A mechanical circulatory assist system comprising: a continuous flow blood pump implantable in fluid communication with a ventricle and an artery of a patient to assist blood flow from the ventricle to the artery; and a controller operatively connected to the blood pump and operable to: control a rotation rate of the blood pump to pump blood from the ventricle to the artery over a first segment of a cardiac cycle of the patient, the rotation rate of the blood pump over the first segment being controlled in accordance with a first segment operational mode for the blood pump; monitor a blood flow rate through the blood pump; based on the monitored blood flow rate through the blood pump, determine whether continuing to control the rotation rate of the blood pump over a second segment of the cardiac cycle in accordance with the first segment operational mode would result in the blood flow rate through the blood pump being less than a target minimum blood flow rate during ventricular diastole; and in response to determining that continuing to control the rotation rate of the blood pump over the second segment in accordance with the first segment operational mode would result in the blood flow rate through the blood pump being less than the target minimum blood flow rate during ventricular diastole, control the rotation rate of the blood pump over the second segment so that the blood flow rate through the blood pump is approximate to the target minimum blood flow rate. a continuous flow blood pump implantable in fluid communication with a ventricle and an artery of a patient to assist blood flow from the ventricle to the artery; and a controller operatively connected to the blood pump and operable to: control a rotation rate of the blood pump to pump blood from the ventricle to the artery over a first segment of a cardiac cycle of the patient, the rotation rate of the blood pump over the first segment being controlled in accordance with a first segment operational mode for the blood pump; monitor a blood flow rate through the blood pump; based on the monitored blood flow rate through the blood pump, determine whether continuing to control the rotation rate of the blood pump over a second segment of the cardiac cycle in accordance with the first segment operational mode would result in the blood flow rate through the blood pump being less than a target minimum blood flow rate during ventricular diastole; and in response to determining that continuing to control the rotation rate of the blood pump over the second segment in accordance with the first segment operational mode would result in the blood flow rate through the blood pump being less than the target minimum blood flow rate during ventricular diastole, control the rotation rate of the blood pump over the second segment so that the blood flow rate through the blood pump is approximate to the target minimum blood flow rate. control a rotation rate of the blood pump to pump blood from the ventricle to the artery over a first segment of a cardiac cycle of the patient, the rotation rate of the blood pump over the first segment being controlled in accordance with a first segment operational mode for the blood pump; monitor a blood flow rate through the blood pump; based on the monitored blood flow rate through the blood pump, determine whether continuing to control the rotation rate of the blood pump over a second segment of the cardiac cycle in accordance with the first segment operational mode would result in the blood flow rate through the blood pump being less than a target minimum blood flow rate during ventricular diastole; and in response to determining that continuing to control the rotation rate of the blood pump over the second segment in accordance with the first segment operational mode would result in the blood flow rate through the blood pump being less than the target minimum blood flow rate during ventricular diastole, control the rotation rate of the blood pump over the second segment so that the blood flow rate through the blood pump is approximate to the target minimum blood flow rate.