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Pure Appl. Chem. 76(2), 295-302, 2004

Pure and Applied Chemistry

Vol. 76, Issue 2

Simulations on many scales: The synapse as an example

K. Tai

Department of Biochemistry, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK

Abstract: Computer simulation methods spanning several temporal and spatial scales are reviewed, focusing on their applications on the neuromuscular synapse. Quantum mechanics treats the enzymatic catalysis of neurotransmitters on the picometer scale. Molecular dynamics reveals conformational changes of the enzyme acetylcholinesterase for nanoseconds. Brownian dynamics follow the substrate molecule in its diffusion on the microsecond level. Methods such as finite elements describe the diffusion of neurotransmitters as a changing concentration continuum in the synapse. Promising directions for future research include integration of methods on several scales, and applying these methods to the acetylcholine receptor.

[full text - pdf 606KB]

*Pure Appl. Chem. 76, 263-319 (2004). A collection of invited, peer-reviewed articles by the winners of the 2003 IUPAC Prize for Young Chemists.

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