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The first would be the difference between the calculated ensemble-average (GAT)ea at the end of the control runs and the individual (GAT)cj values; these would all be different The second would be the difference between the individual model/code (GAT)cj values at the end of the control runs and its (GAT)cj; and so would be 0.0.
Two advantages of the framework are (i) the ability, in principle, to predict stochasticity and therefore quantify uncertainties; (ii) the ability to predict size dependency (in an ensemble-average sense) with conventional boundary conditions.