Dynamics of hard-sphere suspensions

Tokuyama, Michio; Oppenheim, Irwin

doi:10.1103/physreve.50.r16

Cited by 464 publications

(200 citation statements)

References 18 publications

(10 reference statements)

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“…Interestingly, the reduced diffusion seems to obey a temperature-independent master-curve. The experimental D t ðφÞ∕D t ð0Þ agree almost perfectly with the normalized short-time self-diffusion coefficient predicted by colloid theory for charged (19) and noncharged hard spheres (22) (Fig. 4).…”

Section: Resultssupporting

confidence: 73%

“…For t ≫ τ I long-time self-diffusion is observed, affected by both hydrodynamic and direct interactions. For the short-time and long-time regimes, series expansions have been derived for the self-diffusion of spherical colloids with and without charge (18)(19)(20)(21)(22).In this study we report on extensive experimental data on protein self-diffusion in crowded aqueous solutions of bovine serum albumin (BSA) as determined from quasielastic neutron backscattering on nanosecond time and nanometer length scales. Thereby, we investigate the fundamental case where tracer particle and crowding agent are identical proteins.…”

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confidence: 99%

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Protein self-diffusion in crowded solutions

Roosen-Runge

Hennig²,

Zhang³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

216

311

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Macromolecular crowding in biological media is an essential factor for cellular function. The interplay of intermolecular interactions at multiple time and length scales governs a fine-tuned system of reaction and transport processes, including particularly protein diffusion as a limiting or driving factor. Using quasielastic neutron backscattering, we probe the protein self-diffusion in crowded aqueous solutions of bovine serum albumin on nanosecond time and nanometer length scales employing the same protein as crowding agent. The measured diffusion coefficient DðφÞ strongly decreases with increasing protein volume fraction φ explored within 7% ≤ φ ≤ 30%. With an ellipsoidal protein model and an analytical framework involving colloid diffusion theory, we separate the rotational D r ðφÞ and translational D t ðφÞ contributions to DðφÞ. The resulting D t ðφÞ is described by short-time self-diffusion of effective spheres. Protein self-diffusion at biological volume fractions is found to be slowed down to 20% of the dilute limit solely due to hydrodynamic interactions. macromolecular crowding | quasi-elastic neutron scattering | globular proteins T he interior of biological cells is a medium with a macromolecular volume fraction of up to 40%. This crowding crucially affects reaction kinetics and equilibria in the cell (1, 2). Cellular function and structure thus cannot be understood without a systematic understanding of both phase behavior and transport processes in crowded media. Diffusion is the main transport process for systems at low Reynolds numbers, governing many dynamic processes in nature (3). From the perspective of a single tracer molecule, all other molecules act as obstacles. In vivo diffusion coefficients for globular proteins in living cells (4-7) are strongly decreased compared to the in vitro diffusion coefficient in dilute buffer solutions. Systematic measurements of the tracer diffusion of proteins dissolved in concentrated suspensions of crowding agents, i.e., other proteins or polymers, reveal a complex dependence of the slowing down on the combination of tracer molecule and crowding agent (8-10). Furthermore, macromolecular crowding is found to induce subdiffusive behavior in several cases (11,12), being suggested as a slower but more reliable diffusive search process inside the cell (13). This anomalous diffusion process has been found also in theory and simulations (12-15) suggesting a crossover from subdiffusive behavior at small times to diffusive behavior at larger times.Proteins are macromolecules generally with a nonspherical shape and a nonhomogeneous surface charge, showing specific interactions with ligands. Furthermore, proteins not only show global motions like translational and rotational diffusion but also internal and interdomain motions. Therefore, proteins pose a challenge to colloid theory (16,17). In a recent simulation study Ando and Skolnick (4) revealed that using an equivalent-sphere model for macromolecules is a reasonable approximation to describe diffusion. Moreover, ...

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Section: Resultssupporting

confidence: 73%

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confidence: 99%

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Protein self-diffusion in crowded solutions

Roosen-Runge

Hennig²,

Zhang³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

216

311

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“…The obstruction factor depends on the shape, volume fraction, and spatial and orientation distribution of the obstructing molecules [48,[65][66][67]. The simple obstruction models derived to date assumed that all of the obstructing particles have the same size and shape (generally taken to be spheres) and are only valid at very low concentrations [48,[65][66][67][68][69][70][71]. Furthermore, these obstruction models do not account for the effects from electrostatic interactions.…”

Section: Obstructionmentioning

confidence: 99%

“…Lekkerkerker and Dhont [71], on the other hand, provided the obstruction factor using the MSD of interacting Brownian particles. Han and Herzfeld [48] derived a relationship for a hard sphere diffusing among hard spherocylinders while Tokuyama and Oppenheim (T and O) [70,73] used the Navier-Stokes equation to develop a model for the dynamics of concentrated hard-sphere suspensions of interacting Brownian particles with both hydrodynamic and direct interactions. NMR diffusion measurements are usually carried out with solutes or macromolecules present in the millimolar range or above, yet most of the theory used to analyse the diffusion data has been derived on the assumption that diffusion is occurring at infinite dilution.…”

Section: Obstructionmentioning

confidence: 99%

Macromolecular crowding studies of amino acids using NMR diffusion measurements and molecular dynamics simulations

et al. 2015

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Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction). Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance (NMR) measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine) up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

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