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ESPM 228



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Dennis Baldocchi
Professor of Biometeorology
Ecosystem Science Division
Department of Environmental Science, Policy and Management
345 Hilgard Hall
University of California, Berkeley
Berkeley, CA 94720
Email: Baldocchi@berkeley.edu

Phone: 510-642-2874


version Sept 23, 2021

Updating notes with lectures from Spring Semester, 2021


Course Description

This course examines contemporary biometeorological and micrometeorological theories, models, and data that relate to the quantification of mass and energy between the biosphere and atmosphere. Each class meeting will consist of a two-hour lecture/discussion. This course will cover five Broad Topics:

1.Micrometeorological Methods for Measuring Mass and Energy Flux Densities

2. Biosphere/Atmosphere Interactions: Models for Integrating Leaf Scale Fluxes to the Canopy Scale

3. Biosphere/Atmosphere Interactions: Integrating and Scaling from Canopy to Landscape Scales

3. Plant-Canopy Micrometeorology

4. Planetary Boundary Layer Turbulence and Characteristics

5. Plant-Atmosphere Interactions: Trace Gas Deposition and Emissions

Upon completion of this course the student should be able to apply this knowledge in a critical manner to review journal articles, write and critique research proposals and to conduct research.

Student Participation

Students will be assigned weekly reading assignment of key reviews associated with each topic. Students will be expected to participate in lively discussion during the lectures and lead a discussion of the reading during the last half-hour of Class.

External exercises will involve the use of data, computation exercises and application of system model calculations to illustrate points made in the lectures. I encourage the students to buy and learn MATLAB. A growing number of exercises will use MATLAB to plot and visualize data.

This year we will use b-space as a Web interface, in addition to this web site, to exchange data and modeling, email one another, etc.

Each student will produce a term paper on a topic of their choice, that fall within the domain of Biometeorology/Micrometeorology. Students are encouraged to develop and analyze simple models and/or analyze data available on the net through such projects as Fluxnet.

At the end of the semester, each student will be responsible for presenting a 30 minute discussion on

Grade will be determined on the basis:

a. Participation in and Leadership of Class Discussions, 10%

b. External Class Assignments, 30%

c. Class Term Paper, 50%.

d. Paper Presentation, 10%

Class Lecture Material and Figures

Pdf copies of lecture overheads and material that augments the lectures is available for downloading on a lecture by lecture basis from the following table.

 LECTURE Number and Notes Lecture Title and Overheads

Reading Assignments from Alternate Voices or Reinforcement

see b-space for pdf

 Section 1. Micrometeorological Methods of Measuring Mass and Energy Flux Densities    Hicks, Bruce B., and Dennis D. Baldocchi. 2020. 'Measurement of Fluxes Over Land: Capabilities, Origins, and Remaining Challenges', Boundary-Layer Meteorology.



 Lecture 1, Micrometeorological Flux Measurement Methods: Background, History,& Future

Dabberdt, W. F., D. H. Lenschow, T. W. Horst, P. R. Zimmerman, S. P. Oncley, and A. C. Delany. 1993. 'Atmosphere-Surface Exchange Measurements', Science, 260: 1472-81.





Lecture 2, Micrometeorological Flux Measurement Methods: Flux-Gradient Theory



Pattey, E., G. Edwards, I. B. Strachan, R. L. Desjardins, S. Kaharabata, and C. W. Riddle. 2006. 'Towards standards for measuring greenhouse gas fluxes from agricultural fields using instrumented towers', Canadian Journal of Soil Science, 86: 373-400.




 Lecture 3 Micrometeorological Flux Measurement Methods: Eddy Covariance, Application, Part 1

 Rebmann, C., et al.  2018. 'ICOS eddy covariance flux-station site setup: a review', International Agrophysics, 32: 471-+.


Aubinet, M., et al. 2000. 'Estimates of the Annual Net Carbon and Water Exchange of Forests: The EUROFLUX Methodology', Advances in Ecological Research, 30: 113-75.



Process raw turbulence data; compute fluxes with different averaging time constants.

SpectralTranfer Function Code (Matlab)




Lecture 4 Micrometeorological Flux Measurement Methods, Eddy Covariance, Application, Part 2,


Flux Processing Software

Fourier Transform Software





Lecture 5 Micrometeorological Flux Measurement Methods, Eddy Covariance, Part 3


Sabbatini, S., I. Mammarella, N. Arriga, G. Fratini, A. Graf, L. Hortriagl, A. Ibrom, B. Longdoz, M. Mauder, L. Merbold, S. Metzger, L. Montagnani, A. Pitacco, C. Rebmann, P. Sedlak, L. Sigut, D. Vitale, and D. Papale. 2018. 'Eddy covariance raw data processing for CO2 and energy fluxes calculation at ICOS ecosystem stations', International Agrophysics, 32: 495-+.


  Lecture 6, Micromet Flux Methods Eddy Covariance, part 4  Papale, Dario. 2012. 'Data Gap Filling.' in Marc Aubinet, Timo Vesala and Dario Papale (eds.), Eddy Covariance: A Practical Guide to Measurement and Data Analysis (Springer Netherlands: Dordrecht).



Lecture 7, Lessons Learned from Flux Networks Baldocchi, D.D. 2008. 'TURNER REVIEW No. 15. 'Breathing' of the terrestrial biosphere: lessons learned from a global network of carbon dioxide flux measurement systems', Australian Journal of Botany, 56: 1-26.
 Section 2. Biosphere/Atmosphere Interactions 





Lecture 8, Leaf Energy Balance and Photosynthesis Modeling, Part 1



Sellers et al. 1997. Science




Lecture 8, Canopy Modeling, Leaf to Canopy Integration Part 1 


Bonan, Gordon B., Edward G. Patton, John J. Finnigan, Dennis D. Baldocchi, and Ian N. Harman. 2021. 'Moving beyond the incorrect but useful paradigm: reevaluating big-leaf and multilayer plant canopies to model biosphere-atmosphere fluxes – a review', Agricultural and Forest Meteorology, 306: 108435.





 Topic 9, Canopy Modeling, Eulerian and Lagrangian Closure Part 2

Brunet, Yves. 2020. 'Turbulent Flow in Plant Canopies: Historical Perspective and Overview', Boundary-Layer Meteorology, 177: 315-64.

Finnigan, John. 2000. 'Turbulence in Plant Canopies', Annu. Rev. Fluid Mech., 32: 519-71.



Topic 10,  Canopy Modeling, Lessons Learned, part 3



Matlab Code

Basic Code for Leaf Photosynthesis




Topic 12, Integrating or Scaling Information from Canopy to Landscape Scales, part 1: Footprint Models

 Foken, T., and M. Y. Leclerc. 2004. 'Methods and limitations in validation of footprint models', Agricultural and Forest Meteorology, 127: 223-34.

Kljun, N., P. Calanca, M. W. Rotach, and H. P. Schmid. 2015. 'A simple two-dimensional parameterisation for Flux Footprint Prediction (FFP)', Geoscientific Model Development, 8: 3695-713.

Schmid, Hans Peter. 2002. 'Footprint modeling for vegetation atmosphere exchange studies: a review and perspective', Agricultural and Forest Meteorology, 113: 159-83.

Matlab Code for Hseih 2d footprint model




 Topic 13 Integrating or Scaling Information from Canopy to Landscape Scales, part 2; planetary boundary layer

Raupach et al. 1998






14. Trace Gas Emissions





Fuentes et al. (2000)


 15. Trace Gas Deposition





Last Updated: 2021-09-23

  This material is based upon work supported by the National Science Foundation and US Department of Energy. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the supporters.