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Computational Study of Ion Conductance in the KcsA K⁺ Channel Using a Nernst-Planck Model with Explicit Resident Ions

Title: A Computational Study of Ion Conductance in the KcsA K⁺ Channel Using a Nernst-Planck Model with Explicit Resident Ions.
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Name(s): Jung, Yong Woon, 1961-, author
Mascagni, Michael A., professor directing dissertation
Huffer, Fred, university representative
Bowers, Philip, committee member
Klassen, Eric, committee member
Cogan, Nick, committee member
Department of Mathematics, degree granting department
Florida State University, degree granting institution
Type of Resource: text
Genre: Text
Issuance: monographic
Date Issued: 2010
Publisher: Florida State University
Place of Publication: Tallahassee, Florida
Physical Form: computer
online resource
Extent: 1 online resource
Language(s): English
Abstract/Description: In this dissertation, we describe the biophysical mechanisms underlying the relationship between the structure and function of the KcsA K+ channel. Because of the conciseness of electro-diffusion theory and the computational advantages of a continuum approach, Nernst-Planck (NP) type models such as the Goldman-Hodgkin-Katz (GHK) and Poisson-Nernst-Planck (PNP) models have been used to describe currents in ion channels. However, the standard PNP (SPNP) model is known to be inapplicable to narrow ion channels because it cannot handle discrete ion properties. To overcome this weakness, we formulated the explicit resident ions Nernst-Planck (ERINP) model, which applies a local explicit model where the continuum model fails. Then we tested the effects of the ERI Coulomb potential, the ERI induced potential, and the ERI dielectric constant for ion conductance were tested in the ERINP model. Using the current-voltage (I-V ) and current-concentration (I-C) relationships determined from the ERINP model, we discovered biologically significant information that is unobtainable from the traditional continuum model. The mathematical analysis of the K+ ion dynamics revealed a tight structure-function system with a shallow well, a deep well, and two K+ ions resident in the selectivity filter. We also demonstrated that the ERINP model not only reproduced the experimental results with a realistic set of parameters, it also reduced CPU costs.
Identifier: FSU_migr_etd-3741 (IID)
Submitted Note: A Dissertation submitted to the Department of Mathematics in partial fulfillment of the requirements for the degree of Doctor of Philosophy.
Degree Awarded: Spring Semester, 2010.
Date of Defense: March 29, 2010.
Keywords: Explicit Resident Ions Nernst-Planck Model, ERI Coulomb and Induced Potential, Strategic Structure-Function System, ERI Dielectric Constant
Bibliography Note: Includes bibliographical references.
Advisory Committee: Michael A. Mascagni, Professor Directing Dissertation; Fred Huffer, University Representative; Philip Bowers, Committee Member; Eric Klassen, Committee Member; Nick Cogan, Committee Member.
Subject(s): Mathematics
Persistent Link to This Record: http://purl.flvc.org/fsu/fd/FSU_migr_etd-3741
Owner Institution: FSU

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Jung, Y. W. (2010). A Computational Study of Ion Conductance in the KcsA K⁺ Channel Using a Nernst-Planck Model with Explicit Resident Ions. Retrieved from http://purl.flvc.org/fsu/fd/FSU_migr_etd-3741