemical-potential dependent grand potential. By fitting the coefficients to known results of Onsager theory, we are not only able to describe the isotropic-nematic phase transition as function of density, including the well-known density jump, but also the isotropic-nematic planar interface. The resulting theory is applied in calculations of the isotropic core size in a radial hedgehog defect, the density dependence of linear defects of hard rods in square confinem…
Spherically-symmetric atom-centered descriptors of atomic environments have been widely used for constructing potential or free energy surfaces of atomistic and colloidal systems and to characterize local structures using machine learning techniques. However, when particle shapes are non-spherical, as in the case of rods and ellipsoids, standard spherically-symmetric structure functions alone produce imprecise descriptions of local environments. In order to account for the effects of orientation, we introduce two- and three-body orientation-dependent particle-centered descriptors for systems c…
In the presence of a non-adsorbing polymer, monodisperse rod-like particles assemble into colloidal membranes, which are one rod-length thick liquid-like monolayers of aligned rods. Unlike 3D edgeless bilayer vesicles, colloidal monolayer membranes form open structures with an exposed edge, thus presenting an opportunity to study physics of thin elastic sheets. Membranes assembled from single-component chiral rods form flat disks with uniform edge twist. In comparison, membranes comprised of mixture of rods with opposite chiralities can have the edge twist of either handedness. In this limit d…
We analyse a binary mixture of colloidal parallel hard cylindrical particles with identical diameters but dissimilar lengths $L_1$ and $L_2$, with $s=L_2/L_1=3$, confined by two parallel hard walls in a planar slit-pore geometry, using a fundamental--measure density functional theory. This model presents nematic (N) and two types of smectic (S) phases, with first- and second-order N-S bulk transitions and S-S demixing, and surface behaviour at a single hard wall which includes complete wetting by the S phase mediated (or not) by an infinite number of surface-induced layering (SIL) transitions.…
The depletion interaction mediated by non-adsorbing polymers promotes condensation and assembly of repulsive colloidal particles into diverse higher-order structures and materials. One example, with particularly rich emergent behaviors, is the formation of two-dimensional colloidal membranes from a suspension of filamentous $\it{fd}$ viruses, which act as rods with effective repulsive interactions, and dextran, which acts as a condensing, depletion-inducing agent. Colloidal membranes exhibit chiral twist even when the constituent virus mixture lacks macroscopic chirality, change from a circula…
We construct phase diagrams for charged rodlike colloids within the second-virial approximation as a function of rod concentration, salt concentration, and colloidal charge. Besides the expected isotropic-nematic transition, we also find parameter regimes with a coexistence between a nematic and a second, more highly aligned nematic phase including an isotropic-nematic-nematic triple point and a nematic-nematic critical point, which can all be explained in terms of the twisting effect. We compute the Frank elastic constants to see if the twist elastic constant can become negative, which would …
Colloidal rods immersed in a thermotropic liquid-crystalline solvent are at the basis of so-called hybrid liquid crystals which are characterized by tunable nematic fluidity with symmetries ranging from conventional uniaxial nematic or anti-nematic to orthorhombic [Mundoor et al., Science 360, 768 (2018)]. We provide a theoretical analysis of the elastic moduli of such systems by considering interactions between the individual rods with the embedding solvent through surface-anchoring forces, as well as steric and electrostatic interactions between the rods themselves. For uniaxial systems the …
We show by computer simulation of a two-dimensional crystal confined by corrugated walls that confinement can be used to impose a controllable mesoscopic superstructure of predominantly mechanical elastic character. Due to an interplay of the particle density of the system and the width D of the confining channel, "soliton staircases" can be created along both parallel confining boundaries, that give rise to standing strain waves in the entire crystal. The periodicity of these waves is of the same order as D. This mechanism should be useful for structure formation in the self-assembly of vario…
The vertical drying of a colloidal film containing rod-like particles was studied by means of kinetic Monte Carlo (MC) simulation. The problem was approached using a two-dimensional square lattice and the rods were represented as linear $k$-mers (i.e., particles occupying $k$ adjacent sites). The initial state before drying was produced using a model of random sequential adsorption (RSA) with isotropic orientations of the $k$-mers (orientation of the $k$-mers along horizontal $x$ and vertical $y$ directions are equiprobable). In the RSA model, overlapping of the $k$-mers is forbidden. During t…
We study the optimal packing of short, hard spherocylinders confined to lie tangential to a spherical surface, using simulated annealing and molecular dynamics simulations. For clusters of up to twelve particles, we map out the changes in the geometry of the closest-packed configuration as a function of the aspect ratio $L/D$, where $L$ is the cylinder length and $D$ the diameter of the rods. We find a rich variety of cluster structures. For larger clusters, we find that the best-packed configurations up to around 100 particles are highly dependent on the exact number of particles and aspect r…
We report on the dynamics in colloidal suspensions of stiff viral rods, called fd-Y21M. This mutant filamentous virus exhibits a persistence length 3.5 times larger than the wild-type fd-wt. Such a virus system can be used as a model system of rodlike particles for studying their self-diffusion. In this paper, the physical features, such as rod contour length and polydispersity have been determined for both viruses. The effect of viral rod flexibility on the location of the nematic-smectic phase transition has been investigated, with a focus on the underlying dynamics studied more specifically…
The yet virtually unexplored class of soft colloidal rods with small aspect ratio is investigated and shown to exhibit a very rich phase and dynamic behavior, spanning from liquid to nearly melt state. Instead of nematic order, these short and soft nanocylinders alter their organization with increasing concentration from isotropic liquid with random orientation to one with preferred local orientation and eventually a multi-domain arrangement with local orientational order. The latter gives rise to a kinetically suppressed state akin to structural glass with detectable terminal relaxation, whic…
In the wake of previous studies on the rattling-and-jumping diffusion in smectic liquid crystal phases of colloidal rods, we analyze here for the first time the heterogeneous dynamics in columnar phases. More specifically, we perform computer simulations to investigate the relaxation dynamics of a binary mixture of perfectly aligned hard spherocylinders. We detect that the columnar arrangement of the system produces free-energy barriers the particles should overcome to jump from one column to another, thus determining a hopping-type diffusion. This phenomenon accounts for the non-Gaussian inte…
