EE Seminar: The Ribosome Flow Model: Theory and Applications

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Speaker: Yoram Zarai
Ph.D. student under the supervision of Prof. Michael Margaliot

Wednesday, November 25th, 2015 at 15:00
Room 011, Kitot Bldg., Faculty of Engineering

The Ribosome Flow Model: Theory and Applications

Abstract
Gene expression is the process by which information encoded in the genes is transformed into proteins. Protein synthesis begins with the transcription of the genetic information from DNA to mRNA, and proceeds to translation of the mRNA to proteins. During translation, molecular machines called ribosomes move along the mRNA chain, decoding triplets of mRNA nucleotides (called codons) into a chain of amino acids that is then folded into a protein. The translation process occurs in all organisms, in all known cells and in almost all conditions. Thus, understanding translation has important implications in many scientific disciplines, including medicine, biotechnology, and synthetic biology.

The Ribosome Flow Model (RFM) is a deterministic mathematical model for the flow of ribosomes along the mRNA chain. It consists of   first-order, nonlinear ordinary differential equations, and   parameters: the initiation rate   and elongation rates  ,  , between the consecutive sites. The RFM can be derived as a mean-field approximation of an important model from non-equilibrium statistical physics called the Totally Asymmetric Simple Exclusion Process (TASEP).

In this work, we study the RFM using tools from systems and control theory including contraction theory, monotone dynamical systems theory, the analytic theory of continued fractions, controllability and accessibility theory, and convex analysis.

We detail several biological implications of the analysis, provide examples of applications of the RFM other than translation, and discuss several possible directions for future research.