Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory interactions. Here, we use mathematical modeling to show that, additionally, the cell cycle generically influences circadian… (More)
This research presents an evaluation of a recommender system that automatically generates recommendations for articles from an online newspaper. A prototype of a recommender system was built in cooperation with a Dutch newspaper called " Trouw ". With the data retrieved from Trouw, the system was able to recommend articles for news articles that were daily… (More)
Circadian clocks must be able to entrain to time-varying signals to keep their oscillations in phase with the day-night rhythm. On the other hand, they must also exhibit input compensation: their period must remain about one day in different constant environments. The post-translational oscillator of the Kai system can be entrained by transient or… (More)
The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homo-hexamer, with each monomer consisting of two domains, CI and CII. Both domains can bind and hydrolyze ATP, but only the CII domain can be phosphorylated, at two residues, in… (More)
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing biological components, they could create a network that exhibits periodic gene expression, dubbed the repressilator… (More)
The diffusive arrival of transcription factors at the promoter sites on the DNA sets a lower bound on how accurately a cell can regulate its protein levels. Using results from the literature on diffusion-influenced reactions, we derive an analytical expression for the lower bound on the precision of transcriptional regulation. In our theory, transcription… (More)
This paper discusses the problems and possibility of collecting bee dance data in a linguistic corpus and use linguistic instruments such as Zipf's law and entropy statistics to decide on the question whether the dance carries information of any kind. We describe this against the historical background of attempts to analyse nonhuman communication systems.