Joris Paijmans

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Biological systems often have to measure extremely low concentrations of chemicals with high precision. When dealing with such small numbers of molecules, the inevitable randomness of physical transport processes and binding reactions will limit the precision with which measurements can be made. An important question is what the lower bound on the noise(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 homohexamer, 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)
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)
The diffusive arrival of transcription factors at the promoter sites on 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)
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. Elowitz and Leibler [Nature (London) 403, 335 (2000)NATUAS0028-083610.1038/35002125] showed that by rational design of the reaction network, and using existing biological components, they could create a network that exhibits(More)
Traditional approaches to the task of automatic classification of music by genre generally focus on the use of note-duration symbols to represent musical content. As well, most studies generally extract information from a combination of instruments. This paper compares the traditional method of using note-duration symbols with another method based on time(More)
This paper is concerned with information storage and retrieval systems for museums, in particular for museums of art and history. During the last 10 or 15 years quite a few such systems have been built 1 and the time has come to reassess their merits, their impact (or lack of it) on the museum world and the new possibilities opened up in this direction by(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.
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 approximately one day in different constant environments. The posttranslational oscillator of the Kai system can be entrained by transient or(More)