Abstract
The heterogeneity associated with membrane systems poses a huge challenge for computer simulations of membrane dynamics and structure. Unlike proteins or nucleic acids with well-defined three-dimensional structures, membrane components such as lipid bilayers derive a vast majority of their properties and function from their fluid nature. This introduces the problem of setting up the correct bilayer model system for any realistic computer simulation. The model includes: choice of the system size; interatomic force fields; treatment of short and long-range interactions; and, most important, the macroscopic boundary conditions that best mimic experimental conditions. The simulation is thus an integral part of the model.
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References
Albrecht O, Gruler H, Sackman E (1978): Polymorphism of phospholipid bilayers. J Physique 39:301–313
Alper HE, Bassolino D, Stouch TR (1993a): Computer simulation of a phospholipid monolayer-water system. The influence of long range forces on water structure and dynamics. J Chem Phys 98:9798–9807
Alper HE, Bassolino-Klimas D, Stouch TR (1993b): The limiting behavior of water hydrating a phospholipid monolayer: A computer simulation study. J Chem Phys 99:5547–5559
Bakker G (1911): Theorie de la Couche Capillaire Plane dans les Corps Purs. Paris: Gauthier-Villars
Berendsen HJC, Egberts B, Marrink S-J, Ahlstrom P (1992): Molecular dynamics simulations of phospholipid membranes and their interaction with phospholipase A2. In: Membrane Proteins: Structures, Interactions and Models, Pullman A, Jortner J, Pullman B, eds. Dordrecht, The Netherlands: Kluwer Academic Publishers
Berendsen HJC, Grigera JR, Straatsma TP (1987): The missing term in effective pair potentials. J Chem Phys 91:6289–6291
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984): Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3689
Board JA Jr, Causey JW, Leathrum JR Jr, Windemuth A, Schulten K (1992): Accelerated molecular dynamics simulation with the parallel fast multipole algorithm. Chem Phys Lett 198:89
Chiu SW, Gulukota K, Jakobsson E (1992): Computational approaches to understanding the ion channel-lipid system. In: Membrane Proteins: Structures, Interactions, and Models, Pullman A, Jortner J, Pullman B, eds. Dordrecht, The Netherlands: Kluwer Academic Publishers
Chiu SW, Clark M, Balajiv V, Subramaniam S, Scott HL, Jakobsson E (1995): Incorporation of surface tension into molecular dynamics simulation of an interface: A fluid phase lipid bilayer membrane. Biophys J 69:1230–1245
Damodaran KV, Merz KM (1994): A comparison of DMPC- and DLPE-based lipid bilayers. Biophys J 66:1076–1087
Darden T, York D, Pedersen L (1993): Particle mesh Ewald: An N · · log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092
Egberts E (1988): Molecular dynamics simulations of multibilayer membranes (dissertation). University of Groningen, Groningen, The Netherlands
Egberts E, Marrink S J, Berendsen HJC (1994): Molecular dynamics simulation of a phospholipid membrane. Eur Biophys J 22:423–436
Flewelling RF, Hubbell WL (1986): The membrane dipole potential in a total membrane potential model. Applications to hydrophobic ion interactions with membranes. Biophys 7 49:541–552
Helfrich P, Jakobsson E (1990): Calculation of deformation energies and conformations in lipid membranes containing gramicidin channels. Biophys J 57:1075–1084
Heller H, Schaefer M, Schulten K (1993): Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal phases. J Phys Chem 97:8343–8360
Hladky SB, Haydon DA (1973): Membrane conductance and surface potential. Biochim Biophys Acta 318:464–468
Huang P, Perez JJ, Loew GH (1994): Molecular dynamics simulations of phospholipid bilayers. J Biomol Struct Dyn 11:927–956
Lee CY, McCammon JA, Rossky PJ (1984): The structure of liquid water at an extended hydrophobic surface. J Chem Phys 80:4448
MacDonald RC, Simon SA (1987): Lipid monolayer states and their relation to bilayers. Proc Natl Acad Sci USA 84:4089–4093
Marrink SJ, Berendsen HJC (1994): Simulation of water transport through a lipid membrane. J Phys Chem 98:4155–4168
Marrink SJ, Berkowitz M, Berendsen HJC (1993): Molecular dynamics simulation of a membrane water interface—the ordering of water and its relation to the hydration force. Langmuir 9:3122–3131
McLaughlin S (1989): The electrostatic properties of membranes. Ann Rev Biophys Biophys Chem 18:113–136
McLaughlin S (1977): Electrostatic potentials at membrane-solution interfaces. Curr Top Membr Transp 9:71–144
Robinson AJ, Richards WG, Thomas PJ, Hann MM (1994): Head group and chain behavior in biological membranes: A molecular dynamics computer simulation. Biophys J 67:2345–2354
Ryckaert JP, Bellemans A (1978): Molecular dynamics of liquid alkanes. Far Disc Chem Soc 66:95–106
Ryckaert JP, Bellemans A (1975): Molecular dynamics of liquid n-butane near its boiling point. Chem Phys Lett 30:123–125
Vehable RM, Zhang Y, Hardy BJ, Pastor RW (1993): Molecular dynamics simulations of a lipid bilayer and of hexadecane: An investigation of membrane fluidity. Science 262:223–226
von Heijne G (1994): Membrane proteins: From sequence to structure. Annu Rev Biophys Biomol Struct 23:167–192
White SH (1980): Small phospholipid vesicles: Internal pressure, surface tension, and surface free energy. Proc Natl Acad Sci USA 77:4048–4050
Zhou F, Schulten K (1995): Molecular dynamics study of a membrane-water interface. J Phys Chem 99:2194–2208
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Jakobsson, E., Subramaniam, S., Scott, H.L. (1996). Strategic Issues in Molecular Dynamics Simulations of Membranes. In: Merz, K.M., Roux, B. (eds) Biological Membranes. Birkhäuser Boston. https://doi.org/10.1007/978-1-4684-8580-6_4
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DOI: https://doi.org/10.1007/978-1-4684-8580-6_4
Publisher Name: Birkhäuser Boston
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