메뉴 건너뛰기




Volumn 2, Issue 1, 2005, Pages 56-67

Self-consistent particle simulation of ion channels

Author keywords

Brownian dynamics; Ion channel simulation; Ion conduction; Kcsa

Indexed keywords

APPROXIMATION THEORY; BROWNIAN MOVEMENT; CELL MEMBRANES; COMPUTER SIMULATION; FINITE DIFFERENCE METHOD; INTEGRATION; MOLECULAR STRUCTURE; POISSON EQUATION;

EID: 20444388630     PISSN: 15461955     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (5)

References (61)
  • 3
    • 0037066261 scopus 로고    scopus 로고
    • Electrical interfacing of nerve cells and semiconductor chips
    • P. Fromherz, Electrical interfacing of nerve cells and semiconductor chips. Chem. Phys. Chem. 3, 276 (2002).
    • (2002) Chem. Phys. Chem. , vol.3 , pp. 276
    • Fromherz, P.1
  • 4
    • 0038625442 scopus 로고    scopus 로고
    • Semiconductor chips with ion channels, nerve cells and brain
    • P. Fromherz, Semiconductor chips with ion channels, nerve cells and brain. Physica E 16, 24 (2003).
    • (2003) Physica E , vol.16 , pp. 24
    • Fromherz, P.1
  • 5
    • 0042912833 scopus 로고    scopus 로고
    • Simulation of intrinsic parameter fluctuation in decananometer and nanometer-scale mosfets
    • A. Asenov, A. R. Brown, J. H. Davies, S. Kaya, and G. Slavcheva, Simulation of intrinsic parameter fluctuation in decananometer and nanometer-scale mosfets. IEEE Trans. Elec. Dev. 50, 1837 (2003).
    • (2003) IEEE Trans. Elec. Dev. , vol.50 , pp. 1837
    • Asenov, A.1    Brown, A.R.2    Davies, J.H.3    Kaya, S.4    Slavcheva, G.5
  • 8
    • 0032478818 scopus 로고    scopus 로고
    • The structure of the potassium channel: Molecular basis of k+ conduction and selectivity
    • D. A. Doyle et al., The structure of the potassium channel: Molecular basis of k+ conduction and selectivity. Science 280, 69 (1998).
    • (1998) Science , vol.280 , pp. 69
    • Doyle, D.A.1
  • 9
    • 0032725268 scopus 로고    scopus 로고
    • Exploring the open pore of the potassium channel from streptomyces lividans
    • D. Meuser, H. Splitt, R. Wagner, and H. Schrempf, Exploring the open pore of the potassium channel from streptomyces lividans. FEBS Letters 462, 447 (1999).
    • (1999) FEBS Letters , vol.462 , pp. 447
    • Meuser, D.1    Splitt, H.2    Wagner, R.3    Schrempf, H.4
  • 10
    • 0000127690 scopus 로고    scopus 로고
    • Molecular and brownian dynamics study of ion selectivity and conductivity in the potassium channel
    • T. W. Allen, M. Hoyles, S. Kuyucak, and S. H. Chung, Molecular and brownian dynamics study of ion selectivity and conductivity in the potassium channel. Chem. Phys. Lett. 313, 358 (1999).
    • (1999) Chem. Phys. Lett. , vol.313 , pp. 358
    • Allen, T.W.1    Hoyles, M.2    Kuyucak, S.3    Chung, S.H.4
  • 14
    • 0031030225 scopus 로고    scopus 로고
    • Permeation through an open channel: Poisson-nernst-plank theory of a synthetic ionic channel
    • D. Chen, J. Lear, and B. Eisenberg, Permeation through an open channel: Poisson-nernst-plank theory of a synthetic ionic channel. Biophys. J. 72, 97 (1997).
    • (1997) Biophys. J. , vol.72 , pp. 97
    • Chen, D.1    Lear, J.2    Eisenberg, B.3
  • 15
    • 0000381967 scopus 로고    scopus 로고
    • Two- and three-dimensional poisson-nernst-plank simulations of current flow through gramicidin a
    • U. Hollerbach, D. P. Chen, and R. S. Eisenberg, Two- and three-dimensional poisson-nernst-plank simulations of current flow through gramicidin a. J. Scientific Computing 16, 373 (2001).
    • (2001) J. Scientific Computing , vol.16 , pp. 373
    • Hollerbach, U.1    Chen, D.P.2    Eisenberg, R.S.3
  • 16
    • 20444430212 scopus 로고    scopus 로고
    • Simulating ion permeation through the ompf porin ion channel using three-dimensional drift-diffusion theory
    • T. A. van der Straaten, J. M. Tang, U. Ravailoi, R. S. Eisenberg, and N. Aluru, Simulating ion permeation through the ompf porin ion channel using three-dimensional drift-diffusion theory. J. Comp. Elec. 2, 231 (2002).
    • (2002) J. Comp. Elec. , vol.2 , pp. 231
    • van der Straaten, T.A.1    Tang, J.M.2    Ravailoi, U.3    Eisenberg, R.S.4    Aluru, N.5
  • 17
    • 0035695476 scopus 로고    scopus 로고
    • Simulation of biological ionic channels by technology computer aided design
    • K. Hess, U. Ravaioli, N. R. Aluru, M. Gupta, and R. S. Eisenberg, Simulation of biological ionic channels by technology computer aided design. VLSI Design 13, 179 (2001).
    • (2001) VLSI Design , vol.13 , pp. 179
    • Hess, K.1    Ravaioli, U.2    Aluru, N.R.3    Gupta, M.4    Eisenberg, R.S.5
  • 18
    • 20444382896 scopus 로고    scopus 로고
    • A generic particle-mesh framework for the simulation of ionic channels
    • C. Millar, A. Asenov, and S. Roy, A generic particle-mesh framework for the simulation of ionic channels. J. Comp. Elec. 1, 405 (2002).
    • (2002) J. Comp. Elec. , vol.1 , pp. 405
    • Millar, C.1    Asenov, A.2    Roy, S.3
  • 19
    • 20444418804 scopus 로고    scopus 로고
    • Brownian ionic channel simulation
    • C. Millar, A. Asenov, and S. Roy, Brownian ionic channel simulation. J. Comp. Elec. 2, 257 (2003).
    • (2003) J. Comp. Elec. , vol.2 , pp. 257
    • Millar, C.1    Asenov, A.2    Roy, S.3
  • 20
    • 20444362853 scopus 로고    scopus 로고
    • Brownian dynamics based simulation of ionic solutions and channels
    • edited by M. Laudon and B. Romanowicz, MSM/Nanotech, Computational Publications, Cambridge
    • C. Millar, A. Asenov, and S. Roy, Brownian dynamics based simulation of ionic solutions and channels, in Nanotech 2003: Technical Proceedings, edited by M. Laudon and B. Romanowicz, MSM/Nanotech, Computational Publications, Cambridge (2003).
    • (2003) Nanotech 2003: Technical Proceedings
    • Millar, C.1    Asenov, A.2    Roy, S.3
  • 21
    • 0031870447 scopus 로고    scopus 로고
    • Study of ionic currents accross a model membrane channel using brownian dynamics
    • S. Chung, M. Hoyles, T. Allen, and S. Kuyucak, Study of ionic currents accross a model membrane channel using brownian dynamics. Biophys. J. 75, 793 (1998).
    • (1998) Biophys. J. , vol.75 , pp. 793
    • Chung, S.1    Hoyles, M.2    Allen, T.3    Kuyucak, S.4
  • 23
    • 0037143367 scopus 로고    scopus 로고
    • Monte-carlo study of the selectivity of calcium channels: Improved geometric model
    • D. Boda, D. Henderson, and D. D. Busath, Monte-carlo study of the selectivity of calcium channels: Improved geometric model. J. Mol. Phys. 14, 2361 (2002).
    • (2002) J. Mol. Phys. , vol.14 , pp. 2361
    • Boda, D.1    Henderson, D.2    Busath, D.D.3
  • 24
    • 0037007814 scopus 로고    scopus 로고
    • Molecular dynamics of a k channel model: Sensitivity to changes in ions, waters and membrane environment
    • C. E. Capener and M. S. P. Sansom, Molecular dynamics of a k channel model: Sensitivity to changes in ions, waters and membrane environment. J. Phys. Chem. B 106, (2002).
    • (2002) J. Phys. Chem. B , pp. 106
    • Capener, C.E.1    Sansom, M.S.P.2
  • 25
    • 0037007814 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a k channel model: Sensetivity to changes in ions, waters and membrane environment
    • C. E. Capener and M. S. P. Sansom, Molecular dynamics simulations of a k channel model: Sensetivity to changes in ions, waters and membrane environment. J. Phys. Chem. B 106, 4542 (2002).
    • (2002) J. Phys. Chem. B , vol.106 , pp. 4542
    • Capener, C.E.1    Sansom, M.S.P.2
  • 27
    • 20444409591 scopus 로고    scopus 로고
    • Ion channels as natural nanotubes: Electrostatics, permeation and selectivity
    • Berlin
    • M. Saraniti, Ion channels as natural nanotubes: Electrostatics, permeation and selectivity. In MCM 2003, Berlin (2003).
    • (2003) MCM 2003
    • Saraniti, M.1
  • 29
    • 20444428107 scopus 로고
    • A brief account of microscopical observations made in the months of june, july and august 1827 on the particles contained in the pollen of plants; and on the general existence of active molecules in organic and inorganic bodies
    • Taylor, Not Published
    • R. Brown. A brief account of microscopical observations made in the months of june, july and august 1827 on the particles contained in the pollen of plants; and on the general existence of active molecules in organic and inorganic bodies. In Private Publication. Taylor, 1828. Not Published.
    • (1828) Private Publication
    • Brown, R.1
  • 31
    • 20444369303 scopus 로고    scopus 로고
    • Methods for the Atomistic Simulation of Ultrasmall Semiconductor Devices
    • PhD thesis, Glasgow University
    • C. R. Arokianthan, Methods for the Atomistic Simulation of Ultrasmall Semiconductor Devices, PhD thesis, Glasgow University (1998).
    • (1998)
    • Arokianthan, C.R.1
  • 37
    • 20444370038 scopus 로고    scopus 로고
    • Excessive over-relaxation method for multigrid poisson solvers
    • C. Millar, A. Asenov, and J. Watling, Excessive over-relaxation method for multigrid poisson solvers. J. Comp. Electronics 1, 341 (2002).
    • (2002) J. Comp. Electronics , vol.1 , pp. 341
    • Millar, C.1    Asenov, A.2    Watling, J.3
  • 38
    • 0029876860 scopus 로고    scopus 로고
    • Computing the field in channels and proteins
    • R. S. Eisenberg, Computing the field in channels and proteins. J. Membrane Biol. 150, 1 (1996).
    • (1996) J. Membrane Biol. , vol.150 , pp. 1
    • Eisenberg, R.S.1
  • 40
    • 0030126761 scopus 로고    scopus 로고
    • Physical models of ohmic contact for monte carlo device simulation
    • T. Gonzalez and D. Pardo, Physical models of ohmic contact for monte carlo device simulation. Solid-State Electronics 39, 555 (1996).
    • (1996) Solid-State Electronics , vol.39 , pp. 555
    • Gonzalez, T.1    Pardo, D.2
  • 41
    • 20444429525 scopus 로고    scopus 로고
    • 3D Simulation Techniques For Biological Ion Channels
    • PhD thesis, University of Glasgow, Glasgow
    • C. Millar, 3D Simulation Techniques For Biological Ion Channels, PhD thesis, University of Glasgow, Glasgow (2004).
    • (2004)
    • Millar, C.1
  • 48
    • 20444373829 scopus 로고    scopus 로고
    • The Protein Data Bank
    • The Protein Data Bank. http://www.rcsb.org/pdb.
  • 49
    • 0026494358 scopus 로고
    • Crystallographic studies of a transmembrane ion channel, gramicidin a
    • B. A. Wallace, Crystallographic studies of a transmembrane ion channel, gramicidin a. Prog. Biophys. Molec. Biol. 57 (1992).
    • (1992) Prog. Biophys. Molec. Biol. , pp. 57
    • Wallace, B.A.1
  • 50
    • 0040955484 scopus 로고    scopus 로고
    • X-ray crystallograpic structures of gramicidin and their relation to the streptomyces lividans potassium channel structure
    • Wiley, London
    • B. A. Wallace, X-ray crystallograpic structures of gramicidin and their relation to the streptomyces lividans potassium channel structure. In Gramicidin and Related Ion Channel-Forming Peptides, no. 225, Wiley, London (1999).
    • (1999) Gramicidin and Related Ion Channel-Forming Peptides , Issue.225
    • Wallace, B.A.1
  • 51
    • 0034817286 scopus 로고    scopus 로고
    • Stucture of the kcsa channel intracellular gate in the open state
    • Y. Liu, P. Sompornpisut, and E. Perozo, Stucture of the kcsa channel intracellular gate in the open state. Nature Structural Biol. 8, 883 (2OO1).
    • (2001) Nature Structural Biol. , vol.8 , pp. 883
    • Liu, Y.1    Sompornpisut, P.2    Perozo, E.3
  • 52
    • 0015027073 scopus 로고
    • The gramicidin a transmembrane channel
    • D. W. Urry, The gramicidin a transmembrane channel. In Proc Natl Acad Sci USA 68, 672 (1971).
    • (1971) Proc. Natl. Acad. Sci. USA , vol.68 , pp. 672
    • Urry, D.W.1
  • 54
    • 0036787715 scopus 로고    scopus 로고
    • Open-state models of a potassium channel
    • P. C. Biggin and M. S. P. Sansom, Open-state models of a potassium channel. Biophys. J. 83, (2002).
    • (2002) Biophys. J. , pp. 83
    • Biggin, P.C.1    Sansom, M.S.P.2
  • 56
    • 0037380854 scopus 로고    scopus 로고
    • Gramicidina as a test ground for molecular dynamics force fields
    • T. W. Allen, T. Bastug, S. Kuyucak, and S. H. Chung, Gramicidina as a test ground for molecular dynamics force fields. Biophys. J. 84, 2159 (2003).
    • (2003) Biophys. J. , vol.84 , pp. 2159
    • Allen, T.W.1    Bastugs, T.2    Kuyucak, S.3    Chung, S.H.4
  • 57
    • 0033532712 scopus 로고    scopus 로고
    • Effective diffusion coefficients of k+ and cl- ions in ion channel models
    • G. R. Smith and M. S. P. Sansom, Effective diffusion coefficients of k+ and cl- ions in ion channel models. Biophysical Chemistry 79, 129 (1999).
    • (1999) Biophysical Chemistry , vol.79 , pp. 129
    • Smith, G.R.1    Sansom, M.S.P.2
  • 58
    • 0035575826 scopus 로고    scopus 로고
    • Brownian dynamics study of an open-state kcsa potassium channel
    • T. W. Allen and S. H. Chung, Brownian dynamics study of an open-state kcsa potassium channel. Biochimica et Biophysica Acta 1515, 83 (2001).
    • (2001) Biochimica Et Biophysica Acta , vol.1515 , pp. 83
    • Allen, T.W.1    Chung, S.H.2
  • 60
    • 0007165005 scopus 로고    scopus 로고
    • Mobility and solvation of ions in channels
    • R. M. Lynden-Bell, Mobility and solvation of ions in channels. J. Chem. Phys. 105, 9266 (1996).
    • (1996) J. Chem. Phys. , vol.105 , pp. 9266
    • Lynden-Bell, R.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.