Self-diffusion of biomolecules in solution

Tokuyama, Michio; Moriki, Tatsuo; Kimura, Yuto

doi:10.1103/physreve.83.051402

Cited by 25 publications

(39 citation statements)

References 37 publications

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“…When a solute k is only partially included within R cut , that is, when

R^{italiccut} - σ_{k}^{italicstokes} < d_{italicik} < R^{italiccut} + σ_{k}^{italicstokes}

, we account for that portion of solute volume derived by the sphere-sphere intersection. The volume fraction dependent short-time translational diffusion coefficient (

D^{t_{italicshort}} (ϕ_{i})

) is then obtained using the Tokuyama model [20-22], derived for a concentrated hard-sphere suspension of particles interacting with both direct and hydrodynamic interactions. An equation analogous to Equation 2 is used for the rotational motion [12], with the volume fraction dependent short-time rotational diffusion coefficient obtained using the model derived by Cichocki et al which includes lubrication forces as well as two- and three-body expansions of the mobility functions [23].…”

Section: Methodsmentioning

confidence: 99%

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

2014

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BackgroundBrownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to contain the computational costs, especially for the computation of interaction forces and energies. A common approach is to compute interaction forces between macromolecules by precomputing their interaction potentials on three-dimensional discretized grids. For long-range interactions, such as electrostatics, grid-based methods are subject to finite size errors. We describe here the implementation of a Debye-Hückel correction to the grid-based electrostatic potential used in the SDA BD simulation software that was applied to simulate solutions of bovine serum albumin and of hen egg white lysozyme.ResultsWe found that the inclusion of the long-range electrostatic correction increased the accuracy of both the protein-protein interaction profiles and the protein diffusion coefficients at low ionic strength.ConclusionsAn advantage of this method is the low additional computational cost required to treat long-range electrostatic interactions in large biomacromolecular systems. Moreover, the implementation described here for BD simulations of protein solutions can also be applied in implicit solvent molecular dynamics simulations that make use of gridded interaction potentials.

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“…When a solute k is only partially included within R cut , that is, when

R^{italiccut} - σ_{k}^{italicstokes} < d_{italicik} < R^{italiccut} + σ_{k}^{italicstokes}

, we account for that portion of solute volume derived by the sphere-sphere intersection. The volume fraction dependent short-time translational diffusion coefficient (

D^{t_{italicshort}} (ϕ_{i})

Section: Methodsmentioning

confidence: 99%

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

2014

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“…k is the interaction parameter, where k ¼ 1 for complete elastic binary collision of hard spheres [5]. But k for hard disks was found to be k ¼ 3 from our simulation results.…”

Section: Simulation Results and Discussionmentioning

confidence: 65%

Spatial dimensionality dependence of long-time diffusion on two- and three-dimensional systems near glass transition

Terada

Tokuyama

2010

Intermetallics

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“…Another, more simple, method to incorporate the manybody HI is employed in Refs. [13,[47][48][49]. In these studies, the Brownian dynamics simulation is carried out with a theoretical prediction for the short-time diffusion coefficient given in Refs.…”

Section: A Hydrodynamic Interactionmentioning

confidence: 99%

Reduction of self-diffusion coefficient in a coarse-grained model of cytoplasm

Miyaguchi

2020

Phys. Rev. Research

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Theoretical predictions for polydisperse hard-sphere suspensions with and without hydrodynamic interaction are applied to a coarse-grained model of bacterial cytoplasm, which consists of 15 species of spherical particles. Short-time and long-time self-diffusion coefficients of each species are obtained to the first order in concentration. It is shown that the hydrodynamic interaction leads to a large reduction of diffusivity for small particles such as green fluorescent proteins. Moreover, a heuristic modification of the above theory to make it valid at higher concentrations is presented.

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Self-diffusion of biomolecules in solution

Cited by 25 publications

References 37 publications

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

Spatial dimensionality dependence of long-time diffusion on two- and three-dimensional systems near glass transition

Reduction of self-diffusion coefficient in a coarse-grained model of cytoplasm

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