Strategies for Optimize Off-Lattice Aggregate Simulations

We review some computer algorithms for the simulation of off-lattice clusters grown from a seed, with emphasis on the diffusion-limited aggregation, ballistic aggregation and Eden models. Only those methods which can be immediately extended to distinct off-lattice aggregation processes are discussed. The computer efficiencies of the distinct algorithms are compared.Comment: 6 pages, 7 figures and 3 tables; published at Brazilian Journal of Physics 38, march, 2008 (http://www.sbfisica.org.br/bjp/files/v38_81.pdf

Contact process on a Voronoi triangulation

We study the continuous absorbing-state phase transition in the contact process on the Voronoi-Delaunay lattice. The Voronoi construction is a natural way to introduce quenched coordination disorder in lattice models. We simulate the disordered system using the quasistationary simulation method and determine its critical exponents and moment ratios. Our results suggest that the critical behavior of the disordered system is unchanged with respect to that on a regular lattice, i.e., that of directed percolation

Aggregation in a mixture of Brownian and ballistic wandering particles

In this paper, we analyze the scaling properties of a model that has as limiting cases the diffusion-limited aggregation (DLA) and the ballistic aggregation (BA) models. This model allows us to control the radial and angular scaling of the patterns, as well as, their gap distributions. The particles added to the cluster can follow either ballistic trajectories, with probability $P_{ba}$, or random ones, with probability $P_{rw}=1-P_{ba}$. The patterns were characterized through several quantities, including those related to the radial and angular scaling. The fractal dimension as a function of $P_{ba}$ continuously increases from $d_f\approx 1.72$ (DLA dimensionality) for $P_{ba}=0$ to $d_f\approx 2$ (BA dimensionality) for $P_{ba}=1$. However, the lacunarity and the active zone width exhibt a distinct behavior: they are convex functions of $P_{ba}$ with a maximum at $P_{ba}\approx1/2$. Through the analysis of the angular correlation function, we found that the difference between the radial and angular exponents decreases continuously with increasing $P_{ba}$ and rapidly vanishes for $P_{ba}>1/2$, in agreement with recent results concerning the asymptotic scaling of DLA clusters.Comment: 7 pages, 6 figures. accepted for publication on PR

Modelling of epitaxial film growth with a Ehrlich-Schwoebel barrier dependent on the step height

The formation of mounded surfaces in epitaxial growth is attributed to the presence of barriers against interlayer diffusion in the terrace edges, known as Ehrlich-Schwoebel (ES) barriers. We investigate a model for epitaxial growth using a ES barrier explicitly dependent on the step height. Our model has an intrinsic topological step barrier even in the absence of an explicit ES barrier. We show that mounded morphologies can be obtained even for a small barrier while a self-affine growth, consistent with the Villain-Lai-Das Sarma equation, is observed in absence of an explicit step barrier. The mounded surfaces are described by a super-roughness dynamical scaling characterized by locally smooth (faceted) surfaces and a global roughness exponent $\alpha>1$. The thin film limit is featured by surfaces with self-assembled three-dimensional structures having an aspect ratio (height/width) that may increase or decrease with temperature depending on the strength of step barrier.Comment: To appear in J. Phys. Cond. Matter; 3 movies as supplementary materia

A computationally efficient method for calculating the maximum conductance of disordered networks: Application to 1-dimensional conductors

Random networks of carbon nanotubes and metallic nanowires have shown to be very useful in the production of transparent, conducting films. The electronic transport on the film depends considerably on the network properties, and on the inter-wire coupling. Here we present a simple, computationally efficient method for the calculation of conductance on random nanostructured networks. The method is implemented on metallic nanowire networks, which are described within a single-orbital tight binding Hamiltonian, and the conductance is calculated with the Kubo formula. We show how the network conductance depends on the average number of connections per wire, and on the number of wires connected to the electrodes. We also show the effect of the inter-/intra-wire hopping ratio on the conductance through the network. Furthermore, we argue that this type of calculation is easily extendable to account for the upper conductivity of realistic films spanned by tunneling networks. When compared to experimental measurements, this quantity provides a clear indication of how much room is available for improving the film conductivity.Comment: 7 pages, 5 figure

Crystallization, data collection and data processing of maltose-binding protein (MalE) from the phytopathogen Xanthomonas axonopodis pv. citri

Maltose-binding protein is the periplasmic component of the ABC transporter responsible for the uptake of maltose/maltodextrins. The Xanthomonas axonopodis pv. citri maltose-binding protein MalE has been crystallized at 293 Kusing the hanging-drop vapour-diffusion method. The crystal belonged to the primitive hexagonal space group P6_122, with unit-cell parameters a = 123.59, b = 123.59, c = 304.20 Å, and contained two molecules in the asymetric unit. It diffracted to 2.24 Å resolution