Systems and methods for operating a stepper motor of a pump at a desired low velocity include memory for storing information corresponding to an intake velocity profile. The intake velocity profile represents an optimized acceleration curve for operating the stepper motor over a range of motor velocities during an intake cycle. A processor of a system controller dynamically accesses the memory during the intake cycle to acquire the information representing the intake velocity profile and issues a series of pulses to the stepper motor based on this information. In response to the pulses, the stepper motor accelerates in accordance with the optimized acceleration curve represented by the intake velocity profile. The optimized acceleration curve is based on the available torque of the stepper motor across a range of motor velocities and enables the motor to operate with greater torque utilization and less margin than traditional linear acceleration profiles.