-
2
-
-
0000566343
-
Limiting laws and counterion condensation in poly-electrolyte solutions. 8. Mixtures of counterions, specific selectivity, and valence selectivity
-
G.S. Manning Limiting laws and counterion condensation in poly-electrolyte solutions. 8. Mixtures of counterions, specific selectivity, and valence selectivity J. Phys. Chem. US 88 1984 6654 6661
-
(1984)
J. Phys. Chem. US
, vol.88
, pp. 6654-6661
-
-
Manning, G.S.1
-
3
-
-
0017895903
-
The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
-
G.S. Manning The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides Q. Rev. Biophys. 11 1978 179 246
-
(1978)
Q. Rev. Biophys.
, vol.11
, pp. 179-246
-
-
Manning, G.S.1
-
4
-
-
0017411336
-
Theory of the delocalized binding of Mg(II) to DNA: Preliminary analysis for low binding levels
-
G.S. Manning Theory of the delocalized binding of Mg(II) to DNA: preliminary analysis for low binding levels Biophys. Chem. 7 1977 141 145
-
(1977)
Biophys. Chem.
, vol.7
, pp. 141-145
-
-
Manning, G.S.1
-
5
-
-
36848999901
-
Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids
-
Y. Bai, and M. Greenfeld D. Herschlag Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids J. Am. Chem. Soc. 129 2007 14981 14988
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 14981-14988
-
-
Bai, Y.1
Greenfeld, M.2
Herschlag, D.3
-
6
-
-
78649935315
-
Counting ions around DNA with anomalous small-angle x-ray scattering
-
S.A. Pabit, and S.P. Meisburger L. Pollack Counting ions around DNA with anomalous small-angle x-ray scattering J. Am. Chem. Soc. 132 2010 16334 16336
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 16334-16336
-
-
Pabit, S.A.1
Meisburger, S.P.2
Pollack, L.3
-
7
-
-
0038719800
-
A crystallographic study of the binding of 13 metal ions to two related RNA duplexes
-
E. Ennifar, P. Walter, and P. Dumas A crystallographic study of the binding of 13 metal ions to two related RNA duplexes Nucleic Acids Res. 31 2003 2671 2682
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 2671-2682
-
-
Ennifar, E.1
Walter, P.2
Dumas, P.3
-
10
-
-
77954627025
-
Free state conformational sampling of the SAM-I riboswitch aptamer domain
-
C.D. Stoddard, and R.K. Montange R.T. Batey Free state conformational sampling of the SAM-I riboswitch aptamer domain Structure 18 2010 787 797
-
(2010)
Structure
, vol.18
, pp. 787-797
-
-
Stoddard, C.D.1
Montange, R.K.2
Batey, R.T.3
-
11
-
-
33751552991
-
Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
-
K.A. Sharp, and B. Honig Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation J. Phys. Chem. U.S. 94 1990 7684 7692
-
(1990)
J. Phys. Chem. U.S.
, vol.94
, pp. 7684-7692
-
-
Sharp, K.A.1
Honig, B.2
-
12
-
-
0025283002
-
Electrostatic interactions in macromolecules: Theory and applications
-
K.A. Sharp, and B. Honig Electrostatic interactions in macromolecules: theory and applications Annu. Rev. Biophys. Biophys. Chem. 19 1990 301 332
-
(1990)
Annu. Rev. Biophys. Biophys. Chem.
, vol.19
, pp. 301-332
-
-
Sharp, K.A.1
Honig, B.2
-
13
-
-
2342454337
-
Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation
-
A.H. Boschitsch, and M.O. Fenley Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation J. Comput. Chem. 25 2004 935 955
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 935-955
-
-
Boschitsch, A.H.1
Fenley, M.O.2
-
14
-
-
33947707250
-
A new outer boundary formulation and energy corrections for the nonlinear Poisson-Boltzmann equation
-
A.H. Boschitsch, and M.O. Fenley A new outer boundary formulation and energy corrections for the nonlinear Poisson-Boltzmann equation J. Comput. Chem. 28 2007 909 921
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 909-921
-
-
Boschitsch, A.H.1
Fenley, M.O.2
-
15
-
-
79955915303
-
A fast and robust Poisson-Boltzmann solver based on adaptive Cartesian grids
-
A.H. Boschitsch, and M.O. Fenley A fast and robust Poisson-Boltzmann solver based on adaptive Cartesian grids J. Chem. Theory Comput. 7 2011 1524 1540
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1524-1540
-
-
Boschitsch, A.H.1
Fenley, M.O.2
-
16
-
-
0035913537
-
Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
-
W. Rocchia, E. Alexov, and B. Honig Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions J. Phys. Chem. B 105 2001 6507 6514
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6507-6514
-
-
Rocchia, W.1
Alexov, E.2
Honig, B.3
-
18
-
-
14544303670
-
Recognition of the spliceosomal branch site RNA helix on the basis of surface and electrostatic features
-
D. Xu, N.L. Greenbaum, and M.O. Fenley Recognition of the spliceosomal branch site RNA helix on the basis of surface and electrostatic features Nucleic Acids Res. 33 2005 1154 1161
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 1154-1161
-
-
Xu, D.1
Greenbaum, N.L.2
Fenley, M.O.3
-
19
-
-
34547119333
-
The electrostatic characteristics of G·U wobble base pairs
-
D. Xu, and T. Landon M.O. Fenley The electrostatic characteristics of G·U wobble base pairs Nucleic Acids Res. 35 2007 3836 3847
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 3836-3847
-
-
Xu, D.1
Landon, T.2
Fenley, M.O.3
-
20
-
-
6244273869
-
Steric effects in electrolytes: A modified Poisson-Boltzmann equation
-
I. Borukhov, D. Andelman, and H. Orland Steric effects in electrolytes: a modified Poisson-Boltzmann equation Phys. Rev. Lett. 79 1997 435 438
-
(1997)
Phys. Rev. Lett.
, vol.79
, pp. 435-438
-
-
Borukhov, I.1
Andelman, D.2
Orland, H.3
-
21
-
-
38949141177
-
Continuum molecular electrostatics, salt effects, and counterion binding - A review of the Poisson-Boltzmann theory and its modifications
-
P. Grochowski, and J. Trylska Continuum molecular electrostatics, salt effects, and counterion binding - a review of the Poisson-Boltzmann theory and its modifications Biopolymers 89 2008 93 113
-
(2008)
Biopolymers
, vol.89
, pp. 93-113
-
-
Grochowski, P.1
Trylska, J.2
-
22
-
-
78651328563
-
Comparing the predictions of the nonlinear Poisson-Boltzmann equation and the ion size-modified Poisson-Boltzmann equation for a low-dielectric charged spherical cavity in an aqueous salt solution
-
A.R.J. Silalahi, and A.H. Boschitsch M.O. Fenley Comparing the predictions of the nonlinear Poisson-Boltzmann equation and the ion size-modified Poisson-Boltzmann equation for a low-dielectric charged spherical cavity in an aqueous salt solution J. Chem. Theory Comput. 6 2010 3631 3639
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3631-3639
-
-
Silalahi, A.R.J.1
Boschitsch, A.H.2
Fenley, M.O.3
-
23
-
-
36048952831
-
Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory
-
V.B. Chu, and Y. Bai S. Doniach Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory Biophys. J. 93 2007 3202 3209
-
(2007)
Biophys. J.
, vol.93
, pp. 3202-3209
-
-
Chu, V.B.1
Bai, Y.2
Doniach, S.3
-
24
-
-
67651163671
-
Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA
-
S.A. Pabit, and X.Y. Qiu L. Pollack Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA Nucleic Acids Res. 37 2009 3887 3896
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 3887-3896
-
-
Pabit, S.A.1
Qiu, X.Y.2
Pollack, L.3
-
25
-
-
33746907422
-
Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure
-
J.P. Piquemal, and L. Perera T.A. Darden Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: from energetics to structure J. Chem. Phys. 125 2006 054511
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 054511
-
-
Piquemal, J.P.1
Perera, L.2
Darden, T.A.3
-
26
-
-
33749646478
-
2+ solvation using polarizable atomic multipole potential
-
2+ solvation using polarizable atomic multipole potential J. Phys. Chem. B 110 2006 18553 18559
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 18553-18559
-
-
Jiao, D.1
King, C.2
Ren, P.3
-
27
-
-
84857311171
-
RNA and its ionic cloud: Solution scattering experiments and atomically detailed simulations
-
S. Kirmizialtin, and S.A. Pabbitt R. Elber RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations Biophys. J. 102 2012 819 828
-
(2012)
Biophys. J.
, vol.102
, pp. 819-828
-
-
Kirmizialtin, S.1
Pabbitt, S.A.2
Elber, R.3
-
28
-
-
33751005022
-
Condensation of monovalent counterions around DNA
-
A. Savelyev, and G.A. Papoian Condensation of monovalent counterions around DNA J. Am. Chem. Soc. 128 2006 815 824
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 815-824
-
-
Savelyev, A.1
Papoian, G.A.2
-
29
-
-
77956565237
-
Simulations of RNA interactions with monovalent ions
-
H. Daniel, Academic Press New York
-
A.A. Chen, and M. Marucho R.V. Pappu Simulations of RNA interactions with monovalent ions H. Daniel, Methods in Enzymology 2009 Academic Press New York 411 432
-
(2009)
Methods in Enzymology
, pp. 411-432
-
-
Chen, A.A.1
Marucho, M.2
Pappu, R.V.3
-
31
-
-
84956269912
-
Polyelectrolyte solutions between charged surfaces
-
I. Borukhov, D. Andelman, and H. Orland Polyelectrolyte solutions between charged surfaces EuroPhys Lett. 32 1995 499
-
(1995)
EuroPhys Lett.
, vol.32
, pp. 499
-
-
Borukhov, I.1
Andelman, D.2
Orland, H.3
-
33
-
-
76749157270
-
AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation
-
P. Koehl, and M.M. Delarue AQUASOL: an efficient solver for the dipolar Poisson-Boltzmann-Langevin equation J. Chem. Phys. 132 2010 064101 064116
-
(2010)
J. Chem. Phys.
, vol.132
, pp. 064101-064116
-
-
Koehl, P.1
Delarue, M.M.2
-
34
-
-
0037076079
-
Fast boundary element method for the linear Poisson-Boltzmann equation
-
A.H. Boschitsch, M.O. Fenley, and H.-X. Zhou Fast boundary element method for the linear Poisson-Boltzmann equation J. Phys. Chem. B 106 2003 2741 2754
-
(2003)
J. Phys. Chem. B
, vol.106
, pp. 2741-2754
-
-
Boschitsch, A.H.1
Fenley, M.O.2
Zhou, H.-X.3
-
35
-
-
34249039431
-
Do electrostatic interactions destabilize protein-nucleic acid binding?
-
S. Qin, and H.-X. Zhou Do electrostatic interactions destabilize protein-nucleic acid binding? Biopolymers 86 2007 112 118
-
(2007)
Biopolymers
, vol.86
, pp. 112-118
-
-
Qin, S.1
Zhou, H.-X.2
-
36
-
-
0000216904
-
Local dielectric environment of B-DNA in solution: Results from a 14 ns molecular dynamics trajectory
-
M.A. Young, B. Jayaram, and D.L. 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
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 7666-7669
-
-
Young, M.A.1
Jayaram, B.2
Beveridge, D.L.3
-
37
-
-
77953802958
-
Computational exploration of mobile ion distributions around RNA duplex
-
S. Kirmizialtin, and R. Elber Computational exploration of mobile ion distributions around RNA duplex J. Phys. Chem. B 114 2010 8207 8220
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 8207-8220
-
-
Kirmizialtin, S.1
Elber, R.2
-
38
-
-
58749107160
-
Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics
-
C. Azuara, and H. Orland M. Delarue Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics Biophys. J. 95 2008 5587 5605
-
(2008)
Biophys. J.
, vol.95
, pp. 5587-5605
-
-
Azuara, C.1
Orland, H.2
Delarue, M.3
-
39
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Y. Sugita, and Y. Okamoto Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 314 1999 141 151
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
40
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
W.L. Jorgensen, and J. Chandrasekhar M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Klein, M.L.3
-
41
-
-
84857250215
-
MOIL: A molecular dynamics program with emphasis on conformational searches and reaction path calculations
-
S. Doniach, Plenum Press New York
-
R. Elber, and A. Roitberg A. Ulitsky MOIL: a molecular dynamics program with emphasis on conformational searches and reaction path calculations S. Doniach, NATO ASI Series Series B Physics; Statistical Mechanistics, Protein Structure, and Protein Substrate Interactions 1994 Plenum Press New York 165 191
-
(1994)
NATO ASI Series Series B Physics; Statistical Mechanistics, Protein Structure, and Protein Substrate Interactions
, pp. 165-191
-
-
Elber, R.1
Roitberg, A.2
Ulitsky, A.3
-
42
-
-
0025728614
-
OPLS potential functions for nucleotide bases - Relative association constants of hydrogen-bonded base-pairs in chloroform
-
J. Pranata, S.G. Wierschke, and W.L. Jorgensen OPLS potential functions for nucleotide bases - relative association constants of hydrogen-bonded base-pairs in chloroform J. Am. Chem. Soc. 113 1991 2810 2819
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 2810-2819
-
-
Pranata, J.1
Wierschke, S.G.2
Jorgensen, W.L.3
-
43
-
-
33646940952
-
Numerical integration of Cartesian equations of motion of a system with constraints - Molecular dynamics of n-alkanes
-
J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of Cartesian equations of motion of a system with constraints - molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
44
-
-
20344362895
-
Revisiting and parallelizing SHAKE
-
Y. Weinbach, and R. Elber Revisiting and parallelizing SHAKE J. Comput. Phys. 209 2005 193 206
-
(2005)
J. Comput. Phys.
, vol.209
, pp. 193-206
-
-
Weinbach, Y.1
Elber, R.2
-
46
-
-
0032851951
-
Sodium and chlorine ions as part of the DNA solvation shell
-
M. Feig, and B.M. Pettitt Sodium and chlorine ions as part of the DNA solvation shell Biophys. J. 77 1999 1769 1781
-
(1999)
Biophys. J.
, vol.77
, pp. 1769-1781
-
-
Feig, M.1
Pettitt, B.M.2
-
48
-
-
0032707625
-
Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function
-
K. Chin, and K.A. Sharp A.M. Pyle Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function Nat. Struct. Biol. 6 1999 1055 1061
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 1055-1061
-
-
Chin, K.1
Sharp, K.A.2
Pyle, A.M.3
-
51
-
-
51949119253
-
Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble
-
Y. Bai, and V.B. Chu S. Doniach Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble J. Am. Chem. Soc. 130 2008 12334 12341
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 12334-12341
-
-
Bai, Y.1
Chu, V.B.2
Doniach, S.3
|