Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Extended kinetic lattice grand canonical Monte Carlo simulation method for transport of multicomponent ion mixtures through a model nanopore system

Journal Article · · Bulletin of the Korean Chemical Society (Online)
DOI: https://doi.org/10.1002/bkcs.12466 · OSTI ID:1838083
 [1];  [2];  [1];  [3];  [1]
  1. Department of Chemistry and Institute for Molecular Science and Fusion Technology Kangwon National University Chuncheon Gangwon‐do Republic of Korea
  2. Department of Biochemistry Kangwon National University Chuncheon Gangwon‐do Republic of Korea
  3. Department of Chemistry Northwestern University Evanston Illinois USA
+ Show Author Affiliations

Abstract An extended version of the original kinetic lattice grand canonical Monte Carlo simulation method combined with mean field theory (KLGCMC/MF) ( J. Chem. Phys. 2007 , 127, 024706) is presented for the study of transport of multicomponent ion mixtures through a model nanopore. Comparison of the extended KLGCMC/MF (eKLGCMC/MF) simulation results with Poisson–Nernst–Planck (PNP) calculations is also made to confirm the validity of the extended simulation approach. Unlike the original version of KLGCMC/MF simulation method that treats only a binary ionic solution with one cation and one anion species, this extended version can deal with a system that includes ternary ion mixtures. A diffusion probability algorithm is also added to the extended version of the simulation method to describe the inhomogeneous diffusivity of ions that is often observed in the ion permeation through nanopores. Both Legendre and Chebyshev polynomials of the second kind were tested as a basis set for the basis set expansion (BSE) method with which to calculate the reaction field energy in the eKLGCMC/MF simulation. It turned out that the Legendre polynomials perform better than the Chebyshev polynomials, and as a result, the Legendre polynomials were implemented in the current version of eKLGCMC/MF simulation algorithm. The presented eKLGCMC/MF simulation method with new features finds its potential applications in nanopore systems where the correlation between ion species with the same sign of charges plays a key role such as oscillating ion currents or anomalous mole fraction effects.

Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1838083
Journal Information:
Bulletin of the Korean Chemical Society (Online), Journal Name: Bulletin of the Korean Chemical Society (Online) Journal Issue: 3 Vol. 43; ISSN 1229-5949
Publisher:
Wiley Blackwell (John Wiley & Sons)Copyright Statement
Country of Publication:
Korea, Republic of
Language:
English

References (42)

Energetic and Frictional Effects in the Transport of Ions in a Cyclic Peptide Nanotube: Energetic and Frictional Effects in the Transport of Ions journal December 2016
Saccharide Insertion in Carbon Nanotube: Molecular Dynamics Simulation Studies journal February 2020
Empirical force fields for biological macromolecules: Overview and issues journal January 2004
Calculation of ionic diffusion coefficients on the basis of migration test results journal April 2003
A Grand Canonical Monte Carlo–Brownian Dynamics Algorithm for Simulating Ion Channels journal August 2000
Tests of Continuum Theories as Models of Ion Channels. II. Poisson–Nernst–Planck Theory versus Brownian Dynamics journal May 2000
Gramicidin A Channel as a Test Ground for Molecular Dynamics Force Fields journal April 2003
Dielectric Self-Energy in Poisson-Boltzmann and Poisson-Nernst-Planck Models of Ion Channels journal June 2003
The Role of the Dielectric Barrier in Narrow Biological Channels: A Novel Composite Approach to Modeling Single-Channel Currents journal June 2003
Influence of the membrane potential on the free energy of an intrinsic protein journal December 1997
Statistical Mechanical Equilibrium Theory of Selective Ion Channels journal July 1999
A Lattice Relaxation Algorithm for Three-Dimensional Poisson-Nernst-Planck Theory with Application to Ion Transport through the Gramicidin A Channel journal February 1999
PACO: PArticle COunting Method To Enforce Concentrations in Dynamic Simulations journal February 2016
Energetic and Dynamic Analysis of Transport of Na + and K + through a Cyclic Peptide Nanotube in Water and in Lipid Bilayers journal November 2016
Synthetic Ion Channels: From Pores to Biological Applications journal June 2013
Theory and Simulation of Ion Conduction in the Pentameric GLIC Channel journal March 2012
Three-Dimensional Brownian Dynamics Simulator for the Study of Ion Permeation through Membrane Pores journal July 2014
Simulating Current–Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method journal March 2015
Simulation of water transport through a lipid membrane journal April 1994
Electrical double layers. 4. Limitations of the Gouy-Chapman theory journal August 1982
Dynamics of Simultaneous, Single Ion Transport through Two Single-Walled Carbon Nanotubes: Observation of a Three-State System journal January 2011
Steered Molecular Dynamics Studies of the Potential of Mean Force of a Na + or K + Ion in a Cyclic Peptide Nanotube journal December 2006
Incorporation of Inhomogeneous Ion Diffusion Coefficients into Kinetic Lattice Grand Canonical Monte Carlo Simulations and Application to Ion Current Calculations in a Simple Model Ion Channel journal October 2007
Multiple Scales in the Simulation of Ion Channels and Proteins journal October 2010
Precipitation-Induced Voltage-Dependent Ion Current Fluctuations in Conical Nanopores journal April 2010
Local Dielectric Environment of B-DNA in Solution:  Results from a 14 ns Molecular Dynamics Trajectory journal September 1998
Carbon nanotubes as nanoscale mass conveyors journal April 2004
Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry journal September 2001
Simulating prescribed particle densities in the grand canonical ensemble using iterative algorithms journal March 2008
An efficient iterative grand canonical Monte Carlo algorithm to determine individual ionic chemical potentials in electrolytes journal June 2010
Primitive model electrolytes. I. Grand canonical Monte Carlo computations journal June 1980
Electrical double layers. I. Monte Carlo study of a uniformly charged surface journal December 1980
Molecular dynamics and Monte Carlo simulations in the grand canonical ensemble: Local versus global control journal March 1993
Dielectric constant of water as a function of separation in a slab geometry: A molecular dynamics study journal May 2015
Surface diffusion on a stepped surface journal June 1993
Combined ab initio and kinetic Monte Carlo simulations of C diffusion on the 3 × 3 β − Si C ( 111 ) surface journal February 2005
Computing induced charges in inhomogeneous dielectric media: Application in a Monte Carlo simulation of complex ionic systems journal April 2004
Molecular Dynamics Simulation of Continuous Current Flow through a Model Biological Membrane Channel journal March 2001
Non-selective conductance in calcium channels of frog muscle: calcium selectivity in a single-file pore. journal August 1984
Coherence Resonance in a Single-Walled Carbon Nanotube Ion Channel journal September 2010
Theoretical Studies of the M2 Transmembrane Segment of the Glycine Receptor: Models of the Open Pore Structure and Current-Voltage Characteristics journal September 2005
Energetics of Divalent Selectivity in a Calcium Channel: The Ryanodine Receptor Case Study journal February 2008

Similar Records

Poisson-Boltzmann-Nernst-Planck model
Journal Article · 2011 · Journal of Chemical Physics · OSTI ID:21560243
Fifth-kind orthonormal Chebyshev polynomial solutions for fractional differential equations
Journal Article · 2018 · Computational and Applied Mathematics · OSTI ID:22769289
Fluctuating hydrodynamics of electrolytes at electroneutral scales
Journal Article · 2019 · Physical Review Fluids · OSTI ID:1526544
+2 more

Related Subjects