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TASEP models

The TASEP, or "totally asymmetric exclusion process", is a statistical physics model in which particles move along a one-dimensional lattice, hopping in one direction between discrete sites, such that each site can only be occupied by one particle at a time. This model is interesting because it is very generic: it can be used to model problems ranging from traffic queuing all the way to protein production in biological cells. Philip Greulich, a postdoc working with me in Edinburgh, worked together with Luca Ciandrini, a PhD student working with Mamen Romano at Aberdeen University, and me, on a project in which we used the TASEP to model cellular protein production. In a biological cell, protein is produced ina 2-step process. First, the DNA sequence that encodes a protein is copied, or transcribed, into an mRNA molecule. Next, ribosome protein complexes move along the mRNA, translating the coding sequence into a protein molecule. Our project was inspired by the fact that in cells, different mRNA molecules have to compete for a limited pool of ribosomes. This led us to investigate a model in which several TASEP processes compete for a shared reservoir of particles. We studied this model by constructing a mean field model in which the density of "free" particles is described by a single equation. The input to this equation is the known statistical physics behaviour of the TASEP. This model turns out to show interesting behaviour, including a "buffering" effect, in which the presence of a subpopulation of "particle-hungry" TASEPs can prevent fluctuations in the particle number being felt by other TASEPs.

 

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25/08/2022

Here is a great 3 minute video of our PhD student Freya Bull describing her research modelling bacterial infection of a urinary catheter!

25/08/2022

We are searching for a part-time computer systems administrator for our group in Jena. Please contact us if you are interested!

18/08/2022

Welcome to Ariane Zander who has joined us as a technician in our lab!

 
 

 

 
 
 
 
 
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