Difference between Zonal Centrifugation and Isopycnic Centrifugation Rate Zonal Centrifugation Isopycnic Centrifugation Low speed. High speed. Swing Rotor was used. Fixed Angle or Swing Rotor was used. Not completely sedimented. Completely sedimented. Short running time (Short duration). Long running time (Long duration). Gradient type is Continuous. Gradient type is Continuous or Discontinious. Separation was based on Size of molecules. Separation was based on Density of molecules. Particles are separated on the basis of Sedimentation rate. Particles are separated on the basis of Sedimentation equilibrium. Similar density but different molecular weight. Similar molecular weight but different density. Used for the separation of Proteins, Enzym