-
1
-
-
0035327194
-
Interfacing molecular dynamics with continuum dynamics in computer simulation: towards an application to biological membranes
-
Ayton G., Bardenhagen S., et al. Interfacing molecular dynamics with continuum dynamics in computer simulation: towards an application to biological membranes. IBM J. Res. Dev. 45 (2001) 417-426
-
(2001)
IBM J. Res. Dev.
, vol.45
, pp. 417-426
-
-
Ayton, G.1
Bardenhagen, S.2
-
2
-
-
22244446431
-
Coupling field theory with continuum mechanics: a simulation of domain formation in giant unilamellar vesicles
-
Ayton G.S., McWhirter J.L., et al. Coupling field theory with continuum mechanics: a simulation of domain formation in giant unilamellar vesicles. Biophys. J. 88 (2005) 3855-3869
-
(2005)
Biophys. J.
, vol.88
, pp. 3855-3869
-
-
Ayton, G.S.1
McWhirter, J.L.2
-
3
-
-
36049017896
-
A second generation mesoscopic lipid bilayer model: connections to field-theory descriptions of membranes and nonlocal hydrodynamics J
-
Ayton G.S., McWhirter J.L., et al. A second generation mesoscopic lipid bilayer model: connections to field-theory descriptions of membranes and nonlocal hydrodynamics J. Chem. Phys. 124 (2005) 064906
-
(2005)
Chem. Phys.
, vol.124
, pp. 064906
-
-
Ayton, G.S.1
McWhirter, J.L.2
-
4
-
-
0036200766
-
Calculating the bulk modulus for a lipid bilayer using non-equilibrium molecular dynamics
-
Ayton G., Smondyrev A.M., et al. Calculating the bulk modulus for a lipid bilayer using non-equilibrium molecular dynamics. Biophys. J. 82 (2002) 1226-1238
-
(2002)
Biophys. J.
, vol.82
, pp. 1226-1238
-
-
Ayton, G.1
Smondyrev, A.M.2
-
5
-
-
0035997053
-
Interfacing molecular dynamics and macro-scale simulations for lipid bilayer vesicles
-
Ayton G., Smondyrev A.M., et al. Interfacing molecular dynamics and macro-scale simulations for lipid bilayer vesicles. Biophys. J. 83 (2002) 1026-1038
-
(2002)
Biophys. J.
, vol.83
, pp. 1026-1038
-
-
Ayton, G.1
Smondyrev, A.M.2
-
6
-
-
1842528793
-
A new perspective on the coarse-grained dynamics of fluids
-
Ayton G.S., Tepper H., et al. A new perspective on the coarse-grained dynamics of fluids. J. Chem. Phys. 120 (2004) 4074-4088
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 4074-4088
-
-
Ayton, G.S.1
Tepper, H.2
-
7
-
-
0036928383
-
Bridging microscopic and mesoscopic simulations of lipid bilayers
-
Ayton G., and Voth G.A. Bridging microscopic and mesoscopic simulations of lipid bilayers. Biophys. J. 83 (2002) 3357-3370
-
(2002)
Biophys. J.
, vol.83
, pp. 3357-3370
-
-
Ayton, G.1
Voth, G.A.2
-
8
-
-
16344393515
-
The simulation of biomolecular systems at multiple length and timescales
-
Ayton G.S., and Voth G.A. The simulation of biomolecular systems at multiple length and timescales. Int. J. Mult. Comp. Eng. 2 (2004) 291-311
-
(2004)
Int. J. Mult. Comp. Eng.
, vol.2
, pp. 291-311
-
-
Ayton, G.S.1
Voth, G.A.2
-
9
-
-
33644644163
-
Insertion and assembly of membrane proteins via simulation
-
Bond P.J., and Sansom M.S.P. Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 128 (2006) 2697-2704
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 2697-2704
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
10
-
-
0001482698
-
Frequency spectrum of the flicker phenomenon in erythrocytes
-
Brochard F., and Lennon J.F. Frequency spectrum of the flicker phenomenon in erythrocytes. J. Phys. (France) 11 (1975) 1035-1047
-
(1975)
J. Phys. (France)
, vol.11
, pp. 1035-1047
-
-
Brochard, F.1
Lennon, J.F.2
-
11
-
-
34548090976
-
Multiscale coupling of mesoscopic and atomistic-level lipid bilayer simulations
-
Chang R., Ayton G.S., et al. Multiscale coupling of mesoscopic and atomistic-level lipid bilayer simulations. J. Chem. Phys. 122 (2005) 244716
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 244716
-
-
Chang, R.1
Ayton, G.S.2
-
12
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell W.D., Cieplak P., et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
-
13
-
-
0037159065
-
A second generation multistate empirical valence bond model for proton transport in aqueous systems
-
Day T.F., Soudackov A.V., et al. A second generation multistate empirical valence bond model for proton transport in aqueous systems. J. Chem. Phys. 117 (2002) 5839-5849
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 5839-5849
-
-
Day, T.F.1
Soudackov, A.V.2
-
14
-
-
0037864422
-
Continuum-particle hybrid coupling for mass, momentum, and energy transfers in unsteady fluid flow
-
Delgado-Buscalioni R., and Coveney P.V. Continuum-particle hybrid coupling for mass, momentum, and energy transfers in unsteady fluid flow. Phys. Rev. E 67 (2003) 046704
-
(2003)
Phys. Rev. E
, vol.67
, pp. 046704
-
-
Delgado-Buscalioni, R.1
Coveney, P.V.2
-
15
-
-
0026785994
-
The transmembrane domain of influenza A M2 protein forms amantadine-sensitive proton channels in planar lipid bilayer
-
Duff K.C., and Ashley R.H. The transmembrane domain of influenza A M2 protein forms amantadine-sensitive proton channels in planar lipid bilayer. Virology 190 (1992) 485-489
-
(1992)
Virology
, vol.190
, pp. 485-489
-
-
Duff, K.C.1
Ashley, R.H.2
-
16
-
-
36549093652
-
The Nose-Hoover thermostat
-
Evans D.J., and Holian B.L. The Nose-Hoover thermostat. J. Chem. Phys. 83 (1985) 4069-4074
-
(1985)
J. Chem. Phys.
, vol.83
, pp. 4069-4074
-
-
Evans, D.J.1
Holian, B.L.2
-
17
-
-
0036864627
-
The fluctuation theorem
-
Evans D.J., and Searles D.J. The fluctuation theorem. Adv. Phys. 51 (2002) 1529-1585
-
(2002)
Adv. Phys.
, vol.51
, pp. 1529-1585
-
-
Evans, D.J.1
Searles, D.J.2
-
18
-
-
0029767694
-
On simulating lipid bilayers with an applied surface tension: Periodic boundary conditions and undulations
-
Feller S.E., and Pastor R.W. On simulating lipid bilayers with an applied surface tension: Periodic boundary conditions and undulations. Biophys. J. 71 (1996) 1350-1355
-
(1996)
Biophys. J.
, vol.71
, pp. 1350-1355
-
-
Feller, S.E.1
Pastor, R.W.2
-
19
-
-
0032614136
-
Constant surface tension simulations of lipid bilayers: the sensitivity of surface areas and compressibilities
-
Feller S.E., and Pastor R.W. Constant surface tension simulations of lipid bilayers: the sensitivity of surface areas and compressibilities. J. Chem. Phys. 111 (1999) 1281-1287
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 1281-1287
-
-
Feller, S.E.1
Pastor, R.W.2
-
20
-
-
36449007043
-
Computer simulation of liquid/liquid interfaces II : surface tension-area dependence of a bilayer and monolayer
-
Feller S.E., Zhang Y., et al. Computer simulation of liquid/liquid interfaces II : surface tension-area dependence of a bilayer and monolayer. J. Chem. Phys. 103 (1995) 10267-10276
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 10267-10276
-
-
Feller, S.E.1
Zhang, Y.2
-
21
-
-
0034030929
-
Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer
-
Forrest L.R., Kukol A., et al. Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer. Biophys. J. 78 (2000) 55-69
-
(2000)
Biophys. J.
, vol.78
, pp. 55-69
-
-
Forrest, L.R.1
Kukol, A.2
-
22
-
-
0031386328
-
From semi-flexible polymers to membranes: anomalous diffusion and reputation
-
Granek R. From semi-flexible polymers to membranes: anomalous diffusion and reputation. J. Phys. (France) 7 (1997) 1761-1788
-
(1997)
J. Phys. (France)
, vol.7
, pp. 1761-1788
-
-
Granek, R.1
-
23
-
-
33645519597
-
A role for direct interactions in the modulation of rhodopsin by ω-3 polyunsaturated lipids
-
Grossfield A., Feller S.E., et al. A role for direct interactions in the modulation of rhodopsin by ω-3 polyunsaturated lipids. Proc. Nat. Acad. Sci. 103 (2006) 4888-4893
-
(2006)
Proc. Nat. Acad. Sci.
, vol.103
, pp. 4888-4893
-
-
Grossfield, A.1
Feller, S.E.2
-
24
-
-
0035039272
-
Structural determinants of Mscl gating studied by molecular dynamics simulations
-
Gullingsrud J., Kosztin D., et al. Structural determinants of Mscl gating studied by molecular dynamics simulations. Biophys. J. 80 (2001) 2074-2081
-
(2001)
Biophys. J.
, vol.80
, pp. 2074-2081
-
-
Gullingsrud, J.1
Kosztin, D.2
-
25
-
-
0141754098
-
Gating of Mscl studied by steered molecular dynamics
-
Gullingsrud J., and Schulten K. Gating of Mscl studied by steered molecular dynamics. Biophys. J. 85 (2003) 2087-2099
-
(2003)
Biophys. J.
, vol.85
, pp. 2087-2099
-
-
Gullingsrud, J.1
Schulten, K.2
-
26
-
-
84943997802
-
Elastic properties of lipid bilayers: theory and possible experiments
-
Helfrich W. Elastic properties of lipid bilayers: theory and possible experiments. Z. Naturforsch. (c) 28 (1973) 693-703
-
(1973)
Z. Naturforsch. (c)
, vol.28
, pp. 693-703
-
-
Helfrich, W.1
-
27
-
-
19944362820
-
Patch dynamics for multiscale problems
-
Hyman J.M. Patch dynamics for multiscale problems. Comp. Sci. Eng. 7 (2005) 47-53
-
(2005)
Comp. Sci. Eng.
, vol.7
, pp. 47-53
-
-
Hyman, J.M.1
-
28
-
-
14544291957
-
A multiscale coarse-graining method for biomolecular systems
-
Izvekov S., and Voth G.A. A multiscale coarse-graining method for biomolecular systems. J. Phys. Chem. B 109 (2005) 2469-2473
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 2469-2473
-
-
Izvekov, S.1
Voth, G.A.2
-
29
-
-
33748250745
-
Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers
-
Izvekov S., and Voth G.A. Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers. J. Chem. Theor. Comp. 2 (2006) 637-648
-
(2006)
J. Chem. Theor. Comp.
, vol.2
, pp. 637-648
-
-
Izvekov, S.1
Voth, G.A.2
-
30
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen W.L., Chandrasekhar J., et al. 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
-
31
-
-
22944466441
-
Coarse-grained computations for a micellar system
-
Kopelevich D.I., Panagiotopoulos A.Z., et al. Coarse-grained computations for a micellar system. J. Chem. Phys. 122 (2005) 0449071-0490714
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 0449071-0490714
-
-
Kopelevich, D.I.1
Panagiotopoulos, A.Z.2
-
32
-
-
0030777711
-
Transmembrane four-helix bundle of influenza A M2 protein channel: structural implications from helix tilt and orientation
-
Kovacs F.A., and Cross T.A. Transmembrane four-helix bundle of influenza A M2 protein channel: structural implications from helix tilt and orientation. Biophys. J. 73 (1997) 2511-2517
-
(1997)
Biophys. J.
, vol.73
, pp. 2511-2517
-
-
Kovacs, F.A.1
Cross, T.A.2
-
33
-
-
0033932839
-
Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations
-
Lindahl E., and Edholm O. Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys. J. 79 (2000) 426-433
-
(2000)
Biophys. J.
, vol.79
, pp. 426-433
-
-
Lindahl, E.1
Edholm, O.2
-
34
-
-
1642485164
-
Coarse grained model for semiquantitative lipid Simulations
-
Marrink S.J., deVries A.H., et al. Coarse grained model for semiquantitative lipid Simulations. J. Phys. Chem. B 108 (2004) 750-760
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 750-760
-
-
Marrink, S.J.1
deVries, A.H.2
-
35
-
-
0035812110
-
Effect of undulations on surface tension in simulated bilayers
-
Marrink S.J., and Mark A.E. Effect of undulations on surface tension in simulated bilayers. J. Phys. Chem. B 105 (2001) 6122-6127
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6122-6127
-
-
Marrink, S.J.1
Mark, A.E.2
-
36
-
-
16344388803
-
Coupling field theory with mesoscopic dynamical simulations of multi-component lipid bilayers
-
McWhirter J.L., Ayton G.S., et al. Coupling field theory with mesoscopic dynamical simulations of multi-component lipid bilayers. Biophys. J. 87 (2004) 3242-3263
-
(2004)
Biophys. J.
, vol.87
, pp. 3242-3263
-
-
McWhirter, J.L.1
Ayton, G.S.2
-
37
-
-
0030881872
-
A functionally defined model for the M2 proton channel of influenza A virus suggests a mechanism for its ion selectivity
-
Pinto L.H., Dieckmann G.R., et al. A functionally defined model for the M2 proton channel of influenza A virus suggests a mechanism for its ion selectivity. Proc. Nat. Acad. Sci. 94 (1997) 11301-11306
-
(1997)
Proc. Nat. Acad. Sci.
, vol.94
, pp. 11301-11306
-
-
Pinto, L.H.1
Dieckmann, G.R.2
-
38
-
-
0028275812
-
Membrane bending energy concept of vesicle- and cell-shapes and shape-transitions
-
Sackmann E. Membrane bending energy concept of vesicle- and cell-shapes and shape-transitions. FEBS Lett. 346 (1994) 3-16
-
(1994)
FEBS Lett.
, vol.346
, pp. 3-16
-
-
Sackmann, E.1
-
39
-
-
0030803839
-
The influenza A virus M2 channel: A molecular modeling and simulation study
-
Sansom M.S., Kerr I.D., et al. The influenza A virus M2 channel: A molecular modeling and simulation study. Virology 233 (1997) 163-173
-
(1997)
Virology
, vol.233
, pp. 163-173
-
-
Sansom, M.S.1
Kerr, I.D.2
-
40
-
-
0034039757
-
Computer simulation of ion channel gating: The M2 channel of influenza A virus in a lipid bilayer
-
Schweighofer K.J., and Pohorille A. Computer simulation of ion channel gating: The M2 channel of influenza A virus in a lipid bilayer. Biophys. J. 78 (2000) 150-163
-
(2000)
Biophys. J.
, vol.78
, pp. 150-163
-
-
Schweighofer, K.J.1
Pohorille, A.2
-
41
-
-
0030735760
-
Configurations of fluid membranes and vesicles
-
Seifert U. Configurations of fluid membranes and vesicles. Adv. Phys. 46 (1997) 13-137
-
(1997)
Adv. Phys.
, vol.46
, pp. 13-137
-
-
Seifert, U.1
-
42
-
-
0035902367
-
A coarse grain model for phospholipid simulation
-
Shelley J.C., Shelley M.Y., et al. A coarse grain model for phospholipid simulation. J. Phys. Chem. B 105 (2001) 4464-4470
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 4464-4470
-
-
Shelley, J.C.1
Shelley, M.Y.2
-
43
-
-
33644893631
-
Coarse grained protein-lipid model with applications to lipoprotein particles
-
Shih A.Y., Arkhipov A., et al. Coarse grained protein-lipid model with applications to lipoprotein particles. J. Phys. Chem. B 110 (2006) 3674-3684
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 3674-3684
-
-
Shih, A.Y.1
Arkhipov, A.2
-
44
-
-
33847225473
-
-
Smith, W. and T.R. Forester (1999). The DL_POLY Molecular Simulation Package, http://www.dl.ac.uk/TCSC/Software/DL_POLY/main.html.
-
-
-
-
45
-
-
5244326635
-
United atom force field for phospholipid membranes: constant pressure molecular dynamics simulation of dipalmitoylphosphatidylcholine/water system
-
Smondyrev A.M., and Berkowitz M.L. United atom force field for phospholipid membranes: constant pressure molecular dynamics simulation of dipalmitoylphosphatidylcholine/water system. J. Comp. Chem. 20 (1999) 531-545
-
(1999)
J. Comp. Chem.
, vol.20
, pp. 531-545
-
-
Smondyrev, A.M.1
Berkowitz, M.L.2
-
46
-
-
0036789499
-
Molecular dynamics simulation of proton transport through the Influenza A virus M2 channel
-
Smondyrev A.M., and Voth G.A. Molecular dynamics simulation of proton transport through the Influenza A virus M2 channel. Biophys. J. 83 (2002) 1987-1996
-
(2002)
Biophys. J.
, vol.83
, pp. 1987-1996
-
-
Smondyrev, A.M.1
Voth, G.A.2
-
47
-
-
11044233935
-
Coarse-grained simulations of lipid bilayers
-
Stevens M.J. Coarse-grained simulations of lipid bilayers. J. Chem. Phys. 121 (2004) 11942-11948
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 11942-11948
-
-
Stevens, M.J.1
-
48
-
-
27644502867
-
Complementary matching in domain formation within lipid bilayers
-
Stevens M.J. Complementary matching in domain formation within lipid bilayers. J. Am. Chem. Soc. 127 (2005) 15330-15331
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 15330-15331
-
-
Stevens, M.J.1
-
49
-
-
4344685227
-
Global ribosome motions revealed with elastic network model
-
Wang Y., Rader A.J., et al. Global ribosome motions revealed with elastic network model. J. Struct. Biol. 147 (2004) 302-314
-
(2004)
J. Struct. Biol.
, vol.147
, pp. 302-314
-
-
Wang, Y.1
Rader, A.J.2
-
50
-
-
0037194057
-
Experimental demonstration of violations of the Second Law of Thermodynamics for small systems and short time scales
-
Wang G.M., Sevick E., et al. Experimental demonstration of violations of the Second Law of Thermodynamics for small systems and short time scales. Phys. Rev. Lett. 89 (2002) 0506011-0506014
-
(2002)
Phys. Rev. Lett.
, vol.89
, pp. 0506011-0506014
-
-
Wang, G.M.1
Sevick, E.2
-
51
-
-
25844476272
-
A computational study of the closed and open states of the influenza A M2 proton channel
-
Wu Y., and Voth G.A. A computational study of the closed and open states of the influenza A M2 proton channel. Biophys. J. 89 (2005) 2402-2411
-
(2005)
Biophys. J.
, vol.89
, pp. 2402-2411
-
-
Wu, Y.1
Voth, G.A.2
-
52
-
-
0032434323
-
The M2 channel of influenza A virus: a molecular dynamics study
-
Zhong Q., Husslein T., et al. The M2 channel of influenza A virus: a molecular dynamics study. FEBS Lett. 434 (1998) 265-271
-
(1998)
FEBS Lett.
, vol.434
, pp. 265-271
-
-
Zhong, Q.1
Husslein, T.2
|