Agent-Based Modeling for the 2D Molecular Self-Organization of Realistic Molecules

Authored by Sara Fortuna, Alessandro Troisi

Date Published: 2010-08-12

DOI: 10.1021/jp103950m

Sponsors: Leverhulme Trust

Platforms: TINKER

Model Documentation: Other Narrative

Model Code URLs: Model code not found

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.

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