This README file was generated on 2022-09-04 by Artem Kalinin.


GENERAL INFORMATION

Dataset for the calibration of the photosynthetic unit (PSU)-model developed at KIT

Author:		Artem Kalinin
Institution:	Karlsruhe Institute of Technology (KIT)
			Institute of Process Engineering in Life Sciences – Bioprocess Engineering
			Building 30.44, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
Email:		artem.kalinin@kit.edu

Co-author:		Prof. Dr.-Ing. Clemens Posten
Institution:	Karlsruhe Institute of Technology (KIT)
			Institute of Process Engineering in Life Sciences – Bioprocess Engineering
			Building 30.44, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
Email:		clemens.posten@kit.edu

The presented dataset was used to develop and calibrate (estimate the model parameters) a photosynthetic unit (PSU)-model. The PSU-model and the data were generated at the Institute of Process Engineering in Life Sciences – Bioprocess Engineering of the KIT under the supervision of Prof. Dr.-Ing. Clemens Posten. Please use this data to familiarize yourself with the PSU-model and as an example dataset. If you want to use your own data in this context, organize it like the sample data listed here. As an alternative, you should adapt the model scripts to your data accordingly.

Date of data collection: The data were generated as a part of the author’s PhD program between 2018-2022 at Karlsruhe Institute of Technology (KIT).


SHARING/ACCESS INFORMATION

This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.

Please cite the following relevant reference when using the present dataset or parts of it in any publication:
	DOI: 10.5445/IR/1000156200

DOI of the PSU-model that uses this dataset: 10.5281/zenodo.7054799

The in vivo absorption coefficients of the pigments (Ea_i in m²/kg; in this case, only data of Chlorophyll a, Chlorophyll b and the photoprotective Carotenoids are required) can be found in the following literature:

Bidigare, R. R.; Ondrusek, M. E.; Morrow, J. H.; Kiefer, D. A. (1990): In-vivo absorption properties of algal pigments. In: Richard W. Spinrad (Hg.): Ocean Optics X. Orlando '90, 16-20 April. Orlando, FL, United States: SPIE (SPIE Proceedings), S. 290.

And/or

Dauchet, J.; Blanco, S.; Cornet, J.-F.; Fournier, R. (2015): Calculation of the radiative properties of photosynthetic microorganisms. In: Journal of Quantitative Spectroscopy and Radiative Transfer 161, S. 60–84. DOI: 10.1016/j.jqsrt.2015.03.025.
Link to the data base: http://edstar.lmd.jussieu.fr/databases (last checked: 2022-09-04)


DATA & FILE OVERVIEW FOR: accl_fast_data.mat

Nomenclature:

accl: photoacclimated cells

avrg: average/mean

dzR: steps along the depth of the corresponding apparatus (flat-panel photobioreactor (PBR) or photosynthesis measurement cell (PMC))

fast: acclimated data used during the experiments to determine fast photosynthesic rate (P) vs. irradiance (I)-curves (fast PI-curves)

fit: fitted data or is based on fitted data

LL, ML & HL: low light, medium light & high light

spctrm: spectral data or spectrum of a LED-array

ss: steady state/stationary data

Experimental data:

1)	avrg_LED_PMC_spctrm: spectrum of the LEDs used in the PMC

2)	avrg_LED_R_spctrm: spectrum of the LEDs used in the PBRs

3)	LLMLHL_fast_P_Netto: Chlorophyll-specific oxygenic photosynthesis rates of Chlorella 	vulgaris acclimated to LL, ML & HL (fast PI-curves in mol O2/mol Chl/s)
	-> dimensions: [acclimation states x number of measurements]

4)	PMC_PFD0: set actinic photon flux densities (PFDs; in µmol/m²/s) on the surface of the PMC 	(fast PI-curves); corresponds to the number of measurements for each acclimation state

5)	ss_accl_PFD0: the set actinic PFDs on each of the two surfaces of a PBR; corresponds to the 	number of photoacclimated states of C. vulgaris

6)	ss_accl_c_bdm: bio-dry mass (bdm) concentration (in g/L or kg/m³)

7)	ss_accl_w_chla: weight-fraction of Chlorophyll a in photoacclimated C. vulgaris (in g Chla/g 	bdm)

8)	ss_accl_w_chlb: weight-fraction of Chlorophyll b in photoacclimated C. vulgaris (in g Chlb/g 	bdm)

9)	ss_accl_w_car: weight-fraction of Carotenoids in photoacclimated C. vulgaris (in g Car/g 	bdm)

10)	ss_accl_phi_RCII: maximum efficiency of a reaction center II (RCII) in a given photoacclimated 	state; corresponds to Fv’/Fm’ in common literature; note: ss_accl_phi_RCII was not 	measured for the photoacclimated state with ss_accl_PFD0 = 77.03 µmol/m²/s!

11)	ss_fast_PFD0: same as ss_accl_PFD0, but used exclusively to determine/simulate fast PI-	curves

12)	ss_fast_c_bdm: same as ss_accl_c_bdm, but used exclusively to determine/simulate fast PI-	curves

13)	ss_fast_w_chla: same as ss_accl_w_chla, but used exclusively to determine/simulate fast PI-	curves

14)	ss_fast_w_chlb: same as ss_accl_w_chlb, but used exclusively to determine/simulate fast PI-	curves

15)	ss_fast_w_car: same as ss_accl_w_car, but used exclusively to determine/simulate fast PI-	curves

16)	ss_fast_phi_RCII: same as ss_accl_phi_RCII, but used exclusively to determine/simulate fast 	PI-curves

17)	Ea_chla, Ea_chlb & Ea_car: see “SHARING/ACCESS INFORMATION”; experimental data not 	provided here, but required

Data from literature:

1)	M_chla & M_chlb: molecular weight of Chlorophyll a & Chlorophyll b, respectively (in g/mol)

2)	ss_accl_r_mnt_bdm: bdm-specific maintenance respiration rate (in mol/g/s)*

3)	ss_accl_y_resp_P_Brutto: relative cost of synthesis of new biomass**

*: Kliphuis, A. M. J.; Klok, A. J.; Martens, D. E.; Lamers, P. P.; Janssen, M.; Wijffels, R. H. (2012): Metabolic modeling of Chlamydomonas reinhardtii: energy requirements for photoautotrophic growth and maintenance. In: J Appl Phycol 24 (2), S. 253–266. DOI: 10.1007/s10811-011-9674-3.
**: Geider, R. J.; Osborne, B. A. (1989): Respiration and microalgal growth: a review of the quantitative relationship between dark respiration and growth. In: New Phytol 112 (3), S. 327–341. DOI: 10.1111/j.1469-8137.1989.tb00321.x.

Computed input data:

1)	LLMLHL_fast_PMC_PFD_dzR: computed light profiles for each data point in 	LLMLHL_fast_P_Netto (in µmol/m²/s) -> dimensions:
	[acclimation states x number of measurements x steps along the PMC depth]

2)	sim_PMC_PFD0: additional simulated PMC_PFD0-values (e.g.: sim_PMC_PFD0 = (0:10:1500)’;);
	optional, only required if line plots are desired

3)	sim_PMC_PFD_dzR: resulting light profiles (in µmol/m²/s); optional, only required if line plots 	are desired -> dimensions: [acclimation states x number of measurements x steps along the PMC depth]

4)	spctrm: light wavelengths between 400-700 nm (spctrm = (400:1:700)’;)

5)	ss_accl_m_ccell: computed refractive index (RI) of the cell core****

6)	ss_accl_n_Rubisco_max_bdm: maximum number of Rubisco per g bdm***

7)	ss_accl_p_phi_RCII: parameters of the logistic function fitted to the phi_RCII data

8)	ss_accl_p_w_chla, ss_accl_p_w_chlb, ss_accl_p_w_car: parameters of the logistic function 	fitted to the respective weight-fraction data

9)	ss_accl_PFD: averaged (over the PBR depth) actinic PFD (in µmol/m²/s)

10)	ss_fast_PFD: same as ss_accl_PFD, but used exclusively to determine/simulate fast PI-curves

11)	ss_fast_fit_m_ccell: same as ss_fast_m_ccell, but computed with fitted values of 	ss_fast_w_chla, ss_fast_w_chlb & ss_fast_w_car****

12)	ss_fast_m_ccell: same as ss_accl_m_ccell, but used exclusively to compute the light profiles 	for the determination/simulation of fast PI-curves****

***: the exact computation is shown in the PhD thesis (DOI: 10.5445/IR/1000156200)
****: the exact computation is shown in the PhD thesis (DOI: 10.5445/IR/1000156200) or in:

Kandilian, R.; Pruvost, J.; Artu, A.; Lemasson, C.; Legrand, J.; Pilon, L. (2016): Comparison of experimentally and theoretically determined radiation characteristics of photosynthetic microorganisms. In: Journal of Quantitative Spectroscopy and Radiative Transfer 175, S. 30–45. DOI: 10.1016/j.jqsrt.2016.01.031.

And (also the required Kramers-Kronig script can be found here)

Lucarini, V.; Peiponen, K.-E.; Saarinen, J. J.; Vartiainen, E. M. (2005): Kramers-Kronig relations in optical materials research. Berlin, Heidelberg: Springer-Verlag Berlin Heidelberg (Springer Series in Optical Sciences, 110).

Results (not required as model inputs):

1)	k_PSU_model: estimated kinetic parameters of the PSU-model (rate constants k_RCII,lim & 	k_PSU,lim; in 1/s)

2)	sim_LLMLHL_fast_P_Netto_dzR: simulated Chlorophyll-specific oxygenic photosynthesis 	rates of C. vulgaris acclimated to LL, ML & HL (fast PI-curves in mol O2/mol Chl/s)
	-> dimensions:
	[acclimation states x number of simulated measurements x steps along the PMC depth]

3)	sim_LLMLHL_fast_PMC_PFD_dzR: computed light profiles for each data simulated PFD0 (in 	µmol/m²/s)
	-> dimensions: [acclimation states x number of measurements x steps along the PMC depth]

4)	sim_LLMLHL_fast_r_diss_dzR: simulated PSU-specific energy dissipation rate (in 1/s)
	-> dimensions: [acclimation states x number of measurements x steps along the PMC depth]

5)	sim_LLMLHL_fast_x_dzR: simulated fractions of the modelled PSU-components (RCII_open, 	RCII_closed, PQ_open & PQ_closed)
	-> dimensions: [acclimation states x number of measurements x steps along the PMC depth]

6)	ss_accl_b634: fraction of light (wavelength = 634 nm) backscattered from photoacclimated C. 	vulgaris cells

7)	ss_accl_spctrm_kappa_bdm: bdm-specific scattering cross-section of photoacclimated C. 	vulgaris cells (in m²/kg)

8)	ss_accl_spctrm_sigma_bdm: bdm-specific absorption cross-section of photoacclimated C. 	vulgaris cells (in m²/kg)

9)	ss_fast_b634: same as ss_accl_b634, but used exclusively to determine/simulate fast PI-	curves

10)	ss_fast_spctrm_kappa_bdm: same as ss_accl_spctrm_kappa_bdm, but used exclusively to 	determine/simulate fast PI-curves

11)	ss_fast_spctrm_sigma_bdm: same as ss_accl_spctrm_sigma_bdm, but used exclusively to 	determine/simulate fast PI-curves

12)	stat_tbl_phi_RCII, stat_tbl_pigm & stat_tbl_PSU_model: tables with statistical parameters for 	quantifying the respective goodness of fit


METHODOLOGICAL INFORMATION

The generation of experimental data is described in detail here (in German):
	DOI: 10.5445/IR/1000156200

All photoacclimated states of C. vulgaris were reproduced twice in identical flat-panel PBRs (1 L working volume, double-sided illumination). The C. vulgaris cells were acclimated for at least 72 h to each PFD before sampling. To achieve a stationary acclimation state of the cells, continuous cultivations with optically thin C. vulgaris cultures were performed. Each analytical method was performed in triplicates. Therefore, each experimental value presented is the average of a total of 6 measurements. However, obvious outliers were removed in the respective cases. This applies only to own experimental data, except in the case of avrg_LED_PMC_spctrm, avrg_LED_R_spctrm, PMC_PFD0, ss_accl_PFD0 & ss_fast_PFD0.

LED spectra and PFD0:

The respective LED spectra (avrg_LED_PMC_spctrm & avrg_LED_R_spctrm) were measured with the spectrophotometer AvaSpec-3648. The PFD0 values (PMC_PFD0, ss_accl_PFD0 & ss_fast_PFD0) were determined with a planar quantum sensor (LI-COR LI-190SA with LI-250 light meter).

Bdm-concentrations:

A gravimetrical method & also an optical density (OD)-based method were applied to quantify the bdm-concentrations (ss_accl_c_bdm & ss_fast_c_bdm).

Concentrations of pigments:

The concentrations of the respective pigments were determined photometrically according to the method presented by Wellburn (see reference below). The extraction of the pigments was done with DMSO. For this purpose, 950 µL were added to the cell samples (50 µL) and incubated at 45 °C and 600 rpm for 20 minutes in a thermal incubator. Subsequently, the cell-free supernatant was photometrically measured at the following light wavelengths: 665, 649 & 480 nm (PerkinElmer LAMBDA 35 UV/Vis). The equations used to calculate the concentrations based on the absorbance values can be found in the source material. The respective pigment concentrations were divided by the corresponding bdm-concentrations to get ss_accl_w_chla, ss_accl_w_chlb, ss_accl_w_car, ss_fast_w_chla, ss_fast_w_chlb & ss_fast_w_car.
Wellburn, A. R. (1994): The spectral determination of chlorophylls a and b, as well as total carotenoids, using various solvents with spectrophotometers of different resolution. In: Journal of Plant Physiology 144 (3), S. 307–313. DOI: 10.1016/S0176-1617(11)81192-2.

Fluorometer measurements:

The Fluorometer FL 6000-F (with FluorWin Software 3.7) was used for the measurement of ss_accl_phi_RCII & ss_fast_phi_RCII (both correspond to Fv’/Fm’ in common literature; see references below) in each photoacclimated state of C. vulgaris.

The following parameters were set during each measurement (protocol: “Quenching Analysis”):

1)	act. light voltage [%]: variable, depending on the photoacclimated state of C. vulgaris
2)	sat. pulse voltage [%]: 80 %
3)	actinic light exposure duration [s]: 180
4)	dark relaxation duration [s]: 120
5)	only measuring flash 1 was used
6)	m. flash voltage [%]: 10
7)	gain: 10 %
8)	offset: 15 %

For each measurement, 4 mL of a fresh sample was used. The microalgal cells were incubated in the dark for approx. 15 min before each measurement.
Baker, N. R. (2008): Chlorophyll fluorescence: a probe of photosynthesis in vivo. In: Annual review of plant biology 59, S. 89–113. DOI: 10.1146/annurev.arplant.59.032607.092759.
Photon Systems Instruments (2019): Dual-modulation kinetic fluorometer FL 6000. Manual and user guide. Hg. v. Photon Systems Instruments.

Measurement of the oxygenic photosynthetic rates:

For the measurement of the oxygenic photosynthesis rate a custom measuring cell (PMC) was build at the Institute of Process Engineering in Life Sciences – Bioprocess Engineering (KIT) based on the setup presented in:
Brindley, C.; Acién, F. G.; Fernández-Sevilla, J. M. (2010): The oxygen evolution methodology affects photosynthetic rate measurements of microalgae in well-defined light regimes. In: Biotechnology and bioengineering 106 (2), S. 228–237. DOI: 10.1002/bit.22676.
The exact setup and measurement process can be found here:
	DOI: 10.5445/IR/1000156200