A generalized numerical model for clonal growth in scleractinian coral colonies.

Coral reefs, vital ecosystems supporting diverse marine life, are primarily shaped by the clonal expansion of coral colonies. Although the principles of coral clonal growth, involving polyp division for spatial extension, are well-understood, numerical modelling efforts are notably scarce in the literature. In this article, we present a parsimonious numerical model based on the cloning of polyps, using five key parameters to simulate a range of coral shapes.

Dynamic response of a ferromagnetic nanofilament under rotating fields: effects of flexibility, thermal fluctuations and hydrodynamics.

Using nonequilibrium computer simulations, we study the response of ferromagnetic nanofilaments, consisting of stabilized one dimensional chains of ferromagnetic nanoparticles, under external rotating magnetic fields. In difference with their analogous microscale and stiff counterparts, which have been actively studied in recent years, nonequilibrium properties of rather flexible nanoparticle filaments remain mostly unexplored. By progressively increasing the modeling details, we are able to evidence the qualitative impact of main interactions that can not be neglected at the nanoscale, showing that filament flexibility, thermal fluctuations and hydrodynamic interactions contribute independently to broaden the range of synchronous frequency response in this system.

Depletion Interactions at Interfaces Induced by Ferromagnetic Colloidal Polymers.

The pair-interaction force profiles for two non-magnetic colloids immersed in a suspension of ferromagnetic colloidal polymers are investigated via Langevin simulations. A quasi-two-dimensional approach is taken to study the interface case and a range of colloidal size ratios (non-magnetic:magnetic) from 6:1 up to 20:1 have been considered in this work. Simulations show that when compared with non-magnetic suspensions, the magnetic polymers strongly modify the depletion force profiles leading to strongly oscillatory behavior.

Self-organized sulfide-driven traveling pulses shape seagrass meadows.

Seagrasses provide multiple ecosystem services and act as intense carbon sinks in coastal regions around the globe but are threatened by multiple anthropogenic pressures, leading to enhanced seagrass mortality that reflects in the spatial self-organization of the meadows. Spontaneous spatial vegetation patterns appear in such different ecosystems as drylands, peatlands, salt marshes, or seagrass meadows, and the mechanisms behind this phenomenon are still an open question in many cases. Here, we report on the formation of vegetation traveling pulses creating complex spatiotemporal patterns and rings in Mediterranean seagrass meadows.

Colloidal magnetic brushes: influence of the magnetic content and presence of short-range attractive forces in the micro-structure and field response.

The behaviour of supramolecular brushes, whose filaments are composed of sequences of magnetic and non-magnetic colloidal particles, has been studied using Langevin dynamics simulations. Two types of brushes have been considered: sticky or Stockmayer brushes (SB) and non-sticky magnetic brushes (NSB). In both cases, the microstructure and the collective behaviour have been analysed for a wide range of magnetic field strengths including the zero-field case, and negative fields.

Adsorption transition of a grafted ferromagnetic filament controlled by external magnetic fields.

Extensive Langevin dynamics simulations are used to characterize the adsorption transition of a flexible magnetic filament grafted onto an attractive planar surface. Our results identify different structural transitions at different ratios of the thermal energy to the surface attraction strength: filament straightening, adsorption, and the magnetic flux closure. The adsorption temperature of a magnetic filament is found to be higher in comparison to an equivalent nonmagnetic chain.

Magnetic responsive brushes under flow in strongly confined slits: external field control of brush structure and flowing particle mixture separation.

In the present work magnetic brushes under flow conditions and confined inside narrow slits have been studied using Langevin dynamics simulations. It has been observed that the structural properties of these confined magnetic brushes can be tuned via the application of an external magnetic field, and this control can be exerted with a relatively low content of magnetic colloidal particles in the filaments that form the brushes (20% in the present study). The potential of these brushes to perform a separation process of a size-bidispersed mixture of free non-magnetic colloidal particles flowing through the slit has also been explored.

Fairy circle landscapes under the sea.

Short-scale interactions yield large-scale vegetation patterns that, in turn, shape ecosystem function across landscapes. Fairy circles, which are circular patches bare of vegetation within otherwise continuous landscapes, are characteristic features of semiarid grasslands. We report the occurrence of submarine fairy circle seascapes in seagrass meadows and propose a simple model that reproduces the diversity of seascapes observed in these ecosystems as emerging from plant interactions within the meadow.

Scattering properties and internal structure of magnetic filament brushes.

Practical applications of polymer brush-like systems rely on a clear understanding of their internal structure. In the case of magnetic nanoparticle filament brushes, the competition between bonding and nonbonding interactions-including long range magnetic dipole-dipole interactions-makes the microstructure of these polymer brush-like systems rather complex. On the other hand, the same interactions open up the possibility to manipulate the meso- and macroscopic responses of these systems by applying external magnetic fields or by changing the background temperature.

The behavior of a magnetic filament in flow under the influence of an external magnetic field.

We present an extensive numerical study of the behaviour of a filament made of ferromagnetic colloidal particles subjected to the simultaneous action of a fluid flow and a stationary external magnetic field perpendicular to the flow lines. We found that in the presence of a shear flow, the tumbling motion observed at zero field is strongly inhibited when the external magnetic field is applied. The field is able to stabilise the filament with a well defined degree of alignment that depends on the balance between hydrodynamic and magnetic torques.

Flexible magnetic filaments under the influence of external magnetic fields in the limit of infinite dilution.

In the present work we use Langevin dynamics computer simulations to understand how the presence of a constant external magnetic field modifies the conformational phase diagram of magnetic filaments in the limit of infinite dilution. We have considered the filaments immersed in either a good (non-sticky filaments) or a poor (Stockmayer polymers) solvent. It has been found that in the presence of an applied field, filaments turn out to be much more susceptible to parameters such as temperature and solvent conditions.

Magnetic filament brushes: tuning the properties of a magnetoresponsive supracolloidal coating.

We present a theoretical study on the design of a supramolecular magnetoresponsive coating. The coating is formed by a relatively dense array of supracolloidal magnetic filaments grafted to a surface in a polymer brush-like arrangement. In order to determine and optimise the properties of the magnetic filament brush, we perform extensive computer simulations with a coarse-grained model that takes into account the correlations between the magnetic moments of the particles and the backbone crosslinks.

Supramolecular Magnetic Brushes: The Impact of Dipolar Interactions on the Equilibrium Structure.

The equilibrium structure of supramolecular magnetic filament brushes is analyzed at two different scales. First, we study the density and height distributions for brushes with various grafting densities and chain lengths. We use Langevin dynamics simulations with a bead-spring model that takes into account the cross-links between the surface of the ferromagnetic particles, whose magnetization is characterized by a point dipole.

The effect of links on the interparticle dipolar correlations in supramolecular magnetic filaments.

We present a combined computational and analytical study of supramolecular magnetic filaments, i.e., permanently linked chains of ferromagnetic nanocolloids.

Effects of the dipolar interaction on the equilibrium morphologies of a single supramolecular magnetic filament in bulk.

We study the equilibrium morphologies of a single supramolecular magnetic filament in a three-dimensional system as a function of the effective strength of the magnetic dipolar interactions. The study is performed by means of Langevin dynamics simulations with a bead-spring chain model of freely rotating dipoles. We demonstrate the existence of three structural regimes as the value of the dipolar coupling parameter is increased: a coil compaction regime, a coil expansion regime, and a closed chain regime in which the structures tend progressively to an ideal ring configuration.

Ice polyamorphism in the minimal Mercedes-Benz model of water.

We investigate ice polyamorphism in the context of the two-dimensional Mercedes-Benz model of water. We find a first-order phase transition between a crystalline phase and a high-density amorphous phase. Furthermore, we find a reversible transformation between two amorphous structures of high and low density; however, we find this to be a continuous and not an abrupt transition, as the low-density amorphous phase does not show structural stability.

Implications of extreme life span in clonal organisms: millenary clones in meadows of the threatened seagrass Posidonia oceanica.

The maximum size and age that clonal organisms can reach remains poorly known, although we do know that the largest natural clones can extend over hundreds or thousands of metres and potentially live for centuries. We made a review of findings to date, which reveal that the maximum clone age and size estimates reported in the literature are typically limited by the scale of sampling, and may grossly underestimate the maximum age and size of clonal organisms. A case study presented here shows the occurrence of clones of slow-growing marine angiosperm Posidonia oceanica at spatial scales ranging from metres to hundreds of kilometres, using microsatellites on 1544 sampling units from a total of 40 locations across the Mediterranean Sea.

Influence of microstructure on the transitions between mesoscopic thin-film morphologies in ballistic-diffusive models.

We study the influence of the symmetries of competing microstructures on the emergence of different mesoscopic morphologies in the growth by vapor deposition of thin solid films. We show the results of numerical simulations in (1+1) - and (2+1) -dimensional systems including different microstructures, as well as thermally activated surface diffusion in combination with a ballistic algorithm to model the deposition process. We focus on the characterization of the transitional structures that appear in the empirical structure zone model (SZM) through the evaluation of the mean packing density and the mean coordination number.

Spherical brushes within spherical cavities: a self-consistent field and Monte Carlo study.

We present an extensive numerical study on the behavior of spherical brushes confined into a spherical cavity. Self-consistent field (SCF) and off-lattice Monte Carlo (MC) techniques are used in order to determine the monomer and end-chain density profiles and the cavity pressure as a function of the brush properties. A comparison of the results obtained via SCF, MC, and the Flory theory for polymer solutions reveals SCF calculations to be a valuable alternative to MC simulations in the case of free and softly compressed brushes, while the Flory's theory accounts remarkably well for the pressure in the strongly compressed regime.

Shear effects on crystal nucleation in colloidal suspensions.

Extensive two-dimensional Langevin dynamics simulations are used to determine the effect of steady shear flows on the crystal nucleation kinetics of charge stabilized colloids and colloids whose pair potential possess an attractive shallow well of a few k_{B}T 's (attractive colloids). Results show that in both types of systems small amounts of shear speeds up the crystallization process and enhances the quality of the growing crystal significantly. Moderate shear rates, on the other hand, destroy the ordering in the system.

Stiff polymer adsorption. Onset to pattern recognition.

We present the results of extensive off-lattice Monte-Carlo simulations of a stiff polymer chain adsorbing onto a sticky periodic stripe-like pattern of variable width. We have analyzed, in terms of the chain length and rigidity, the adsorption and the pattern recognition process as a function of the stripe width. We have seen that this process is twofold: (i) the chain adsorbs rather isotropically onto the surface at a characteristic temperature T(c) and (ii) a further reduction in the temperature is needed for the chain to reorganize and adjust to the specific pattern.

Structure factor scaling in colloidal phase separation.

The dynamical scaling hypothesis for the structure factor, S (q) , in depletion-driven colloidal phase separation is studied by carrying out Brownian dynamics simulations. A true dynamical scaling is observed for shallow quenches into the two-phase coexistence region. In such a quench, compact clusters nucleate and grow with time and there is only one characteristic length scale in the system after an initial transient period.

Kinetics of phase transformations in depletion-driven colloids.

We present results from a detailed numerical study of the kinetics of phase transformations in a model two-dimensional depletion-driven colloidal system. Transition from a single, dispersed phase to a two-phase coexistence of monomers and clusters is obtained as the depth of the interaction potential among the colloidal particles is changed. Increasing the well depth further, fractal clusters are observed in the simulation.

Enhanced kinetics and free-volume universality in dense aggregating systems.

Aggregation kinetics and cluster-size distributions are studied with off-lattice, diffusion-limited cluster-cluster simulations. With increased cluster crowding (occurring at late times) as measured by the normalized free volume, Omega, both the kinetics speeds up and the size distribution broadens. The exponents characterizing each, z and lambda, respectively, are found to be universal functions of Omega.