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<article xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:oasis="http://docs.oasis-open.org/ns/oasis-exchange/table" dtd-version="3.0"><?xmltex \makeatother\@nolinetrue\makeatletter?><?xmltex \bartext{}?>
  <front>
    <journal-meta>
<journal-id journal-id-type="publisher">GMD</journal-id>
<journal-title-group>
<journal-title>Geoscientific Model Development</journal-title>
<abbrev-journal-title abbrev-type="publisher">GMD</abbrev-journal-title>
<abbrev-journal-title abbrev-type="nlm-ta">Geosci. Model Dev.</abbrev-journal-title>
</journal-title-group>
<issn pub-type="epub">1991-9603</issn>
<publisher><publisher-name>Copernicus Publications</publisher-name>
<publisher-loc>Göttingen, Germany</publisher-loc>
</publisher>
</journal-meta>

    <article-meta>
      <article-id pub-id-type="doi">10.5194/gmd-9-587-2016</article-id><title-group><article-title><?xmltex \hack{\vskip-6mm}?>A global scale mechanistic model of photosynthetic capacity (LUNA V1.0)</article-title>
      </title-group><?xmltex \runningtitle{A global scale mechanistic model of photosynthetic capacity}?><?xmltex \runningauthor{A.~A.~Ali et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="no" rid="aff1 aff2">
          <name><surname>Ali</surname><given-names>A. A.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>Xu</surname><given-names>C.</given-names></name>
          <email>xuchongang@gmail.com</email>
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Rogers</surname><given-names>A.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-9262-7430</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff4">
          <name><surname>Fisher</surname><given-names>R. A.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff5">
          <name><surname>Wullschleger</surname><given-names>S. D.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Massoud</surname><given-names>E. C.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-1772-5361</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2 aff6">
          <name><surname>Vrugt</surname><given-names>J. A.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Muss</surname><given-names>J. D.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>McDowell</surname><given-names>N. G.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff7">
          <name><surname>Fisher</surname><given-names>J. B.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff8 aff9">
          <name><surname>Reich</surname><given-names>P. B.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Wilson</surname><given-names>C. J.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-9896-0912</ext-link></contrib>
        <aff id="aff1"><label>1</label><institution>Earth and Environmental Sciences Division, Los Alamos National Laboratory,
Los Alamos, New Mexico, USA</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>Department of Civil and Environmental Engineering, University of California
Irvine, Irvine, California, USA</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>Environmental and Climate Sciences Department, Brookhaven
National Laboratory, Upton, New York, USA</institution>
        </aff>
        <aff id="aff4"><label>4</label><institution>Climate and Global Dynamics, National Center for Atmospheric Research,
Boulder, Colorado, USA</institution>
        </aff>
        <aff id="aff5"><label>5</label><institution>Climate Change Science Institute, Environmental Sciences Division, Oak Ridge
National Laboratory, <?xmltex \hack{\newline}?>Oak Ridge, Tennessee, USA</institution>
        </aff>
        <aff id="aff6"><label>6</label><institution>Department of Earth System Science, University of California Irvine, Irvine,
California, USA</institution>
        </aff>
        <aff id="aff7"><label>7</label><institution>Jet Propulsion Laboratory, California Institute of Technology, Pasadena,
California, USA</institution>
        </aff>
        <aff id="aff8"><label>8</label><institution>Department of Forest Resources, University of Minnesota, St. Paul,
Minnesota, USA</institution>
        </aff>
        <aff id="aff9"><label>9</label><institution>Hawkesbury Institute for the Environment, University of Western Sydney,
Penrith, New South Wales, Australia</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">C. Xu (xuchongang@gmail.com)</corresp></author-notes><pub-date><day>12</day><month>February</month><year>2016</year></pub-date>
      
      <volume>9</volume>
      <issue>2</issue>
      <fpage>587</fpage><lpage>606</lpage>
      <history>
        <date date-type="received"><day>8</day><month>July</month><year>2015</year></date>
           <date date-type="rev-request"><day>10</day><month>August</month><year>2015</year></date>
           <date date-type="rev-recd"><day>12</day><month>December</month><year>2015</year></date>
           <date date-type="accepted"><day>6</day><month>January</month><year>2016</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://gmd.copernicus.org/articles/.html">This article is available from https://gmd.copernicus.org/articles/.html</self-uri>
<self-uri xlink:href="https://gmd.copernicus.org/articles/.pdf">The full text article is available as a PDF file from https://gmd.copernicus.org/articles/.pdf</self-uri>


      <abstract>
    <p>Although plant photosynthetic capacity as determined by the maximum
carboxylation rate (i.e., <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and the maximum electron transport
rate (i.e., <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> at a reference temperature (generally 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C) is
known to vary considerably in space and time in response to environmental
conditions, it is typically parameterized in Earth system models (ESMs) with
tabulated values associated with plant functional types. In this study, we
have developed a mechanistic model of leaf utilization of nitrogen for
assimilation (LUNA) to predict photosynthetic capacity at the
global scale under different environmental conditions. We adopt an
optimality hypothesis to nitrogen allocation among light capture, electron
transport, carboxylation and respiration. The LUNA model is able to
reasonably capture the measured spatial and temporal patterns of
photosynthetic capacity as it explains <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 55 % of the global
variation in observed values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 65 % of the variation in the observed values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. Model
simulations with LUNA under current and future climate conditions
demonstrate that modeled values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> are most affected in
high-latitude regions under future climates. ESMs that relate the values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> or <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> to plant functional types only are likely to
substantially overestimate future global photosynthesis.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>
      <p>Photosynthesis is one of the major components of the ecosystem carbon cycle
(Canadell et al., 2007; Sellers et al., 1997) and is thus a key
ingredient of Earth system models (ESMs)   (Block and Mauritsen, 2013;
Hurrell et al., 2013). Most ESMs are based on the photosynthesis model
developed by Farquhar et al. (1980). The maximum carboxylation rate
scaled to 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C (i.e., <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>; <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 the maximum electron transport rate scaled to 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C
(i.e., <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>; <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron 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 the
model have been generally accepted as the main proxies of photosynthetic
capacity. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> are key biochemical parameters in
photosynthesis models as they control the carbon fixation process
(Farquhar et al., 1980). Large spatial and temporal
variations in estimates of the gross primary productivity exist across ESMs
(Schaefer et al., 2012), which have been partly attributed to
uncertainties in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>  (Bonan et al., 2011).
Accurate estimates of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> are of paramount
importance to simulate the gross primary productivity as errors in these two
entities may be exacerbated when upscaling from leaf to ecosystem level
(Hanson et al., 2004).</p>
      <p>Many studies have demonstrated that it is particularly difficult to predict
accurately the global scale variations in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>
(Bonan et al., 2011; Rogers, 2014). One important reason
that contributes to this rather poor predictability is a lack of
understanding of the processes that control the values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>          (Maire et al., 2012; Xu et al., 2012)
despite the fact that <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> has been measured and studied more
extensively than most other photosynthetic parameters   (Kattge and Knorr,
2007; Leuning, 1997; Wullschleger, 1993). Many empirical studies have shown
that <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (or field-based surrogates) correlate
with leaf nitrogen content   (Medlyn et al., 1999; Prentice et al., 2014;
Reich et al., 1998; Ryan, 1995; Walker et al., 2014). Therefore, a constant
relationship between the leaf nitrogen content and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> or
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is commonly utilized by many ecosystem models   (Bonan et al.,
2003; Haxeltine and Prentice, 1996; Kattge et al., 2009). However, the
relationship between leaf nitrogen content, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> varies with light intensity, temperature, nitrogen
availability and the 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> concentration   (Friend, 1991;
Reich et al., 1995; Ripullone et al., 2003). Thus, the presumed relationship
between <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> and leaf nitrogen content might introduce
significant simulation biases of future photosynthetic rates, which in turn
may also affect predictions of the downstream carbon cycle and other climate
processes that are dependent on the modeled photosynthetic rates   (Bonan
et al., 2011; Knorr and Kattge, 2005; Rogers, 2014).</p>
      <p>To better describe the relationship between photosynthetic capacity and
its driving environmental conditions, we have developed a global scale
mechanistic model of leaf utilization of nitrogen for assimilation (LUNA). This
model takes into explicit consideration the key environmental
variables including temperature, radiation, humidity, 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 day length to explain the complex dependencies between
leaf nitrogen, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. Using an optimality
hypothesis, the LUNA model allocates leaf nitrogen to different processes,
thereby predicting the values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> under
different environmental conditions. We estimate the parameters of LUNA by
fitting the model against globally distributed observations of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. We then use the calibrated LUNA model to
assess the impacts of future climate change on photosynthesis by estimating
the summer-season net photosynthetic rate using LUNA's predicted values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> under historic and future climate conditions.</p>
</sec>
<sec id="Ch1.S2">
  <title>Methodology</title>
<sec id="Ch1.S2.SS1">
  <title>Overview</title>
      <p>The LUNA model (version 1.0) is based on the nitrogen allocation model
developed by Xu et al. (2012), which optimizes nitrogen
allocated to light capture, electron transport, carboxylation and
respiration. Xu et al. (2012) considered a few model
assumptions to derive the optimized nitrogen distributions, including (i)
storage nitrogen is allocated to meet requirements to support new tissue
production; (ii) respiratory nitrogen is equal to the demand implied by the
sum of maintenance respiration and growth respiration; and (iii) light capture,
electron transport and carboxylation are co-limiting to maximize
photosynthesis. The model of Xu et al. (2012) has been tested for three
different sites only without global-scale calibration of its parameters.
Here, we expand the work of Xu et al. (2012) by using a global data set of
observations of photosynthetic capacity to derive accurate values of the
model parameters and by incorporation of several refinements to support
global-scale prediction of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. Specifically, this
revised model considers additional environmental variables such as day
length and humidity, and honors variations in the balance between the
light-limited electron transport rate and the Rubisco-limited carboxylation
rate. We use an efficient Markov chain Monte Carlo simulation approach, the
Differential Evolution Adaptive Metropolis algorithm (DREAM<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>(ZS)</mml:mtext></mml:msub></mml:math></inline-formula>)
(Laloy and Vrugt, 2012; Vrugt et al., 2008, 2009), to fit
the nitrogen allocation model to a large data set of observed <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> values collected across a wide range of environmental gradients
(Ali et al., 2015). After model fitting, sensitivity
analyses are performed to gauge the response of the model to changes in its
parameter values and the key environmental drivers including temperature,
photosynthetic active radiation, day length, relative humidity and
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> concentration. Finally, mean summer-season
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values and their impacts on net photosynthesis
are estimated for the globe, using climate projections from the Community
Climate System Model (CCSM)  (Gent et al., 2011).</p>
</sec>
<sec id="Ch1.S2.SS2">
  <title>Model description </title>
      <p>The structure of the LUNA model is based on Xu et al. (2012),
where the leaf nitrogen is divided into four different pools including
structural nitrogen, photosynthetic nitrogen, storage nitrogen and
respiratory nitrogen. We assume that plants optimize their nitrogen
allocation to maximize the net photosynthetic carbon gain, defined as the
gross photosynthesis (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>A</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> minus the maintenance respiration for photosynthetic
enzymes (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mtext>psn</mml:mtext></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, under given environmental conditions and a leaf nitrogen
use strategy as determined by the parameters of the LUNA model. The model
includes the following four unitless parameters: (1) <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb0</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, which
specifies the baseline proportion of nitrogen allocated for electron
transport rate; (2) <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb1</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, which determines response of electron
transport rate to light; (3) <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, which defines the baseline ratio of
Rubisco-limited rate to light-limited rate; and (4) <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula>, which determines the
response of electron transport rate to relative humidity. The LUNA model
predicts the values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> based on the optimal
amounts of nitrogen allocated for carboxylation and electron transport. The
model inputs are area-based leaf nitrogen content, leaf mass per unit leaf
area and the driving environmental conditions including temperature,
CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, radiation, relative humidity and day length.</p>
      <p>It is important to stress here that the outcome of the optimality concept
used in LUNA is conditional on the plant's nitrogen use strategies built
into the model. Thus, it is possible that the optimal values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> predicted by the LUNA model for future
climate conditions could produce lower values of the net photosynthetic
carbon gain than fixed values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> without
the use of a nitrogen use strategy. An example of this is shown in Fig. S1 in
the Supplement,
where the net photosynthetic carbon gain pertaining to the optimal
nitrogen allocations predicted by the LUNA model for the elevated
temperature is lower than its counterpart derived from a fixed nitrogen
allocation for the ambient temperature. A complete description of the LUNA
model and the associated optimality hypothesis and algorithms appears in
Appendix A. This optimality approach is introduced and tested by Xu et al.
(2012) for only three different sites, and here we evaluate
its usefulness and applicability at the global scale with improvements to
account for large-scale variability. Optimality approaches are important
tools for land surface models because they provide testable hypotheses for
specific plant functions   (Dewar, 2010; Franklin et al., 2012; Schymanski
et al., 2009; Thomas and Williams, 2014).</p>
</sec>
<sec id="Ch1.S2.SS3">
  <title>Data and temperature response functions</title>
      <p>Details of data collection are reported in Ali et al. (2015).
Specifically, we conducted an exhaustive literature search with Google Scholar
to obtain publications that contained the words <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>,
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, maximum carboxylation rate or maximum electron
transport rate. To rapidly subset the most appropriate and relevant
publications, we use simultaneously the wording leaf nitrogen content,
leaf mass per area or specific leaf area. Individual values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, area-based leaf nitrogen content (LNC<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:math></inline-formula>; g N 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> leaf) and leaf mass per unit leaf area (LMA; g dry mass 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> leaf)
are then obtained by digitizing the experimental data depicted
graphically in the selected papers. We use all of the data from Ali et al.
(2015) with the exception of one study that collected
seasonal data on <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> during a prolonged drought
(Xu and Baldocchi, 2003), as the LUNA model does not take into
consideration the potential enzyme deterioration due to water stress but
rather simulates only the optimal nitrogen allocation based on monthly
climate conditions. This resulted in a data set of 766 observations of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> and 643 data points of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> ranging from the tropics to the
arctic with a total of 125 species. The data include evergreen and
deciduous species from arctic, boreal, temperate and tropical areas at
different times of the year and from various canopy locations (Fig. S2).</p>
      <p>To allow comparisons of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> data collected at
different temperatures, we first standardize our data to a common reference
temperature (25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C). To do this, we employ temperature response
functions (TRFs) for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>. Because of issues related to
the possibility of acclimation to temperature, there is not yet scientific
consensus on which TRF to use (Yamori et al., 2006).
Therefore, we use two alternative temperature response functions to evaluate
the potential impact of our selection of the TRFs on the outcome of our
analysis. The first temperature response function (TRF1) uses the formula of Kattge and
Knorr (2007), which accounts empirically for the potential
of thermal acclimation to growth temperature. Following the Community Land
Model version 4.5, the growth temperature is constrained between
11 and 35 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C
(Oleson et al., 2013) to limit
the extent of acclimation to growth temperatures found in the calibration
data set. The second temperature response function (TRF2) does not consider
the thermal acclimation by fixing the acclimation coefficients in TRF1
(Kattge and Knorr, 2007). Please refer to Appendix B for details on
TRF1 and TRF2 used herein.</p>
      <p>Because the LUNA model is based on the C<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> photosynthetic pathway, in
this study, we only consider C<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> species. Typically, plant species are
grouped into several simple plant functional types (PFTs) in ESMs because of
computational limitations and gaps in ecological knowledge. The LUNA model
does not differentiate among the PFTs of C<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> species due to a limited
coverage of environmental conditions for individual PFTs. Thus, a single set
of parameter estimates is used for the PFTs of all C<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> species.</p>
</sec>
<sec id="Ch1.S2.SS4">
  <title>Parameter estimation</title>
      <p>The four parameters of LUNA are difficult to measure directly in the field.
In this study, we estimate their values by fitting our model against
observations of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> using the DREAM<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>(ZS)</mml:mtext></mml:msub></mml:math></inline-formula>
algorithm (Vrugt et al., 2008, 2009; Laloy and Vrugt, 2012). This method
uses differential evolution as a genetic algorithm for population evolution
with a Metropolis selection rule to decide whether candidate points should
replace their parents or not. This simple Markov chain Monte Carlo (MCMC)
method exhibits excellent sampling efficiencies on a wide range of model
calibration problems, including multimodal and high-dimensional search
problems. A detailed description of DREAM<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>(ZS)</mml:mtext></mml:msub></mml:math></inline-formula> appears in Vrugt et al. (2008, 2009) and Laloy and Vrugt (2012) and interested readers are referred
to these publications for further details. Uniform prior parameter
distributions are used to constrain the potential parameter values and the
Gaussian likelihood function is used to quantify the distance between the
modeled <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values and their observed
counterparts. Convergence plots of the DREAM<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>(ZS)</mml:mtext></mml:msub></mml:math></inline-formula> sampled LUNA
parameters to the posterior distribution are presented in Figs. S3 and S4.</p>
</sec>
<sec id="Ch1.S2.SS5">
  <title>Model evaluations</title>
      <p>In this study, two different goodness-of-fit metrics are used to quantify
the performance of the LUNA model against the <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> data. These are the coefficient of determination (<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>
(Whitley et al., 2011) and the model efficiency (ME)
(Whitley et al., 2011). The <inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> metric ranges between 0
and 1 and measures how much of the observed dispersion of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> or
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> is explained by the model. A related metric, the model efficiency
is calculated using

                <disp-formula id="Ch1.E1" content-type="numbered"><mml:math display="block"><mml:mrow><mml:mi mathvariant="normal">ME</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:mo>∑</mml:mo><mml:msup><mml:mfenced open="(" close=")"><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mover accent="true"><mml:mi>y</mml:mi><mml:mo stretchy="false" mathvariant="normal">^</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub></mml:mfenced><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow><mml:mrow><mml:mo>∑</mml:mo><mml:msup><mml:mfenced open="(" close=")"><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:mover accent="true"><mml:mi>y</mml:mi><mml:mo mathvariant="normal">¯</mml:mo></mml:mover></mml:mfenced><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mover accent="true"><mml:mi>y</mml:mi><mml:mo stretchy="false" mathvariant="normal">^</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> denote the observed and LUNA-simulated
values, respectively, and <inline-formula><mml:math display="inline"><mml:mover accent="true"><mml:mi>y</mml:mi><mml:mo mathvariant="normal">¯</mml:mo></mml:mover></mml:math></inline-formula> signifies the mean of the observations.
This metric measures the proportion of the variance in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> or
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> explained by the <inline-formula><mml:math display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula> line between model predictions and
observations    (Mayer and Butler, 1993; Medlyn et al., 2005).
The ME ranges between 0 and 1, where a ME of unity corresponds to a perfect
match between the modeled and measured data and a ME of zero indicates that
the model predictions are only as accurate as the mean of the measured data.</p>
</sec>
<sec id="Ch1.S2.SS6">
  <title>Model sensitivity analysis</title>
      <p>To better understand how the simulated LUNA output of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> depends on its four parameters and the key model inputs, a
one-at-a-time (OAT) sensitivity analysis is performed. In the first
analysis, we focus on the model parameters only, and perturb their
calibrated values, one at a time, with <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>15 %. The second sensitivity
analysis considers separately the effect of the key environmental variables
on the simulated values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> and perturbs
the mean values of the day length (hours), daytime radiation (W m<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>,
temperature (<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C), relative humidity (unitless) and carbon dioxide
(ppm) with <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>15 %.</p>
</sec>
<sec id="Ch1.S2.SS7">
  <?xmltex \opttitle{Changes in $V_{\mathrm{c,max25}}$ and $J_{\mathrm{max25}}$ under future climate projections}?><title>Changes in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> under future climate projections</title>
      <p>The global surface temperature could increase as much of 3.9 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C by
the year 2100 relative to present day    (Friedlingstein et al.,
2014), with large variations across different regions of the globe
(Raddatz et al., 2007). Given the dependence of
photosynthesis on temperature, it is critical to examine how much future
photosynthesis is likely to change in different regions. In this study, we
investigate how the LUNA predicted values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> will change under future climate conditions and how they will
affect future estimates of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mtext>net</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, the net photosynthesis rate. The
impacts of future climate on <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub><mml:mo>,</mml:mo><mml:mspace linebreak="nobreak" width="0.25em"/><mml:msub><mml:mi>J</mml:mi><mml:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mtext>net</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> are
quantified by calculating their values for the leaf layer at the top canopy
during the summer season under historic and future climate conditions.
Appendix C summarizes the calculation of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mtext>net</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>.</p>
      <p>We use model outputs from the climate carbon cycle Coupled Model Intercomparison Project Phase 5 (CMIP5)     (Meehl et al.,
2000) to obtain projections of future climate. Climate modelers have
developed four representative concentration pathways (RCPs) for the
21st century     (Taylor et al., 2013). Each of them corresponds
to a different level of greenhouse gas emission. In this study, we use
historic and future climate conditions simulated by the CCSM 4.0 model under
scenario RCP8.5, which considers the largest greenhouse gas emissions. We do
not consider herein other models and emission scenarios as the main purpose
of our study is not to do a complete analysis under all CMIP5 outputs but
rather to estimate the potential impact of nitrogen allocation on
photosynthesis. Specifically, the 10-year climate record between 1995 and
2004 is used as a benchmark for historic conditions, whereas the climate
data between 2090 and 2099 is used for future conditions. We present the
LUNA's predicted <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values for the months of the
peak growing season. Data from the NOAA Earth System Research Laboratory
(Riebeek, 2011) showed that the maximum amount of carbon dioxide drawn
from the atmosphere occurs in August and February for the large land masses
of the Northern and Southern hemispheres, respectively. As a result, June,
July and August are assumed herein to best represent the summer season for
the Northern Hemisphere and December, January and February are considered
representative for the summer season on the Southern Hemisphere. In this
study, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values are predicted by LUNA using the
average values of climate variables for the summer season.</p>
      <p>We conduct a third sensitivity analysis to quantify the impacts of future
changes in climate variables such as temperature, 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,
radiation and relative humidity on the simulated values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. While the first two sensitivity analyses in section 2.6
assume current mean climate conditions, this sensitivity analysis
investigates global patterns in sensitivity of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> to future changes in climate variables across different biomes.
Specifically, we calculate the percentage difference in the LUNA predicted
values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> using historic and future values of
each climate variable. All other climate variables are set at their default
(or historic) values.</p>
</sec>
</sec>
<sec id="Ch1.S3">
  <title>Results</title>
<sec id="Ch1.S3.SS1">
  <?xmltex \opttitle{Model--data comparison of $V_{\mathrm{c,max25}}$  and
$J_{\mathrm{max25}}$}?><title>Model–data comparison of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula></title>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1" specific-use="star"><caption><p>Mean values and standard deviations (parentheses) of LUNA parameters
estimated by using the Differential Evolution Adaptive Metropolis Snooker
updater (DREAM<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>(ZS)</mml:mtext></mml:msub></mml:math></inline-formula>) sampling technique for temperature response functions TRF1
and TRF2. The parameters include (1) <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb0</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (unitless): baseline
proportion of nitrogen allocated for electron transport rate,
(2) <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb1</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (unitless): electron transport rate response to light
availability, (3) <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (unitless): baseline ratio of Rubisco
limited rate to light limited rate and (4) <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> (unitless): electron
transport rate response to relative humidity.</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="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:colspec colnum="5" colname="col5" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">Statistics</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">maxb</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></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>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">maxb</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5"><inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula></oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">TRF1</oasis:entry>  
         <oasis:entry colname="col2">0.0311 (0.0004)</oasis:entry>  
         <oasis:entry colname="col3">0.1745 (0.0002)</oasis:entry>  
         <oasis:entry colname="col4">0.8054 (0.0015)</oasis:entry>  
         <oasis:entry colname="col5">6.0999 (0.2416)</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">TRF2</oasis:entry>  
         <oasis:entry colname="col2">0.0322 (0.0002)</oasis:entry>  
         <oasis:entry colname="col3">0.1695 (0.0006)</oasis:entry>  
         <oasis:entry colname="col4">0.7760 (0.0031)</oasis:entry>  
         <oasis:entry colname="col5">5.7139 (0.0354)</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <p>The DREAM<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mrow><mml:mo>(</mml:mo><mml:mi mathvariant="normal">ZS</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:msub></mml:math></inline-formula> algorithm provides us with the posterior means and standard deviations
of the four LUNA parameters (Table 1). The calibrated LUNA model explains
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 54 % of the variance in the observed values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> across all species (Fig. 1a) and <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 65 % of the variance in the observed values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 1b)
using the temperature response function TRF1. This response function considers
explicitly the thermal acclimation. If TRF2 is used in LUNA, the model is
able to explain <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 57 % of the variance in the observed
values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 1c) and <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 66 % of the
variance in the observed values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 1d) across all
species. When the LUNA predictions with TRF1 are compared with the
observation data with seasonal cycles, the model explains <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 67 and
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 53 % of the variance in the observed values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, respectively (see Fig. S5a, b in the
Supplement). The model performs similarly when TRF2 is used
(Fig. S5c, d).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1"><caption><p>Percentage of variance (<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> and ME) in observed values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> (<bold>a</bold>, TRF1; <bold>c</bold>, TRF2)
and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron 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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> (<bold>b</bold>, TRF1; <bold>d</bold>, TRF2) explained
by the LUNA model for all the species. The <inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> is derived by a linear
regression between observed and modeled values. The dashed line is the <inline-formula><mml:math display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula>
line between observed and modeled values.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/9/587/2016/gmd-9-587-2016-f01.png"/>

        </fig>

      <p>Our model also performs well for different PFTs.  With TRF1, the LUNA model
explains about 57, 58 and 47 % of the variance in the observed values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> for herbaceous plants (Fig. S6a), shrubs (Fig. S6b) and trees
(Fig. S6c), respectively. For <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, LUNA explains approximately 49, 85
and 46 % of the variances in the observed values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> for
herbaceous plants (Fig. S6d), shrubs (Fig. S6e) and trees (Fig. S6f),
respectively. The predictive power of LUNA increases for shrubs when TRF2 is
used. About 63 % of the variance in the observed <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values is
explained by the model (Fig. S7b), yet a similar performance is observed
for herbaceous plants and trees (Fig. S7a, c). The statistics for the predictions
of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> are very similar to those reported previously for TRF1
(Fig. S6d–f).</p>
</sec>
<sec id="Ch1.S3.SS2">
  <title>Model sensitivity analysis</title>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2"><caption><p>Sensitivities of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> (<bold>a</bold>, TRF1; <bold>c</bold>, TRF2) and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron 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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>
(<bold>b</bold>, TRF1; <bold>d</bold>, TRF2) to changes in model parameters. Each parameter
(<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb0</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb1</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, and <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>H</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is varied one at a time by
<inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>15 % of its fitted value. The values of environmental variables are
held fixed at their mean values with day length <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 14 h, daytime
radiation <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 182 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>, temperature <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 14 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, relative humidity <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.6
(unitless) and 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 <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 393 ppm. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values are first obtained at changed parameter values
and the percentage changes in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> are then
calculated relative to the baseline values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> predicted based the default parameter values. Positive values
indicate that the increase in a specific model parameter leads to larger
values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> or <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, while negative values indicate that
the increase in a specific model parameter leads to smaller values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> or <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/9/587/2016/gmd-9-587-2016-f02.png"/>

        </fig>

      <p>Sensitivity analysis shows that all four LUNA model parameters (Table 1)
have a positive effect on <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 2a, c) and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>
(Fig. 2b, d) regardless which temperature response function is used. The
parameter <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> has the strongest effect on
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 2a, c) while <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb0</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> has the strongest impact on
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>(Fig. 2b, d). Parameter <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> has a much lesser control on the
simulated values of both <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 2a–d).</p>
      <p>Sensitivity analysis of the LUNA model output to its main climate variables
shows that radiation most strongly affects the simulated <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> values, whereas an increasingly smaller impact is observed for the day
length, temperature, 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 relative humidity (Fig. 3a, c). The LUNA predicted values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> appear most sensitive to day
length, followed by temperature, radiation, relative humidity and 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 (Fig. 3b, d). These findings are independent of the TRF being
used.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3"><caption><p>Sensitivities of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>
(<bold>a</bold>: TRF1, <bold>c</bold>: TRF2) and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron 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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> (<bold>b</bold>: TRF1, <bold>d</bold>: TRF2) to changes in environmental variables including
day length (<inline-formula><mml:math display="inline"><mml:mi>D</mml:mi></mml:math></inline-formula>), daytime radiation (<inline-formula><mml:math display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula>), temperature (<inline-formula><mml:math display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula>), relative humidity
(RH) and 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. Each environmental variable is varied one
at a time by <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>15 % around their mean values with day length <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 14 h, daytime radiation <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 182 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>, temperature <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 14 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C,
relative humidity <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 0.6 (unitless) and 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 <inline-formula><mml:math display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 393 ppm. The model parameters (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb0</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb1</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, and <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>H</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> are held
fixed at their fitted values. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values are first
obtained at changed environmental conditions and percentage
changes in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> are calculated relative to the
baseline values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> under the mean climate
conditions in the data. Positive values indicate that the increase in a
specific environmental variable leads to larger values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mtext>max25,</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> while negative values indicate that the increase in a specific
environmental variable leads to smaller values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/9/587/2016/gmd-9-587-2016-f03.png"/>

        </fig>

</sec>
<sec id="Ch1.S3.SS3">
  <?xmltex \opttitle{Impacts of climate change on $V_{\mathrm{c,max25}}$ and
$J_{\mathrm{max25}}$}?><title>Impacts of climate change on <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula></title>
      <p>Across the globe, a similar pattern is observed for TRF1 and TRF2 in the
simulated values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (Figs. 4 and S8).
Under historical climate conditions, the higher latitudes are predicted to
have relatively high values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> while lower
latitudes are predicted to have relatively low values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 4a, c for TRF1; Fig. S8a, c for TRF2). Future climate
conditions are likely to decrease significantly the <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values for
most vegetated lands in large part due to a predicted rise in the
temperature and 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 (Fig. 4b for TRF1 and Fig. S8b for
TRF2). A somewhat opposite trend is observed for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> with decreasing
values at higher latitudes and increasing values at the lower latitudes
(Fig. 4d for TRF1 and Fig. S8b for TRF2).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4" specific-use="star"><caption><p>Summer-season photosynthetic capacity for the top leaf layer in the
canopy under historical climatic conditions (<bold>a</bold>: <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<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>), <bold>b</bold>: <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron 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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>)
and the difference in either <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> <bold>(b)</bold> or
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> <bold>(d)</bold> due to changed climatic conditions in the future. The
difference is calculated by subtracting the photosynthetic capacity
predicted by the LUNA model under the historical climate conditions from
that under the future climate conditions. The historical climate is
represented by the 10-year monthly averages over years 1995–2004 and the
future climate is represented by the 10-year monthly averages over years
2090–2099. The model is run by using TRF1, which is a temperature response
function that considered the thermal acclimation.</p></caption>
          <?xmltex \igopts{width=327.206693pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/9/587/2016/gmd-9-587-2016-f04.png"/>

        </fig>

      <p>Our results show that the LUNA-simulated <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values are most
sensitive to the changes in 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, followed by temperature,
radiation and relative humidity (Fig. 5a–d for TRF1 and Fig. S9a–d for
TRF2). The variable <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> appears most sensitive to the changes in
temperature, and then radiation, relative humidity and CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> (Fig. 6a–d
for TRF1 and Fig. S10a–d for TRF2). Across the globe, temperature has
negative impacts on <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> when using TRF1 (Fig. 5a); however, when
TRF2 is used, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> is found to increase at the lower latitudes
(Fig. S9a).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5" specific-use="star"><caption><p>Sensitivity of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (<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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> to
projected future changes in environmental variables including temperature
<bold>(a)</bold>, radiation <bold>(b)</bold>, humidity <bold>(c)</bold> and CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> <bold>(d)</bold> at the global scale for
TRF1. The sensitivity analysis is conducted by changing the value of an
individual environmental variable from its 10-year monthly averages in the
past (1995–2004) to those in the future (2090–2099) for each individual grid
cell across the globe. Positive values indicate that the increase in a
specific environmental variable leads to larger values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>,
while negative values indicate that the increase in a specific environmental
variable leads to smaller values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>.</p></caption>
          <?xmltex \igopts{width=327.206693pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/9/587/2016/gmd-9-587-2016-f05.png"/>

        </fig>

      <p>The simulations of LUNA demonstrate that the future summer-season mean
photosynthetic rate at the top leaf layer might be substantially
overestimated if acclimation of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>  under
future climate conditions (i.e., using historic values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is not explicitly considered (Fig. 7a, b). This is especially
true for regions with high temperatures (Fig. S11). Future estimates of the
summer-season mean photosynthesis rate are much higher under TRF1 than TRF2
(Fig. 7b). The omission of acclimation could lead to a 10.1 and 16.3 %
overestimation in the global net photosynthetic rate at the top canopy layer
for TRF1 and TRF2, respectively.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6" specific-use="star"><caption><p>Sensitivity of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron 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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> to projected future changes in environmental variables including
temperature <bold>(a)</bold>, radiation <bold>(b)</bold>, humidity <bold>(c)</bold> and CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> <bold>(d)</bold> at the global
scale using TRF1. The sensitivity analysis is conducted by changing the
value of an individual environmental variable from its 10-year monthly
averages in the past (1995–2004) to those in the future (2090–2099) for each
individual grid cell across the globe. Positive values indicate that the
increase in a specific environmental variable leads to larger values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, while negative values indicate that the increase in a specific
environmental variable leads to smaller values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>.</p></caption>
          <?xmltex \igopts{width=327.206693pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/9/587/2016/gmd-9-587-2016-f06.png"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F7"><caption><p>Percentage differences in estimated net photosynthetic rate for the leaf layer at the top of the canopy (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mtext>net</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, <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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> under future climate
conditions (<bold>a</bold>: TRF1, <bold>b</bold>: TRF2) by using LUNA predicted values of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (<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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron 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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> under historic versus future climate
conditions. Positive values indicate overestimation by using fixed (or
historic) <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> while negative values indicate
underestimation. The historic climate is represented by the 10-year monthly
averages over years 1995–2004 and the future climate is represented by the
10-year monthly averages over years 2090–2099.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/9/587/2016/gmd-9-587-2016-f07.png"/>

        </fig>

</sec>
</sec>
<sec id="Ch1.S4" sec-type="conclusions">
  <title>Discussion</title>
<sec id="Ch1.S4.SS1">
  <title>Model limitations</title>
      <p>The LUNA model built on the assumption that nitrogen is allocated according
to optimality principles explains a large part of the global-scale
variability observed in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 55 %) and
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 65 %), regardless which TRF is used. This
approach used by LUNA also mimics accurately seasonal cycles and
PFT-specific values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (Figs. S5–S7), and
has a much better overall predictive power than a multiple linear regression
with LNC<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:math></inline-formula> and LMA as main predictors. Such a linear model is able to
explain only, for both TRFs, about 22 % of the variance in the observed
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values (Fig. S12a, d) and approximately 13 % of the variance
in the observed <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> values (Fig. S12b, d). These results
suggest that our model includes many of the key variables that determine the
spatial and temporal variation of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> across the globe. The remaining portion of the variance that cannot be
explained by the LUNA model can be related to variability within the 125
species considered in this study. There are inherent intraspecific
variations in leaf traits      (Valladares et al., 2000) and in
photosynthetic capacity   (Moran et al., 2016). Data availability
limits the number of species that can be considered in the present analysis
and favors a single LUNA calibration for all species. Indeed, the data for
individual species normally did not cover a sufficiently large range of
environmental conditions. When more data become available for individual
species in the future, we can revisit the calibration procedure and fit our
model to specific PFTs pending a sufficiently large enough coverage of
environmental conditions. We posit that such a model will be able to adequately capture
a larger portion of the variability observed in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>.</p>
      <p>Other deficiencies of LUNA might be related to unexplored nutrient
limitations and other plant physiological properties. For example, low
phosphorus concentrations can reduce considerably the nitrogen use
efficiency of tropical plants with typically modest to low nitrogen
(Cernusak et al., 2010; Reich and Oleksyn, 2004), suggesting
that our LUNA model can be enhanced by considering multiple different
nutrient limitations simultaneously   (Goll et al., 2012; Walker et al.,
2014; Wang et al., 2010). Our treatment of the photosynthetic capacity can
also be improved by incorporating a species-specific mesophyll and stomatal
conductance       (Medlyn et al., 2011), by analyzing
properties such as leaf life span
(Wright et al., 2004),
and by considering soil pH, nutrient availability and water availability
(Maire et al., 2015). Unexplored nutrient limitations and
other plant physiological properties could also play a factor in the
limitation of our model. For example, the nitrogen use efficiency of
tropical plants (typically modest to low nitrogen) can be diminished by low
phosphorus   (Cernusak et al., 2010; Reich and Oleksyn, 2004),
suggesting that our model could be improved by considering multiple nutrient
limitations   (Goll et al., 2012; Walker et al., 2014; Wang et al., 2010).
Our treatment of photosynthetic capacity could also be improved by
incorporating species-specific mesophyll and stomatal conductance
(Medlyn et al., 2011), by analyzing leaf properties
such as leaf life span
(Wright et al., 2004), or
by considering soil nutrient, soil water availability and soil pH
(Maire et al., 2015).</p>
      <p>Measurement errors of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> also affect negatively
the ability of LUNA to describe perfectly the observational data. These
errors can originate from many different sources but are rarely quantified
in the literature. They can play a significant role in parameter fitting.
Indeed, previous research has shown that the value of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> in the Farquhar
et al. (1980) model used to differentiate between Rubisco and Ribulose-1,5-bisphosphate (RuBP) limitations,
could be estimated from different methods in the literature
(Miao et al., 2009). Furthermore, it is particularly
difficult to obtain accurate and biologically realistic estimates of dark
respiration        (but see Dubois et al., 2007), and
consequently, dark respiration is sometimes not reported
(Medlyn et al., 2002b).<?xmltex \hack{\newpage}?></p>
</sec>
<sec id="Ch1.S4.SS2">
  <?xmltex \opttitle{Importance of environmental control on $V_{\text{c,max25}}$ and
$J_{\mathrm{max25}}$}?><title>Importance of environmental control on <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula></title>
      <p>Our model predicts that higher temperatures generally lead to lower values
of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 3a, c). As temperature
increases, the nitrogen use efficiencies of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> also
increase and thus plants need a lower amount of nitrogen allocated for
carboxylation and electron transport. This is true for all the sites except
for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> in the warmest regions of our planet when TRF2 is used
(Fig. S9a). This is explained by a large increase in the nighttime
temperature of LUNA (e.g., 22 to 30 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C) as the daytime temperature
(e.g., from 31 to 33 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C) is constrained by the maximum temperature for
optimization in TRF2 (i.e., 33 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C). To maximize the net photosynthetic
carbon gain, the model predicts a higher proportion of nitrogen allocated to
carboxylation to compensate for a higher nighttime respiration rate.
Therefore, the LUNA model predicts higher values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. Yet, this
may result from a deficiency of TRF2 in that this response function does not
allow for thermal acclimation under global warming
(Lombardozzi et al., 2015).</p>
      <p>Our model predicts that the future changes in 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>
concentration has a negligible effect on <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, a finding that is in
agreement with results from other studies       (e.g., Maroco et
al., 2002). A meta-analysis of 12 Free-Air Carbon dioxide Enrichment (FACE) experiments demonstrated reductions
in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> on the order of 5 % but with a 10 % reduction in
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> under elevated 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     (Long
et al., 2004). Our model also predicts that the relative humidity has a
relatively minor effect on <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. This may be due to the fact that
most of the values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> in our data set
coincide with relatively high values of the humidity. As LUNA does not
consider the effects of drought on photosynthesis, it may have
underestimated the effects of water scarcity on <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> under low
humidity conditions   (Xu and Baldocchi, 2003). Under prolonged
drought, plants close their stomata and photosynthesis is greatly reduced
(Breshears et al., 2008; McDowell, 2011). Without
sufficient carbon input, photosynthetic enzymes may degenerate during the
high temperatures of a drought, which could decrease <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> substantially   (Limousin et al., 2010; Xu and Baldocchi, 2003).</p>
      <p>There are many different ways to incorporate environmental controls on
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. One such approach is to use relatively simple
empirical relationships between environmental variables and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>   (e.g., Ali et al., 2015; Verheijen et al., 2013). Such
functions can improve the model performance    (Verheijen et al.,
2015), yet may exhibit rather poor extrapolative capabilities under future
climate conditions. The optimality hypothesis used by LUNA is arguably
better rooted in ecologic theory, and is therefore expected to exhibit a
better predictive quality when confronted with novel future climate
conditions. Indeed, the concept of optimality has been applied to the
prediction of many different plant functions and structures under a
wide array of environmental conditions. Examples include carbon allocation
(Franklin et al., 2012), leaf C <inline-formula><mml:math display="inline"><mml:mo>:</mml:mo></mml:math></inline-formula> N    (Thomas and
Williams, 2014), root distribution     (McMurtrie et al., 2012)
and stomatal conductance  (Cowan and Farquhar, 1977). For photosynthetic
capacity optimization, Haxeltine and Prentice (1996) have predicted
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> based on a trade-off analysis of photosynthesis and
respiration. This concept has been incorporated in different land surface
models such as LPJ-GUESS      (Smith et al., 2001) and LPJmL
(Sitch et al., 2003). Both LUNA and the model of
Haxeltine and Prentice (1996), hereafter conveniently referred to as
HP, consider <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> and respiration. The LUNA model is currently
limited to prediction at the leaf level only while the HP model is
applicable for both the leaf and canopy level. Nevertheless, key
improvements of LUNA over HP include an explicit consideration of light
capture, electron transport and storage. Furthermore, the parameters of LUNA
have been derived from a much larger global data set, with many different
environmental conditions.</p>
</sec>
<sec id="Ch1.S4.SS3">
  <?xmltex \opttitle{Importance of changes in $V_{\text{c,max25}}$ and $J_{\mathrm{max25}}$ to future photosynthesis estimation}?><title>Importance of changes in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> to future photosynthesis estimation</title>
      <p>Our model suggests that most regions of the world will likely experience
reductions in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (Figs. 4b and S8b) due to global warming. An
increase of the temperature (Fig. S13) and 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>
concentration is expected to increase the nitrogen use efficiency of Rubisco
and thus plants are able to reduce the amount of nitrogen allocated for
Rubisco to reduce the carbon cost required for enzyme maintenance.
Similarly, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> will also decrease globally, except in regions where
the present temperatures of the growing season are relatively high (Fig. S12b). The increase of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> can be attributed to leaf temperature
limitations and increased shortwave radiation (Figs. S14 and S15).
Temperature will have a relatively small impact on nitrogen allocation in
regions with historically high temperatures during the growing season
because leaf temperature is already close to or higher than the upper limit
of optimal nitrogen allocation (42 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C for TRF1 and 33 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C for TRF2).
Based on Eq. (A11), higher levels of shortwave solar radiation will increase
nitrogen allocation to electron transport   (Evans and Poorter, 2001).
<?xmltex \hack{\newpage}?>
If we do not account for the potential acclimation of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> under future climate conditions, our analysis based on the
LUNA model indicates that ESM  predictions of future global photosynthesis at
the uppermost leaf layer will likely be overestimated by as much as
10–16 % if <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> are held fixed (Fig. 7). This
overestimation is larger for TRF2 (16.3 %) than TRF1 (10.1 %) and can
result from the fact that TFR2 does not account for thermal acclimation
under future climate conditions. Consequently, LUNA predicts a large
nitrogen allocation acclimation under climate change. In both cases, our
results suggest that, to reliably predict global plant responses to future
climate change, ESMs should take into explicit consideration environmental
controls on <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. It has been suggested recently
that nitrogen-related factors are not well represented in ESMs
(Houlton et al., 2015; Wieder et al., 2015). Our
nitrogen partitioning scheme would help remove the prediction bias of future
photosynthetic rates, which will also improve considerably related climate
processes that are dependent on these predictions   (Bonan et al., 2011;
Knorr and Kattge, 2005; Rogers, 2014).</p>
</sec>
<sec id="Ch1.S4.SSx1" specific-use="unnumbered">
  <title>Code availability</title>
      <p>The LUNA model has been implemented in CLM5.0 and will be made publicly
available with its release in 2016. Stand-alone codes of LUNA are available
in MATLAB, FORTRAN and C. These source codes can be obtained from the
corresponding author upon request.</p><?xmltex \hack{\clearpage}?>
</sec>
</sec>

      
      </body>
    <back><app-group>

<app id="App1.Ch1.S1">
  <title>Leaf utilization of nitrogen for assimilation (LUNA) model</title>
      <p>The LUNA model considers nitrogen allocation within a given leaf layer in
the canopy that has a predefined leaf-area-based plant leaf nitrogen content
availability (LNC<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:math></inline-formula>; g N 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> leaf) to support its growth and
maintenance. The structure of the LUNA model is adapted from Xu et al. (2012), where the plant nitrogen at the leaf level is divided
into four pools: structural nitrogen (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>str</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>; g N 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> leaf),
photosynthetic nitrogen (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>psn</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>; g N 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> leaf), storage nitrogen
(<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>store</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>; g N 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> leaf) and respiratory nitrogen
(<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>resp</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>; g N 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> leaf). Namely,

              <disp-formula id="App1.Ch1.E1" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi mathvariant="normal">LNC</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">psn</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">str</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">store</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">resp</mml:mi></mml:msub><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula></p>
      <p>The photosynthetic nitrogen, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>psn</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, is further divided into
nitrogen for light capture (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>lc</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>; g N 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> leaf), nitrogen for
electron transport (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>et</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>; g N 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> leaf) and nitrogen for
carboxylation (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>cb</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>; g N 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> leaf). Namely,

              <disp-formula id="App1.Ch1.E2" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">psn</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">et</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">cb</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">lc</mml:mi></mml:msub><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula></p>
      <p>The structural nitrogen, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">str</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, is calculated as the
multiplication of leaf mass per unit area (LMA; g biomass 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> leaf), and
the structural nitrogen content (SNC; g N g<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> biomass). Namely,

              <disp-formula id="App1.Ch1.E3" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">str</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mi mathvariant="normal">SNC</mml:mi><mml:mo>⋅</mml:mo><mml:mi mathvariant="normal">LMA</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where SNC is set to be fixed at 0.002 (g N g<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> biomass), based on data
on C <inline-formula><mml:math display="inline"><mml:mo>:</mml:mo></mml:math></inline-formula> N ratio from dead wood   (White et al., 2000). The functional
leaf nitrogen content (FNC<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:math></inline-formula>; g N 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> leaf) is defined by
subtracting structural nitrogen content, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>str</mml:mtext></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:math></inline-formula> from the total leaf
nitrogen content (LNC<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:math></inline-formula>; g N 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> leaf),

              <disp-formula id="App1.Ch1.E4" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi mathvariant="normal">FNC</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi mathvariant="normal">LNC</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">str</mml:mi></mml:msub><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula></p>
      <p>We assume that plants optimize their nitrogen allocations (i.e.,
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>store</mml:mtext></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mtext>resp</mml:mtext></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mtext>lc</mml:mtext></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mtext>et</mml:mtext></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mtext>cb</mml:mtext></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> to
maximize the net photosynthetic carbon gain, defined as the gross
photosynthesis (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>A</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> minus the maintenance respiration for photosynthetic
enzymes (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mtext>psn</mml:mtext></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, under specific environmental conditions and given
plant's strategy of leaf nitrogen use. Namely, the solutions of nitrogen
allocations <inline-formula><mml:math display="inline"><mml:mrow><mml:mo mathvariant="italic">{</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mtext>store</mml:mtext></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mtext>resp</mml:mtext></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mtext>lc</mml:mtext></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mtext>et</mml:mtext></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mtext>cb</mml:mtext></mml:msub><mml:mo mathvariant="italic">}</mml:mo></mml:mrow></mml:math></inline-formula> can be estimated as follows,

              <disp-formula specific-use="align" content-type="numbered"><mml:math display="block"><mml:mtable displaystyle="true"><mml:mtr><mml:mtd/><mml:mtd><mml:mrow><mml:mo mathvariant="italic">{</mml:mo><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo stretchy="false" mathvariant="normal">^</mml:mo></mml:mover><mml:mrow><mml:mi mathvariant="normal">store</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:msub><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo mathvariant="normal" stretchy="false">^</mml:mo></mml:mover><mml:mrow><mml:mi mathvariant="normal">resp</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:msub><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo mathvariant="normal" stretchy="false">^</mml:mo></mml:mover><mml:mi mathvariant="normal">lc</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo stretchy="false" mathvariant="normal">^</mml:mo></mml:mover><mml:mrow><mml:mi mathvariant="normal">et</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:msub><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo mathvariant="normal" stretchy="false">^</mml:mo></mml:mover><mml:mi mathvariant="normal">cb</mml:mi></mml:msub><mml:mo mathvariant="italic">}</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mo>=</mml:mo></mml:mrow></mml:mtd></mml:mtr><mml:mlabeledtr id="App1.Ch1.E5"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:mspace linebreak="nobreak" width="1em"/><mml:mspace width="0.125em" linebreak="nobreak"/><mml:munder><mml:mi mathvariant="normal">argmax</mml:mi><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">store</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">resp</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">lc</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">et</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">cb</mml:mi></mml:msub><mml:mo>&lt;</mml:mo><mml:msub><mml:mi mathvariant="normal">FNC</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow></mml:munder><mml:mo>(</mml:mo><mml:mi>A</mml:mi><mml:mo>-</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">psn</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula></p>
      <p>The gross photosynthesis, <inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula>, is calculated with a coupled leaf gas exchange
model based on the Farquhar et al. (1980) model of photosynthesis and
Ball–Berry-type stomatal conductance model   (Ball et al., 1987)
(See Appendix C for details). The maintenance respiration for photosynthetic
enzymes, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mtext>psn</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, is calculated by the multiplication of total
photosynthetic nitrogen (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">N</mml:mi><mml:mtext>psn</mml:mtext></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and the maintenance respiration
cost for photosynthetic enzyme (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">rp</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, see Appendix D), namely,

              <disp-formula id="App1.Ch1.E6" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">psn</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">rp</mml:mi></mml:msub><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">psn</mml:mi></mml:msub><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula>

        In the LUNA model, the maximum electron transport rate (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>; <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron 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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is simulated to have a baseline
allocation of nitrogen and additional nitrogen allocation to change
depending on the average daytime photosynthetic active radiation (PAR; <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron 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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, day length (hours) and air humidity.
Specifically, we have

              <disp-formula id="App1.Ch1.E7" content-type="numbered"><mml:math display="block"><mml:mrow><?xmltex \hack{\hbox\bgroup\fontsize{8.5}{8.5}\selectfont$\displaystyle}?><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">maxb</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msub><mml:mi>f</mml:mi><mml:mfenced close=")" open="("><mml:mi mathvariant="normal">day</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">length</mml:mi></mml:mfenced><mml:mi>f</mml:mi><mml:mfenced close=")" open="("><mml:mi mathvariant="normal">humidity</mml:mi></mml:mfenced><mml:mi mathvariant="italic">α</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">PAR</mml:mi><mml:mo>.</mml:mo><?xmltex \hack{$\egroup}?></mml:mrow></mml:math></disp-formula></p>
      <p>The baseline electron transport rate, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max0</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>  (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron 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>), is calculated as
follows,

              <disp-formula id="App1.Ch1.E8" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">maxb</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi mathvariant="normal">FNC</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb0</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (unitless) is the baseline proportion of nitrogen allocated
for electron transport rate. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mtext>NUE</mml:mtext><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron 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> g<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> N) is the nitrogen use efficiency of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (see Eq. D2
for details). <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb1</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (unitless) is a coefficient determining the
response of the electron transport rate to amount of absorbed light
(i.e. <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="italic">α</mml:mi><mml:mi mathvariant="normal">PAR</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>f</mml:mi><mml:mfenced close=")" open="("><mml:mi mathvariant="normal">day</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">length</mml:mi></mml:mfenced></mml:mrow></mml:math></inline-formula> is a
function specifies the impact of day length (hours) on <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> in
view that longer day length has been demonstrated by previous studies to
alter <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>         (Bauerle et al., 2012; Comstock and Ehleringer,
1986) through photoperiod sensing and regulation    (e.g., Song et
al., 2013). Following Bauerle et al. (2012), <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>f</mml:mi><mml:mfenced open="(" close=")"><mml:mi mathvariant="normal">day</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">length</mml:mi></mml:mfenced></mml:mrow></mml:math></inline-formula> is simulated as follows,

              <disp-formula id="App1.Ch1.E9" content-type="numbered"><mml:math display="block"><mml:mrow><mml:mi>f</mml:mi><mml:mfenced close=")" open="("><mml:mi mathvariant="normal">day</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">length</mml:mi></mml:mfenced><mml:mo>=</mml:mo><mml:msup><mml:mfenced close=")" open="("><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mi mathvariant="normal">day</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">length</mml:mi></mml:mrow><mml:mn>12</mml:mn></mml:mfrac></mml:mstyle></mml:mfenced><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>f</mml:mi><mml:mfenced close=")" open="("><mml:mi mathvariant="normal">humidity</mml:mi></mml:mfenced></mml:mrow></mml:math></inline-formula> represents the impact of air humidity on
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. We assume that higher humidity leads to higher
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> with less water limitation on stomata opening and that low
relative humidity has a stronger impact on nitrogen allocation due to
greater water limitation. When relative humidity (RH; unitless) is too low,
we assume that plants are physiologically unable to reallocate nitrogen. We
therefore assume that there exists a critical value of relative humidity
(RH<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi/><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>=</mml:mo><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:math></inline-formula>.25; unitless), below which there is no optimal nitrogen
allocation. Based on the above assumptions, we have

              <disp-formula id="App1.Ch1.E10" content-type="numbered"><mml:math display="block"><mml:mrow><mml:mi>f</mml:mi><mml:mfenced close=")" open="("><mml:mi mathvariant="normal">humidity</mml:mi></mml:mfenced><mml:mo>=</mml:mo><mml:mfenced open="(" close=")"><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mfenced open="(" close=")"><mml:mo>-</mml:mo><mml:mi>H</mml:mi><mml:mfrac><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mfenced close=")" open="("><mml:mi mathvariant="normal">RH</mml:mi><mml:mo>-</mml:mo><mml:msub><mml:mi mathvariant="normal">RH</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:mn> 0</mml:mn></mml:mfenced></mml:mrow><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:msub><mml:mi mathvariant="normal">RH</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:mfrac></mml:mfenced></mml:mrow></mml:msup></mml:mfenced><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where <inline-formula><mml:math display="inline"><mml:mi>H</mml:mi></mml:math></inline-formula> (unitless) specifies the impact of relative humidity on electron
transport rate. Replacing Eq. (A7) with Eqs. (A8), (A9) and (A10), we have

              <disp-formula specific-use="align" content-type="numbered"><mml:math display="block"><mml:mtable displaystyle="true"><mml:mtr><mml:mtd><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub><mml:mo>=</mml:mo></mml:mrow></mml:mtd><mml:mtd><mml:mrow><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">maxb</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi mathvariant="normal">FNC</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd/><mml:mtd><mml:mrow><mml:mo>+</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">maxb</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msub><mml:msup><mml:mfenced close=")" open="("><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mi mathvariant="normal">day</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">length</mml:mi></mml:mrow><mml:mn>12</mml:mn></mml:mfrac></mml:mstyle></mml:mfenced><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow></mml:mtd></mml:mtr><mml:mlabeledtr id="App1.Ch1.E11"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:mfenced open="(" close=")"><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:msup><mml:mi mathvariant="normal">e</mml:mi><mml:mrow><mml:mfenced close=")" open="("><mml:mo>-</mml:mo><mml:mi>H</mml:mi><mml:mfrac><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mfenced close=")" open="("><mml:mi mathvariant="normal">RH</mml:mi><mml:mo>-</mml:mo><mml:msub><mml:mi mathvariant="normal">RH</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:mn mathvariant="normal">0</mml:mn></mml:mfenced></mml:mrow><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:msub><mml:mi mathvariant="normal">RH</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:mfrac></mml:mfenced></mml:mrow></mml:msup></mml:mfenced><mml:mi mathvariant="italic">α</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">PAR</mml:mi><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

          The efficiency of light energy absorption (unitless), <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>, is
calculated depending on the amount of nitrogen allocated for light capture,
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>lc</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>. Following Niinemets and Tenhunen   (1997) we have,

              <disp-formula id="App1.Ch1.E12" content-type="numbered"><mml:math display="block"><mml:mrow><mml:mi mathvariant="italic">α</mml:mi><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mn>0.292</mml:mn><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>+</mml:mo><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mn>0.076</mml:mn><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">lc</mml:mi></mml:msub><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">b</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where 0.292 is the conversion factor from photon to electron. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">b</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the
conversion factor (1.78) from nitrogen to chlorophyll. After we estimate
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> , the actual electron transport rate with the daily maximum
radiation (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> can be calculated using the empirical expression of Smith
(1937),

              <disp-formula id="App1.Ch1.E13" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mi mathvariant="italic">α</mml:mi><mml:msub><mml:mi mathvariant="normal">PAR</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msup><mml:mfenced open="(" close=")"><mml:mn mathvariant="normal">1</mml:mn><mml:mo>+</mml:mo><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mrow><mml:msup><mml:mi mathvariant="italic">α</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:msubsup><mml:mi mathvariant="normal">PAR</mml:mi><mml:mi mathvariant="normal">max</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msubsup></mml:mrow><mml:mrow><mml:msubsup><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msubsup></mml:mrow></mml:mfrac></mml:mstyle></mml:mfenced><mml:mn>0.5</mml:mn></mml:msup></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where PAR<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>max</mml:mtext></mml:msub></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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is the maximum
photosynthetically active radiation during the day.</p>
      <p>Based on Farquhar et al. (1980) and Wullschleger (1993), we
calculate the electron-limited photosynthetic rate under daily maximum
radiation (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>  and the Rubisco-limited photosynthetic rate (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>
as follows,

              <disp-formula specific-use="align" content-type="numbered"><mml:math display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="App1.Ch1.E14"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="App1.Ch1.E15"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

          where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <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> are the conversion factors from <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and from <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">W</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, respectively
(see Eqs. C4 and C6 in Appendix C for details of calculation). Based on
Xu et al. (2012), Maire et al. (2012) and Walker et al. (2014), we assume that <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is proportional to
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. Specifically, we have

              <disp-formula id="App1.Ch1.E16" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mi>W</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the ratio of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. We
recognize that this ratio may change depending on the nitrogen use
efficiency of carboxylation and electron transport   (Ainsworth and
Rogers, 2007) and therefore introduce the modification as follows,

              <disp-formula id="App1.Ch1.E17" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:msub><mml:msup><mml:mfenced open="(" close=")"><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mrow><mml:mfenced close="" open="/"><mml:mphantom style="vphantom"><mml:mpadded width="0pt" style="vphantom"><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">j</mml:mi></mml:msub></mml:mpadded></mml:mphantom></mml:mfenced></mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">j</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:mrow><mml:mfenced open="/" close=""><mml:mphantom style="vphantom"><mml:mpadded width="0pt" style="vphantom"><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mpadded></mml:mphantom></mml:mfenced></mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle></mml:mfenced><mml:mn>0.5</mml:mn></mml:msup><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (unitless) is the ratio of
Rubisco limited rate to light limited rate, NUE<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:math></inline-formula> (<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> 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> g<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> N) and NUE<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mrow><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:math></inline-formula> (<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> 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> g<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> N)
are the daily nitrogen use efficiency of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
under reference climate conditions defined as the 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C leaf
temperature and 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> concentration of 380 ppm, with leaf
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 set as 70 % of the 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>
concentration. NUE<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:math></inline-formula>
(<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> 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> g<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> N) and
NUE<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi>j</mml:mi></mml:msub></mml:math></inline-formula> (<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> 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> g<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> N) are the nitrogen use
efficiency of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> at the current climate conditions. See
Eqs. (D6) and (D7) for details of calculation. The term
<inline-formula><mml:math display="inline"><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mrow><mml:mfenced open="/" close=""><mml:mphantom style="vphantom"><mml:mpadded style="vphantom" width="0pt"><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mpadded></mml:mphantom></mml:mfenced></mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:mrow><mml:mfenced open="/" close=""><mml:mphantom style="vphantom"><mml:mpadded style="vphantom" width="0pt"><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mpadded></mml:mphantom></mml:mfenced></mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle></mml:math></inline-formula> assumes
that the higher nitrogen use efficiency of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> compared to that of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> will lead to a higher value of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> given the
same value of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. The exponent 0.5 is used to ensure that the response
of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> to elevated CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> is down-regulated by approximately
10 % when CO<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> increased from 365 to 567 ppm as reported by
Ainsworth and Rogers (2007).</p>
      <p>Replacing Eq. (A16) with Eqs. (A14), (A15) and (A17), we are able to
estimate the maximum carboxylation rate (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>; <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:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> as follows,

              <disp-formula id="App1.Ch1.E18" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:msub><mml:msup><mml:mfenced open="(" close=")"><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mrow><mml:mfenced open="/" close=""><mml:mphantom style="vphantom"><mml:mpadded style="vphantom" width="0pt"><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mpadded></mml:mphantom></mml:mfenced></mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">j</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:mrow><mml:mfenced close="" open="/"><mml:mphantom style="vphantom"><mml:mpadded width="0pt" style="vphantom"><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mpadded></mml:mphantom></mml:mfenced></mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle></mml:mfenced><mml:mn>0.5</mml:mn></mml:msup><mml:mfenced close=")" open="("><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle></mml:mfenced><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula>

        Following Collatz et al. (1991), the total respiration
(<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">t</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is calculated in proportion to <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>,

              <disp-formula id="App1.Ch1.E19" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">t</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>0.015</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula></p>
      <p>Accounting for the daytime and nighttime temperature, we are able to
estimate the daily respiration as follows,

              <disp-formula id="App1.Ch1.E20" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">td</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">t</mml:mi></mml:msub><mml:mo>[</mml:mo><mml:msub><mml:mi>D</mml:mi><mml:mi mathvariant="normal">day</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>D</mml:mi><mml:mi mathvariant="normal">night</mml:mi></mml:msub><mml:msub><mml:mi>f</mml:mi><mml:mi mathvariant="normal">r</mml:mi></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">night</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>/</mml:mo><mml:msub><mml:mi>f</mml:mi><mml:mi mathvariant="normal">r</mml:mi></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">day</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>]</mml:mo><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>D</mml:mi><mml:mi mathvariant="normal">day</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>D</mml:mi><mml:mi mathvariant="normal">night</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are daytime and nighttime
durations in seconds. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mi mathvariant="normal">r</mml:mi></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">night</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">and</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msub><mml:mi>f</mml:mi><mml:mi mathvariant="normal">r</mml:mi></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">day</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> are the temperature response functions for
respiration (see Eq. B1 for details).</p>
      <p>In summary, given an initial estimation of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>lc</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, we are able to first
estimate the efficiency of light energy absorption <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> using Eq. (A12). With that, we are able to estimate the maximum electron transport
rate , <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, using Eq. (A11). The nitrogen allocated for
electron transport can thus be calculated as follows,

              <disp-formula id="App1.Ch1.E21" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">et</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula></p>
      <p>Then, based on Eq. (A18), we are able to estimate the corresponding the
maximum carboxylation rate <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>  and the nitrogen allocated for
carboxylation as follows,

              <disp-formula id="App1.Ch1.E22" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">cb</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><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">NUE</mml:mi><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the nitrogen use efficiency
for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. See Eq. (D1) for details of calculation. Using Eq. (A20), we
are able to estimate <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mtext>td</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> and thus the nitrogen allocated for
respiration as follows,

              <disp-formula id="App1.Ch1.E23" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">resp</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">td</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">r</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><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">NUE</mml:mi><mml:mi mathvariant="normal">r</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is nitrogen use efficiency of enzymes
for respiration. See Eq. (D3) for details of calculation. Finally, the
storage nitrogen is calculated as follows,

              <disp-formula id="App1.Ch1.E24" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">store</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mtext>FNC</mml:mtext><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">resp</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">cb</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">lc</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">et</mml:mi></mml:msub><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula></p>
      <p>Note that this storage nitrogen is mainly a remaining component of
FNC<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:math></inline-formula>. Its formulation is different from the formulation of Xu et
al.
(2012) where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">store</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is set as a linear function
of net photosynthetic rate. This modification is based on the observation
that the preliminary fitting to data using the linear function shows no
dependence of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">store</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> on net photosynthetic rate. To make the
solutions realistic, we set the minimum of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">store</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> as 5 % of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">FNC</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> in view of potential nitrogen for plant
functionality that is not accounted for by photosynthesis and respiration.
By exploring different values of nitrogen allocated for light capture
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>lc</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> and using the Eqs. (A21)–(A23), we will find the optimal nitrogen
allocations (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo stretchy="false" mathvariant="normal">^</mml:mo></mml:mover><mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">store</mml:mi></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:msub><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo mathvariant="normal" stretchy="false">^</mml:mo></mml:mover><mml:mrow class="chem"><mml:mi mathvariant="normal">resp</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:msub><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo mathvariant="normal" stretchy="false">^</mml:mo></mml:mover><mml:mrow class="chem"><mml:mi mathvariant="normal">lc</mml:mi></mml:mrow></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo mathvariant="normal" stretchy="false">^</mml:mo></mml:mover><mml:mrow class="chem"><mml:mi mathvariant="normal">et</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:msub><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo mathvariant="normal" stretchy="false">^</mml:mo></mml:mover><mml:mrow class="chem"><mml:mi mathvariant="normal">cb</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> until the net photosynthetic rate is maximized (see
Eq. A5) given a specific set of nitrogen allocation coefficients (i.e.,
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb0</mml:mtext></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mtext>maxb1</mml:mtext></mml:msub><mml:mo>,</mml:mo><mml:mi>H</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:math></inline-formula> and  <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. The detailed optimization algorithms are
implemented as follows:
<list list-type="order"><list-item><p>increase the nitrogen allocated (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mtext>lc</mml:mtext></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> for light capture (from a small
initial value of 0.05) and calculate the corresponding light absorption rate
<inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula> with Eq. (A12);</p></list-item><list-item><p>calculate <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> from Eq. (A11) and derive the nitrogen
allocated to electron transport, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">et</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, using Eq. (A21);</p></list-item><list-item><p>calculate <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> from Eq. (A18) and derive the nitrogen
allocated to Rubisco, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">cb</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, using Eq. (A22);</p></list-item><list-item><p>calculate the total respiration <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mtext>td</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> from Eq. (A20) and derive the
nitrogen allocated to respiration, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant="normal">resp</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, using Eq. (A23);</p></list-item><list-item><p>calculate the total nitrogen invest in photosynthetic enzymes including
nitrogen for electron transport, carboxylation and light capture using Eq. (A2);</p></list-item><list-item><p>calculate the gross photosynthetic rate, <inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula>, and the maintenance respiration
for photosynthetic enzymes, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mtext>psn</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, by Eq. (A6);</p></list-item><list-item><p>repeat steps (1) to (6) until the increase from previous time step in <inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> is
smaller than or equal to the increase in <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mtext>psn</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>.</p></list-item></list></p>
      <p>Since the response of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> to increasing temperature
shows a steady rise to an optimum followed by a relatively rapid decline
(Bernacchi et al., 2003; Kattge and Knorr, 2007; Leuning, 2002; Medlyn et
al., 2002a), we postulate that the detrimental heat stress on leaf enzymatic
activity beyond this optimum   (Crafts-Brandner and Law, 2000;
Crafts-Brandner and Salvucci, 2000; Law and Crafts-Brandner, 1999; Spreitzer
and Salvucci, 2002) will cause the leaf to fail to optimize its nitrogen
allocation. Consequently, we hypothesized that plants only optimize nitrogen
allocation up to their optimum enzymatic activity, which is 42 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C
for TRF1 and 33 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C for TRF2. Regardless of whether plants
acclimate to temperature or not, we assume that they do not optimally
allocate nitrogen when leaf temperature is below 5 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C because low
temperatures could substantially limit plant enzymes   (Martin et al.,
1978; Öquist et al., 1980; Strand and Öquist, 1988).</p>
      <p>After we get the optimal nitrogen allocations (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo stretchy="false" mathvariant="normal">^</mml:mo></mml:mover><mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">store</mml:mi></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:msub><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo stretchy="false" mathvariant="normal">^</mml:mo></mml:mover><mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">resp</mml:mi></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:msub><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo mathvariant="normal" stretchy="false">^</mml:mo></mml:mover><mml:mrow class="chem"><mml:mi mathvariant="normal">lc</mml:mi></mml:mrow></mml:msub><mml:mo>,</mml:mo><mml:mrow class="chem"><mml:mspace linebreak="nobreak" width="0.125em"/></mml:mrow><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo mathvariant="normal" stretchy="false">^</mml:mo></mml:mover><mml:mrow class="chem"><mml:mi mathvariant="normal">et</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:msub><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo stretchy="false" mathvariant="normal">^</mml:mo></mml:mover><mml:mrow class="chem"><mml:mi mathvariant="normal">cb</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, we are able to estimate
the <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> by rearranging Eqs. (A21) and (A22)
as follows:

              <disp-formula specific-use="align" content-type="numbered"><mml:math display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="App1.Ch1.E25"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo mathvariant="normal" stretchy="false">^</mml:mo></mml:mover><mml:mrow class="chem"><mml:mi mathvariant="normal">cb</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="App1.Ch1.E26"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mo>max⁡</mml:mo><mml:mn>25</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mover accent="true"><mml:mi>N</mml:mi><mml:mo mathvariant="normal" stretchy="false">^</mml:mo></mml:mover><mml:mrow class="chem"><mml:mi mathvariant="normal">cb</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

          where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>
are the nitrogen use efficiency for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></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:mtext>max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>. See
Eqs. (D1) and (D2) in Appendix D for details of calculations.</p>
</app>

<app id="App1.Ch1.S2">
  <title>Temperature response functions</title>
<sec id="App1.Ch1.S2.SS1">
  <title>Temperature dependence of Rubisco properties and respiration</title>
      <p>The temperature dependence of Rubisco kinetic parameters (<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>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">o</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>,
<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="italic">τ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and mitochondrial respiration in light (<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:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>   (Farquhar
et al., 1980) is an Arrhenius function taken from Bernacchi et al. (2001). The temperature response functions of Rubisco kinetic
parameters used are outlined below, which are the same irrespective of
whether plants are assumed to acclimate to growth temperatures (Temperature
response function one; TRF1) or not (Temperature response function two;
TRF2).</p>
      <p>Community land model version 4.5 (CLM4.5)
(Oleson et al., 2013) uses the
partial pressures of oxygen, <inline-formula><mml:math display="inline"><mml:mi>O</mml:mi></mml:math></inline-formula> as  20 900 Pa. The kinetic properties of
Rubisco,
which depend on temperature are Rubisco-specific factor, <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">τ</mml:mi></mml:math></inline-formula>
(Jordan and Ogren, 1984), <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mtext>cc</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">o</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, which are the
Michaelis–Menten constants for 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>, respectively. The
temperature response function of <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> and kinetic properties of Rubisco
(<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">cc</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">o</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="italic">τ</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> are described below, where the fixed coefficients
of the equations are values at 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C.

                <disp-formula specific-use="align" content-type="numbered"><mml:math display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="App1.Ch1.E27"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mi mathvariant="normal">r</mml:mi></mml:msub><mml:mfenced open="(" close=")"><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mfenced><mml:mo>=</mml:mo><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mfenced open="[" close="]"><mml:mfenced close=")" open="("><mml:mn>46 390</mml:mn><mml:mo>/</mml:mo><mml:mi>R</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mfenced><mml:mfenced open="(" close=")"><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mfenced></mml:mfenced></mml:mrow></mml:msup></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="App1.Ch1.E28"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mfenced open="(" close=")"><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mfenced><mml:mo>=</mml:mo><mml:mn>27 840</mml:mn><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mfenced open="[" close="]"><mml:mfenced close=")" open="("><mml:mn>36380</mml:mn><mml:mo>/</mml:mo><mml:mi>R</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mfenced><mml:mfenced close=")" open="("><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mfenced></mml:mfenced></mml:mrow></mml:msup></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="App1.Ch1.E29"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mfenced open="(" close=")"><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mfenced><mml:mo>=</mml:mo><mml:mn>40.49</mml:mn><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mfenced open="[" close="]"><mml:mfenced close=")" open="("><mml:mn>79 430</mml:mn><mml:mo>/</mml:mo><mml:mi>R</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mfenced><mml:mfenced close=")" open="("><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mfenced></mml:mfenced></mml:mrow></mml:msup></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="App1.Ch1.E30"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:mi mathvariant="italic">τ</mml:mi><mml:mfenced open="(" close=")"><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mfenced><mml:mo>=</mml:mo><mml:mn>2407.834</mml:mn><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mfenced open="[" close="]"><mml:mfenced open="(" close=")"><mml:mn>37 830</mml:mn><mml:mo>/</mml:mo><mml:mi>R</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mfenced><mml:mfenced open="(" close=")"><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mfenced></mml:mfenced></mml:mrow></mml:msup></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

            In the above equations, <inline-formula><mml:math display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula> is the universal gas constant (8.314 J mol<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> K<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>,
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> is the leaf temperature (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>K</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and the reference temperature,
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>=</mml:mo><mml:mn>298.15</mml:mn></mml:mrow></mml:math></inline-formula> K.</p>
</sec>
<sec id="App1.Ch1.S2.SS2">
  <?xmltex \opttitle{Temperature dependence of $V_{\mathrm{c,max}}$  and $J_{\text{max}}$}?><title>Temperature dependence of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula></title>
      <p>Temperature sensitivities of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> are simulated using a
modified Arrhenius function   (e.g., Kattge and Knorr, 2007; Medlyn et al.,
2002a; Walker et al., 2014). Because the temperature relationship could
acclimate, we examined Kattge and Knorr  (2007)'s formulation of with
and without temperature acclimation to plant growth temperature. We use two
temperature dependence functions of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, which are
described below.</p>
</sec>
<sec id="App1.Ch1.S2.SS3">
  <title>Temperature response function one (TRF1)</title>
      <p>Fundamentally, TRF1 is a temperature dependence function for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> , which is based on the formulation and parameterization as
in Medlyn et al. (2002a) but further modified by Kattge
and Knorr (2007) to make the temperature optima a function of growth
temperature (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>; <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C). It is specified for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> as
follows:

                <disp-formula id="App1.Ch1.E31" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi>f</mml:mi><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

          with

                <disp-formula specific-use="align" content-type="numbered"><mml:math display="block"><mml:mtable displaystyle="true"><mml:mtr><mml:mtd/><mml:mtd><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mfenced open="(" close=")"><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mfenced><mml:mo>=</mml:mo></mml:mrow></mml:mtd></mml:mtr><mml:mlabeledtr id="App1.Ch1.E32"><mml:mtd/><mml:mtd/><mml:mtd><mml:mrow><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mfenced open="(" close=")"><mml:mn mathvariant="normal">1</mml:mn><mml:mo>+</mml:mo><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mfenced open="[" close="]"><mml:mfenced close=")" open="("><mml:msub><mml:mi>S</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>H</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub></mml:mfenced><mml:mrow><mml:mfenced open="/" close=""><mml:mphantom style="vphantom"><mml:mpadded width="0pt" style="vphantom"><mml:mfenced close=")" open="("><mml:msub><mml:mi>S</mml:mi><mml:mi mathvariant="normal">v</mml:mi></mml:msub><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>H</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub></mml:mfenced><mml:mfenced close=")" open="("><mml:mi>R</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mfenced></mml:mpadded></mml:mphantom></mml:mfenced></mml:mrow><mml:mfenced close=")" open="("><mml:mi>R</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mfenced></mml:mfenced></mml:mrow></mml:msup></mml:mfenced><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mfenced close="]" open="["><mml:mfenced close=")" open="("><mml:msub><mml:mi>H</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mrow><mml:mfenced close="" open="/"><mml:mphantom style="vphantom"><mml:mpadded style="vphantom" width="0pt"><mml:msub><mml:mi>H</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mi>R</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mpadded></mml:mphantom></mml:mfenced></mml:mrow><mml:mi>R</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mfenced><mml:mfenced open="(" close=")"><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mrow><mml:mfenced open="/" close=""><mml:mphantom style="vphantom"><mml:mpadded style="vphantom" width="0pt"><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mpadded></mml:mphantom></mml:mfenced></mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mfenced></mml:mfenced></mml:mrow></mml:msup></mml:mrow><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>+</mml:mo><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mfenced open="[" close="]"><mml:mfenced close=")" open="("><mml:msub><mml:mi>S</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>H</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub></mml:mfenced><mml:mrow><mml:mfenced open="/" close=""><mml:mphantom style="vphantom"><mml:mpadded style="vphantom" width="0pt"><mml:mfenced open="(" close=")"><mml:msub><mml:mi>S</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>H</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub></mml:mfenced><mml:mfenced open="(" close=")"><mml:mi>R</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mfenced></mml:mpadded></mml:mphantom></mml:mfenced></mml:mrow><mml:mfenced close=")" open="("><mml:mi>R</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub></mml:mfenced></mml:mfenced></mml:mrow></mml:msup></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

            where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> is the value of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> at the
reference temperature <inline-formula><mml:math display="inline"><mml:mrow><mml:mfenced open="(" close=")"><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>=</mml:mo><mml:mn>298.15</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">K</mml:mi></mml:mfenced></mml:mrow></mml:math></inline-formula>. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>H</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (J mol<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>
is energy of activation and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>H</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (J mol<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is the energy of
deactivation. <inline-formula><mml:math display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula> is the universal gas constant (8.314 J mol<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> K<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>
and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub><mml:mo>(</mml:mo><mml:mi>K</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is the leaf temperature. The entropy term, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mi>v</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (J mol<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> K<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, is now a function of temperature  (Kattge and
Knorr, 2007),

                <disp-formula id="App1.Ch1.E33" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mi>a</mml:mi><mml:mo>+</mml:mo><mml:mi>b</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mi>b</mml:mi></mml:math></inline-formula> are acclimation parameters.</p>
      <p>TRF1 is implemented in CLM4.5 by Oleson et al. (2013), who use the form of
temperature dependence function for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mtext>c,max</mml:mtext></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> as shown in
Eq. (B5), but with limited temperature acclimation, where
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>668.39</mml:mn><mml:mo>-</mml:mo><mml:mn>1.07</mml:mn><mml:mi mathvariant="normal">min</mml:mi><mml:mfenced close=")" open="("><mml:mi mathvariant="normal">max</mml:mi><mml:mfenced open="(" close=")"><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:mn>11</mml:mn></mml:mfenced><mml:mo>,</mml:mo><mml:mn>35</mml:mn></mml:mfenced></mml:mrow></mml:math></inline-formula> with <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> representing the
monthly mean air temperature (<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C). Other parameters present in
CLM4.5 model include, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>H</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>72</mml:mn></mml:mrow></mml:math></inline-formula> 000 J mol<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 <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>H</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>200</mml:mn></mml:mrow></mml:math></inline-formula> 000 J mol<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 values of the acclimation parameters (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>a</mml:mi><mml:mo>=</mml:mo><mml:mn>668</mml:mn></mml:mrow></mml:math></inline-formula>.39 and <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>b</mml:mi><mml:mo>=</mml:mo><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula>.07)
are taken from Table 3 of Kattge and Knorr  (2007).</p>
      <p>An equation similar to Eq. (B6), <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow></mml:msub><mml:mfenced open="(" close=")"><mml:msub><mml:mi>T</mml:mi><mml:mn mathvariant="normal">1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mfenced></mml:mrow></mml:math></inline-formula>, is used to describe the temperature dependence of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> that
considers temperature acclimation based on the <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mi>v</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> term. The values of
the acclimation parameters (<inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>b</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mi>v</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are taken from Table 3 of
Kattge and Knorr  (2007). Following Kattge and Knorr  (2007)
and CLM4.5, we set <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>H</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>H</mml:mi><mml:mi mathvariant="normal">d</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mo>max⁡</mml:mo></mml:msub></mml:mrow></mml:math></inline-formula> as 50 000 and 200 000 J mol<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>, respectively.</p>
</sec>
<sec id="App1.Ch1.S2.SS4">
  <title>Temperature response function two (TRF2)</title>
      <p>TRF2 does not consider the thermal acclimation. The formulation of TRF2 is
same as TRF1 except that in TRF2, the entropy term; <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mi>v</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (J mol<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> K<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is fixed across our data set. The values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mi>v</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are
taken from Table 3 of Kattge and Knorr (2007). <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>S</mml:mi><mml:mi>v</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is set as 649.12 J mol<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> K<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 646.22 J mol<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> K<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> for
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, respectively.</p>
</sec>
</app>

<app id="App1.Ch1.S3">
  <title>The Farquhar photosynthesis and  Ball–Berry model</title>
<sec id="App1.Ch1.S3.SS1">
  <title>Overview</title>
      <p>Photosynthesis is described using a system of three equations and three
unknown variables. The three unknown variables include (1) the net rate of
leaf photosynthesis (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>A</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, (2) the stomatal conductance (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>g</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and (3) the
intercellular partial pressure of CO<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. All of the unknown
variables influence one another. The three equations include (1) the
Farquhar's non-linear equation (<inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> vs. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, (2) the Ball–Berry equation
(<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>g</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> vs. <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>A</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and (3) the diffusion equation (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>A</mml:mi><mml:mo>=</mml:mo><mml:msub><mml:mi>g</mml:mi><mml:mi mathvariant="normal">s</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">a</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>. We solved all of these equations simultaneously by taking an
iterative approach   (Collatz et al., 1991; Harley et al., 1992; Leuning,
1990). The detailed algorithm for modeling photosynthesis is described
below.</p>
</sec>
<sec id="App1.Ch1.S3.SS2">
  <title>Modeling photosynthesis</title>
      <p>The photosynthetic rate (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>A</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> depends upon (i) the amount, activity and kinetic
properties of Rubisco, and (ii) the rate of ribulose-l,5 bisphosphate (RuBP)
regeneration via electron transport    (Farquhar et al., 1980). The
minimum of these two limiting conditions yields the following expression,

                <disp-formula id="App1.Ch1.E34" content-type="numbered"><mml:math display="block"><mml:mrow><mml:mi>A</mml:mi><mml:mo>=</mml:mo><mml:mo movablelimits="false">min⁡</mml:mo><mml:mfenced close=")" open="("><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">j</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>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the Rubisco limited rate and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">j</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is
the electron transport limited rate. The Rubisco-limited carboxylation can
be described by

                <disp-formula id="App1.Ch1.E35" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

          with

                <disp-formula id="App1.Ch1.E36" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mo>(</mml:mo><mml:mn mathvariant="normal">0</mml:mn><mml:mo>,</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mrow><mml:mn>0.5</mml:mn><mml:mi>O</mml:mi></mml:mrow><mml:mi mathvariant="italic">τ</mml:mi></mml:mfrac></mml:mstyle><mml:mo>)</mml:mo></mml:mrow><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">cc</mml:mi></mml:msub><mml:mfenced open="(" close=")"><mml:mn mathvariant="normal">1</mml:mn><mml:mo>+</mml:mo><mml:mi>O</mml:mi><mml:mo>/</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">o</mml:mi></mml:msub></mml:mfenced></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the maximum rate of carboxylation, competitive
with respect to 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 oxygen, and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mtext>cc</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">o</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are Michaelis
constants for carboxylation and oxygenation, respectively. <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">τ</mml:mi></mml:math></inline-formula> is the
specificity factor for Rubisco    (Jordan and Ogren, 1984), while
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mi>O</mml:mi></mml:math></inline-formula> are the partial pressures 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> 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> in the
intercellular air space, respectively. Likewise, the electron-limited rate
of carboxylation can be expressed by

                <disp-formula id="App1.Ch1.E37" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi mathvariant="normal">j</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">j</mml:mi></mml:msub><mml:mi>J</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

          with

                <disp-formula id="App1.Ch1.E38" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">j</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mo>(</mml:mo><mml:mn mathvariant="normal">0</mml:mn><mml:mo>,</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mrow><mml:mi mathvariant="normal">i</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mrow><mml:mn>0.5</mml:mn><mml:mi>O</mml:mi></mml:mrow><mml:mi mathvariant="italic">τ</mml:mi></mml:mfrac></mml:mstyle><mml:mo>)</mml:mo></mml:mrow><mml:mrow><mml:mn mathvariant="normal">4</mml:mn><mml:mfenced open="(" close=")"><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">i</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:mn mathvariant="normal">2</mml:mn><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mrow><mml:mn>0.5</mml:mn><mml:mi>O</mml:mi></mml:mrow><mml:mi mathvariant="italic">τ</mml:mi></mml:mfrac></mml:mstyle></mml:mfenced></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math display="inline"><mml:mi>J</mml:mi></mml:math></inline-formula> is the potential rate of electron transport, and the factor 4
indicates that the transport of four electrons will generate sufficient ATP
and NADPH for the regeneration of RuBP in the Calvin cycle
(Farquhar and von Caemmerer, 1982). The potential rate of
electron transport is dependent upon irradiance, <inline-formula><mml:math display="inline"><mml:mi>I</mml:mi></mml:math></inline-formula>, according to the
empirical expression of Smith   (1937):

                <disp-formula id="App1.Ch1.E39" content-type="numbered"><mml:math display="block"><mml:mrow><mml:mi>J</mml:mi><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mi mathvariant="italic">α</mml:mi><mml:mi>I</mml:mi></mml:mrow><mml:mrow><mml:msup><mml:mfenced open="(" close=")"><mml:mn mathvariant="normal">1</mml:mn><mml:mo>+</mml:mo><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mrow><mml:msup><mml:mi mathvariant="italic">α</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:msup><mml:mi>I</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:mrow><mml:mrow><mml:msubsup><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msubsup></mml:mrow></mml:mfrac></mml:mstyle></mml:mfenced><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mrow><mml:mfenced open="/" close=""><mml:mphantom style="vphantom"><mml:mpadded style="vphantom" width="0pt"><mml:mn>12</mml:mn></mml:mpadded></mml:mphantom></mml:mfenced></mml:mrow><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>, the efficiency of light energy conversion is considered as
0.292 (unitless)   (Niinemets and Tenhunen, 1997) and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> <italic>is</italic> the
maximum rate of electron transport.</p>
</sec>
<sec id="App1.Ch1.S3.SS3">
  <title>Ball–Berry model</title>
      <p>The stomatal conductance (<inline-formula><mml:math display="inline"><mml:mi>g</mml:mi></mml:math></inline-formula>, m 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>) is evaluated by the Ball–Berry empirical
stomatal conductance model   (Ball et al., 1987):

                <disp-formula id="App1.Ch1.E40" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>g</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>g</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub><mml:mo>+</mml:mo><mml:mi>m</mml:mi><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mi>A</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">RH</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

          where RH is the relative humidity (unitless) at the leaf surface, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is
the 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 at the leaf surface, and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>g</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (0.0005 m 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
<inline-formula><mml:math display="inline"><mml:mi>m</mml:mi></mml:math></inline-formula> are the minimum stomatal conductance and slope (9; constant across all
C<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> species), respectively.</p>
      <p>The estimation of <inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> could be sensitive to the choice of maximum
stomatal conductance slope, as this parameter varies both within and across
species     (Harley and Baldocchi, 1995; Wilson et al., 2001). A
recent synthesis provides the first analysis of the global variation in
stomatal slope based on an alternative algorithm that considers
representation of optimal stomatal behavior   (Lin et al., 2015). However,
following CLM4.5, which uses the Ball–Berry empirical stomatal conductance
model   (Ball et al., 1987), we fixed the value of stomatal slope
(<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>m</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> as 9 for all PFTs in our study.</p>
</sec>
<sec id="App1.Ch1.S3.SS4">
  <title>Calculation of photosynthesis and stomatal conductance</title>
      <p>We solved Farquhar's non-linear equation (<inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> vs. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, the Ball–Berry
equation (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>g</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> vs. <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>A</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and the diffusion equation (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>A</mml:mi><mml:mo>=</mml:mo><mml:msub><mml:mi>g</mml:mi><mml:mi mathvariant="normal">s</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">a</mml:mi></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> simultaneously by taking an iterative approach   (Collatz et al.,
1991; Harley et al., 1992; Leuning, 1990) until values of <inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>g</mml:mi><mml:mi mathvariant="normal">s</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>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are obtained. The three equations are solved in two phases;
the first phase included solving the equations for which Rubisco is limiting
while the second phase considered light limitation. The following steps are
followed:
<list list-type="order"><list-item><p>Given the initial values of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (where initial value of C<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi>i</mml:mi></mml:msub></mml:math></inline-formula> is
assumed 0.7 <inline-formula><mml:math display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> ambient 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), the temperature dependence
functions of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></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:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> (see Appendix B), and the temperature
dependence of Rubisco kinetics (<inline-formula><mml:math display="inline"><mml:mi>O</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">τ</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>o</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, Appendix B),
<inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> is calculated from Eq. (C2).</p></list-item><list-item><p>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 at the leaf surface (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is determined by
calculating the difference between <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and the partial
pressure due to <inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula>, wind speed and the dimension of the leaf.</p></list-item><list-item><p>Given <inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, the stomatal conductance (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>g</mml:mi><mml:mi mathvariant="normal">s</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is determined using Eq. (C8).</p></list-item><list-item><p><inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is determined by calculating the difference between <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and
partial pressure due to <inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> and boundary conditions of the stomata.</p></list-item><list-item><p>Using the leaf energy balance based on absorbed shortwave radiation, molar
latent heat content of water vapor, air temperature, and a parameter that
governs the rate of convective cooling (38.4 J 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> K<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>
(Jarvis, 1986; Moorcroft et al., 2001), leaf
temperature is calculated.</p></list-item></list>
The above five steps are repeated in a systematic way until <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is
equilibrated and the final value of <inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> is then recorded. The net
photosynthetic rate, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mtext>net</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula>, is then calculated by subtracting the
respiration from <inline-formula><mml:math display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> as follows:

                <disp-formula id="App1.Ch1.E41" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant="normal">net</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mi>A</mml:mi><mml:mo>-</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">t</mml:mi></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

          where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">t</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is respiration calculated by Eq. (A19).</p>
</sec>
</app>

<app id="App1.Ch1.S4">
  <title>Nitrogen use efficiencies</title>
      <p>The nitrogen use efficiency for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, <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> g<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> N s<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is estimated from a baseline nitrogen
use efficiency 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C (<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> and a
corresponding temperature response function at as follows:

              <disp-formula id="App1.Ch1.E42" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>×</mml:mo><mml:msub><mml:mi>f</mml:mi><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>(</mml:mo><mml:mi>T</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub><mml:mo>)</mml:mo><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        with

              <disp-formula id="App1.Ch1.E43" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mn>47.3</mml:mn><mml:mo>×</mml:mo><mml:mrow class="chem"><mml:mn>6.25</mml:mn></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where the constant 47.3 is the specific Rubisco activity (<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> g<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> Rubisco s<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> measured at 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C and the constant 6.25 is
the nitrogen binding factor for Rubisco (<inline-formula><mml:math display="inline"><mml:mi>g</mml:mi></mml:math></inline-formula> Rubisco g<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> N)   (Rogers,
2014). <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>(</mml:mo><mml:mi>T</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is the function
specifying the temperature dependence of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> with <inline-formula><mml:math display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula> as the
leaf temperature (K) and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> as the growth air temperature (see
Appendix B for details of the temperature dependence
of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo></mml:mrow><mml:mspace width="0.25em" linebreak="nobreak"/><mml:mrow class="chem"><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>.</p>
      <p>The nitrogen use efficiency for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>,
<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron g<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> N s<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is estimated based on a characteristic
protein cytochrome <inline-formula><mml:math display="inline"><mml:mi>f</mml:mi></mml:math></inline-formula>   (Evans and Poorter, 2001),

              <disp-formula id="App1.Ch1.E44" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">J</mml:mi></mml:mrow><mml:mrow><mml:mo>max⁡</mml:mo><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>×</mml:mo><mml:msub><mml:mi>f</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>(</mml:mo><mml:mi>T</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        with

              <disp-formula id="App1.Ch1.E45" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mrow class="chem"><mml:mn>8.06</mml:mn></mml:mrow><mml:mo>×</mml:mo><mml:mrow class="chem"><mml:mn>156</mml:mn></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where the coefficient 156 is the maximum electron transport rate for
cytochrome <inline-formula><mml:math display="inline"><mml:mi>f</mml:mi></mml:math></inline-formula> at 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol electron/<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol cytochrome <inline-formula><mml:math display="inline"><mml:mrow><mml:mi>f</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>; 8.06 is the nitrogen
binding coefficient for cytochrome <inline-formula><mml:math display="inline"><mml:mi>f</mml:mi></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>mol cytochrome <inline-formula><mml:math display="inline"><mml:mi>f</mml:mi></mml:math></inline-formula> g<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> N in
bioenergetics). <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>(</mml:mo><mml:mi>T</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is a function
specifies the dependence of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> on temperature (see Appendix B for
details of the temperature dependence of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>.</p>
      <p>The nitrogen use efficiency of enzymes for respiration (<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> g<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> N day<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">r</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, is assumed to be
temperature-dependent. Specifically, it is calculated as follows,

              <disp-formula id="App1.Ch1.E46" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">r</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mn>33.69</mml:mn><mml:mspace linebreak="nobreak" width="0.25em"/><mml:mo>[</mml:mo><mml:msub><mml:mi>D</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">day</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mi>f</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">r</mml:mi></mml:mrow></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">day</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo><mml:mo>+</mml:mo><mml:msub><mml:mi>D</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">night</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mi>f</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">r</mml:mi></mml:mrow></mml:msub><mml:mo>(</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">night</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo><mml:mo>]</mml:mo><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where 33.69 is the specific nitrogen use efficiency for respiration at
25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C (<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> g<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> N s<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula>     (Makino and Osmond,
1991) and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">r</mml:mi></mml:mrow></mml:msub><mml:mo>(</mml:mo><mml:mi>T</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> specifies the dependence of respiration on
temperature. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>D</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">day</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>D</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">night</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the daytime and
nighttime length in seconds.</p>
      <p>The maintenance respiration cost for all photosynthetic enzymes (NUE<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>rp</mml:mtext></mml:msub></mml:math></inline-formula>,
<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> g<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>N s<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is calculated as follows:

              <disp-formula id="App1.Ch1.E47" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">rp</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mrow class="chem"><mml:mo>=</mml:mo><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">rp</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi>f</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">r</mml:mi></mml:mrow></mml:msub><mml:mo>(</mml:mo><mml:mi>T</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">rp</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the nitrogen use efficiency at 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">rp</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is estimated from the observation of
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> as follows:

              <disp-formula id="App1.Ch1.E48" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">rp</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mn>0.8</mml:mn><mml:mo>×</mml:mo><mml:mn>0.5</mml:mn><mml:mo>×</mml:mo><mml:mn>0.015</mml:mn><mml:mo>×</mml:mo><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mrow class="chem"><mml:mo>+</mml:mo></mml:mrow><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>+</mml:mo><mml:mn>0.2</mml:mn></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where the total respiration is set as 1.5 % of <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> (Collatz et al., 1991). We assume that 50 % of the total
respiration is used for maintenance respiration   (Van Oijen et al., 2010)
and 80 % of the maintenance respiration is used for photosynthetic enzyme.
In view that the light absorption rate is generally around 80 %
(Evans and Poorter, 2001), we set the nitrogen for light capture as
0.2 based on Eq. (A12) in Appendix A. <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> and
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> are the nitrogen use efficiency for
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mrow><mml:mi mathvariant="normal">max</mml:mi><mml:mn>25</mml:mn></mml:mrow></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:mtext>c,max25</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> estimated from Eqs. (D1) and (D2). In this
study, we use the estimated mean value of 0.715 for
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mrow class="chem"><mml:mi mathvariant="normal">NUE</mml:mi></mml:mrow><mml:mrow class="chem"><mml:mi mathvariant="normal">rp</mml:mi><mml:mn>25</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> based on the data of Ali et al. (2015).
<?xmltex \hack{\newpage}?>
The nitrogen use efficiency for carboxylation (NUE<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi/><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is calculated as
the multiplication of conversion factor <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> and the nitrogen use
efficiency for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> follows:

              <disp-formula id="App1.Ch1.E49" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">max</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where <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> is calculated based on the actual 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>
concentrations and leaf temperature (see Eq. C4 for details).
Correspondingly, the reference nitrogen use efficiency for carboxylation
(NUE<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi/><mml:mrow><mml:mi mathvariant="normal">c</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is calculated using the Eq. (D5) except that <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> is
calculated based on the reference 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 26.95 Pa
and the reference leaf temperature of 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C. The reference 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 is estimated by assuming 70 % of the 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> concentration of 380 ppm and an air pressure of 101, 325 Pa.</p>
      <p>The nitrogen use efficiency for electron transport (NUE<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi/><mml:mi>j</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is calculated
as the multiplication of conversion factor <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and the nitrogen use
efficiency for <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mtext>max</mml:mtext></mml:msub></mml:mrow></mml:math></inline-formula> follows:

              <disp-formula id="App1.Ch1.E50" content-type="numbered"><mml:math display="block"><mml:mrow><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>K</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msub><mml:mi mathvariant="normal">NUE</mml:mi><mml:mrow><mml:msub><mml:mi>J</mml:mi><mml:mi mathvariant="normal">max</mml:mi></mml:msub></mml:mrow></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>

        where <inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is calculated based on the actual 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>
concentrations and leaf temperature (see Eq. C6 in Appendix C for
details). Correspondingly, the reference nitrogen use efficiency for
electron transport (NUE<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi/><mml:mrow><mml:mi>j</mml:mi><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is calculated using the Eq. (D6) except that
<inline-formula><mml:math display="inline"><mml:mrow><mml:msub><mml:mi>K</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is calculated based on the reference 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 26.95 Pa and the reference leaf temperature of 25 <inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C.
The reference 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 is estimated by assuming
70 % of the 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> concentration of 380 ppm and an air
pressure of 101, 325 Pa.
<?xmltex \hack{\clearpage}?>
<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/gmd-9-587-2016-supplement" xlink:title="pdf">doi:10.5194/gmd-9-587-2016-supplement</inline-supplementary-material>.</bold></p></supplementary-material></p>
</app>
  </app-group><ack><title>Acknowledgements</title><p>This work is funded by UC Lab Research Program (ID: 237285)
and by the DOE Office of Science, Next Generation Ecosystem Experiment
(NGEE) programs in the arctic and in the tropics. This submission is under
public release with the approved LA-UR-14-23309.
<?xmltex \hack{\newline}?><?xmltex \hack{\newline}?>Edited by:  G. A. Folberth</p></ack><ref-list>
    <title>References</title>

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    <!--<article-title-html>A global scale mechanistic model of photosynthetic capacity (LUNA V1.0)</article-title-html>
<abstract-html><p class="p">Although plant photosynthetic capacity as determined by the maximum
carboxylation rate (i.e., <i>V</i><sub>c, max25</sub>) and the maximum electron transport
rate (i.e., <i>J</i><sub>max25</sub>) at a reference temperature (generally 25 °C) is
known to vary considerably in space and time in response to environmental
conditions, it is typically parameterized in Earth system models (ESMs) with
tabulated values associated with plant functional types. In this study, we
have developed a mechanistic model of leaf utilization of nitrogen for
assimilation (LUNA) to predict photosynthetic capacity at the
global scale under different environmental conditions. We adopt an
optimality hypothesis to nitrogen allocation among light capture, electron
transport, carboxylation and respiration. The LUNA model is able to
reasonably capture the measured spatial and temporal patterns of
photosynthetic capacity as it explains  ∼  55 % of the global
variation in observed values of <i>V</i><sub>c, max25</sub> and  ∼  65 % of the variation in the observed values of <i>J</i><sub>max25</sub>. Model
simulations with LUNA under current and future climate conditions
demonstrate that modeled values of <i>V</i><sub>c, max25</sub> are most affected in
high-latitude regions under future climates. ESMs that relate the values of
<i>V</i><sub>c, max25</sub> or <i>J</i><sub>max25</sub> to plant functional types only are likely to
substantially overestimate future global photosynthesis.</p></abstract-html>
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