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References

[1] R. Henderson, J. M. Baldwin, T. A. Ceska, F. Zemlin, E. Beckmann, K. H. Downing. Model for the Structure of Bacteriorhodopsin Based on High-Resolution Electron Cryo-microscopy. J. Mol. Biol, 231:899-929, 1990.

[2] Marco Nonella, Andreas Windemuth, and Klaus Schulten. Structure of Bacteriorhodopsin and in situ isomerization of retinal: A molecular dynamics study. J. Photochem. Photobiol., 54(6):937-948, 1991.

[3] Feng Zhou, Andreas Windemuth, and Klaus Schulten. Molecular dynamics investigation of the proton pump cycle of Bacteriorhodopsin. Biochemistry, 32(9)2291-2306, 1993.

[4] William Humphrey and Andrew Dalke. VMD user guide (Version 0.94). Beckman Intitute Technical Report TB-94-07, Univerity of Illinois, 1994.

[5] Klaus Schulten, Zan Schulten, and Paul Tavan. An isomerization model for the pump cycle of Bacteriorhodopsin. In L. Bolis, E. J. M. Helmreich, and H. Passow, editors, Information and Energy Transduction in Biological Membranes, pages 113-131. Allan. R. Liss, Inc., New York, 1984.

[6] S. Scheiner and X. Duan. Effect of intermolecular orientation upon proton transfer within a polarizable medium. Biophys. J., 60:874-883, 1991.

[7] E. Clementi. Computational Aspects for Large Chemical Systems. In Lecture Notes In Chemistry. Springer, New York, 1980.

[8] U. C. Singh and P. A. Kollman. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: applications to the CH_3/Cl+Cl- echange reaction and gas phase protonation. J. Comp. Chem., 7:718, 1986.

[9] M. J. Field, P. A. Bash, and M. Karplus. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comp. Chem., 11(6):700-733, 1990.

[10] L. Song, M. A. El-Sayed, and J. K. Lanyi. Protein catalysis of the retinal subpicosecond photoisomerization in the primary process of Bacteriorhodopsin photosynthesis. Science, 261:891-894, 1993.