Mathematical models of physical systems are subject to many uncertainties
such as measurement errors and uncertain initial and boundary conditions. After
accounting for these uncertainties, it is often revealed that discrepancies
between the model output and the observations remain; if so, the model is said
to be inadequate. In practice, the inadequate model may be the best that is
available or tractable, and so despite its inadequacy the model may be used to
make predictions of unobserved quantities. In this case, a representation of
the inadequacy is necessary, so the impact of the observed discrepancy can be
determined. We investigate this problem in the context of chemical kinetics and
propose a new technique to account for model inadequacy that is both
probabilistic and physically meaningful. A stochastic inadequacy operator
S is introduced which is embedded in the ODEs describing the
evolution of chemical species concentrations and which respects certain
physical constraints such as conservation laws. The parameters of S
are governed by probability distributions, which in turn are characterized by a
set of hyperparameters. The model parameters and hyperparameters are calibrated
using high-dimensional hierarchical Bayesian inference. We apply the method to
a typical problem in chemical kinetics---the reaction mechanism of hydrogen
combustion