METEO 563: Biometeorology

Instructor: Jose D Fuentes, Tuesday and Thursday 12:05 - 1:20 PM in 109 Electrical Engineering West Building.

METEO 563: Biometeorology

Spring 2017
Course Syllabus 

  • Instructor: Jose D Fuentes
  • Office: 508 Walker Building
  • Telephone: 814 863 1585
  • Email:
  • Web page:

Class meeting time and location: Tuesday and Thursday 12:05 - 1:20 PM in 109 Electrical Engineering West Building

Office hours: 1:00-3:30 PM Monday, 1:00 – 3:30 PM Wednesday, or by appointment 

Course Description

This course introduces concepts to understand the interactions between atmospheric processes and living organisms. It also covers basic concepts to understand how the atmospheric environment influences the functioning of vegetated ecosystems and how plants in turn modify the surrounding environment. The processes governing the exchanges of energy, mass, and momentum between various landscape types and overlying atmosphere are emphasized as well. We discuss micro- and meso-scale weather and climate processes relevant to applications in air quality, hydrology, forestry, and agriculture. To learn how to scale processes from small (e.g., a single plant leaf or a soil plot) to large (e.g., a forest ecosystem) dimensions, one-dimensional numerical models are introduced. With these models, processes such as trace gas (e.g., carbon dioxide, ozone, isoprene) exchange between vegetation and atmosphere will be diagnosed and predicted. Students will visit the laboratory to learn the contemporary types of technologies needed to investigate surface-atmosphere interactions. 

Course Goals

The goals of this course are to learn and apply concepts to study the interactions between the biosphere and the atmosphere, and to understand how surface-atmosphere feedbacks respond to environmental change.



  • An introduction to environmental biophysics (2nd Edition) by GS Campbell and JM Norman, 1998.

Additional texts:

  • Plants and microclimate by HG Jones, 1992.
  • Principles of environmental physics by JL Monteith and MH Unsworth, 2013.
  • Plants and microclimate by H.G. Jones, 2015 

Relevant Journals:

Throughout the semester, several journal review articles will be studied and discussed.  Articles will come from the following journals:

  • Agricultural and Forest Meteorology
  • Journal of Applied Meteorology and Climatology
  • Boundary-Layer Meteorology
  • Journal of Geophysical Research-Atmospheres
  • Journal of Geophysical Research-Biogeosciences
  • Global Change Biology
  • Biogeosciences 

Course load and evaluation

This course will have two 1.25-hour lectures or class discussions per week.  It is expected that students and instructor will closely interact through joint discussions on research topics of interest to students’ own research.  The current literature will be surveyed and discussed.  Literature review will be incorporated in assignments and term papers.  Course evaluation will entail assignments, a mid-term exam, and a term paper. The paper will be based on students’ research interest and must include and apply the concepts covered in class.  Also, the paper must follow the format of peer-reviewed journals.  Marks for the course will be allocated as follows:

  • Assignments (4) 15 % (last assignment will be due on 27 April)
  • Mid-term paper:
    • Outline 10 % (23 March)
    • First draft 15 % (13 April)
    • Final draft 15 % (due anytime before 25 April)
    • Paper presentation 10 % (27 April)
  • Mid-term exam 35 % (4 April) 

The final grade will be determined according to the following scale:

  • A: Above 90 %             
  • A-: 85-89 %
  • B+: 80-84 %
  • B: 75-79 %
  • B-: 70-74 %
  • C+: 65-69 %
  • C: 60-64 %
  • D: 55-59 %
  • F: Less than 55 % 


Assignments will not be accepted beyond the assigned due date. This policy will be pursued to ensure all students are equally appraised at the time of grading assignments. Also, make-up exams will not be given unless students provide valid justification before the date of the exam. Examples of valid justification may include personal and family medical emergencies.

Academic integrity

Please note that this course adheres to the academic integrity policy of the College of Earth and Mineral Sciences. The policy can be obtained from Students are expected to present their own work. Classmates may collaborate on assignments. However, each student must write up his or her answers separately.  Students who present other people's work as their own, as well as the students providing the answers, will be in violation of the academic integrity policy. It is never acceptable to copy the work of another person. Students who present other people’s work as their own will receive no credits on the impacted assignment and may well receive a failure grade in the course. Plagiarism is also a serious academic misconduct. Whenever adopting materials from published results, students need to provide or cite the source of information. 

Other considerations  

Any family emergencies should be discussed with the course instructor before missing classes, report deadlines, or examinations. This course abides by the Penn State University Class Attendance policy given at Students should attend every class and should be responsible for the work covered in class. 

Accommodations for students with disabilities

Let course instructor know in advance of religious observances or any required disability accommodation.  The Office of Disability Services ( requests and maintains disability-related documents, certifies eligibility for services; determines academic adjustments, auxiliary aids, and/or services; and develops plans for the provision of academic adjustments, auxiliary aids, and/or services as mandated under Title II of the ADA Amendments Act (ADAAA) of 2008 and Section 504 of the Rehabilitation Act of 1973. A list of these services is provided at 

Campus emergencies, including weather delays

Campus emergencies, including weather delays, are announced on Penn State Live ( and communicated to cellphones, email, the Penn State Facebook page, and Twitter via PSUTXT (to sign up, please see 

Diversity, inclusion, and respect

Penn State is “committed to creating an educational environment which is free from intolerance directed toward individuals or groups and strives to create and maintain an environment that fosters respect for others” as stated in Policy AD29 Statement on Intolerance. All members of this class are expected to contribute to a respectful, welcoming and inclusive environment and to interact with civility. For additional information, see

  • Penn State Affirmative Action non-discrimination statement:
  • Policy AD 85 Sexual and gender-based harassment and misconduct, Title IX
  • Policy AD91 Discrimination and Harassment, and Related inappropriate Conduct:
  • Penn State Statement on Diversity, Equity, and Inclusive Excellence:
  • Penn State Values:
  • Penn State Principles:
  • All In at Penn State: A Commitment to Diversity and Inclusion: 

Mandated reporting statement

Penn State’s policies require me, as a faculty member, to share information about incidents of sex-based discrimination and harassment (discrimination, harassment, sexual harassment, sexual misconduct, dating violence, domestic violence, stalking, and retaliation) with Penn State’s Title IX coordinator or deputy coordinators, regardless of whether the incidents are stated to me in person or shared by students as part of their coursework.  For more information regarding the University's policies and procedures for responding to reports of sexual or gender-based harassment or misconduct, please visit Additionally, I am required to make a report on any reasonable suspicion of child abuse in accordance with the Pennsylvania Child Protective Services Law.

Course Outline - BOOK CHAPTER

    A. Biometeorology overview
    B. Concepts of energy and mass flux densities
    C. Measurement terminology
  2. RADIATION - 10, 11, 15
    A. Solar radiation 
    Solar constant, spectral distribution
    Planck’s law, Wien’s law
    B.Terrestrial radiation
    Spectral distribution
    Stefan-Boltzmann law, Kirchoff’s law
    C. Radiative properties of natural materials
    D. Net radiation balance
    E. Radiative transfer in plant canopies
    Observations and numerical modeling
    Remote sensing
    F. Measurements and estimation
    A. Patterns of atmospheric and soil temperature
    B. Kinetics of photosynthesis, respiration, isoprene emission
    C. Growth and phenology based on temperature summation units
    D. First and second laws of thermodynamics
    E. Thermal indices
    F. Measurements
    A. Gas Laws
    B. Physical and chemical properties of water
    C. Measures of atmospheric water vapor 
    Relative humidity
    Absolute humidity
    Virtual temperature
    Saturation vapor pressure
    Clausius-Clapyeron equation
    D. Diurnal and seasonal patterns of humidity
    E. Vertical gradients of humidity
    F. Field measurements
    A. Characteristics of atmospheric turbulence
    B. Wind profiles above uniform surfaces
    C. Influences of atmospheric stability on wind profiles
    D. Wind flow within plant canopies
    E. Reynold’s averaging and turbulence intensities
    F. Spectrum of turbulence
    G. Observations
    A. Forced convection
    B. Free convection
    C. Molecular diffusion
    D. Molar fluxes
    E. Resistances and conductances
    F. Calculations of fluxes
    A. Leaf temperature
    B. Aerodynamic temperature of plant canopies
    C. Radiometric temperature of vegetation
    D. Leaf energy balance
    E. Canopy transpiration and photosynthesis
    F. Assimilation models
    G. Control on stomatal conductance and response to forcings
    H. Evaporation, potential evaporation, equilibrium evaporation, and transpiration
    A. Aerodynamic
    B. Bowen-ratio energy balance
    C. Dry deposition of airborne pollutants and aerosols
    D. Eddy covariance
    E. Relaxed eddy accumulation