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  <front>
    <journal-meta>
<journal-id journal-id-type="publisher">BG</journal-id>
<journal-title-group>
<journal-title>Biogeosciences</journal-title>
<abbrev-journal-title abbrev-type="publisher">BG</abbrev-journal-title>
<abbrev-journal-title abbrev-type="nlm-ta">Biogeosciences</abbrev-journal-title>
</journal-title-group>
<issn pub-type="epub">1726-4189</issn>
<publisher><publisher-name>Copernicus GmbH</publisher-name>
<publisher-loc>Göttingen, Germany</publisher-loc>
</publisher>
</journal-meta>

    <article-meta>
      <article-id pub-id-type="doi">10.5194/bg-12-4067-2015</article-id><title-group><article-title>Investigating the usefulness of satellite-derived fluorescence data in
inferring gross primary productivity within the carbon cycle data
assimilation system</article-title>
      </title-group><?xmltex \runningtitle{Investigating the usefulness of satellite-derived fluorescence data}?><?xmltex \runningauthor{E.~N.~Koffi et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1 aff5">
          <name><surname>Koffi</surname><given-names>E. N.</given-names></name>
          <email>ernest.koffi@jrc.ec.europa.eu</email>
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Rayner</surname><given-names>P. J.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-7707-6298</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Norton</surname><given-names>A. J.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Frankenberg</surname><given-names>C.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-0546-5857</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff4">
          <name><surname>Scholze</surname><given-names>M.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-3474-5938</ext-link></contrib>
        <aff id="aff1"><label>1</label><institution>Laboratoire des Sciences du Climat et de l'Environnement (LSCE),
UMR8212, Ormes des merisiers,<?xmltex \hack{\newline}?> 91191 Gif-sur-Yvette, France</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>School of Earth Sciences, University of Melbourne, Melbourne,
Australia</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>Jet Propulsion Laboratory, California Institute of Technology,
Pasadena, USA</institution>
        </aff>
        <aff id="aff4"><label>4</label><institution>Department of Physical Geography and Ecosystem Science, Lund
University, Lund, Sweden</institution>
        </aff>
        <aff id="aff5"><label>a</label><institution>now at: the European Commission Joint Research Centre, Institute for
Environment and Sustainability,<?xmltex \hack{\newline}?> 21027 Ispra (Va), Italy</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">E. N. Koffi (ernest.koffi@jrc.ec.europa.eu)</corresp></author-notes><pub-date><day>07</day><month>July</month><year>2015</year></pub-date>
      
      <volume>12</volume>
      <issue>13</issue>
      <fpage>4067</fpage><lpage>4084</lpage>
      <history>
        <date date-type="received"><day>01</day><month>December</month><year>2014</year></date>
           <date date-type="rev-request"><day>13</day><month>January</month><year>2015</year></date>
           <date date-type="rev-recd"><day>18</day><month>June</month><year>2015</year></date>
           <date date-type="accepted"><day>18</day><month>June</month><year>2015</year></date>
      </history>
      <permissions>
<license license-type="open-access">
<license-p>This work is licensed under a Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link></license-p>
</license>
</permissions><self-uri xlink:href="https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015.html">This article is available from https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015.html</self-uri>
<self-uri xlink:href="https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015.pdf">The full text article is available as a PDF file from https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015.pdf</self-uri>


      <abstract>
    <p>Simulations of carbon fluxes with terrestrial biosphere models still exhibit
significant uncertainties, in part due to the uncertainty in model parameter
values. With the advent of satellite measurements of solar induced
chlorophyll fluorescence (SIF), there exists a novel pathway for constraining
simulated carbon fluxes and parameter values. We investigate the utility of
SIF in constraining gross primary productivity (GPP). As a first test we
assess whether SIF simulations are sensitive to important parameters in a
biosphere model. SIF measurements at the wavelength of 755 nm are simulated
by the Carbon-Cycle Data Assimilation System (CCDAS) which has been augmented
by the fluorescence component of the Soil Canopy Observation, Photochemistry
and Energy fluxes (SCOPE) model.</p>
    <p>Idealized sensitivity tests of the SCOPE model stand-alone indicate strong
sensitivity of GPP to the carboxylation capacity (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) and of
SIF to the chlorophyll AB content (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) and incoming short wave
radiation. Low sensitivity is found for SIF to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, however the
relationship is subtle, with increased sensitivity under high radiation
conditions and lower <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> ranges.</p>
    <p>CCDAS simulates well the patterns of satellite-measured SIF suggesting the
combined model is capable of ingesting the data. CCDAS supports the idealized
sensitivity tests of SCOPE, with SIF exhibiting sensitivity to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and incoming radiation, both of which are treated as
perfectly known in previous CCDAS versions. These results demonstrate the
need for careful consideration of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and incoming radiation when
interpreting SIF and the limitations of utilizing SIF to constrain
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> in the present set-up in the CCDAS system.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>
      <p>The terrestrial carbon flux has been identified as the most uncertain term in
the global carbon budget (Le Quéré et al., 2013). The gross primary
productivity (GPP), which is the flux of CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> assimilated by plants
during photosynthesis, is the input to the system used to characterize carbon
flux so its variation can significantly contribute to the uncertainties in
terrestrial CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes.</p>
      <p>Complex systems have been built to reduce the uncertainties in GPP. These
algorithms are either based on up-scaling or atmospheric inverse modelling
methods. Up-scaling methods estimate GPP at global scale by establishing
relationships between local GPP measurements and environmental variables
then using these variables to calculate GPP globally (e.g., Jung et al.,
2011; Beer et al., 2010 and references therein). The inverse modelling
approach uses CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> concentration observations at a global scale to
constrain the process parameters of carbon models that compute the
terrestrial fluxes. This inverse method is an example of Carbon Cycle Data
Assimilation Systems (CCDAS). The CCDAS considered in the present study has
two main components:
<list list-type="bullet"><list-item><p>A deterministic dynamical model that computes the evolution of both the biosphere
and soil carbon stores given an initial condition, forcing and a set of the model process
parameters.</p></list-item><list-item><p>An assimilation algorithm that allows the adjustment of a subset of the state variables, initial
conditions and/or process parameters to reduce the mismatch between the model simulations and observations.
Usually any prior information on the variables which are adjusted are also taken into account
(see e.g., Kaminski et al., 2002, 2003; Rayner et al., 2005, and references therein for the underlying
methodology).</p></list-item></list>
Rayner et al. (2005) built such a CCDAS around the biosphere model BETHY
(Biosphere Energy-Transfer Hydrology; Knorr, 2000) coupled to an atmospheric
transport model together with CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fluxes representing ocean flux, land
use change, and fossil fuel emission, see also Scholze at al. (2007) and
Kaminski et al. (2013) for an overview on further developments and
applications. Koffi et al. (2012) used this CCDAS to investigate the
sensitivity of estimates of GPP to transport models and observational
networks of CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> concentrations. Large differences in GPP in the tropics
were found between the GPP estimates of Koffi et al. (2012) and those from either
satellite-based products or up-scaling methods (e.g., Jung et al., 2011; Beer
et al., 2010). Koffi et al. (2012) found significantly larger GPP in the
tropics compared to the other GPP products. In fact, due to few CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
concentration observations available in the tropics, the parameters of BETHY
are mainly constrained by observations from other regions. Consequently, the
optimized parameters can be uncertain.</p>
      <p>Recent work has inferred sun-induced plant fluorescence (hereafter SIF) from
the Greenhouse gas Observing Satellite (GOSAT; e.g., Frankenberg et al.,
2011, 2012; Joiner et al., 2011; Guanter et al., 2012), ENVISAT/SCIAMACHY
(Joiner et al., 2012), and MetOp-A/GOME-2 (Joiner et al., 2013). They showed
that SIF data at a global scale is promising for inferring GPP. They found a
strong linear correlation between satellite-based SIF and GPP estimated from
either up-scaling methods (Jung et al., 2011) or satellite products (MODIS
data). The satellite-based SIF data cover large areas of the globe including
tropical zones where estimates from a CCDAS are found to be uncertain. It is
worth asking whether such fluorescence data is useful to constrain GPP in
the CCDAS framework.</p>
      <p>The relationship between fluorescence and photochemistry at leaf level is
reasonably well understood. Light energy absorbed by chlorophyll molecules
has one of three fates: photosynthesis, dissipation as heat
(non-photochemical quenching) or chlorophyll fluorescence. The total amount
of chlorophyll fluorescence is only 1 to 2 % of total light absorbed. The
spectrum of fluorescence is different to that of absorbed light. The peak of
the fluorescence spectrum lies between 650 and 850 nm. Under low-light
conditions, a negative correlation has been found between fluorescence and
photosynthesis light use efficiencies (e.g., Genty et al., 1989; Rosema et
al., 1998; Seaton and Walker, 1990; Maxwell and Johnson, 2000; van der Tol et
al., 2009a). At high-light
conditions (i.e., high irradiance and moisture stress), a positive
correlation has been observed between fluorescence and photosynthesis light
use efficiencies (Gilmore and Yamamoto, 1992; Gilmore et al., 1994; Maxwell
and Johnson, 2000; van der Tol et al., 2009a). Regarding the water stress, more recently, Lee et
al. (2013) showed a negative correlation between vapour pressure deficit and
SIF.</p>
      <p>The cited works above show that the link between fluorescence and
photosynthesis is complex. Thus, before using fluorescence observations to
constrain gross primary productivity in the framework of CCDAS, first we need
to ensure that there is a common parameter or set of parameters relevant to
both the fluorescence and photosynthesis process models of the CCDAS. So, if
there are common parameters, we can assess the sensitivities of GPP and SIF
to them. This requires implementing in CCDAS a model that allows for the computing
of both fluorescence and photosynthesis. We build such a CCDAS by using the
SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes) model (van
der Tol et al., 2009a, 2014). SCOPE is based on the existing theory of
chlorophyll fluorescence and photosynthesis. The photosynthesis scheme of C3
plants uses the formulations of Collatz et al. (1991), while for the C4
photosynthesis pathway, the formulations of Collatz et al. (1992) are
considered. In these formulations of the photosynthesis, the maximum
carboxylation rate <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is a key process parameter. The
fluorescence model is based on the work of Genty et al. (1989), Rosema et
al. (1998), and van der Tol et al. (2014). The model is formulated such that
the sum of the probabilities of an absorbed photon to result in fluorescence,
photochemistry, and heat is unity. Hence, the fluorescence model also
utilizes <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> as a process parameter.</p>
      <p>CCDAS operates in two modes (Scholze et al., 2007). The calibration mode that
derives an optimal parameter set including posterior uncertainties of the
dynamical carbon model (here the biosphere model) by constraining the process
parameters of the model with observations. The diagnostic/prognostic
(referred hereafter as forward) mode allows deriving the various quantities
of interest (e.g., terrestrial carbon fluxes or atmospheric CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
concentrations) and their uncertainties. These quantities are calculated from
the optimized parameter vector obtained from the calibration step. CCDAS has
been widely applied to investigate terrestrial carbon cycling (e.g., Rayner
et al., 2005; Scholze et al., 2007) and in particular more recently to (i)
estimate the GPP at global scale (Koffi et al., 2012) and (ii) to quantify
the uncertainty in the parameters of BETHY by using both CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
concentration and flux observational networks (Kaminski et al., 2012; Koffi
et al., 2013). To assess the usefulness of satellite-based fluorescence data
(SIF) to constrain GPP within CCDAS, in this study, we investigate the
sensitivities of both GPP and SIF to the biochemical parameters as well as
environmental conditions by using the SCOPE model alone and the forward mode
of the CCDAS built around it. The work is organized as follows: in Sect. 2, we describe both the model SCOPE and its coupling with CCDAS and
the fluorescence data retrieved from the satellite GOSAT. In Sect. 3, we
perform various idealized sensitivity tests to investigate the strength of
the relationships between SIF and GPP by using the SCOPE model alone. These
tests are performed by studying the sensitivity of GPP and SIF to the
biochemical parameters (i.e., <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and the chlorophyll AB
content <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) and the environmental conditions (e.g., incoming
short wave radiation <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>). In the idealized tests, the vegetation
is characterized by different values of the leaf area index (LAI). In
Sect. 4, by using the forward mode of the CCDAS coupled to SCOPE, we compute
both SIF and GPP at global scale and results are compared to the GOSAT SIF
from June 2009 until December 2010. The simulations are based on the
different settings of LAI, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, and
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values. In Sect. 5, results are discussed. Finally,
conclusions are presented in Sect. 6.</p>
</sec>
<sec id="Ch1.S2">
  <title>Models and data</title>
<sec id="Ch1.S2.SS1">
  <title>Models</title>
<sec id="Ch1.S2.SS1.SSS1">
  <title>SCOPE model</title>
      <p>The model SCOPE is a 1-D model based on radiative transfer, micrometeorology,
and plant physiology (van der Tol et al., 2009b). Version 1.53 of SCOPE is
used in this study with the default version of the biochemical code
(referred as fluorescence model choice 0; van der Tol et al., 2014).
SCOPE treats canopy radiative transfer in the visible and infrared and
chlorophyll fluorescence, as well as the energy balance. The modules of
SCOPE are executed in the following order:
<list list-type="order"><list-item><p>A semi-empirical radiative transfer model for incident sun and sky radiation, based on the SAIL model
(Verhoef and Bach, 2007). This module calculates the outgoing radiation
spectrum (0.4 to 50 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m) at the top of the canopy (hereafter TOC),
as well as the net radiation and absorbed photosynthetically active radiation
(aPAR) per surface element.</p></list-item><list-item><p>A numerical radiative transfer model for thermal radiation generated internally by soil and vegetation, based on
Verhoef et al. (2007). This module computes the TOC outgoing thermal
radiation and net radiation per surface element, but for heterogeneous leaf
and soil temperatures.</p></list-item><list-item><p>A biochemistry model for C3 and C4 plants, which allows the computation of quantities relevant for photosynthesis
and chlorophyll fluorescence at leaf level. At leaf level, the model calculates a fluorescence scaling factor relative to
that of a leaf in low-light, unstressed conditions from absorbed radiative fluxes, canopy and ambient environmental conditions
(radiation, temperature, air vapour pressure, CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, and O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
concentrations).</p></list-item><list-item><p>A radiative transfer model for chlorophyll fluorescence based on the FluorSAIL model (Miller et al., 2005) that
calculates the TOC radiance spectrum of fluorescence over 640–850 nm from
the geometry of the canopy and a calculated fluorescence spectrum that is
linearly scaled by the leaf level chlorophyll fluorescence scaling factor.</p></list-item></list></p>
      <p>In this study, SCOPE uses a canopy structure characterized by a spherical
leaf angle distribution (parameters LIDF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:math></inline-formula> and LIDF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">b</mml:mi></mml:msub></mml:math></inline-formula>
in Table 1) as a function of LAI with 60 distributed elementary layers. The
geometry of the vegetation is treated stochastically. SCOPE calculates the
illumination of leaves with respect to their position and orientation in the
canopy. The spectra of reflected and emitted radiation as observed above the
canopy in the satellite observation direction are computed. It is worth
noting that SCOPE permits variation only in the vertical dimension. Thus, it
is valid for vegetation in which variations in the horizontal are smaller
than in the vertical dimension. This is maybe a limitation for some natural
canopies, especially when coupling to the CCDAS as performed in Sect. 2.1.2.
However, the sensitivity of this limitation to the CCDAS results is beyond
the scope of this study.</p>
      <p>We briefly describe the fluorescence model at leaf level (more detail is
given in van der Tol et al., 2009a, 2014) with focus on the variables and
parameters relevant for the photosynthesis. The model of Faquahar et
al. (1980) divides photosynthesis into two main processes: (1) regeneration
of the ribulose bisphosphate (RuP2), which depends on the light and (2) the
maximum carboxylation rate at RuP2 saturated conditions in the presence of
sufficient light. The regeneration of RuP2 for two photosystems (PSII and
PSI) gives the link between photosynthesis and fluorescence.</p>
      <p>As already mentioned above, the fluorescence model in SCOPE is formulated
such that the sum of the probabilities of an absorbed photon to result in
fluorescence, photochemistry, and heat is unity. Following this, the
fluorescence <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Ft</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> from a single leaf is calculated over the
spectrum window of 640–850 nm as follows:
              <disp-formula id="Ch1.E1" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Ft</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Fm</mml:mi></mml:msub><mml:mfenced close=")" open="("><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub></mml:mfenced><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
            where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Fm</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the fluorescence yield and computed as follows:
              <disp-formula id="Ch1.E2" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Fm</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">f</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:mfenced close=")" open="("><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">f</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula>
            With <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> being the rate coefficient relative to nonphotochemical
quenching (NPQ), a parameter obtained from Pulse amplitude modulated
(PAM) fluorometry. PAM measures the photosynthetic efficiency of photosystem
II (PSII). <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is parametrized by using Flexas et al. (2002)'s data set as
follows:
              <disp-formula id="Ch1.E3" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mfenced close=")" open="("><mml:mn>6.2473</mml:mn><mml:mo>×</mml:mo><mml:mi>x</mml:mi><mml:mo>-</mml:mo><mml:mn>0.5944</mml:mn></mml:mfenced><mml:mo>×</mml:mo><mml:mi>x</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
            where <inline-formula><mml:math display="inline"><mml:mi>x</mml:mi></mml:math></inline-formula> stands for the degree of light saturation and defined as:
              <disp-formula id="Ch1.E4" content-type="numbered"><mml:math display="block"><mml:mrow><mml:mi>x</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mrow><mml:mi mathvariant="normal">p</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula>
            <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mrow><mml:mi mathvariant="normal">p</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (given by the following
expressions) stand for the fractions of actual and dark photochemistry
yields, respectively:
              <disp-formula id="Ch1.E5" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mrow><mml:mi mathvariant="normal">p</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:mfenced close=")" open="("><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">f</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub></mml:mfenced></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula>
            <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">f</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the rate constant for fluorescence and sets to 0.05,
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the rate constant for photochemistry with a value of 4.0,
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, with a value of 0.95, is the rate constant for thermal
deactivation at <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Fm</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
              <disp-formula id="Ch1.E6" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mrow><mml:mi mathvariant="normal">p</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">e</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula>
            <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">e</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> stand for the actual and potential electron
transport rates, respectively. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the electron transport rate
used for gross primary productivity (GPP). van der Tol et al. (2014) used
Pulse-Amplitude fluorescence measurements to derive an empirical relation
between the efficiencies of photochemistry and fluorescence. This
relationship was derived after analysing the response of non-photochemical
quenching (NPQ) in plants to light saturation. The formulations of GPP in
SCOPE follow that of Collatz et al. (1991) and Collatz et al. (1992) for C3
and C4 plants, respectively. The potential electron transport rate
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">e</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is related to the rate of absorbed photons (or absorbed
photosynthetically active radiation, i.e. aPAR), hence to the visible
radiation. The fluorescence is linearly related to the short wave (visible)
radiation, while it is related to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> mainly when the gross
primary productivity GPP is limited by the carboxylation enzyme Rubisco and
the capacity for the export or the utilization of the products of
photosynthesis.</p>
      <p>The total top-of-canopy fluorescent radiance is obtained from the
fluorescence flux (i.e., <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Ft</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> in Eq. 1) and the spectral
radiance of single leaves over all layers and orientations, taking into
account the probabilities of viewing sunlit and shaded components. The model
then calculates radiation transport in a multilayer canopy as a function of
the solar zenith angle and leaf orientation to simulate fluorescence in the
direction of satellite observation (van der Tol et al., 2009b).</p>
      <p>Leaf biochemistry affects reflectance, transmittance, transpiration,
photosynthesis, stomatal resistance, and chlorophyll fluorescence.
Reflectance and transmittance coefficients, which are a function of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are calculated by following the PROSPECT model (Jacquemoud
and Baret, 1990). Two excitation fluorescence matrices (EF-matrices)
representing fluorescence from both sides of the leaf are computed. The
matrices convert a spectrum of aPAR into a spectrum of fluorescence. Details
on the radiative transfer model of the fluorescence at the TOC level are
given in van der Tol et al. (2009b).</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1" specific-use="star"><caption><p>SCOPE parameters.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="4">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">Parameters</oasis:entry>  
         <oasis:entry colname="col2">Symbol</oasis:entry>  
         <oasis:entry colname="col3">Units</oasis:entry>  
         <oasis:entry colname="col4">Range or values</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Incoming short wave radiation</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0–1200</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Maximum carboxylation rate</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">1–250</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Chlorophyll <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>a</mml:mi><mml:mo>+</mml:mo><mml:mi>b</mml:mi></mml:mrow></mml:math></inline-formula> content</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">1–80</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Dry matter content</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">dm</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">g cm</oasis:entry>  
         <oasis:entry colname="col4">0.012</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Leaf equivalent water thickness</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">w</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">cm</oasis:entry>  
         <oasis:entry colname="col4">0.009</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Senescent material</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.0</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Leaf structure</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mi>N</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">1.4</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Leaf angle distribution parameter <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col2">LIDF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi>a</mml:mi></mml:msub></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.35</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Leaf angle distribution parameter <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col2">LIDF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi>b</mml:mi></mml:msub></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.15</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Leaf width</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mi>w</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">m</oasis:entry>  
         <oasis:entry colname="col4">0.1</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Ball-Berry stomatal conductance parameter</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mi>m</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">8</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Dark respiration rate at 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C as fraction of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.015</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Cowan's water use efficiency parameter</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">700</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Leaf thermal reflectance</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">ρ</mml:mi></mml:math></inline-formula>(thermal)</oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.01</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Leaf thermal transmittance</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">τ</mml:mi></mml:math></inline-formula>(thermal)</oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.01</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Soil thermal reflectance</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ρ</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>(thermal)</oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.06</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Leaf area index LAI</oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.1–6</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">fluorescence quantum yield efficiency at photosystem level</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mi mathvariant="normal">qe</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">0.02</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Canopy height</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>h</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">m</oasis:entry>  
         <oasis:entry colname="col4">1</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

</sec>
<sec id="Ch1.S2.SS1.SSS2">
  <title>Coupling SCOPE to CCDAS</title>
      <p>Within CCDAS we replace the canopy radiative transfer and photosynthesis
schemes of BETHY with their corresponding schemes from SCOPE and add the
fluorescence model of SCOPE. The spatial resolution, vegetation
characteristics as well as the meteorological and phenological data of BETHY
are used to force SCOPE. The spatial resolution is
2<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 2<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> with 3462 land grid points for the globe.
CCDAS uses 13 plant functional types (PFT; see Table 2), which have been
derived by a condensation (grouping different crop types into one crop PFT)
of the original 23 PFTs in BETHY (Knorr, 1997, based on Wilson and
Henderson-Sellers, 1985). A grid cell can contain up to three different PFTs,
with the amount specified by their fractional coverage.</p>
</sec>
</sec>
<sec id="Ch1.S2.SS2">
  <title>Data</title>
<sec id="Ch1.S2.SS2.SSS1">
  <title>GOSAT fluorescence data</title>
      <p>Frankenberg et al. (2011, 2012), Joiner et al. (2011), and Guanter et al.,
(2012) have published maps of SIF from GOSAT (Kuze et al, 2009). The
retrieval measures terrestrial emission at the frequencies of solar
Fraunhofer lines (gaps in the solar spectrum). Chlorophyll fluorescence is
the main contributor to emissions at these frequencies. GOSAT carries a
Fourier Transform Spectrometer (FTS) measuring with high spectral resolution
in the 755–775 nm range, which allows resolving individual Fraunhofer lines
overlapping the fluorescence emission. The method described in Frankenberg et
al. (2011) makes use of two spectral windows centred at 755 and 770 nm to
derive SIF. Results from the line centred around 755 nm for the period
June 2009 to December 2010 are used in this study. The fluorescence data we
are using are monthly means mapped onto 2<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula>  2<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>
spatial resolution at global scale. The fluorescence product includes
uncertainties.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T2" specific-use="star"><caption><p>Main controlling parameters for the photosynthesis and fluorescence
models are given<bold>. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></bold> stands for carboxylation maximum
capacity and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> for the chlorophyll AB content for 13 plant
functional types (PFT) as used in the CCDAS.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry namest="col3" nameend="col4" align="center"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry namest="col3" nameend="col4" align="center">(<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol(CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) </oasis:entry>  
         <oasis:entry colname="col5">(<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>)</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">PFT</oasis:entry>  
         <oasis:entry colname="col2">Plant Function Type (PFT)</oasis:entry>  
         <oasis:entry colname="col3">Prior value</oasis:entry>  
         <oasis:entry colname="col4">Optmized values</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">number</oasis:entry>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3"/>  
         <oasis:entry colname="col4">Koffi et al. (2012)</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">1</oasis:entry>  
         <oasis:entry colname="col2">Tropical broadleaved evergreen tree</oasis:entry>  
         <oasis:entry colname="col3">60</oasis:entry>  
         <oasis:entry colname="col4">63.8</oasis:entry>  
         <oasis:entry colname="col5">40</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">2</oasis:entry>  
         <oasis:entry colname="col2">Tropical broadleaved deciduous tree</oasis:entry>  
         <oasis:entry colname="col3">90</oasis:entry>  
         <oasis:entry colname="col4">73.5</oasis:entry>  
         <oasis:entry colname="col5">15</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">3</oasis:entry>  
         <oasis:entry colname="col2">Temperate broadleaved evergreen tree</oasis:entry>  
         <oasis:entry colname="col3">41</oasis:entry>  
         <oasis:entry colname="col4">39.7</oasis:entry>  
         <oasis:entry colname="col5">15</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">4</oasis:entry>  
         <oasis:entry colname="col2">Temperate broadleaved deciduous tree</oasis:entry>  
         <oasis:entry colname="col3">35</oasis:entry>  
         <oasis:entry colname="col4">149.2</oasis:entry>  
         <oasis:entry colname="col5">10</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">5</oasis:entry>  
         <oasis:entry colname="col2">Evergreen coniferous tree</oasis:entry>  
         <oasis:entry colname="col3">29</oasis:entry>  
         <oasis:entry colname="col4">21.9</oasis:entry>  
         <oasis:entry colname="col5">10</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">6</oasis:entry>  
         <oasis:entry colname="col2">Deciduous coniferous tree</oasis:entry>  
         <oasis:entry colname="col3">53</oasis:entry>  
         <oasis:entry colname="col4">136.4</oasis:entry>  
         <oasis:entry colname="col5">10</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">7</oasis:entry>  
         <oasis:entry colname="col2">Evergreen shrub</oasis:entry>  
         <oasis:entry colname="col3">52</oasis:entry>  
         <oasis:entry colname="col4">168.9</oasis:entry>  
         <oasis:entry colname="col5">10</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">8</oasis:entry>  
         <oasis:entry colname="col2">Deciduous shrub</oasis:entry>  
         <oasis:entry colname="col3">160</oasis:entry>  
         <oasis:entry colname="col4">96.1</oasis:entry>  
         <oasis:entry colname="col5">10</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">9</oasis:entry>  
         <oasis:entry colname="col2">C3 grass</oasis:entry>  
         <oasis:entry colname="col3">42</oasis:entry>  
         <oasis:entry colname="col4">18.9</oasis:entry>  
         <oasis:entry colname="col5">10</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">10</oasis:entry>  
         <oasis:entry colname="col2">C4 grass</oasis:entry>  
         <oasis:entry colname="col3">8</oasis:entry>  
         <oasis:entry colname="col4">0.7</oasis:entry>  
         <oasis:entry colname="col5">5</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">11</oasis:entry>  
         <oasis:entry colname="col2">Tundra</oasis:entry>  
         <oasis:entry colname="col3">20</oasis:entry>  
         <oasis:entry colname="col4">8.5</oasis:entry>  
         <oasis:entry colname="col5">10</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">12</oasis:entry>  
         <oasis:entry colname="col2">Swamp</oasis:entry>  
         <oasis:entry colname="col3">20</oasis:entry>  
         <oasis:entry colname="col4">9.3</oasis:entry>  
         <oasis:entry colname="col5">10</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">13</oasis:entry>  
         <oasis:entry colname="col2">Crop</oasis:entry>  
         <oasis:entry colname="col3">117</oasis:entry>  
         <oasis:entry colname="col4">47.9</oasis:entry>  
         <oasis:entry colname="col5">20</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

</sec>
<sec id="Ch1.S2.SS2.SSS2">
  <title>Data relevant for models</title>
      <p>The input data for the models we are using are of three main kinds: (i) the
data for the canopy radiative transfer modules of SCOPE, (ii) the data
characterizing the environmental conditions (i.e. meteorological and short
and long wave radiation) relevant for both the canopy radiative transfer and
biochemistry models, and (iii) the process parameters of the biochemistry
models.</p>
      <p>The model SCOPE requires incident radiation at the top-of-canopy as input. To
take into account the atmospheric absorption bands properly, these data are
needed at high resolution. The spectra of sun and sky fluxes at the top of
the canopy are obtained from the atmospheric radiative transfer model MODTRAN
(Berk et al., 2000). MODTRAN was run for 16 atmospheric situations
representative of different regions (Verhoef et al., 2014). We use 4 types of
these generated atmospheres. They are tropical atmosphere for the tropical
zones, winter and summer atmospheres for high and middle latitudes. In
addition, we have at our disposal data for an atmosphere which is
representative of the whole globe (hereafter standard atmosphere). We
have tested the sensitivity of SIF and GPP to these four types of
atmospheres. Results show only negligible differences between the inferred
SIF and GPP. We consider the standard atmosphere for the idealized tests
(Sect. 4.1) and the seasonal atmosphere for the simulations at global scale
by using the CCDAS (Sect. 4.2).</p>
      <p>The system needs forcing data to drive SCOPE within the CCDAS framework.
Monthly observed climate, incident radiation, and fractional soil moisture
for the period 2009–2010 are used (Weedon et al., 2011). The LAIs are
obtained from BETHY simulation.</p>
      <p>The main parameters that affect both the photosynthesis and fluorescence
schemes are given in Table 2. The parameters are of two kinds: parameters
that are PFT-specific (e.g., <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) and
global parameters. Prior and optimized values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> obtained
by Koffi et al. (2012) are shown. The chlorophyll content <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is
related to the nitrogen content of the leaf which itself is linked to the
maximum rate of carboxylation through the proteins of the Calvin Cycle and
the thylakoids. Some investigators have related the photosynthetic capacity
of leaves of some specific plants to their nitrogen content (e.g., Evans,
1989; Kattge et al., 2009; Houborg et al., 2013). Other investigators have
derived some empirical relationships between the nitrogen content and the
chlorophyll content (e.g., Shaahan et al., 1999; van den Berg and Perkins,
2004; Ghasemi et al., 2011). Since the current version of the model SCOPE
does not include the nitrogen scheme of a leaf, we first use the same value
of chlorophyll content <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> for all 13 PFTs. As a second step,
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values for each of the 13 PFTs are optimized so that the
simulated SIF reproduces the main spatial characteristics of observed SIF.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1"><caption><p>The simulated fluorescence (SIF) at the top of the canopy as a
function of the radiation wavelength and for C3 (black solid line) and C4
(red dashed line) plants from the model SCOPE are shown, respectively. The
blue solid line corresponds to wavelength value (i.e., 755 nm) at which the
simulated SIF is calculated in this study, i.e., the equivalent of the
satellite GOSAT based SIF.</p></caption>
            <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015-f01.png"/>

          </fig>

</sec>
</sec>
</sec>
<sec id="Ch1.S3">
  <title>Experimental set ups</title>
<sec id="Ch1.S3.SS1">
  <title>Idealized tests</title>
      <p>We carry out some idealized sensitivity tests by using the SCOPE model alone.
We investigate the sensitivity of SIF and GPP to biochemical parameters
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, environmental variables (atmospheric
temperature and vapour pressure, etc), visible radiation, and LAI. We assume
throughout the following sections the concentrations of both CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and
O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> at the interface of the canopy to be constant. We will focus our
discussions on the assessment of the sensitivity of the simulated SIF and GPP
to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, LAI, and the short wave radiation. All
the simulations in these tests are performed at noon.</p>
      <p>We present a spectrum of simulated fluorescence for C3 and C4 plants in
Fig. 1. Two peaks in the simulated fluorescence spectrum are shown at 680 and
725 nm. In agreement with van der Tol et al. (2009a), C4 plants exhibit
larger SIF than C3 plants over the wavelength range 625 to 755 nm. These
differences are amplified around the two peaks. We are using as observations
the GOSAT satellite-derived SIF, which retrieved SIF around 755 nm.
Therefore, the simulated fluorescence in this study corresponds to the SIF
value at this wavelength. In Fig. 1, this is around
1.2 Wm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> sr<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>.</p>
      <p>For all of the idealized tests presented hereafter, we use eight values of
LAI: 0.1, 0.5, 1, 2, 3, 4, 5, and 6. Also, the pressure, the temperature, and
the vapour pressure of the air surrounding the leaf used to compute the
internal CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> concentration of the leaf are set to 1000 hPa,
25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, and 10 hPa, respectively. The carbon dioxide (CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) and
the oxygen (O<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) concentrations are set to 355 ppm and
210 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula> ppm, respectively. The other settings of SCOPE
relevant for this study are given in Table 1.
<list list-type="bullet"><list-item><p>To investigate the sensitivity of SIF and GPP to the maximum carboxylation capacity <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>,
we choose <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values ranging from 10 to
250 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol(CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> every
10 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. In addition, two small
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values of 0.5 and 5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> are
considered.</p></list-item><list-item><p>To study the sensitivity of SIF and GPP to the chlorophyll AB content (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>), we select <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values
that span 10 to 80 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> range every
5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. Additionally, a small <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> value of
1 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> is considered.</p></list-item><list-item><p>To assess the sensitivity of the SIF and GPP to the broadband incoming shortwave radiation (0.4–2.5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m; hereafter
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) at the top of the canopy, we select <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values
that range from 100 to 1200 W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> every 100 W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. We add small
values of 1, 5, 10, 25, 50, and 75 W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>.</p></list-item><list-item><p>Finally, to investigate the diurnal variations, we simulate SIF and GPP by using the short time series of half-hourly
data over 15–20 July 2004 over a canopy located at the Hyytiala research
site in Finland (61.85<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> latitude and 24.29<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> longitude), which
is one of the sites of the FLUXNET network (e.g., Baldocchi, 2003; Papale et
al., 2006; see the dedicated website: <uri>http://www.fluxnet.ornl.gov</uri>).
SCOPE GPPs are compared to the observationally derived GPP data.
Unfortunately, we do not have observed SIF for this period.</p></list-item></list></p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T3" specific-use="star"><caption><p>Set-ups for the CCDAS simulations based on the carboxylation maximum
capacity (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) and chlorophyll AB content (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) are
given. The values of prior and optimized <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> as well as
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> PFT-specific are given in Table 2. The constant value of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> for all 13 PFTs is set to 40 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="3">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">Model configuration</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">S1</oasis:entry>  
         <oasis:entry colname="col2">Prior values</oasis:entry>  
         <oasis:entry colname="col3">Constant value for all the 13 PFTs</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S2</oasis:entry>  
         <oasis:entry colname="col2">Prior values</oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> PFT-specific</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S3</oasis:entry>  
         <oasis:entry colname="col2">Optimized values</oasis:entry>  
         <oasis:entry colname="col3">Constant value for all the 13 PFTs</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S4</oasis:entry>  
         <oasis:entry colname="col2">Optimized values</oasis:entry>  
         <oasis:entry colname="col3"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> PFT-specific</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

</sec>
<sec id="Ch1.S3.SS2">
  <title>CCDAS simulations</title>
      <p>Since the idealized tests may give a partial picture of the relationship
between SIF and GPP, we use the CCDAS built around SCOPE to perform
additional sensitivity tests by using actual meteorological, radiation, and
phenological data over 2009–2010. Overall, the values of the short wave
radiation <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> used in the CCDAS are mostly under moderate light
conditions (around 400–600 W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), but at some pixels <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
values can be larger than 800 W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (see Sect. S3 in the Supplement).
The relationship between SIF and GPP is then investigated along with
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. We make simulations of SIF and GPP by
using prior values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and their optimized values from Koffi
et al. (2012). We also carry out simulations by using a constant value of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> for all the 13 PFTs and a set of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values for
each of them. We perform four experiments (i.e., S1 to S4), which are
summarized in Table 3. The experiments S1 and S3 use a constant value of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> for all of the 13 PFTs, while simulations S2 and S4 consider
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> to be PFT dependent (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values are reported in
Table 2). The experiments S1 and S2 consider the prior values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, while S3 and S4 their optimized values. The differences
between S1 and S3 or between S2 and S4 give the sensitivity of SIF and GPP to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. The differences between S1 and S2 or between S3 and S4
mainly give the sensitivity of SIF to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>.</p>
      <p>The CCDAS simulates hourly SIF and GPP for one representative day in a month.
Since the computation of fluorescence is time consuming, we compute both SIF
and GPP only at 12 h local time, i.e., around the time of their peaks during
a sunny day. For the simulated SIF, the computations are assigned to the 15th
day of the month by using the monthly climate data and phenological variables
of BETHY, as described in Sect. 2.2.2. We also neglect the energy balance
scheme in SCOPE which weakly affects SIF.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2"><caption><p>The sensitivities of SCOPE fluorescence (SIF) at the top of the
canopy of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> plant to the carboxylation maximum capacity
(<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>), chlorophyll AB content (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>), and to the
broadband incoming shortwave radiation (0.4-2.5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m)
(<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) for several leaf area indices (LAI) are shown. Graphs
(<bold>a</bold>
and <bold>b</bold>) stand for SIF and GPP as function of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, respectively.
Graphs (<bold>c</bold> and <bold>d</bold>) give the sensitivities of SIF and GPP to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, respectively. Graphs (<bold>e</bold> and <bold>f</bold>) show SIF and GPP as a
function of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, respectively.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015-f02.png"/>

        </fig>

</sec>
</sec>
<sec id="Ch1.S4">
  <title>Results</title>
<sec id="Ch1.S4.SS1">
  <title>Idealized sensitivity tests using SCOPE</title>
      <p>The results of these idealized sensitivity tests for the various LAI values
are summarized in Figs. 2 and 3. For clarity, results from C3 plant are
discussed. Then, some conclusions are given for C4 plant.</p><?xmltex \hack{\newpage}?>
<sec id="Ch1.S4.SS1.SSS1">
  <title>Sensitivity of SIF and GPP to biochemistry parameters</title>
      <p>Figure 2 shows the sensitivity of both SIF and GPP to LAI, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>,
and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> under moderate light conditions (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>500</mml:mn></mml:mrow></mml:math></inline-formula> W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). As expected, both the fluorescence SIF and GPP increase
with the increase of LAI (Fig. 2). However, a weak sensitivity is found for
LAI values greater than 4. As an illustration for the increase, for
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>50</mml:mn></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, SIF values of 0.5
and 1.25 W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> sr<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> are found for LAI of 0.5
and 2, respectively (Fig. 2a). The fluorescence slightly increases with an
increase of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. The sensitivity is relatively large for
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, less than 70 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. Then, SIF
remains almost constant for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> higher than
125 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>molm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (Fig. 2a). As an illustration, for
LAI <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 2, the largest increase is of only 50 % of SIF for
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> between 10 and 70 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. Under
the studied configurations SIF increases with <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> when the GPP
is controlled by the carboxylation enzyme Rubisco, and remains almost
constant when photosynthesis is limited by electron transport.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3"><caption><p>The sensitivities of the SCOPE fluorescence SIF (<bold>a</bold> and <bold>c</bold>) and
gross primary productivity (GPP) (<bold>b</bold> and <bold>d</bold>) to the incoming short wave
radiation (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) and absorbed photosynthetically active radiation
(aPAR) and for several <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are presented. LAI and
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are set to 2 and 40 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, respectively.
Results for a <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> plant are shown.</p></caption>
            <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015-f03.png"/>

          </fig>

      <p>GPP monotonically increases as <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> increases with large
sensitivity for small <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (less than
75 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), then it becomes weakly sensitive for
large values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 2b). A moderate positive correlation
is found between SIF and GPP for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> less than
125 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, as shown by the increase of both SIF
and GPP with <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 2a and b). Then, for larger <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
(i.e., 125 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), a very weak negative
correlation between SIF and GPP is obtained. The reason for this weak
negative correlation is that SIF slightly decreases for large
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, while GPP even limited by the carboxylation enzyme Rubisco
still slightly increases (Fig. 2a and b). In fact, the value of irradiance at
which the fluorescence yield at leaf level <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Ft</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Eq. 1) or SIF
peaks increases with the increase of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. Thus, for the case
presented in Fig. 2a with the short wave radiation <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> of
500 W m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, the peak of SIF occurs at about <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>200</mml:mn></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>.</p>
      <p>In the current version of the fluorescence model in SCOPE, the concentration
of chlorophyll <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is set as a parameter and it is linked to SIF
through the transmittance and reflectance of the leaves. Figure 2c portrays
the variations of SIF as a function of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and for various LAIs.
For a given LAI, SIF increases with <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> with large sensitivity
for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> less than 20 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. For larger
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values (i.e., <inline-formula><mml:math display="inline"><mml:mo>&gt;</mml:mo></mml:math></inline-formula> 50 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), SIF remains
almost constant with a tendency to slightly decrease as <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
increases. For a given <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, the variance in SIF due to the LAI
can be significant.</p>
      <p>Fig. 2d displays GPP as a function of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 2d). Except for
small values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (less than 5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), GPP is
not sensitive to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. The very weak sensitivity of GPP to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> comes from the impact of the chlorophyll content on the
transmittance and reflectance at the top of the canopy when computing the
aPAR. This lack of sensitivity of GPP to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> contradicts the
established positive relationship between the two variables as reported in
Fleischer (1935) and more recently in
Gitelson et al. (2006).</p>
</sec>
<sec id="Ch1.S4.SS1.SSS2">
  <title>Sensitivity of SIF and GPP to short wave radiation</title>
      <p>For a given LAI, both SIF and GPP increase with the top of canopy short wave
radiation (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) (Fig. 2e and f). Thus, a strong positive linear
correlation is obtained between SIF and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 2e), while a
non-linear (i.e., curvilinear) relationship is obtained between GPP and
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 2f). For large <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, GPP increases with a
slower rate indicating that the photosynthesis is limited by the
carboxylation enzyme Rubisco. For the selected values of LAI, large variance
is found between SIF and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 2e). We also investigate the
relationship between the simulated aPAR and both computed SIF and GPP (see
Sect. S1 in the Supplement). As expected, a very strong linear relationship
between SIF and aPAR is obtained. This relationship is less sensitive to the
LAI as it is for the relation between SIF and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (as shown in
Fig. 2e). GPP shows similar variations with aPAR as it does with the short
wave radiation in Fig. 2f.</p>
      <p>Finally, the sensitivities of SIF and GPP to both <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and aPAR
for various <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are also investigated (Fig. 3). A strong linear
relationship between SIF and both <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and aPAR is obtained with
slopes which are less sensitive to the values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 3a
and c). Also, results clearly show that the sensitivity of SIF to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> increases with the increase of aPAR (or <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>),
with almost no sensitivity for low values of aPAR
(<inline-formula><mml:math display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula> 250 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). However, even with large
values of aPAR (or <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>), the sensitivity of SIF to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> remains small. In fact, the sensitivity of SIF to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> slightly increases with increasing of incoming radiation
only when <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> rapidly increases from low to high values (e.g. 5
to 250 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>; Fig. 3a and c). Such a rapid
increase of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> does occur only during the growing season of
the plant. As expected, a curvilinear relationship is found between GPP and
both <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and aPAR with large variance in this relation for the
selected <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 3b and d).</p>
      <p>It is worth noting that SIF values present in Fig. 3 in this study differ
(here lower) from the fluorescence flux at leaf level shown in van der Tol et
al. (2014). In fact, the authors argued that in the canopy, leaf illumination
is variable among leaves, and the relationship after aggregating over all
leaves (i.e., SIF) may differ from the fluorescence flux at leaf level.</p>
      <p>The conclusions found from C3 plant relevant for the sensitivity of both SIF
and GPP to the input variables (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, and
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) are valid for C4 plant (see Sect. S1). However, the
amplitude of these sensitivities is slightly larger for C4 plant.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4"><caption><p>SCOPE simulations of fluorescence SIF, gross primary productivity
(GPP), and absorbed photosynthetically active radiation (aPAR) from in situ
measurements at Hyytiala (acronym FI-Hyy and having longitude/latitude of
24.295<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> E/61.847<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N) in Finland during 2004 over the
15 July to 20 July period. Graph <bold>(a)</bold> presents the temporal
variations of the observed temperature (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>). Graph <bold>(b)</bold>
shows the temporal variations of both observed incoming short wave radiation
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (black) and SCOPE simulated aPAR (red). Graphs <bold>(c)</bold>
(SIF) and <bold>(d)</bold> (GPP) present SCOPE simulations by using two values of
both <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (blue: SCOPE<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>SIM1</mml:mtext></mml:msub></mml:math></inline-formula>: 
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>/<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>29</mml:mn></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>/10 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>; red:
SCOPE<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>SIM2</mml:mtext></mml:msub></mml:math></inline-formula>: 21.91/10.; green SCOPE<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>SIM3</mml:mtext></mml:msub></mml:math></inline-formula>: 21.91/40). The
observed GPP is in black. The other SCOPE parameters are given in Table 1.
The C3 plant is considered in SCOPE simulations.</p></caption>
            <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015-f04.png"/>

          </fig>

</sec>
<sec id="Ch1.S4.SS1.SSS3">
  <title>Simulations of in situ measurements</title>
      <p>The time series of both simulated SIF and GPP for 15–20 July 2004 are
presented in Fig. 4. As expected, there is a strong correlation between aPAR
and the short wave radiation <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 4b), hence we discuss the
results as a function of the observed <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. The temporal
variations of SIF and GPP mainly follow that of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>.
Particularly, the variations of SIF mirror that of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, showing
that the variance in SIF due to the temperature is low in this case study
(Fig. 4a). At high irradiance GPP shows limitation by the carboxylation
enzyme Rubisco, peaking early in the day whereas SIF follows <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">in</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
throughout the day. The small variations in GPP at certain episodes can be
explained by the temporal variations of the temperature (Fig. 4a). Note that
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, and LAI are set constant during this
period. Consequently, for this case study, the short wave radiation (hence
aPAR) is the main driver of the relationship between simulated SIF and GPP. A
curvilinear relation is obtained between GPP and SIF. However, a relatively
strong linear correlation coefficient of 0.95 is derived. This suggests that
SIF is a good constraint of GPP even if it does not directly constrain
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. The SCOPE model reproduces the observed diurnal GPP quite
well with meaningful choices of both LAI and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values
(Fig. 4d). Again, the simulated SIF is sensitive to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, while GPP
is insensitive to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Figs. 4c and d).</p>
      <p>Furthermore, we have computed the seasonal variations of these quantities for
some years at Hyytiala and Roccarespampani1 (acronym IT-Ro1,
longitude/latitude of 11.93/42.408) (see Sect. S2 in the Supplement). Overall, the model
reproduces quite well the observed GPP. However, the simulated SCOPE GPP peak
over a year occurs earlier (within 1–2 months) than observed ones. This
result is maybe caused by both LAI and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> used for the
simulation, which seem apparently large during the growing season of the
vegetation at these sites. The results of these preliminary analyses can be
then reinforced by using e.g., the satellite MODIS weekly LAI data relevant
for these stations.</p>
      <p>In summary, these idealized tests clearly show that the fluorescence SIF is
more sensitive to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, while GPP is more sensitive to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and both quantities are strongly sensitive to the short
wave radiation (or aPAR). However, GPP is limited by the carboxylation enzyme
Rubisco for large values of short wave radiation (or aPAR). Consequently, in
this case the relationship between SIF and GPP mainly driven by the short
wave radiation (or aPAR) is curvilinear. The part of the variance in this
relationship due to the GPP can be explained by <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and
environment conditions, while the variance in SIF is mainly due to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and possibly to the geometrical parameters (i.e., solar
zenith angle and observation zenith angle) used in the retrieval of SIF.</p>
      <p>Recent investigations by Zhang et al. (2014) show a strong sensitivity of SIF
to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> at in situ level at light saturation for cropland (corn
and soybean) using SCOPE version 1.52. Zhang et al. (2014) found about 4
times our sensitivity of SIF (here computed at 755 nm; Fig. 3a) to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> in the range of 10–200 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>.
We have modified our experiments to bring them closer to those of Zhang et
al. (2014). First, Zhang et al. (2014) calculate SIF at 740 nm vs.
755 nm in this study. Secondly, Zhang et al. (2014) average their calculations
from 9:00–12:00 local time (LT), while we sample at 12:00 LT. Results show
that:
<list list-type="bullet"><list-item><p>The sensitivity of SIF to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is slightly larger at 740 than 755 nm
and the difference increases with aPAR. However, as an example, for a
relatively large aPAR (1400 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>), SIF at
740 nm is only 25 % higher than SIF at 755 nm.</p></list-item><list-item><p>The averaging period makes little difference to the sensitivity.</p></list-item><list-item><p>Optimal choices of temperature and LAI produce a sensitivity about <inline-formula><mml:math display="inline"><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>/</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:math></inline-formula> that shown in
Zhang et al. (2014). Details on these comparisons are given in the Supplement
(Sect. S4).</p></list-item></list></p>
</sec>
</sec>
<sec id="Ch1.S4.SS2">
  <title>CCDAS simulations</title>
      <p>To assess the relationship between SIF and GPP at global scale, we perform
CCDAS simulations for the four experiments described in Table 3. The observed
(SIF) and modelled (SIF, GPP, and aPAR) quantities are generated at monthly
time resolution as described in Sects. 2.2.1 and 3.1, respectively. The
results of these simulations are discussed along with the satellite-based
SIF. We first analyze the correlations between the simulated quantities and
also the correlations between these simulations and the satellite-based SIF.
Secondly, their mean spatial patterns are discussed and finally, the time
series of their global and regional means as well as their zonal averages are
discussed.</p>
<sec id="Ch1.S4.SS2.SSS1">
  <title>Correlations between SIF and GPP</title>
      <p>For the discussion of the time series of modelled SIF and GPP at each CCDAS
land pixel and the corresponding observed SIF we analyze only pixels for
which we have at least 1 year satellite-based SIF data. Moreover, we
consider only the time series of these quantities for which the
satellite-based SIF data show consecutive values equal or greater than zero.
Indeed, the SCOPE model does not allow simulating negative SIF values.
Overall, the seasonality of the satellite-derived SIF is reasonably well
reproduced by both the simulated SIF and GPP as illustrated in Fig. 5. In
accordance with the idealized tests, the amplitudes of the satellite-derived
SIF can be better fitted by appropriate values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 5a),
while the simulated GPP is only weakly sensitive to small <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
values as discussed in Sect. 4.1. As expected, the amplitudes of the
simulated GPP are strongly sensitive to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 5b).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5"><caption><p>Temporal variations (June 2009 to December 2010) of CCDAS
simulations of the fluorescence SIF and GPP for different values of the
carboxylation maximum capacity (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) and the chlorophyll AB
content (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) and for <bold>(a)</bold> plant functional type (PFT 2: Tropical
broadleaved evergreen tree) are shown. In both graphs (<bold>a</bold> and <bold>b</bold>), the
satellite GOSAT based SIF is shown in black solid line with big dots.
<?xmltex \hack{\newline}?>
In graph <bold>(a)</bold>, SIF and GPP are simulated by using <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> value
of 73.5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol(CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and two <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
values of 40 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (SIF in blue dashed line with triangles
and GPP in red solid line with crosses) and 15 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (SIF
in green dashed line with diamond and GPP in orange solid line with
rectangles), respectively. For <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> value of 15 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, the correlation coefficient <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> between simulated SIF and
satellite based SIF is given on the top of the graph.
<?xmltex \hack{\newline}?>
In graph <bold>(b)</bold>, SIF and GPP are simulated by using <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> value of 15 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> and two <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values of
90 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol(CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (SIF in blue dashed line with
triangles and GPP in orange solid line with rectangles) and
73.5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol(CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> (SIF in green dashed line with
diamonds and GPP in red solid line with crosses), respectively. For
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> value of 73.5 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol(CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>) m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>,
the correlation coefficient <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> between simulated GPP and satellite based
SIF is given on the top of the graph.</p></caption>
            <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015-f05.png"/>

          </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6"><caption><p>Correlations between CCDAS simulated quantities (i.e., SIF,
GPP, aPAR) and between these simulated quantities and satellite GOSAT based
fluorescence SIF are shown. Graph <bold>(a)</bold> presents the correlation between
CCDAS simulated SIF (SIF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>SIM</mml:mtext></mml:msub></mml:math></inline-formula>) and the simulated absorbed
photosynthetically active radiation (aPAR). Graph <bold>(b)</bold> shows the simulated
gross primary productivity (GPP) as function of aPAR. Graph <bold>(c)</bold> displays
the scatter plot between simulated GPP and simulated SIF. Graph <bold>(d)</bold>
presents the correlation between SIF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>SIM</mml:mtext></mml:msub></mml:math></inline-formula> and SIF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>OBS</mml:mtext></mml:msub></mml:math></inline-formula>. Graph <bold>(e)</bold>
displays simulated GPP as function of SIF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>OBS</mml:mtext></mml:msub></mml:math></inline-formula>. Graph <bold>(f)</bold> shows
SIF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>OBS</mml:mtext></mml:msub></mml:math></inline-formula> as a function of aPAR. The dominant plant functional types (PFT)
in the grid cell, characterized by the PFTs having at least 50 % of the
spatial coverage, are shown by different colours on the right hand side of
graph <bold>(b)</bold>. The pixels of the CCDAS are at the spatial resolution of
2<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 2<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> (longitude <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> latitude). Results at global scale are
shown. The number of pair of data is 2857. The Pearson coefficient of the
linear correlation <inline-formula><mml:math display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula> is indicated. Data for June 2009 to December 2010 period
are considered.</p></caption>
            <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015-f06.png"/>

          </fig>

      <p>We have computed the Pearson correlation coefficient between the time series
of satellite-based SIF and modelled SIF and GPP at each pixel. For each
pixel, we consider only the pair of data for which the satellite-based SIF is
greater than or equal to zero. At most, 18 pairs of data are available for
each pixel. We treat only pixels with at least 14 data points for which the
linear correlation is significant at least 10 % of level of significance
for Pearson coefficient <inline-formula><mml:math display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula> greater than 0.43. For about half of the 3462
land pixels of CCDAS, the linear correlation coefficient <inline-formula><mml:math display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula> between the
satellite-based SIF and either simulated SIF or GPP is less than 0.43. For
these latter pixels, we have analyzed the time series of the satellite-based
SIF (with their uncertainty) jointly with the simulated SIF and GPP together
with the aPAR as representative of the short wave radiation. For brevity
sake, we only enumerate the different cases with low correlation (i.e.,
<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>R</mml:mi><mml:mo>&lt;</mml:mo></mml:mrow></mml:math></inline-formula> 0.43) without quantification since this does not add anything valuable
to our demonstration in the current study. We have cases for which:
<list list-type="bullet"><list-item><p>The peaks in simulated quantities (i.e., SIF and GPP) lag the satellite-based SIF peak by at least 1 month. Other cases show opposite
behaviour.</p></list-item><list-item><p>The simulated SIF remain almost constant, while the satellite-based SIF show a weak seasonality. Such cases predominantly occur in the
tropics.</p></list-item><list-item><p>The satellite-based SIF are larger (<inline-formula><mml:math display="inline"><mml:mo>&gt;</mml:mo></mml:math></inline-formula> 2 Wm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> sr<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) than modelled SIF
(around 1.2 Wm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> sr<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). Such cases are mainly
obtained in the tropics and for the PFT 1 (i.e., tropical broadleaved
evergreen tree).</p></list-item><list-item><p>The simulated SIF are larger than satellite based SIF. Such cases are mainly obtained from the PFT 9 (i.e., C3
grass).</p></list-item><list-item><p>The satellite-based SIF show some unexpected peaks during period where they are not expected and hence not
modelled.</p></list-item></list>
Secondly, we investigate the correlations between the simulated quantities
(SIF, GPP, and aPAR) at regional scales by using our best set up (i.e.,
experiment S4 in Table 3). We then assess the correlations between the
simulated quantities (SIF, GPP, and aPAR) and between simulated quantities
and the satellite-based SIF. We select data at each pixel such that the
satellite-based SIF is greater or equal to zero and CCDAS land pixel (i.e.,
the maximum fraction of coverage of the dominant PFT of the pixel) is greater
than zero. Data from June 2009 to end of 2010 are analyzed. We also give
information about the dominant PFT of the pixels over the studied time
period. To sample only over grid cells which are dominated by only one PFT,
we consider only pixels for which the dominant PFT has a fraction of coverage
greater than 50 %. Correlations are computed at global and regional
(southern hemisphere, tropics, and southern hemisphere) scales and over the
studied period. The results at global scale are shown in Fig. 6. A strong
linear correlation is found between the computed SIF and aPAR. This relation
is weakly sensitive to the PFTs (Fig. 6a). In contrast, the relationship
between GPP and aPAR is PFT dependent (Fig. 6b). A good linear relationship
between computed GPP and simulated SIF is obtained and again the slopes of
this relationship are PFT dependent (Fig. 6c). The correlation coefficient R
derived from GPP as a function of SIF value is around 0.8.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F7" specific-use="star"><caption><p>Mean spatial patterns over the year 2010 of <bold>(a)</bold> satellite GOSAT
based fluorescence SIF, <bold>(b)</bold> CCDAS simulated SIF by using constant value of
the chlorophyll AB content (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) for all the 13 PFTs (setting S3
in Table 3), <bold>(c)</bold> <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> PFT specific (setting S4 in Table 3) are
shown. Graph d) displays the mean spatial patterns of the gross primary
productivity (GPP) by using both <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> PFT specific and optimized
carboxylation maximum capacity (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) (setting S4 in Table 3).</p></caption>
            <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015-f07.png"/>

          </fig>

      <p>The model SCOPE simulates quite well the observed SIF (Fig. 6d). However,
large observed SIF (<inline-formula><mml:math display="inline"><mml:mo>&gt;</mml:mo></mml:math></inline-formula> 2 Wm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> sr<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) are not
simulated. Such large observed SIF mainly occur in the tropics. This result
points out that short wave radiation used in the CCDAS simulations may be
smaller than actual values. Also, the parameter <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Eq. 3) in the SCOPE
model may explain part of these low SIF. In fact, the computation of the
fluorescence yield <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Fm</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Eq. 2) depends on the parameter
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, which is unknown and there is no theoretical basis to constrain it.
Thus, an empirical relationship of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is used to calculate
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Fm</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. In the current version of the model SCOPE, there are two
parametrizations of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. In this paper, we use the parameterization of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> from Flexas et al. (2002)'s data set that includes drought stress
(see Eq. 3). Nevertheless, we have tested the other parameterization and
large differences are found from their SIF output. The contribution of
chlorophyll content <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is low since the assigned value in
tropics is already large (40 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) and as shown by the
idealized tests, the simulated fluorescence SIF remains almost constant for
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> value larger or equal to 40 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g cm<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>
(Fig. 2c). The correlation coefficient between modelled GPP and
satellite-based SIF is 0.70. This rises to 0.8 when we aggregate both
quantities to 4 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 4 degrees in agreement with Frankenberg et
al. (2011). Finally, as expected, a relatively good correlation is found
between aPAR and satellite-based SIF (Fig. 6f).</p>
      <p>Correlations are found to be larger between simulated quantities and
satellite-derived SIF in the northern hemisphere and moderate in the tropics
and lower in the southern hemisphere (not shown).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F8"><caption><p>Global <bold>(a)</bold> and regional (<bold>b</bold> to <bold>d</bold>) means of fluorescence SIF and
gross primary productivity GPP over June 2009 to December 2010 period are
shown. The satellite GOSAT based SIF (SIF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>OBS</mml:mtext></mml:msub></mml:math></inline-formula>: black solid line with big
dot), simulated SIF (SIF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>SIM</mml:mtext></mml:msub></mml:math></inline-formula>: green dashed line with triangles), and the
simulated gross primary productivity (GPP: red solid line with crosses) are
displayed. The CCDAS set up S4 (Table 3) is considered.</p></caption>
            <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015-f08.png"/>

          </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F9"><caption><p>Latitudinal distributions of the satellite GOSAT based SIF
(SIF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>OBS</mml:mtext></mml:msub></mml:math></inline-formula>: black solid line with big dot), simulated SIF (SIF<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>SIM</mml:mtext></mml:msub></mml:math></inline-formula>:
green solid line with diamonds), and gross primary productivity (GPP: red
solid line with triangles) within 5<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> latitudinal band are shown. The
CCDAS set up S4 (Table 3) is considered. The period of June 2009 and December 2010 period is considered.</p></caption>
            <?xmltex \igopts{width=170.716535pt}?><graphic xlink:href="https://bg.copernicus.org/articles/12/4067/2015/bg-12-4067-2015-f09.png"/>

          </fig>

</sec>
<sec id="Ch1.S4.SS2.SSS2">
  <title>Mean spatial patterns of SIF and GPP</title>
      <p>We compute the mean annual patterns of the satellite-based SIF and simulated
SIF and GPP for 2010. We discuss the simulated quantities by using the
experiments S3 (i.e., optimized <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and constant
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> for all the 13 PFTs) and S4 (optimized <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> PTF-specific) (See Table 3).</p>
      <p>Figure 7 displays the annual mean observed and simulated SIF as well as
simulated GPP. Figure 7a shows the satellite-based SIF. Figure 7b displays
the modelled SIF by using constant <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> for the 13 PFTs
(experiment S3; Table 3), while Fig. 7c presents model results of SIF for
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> PTF-specific (experiment S4). Figure 7d exhibits the
simulated GPP by using both <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> PFT-specific and optimized
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi>c</mml:mi><mml:mi>m</mml:mi><mml:mi>a</mml:mi><mml:mi>x</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (experiment S4). The model can reasonably reproduce the mean
spatial patterns of the satellite-based SIF with an appropriate choice of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> values for each of the 13 PFTs (Fig. 7a and c). The model
with constant <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> cannot reproduce the locations of maximum
observed SIF (Fig. 7a and b). Despite the good correlation, the computed SIF
with PFT-specific <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Table 3) underestimates the
satellite-based data (Fig. 7a and c). Some of this mismatch corresponds to
unlikely simulated SIF, for example, in central Australia.</p>
      <p>A good agreement between the spatial patterns of GPP and satellite-based SIF
is found (Fig. 7a and d). Overall, we have a co-occurrence of hot spots of
observed SIF and simulated SIF and GPP. Moreover, maximum simulated SIF
coincides with maximum aPAR (not shown).</p>
      <p>The small sensitivity of simulated SIF to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> suggests that it may
be difficult to use observations of SIF to constrain it. We can test this in
a more realistic context by comparing the differences between simulated SIF
for prior and optimized values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. If differences are large
compared to uncertainties in the observation then SIF observations would
allow constraining <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. We compute the differences between
simulated SIF by using prior <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (experiment S2 in Table 3) and
optimized <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (experiment S4). Then, we normalize these
differences by the uncertainties in satellite-based SIF. The derived root
mean square over the year 2010 at pixel level can reach up to 67 % of the
observed uncertainties, but the global average is only 6 %. This suggests
that SIF measurements can only weakly constrain <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> within the
current CCDAS.</p>
</sec>
<sec id="Ch1.S4.SS2.SSS3">
  <title>Global and regional means of SIF and GPP</title>
      <p>We compute the global and regional (i.e., Northern hemisphere
[30<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N–90<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N] Tropics [30<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S–30<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N] and
Southern hemisphere [90<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S–30<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S]) means at each month of
the year and over June 2009 to December 2010 over land pixels. Results of
both simulated SIF and GPP from our best experimental set up (i.e., optimized
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> with <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> PTF-specific; experiment S4 in
Table 3) are discussed. The results show a reasonably good agreement between
satellite-based SIF and both simulated SIF and GPP in terms of seasonality
(Fig. 8). However, on average, the simulated quantities peak 1 month earlier
than the peak of the satellite-based SIF (Fig. 8a). In the Northern
hemisphere, satellite-based SIF peaks in July, while simulated SIF reaches
its maximum in June (Fig. 8b). The seasonality at global scale is dominated
by the Northern hemisphere (Fig. 8a and b). In the Tropics, there is no
significant seasonality in the satellite-based SIF, which is also reproduced
by the model (Fig. 8c). In the Southern hemisphere, the satellite-based SIF
peaks in January, while modelled peaks in December (Fig. 8d). This weak
seasonality shift in the CCDAS simulations is driven by the visible radiation
at the top of the canopy (or aPAR) and LAI.</p>
      <p>Quantitatively, the mean values of the simulated SIF are slightly smaller
than that of satellite-based (about 93 %) in the Northern hemisphere and the
Tropics. Since the above-mentioned regions dominated the amplitude of SIF, a
good agreement between simulated and satellite-based SIF is consequently
found at global scale. The simulated SIF in the Southern hemisphere is about
1.47 times the value of satellite-based SIF. The main differences occur in
Australia where the relatively large values of modelled SIF are not shown in
the satellite-based SIF data (see Fig. 7a and c).</p>
      <p>The zonal averages over the CCDAS land pixels of the satellite-based SIF and
the simulated quantities (SIF and GPP) are shown in Fig. 9. A good agreement
is found between the latitudinal variations of the satellite-based SIF and
the simulated SIF by using the <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> PFT-specific (Fig. 9). Also, a
good agreement is obtained between the satellite-based SIF and the GPP
(Fig. 9) and between SIF and aPAR (see Sect. S3 in the Supplement). All of these quantities show maxima in the tropics and around
45<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N. Simulated SIF values are smaller than the satellite-based SIF
in the tropics. Between <inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>15<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>45<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>, the differences
are mainly due to C4 grass for which both the model's <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are apparently small. Around <inline-formula><mml:math display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>35<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> latitude, the
differences are mainly due to the fact that the model simulates a large SIF
signal over Australia, while the satellite-based SIF shows only a small SIF
signal. This discrepancy might be explained by the uncertainty in the LAIs
set to the evergreen shrub in the CCDAS in this area. Apparently, the LAIs in
the CCDAS seem larger than expected values that give satellite based SIF
measurements.</p>
      <p>In summary, the agreement between simulated and observed SIF is better as we
move to larger and larger scales.</p>
</sec>
</sec>
</sec>
<sec id="Ch1.S5">
  <title>Discussion and concluding remarks</title>
      <p>The first global maps of SIF retrieved from GOSAT measurements show promise
in estimating the terrestrial gross photosynthetic uptake flux of CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
(GPP) (Frankenberg et al., 2011; Joiner et al., 2011). We have investigated
the usefulness of these data in constraining GPP in the framework of CCDAS.
We have augmented CCDAS with SCOPE, which allows the calculation of GPP and
SIF at leaf and canopy level. In CCDAS, the relationship between SIF and GPP
is mediated by process parameters, principally the maximum carboxylation
capacity (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>). Parameters not currently included in CCDAS such
as the chlorophyll content (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) of the leaves also affects the
observed fluorescence and so constitutes a nuisance variable in an
assimilation of SIF into CCDAS. We first calculate the sensitivity of SIF and
GPP in the stand alone SCOPE model to a series of parameters, inputs or
nuisance variables. SIF and GPP both respond strongly to incoming radiation
suggesting that, insofar as this input is uncertain, SIF can provide a useful
constraint. This uncertainty is currently not considered in the CCDAS under
study.</p>
      <p>The relationship between <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and SIF is more complicated and
weaker suggesting that the CCDAS approach of using model parameters to
mediate information from SIF to GPP is unlikely to work. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> also
controls SIF while it has little impact on the desired GPP making it a
classical nuisance variable. Hence, in the relationship between simulated SIF
and GPP, part of the variance is due to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. This study also
shows that the use of SIF measurements in the model should account for
chlorophyll concentration.</p>
      <p>The simulations of CCDAS confirm the results from the idealized tests. Thus,
the relationship between the simulated GPP and computed SIF is again found to
be mainly controlled by the short wave radiation or aPAR. The analyses also
show that a robust linear relationship between SIF and GPP can be inferred
for each PFT. This result is in agreement with the findings of Guanter et
al. (2012) and Parazoo et al. (2014).</p>
      <p>We compared observed SIF with simulated SIF and GPP at global scale within
the CCDAS. The analyses showed a need to select meaningful values for the
chlorophyll content <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> for each of the 13 PFTs to better
reproduce the satellite-based SIF. The use of PFT-specific <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
allows a better reproduction of the satellite-based SIF, with good
co-location of the hot spots. Timing of large-scale means is also good but
this breaks down at pixel level. The global and regional as well as the zonal
averages of the simulated quantities (SIF and GPP) are in good agreement with
the satellite-based SIF. On average, the peaks in simulated SIF and GPP lag
by 1 month the peaks in satellite-derived SIF in both Southern and Northern
hemispheres. The simulated quantities are found to be better correlated to
the satellite-based SIF when integrating the data at global and regional
scales. More particularly, we found a significant linear correlation between
simulated GPP and observed SIF, but a large scatter within the data is
obtained. Such a variance can be attributed partly to the type of vegetation
(Guanter et al., 2012; Parazoo et al., 2014). Also, part of this variance is
caused by both <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. Indeed, simulated GPP
is more sensitive to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, while simulated SIF is sensitive to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>.</p>
      <p>The study suggests some prospects for the use of satellite-based SIF to
constrain GPP. While we found a good correlation between the global and
regional and zonal averages of simulated quantities and satellite-based SIF,
we do not find a common process parameter that propagates the information
from the fluorescence to the GPP. Indeed, the relationship between GPP and
satellite-based SIF is mainly driven by the short wave radiation or aPAR.
Consequently, the mechanistic formulations of both SIF and GPP under study do
not allow us to constrain GPP through <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>.</p>
      <p>On the other hand, the results clearly show the good correlation between
aPAR and both the fluorescence SIF and GPP, which support previous
investigations. This both points to a simpler application of SIF in
constraining GPP and a problem with the foregoing study. aPAR is an external
forcing for the biochemical modules of the biosphere model (e.g., SCOPE or
BETHY) which is taken to be well known. Errors in forcing (like other
nonparametric errors) are added to the observational error in CCDAS (Rayner
et al., 2005), but the observations are unable to improve estimates of
forcing. The parametric studies above hence miss a potential role of the SIF
measurements in constraining GPP even if they cannot constrain process
parameters.</p>
      <p>Monteith (1972) proposed an empirical linear relation between GPP and aPAR
which has been widely used by the satellite community to derive the GPP. The
slope of this relationship is the efficiency (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ε</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) with
which the absorbed radiation is converted to fixed carbon. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ε</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> varies with physiological stress. We have seen a good linear
relationship between the fluorescence SIF and aPAR. Thus, the GPP is directly
linked to SIF by the ratio <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ε</mml:mi><mml:mi mathvariant="normal">p</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="italic">ε</mml:mi><mml:mi mathvariant="normal">f</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. Such an approach is described in a recent report of Berry et
al. (2013). Moreover, Yang et al. (2015), when investigating a temperate
deciduous forest, found that SIF incorporated information about both
aPAR and light use efficiency (LUE), the two main components of GPP. The
empirical approach would be easier to implement. It could be combined with
other pertinent data for GPP (e.g., CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> or Carbonyl sulfide (COS)
concentration) within a simplified CCDAS. This approach will be applied in a
future study.</p>
      <p>This study also shows a very weak sensitivity of GPP to the chlorophyll
content (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) which is obtained for only small <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>.
This model result contradicts the established positive relationship between
the two variables as reported in Fleischer (1935) and more recently in
Gitelson et al. (2006). In the current version of the SCOPE model,
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are independent parameters, but in
reality they are correlated. In fact, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is related to the
nitrogen content of the leaf which itself is linked to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
(e.g., Kattge et al., 2009; Houborg et al., 2013). In addition, the nitrogen
content of the leaf affects both the leaf transmittance and reflectance which
influences the aPAR and then the GPP. Thus, through the inclusion of a
nitrogen scheme a more apparent link between <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and GPP and
greater sensitivity could be achieved.</p>
      <p>As the SCOPE model development, as stated in van der Tol et al. (2014), the
computation of the fluorescence yield <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Fm</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Eq. 2 in this
paper) depend on the parameter <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, which is unknown and there is no
theoretical basis to constrain it. Thus, an empirical relationship of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
is used to change <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Φ</mml:mi><mml:mi mathvariant="normal">Fm</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. In the current version of the model
SCOPE, there are two parametrizations of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. In this paper, we use the
parameterization of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> from a Flexas' data set that includes drought
stress, as noted within the model. Nevertheless, we have tested the other
parameterization and large differences are found from their SIF output.
Consequently, more research is needed to consolidate SIF modelling in SCOPE
biochemistry model as there can be a notable effect of different models for
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> on the photosystem yields and subsequent sensitivity of SIF.</p>
      <p>Finally, in this study we have investigated the sensitivity of simulated SIF
to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> at the frequency of 755 nm. Other frequencies in the
fluorescence spectrum need to be checked.</p>
</sec>
<sec id="Ch1.S6" sec-type="conclusions">
  <title>Conclusions</title>
      <p>We have investigated the usefulness of satellite-derived fluorescence data to
constrain GPP within CCDAS. We have coupled the SCOPE model to CCDAS to allow for the
computing of both fluorescence SIF and GPP. We have assessed the sensitivity of
both SIF and GPP to the environmental conditions at the interface of the
canopy (short wave radiation and meteorological variables) and the
biophysical parameters (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) by using
idealized and CCDAS simulations. Our results show:
<list list-type="bullet"><list-item><p>As expected, GPP is strongly sensitive to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, while SIF is more sensitive to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">ab</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
and only weakly sensitive to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> under high radiation conditions and lower <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
ranges.</p></list-item><list-item><p>The relationship between simulated SIF and GPP is mainly driven by aPAR. The variance in this relationship is
mostly explained by the <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and the chlorophyll content. This highlights the need for better treatment of chlorophyll content in biosphere
models.</p></list-item><list-item><p>The global and regional means as well as the zonal averages of both simulated SIF and GPP are in good agreement
with the satellite-based SIF. The seasonality of the satellite-based SIF is
quite well reproduced by the simulated SIF and GPP. However, the peaks of the
simulated quantities lag by 1 month that of the satellite-based SIF in the
Northern and Southern Hemispheres.</p></list-item><list-item><p>A good agreement is found between the simulated SIF and computed GPP. The relationship is PFT
dependent.</p></list-item><list-item><p>A good agreement is found between the satellite-based SIF and the simulated quantities (SIF and
GPP).</p></list-item></list>
The study shows that the models of GPP and SIF in the CCDAS built around
SCOPE do not allow us to propagate observations of SIF through constraint of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> to improve estimates of GPP. For this version of CCDAS,
this study would rather recommend the use of an empirical relationship
between GPP and the satellite-based SIF especially taking account
uncertainties in the radiation. Moreover, this empirical approach would be
easier to implement and combined with other relevant data for the GPP would
help to better estimate this quantity. However, a version of CCDAS which
includes the full energy balance (including hydrological scheme) and
prognostic photosynthesis (e.g., Knorr et al., 2010; Kaminski et al., 2013)
and especially nitrogen scheme may give a slightly different conclusion about
the sensitivity of the fluorescence to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mi mathvariant="normal">cmax</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>.</p>
</sec>

      
      </body>
    <back><app-group>
        <supplementary-material position="anchor"><p><bold>The Supplement related to this article is available online at <inline-supplementary-material xlink:href="http://dx.doi.org/10.5194/bg-12-4067-2015-supplement" xlink:title="pdf">doi:10.5194/bg-12-4067-2015-supplement</inline-supplementary-material>.</bold></p></supplementary-material>
        </app-group><ack><title>Acknowledgements</title><p>Rayner is in receipt of an Australian Professorial Fellowship (DP1096309).
We are grateful to Christiaan van der Tol for providing the model SCOPE and
his initial support. We are also grateful to both Timo Vesala and Dario
Papale for providing FLUXNET data at the stations Hyytiala and
Roccarespampani 1, respectively.
<?xmltex \hack{\newline}?><?xmltex \hack{\newline}?>
Edited by: G. Wohlfahrt</p></ack><ref-list>
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