NDLI: A Coupled 3-D PNP/ECP Model for Ion Transport in Biological Ion Channels

Content Provider	Springer Nature Link
Author	Yang, Zhicheng Van, Trudy A. Straaten, Der Ravaioli, Umberto Liu, Yang
Copyright Year	2005
Abstract	The Poisson-Nernst-Planck (PNP) or Drift-Diffusion theory can be used to compute macroscopic current in ion channels in an efficient manner. The major drawback of the standard PNP theory is that it is based on a continuum model for the charge flow, therefore it models ions as a gas of point particles. Water is also not simulated explicitly, but introduced as a background medium with a given permittivity. The PNP model can be modified to include effects of finite ion size and water occupation by including a correction term, the Excess Chemical Potential (ECP), in the standard model. Gillespie et al. [1] developed a model for ECP correction, based on Density Functional theory, which is introduced in an existing 3-D PNP solver for ion transport in biological ion channels realized using the numerical computational platform PROPHET. Since incorporation of the ECP correction directly into the PNP matrix formulation is not an easy task, for demonstration purposes we developed a relatively simple decoupled relaxed iteration algorithm. Preliminary tests were conducted on idealized channel geometries, showing how the adopted ECP correction model alters significantly the ion densities inside the channel from those predicted by the conventional PNP theory alone.
Starting Page	167
Ending Page	170
Page Count	4
File Format	PDF
ISSN	15698025
Journal	Journal of Computational Electronics
Volume Number	4
Issue Number	1-2
e-ISSN	15728137
Language	English
Publisher	Kluwer Academic Publishers
Publisher Date	2005-01-01
Publisher Place	Boston
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	ion channel Poisson-Nernst-Planck (PNP) Excess Chemical Potential (ECP) Density Functional Theory (DFT) Mathematical and Computational Physics ApplicationMathematics/Computational Methods of Engineering Mechanical Engineering Optical and Electronic Materials Electronic and Computer Engineering
Content Type	Text
Resource Type	Article
Subject	Atomic and Molecular Physics, and Optics Electronic, Optical and Magnetic Materials Electrical and Electronic Engineering Modeling and Simulation

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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