Self-assembly of particles with certain surface properties is a topic which becomes more and more interesting in many research areas. The main problems of self-assembly of different particles are of two kinds: First, one has to find a method that determines a set of particles with certain properties so that an assembly into a desired structure is achieved. Second, once these particles are found, they have to be created as real chemical or biological components. The model proposed in this paper addresses the first problem: finding a set of particles that self-assemble into higher order structures. It uses a newly developed version of the so called Cellular Potts Model, a simulation technique that has become increasingly popular in the last years for simulating biological cells and their mechanical interactions. The cells are created with binding sites on their surfaces, and these binding sites allow the particles to attach to each other in a way that is generic enough to allow for the formation of a broad range of different structures. The model also includes the possibility to add growth and division, as these mechanisms may have critical influence on the self assembly process. One advantage with this model structure is that one can directly add reaction-diffusion dynamics to the simulation model. The software is available as part of Deliverable D22, including a report (Nyström, 2008).
The following simulation illustrates the growth of cells with division and aggregation based on one binding site per cell.
--> Simulation of Potts-based model for growth and aggregation
Reference:
Nyström, J. (2008). Report on simulation package for physically self-assembling units. (preprint) included in Deliverable D22.