The process of polymerizing a protein by a ribosome, using a messenger RNA
(mRNA) as the corresponding template, is called {\it translation}. Ribosome may
be regarded as a molecular motor for which the mRNA template serves also as the
track. Often several ribosomes may translate the same (mRNA) simultaneously.
The ribosomes bound simultaneously to a single mRNA transcript are the members
of a polyribosome (or, simply, {\it polysome}). Experimentally measured {\it
polysome profile} gives the distribution of polysome {\it sizes}. Recently a
breakthrough in determining the instantaneous {\it positions} of the ribosomes
on a given mRNA track has been achieved and the technique is called {\it
ribosome profiling} \cite{ingolia10,guo10}. Motivated by the success of these
techniques, we have studied the spatio-temporal organization of ribosomes by
extending a theoretical model that we have reported elsewhere \cite{sharma11}.
This extended version of our model incorporates not only (i) mechano-chemical
cycle of individual ribomes, and (ii) their steric interactions, but also (iii)
the effects of (a) kinetic proofreading, (b) translational infidelity, (c)
ribosome recycling, and (d) sequence inhomogeneities. The theoretical framework
developed here will serve in guiding further experiments and in analyzing the
data to gain deep insight into various kinetic processes involved in
translation.Comment: Minor revisio
