-
1
-
-
4143138518
-
Methodological issues in lipid bilayer simulations
-
Anezo C., de Vries A.H., Höltje H., Tieleman D.P., and Marrink S.J. Methodological issues in lipid bilayer simulations. J. Phys. Chem. 107 (2003) 9424-9433
-
(2003)
J. Phys. Chem.
, vol.107
, pp. 9424-9433
-
-
Anezo, C.1
de Vries, A.H.2
Höltje, H.3
Tieleman, D.P.4
Marrink, S.J.5
-
2
-
-
0021098283
-
Effect of poly(ethylene glycol) on phospholipid hydration and polarity of the external phase
-
Arnold K., Pratsch L., and Gawrisch K. Effect of poly(ethylene glycol) on phospholipid hydration and polarity of the external phase. Biochim. Biophys. Acta 728 (1983) 121-128
-
(1983)
Biochim. Biophys. Acta
, vol.728
, pp. 121-128
-
-
Arnold, K.1
Pratsch, L.2
Gawrisch, K.3
-
3
-
-
0346002802
-
A parallel computer for molecular dynamics simulations
-
de Groot R.A., and Nadrchal J. (Eds), World Scientific, Singapore
-
Bekker H., Berendsen H.J.C., Dijkstra E.J., Achterop S., van Drunen R., van der Spoel D., Sijbers A., Keegstra H., Reitsma B., Renardus M.K.R., and Gromacs. A parallel computer for molecular dynamics simulations. In: de Groot R.A., and Nadrchal J. (Eds). Physics Computing 92 (1993), World Scientific, Singapore
-
(1993)
Physics Computing 92
-
-
Bekker, H.1
Berendsen, H.J.C.2
Dijkstra, E.J.3
Achterop, S.4
van Drunen, R.5
van der Spoel, D.6
Sijbers, A.7
Keegstra, H.8
Reitsma, B.9
Renardus, M.K.R.10
Gromacs11
-
6
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
-
Berger O., Edholm O., and Jahnig F. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys. J. 72 (1997) 2002-2013
-
(1997)
Biophys. J.
, vol.72
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jahnig, F.3
-
8
-
-
0036585607
-
A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phase
-
Chandrasekhar I., and van Gunsteren W.F. A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phase. Eur. Biophys. J. 31 (2002) 89-101
-
(2002)
Eur. Biophys. J.
, vol.31
, pp. 89-101
-
-
Chandrasekhar, I.1
van Gunsteren, W.F.2
-
9
-
-
0029099308
-
Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane
-
Chiu S.W., Clark M., Balaji V., Subramaniam S., Scott H.L., and Jakobsson E. Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. Biophys. J. 69 (1995) 1230-1245
-
(1995)
Biophys. J.
, vol.69
, pp. 1230-1245
-
-
Chiu, S.W.1
Clark, M.2
Balaji, V.3
Subramaniam, S.4
Scott, H.L.5
Jakobsson, E.6
-
10
-
-
0032706178
-
Combined Monte Carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers
-
Chiu S.W., Jakobsson E., Subramaniam S., and Scott H.L. Combined Monte Carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers. Biophys. J. 77 (1999) 2462-2469
-
(1999)
Biophys. J.
, vol.77
, pp. 2462-2469
-
-
Chiu, S.W.1
Jakobsson, E.2
Subramaniam, S.3
Scott, H.L.4
-
11
-
-
33846823909
-
Particule mesh Ewald: an Nlog(N) method for Ewald sums in large systems
-
Darden T.D., York D., and Pedersen I. Particule mesh Ewald: an Nlog(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.D.1
York, D.2
Pedersen, I.3
-
13
-
-
33645961739
-
A smooth particule mesh Ewald method
-
Essmann U., Pereira-Maia E., Berkowitz M.L., Darden T.D., Lee B.W., and Pedersen I. A smooth particule mesh Ewald method. J. Chem. Phys. 103 (1995) 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Pereira-Maia, E.2
Berkowitz, M.L.3
Darden, T.D.4
Lee, B.W.5
Pedersen, I.6
-
14
-
-
0037962802
-
The effect of cholesterol on the lateral diffusion of phospholipids in oriented bilayers
-
Filippov A., Oradd G., and Lindblom G. The effect of cholesterol on the lateral diffusion of phospholipids in oriented bilayers. Biophys. J. 84 (2003) 3079-3086
-
(2003)
Biophys. J.
, vol.84
, pp. 3079-3086
-
-
Filippov, A.1
Oradd, G.2
Lindblom, G.3
-
15
-
-
0034902578
-
Quantitative determination of fat emulsion using 1,6-diphenyl-1,3,5-hexatriene as fluorescence probe: application to the compounding of all-in-one parenteral nutrition admixtures
-
Hernando V., Zhou J.Y., Nouaille-Degorce B., Prognon P., Brion F., and Rieutord A. Quantitative determination of fat emulsion using 1,6-diphenyl-1,3,5-hexatriene as fluorescence probe: application to the compounding of all-in-one parenteral nutrition admixtures. J. Pharm. Biomed. Anal. 26 (2001) 487-493
-
(2001)
J. Pharm. Biomed. Anal.
, vol.26
, pp. 487-493
-
-
Hernando, V.1
Zhou, J.Y.2
Nouaille-Degorce, B.3
Prognon, P.4
Brion, F.5
Rieutord, A.6
-
16
-
-
0000388705
-
Lincs: a linear constraint solver for molecular simulations
-
Hess B., Bekker, Berendsen H.J., and Fraaije. Lincs: a linear constraint solver for molecular simulations. J. Comput. Chem. 18 (1997) 1463-1472
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker2
Berendsen, H.J.3
Fraaije4
-
17
-
-
33746897341
-
A molecular dynamics investigation of the influence of hydration and temperature on structural and dynamical properties of a dimyristoylphosphatidylcholine bilayer
-
Hogberg C.J., and Lyubartsev A.P. A molecular dynamics investigation of the influence of hydration and temperature on structural and dynamical properties of a dimyristoylphosphatidylcholine bilayer. J. Phys. Chem. B Condens. Matter Mater. Surf. Interfaces Biophys. 110 (2006) 14326-14336
-
(2006)
J. Phys. Chem. B Condens. Matter Mater. Surf. Interfaces Biophys.
, vol.110
, pp. 14326-14336
-
-
Hogberg, C.J.1
Lyubartsev, A.P.2
-
19
-
-
0037044599
-
Comparative analysis of different plant oils by high-performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry
-
Jakab A., Heberger K., and Forgacs E. Comparative analysis of different plant oils by high-performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry. J. Chromatogr. A. 976 (2002) 255-263
-
(2002)
J. Chromatogr. A.
, vol.976
, pp. 255-263
-
-
Jakab, A.1
Heberger, K.2
Forgacs, E.3
-
20
-
-
33645941402
-
The OPLS potential functions for proteins: energy minimization for crystals of cyclic peptides and crambin
-
Jorgensen W.L., and Tirado-Rives J. The OPLS potential functions for proteins: energy minimization for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110 (1988) 1657-1666
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
21
-
-
33749343217
-
How phospholipid-cholesterol interactions modulate lipid lateral diffusion, as revealed by fluorescence correlation spectroscopy
-
Kahya N., and Schwille P. How phospholipid-cholesterol interactions modulate lipid lateral diffusion, as revealed by fluorescence correlation spectroscopy. J. Fluoresc. 16 (2006) 671-678
-
(2006)
J. Fluoresc.
, vol.16
, pp. 671-678
-
-
Kahya, N.1
Schwille, P.2
-
22
-
-
22144486884
-
Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles
-
Kucerka N., Liu Y., Chu N., Petrache H.I., Tristram-Nagle S., and Nagle J.F. Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles. Biophys. J. 88 (2005) 2626-2637
-
(2005)
Biophys. J.
, vol.88
, pp. 2626-2637
-
-
Kucerka, N.1
Liu, Y.2
Chu, N.3
Petrache, H.I.4
Tristram-Nagle, S.5
Nagle, J.F.6
-
23
-
-
33646446451
-
Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains
-
Kucerka N., Tristram-Nagle S., and Nagle J.F. Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains. J. Membr. Biol. 208 (2005) 193-202
-
(2005)
J. Membr. Biol.
, vol.208
, pp. 193-202
-
-
Kucerka, N.1
Tristram-Nagle, S.2
Nagle, J.F.3
-
24
-
-
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
-
25
-
-
0035789518
-
GROMACS 3.0: a package for molecular simulation and trajectory analysis
-
Lindahl E., Hess B., and Van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Mod. 7 (2001) 306-317
-
(2001)
J. Mol. Mod.
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van der Spoel, D.3
-
26
-
-
0019879642
-
Effect of cholesterol in membranes. Pulsed nuclear magnetic resonance measurements of lipid lateral diffusion
-
Lindblom G., Johansson L.B., and Arvidson G. Effect of cholesterol in membranes. Pulsed nuclear magnetic resonance measurements of lipid lateral diffusion. Biochemistry 20 (1981) 2204-2207
-
(1981)
Biochemistry
, vol.20
, pp. 2204-2207
-
-
Lindblom, G.1
Johansson, L.B.2
Arvidson, G.3
-
27
-
-
33745760606
-
Phase transition of a DPPC bilayer induced by an external surface pressure: from bilayer to monolayer behavior. A molecular dynamics simulation study
-
Lopez Cascales J.J., Otero T.F., Fernandez Romero A.J., and Camacho L. Phase transition of a DPPC bilayer induced by an external surface pressure: from bilayer to monolayer behavior. A molecular dynamics simulation study. Langmuir 22 (2006) 5818-5824
-
(2006)
Langmuir
, vol.22
, pp. 5818-5824
-
-
Lopez Cascales, J.J.1
Otero, T.F.2
Fernandez Romero, A.J.3
Camacho, L.4
-
28
-
-
84986440341
-
Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
Miyamoto S., and Kollman P. Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13 (1992) 952-962
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.2
-
29
-
-
0034759459
-
Dynamical properties of a hydrated lipid bilayer from a multinanosecond molecular dynamics simulation
-
Moore P.B., Lopez C.F., and Klein M.L. Dynamical properties of a hydrated lipid bilayer from a multinanosecond molecular dynamics simulation. Biophys. J. 81 (2001) 2484-2494
-
(2001)
Biophys. J.
, vol.81
, pp. 2484-2494
-
-
Moore, P.B.1
Lopez, C.F.2
Klein, M.L.3
-
30
-
-
0034950798
-
Effects of phospholipid unsaturation on the membrane/water interface: a molecular simulation study
-
Murzyn K., Rog T., Jezierski G., Takaoka Y., and Pasenkiewicz-Gierula M. Effects of phospholipid unsaturation on the membrane/water interface: a molecular simulation study. Biophys. J. 81 (2001) 170-183
-
(2001)
Biophys. J.
, vol.81
, pp. 170-183
-
-
Murzyn, K.1
Rog, T.2
Jezierski, G.3
Takaoka, Y.4
Pasenkiewicz-Gierula, M.5
-
31
-
-
0027198849
-
Evidence of partial rotational order in gel phase DPPC
-
Nagle J.F. Evidence of partial rotational order in gel phase DPPC. Biophys. J. 64 (1993) 1110-1112
-
(1993)
Biophys. J.
, vol.64
, pp. 1110-1112
-
-
Nagle, J.F.1
-
33
-
-
0037678992
-
Molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer with NaCl
-
Pandit S.A., Bostick D., and Berkowitz M.L. Molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer with NaCl. Biophys. J. 84 (2003) 3743-3750
-
(2003)
Biophys. J.
, vol.84
, pp. 3743-3750
-
-
Pandit, S.A.1
Bostick, D.2
Berkowitz, M.L.3
-
34
-
-
33846833769
-
Cholesterol surrogates: a comparison of cholesterol and 16:0 ceramide in POPC bilayers
-
Pandit S.A., Chiu S.W., Jakobsson E., Grama A., and Scott H.L. Cholesterol surrogates: a comparison of cholesterol and 16:0 ceramide in POPC bilayers. Biophys. J. 92 (2007) 920-927
-
(2007)
Biophys. J.
, vol.92
, pp. 920-927
-
-
Pandit, S.A.1
Chiu, S.W.2
Jakobsson, E.3
Grama, A.4
Scott, H.L.5
-
35
-
-
0030933013
-
Determination of component volumes of lipid bilayers from simulations
-
Petrache H.I., Feller S.E., and Nagle J.F. Determination of component volumes of lipid bilayers from simulations. Biophys. J. 72 (1997) 2237-2242
-
(1997)
Biophys. J.
, vol.72
, pp. 2237-2242
-
-
Petrache, H.I.1
Feller, S.E.2
Nagle, J.F.3
-
36
-
-
10744228856
-
Effects of phospholipid unsaturation on the bilayer nonpolar region: a molecular simulation study
-
Rog T., Murzyn K., Gurbiel R., Takaoka Y., Kusumi A., and Pasenkiewicz-Gierula M. Effects of phospholipid unsaturation on the bilayer nonpolar region: a molecular simulation study. J. Lipid Res. 45 (2004) 326-336
-
(2004)
J. Lipid Res.
, vol.45
, pp. 326-336
-
-
Rog, T.1
Murzyn, K.2
Gurbiel, R.3
Takaoka, Y.4
Kusumi, A.5
Pasenkiewicz-Gierula, M.6
-
37
-
-
0037028696
-
The dynamics of water at the phospholipid bilayer surface: a molecular dynamics simulation study
-
Rog T., Murzyn K., and Pasenkiewicz-Gierula M. The dynamics of water at the phospholipid bilayer surface: a molecular dynamics simulation study. Chem. Phys. Lett. 352 (2002) 323-327
-
(2002)
Chem. Phys. Lett.
, vol.352
, pp. 323-327
-
-
Rog, T.1
Murzyn, K.2
Pasenkiewicz-Gierula, M.3
-
38
-
-
17044450798
-
Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions
-
Rog T., Murzyn K., and Pasenkiewicz-Gierula M. Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions. Acta Biochim. Pol. 50 (2003) 789-798
-
(2003)
Acta Biochim. Pol.
, vol.50
, pp. 789-798
-
-
Rog, T.1
Murzyn, K.2
Pasenkiewicz-Gierula, M.3
-
39
-
-
49549141675
-
Molecular dynamics of liquid n-butane near its boiling point
-
Ryckaert J.-P., and Bellemans A. Molecular dynamics of liquid n-butane near its boiling point. Chem. Phys. Lett. 30 (1975) 123-125
-
(1975)
Chem. Phys. Lett.
, vol.30
, pp. 123-125
-
-
Ryckaert, J.-P.1
Bellemans, A.2
-
40
-
-
0000373167
-
Order parameter profile of docosahexaenoic acid as determined frim deuterium-NMR experiments
-
Safley A.M., Polozov I.V., and Gawrisch K. Order parameter profile of docosahexaenoic acid as determined frim deuterium-NMR experiments. Biophys. J. 78 (2000) 412A
-
(2000)
Biophys. J.
, vol.78
-
-
Safley, A.M.1
Polozov, I.V.2
Gawrisch, K.3
-
41
-
-
0031860932
-
A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer
-
Tieleman D.P., and Berendsen H.J. A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys. J. 74 (1998) 2786-2801
-
(1998)
Biophys. J.
, vol.74
, pp. 2786-2801
-
-
Tieleman, D.P.1
Berendsen, H.J.2
-
42
-
-
0032534843
-
Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: molecular dynamics simulations
-
Tieleman D.P., Forrest L.R., Sansom M.S., and Berendsen H.J. Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: molecular dynamics simulations. Biochemistry 37 (1998) 17554-17561
-
(1998)
Biochemistry
, vol.37
, pp. 17554-17561
-
-
Tieleman, D.P.1
Forrest, L.R.2
Sansom, M.S.3
Berendsen, H.J.4
-
43
-
-
0031438285
-
A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems
-
Tieleman D.P., Marrink S.J., and Berendsen H.J. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta 1331 (1997) 235-270
-
(1997)
Biochim. Biophys. Acta
, vol.1331
, pp. 235-270
-
-
Tieleman, D.P.1
Marrink, S.J.2
Berendsen, H.J.3
-
44
-
-
0032951553
-
Alamethicin helices in a bilayer and in solution: molecular dynamics simulations
-
Tieleman D.P., Sansom M.S., and Berendsen H.J. Alamethicin helices in a bilayer and in solution: molecular dynamics simulations. Biophys. J. 76 (1999) 40-49
-
(1999)
Biophys. J.
, vol.76
, pp. 40-49
-
-
Tieleman, D.P.1
Sansom, M.S.2
Berendsen, H.J.3
-
45
-
-
0030031374
-
Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer
-
Tu K., Tobias D.J., Blasie J.K., and Klein M.L. Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer. Biophys. J. 70 (1996) 595-608
-
(1996)
Biophys. J.
, vol.70
, pp. 595-608
-
-
Tu, K.1
Tobias, D.J.2
Blasie, J.K.3
Klein, M.L.4
-
46
-
-
27344454932
-
GROMACS: fast, flexible and free
-
Van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., and Berendsen H.J. GROMACS: fast, flexible and free. J. Comp. Chem. 26 (2005) 1701-1718
-
(2005)
J. Comp. Chem.
, vol.26
, pp. 1701-1718
-
-
Van der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.6
|