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  • 1
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    Analysis and Hindcast Experiments of the 2009 Sudden Stratospheric Warming in WACCMX+DART (2018)
    Wiley
    Details
    Publication Date: 2018-03-16
    Description: The ability to perform data assimilation in the Whole Atmosphere Community Climate Model eXtended version (WACCMX) is implemented using the Data Assimilation Research Testbed (DART) ensemble adjustment Kalman filter. Results are presented demonstrating that WACCMX+DART analysis fields reproduce the middle and upper atmosphere variability during the 2009 major sudden stratospheric warming (SSW) event. Compared to specified dynamics WACCMX, which constrains the meteorology by nudging towards an external reanalysis, the large-scale dynamical variability of the stratosphere, mesosphere, and lower thermosphere are improved in WACCMX+DART. This leads to WACCMX+DART better representing the downward transport of chemical species from the mesosphere into the stratosphere following the SSW. WACCMX+DART also reproduces most aspects of the observed variability in ionosphere total electron content (TEC) and equatorial vertical plasma drift during the SSW. Hindcast experiments initialized on January 5, 10, 15, 20, and 25 are used to assess the middle and upper atmosphere predictability in WACCMX+DART. A SSW, along with the associated middle and upper atmosphere variability, is initially predicted in the hindcast initialized on January 15, which is ∼10 days prior to the warming. However, it is not until the hindcast initialized on January 20 that a major SSW is forecast to occur. The hindcast experiments reveal that dominant features of the TEC can be forecast ∼10-20 days in advance. This demonstrates that whole atmosphere models that properly account for variability in lower atmosphere forcing can potentially extend the ionosphere-thermosphere forecast range.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
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    Towards a chemical reanalysis in a coupled chemistry-climate model: An evaluation of MOPITT CO assimilation and its impact on tropospheric composition (2016)
    Wiley
    Details
    Publication Date: 2016-05-29
    Description: We examine in detail a one-year global reanalysis of carbon monoxide (CO) that is based on joint assimilation of conventional meteorological observations and Measurement of Pollution in The Troposphere (MOPITT) multispectral CO retrievals in the Community Earth System Model (CESM). Our focus is to assess the impact to the chemical system when CO distribution is constrained in a coupled full chemistry-climate model like CESM. To do this, we first evaluate the joint reanalysis (MOPITT Reanalysis) against four sets of independent observations and compare its performance against a reanalysis with no MOPITT assimilation (Control Run). We then investigate the CO burden and chemical response with the aid of tagged sectoral CO tracers. We estimate the total tropospheric CO burden in 2002 (from ensemble mean and spread) to be 371 ±12% Tg for MOPITT Reanalysis and 291 ± 9 % Tg for Control Run. Our multi-species analysis of this difference suggests that: a) direct emissions of CO and hydrocarbons are too low in the inventory used in this study; and b) chemical oxidation, transport, and deposition processes are not accurately and consistently represented in the model. Increases in CO led to net reduction of OH and subsequent longer lifetime of CH 4 (Control Run: 8.7 years versus MOPITT Reanalysis: 9.3 years). Yet, at the same time, this increase led to 5-10% enhancement of northern hemisphere O 3 and overall photochemical activity via HO X recycling. Such nonlinear effects further complicate the attribution to uncertainties in direct emissions alone. This has implications to chemistry-climate modeling and inversion studies of longer-lived species.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
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  • 3
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    Assimilation of FORMOSAT-3/COSMIC electron density profiles into a coupled thermosphere/ionosphere model using ensemble Kalman filtering (2012)
    Wiley
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    Publication Date: 2012-10-13
    Description: This paper presents our effort to assimilate FORMOSAT-3/COSMIC (F3/C) GPS Occultation Experiment (GOX) observations into the National Center for Atmospheric Research (NCAR) Thermosphere Ionosphere Electrodynamics General Circulation Model (TIE-GCM) by means of ensemble Kalman filtering (EnKF). The F3/C electron density profiles (EDPs) uniformly distributed around the globe which provide an excellent opportunity to monitor the ionospheric electron density structure. The NCAR TIE-GCM simulates the Earth's thermosphere and ionosphere by using self-consistent solutions for the coupled nonlinear equations of hydrodynamics, neutral and ion chemistry, and electrodynamics. The F3/C EDP are combined with the TIE-GCM simulations by EnKF algorithms implemented in the NCAR Data Assimilation Research Testbed (DART) open-source community facility to compute the expected value of electron density, which is ‘the best’ estimate of the current ionospheric state. Assimilation analyses obtained with real F3/C electron density profiles are compared with independent ground-based observations as well as the F3/C profiles themselves. The comparison shows the improvement of the primary ionospheric parameters, such as NmF2 and hmF2. Nevertheless, some unrealistic signatures appearing in the results and high rejection rates of observations due to the applied outlier threshold and quality control are found in the assimilation experiments. This paper further discusses the limitations of the model and the impact of ensemble member creation approaches on the assimilation results, and proposes possible methods to avoid these problems for future work.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
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  • 4
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    Demonstration of ensemble data assimilation for Mars using DART, MarsWRF, and radiance observations from MGS TES (2011)
    Wiley
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    Publication Date: 2011-11-29
    Description: We describe a global atmospheric data assimilation scheme that has been adapted for use with a Martian General Circulation Model (GCM), with the ultimate goal of creating globally and temporally interpolated “reanalysis” data sets from planetary atmospheric observations. The system uses the Data Assimilation Research Testbed (DART) software to apply an Ensemble Kalman Filter (EnKF) to the MarsWRF GCM. Specific application to Mars also required the development of a radiance forward model for near-nadir Thermal Emission Spectrometer (TES) observations. Preliminary results from an assimilation of 40 sols of TES radiance data, taken around Ls = 150° (August 1999, Mars Year 24), are provided. 1.3 million TES observations are ingested and used to improve the state prediction by the GCM, with bias and error reductions obtained throughout the state vector. Results from the assimilation suggest steepening of the latitudinal and vertical thermal gradients with concurrent strengthening of the mid-latitude zonal jets, and a slower recession of the southern polar ice edge than predicted by the unaided GCM. Limitations of the prescribed dust model are highlighted by the presence of an atmospheric radiance bias. Preliminary results suggest the prescribed dust vertical profile might not be suitable for all seasons, in accordance with more recent observations of the vertical distribution of dust by the Mars Climate Sounder. The tools developed using this DA system are available at http://www.marsclimatecenter.com. A tutorial and example TES radiance assimilation are also provided.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
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  • 5
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    Ensemble Data Assimilation in the Whole Atmosphere Community Climate Model (2014)
    Wiley
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    Publication Date: 2014-08-13
    Description: We present results pertaining to the assimilation of real lower, middle, and upper atmosphere observations in the Whole Atmosphere Community Climate Model (WACCM) using the Data Assimilation Research Testbed (DART) ensemble adjustment Kalman filter. The ability to assimilate lower atmosphere observations of aircraft and radiosonde temperature and winds, satellite drift winds, and COSMIC refractivity along with middle/upper atmosphere temperature observations from SABER and Aura MLS is demonstrated. The WACCM + DART data assimilation system is shown to be able to reproduce the salient features, and variability, of the troposphere present in the NCEP/NCAR reanalysis. In the mesosphere, the fit of WACCM + DART to observations is found to be slightly worse when only lower atmosphere observations are assimilated compared to a control experiment that is reflective of the model climatological variability. This differs from previous results which found that assimilation of lower atmosphere observations improves the fit to mesospheric observations. This discrepancy is attributed to the fact that, due to the gravity wave drag parameterizations, the model climatology differs significantly from the observations in the mesosphere, and this is not corrected by the assimilation of lower atmosphere observations. The fit of WACCM + DART to mesospheric observations is, however, significantly improved compared to the control experiment when middle/upper atmosphere observations are assimilated. We find that assimilating SABER observations reduces the root mean square error and bias of WACCM + DART relative to the independent Aura MLS observations by ~50%, demonstrating that assimilation of middle/upper atmosphere observations is essential for accuratespecification of the MLT region in WACCM + DART. Last, we demonstrate that WACCM + DART is able to follow the dynamical and chemical variability during the 2009 sudden stratosphere warming, illustrating the capability of WACCM + DART to generate high quality atmospheric reanalysis from the surface to the lower thermosphere.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
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  • 6
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    Design and engineering of an O(2) transport protein (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-03-20
    Description: The principles of natural protein engineering are obscured by overlapping functions and complexity accumulated through natural selection and evolution. Completely artificial proteins offer a clean slate on which to define and test these protein engineering principles, while recreating and extending natural functions. Here we introduce this method with the design of an oxygen transport protein, akin to human neuroglobin. Beginning with a simple and unnatural helix-forming sequence with just three different amino acids, we assembled a four-helix bundle, positioned histidines to bis-histidine ligate haems, and exploited helical rotation and glutamate burial on haem binding to introduce distal histidine strain and facilitate O(2) binding. For stable oxygen binding without haem oxidation, water is excluded by simple packing of the protein interior and loops that reduce helical-interface mobility. O(2) affinities and exchange timescales match natural globins with distal histidines, with the remarkable exception that O(2) binds tighter than CO.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539743/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539743/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koder, Ronald L -- Anderson, J L Ross -- Solomon, Lee A -- Reddy, Konda S -- Moser, Christopher C -- Dutton, P Leslie -- R01 GM041048/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Mar 19;458(7236):305-9. doi: 10.1038/nature07841.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295603" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Transport ; Carbon Monoxide/metabolism ; Carrier Proteins/*chemical synthesis/chemistry/*metabolism ; Drug Design ; Globins/chemistry ; Glutamic Acid/metabolism ; Heme/metabolism ; Histidine/metabolism ; Humans ; Kinetics ; Ligands ; Nerve Tissue Proteins/chemistry ; Oxidation-Reduction ; Oxygen/*metabolism ; *Protein Engineering ; Protein Structure, Secondary ; Rotation ; Spectroscopy, Fourier Transform Infrared ; Substrate Specificity ; Water/analysis/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Footwall refrigeration along a detachment fault: implications for the thermal evolution of core complexes (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-01-09
    Description: Oxygen isotope compositions of epidote and quartz from chloritic breccias that underlie the detachment fault in the metamorphic core complex of the Whipple Mountains yielded quartz-epidote fractionations that range from 4.1 to 6.4 per mil and increase systematically toward the fault. These fractionations give mean temperatures that decrease from approximately 432 degrees C at 50 meters below the fault to approximately 350 degrees C at 12 meters below the fault. This extreme thermal gradient of 82 degrees C over 38 meters (2160 degrees C per kilometer) is best explained by advective heat extraction by means of circulating surface-derived fluids. Models of lithospheric extension consider only conductive cooling resulting from tectonic denudation and thus require revision to include fluid-induced fault-zone refrigeration.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morrison -- Anderson -- New York, N.Y. -- Science. 1998 Jan 2;279(5347):63-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089-0740, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9417023" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Short-term nonmigrating tide variability in the mesosphere, thermosphere, and ionosphere (2016)
    Wiley
    Details
    Publication Date: 2016-04-01
    Description: The intraseasonal variability of the eastward propagating nonmigrating diurnal tide with zonal wavenumber 3 ( D E 3) during 2007 in the mesosphere, ionosphere, and thermosphere is investigated using a whole atmosphere model reanalysis and satellite observations. The atmospheric reanalysis is based on implementation of data assimilation in the Whole Atmosphere Community Climate Model (WACCM) using the Data Assimilation Research Testbed (DART) ensemble Kalman filter. The tidal variability in the WACCM+DART reanalysis is compared to the observed variability in the mesosphere and lower thermosphere (MLT) based on the Thermosphere Ionosphere Mesosphere Energetics Dynamics satellite Sounding of the Atmosphere using Broadband Emission Radiometry (TIMED/SABER) observations, in the ionosphere based on Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) observations, and in the upper thermosphere (∼475 km) based on Gravity Recovery and Climate Experiment (GRACE) neutral density observations. To obtain the short-term D E 3 variability in the MLT and upper thermosphere, we apply the method of tidal deconvolution to the TIMED/SABER observations, and difference the ascending and descending longitudinal wavenumber 4 structure in the GRACE observations. The results reveal that tidal amplitude changes of 5-10 K regularly occur on short time scales (∼10-20 days) in the MLT. Similar variability occurs in the WACCM+DART reanalysis and TIMED/SABER observations, demonstrating that the short-term variability can be captured in both whole atmosphere models that employ data assimilation as well as by the technique of tidal deconvolution. The impact of the short-term D E 3 variability in the MLT on the ionosphere and thermosphere is also clearly evident in the COSMIC and GRACE observations. Analysis of the troposphere forcing in WACCM+DART and simulations of the Global Scale Wave Model (GSWM) show that the short-term D E 3 variability in the MLT is not related to a single source; rather, it is due to a combination of changes in troposphere forcing, zonal mean atmosphere, and wave-wave interactions.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
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  • 9
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    Economics. Sustainability and global seafood (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Martin D -- Roheim, Cathy A -- Crowder, Larry B -- Halpern, Benjamin S -- Turnipseed, Mary -- Anderson, James L -- Asche, Frank -- Bourillon, Luis -- Guttormsen, Atle G -- Khan, Ahmed -- Liguori, Lisa A -- McNevin, Aaron -- O'Connor, Mary I -- Squires, Dale -- Tyedmers, Peter -- Brownstein, Carrie -- Carden, Kristin -- Klinger, Dane H -- Sagarin, Raphael -- Selkoe, Kimberly A -- New York, N.Y. -- Science. 2010 Feb 12;327(5967):784-6. doi: 10.1126/science.1185345.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Nicholas School of the Environment, Duke University, Durham, NC 27708, USA. marsmith@duke.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20150469" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Aquaculture/economics/legislation & jurisprudence/organization & administration ; *Commerce/legislation & jurisprudence ; Developed Countries/economics ; Developing Countries/economics ; *Ecosystem ; *Fisheries/economics/legislation & jurisprudence ; *Fishes ; Food Supply ; Government ; Humans ; Malnutrition/epidemiology ; *Seafood/economics ; *Shellfish
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Sustainability. Secure sustainable seafood from developing countries (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-05-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sampson, Gabriel S -- Sanchirico, James N -- Roheim, Cathy A -- Bush, Simon R -- Taylor, J Edward -- Allison, Edward H -- Anderson, James L -- Ban, Natalie C -- Fujita, Rod -- Jupiter, Stacy -- Wilson, Jono R -- New York, N.Y. -- Science. 2015 May 1;348(6234):504-6. doi: 10.1126/science.aaa4639. Epub 2015 Apr 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, Davis, Davis, CA 95616, USA. ; University of California, Davis, Davis, CA 95616, USA. Resources for the Future, Washington, DC 20036, USA. jsanchirico@ucdavis.edu. ; University of Idaho, Moscow, ID 83844, USA. ; Wageningen University, Wageningen 6708 LX, Netherlands. ; University of Washington, Seattle, WA 98105, USA. ; University of Florida, Gainesville, FL 32611, USA. ; University of Victoria, Victoria, British Columbia V8W 2Y2, Canada. ; Environmental Defense Fund, San Francisco, CA 94105, USA. ; Wildlife Conservation Society, Suva, Fiji. ; The Nature Conservancy, Santa Barbara, CA 93106, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25931542" target="_blank"〉PubMed〈/a〉
    Keywords: *Developing Countries ; Fisheries/*standards ; Humans ; Seafood/*standards
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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