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Sara Fortuna

The Agent-Based model


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 on a 2-D lattice following a combination of stochastic, deterministic and adaptive rules with less computational effort than comparable Monte Carlo simulations.

The aim of our research is the study of the multiscale assembly of realistic systems [1,2]: a code based on a new set of rules (Fig.1) has been developed for the prediction of the self assembled structure of a set of idealized shapes in the 3D space [4].

The performance of the algorithm have been assessed by comparison with a conventional Metropolis Monte Carlo algorithm (Fig.2), 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.


Comparison between AB and MC simulations

Fig.2: the Agent-Based technique allows a system of rigid shapes to evolve to a better packed configuration than a comparable Monte Carlo simulation.


[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).




Talks:

The seminar "Agent Based Modelling for the study of Molecular Self-Organisation" was given a the ELETTRA Synchrotron Light Laboratory (Trieste, Italy, 7 April 2010).

The seminar "Agent Based Modelling for the study of Molecular Self-Organisation" (PDF   Document) was given at the Complexity Forum (Complexity Science Doctoral Training Centre, University of Warwick, UK, 17 February 2010).

The talk "Agent Based algorithm for the study of molecular self-organisation" (PDF Document) was given at the "European Conference on Complex Systems" (University of Warwick, UK, 21-25 September 2009).

The talk "Agent Based modelling for molecular self-organisation" (PDF Document) was given at the "European Dynamics Days 2009" (Göttingen, DE, 31 August, 4 September 2009).

The talk "Agent Based algorithm for the study of molecular self-organisation" (PDF Document) was given at the "EPSRC Network Mathematical Challenges of Molecular Dynamics, Second Annual Conference" (University of Bath, UK, 13-15 July 2009).

The talk "Agent Based algorithm for the study of molecular self-organisation" (PDF Document) was given at the "Chemistry Postgraduate Research Symposium 2009" (University of Warwick, UK, 10 June 2009).

The seminar "An Agent-Based Model for Molecular Self-Organization" (PDF Document) was given as a CSC@Lunch Seminar (Centre for Scientific Computing, University of Warwick, UK, 2 February 2009).


Posters:

The poster "Agent-based modelling for molecular self-organization" (PDF Document) has been presented at the "42nd IUPAC Congress - Chemistry Solutions" (Glasgow, UK, 2-7 August 2009).

The poster "Agent-based modelling for molecular self-organization" (PDF Document) has been presented at the "Faraday Discussion 144: Multiscale Modelling of Soft Matter" (University of Groningen, The Netherlands, 20-22 July 2009).

The poster "Agent-based modelling for molecular self-organization" (PDF Document) has been presented at the "EPSRC Symposium Workshop on Molecular Dynamics" (University of Warwick, UK 1-5 June 2009).

The poster "Agent-based modelling for molecular self-organization" (PDF Document) has been presented at the "Warwick PhD Poster Competition" (University of Warwick, UK, 5 May 2009).

The poster "An agent-based approach for modeling self-organization" (PDF Document) has been presented at the "Conference on Structure and Dynamics in Soft Matter and Biomolecules: From Single Molecules to Ensembles" (ICTP Trieste - Italy, 4-8 June 2007).

Agent-Based Modelling for Molecular Self-Organization
Poster presented at the
"Warwick PhD Poster Competition"
5 May 2009, Warwick University

motivation




AB kernel

Fig.1: the Agent-Based kernel code for the study of molecular self-organization.












Gottingen Oral Presentation
Presenting my work in Göttingen




warwick
CSC@Lunch




glasgow
Presenting my poster in Groningen