Calculation of the radiative properties of photosynthetic microorganisms

Journal of Quantitative Spectroscopy and Radiative Transfer

Volumn 161, Issue , 2015, Pages 60-84

  Dauchet, Jérémi ^a,b   Blanco, Stéphane ^b,c   Cornet, Jean François ^a,b   Fournier, Richard ^b,c  

^a UNIVERSITÉ CLERMONT AUVERGNE   (France)

^b CNRS   (France)

^c d'Hydraulique et des Telecommunications   (France)

Author keywords

Anomalous diffraction approximation; Light scattering; Optical properties; Photobioreactor; Photosynthetic microorganisms; Schiff approximation

Indexed keywords

ABSORPTION SPECTROSCOPY; ASTROPHYSICS; BACTERIA; CHAINS; CHEMICAL ANALYSIS; HEAT RADIATION; LIGHT SCATTERING; MICROBIOLOGY; OPTICAL PROPERTIES; PARTICLE SIZE ANALYSIS; PHOTOBIOREACTORS; REFRACTIVE INDEX;

ANOMALOUS DIFFRACTION APPROXIMATIONS; HEMISPHERICAL TRANSMITTANCE; LIGHT SCATTERING AND ABSORPTIONS; PHOTOBIORE-ACTOR; PHOTOSYNTHETIC MICROORGANISMS; PHOTOSYNTHETIC PIGMENT CONTENTS; SCHIFF APPROXIMATION; STRUCTURAL CHARACTERISTICS;

MICROORGANISMS;

BIOREACTOR; LIGHT SCATTERING; MICROORGANISM; OPTICAL PROPERTY; PHOTOSYNTHESIS; RADIATIVE TRANSFER; REFRACTIVE INDEX;

ARTHROSPIRA PLATENSIS; CHLAMYDOMONAS REINHARDTII; CYANOBACTERIA; EUKARYOTA; PHOTOBACTERIA; RHODOSPIRILLUM RUBRUM;

EID: 84927725730     PISSN: 00224073     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jqsrt.2015.03.025     Document Type: Article

References (107)

1. Aiba S. Growth kinetics of photosynthetic micro-organisms. Adv Biochem Eng 1982, 23:85-156.
2. Cornet J.F., Dussap C.G., Dubertret G. A structured model for simulation of cultures of the cyanobacterium spirulina platensis in photobioreactors. I. Coupling between light transfer and growth kinetics. Biotechnol Bioeng 1992, 40(7):817-825.
3. Cornet J-F, Dussap C, Gros J-B. Kinetics and energetics of photosynthetic micro-organisms in photobioreactors. In: Bioprocess and algae reactor technology, apoptosis. Advances in biochemical engineering biotechnology, vol. 59. Berlin Heidelberg: Springer; 1998. p. 153-224.
4. Cornet J.F., Dussap C.G. A simple and reliable formula for assessment of maximum volumetric productivities in photobioreactors. Biotechnol Prog 2009, 25(2):424-435.
5. Cornet J.F. Calculation of optimal design and ideal productivities of volumetrically lightened photobioreactors using the constructal approach. Chem Eng Sci 2010, 65(2):985-998.
6. Pruvost J., Cornet J.F. Knowledge models for the engineering and optimization of photobioreactors. Microalgal biotechnology: potential and production 2012, De Gruyter, Berlin, Germany. C. Posten, C. Walter (Eds.).
7. Takache H., Christophe G., Cornet J.-F., Pruvost J. Experimental and theoretical assessment of maximum productivities for the microalgae Chlamydomonas reinhardtii in two different geometries of photobioreactors. Biotechnol Prog 2010, 26(2):431-440.
8. Pilon L., Berberoglu H., Kandilian R. Radiation transfer in photobiological carbon dioxide fixation and fuel production by microalgae. J Quant Spectrosc Radiat Transf 2011, 112(17):2639-2660.
9. Cassano A.E., Martin C.A., Brandi R.J., Alfano O.M. Photoreactor analysis and design. fundamentals and applications. Ind Eng Chem Res 1995, 34:2155-2201.
10. Csogor Z., Herrenbauer M., Schmidt K., Posten C. Light distribution in a novel photobioreactor-modelling for optimization. J Appl Phycol 2001, 13:325-333.
11. Pottier L., Pruvost J., Deremetz J., Cornet J.F., Legrand J., Dussap C.G. A fully predictive model for one-dimensional light attenuation by Chlamydomonas reinhardtii in a torus photobioreactor. Biotechnol Bioeng 2005, 91(5):569-582.
12. Dauchet J., Blanco S., Cornet J.-F., El Hafi M., Eymet V., Fournier R. The practice of recent radiative transfer monte carlo advances and its contribution to the field of microorganisms cultivation in photobioreactors. J Quant Spectrosc Radiat Transf 2013, 128(0):52-59.
13. Mengüç MP. Characterization of fine particles via elliptically-polarized light scattering. Purdue Heat Transfer Celebration; 2002.
14. Muñoz O., Hovenier J.W. Laboratory measurements of single light scattering by ensembles of randomly oriented small irregular particles in air. A review. J Quant Spectrosc Radiat Transf 2011, 112(11):1646-1657.
15. Berberoglu H., Pilon L., Melis A. Radiation characteristics of Chlamydomonas reinhardtii cc125 and its truncated chlorophyll antenna transformants tla1, tlax and tla1-cw. Int J Hydrog Energy 2008, 33(22):6467-6483.
16. Berberoglu H., Gomez P.S., Pilon L. Radiation characteristics of Botryococcus braunii, Chlorococcum littorale, and Chlorella sp. used for co2 fixation and biofuel production. J Quant Spectrosc Radiat Transf 2009, 110(17):1879-1893.
17. Vaillon R., Geffrin J.M., Eyraud C., Merchiers O., Sabouroux P., Lacroix B. A novel implementation of a microwave analog to light scattering measurement set-up. J Quant Spectrosc Radiat Transf 2011, 112(11):1753-1760.
18. Wriedt T. Light scattering theories and computer codes. J Quant Spectrosc Radiat Transf 2009, 110(11):833-843.
19. Kahnert F.M. Numerical methods in electromagnetic scattering theory. J Quant Spectrosc Radiat Transf 2003, 7980(0):775-824.
20. Fernandes B., Dragone G., Teixeira J., Vicente A. Light regime characterization in an airlift photobioreactor for production of microalgae with high starch content. Appl Biochem Biotechnol 2010, 161:218-226.
21. Franco-Lara E., Havel J., Peterat F., Weuster-Botz D. Model-supported optimization of phototrophic growth in a stirred-tank photobioreactor. Biotechnol Bioeng 2006, 95(6):1177-1187.
22. Suh I.S., Lee S.B. A light distribution model for an internally radiating photobioreactor. Biotechnol Bioeng 2003, 82(2):180-189.
23. Suh I.S., Lee S.B. Optimization of radiator position in an internally radiating photobioreactor. a model simulation study. J Microbiol Biotechnol 2003, 13:789-793.
24. Suh I.S., Lee S.B. Cultivation of a cyanobacterium in an internally radiating air-lift photobioreactor. J Appl Phycol 2001, 13:381-388.
25. Su W.W., Li J., Xu N.S. State and parameter estimation of microalgal photobioreactor cultures based on local irradiance measurement. J Biotechnol 2003, 105(1-2):165-178.
26. Cornet J.F., Dussap C.G., Cluzel P., Dubertret G. A structured model for simulation of cultures of the cyanobacterium spirulina platensis in photobioreactors. II. Identification of kinetic parameters under light and mineral limitations. Biotechnol Bioeng 1992, 40(7):826-834.
27. Farges B., Laroche C., Cornet J.F., Dussap C.G. Spectral kinetic modeling and long-term behavior assessment of Arthrospira platensis growth in photobioreactor under red (620nm) light illumination. Biotechnol Prog 2009, 25(1):151-162.
28. van de Hulst H.C. Light scattering by small particles 1981, Dover Publication, Inc., New York.
29. Bohren C.F., Huffman D.R. Absorption and scattering of light by small particles 1983, Wiley-Interscience, New York.
30. Mishchenko M.I., Hovenier J.W., Travis L.D. Light scattering by nonspherical particles: theory, measurements, and applications 2000, USA: Academic Press, San Diego.
31. Mishchenko M, Travis L, Lacis A. Scattering, absorption, and emission of light by small particles. Cambridge, UK: Cambridge Univ Press; 2002. The Lorenz-Mie code used in the present article is available at http://www.giss.nasa.gov/staff/mmishchenko.
32. Bernard S., Probyn T.A., Quirantes A. Simulating the optical properties of phytoplankton cells using a two-layered spherical geometry. Biogeosci Discus 2009, 6(1):1497-1563.
33. Wu T.T., Qu J.Y., Xu M. Unified Mie and fractal scattering by biological cells and subcellular structures. Opt Lett 2007, 32(16):2324-2326.
34. Choi W., Yu C.-C., Fang-Yen C., Badizadegan K., Dasari R., Feld M.S. Field-based angle-resolved light-scattering study of single live cells. Opt Lett 2008, 33(14):1596-1598.
35. Kolokolova L., Gustafsonm B.A.S. Scattering by inhomogeneous particles: microwave analog experiments and comparison to effective medium theories. J Quant Spectrosc Radiat Transf 2001, 70(4-6):611-625.
36. Dauchet J. Analyse radiative des photobioréacteurs [Ph.D. thesis]. University Blaise Pascal - Clermont II, The corresponding publication is being prepared; 2012.
37. Wang Z.P., Zhao Y. Morphological reversion of spirulina (Arthrospira) platensis (cyanophyta). from linear to helical. J Phycol 2005, 41(3):622-628.
38. Hoepffner N., Sathyendranath S. Effect of pigment composition on absorption properties of phytoplankton. Mar Ecol Prog Ser 1991, 73(1):11-23.
39. Morel A., Bricaud A. Theoretical results concerning light absorption in a discrete medium, and application to specific absorption of phytoplankton. Mar Ecol Prog Ser 1981, Papers 28(11):1375-1393.
40. Bricaud A., Morel A. Light attenuation and scattering by phytoplanktonic cells. a theoretical modeling. Appl Opt 1986, 25(4):571-580.
41. Bidigare RR, Ondrusek ME, Morrow JH, Kiefer DA. In-vivo absorption properties of algal pigments, vol. 1302. Orlando, FL, United States: SPIE; 1990. p. 290-302, http://dx.doi.org/10.1117/12.21451.
42. Wozniak B., Dera J., Ficek D., Majchrowski R., Kaczmarek S., Ostrowska M., et al. Model of the in vivo spectral absorption of algal pigments. Part 1. mathematical apparatus. Oceanologia 2000, 42(2):177-190.
43. Aas E. Refractive index of phytoplankton derived from its metabolite composition. J Plankton Res 1996, 18(12):2223-2249.
44. Wyatt P.J. Differential light scattering. a physical method for identifying living bacterial cells. Appl Opt 1968, 7(10):1879-1896.
45. Wyatt P.J. Cell wall thickness, size distribution, refractive index ratio and dry weight content of living bacteria (Stapylococcus aureus). Nature 1970, 226(5242):277-279.
46. Wyatt P.J. Light scattering in the microbial world. J Colloid Interface Sci 1972, 39(3):479-491.
47. Tychinsky V., Tikhonov A. Interference microscopy in cell biophysics. 1. Principles and methodological aspects of coherent phase microscopy. Cell Biochemistry and Biophysics 2010, 58:107-116.
48. Tychinsky V., Tikhonov A. Interference microscopy in cell biophysics. 2. Visualization of individual cells and energy-transducing organelles. Cell Biochem Biophys 2010, 58:117-128.
49. Tychinsky V. The metabolic component of cellular refractivity and its importance for optical cytometry. J Biophotonics 2009, 2(8-9):494-504.
50. Lue N., Popescu G., Ikeda T., Dasari R.R., Badizadegan K., Feld M.S. Live cell refractometry using microfluidic devices. Opt Lett 2006, 31(18):2759-2761.
51. Choi W., Fang-Yen C., Badizadegan K., Oh S., Lue N., Dasari R.R. Tomographic phase microscopy. Nat Methods 2007, 4(9):717-719.
52. Park Y., Diez-Silva M., Popescu G., Lykotrafitis G., Choi W., Feld M.S., et al. Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum. Proc Natl Acad Sci 2008, 105(37):13730-13735.
53. Loparev A., Kretushev A., Tychinsky V. Coherent phase microscopy. a new method of identification of intracellular structures based on their optical and morphometric parameters. Biofizika 2008, 53(2):299-304.
54. Cisek R., Spencer L., Prent N., Zigmantas D., Espie G., Barzda V. Optical microscopy in photosynthesis. Photosynth Res 2009, 102:111-141.
55. Virtual chemistry laboratory, University of Oxford, http://www.chem.ox.ac.uk/vrchemistry.
56. Harris E.H. The Chlamydomonas sourcebook: introduction to Chlamydomonas and its laboratory use 2009, Academic Press, San Diego, California, USA. Second ed.
57. Tuminello P.S., Arakawa E.T., Khare B.N., Wrobel J.M., Querry M.R., Milham M.E. Optical properties of Bacillus subtilis spores from 0.2 to 2.5νm. Appl Opt 1997, 36(13):2818-2824.
58. Perrin J.M., Lamy P.L. On the validity of effective-medium theories in the case of light extinction by inhomogeneous dust particles. Astrophys J 1990, 364:146-151.
59. Voshchinnikov N.V., Videen G., Henning T. Effective medium theories for irregular fluffy structures. aggregation of small particles. Appl Opt 2007, 46(19):4065-4072.
60. Bohren C.F., Battan L.J. Radar backscattering by inhomogeneous precipitation particles. J Atmos Sci 1980, 37(8):1821-1827.
61. Erlick C. Effective refractive indices of water and sulfate drops containing absorbing inclusions. J Atmos Sci 2006, 63(2):754-763.
62. Worringen A., Ebert M., Trautmann T., Weinbruch S., Helas G. Optical properties of internally mixed ammonium sulfate and soot particles - a study of individual aerosol particles and ambient aerosol populations. Appl Opt 2008, 47(21):3835-3845.
63. Sihvola A.H. Electromagnetic mixing formulas and applications 1999, IEE, London.
64. Bernard S., Probyn T.A., Barlow R.G. Measured and modelled optical properties of particulate matter in the southern benguela. S Afr J Sci 2001, 97(9-10):410-420.
65. van Kampen N.G., Lurçat F. Causalité et relations de Kramers-Kronig. J Phys Radium 1961, 22(3):179-191.
66. Toll J.S. Causality and the dispersion relation. logical foundations. Phys Rev 1956, 104(6):1760-1770.
67. Lucarini V. Kramers-Kronig relations in optical materials research 2005, Springer, Berlin, Heidelberg.
68. Naqvi K.R., Merzlyak M.N., Melo T.B. Absorption and scattering of light by suspensions of cells and subcellular particles. an analysis in terms of Kramers-Kronig relations. Photochem Photobiol Sci 2004, 3:132-137.
69. de Sousa Meneses D., Rousseau B., Echegut P., Simon P. Retrieval of linear optical functions from finite range spectra. Appl Spectrosc 2007, 61(12):1390-1397.
70. Roels J.A. Kinetics and energetics in biotechnology 1983, Elsevier Biomedical Press, Amsterdam.
71. Stier P., Seinfeld J.H., Kinne S., Boucher O. Aerosol absorption and radiative forcing. Atmos Chem Phys 2007, 7(3):7171-7233.
72. Schmid O., Chand D., Karg E., Guyon P., Frank G.P., Swietlicki E., et al. Derivation of the density and refractive index of organic matter and elemental carbon from closure between physical and chemical aerosol properties. Environ Sci Technol 2009, 43(4):1166-1172.
73. Yang P., Zhang Z., Baum B.A., Huang H.-L., Hu Y. A new look at anomalous diffraction theory (adt). algorithm in cumulative projected-area distribution domain and modified adt. J Quant Spectrosc Radiat Transf 2004, 89(1-4):421-442.
74. Nousiainen T. Optical modeling of mineral dust particles. a review. J Quant Spectrosc Radiat Transf 2009, 110(14-16):1261-1279.
75. Liu L., Mishchenko M.I., Arnott W.P. A study of radiative properties of fractal soot aggregates using the superposition T-matrix method. J Quant Spectrosc Radiat Transf 2008, 109(15):2656-2663.
76. Baran A.J. A review of the light scattering properties of cirrus. J Quant Spectrosc Radiat Transf 2009, 110(14-16):1239-1260.
77. Bond T.C., Bergstrom R.W. Light absorption by carbonaceous particles. an investigative review. Aerosol Sci Technol 2006, 40(1):27-67.
78. Sorensen C.M. Light scattering by fractal aggregates. a review. Aerosol Sci Technol 2001, 35(2):648-687.
79. Asano S., Sato M. Light scattering by randomly oriented spheroidal particles. Appl Opt 1980, 19(6):962-974.
80. Hellmers J., Schmidt V., Wriedt T. Improving the numerical stability of T-matrix light scattering calculations for extreme particle shapes using the nullfield method with discrete sources. J Quant Spectrosc Radiat Transf 2011, 112(11):1679-1686.
81. Schiff L.I. Approximation method for high-energy potential scattering. Phys Rev 1956, 103(2):443-453.
82. Xu M, Katz A. Statistical interpretation of light anomalous diffraction by small particles and its applications in bio-agent detection and monitoring. In: Light scattering reviews 3. Berlin, Heidelberg: Springer Praxis Books; 2008. p. 27-67.
83. Zhao J.Q., Hu Y.Q. Bridging technique for calculating the extinction efficiency of arbitrary shaped particles. Appl Opt 2003, 42(24):4937-4945.
84. Zhao J.Q., Shi G., Che H., Cheng G. Approximations of the scattering phase functions of particles. Adv Atmos Sci 2006, 23:802-808.
85. Farone W.A., Robinson M.J.I. The range of validity of the anomalous diffraction approximation to electromagnetic scattering by a sphere. Appl Opt 1968, 7(4):643-645.
86. Liu Y., Arnott W.P., Hallett J. Anomalous diffraction theory for arbitrarily oriented finite circular cylinders and comparison with exact T-matrix results. Appl Opt 1998, 37(21):5019-5030.
87. Dudley B.F., Steiber B.A., Latimer P. Absolute optical cross sections of cells and chloroplasts. Arch Biochem Biophys 1969, 135:79-108.
88. Pullerits T., Sundström V. Photosynthetic light-harvesting pigment-protein complexes. toward understanding how and why. Acc Chem Res 1996, 29(8):381-389.
89. StarWest, Edstar development environment project, http://edstar.lmd.jussieu.fr/databases.
90. Myers J., Kratz K.A. Relation between pigment content and photosynthetic characteristics in blue green alga. J Gen Physiol 1955, 39:11-22.
91. Bennet A., Bogorad L. Complementary chromatic adaptation in a filamentous blue-green alga. J Cell Biol 1973, 58:419-435.
92. Strickland JDH, Parsons TR. A practical handbook of seawater analysis: pigment analysis. Bull Fish Res Board Can (Bulletin number 167); 1972, http://www.dfo-mpo.gc.ca/Library/1507.pdf.
93. Vernon LP, Garcia AF. Pigment-protein complexes derived from Rhodospirillum rubrum chromatophores by enzymatic digestion, Biochim Biophys Acta 1967;143:144-53.
94. Bratbak G, Dundas I. Bacterial dry matter content and biomass estimations. Appl Environ Microbiol 1984; 48:755-7.
95. Inoue K., Nishimura M., Nayak B.B., Kogure K. Separation of marine bacteria according to buoyant density by use of the density-dependent cell sorting method. Appl Environ Microbiol 2007, 73:1049-1053.
96. Ross K.F.A., Billing E. The water and solid content of living bacterial spores and vegetative cells as indicated by refractive index measurements. J Gen Microbiol 1957, 16(2):418-425.
97. Thormählen I., Straub J., Grigull U. Refractive index of water and its dependence on wavelength, temperature, and density. J Phys Chem Ref Data 1985, 14:933-945.
98. Lambeek G., Vorenkamp E., Schouten A.J. Structural study of Langmuir-Blodgett mono- and multilayers of poly(béta-hydroxybutyrate). Macromolecules 1995, 28:2023-2032.
99. Schötz F., Bathelt H., Arnold C.G., Schimmer O. Die architektur und organization der chlamydomonas-zelle. Protoplasma 1972, 75:229-254.
100. Howell J.R. The monte carlo method in radiative heat transfer. J Heat Transf 1998, 120(3):547-560.
101. Modest M.F. Radiative heat transfer 2003, Academic Press. Second ed.
102. Delatorre J., Baud G., Bézian J.-J., Blanco S., Caliot C., Cornet J.-F., et al. Monte carlo advances and concentrated solar applications. Solar Energy 2014, 103(0):653-681. 10.1016/j.solener.2013.02.035.
103. Roger M., Blanco S., el Hafi M., Fournier R. Monte carlo estimates of domain-deformation sensitivities. Phys Rev Lett 2005, 95(18):180601.
104. Weisstein E.W. CRC concise encyclopedia of mathematics 2003, Chapman and Hall/CRC, (ISBN-10: 1584883472/ISBN-13: 978-1584883470). 2nd ed.
105. Mugnai A., Wiscombe W.J. Scattering from nonspherical chebyshev particles. i. cross sections, single-scattering albedo, asymmetry factor and backscattered fraction. Appl Opt 1986, 25:1235-1244.
106. Mishchenko M.I., Travis L.D. Capabilities and limitations of a current fortran implementation of the T-matrix method for randomly oriented, rotationally symmetric scatterers. J Quant Spectrosc Radiat Transf 1998, 60:309-324.
107. Gielis J. A generic geometric transformation that unifies a wide range of natural and abstract shapes. Am J Bot 2003, 90(3):333-338.