Building artificial systems using self-assembly is one of the main issues of artificial life [17]. Scientists are trying to understand this process either using experimental approaches or computer simulation approaches. This paper aims at supporting research using computer simulation approaches mimicking self-assembly as it occurs in the real world using basic principles in physics such as Brownian motion and basic concepts in Chemistry such as activation energy required to build molecules at molecular level. In this paper, a simulator has been implemented to mimic the process of self-assembly. In this simulator, objects are modeled by shapes such as cubes, tetrahedrons, wedges and pyramids with colors in their faces. The objects move randomly in Brownian motion, and the faces' colors determine how the objects interact with each other. Each object has its own probability to move which depends on the energy that the object gains through its interaction with other objects. The high...