Modelling the effect of ribosome mobility on the rate of protein synthesis

Abstract: Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally, while unbound ribosomes diffuse in the cytoplasm. It has been hypothesized that finite diffusion of ribosomes plays an important role in ribosome recycling and that mRNA circularization enhances the efficiency of translation, see e.g. Lodish et al. (Molecular cell biology, 8th edn, W.H. Freeman and Company, San Francisco, 2016). In order to estimate the effect of cytoplasmic diffusion on the rate of translation, we consider a totally asymmetric simple exclusion process coupled to a finite diffusive reservoir, which we call the ribosome transport model with diffusion. In this model, we derive an analytical expression for the rate of protein synthesis as a function of the diffusion constant of ribosomes, which is corroborated with results from continuous-time Monte Carlo simulations. Using a wide range of biological relevant parameters, we conclude that diffusion is not a rate limiting factor in translation initiation because diffusion is fast enough in biological cells. Graphic abstract: [Figure not available: see fulltext.].

Opinion dynamics with emergent collective memory: The impact of a long and heterogeneous news history

In modern society people are being exposed to numerous information, with some of them being frequently repeated or more disruptive than others. In this paper we use a model of opinion dynamics to study how this news impact the society. In particular, our study aims to explain how the exposure of the society to certain events deeply change peopletextquoterights perception of the present and future. The evolution of opinions which we consider is influenced both by external information and the pressure of the society. The latter includes imitation, differentiation, homophily and its opposite, xenophobia. The combination of these ingredients gives rise to a collective memory effect, which is triggered by external information. In this paper we focus our attention on how this memory arises when the order of appearance of external news is random. We will show which characteristics a piece of news needs to have in order to be embedded in the societytextquoterights memory. We will also provide an analytical way to measure how many information a society can remember when an extensive number of news items is presented. Finally we will show that, when a certain piece of news is present in the societytextquoterights history, even a distorted version of it is sufficient to trigger the memory of the originally stored information.