Brownian dynamics simulation of charge transport in ion channels

Marreiro, David; Saraniti, Marco; Aboud, Shela

doi:10.1088/0953-8984/19/21/215203

Cited by 10 publications

(15 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In order to validate the analytical model, we performed a full 3-D simulation of the nanopore using the Brownian dynamics [1,9] simulation software described in detail in [1]. The water environment here is modeled as a continuum dielectric, while each ion is an explicit Brownian particle with its dynamics tracked through the six-dimensional phase space.…”

Section: -D Particle-based Simulationmentioning

confidence: 99%

See 1 more Smart Citation

Silicon nanopores as bioelectronic devices: a simulation study

Smolyanitsky

Saraniti

2009

J Comput Electron

Self Cite

View full text Add to dashboard Cite

Solid-state aqueous pores of nanoscale dimensions are now a reality, thanks to the advancing fabrication techniques. The interest in such devices has been high in the last decade, due to their potential as molecular sensing elements (Kirby and Hasselbrink in Electrophoresis 25(2): [187][188][189][190][191][192][193][194][195][196][197][198][199][200][201][202] 2004) and in fast DNA sequencing (Smeets et al. in Nano Lett. 6(1), 2006). This work focuses on the theoretical characterization and numerical modeling of the role of oxidated surface electric charge in the ionic conduction process through man-made silicon nanopores. We have extended the model presented in (Behrens and Grier in J. Chem. Phys. 115(14), 2001) by including potassium adsorption on the oxidated silicon (silica) surface, as well as taking the cylindrical curvature of the surface into account. Being able to calculate the surface charge density, we have used a particle-based Brownian dynamics simulation tool to characterize the ionic population in nanopores and simulate conduction through nanopores at various bulk electrolyte concentrations.

show abstract

Section: -D Particle-based Simulationmentioning

confidence: 99%

“…Hence, the number of silanol groups occupied by protons is at least 10 7 times larger than the number of those occupied by the potassium ions, if the concentrations of protons and potassium ions are the same, and assuming that the concentrations in the vicinity of the wall satisfy (8) and (9).…”

Section: Surface Charge and Surface Zeta Potentialmentioning

confidence: 99%

Silicon nanopores as bioelectronic devices: a simulation study

Smolyanitsky

Saraniti

2009

J Comput Electron

Self Cite

View full text Add to dashboard Cite

show abstract

“…Modeling full I‐V characteristics is computationally expensive; this can be a bottleneck for large sets of model structure candidates. There are computational methods potentially applicable for this task, such as molecular dynamics (MD), which treats the pore and ions in a fully discrete way, and Brownian dynamics (BD), which treats the pore and the solute in a continuous manner and the ions discretely. However, both methods are slow.…”

Section: Introductionmentioning

confidence: 99%

Optimization of 3D Poisson-Nernst-Planck model for fast evaluation of diverse protein channels

2013

View full text Add to dashboard Cite

International audienceWe show the accuracy and applicability of our fast algorithmic implementation of a three-dimensional Poisson-Nernst-Planck (3D-PNP) flow model for characterizing different protein channels. Due to its high computational efficiency, our model can predict the full current-voltage characteristics of a channel within minutes, based on the experimental 3D structure of the channel or its computational model structure. Compared with other methods, such as Brownian dynamics, which currently needs a few weeks of the computational time, or even much more demanding molecular dynamics modeling, 3D-PNP is the only available method for a function-based evaluation of very numerous tentative structural channel models. Flow model tests of our algorithm and its optimal parametrization are provided for five native channels whose experimental structures are available in the protein data bank (PDB) in an open conductive state, and whose experimental current-voltage characteristics have been published. The channels represent very different geometric and structural properties, which makes it the widest test to date of the accuracy of 3D-PNP on real channels. We test whether the channel conductance, rectification, and charge selectivity obtained from the flow model, could be sufficiently sensitive to single-point mutations, related to unsignificant changes in the channel structure. Our results show that the classical 3D-PNP model, under proper parametrization, is able to achieve a qualitative agreement with experimental data for a majority of the tested characteristics and channels, including channels with narrow and irregular conductivity pores. We propose that although the standard PNP model cannot provide insight into complex physical phenomena due to its intrinsic limitations, its semiquantitative agreement is achievable for rectification and selectivity at a level sufficient for the bioinformatical purpose of selecting the best structural models with a great advantage of a very short computational time

show abstract

“…63,486 However, the X-ray structure of an ion channel can be used to create a more realistic model of the channel by computing electrostatic and core repulsion potential maps from the all-atom structure. Brownian dynamics simulations have been applied to several biological channels including OmpF, 55,62–64 K + channels, 110–115,117 α -hemolysin, 88,95 VDAC, 268 and gramicidin. 16,17 Roux and coworkers have developed a grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) method 62,63,103 to allow for fluctuations in the total number of ions in the system and asymmetric ion concentration conditions.…”

Section: Most Common Simulation Methodsmentioning

confidence: 99%