Ian Stansfield | Searcharxiv

arXiv2021

Two-species TASEP model: from a simple description to intermittency and travelling traffic jams

We extend the paradigmatic and versatile TASEP (Totally Asymmetric Simple Exclusion Process) for stochastic 1d transport to allow for two different particle species, each having specific entry and exit rates. We offer a complete mean-field analysis, including a phase diagram, by mapping this model onto an effective one-species TASEP. Stochastic simulations confirm the results, but indicate deviations when the particle species have very different exit rates. We illustrate that this is due to a phenomenon of intermittency, and formulate a refined 'intermittent' mean-field (iMF) theory for this regime. We discuss how non-stationary effects may further enrich the phenomenology.

cond-mat.stat-mech↗

arXiv2021

ExpressInHost: A codon tuning tool for the expression of recombinant proteins in host microorganisms

ExpressInHost (https://gitlab.com/a.raguin/expressinhost) is a GTK/C++ based user friendly graphical interface that allows tuning the codon sequence of an mRNA for recombinant protein expression in a host microorganism. Heterologous gene expression is widely implemented in biotechnology companies and academic research laboratories. However, expression of recombinant proteins can be challenging. On the one hand, maximising translation speed is important, especially in scalable production processes relevant to biotechnology companies, but on the other hand, solubility problems often arise as a consequence, since translation "pauses" might be key to allow the nascent polypeptide chain to fold appropriately. To address this challenge, we have developed a software that offers three distinct modes to tune codon sequences using the genetic code redundancy. The tuning strategies implemented take into account the specific tRNA resources of the host and that of the native organism. They balance rapid translation and native speed mimicking, which might be important to allow proper protein folding, thereby avoiding protein solubility problems.

physics.bio-ph↗