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1.
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).
Found in: ključnih besedah
Keywords: Self-assembly, self-organisation, agent based, Monte Carlo, rigid molecules, simulation
Published: 10.10.2016; Views: 3057; Downloads: 0
.pdf Fulltext (2,25 MB)

2.
Agent based modelling for the 2D molecular self-organization of realistic molecules
Sara Fortuna, Alessandro Troisi, 2010, original scientific article

Abstract: We extend our previously developed agent-based (AB) algorithm to the study of the self-assembly of a fully atomistic model of experimental interest. We study the 2D self-assembly of a rigid organic molecule (1,4-benzene-dicarboxylic acid or TPA), comparing the AB results with Monte Carlo (MC) and MC simulated annealing, a technique traditionally used to solve the global minimization problem. The AB algorithm gives a lower energy configuration in the same simulation time than both of the MC simulation techniques. We also show how the AB algorithm can be used as a part of the protocol to calculate the phase diagram with less computational effort than standard techniques.
Found in: ključnih besedah
Keywords: self-assembly, self-organisation, 1, 4-benzene-dicarboxylic acid, TPA, agent based, Monte Carlo, simulation, phase diagram
Published: 11.10.2016; Views: 3211; Downloads: 0
.pdf Fulltext (4,00 MB)

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