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Molecular Simulation Volume 31, 2005 - Issue 2-3
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Original Articles

Hybrid MD-Nernst Planck model of α-hemolysin conductance properties

Ioana Cozmuta NASA Ames Research Center, Eloret Corporation, USA, 94035, Moffett Field, CA
,
James T. O'Keeffe ‡NASA AMES Research Center, Mail Stop, USA, 94035, Moffett Field, CA
,
Deepak Bose NASA Ames Research Center, Eloret Corporation, USA, 94035, Moffett Field, CA
&
Viktor Stolc ‡NASA AMES Research Center, Mail Stop, USA, 94035, Moffett Field, CACorrespondence[email protected]
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Pages 79-93 | Received 01 Mar 2004, Accepted 01 Jun 2004, Published online: 06 Aug 2006

Citations (19)

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J. Marañón Di Leo & J. Marañón. (2009) Cation transport in nanopores. Molecular Simulation 35:4, pages 280-286.
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Articles from other publishers (18)

Kiran Prakash, Dheeraj K V S, Sridhar Kumar Kannam & Sarith P Sathian. (2020) Non-isothermal flow of an electrolyte in a charged nanochannel. Nanotechnology 31:42, pages 425403.
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Nathalie Basdevant, Delphine Dessaux & Rosa Ramirez. (2019) Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study. Scientific Reports 9:1.
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Monasadat Talarimoghari, Gerhard Baaken, Ralf Hanselmann & Jan C. Behrends. (2018) Size-dependent interaction of a 3-arm star poly(ethylene glycol) with two biological nanopores. The European Physical Journal E 41:6.
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Monika Kurczyńska, Bogumił M. Konopka & Małgorzata Kotulska. 2017. Transport Across Natural and Modified Biological Membranes and its Implications in Physiology and Therapy. Transport Across Natural and Modified Biological Membranes and its Implications in Physiology and Therapy 17 37 .
Jirasak Wong-ekkabut & Mikko Karttunen. (2015) Molecular dynamics simulation of water permeation through the alpha-hemolysin channel. Journal of Biological Physics 42:1, pages 133-146.
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Witold Dyrka, Maciej M. Bartuzel & Malgorzata Kotulska. (2013) Optimization of 3D Poisson-Nernst-Planck model for fast evaluation of diverse protein channels. Proteins: Structure, Function, and Bioinformatics 81:10, pages 1802-1822.
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Elisa Campos, Alina Asandei, Colin E. McVey, João C. Dias, A. Sofia F. Oliveira, Cláudio M. Soares, Tudor Luchian & Yann Astier. (2012) The Role of Lys147 in the Interaction between MPSA-Gold Nanoparticles and the α-Hemolysin Nanopore. Langmuir 28:44, pages 15643-15650.
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Jirasak Wong-ekkabut & Mikko Karttunen. (2012) Assessment of Common Simulation Protocols for Simulations of Nanopores, Membrane Proteins, and Channels. Journal of Chemical Theory and Computation 8:8, pages 2905-2911.
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Chen Song & Ben Corry. (2011) Testing the Applicability of Nernst-Planck Theory in Ion Channels: Comparisons with Brownian Dynamics Simulations. PLoS ONE 6:6, pages e21204.
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M. Aguilella-Arzo & V. M. Aguilella. (2010) Continuum electrostatic calculations of the pKa of ionizable residues in an ion channel: Dynamic vs. static input structure. The European Physical Journal E 31:4, pages 429-439.
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Bernhard Egwolf, Yun Luo, D. Eric Walters & Benoît Roux. (2010) Ion Selectivity of α-Hemolysin with β-Cyclodextrin Adapter. II. Multi-Ion Effects Studied with Grand Canonical Monte Carlo/Brownian Dynamics Simulations. The Journal of Physical Chemistry B 114:8, pages 2901-2909.
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J M Xue, X Q Zou, Y B Xie & Y G Wang. (2009) Molecular dynamics simulations on the ionic current through charged nanopores. Journal of Physics D: Applied Physics 42:10, pages 105308.
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Simone Furini, Carmen Domene, Michele Rossi, Marco Tartagni & Silvio Cavalcanti. (2008) Model-Based Prediction of the α-Hemolysin Structure in the Hexameric State. Biophysical Journal 95:5, pages 2265-2274.
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Witold Dyrka, Andy T. Augousti & Malgorzata Kotulska. (2008) Ion flux through membrane channels—An enhanced algorithm for the Poisson‐Nernst‐Planck model. Journal of Computational Chemistry 29:12, pages 1876-1888.
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G. Oukhaled, L. Bacri, J. Mathé, J. Pelta & L. Auvray. (2008) Effect of screening on the transport of polyelectrolytes through nanopores. EPL (Europhysics Letters) 82:4, pages 48003.
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James O’Keeffe, Ioana Cozmuta, Deepak Bose & Viktor Stolc. (2007) A predictive MD-Nernst–Planck model for transport in alpha-hemolysin: Modeling anisotropic ion currents. Chemical Physics 342:1-3, pages 25-32.
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Emad Tajkhorshid, Jordi Cohen, Aleksij Aksimentiev, Marcos Sotomayor & Klaus Schulten. 2005. Bacterial Ion Channels and Their Eukaryotic Homologs. Bacterial Ion Channels and Their Eukaryotic Homologs 153 190 .
Aleksij Aksimentiev & Klaus Schulten. (2005) Imaging α-Hemolysin with Molecular Dynamics: Ionic Conductance, Osmotic Permeability, and the Electrostatic Potential Map. Biophysical Journal 88:6, pages 3745-3761.
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