A method of analyzing a partition of a circuit design, comprising: partitioning a netlist of a circuit design to determine the partition of the circuit design, the partition of the circuit design having one or more local inputs; configuring an emulator to emulate the partition of the circuit design; sampling the emulator to obtain one or more input values provided at a first time to the one or more local inputs of the partition of the circuit design; sampling the emulator to obtain one or more first state values produced by the circuit design partition at the first time; using the one or more input values and the one or more first state values to, based on execution of a software model by a computing device in communication with the emulator, calculate one or more second state values produced by the partition of the circuit design at a second time, the software model describing the operation of the partition of the circuit design; and registering the one or more second state values in a tangible medium, characterized in that the partition of the circuit design includes a plurality of time domains; and the software model includes a portion describing the operation of each time domain, wherein the partition of the circuit design has one or more cross-domain inputs, and wherein the method further comprises: sampling an emulator to obtain: one or more cross-domain input values provided to the one or more cross-domain inputs of the partition of the circuit design at one or more times prior to the first time, and a time of arrival of each sampled cross-domain input; and wherein in addition to the one or more input values and the one or more first state values, the one or more cross-domain input values and the time of arrival of each sampled cross-domain input are used to, based on execution of the software model by the computing device, calculate the one or more second state values produced by the partition of the circuit design at the second time. partitioning a netlist of a circuit design to determine the partition of the circuit design, the partition of the circuit design having one or more local inputs; configuring an emulator to emulate the partition of the circuit design; sampling the emulator to obtain one or more input values provided at a first time to the one or more local inputs of the partition of the circuit design; sampling the emulator to obtain one or more first state values produced by the circuit design partition at the first time; using the one or more input values and the one or more first state values to, based on execution of a software model by a computing device in communication with the emulator, calculate one or more second state values produced by the partition of the circuit design at a second time, the software model describing the operation of the partition of the circuit design; and registering the one or more second state values in a tangible medium, characterized in that the partition of the circuit design includes a plurality of time domains; and the software model includes a portion describing the operation of each time domain, wherein the partition of the circuit design has one or more cross-domain inputs, and wherein the method further comprises: sampling an emulator to obtain: one or more cross-domain input values provided to the one or more cross-domain inputs of the partition of the circuit design at one or more times prior to the first time, and a time of arrival of each sampled cross-domain input; and wherein in addition to the one or more input values and the one or more first state values, the one or more cross-domain input values and the time of arrival of each sampled cross-domain input are used to, based on execution of the software model by the computing device, calculate the one or more second state values produced by the partition of the circuit design at the second time. sampling an emulator to obtain: one or more cross-domain input values provided to the one or more cross-domain inputs of the partition of the circuit design at one or more times prior to the first time, and a time of arrival of each sampled cross-domain input; and one or more cross-domain input values provided to the one or more cross-domain inputs of the partition of the circuit design at one or more times prior to the first time, and a time of arrival of each sampled cross-domain input; and wherein in addition to the one or more input values and the one or more first state values, the one or more cross-domain input values and the time of arrival of each sampled cross-domain input are used to, based on execution of the software model by the computing device, calculate the one or more second state values produced by the partition of the circuit design at the second time.