From Metabolites to Cells: A Perspective on Non-Equilibrium Thermodynamics

Cells may be seen as chemical factories, processing a fuel source taken from the environment and producing the chemical building blocks vital for life. However, cells are rarely found in isolation with many biological systems being spatially organised. Understanding the non-equilibrium thermodynamics behind cell growth, cell death, and self-organisation is of great importance for when we want to program bio-systems for "useful" work such as biofuel production or industrial chemical synthesis.

We can model these processes using a systems approach and represent the chemical conversions by chemical reaction networks. By regulating the protein translation and cost behind the production of reaction catalysing enzymes, the flux through the reaction pathways can be controlled to change the chemical concentrations and selectively produce metabolites. By controlling the chemical reactions within a cell these processes can be altered to produce select byproducts, such as biofuels. This however requires a firm understanding of the chemistry and reaction regulation that occurs within each cell.

Investigations into these cellular systems require a multi-scale approach. Cells interact with their environment to form ecological niches through the excretion and uptake of chemicals, which form chemical gradients that influence organisation and can provide a strong cumulative impact of the cells onto their environment. Therefore we require a range of modelling paradigms as we transition from discussing metabolites to studying cells and the ecosystem.

In this talk, we will provide an overview of field from the perspective of cells as chemical factories and discuss a selection of methods used to study cell systems.