methanogenesis.time: Steps through time during a methanogenesis reaction

In hoehler-labgroup/methanogenlab: Methanogenesis Model

Steps through time during a methanogenesis reaction

Description

'methanogenesis.time()' calculates CH4 produced, H2 consumed, CO2 consumed, pH, and Gibbs free energy changes as dissolved inorganic carbon is consumed over time.

Usage

methanogenesis.time(
  CH4.initial,
  K.CH4 = NA,
  H2.initial,
  K.H2 = NA,
  is.H2.limiting = NA,
  Ks.H2,
  DIC.initial,
  pH.initial,
  K.CO2 = NA,
  is.CO2.limiting = NA,
  Ks.CO2,
  umax,
  temperature,
  VolumeSolution,
  VolumeHeadspace,
  K.CO2HCO3 = NA,
  K.HCO3CO3 = NA,
  time.step = 0.1,
  total.time = 5,
  inoculum.cell.number = 1e+06,
  biomass.yield = 2.4,
  carbon.fraction = 0.44,
  cell.weight = 3e-14
)

Arguments

CH4.initial	Concentration of initial dissolved CH4, in molarity.
K.CH4	Henry's constant for CH4. NA by default (calculated by CHNOSZ).
H2.initial	Concentration of initial dissolved H2, in molarity.
K.H2	Henry's constant for H2. NA by default (calculated by CHNOSZ).
is.H2.limiting	Boolean. Determines whether to use the Monod equation for H2. NA by default (limiting contribution determined by the proportion of current H2 and Ks.H2).
Ks.H2	Half-saturation constant for H2 (microorganism dependent), in molarity.
DIC.initial	Concentration of initial dissolved inorganic carbon, in molarity.
pH.initial	initial pH.
K.CO2	Henry's constant for CH4. NA by default (calculated by CHNOSZ).
is.CO2.limiting	Boolean. Determines whether to use the Monod equation for CO2. NA by default (limiting contribution determined by the proportion of current CO2 and Ks.CO2).
Ks.CO2	Half-saturation constant for CO2 (microorganism dependent), in molarity.
umax	Maximum growth rate for the microorganism, hr-1
temperature	Temperature of the system, in Kelvin.
VolumeSolution	Volume of liquid in the closed system, in liters.
VolumeHeadspace	Volume of gaseous head space in the closed system, in liters.
K.CO2HCO3	Equilibrium constant for the dissociation of CO2(aq) to HCO3-(aq). NA by default (calculated by CHNOSZ).
K.HCO3CO3	Equilibrium constant for the dissociation of HCO3- (aq) to CO3– (aq). NA by default (calculated by CHNOSZ).
time.step	Step size in time, in hours. 0.1 hrs by default.
total.time	Length of time the model will run, in hours. Note: the model may break before the total.time is reached if H2 or DIC runs out.
inoculum.cell.number	Initial number of cells. 1e6 by default.
biomass.yield	mass of dry biomass produced per mol of product. 2.4 g/mol product by default.
carbon.fraction	w/w percent C of biomass, expressed as a decimal. 0.44 by default.
cell.weight	individual cell mass, in grams. 30e-15 by default.

Value

A data frame of the model results

Examples

methanogenesis.time(
CH4.initial= 1e-6,
H2.initial= 5e-4,
is.H2.limiting=FALSE,
Ks.H2=10e-6,
DIC.initial= 3.2e-3,
pH.initial= 7.5,
is.CO2.limiting=TRUE,
Ks.CO2=20e-6,
umax=0.6,
temperature= 273.15+40,
VolumeSolution = 80e-3,
VolumeHeadspace = 20e-3,
time.step=0.1,
total.time=50,
inoculum.cell.number = 1e6,
biomass.yield=2.4,
carbon.fraction=0.44,
cell.weight=30e-15)

hoehler-labgroup/methanogenlab documentation built on April 25, 2022, 11:42 a.m.