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The electromagnetic nature of protein–protein interactions
Published in Ze Zhang, Mahmoud Rouabhia, Simon E. Moulton, Conductive Polymers, 2018
Anna Katharina Hildebrandt, Thomas Kemmer, Andreas Hildebrandt
To simulate the kinetics of protein association, we essentially need to simulate the Brownian trajectories of the interaction partners toward the encounter complex, where the motion is biased by the electrostatic interaction. A fully atomistic simulation would again lead to an MD approach with its associated computational cost. To simplify matters, it is a common practice to ignore intramolecular degrees of freedom (i.e., molecular flexibility) and to use macroscopic continuum electrostatics instead of an explicit solvent representation. The resulting techniques are known as Brownian dynamics (BD) simulations. Since BD would essentially require a recomputation of the electrostatic potentials in each step—at least when the proteins are close, as influence of the low-dielectric cavities of the binding partners on their potentials can then not be ignored—practical applications typically rely on cost-effective approximations, such as the Coulombic treatment of one of the molecules.
Trapping characteristics of magnetic rod-like particles flowing in a cylindrical pipe by means of a non-uniform magnetic field (Brownian dynamics simulations)
Published in Molecular Physics, 2020
Takeru Yamanouchi, Akira Satoh
In the Brownian dynamics method, the solvent molecules composing the base liquid are not separately treated but rather the base liquid is regarded as a continuum medium in which the dispersed colloidal particles are assumed to perform a random motion [58]. The influence of the solvent will appear through the stochastic random forces and torques acting on the dispersed particles. In the case of an axisymmetric particle such as the spherocylinder treated in the present study, we can treat the translation and the rotational motion separately. Moreover, the translational motion can be decomposed into the motion parallel and normal to the particle axis direction. Similarly, the rotational motion can be decomposed into the rotation about the particle axis and about the direction through the particle centre normal to the particle axis. However, since the present rod-like particle is magnetised along the particle axis, it is sufficient to treat only the latter rotational motion. In the following, the quantities related to the direction parallel and normal to the particle axis are described using subscripts | | and ⊥, respectively.
Brownian dynamics simulations of a cubic haematite particle suspension with a more effective treatment of steric layer interactions
Published in Molecular Physics, 2020
We now address a simulation method suitable for analysing the above-mentioned magnetorheological effects and the characteristics of the heat generation in an alternating magnetic field at the microscopic scale. For this objective, Brownian dynamics is considered to be a useful simulation tool for a suspension of axisymmetric particles such as spherical, rod-like and disk-like particles [22] that perform Brownian motion in a base liquid. However, Brownian dynamics method is not directly applicable to a suspension composed of non-axisymmetric particles such as cube-like particles because the relationship between the components of the friction or diffusion tensor in the case of cubic particles has not fully been clarified at the present. Therefore in order to develop a Brownian dynamic simulation for a cube-like particle suspension, there have been several simulation-based studies with respect to the friction coefficients of cubic particles [23,24]. In related studies, Bet et al. calculated the translational and rotational friction coefficients for the platonic solids such as tetrahedron, cube and octahedron by means of numerical bead-shell model calculations from the viewpoint of an application to micro-swimmers [23]. In our previous study [24] we focused only on cubic particles and clarified that there is no coupling between the translational motion and the rotational motion as in the case of spherical particles in the situation of the Reynolds number being sufficiently smaller than unity. Moreover, it was shown that the lack of coupling between the friction or diffusion coefficients for a cubic particle suspension enabled the development of a relatively straightforward Brownian dynamics simulation [24].