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Title: Agent Based modelling for the study molecular self-organisation

Abstract:

 If we consider chemical systems, such as the crystal structure [1] or the supramolecular assembly [2] of an ensemble of molecules, a common question will arise: given N molecules, what is the lowest-energy organized structure that they can form?

This problem can be solved with the decomposition of the system in N agents.  An agent is a system capable of exchanging information with other agents and its environment, taking decisions and performing autonomous actions.

The agent-based technique, previously used to study social phenomena, was first applied to a chemical system by Troisi et al. [3].  This technique allows a system of rigid shapes to evolve to the lowest-energy ordered structure lattice following a combination of stochastic, deterministic and adaptive rules with less computational effort than comparable Monte Carlo simulations.

Now, a code based on a new set of rules [4] has been developed for the prediction of the self assembled structure of a set of idealized shapes in the 3D space.

The performance of the algorithm have been assessed by comparison with a conventional Metropolis Monte Carlo algorithm , and this have been 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).

Current research is focused on linking the existing code to Tinker [5], software able to calculate the force field of real molecules.

[1] G.M.Day, W.D.S.Motherwell, H.L.Ammon, et al., Acta Crystall. B 61, 511 (2005).
[2] Y.Kato, N.Mizoshita and K.Kishimoto, Angew. Chem. Int. 45, 38 (2006).
[3] A.Troisi, V.Wong and M.A.Ratner, PNAS 102, 255 (2005).
[4] S.Fortuna and A.Troisi, J. Phys. Chem. B, 113 (29), 9877 (2009).
[5] J.W.Ponder and F.M.Richards, J. Comput. Chem. 8, 1016 (1987).