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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 Feb 12, 2019

Updating notes with lectures from Spring Semester, 2019

Mondays 14-16

Office Hours: By Appointment

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 Assignment

see b-space for pdf

 Section 1. Micrometeorological Methods of Measuring Mass and Energy Flux Densities    



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

Dabberdt et ak, 1993 Science





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



Pattey et al. 2006 Can J Soil Sci




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


Moore 1986. BLM

Burba and Anderson. LICOR Eddy Covariance Manual



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,

Hollinger et al. 2004. GCB

Flux Processing Software

Fourier Transform Software





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


Moffat et al. 2007. AgForestMet





Lecture 6, Lessons Learned from Flux Networks Baldocchi. 2008. Aust J Bot
 Section 2. Biosphere/Atmosphere Interactions 





Lecture 7, Leaf Energy Balance and Photosynthesis Modeling, Part 1



Sellers et al. 1997. Science




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


duPury & Farquhar. 1997. Plant, Cell, Environment

Mat Williams et al 2009 Biogeosciences





 Topic 9, Canopy Modeling, Eulerian Closure Part 2

Finnigan 2000. Annual Review Fluid Mechanics



Topic 10,  Canopy Modeling, Lagrangian framework, part 3


Nikolov et al.(1995)

Matlab Code

Basic Code for Leaf Photosynthesis

11. Topic 11, Canopy Modeling, Lessons Learned  



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


Schmid 2002. AgForestMet

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: 2019-03-15

  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.