aiSee: Network Artificial Chemistry Simulation

Network Artificial Chemistry Simulation

“Network artificial chemistry (NAC) is a new method of artificial chemistry that represents spatial structure and molecular interactions purely with a network. The NAC’s nodes are abstract representations of biological molecules or atomic clusters. In imitation of the forces governing biochemical processes, the NAC has three types of edges: covalent, ionic, and van der Waals.

Using a method of statistical mechanics, the NAC edges are rewired according to pas­sive and active rewiring rules. The active rewiring only occurs catalized by active nodes or clusters (as compared to biological protein), whereas the passive rewiring incessantly creates and deletes the weakest (i.e. van der Waals) edges so as to emulate spatial movement and collisions between molecules.

The above picture is a part of a sample NAC network after a hundred thousand time steps of the rewiring. Yellow nodes are hydrophilic, and red nodes are hydrophobic. ”The big hydrophilic cluster is dividing itself. The snapshot was created using aiSee.

Hideaki Suzuki, National Institute of Information and Communications Technology, Kobe, Japan, and ATR Network Informatics Laboratories, Kyoto, Japan, and Naoaki Ono, Complex Systems Biology Project, ERATO, JST, Osaka University, Japan.