Many-particle diffusion in continuum: Influence of a periodic surface potential

Effect of Protein–Protein Interactions on Translational Diffusion of Spheroidal Proteins

One of the commonly accepted approaches to estimate protein–protein interactions (PPI) in aqueous solutions is the analysis of their translational diffusion. The present review article observes a phenomenological approach to analyze PPI effects via concentration dependencies of self- and collective translational diffusion coefficient for several spheroidal proteins derived from the pulsed field gradient NMR (PFG NMR) and dynamic light scattering (DLS), respectively. These proteins are rigid globular α-chymotrypsin (ChTr) and human serum albumin (HSA), and partly disordered α-casein (α-CN) and β-lactoglobulin (β-Lg). The PPI analysis enabled us to reveal the dominance of intermolecular repulsion at low ionic strength of solution (0.003–0.01 M) for all studied proteins. The increase in the ionic strength to 0.1–1.0 M leads to the screening of protein charges, resulting in the decrease of the protein electrostatic potential. The increase of the van der Waals potential for ChTr and α-CN characterizes their propensity towards unstable weak attractive interactions. The decrease of van der Waals interactions for β-Lg is probably associated with the formation of stable oligomers by this protein. The PPI, estimated with the help of interaction potential and idealized spherical molecular geometry, are in good agreement with experimental data.

Sedimentation dynamics of spherical particles in confined geometries

We study the steady-state dynamics of sedimenting non-Brownian particles in confined geometries with full hydrodynamic interactions at small but finite Reynolds numbers. We employ extensive computer simulations using a method where a continuum liquid phase is coupled through Stokesian friction to a discrete particle phase. In particular, we consider a sedimentation box which is otherwise periodic except that it is confined by two parallel walls parallel to gravity with a spacing Lx. By systematically varying Lx we explore the change in dynamics from a quasi-two-dimensional (2D) case to a three-dimensional case. We find that in such confined geometries there is a depletion of particle number density at the walls for small volume fractions, while for large volume fractions there is an excess number of particles at the walls. For the average sedimentation velocity, we find that the Richardson-Zaki law is well obeyed but the decrease of the velocity for dilute systems is slower for smaller values of Lx. We study the anisotropy of the velocity fluctuations and find that in the direction of gravity there is excellent agreement with the predicted scaling with respect to Lx. We also find that the behavior of the corresponding diffusion coefficients as a function of Lx is qualitatively different in the direction parallel to gravity and perpendicular to it. In the quasi-2D limit where particles block each other, the velocity fluctuations behave differently from the other confined systems.