http://lod.bco-dmo.org/id/dataset/721940
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-12-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Estimation of the parameters of a simple model of thorium and particle cycling in the ocean water column, based on a fit to radionuclide and particle data from the US GEOTRACES North Atlantic Section (GA03)
2018-02-26
publication
2018-02-26
revision
BCO-DMO Linked Data URI
2018-02-26
creation
http://lod.bco-dmo.org/id/dataset/721940
Olivier Marchal
Woods Hole Oceanographic Institution
principalInvestigator
Phoebe J. Lam
University of California-Santa Cruz
principalInvestigator
Paul Lerner
Woods Hole Oceanographic Institution
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Marchal, O., Lam, P. J., Lerner, P. (2018) Estimation of the parameters of a simple model of thorium and particle cycling in the ocean water column, based on a fit to radionuclide and particle data from the US GEOTRACES North Atlantic Section (GA03). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2018-02-26 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/721940 [access date]
Thorium and Particle Cycling Inverse Model and parameter estimates Dataset Description: <p>This dataset contains model code and output from a thorium and particle cycling model.&nbsp;</p>
<p>The model code and documentation are available for download as a .zip file:&nbsp;<a href="http://datadocs.bco-dmo.org/docs/GEOTRACES_Particle_Dynamics/data_docs/Lerner_Th_P_inverseModel.zip" target="_blank">Lerner_Th_P_InverseModel.zip (2.6 MB)</a></p>
<p>Model output data are available by clicking the "Get Data" button above.&nbsp; These data are parameter estimates from fitting the model to radionuclide and particle data from the US GEOTRACES North Atlantic Section,&nbsp;not samples collected in the field.&nbsp;</p>
<p>Both the model and inverse method are described in detail in the model manual “<a href="http://datadocs.bco-dmo.org/docs/GEOTRACES_Particle_Dynamics/data_docs/Lerner_Th_P_inversion_manual.pdf" target="_blank">Manual of Matlab Code: Nonlinear Inversion of Thorium and Particle Data</a>,” as well as in Lerner et al., 2017.&nbsp;&nbsp;&nbsp;This document describes how to use the routine submitted here to fit a 1-d thorium and particle cycling model to radionuclide and particle data</p>
<p>These data and model were&nbsp;published in:</p>
<p>Lerner, P., Marchal, O., Lam, P. J., Buesseler, K., and Charette, M. (2017). Kinetics of thorium and particle cycling along the US GEOTRACES North Atlantic Transect. Deep Sea Research Part I: Oceanographic Research Papers, 125, 106-128, Fig. 12, Supplementary Figs. S1-S3. doi: <a href="https://doi.org/10.1016/j.dsr.2017.05.003" target="_blank">10.1016/j.dsr.2017.05.003</a></p> Methods and Sampling: <p><strong>Location: </strong>The model is fit to&nbsp;<sup>228,230,234</sup>Th,&nbsp;<sup>234,238</sup>U,&nbsp;<sup>228</sup>Ra, and particle concentration data collected from a section from Bermuda to a station just off the coast of Mauritania. The section crosses the Mid-Atlantic Ridge and the southeastern portion of the North Atlantic Subtropical gyre. The locations and depth ranges of data used to estimate model parameters are listed below (Table 1 of Lerner et al., 2017).</p>
<div><img alt="locations" src="http://datadocs.bco-dmo.org/docs/GEOTRACES_Particle_Dynamics/data_docs/Lerner_et_al_Table1.png" /></div>
<div>
<p><strong>Data: </strong>The thorium and particle cycling model is fit to radionuclide and particle data from the US GEOTRACES North Atlantic Section (GA03). The following lists these data, along with their associated references, in which analytical methods associated with these data are published. The subscript “p” denotes particulate data and “d” denotes “dissolved” data, where particulate and dissolved material are separated by filters with a pore size of 0.8 µm. &nbsp;These data have all been submitted to BCO-DMO, and all except&nbsp;<sup>228</sup>Th are published. These data are also available as part of the GEOTRACES Intermediate Data Product (Mawji et al., 2014).&nbsp;</p>
<div><sup>234,238</sup>U (obtained from salinity) - Owens et al., 2011 (available in datasets of project:&nbsp;<a href="https://www.bco-dmo.org/project/2066" target="_blank">https://www.bco-dmo.org/project/2066</a>)</div>
<div><sup>234</sup>Th<sub>d,p</sub>&nbsp;(dpm&nbsp;m-3) - Owens et al., 2015&nbsp;(available in datasets of project:&nbsp;<a href="https://www.bco-dmo.org/project/2066" target="_blank">https://www.bco-dmo.org/project/2066</a>)</div>
<div><sup>230</sup>Th<sub>d</sub>&nbsp;(dpm&nbsp;m-3)&nbsp; - Hayes et al., 2015a (available in dataset&nbsp;<a href="https://www.bco-dmo.org/dataset/3847" target="_blank">https://www.bco-dmo.org/dataset/3847</a>)</div>
<div><sup>230</sup>Th<sub>p</sub>&nbsp;(dpm&nbsp;m-3)&nbsp; - Hayes et al., 2015b (available in dataset&nbsp;<a href="https://www.bco-dmo.org/dataset/3847" target="_blank">https://www.bco-dmo.org/dataset/3847</a>)</div>
<div><sup>228</sup>Ra (dpm&nbsp;m-3)&nbsp; - Charrette et al., 2015 (available in dataset&nbsp;<a href="https://www.bco-dmo.org/dataset/3847" target="_blank">https://www.bco-dmo.org/dataset/3847</a>)</div>
<div><sup>228</sup>Th<sub>d,p</sub>&nbsp;(dpm&nbsp;m-3) - unpublished (available on BCO-DMO dataset page: <a href="http://lod.bco-dmo.org/id/dataset/3846" target="_blank">http://lod.bco-dmo.org/id/dataset/3846</a>, Charrette et al., 2014)&nbsp;</div>
<div>Particle concentration (mg m-3) - Lam et al., 2015 (available in dataset&nbsp;<a href="https://www.bco-dmo.org/dataset/3871" target="_blank">https://www.bco-dmo.org/dataset/3871</a>)</div>
<div>&nbsp;</div>
<div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The depths at which the radiochemical and particle data are available do not generally coincide. Hence, at each station, an objective interpolation procedure was used to interpolate the data onto an irregular grid (the grid varies with each station and the range of the grid is the same as the “depth range” ). This procedure is described in detail in section 2.4 of Lerner et al., 2016.</div>
<p><strong>Inverse Method:&nbsp;</strong>The algorithm used to fit the model (eqs. 1-3 available in the<a href="http://datadocs.bco-dmo.org/docs/GEOTRACES_Particle_Dynamics/data_docs/Lerner_Th_P_inversion_manual.pdf" target="_blank"> model manual</a>) to the radionuclide and particle data is a nonlinear programming technique as implemented in Matlab’s FMINCON (Matlab R2016b), a constrained optimization routine used to solve nonlinear problems. This algorithm takes as its argument a vector&nbsp;<strong><em>x</em></strong><sub>0&nbsp;</sub>&nbsp;containing radionuclide activities, particle concentration, and prior estimates of the rate parameters (parameters listed in “Parameter&nbsp;names…” section, all at different depths of the model grid, as well as an error covariance matrix,&nbsp;<strong>C<sub>0</sub></strong>, whose diagonal elements are the variances in&nbsp;<strong><em>x</em></strong><sub>0</sub>&nbsp;and whose off-diagonal elements are the error covariances in&nbsp;<strong><em>x</em></strong><sub>0</sub>. FMINCON seeks a vector&nbsp;<strong><em>x&nbsp;</em></strong>which both perfectly satisfies the model (that is, the&nbsp;rhs&nbsp;of equations (1-3) equal 0 when a solution is found), and fits radionuclide and particle concentration data, as well as prior estimates of rate parameters, in a least squares sense, with due consideration for the errors in the data and in the estimates (see equation Further details on the procedure used by FMINCON are reported in Byrd et al. (2000) and Waltz et al. (2005).</p>
</div>
<p>For more detail see the model manual “<a href="http://datadocs.bco-dmo.org/docs/GEOTRACES_Particle_Dynamics/data_docs/Lerner_Th_P_inversion_manual.pdf" target="_blank">Manual of Matlab Code: Nonlinear Inversion of Thorium and Particle Data</a>."</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1232578 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1232578
completed
Olivier Marchal
Woods Hole Oceanographic Institution
5082893374
266 Woods Hole Road
Woods Hole
MA
025431041
US
omarchal@whoi.edu
pointOfContact
Phoebe J. Lam
University of California-Santa Cruz
831-459-4587
1156 High St. Department of Ocean Sciences
Santa Cruz
CA
95064
USA
pjlam@ucsc.edu
pointOfContact
Paul Lerner
Woods Hole Oceanographic Institution
508-289-3279
Clark 456, MS#25 266 Woods Hole Rd
Woods Hole
MA
02543
United States
plerner@whoi.edu
pointOfContact
asNeeded
Unknown
CRUISE
Station_ID
STATION
LAT
LONG
DEPTH
Th_absorp
Th_absorp_1sd
Th_desorp
Th_desorp_1sd
particle_degred
particle_degred_1sd
partile_sink_speed
particle_sink_speed_1sd
theme
None, User defined
Cruise identfier
station
latitude
longitude
depth
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
KN199-04
KN204-01
service
Deployment Activity
Subtropical northern Atlantic Ocean
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Selecting and Applying an Inverse Method to Infer Particle Dynamics from GEOTRACES Data
https://osprey.bco-dmo.org/project/721934
Selecting and Applying an Inverse Method to Infer Particle Dynamics from GEOTRACES Data
<p>NSF abstract:</p>
<p>Processes affecting ocean particles have important consequences for the marine biogeochemical cycles of trace elements; however, our present understanding of these processes is incomplete, as shown by the very large uncertainties (spanning orders of magnitude) of current estimates of particle cycling rates in the ocean. The extensive trace element dataset being generated as part of the GEOTRACES program provides an opportunity to enhance our knowledge of particle processes in a variety of oceanic environments. A scientist from Woods Hole Oceanographic Institution plans to determine the adequacy of different inverse methods to constrain particle processes such as solid-solution exchange and particle processes in the water column from measurements of thorium isotope activity, particle composition, and particle concentration in different size fractions. To attain this goal, the researcher would first assess the adequacy of different inverse methods to infer, from such an eclectic dataset, rate constants of sorption reactions (adsorption and desorption) and particle dynamics (aggregation, disaggregation, sinking, and remineralization). The second step would involve applying the selected method to estimate these constants and their uncertainties at the "superstations" of the GEOTRACES North Atlantic Zonal Section. Once the model is in place, the scientist would test the hypotheses that the rate constants varied (1) vertically within the mesopelagic layer and the deeper layers at these stations and (2) horizontally across the diverse environments sampled along the section.</p>
<p>Broader Impacts: The software to be developed would be archived with the Biological and Chemical Oceanography Data Management Office with instructions so other scientist can use it. One graduate student would be trained on the use of inverse methods in data analyses.</p>
GEOTRACES Particle Dynamics
largerWorkCitation
project
eng; USA
oceans
Subtropical northern Atlantic Ocean
2018-02-26
0
BCO-DMO catalogue of parameters from Estimation of the parameters of a simple model of thorium and particle cycling in the ocean water column, based on a fit to radionuclide and particle data from the US GEOTRACES North Atlantic Section (GA03)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/728409.rdf
Name: CRUISE
Units: unitless
Description: <p>Cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/728410.rdf
Name: Station_ID
Units: unitless
Description: <p>Station identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/728411.rdf
Name: STATION
Units: unitless
Description: <p>Station number (same as station ID)</p>
http://lod.bco-dmo.org/id/dataset-parameter/728412.rdf
Name: LAT
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/728413.rdf
Name: LONG
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/728414.rdf
Name: DEPTH
Units: meters (m)
Description: <p>Water column depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/728415.rdf
Name: Th_absorp
Units: per year (yr -1)
Description: <p>Thorium adsorption rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/728416.rdf
Name: Th_absorp_1sd
Units: per year (yr -1)
Description: <p>One standard deviation of the Thorium adsorption rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/728417.rdf
Name: Th_desorp
Units: per year (yr -1)
Description: <p>Thorium desorption rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/728418.rdf
Name: Th_desorp_1sd
Units: per year (yr -1)
Description: <p>One standard deviation of the Thorium desorption rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/728419.rdf
Name: particle_degred
Units: per year (yr -1)
Description: <p>Particle degradation rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/728420.rdf
Name: particle_degred_1sd
Units: per year (yr -1)
Description: <p>One standard deviation of the Particle degradation rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/728421.rdf
Name: partile_sink_speed
Units: per year (yr -1)
Description: <p>Particle sinking speed</p>
http://lod.bco-dmo.org/id/dataset-parameter/728422.rdf
Name: particle_sink_speed_1sd
Units: meters per year (m/yr)
Description: <p>One standard deviation of the Particle sinking speed</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
48169
https://datadocs.bco-dmo.org/file/1VVMO6jcn1gp35/Lerner_Th_P_model_parameters.csv
Lerner_Th_P_model_parameters.csv
Primary data file for dataset ID 721940
download
https://osprey.bco-dmo.org/dataset/721940/data/download
download
onLine
dataset
<p><strong>Location: </strong>The model is fit to&nbsp;<sup>228,230,234</sup>Th,&nbsp;<sup>234,238</sup>U,&nbsp;<sup>228</sup>Ra, and particle concentration data collected from a section from Bermuda to a station just off the coast of Mauritania. The section crosses the Mid-Atlantic Ridge and the southeastern portion of the North Atlantic Subtropical gyre. The locations and depth ranges of data used to estimate model parameters are listed below (Table 1 of Lerner et al., 2017).</p>
<div><img alt="locations" src="http://datadocs.bco-dmo.org/docs/GEOTRACES_Particle_Dynamics/data_docs/Lerner_et_al_Table1.png" /></div>
<div>
<p><strong>Data: </strong>The thorium and particle cycling model is fit to radionuclide and particle data from the US GEOTRACES North Atlantic Section (GA03). The following lists these data, along with their associated references, in which analytical methods associated with these data are published. The subscript “p” denotes particulate data and “d” denotes “dissolved” data, where particulate and dissolved material are separated by filters with a pore size of 0.8 µm. &nbsp;These data have all been submitted to BCO-DMO, and all except&nbsp;<sup>228</sup>Th are published. These data are also available as part of the GEOTRACES Intermediate Data Product (Mawji et al., 2014).&nbsp;</p>
<div><sup>234,238</sup>U (obtained from salinity) - Owens et al., 2011 (available in datasets of project:&nbsp;<a href="https://www.bco-dmo.org/project/2066" target="_blank">https://www.bco-dmo.org/project/2066</a>)</div>
<div><sup>234</sup>Th<sub>d,p</sub>&nbsp;(dpm&nbsp;m-3) - Owens et al., 2015&nbsp;(available in datasets of project:&nbsp;<a href="https://www.bco-dmo.org/project/2066" target="_blank">https://www.bco-dmo.org/project/2066</a>)</div>
<div><sup>230</sup>Th<sub>d</sub>&nbsp;(dpm&nbsp;m-3)&nbsp; - Hayes et al., 2015a (available in dataset&nbsp;<a href="https://www.bco-dmo.org/dataset/3847" target="_blank">https://www.bco-dmo.org/dataset/3847</a>)</div>
<div><sup>230</sup>Th<sub>p</sub>&nbsp;(dpm&nbsp;m-3)&nbsp; - Hayes et al., 2015b (available in dataset&nbsp;<a href="https://www.bco-dmo.org/dataset/3847" target="_blank">https://www.bco-dmo.org/dataset/3847</a>)</div>
<div><sup>228</sup>Ra (dpm&nbsp;m-3)&nbsp; - Charrette et al., 2015 (available in dataset&nbsp;<a href="https://www.bco-dmo.org/dataset/3847" target="_blank">https://www.bco-dmo.org/dataset/3847</a>)</div>
<div><sup>228</sup>Th<sub>d,p</sub>&nbsp;(dpm&nbsp;m-3) - unpublished (available on BCO-DMO dataset page: <a href="http://lod.bco-dmo.org/id/dataset/3846" target="_blank">http://lod.bco-dmo.org/id/dataset/3846</a>, Charrette et al., 2014)&nbsp;</div>
<div>Particle concentration (mg m-3) - Lam et al., 2015 (available in dataset&nbsp;<a href="https://www.bco-dmo.org/dataset/3871" target="_blank">https://www.bco-dmo.org/dataset/3871</a>)</div>
<div>&nbsp;</div>
<div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The depths at which the radiochemical and particle data are available do not generally coincide. Hence, at each station, an objective interpolation procedure was used to interpolate the data onto an irregular grid (the grid varies with each station and the range of the grid is the same as the “depth range” ). This procedure is described in detail in section 2.4 of Lerner et al., 2016.</div>
<p><strong>Inverse Method:&nbsp;</strong>The algorithm used to fit the model (eqs. 1-3 available in the<a href="http://datadocs.bco-dmo.org/docs/GEOTRACES_Particle_Dynamics/data_docs/Lerner_Th_P_inversion_manual.pdf" target="_blank"> model manual</a>) to the radionuclide and particle data is a nonlinear programming technique as implemented in Matlab’s FMINCON (Matlab R2016b), a constrained optimization routine used to solve nonlinear problems. This algorithm takes as its argument a vector&nbsp;<strong><em>x</em></strong><sub>0&nbsp;</sub>&nbsp;containing radionuclide activities, particle concentration, and prior estimates of the rate parameters (parameters listed in “Parameter&nbsp;names…” section, all at different depths of the model grid, as well as an error covariance matrix,&nbsp;<strong>C<sub>0</sub></strong>, whose diagonal elements are the variances in&nbsp;<strong><em>x</em></strong><sub>0</sub>&nbsp;and whose off-diagonal elements are the error covariances in&nbsp;<strong><em>x</em></strong><sub>0</sub>. FMINCON seeks a vector&nbsp;<strong><em>x&nbsp;</em></strong>which both perfectly satisfies the model (that is, the&nbsp;rhs&nbsp;of equations (1-3) equal 0 when a solution is found), and fits radionuclide and particle concentration data, as well as prior estimates of rate parameters, in a least squares sense, with due consideration for the errors in the data and in the estimates (see equation Further details on the procedure used by FMINCON are reported in Byrd et al. (2000) and Waltz et al. (2005).</p>
</div>
<p>For more detail see the model manual “<a href="http://datadocs.bco-dmo.org/docs/GEOTRACES_Particle_Dynamics/data_docs/Lerner_Th_P_inversion_manual.pdf" target="_blank">Manual of Matlab Code: Nonlinear Inversion of Thorium and Particle Data</a>."</p>
Specified by the Principal Investigator(s)
<p><strong>Problem report:&nbsp;</strong>Beyond issue with gaps in previously reported radionuclide and particle measurements, there are no known issues with rate parameters and&nbsp;routine&nbsp;provided.&nbsp;</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Cruise: KN199-04
KN199-04
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel
KN199-04
William J. Jenkins
Woods Hole Oceanographic Institution
http://bcodata.whoi.edu/US_GEOTRACES/AtlanticSection/Cruise_Report_for_Knorr_199_Final_v3.pdf
Report describing KN199-04
Cruise: KN204-01
KN204-01
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel
KN204-01
Edward A. Boyle
Massachusetts Institute of Technology
http://bcodata.whoi.edu/US_GEOTRACES/AtlanticSection/STS_Prelim_GT11_Doc.pdf
Report describing KN204-01
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel