-
1
-
-
66549111828
-
Asymptotic expansions of I-V relations via a Poisson-Nernst-Planck system
-
Abaid N., Eisenberg R.S., Liu W.S. Asymptotic expansions of I-V relations via a Poisson-Nernst-Planck system. SIAM J. Appl. Dyn. Syst. 2008, 7(4):1507-1526.
-
(2008)
SIAM J. Appl. Dyn. Syst.
, vol.7
, Issue.4
, pp. 1507-1526
-
-
Abaid, N.1
Eisenberg, R.S.2
Liu, W.S.3
-
2
-
-
0035723018
-
Electrostatic potential inside ionic solutions confined by dielectrics: a variational approach
-
Allen R., Hansen J.-P., Melchionna S. Electrostatic potential inside ionic solutions confined by dielectrics: a variational approach. Phys. Chem. Chem. Phys. 2001, 3:4177-4186.
-
(2001)
Phys. Chem. Chem. Phys.
, vol.3
, pp. 4177-4186
-
-
Allen, R.1
Hansen, J.-P.2
Melchionna, S.3
-
3
-
-
0000024779
-
The finite element method for elliptic equations with discontinuous coefficients
-
Babuška I. The finite element method for elliptic equations with discontinuous coefficients. Computing 1970, 5:207-213.
-
(1970)
Computing
, vol.5
, pp. 207-213
-
-
Babuška, I.1
-
4
-
-
0026930493
-
Ion flow through narrow membran channels: part I
-
Barcilon V. Ion flow through narrow membran channels: part I. SIAM J. Appl. Math. 1992, 52(5):1391-1404.
-
(1992)
SIAM J. Appl. Math.
, vol.52
, Issue.5
, pp. 1391-1404
-
-
Barcilon, V.1
-
5
-
-
0026929304
-
Ion flow through narrow membrane channels: Part ii
-
Barcilon V., Chen D., Eisenberg R. Ion flow through narrow membrane channels: Part ii. SIAM J. Appl. Math. 1992, 52:1405-1425.
-
(1992)
SIAM J. Appl. Math.
, vol.52
, pp. 1405-1425
-
-
Barcilon, V.1
Chen, D.2
Eisenberg, R.3
-
6
-
-
84962460748
-
Discretization of the induced-charge boundary integral equation
-
Bardhan J.P., Eisenberg R.S., Gillespie D. Discretization of the induced-charge boundary integral equation. Phys. Rev. E, Stat. Nonlinear Soft Matter Phys. 2009, 80(1):11906-11910.
-
(2009)
Phys. Rev. E, Stat. Nonlinear Soft Matter Phys.
, vol.80
, Issue.1
, pp. 11906-11910
-
-
Bardhan, J.P.1
Eisenberg, R.S.2
Gillespie, D.3
-
7
-
-
67650932053
-
Geometric and potential driving formation and evolution of biomolecular surfaces
-
Bates P.W., Chen Z., Sun Y.H., Wei G.W., Zhao S. Geometric and potential driving formation and evolution of biomolecular surfaces. J. Math. Biol. 2009, 59:193-231.
-
(2009)
J. Math. Biol.
, vol.59
, pp. 193-231
-
-
Bates, P.W.1
Chen, Z.2
Sun, Y.H.3
Wei, G.W.4
Zhao, S.5
-
8
-
-
38349095051
-
Minimal molecular surfaces and their applications
-
Bates P.W., Wei G.W., Zhao S. Minimal molecular surfaces and their applications. J. Comput. Chem. 2008, 29(3):380-391.
-
(2008)
J. Comput. Chem.
, vol.29
, Issue.3
, pp. 380-391
-
-
Bates, P.W.1
Wei, G.W.2
Zhao, S.3
-
9
-
-
42749109091
-
Diffuse-charge dynamics in electrochemical systems
-
Bazant M.Z., Thornton K., Ajdari A. Diffuse-charge dynamics in electrochemical systems. Phys. Rev. E 2004, 70:021506.
-
(2004)
Phys. Rev. E
, vol.70
, pp. 021506
-
-
Bazant, M.Z.1
Thornton, K.2
Ajdari, A.3
-
10
-
-
42749100087
-
Computing induced charges in inhomogeneous dielectric media: application in a Monte Carlo simulation of complex ionic systems
-
Boda D., Gillespie D., Nonner W., Henderson D., Eisenberg B. Computing induced charges in inhomogeneous dielectric media: application in a Monte Carlo simulation of complex ionic systems. Phys. Rev. E, Stat. Nonlinear Soft Matter Phys. 2004, 69:046702.
-
(2004)
Phys. Rev. E, Stat. Nonlinear Soft Matter Phys.
, vol.69
, pp. 046702
-
-
Boda, D.1
Gillespie, D.2
Nonner, W.3
Henderson, D.4
Eisenberg, B.5
-
11
-
-
43649092750
-
Volume exclusion in calcium selective channels
-
Boda D., Nonner W., Henderson D., Eisenberg B., Gillespie D. Volume exclusion in calcium selective channels. Biophys. J. 2008, 94:3486-3496.
-
(2008)
Biophys. J.
, vol.94
, pp. 3486-3496
-
-
Boda, D.1
Nonner, W.2
Henderson, D.3
Eisenberg, B.4
Gillespie, D.5
-
12
-
-
34548717678
-
Steric selectivity in Na channels arising from protein polarization and mobile side chains
-
Boda D., Nonner W., Valisko M., Henderson D., Eisenberg B., Gillespie D. Steric selectivity in Na channels arising from protein polarization and mobile side chains. Biophys. J. 2007, 93(6):1960-1980.
-
(2007)
Biophys. J.
, vol.93
, Issue.6
, pp. 1960-1980
-
-
Boda, D.1
Nonner, W.2
Valisko, M.3
Henderson, D.4
Eisenberg, B.5
Gillespie, D.6
-
13
-
-
34247260951
-
The combined effect of pore radius and protein dielectric coefficient on the selectivity of a calcium channel
-
Boda D., Valisko M., Eisenberg B., Nonner W., Henderson D., Gillespie D. The combined effect of pore radius and protein dielectric coefficient on the selectivity of a calcium channel. Phys. Rev. Lett. 2007, 98:168102.
-
(2007)
Phys. Rev. Lett.
, vol.98
, pp. 168102
-
-
Boda, D.1
Valisko, M.2
Eisenberg, B.3
Nonner, W.4
Henderson, D.5
Gillespie, D.6
-
14
-
-
3042835846
-
Monte carlo simulation study of a system with a dielectric boundary: application to calcium channel selectivity
-
Boda D., Varga T., Henderson D., Busath D., Nonner W., Gillespie D., Eisenberg B. Monte carlo simulation study of a system with a dielectric boundary: application to calcium channel selectivity. Mol. Simul. 2004, 30:89-96.
-
(2004)
Mol. Simul.
, vol.30
, pp. 89-96
-
-
Boda, D.1
Varga, T.2
Henderson, D.3
Busath, D.4
Nonner, W.5
Gillespie, D.6
Eisenberg, B.7
-
15
-
-
21444439361
-
A finite element method for interface problems in domains with smooth boundaries and interfaces
-
Bramble J., King J. A finite element method for interface problems in domains with smooth boundaries and interfaces. Adv. Comput. Math. 1996, 6:109-138.
-
(1996)
Adv. Comput. Math.
, vol.6
, pp. 109-138
-
-
Bramble, J.1
King, J.2
-
16
-
-
0043239420
-
Three-dimensional Poisson-Nernst-Planck theory studies: influence of membrane electrostatics on Gramicidin A channel conductance
-
Cardenas A.E., Coalson R.D., Kurnikova M.G. Three-dimensional Poisson-Nernst-Planck theory studies: influence of membrane electrostatics on Gramicidin A channel conductance. Biophys. J. 2000, 79:80-93.
-
(2000)
Biophys. J.
, vol.79
, pp. 80-93
-
-
Cardenas, A.E.1
Coalson, R.D.2
Kurnikova, M.G.3
-
17
-
-
79251528566
-
MIBPB: a software package for electrostatic analysis
-
Chen D., Chen Z., Chen C., Geng W.H., Wei G.W. MIBPB: a software package for electrostatic analysis. J. Comput. Chem. 2011, 32:657-670.
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 657-670
-
-
Chen, D.1
Chen, Z.2
Chen, C.3
Geng, W.H.4
Wei, G.W.5
-
18
-
-
45849096468
-
Piecewise-polynomial discretization and Krylov-accelerated multigrid for elliptic interface problems
-
Chen T., Strain J. Piecewise-polynomial discretization and Krylov-accelerated multigrid for elliptic interface problems. J. Comput. Phys. 2008, 16:7503-7542.
-
(2008)
J. Comput. Phys.
, vol.16
, pp. 7503-7542
-
-
Chen, T.1
Strain, J.2
-
19
-
-
77956414486
-
Differential geometry based solvation models I: Eulerian formulation
-
Chen Z., Baker N.A., Wei G.W. Differential geometry based solvation models I: Eulerian formulation. J. Comput. Phys. 2010, 229:8231-8258.
-
(2010)
J. Comput. Phys.
, vol.229
, pp. 8231-8258
-
-
Chen, Z.1
Baker, N.A.2
Wei, G.W.3
-
20
-
-
12344297727
-
An accurate and efficient empirical approach for calculating the dielectric self-energy and ion-ion pair potential in continuum models of biological ion channels
-
Cheng M.H., Coalson R.D. An accurate and efficient empirical approach for calculating the dielectric self-energy and ion-ion pair potential in continuum models of biological ion channels. J. Phys. Chem. B 2005, 109(1):488-498.
-
(2005)
J. Phys. Chem. B
, vol.109
, Issue.1
, pp. 488-498
-
-
Cheng, M.H.1
Coalson, R.D.2
-
21
-
-
78649979016
-
Molecular dynamics and Brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel
-
Cheng M.H., Coalson R.D., Tang P. Molecular dynamics and Brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel. J. Am. Chem. Soc. 2010, 132(46):16442-16449.
-
(2010)
J. Am. Chem. Soc.
, vol.132
, Issue.46
, pp. 16442-16449
-
-
Cheng, M.H.1
Coalson, R.D.2
Tang, P.3
-
22
-
-
33846682092
-
Accurate evaluation of electrostatics for macromolecules in solution
-
Chern I.L., Liu J.-G., Weng W.-C. Accurate evaluation of electrostatics for macromolecules in solution. Methods Appl. Anal. 2003, 10(2):309-328.
-
(2003)
Methods Appl. Anal.
, vol.10
, Issue.2
, pp. 309-328
-
-
Chern, I.L.1
Liu, J.-G.2
Weng, W.-C.3
-
23
-
-
77949332587
-
The electrostatics of VDAC: implications for selectivity and gating
-
Choudhary O.P., Ujwal R., Kowallis W., Coalson R., Abramson J., Grabe M. The electrostatics of VDAC: implications for selectivity and gating. J. Mol. Biol. 2010, 396(3):580-592.
-
(2010)
J. Mol. Biol.
, vol.396
, Issue.3
, pp. 580-592
-
-
Choudhary, O.P.1
Ujwal, R.2
Kowallis, W.3
Coalson, R.4
Abramson, J.5
Grabe, M.6
-
24
-
-
0037064260
-
Recent advances in ion channel research
-
Chung S.-H., Kuyucak S. Recent advances in ion channel research. Biochim. Biophys. Acta 2002, 1565:267-286.
-
(2002)
Biochim. Biophys. Acta
, vol.1565
, pp. 267-286
-
-
Chung, S.-H.1
Kuyucak, S.2
-
25
-
-
15244344856
-
Poisson-Nernst-Planck theory approach to the calculation of current through biological ion channels
-
Coalson R.D., Kurnikova M.G. Poisson-Nernst-Planck theory approach to the calculation of current through biological ion channels. IEEE Trans. Nanobiosci. 2005, 4(1):81-93.
-
(2005)
IEEE Trans. Nanobiosci.
, vol.4
, Issue.1
, pp. 81-93
-
-
Coalson, R.D.1
Kurnikova, M.G.2
-
26
-
-
0036788529
-
Noncontact dipole effects on channel permeation. vi. 5f- and 6F-Trp gramicidin channel currents
-
Cole C.D., Frost A.S., Thompson N., Cotten M., Cross T.A., Busath D.D. Noncontact dipole effects on channel permeation. vi. 5f- and 6F-Trp gramicidin channel currents. Biophys. J. 2002, 83:1974-1986.
-
(2002)
Biophys. J.
, vol.83
, pp. 1974-1986
-
-
Cole, C.D.1
Frost, A.S.2
Thompson, N.3
Cotten, M.4
Cross, T.A.5
Busath, D.D.6
-
27
-
-
34547559704
-
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
Dolinsky T.J., Czodrowski P., Li H., Nielsen J.E., Jensen J.H., Klebe G., Baker N.A. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucl. Acids Res. 2007, 35(S2):W522-W525.
-
(2007)
Nucl. Acids Res.
, vol.35
, Issue.S2
-
-
Dolinsky, T.J.1
Czodrowski, P.2
Li, H.3
Nielsen, J.E.4
Jensen, J.H.5
Klebe, G.6
Baker, N.A.7
-
28
-
-
37649032736
-
Improved local lattice approach for Coulombic simulations
-
Duncan A., Sedgewick R.D., Coalson R.D. Improved local lattice approach for Coulombic simulations. Phys. Rev. E, Stat. Nonlinear Soft Matter Phys. 2005, 71:046702.
-
(2005)
Phys. Rev. E, Stat. Nonlinear Soft Matter Phys.
, vol.71
, pp. 046702
-
-
Duncan, A.1
Sedgewick, R.D.2
Coalson, R.D.3
-
29
-
-
77956944534
-
Energy variational analysis of ions in water and channels: field theory for primitive models of complex ionic fluids
-
Eisenberg B., Hyon Y., Liu C. Energy variational analysis of ions in water and channels: field theory for primitive models of complex ionic fluids. J. Chem. Phys. 2010, 133(104104).
-
(2010)
J. Chem. Phys.
, vol.133
, pp. 104104
-
-
Eisenberg, B.1
Hyon, Y.2
Liu, C.3
-
30
-
-
34548804174
-
Poisson-Nernst-Planck systems for ion channels with permanent charges
-
Eisenberg B., Liu W.S. Poisson-Nernst-Planck systems for ion channels with permanent charges. SIAM J. Appl. Dyn. Syst. 2006, 38(6):1932-1966.
-
(2006)
SIAM J. Appl. Dyn. Syst.
, vol.38
, Issue.6
, pp. 1932-1966
-
-
Eisenberg, B.1
Liu, W.S.2
-
31
-
-
4243514587
-
Poisson-Nernst-Planck (PNP) theory of an open ionic channel
-
Eisenberg R., Chen D. Poisson-Nernst-Planck (PNP) theory of an open ionic channel. Biophys. J. 1993, 64:A22.
-
(1993)
Biophys. J.
, vol.64
-
-
Eisenberg, R.1
Chen, D.2
-
32
-
-
0029876860
-
Computing the field in proteins and channels
-
Eisenberg R.S. Computing the field in proteins and channels. J. Membrane Biol. 1996, 150:1-25.
-
(1996)
J. Membrane Biol.
, vol.150
, pp. 1-25
-
-
Eisenberg, R.S.1
-
33
-
-
0346837922
-
A non-oscillatory Eulerian approach to interfaces in multimaterial flows (the ghost fluid method)
-
Fedkiw R.P., Aslam T., Merriman B., Osher S. A non-oscillatory Eulerian approach to interfaces in multimaterial flows (the ghost fluid method). J. Comput. Phys. 1999, 152:457-492.
-
(1999)
J. Comput. Phys.
, vol.152
, pp. 457-492
-
-
Fedkiw, R.P.1
Aslam, T.2
Merriman, B.3
Osher, S.4
-
34
-
-
34547690932
-
Ion channel gene expression in the inner ear
-
Gabashvili I.S., Sokolowski B.H.A., Morton C.C., Giersch A.B.S. Ion channel gene expression in the inner ear. J. Assoc. Res. Otolaryngol. 2007, 8(3):305-328.
-
(2007)
J. Assoc. Res. Otolaryngol.
, vol.8
, Issue.3
, pp. 305-328
-
-
Gabashvili, I.S.1
Sokolowski, B.H.A.2
Morton, C.C.3
Giersch, A.B.S.4
-
35
-
-
34648817162
-
Treatment of charge singularities in implicit solvent models
-
Geng W., Yu S., Wei G.W. Treatment of charge singularities in implicit solvent models. J. Chem. Phys. 2007, 127:114106.
-
(2007)
J. Chem. Phys.
, vol.127
, pp. 114106
-
-
Geng, W.1
Yu, S.2
Wei, G.W.3
-
36
-
-
38949090423
-
Energetics of divalent selectivity in a calcium channel: the ryanodine receptor case study
-
Gillespie D. Energetics of divalent selectivity in a calcium channel: the ryanodine receptor case study. Biophys. J. 2008, 94(4):1169-1184.
-
(2008)
Biophys. J.
, vol.94
, Issue.4
, pp. 1169-1184
-
-
Gillespie, D.1
-
37
-
-
26444537377
-
Density functional theory of the electrical double layer: the RFD functional
-
Gillespie D., Valisko M., Boda D. Density functional theory of the electrical double layer: the RFD functional. J. Phys.: Condens. Matter 2005, 17:6609-6626.
-
(2005)
J. Phys.: Condens. Matter
, vol.17
, pp. 6609-6626
-
-
Gillespie, D.1
Valisko, M.2
Boda, D.3
-
38
-
-
84916430884
-
A self-consistent iterative scheme for the one-dimensional steady-state transistor calculations
-
Gummel H.K. A self-consistent iterative scheme for the one-dimensional steady-state transistor calculations. IEEE Trans. Electron Dev. 1964, 11:455-465.
-
(1964)
IEEE Trans. Electron Dev.
, vol.11
, pp. 455-465
-
-
Gummel, H.K.1
-
40
-
-
0000381967
-
Two- and three-dimensional Poisson-Nernst-Planck simulations of current flow through Gramicidin A
-
Hollerbach U., Chen D.P., Eisenberg R.S. Two- and three-dimensional Poisson-Nernst-Planck simulations of current flow through Gramicidin A. J. Sci. Comput. 2002, 16(4):373-409.
-
(2002)
J. Sci. Comput.
, vol.16
, Issue.4
, pp. 373-409
-
-
Hollerbach, U.1
Chen, D.P.2
Eisenberg, R.S.3
-
41
-
-
85189839931
-
-
The Poisson-Boltzmann equation: analysis and multilevel numerical solution, PhD Thesis, California Institute of Technology
-
M. Holst, The Poisson-Boltzmann equation: analysis and multilevel numerical solution, PhD Thesis, California Institute of Technology, 1994.
-
(1994)
-
-
Holst, M.1
-
42
-
-
38049129674
-
Incorporation of inhomogeneous ion diffusion coefficients into kinetic lattice grand canonical Monte Carlo simulations and application to ion current calculations in a simple model ion channel
-
Hwang H., Schatz G.C., Ratner M.A. Incorporation of inhomogeneous ion diffusion coefficients into kinetic lattice grand canonical Monte Carlo simulations and application to ion current calculations in a simple model ion channel. J. Phys. Chem. A 2007, 111(49):12506-12512.
-
(2007)
J. Phys. Chem. A
, vol.111
, Issue.49
, pp. 12506-12512
-
-
Hwang, H.1
Schatz, G.C.2
Ratner, M.A.3
-
43
-
-
0036389892
-
Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory
-
Im W., Roux B. Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory. J. Mol. Biol. 2002, 322:851-869.
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 851-869
-
-
Im, W.1
Roux, B.2
-
46
-
-
72049087484
-
A computational study of ion conductance in the KcsA K+ channel using a Nernst-Planck model with explicit resident ions
-
Jung Y.W., Lu B.Z., Mascagni M. A computational study of ion conductance in the KcsA K+ channel using a Nernst-Planck model with explicit resident ions. J. Chem. Phys. 2009, 131(215101).
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 215101
-
-
Jung, Y.W.1
Lu, B.Z.2
Mascagni, M.3
-
47
-
-
0033032906
-
A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the Gramicidin A channel
-
Kurnikova M.G., Coalson R.D., Graf P., Nitzan A. A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the Gramicidin A channel. Biophys. J. 1999, 76:642-656.
-
(1999)
Biophys. J.
, vol.76
, pp. 642-656
-
-
Kurnikova, M.G.1
Coalson, R.D.2
Graf, P.3
Nitzan, A.4
-
49
-
-
0028485385
-
The immersed interface method for elliptic equations with discontinuous coefficients and singular sources
-
LeVeque R.J., Li Z.L. The immersed interface method for elliptic equations with discontinuous coefficients and singular sources. SIAM J. Numer. Anal. 1994, 31:1019-1044.
-
(1994)
SIAM J. Numer. Anal.
, vol.31
, pp. 1019-1044
-
-
LeVeque, R.J.1
Li, Z.L.2
-
50
-
-
0022522698
-
Interpretation of biological ion channel flux data-reaction-rate versus continuum theory
-
Levitt D.G. Interpretation of biological ion channel flux data-reaction-rate versus continuum theory. Annu. Rev. Biophys. Biophys. Chem. 1986, 15:29-57.
-
(1986)
Annu. Rev. Biophys. Biophys. Chem.
, vol.15
, pp. 29-57
-
-
Levitt, D.G.1
-
51
-
-
0033010064
-
Modeling of ion channels
-
Levitt D.G. Modeling of ion channels. J. Gen. Physiol. 1999, 113(6):789-794.
-
(1999)
J. Gen. Physiol.
, vol.113
, Issue.6
, pp. 789-794
-
-
Levitt, D.G.1
-
52
-
-
0036208213
-
Maximum principle preserving schemes for interface problems with discontinuous coefficients
-
Li Z.L., Ito K. Maximum principle preserving schemes for interface problems with discontinuous coefficients. SIAM J. Sci. Comput. 2001, 23:339-361.
-
(2001)
SIAM J. Sci. Comput.
, vol.23
, pp. 339-361
-
-
Li, Z.L.1
Ito, K.2
-
53
-
-
30944434458
-
Immersed finite element method and its applications to biological systems
-
Liu W.K., Liu Y., Farrell D., Zhang L., Wang X., Fukui Y., Patankar N., Zhang Y., Bajaj C., Chen X., Hsu H. Immersed finite element method and its applications to biological systems. Comput. Methods Appl. Mech. Eng. 2006, 195:1722-1749.
-
(2006)
Comput. Methods Appl. Mech. Eng.
, vol.195
, pp. 1722-1749
-
-
Liu, W.K.1
Liu, Y.2
Farrell, D.3
Zhang, L.4
Wang, X.5
Fukui, Y.6
Patankar, N.7
Zhang, Y.8
Bajaj, C.9
Chen, X.10
Hsu, H.11
-
54
-
-
21244486362
-
Geometric singular perturbation approach to steady-state Poisson-Nernst-Planck systems
-
Liu W.S. Geometric singular perturbation approach to steady-state Poisson-Nernst-Planck systems. SIAM J. Appl. Math. 2005, 65(3):754-766.
-
(2005)
SIAM J. Appl. Math.
, vol.65
, Issue.3
, pp. 754-766
-
-
Liu, W.S.1
-
55
-
-
0001491689
-
A boundary condition capturing method for Poisson's equation on irregular domains
-
Liu X.D., Fedkiw R.P., Kang M. A boundary condition capturing method for Poisson's equation on irregular domains. J. Comput. Phys. 2000, 160:151-178.
-
(2000)
J. Comput. Phys.
, vol.160
, pp. 151-178
-
-
Liu, X.D.1
Fedkiw, R.P.2
Kang, M.3
-
56
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell A.D., Bashford D., Bellot M., Dunbrack R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Reiher W.E., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiórkiewicz-Kuczera J., Yin D., Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102(18):3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellot, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiórkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
57
-
-
33750621301
-
Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods
-
Mamonov A.B., Kurnikova M.G., Coalson R.D. Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods. Biophys. Chem. 2006, 124:268-278.
-
(2006)
Biophys. Chem.
, vol.124
, pp. 268-278
-
-
Mamonov, A.B.1
Kurnikova, M.G.2
Coalson, R.D.3
-
58
-
-
0000323669
-
Ab initio molecular dynamics: theory and implementation
-
John von Neumann Institute for Computing, Jülich, J. Grotendorst (Ed.) Modern Methods and Algorithms of Quantum Chemistry
-
Marx D., Hutter J. Ab initio molecular dynamics: theory and implementation. NIC Series 2000, vol. 3:329-477. John von Neumann Institute for Computing, Jülich. J. Grotendorst (Ed.).
-
(2000)
NIC Series
, vol.3
, pp. 329-477
-
-
Marx, D.1
Hutter, J.2
-
59
-
-
67049160490
-
A multigrid method for the Poisson-Nernst-Planck equations
-
Mathur S.R., Murthy J.Y. A multigrid method for the Poisson-Nernst-Planck equations. SIAM J. Appl. Math. 2009, 52(17-18):4031-4039.
-
(2009)
SIAM J. Appl. Math.
, vol.52
, Issue.17-18
, pp. 4031-4039
-
-
Mathur, S.R.1
Murthy, J.Y.2
-
60
-
-
0021417514
-
The fast solution of Poisson's and the biharmonic equations on irregular regions
-
Mayo A. The fast solution of Poisson's and the biharmonic equations on irregular regions. SIAM J. Numer. Anal. 1984, 21:285-299.
-
(1984)
SIAM J. Numer. Anal.
, vol.21
, pp. 285-299
-
-
Mayo, A.1
-
61
-
-
33750614424
-
A cartesian grid finite volume method for elliptic equations with variable coefficients and embedded interfaces
-
Oevermann M., Klein R. A cartesian grid finite volume method for elliptic equations with variable coefficients and embedded interfaces. J. Comput. Phys. 2006, 219:749-769.
-
(2006)
J. Comput. Phys.
, vol.219
, pp. 749-769
-
-
Oevermann, M.1
Klein, R.2
-
62
-
-
0017424014
-
Numerical analysis of blood flow in the heart
-
Peskin C.S. Numerical analysis of blood flow in the heart. J. Comput. Phys. 1977, 25(3):220-252.
-
(1977)
J. Comput. Phys.
, vol.25
, Issue.3
, pp. 220-252
-
-
Peskin, C.S.1
-
63
-
-
0003631524
-
-
Sinauer Associates, Sunderland, MA
-
Purves D., Augustine G.J., Fitzpatrick D., Katz L.C., LaMantia A.S., McNamara J.O., Williams S.M. Neuroscience 2001, Sinauer Associates, Sunderland, MA. second ed.
-
(2001)
Neuroscience
-
-
Purves, D.1
Augustine, G.J.2
Fitzpatrick, D.3
Katz, L.C.4
LaMantia, A.S.5
McNamara, J.O.6
Williams, S.M.7
-
64
-
-
0017429069
-
Areas, volumes, packing, and protein structure
-
Richards F.M. Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng. 1977, 6(1):151-176.
-
(1977)
Annu. Rev. Biophys. Bioeng.
, vol.6
, Issue.1
, pp. 151-176
-
-
Richards, F.M.1
-
65
-
-
3142652094
-
Theoretical and computational models of biological ionchannels
-
Roux B., Allen T., Berneche S., Im W. Theoretical and computational models of biological ionchannels. Q. Rev. Biophys. 2004, 7(1):1-103.
-
(2004)
Q. Rev. Biophys.
, vol.7
, Issue.1
, pp. 1-103
-
-
Roux, B.1
Allen, T.2
Berneche, S.3
Im, W.4
-
67
-
-
0030040323
-
Reduced surface: an efficient way to compute molecular surfaces
-
Sanner M.F., Olson A.J., Spehner J.C. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996, 38:305-320.
-
(1996)
Biopolymers
, vol.38
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.C.3
-
68
-
-
0035441903
-
Derivation of Poisson and Nernst-Planck equations in a bath and channel from a molecular model
-
Schuss Z., Nadler B., Eisenberg R. Derivation of Poisson and Nernst-Planck equations in a bath and channel from a molecular model. Phys. Rev. E, Stat. Nonlinear Soft Matter Phys. 2001, 64:036116.
-
(2001)
Phys. Rev. E, Stat. Nonlinear Soft Matter Phys.
, vol.64
, pp. 036116
-
-
Schuss, Z.1
Nadler, B.2
Eisenberg, R.3
-
69
-
-
23844506931
-
Limitations of atom-centered dielectric functions in implicit solvent models
-
Swanson J.M.J., Mongan J., McCammon J.A. Limitations of atom-centered dielectric functions in implicit solvent models. J. Phys. Chem. B 2005, 109(31):14769-14772.
-
(2005)
J. Phys. Chem. B
, vol.109
, Issue.31
, pp. 14769-14772
-
-
Swanson, J.M.J.1
Mongan, J.2
McCammon, J.A.3
-
70
-
-
77951687164
-
An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries
-
Tyagi S., Suzen M., Sega M., Barbosa M., Kantorovich S.S., Holm C. An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries. J. Chem. Phys. 2010, 132(15):154112-154119.
-
(2010)
J. Chem. Phys.
, vol.132
, Issue.15
, pp. 154112-154119
-
-
Tyagi, S.1
Suzen, M.2
Sega, M.3
Barbosa, M.4
Kantorovich, S.S.5
Holm, C.6
-
71
-
-
77955229645
-
Differential geometry based multiscale models
-
Wei G.W. Differential geometry based multiscale models. Bull. Math. Biol. 2010, 72:1562-1622.
-
(2010)
Bull. Math. Biol.
, vol.72
, pp. 1562-1622
-
-
Wei, G.W.1
-
72
-
-
36749034166
-
A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
-
Xie D., Zhou S.Z. A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation. BIT Numer. Math. 2007, 47:853-871.
-
(2007)
BIT Numer. Math.
, vol.47
, pp. 853-871
-
-
Xie, D.1
Zhou, S.Z.2
-
73
-
-
34547352376
-
Treatment of geometric singularities in implicit solvent models
-
Yu S., Geng W., Wei G.W. Treatment of geometric singularities in implicit solvent models. J. Chem. Phys. 2007, 126:244108.
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 244108
-
-
Yu, S.1
Geng, W.2
Wei, G.W.3
-
74
-
-
35348917599
-
Three-dimensional matched interface and boundary (MIB) method for treating geometric singularities
-
Yu S., Wei G.W. Three-dimensional matched interface and boundary (MIB) method for treating geometric singularities. J. Comput. Phys. 2007, 227:602-632.
-
(2007)
J. Comput. Phys.
, vol.227
, pp. 602-632
-
-
Yu, S.1
Wei, G.W.2
-
75
-
-
34248596727
-
Matched interface and boundary (MIB) method for elliptic problems with sharp-edged interfaces
-
Yu S., Zhou Y., Wei G.W. Matched interface and boundary (MIB) method for elliptic problems with sharp-edged interfaces. J. Comput. Phys. 2007, 224(2):729-756.
-
(2007)
J. Comput. Phys.
, vol.224
, Issue.2
, pp. 729-756
-
-
Yu, S.1
Zhou, Y.2
Wei, G.W.3
-
76
-
-
4544354197
-
High-order FDTD methods via derivative matching for Maxwell's equations with material interfaces
-
Zhao S., Wei G.W. High-order FDTD methods via derivative matching for Maxwell's equations with material interfaces. J. Comput. Phys. 2004, 200(1):60-103.
-
(2004)
J. Comput. Phys.
, vol.200
, Issue.1
, pp. 60-103
-
-
Zhao, S.1
Wei, G.W.2
-
77
-
-
64049109900
-
Matched interface and boundary (MIB) for the implementation of boundary conditions in high order central finite differences
-
Zhao S., Wei G.W. Matched interface and boundary (MIB) for the implementation of boundary conditions in high order central finite differences. Int. J. Numer. Methods Eng. 2009, 77:1690-1730.
-
(2009)
Int. J. Numer. Methods Eng.
, vol.77
, pp. 1690-1730
-
-
Zhao, S.1
Wei, G.W.2
-
78
-
-
37649005586
-
Highly accurate biomolecular electrostatics in continuum dielectric environments
-
Zhou Y.C., Feig M., Wei G.W. Highly accurate biomolecular electrostatics in continuum dielectric environments. J. Comput. Chem. 2008, 29:87-97.
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 87-97
-
-
Zhou, Y.C.1
Feig, M.2
Wei, G.W.3
-
79
-
-
33750356476
-
On the fictitious-domain and interpolation formulations of the matched interface and boundary (MIB) method
-
Zhou Y.C., Wei G.W. On the fictitious-domain and interpolation formulations of the matched interface and boundary (MIB) method. J. Comput. Phys. 2006, 219(1):228-246.
-
(2006)
J. Comput. Phys.
, vol.219
, Issue.1
, pp. 228-246
-
-
Zhou, Y.C.1
Wei, G.W.2
-
80
-
-
31744448526
-
High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources
-
Zhou Y.C., Zhao S., Feig M., Wei G.W. High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources. J. Comput. Phys. 2006, 213(1):1-30.
-
(2006)
J. Comput. Phys.
, vol.213
, Issue.1
, pp. 1-30
-
-
Zhou, Y.C.1
Zhao, S.2
Feig, M.3
Wei, G.W.4
-
81
-
-
85033849708
-
Finite-difference solution of the Poisson-Boltzmann equation: complete elimination of self-energy
-
Zhou Z., Payne P., Vasquez M., Kuhn N., Levitt M. Finite-difference solution of the Poisson-Boltzmann equation: complete elimination of self-energy. J. Comput. Chem. 1996, 17:1344-1351.
-
(1996)
J. Comput. Chem.
, vol.17
, pp. 1344-1351
-
-
Zhou, Z.1
Payne, P.2
Vasquez, M.3
Kuhn, N.4
Levitt, M.5
|