Translational Diffusion of Macromolecules and Nanoparticles Modeled as Non-overlapping Bead Arrays in an Effective Medium

详细信息    查看全文

• 作者：Stuart Allison ; Hongxia Pei ; Margaret Haynes ; Yao Xin ; Lydia Law ; Josh Labrum ; Daphne Augustin
• 刊名：Journal of Physical Chemistry B
• 出版年：2008
• 出版时间：May 8, 2008
• 年：2008
• 卷：112
• 期：18
• 页码：5858 - 5866
• 全文大小：98K
• 年卷期：v.112,no.18(May 8, 2008)
• ISSN：1520-5207

文摘

There are three objectives to the present work. First, starting from a boundary element (BE) formulation oflow Reynolds number hydrodynamics, model the translational diffusion of macromolecules modeled as anarray of non-overlapping beads, and show how this approach is equivalent to previous formulations of "beadhydrodynamics" and under what conditions. Second, show how this approach can be improved upon byaccounting for the variation in forces over the surfaces of individual beads and also extending the approachto a gel modeled as an effective medium, EM. Third, develop a "combined obstruction and hydrodynamiceffect" model of the translational diffusion of irregularly shaped macromolecules in a gel. In one of the casesstudied, the BE approach is shown to be equivalent to previous "bead model" formulations in which intersubunithydrodynamic interaction is modeled using the Rotne-Prager tensor. A bead model that accounts for thevariation in hydrodynamic stress forces over the individual bead surfaces is shown to be in best agreementwith exact results for simple bead arrays made up of 2-4 subunits. The translational diffusion of rods, modeledas strings of from 2 to 100 touching beads in dilute gels is examined. Interpolation formulas valid over arange of gel concentrations and rod lengths are derived for the parallel and perpendicular components of thediffusion tensor as well as the orientationally averaged diffusion tensor. The EM model accounts for thelong-range hydrodynamic interaction exerted by the gel support matrix on the diffusing particle of interestbut does not account for the reduction in diffusion caused by the direct obstruction of the gel, or steric effect.Both effects are accounted for by writing the translational diffusion in a gel as the product of two termsrepresenting long-range hydrodynamic interaction and steric effects. Finally, the diffusion of a 564 base pairDNA in a 2% agarose gel is examined and model results are compared to experiment (Pluen, A.; Netti, P. A.;Jain, R. K.; Berk, D. A. Biophys. J. 1999, 77, 542-552). For reasonable choices of model parameters, fairagreement between theory and experiment is achieved.