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21.
An artificial intelligence approach for modeling molecular self-assembly: Agent Based simulations of rigid molecules
Sara Fortuna, Alessandro Troisi, 2009, original scientific article

Abstract: Agent-based simulations are rule-based models traditionally used for the simulations of complex systems. In this paper, an algorithm based on the concept of agent-based simulations is developed to predict the lowest energy packing of a set of identical rigid molecules. The agents are identified with rigid portions of the system under investigation, and they evolve following a set of rules designed to drive the system toward the lowest energy minimum. The algorithm is compared with a conventional Metropolis Monte Carlo algorithm, and it is applied on a large set of representative models of molecules. For all the systems studied, the agent-based method consistently finds a significantly lower energy minima than the Monte Carlo algorithm because the system evolution includes elements of adaptation (new configurations induce new types of moves) and learning (past successful choices are repeated).
Keywords: Self-assembly, self-organisation, agent based, Monte Carlo, rigid molecules, simulation
Published in RUNG: 10.10.2016; Views: 4796; Downloads: 0
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22.
Packing patterns of silica nanoparticles on surfaces of armored polystyrene latex particles
Sara Fortuna, Catheline A. L. Colard, Stefan A. F. Bon, Alessandro Troisi, 2009, original scientific article

Abstract: Fascinating packing patterns of identical spherical and discotic objects on curved surfaces occur readily in nature and science. Examples include C60 fullerenes,(1, 2)13-atom cuboctahedral metal clusters,(3) and S-layer proteins on outer cell membranes.(4) Numerous situations with surface-arranged objects of variable size also exist, such as the lenses on insect eyes, biomineralized shells on coccolithophorids,(5) and solid-stabilized emulsion droplets(6) and bubbles.(7) The influence of size variations on these packing patterns, however, is studied sparsely. Here we investigate the packing of nanosized silica particles on the surface of polystyrene latex particles fabricated by Pickering miniemulsion polymerization of submicrometer-sized armored monomer droplets. We are able to rationalize the experimental morphology and the nearest-neighbor distribution with the help of Monte Carlo simulations. We show that broadening of the nanoparticle size distribution has pronounced effects on the self-assembled equilibrium packing structures, with original 12-point dislocations or grain-boundary scars gradually fading out.
Keywords: packing patterns, silica, simulation, Monte Carlo, order, disorder, transition, armored particles, nanoparticles, Pickering emulsion
Published in RUNG: 10.10.2016; Views: 4622; Downloads: 0
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23.
Computational design of customised nanobodies for biotechnological applications
Miguel Soler, Ario De Marco, Sara Fortuna, 2016, unpublished conference contribution

Abstract: In silico modeling to improve the biophysical characteristics of recombinant single-domain antibodies
Keywords: nanobodies, modeling, protein stability, antibody humanization, molecular dynamics
Published in RUNG: 26.04.2016; Views: 4639; Downloads: 0
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