Monte Carlo Simulation Study of a System with a Dielectric Boundary: Application to Calcium Channel Selectivity

Boda, Dezső; Varga, Tibor; Henderson, Douglas; Busath, David D.; Nonner, Wolfgang; Gillespie, Dirk; Eisenberg, Robert S.

doi:10.1080/0892702031000152226

Cited by 45 publications

(60 citation statements)

References 9 publications

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“…[16][17][18][19][20][21] However, phenomena such as the DNA condensation are induced by the addition of multivalent electrolytes to a solution at physiological conditions (0.1 M of NaCl). 22 Therefore, a study of EDLs in solutions comprised of counterions with dissimilar valences and realistic sizes appears as an important issue toward the better understanding of this type of phenomena.…”

Section: Introductionmentioning

confidence: 99%

Electric Double Layers with Electrolyte Mixtures: Integral Equations Theories and Simulations

2005

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A study of a planar electric double layer (EDL) in the presence of mixtures of electrolyte is presented. In particular, results from the Hyper-Netted-Chain/Mean-Spherical-Approximation (HNC/MSA) theory are compared with Monte Carlo (MC) simulations. In this way, the charge inversion induced by mixtures of multivalent and monovalent counterions is probed. Since overcharging phenomena in nature emerge under such conditions, the role of ion-ion correlations in the EDL appears as a crucial point in this kind of study. Unlike previous related works, a realistic hydrated ion size is used in the HNC/MSA calculations and simulations. In this way, a qualitative agreement between the results obtained from the theory and MC simulations is found. However, some discrepancies arise when the charge inversion is expected to be more noticeable, namely at high surface charges and/or elevated concentrations of multivalent electrolytes. Such differences are explained in terms of an overestimation of the charge inversion by the integral equation (IE) formalism.

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Section: Introductionmentioning

confidence: 99%

Electric Double Layers with Electrolyte Mixtures: Integral Equations Theories and Simulations

2005

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“…The im- age charge solution, therefore, could be a suitable approximation for this energy term. As a matter of fact, we used this approximation in our earlier study 29 though, at that time, we were not aware of all the subtleties discussed in this work.…”

Section: Results For An Ion Crossing a Flat Dielectric Boundarymentioning

confidence: 99%

“…This also justifies our simplified treatment in our earlier work. 29 In a general case, however, a simple solution from image charges is not available. In such cases, a numerical method and the algorithm that interpolates for the overlap-region is necessary.…”

Section: Results For An Ion Crossing a Flat Dielectric Boundarymentioning

confidence: 99%

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A method for treating the passage of a charged hard sphere ion as it passes through a sharp dielectric boundary

Boda

Henderson

Eisenberg

et al. 2011

The Journal of Chemical Physics

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In the implicit solvent models of electrolytes (such as the primitive model (PM)), the ions are modeled as point charges in the centers of spheres (hard spheres in the case of the PM). The surfaces of the spheres are not polarizable which makes these models appropriate to use in computer simulations of electrolyte systems where these ions do not leave their host dielectrics. The same assumption makes them inappropriate in simulations where these ions cross dielectric boundaries because the interaction energy of the point charge with the polarization charge induced on the dielectric boundary diverges. In this paper, we propose a procedure to treat the passage of such ions through dielectric interfaces with an interpolation method. Inspired by the "bubble ion" model (in which the ion's surface is polarizable), we define a space-dependent effective dielectric coefficient, eff (r), for the ion that overlaps with the dielectric boundary. Then, we replace the "bubble ion" with a point charge that has an effective charge q/ eff (r) and remove the portion of the dielectric boundary where the ion overlaps with it. We implement the interpolation procedure using the induced charge computation method [D. Boda, D. Gillespie, W. Nonner, D. Henderson, and B. Eisenberg, Phys. Rev. E 69, 046702 (2004)]. We analyze the various energy terms using a spherical ion passing through an infinite flat dielectric boundary as an example.

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“…Using a force-field scheme based on a Poisson particle-particle-particle-mesh algorithm, they made, "an initial step toward the development of an efficient and robust simulation tool for the particle-basedmodeling of complex inhomogeneous biological systems, such as lipid membranes and ion channels." [5] Monte Carlo simulations were used to examine ion channel selectivity [6], induced charges in an inhomogeneous dielectric [7], and the equilibrium structure of electrolytes [8]. A three dimensional ion channel simulator was developed, "as an alternative to the computationally intensive Molecular Dynamics approach for simulating ion transport through channels...a promising tool for studying conduction through ionic channels on a timescale relevant to experimental observations."…”

Section: -Expansion Of Theoretical Knowledge Of Ion Channelsmentioning

confidence: 99%

Ionic Channels as Natural Nanodevices

Eisenberg¹

2006

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Monte Carlo Simulation Study of a System with a Dielectric Boundary: Application to Calcium Channel Selectivity

Cited by 45 publications

References 9 publications

Electric Double Layers with Electrolyte Mixtures: Integral Equations Theories and Simulations

Electric Double Layers with Electrolyte Mixtures: Integral Equations Theories and Simulations

A method for treating the passage of a charged hard sphere ion as it passes through a sharp dielectric boundary

Ionic Channels as Natural Nanodevices

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