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Cell growth is determined by substrate availability and the cell's metabolic capacity to assimilate substrates into building blocks. Metabolic genes that determine growth rate may interact synergistically or antagonistically, and can…
Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Escherichia coli that regulates…
Metabolic models condense biochemical knowledge about organisms in a structured and standardised way. As large-scale network reconstructions are readily available for many organisms, genome-scale models are being widely used among modellers…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense,…
One of the major characteristics of living organisms is metabolic rate, which is the amount of energy produced per unit of time. When the mass of organisms increases, the metabolic rate also increases (usually as a power function of mass),…
We study an optimal control problem arising from a resource allocation problem in cellular metabolism. A minimalistic model that describes the production of enzymatic vs. non-enzymatic biomass components from a single nutrient source is…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
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 metabolic networks. Our graphs encode the directionality of…
Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to…
The heterogeneity of reaction fluxes present in a metabolic network within a single flux state can be exploited to construct the so-called backbone as a reduced version of metabolism. The backbone maintains all significant fluxes producing…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
Growth rate is one of the most important and most complex phenotypic characteristics of unicellular microorganisms, which determines the genetic mutations that dominate at the population level, and ultimately whether the population will…
I consider how cell shape and environmental geometry affect the rate of nutrient capture and the consequent maximum growth rate of a cell, focusing on rod-like species like \textit{E.\ coli}. Simple modeling immediately implies that it is…
Cell colonies of bacteria, tumour cells and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell…
The interplay between energy efficiency and evolutionary mechanisms is addressed. One important question is how evolutionary mechanisms can select for the optimised usage of energy in situations where it does not lead to immediate…
Bacterial growth depends crucially on metabolic fluxes, which are limited by the cell's capacity to maintain metabolic enzymes. The necessary enzyme amount per unit flux is a major determinant of metabolic strategies both in evolution and…
Organisms must acquire and use environmental information to guide their behaviors. However, it is unclear whether and how information quantitatively limits behavioral performance. Here, we relate information to behavioral performance in…