1. A molecular modeling system for use in assembling a plurality of structural elements comprising: a node element comprising: a body; at least one connection port disposed relative to the body and configured to be coupled to an adjacent structural element; a computational unit disposed within the body configured to receive information of physical characteristics of the node element from the connection port; the computational unit including: a memory device for storing embedded rules of the body and operational instructions associated with functioning of the node element, the instructions including: unique characteristics of the node element, input data from a communications device, output data from a transmission device, communication rules for determining a state of the body, rules for building the body, and computational functions for processing of the instructions and interpreting the communication rules and the rules for building; and the communications device capable of providing data from the computational unit to an external computer system; and a bond element comprising: a body; a first and a second connection port disposed relative to the body, at least one of the first and the second connection ports capable of being coupled to the node element; and a computational unit disposed within the body, wherein the computational unit receives information of physical characteristics of the bond element from at least one of the first and second connection ports.