Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods

To mimic the unique properties of capsid (protein shell of a virus), we performed Brownian dynamics simulations of the self-assembly of amphiphilic truncated cone particles with anisotropic interactions.

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Analysis of a Stokes Flow Past a Cube (Friction and Diffusion Coefficients for Brownian Dynamics Simulations)

Volume 7: Fluids Engineering ◽

10.1115/imece2019-10549 ◽

2019 ◽

Author(s):

Kazuya Okada ◽

Akira Satoh

Keyword(s):

Reynolds Number ◽

Flow Field ◽

Stokes Flow ◽

Diffusion Coefficients ◽

Brownian Dynamics ◽

Particle Suspension ◽

Rotational Flow ◽

Friction Coefficients ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations

Abstract Magnetorheological properties significantly depend on the regime of aggregate structures. In the case of cubic particles, closely-packed clusters that are significantly different from those for the case of spherical or rod-like particles are formed in the system since magnetic cube-like particles prefer a face-to-face contact with the neighboring particles. Therefore, a cubic particle suspension is expected to exhibit a sufficiently strong magnetorheological effect, which may be investigated by means of Brownian dynamics simulations. However, the translational and rotational diffusion (or friction) coefficients of a cube are not known and indispensable in order to develop this simulation technique. From this background, in the present study, we have analyzed the flow field around a cube in a Stokes flow regime in order to estimate the diffusion (or friction) coefficients of cube-like particles that are required for performing Brownian dynamics simulations of a cubic particle suspension. In the situation of a uniform flow field with a Reynolds number sufficiently smaller than unity, the force acts on the cube only in the flow field direction, and the torque acting on the cube may be regarded as negligible. In the situation of a rotational flow field with a sufficiently low Reynolds number, the torque acts on the cube only in the direction of angular velocity of the rotational flow field, and the force negligibly act on the cube. These characteristics are in significantly similar to those for the case of spheres in a Stokes flow situation. From these results, we may conclude that the diffusion coefficients of cube-like particles can be expressed by introducing a correction factor to those of the spherical particles.

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Brownian Dynamics Simulations of Rotational Diffusion Using the Cartesian Components of the Rotation Vector as Generalized Coordinates

Macromolecular Theory and Simulations ◽

10.1002/mats.200800031 ◽

2008 ◽

Vol 17 (7-8) ◽

pp. 403-409 ◽

Cited By ~ 7

Author(s):

Tom Richard Evensen ◽

Stine Nalum Naess ◽

Arnljot Elgsaeter

Keyword(s):

Brownian Dynamics ◽

Rotational Diffusion ◽

Rotation Vector ◽

Generalized Coordinates ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations

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Noncentral forces mediated between two inclusions in a bath of active Brownian rods

Scientific Reports ◽

10.1038/s41598-021-02295-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mahmoud Sebtosheikh ◽

Ali Naji

Keyword(s):

Brownian Dynamics ◽

Effective Interaction ◽

Longitudinal Axis ◽

The Self ◽

Reference Case ◽

Effective Interactions ◽

Spatial Dimensions ◽

Force Components ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations

AbstractUsing Brownian Dynamics simulations, we study effective interactions mediated between two identical and impermeable disks (inclusions) immersed in a bath of identical, active (self-propelled), Brownian rods in two spatial dimensions, by assuming that the self-propulsion axis of the rods may generally deviate from their longitudinal axis. When the self-propulsion is transverse (perpendicular to the rod axis), the accumulation of active rods around the inclusions is significantly enhanced, causing a more expansive steric layering (ring formation) of the rods around the inclusions, as compared with the reference case of longitudinally self-propelling rods. As a result, the transversally self-propelling rods also mediate a significantly longer ranged effective interaction between the inclusions. The bath-mediated interaction arises due to the overlaps between the active-rod rings formed around the inclusions, as they are brought into small separations. When the self-propulsion axis is tilted relative to the rod axis, we find an asymmetric imbalance of active-rod accumulation around the inclusion dimer. This leads to a noncentral interaction, featuring an anti-parallel pair of transverse force components and, hence, a bath-mediated torque on the dimer.

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Diffusion coefficients of elastic macromolecules

Journal of Fluid Mechanics ◽

10.1017/jfm.2019.652 ◽

2019 ◽

Vol 878 ◽

Cited By ~ 2

Author(s):

Bogdan Cichocki ◽

Marcin Rubin ◽

Anna Niedzwiecka ◽

Piotr Szymczak

Keyword(s):

Diffusion Coefficient ◽

Diffusion Coefficients ◽

Reference Point ◽

Brownian Dynamics ◽

The Other ◽

Long Time ◽

Computationally Expensive ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations ◽

Short Time

In elastic macromolecules, the value of the short-time diffusion coefficient depends on the choice of the point the displacement of which is tracked. On the other hand, the experimentally more relevant long-time diffusion coefficient is independent of the reference point, but its estimation usually requires computationally expensive Brownian dynamics simulations. Here we show how to obtain a precise estimate of the long-time diffusion coefficient of elastic macromolecules in a fast and robust manner, without invoking Brownian dynamics.

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Dynamics of Complexation of a Charged Dendrimer by Linear Polyelectrolyte: Computer Modelling

e-Polymers ◽

10.1515/epoly.2007.7.1.1110 ◽

2007 ◽

Vol 7 (1) ◽

Author(s):

Sergey Lyulin ◽

Anatolij Darinskii ◽

Alexey Lyulin

Keyword(s):

Brownian Dynamics ◽

Computer Modelling ◽

Rotational Diffusion ◽

Linear Chain ◽

Relaxation Times ◽

Linear Polymer ◽

Dynamics Simulations ◽

The Individual ◽

Brownian Dynamics Simulations ◽

Oppositely Charged

AbstractBrownian-dynamics simulations have been performed for complexes formed by a charged dendrimer and a long oppositely charged linear polyelectrolyte when overcharging phenomenon is always observed. After complex formation the orientational mobility of the individual dendrimer bonds, the fluctuations of the dendrimer size, and the dendrimer rotational diffusion have been simulated. Corresponding relaxation times do not depend on the linear-chain length in a complex and are close to those for a single neutral dendrimer. At the same time fluctuations of the size of a complex are completely defined by the corresponding fluctuations of a linear polyelectrolyte size. Adsorbed polyelectrolyte practically does not feel the rotation of a dendrimer; simulated complexes may be considered as nuts with light core (dendrimer) and heavy shell (adsorbed linear polymer); the electrostatic contacts between dendrimer and oppositely charged linear polymer are easily broken due to the very fast dendrimer-size fluctuations.

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