Optimizing Event-Driven Simulations

Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model has been indeed widely used both for computational and theoretical description of physical systems. Recently further developments of computational techniques allow simulations of hard rigid objects of generic shape. In present paper we will present some optimizations for event-driven simulations that offered significant speedup over previous methods. In particular we will describe a generalization of well known linked list method and an improvement on nearest neighbor lists method recently proposed by us.Comment: Submitted to Comp. Phys. Comm. Special Issue for CCP201

Exploiting limited valence patchy particles to understand autocatalytic kinetics

Autocatalysis, i.e., the speeding up of a reaction through the very same molecule which is produced, is common in chemistry, biophysics, and material science. Rate-equation-based approaches are often used to model the time dependence of products, but the key physical mechanisms behind the reaction cannot be properly recognized. Here, we develop a patchy particle model inspired by a bicomponent reactive mixture and endowed with adjustable autocatalytic ability. Such a coarse-grained model captures all general features of an autocatalytic aggregation process that takes place under controlled and realistic conditions, including crowded environments. Simulation reveals that a full understanding of the kinetics involves an unexpected effect that eludes the chemistry of the reaction, and which is crucially related to the presence of an activation barrier. The resulting analytical description can be exported to real systems, as confirmed by experimental data on epoxy-amine polymerizations, solving a long-standing issue in their mechanistic description

Scaling in soft spheres: fragility invariance on the repulsive potential softness

We address the question of the dependence of the fragility of glass forming supercooled liquids on the softness of an interacting potential by performing numerical simulation of a binary mixture of soft spheres with different power n of the interparticle repulsive potential. We show that the temperature dependence of the diffusion coefficients for various $n$ collapses onto a universal curve, supporting the unexpected view that fragility is not related to the hard core repulsion. We also find that the configurational entropy correlates with the slowing down of the dynamics for all studied n.Comment: 4 pages, 4 figure

Self-assembly of bi-functional patchy particles with anisotropic shape into polymers chains: theory and simulations

Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes their aggregation into poly-disperse chains with a significant persistence length. Experiments show that liquid crystals phases form above a critical volume fraction depending on the duplex length. We introduce and investigate via numerical simulations, a coarse-grained model of DNA double-helical duplexes. Each duplex is represented as an hard quasi-cylinder whose bases are decorated with two identical reactive sites. The stacking interaction between terminal sites is modeled via a short-range square-well potential. We compare the numerical results with predictions based on a free energy functional and find satisfactory quantitative matching of the isotropic-nematic phase boundary and of the system structure. Comparison of numerical and theoretical results with experimental findings confirm that the DNA duplexes self-assembly can be properly modeled via equilibrium polymerization of cylindrical particles and enables us to estimate the stacking energy

Scaling between Structural Relaxation and Particle Caging in a Model Colloidal Gel

In polymers melts and supercooled liquids, the glassy dynamics is characterized by the rattling of monomers or particles in the cage formed by their neighbors. Recently, a direct correlation in such systems, described by a universal scaling form, has been established between the rattling amplitude and the structural relaxation time. In this paper we analyze the glassy dynamics emerging from the formation of a persistent network in a model colloidal gel at very low density. The structural relaxation time of the gel network is compared with the mean squared displacement at short times, corresponding to the localization length associated to the presence of energetic bonds. Interestingly, we find that the same type of scaling as for the dense glassy systems holds. Our findings well elucidate the strong coupling between the cooperative rearrangements of the gel network and the single particle localization in the structure. Our results further indicate that the scaling captures indeed fundamental physical elements of glassy dynamics.Comment: Submitted to Soft Matter for web theme on ISM

Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link

Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on temperature and duplex length, such chains order into liquid crystal phases. Here, we investigate the self-assembly of such double-helical duplexes with a combined numerical and theoretical approach. We simulate the bulk system employing the coarse-grained DNA model recently proposed by Ouldridge et al. [ J. Chem. Phys. 134, 08501 (2011) ]. Then we evaluate the input quantities for the theoretical framework directly from the DNA model. The resulting parameter-free theoretical predictions provide an accurate description of the simulation results in the isotropic phase. In addition, the theoretical isotropic-nematic phase boundaries are in line with experimental findings, providing a route to estimate the stacking free energy.Comment: 13 pages, 10 figure

Slow dynamics in a primitive tetrahedral network model

We report extensive Monte Carlo and event-driven molecular dynamics simulations of the fluid and liquid phase of a primitive model for silica recently introduced by Ford, Auerbach and Monson [J. Chem. Phys. 17, 8415 (2004)]. We evaluate the iso-diffusivity lines in the temperature-density plane to provide an indication of the shape of the glass transition line. Except for large densities, arrest is driven by the onset of the tetrahedral bonding pattern and the resulting dynamics is strong in the Angell's classification scheme. We compare structural and dynamic properties with corresponding results of two recently studied primitive models of network forming liquids -- a primitive model for water and a angular-constraint free model of four-coordinated particles -- to pin down the role of the geometric constraints associated to the bonding. Eventually we discuss the similarities between "glass" formation in network forming liquids and "gel" formation in colloidal dispersions of patchy particles.Comment: 9 pages, 10 figure

A molecular dynamics study of chemical gelation in a patchy particle model

We report event-driven molecular dynamics simulations of the irreversible gelation of hard ellipsoids of revolution containing several associating groups, characterizing how the cluster size distribution evolves as a function of the extent of reaction, both below and above the gel point. We find that in a very large interval of values of the extent of reaction, parameter-free mean-field predictions are extremely accurate, providing evidence that in this model the Ginzburg zone near the gel point, where non-mean field effects are important, is very limited. We also find that the Flory's hypothesis for the post-gelation regime properly describes the connectivity of the clusters even if the long-time limit of the extent of reaction does not reach the fully reacted state. This study shows that irreversibly aggregating asymmetric hard-core patchy particles may provide a close realization of the mean-field model, for which available theoretical predictions may help control the structure and the connectivity of the gel state. Besides chemical gels, the model is relevant to network-forming soft materials like systems with bioselective interactions, functionalized molecules and patchy colloids.Comment: 6 pages, 4 figures, to be published in Soft Matte