On the theory of concentrated hard-sphere suspensions

Tokuyama, Michio; Oppenheim, Irwin

doi:10.1016/0378-4371(94)00280-7

Cited by 94 publications

(84 citation statements)

References 29 publications

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“…The benchmark model for simple crowding is a solution of hard, monodisperse spheres. A good experimental realization of this system is a solution of spherical, monodisperse colloidal particles; these have been well studied both experimentally and theoretically (2,34). The observed falloff of D/D 0 is about a factor of 10 as increases from 0 to 0.4, the range of interest in our work.…”

Section: Resultsmentioning

confidence: 64%

Cytoplasmic Protein Mobility in Osmotically Stressed Escherichia coli

Konopka¹,

Sochacki²,

Bratton³

et al. 2009

J Bacteriol

102

177

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Section: Resultsmentioning

confidence: 64%

Cytoplasmic Protein Mobility in Osmotically Stressed Escherichia coli

Konopka¹,

Sochacki²,

Bratton³

et al. 2009

J Bacteriol

102

177

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“…For monodisperse, hard sphere spherical particles, analytical equations that describe the concentration dependence of the short-time and long-time self-diffusion coefficients have been derived by Tokuyama and Oppenheim (41,42). These theoretical values are in good agreement with experimental results on diffusivity even for condensed systems.…”

Section: Discussionmentioning

confidence: 99%

“…On including HI, in principle, the diffusion tensor of each molecule depends on the instantaneous configuration of the entire system (but we would expect screening to emerge at higher concentrations). To explore the role of HI, the modified [40][41][42]. In this model, the surface roughness of macromolecule was also considered by including a correction factor.…”

Section: Estimation Of Diffusion Tensor Of a Macromolecule From Its Amentioning

confidence: 99%

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

Ando

Skolnick

2010

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

368

455

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To begin to elucidate the principles of intermolecular dynamics in the crowded environment of cells, employing Brownian dynamics (BD) simulations, we examined possible mechanism(s) responsible for the great reduction in diffusion constants of macromolecules in vivo from that at infinite dilution. In an Escherichia coli cytoplasm model comprised of 15 different macromolecule types at physiological concentrations, BD simulations of molecular-shaped and equivalent sphere representations were performed with a soft repulsive potential. At cellular concentrations, the calculated diffusion constant of GFP is much larger than experiment, with no significant shape dependence. Next, using the equivalent sphere system, hydrodynamic interactions (HI) were considered. Without adjustable parameters, the in vivo experimental GFP diffusion constant was reproduced. Finally, the effects of nonspecific attractive interactions were examined. The reduction in diffusivity is very sensitive to macromolecular radius with the motion of the largest macromolecules dramatically slowed down; this is not seen if HI dominate. In addition, long-lived clusters involving the largest macromolecules form if attractions dominate, whereas HI give rise to significant, size independent intermolecular dynamic correlations. These qualitative differences provide a testable means of differentiating the importance of HI vs. nonspecific attractive interactions on macromolecular motion in cells. Brownian dynamics | correlated motionO ne of the most characteristic features of the interiors of cells is the high total concentration of biological macromolecules. Typically, 20%-40% of the cytoplasmic volume is occupied by proteins, nucleic acids, and other macromolecules (1-3). Under these conditions, although the molar concentration of each protein ranges from nM to μM, the distance between neighboring proteins is comparable to the size of the proteins. Therefore, simulating the crowded intracellular environment is crucial to understanding the nature of living systems.Macromolecular crowding exerts surprisingly large effects on the thermodynamics and kinetics of processes such as macromolecular association, protein stability, and enzyme activity (1, 4, 5). The diffusion and partitioning of macromolecules are highly restricted by intermolecular steric repulsions as well as nonspecific attractive interactions. Consequently, the in vivo and in vitro rates and equilibria of biological reactions can differ by orders of magnitude. While there have been several models of metabolic networks or signaling pathways designed to elucidate the relationship between molecular and cellular behavior (6), effects of macromolecular crowding are at best only partially considered (7).Diffusion is one of the most important physical parameters that describe motions of molecules in a fluid. The diffusion constants of macromolecules in the cytoplasm as well as in membranes have been measured by various techniques including "single-particle tracking" (8), "fluorescence recovery after phot...

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“…For highly packed hard-sphere systems, theoretical and experimental studies suggest that the diffusion coefficient vanishes as a power-law [28,29,30]. Hence we will assume that the mobility Γ(ρ) vanishes as…”

Section: A Nonlinear Diffusion Equationmentioning

confidence: 99%

Slow dynamics under gravity: a nonlinear diffusion model

Arenzon

Levin

Sellitto

2003

Physica A: Statistical Mechanics and its Applications

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We present an analytical and numerical study of a nonlinear diffusion model which describes density relaxation of loosely packed particles under gravity and weak random (thermal) vibration, and compare the results with Monte Carlo simulations of a lattice gas under gravity. The dynamical equation can be thought of as a local density functional theory for a class of lattice gases used to model slow relaxation of glassy and granular materials. The theory predicts a jamming transition line between a low density fluid phase and a high density glassy regime, characterized by diverging relaxation time and logarithmic or power-law compaction according to the specific form of the diffusion coefficient. In particular, we show that the model exhibits history dependent properties, such as quasi reversible-irreversible cycle and memory effects -as observed in recent experiments, and dynamical heterogeneities.

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On the theory of concentrated hard-sphere suspensions

Cited by 94 publications

References 29 publications

Cytoplasmic Protein Mobility in Osmotically Stressed Escherichia coli

Cytoplasmic Protein Mobility in Osmotically Stressed Escherichia coli

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

Slow dynamics under gravity: a nonlinear diffusion model

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