Most bacteria form organized sessile communities, known as biofilms. Their ubiquity and relevance have stimulated the development of efficient mathematical models able to predict biofilm evolution and characteristics at different conditions. Here we present a study of the early stages of bacterial biofilm formation modeled by means of individual cell-based computer simulation. Simulation showed that clusters with different degrees of internal and orientational order were formed as a function of the aspect ratio of the individual particles and the relation between the diffusion and growth rates. Analysis of microscope images of early biofilm formation by the Gram-negative bacterium Pseudomonas putida at varying diffusion rates revealed a good qualitative agreement with the simulation results. Our model is a good predictor of microcolony morphology during early biofilm development, showing that the competition between diffusion and growth rates is a key aspect in the formation of stable biofilm microcolonies.

We investigate the phase behavior of a model for colloidal hard platelets and rigid discotic molecules: oblate hard spherocylinders (OHSC). We perform free energy calculations using Monte Carlo simulations to map out the phase diagram as a function of the aspect ratio L/D of the particles. The phase diagram displays a stable isotropic phase, a nematic liquid crystal phase for L/D ≤ 0.12, a columnar phase for L/D 0.3, a tilted crystal phase for L 0.45, and an aligned crystal phase for L/D 0.45. We compare the results to the known phase diagram of hard cut spheres. Thin cut spheres are almost cylinder-shaped, while the interactions between real discotic mesogens and colloidal platelets are more consistent with the toroidal rims of the OHSC. Since the shapes of the OHSC and the cut spheres are otherwise similar, the phase diagrams of the two types of particles are quite akin. However, the tilted crystal phase for OHSC, which is of a crystal type that is frequently found in experiments on disklike molecules, has not been found for hard cut spheres. Furthermore, although we have found a cubatic phase, it was shown to be definitely unstable, whereas the stability of the cubatic phase of cut spheres is still disputed. Finally, we also show that the phase boundaries differ significantly from those for cut spheres. These are remarkable consequences of a subtle change in particle shape, which show that for a detailed comparison with the phase behavior of experimental particles, the OHSC should be used as a model particle.

We examine the phase behaviour of colloidal suspensions of hard board-like particles (HBPs) as a function of their shape anisotropy, and observe a fascinating spectrum of nematic, smectic, and columnar liquid-crystalline phases, whose formation is entirely driven by excluded volume effects. We map out the phase diagram of short and long HBPs by gradually modifying their shape from prolate to oblate and investigate the long-range order of the resulting morphologies along the phase directors and perpendicularly to them. The intrinsic biaxial nature of these particles promotes the formation of translationally ordered biaxial phases, but does not show solid evidence that it would, per se, promote the formation of the biaxial nematic phase. Our simulations shed light on the controversial existence of the discotic smectic phase, whose layers are as thick as the minor particle dimension, which is stable in a relatively large portion of our phase diagrams. Additionally, we modify the Onsager theory to describe the isotropic-nematic phase transition of freely rotating biaxial particles as a function of the particle width, and find a relatively strong first-order signature, in excellent agreement with our simulations. In an attempt to shed light on the elusive formation of the biaxial nematic phase, we apply this theory to predict the uniaxial-biaxial nematic phase transition and confirm, again in agreement with simulations, the prevailing stability of the translationally ordered smectic phase over the orientationally ordered biaxial nematic phase.

We study the kinetic pathways for the isotropic-to-nematic transition in a fluid of colloidal hard rods. In order to follow the formation of the nematic phase, we develop a new cluster criterion that distinguishes nematic clusters from the isotropic phase. Applying this criterion in Monte Carlo simulations, we find spinodal decomposition as well as nucleation and growth depending on the supersaturation. We determine the height of the nucleation barrier and we study the shape and structure of the cluster. More specifically, we find ellipsoidal nematic clusters with an aspect ratio of about 1.7 and a homogeneous nematic director field. Our results are consistent with theoretical predictions on the shape and director field of nematic tactoids. Classical nucleation theory gives reasonable predictions for the height of the nucleation barrier and the critical nucleus size.

We report on the diffusion of purely repulsive and freely rotating colloidal rods in the isotropic, nematic, and smectic liquid crystal phases to probe the agreement between Brownian and Monte Carlo dynamics under the most general conditions. By properly rescaling the Monte Carlo time step, being related to any elementary move via the corresponding self-diffusion coefficient, with the acceptance rate of simultaneous trial displacements and rotations, we demonstrate the existence of a unique Monte Carlo time scale that allows for a direct comparison between Monte Carlo and Brownian dynamics simulations. To estimate the validity of our theoretical approach, we compare the mean square displacement of rods, their orientational autocorrelation function, and the self-intermediate scattering function, as obtained from Brownian dynamics and Monte Carlo simulations. The agreement between the results of these two approaches, even under the condition of heterogeneous dynamics generally observed in liquid crystalline phases, is excellent.

The fluorescence quenching by electron transfer of a fluorophore, 2,5-bis(dimethylamino)-1,3-benzenedicarbonitrile, to 1,3-dimethyl-2-nitrobenzene, has been studied by means of time-resolved and steady-state experiments at different viscosities and up to large quencher concentrations. Differential Encounter Theory (DET) has been used to rationalize the results, in combination with electron transfer modelled by the Marcus theory. Additionally, the solvent structure and the hydrodynamic effect on the diffusion coefficient have been taken into account. Any simpler model failed to simultaneously fit all the results. The large number of quencher concentrations used is crucial to unambiguously extract the electron transfer parameters.

The liquid crystal phase diagram of the discotic hard spherocylinder fluid is investigated by Monte Carlo simulations. Thickness-to-diameter aspect ratios within L/D=0.2-0.5 are considered. Three distinct columnar phases are found, namely, a hexatic interdigitated phase (D(hi)), a hexatic ordered phase (D(ho)), both with long-range spatial correlations, and a hexatic disordered phase (D(hd)), in which the columns become fluidlike. Local domains of stacked particles are also observed in the isotropic phase. The stability of the D(ho) and D(hd) phases is favored with increasing anisotropy of the particle shape. As a consequence, the packing fraction versus the aspect ratio representation of the phase diagram features D(ho)-D(hd)-I and D(hi)-D(ho)-I triple points. The study involved the development of an efficient algorithm to compute the shortest distance between two oblate spherocylinder particles. The study provides a general coarse-grain methodology to explore discotic behavior, with fundamental advantages against alternative molecular models.

The liquid crystal phases of the Kihara fluid have been studied in computer simulations. The work focuses on the isotropic-nematic-smectic-A triple point region, especially relevant for the understanding of the properties and the design of real mesogens with specific phase diagrams. The Kihara interaction resembles more appropriately than other related models, the shape of elongated polymers and biomolecules, and a closer assertion is provided for the role of the configurational entropy and the dispersive interactions in the behavior of such molecules in dense phases or under macromolecular crowding conditions.