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Open Access Research article

System size reduction in stochastic simulations of the facilitated diffusion mechanism

Nicolae Radu Zabet

Author Affiliations

Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK

Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK

BMC Systems Biology 2012, 6:121  doi:10.1186/1752-0509-6-121

Published: 8 September 2012

Additional files

Additional file 1:

Supplementary Material. The Supplementary Material contains extra figures which confirm that the measured one-dimensional parameters are conserved in the subsystems. These parameters include: residence time, sliding length, actual sliding length and proportion of time the molecules spend on the DNA. In addition, the Supplementary Material contains an alternative method to scale the system which assumes that λ (the scaling factor) is determined by the ratio between sum of all waiting times in the subsystem and sum of all waiting times in the full system.

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