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This publication constitutes the refereed complaints of the overseas convention on Computational tools in structures Biology, CMSB 2007, held in Edinburgh, Scotland, September 20-21, 2007.
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Federica Ciocchetta and Jane Hillston are supported by the EPSRC under the CODA project “Process Algebra Approaches for Collective Dynamics” (EP/c54370x/01 and ARF EP/c543696/01). Martin Kos is supported by European Commision (LSHG-CT-2005-518280) and David Tollervey is supported by The Wellcome Trust. References 1. : Ribosomal RNA processing and ribosome biogenesis in eukaryotes. IUBMB Life 56(8), 457–465 (2004) 2. : Crosstalk in gene expression: coupling and coregulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing.
We investigate by means of our model the influence of the point where CoTC happens on the growth of 20S and of 27S2. The results are reported in Fig. 8. The graph on the left concerns 20S and considers as point of CoTC the end of region 7, the end of region 13 and the end of the region 15. We see that the discrepancy between the different curves is minimal. However we can observe that the initial growth of 20S depends on the point of CoTC, in particular if CoTC happens towards the end of the transcription 20S increases slowly.
X(tR ), τR )) = R p(t0 ) (x0 ) · αmi−1 (x(ti−1 )) exp (α0 (x(ti−1 ))τi−1 ) (11) i=1 where α0 (x(ti−1 )) := α1 (x(ti−1 ))+· · · αM (x(ti−1 )), similarly as explained before and used in the direct generation of CTMC trajectories. Note that for a given time horizon over which the system is observed (and should be simulated) the number R of reactions is not known in advance and in particular not deterministic. Formally, R is a random stopping time2 which is in accordance with the requirement of dP being a density of a probability measure P defined on the path space of the Markov process.