Neil Dalchau

November 1, 2007


Neil Dalchau obtained an undergraduate masters degree in Mathematics (MMath) from the University of Oxford in 2005. During the final year, he also spent some time working on finite element methods for electromagnetic problems at Vector Fields Ltd. He is currently (2007) at the beginning of his third year at the University of Cambridge working in a collaborative project between Alex Webb (Dept. of Plant Sciences) and Jorge Goncalves (Dept. of Engineering). He is interested in Systems Identification techniques for linear and nonlinear systems, and network reconstruction methods. His research has used these tools to learn properties of uncharacterised mechanisms in the face of noisy biological observations. .


Almost all organisms have evolved a circadian clock, a genetic network of interlocking feedback loops which provide temporal information at the cellular level. The circadian clock controls many physiological processes, conferring great advantages to the fitness of the organism. Circadian biology has seen great interest from mathematical modellers in recent years, due to the complex network of feedback loops. This work is predominately concerned with the core mechanism which generates the oscillations, the components of which are often known. In Arabidopsis thaliana, the model plant organism, many of the central oscillator genes are known, but the pathways through which they regulate physiology are often completely uncharacterised. We have been investigating experimentally and mathematically the interplay between the circadian clock and the uncharacterised signalling pathways of calcium (Ca2+), light and sugars.

In this talk, two studies will be presented. With a careful choice of training data, we show how linear systems can be used to predict Ca2+ dynamics resulting from uncharacterised pathways. These pathways are replaced with explicit time delays, and the resulting models show the necessity for two inputs controlling Ca2+ signals through extensive validation. Also, a bifurcation matching method is proposed for adjusting existing clock models to different experimental conditions (the external availability of sugars). This leads to testable hypotheses for the targets of sugar signalling in the circadian clock.