Abstract
Computer simulation is a quickly expanding discipline that is entering fields as diverse as astrophysics, polymer physics, chemical physics, and even molecular biology and biochemistry. Our own field is theoretical biophysics where we collaborate with a number of experimental biological groups. Although standard algorithms have emerged since the 1960s, and have been implemented in a number of freely available or commercial simulation packages, there is a constant need for new developments that open up new areas of research. Here, two approaches are described where standard simulation methodology is being expanded to treat diffusional dynamics of multi-protein systems and to treat proton transport in macromolecules.
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References
D.J. Bicout and M.J. Field, J. Phys. Chem. 100 (1996) 2489.
D.L. Ermak and J.A. McGammon, J. Chem. Phys. 69 (1978) 1352.
E. Dickinson, S.A. Allison and J.A. McCarnmon, J. Chem. Soc. Farad. Trans. 2 81 (1985) 591.
P. Mazur and W. van Saarloos, Physica 115A (1982) 21.
S.H. Northrup, in Cytochrome C: A Multi disciplinary Approach; (University Science Books, 1996) pp. 543.
R. G. Schmidt and J. Brickmann, Ber. Bunsenges. Phys. Chem. 101 (1997) 1816.
R. Vuilleumier and D. Borgis, Chem. Phys. Lett. 284 (1998) 71.
U. W. Schmitt and G. A. Voth, J. Phys. Chem. B102 (1998) 5547.
U. W. Schmitt and G. A. Voth, J. Chem. Phys. 111 (1999) 9361.
D. Marx, M. E. Tuckerman, J. Hutter, and M. Parrinello, Nature 397 (1999) 601.
M. E. Tuckerman, D. Marx, M. L. Klein, and M. Parrinello, Science 275 (1997) 817.
M.A. Lill and V. Helms, J. Chem. Phys. 114 (2001) 1125.
M.A. Lill, M.C. Hutter and V. Helms, J. Phys. Chem. A104 (2000) 8283.
M.A. Lill and V. Helms, J. Chem. Phys. 114 (2001) 7985.
M.A. Lill and V. Helms, J. Chem. Phys. 114 (2001) 7993.
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© 2003 Springer Science+Business Media New York
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Helms, V., Gorba, C., Lill, M. (2003). Computer Simulation Meets Molecular Biology. In: Macias, A., Uribe, F., Diaz, E. (eds) Developments in Mathematical and Experimental Physics. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-0207-4_9
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DOI: https://doi.org/10.1007/978-1-4615-0207-4_9
Publisher Name: Springer, Boston, MA
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