Growth of hard--rod monolayers via deposition is studied in a lattice model using rods with discrete orientations and in a continuum model with hard spherocylinders. The lattice model is treated with kinetic Monte Carlo simulations and dynamic density functional theory while the continuum model is studied by dynamic Monte Carlo simulations equivalent to diffusive dynamics. The evolution of nematic order (excess of upright particles, "standing--up" transition) is an entropic effect and is mainly governed by the equilibrium solution, {rendering a continuous transition} (paper I, J. Chem. Phys. 145, 074902 (2016)). Strong non--equilibrium effects (e.g. a noticeable dependence on the ratio of rates for translational and rotational moves) are found for attractive substrate potentials favoring lying rods. Results from the lattice and the continuum models agree qualitatively if the relevant characteristic times for diffusion, relaxation of nematic order and deposition are matched properly. Applicability of these monolayer results to multilayer growth is discussed for a continuum--model realization in three dimensions where spherocylinders are deposited continuously onto a substrate via diffusion.
The equilibrium properties of hard rod monolayers are investigated in a lattice model (where position and orientation of a rod are restricted to discrete values) as well as in an off--lattice model featuring spherocylinders with continuous positional and orientational degrees of freedom. Both models are treated using density functional theory and Monte Carlo simulations. Upon increasing the density of rods in the monolayer, there is a continuous ordering of the rods along the monolayer normal ("standing up" transition). The continuous transition also persists in the case of an external potenti…
Using the Parsons Lee theory we examined the effect of shape anisotropy and the wall to wall separation on the phase behavior of the hard parallelepiped rods with dimensions L, D, and D (L>D) in such narrow slitlike pores which only one homeotropic layer can form. The phase structures, including biaxiality, planar nematic layering transition as well as planar to homeotropic, were studied for some separations in the range 2.5D<H<10.0D for H-D<L<H.
Orientational ordering driven by mechanical distortion of soft substrates plays a major role in material transformation processes such as elastocapillarity and surface anchoring. We present a theoretical model of the orientational response of anisotropic rods deposited onto a surface of a soft, elastic substrate of finite thickness. We show that anisotropic rods exhibit a continuous isotropic-nematic phase transition, driven by orientational interactions between surface deposited rods. This interaction is mediated by the deformation of the underlying elastic substrate, and is quantified by the…
We report on an observation of propagating compression waves in a quasi-two-dimensional monolayer of apolar granular rods fluidized by an upflow of air. The collective wave speed is an order of magnitude faster than the speed of the particles. This gives rise to anomalously large number fluctuations dN ~ $N^{0.72 \pm 0.04}$, which are greater than ordinary number fluctuations of N^{1/2}. We characterize the waves by calculating the spatiotemporal power spectrum of the density. The position of observed peaks, as a function of frequency w and wavevector k, yields a linear dispersion relationship…
The propagation of chirality across scales is a common but poorly understood phenomenon in soft matter. In this work, we use computer simulations to study chiral monolayer assemblies formed by hard rod-like colloidal particles in the presence of non-adsorbing polymer and characterize the thermodynamic driving forces responsible for the twisting. Simulations show that straight (achiral) rods assemble into monolayers with a spontaneous twist that is either left- or right-handed, while helical (chiral) rods lead to assemblies with preferential chiral features that depend on their handedness and c…
We elucidate the molecular forces leading to assembly of two dimensional membrane-like structures composed of a one rod-length thick monolayer of aligned rods from an immiscible suspension of hard rods and depleting polymers. We perform simulations which predict that monolayer membranes are thermodynamically stable above a critical rod aspect ratio and below a critical depletion interaction length scale. Outside of these conditions alternative structures such as stacked smectic columns or nematic droplets are thermodynamically stable. These predictions are confirmed using an experimental model…
The orientational order in vertically agitated granular rod monolayers is investigated experimentally and compared quantitatively with equilibrium Monte Carlo simulations and density functional theory. At sufficiently high number density, short rods form a tetratic state and long rods form a uniaxial nematic state. The length-to-width ratio at which the order changes from tetratic to uniaxial is around $7.3$ in both experiments and simulations. This agreement illustrates the universal aspects of the ordering of rod-shaped particles across equilibrium and nonequilibrium systems. Moreover, the a…
The colonisation of a soft passive material by motile cells such as bacteria is common in biology. The resulting colonies of the invading cells are often observed to exhibit intricate patterns whose morphology and dynamics can depend on a number of factors, particularly the mechanical properties of the substrate and the motility of the individual cells. We use simulations of a minimal 2D model of self-propelled rods moving through with a passive compliant medium consisting of particles that offer elastic resistance before being plastically displaced from their equilibrium positions. It is obse…
A density functional of fundamental measure type for a lattice model of anisotropic particles with hard-core repulsions and effective attractions is derived in the spirit of the Asakura-Oosawa model. Through polymeric lattice particles of various size and shape, effective attractions of different strength and range between the colloids can be generated. The functional is applied to the determination of phase diagrams for sticky rods of length $L$ in two dimensions, in three dimensions and in a monolayer system on a neutral substrate. In all cases, there is a competition between ordering and ga…
Spatially ordered systems confined to surfaces such as spheres exhibit interesting topological structures because of curvature induced frustration in orientational as well as translational order. The study of these structures is important for investigating the interplay between geometry, topology, and elasticity, and for their potential applications in materials science. In this work we numerically simulate a spherical monolayer of soft repulsive spherocylinders (SRS) and study the packing of rods and their ordering transition as a function of the packing fraction. In the model that we study, …
We investigate the ordering properties of vertically-vibrated monolayers of granular cylinders in a circular container at high packing fraction. In line with previous works by other groups, we identify liquid-crystalline ordering behaviour similar to that of two-dimensional hard rectangular particles subject to thermal equilibrium fluctuations. However, due to dissipation, there is a much stronger tendency for particles to cluster into parallel arrangements in the granular system. These clusters behave as a polydisperse mixture of long life-time `superparticles', and some aspects of the system…
We present a model for wave propagation in a monolayer of spheres on an elastic substrate. The model, which considers sagittally polarized waves, includes: horizontal, vertical, and rotational degrees of freedom; normal and shear coupling between the spheres and substrate, as well as between adjacent spheres; and the effects of wave propagation in the elastic substrate. For a monolayer of interacting spheres, we find three contact resonances, whose frequencies are given by simple closed-form expressions. For a monolayer of isolated spheres, only two resonances are present. The contact resonanc…
Monodisperse suspensions of rodlike chiral $fd$ viruses are condensed into a rod-length thick colloidal monolayers of aligned rods by depletion forces. Twist deformations of the molecules are expelled to the monolayer edge as in a chiral smectic $A$ liquid crystal, and a cholesteric band forms at the edge. Coalescence of two such isolated membranes results in a twist wall sandwiched between two regions of aligned rods, dubbed $π$-walls. By modeling the membrane as a binary fluid of coexisting cholesteric and chiral smectic $A$ liquid-crystalline regions, we develop a unified theory of the $π$-…
Motivated by recent simulations and by experiments on aggregation of gliding bacteria, we study a model of the collective dynamics of self-propelled hard rods on a substrate in two dimensions. The rods have finite size, interact via excluded volume and their dynamics is overdamped by the interaction with the substrate. Starting from a microscopic model with non-thermal noise sources, a continuum description of the system is derived. The hydrodynamic equations are then used to characterize the possible steady states of the systems and their stability as a function of the particles packing fract…
Within an Onsager-like density functional theory we explore the thermodynamic and structural properties of an isotropic and nematic fluid of hard needle-like colloids in contact with a hard substrate coated with a soft short-ranged attractive or repulsive layer. As a function of the range and the strength of the soft interactions we find wetting and drying transitions, a pre-drying line, and a symmetry-breaking transition from uniaxial to biaxial in the wetting and drying film.
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…
We experimentally investigate the structural behavior of an interacting colloidal monolayer being driven across a decagonal quasiperiodic potential landscape created by an optical interference pattern. When the direction of the driving force is varied, we observe the monolayer to be directionally locked on angles corresponding to the symmetry axes of the underlying potential. At such locking steps we observe a dynamically ordered smectic phase in agreement with recent simulations. We demonstrate, that such dynamical ordering is due to the interaction of particle lanes formed by interstitial an…
We investigate the directional locking effects that arise when a monolayer of paramagnetic colloidal particles is driven across a triangular lattice of magnetic bubbles. We use an external rotating magnetic field to generate a two dimensional traveling wave ratchet forcing the transport of particles along a direction that intersects two crystallographic axes of the lattice. We find that, while single particles show no preferred direction, collective effects induce transversal current and directional locking at high density via a spontaneous symmetry breaking. The colloidal current may be polar…
The molecular structure of dimyristoyl phosphatidylserine (DMPS) monolayers on a water substrate in different phase states has been investigated under normal conditions by X-ray reflectometry with a photon energy of ~ 8 keV. According to the experimental data, the transition from a two-dimensional expanded liquid state to a solid gel state (liquid crystal) accompanied by the ordering of the hydrocarbon tails of the DMPS molecule occurs in the monolayer as the surface pressure rises. The monolayer thickness is (20 +/- 3) Angstrom and (28 +/- 2) Angstrom in the liquid and solid phases, respectiv…
We study experimentally the nonequilibrium phase behaviour of a horizontal monolayer of macroscopic rods. The motion of the rods in two dimensions is driven by vibrations in the vertical direction. Aside from the control variables of packing fraction and aspect ratio that are typically explored in molecular liquid crystalline systems, due to the macroscopic size of the particles we are also able to investigate the effect of the precise shape of the particle on the steady states of this driven system. We find that the shape plays an important role in determining the nature of the orientational …
We study a quasi-two-dimensional monolayer of granular rods fluidized by a spatially and temporally homogeneous upflow of air. By tracking the position and orientation of the particles, we characterize the dynamics of the system with sufficient resolution to observe ballistic motion at the shortest time scales. Particle anisotropy gives rise to dynamical anisotropy and superdiffusive dynamics parallel to the rod's long axis, causing the parallel and perpendicular mean squared displacements to become diffusive on different timescales. The distributions of free times and free paths between colli…
We study the behavior of negatively charged colloids with two positively charged polar caps close to a planar patterned surface. The competition between the different anisotropic components of the particle-particle interaction patterns is able by itself to give rise to a rich assembly scenario: colloids with charged surface patterns form different crystalline domains when adsorbed to a homogeneously charged substrate. Here we consider substrates composed of alternating (negative/neutral, positive/neutral and positive/negative) parallel stripes and, by means of Monte Carlo simulations, we inves…
We study long-range morphological changes in atomic monolayers on solid substrates induced by different types of defects; e.g., by monoatomic steps in the surface, or by the tip of an atomic force microscope (AFM), placed at some distance above the substrate. Representing the monolayer in terms of a suitably extended Frenkel-Kontorova-type model, we calculate the defect-induced density profiles for several possible geometries. In case of an AFM tip, we also determine the extra force exerted on the tip due to the tip-induced de-homogenization of the monolayer.
The effect of strong confinement on the positional and orientational ordering is examined in a system of hard rectangular rods with length L and diameter D (L>D) using the Parsons-Lee modification of the second virial density functional theory. The rods are nonmesogenic (L/D<3)and confined between two parallel hard walls, where the width of the pore (H) is chosen in such a way that both planar (particle's long axis parallel to the walls) and homeotropic (particle's long axis perpendicular to the walls) orderings are possible and a maximum of two layers are allowed to form in the pore. In the e…
We have studied the electronic properties, in relation to their structural properties, of monolayers of 1-octadecene attached on a hydrogen-terminated (111) silicon surface. The molecules are attached using the free-radical reaction between C=C and Si-H activated by an ultraviolet illumination. We have compared the structural and electrical properties of monolayers formed on silicon substrate of different types (n-type and p-type) and different doping concentrations from low-doped (~1E14 cm-3) to highly doped (~1E19 cm-3) silicon substrates. We show that the monolayers on n-, p- and p+ silicon…
The surface phase behavior of binary mixtures of colloidal hard rods in contact with a solid substrate (hard wall) is studied, with special emphasis on the region of the phase diagram that includes the smectic A phase. The colloidal rods are modelled as hard cylinders of the same diameter and different lengths, in the approximation of perfect alignment. A fundamental--measure density functional is used to obtain equilibrium density profiles and thermodynamic properties such as surface tensions and adsorption coefficients. The bulk phase diagram exhibits nematic-smectic and smectic-smectic demi…
We study acoustic modes of a close-packed hexagonal lattice of spheres adhered to a substrate, propagating along a high-symmetry direction. The model, accounting for both normal and shear coupling between the spheres and between the spheres and the substrate, yields three contact-based vibrational modes involving both translational and rotational motion of the spheres. Furthermore, we study the effect of sphere-substrate and sphere-sphere contacts on spheroidal vibrational modes of the spheres within a perturbative approach. The sphere-substrate interaction results in a frequency upshift for t…
Coordinated and cooperative motion of cells is essential for embryonic development, tissue morphogenesis, wound healing and cancer invasion. A predictive understanding of the emergent mechanical behaviors in collective cell motion is challenging due to the complex interplay between cell-cell interactions, cell-matrix adhesions and active cell behaviors. To overcome this challenge, we develop a predictive cellular vertex model that can delineate the relative roles of substrate rigidity, tissue mechanics and active cell properties on the movement of cell collectives. We apply the model to the sp…
When a plate is withdrawn from a liquid bath, either a static meniscus forms in the transition region between the bath and the substrate or a liquid film of finite thickness (a Landau-Levich film) is transferred onto the moving substrate. If the substrate is inhomogeneous, e.g., has a prestructure consisting of stripes of different wettabilities, the meniscus can be deformed or show a complex dynamic behavior. Here we study the free surface shape and dynamics of a dragged meniscus occurring for striped prestructures with two orientations, parallel and perpendicular to the transfer direction. A…
Density functional theory is used to study colloidal hard-rod fluids near an individual right-angled wedge or edge as well as near a hard wall which is periodically patterned with rectangular barriers. The Zwanzig model, in which the orientations of the rods are restricted to three orthogonal orientations but their positions can vary continuously, is analyzed by numerical minimization of the grand potential. Density and orientational order profiles, excess adsorptions, as well as surface and line tensions are determined. The calculations exhibit an enrichment [depletion] of rods lying parallel…
We study the effect of the presence of a regular substrate pattern on the irreversible adsorption of nanosized and colloid particles. Deposition of disks of radius $r_0$ is considered, with the allowed regions for their center attachment at the planar surface consisting of square cells arranged in a square lattice pattern. We study the jammed state properties of a generalized version of the random sequential adsorption model for different values of the cell size, $a$, and cell-cell separation, $b$. The model shows a surprisingly rich behavior in the space of the two dimensionless parameters $α…
Epithelial-substrate coupling strength regulates the landscape of the traction in cohesive monolayers: a parametric study and a revisit to "size effect"
Collective cell migration plays a crucial role in many developmental processes that underlie morphogenesis, wound healing, or cancer progression. In such coordinated behaviours, cells are organised in coherent structures and actively migrate to serve different biological purposes. In some contexts, namely during epithelial wound healing, it is well known that a migrating free-edge monolayer develops finger-like instabilities, yet the onset is still under debate. Here, by means of theory and numerical simulations, we shed light on the main mechanisms driving the instability process, analysing t…
