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Volumn 15, Issue 1, 2014, Pages 93-125

A stabilized finite element method for modified Poisson-Nernst-Planck equations to determine ion flow through a nanopore

Author keywords

Continuum transport theory; Finite element method; Ion channels; Ionic current; Nucleic acids; PNP; Steric effects; SUPG

Indexed keywords


EID: 84887796020     PISSN: 18152406     EISSN: 19917120     Source Type: Journal    
DOI: 10.4208/cicp.101112.100413a     Document Type: Article
Times cited : (44)

References (66)
  • 1
    • 0017841119 scopus 로고
    • The extracellular patch clamp: A method for resolving currents through individual open channels in biological membranes
    • E. Neher, B. Sakmann, J. Steinbach, The extracellular patch clamp: A method for resolving currents through individual open channels in biological membranes, Pflug. Arch. Eur. J. Physiol. 375 (1978) 219-228. (Pubitemid 8383955)
    • (1978) Pflugers Archiv European Journal of Physiology , vol.375 , Issue.2 , pp. 219-228
    • Neher, E.1    Sakmann, B.2    Steinbach, J.H.3
  • 2
    • 0021288941 scopus 로고
    • Patch clamp techniques for studying ionic channels in excitable membranes
    • B. Sakmann, E.Neher, Patch clamp techniques for studying ionic channels in excitablemembranes, Ann. Rev. Physiol. 46 (1984) 455-472. (Pubitemid 14147809)
    • (1984) Annual Review of Physiology , vol.VOL. 46 , pp. 455-472
    • Sakmann, B.1    Neher, E.2
  • 3
    • 14844318136 scopus 로고    scopus 로고
    • Nanopore unzipping of individual DNA hairpin molecules
    • DOI 10.1529/biophysj.104.047274
    • J. Mathé, H. Visram, V. Viasnoff, Y. Rabin, A. Meller, Nanopore unzipping of individual DNA hairpin molecules, Biophys. J. 87 (2004) 3205-3212. (Pubitemid 40468577)
    • (2004) Biophysical Journal , vol.87 , Issue.5 , pp. 3205-3212
    • Mathe, J.1    Visram, H.2    Viasnoff, V.3    Rabin, Y.4    Meller, A.5
  • 8
    • 0032762996 scopus 로고    scopus 로고
    • Microsecond timescale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within singe RNAmolecules
    • M. Akeson, D. Branton, J. J. Kasianowicz, E. Brandin, D. W. Deamer, Microsecond timescale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within singe RNAmolecules, Biophys. J. 77 (1999) 3227-3233.
    • (1999) Biophys. J , vol.77 , pp. 3227-3233
    • Akeson, M.1    Branton, D.2    Kasianowicz, J.J.3    Brandin, E.4    Deamer, D.W.5
  • 10
    • 64449088698 scopus 로고    scopus 로고
    • Continuous base identification for single-molecule nanopore DNA sequencing
    • J. Clarke, H. Wu, L. Jayasinghe, A. Patel, S. Reid, H. Bayley, Continuous base identification for single-molecule nanopore DNA sequencing, Nature Nanotech. 4 (2009) 265-270.
    • (2009) Nature Nanotech , vol.4 , pp. 265-270
    • Clarke, J.1    Wu, H.2    Jayasinghe, L.3    Patel, A.4    Reid, S.5    Bayley, H.6
  • 12
    • 0036301334 scopus 로고    scopus 로고
    • Ions and counterions in a biological channel: A molecular dynamics simulation of ompf porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution
    • DOI 10.1016/S0022-2836(02)00380-7
    • W. Im, B. Roux, Ions and counterions in a biological channel: a molecular dynamics study of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution, J. Mol. Biol. 319 (2002) 1177-1197. (Pubitemid 34729427)
    • (2002) Journal of Molecular Biology , vol.319 , Issue.5 , pp. 1177-1197
    • Im, W.1    Roux, B.2
  • 13
    • 0036389892 scopus 로고    scopus 로고
    • Ion permeation and selectivity of OmpF porin: A theoretical study based on molecular dynamics brownian dynamics and continuum electrodiffusion theory
    • W. Im, B. Roux, Ion permeation and selectivity of OmpF porin: A theoretical study based on molecular dynamics, brownian dynamics, and continuum electrodiffusion theory, J. Mole. Bio. 322 (2002) 851-869.
    • (2002) J. Mole. Bio , vol.322 , pp. 851-869
    • Im, W.1    Roux, B.2
  • 14
    • 15244338641 scopus 로고    scopus 로고
    • Ion permeation through the α-hemolysin channel: Theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory
    • DOI 10.1529/biophysj.104.044008
    • S. Y. Noskov, W. Im, B. Roux, Ion permeation through the α-hemolysin channel: Theoretical studies based on Brownian Dynamics and Poisson-Nernst-Plank electrodiffusion theory, Biophys. J. 87 (2004) 2299-2309. (Pubitemid 41071331)
    • (2004) Biophysical Journal , vol.87 , Issue.4 , pp. 2299-2309
    • Noskov, S.Yu.1    Im, W.2    Roux, B.3
  • 15
    • 4444234147 scopus 로고    scopus 로고
    • Microscopic kinetics of DNA translocation through synthetic nanopores
    • DOI 10.1529/biophysj.104.042960
    • A. Aksimentiev, J. B. Heng, G. Timp, K. Schulten,Microscopic kinetics of DNA translocation through synthetic nanopores, Biophys. J. 87 (2004) 2086-2097. (Pubitemid 39172203)
    • (2004) Biophysical Journal , vol.87 , Issue.3 , pp. 2086-2097
    • Aksimentiev, A.1    Heng, J.B.2    Timp, G.3    Schulten, K.4
  • 16
    • 22244445788 scopus 로고    scopus 로고
    • Imaging α-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map
    • DOI 10.1529/biophysj.104.058727
    • A. Aksimentiev, K. Schulten, Imaging alpha-hemolysin withmolecular dynamics: Ionic conductance, osmotic permeability and the electrostatic potential map, Biophys. J. 88 (2005) 3745-3761. (Pubitemid 40991090)
    • (2005) Biophysical Journal , vol.88 , Issue.6 , pp. 3745-3761
    • Aksimentiev, A.1    Schulten, K.2
  • 17
    • 58849087632 scopus 로고    scopus 로고
    • Microscopic mechanics of hairpin DNA translocation through synthetic nanopores
    • J. Comer, V. Dimitrov, Q. Zhao, G. Timp, A. Aksimentiev, Microscopic mechanics of hairpin DNA translocation through synthetic nanopores, Biophys. J. 96 (2009) 593-608.
    • (2009) Biophys. J , vol.96 , pp. 593-608
    • Comer, J.1    Dimitrov, V.2    Zhao, Q.3    Timp, G.4    Aksimentiev, A.5
  • 18
    • 70350035648 scopus 로고    scopus 로고
    • Understanding ion conductance on a molecular level: An all-atom modeling of the bacterial porin OmpF
    • S. Pezeshki, C. Chimerel, A.N. Bessonov,M.Winterhalter, U. Kleinekathofer, Understanding ion conductance on a molecular level: An all-atom modeling of the bacterial porin OmpF, Biophys. J. 97 (2009) 1898-1906.
    • (2009) Biophys. J , vol.97 , pp. 1898-1906
    • Pezeshki, S.1    Chimerel, C.2    Bessonov, A.N.3    Winterhalter, M.4    Kleinekathofer, U.5
  • 19
    • 84856918802 scopus 로고    scopus 로고
    • Ion selectivity of α-hemolysin with a β-cyclodextrin adapter. I. Single ion potential ofmean force and diffusion coefficient
    • Y. Luo, B. Egwolf, D. Walters, B. Roux, Ion selectivity of α-hemolysin with a β-cyclodextrin adapter. I. Single ion potential ofmean force and diffusion coefficient, J. Phys. Chem. B (2009) 2035-2042.
    • (2009) J. Phys. Chem. B , pp. 2035-2042
    • Luo, Y.1    Egwolf, B.2    Walters, D.3    Roux, B.4
  • 20
    • 77953677764 scopus 로고    scopus 로고
    • Deciphering ionic current signatures of DNA transport through a nanopore
    • A. Aksimentiev, Deciphering ionic current signatures of DNA transport through a nanopore, Nanoscale 2 (2010) 468-483.
    • (2010) Nanoscale , vol.2 , pp. 468-483
    • Aksimentiev, A.1
  • 23
    • 80054982153 scopus 로고    scopus 로고
    • Atoms-to-microns model for small solute transport through sticky nanochannels
    • R. Carr, J. Comer, M. Ginsberg, A. Aksimentiev, Atoms-to-microns model for small solute transport through sticky nanochannels, Lab Chip 11 (2011) 3766-3773.
    • (2011) Lab Chip , vol.11 , pp. 3766-3773
    • Carr, R.1    Comer, J.2    Ginsberg, M.3    Aksimentiev, A.4
  • 24
    • 84856812308 scopus 로고    scopus 로고
    • Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics
    • J. Comer, A. Aksimentiev, Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics, J. Phys. Chem. C 116 (2012) 3376-3393.
    • (2012) J. Phys. Chem. C , vol.116 , pp. 3376-3393
    • Comer, J.1    Aksimentiev, A.2
  • 25
    • 4243463817 scopus 로고
    • Electrostatics in biomolecular structure and dynamics
    • M. E. Davis, J. A.McCammon, Electrostatics in biomolecular structure and dynamics, Chem. Rev. 90 (1990) 509-521.
    • (1990) Chem. Rev , vol.90 , pp. 509-521
    • Davis, M.E.1    McCammon, J.A.2
  • 27
    • 0033032906 scopus 로고    scopus 로고
    • A lattice relaxation algorithm for three-dimensional Poisson-Nernst- Planck theory with application to ion transport through the gramicidin A channel
    • M. G. Kurnikova, R. D. Coalson, P. Graf, A. Nitzan, A lattice relaxation algorithm for threedimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel, Biophys J. 76 (1999) 642-656. (Pubitemid 29264548)
    • (1999) Biophysical Journal , vol.76 , Issue.2 , pp. 642-656
    • Kurnikova, M.G.1    Coalson, R.D.2    Graf, P.3    Nitzan, A.4
  • 28
    • 34948887808 scopus 로고    scopus 로고
    • Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution
    • (17 pages)
    • B. Lu, Y. Zhou, G. A. Huber, S. D. Bond, M. J. Holst, J. A. McCammon, Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution, J. Chem. Phys. 127 (2007) 135102 (17 pages).
    • (2007) J. Chem. Phys , vol.127 , pp. 135102
    • Lu, B.1    Zhou, Y.2    Huber, G.A.3    Bond, S.D.4    Holst, M.J.5    McCammon, J.A.6
  • 29
    • 33847295668 scopus 로고    scopus 로고
    • Steric effects in the dynamics of electrolytes at large applied voltages. II. Modified Poisson-Nernst-Planck equations
    • M. S. Kilic, M. Z. Bazant, A. Ajdari, Steric effects in the dynamics of electrolytes at large applied voltages. II. Modified Poisson-Nernst-Planck equations, Phys. Rev. E 75 (2007) 021503.
    • (2007) Phys. Rev. e , vol.75 , pp. 021503
    • Kilic, M.S.1    Bazant, M.Z.2    Ajdari, A.3
  • 30
    • 59149103015 scopus 로고    scopus 로고
    • Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore
    • D. S. Bolintineanu, A. Sayyed-Ahmad, H. T. Davis, Y. N. Kaznessis, Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore, PLoS Comput. Biol. 5 (1) (2009) e1000277.
    • (2009) PLoS Comput. Biol , vol.5 , Issue.1
    • Bolintineanu, D.S.1    Sayyed-Ahmad, A.2    Davis, H.T.3    Kaznessis, Y.N.4
  • 31
    • 0043239420 scopus 로고    scopus 로고
    • Three-dimensional Poisson-Nernst-Planck theory studies: Influence of membrane electrostatics on gramicidin a channel conductance
    • A. E. Cardenas, R. D. Coalson, M. G. Kurnikova, Three-dimensional Poisson-Nernst-Planck theory studies: Influence of membrane electrostatics on gramicidin A channel conductance, Biophys. J. 79 (1) (2000) 80-93. (Pubitemid 30436729)
    • (2000) Biophysical Journal , vol.79 , Issue.1 , pp. 80-93
    • Cardenas, A.E.1    Coalson, R.D.2    Kurnikova, M.G.3
  • 32
    • 0001170937 scopus 로고
    • The numerical solution of the time-dependentNernst-Planck equations
    • H. Cohen, J. Cooley, The numerical solution of the time-dependentNernst- Planck equations, Biophys. J. 5 (1965) 145-162.
    • (1965) Biophys. J , vol.5 , pp. 145-162
    • Cohen, H.1    Cooley, J.2
  • 33
    • 34948887808 scopus 로고    scopus 로고
    • Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution
    • B. Lu, Y. C. Zhou, G. A. Huber, S. D. Bond, M. J. Holst, J. A. McCammon, Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution, J. Chem. Phys. 127 (2007) 135102.
    • (2007) J. Chem. Phys , vol.127 , pp. 135102
    • Lu, B.1    Zhou, Y.C.2    Huber, G.A.3    Bond, S.D.4    Holst, M.J.5    McCammon, J.A.6
  • 34
    • 77955272371 scopus 로고    scopus 로고
    • Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutions
    • B. Lu, M. J. Holst, J. Andrew McCammon, Y. C. Zhou, Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutions, J. Comput. Phys. 229 (2010) 6979-6994.
    • (2010) J. Comput. Phys , vol.229 , pp. 6979-6994
    • Lu, B.1    Holst, M.J.2    Andrew McCammon, J.3    Zhou, Y.C.4
  • 35
    • 79959636026 scopus 로고    scopus 로고
    • Poisson-Nernst-Planck equations for simulating biomolecular diffusionreaction processes II: Size effects on ionic distributions and diffusion-reaction rates
    • B. Lu, Y. Zhou, Poisson-Nernst-Planck equations for simulating biomolecular diffusionreaction processes II: Size effects on ionic distributions and diffusion-reaction rates, Biophys. J. 100 (2011) 2475-2485.
    • (2011) Biophys. J , vol.100 , pp. 2475-2485
    • Lu, B.1    Zhou, Y.2
  • 36
    • 79955476670 scopus 로고    scopus 로고
    • Second-order Poisson-Nernst-Planck solver for ion transport
    • Q. Zheng, D. Chen, G.-W.Wei, Second-order Poisson-Nernst-Planck solver for ion transport, J. Comput. Phys. 230 (2011) 5239-5262.
    • (2011) J. Comput. Phys , vol.230 , pp. 5239-5262
    • Zheng, Q.1    Chen, D.2    Wei, G.-W.3
  • 37
    • 76249096812 scopus 로고    scopus 로고
    • DOLFIN: Automated finite element computing
    • A. Logg, G. N. Wells, DOLFIN: Automated finite element computing, ACM Trans. Math. Softw. 37 (2010) 20:1-20:28.
    • (2010) ACM Trans. Math. Softw , vol.37 , pp. 201-2028
    • Logg, A.1    Wells, G.N.2
  • 39
    • 14344258977 scopus 로고    scopus 로고
    • Stability of the SUPG finite element method for transient advection-diffusion problems
    • DOI 10.1016/j.cma.2004.01.026, PII S0045782504000830
    • P. B. Bochev,M. D. Gunzburger, J.N. Shadid, Stability of the SUPG finite elementmethod for transient advection-diffusion problems, Comp. Meth. Appl. Mech. Engr. 193 (23-26) (2004) 2301-2323. (Pubitemid 38503358)
    • (2004) Computer Methods in Applied Mechanics and Engineering , vol.193 , Issue.23-26 , pp. 2301-2323
    • Bochev, P.B.1    Gunzburger, M.D.2    Shadid, J.N.3
  • 40
    • 0023525478 scopus 로고
    • Recent progress in the development and understanding of SUPG methods with special reference to the compressible Euler and Navier-Stokes equations
    • T. J. R. Hughes, Recent progress in the development and understanding of SUPG methods with special reference to the compressible Euler and Navier-Stokes equations, Int. J. Numer. Meth. Fluids 7 (1987) 1261-1275.
    • (1987) Int. J. Numer. Meth. Fluids , vol.7 , pp. 1261-1275
    • Hughes, T.J.R.1
  • 41
    • 45149144830 scopus 로고
    • A new finite element formulation for computational fluid dynamics: VIII. The galerkin/least-squares method for advective-diffusive equations
    • T. J. R. Hughes, L. P. Franca, G. M. Hulbert, A new finite element formulation for computational fluid dynamics: VIII. The galerkin/least-squares method for advective-diffusive equations, Comp. Meth. Appl. Mech. Engr. 73 (1989) 173-189.
    • (1989) Comp. Meth. Appl. Mech. Engr , vol.73 , pp. 173-189
    • Hughes, T.J.R.1    Franca, L.P.2    Hulbert, G.M.3
  • 42
    • 0026835579 scopus 로고
    • Stabilized finite element methods: I. Application to the advective-diffusivemodel
    • L. P. Franca, S. L. Frey, T. J. R. Hughes, Stabilized finite element methods: I. Application to the advective-diffusivemodel, Comp. Meth. Appl. Mech. Engr. 95 (1992) 253-276.
    • (1992) Comp. Meth. Appl. Mech. Engr , vol.95 , pp. 253-276
    • Franca, L.P.1    Frey, S.L.2    Hughes, T.J.R.3
  • 43
    • 77956849889 scopus 로고
    • Stabilized finite element formulations for incompressible flow computations
    • T. T. Eu, Stabilized finite element formulations for incompressible flow computations, Adv. Appl. Mech. 28 (1991) 1-44.
    • (1991) Adv. Appl. Mech , vol.28 , pp. 1-44
    • Eu, T.T.1
  • 44
    • 0022681271 scopus 로고
    • A new finite element formulation for computational fluid dynamics: II. Beyond SUPG
    • T. J. Hughes, M.Mallet,M. Akira, A new finite element formulation for computational fluid dynamics: II. Beyond SUPG, Comp. Meth. Appl. Mech. Engr. 54 (1986) 341-355.
    • (1986) Comp. Meth. Appl. Mech. Engr , vol.54 , pp. 341-355
    • Hughes, T.J.1    Akira, M.MalletM.2
  • 45
    • 0001585447 scopus 로고
    • Computation of electrostatic forces on solvatedmolecules using the poisson-boltzmann equation
    • M. K. Gilson, M. E. Davis, B. A. Luty, J. A. McCammon, Computation of electrostatic forces on solvatedmolecules using the poisson-boltzmann equation, J. Phys. Chem. 97 (1993) 3591-3600.
    • (1993) J. Phys. Chem , vol.97 , pp. 3591-3600
    • Gilson, M.K.1    Davis, M.E.2    Luty, B.A.3    McCammon, J.A.4
  • 46
    • 85033849708 scopus 로고    scopus 로고
    • Finite-difference solution of the Poisson - Boltzmann equation: Complete elimination of self-energy
    • Z. Zhou, P. Payne,M. Vasquez, N. Kuhn,M. Levitt, Finite-difference solution of the Poisson- Boltzmann equation: Complete elimination of self-energy, J. Comput. Chem. 17 (1996) 1344-1351. (Pubitemid 126576751)
    • (1996) Journal of Computational Chemistry , vol.17 , Issue.11 , pp. 1344-1351
    • Zhou, Z.1    Payne, P.2    Vasquez, M.3    Kuhn, N.4    Levitt, M.5
  • 47
    • 79959545610 scopus 로고    scopus 로고
    • Finite element approximation to a finite-size modified Poisson-Boltzmann equation
    • 10.1007/s10915-010-9441-7
    • J. Chaudhry, S. Bond, L. Olson, Finite element approximation to a finite-size modified Poisson-Boltzmann equation, J. Sci. Comput. 47 (2011) 347-364, 10.1007/s10915-010-9441-7.
    • (2011) J. Sci. Comput , vol.47 , pp. 347-364
    • Chaudhry, J.1    Bond, S.2    Olson, L.3
  • 48
    • 77952378191 scopus 로고    scopus 로고
    • A first-order system least-squares finite element method for the Poisson-Boltzmann equation
    • S. D. Bond, J. H. Chaudhry, E. C. Cyr, L. N. Olson, A first-order system least-squares finite element method for the Poisson-Boltzmann equation, J. Comput. Chem. 31 (8) (2010) 1625-1635.
    • (2010) J. Comput. Chem , vol.31 , Issue.8 , pp. 1625-1635
    • Bond, S.D.1    Chaudhry, J.H.2    Cyr, E.C.3    Olson, L.N.4
  • 49
    • 33846682092 scopus 로고    scopus 로고
    • Accurate evaluation of electrostatics for macromolecules in solution
    • I.-L. Chern, J.-G. Liu, W.-C. Wang, Accurate evaluation of electrostatics for macromolecules in solution, Meth. Appl. Anal. 10 (2003) 309-328. (Pubitemid 38825116)
    • (2003) Meth. Appl. Anal. , vol.10 , Issue.2 , pp. 309-328
    • Chern, I.-L.1    Liu, J.-G.2    Wang, W.-C.3
  • 50
    • 84861455916 scopus 로고    scopus 로고
    • Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
    • B. Aksoylu, S. D. Bond, E. C. Cyr, M. J. Holst, Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation, J. Sci. Comput. 52 (2012) 202-225.
    • (2012) J. Sci. Comput , vol.52 , pp. 202-225
    • Aksoylu, B.1    Bond, S.D.2    Cyr, E.C.3    Holst, M.J.4
  • 51
    • 70350711984 scopus 로고    scopus 로고
    • Towards an understanding of inducedcharge electrokinetics at large applied voltages in concentrated solutions
    • M. Z. Bazant, M. S. Kilic, B. D. Storey, A. Ajdari, Towards an understanding of inducedcharge electrokinetics at large applied voltages in concentrated solutions, Adv. Colloid Interface Sci. 152 (1-2) (2009) 48-88.
    • (2009) Adv. Colloid Interface Sci , vol.152 , Issue.1-2 , pp. 48-88
    • Bazant, M.Z.1    Kilic, M.S.2    Storey, B.D.3    Ajdari, A.4
  • 54
    • 84887719445 scopus 로고    scopus 로고
    • URL http://www.rcsb.org/pdb/
  • 55
    • 34547559704 scopus 로고    scopus 로고
    • Pdb2pqr: Expanding and upgrading automated preparation of biomolecular structures formolecular simulations
    • T. Dolinsky, P. Czodrowski, H. Li, J. Nielsen, J. Jensen, G. K. N. Baker, Pdb2pqr: Expanding and upgrading automated preparation of biomolecular structures formolecular simulations, Nucleic Acids Res. 35 (2007)W522-W525.
    • (2007) Nucleic Acids Res , vol.35
    • Dolinsky, T.1    Czodrowski, P.2    Li, H.3    Nielsen, J.4    Jensen, J.5    Baker, G.K.N.6
  • 56
    • 3242886771 scopus 로고    scopus 로고
    • PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    • DOI 10.1093/nar/gkh381
    • T. Dolinsky, J. Nielsen, J. McCammon, N. Baker, Pdb2pqr: An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations, Nucleic Acids Res. 35 (2004)W665-W667. (Pubitemid 38997419)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS.
    • Dolinsky, T.J.1    Nielsen, J.E.2    McCammon, J.A.3    Baker, N.A.4
  • 57
    • 42749086211 scopus 로고    scopus 로고
    • Feature-preserving adaptivemesh generation for molecular shape modeling and simulation
    • Z. Yu,M. J.Holst, Y. Cheng, J. A.McCammon, Feature-preserving adaptivemesh generation for molecular shape modeling and simulation, J. Mol. Graph. Model. 26 (2008) 1370-1380.
    • (2008) J. Mol. Graph. Model , vol.26 , pp. 1370-1380
    • Yu, Z.1    Holst, M.J.2    Cheng, Y.3    McCammon, J.A.4
  • 58
    • 67650149648 scopus 로고    scopus 로고
    • Gmsh: A 3-d finite element mesh generator with built-in preand post-processing facilities
    • C. Geuzaine, J.-F. Remacle, Gmsh: A 3-d finite element mesh generator with built-in preand post-processing facilities, Int. J. Numer. Meth. Engr. 79 (2009) 1309-1331.
    • (2009) Int. J. Numer. Meth. Engr , vol.79 , pp. 1309-1331
    • Geuzaine, C.1    Remacle, J.-F.2
  • 59
    • 31544471731 scopus 로고    scopus 로고
    • Salt dependence of ion transport and DMA translocation through solid-state nanopores
    • DOI 10.1021/nl052107w
    • R.M.M. Smeets, U. F. Keyser, D. Krapf,M.-Y.Wu, N. H. Dekker, C. Dekker, Salt dependence of ion transport and dna translocation through solid-state nanopores, Nano Letters 6 (2006) 89-95. (Pubitemid 43166107)
    • (2006) Nano Letters , vol.6 , Issue.1 , pp. 89-95
    • Smeets, R.M.M.1    Keyser, U.F.2    Krapf, D.3    Wu, M.-Y.4    Dekker, N.H.5    Dekker, C.6
  • 60
    • 0000216904 scopus 로고    scopus 로고
    • Local dielectric environment of B-DNA in solution: Results from a 14 ns molecular dynamics trajectory
    • M. Young, B. Jayaram, D. Beveridge, Local dielectric environment of B-DNA in solution: Results from a 14 ns molecular dynamics trajectory, J. Phys. Chem. B 102 (1998) 7666-7669. (Pubitemid 128578404)
    • (1998) Journal of Physical Chemistry B , vol.102 , Issue.39 , pp. 7666-7669
    • Young, M.A.1    Jayaram, B.2    Beveridge, D.L.3
  • 61
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • B. Roux, The calculation of the potential of mean force using computer simulations, Comp. Phys. Commun. 91 (1995) 275-282.
    • (1995) Comp. Phys. Commun , vol.91 , pp. 275-282
    • Roux, B.1
  • 64
    • 0001655657 scopus 로고
    • Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
    • D. Beglov, B. Roux, Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations, J. Chem. Phys. 100 (1994) 9050-9063.
    • (1994) J. Chem. Phys , vol.100 , pp. 9050-9063
    • Beglov, D.1    Roux, B.2
  • 65
    • 0035828343 scopus 로고    scopus 로고
    • Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry
    • W. Im, B. Roux, Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry, J. Chem. Phys. 115 (2001) 4580.
    • (2001) J. Chem. Phys , vol.115 , pp. 4580
    • Im, W.1    Roux, B.2
  • 66
    • 34848830419 scopus 로고    scopus 로고
    • Exploring transmembrane transport through α-hemolysin with grid-steered molecular dynamics
    • D. B. Wells, V. Abramkina, A. Aksimentiev, Exploring transmembrane transport through α-hemolysin with grid-steered molecular dynamics, J. Chem. Phys. 127 (2007) 125101.
    • (2007) J. Chem. Phys , vol.127 , pp. 125101
    • Wells, D.B.1    Abramkina, V.2    Aksimentiev, A.3


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