ESPM 228
ADVANCED TOPICS IN BIOMETEOROLOGY AND MICROMETEOROLOGY, 2019
Instructor:
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: 5106422874
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 twohour 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. PlantCanopy Micrometeorology
4. Planetary Boundary Layer Turbulence and Characteristics
5. PlantAtmosphere 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 halfhour 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 bspace 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 bspace 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', BoundaryLayer 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. 'AtmosphereSurface Exchange Measurements', Science, 260: 147281. 

Lecture 2, Micrometeorological Flux Measurement Methods: FluxGradient 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: 373400. 

Lecture 3 Micrometeorological Flux Measurement Methods: Eddy Covariance, Application, Part 1 
Rebmann, C., et al. 2018. 'ICOS eddy covariance fluxstation 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: 11375. Assignment Process raw turbulence data; compute fluxes with different averaging time constants. 

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

6.  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). 
7. 
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: 126. 
Section 2. Biosphere/Atmosphere InteractionsÂ 


Lecture 8, Leaf Energy Balance and PhotosynthesisÂ 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 bigleaf and multilayer plant canopies to model biosphereatmosphere fluxes â€“ 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', BoundaryLayer Meteorology, 177: 31564. Finnigan, John. 2000. 'Turbulence in Plant Canopies', Annu. Rev. Fluid Mech., 32: 51971. 

Topic 10, Canopy Modeling, Lessons Learned, part 3 
Matlab Code 

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: 22334. Kljun, N., P. Calanca, M. W. Rotach, and H. P. Schmid. 2015. 'A simple twodimensional parameterisation for Flux Footprint Prediction (FFP)', Geoscientific Model Development, 8: 3695713. Schmid, Hans Peter. 2002. 'Footprint modeling for vegetation atmosphere exchange studies: a review and perspective', Agricultural and Forest Meteorology, 113: 15983. 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 

Fuentes et al. (2000) 

15.  Trace Gas Deposition 

Last Updated: 20231014