A computer simulation of charged particles in solution. I. Technique and equilibrium properties

Ermak, D.L.

doi:10.1063/1.430300

Cited by 405 publications

(226 citation statements)

References 19 publications

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“…Equation ͑7͒ corresponds to the well-known restricted primitive model with soft core which has been frequently used in statistical mechanical studies of ionic solutions. [11][12][13]27 The contribution from the static field is…”

Section: ͑2͒mentioning

confidence: 99%

“…[1][2][3][4][5][6][7][8][9][10] The approach consists in generating the chaotic trajectory of the ions as a function of time by numerically integrating stochastic equation of motions using some effective potential function to calculate the microscopic forces operating between them. [11][12][13] In such BD simulations, the potential function itself is a central element because it provides the underlying thermodynamic structure of the theory, i.e., it completely determines all the equilibrium properties of the system. From a microscopic point of view, this effective potential is a manybody potential of mean force ͑PMF͒ which corresponds rigorously to the reversible thermodynamic work function ͑free energy͒ to assemble a particular configuration of the ions in the system while averaging over the remaining degrees of freedom ͑e.g., solvent molecules, protein channel, bilayer membrane, and remote counterions͒.…”

Section: Introductionmentioning

confidence: 99%

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Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

Im¹,

Roux²

2001

The Journal of Chemical Physics

105

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A general method has been developed to include the electrostatic reaction field in Brownian dynamics ͑BD͒ simulations of ions diffusing through complex molecular channels of arbitrary geometry. Assuming that the solvent is represented as a featureless continuum dielectric medium, a multipolar basis-set expansion is developed to express the reaction field Green's function. A reaction field matrix, which provides the coupling between generalized multipoles, is calculated only once and stored before the BD simulations. The electrostatic energy and forces are calculated at each time step by updating the generalized multipole moments. The method is closely related to the generalized solvent boundary potential ͓Im et al., J. Chem. Phys. 114, 2924 ͑2001͔͒ which was recently developed to include the influence of distant atoms on a small region part of a large macromolecular system in molecular dynamics simulations. It is shown that the basis-set expansion is accurate and computationally inexpensive for three simple models such as a spherical ionic system, an impermeable membrane system, and a cylindrical pore system as well as a realistic system such as OmpF porin with all atomic details. The influence of the static field and the reaction field on the ion distribution and conductance in the OmpF channel is studied and discussed.

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Section: ͑2͒mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

Im¹,

Roux²

2001

The Journal of Chemical Physics

105

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“…This choice of potential is motivated by previous investigations of the equilibrium structure, where we found a very good agreement with experiments [25,26]. Our investigations are based on standard BD simulations in three dimensions, where the position of particle i is advanced according to [38] …”

Section: Model and Simulation Detailsmentioning

confidence: 97%

Shear-induced laning transition in a confined colloidal film

2017

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Using Brownian dynamics (BD) simulations we investigate a dense system of charged colloids exposed to shear flow in a confined (slit-pore) geometry. The equilibrium system at zero flow consists of three, well-pronounced layers with square-like crystalline in-plane structure. We demonstrate that, for sufficiently large shear rates, the middle layer separates into two sublayers where the particles organize into moving lanes with opposite velocities. The formation of this micro-laned state results in a destruction of the applied shear profile. It has a strong impact not only on the structure of the system, but also on its rheology as measured by the stress tensor. At higher shear rates we observe a disordered state and finally a recrystallization reminiscent of the behavior of bilayer films. We expect the shear-induced laning to be a generic feature of thin films with three or more layers.

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“…Eqs. 14 and 15 are numerically solved using the standard Euler-forward scheme for stochastic differential equations [59] (20) and (going into the body frame)…”

Section: B Brownian Dynamics Simulationmentioning

confidence: 99%

Colloidal suspensions of C-particles: Entanglement, percolation and microrheology

Hoell

Löwen

2016

The Journal of Chemical Physics

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We explore structural and dynamical behavior of concentrated colloidal suspensions made up by C-shape particles using Brownian dynamics computer simulations and theory. In particular, we focus on the entanglement process between nearby particles for almost closed C-shapes with a small opening angle. Depending on the opening angle and the particle concentration, there is a percolation transition for the cluster of entangled particles which shows the classical scaling characteristics. In a broad density range below the percolation threshold, we find a stretched exponential function for the dynamical decorrelation of the entanglement process. Finally, we study a set-up typical in microrheology by dragging a single tagged particle with constant speed through the suspension. We measure the cluster connected to and dragged with this tagged particle. In agreement with a phenomenological theory, the size of the dragged cluster depends on the dragging direction and increases markedly with the dragging speed.

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A computer simulation of charged particles in solution. I. Technique and equilibrium properties

Cited by 405 publications

References 19 publications

Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

Shear-induced laning transition in a confined colloidal film

Colloidal suspensions of C-particles: Entanglement, percolation and microrheology

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