The Tools

The Next Subvolume Method (Elf and Ehrenberg, IEE Systems Biology, 2004) is a very efficient method for simulating stochastic reaction diffusion kinetics.  The algorithm is for instance implemented in our MesoRD software (Hattne et al. Bioinformatics, 2005, Fange et al. PNAS 2010). MesoRD has for instance been used to understand the noise induced phenotypes of the E. coli Min system (Fange and Elf PLoS CB, 2006; Fange Bioinformatics 2012).

We have developed new methods for probing transcription factor dynamics at the level of single molecule in living cells (Hammar et al. Science 2012). These methods make it possible to study gene regulation directly and at a higher time resolution than methods based on expression of reporter genes.
We are also developing new methods for tracking individual proteins molecules in living cells at ms time resolution (English et al. PNAS 2011).

The theory for selective charging of tRNA (Elf et al. Science 2003) explains how the genetic code is used under amino acid limitation.  The theory has now been tested in a number of experimental studies (EMBO rep, 2005, EMBO rep, 2005 JMB, 2005).

The generalization of zero order kinetics to several dimensions (Elf et al. Biophys J, 2003, Genome Res, 2003), that implies that the substrate pools to multi substrate reactions can display huge stochastic fluctuations and ultra sensitivity because the increase in one pool is compensated by the decrease in an other so that the overall flux is conserved. The observation has consequences for the flux of amino acids in protein synthesis (Biophys J, 2005).

New theoretical methods to analyze stochastic processes makes it possible to investigate the consequences of time delays in gene regulatory control circuits (Grönlund et al. PNAS 2009, Nature Communications 2010)