-
6
-
-
33646063018
-
-
DelPhi V3.0; Columbia University, New York
-
Nicholls, A.; Sharp, K. A.; Honig, B. DelPhi V3.0; Columbia University, New York, 1990.
-
(1990)
-
-
Nicholls, A.1
Sharp, K.A.2
Honig, B.3
-
7
-
-
33751385054
-
-
Honig, B.; Sharp, K.; Yana, A. S. J. Pliys. Client. 1993, 97, 1101.
-
(1993)
J. Pliys. Client.
, vol.97
, pp. 1101
-
-
Honig, B.1
Sharp, K.2
Yana, A.S.3
-
12
-
-
0033014096
-
-
Nonner, W.; Chen, D. P.; Eisenberg, R. S. J. Gen. Physiol. 1999, 113, 773.
-
(1999)
J. Gen. Physiol.
, vol.113
, pp. 773
-
-
Nonner, W.1
Chen, D.P.2
Eisenberg, R.S.3
-
16
-
-
0033032906
-
-
Kurnikova, M. G.; Coalson, R. D.; Graf, P.; Nitzan, A. Biophys. J. 1999, 76, 642.
-
(1999)
Biophys. J.
, vol.76
, pp. 642
-
-
Kurnikova, M.G.1
Coalson, R.D.2
Graf, P.3
Nitzan, A.4
-
18
-
-
0034207477
-
-
Hollerbach, U.; Chen, D. P.; Busath, D. D.; Eisenberg, B. Langmuir 2000, 16, 5509.
-
(2000)
Langmuir
, vol.16
, pp. 5509
-
-
Hollerbach, U.1
Chen, D.P.2
Busath, D.D.3
Eisenberg, B.4
-
19
-
-
0000391365
-
-
and references therein
-
See, e.g., Caillol, J. M. J. Chem. Phys. 1999, 111, 6528, and references therein.
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 6528
-
-
Caillol, J.M.1
-
20
-
-
0031870447
-
-
Chung, S.-Ho; Hoyles, M.; Allen, T.; Kuyucak, S. Biophys. J. 1998, 75, 793.
-
(1998)
Biophys. J.
, vol.75
, pp. 793
-
-
Chung, S.-H.1
Hoyles, M.2
Allen, T.3
Kuyucak, S.4
-
21
-
-
0032158469
-
-
Hoyles, M.; Kuyucak, S.; Chung, S.-Ho Phys. Rev. E 1998, 55, 3654.
-
(1998)
Phys. Rev. E
, vol.55
, pp. 3654
-
-
Hoyles, M.1
Kuyucak, S.2
Chung, S.-H.3
-
22
-
-
0032827130
-
-
Corry, B.; Kuyucak, S.; Chung, S.-Ho J. Gen. Physiol. 1999,114, 597.
-
(1999)
J. Gen. Physiol.
, vol.114
, pp. 597
-
-
Corry, B.1
Kuyucak, S.2
Chung, S.-H.3
-
23
-
-
0032708637
-
-
Chung, S. H.; Allen, T. W.; Hoyles, M.; Kuyucak, S. Biophys. J. 1999, 77, 2517.
-
(1999)
Biophys. J.
, vol.77
, pp. 2517
-
-
Chung, S.H.1
Allen, T.W.2
Hoyles, M.3
Kuyucak, S.4
-
24
-
-
0000127690
-
-
Allen, T. W.; Hoyles, M.; Kuyucak, S.; Chung, S. H. Chem. Phys. Lett. 1999, 313, 358.
-
(1999)
Chem. Phys. Lett.
, vol.313
, pp. 358
-
-
Allen, T.W.1
Hoyles, M.2
Kuyucak, S.3
Chung, S.H.4
-
25
-
-
0034106946
-
-
describes Brownian dynamics simulations of ion transport through a pore with comparison to mean field (PB and PNP) calculations. Our methodology is different from the approach taken in these papers. Nevertheless our results are consistent with the observations made in these works
-
Three relevant papers have appeared after our paper was submitted, (a) Moy, G.; Corry, B.; Kuyucak, S.; Chung, S.-Ho Biophys. J. 2000, 78, 2349-2363,2364-2381, describes Brownian dynamics simulations of ion transport through a pore with comparison to mean field (PB and PNP) calculations. Our methodology is different from the approach taken in these papers. Nevertheless our results are consistent with the observations made in these works.
-
(2000)
Biophys. J.
, vol.78
, pp. 2349-2363
-
-
Moy, G.1
Corry, B.2
Kuyucak, S.3
Chung, S.-H.4
-
26
-
-
0033884302
-
-
describes a Brownian dynamics simulation of ion motion in a Porin channel. In this paper dielectric effects on self-energy and interparticle interactions of mobile ions are disregarded
-
(b) Im, W.; Seefeld, S.; Roux, B. Biophys. J. 2000, 79, 788, describes a Brownian dynamics simulation of ion motion in a Porin channel. In this paper dielectric effects on self-energy and interparticle interactions of mobile ions are disregarded.
-
(2000)
Biophys. J.
, vol.79
, pp. 788
-
-
Im, W.1
Seefeld, S.2
Roux, B.3
-
27
-
-
0028901238
-
-
Elber, R.; Chen, D. P.; Rojewska, D.; Eisenberg, R. Biophys. J. 1995, 68, 906.
-
(1995)
Biophys. J.
, vol.68
, pp. 906
-
-
Elber, R.1
Chen, D.P.2
Rojewska, D.3
Eisenberg, R.4
-
30
-
-
0028430608
-
-
Knödler, D.; Pendzig, P.; Dieterich, W. 1994, 70, 356.
-
(1994)
, vol.70
, pp. 356
-
-
Knödler, D.1
Pendzig, P.2
Dieterich, W.3
-
31
-
-
33646049508
-
-
Knödler, D.; Dieterich, W.; Lonsky, C.; Nitzan, A. J. Client. Phys. 1995, 702, 465.
-
(1995)
J. Client. Phys.
, vol.702
, pp. 465
-
-
Knödler, D.1
Dieterich, W.2
Lonsky, C.3
Nitzan, A.4
-
32
-
-
0000310928
-
-
Pendzig, P.; Dieterich, W.; Nitzan, A. J. Noncryst. Solids. 1998, 235, 748.
-
(1998)
J. Noncryst. Solids.
, vol.235
, pp. 748
-
-
Pendzig, P.1
Dieterich, W.2
Nitzan, A.3
-
33
-
-
0001525103
-
-
For an impressive demonstration of such a program in the study of fracture dynamics in silicon see: Abraham, F. F.; Broughton, J. Q.; Bernstein, N.; Kaxiras, E. Comput. Phys. 1998, 12, 538.
-
(1998)
Comput. Phys.
, vol.12
, pp. 538
-
-
Abraham, F.F.1
Broughton, J.Q.2
Bernstein, N.3
Kaxiras, E.4
-
34
-
-
0033019968
-
-
A description of an equilibrium ionic channel in which the system is separated into an inner and an outer subsystems was recently presented by: Roux, B. Biophys. J. 1999, 77, 139.
-
(1999)
Biophys. J.
, vol.77
, pp. 139
-
-
Roux, B.1
-
35
-
-
36448999716
-
-
See, e.g.: Barcilon, V.; Chen, D.; Eisenberg, R. S.; Ratner, M. A. J. Chem. Phys. 1993, 98, 1193.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 1193
-
-
Barcilon, V.1
Chen, D.2
Eisenberg, R.S.3
Ratner, M.A.4
-
39
-
-
33646031336
-
-
In the application of these periodic boundary conditions in the present work the corresponding interion interactions were computed with the minimum image approximation
-
In the application of these periodic boundary conditions in the present work the corresponding interion interactions were computed with the minimum image approximation.
-
-
-
-
40
-
-
0002621511
-
-
For example, composite grids could be used: one grid for the calculation of the electrostatic potential and a different, finer grid to represent ion configuration and ionic motion where the ion occupies more than a single grid cell. For the use of composite grids in electrostatic calculations see: Beck, T. L. J. Comput. Chem. 1999, 20, 1731-1739.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1731-1739
-
-
Beck, T.L.1
-
42
-
-
0001835044
-
-
Monte Carlo Investigations of Phase Transitions and Critical Phenomena. Academic Press: New York, Chapter 1
-
See, e.g.: Binder, K. Monte Carlo Investigations of Phase Transitions and Critical Phenomena. Phase Transitions and Critical Phenomena; Academic Press: New York, 1976; Vol. 5b, Chapter 1, pp 1-105.
-
(1976)
Phase Transitions and Critical Phenomena
, vol.5 B
, pp. 1-105
-
-
Binder, K.1
-
43
-
-
85088886880
-
-
2/(2a))(1/ε - 1)
-
2/(2a))(1/ε - 1).
-
-
-
-
44
-
-
0001539165
-
-
and references therein. Controlling these errors is important in situations where system properties are dominated by the balance between opposing interactions, e.g., Coulombic repulsion vs dielectric attraction in solvated ions of the same charge sign
-
Using Coulomb potentials with a cutoff is a potential source of error. Alternatively, using Ewald summation in inhomogeneous restricted geometry systems (in our case a 2-dimensional Ewald summation is required) is computationally very demanding. Moreover, the inhomogeneous net charge distribution of mobile ions in our system would lead to unphysical interactions between periodic extensions of the system in the Ewald method. There are indications that the errors introduced by using Coulomb interactions with cutoff are not very large for many applications, see, e.g.: Schweighofer, K.; Benjamin, I. J. Chem. Phys. 2000,112, 1474-1482 and references therein. Controlling these errors is important in situations where system properties are dominated by the balance between opposing interactions, e.g., Coulombic repulsion vs dielectric attraction in solvated ions of the same charge sign
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 1474-1482
-
-
Schweighofer, K.1
Benjamin, I.2
-
46
-
-
85088886622
-
-
note
-
c.
-
-
-
-
47
-
-
85088886806
-
-
(0) reflects in the usual way the periodic boundary condition in the x- and y-direction and the finite system size in the z-direction
-
(0) reflects in the usual way the periodic boundary condition in the x- and y-direction and the finite system size in the z-direction.
-
-
-
-
48
-
-
85088886817
-
-
6
-
6
-
-
-
-
49
-
-
33646030745
-
-
note
-
The unphysical image of polarization charges, induced by individual ions on the internal dielectric interfaces, on the imposed boundaries is not eliminated by this procedure. If, however, the imposed boundaries are far from the dielectric interfaces the resulting unphysical contribution to the total energy is small.
-
-
-
-
50
-
-
0004179874
-
-
Wiley: New York
-
2 = |r - (0, d)| are the distances between point r and the charges q and q′, respectively. (Note that we compute here only the polarization contribution to the potential Φ. These expressions, which diverge on the interface, become valid far enough (from distances of order a, or our grid spacing) from the interface.
-
(1975)
Classical Electrodynamics, 2nd Ed.
-
-
Jackson, J.D.1
-
52
-
-
33646018762
-
-
As in section 6b, a part that is not eliminated comes from the image of the polarization charges induced at the internal dielectric boundaries; however, this contribution can be made small (see footnote 47)
-
As in section 6b, a part that is not eliminated comes from the image of the polarization charges induced at the internal dielectric boundaries; however, this contribution can be made small (see footnote 47).
-
-
-
-
53
-
-
85088886533
-
-
B = 80 is used in all calculations reported here, because in anticipated applications ions reside in a water environment
-
B = 80 is used in all calculations reported here, because in anticipated applications ions reside in a water environment.
-
-
-
-
54
-
-
0003668078
-
-
Elsevier: Amsterdam, This would, however, raise the issue of validity of the PB approximation for computing solvation energies near a system's boundary
-
An alternative procedure would be to calculate the contribution of the outer medium to the solvation energy of an ion near the boundary using, e.g., a Poisson-Boltzmann description of the outer medium (see, e.g.: Sadus, R. J. Molecular Simulations of Fluids; Elsevier: Amsterdam, 1999). This would, however, raise the issue of validity of the PB approximation for computing solvation energies near a system's boundary.
-
(1999)
Molecular Simulations of Fluids
-
-
Sadus, R.J.1
-
56
-
-
0000937109
-
-
Mafé, S.; Pellicer, J.; Aguilella, V. M. J. Phys. Chem. 1986, 90, 6045.
-
(1986)
J. Phys. Chem.
, vol.90
, pp. 6045
-
-
Mafé, S.1
Pellicer, J.2
Aguilella, V.M.3
-
57
-
-
0023312268
-
-
Aguilella, V. M.; Mafé, S.; Pellicer, J. Electrochim. Ada 1987, 32, 483.
-
(1987)
Electrochim. Ada
, vol.32
, pp. 483
-
-
Aguilella, V.M.1
Mafé, S.2
Pellicer, J.3
-
58
-
-
0024976565
-
-
Riveros, O. J.; Croxton, T. L.; Armstrong, W. McD. J. Theor. Biol. 1989, 140, 221.
-
(1989)
J. Theor. Biol.
, vol.140
, pp. 221
-
-
Riveros, O.J.1
Croxton, T.L.2
McD, A.W.3
-
59
-
-
33646070718
-
-
In fact, the correspondence between the two approaches is not complete because the PNP theory disregards the retarding effect of the ionic solvation atmosphere on an ion's motion. This retardation affects the conductivity of a dilute homogeneous electrolyte solution by a few percent
-
In fact, the correspondence between the two approaches is not complete because the PNP theory disregards the retarding effect of the ionic solvation atmosphere on an ion's motion. This retardation affects the conductivity of a dilute homogeneous electrolyte solution by a few percent.
-
-
-
-
60
-
-
85088887536
-
-
R = 0.096 M that correspond to the bulk concentration obtained in the equilibrium DLMC simulation. See Figure 5 and ensuing discussion
-
R = 0.096 M that correspond to the bulk concentration obtained in the equilibrium DLMC simulation. See Figure 5 and ensuing discussion.
-
-
-
-
61
-
-
0032989631
-
-
Dieckmann, G. R.; Lear, J. D.; Zhong, Q.; Klein, M. L.; DeGrado, W. F.; Sharp, K. A. Biophys. J. 1999, 76, 618.
-
(1999)
Biophys. J.
, vol.76
, pp. 618
-
-
Dieckmann, G.R.1
Lear, J.D.2
Zhong, Q.3
Klein, M.L.4
Degrado, W.F.5
Sharp, K.A.6
-
62
-
-
0020538940
-
-
In realistic biological channels, which may contain internal structural barriers, blocking of ionic motion as a result of ions being trapped for a relatively long time inside the channel may actually lead to a sublinear I/ΔΦ characteristic. See, e.g.: Andersen, O. S. Biophys. J. 1983, 41, 135.
-
(1983)
Biophys. J.
, vol.41
, pp. 135
-
-
Andersen, O.S.1
-
63
-
-
0010624785
-
-
Sham, Y. Y.; Muegge, I.; Warshel, A. Biophys. J. 1998, 74, 1744-1753.
-
(1998)
Biophys. J.
, vol.74
, pp. 1744-1753
-
-
Sham, Y.Y.1
Muegge, I.2
Warshel, A.3
-
64
-
-
0032031405
-
-
(b) Muegge, I.; Schweins, T.; Warshel, A. Proteins: Struct. Fund. Genet. 1998, 30, 407-423.
-
(1998)
Proteins: Struct. Fund. Genet.
, vol.30
, pp. 407-423
-
-
Muegge, I.1
Schweins, T.2
Warshel, A.3
-
66
-
-
0004161838
-
-
Cambridge University Press: London
-
See, e.g.: Press: W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. P. Numerical Recipes in FORTRAN: The An of Scientific Computing, 2nd ed.; Cambridge University Press: London, 1992.
-
(1992)
Numerical Recipes in FORTRAN: the An of Scientific Computing, 2nd Ed.
-
-
Press, W.H.1
Teukolsky, S.A.2
Vetterling, W.T.3
Flannery, B.P.P.4
|