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

Glass transition of an epoxy resin induced by temperature, pressure and chemical conversion: a configurational entropy rationale

A comparative study is reported on the dynamics of a glass-forming epoxy resin when the glass transition is approached through different paths: cooling, compression, and polymerization. In particular, the influence of temperature, pressure and chemical conversion on the dynamics has been investigated by dielectric spectroscopy. Deep similarities are found in dynamic properties. A unified reading of our experimental results for the structural relaxation time is given in the framework of the Adam-Gibbs theory. The quantitative agreement with the experimental data is remarkable, joined with physical values of the fitting parameters. In particular, the fitting function of the isothermal tau(P) data gives a well reasonable prediction for the molar thermal expansion of the neat system, and the fitting function of the isobaric-isothermal tau(C) data under step- polymerization conforms to the prediction of diverging tau at complete conversion of the system.Comment: 16 pages, 8 figures, from the talk given at the 4th International Discussion Meeting on Relaxations in Complex Systems (IDMRCS), Hersonissos, Helaklion, Crete (Greece), 17-23 June 200

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

Connecting Irreversible to Reversible Aggregation: Time and Temperature

We report molecular dynamics simulations of a gel-forming mixture of ellipsoidal patchy particles with different functionality. We show that in this model, which disfavors the formation of bond-loops, elapsed time during irreversible aggregation -- leading to the formation of an extended network -- can be formally correlated with equilibrium temperature in reversible aggregation. We also show that it is possible to develop a parameter-free description of the self-assembly kinetics, bringing reversible and irreversible aggregation of loopless branched systems to the same level of understanding as equilibrium polymerization.Comment: 5 pages, 4 figure

Simulating Hard Rigid Bodies

Several physical systems in condensed matter have been modeled approximating their constituent particles as hard objects. The hard spheres model has been indeed one of the cornerstones of the computational and theoretical description in condensed matter. The next level of description is to consider particles as rigid objects of generic shape, which would enrich the possible phenomenology enormously. This kind of modeling will prove to be interesting in all those situations in which steric effects play a relevant role. These include biology, soft matter, granular materials and molecular systems. With a view to developing a general recipe for event-driven Molecular Dynamics simulations of hard rigid bodies, two algorithms for calculating the distance between two convex hard rigid bodies and the contact time of two colliding hard rigid bodies solving a non-linear set of equations will be described. Building on these two methods, an event-driven molecular dynamics algorithm for simulating systems of convex hard rigid bodies will be developed and illustrated in details. In order to optimize the collision detection between very elongated hard rigid bodies, a novel nearest-neighbor list method based on an oriented bounding box will be introduced and fully explained. Efficiency and performance of the new algorithm proposed will be extensively tested for uniaxial hard ellipsoids and superquadrics. Finally applications in various scientific fields will be reported and discussed.Comment: 36 pages, 17 figure

Chaos and thermal conductivity

Article discussing research on chaos and thermal conductivity