Data collected and models code developed during the ATB project.
For further information contact Joe
Vallino listed on the ATB Home page
Microcosm Data
Below are the data collected on-line associated with O2, CO2
and CH4
gas concentrations and electrodes (pH and DO, but the latter became
unreliable due to probe drift). Concentration of nutrients in the
bioreactors were also periodically sampled and analyzed as given below.
ATBexp1.dat: Contains gas
concentrations in the reactor head space. See ATBexp.hdr header file for a
description of each data column. The .dat file can be read by
Tecplot.
ATBexp1.csv: Comma separated
values file for dissolved oxygen (mg/L), pH and ORP (mV) for each
microcosm.
ATBexp1.info:
File contains experimental notes, such as instrument calibrations,
etc.
ATBexp1.OnOff: Date, time
and experimental time when methane to MCs #1 and #4 was turned on (0)
and turned off (1).
ATBexp1_dCH4.dat:
Concentration of dissolved methane form experimental probe (see here). The
experimental probe only worked for a short time, but data was recorded
anyway.
MonitorGases_4.03.f90:
Fortran code compiled with Intel Visual Fortran used to monitor
bioreactors.
julday.for: Used to calculated
experimental elapsed time in days.
NO3alldata.csv:
Nitrate+nitrite concentration in all four MCs plus in the feed medium
(microMolar)
CHN.dat: Particulate organic C
and N in all four MCs and feed (microMolar)
DOC-DON-TDN.dat:
Dissolved organic C and N, and total dissolved organic N (microMolar)
NH4.dat: Ammonium concentration
(microMolar)
PO4.csv: Inorganic phosphate
concentration (microMolar). Note, on 19-May-2011 (t = 272.60
d), 10 mM phosphate buffer was added to feed medium, so collection of
phosphate samples stopped.
Sequence Data
DNA sequences of V4-V6 16S tags is publicly available on VAMPS under the
project JAH_ENT_Bv6v4.
Raw reads for V6 are available in the NCBI Short Read Archive
under Accession Number PRJNA322031.
Models 
Below is the Fortran code and output associate with the modeling work
described
in the Vallino et. al (2014) paper listed under the Publications tab.
All source code was compiled with Intel Visual Fortran (without
MKL), so there may be some complier associated function calls that may
not compile without errors with other compilers, such as gfortran
(this has not been tested though).
Methanotroph_BOBYQA_2_V4.1.f90:
Main program for simulating both control and cycled microcosms
described
on this web site and in Vallino et al. (2014)..
Module_Thermo_V2.F90:
Associated modules.
bobyqa_ArraysSpecified.f:
Slightly modified version of Powell's BOBYQA for finding local optima
without derivatives (also see here
and here).
bim_NoWrite.f:
Slightly modified version of BiM
used to solve the set of
governing ordinary differential equations.
subbim.f:
Supporting routines used by BiM.
Below are the input files and all model output for simulations of both
the control and cycled microcosms using different integration intervals
in the receding horizon optimal control problem. These runs
correspond to the data presented in Table 18.2 in the above reference
manuscript. The zip archives also contain Tecplot files for
visualizing output.
Interval_0.1-0.1.zip: Input and solutions for Δt = 0.1 and Δt* =
0.1 d
Interval_0.1-1.zip: Input and solutions for Δt = 0.1 and Δt* = 1 d
Interval_1-1.zip: Input and solutions for Δt = 1 and Δt* = 1 d
Interval_1-5.zip: Input and solutions for Δt = 1 and Δt* = 5 d
Interval_10-20.zip: Input and solutions for Δt = 10 and Δt* = 20 d
Interval_20-40.zip: Input and solutions for Δt = 20 and Δt* = 40 d
Interval_20-50.zip: Input and solutions for Δt = 20 and Δt* = 50 d