1. A method for enabling a simulation environment for experimental design, the method comprising: receiving a request to initiate a simulation of a biological model of a cell having organelles (cell model), wherein the request comprises a selection of initial entities comprising one or more organelles of the cell model and one or more molecule types contained within, or associated with the one or more organelles of the cell model, wherein each entity has one or more interaction points, and wherein each interaction point describes an input and an outcome of a biological event; instantiating the initial entities of the request to a data structure representing a virtual three-dimensional (3-D) geometric space, wherein the instantiated data structure comprises the selection of initial entities at locations within the virtual 3-D geometric space, wherein the instantiated data structure describes an initial state of each instantiated entity and describes a plurality of available behaviors for each instantiated entity, and wherein one or more of the available behaviors is to be determined and performed upon an interaction event; performing a periodic iteration to evaluate each interaction point of each instantiated entity within the virtual 3-D geometric space to identify interactions with other instantiated entities that would result in performance of a determined behavior, wherein each periodic iteration command demarks the beginning of a new action cycle; wherein, in the periodic iteration, each of the instantiated entities: updates its position and velocity within the virtual 3-D geometric space; identifies occurrence of a collision, if present, with other instantiated entities and performs one or more determined behaviors from anon the plurality of available behaviors, wherein the plurality of available behaviors includes, at least each of: binding or releasing of an instantiated entity, changing the secondary, tertiary, or quaternary structure of an instantiated entity, and transforming an instantiated entity to a different entity type; performs the determined one or more behaviors; and waits for a next periodic iteration command.