Simulation of the time course of macromolecular separations in an ultracentrifuge. II. Controlling the solute concentrations.

We describe algorithms, based on a simulation described in Part I of this series of papers, for the control of the distribution of one or more solutes in preparative or analytical ultracentrifuges equipped with programmable speed control. All of the methods involve the determination, during numerical integration of the Lamm equation, of protocols for continuously varying the rotor speed. We show one such protocol that has been used for the prevention of cesium chloride crystallization during DNA plasmid purification in the preparative ultracentrifuge. Other protocols that are described involve the in situ controlled mixing of two solutes. Limitations of the method owing to problems with input parameter imprecision, fundamental physical constraints, and mechanical limitations are discussed.