Gene expression is a complex multistage process in which information encoded in the DNA is used to generate proteins or other gene products. Gene expression involves two primary stages:  transcription and translation. Each of these stages involves the sequential movement of "molecular machines" along the genetic material. During transcription, RNA copies of the DNA genes are synthesized by enzymes called RNA polymerase. The product is the messenger RNA (mRNA), which codes, by a series of nucleotide triplets (called codons), the order in which amino-acids need to be combined to synthesize the protein.

Translation is the process in which the information in the mRNA is decoded and the protein is synthesized. During translation, complex macromolecules called ribosomes bind to the start codon in the mRNA and sequentially decode each codon to its corresponding amino-acid that is delivered to the awaiting ribosome by transfer RNA (tRNA) molecules. The amino-acid peptide is elongated until the ribosome reaches a stop codon, detaches from the mRNA and the resulting amino-chain peptide is released, folded and becomes a functional protein. The detached ribosome may re-initiate the same mRNA molecule (ribosome recycling) or become available to translate other mRNAs. To increase translation efficiency, multiple ribosomes may decode the same mRNA molecule simultaneously (forming a polysome).

mRNA translation is a fundamental process in all living cells of all organisms. Thus, a better understanding of its bio-physical properties has numerous potential applications in many scientific disciplines including medicine, systems biology, biotechnology and evolutionary biology.

Mechanistic models of translation are essential for:analyzing the flow of ribosomes along the mRNA molecule and integrating and understanding the rapidly increasing experimental findings related to translation and its role in the dynamic regulation of gene expression.

The ribosome flow model (RFM) is a deterministic model for the flow of particles satisfying a relaxed simple exclusion principle i.e. two particles cannot be in the same place at the same time. It has been extensively used to model and analyze ribosome flow along a single mRNA molecule and in networks of interconnected mRNAs.