Brownian dynamics simulation of analytical ultracentrifugation experiments

Simulations are carried out for four molecules covering a wide range of the ratio of sedimentation and diffusion coefficients. The evaluation is done by extracting the molecular parameters that were initially employed in the simulation by analyzing the profiles with an independent tool, the well-proved SEDFIT software. The code of simulation algorithm has been parallelized in order to take advantage of current multi-core computers.Our Brownian dynamics simulation procedure may be considered as an alternative to other predictors based in numerical solutions of the Lamm equation, and its efficiency could make it useful in the most relevant, inverse problem, which is that of extracting the molecular parameters from experimentally determined concentration profiles.Since the invention of the analytical ultracentrifuge by Svedberg [1], the technique of analytical ultracentrifugation (AUC) has been a classical - and, thanks to advances in instrumentation and analysis software, it is still a most modern - technique for characterization of macromolecules and nanoparticles in solution. The reader may grasp the recent importance of this field in monographs [2-4] and thematic issues of other journals [5-7].In the AUC, particles move under influence of a centrifugal field, caused by rotation of the sample with angular velocity ω, which produces a centrifugal force (corrected by buoyancy) equal to ω 2 r m ( 1 ？ v ˉ ρ ) , where r is the instantaneous distance from the particle to the rotation axis, m is the mass of the particle (m = M/NA where M is the molecular weight and NA is Avogadro's number), v ˉ is the partial specific volume of the solute particles and ρ is the solution density (nearly equal to the solvent density, if the solution is dilute). The velocity that the solute particles may acquire due to this effect is proportional to the centrifugal acceleration, υ = sω2r, where the s is the sedimentation coefficient, and modulated also by the friction coefficient f of