86 citations · 450 across the 18 of their papers we have counts for
18 papers
Paused in translation: A model for the transcript length-dependent impact of ribosome-targeting antibiotics
Johannes Keisers, Norbert Kern, Luca Ciandrini
Ribosome-targeting antibiotics, such as chloramphenicol, stall elongating ribosomes during protein synthesis, disrupting mRNA translation. These antibiotic-induced pauses occur sto…
The Hands-On Growth Laws Theory Cookbook
Rossana Droghetti, Mattia Corigliano, Ludovico Calabrese +6
This tutorial covers the emerging field of coarse-grained cellular growth modeling, and aims to bridge the gap between theoretical foundations and practical application. By adoptin…
Biologically relevant finite-size effects in a driven lattice gas with particle pausing and dynamical defects
Johannes Keisers, Lorenzo Vito Dal Zovo, Norbert Kern +1
In this article we present a comprehensive study of the totally asymmetric simple exclusion process with pausing particles (pTASEP), a model initially introduced to describe RNAP d…
Optimal control of ribosome population for gene expression under periodic nutrient intake
Clément Soubrier, Eric Foxall, Luca Ciandrini +1
Translation of proteins is a fundamental part of gene expression that is mediated by ribosomes. As ribosomes significantly contribute to both cellular mass and energy consumption,…
TASEPy: a Python-based package to iteratively solve the inhomogeneous exclusion process
Luca Ciandrini, Richmond L. Crisostomo, Juraj Szavits-Nossan
The totally asymmetric simple exclusion process (TASEP) is a paradigmatic lattice model for one-dimensional particle transport subject to excluded-volume interactions. Solving the…
An equilibrium model for ribosome competition
Pascal S. Rogalla, Timothy J. Rudge, Luca Ciandrini
The number of ribosomes in a cell is considered as limiting, and gene expression is thus largely determined by their cellular concentration. In this work we develop a toy model to…