HabitabilityTheOry 0.0.3

This package contains some useful functions to assess habitability of Chemostat-like environments to energy-limited microbes.

HaThOr

Habitable TheOry

Rationale and goals

Here, we use habitable theory to build a tool to assess habitability at a large spectrum

We have a model frame for growth:

[ k_g = A \lambda \tau e^{-\frac{\Delta G_{ac}}{RT}} - A e^{-\frac{\Delta G_{am}}{RT}} ] where

• $k_g$ is the specific growth rate (s$^{-1}$)
• $A$ pre-exponential factor (s$^{-1}$)
• $\lambda = - \Delta_rG_c/E_{ana}$ the catabolic yield
• $\tau$ active biomass fraction (mol enzyme per mole biomass)
• $\Delta G_{ac}$ activation gibbs free energy of the catabolic reaction (J/mol)
• $\Delta G_{am}$ activation gibbs free energy of the maintenance reaction (J/mol)
• $R=8.314$ (J/(K mol)) is the perfect gas constant
• $T$ absolute temperature (K)

Some of these parameters can be estimated from growth curves (see Guyot and Affholder in prep).

Structure of the package HaThOr:

• chem_helper contains some helper functions and stoichiometric data for some organisms
• Metabolisms contains the classes metabolism and organism that are designed to build objects representing a functional type with a given metabolism and a given set of parameters
• Chemostat contains the chemostat class, used to define an environment and calculate biomass etc.