Patent Document ID: 9805159
Application ID: 14790400
Patent Flag: 1

Claim One:
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, wherein the initial state of each instantiated entity comprises each of, a mass of the instantiated entity, a number of copies of the instantiated entity, an initial position of each instantiated instance of the entity within the virtual 3-D geometric space, and an initial velocity of each instance of the instantiated entity, and wherein one or more of the available behaviors is to be determined and performed upon an interaction event; dividing the virtual 3-D geometric space into one or more geometric portions sized in accordance with available work nodes; distributing the one or more geometric portions to the available work nodes for processing, wherein each geometric portion comprises a subset of the instantiated entities; 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 among 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.