HabitabilityTheOry 0.0.4

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

HaThOr

Habitable TheOry

Install

pip install HabitabilityTheOry

Import

import HaThOr

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.

Example

import HaThOr.chem_helper as chem
import HaThOr.Metabolisms as mtb
mgis = chem.Reaction(**chem.hydrogenotrophy_dat) # The reaction for methanogenesis
HMG = mtb.Metabolism(reaction=mgis)
parameters = {'tau': 8.8e-3,'A': 5e13,'DGac': 72421.0,'DGam': 92626.0,'d':0.005}
FT_HMG = mtb.Organism(metabolism=HMG,**parameters)
# Get the limit viability Gibbs free energy at pH=7 and T=320
FT_HMG.DeltaGstar(320,pH=7.0)