Prediction and analysis of analytical ultracentrifugation experiments for heterogeneous macromolecules and nanoparticles based on Brownian dynamics simulation

In the prediction of sedimentation profiles in analytical ultracentrifugation, the counterflow due to diffusion must be taken into account for a proper analysis of experimental data in the determination of molecular properties. This is usually achieved by numerical solution of the Lamm equation. This paper presents an alternative approach, in which the displacement of the solute in the cell, resulting from the opposite effects of ultracentrifugal force and diffusional drift, is described by Brownian dynamics simulation of the solute particles. The formalism is developed for heterogeneous solutes, composed of several species, and implemented in computational schemes and tools. The accuracy of the procedure is verified by comparison with other methods based on the Lamm equation, and its efficiency is illustrated. The possibilities offered by the Brownian dynamics methods in the determination of solute properties and sample composition are demonstrated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00249-018-1322-2) contains supplementary material, which is available to authorized users.