4 papers
Stochastic modelling reveals mechanisms of metabolic heterogeneity
Mona K. Tonn, Philipp Thomas, Mauricio Barahona +1
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth varia…
Flux-dependent graphs for metabolic networks
Mariano Beguerisse-Díaz, Gabriel Bosque, Diego Oyarzún +2
Cells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide…
Shaping Pulses to Control Bistable Biological Systems
Aivar Sootla, Diego Oyarzun, David Angeli +1
In this paper we study how to shape temporal pulses to switch a bistable system between its stable steady states. Our motivation for pulse-based control comes from applications in…
Dynamic optimization of metabolic networks coupled with gene expression
Steffen Waldherr, Diego A. Oyarzún, Alexander Bockmayr
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at stea…