<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD Journal Publishing with OASIS Tables v3.0 20080202//EN" "journalpub-oasis3.dtd">
<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" xml:lang="en" dtd-version="3.0"><?xmltex \makeatother\@nolinetrue\makeatletter?>
  <front>
    <journal-meta><journal-id journal-id-type="publisher">ACP</journal-id><journal-title-group>
    <journal-title>Atmospheric Chemistry and Physics</journal-title>
    <abbrev-journal-title abbrev-type="publisher">ACP</abbrev-journal-title><abbrev-journal-title abbrev-type="nlm-ta">Atmos. Chem. Phys.</abbrev-journal-title>
  </journal-title-group><issn pub-type="epub">1680-7324</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/acp-18-2011-2018</article-id><title-group><article-title>Contributions of natural and anthropogenic sources to ambient ammonia in the Athabasca Oil Sands and north-western Canada</article-title><alt-title>Sources of atmospheric NH<inline-formula><mml:math id="M1" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> in Alberta and Saskatchewan</alt-title>
      </title-group><?xmltex \runningtitle{Sources of atmospheric NH${}_{3}$ in Alberta and Saskatchewan}?><?xmltex \runningauthor{C. H. Whaley et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1 aff2">
          <name><surname>Whaley</surname><given-names>Cynthia H.</given-names></name>
          <email>cynthia.whaley@canada.ca</email>
        <ext-link>https://orcid.org/0000-0002-0028-1514</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Makar</surname><given-names>Paul A.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Shephard</surname><given-names>Mark W.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-2867-9612</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Zhang</surname><given-names>Leiming</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-5437-5412</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Zhang</surname><given-names>Junhua</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Zheng</surname><given-names>Qiong</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Akingunola</surname><given-names>Ayodeji</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3 aff4">
          <name><surname>Wentworth</surname><given-names>Gregory R.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Murphy</surname><given-names>Jennifer G.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-8865-5463</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Kharol</surname><given-names>Shailesh K.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff5">
          <name><surname>Cady-Pereira</surname><given-names>Karen E.</given-names></name>
          
        </contrib>
        <aff id="aff1"><label>1</label><institution>Air Quality Research Division, Environment and Climate Change Canada, 4905 Dufferin Street,<?xmltex \hack{\break}?> Toronto, Ontario, Canada</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>Climate Research Division, Environment and Climate Change Canada, 4905 Dufferin Street, Toronto, Ontario, Canada</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>Department of Chemistry, University of Toronto, 80 St George Street, Toronto, Ontario, Canada</institution>
        </aff>
        <aff id="aff4"><label>4</label><institution>Environmental Monitoring and Science Division, Alberta Environment and Parks, 9888 Jasper Ave NW, <?xmltex \hack{\break}?>Edmonton, Alberta, Canada</institution>
        </aff>
        <aff id="aff5"><label>5</label><institution>Atmospheric and Environmental Research, Lexington, Massachusetts, USA</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Cynthia H. Whaley (cynthia.whaley@canada.ca)</corresp></author-notes><pub-date><day>13</day><month>February</month><year>2018</year></pub-date>
      
      <volume>18</volume>
      <issue>3</issue>
      <fpage>2011</fpage><lpage>2034</lpage>
      <history>
        <date date-type="received"><day>4</day><month>July</month><year>2017</year></date>
           <date date-type="rev-request"><day>17</day><month>October</month><year>2017</year></date>
           <date date-type="rev-recd"><day>25</day><month>January</month><year>2018</year></date>
           <date date-type="accepted"><day>26</day><month>January</month><year>2018</year></date>
      </history>
      <permissions>
        
        
      <license license-type="open-access"><license-p>This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this licence, visit <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">https://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><self-uri xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018.html">This article is available from https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018.html</self-uri><self-uri xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018.pdf">The full text article is available as a PDF file from https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018.pdf</self-uri>
      <abstract>
    <p id="d1e212">Atmospheric ammonia (NH<inline-formula><mml:math id="M2" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>) is a short-lived pollutant that plays an
important role in aerosol chemistry and nitrogen deposition. Dominant NH<inline-formula><mml:math id="M3" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>
emissions are from agriculture and forest fires, both of which are increasing
globally. Even remote regions with relatively low ambient NH<inline-formula><mml:math id="M4" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>
concentrations, such as northern Alberta and Saskatchewan in northern Canada,
may be of interest because of industrial oil sands emissions and a sensitive
ecological system. A previous attempt to model NH<inline-formula><mml:math id="M5" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> in the region showed a
substantial negative bias compared to satellite and aircraft observations.
Known missing sources of NH<inline-formula><mml:math id="M6" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> in the model were re-emission of NH<inline-formula><mml:math id="M7" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> from
plants and soils (bidirectional flux) and forest fire emissions, but the
relative impact of these sources on NH<inline-formula><mml:math id="M8" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> concentrations was unknown. Here
we have used a research version of the high-resolution air quality
forecasting model, GEM-MACH, to quantify the relative impacts of semi-natural
(bidirectional flux of NH<inline-formula><mml:math id="M9" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> and forest fire emissions) and direct
anthropogenic (oil sand operations, combustion of fossil fuels, and
agriculture) sources on ammonia volume mixing ratios, both at the surface and
aloft, with a focus on the Athabasca Oil Sands region during a
measurement-intensive campaign in the summer of 2013. The addition of fires
and bidirectional flux to GEM-MACH has improved the model bias, slope, and
correlation coefficients relative to ground, aircraft, and satellite NH<inline-formula><mml:math id="M10" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>
measurements significantly.</p>
    <p id="d1e297">By running the GEM-MACH-Bidi model in three configurations and calculating
their differences, we find that averaged over Alberta and Saskatchewan during
this time period an average of 23.1 % of surface NH<inline-formula><mml:math id="M11" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> came from direct
anthropogenic sources, 56.6 % (or 1.24 ppbv) from bidirectional flux
(re-emission from plants and soils), and 20.3 % (or 0.42 ppbv) from forest
fires. In the NH<inline-formula><mml:math id="M12" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> total column, an average of 19.5 % came from direct
anthropogenic sources, 50.0 % from bidirectional flux, and 30.5 % from
forest fires. The addition of bidirectional flux and fire emissions caused
the overall average net deposition of NH<inline-formula><mml:math id="M13" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> across the domain to be
increased by 24.5 %. Note that forest fires are very episodic and their
contributions will vary significantly for different time periods and regions.</p>
    <p id="d1e327">This study is the first use of the bidirectional flux scheme in GEM-MACH,
which could be generalized for other volatile or semi-volatile species. It
is also the first time CrIS (Cross-track Infrared
Sounder) satellite observations of NH<inline-formula><mml:math id="M14" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> have been used
for model evaluation, and the first use of fire emissions in GEM-MACH at
2.5 km resolution.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

      <?xmltex \hack{\newpage}?>
<?pagebreak page2012?><sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>
      <p id="d1e348">Ammonia (NH<inline-formula><mml:math id="M15" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>) is a short-lived pollutant that is receiving
global attention because of its increasing concentrations. Emissions of
NH<inline-formula><mml:math id="M16" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> – which are in large part from agricultural fertilizer, livestock
<xref ref-type="bibr" rid="bib1.bibx7 bib1.bibx23" id="paren.1"/>, and biomass burning <xref ref-type="bibr" rid="bib1.bibx67 bib1.bibx45" id="paren.2"/> –
have not been regulated to the same extent as other nitrogen species. NH<inline-formula><mml:math id="M17" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>
is the only aerosol precursor whose global emissions are projected to rise
throughout the next century <xref ref-type="bibr" rid="bib1.bibx62 bib1.bibx46 bib1.bibx18" id="paren.3"/>.</p>
      <p id="d1e388">NH<inline-formula><mml:math id="M18" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> has an atmospheric lifetime of hours to a day
<xref ref-type="bibr" rid="bib1.bibx78 bib1.bibx1" id="paren.4"/>. It is a base that reacts in the atmosphere with
sulphuric acid (H<inline-formula><mml:math id="M19" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>SO<inline-formula><mml:math id="M20" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>) and nitric acid (HNO<inline-formula><mml:math id="M21" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>) to form crystalline
sulphate, nitrate salts (e.g., (NH<inline-formula><mml:math id="M22" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>)<inline-formula><mml:math id="M23" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>SO<inline-formula><mml:math id="M24" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>, NH<inline-formula><mml:math id="M25" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>HSO<inline-formula><mml:math id="M26" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>,
NH<inline-formula><mml:math id="M27" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula>NO<inline-formula><mml:math id="M28" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>) and aqueous ions (SO<inline-formula><mml:math id="M29" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula>, HSO<inline-formula><mml:math id="M30" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, NO<inline-formula><mml:math id="M31" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>)
<xref ref-type="bibr" rid="bib1.bibx66 bib1.bibx51" id="paren.5"/>, which are significant components of fine particulate
matter (PM<inline-formula><mml:math id="M32" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2.5</mml:mn></mml:msub></mml:math></inline-formula>; e.g., <xref ref-type="bibr" rid="bib1.bibx41" id="author.6"/>, <xref ref-type="bibr" rid="bib1.bibx41" id="year.7"/>;
<xref ref-type="bibr" rid="bib1.bibx25" id="author.8"/>, <xref ref-type="bibr" rid="bib1.bibx25" id="year.9"/>), thus having health <xref ref-type="bibr" rid="bib1.bibx73 bib1.bibx48" id="paren.10"/>
and climate impacts <xref ref-type="bibr" rid="bib1.bibx40" id="paren.11"/>. A large portion of NH<inline-formula><mml:math id="M33" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> is readily
deposited in the first 4–5 km from its source, but when in fine particulate
form (as NH<inline-formula><mml:math id="M34" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>), its lifetime is days to several weeks
<xref ref-type="bibr" rid="bib1.bibx32 bib1.bibx68 bib1.bibx7 bib1.bibx70" id="paren.12"/>, and it can be transported
hundreds of kilometres <xref ref-type="bibr" rid="bib1.bibx45 bib1.bibx31 bib1.bibx52" id="paren.13"/>. Deposition of
NH<inline-formula><mml:math id="M35" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> and these aerosols can lead to nitrogen eutrophication and soil
acidification <xref ref-type="bibr" rid="bib1.bibx26 bib1.bibx84 bib1.bibx21 bib1.bibx15" id="paren.14"/>. NH<inline-formula><mml:math id="M36" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> is
listed as a “criteria air contaminant” <xref ref-type="bibr" rid="bib1.bibx24" id="paren.15"/> in order to help address
air quality issues such as smog and acid rain.</p>
      <p id="d1e618">Modelling can be used to better understand NH<inline-formula><mml:math id="M37" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> processes. Recent NH<inline-formula><mml:math id="M38" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>
models have focused on improving bidirectional flux processes and impacts of
livestock. Measurements of NH<inline-formula><mml:math id="M39" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> bidirectional flux include those in
<xref ref-type="bibr" rid="bib1.bibx27 bib1.bibx85 bib1.bibx86 bib1.bibx2" id="text.16"/>; and <xref ref-type="bibr" rid="bib1.bibx65" id="text.17"/>, with indirect support
for bidirectional flux also in <xref ref-type="bibr" rid="bib1.bibx22" id="text.18"/>. Thus, these studies were the
motivation for the recent design of parameterizations to describe this
important process <xref ref-type="bibr" rid="bib1.bibx97 bib1.bibx94 bib1.bibx57 bib1.bibx101 bib1.bibx103 bib1.bibx30 bib1.bibx36" id="paren.19"/>.
Additionally, satellite observations are providing valuable insight into
ammonia concentrations and emissions both on regional and global scales
<xref ref-type="bibr" rid="bib1.bibx6 bib1.bibx20 bib1.bibx80 bib1.bibx79 bib1.bibx88 bib1.bibx102" id="paren.20"/>.</p>
      <p id="d1e664">The Athabasca Oil Sands region (AOSR), located in the north-eastern part of
the province of Alberta, Canada, is a large source of pollution to air
<xref ref-type="bibr" rid="bib1.bibx35 bib1.bibx50 bib1.bibx49" id="paren.21"/> and ecosystems <xref ref-type="bibr" rid="bib1.bibx42 bib1.bibx44 bib1.bibx39" id="paren.22"/>,
as well as a source of greenhouse gases <xref ref-type="bibr" rid="bib1.bibx17" id="paren.23"/> due to mining
and processing by the oil industry. While NH<inline-formula><mml:math id="M40" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> volume mixing ratios (VMRs)
surrounding the AOSR in northern Alberta and Saskatchewan remain relatively
low – around 0.6 to 1.2 ppbv background (this study and
<xref ref-type="bibr" rid="bib1.bibx81" id="author.24"/>, <xref ref-type="bibr" rid="bib1.bibx81" id="year.25"/>) – due to low population
and lack of agriculture, the northern Alberta and Saskatchewan ecosystems are
sensitive to nitrogen deposition
<xref ref-type="bibr" rid="bib1.bibx19 bib1.bibx95 bib1.bibx96 bib1.bibx90 bib1.bibx55" id="paren.26"/>, and the modelled
background NH<inline-formula><mml:math id="M41" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> must be correct in order to understand the relative impacts
of the oil sand operations. It is important to understand if the AOSR
facilities or other sources (e.g., fires, re-emissions) are causing NH<inline-formula><mml:math id="M42" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> to
reach levels that cause ecosystem damage. A monitoring study from 2005 to
2008 found NH<inline-formula><mml:math id="M43" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs near Fort McMurray and Fort McKay (population centers
in the vicinity of the oil sand facilities) to be highly variable in space
and time with a range of 1.1 to 8.8 ppbv (where the upper end corresponds to
NH<inline-formula><mml:math id="M44" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> levels found in agricultural regions of Canada and the U.S.), with
NH<inline-formula><mml:math id="M45" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> concentrations 1.5–3 times higher than HNO<inline-formula><mml:math id="M46" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> concentrations
<xref ref-type="bibr" rid="bib1.bibx14" id="paren.27"/>. <xref ref-type="bibr" rid="bib1.bibx38" id="text.28"/> also found NH<inline-formula><mml:math id="M47" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> concentrations in the
AOSR to be much higher than HNO<inline-formula><mml:math id="M48" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>, NO<inline-formula><mml:math id="M49" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, and NH<inline-formula><mml:math id="M50" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> concentrations
(by <inline-formula><mml:math id="M51" display="inline"><mml:mspace linebreak="nobreak" width="0.25em"/></mml:math></inline-formula>5, 23, and 1.8 times, respectively). Thus, NH<inline-formula><mml:math id="M52" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> may contribute the
largest fraction of deposited nitrogen in the AOSR compared to other nitrogen
species. Estimates of deposition of nitrogen compounds in the AOSR are
described in <xref ref-type="bibr" rid="bib1.bibx55" id="text.29"/>; however, they did not include NH<inline-formula><mml:math id="M53" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>
bidirectional flux or forest fires in their model simulations.</p>
      <p id="d1e827">In a previous study by <xref ref-type="bibr" rid="bib1.bibx81" id="normal.30"/>, it was found that the GEM-MACH air
quality forecasting model <xref ref-type="bibr" rid="bib1.bibx61 bib1.bibx59 bib1.bibx53 bib1.bibx54 bib1.bibx34" id="paren.31"/>,
using a domain covering the Canadian provinces of Alberta and Saskatchewan
at 2.5 km resolution, under-predicted summertime tropospheric ammonia VMRs by
0.4–0.6 ppbv (which is 36–100 % depending on altitude – see Fig. 16 in
<xref ref-type="bibr" rid="bib1.bibx81" id="author.32"/>, <xref ref-type="bibr" rid="bib1.bibx81" id="year.33"/>) in the AOSR when compared
to the Tropospheric Emission Spectrometer (TES) satellite measurements and
aircraft measurements. Having too much modelled NH<inline-formula><mml:math id="M54" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> deposition is a
cause that was ruled out when <xref ref-type="bibr" rid="bib1.bibx55" id="text.34"/> showed that GEM-MACH actually
underestimates NH<inline-formula><mml:math id="M55" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> deposition. Underestimating anthropogenic and
agricultural emissions was also ruled out as a cause since the GEM-MACH model
performs well in southern Canada and the U.S. when compared to the U.S.
Ambient Ammonia Monitoring Network (AMoN). NH<inline-formula><mml:math id="M56" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> sources known to be missing
from the GEM-MACH model were forest fire emissions and re-emission of
deposited NH<inline-formula><mml:math id="M57" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> from soils and plants (the latter referred to as
bidirectional flux, hereafter), which would have the greatest impact in
background areas, such as northern Alberta and Saskatchewan. Therefore, these
two sources were added to an updated version of GEM-MACH and model
simulations were repeated for a 2013 summer period (12 August to 7 September
2013), during which an intensive measurement<?pagebreak page2013?> campaign occurred. We utilize
ground, aircraft, and satellite measurements of NH<inline-formula><mml:math id="M58" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> and related species to
evaluate the model and to quantify the impacts of the different sources on
atmospheric NH<inline-formula><mml:math id="M59" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> and its deposition.</p>
      <p id="d1e900">Section <xref ref-type="sec" rid="Ch1.S2"/> provides the model description. Section <xref ref-type="sec" rid="Ch1.S3"/> provides a brief description of ammonia measurements during
the campaign. Section <xref ref-type="sec" rid="Ch1.S4"/> presents the evaluation of
three model scenarios against three different types of measurements (surface,
aircraft, and satellite), and Sect. <xref ref-type="sec" rid="Ch1.S5"/> presents our
quantitative assessment on the impacts of different sources of NH<inline-formula><mml:math id="M60" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> to
ambient VMRs and NH<inline-formula><mml:math id="M61" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> fluxes in the region. Our conclusions appear in
Sect. <xref ref-type="sec" rid="Ch1.S6"/>.</p>
</sec>
<sec id="Ch1.S2">
  <title>GEM-MACH model description</title>
      <p id="d1e938">GEM-MACH (Global Environment Multiscale-Modelling Air
quality and CHemistry) is an online chemical transport model, which is
embedded in GEM, Environment and Climate Change Canada's (ECCC) numerical
weather prediction model <xref ref-type="bibr" rid="bib1.bibx61" id="paren.35"/>. This means that the chemical
processes of the model (gas-phase chemistry, plume rise emissions
distribution, vertical diffusion and surface fluxes of tracers, and a
particle chemistry package including particle microphysics, cloud processes,
and inorganic heterogeneous chemistry) are imbedded within GEM's physics
package, which in turn is imbedded within GEM's dynamics package, the latter
handling chemical tracer advection. A detailed description of the process
representation of GEM-MACH, and an evaluation of its performance for
pollutants such as ozone and particulate matter (PM) appears in
<xref ref-type="bibr" rid="bib1.bibx59 bib1.bibx53 bib1.bibx54" id="text.36"/>; and <xref ref-type="bibr" rid="bib1.bibx34" id="text.37"/>.</p>
      <p id="d1e950">GEM-MACHv2 is used operationally to issue twice-daily, 48 h public
forecasts of criteria air pollutants (ozone, nitrogen oxides, PM), as well as
the Air Quality Health Index (<uri>https://ec.gc.ca/cas-aqhi/</uri>). Any
improvements to NH<inline-formula><mml:math id="M62" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> in the model may result in better Air Quality Health Index predictions,
since NH<inline-formula><mml:math id="M63" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> is a major precursor of PM<inline-formula><mml:math id="M64" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2.5</mml:mn></mml:msub></mml:math></inline-formula>, as mentioned in the
introduction. We start with a similar research version of GEM-MACHv2
(rev2285) to make the bidirectional flux modifications. The key differences
between this and older versions are the use of a more recent meteorological
package (GEMv4.8), the capability to nest in the vertical dimension as well
as the horizontal dimension, and improvements to the treatment of fluxes,
vertical diffusion, and advection.</p>
      <p id="d1e983">GEM-MACH can be run for many different spatial domains, at various spatial
resolutions, and in 2-bin or 12-bin aerosol-size-distribution modes. For this
study, we run the model in the 2-bin mode (for computational efficiency),
using a nested set of domains. The outer domain at 10 km resolution covers
North America and the inner domain at 2.5 km resolution covers the provinces
of Alberta and Saskatchewan. The latter is referred to as the 2.5 km oil
sands domain. This setup, along with the emissions described in the next
section, is hereafter called our “base” simulation.</p>
<sec id="Ch1.S2.SS1">
  <title>Emissions</title>
      <p id="d1e991">The emissions of 25 species (SO<inline-formula><mml:math id="M65" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, SO<inline-formula><mml:math id="M66" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> gas,
sulphate, nitrate, NH<inline-formula><mml:math id="M67" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, NO, NO<inline-formula><mml:math id="M68" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, NH<inline-formula><mml:math id="M69" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>, CO, nitrous acid, benzene,
propane, higher alkanes, higher alkenes, ethene, toluene, aromatics,
formaldehyde, aldehydes, methyl ethyl ketone, creosol, isoprene, crustal
material, elemental carbon, and primary carbon) used in GEM-MACH (base case)
come from Canadian and U.S. emissions inventories: the 2011 National Emissions
Inventory (known as NEI) version 1 for U.S. emissions and the Air Pollutant Emission
Inventory (APEI) 2013 for Canadian emissions (2010 for on-road and off-road
emissions). Emissions were processed with SMOKE (Sparse Matrix Operator
Kernel Emissions, <uri>https://www.cmascenter.org/smoke/</uri>) to convert the
inventories into model-ready gridded hourly emissions files for modelling,
separated into major point emissions (typically industrial emissions from
stacks, emitted into the model layers that correspond to the stack height at
the reported temperature and velocity in the inventory's stack parameters),
and area emissions (emissions from spread-out sources, such as transportation
and agriculture, emitted into the first model layer). For more details about
these emissions, see <xref ref-type="bibr" rid="bib1.bibx60" id="text.38"/> and <xref ref-type="bibr" rid="bib1.bibx98" id="text.39"/>.</p>
      <p id="d1e1052">The emissions data for NH<inline-formula><mml:math id="M70" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> from oil sand sources are reported to the
Canadian National Pollutant Release Inventory (NPRI) on a “total annual
emissions per facility” basis. NH<inline-formula><mml:math id="M71" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> emissions are generally more uncertain
than SO<inline-formula><mml:math id="M72" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and NO<inline-formula><mml:math id="M73" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> emissions because NH<inline-formula><mml:math id="M74" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> emissions are not
measured to the same extent as those two. The oil sands represent only 1 %
of total Alberta NH<inline-formula><mml:math id="M75" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> emissions, at approximately 1438 t in 2013. For
comparison, about 18 times more NO<inline-formula><mml:math id="M76" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> and 57 times more SO<inline-formula><mml:math id="M77" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> was
emitted from the oil sand facilities that year
(<uri>http://www.ec.gc.ca/inrp-npri/donnees-data/index.cfm?lang=En</uri>).
However, we found an issue with NH<inline-formula><mml:math id="M78" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> in this inventory that impacted our
model evaluation in the region, which we describe below.</p>
      <?pagebreak page2014?><p id="d1e1140">If stack parameters (e.g., stack height and diameter, volume flow rates,
temperatures, etc.) are included as part of those NPRI data, then the
emissions are allocated to large stacks in our configuration of the SMOKE
emissions processing system. In the absence of this information, SMOKE will
assign default stack parameters based on its source category code. For the
Syncrude Canada Ltd. – Mildred Lake plant site, NPRI ID 2274 (a facility in
the AOSR), the default stack parameters were the following: 18.90 m for the stack height
(which is within the first model layer), 0.24 m for the stack diameter, 320.0
K for the exhaust temperature, and 0.58 m s<inline-formula><mml:math id="M79" 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 the exhaust velocity.
However, when these defaults were applied to NH<inline-formula><mml:math id="M80" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> emissions in initial
model simulations, they were found to result in erroneous short-term plume
events with simulated surface NH<inline-formula><mml:math id="M81" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> levels up to 2 orders of magnitude
higher than ground observations, and modelled VMRs aloft too low compared to
aircraft measurements. Conversely, for species such as SO<inline-formula><mml:math id="M82" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, for which
stack parameters were reported, the model was able to correctly place the
SO<inline-formula><mml:math id="M83" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> enhancements in space and time, relative to observations. When we
applied those same stack parameters for NH<inline-formula><mml:math id="M84" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> emissions as well (stack
height <inline-formula><mml:math id="M85" display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 183 m, stack diameter <inline-formula><mml:math id="M86" display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 7.9 m, exit temperature <inline-formula><mml:math id="M87" display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 513 K, exit
velocity <inline-formula><mml:math id="M88" display="inline"><mml:mo>=</mml:mo></mml:math></inline-formula> 23.9 m s<inline-formula><mml:math id="M89" 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>, from the NPRI website), the simulation of surface NH<inline-formula><mml:math id="M90" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>
was greatly improved. All subsequent simulations reported here make use of
this correction, and we advise the reporting of stack parameters for all
species for future inventories in order to avoid this kind of error for
models.</p>
</sec>
<sec id="Ch1.S2.SS2">
  <title>Ammonia bidirectional flux parameterization</title>
      <p id="d1e1258">NH<inline-formula><mml:math id="M91" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> can be both deposited from the atmosphere to the ground and
re-emitted from soils and plants back to the atmosphere. The two taken
together are called bidirectional flux, since the flux of NH<inline-formula><mml:math id="M92" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> can go both
up and down. The sources of NH<inline-formula><mml:math id="M93" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> available for re-emissions are from the
accumulated NH<inline-formula><mml:math id="M94" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> in the soil and stomatal water, which can arise from
increased deposition from anthropogenic sources, as well as from organic
nitrogen decomposition <xref ref-type="bibr" rid="bib1.bibx10" id="paren.40"/>, N<inline-formula><mml:math id="M95" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-fixation <xref ref-type="bibr" rid="bib1.bibx89" id="paren.41"/>, and
natural microbial action <xref ref-type="bibr" rid="bib1.bibx58" id="paren.42"/>.</p>
      <p id="d1e1316">The bidirectional flux scheme of <xref ref-type="bibr" rid="bib1.bibx101" id="text.43"/> was applied within the
GEM-MACHv2 model, replacing the original deposition velocity for NH<inline-formula><mml:math id="M96" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> only
(deposition velocity of other gas species follows a scheme based on a
multiple resistance approach and a single-layer “big leaf” approach;
<xref ref-type="bibr" rid="bib1.bibx93 bib1.bibx99 bib1.bibx75 bib1.bibx74" id="altparen.44"/>). The bidirectional flux
scheme is described in detail in <xref ref-type="bibr" rid="bib1.bibx101" id="text.45"/>, but we summarize it here.</p>
      <p id="d1e1337">Bidirectional exchange occurs between air–soil and air–stomata interfaces.
The bidirectional flux (<inline-formula><mml:math id="M97" display="inline"><mml:mrow><mml:msub><mml:mi>F</mml:mi><mml:mi>t</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) equation is
            <disp-formula id="Ch1.E1" content-type="numbered"><mml:math id="M98" display="block"><mml:mrow><mml:msub><mml:mi>F</mml:mi><mml:mi>t</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mo>-</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><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 mathvariant="normal">c</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi>b</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 id="M99" display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M100" display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi>b</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are the aerodynamic and quasi-laminar resistances,
respectively. <inline-formula><mml:math id="M101" 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 NH<inline-formula><mml:math id="M102" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> concentration in the air, and <inline-formula><mml:math id="M103" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> is the
canopy compensation point concentration, given by Eq. (<xref ref-type="disp-formula" rid="Ch1.E2"/>).
            <disp-formula id="Ch1.E2" content-type="numbered"><mml:math id="M104" display="block"><mml:mrow><?xmltex \hack{\hbox\bgroup\fontsize{9.5}{9.5}\selectfont$\displaystyle}?><mml:msub><mml:mi>C</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:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi>b</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>+</mml:mo><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">st</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">st</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>+</mml:mo><mml:mstyle displaystyle="false"><mml:mfrac style="text"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">ac</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mstyle></mml:mrow><mml:mrow><mml:mo>(</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi>b</mml:mi></mml:msub><mml:msup><mml:mo>)</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>+</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">st</mml:mi></mml:msub><mml:msup><mml:mo>)</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>+</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">ac</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub><mml:msup><mml:mo>)</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mo>+</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">cut</mml:mi></mml:msub><mml:msup><mml:mo>)</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:mfrac></mml:mstyle><?xmltex \hack{$\egroup}?><mml:mo>,</mml:mo></mml:mrow></mml:math></disp-formula>
          where <inline-formula><mml:math id="M105" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">st</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M106" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are the stomatal and ground compensation points, respectively, and
<inline-formula><mml:math id="M107" display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> are the resistances in s m<inline-formula><mml:math id="M108" 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> of the ground/soil (<inline-formula><mml:math id="M109" display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>), stomata
(<inline-formula><mml:math id="M110" display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">st</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>), cuticle (<inline-formula><mml:math id="M111" display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">cut</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>), and in-canopy aerodynamic (<inline-formula><mml:math id="M112" display="inline"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi mathvariant="normal">ac</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>). All
resistance formulas can be found in <xref ref-type="bibr" rid="bib1.bibx100" id="text.46"/>.</p>
      <p id="d1e1708">Stomata (st) and ground (g) compensation points are both calculated using Eq. (<xref ref-type="disp-formula" rid="Ch1.E3"/>):
            <disp-formula id="Ch1.E3" content-type="numbered"><mml:math id="M113" display="block"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mi>A</mml:mi><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mi>exp⁡</mml:mi><mml:mo>(</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mo>-</mml:mo><mml:mi>B</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>)</mml:mo><mml:msub><mml:mi mathvariant="normal">Γ</mml:mi><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula>
          <inline-formula><mml:math id="M114" display="inline"><mml:mi>A</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M115" display="inline"><mml:mi>B</mml:mi></mml:math></inline-formula> are constants derived from the equilibria constants for NH<inline-formula><mml:math id="M116" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>(g)
in leaves' stomatal cavities to NH<inline-formula><mml:math id="M117" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> and OH<inline-formula><mml:math id="M118" display="inline"><mml:msup><mml:mi/><mml:mo>-</mml:mo></mml:msup></mml:math></inline-formula> in the water contained in
the apoplast within the leaf and in the soil where NH<inline-formula><mml:math id="M119" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>(g) in the soil pore
air space is in equilibrium with the NH<inline-formula><mml:math id="M120" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> and OH<inline-formula><mml:math id="M121" display="inline"><mml:msup><mml:mi/><mml:mo>-</mml:mo></mml:msup></mml:math></inline-formula> dissolved in soil
water <xref ref-type="bibr" rid="bib1.bibx72" id="paren.47"/>. <inline-formula><mml:math id="M122" display="inline"><mml:mrow><mml:mi>A</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 16 1500 mol K L<inline-formula><mml:math id="M123" 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> <xref ref-type="bibr" rid="bib1.bibx64" id="paren.48"/>, or 2.7457 <inline-formula><mml:math id="M124" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M125" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">15</mml:mn></mml:msup></mml:math></inline-formula> <inline-formula><mml:math id="M126" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g K m<inline-formula><mml:math id="M127" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> <xref ref-type="bibr" rid="bib1.bibx72" id="paren.49"/>
for NH<inline-formula><mml:math id="M128" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> for both stomata and soil.
<inline-formula><mml:math id="M129" display="inline"><mml:mrow><mml:mi>B</mml:mi><mml:mo>=</mml:mo></mml:mrow></mml:math></inline-formula> 10 380 K <xref ref-type="bibr" rid="bib1.bibx64" id="paren.50"/>. <inline-formula><mml:math id="M130" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Γ</mml:mi><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> is the emission potential of the
stomata and ground, respectively and, in theory, is equal to the NH<inline-formula><mml:math id="M131" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>
concentration over the H<inline-formula><mml:math id="M132" display="inline"><mml:msup><mml:mi/><mml:mo>+</mml:mo></mml:msup></mml:math></inline-formula> concentration in the apoplast water of the
canopy leaves or soil water:
            <disp-formula id="Ch1.E4" content-type="numbered"><mml:math id="M133" display="block"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Γ</mml:mi><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mo>[</mml:mo><mml:msubsup><mml:mrow class="chem"><mml:mi mathvariant="normal">NH</mml:mi></mml:mrow><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:msub><mml:mo>]</mml:mo><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:mo>[</mml:mo><mml:msup><mml:mrow class="chem"><mml:mi mathvariant="normal">H</mml:mi></mml:mrow><mml:mo>+</mml:mo></mml:msup><mml:msub><mml:mo>]</mml:mo><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>.</mml:mo></mml:mrow></mml:math></disp-formula>
          However, since there are no modelled NH<inline-formula><mml:math id="M134" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> and H<inline-formula><mml:math id="M135" display="inline"><mml:msup><mml:mi/><mml:mo>+</mml:mo></mml:msup></mml:math></inline-formula> apoplast water
concentrations to use, we use <inline-formula><mml:math id="M136" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Γ</mml:mi><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> from <xref ref-type="bibr" rid="bib1.bibx91" id="text.51"/>, which is
based on long-term empirical averages. <xref ref-type="bibr" rid="bib1.bibx91" id="text.52"/> gives a range of values
for emission potentials for 26 land use categories (LUCs), and we use the
low end of the values in our model with the following exceptions: we further
lower the <inline-formula><mml:math id="M137" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Γ</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> for agriculture LUCs to 800, and increase <inline-formula><mml:math id="M138" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Γ</mml:mi><mml:mi mathvariant="normal">st</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
of boreal forest LUCs to 3000, all of which were necessary in order to
achieve realistic NH<inline-formula><mml:math id="M139" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> concentrations (e.g., compared to reported AMoN
values), while staying consistent with <inline-formula><mml:math id="M140" display="inline"><mml:mi mathvariant="normal">Γ</mml:mi></mml:math></inline-formula> findings from the literature.</p>
      <p id="d1e2130">This version of the model, which we call GEM-MACH-Bidi (or just “bidi”
hereafter) was quite sensitive to the selection of these emission potentials,
which are themselves highly uncertain <xref ref-type="bibr" rid="bib1.bibx91" id="paren.53"/>. GEM-MACH-Bidi uses the
exact same emissions as in the base case, described in the previous section.
However, when the sign of <inline-formula><mml:math id="M141" display="inline"><mml:mrow><mml:msub><mml:mi>F</mml:mi><mml:mi>t</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> in Eq. (<xref ref-type="disp-formula" rid="Ch1.E1"/>) becomes positive
(that is, when <inline-formula><mml:math id="M142" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">a</mml:mi></mml:msub><mml:mo>&lt;</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">c</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>), the bidirectional flux acts effectively as an
additional source of NH<inline-formula><mml:math id="M143" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> gas, releasing stored NH<inline-formula><mml:math id="M144" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> until and unless the
ambient concentration rises to the compensation point concentration. When the
flux is negative, net deposition of NH<inline-formula><mml:math id="M145" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> occurs.</p>
      <?pagebreak page2015?><p id="d1e2195">It is important to note that <inline-formula><mml:math id="M146" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values are exponentially dependent on
temperature (Fig. <xref ref-type="fig" rid="Ch1.F1"/> shows an example of this relationship for
the dominant LUCs in the northern part of the domain), and the higher the
compensation point, the greater the likelihood there will be upward flux. The
lower the <inline-formula><mml:math id="M147" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, the more likely there will be deposition. Since our
simulation period was August and September 2013, when the average temperature
in the AOSR was about 18 <inline-formula><mml:math id="M148" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C
(<uri>http://agriculture.alberta.ca/acis/alberta-weather-data-viewer.jsp</uri>), we
expect to have more NH<inline-formula><mml:math id="M149" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> re-emission than at other times of the year.
During the rest of the year (e.g., the preceding winter and spring), the
compensation point would be much lower, greatly increasing the likelihood to
have net deposition, even in northern Alberta and Saskatchewan where ambient
NH<inline-formula><mml:math id="M150" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> concentrations are low. Other meteorological factors affect the
magnitude of bidirectional flux via the resistance terms. For example, canopy
compensation points have been observed to decrease with decreasing wind
velocity and increased precipitation
<xref ref-type="bibr" rid="bib1.bibx28 bib1.bibx29 bib1.bibx8 bib1.bibx101" id="paren.54"/>. In other words, we expect more
re-emission during higher winds and drier conditions.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1"><caption><p id="d1e2268">Compensation point (<inline-formula><mml:math id="M151" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) relationship to temperature;
<inline-formula><mml:math id="M152" display="inline"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> for evergreen needleleaf LUC shown as example.</p></caption>
          <?xmltex \igopts{width=199.169291pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f01.pdf"/>

        </fig>

      <p id="d1e2299">Other chemical transport models, such as GEOS-Chem and CMAQ, use a similar
method as <xref ref-type="bibr" rid="bib1.bibx101" id="text.55"/>; however, instead of the constant average soil
emission potentials used here, they utilize a CMAQ–agroecosystem coupled
simulation to calculate a soil pool from which to estimate <inline-formula><mml:math id="M153" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Γ</mml:mi><mml:mi mathvariant="normal">g</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
<xref ref-type="bibr" rid="bib1.bibx5 bib1.bibx72 bib1.bibx103" id="paren.56"/>. In this case, the emission potential will vary
and can go to zero if the NH<inline-formula><mml:math id="M154" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> in the pool is depleted. However, it was
shown in <xref ref-type="bibr" rid="bib1.bibx91" id="text.57"/> that their <inline-formula><mml:math id="M155" display="inline"><mml:mrow><mml:msub><mml:mi mathvariant="normal">Γ</mml:mi><mml:mrow><mml:mi mathvariant="normal">st</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant="normal">g</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> worked well during the same
time of year as this investigation (August and September). This time of year
was also shown in <xref ref-type="bibr" rid="bib1.bibx103" id="text.58"/> to not have a large effect on emissions from
the NH<inline-formula><mml:math id="M156" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> pool. Additionally, <xref ref-type="bibr" rid="bib1.bibx92" id="text.59"/> calculated the
approximate relative abundances of NH<inline-formula><mml:math id="M157" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> in the boundary layer versus
NH<inline-formula><mml:math id="M158" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> in the soil pool to assess whether surface-to-air fluxes were
sustainable. They found that soil NH<inline-formula><mml:math id="M159" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> concentrations were much greater
than boundary layer NH<inline-formula><mml:math id="M160" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> (by over 2 orders of magnitude), further
supporting the assumption made here. In addition, the turnover time for soil
NH<inline-formula><mml:math id="M161" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> is on the order of 1 day, hence it is unlikely that NH<inline-formula><mml:math id="M162" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>
bidirectional fluxes would significantly deplete or enhance soil NH<inline-formula><mml:math id="M163" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>
pools. Finally, given that GEM-MACH is used for real-time air quality
forecasts at ECCC, it is not desirable for our bidirectional flux scheme to
have to rely in advance on another model's output. Therefore, we use this
simplified version, and assess whether its results provide an improvement
(smaller biases and better correlations to measurements) to simulated NH<inline-formula><mml:math id="M164" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>.</p>
</sec>
<sec id="Ch1.S2.SS3">
  <title>Addition of forest fire emissions</title>
      <p id="d1e2460">Our third model scenario (called “fire <inline-formula><mml:math id="M165" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi” hereafter) uses the
GEM-MACH-Bidi model, and the exact same area emissions and anthropogenic
major point emissions as the base and bidi scenarios. However, in addition,
we add hourly North American forest fire emissions for all species to the
major point emissions. The forest fire emissions system for GEM-MACH (called
“FireWork is described in detail in <xref ref-type="bibr" rid="bib1.bibx71" id="text.60"/>. Briefly, to
calculate the fire emissions for input to FireWork, biomass burning areas are
first identified in near-real-time by the Canadian Wildland Fire Information
System (CWFIS), which is operated by the Canadian Forest Service
(<uri>http://cwfis.cfs.nrcan.gc.ca/home</uri>). CWFIS uses fire hotspots detected
by NASA's Moderate Resolution Imaging Spectroradiometer (MODIS) and
NOAA's Advanced Very High Resolution Radiometer and Visible Infrared
Imaging Radiometer Suite imagery as inputs. Daily total emissions per hotspot
are then estimated by the Fire Emission Production Simulator module of the
BlueSky modelling framework <xref ref-type="bibr" rid="bib1.bibx47" id="paren.61"/>. SMOKE was then used to prepare
model-ready hourly emissions of several species (including NH<inline-formula><mml:math id="M166" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>) in a
point-source format for model input.</p>
      <p id="d1e2488">In ECCC's operational forest fire forecasts, these emissions are used at
10 km resolution for the domain encompassing North America, with forest fires
being treated as point sources with specific plume rise <xref ref-type="bibr" rid="bib1.bibx71" id="paren.62"/>.
We have added 2013 forest fire emissions which were originally created for
the 2013 FireWork forecasts to the anthropogenic point-source emissions used
in the base case simulation, and have modified the GEM-MACH model to be able
to accommodate the changing number of major point sources each day (as the
number of fires changes daily). Fire plume rise is an ongoing area of
investigation (e.g., <xref ref-type="bibr" rid="bib1.bibx37" id="author.63"/>, <xref ref-type="bibr" rid="bib1.bibx37" id="year.64"/>;
<xref ref-type="bibr" rid="bib1.bibx69" id="author.65"/>, <xref ref-type="bibr" rid="bib1.bibx69" id="year.66"/>); smoldering emissions tend to be
emitted directly at the surface, whereas flaming emissions can inject plumes
to the upper troposphere. Here, we have set all fire emissions to be
distributed evenly throughout the boundary layer, which is a simplification
but one that averages out smouldering and flaming plume heights. Different
parameterizations of fire plume rise are currently under development in
GEM-MACH. The FireWork fire emissions are described in detail in
<xref ref-type="bibr" rid="bib1.bibx98" id="text.67"/>, and this study represents the first time they have been used
at a 2.5 km horizontal resolution.</p>
</sec>
<sec id="Ch1.S2.SS4">
  <title>Model setup for three scenarios</title>
      <p id="d1e2516">The base, bidi, and fire <inline-formula><mml:math id="M167" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi models were all run in the
following way: each scenario was run from 1 August to 7 September 2013,
where the first 11 days were “spin up” in order to allow chemical
concentrations to stabilize, and are not used in our evaluation. This is a
sufficient amount of spinup time, given that the atmospheric lifetime of
NH<inline-formula><mml:math id="M168" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> is typically up to 1 day <xref ref-type="bibr" rid="bib1.bibx78 bib1.bibx1" id="paren.68"/>, and given that it
is close to the transport time of air crossing the larger North American
domain. The time period from 12 August to 7 September was chosen to coincide
with the intensive measurement campaign described in Sect. <xref ref-type="sec" rid="Ch1.S3"/>.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2" specific-use="star"><caption><p id="d1e2542">Map of 10 km resolution continental piloting model domain
(green) and 2.5 km resolution nested model domain (purple).</p></caption>
          <?xmltex \igopts{width=312.980315pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f02.png"/>

        </fig>

      <?pagebreak page2016?><p id="d1e2551">The model was run in a nested setup, whereby the North American domain was
run at 10 km resolution using “climatological” chemical initial and boundary
conditions from a 1-year MOZART simulation for all pollutants
<xref ref-type="bibr" rid="bib1.bibx33" id="paren.69"/>. The nested oil sands region (which covers most of Alberta
and Saskatchewan) was run at 2.5 km horizontal resolution, using the initial
and boundary conditions from the 10 km North American model run. Figure <xref ref-type="fig" rid="Ch1.F2"/> shows the two model domains.</p>
      <p id="d1e2559">The model simulations for the pilot and nested domains were not run as a
continuous multi-day forecast but rather following the operational air
quality forecast process, where the meteorological values are updated
regularly with new analyses (products of meteorological data assimilation
which provide optimized initial conditions for the 12 UTC hour of each day).
The analyses were obtained from ECCC archives
(<xref ref-type="bibr" rid="bib1.bibx12 bib1.bibx13 bib1.bibx16" id="altparen.70"/>), in order to prevent chaotic drift of
the model meteorology from observations. Consequently, our simulation setup
comprises simulations on the North American domain in 30 h cycles starting
at 12:00 UTC, and the oil sands domain in 24 h cycles starting at 18:00 UTC (the
6 h lag being required to allow meteorological spinup of the lower
resolution model). The next cycle uses the chemical mass mixing ratios from
the end of the last cycle as initial conditions for the next 24–30 h.
This system of staggered meteorological driving forecasts with a continuous
chemical record continues until the full time period completes.</p>
      <p id="d1e2566">We run GEM-MACH in the 2-bin particle mode, which means that particles fall
in either fine mode (diameter 0–2.5 <inline-formula><mml:math id="M169" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m) or coarse mode (diameter 2.5–10 <inline-formula><mml:math id="M170" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m), for computational
efficiency (although sub-binning is used in some
particle microphysics processes in order to ensure an accurate representation
of particle microphysics; <xref ref-type="bibr" rid="bib1.bibx61" id="altparen.71"/>), and in order to follow the setup
used for the operational 10 km resolution GEM-MACH forecast.</p>
</sec>
</sec>
<sec id="Ch1.S3">
  <title>Measurements</title>
      <p id="d1e2593">Our three model simulations (base, bidi, and fire <inline-formula><mml:math id="M171" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi) are evaluated with
surface, aircraft, and Cross-track Infrared Sounder (CrIS) satellite
measurements. We briefly describe each of these observation datasets below.</p>
<sec id="Ch1.S3.SS1">
  <title>AMS13 ground measurements</title>
      <p id="d1e2608">An extensive suite of instrumentation was deployed at monitoring site AMS13
(57.1492<inline-formula><mml:math id="M172" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N, 111.6422<inline-formula><mml:math id="M173" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> W; 270 m a.s.l.; Fig. <xref ref-type="fig" rid="Ch1.F3"/>) from 7 August 2013 until 12 September 2013. Mining
operations and bitumen upgrading facilities are 5 km to the south and
north of the site, which is surrounded by boreal forest with dominant winds
from the west averaging 1.9 m s<inline-formula><mml:math id="M174" 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> throughout the year. The average
temperatures in the region for August are highs between 20–25 <inline-formula><mml:math id="M175" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C
and lows around 10 <inline-formula><mml:math id="M176" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, which is warm enough to make upward NH<inline-formula><mml:math id="M177" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>
flux more likely (recall Fig. <xref ref-type="fig" rid="Ch1.F1"/>). However, temperatures drop rapidly
at the end of August, into September, where the September highs average
around 15 <inline-formula><mml:math id="M178" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C and lows around 5 <inline-formula><mml:math id="M179" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C. The skies are the clearest
during August, with at least partly clear skies 50 % of the time. That
said, the warm season (May through September) is the wetter season (average
of 20 % chance of precipitation daily), with more precipitation than during
the cold season (when there is an average of 7 % chance of precipitation
daily). However, year-round precipitation, as well as relative humidity, are both
relatively low in the AOSR. During the cold season (November through
February), the average temperatures range from <inline-formula><mml:math id="M180" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>21 to
<inline-formula><mml:math id="M181" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>5 <inline-formula><mml:math id="M182" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, when the forest and soils are more likely to be a deposition
sink for NH<inline-formula><mml:math id="M183" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>. During November to April, it is also much cloudier, with
February having cloudy conditions 77 % of the time. (All weather data cited
here are from the annual<?pagebreak page2017?> report at Fort McMurray:
<uri>https://weatherspark.com/y/2795/Average-Weather-in-Fort-McMurray-Canada-Year-Round</uri>).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3"><caption><p id="d1e2729">Flight path on 13 August 2013, where elevation (in metres) is
denoted by the colour scale and the AMS13 site is indicated by a black circle.</p></caption>
          <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f03.pdf"/>

        </fig>

      <p id="d1e2738">NH<inline-formula><mml:math id="M184" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>, fine particulate ammonium and nitrate, and other species were
measured by an ambient ion monitor ion chromatograph via an inlet
4.55 m off the ground. The uncertainty of these measurements is <inline-formula><mml:math id="M185" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>15 %.
These measurements are described in more detail in <xref ref-type="bibr" rid="bib1.bibx56" id="text.72"/>.</p>
      <p id="d1e2760">Data gaps sometimes appeared in the surface NH<inline-formula><mml:math id="M186" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> time series for the
following reasons: instrument zero (14–15 and 17–18 August), instrument
maintenance (19 August), and a power outage (27–28 August).</p>
</sec>
<sec id="Ch1.S3.SS2">
  <title>Aircraft measurements</title>
      <p id="d1e2778">During the oil sands monitoring intensive campaign, there were a total of 22
flights spanning 13 August to 7 September 2013. These measurements are
described in detail in <xref ref-type="bibr" rid="bib1.bibx81 bib1.bibx35 bib1.bibx50" id="text.73"/>; and <xref ref-type="bibr" rid="bib1.bibx49" id="text.74"/>, and are
summarized here. Aircraft NH<inline-formula><mml:math id="M187" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> measurements were conducted with a dual
quantum cascade laser (QCL) trace gas monitor (Aerodyne Inc., Billerica, MA,
USA; McManus et al., 2008), collecting data every 1 s. Outside air was
sampled through a heated Teflon inlet tube shared with a high-resolution
time-of-flight chemical ionization mass spectrometer (HR-ToF-CIMS); the flow
rate through the QCL was 10.8 L min<inline-formula><mml:math id="M188" 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 1<inline-formula><mml:math id="M189" display="inline"><mml:mi mathvariant="italic">σ</mml:mi></mml:math></inline-formula> uncertainty for
each measurement was estimated to be <inline-formula><mml:math id="M190" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>0.3 ppbv (<inline-formula><mml:math id="M191" display="inline"><mml:mo lspace="0mm">±</mml:mo></mml:math></inline-formula>35 %;
<xref ref-type="bibr" rid="bib1.bibx81" id="altparen.75"/>).</p>
      <p id="d1e2833">Particulate NH<inline-formula><mml:math id="M192" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> (0 to <inline-formula><mml:math id="M193" display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula>1 <inline-formula><mml:math id="M194" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m in diameter) was measured by the
Aerodyne high-resolution time-of-flight aerosol mass spectrometer
(HR-ToF-AMS) instrument on board the same flights, which collected data every
10 s. The ambient air was drawn through a forward-facing shrouded isokinetic
particle inlet from which the HR-ToF-AMS sub-sampled. The total residence
time in the inlet and associated tubing was approximately 1 s. The error
on these measurements is <inline-formula><mml:math id="M195" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>9 %. <xref ref-type="bibr" rid="bib1.bibx50" id="paren.76"/></p>
      <p id="d1e2871">Figure <xref ref-type="fig" rid="Ch1.F3"/> shows a sample flight path from the campaign from
13 August 2013 – one of the 13 flights with valid NH<inline-formula><mml:math id="M196" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> measurements.
The others took place on 15–17, 19 (two this day), 22–24, 26, 28 August, and
5–6 September 2013. NH<inline-formula><mml:math id="M197" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> data on the other nine flights were invalidated
due to instrument issues (those on 14, 20–21, 29, 31 August, and 2–4
September 2013), but were successful for the NH<inline-formula><mml:math id="M198" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> measurements.</p>
</sec>
<sec id="Ch1.S3.SS3">
  <title>CrIS satellite measurements</title>
      <p id="d1e2912">CrIS was launched in late October 2011 on board the Suomi NPP platform. CrIS
follows a sun-synchronous orbit with a daytime overpass time at 13:30 LT
(local time, ascending) and a night time equator overpass at 01:30 LT (descending). The instrument scans along a 2200 km swath using a 3 <inline-formula><mml:math id="M199" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 3 array of
circular pixels with a diameter of 14 km at nadir for each pixel. The CrIS
“fast physical retrieval” described by <xref ref-type="bibr" rid="bib1.bibx79" id="text.77"/> is used to
perform satellite profile retrievals of NH<inline-formula><mml:math id="M200" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMR given the infrared
emission spectrum from the atmosphere. This retrieval uses an optimal
estimation approach <xref ref-type="bibr" rid="bib1.bibx76" id="paren.78"/> that provides the satellite vertical
sensitivity (averaging kernels) and an estimate of the total errors (error
covariance matrix).</p>
      <p id="d1e2937">We take the CrIS retrieved profile and match it up with the closest model
profile in both distance and time, compute the distance between the CrIS
pixel and model field for each time step, and then select the time step that
best matches the satellite overpass time. Since the model time steps are
every hour with a 10 km spatial resolution they are always matched up to
better than half an hour, and within 5 km.</p>
</sec>
</sec>
<sec id="Ch1.S4">
  <title>Model evaluation</title>
      <p id="d1e2948">An older version of GEM-MACH (v1.5.1) has been compared to TES satellite and
aircraft measurements of ammonia over the AOSR <xref ref-type="bibr" rid="bib1.bibx81" id="paren.79"/>.
Simulations with that version of the model were shown to be biased low, by
about <inline-formula><mml:math id="M201" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.5 ppbv throughout the lower-tropospheric vertical profile. This
represented a substantial deficit in the model predicted sources of NH<inline-formula><mml:math id="M202" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>,
prompting the current work. We now compare our three GEM-MACHv2 simulations
(base, bidi, and fire <inline-formula><mml:math id="M203" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi) against surface point measurements at the
measurement site near an oil sands facility (AMS13), aircraft measurements
over the broader AOSR, and satellite measurements over the Alberta and
Saskatchewan area. We will discuss which simulation agrees best with
measurements and where there may still be room for additional model
improvement.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4" specific-use="star"><caption><p id="d1e2979">Surface daily average VMR of <bold>(a)</bold> NH<inline-formula><mml:math id="M204" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>, and concentrations of
<bold>(b)</bold> fine particulate NH<inline-formula><mml:math id="M205" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, <bold>(c)</bold> NO<inline-formula><mml:math id="M206" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, and <bold>(d)</bold> SO<inline-formula><mml:math id="M207" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> at the AMS13 ground
site in the AOSR. Measurements (Meas) in orange, base model in green, bidirectional flux model (Bidi) in blue, and fire <inline-formula><mml:math id="M208" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model (Fire) in red.</p></caption>
        <?xmltex \igopts{width=369.885827pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f04.pdf"/>

      </fig>

<?pagebreak page2018?><sec id="Ch1.S4.SS1">
  <title>At the AMS13 ground site</title>
      <p id="d1e3061">Figure <xref ref-type="fig" rid="Ch1.F4"/> shows the time series of the daily average (for
clarity) VMRs of NH<inline-formula><mml:math id="M209" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> and concentrations of fine-particulate NH<inline-formula><mml:math id="M210" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>,
NO<inline-formula><mml:math id="M211" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, and SO<inline-formula><mml:math id="M212" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> at the AMS13 oil sands ground site for the
observations and three model simulations. The hourly data were also studied,
but are not shown in the time series.</p>
      <p id="d1e3114">We first note that the NH<inline-formula><mml:math id="M213" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs in the measured time series are relatively
low with mean, median, and maximum of 0.6, 0.426, and 2.98 ppbv,
respectively, in the hourly data, which are lower than the 1–8 ppbv range in
<xref ref-type="bibr" rid="bib1.bibx14" id="text.80"/> and the 2.7 ppbv summertime mean given in
<xref ref-type="bibr" rid="bib1.bibx38" id="text.81"/>. However, this may be due to the different time periods and
locations measured. Our mean measured values at the AMS13 site are similar to
the VMRs found at U.S. AMoN background sites
(<uri>http://nadp.sws.uiuc.edu/amon/</uri>).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5" specific-use="star"><caption><p id="d1e3137">Hourly model–measurement bias in surface <bold>(a)</bold> NH<inline-formula><mml:math id="M214" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMR, and
<bold>(b)</bold> NH<inline-formula><mml:math id="M215" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, <bold>(c)</bold> NO<inline-formula><mml:math id="M216" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, and <bold>(d)</bold> SO<inline-formula><mml:math id="M217" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> concentrations at the AMS13 ground site in the AOSR.</p></caption>
          <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f05.pdf"/>

        </fig>

      <p id="d1e3207">Figure <xref ref-type="fig" rid="Ch1.F4"/>a shows that the base model (green) background VMRs
of NH<inline-formula><mml:math id="M218" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> are very low (nearly 0 ppbv when there is no plume influence)
compared to the measurements (orange). Only during the spike on 3–4 September
does the base model exceed the measured values, probably indicating a
local plume event fumigating to a lesser extent in the observations than was
predicted by the model. The NH<inline-formula><mml:math id="M219" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs of the base case are biased low
compared to the surface measurements by a median of <inline-formula><mml:math id="M220" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.35 ppbv (Fig. <xref ref-type="fig" rid="Ch1.F5"/>a) over the time period of the campaign.
In Fig. <xref ref-type="fig" rid="Ch1.F4"/>, the bidi model (blue line) and fire <inline-formula><mml:math id="M221" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model (red line)
show a significant improvement to the NH<inline-formula><mml:math id="M222" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs compared to the base model
(green line). Unfortunately, during some time periods, these two versions of
the model overestimate NH<inline-formula><mml:math id="M223" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>: during 13 August, the model adds a
significant level of NH<inline-formula><mml:math id="M224" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> due to fire emissions; however, the surface
in situ observations show no evidence of fire impact. During other
time periods (e.g., 30 August to 3 September, and 4–7 September), the bidi
model appears to have put too much NH<inline-formula><mml:math id="M225" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> into the system. Therefore, the
bidi model bias (Fig. <xref ref-type="fig" rid="Ch1.F5"/>a) is now 0.30 ppbv too high
(median), and the fire <inline-formula><mml:math id="M226" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi bias is 0.32 ppbv high (median) over the time
period of the campaign, resulting in an overall improvement of only 0.03 ppbv
in the model bias.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6" specific-use="star"><caption><p id="d1e3298">Hourly modelled vs. measured surface <bold>(a)</bold> NH<inline-formula><mml:math id="M227" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMR, and
<bold>(b)</bold> NH<inline-formula><mml:math id="M228" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, <bold>(c)</bold> NO<inline-formula><mml:math id="M229" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, and <bold>(d)</bold> SO<inline-formula><mml:math id="M230" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> concentrations at the AMS13 ground
site in the AOSR. Base model is in grey, bidirectional flux model in blue, and fire <inline-formula><mml:math id="M231" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model in red.</p></caption>
          <?xmltex \igopts{width=341.433071pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f06.pdf"/>

        </fig>

      <p id="d1e3375">While the bias improvement is small, the bidi and fire <inline-formula><mml:math id="M232" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi both have greatly
improved correlation coefficients (from <inline-formula><mml:math id="M233" display="inline"><mml:mrow><mml:mi>R</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">0.1</mml:mn></mml:mrow></mml:math></inline-formula> to 0.4) and slopes much closer
to 1 (from 0.1 to 0.7), showing that those added sources are important to
improve model results (Fig. <xref ref-type="fig" rid="Ch1.F6"/>a). Additionally, the
diurnal cycle (not shown) was improved in the bidi simulation, with both it
and the measurements shaped like a sine curve with a minimum at
03:00–04:00 LT, and a maximum at noon local time, although the amplitude of the
cycle was underestimated. Whereas, the base model diurnal cycle was flat from
midnight to noon local time, and spiky from noon to midnight.</p>
      <p id="d1e3399">While Figs. <xref ref-type="fig" rid="Ch1.F4"/>a to <xref ref-type="fig" rid="Ch1.F6"/>a show that the
addition of bidirectional flux improves the model correlation coefficient,
slope, and bias, there is still room for further improvement. Paired <inline-formula><mml:math id="M234" display="inline"><mml:mi>t</mml:mi></mml:math></inline-formula>-test
results indicate that the fire <inline-formula><mml:math id="M235" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi and measurements are still significantly
different (see Table <xref ref-type="table" rid="Ch1.T2"/> for comparison statistics of
all three simulations). While inherent limitations from<?pagebreak page2019?> model resolution and
uncertainties may be responsible for the remaining bias, it is likely that
(a) the emission potentials for the LUCs in the region
may be causing too much re-emission of NH<inline-formula><mml:math id="M236" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>, and need refinement, and (b)
the fire emissions of NH<inline-formula><mml:math id="M237" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> are not properly distributed in the vertical,
placing too much NH<inline-formula><mml:math id="M238" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> near the surface and/or the fire emission factors for
NH<inline-formula><mml:math id="M239" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> are too high.</p>
      <p id="d1e3459">Refinement needed for the emission potentials and LUCs may be a significant
cause of the bidi and fire <inline-formula><mml:math id="M240" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model biases. <xref ref-type="bibr" rid="bib1.bibx77" id="text.82"/> have shown
that about 64 % of the AOSR are wetlands (fens, bogs, and marshes), which
should be mapped to the swamp LUC. However, our model currently assigns the
AOSR landscape to evergreen needleleaf trees, deciduous broadleaf trees,
inland lake, mixed shrubs, and mixed forests (and none of the region to
swamp). This would lead to an overestimation of re-emission given that bogs
are fairly acidic and our swamp emission potential is lower than the
aforementioned LUCs. Other evidence for these two explanations will be
presented below in Sect. <xref ref-type="sec" rid="Ch1.S4.SS3"/>.</p>
      <p id="d1e3474">For NH<inline-formula><mml:math id="M241" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>,  NO<inline-formula><mml:math id="M242" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> and SO<inline-formula><mml:math id="M243" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> the time series, model biases, and model-vs.-measured correlations are shown in
Figs. <xref ref-type="fig" rid="Ch1.F4"/>, <xref ref-type="fig" rid="Ch1.F5"/>, and <xref ref-type="fig" rid="Ch1.F6"/>,
respectively. There is very little change in NH<inline-formula><mml:math id="M244" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> (Figs. <xref ref-type="fig" rid="Ch1.F4"/>b, <xref ref-type="fig" rid="Ch1.F5"/>b,
and <xref ref-type="fig" rid="Ch1.F6"/>b) and SO<inline-formula><mml:math id="M245" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> (Figs. <xref ref-type="fig" rid="Ch1.F4"/>d, <xref ref-type="fig" rid="Ch1.F5"/>d, and <xref ref-type="fig" rid="Ch1.F6"/>d) despite the increase in NH<inline-formula><mml:math id="M246" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> that
the bidirectional flux yields. The bias is very small for all three model
scenarios, and the correlation coefficients are all relatively poor. So while
there is an improvement to modelled NH<inline-formula><mml:math id="M247" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> with bidirectional flux, there is
a neutral affect on fine particulate NH<inline-formula><mml:math id="M248" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>. This may be because the charge
of NH<inline-formula><mml:math id="M249" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> in the particles is already enough in the base model to balance
the charge of 2 <inline-formula><mml:math id="M250" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> SO<inline-formula><mml:math id="M251" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup><mml:mo>+</mml:mo></mml:mrow></mml:math></inline-formula> NO<inline-formula><mml:math id="M252" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> in the aerosols, thus causing
any additional NH<inline-formula><mml:math id="M253" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> (from bidi and<?pagebreak page2020?> fires) to remain in the gas phase.
Alternatively, the minimal change in NH<inline-formula><mml:math id="M254" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> could be due to additional wet
scavenging of the additional NH<inline-formula><mml:math id="M255" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>, which will be discussed in Sect. <xref ref-type="sec" rid="Ch1.S5.SS2"/>.
The change in NH<inline-formula><mml:math id="M256" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMR has no effect on SO<inline-formula><mml:math id="M257" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula>
since particulate SO<inline-formula><mml:math id="M258" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> is not sensitive to the amount of
NH<inline-formula><mml:math id="M259" display="inline"><mml:mrow><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub><mml:mo>/</mml:mo></mml:mrow></mml:math></inline-formula>NH<inline-formula><mml:math id="M260" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> available, and is dominated by anthropogenic and fire
emissions. For NO<inline-formula><mml:math id="M261" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> (Fig. <xref ref-type="fig" rid="Ch1.F5"/>c), the base model bias was quite small at 0.01 <inline-formula><mml:math id="M262" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g m<inline-formula><mml:math id="M263" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>; however, the addition of bidi and fire <inline-formula><mml:math id="M264" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi further reduced that
bias to 0.0011 and 0.0004 <inline-formula><mml:math id="M265" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g m<inline-formula><mml:math id="M266" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, respectively, which is a significant
improvement. The correlation coefficient for NO<inline-formula><mml:math id="M267" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> also improved from
about 0.1 to 0.3 (Fig. <xref ref-type="fig" rid="Ch1.F6"/>c).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F7" specific-use="star"><caption><p id="d1e3816">NH<inline-formula><mml:math id="M268" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs aloft (colour scale) over the oil sands region during the 13 August 2013
flight. <bold>(a)</bold> Measurements, <bold>(b)</bold> base model, <bold>(c)</bold> fire <inline-formula><mml:math id="M269" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model, and <bold>(d)</bold> bidi model.</p></caption>
          <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f07.png"/>

        </fig>

</sec>
<sec id="Ch1.S4.SS2">
  <title>Along the oil sands campaign flight paths</title>
      <p id="d1e3860">There were 13 flights during the oil sands campaign that had
valid (above detection limit, and no instrument error) NH<inline-formula><mml:math id="M270" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> measurements,
and 22 flights that had valid NH<inline-formula><mml:math id="M271" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> (0–1 <inline-formula><mml:math id="M272" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>m diameter) measurements.
The flight path of the first flight, which occurred on 13 August 2013, is
shown in Fig. <xref ref-type="fig" rid="Ch1.F3"/>; chosen as an example because this flight
sampled mainly background NH<inline-formula><mml:math id="M273" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> (rather than facility plumes).</p>
      <p id="d1e3902">Figure <xref ref-type="fig" rid="Ch1.F7"/> shows the NH<inline-formula><mml:math id="M274" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs along this flight path over
time. Here the hourly model output is interpolated to the same time frequency
as the measurements. The model output also has spatial resolution limits when
comparing to the aircraft. However, we clearly see that for this flight, the
bidirectional flux has increased NH<inline-formula><mml:math id="M275" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs, bringing them closer to the
measured values (median biases for this flight are <inline-formula><mml:math id="M276" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>1.38, 0.68, and 0.69 ppbv
in the base, bidi, and fire <inline-formula><mml:math id="M277" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi simulations, respectively). There is little change when
fires are added (Fig. <xref ref-type="fig" rid="Ch1.F7"/>d vs. c) because this flight did not
pass through a fire plume.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F8" specific-use="star"><caption><p id="d1e3944">Hourly averages along all flight paths over the oil sands region during the summer 2013
campaign: model–measurement bias in <bold>(a)</bold> NH<inline-formula><mml:math id="M278" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> and <bold>(b)</bold> NH<inline-formula><mml:math id="M279" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>. Modelled vs. measured
<bold>(c)</bold> NH<inline-formula><mml:math id="M280" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMR and <bold>(d)</bold> NH<inline-formula><mml:math id="M281" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> concentrations aloft. Base model is in grey, bidirectional
flux model in blue, and fire <inline-formula><mml:math id="M282" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model in red.</p></caption>
          <?xmltex \igopts{width=369.885827pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f08.pdf"/>

        </fig>

      <p id="d1e4015">Figure <xref ref-type="fig" rid="Ch1.F8"/> shows the model–measurement differences and
the model vs. measurement scatter plots for the combined set of all flight
paths for hourly average NH<inline-formula><mml:math id="M283" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> and NH<inline-formula><mml:math id="M284" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>. For NH<inline-formula><mml:math id="M285" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> the median base
model bias is <inline-formula><mml:math id="M286" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.75 ppbv, comparable to the bias observed in
<xref ref-type="bibr" rid="bib1.bibx81" id="author.83"/>, <xref ref-type="bibr" rid="bib1.bibx81" id="year.84"/>, with the bidi model bias
improving to <inline-formula><mml:math id="M287" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.24 ppbv and the fire <inline-formula><mml:math id="M288" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi bias improving to <inline-formula><mml:math id="M289" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.23 ppbv. Also, the best
correlation coefficient and slope is achieved by the fire <inline-formula><mml:math id="M290" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi scenario. The
use of the bidirectional flux has thus reduced the model bias relative to the
aircraft observations by a factor of 3. The fire <inline-formula><mml:math id="M291" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi simulation has the
best statistics compared to measurements, as summarized in Table <xref ref-type="table" rid="Ch1.T2"/>.</p>
      <p id="d1e4103">Again, the NH<inline-formula><mml:math id="M292" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> results show little change despite the increase in
NH<inline-formula><mml:math id="M293" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>. The small bias from the base case gets insignificantly smaller, and
the slope and correlation coefficients are all negligibly changed.</p>
</sec>
<sec id="Ch1.S4.SS3">
  <title>In the vertical profiles across the region</title>
      <p id="d1e4134">The CrIS satellite has many observations over North America during the 2013
oil sands campaign. We have evaluated the model with these observations in two ways:
<list list-type="order"><list-item>
      <p id="d1e4139">All daytime data from 12 August–7 September  2013, with model–measurement comparisons
over a large region encompassing Alberta and Saskatchewan
(latitude range: 48–60<inline-formula><mml:math id="M294" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N, longitude range: 100–122<inline-formula><mml:math id="M295" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> W), which contains agricultural areas, a number of cities, the northern
boreal forest, and oil sand facilities.</p></list-item><list-item>
      <p id="d1e4161">Case studies where we attempt to isolate fire emissions and non-fire conditions to evaluate both new components (fires and bidi) of the model.</p></list-item></list>
The latitude and longitude ranges of our model–measurement pairs are given in
Table <xref ref-type="table" rid="Ch1.T1"/>. The satellite passes over these regions at
approximately 13:00 LT and 01:00 LT.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1" specific-use="star"><caption><p id="d1e4170">Latitude and longitude ranges that the model was evaluated over with the CrIS satellite measurements.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="4">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">Domain</oasis:entry>
         <oasis:entry colname="col2">Date (in 2013)</oasis:entry>
         <oasis:entry colname="col3">Lat. range</oasis:entry>
         <oasis:entry colname="col4">Long. range</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">Alberta and Saskatchewan large domain</oasis:entry>
         <oasis:entry colname="col2">12 Aug to 7 Sep</oasis:entry>
         <oasis:entry colname="col3">48 to 60<inline-formula><mml:math id="M296" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M297" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>122.0 to <inline-formula><mml:math id="M298" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>100.0<inline-formula><mml:math id="M299" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> W</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Northern, no-fire case study</oasis:entry>
         <oasis:entry colname="col2">03 Sep</oasis:entry>
         <oasis:entry colname="col3">55 to 60<inline-formula><mml:math id="M300" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M301" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>120.0 to <inline-formula><mml:math id="M302" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>110.0<inline-formula><mml:math id="M303" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> W</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Southern, no-fire case study</oasis:entry>
         <oasis:entry colname="col2">01 Sep</oasis:entry>
         <oasis:entry colname="col3">49 to 53.5<inline-formula><mml:math id="M304" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M305" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>117.0 to <inline-formula><mml:math id="M306" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>106.0<inline-formula><mml:math id="M307" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> W</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Northern, fire case study</oasis:entry>
         <oasis:entry colname="col2">12 Aug</oasis:entry>
         <oasis:entry colname="col3">56.5 to 60<inline-formula><mml:math id="M308" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M309" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>110.0 to <inline-formula><mml:math id="M310" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>104.4<inline-formula><mml:math id="M311" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> W</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <?xmltex \floatpos{t}?><fig id="Ch1.F9" specific-use="star"><caption><p id="d1e4394"><bold>(a)</bold> (i) NH<inline-formula><mml:math id="M312" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> vertical profiles as measured by CrIS satellite from
12 August to 7 September 2013; difference between measurement and (ii) base model, (iii) bidi model, and
(iv) fire <inline-formula><mml:math id="M313" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model; and (v) averaging kernel (labelled AK) of CrIS satellite for NH<inline-formula><mml:math id="M314" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> retrieval. <bold>(b)</bold> Average
(12 August–7 September 2013) surface NH<inline-formula><mml:math id="M315" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs given by the (i) base model, (ii) fire <inline-formula><mml:math id="M316" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model, and (iii) CrIS satellite.</p></caption>
          <?xmltex \igopts{width=426.791339pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f09.jpg"/>

        </fig>

      <p id="d1e4451">There were over 60 000 model–measurement pairs between the model and the CrIS
satellite over the model domain during 12 August  to 7 September  2013.
Figure <xref ref-type="fig" rid="Ch1.F9"/>a presents model biases for the entire dataset
in a box and whiskers plot of the vertical NH<inline-formula><mml:math id="M317" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> profiles at five vertical
levels. The left-most panel (panel i) shows the NH<inline-formula><mml:math id="M318" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs measured by CrIS, and
the right-most panel (v) shows the diagonal elements of the CrIS averaging
kernels, illustrating the sensitivity of the satellite measurements to each
vertical level. The NH<inline-formula><mml:math id="M319" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs over Alberta and Saskatchewan measured by
CrIS are very similar to those found by TES in the <xref ref-type="bibr" rid="bib1.bibx81" id="text.85"/> study
for the AOSR region.</p>
      <p id="d1e4486">The middle panels (Fig. <xref ref-type="fig" rid="Ch1.F9"/>a, ii–iv) show the model
biases from the three simulations. The base model has a very similar bias to
CrIS as the older version of GEM-MACH (v.1.5.1) had compared to TES
observations in the <xref ref-type="bibr" rid="bib1.bibx81" id="text.86"/> study – thus showing that the
negative NH<inline-formula><mml:math id="M320" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> biases were not improved with the use of the newer GEM-MACH
version (v2) itself. The fire <inline-formula><mml:math id="M321" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model has the smallest bias in the highest
three layers, but the bidi model has the smallest bias in the two lowest
layers. In those lower layers, the fire <inline-formula><mml:math id="M322" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model increases NH<inline-formula><mml:math id="M323" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs too
far (though still a smaller absolute bias compared to the base case; Fig. <xref ref-type="fig" rid="Ch1.F9"/>a). The fire <inline-formula><mml:math id="M324" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi positive bias could be due to an
overestimate of the bidirectional flux re-emissions or of the fire emissions,
or to an underestimate of the altitude of the fire emissions, or a
combination of all three factors. In order to distinguish between these
possibilities, two case studies were examined further in the next section.
The statistics from the model–CrIS comparison can be found in Table <xref ref-type="table" rid="Ch1.T2"/>. That summary shows that the fire <inline-formula><mml:math id="M325" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi simulation
performs better than the base and the bidi simulations.</p>
      <?pagebreak page2021?><p id="d1e4545">The spatial distribution of modelled NH<inline-formula><mml:math id="M326" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> can also be evaluated with CrIS
measurements, as shown in Fig. <xref ref-type="fig" rid="Ch1.F9"/>b. These are maps of
the average surface NH<inline-formula><mml:math id="M327" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> from the base model, the fire <inline-formula><mml:math id="M328" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model, and the
CrIS satellite. The fire <inline-formula><mml:math id="M329" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model over-predicts the effect of fires in the
middle of northern Saskatchewan, but appears to be missing fires in
north-western Manitoba. Other than fire influence, the spatial distribution
in the fire <inline-formula><mml:math id="M330" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model is the same as that of the base model, but with
significant increases in overall VMR. The spatial distribution of the model
simulations is different from the spatial distribution that CrIS measures.
For example, the model predicts much higher NH<inline-formula><mml:math id="M331" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> near the city of Edmonton
than CrIS shows. That said, the addition of bidirectional flux has greatly
improved the NH<inline-formula><mml:math id="M332" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> simulation in the northern part of the province, where it
was almost zero in the base model.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T2" specific-use="star"><caption><p id="d1e4611">Model–measurement NH<inline-formula><mml:math id="M333" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> comparison statistics from 12 August to 7 September 2013: <inline-formula><mml:math id="M334" display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula> is correlation coefficient; slope
is of the line-of-best-fit between model vs. measurement; <inline-formula><mml:math id="M335" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M336" display="inline"><mml:mi>t</mml:mi></mml:math></inline-formula> are from a paired <inline-formula><mml:math id="M337" display="inline"><mml:mi>t</mml:mi></mml:math></inline-formula> test between model and measurement data pairs
(<inline-formula><mml:math id="M338" display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mo>&gt;</mml:mo></mml:mrow></mml:math></inline-formula> 0.05 and <inline-formula><mml:math id="M339" display="inline"><mml:mrow><mml:mo>|</mml:mo><mml:mi>t</mml:mi><mml:mo>|</mml:mo><mml:mo>&lt;</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula> means that the model is statistically indistinguishable from measurements); the median model bias;
RMSE is the root mean square error; and FE is the fractional error of the models.
CrIS (troposphere) results are for the entire model domain at all tropospheric levels shown in Fig. <xref ref-type="fig" rid="Ch1.F9"/>(top),
and CrIS (surface) results are for the lowest retrieval level (both are during mid-day satellite overpass times); aircraft results
are from the 12 flight paths over the oil sand facilities, hourly averages during the daytime; and AMS13 results are from hourly
data (day and night) at the one ground station.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="8">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right"/>
     <oasis:colspec colnum="6" colname="col6" align="right"/>
     <oasis:colspec colnum="7" colname="col7" align="right"/>
     <oasis:colspec colnum="8" colname="col8" align="right"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2"><inline-formula><mml:math id="M340" display="inline"><mml:mi>R</mml:mi></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col3">Slope</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M341" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col5"><inline-formula><mml:math id="M342" display="inline"><mml:mi>t</mml:mi></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col6">Bias (ppbv)</oasis:entry>
         <oasis:entry colname="col7">RMSE (ppbv)</oasis:entry>
         <oasis:entry colname="col8">FE</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">CrIS (troposphere)</oasis:entry>
         <oasis:entry colname="col2"/>
         <oasis:entry colname="col3"/>
         <oasis:entry colname="col4"/>
         <oasis:entry colname="col5"/>
         <oasis:entry colname="col6"/>
         <oasis:entry colname="col7"/>
         <oasis:entry colname="col8"/>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">base</oasis:entry>
         <oasis:entry colname="col2">0.248</oasis:entry>
         <oasis:entry colname="col3">0.076</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M343" display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula>2E-16</oasis:entry>
         <oasis:entry colname="col5"><inline-formula><mml:math id="M344" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>247.5</oasis:entry>
         <oasis:entry colname="col6"><inline-formula><mml:math id="M345" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.430</oasis:entry>
         <oasis:entry colname="col7">2.02</oasis:entry>
         <oasis:entry colname="col8"><inline-formula><mml:math id="M346" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>5.3E-6</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">bidi</oasis:entry>
         <oasis:entry colname="col2">0.302</oasis:entry>
         <oasis:entry colname="col3">0.205</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M347" display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula>2E-16</oasis:entry>
         <oasis:entry colname="col5"><inline-formula><mml:math id="M348" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>77.4</oasis:entry>
         <oasis:entry colname="col6"><inline-formula><mml:math id="M349" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.176</oasis:entry>
         <oasis:entry colname="col7">1.93</oasis:entry>
         <oasis:entry colname="col8"><inline-formula><mml:math id="M350" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>1.2E-6</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">fire <inline-formula><mml:math id="M351" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi</oasis:entry>
         <oasis:entry colname="col2">0.338</oasis:entry>
         <oasis:entry colname="col3">0.425</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M352" display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula>2E-16</oasis:entry>
         <oasis:entry colname="col5">36.2</oasis:entry>
         <oasis:entry colname="col6"><inline-formula><mml:math id="M353" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.126</oasis:entry>
         <oasis:entry colname="col7">2.45</oasis:entry>
         <oasis:entry colname="col8">5.9E-7</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">CrIS (surface)</oasis:entry>
         <oasis:entry colname="col2"/>
         <oasis:entry colname="col3"/>
         <oasis:entry colname="col4"/>
         <oasis:entry colname="col5"/>
         <oasis:entry colname="col6"/>
         <oasis:entry colname="col7"/>
         <oasis:entry colname="col8"/>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">base</oasis:entry>
         <oasis:entry colname="col2">0.272</oasis:entry>
         <oasis:entry colname="col3">0.118</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M354" display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula>2E-16</oasis:entry>
         <oasis:entry colname="col5"><inline-formula><mml:math id="M355" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>19.0</oasis:entry>
         <oasis:entry colname="col6"><inline-formula><mml:math id="M356" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>1.11</oasis:entry>
         <oasis:entry colname="col7">5.72</oasis:entry>
         <oasis:entry colname="col8"><inline-formula><mml:math id="M357" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>1.6E-3</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">bidi</oasis:entry>
         <oasis:entry colname="col2">0.289</oasis:entry>
         <oasis:entry colname="col3">0.162</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M358" display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula>2E-16</oasis:entry>
         <oasis:entry colname="col5"><inline-formula><mml:math id="M359" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>12.8</oasis:entry>
         <oasis:entry colname="col6"><inline-formula><mml:math id="M360" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.66</oasis:entry>
         <oasis:entry colname="col7">5.32</oasis:entry>
         <oasis:entry colname="col8"><inline-formula><mml:math id="M361" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>8.9E-4</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">fire <inline-formula><mml:math id="M362" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi</oasis:entry>
         <oasis:entry colname="col2">0.566</oasis:entry>
         <oasis:entry colname="col3">1.195</oasis:entry>
         <oasis:entry colname="col4">1.4E-06</oasis:entry>
         <oasis:entry colname="col5">4.9</oasis:entry>
         <oasis:entry colname="col6"><inline-formula><mml:math id="M363" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.19</oasis:entry>
         <oasis:entry colname="col7">8.67</oasis:entry>
         <oasis:entry colname="col8">3.7E-4</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">Aircraft (hourly)</oasis:entry>
         <oasis:entry colname="col2"/>
         <oasis:entry colname="col3"/>
         <oasis:entry colname="col4"/>
         <oasis:entry colname="col5"/>
         <oasis:entry colname="col6"/>
         <oasis:entry colname="col7"/>
         <oasis:entry colname="col8"/>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">base</oasis:entry>
         <oasis:entry colname="col2">0.368</oasis:entry>
         <oasis:entry colname="col3">0.114</oasis:entry>
         <oasis:entry colname="col4">8.5E-14</oasis:entry>
         <oasis:entry colname="col5"><inline-formula><mml:math id="M364" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>10.3</oasis:entry>
         <oasis:entry colname="col6"><inline-formula><mml:math id="M365" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.751</oasis:entry>
         <oasis:entry colname="col7">1.14</oasis:entry>
         <oasis:entry colname="col8"><inline-formula><mml:math id="M366" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>2.5E-3</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">bidi</oasis:entry>
         <oasis:entry colname="col2">0.549</oasis:entry>
         <oasis:entry colname="col3">0.503</oasis:entry>
         <oasis:entry colname="col4">0.0026</oasis:entry>
         <oasis:entry colname="col5"><inline-formula><mml:math id="M367" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>3.2</oasis:entry>
         <oasis:entry colname="col6"><inline-formula><mml:math id="M368" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.244</oasis:entry>
         <oasis:entry colname="col7">0.69</oasis:entry>
         <oasis:entry colname="col8"><inline-formula><mml:math id="M369" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>5.0E-4</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">fire <inline-formula><mml:math id="M370" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi</oasis:entry>
         <oasis:entry colname="col2">0.560</oasis:entry>
         <oasis:entry colname="col3">0.519</oasis:entry>
         <oasis:entry colname="col4">0.0052</oasis:entry>
         <oasis:entry colname="col5"><inline-formula><mml:math id="M371" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>2.9</oasis:entry>
         <oasis:entry colname="col6"><inline-formula><mml:math id="M372" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.233</oasis:entry>
         <oasis:entry colname="col7">0.68</oasis:entry>
         <oasis:entry colname="col8"><inline-formula><mml:math id="M373" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>4.5E-4</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">AMS13 (hourly)</oasis:entry>
         <oasis:entry colname="col2"/>
         <oasis:entry colname="col3"/>
         <oasis:entry colname="col4"/>
         <oasis:entry colname="col5"/>
         <oasis:entry colname="col6"/>
         <oasis:entry colname="col7"/>
         <oasis:entry colname="col8"/>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">base</oasis:entry>
         <oasis:entry colname="col2">0.103</oasis:entry>
         <oasis:entry colname="col3">0.116</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M374" display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula>2E-16</oasis:entry>
         <oasis:entry colname="col5"><inline-formula><mml:math id="M375" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>12.4</oasis:entry>
         <oasis:entry colname="col6"><inline-formula><mml:math id="M376" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.35</oasis:entry>
         <oasis:entry colname="col7">0.92</oasis:entry>
         <oasis:entry colname="col8"><inline-formula><mml:math id="M377" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>1.6E-3</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">bidi</oasis:entry>
         <oasis:entry colname="col2">0.413</oasis:entry>
         <oasis:entry colname="col3">0.652</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M378" display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula>2E-16</oasis:entry>
         <oasis:entry colname="col5">12.1</oasis:entry>
         <oasis:entry colname="col6"><inline-formula><mml:math id="M379" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.30</oasis:entry>
         <oasis:entry colname="col7">0.95</oasis:entry>
         <oasis:entry colname="col8">8.0E-4</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">fire <inline-formula><mml:math id="M380" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi</oasis:entry>
         <oasis:entry colname="col2">0.403</oasis:entry>
         <oasis:entry colname="col3">0.691</oasis:entry>
         <oasis:entry colname="col4"><inline-formula><mml:math id="M381" display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula>2E-16</oasis:entry>
         <oasis:entry colname="col5">13.1</oasis:entry>
         <oasis:entry colname="col6">0.32</oasis:entry>
         <oasis:entry colname="col7">1.04</oasis:entry>
         <oasis:entry colname="col8">9.0E-4</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <?pagebreak page2022?><p id="d1e5410">We selected three sample days (12 August and 1 and 3 September 2013) that we
use for the case studies. The measured surface NH<inline-formula><mml:math id="M382" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> and sample Aqua MODIS
true colour composite maps for those days are shown (Fig. <xref ref-type="fig" rid="Ch1.F10"/>). The four boxed regions on those maps indicate where
model–measurement pairs were sampled for this study. The cyan and black boxes
(in Fig. <xref ref-type="fig" rid="Ch1.F10"/>a and b) are the regions where we sample
clear-sky and no-fire conditions on 3 and 1 September 2013, respectively. The magenta box
in Fig. <xref ref-type="fig" rid="Ch1.F10"/>c is the region where we isolated our fire case
study on 12 August 2013. The blue box is the region we discussed above, which
we analysed for the full time period simulated (12 August–7 September 2013; Fig. <xref ref-type="fig" rid="Ch1.F9"/>a).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F10" specific-use="star"><caption><p id="d1e5433">Images of the Alberta and Saskatchewan region with clouds and fire hotspots
from MODIS (upper panels). Maps of CrIS-measured surface NH<inline-formula><mml:math id="M383" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs, with coloured boxes
showing the regions where model and satellite measurements were sampled (lower panels). These three
examples are for <bold>(a)</bold> northern bidi case study (cyan), <bold>(b)</bold> southern bidi case study (black), and
<bold>(c)</bold> fire case study (magenta), discussed in Sect. <xref ref-type="sec" rid="Ch1.S4.SS3"/>, and the blue box is the region of our overall comparison.</p></caption>
          <?xmltex \igopts{width=455.244094pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f10.jpg"/>

        </fig>

<sec id="Ch1.S4.SS3.SSS1">
  <title>Case study 1: clear-sky days with little fire influence – evaluating bidi</title>
      <p id="d1e5467">In order to evaluate the bidirectional flux component separately from the
fire component, we selected 3 September  (northern, boreal forest and AOSR
region – cyan box in Fig. <xref ref-type="fig" rid="Ch1.F10"/>a) and 1 September (southern,
agricultural region – black box in Fig. <xref ref-type="fig" rid="Ch1.F10"/>b), where the
MODIS maps (EOSDIS NASA Worldview map; <uri>https://worldview.earthdata.nasa.gov/</uri>)
showed very little hotspots from fires and<?pagebreak page2023?> conditions that were relatively
cloud and smoke free, which yield the most CrIS observations (see Table <xref ref-type="table" rid="Ch1.T1"/> for the latitude and longitude ranges).
Figure <xref ref-type="fig" rid="Ch1.F10"/> also shows the surface NH<inline-formula><mml:math id="M384" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs as observed by CrIS on
each of those days. Figure <xref ref-type="fig" rid="Ch1.F11"/>a shows that in the
north, the bidi model improves the bias from <inline-formula><mml:math id="M385" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.84 to <inline-formula><mml:math id="M386" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.07 ppbv in the
lowest vertical level, and smaller, but still significant, improvements to
the bias at the other levels. The fire <inline-formula><mml:math id="M387" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model has a nearly identical
impact as the bidi model, which is expected in a fire-free zone. Therefore,
the GEM-MACH-Bidi model performs very well in northern Alberta and
Saskatchewan where there is mainly boreal forest, and background-level
NH<inline-formula><mml:math id="M388" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>. This also implies that the LUC assignment discussed in Sect. <xref ref-type="sec" rid="Ch1.S4.SS1"/> may only apply to a small region around the AOSR, and
not to the overall large region we have defined here.</p>

      <?xmltex \floatpos{p}?><fig id="Ch1.F11" specific-use="star"><caption><p id="d1e5528">As in Fig. <xref ref-type="fig" rid="Ch1.F9"/>a, but for our <bold>(a)</bold> northern “bidi-only” case study
(3 September 2013), <bold>(b)</bold> southern “bidi-only” case study (1 September 2013), and <bold>(c)</bold> northern
“fire-only”
case study (12 August 2013). These regions are shown in Fig. <xref ref-type="fig" rid="Ch1.F10"/>a (cyan),
<xref ref-type="fig" rid="Ch1.F10"/>b (black), and <xref ref-type="fig" rid="Ch1.F10"/>c (magenta) boxes, respectively.</p></caption>
            <?xmltex \igopts{width=355.659449pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f11.jpg"/>

          </fig>

      <p id="d1e5555">In the southern region (Fig. <xref ref-type="fig" rid="Ch1.F11"/>b), the addition of
bidirectional flux moves the bias from near-zero to <inline-formula><mml:math id="M389" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula>1.02 ppbv in the lowest
level. In this case, the base model with no bidirectional flux appears to be
the most accurate model in areas dominated by agricultural sources. There are
two possible explanations: (a) agricultural emissions are too high in the base
model, and the addition of the bidirectional flux leads to an overestimation
of the NH<inline-formula><mml:math id="M390" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> amounts or (b) re-emissions from bidirectional flux from crops
are not significant. The literature <xref ref-type="bibr" rid="bib1.bibx4 bib1.bibx57 bib1.bibx101 bib1.bibx103" id="paren.87"/>
indicates that crops do indeed re-emit NH<inline-formula><mml:math id="M391" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>, therefore (a) is the more
likely explanation. The agriculture NH<inline-formula><mml:math id="M392" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> emission inventory we used was
created by the NAESI (National Agri-Environmental Standards Initiative)
project <xref ref-type="bibr" rid="bib1.bibx9 bib1.bibx3 bib1.bibx52" id="paren.88"/> and has about 30–200 %
uncertainty associated with it <xref ref-type="bibr" rid="bib1.bibx11 bib1.bibx2" id="paren.89"/>. Therefore, with
improved national NH<inline-formula><mml:math id="M393" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> emission inventories, GEM-MACH-Bidi is likely to
improve model results across the domain.</p>
</sec>
<sec id="Ch1.S4.SS3.SSS2">
  <title>Case study 2: a clear-sky day with significant fire influence – evaluating fires</title>
      <?pagebreak page2024?><p id="d1e5619">In order to evaluate the fire component separately from the bidirectional
flux, we selected 12 August  (a northern region with little-to-no
agricultural contributions) where the MODIS map shows numerous hotspots from
fires and smokey conditions (Fig. <xref ref-type="fig" rid="Ch1.F10"/>c; magenta box). The
base and bidi models underestimate NH<inline-formula><mml:math id="M394" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs (Fig. <xref ref-type="fig" rid="Ch1.F11"/>c) by <inline-formula><mml:math id="M395" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>6.22 and <inline-formula><mml:math id="M396" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>5.84 ppbv, respectively (in the
lowest vertical layer), but the fire <inline-formula><mml:math id="M397" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model overestimates NH<inline-formula><mml:math id="M398" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> by <inline-formula><mml:math id="M399" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula>4.06 ppbv. The fire <inline-formula><mml:math id="M400" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi version of the model still
has the lowest bias of the
three simulations; however, either (a) the fire <inline-formula><mml:math id="M401" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model does not
distribute the fire emissions properly in the vertical, (b) the fire
emissions of NH<inline-formula><mml:math id="M402" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> are too high, or (c) the model's oxidation rate of
NO<inline-formula><mml:math id="M403" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> and SO<inline-formula><mml:math id="M404" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> in the fire may be underestimated, resulting in less
sulfate and nitrate to convert NH<inline-formula><mml:math id="M405" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> to NH<inline-formula><mml:math id="M406" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>. It is potentially a
combination of all three explanations, as both fire-plume rise and fire
emission factors are ongoing areas of study, and we further elaborate below.</p>
      <p id="d1e5736"><xref ref-type="bibr" rid="bib1.bibx82" id="text.90"/> suggest that fire plumes are Gaussian-distributed in a
thin layer aloft, which is not how our current fire-emissions module
distributes the fire plume. In our simulation, the fire emissions are
distributed evenly throughout the boundary layer (the first 3–4 layers in
Fig. <xref ref-type="fig" rid="Ch1.F11"/>c). However, we do not believe our
parameterization of plume distribution causes the fire <inline-formula><mml:math id="M407" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi bias since the
positive bias extends throughout the first three vertical layers and does not
go negative in any layer (Fig. <xref ref-type="fig" rid="Ch1.F11"/>c), as would be
expected if mass redistribution of the plume was the cause of the biases. We
also know that the plume heights for most of the Fort McMurray fires of 2016
reached only up to 3–4 km altitude range based on the NASA Cloud-Aerosol
Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) and Multi-angle
Imaging Spectroradiometer (MISR) satellite observations. Therefore, the fire
plumes are not located above the altitudes we studied.</p>
      <p id="d1e5752">Unfortunately, there were no flights that captured the fine structure of the
fire plumes during the 2013 monitoring intensive campaign that can be used to
further corroborate the vertical distribution of the fire plumes. There will, however,
be flight observations of fires during the planned 2018 AOSR
measurement campaign.</p>
      <?pagebreak page2026?><p id="d1e5755">Explanation (b) seems the most likely, as the uncertainty in emission factors
for NH<inline-formula><mml:math id="M408" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> from wildfires is very large (e.g., <inline-formula><mml:math id="M409" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>50–100 % depending on
the fuel type; <xref ref-type="bibr" rid="bib1.bibx87" id="author.91"/>, <xref ref-type="bibr" rid="bib1.bibx87" id="year.92"/>), and could
easily be overestimated. The NO<inline-formula><mml:math id="M410" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> and SO<inline-formula><mml:math id="M411" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> fire emission factors
have smaller uncertainties of <inline-formula><mml:math id="M412" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula>10–40 % <xref ref-type="bibr" rid="bib1.bibx87" id="paren.93"/>. Therefore,
the model may be further improved with reduced NH<inline-formula><mml:math id="M413" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> emission factors for
fires.</p>
</sec>
</sec>
</sec>
<sec id="Ch1.S5">
  <?xmltex \opttitle{Impacts of bidirectional flux and forest fires on NH${}_{3}$ VMRs}?><title>Impacts of bidirectional flux and forest fires on NH<inline-formula><mml:math id="M414" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs</title>
<sec id="Ch1.S5.SS1">
  <title>Effect on ambient ammonia</title>
      <p id="d1e5841">Given that the overall fire <inline-formula><mml:math id="M415" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model agrees best with measurements in the
greater Alberta/Saskatchewan region (discussed throughout Sect. <xref ref-type="sec" rid="Ch1.S4"/>, and Table <xref ref-type="table" rid="Ch1.T2"/>) and contains
all known missing sources of NH<inline-formula><mml:math id="M416" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>, we can use the model to answer one of
our key questions: what percent contributions to total ambient NH<inline-formula><mml:math id="M417" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs
came from bidirectional flux versus from forest fires during the study time
period? We do so by subtracting the bidi model output from the fire <inline-formula><mml:math id="M418" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi
model output to get the forest fire component, and subtracting the base model
output from the bidi model output to get the bidi component. The absolute
differences are calculated as follows:

                <disp-formula specific-use="align" content-type="numbered"><mml:math id="M419" display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="Ch1.E5"><mml:mtd/><mml:mtd><mml:mstyle displaystyle="true" class="stylechange"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:mi mathvariant="normal">bidicomponent</mml:mi><mml:mo>=</mml:mo><mml:msubsup><mml:mrow class="chem"><mml:mi mathvariant="normal">NH</mml:mi></mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mi mathvariant="normal">bidi</mml:mi></mml:msubsup><mml:mo>-</mml:mo><mml:msubsup><mml:mrow class="chem"><mml:mi mathvariant="normal">NH</mml:mi></mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mi mathvariant="normal">base</mml:mi></mml:msubsup><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E6"><mml:mtd/><mml:mtd><mml:mstyle class="stylechange" displaystyle="true"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:mi mathvariant="normal">firecomponent</mml:mi><mml:mo>=</mml:mo><mml:msubsup><mml:mrow class="chem"><mml:mi mathvariant="normal">NH</mml:mi></mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mrow><mml:mi mathvariant="normal">fire</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mo>+</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">bidi</mml:mi></mml:mrow></mml:msubsup><mml:mo>-</mml:mo><mml:msubsup><mml:mrow class="chem"><mml:mi mathvariant="normal">NH</mml:mi></mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mi mathvariant="normal">bidi</mml:mi></mml:msubsup><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

            which tell us how many ppbv of NH<inline-formula><mml:math id="M420" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> on average is associated with
re-emissions of NH<inline-formula><mml:math id="M421" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> (upward component of bidirectional flux) versus fire
emissions.</p>
      <p id="d1e5974">The percent differences are calculated as follows:

                <disp-formula specific-use="align" content-type="numbered"><mml:math id="M422" display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="Ch1.E7"><mml:mtd/><mml:mtd><mml:mstyle class="stylechange" displaystyle="true"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mi mathvariant="normal">bidipercent</mml:mi><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msubsup><mml:mrow class="chem"><mml:mi mathvariant="normal">NH</mml:mi></mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mi mathvariant="normal">bidi</mml:mi></mml:msubsup><mml:mo>-</mml:mo><mml:msubsup><mml:mrow class="chem"><mml:mi mathvariant="normal">NH</mml:mi></mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mi mathvariant="normal">base</mml:mi></mml:msubsup></mml:mrow><mml:mrow><mml:msubsup><mml:mrow class="chem"><mml:mi mathvariant="normal">NH</mml:mi></mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mrow><mml:mi mathvariant="normal">fire</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mo>+</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">bidi</mml:mi></mml:mrow></mml:msubsup></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:mn mathvariant="normal">100</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="italic">%</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E8"><mml:mtd/><mml:mtd><mml:mstyle class="stylechange" displaystyle="true"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:mi mathvariant="normal">firepercent</mml:mi><mml:mo>=</mml:mo><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:msubsup><mml:mrow class="chem"><mml:mi mathvariant="normal">NH</mml:mi></mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mrow><mml:mi mathvariant="normal">fire</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mo>+</mml:mo><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">bidi</mml:mi></mml:mrow></mml:msubsup><mml:mo>-</mml:mo><mml:msubsup><mml:mrow class="chem"><mml:mi mathvariant="normal">NH</mml:mi></mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mi mathvariant="normal">bidi</mml:mi></mml:msubsup></mml:mrow><mml:mrow><mml:msubsup><mml:mrow class="chem"><mml:mi mathvariant="normal">NH</mml:mi></mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mrow><mml:mi mathvariant="normal">fire</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mo>+</mml:mo><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">bidi</mml:mi></mml:mrow></mml:msubsup></mml:mrow></mml:mfrac></mml:mstyle><mml:mo>×</mml:mo><mml:mn mathvariant="normal">100</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="italic">%</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

            which tell us what percent of total NH<inline-formula><mml:math id="M423" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs on average comes from
re-emissions of NH<inline-formula><mml:math id="M424" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> and from fire emissions, assuming the NH<inline-formula><mml:math id="M425" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> from our
fire <inline-formula><mml:math id="M426" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi simulation is the true total NH<inline-formula><mml:math id="M427" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F12" specific-use="star"><caption><p id="d1e6150">Maps of the modelled <bold>(a)</bold> absolute bidirectional flux contribution, <bold>(b)</bold> absolute fire
contribution, <bold>(c)</bold> percent bidirectional flux contribution, and <bold>(d)</bold> percent fire contribution
to surface NH<inline-formula><mml:math id="M428" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>. These are averages over 12 August to 7 September 2013.</p></caption>
          <?xmltex \igopts{width=497.923228pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f12.pdf"/>

        </fig>

      <p id="d1e6180">We perform this calculation on the averaged model output (12 August to 7
September 2013) over the 2.5 km model domain, and get an average of 20.3 %
(or 0.42 ppbv) and a median of 10.4 % for ambient surface NH<inline-formula><mml:math id="M429" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs that
come from forest fires (Fig. <xref ref-type="fig" rid="Ch1.F12"/>b and d). The mean and median
are so different because fires are sporadic, large contributions to NH<inline-formula><mml:math id="M430" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>
VMRs, and the mean value is more sensitive to the big outliers. We get an
average of 56.6 % (or 1.24 ppbv) from bidirectional flux (56.3 %
median; Fig. <xref ref-type="fig" rid="Ch1.F12"/>a and c), and the remaining 23.1 % average (33.3 % median) comes from direct emissions from anthropogenic sources
(agriculture, fossil fuel combustion, oil sands industry, etc.). These numbers
are summarized in Table <xref ref-type="table" rid="Ch1.T3"/>. The increase in NH<inline-formula><mml:math id="M431" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> due
to the bidirectional flux scheme is of the same order of magnitude as that
found in the <xref ref-type="bibr" rid="bib1.bibx103" id="text.94"/> study using the GEOS-Chem model, during the month
of July in the United States (where they found <inline-formula><mml:math id="M432" display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula>1 ppbv increase in surface
VMRs due to bidirectional flux). It is also similar to values found in Europe
in the <xref ref-type="bibr" rid="bib1.bibx94" id="text.95"/> study.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T3"><caption><p id="d1e6234">Average source contributions to ambient NH<inline-formula><mml:math id="M433" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs over the Alberta and Saskatchewan model domain during 12 August to 7 September 2013.</p></caption><oasis:table frame="topbot"><?xmltex \begin{scaleboxenv}{.85}[.85]?><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right"/>
     <oasis:thead>
       <oasis:row>
         <oasis:entry colname="col1">Source</oasis:entry>
         <oasis:entry colname="col2">Median</oasis:entry>
         <oasis:entry colname="col3">Median</oasis:entry>
         <oasis:entry colname="col4">Average</oasis:entry>
         <oasis:entry colname="col5">Average</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2">(ppbv)</oasis:entry>
         <oasis:entry colname="col3">(%)</oasis:entry>
         <oasis:entry colname="col4">(ppbv)</oasis:entry>
         <oasis:entry colname="col5">(%)</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">Total surface NH<inline-formula><mml:math id="M434" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col2">1.60</oasis:entry>
         <oasis:entry colname="col3">100</oasis:entry>
         <oasis:entry colname="col4">2.53</oasis:entry>
         <oasis:entry colname="col5">100</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">From fires to surface</oasis:entry>
         <oasis:entry colname="col2">0.25</oasis:entry>
         <oasis:entry colname="col3">10.4</oasis:entry>
         <oasis:entry colname="col4">0.42</oasis:entry>
         <oasis:entry colname="col5">20.3</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">From bidi to surface</oasis:entry>
         <oasis:entry colname="col2">0.97</oasis:entry>
         <oasis:entry colname="col3">56.3</oasis:entry>
         <oasis:entry colname="col4">1.24</oasis:entry>
         <oasis:entry colname="col5">56.6</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">From anthro. to surface</oasis:entry>
         <oasis:entry colname="col2">0.38</oasis:entry>
         <oasis:entry colname="col3">33.3</oasis:entry>
         <oasis:entry colname="col4">0.87</oasis:entry>
         <oasis:entry colname="col5">23.1</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Total column NH<inline-formula><mml:math id="M435" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col2">18.8</oasis:entry>
         <oasis:entry colname="col3">100</oasis:entry>
         <oasis:entry colname="col4">25.6</oasis:entry>
         <oasis:entry colname="col5">100</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">From fires to total column</oasis:entry>
         <oasis:entry colname="col2">6.1</oasis:entry>
         <oasis:entry colname="col3">27.7</oasis:entry>
         <oasis:entry colname="col4">8.1</oasis:entry>
         <oasis:entry colname="col5">30.5</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">From bidi to total column</oasis:entry>
         <oasis:entry colname="col2">8.8</oasis:entry>
         <oasis:entry colname="col3">48.1</oasis:entry>
         <oasis:entry colname="col4">11.15</oasis:entry>
         <oasis:entry colname="col5">50.0</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">From anthro. to total column</oasis:entry>
         <oasis:entry colname="col2">3.9</oasis:entry>
         <oasis:entry colname="col3">24.2</oasis:entry>
         <oasis:entry colname="col4">6.35</oasis:entry>
         <oasis:entry colname="col5">19.5</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup><?xmltex \end{scaleboxenv}?></oasis:table></table-wrap>

      <p id="d1e6464">Over the model domain, the minimum bidi influence on surface NH<inline-formula><mml:math id="M436" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> is just
north of Edmonton, where only 1 % of NH<inline-formula><mml:math id="M437" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> comes from bidi. Similarly, two
AOSR facilities north of Fort McMurray stand out as having small bidi
influence (12–40 %, surrounded by values greater than 90 %; Fig. <xref ref-type="fig" rid="Ch1.F12"/>d).
Also, any remote region with fire emissions will have
a small percentage contribution from bidirectional flux during the fires, as
they are in northern Saskatchewan (Fig. <xref ref-type="fig" rid="Ch1.F12"/>d). This is
expected given that the average VMRs in cities and near large sources are
very close to, or exceed, the compensation point. The absolute maximum in the
bidi component map is 4.5 ppbv in the lower right corner (an agricultural
region with high NH<inline-formula><mml:math id="M438" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> emissions), and the minimum is 0 ppbv (Fig. <xref ref-type="fig" rid="Ch1.F12"/>b).
This means that nowhere in the domain did the
bidirectional flux formula result in more net deposition than the base model
calculated via the Welesley–Robichaud–Zhang scheme. The maximum fire
contribution to surface NH<inline-formula><mml:math id="M439" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> is 27.9 ppbv where large fires occurred in
northern Saskatchewan (Fig. <xref ref-type="fig" rid="Ch1.F12"/>c).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F13" specific-use="star"><caption><p id="d1e6514">Maps of the modelled average NH<inline-formula><mml:math id="M440" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> deposition for <bold>(a)</bold> base, <bold>(b)</bold> bidi, and
<bold>(c)</bold> fire <inline-formula><mml:math id="M441" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi models. In all maps, red/positive represents upward flux and blue/negative
represents downward flux. These are daily amounts averaged over 12 August to 7 September 2013.</p></caption>
          <?xmltex \igopts{width=483.69685pt}?><graphic xlink:href="https://acp.copernicus.org/articles/18/2011/2018/acp-18-2011-2018-f13.pdf"/>

        </fig>

</sec>
<sec id="Ch1.S5.SS2">
  <title>Effect on deposition</title>
      <p id="d1e6554">Similar to our analysis from the previous section, we can use the model to
determine how bidirectional flux and fires impact daily NH<inline-formula><mml:math id="M442" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula>
deposition (which equals the dry deposition of NH<inline-formula><mml:math id="M443" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> + the wet deposition of
NH<inline-formula><mml:math id="M444" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>). Figure <xref ref-type="fig" rid="Ch1.F13"/> shows the average daily net deposition
(or net flux) of NH<inline-formula><mml:math id="M445" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> from the base, bidi, and fire <inline-formula><mml:math id="M446" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi models.
Negative (or blue) indicates net deposition (downward flux), and positive (or
red) net emission (upward flux). The base model (Fig. <xref ref-type="fig" rid="Ch1.F13"/>a)
had no re-emission (upward flux) option, thus NH<inline-formula><mml:math id="M447" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> was always net dry
deposited in that scenario. The bidi (Fig. <xref ref-type="fig" rid="Ch1.F13"/>b) and fire <inline-formula><mml:math id="M448" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi
(Fig. <xref ref-type="fig" rid="Ch1.F13"/>c) maps show that most of the Alberta and Saskatchewan
area has net deposition (e.g., near the cities, agriculture, and forest
fires), but that some regions (with low atmospheric NH<inline-formula><mml:math id="M449" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs) have net
emission of NH<inline-formula><mml:math id="M450" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula>. The dry NH<inline-formula><mml:math id="M451" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> flux is net positive over the
domain; however, when the increase in wet NH<inline-formula><mml:math id="M452" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> is accounted for, the net
flux of NH<inline-formula><mml:math id="M453" display="inline"><mml:msub><mml:mi/><mml:mi>x<?pagebreak page2027?></mml:mi></mml:msub></mml:math></inline-formula> is still negative (downward). This is very similar to
what <xref ref-type="bibr" rid="bib1.bibx94" id="text.96"/> found in a 2007 study in Europe; a reduction in dry
NH<inline-formula><mml:math id="M454" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> compensated by an increase in wet NH<inline-formula><mml:math id="M455" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> deposition.</p>
      <p id="d1e6702">Note that the assumption of an infinite soil pool of NH<inline-formula><mml:math id="M456" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> in our
bidirectional flux scheme has not caused an overwhelming upward flux of
NH<inline-formula><mml:math id="M457" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula>. In fact, the average results across the domain actually have
more deposition in the fire <inline-formula><mml:math id="M458" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi scenario than in our base scenario. Table <xref ref-type="table" rid="Ch1.T4"/> shows the mean and median net NH<inline-formula><mml:math id="M459" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> flux for each
scenario (presented as deposition, so negative signs removed). That said,
following the soil pool approach <xref ref-type="bibr" rid="bib1.bibx72 bib1.bibx103" id="paren.97"/>, the soil pool of
NH<inline-formula><mml:math id="M460" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> may eventually get depleted. However, we believe this to be very
unlikely for the following reasons: (1) deposition of NH<inline-formula><mml:math id="M461" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> throughout
the year continually replenishes the soil pool – especially when
temperatures are cooler in winter, spring, and fall since the compensation
point is exponentially dependent on temperature. (2) The short time frame of
this study would not be long enough to deplete the soil pool. For example,
<xref ref-type="bibr" rid="bib1.bibx103" id="text.98"/> needed to spin up their model for three months in order to get
the NH<inline-formula><mml:math id="M462" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:math></inline-formula> soil pool stable, implying both a large pool and a long time
required for it to empty.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T4"><caption><p id="d1e6784">Average NH<inline-formula><mml:math id="M463" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> deposition (downward flux) over the Alberta and Saskatchewan model domain during 12 August to 7 September 2013.</p></caption><oasis:table frame="topbot"><?xmltex \begin{scaleboxenv}{.86}[.86]?><oasis:tgroup cols="4">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:thead>
       <oasis:row>
         <oasis:entry colname="col1">Net flux</oasis:entry>
         <oasis:entry colname="col2">Base</oasis:entry>
         <oasis:entry colname="col3">Bidi</oasis:entry>
         <oasis:entry colname="col4">Fire <inline-formula><mml:math id="M464" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">(moles m<inline-formula><mml:math id="M465" 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> day<inline-formula><mml:math id="M466" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>)</oasis:entry>
         <oasis:entry colname="col2"/>
         <oasis:entry colname="col3"/>
         <oasis:entry colname="col4"/>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">Mean</oasis:entry>
         <oasis:entry colname="col2">3.025 <inline-formula><mml:math id="M467" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M468" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col3">1.811 <inline-formula><mml:math id="M469" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M470" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col4">3.765 <inline-formula><mml:math id="M471" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M472" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Median</oasis:entry>
         <oasis:entry colname="col2">2.061 <inline-formula><mml:math id="M473" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M474" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col3">1.299 <inline-formula><mml:math id="M475" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M476" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col4">2.843 <inline-formula><mml:math id="M477" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M478" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup><?xmltex \end{scaleboxenv}?></oasis:table></table-wrap>

      <p id="d1e7012">In the AOSR near Fort McMurray, we can compare our NH<inline-formula><mml:math id="M479" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> dry deposition
results to those calculated in <xref ref-type="bibr" rid="bib1.bibx39" id="text.99"/>. Their values for nitrogen range from 0.7 to
1.25 kg ha<inline-formula><mml:math id="M480" 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> yr<inline-formula><mml:math id="M481" 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> (or 1.13 to 2.01 <inline-formula><mml:math id="M482" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M483" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> moles m<inline-formula><mml:math id="M484" 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> day<inline-formula><mml:math id="M485" 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>), while
ours are 10 times lower at around 0.13 kg ha<inline-formula><mml:math id="M486" 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> yr<inline-formula><mml:math id="M487" 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> (scaled up to a year,
from 2.12 <inline-formula><mml:math id="M488" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M489" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">6</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> moles m<inline-formula><mml:math id="M490" 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> day<inline-formula><mml:math id="M491" 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>) near Fort McMurray, and do not
vary much among our three model scenarios. These differences in deposition
estimates<?pagebreak page2028?> are likely due to the fact that our study is only during a very
warm time of the year, when deposition will be at a minimum, whereas the
<xref ref-type="bibr" rid="bib1.bibx39" id="text.100"/> study covered both winter and summer time periods for multiple
years. The differences may also be partially due to the fact that our
modelled ambient NH<inline-formula><mml:math id="M492" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs are also low compared to those measured in
<xref ref-type="bibr" rid="bib1.bibx38" id="normal.101"/> near Fort McMurray. They measured an average of 1.55 <inline-formula><mml:math id="M493" display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> 0.6 ppbv (1.9 <inline-formula><mml:math id="M494" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g m<inline-formula><mml:math id="M495" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) at Fort McMurray,
whereas our fire <inline-formula><mml:math id="M496" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model has an
average of 1.01 ppbv there (0.73 ppbv in bidi, and 0.39 in base). There may
also be differences in that our model has more of the NH<inline-formula><mml:math id="M497" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> deposition
coming down as NH<inline-formula><mml:math id="M498" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> rather than as NH<inline-formula><mml:math id="M499" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>.</p>
      <p id="d1e7244">Our fire <inline-formula><mml:math id="M500" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi NH<inline-formula><mml:math id="M501" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> deposition values (Table <xref ref-type="table" rid="Ch1.T4"/>) are
well in line with reported NH<inline-formula><mml:math id="M502" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> deposition in <xref ref-type="bibr" rid="bib1.bibx43" id="text.102"/>, who report
satellite-derived NH<inline-formula><mml:math id="M503" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> deposition of about 2.1 to 7.0 <inline-formula><mml:math id="M504" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M505" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> moles m<inline-formula><mml:math id="M506" 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> day<inline-formula><mml:math id="M507" 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 Alberta, and are at the low end of NH<inline-formula><mml:math id="M508" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> deposition
values reported within <xref ref-type="bibr" rid="bib1.bibx7" id="text.103"/>.</p>
      <p id="d1e7343">The difference in deposition between the fire <inline-formula><mml:math id="M509" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi and bidi cases – which is
the contribution of fires to the total NH<inline-formula><mml:math id="M510" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> flux – showed that the
fires increased downward flux or deposition over large swaths of the domain
(e.g., difference between Fig. <xref ref-type="fig" rid="Ch1.F13"/>c and b). The fires
contributed an average of 1.954 <inline-formula><mml:math id="M511" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M512" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> moles m<inline-formula><mml:math id="M513" 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> day<inline-formula><mml:math id="M514" 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> of NH<inline-formula><mml:math id="M515" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> deposition across the domain.</p>
      <p id="d1e7417">Although the atmospheric concentrations of particulate NH<inline-formula><mml:math id="M516" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> did not change
much in our three simulations (see Sect. <xref ref-type="sec" rid="Ch1.S4.SS1"/> and <xref ref-type="sec" rid="Ch1.S4.SS2"/>), the wet deposition of NH<inline-formula><mml:math id="M517" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> increased significantly
going from the base to bidi to fire <inline-formula><mml:math id="M518" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi models. This is in contrast to what
<xref ref-type="bibr" rid="bib1.bibx103" id="text.104"/> found, which was little change to NH<inline-formula><mml:math id="M519" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> wet deposition due
to bidirectional flux. However, that could be due to other parameters, such as
the meteorological conditions, scavenging parameters, and/or gas-particle
partitioning of NH<inline-formula><mml:math id="M520" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula>. It would seem that in GEM-MACH-Bidi, the
increased NH<inline-formula><mml:math id="M521" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> is scavenged by precipitation. The average NH<inline-formula><mml:math id="M522" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>
deposition from the three simulations had a nearly threefold increase in the
NH<inline-formula><mml:math id="M523" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> deposition due to the increased NH<inline-formula><mml:math id="M524" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> that the fire <inline-formula><mml:math id="M525" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi simulation
yields. The average NH<inline-formula><mml:math id="M526" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> wet deposition for our fire <inline-formula><mml:math id="M527" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi simulation is
5.86 <inline-formula><mml:math id="M528" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M529" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> moles m<inline-formula><mml:math id="M530" 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> day<inline-formula><mml:math id="M531" 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>, which is in between values reported in
the U.S. in <xref ref-type="bibr" rid="bib1.bibx83" id="text.105"/> (where they found an average of
1.9 <inline-formula><mml:math id="M532" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M533" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> moles m<inline-formula><mml:math id="M534" 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> day<inline-formula><mml:math id="M535" 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> over the country), and in Japan in
<xref ref-type="bibr" rid="bib1.bibx63" id="text.106"/> (where they found an average of 10.3 <inline-formula><mml:math id="M536" display="inline"><mml:mo>×</mml:mo></mml:math></inline-formula> 10<inline-formula><mml:math id="M537" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> moles m<inline-formula><mml:math id="M538" 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> day<inline-formula><mml:math id="M539" 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> over the country).</p>
      <?pagebreak page2029?><p id="d1e7686">In the three scenarios, the average daily relative ratio of dry <inline-formula><mml:math id="M540" display="inline"><mml:mo>:</mml:mo></mml:math></inline-formula> wet
deposition was 0.43 for base, <inline-formula><mml:math id="M541" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.77 for bidi, and <inline-formula><mml:math id="M542" display="inline"><mml:mo>-</mml:mo></mml:math></inline-formula>0.51 for fire <inline-formula><mml:math id="M543" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi (the
negative value for the bidi and fire <inline-formula><mml:math id="M544" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi cases are because of the average
upward direction of NH<inline-formula><mml:math id="M545" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>). Since all average ratios are less than 1, this
means that most of the removal process is from wet deposition rather than
dry deposition (even for the base case that had no re-emission of NH<inline-formula><mml:math id="M546" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>).
Therefore, increased monitoring of wet deposition in the region would be
useful. These results may also be useful for Alberta Environment and Parks (AEP) terrestrial or aquatic
scientists interested in nitrogen eutrophication. Maps of these ratios can be
found in the Supplement.</p>
</sec>
</sec>
<sec id="Ch1.S6" sec-type="conclusions">
  <title>Conclusions</title>
      <p id="d1e7750">The GEM-MACHv2 air quality forecasting model was altered to include both the
<xref ref-type="bibr" rid="bib1.bibx101" id="text.107"/> bidirectional flux scheme for NH<inline-formula><mml:math id="M547" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> and forest fire
emissions of all species. This new “fire <inline-formula><mml:math id="M548" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi” model improves the simulated
NH<inline-formula><mml:math id="M549" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> in the modelled oil sands domain at 2.5 km resolution when compared to
independent in situ measurements at the ground (at the AMS13 oil
sands monitoring site) and aloft (aircraft measurements), as well as at 10 km
resolution when compared to cutting-edge satellite measurements from the CrIS
instrument in Alberta and Saskatchewan. Almost all comparison statistics are
best with our fire <inline-formula><mml:math id="M550" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi simulation. This suggests that the fire <inline-formula><mml:math id="M551" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model
shows promise for improving NH<inline-formula><mml:math id="M552" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> model predictions elsewhere and during
other time periods. However, more work is required to validate the model in
other regions of the continent (e.g., with the Wood Buffalo Environmental
Association, WBEA; the AMoN; and further CrIS satellite measurements), and for different time
periods (e.g., springtime fertilizer season, cooler conditions, etc.). We
have also shown that for further improvements in the Alberta and Saskatchewan
region, the NH<inline-formula><mml:math id="M553" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> emission factors for fires, and the NH<inline-formula><mml:math id="M554" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> emissions from
agriculture, likely need to be reduced.</p>
      <p id="d1e7823">Despite the significant increase in atmospheric NH<inline-formula><mml:math id="M555" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs with these
additional sources, the impact on its byproduct, NH<inline-formula><mml:math id="M556" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, was minuscule – as
was the change to SO<inline-formula><mml:math id="M557" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> concentrations (0.02 <inline-formula><mml:math id="M558" display="inline"><mml:mi mathvariant="normal">µ</mml:mi></mml:math></inline-formula>g m<inline-formula><mml:math id="M559" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> for each).
The model bias for those species was not significantly changed in either
direction. This is probably because of the extra NH<inline-formula><mml:math id="M560" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> wet scavenging by
precipitation, and the NH<inline-formula><mml:math id="M561" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> VMRs were already high enough (before adding
the extra sources) to charge balance the SO<inline-formula><mml:math id="M562" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">4</mml:mn><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> and NO<inline-formula><mml:math id="M563" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> in the
aerosols. Thus, any additional NH<inline-formula><mml:math id="M564" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> would remain in the gas phase. That
said, the model bias for NO<inline-formula><mml:math id="M565" display="inline"><mml:mrow><mml:msubsup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula> at the AMS13 ground station was essentially
removed with the fire <inline-formula><mml:math id="M566" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model.</p>
      <p id="d1e7959">By running the base, bidi, and fire <inline-formula><mml:math id="M567" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi model scenarios, and taking the
fire <inline-formula><mml:math id="M568" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi results as “true”, we were able to calculate their differences and
determine the average contributions from each source. We found that, on
average, during the 12 August to 7 September 2013 time period in the
Alberta and Saskatchewan model domain, 23.1 % of surface NH<inline-formula><mml:math id="M569" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> comes from
direct anthropogenic emissions, 56.6 % of surface NH<inline-formula><mml:math id="M570" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> comes from
bidirectional flux (re-emission from soils and plants), and 20.3 % of
NH<inline-formula><mml:math id="M571" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> comes from forest fires. Possible sources of error that remain in the
bidi and fire <inline-formula><mml:math id="M572" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> bidi simulations are the agricultural and fire emissions of
NH<inline-formula><mml:math id="M573" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>, as well as the emission potentials for different LUCs.
The fraction of NH<inline-formula><mml:math id="M574" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula> from fires is highly variable depending on the time
periods and spatial domain analysed; on average from 12 August to 7 September
2013, the largest impact was in northern Saskatchewan. We also expect the
re-emission source to be near the highest at this time of year because of the
high temperatures, and this source should be much lower during the cold
season when deposition is expected to dominate the bidirectional flux
process.</p>
      <p id="d1e8029">The bidirectional flux process has decreased NH<inline-formula><mml:math id="M575" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> deposition on
average across the domain, with some areas having a net emission of NH<inline-formula><mml:math id="M576" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:math></inline-formula>.
However, that upward flux is due to the low atmospheric concentrations and
high temperatures, and does not exceed the amount of NH<inline-formula><mml:math id="M577" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> deposition
that occurs during the cooler winter and spring times. When fires are also
taken into account, the net NH<inline-formula><mml:math id="M578" display="inline"><mml:msub><mml:mi/><mml:mi>x</mml:mi></mml:msub></mml:math></inline-formula> deposition is greater, on average
across the domain, compared to the base model.</p>
</sec>

      
      </body>
    <back><notes notes-type="codedataavailability">

      <p id="d1e8072">The CrIS science data products used in this study
can be made available upon request to Mark W. Shephard (ECCC). Similarly, the AMS13
observations can be made available upon request to Gregory R. Wentworth (AEP). The
aircraft observations are on the ECCC data portal
(<uri>https://www.canada.ca/en/environment-climate-change/services/oil-sands-monitoring/monitoring-air-quality-alberta-oil-sands.html</uri>).</p>

      <p id="d1e8078">GEM-MACH – the atmospheric chemistry library for the GEM
numerical atmospheric model Copyright© 2007–2013 – Air Quality Research
Division and National Prediction Operations division, Environment and Climate
Change Canada. This library is free software which can be redistributed
and/or modified under the terms of the GNU Lesser General Public License as
published by the Free Software Foundation; either version 2.1 of the license,
or any later version. Please contact the lead author (Cynthia Whaley, ECCC)
for access to the GEM-MACH-Bidi code, as there is currently no online link
for download.</p>

      <p id="d1e8081">Much of the emissions data used in our model are
available online: Executive Summary, Joint oil sands monitoring program
emissions inventory report
(<uri>https://www.canada.ca/en/environment-climate-change/services/science-technology/publications/joint-oil-sands-monitoring-emissions-report.html</uri>)
and Joint Oil Sands Emissions Inventory Database
(<uri>http://ec.gc.ca/data_donnees/SSB-OSM_Air/Air/Emissions_inventory_files/</uri>).
For the GEM-MACH-Bidi model output, please contact the lead author (Cynthia
Whaley, ECCC) for hourly netCDF files of the 3-D ammonia fields.</p>
  </notes><app-group>
        <supplementary-material position="anchor"><p id="d1e8090">The supplement related to this article is available online at: <inline-supplementary-material xlink:href="https://doi.org/10.5194/acp-18-2011-2018-supplement" xlink:title="pdf">https://doi.org/10.5194/acp-18-2011-2018-supplement</inline-supplementary-material>.</p></supplementary-material>
        </app-group><notes notes-type="competinginterests">

      <p id="d1e8099">The authors declare that they have no conflict of interest.</p>
  </notes><notes notes-type="sistatement">

      <p id="d1e8105">This article is part of the special issue “Atmospheric emissions from oil sands development and their transport,
transformation and deposition (ACP/AMT inter-journal SI)”. It is not associated with a conference.</p>
  </notes><ack><title>Acknowledgements</title><p id="d1e8111">The project was supported by ECCC's Oil Sands Monitoring program (OSM), and
the Climate Change and Air Quality Program (CCAP). We would also like to
acknowledge the University of Wisconsin, Madison, Space Science and Engineering
Center Atmosphere SIPS team sponsored under NASA contract NNG15HZ38C for
providing us with the CrIS level 1 and 2 input data, in particular Keven Hrpcek and Liam Gumley.
<?xmltex \hack{\newline}?><?xmltex \hack{\newline}?>
Edited by: Jan W. Bottenheim<?xmltex \hack{\newline}?>
Reviewed by: three anonymous referees</p></ack><ref-list>
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    <!--<article-title-html>Contributions of natural and anthropogenic sources to ambient ammonia in the Athabasca Oil Sands and north-western Canada</article-title-html>
<abstract-html><p>Atmospheric ammonia (NH<sub>3</sub>) is a short-lived pollutant that plays an
important role in aerosol chemistry and nitrogen deposition. Dominant NH<sub>3</sub>
emissions are from agriculture and forest fires, both of which are increasing
globally. Even remote regions with relatively low ambient NH<sub>3</sub>
concentrations, such as northern Alberta and Saskatchewan in northern Canada,
may be of interest because of industrial oil sands emissions and a sensitive
ecological system. A previous attempt to model NH<sub>3</sub> in the region showed a
substantial negative bias compared to satellite and aircraft observations.
Known missing sources of NH<sub>3</sub> in the model were re-emission of NH<sub>3</sub> from
plants and soils (bidirectional flux) and forest fire emissions, but the
relative impact of these sources on NH<sub>3</sub> concentrations was unknown. Here
we have used a research version of the high-resolution air quality
forecasting model, GEM-MACH, to quantify the relative impacts of semi-natural
(bidirectional flux of NH<sub>3</sub> and forest fire emissions) and direct
anthropogenic (oil sand operations, combustion of fossil fuels, and
agriculture) sources on ammonia volume mixing ratios, both at the surface and
aloft, with a focus on the Athabasca Oil Sands region during a
measurement-intensive campaign in the summer of 2013. The addition of fires
and bidirectional flux to GEM-MACH has improved the model bias, slope, and
correlation coefficients relative to ground, aircraft, and satellite NH<sub>3</sub>
measurements significantly.</p><p>By running the GEM-MACH-Bidi model in three configurations and calculating
their differences, we find that averaged over Alberta and Saskatchewan during
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