title: Agent-based modeling for the 2D molecular self-organization of realistic molecules.
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.
authors.affiliation: Department of Chemistry and Centre for Scientific Computing, Warwick University, Coventry, United Kingdom. S.Fortuna@csc.warwick.ac.uk
authors.forename: Sara
authors.initials: S
authors.lastname: Fortuna
authors.forename: Alessandro
authors.initials: A
authors.lastname: Troisi
mesh_terms: D000465:Algorithms; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009010:Monte Carlo Method; D010795:Phthalic Acids / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D013816:Thermodynamics
chemical_list: C547494:1,4-benzenedicarboxylate; D010795:Phthalic Acids; D012997:Solvents; C011363:terephthalic acid