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Original Articles

Molecular Dynamics Simulations of Phospholipid Bilayers

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Pages 927-956 | Received 05 Jan 1994, Published online: 21 May 2012

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Read on this site (5)

DavidR. Garmer. (1997) MD Simulations of a 5-HT2A Receptor Model in DOPC Membranes. Journal of Biomolecular Structure and Dynamics 14:5, pages 525-546.
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V. Kothekar, K. Mahajan, K. Raha & D. Gupta. (1996) Molecular Dynamics Simulation of Conformational Flexibility of Alamethicin Fragments in Aqueous and Membranous Environment. Journal of Biomolecular Structure and Dynamics 14:3, pages 303-316.
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V. Kothekar. (1996) 260 ps Molecular Dynamics Simulation of Substance P With Hydrated Dimyristoyl Phosphatidyl Choline Bilayer. Journal of Biomolecular Structure and Dynamics 13:4, pages 601-613.
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Ping Huang & GildaH. Loew. (1995) Interaction of an Amphiphilic Peptide with a Phospholipid Bilayer Surface by Molecular Dynamics Simulation Study. Journal of Biomolecular Structure and Dynamics 12:5, pages 937-956.
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Ping Huang, Ed Bertaccini & GildaH. Loew. (1995) Molecular Dynamics Simulation of Anesthetic-Phospholipid Bilayer Interactions. Journal of Biomolecular Structure and Dynamics 12:4, pages 725-754.
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Slawomir S. Stachura, Chris J. Malajczuk & Ricardo L. Mancera. (2018) Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field. Journal of Molecular Modeling 24:7.
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Jobst Liebau, Weihua Ye & Lena Mäler. (2017) Characterization of fast-tumbling isotropic bicelles by PFG diffusion NMR. Magnetic Resonance in Chemistry 55:5, pages 395-404.
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D. R. Gauger, V. V. Andrushchenko, P. Bouř & W. Pohle. (2010) A spectroscopic method to estimate the binding potency of amphiphile assemblies. Analytical and Bioanalytical Chemistry 398:2, pages 1109-1123.
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Stefan Balaz. (2009) Modeling Kinetics of Subcellular Disposition of Chemicals. Chemical Reviews 109:5, pages 1793-1899.
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Lula Rosso & Ian R. Gould. (2008) Structure and dynamics of phospholipid bilayers using recently developed general all-atom force fields. Journal of Computational Chemistry 29:1, pages 24-37.
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Mary Hongying Cheng, Lu Tian Liu, Alexander C. Saladino, Yan Xu & Pei Tang. (2007) Molecular Dynamics Simulations of Ternary Membrane Mixture:  Phosphatidylcholine, Phosphatidic Acid, and Cholesterol. The Journal of Physical Chemistry B 111:51, pages 14186-14192.
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Carl-Johan Högberg & Alexander P. Lyubartsev. (2006) A Molecular Dynamics Investigation of the Influence of Hydration and Temperature on Structural and Dynamical Properties of a Dimyristoylphosphatidylcholine Bilayer. The Journal of Physical Chemistry B 110:29, pages 14326-14336.
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Anthony G. Lee. 2006. Protein-Lipid Interactions. Protein-Lipid Interactions 141 175 .
Zhanwu Liu, Yan Xu & Pei Tang. (2005) Molecular Dynamics Simulations of C2F6 Effects on Gramicidin A: Implications of the Mechanisms of General Anesthesia. Biophysical Journal 88:6, pages 3784-3791.
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Alex H. de Vries, Indira Chandrasekhar, Wilfred F. van Gunsteren & Philippe H. Hünenberger. (2005) Molecular Dynamics Simulations of Phospholipid Bilayers:  Influence of Artificial Periodicity, System Size, and Simulation Time. The Journal of Physical Chemistry B 109:23, pages 11643-11652.
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Marja T. Hyvönen & Petri T. Kovanen. (2005) Molecular dynamics simulations of unsaturated lipid bilayers: effects of varying the numbers of double bonds. European Biophysics Journal 34:4, pages 294-305.
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J. Stecki. (2004) Correlations in simulated model bilayers. The Journal of Chemical Physics 120:7, pages 3508-3516.
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Tomasz Róg, Krzysztof Murzyn, Ryszard Gurbiel, Yuji Takaoka, Akihiro Kusumi & Marta Pasenkiewicz-Gierula. (2004) Effects of phospholipid unsaturation on the bilayer nonpolar region. Journal of Lipid Research 45:2, pages 326-336.
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A. L. Rabinovich, P. O. Ripatti, N. K. Balabaev & F. A. M. Leermakers. (2003) Molecular dynamics simulations of hydrated unsaturated lipid bilayers in the liquid-crystal phase and comparison to self-consistent field modeling. Physical Review E 67:1.
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S.W. Chiu, Eric Jakobsson, R. Jay Mashl & H. Larry Scott. (2002) Cholesterol-Induced Modifications in Lipid Bilayers: A Simulation Study. Biophysical Journal 83:4, pages 1842-1853.
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. (2002) Gilda H. Loew, Ph.D. list of publications. International Journal of Quantum Chemistry 88:1, pages 5-16.
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R. Jay Mashl, H. Larry Scott, Shankar Subramaniam & Eric Jakobsson. (2001) Molecular Simulation of Dioleoylphosphatidylcholine Lipid Bilayers at Differing Levels of Hydration. Biophysical Journal 81:6, pages 3005-3015.
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István P. Sugár, Ekaterina Michonova-Alexova & Parkson Lee-Gau Chong. (2001) Geometrical Properties of Gel and Fluid Clusters in DMPC/DSPC Bilayers: Monte Carlo Simulation Approach Using a Two-State Model. Biophysical Journal 81:5, pages 2425-2441.
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Els van den Brink-van der Laan, Ross E. Dalbey, Rudy A. Demel, J. Antoinette Killian & Ben de Kruijff. (2001) Effect of Nonbilayer Lipids on Membrane Binding and Insertion of the Catalytic Domain of Leader Peptidase. Biochemistry 40:32, pages 9677-9684.
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Krzysztof Murzyn, Tomasz Róg, Grzegorz Jezierski, Yuji Takaoka & Marta Pasenkiewicz-Gierula. (2001) Effects of Phospholipid Unsaturation on the Membrane/Water Interface: A Molecular Simulation Study. Biophysical Journal 81:1, pages 170-183.
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S. W. Chiu, Eric Jakobsson & H. Larry Scott. (2001) Combined Monte Carlo and molecular dynamics simulation of hydrated dipalmitoyl–phosphatidylcholine–cholesterol lipid bilayers. The Journal of Chemical Physics 114:12, pages 5435-5443.
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S.W. Chiu, Eric Jakobsson & H. Larry Scott. (2001) Combined Monte Carlo and Molecular Dynamics Simulation of Hydrated Lipid-Cholesterol Lipid Bilayers at Low Cholesterol Concentration. Biophysical Journal 80:3, pages 1104-1114.
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Monika Höltje, Thomas Förster, Birte Brandt, Thomas Engels, Wolfgang von Rybinski & Hans-Dieter Höltje. (2001) Molecular dynamics simulations of stratum corneum lipid models: fatty acids and cholesterol. Biochimica et Biophysica Acta (BBA) - Biomembranes 1511:1, pages 156-167.
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M. X. Fernandes, J. García de la Torre & M. A. R. B. Castanho. (2000) A Brownian Dynamics Simulation of an Acyl Chain and a trans -Parinaric Acid Molecule Confined in a Phospholipid Bilayer in the Gel and Liquid-Crystal Phases . The Journal of Physical Chemistry B 104:48, pages 11579-11584.
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Igor Z. Zubrzycki, Yan Xu, Marcela Madrid & Pei Tang. (2000) Molecular dynamics simulations of a fully hydrated dimyristoylphosphatidylcholine membrane in liquid-crystalline phase. The Journal of Chemical Physics 112:7, pages 3437-3441.
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S.W. Chiu, Eric Jakobsson, Shankar Subramaniam & H.Larry Scott. (1999) Combined Monte Carlo and Molecular Dynamics Simulation of Fully Hydrated Dioleyl and Palmitoyl-oleyl Phosphatidylcholine Lipid Bilayers. Biophysical Journal 77:5, pages 2462-2469.
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M.M.G. Krishna & N. Periasamy. (1999) Location and orientation of DODCI in lipid bilayer membranes: effects of lipid chain length and unsaturation. Biochimica et Biophysica Acta (BBA) - Biomembranes 1461:1, pages 58-68.
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Samir Mitragotri, Mark E. Johnson, Daniel Blankschtein & Robert Langer. (1999) An Analysis of the Size Selectivity of Solute Partitioning, Diffusion, and Permeation across Lipid Bilayers. Biophysical Journal 77:3, pages 1268-1283.
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Pei Tang, Jian Hu, Serguei Liachenko & Yan Xu. (1999) Distinctly Different Interactions of Anesthetic and Nonimmobilizer with Transmembrane Channel Peptides. Biophysical Journal 77:2, pages 739-746.
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Scott E. Feller & Richard W. Pastor. (1999) Constant surface tension simulations of lipid bilayers: The sensitivity of surface areas and compressibilities. The Journal of Chemical Physics 111:3, pages 1281-1287.
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Christopher Sheldahl & Stephen C. Harvey. (1999) Molecular Dynamics on a Model for Nascent High-Density Lipoprotein: Role of Salt Bridges. Biophysical Journal 76:3, pages 1190-1198.
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Wataru Shinoda & Susumu Okazaki. (1998) A Voronoi analysis of lipid area fluctuation in a bilayer. The Journal of Chemical Physics 109:4, pages 1517-1521.
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Wataru Shinoda, Nobuo Namiki & Susumu Okazaki. (1997) Molecular dynamics study of a lipid bilayer: Convergence, structure, and long-time dynamics. The Journal of Chemical Physics 106:13, pages 5731-5743.
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Johan Landin, Irmin Pascher & Dieter Cremer. (1997) Effect of a Polar Environment on the Conformation of Phospholipid Head Groups Analyzed with the Onsager Continuum Solvation Model. The Journal of Physical Chemistry A 101:16, pages 2996-3004.
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Peter Walde & Eveline Blöchliger. (1997) Circular Dichroic Properties of Phosphatidylcholine Liposomes. Langmuir 13:6, pages 1668-1671.
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D. P. Tieleman & H. J. C. Berendsen. (1996) Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. The Journal of Chemical Physics 105:11, pages 4871-4880.
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V. Kothekar. (1996) Molecular dynamics study of interaction of dimyristoyl phosphotidyl choline with water. Journal of Biosciences 21:5, pages 577-597.
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