A modeling system is presented that can be used to predict the effects of ventilatory settings on the blood gases of patients on mechanical ventilation. The system uses a physiological model of the patient that includes lungs, body tissue, and brain tissue compartments. The model includes the effects of changes in the cardiac output and cerebral blood flow and lung mechanical factors. The system has applications in critiquing different treatment options and can be used alone or in combination with decision support systems to set ventilatory parameters and optimize treatment for patients on mechanical ventilation.