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Environmental Science & Engineering (ESE) Graduate Courses (2020-21)

ESE 100. Special Problems in Environmental Science and Engineering. Up to 12 units by arrangement: any term. Prerequisites: instructor's permission. Special courses of readings or laboratory instruction. Graded pass/fail. Instructor: Staff.
ESE 101. Earth's Atmosphere. 9 units (3-0-6): first term. Introduction to the fundamental processes governing atmospheric circulations and climate. Starting from an overview of the observed state of the atmosphere and its variation over the past, the course discusses Earth's radiative energy balance including the greenhouse effect, Earth's orbit around the Sun and climatic effects of its variations, and the role of atmospheric circulations in maintaining the energy, angular momentum, and water balances, which determine the distributions of temperatures, winds, and precipitation. The focus throughout is on order-of-magnitude physics that is applicable to climates generally, including those of Earth's past and future and of other planets. Instructor: Schneider.
ESE 102. Earth's Oceans. 9 units (3-0-6): first term. This course will provide a basic introduction to physical, chemical and biological properties of Earth's ocean. Topics to be covered include: oceanographic observational and numerical methods as well as the phenomenology and distribution of temperature, salinity, and tracers. Fundamentals of ocean dynamics, such as Ekman layers, wind-driven gyres, and overturning circulations. Ocean biology and chemistry: simple plankton population models, Redfield ratios, air-sea gas exchange, productivity and respiration, carbon cycle basics. Changes in ocean circulation over Earth's history and its impact on past climate changes. Instructor: Thompson.
ESE 103. Earth's Biogeochemical Cycles. 9 units (3-0-6): second term. Global cycles of carbon, nitrogen and sulfur. Photosynthesis, respiration and net primary production. Soil formation, erosion, and carbon storage. Ecosystem processes, metrics, and function. Nutrient supply and limitation. Microbial processes underlying weathering, decomposition, and carbon remineralization. Stable isotope tracers in the carbon and hydrologic cycles. The human footprint on the Earth. Instructor: Frankenberg.
ESE 104. Current Problems in Environmental Science and Engineering. 1 unit: first term. Discussion of current research by ESE graduate students, faculty, and staff. Instructor: Frankenberg.
Bi/Ge/ESE 105. Evolution. 12 units (3-4-5): second term. Prerequisites: Completion of Core Curriculum Courses. Maximum enrollment: 15, by application only. The theory of evolution is arguably biology's greatest idea and serves as the overarching framework for thinking about the diversity and relationships between organisms. This course will present a broad picture of evolution starting with discussions of the insights of the great naturalists, the study of the genetic basis of variation, and an introduction to the key driving forces of evolution. Following these foundations, we will then focus on a number of case studies including the following: evolution of oxygenic photosynthesis, origin of eukaryotes, multicellularity, influence of symbiosis, the emergence of life from the water (i.e. fins to limbs), the return of life to the water (i.e. limbs to fins), diversity following major extinction events, the discovery of Archaea, insights into evolution that have emerged from sequence analysis, and finally human evolution and the impact of humans on evolution (including examples such as antibiotic resistance). A specific focus for considering these issues will be the island biogeography of the Galapagos. Given in alternate years; not offered 2020-21. Instructors: Phillips, Orphan.
ESE 106. Research in Environmental Science and Engineering. Units by arrangement: any term. Prerequisites: instructor's permission. Exploratory research for first-year graduate students and qualified undergraduates. Graded pass/fail. Instructor: Staff.
ESE 110 abc. Seminar in Environmental Science and Engineering. 1 unit: first, second, third terms. Seminar on current developments and research in environmental science and engineering. Graded pass/fail. Instructor: Callies.
Ge/ESE 118. Methods in Data Analysis. 9 units (3-0-6): first term. Prerequisites: Ma 1 or equivalent. Introduction to methods in data analysis. Course will be an overview of different ways that one can quantitatively analyze data, and will not focus on any one methodology. Topics will include linear regression, least squares inversion, Fourier analysis, principal component analysis, and Bayesian methods. Emphasis will be on both a theoretical understanding of these methods and on practical applications. Exercises will include using numerical software to analyze real data. Not offered 2020-21. Instructor: Staff.
BEM/Ec/ESE 119. Environmental Economics. 9 units (3-0-6): first term. Prerequisites: Ec 11 or equivalent. This course provides a survey from the perspective of economics of public policy issues regarding the management of natural resources and the protection of environmental quality. The course covers both conceptual topics and recent and current applications. Included are principles of environmental and resource economics, management of nonrenewable and renewable resources, and environmental policy with the focus on air pollution problems, both local problems (smog) and global problems (climate change). Not offered 2020-21.
ESE 130. Introduction to Atmosphere and Ocean Dynamics. 9 units (3-0-6): second term. Prerequisites: ESE 101/102 or instructor's permission. This course is an introduction to the fluid dynamics of the atmosphere and ocean, with an emphasis on dynamical concepts that explain the large-scale circulation of both fluids. Starting from the equations of motion, we will develop an understanding of geostrophic and hydrostatic balance, inertia-gravity waves, geostrophic adjustment, potential vorticity, quasi-geostrophic dynamics, Rossby waves, baroclinic instability, and Ekman layers. Instructor: Callies.
ESE 131. Ocean Dynamics. 9 units (3-0-6): third term. Prerequisites: ESE 130 or instructor's permission. This course gives an in-depth discussion of the fluid dynamics of the world ocean. Building on the concepts developed in ESE 130, this course explores the vertical structure of the wind-driven gyre circulation, thermocline theory, the dynamics of the Southern Ocean, eddies and eddy parameterizations, geostrophic turbulence, submesoscale dynamics, the circulation of the deep ocean, tides, internal waves, and turbulent mixing. Instructor: Callies.
ESE 132. Tropical Atmosphere Dynamics. 9 units (3-0-6): third term. Prerequisites: ESE 130 or instructor’s permission. Phenomenological description of tropical atmospheric circulations at different scales, and theories or models that capture the underlying fundamental dynamics, starting from the large-scale energy balance and moving down to cumulus convection and hurricanes. Topics to be addressed include: large-scale circulations such as the Hadley, Walker, and monsoonal circulations, the intertropical convergence zone, equatorial waves, convectively coupled waves, and hurricanes. Offered 2020-21. Instructor: Schneider.
ESE 133. Global Atmospheric Circulations. 9 units (3-0-6): second term. Prerequisites: ESE 130 or instructor's permission. Introduction to the global-scale fluid dynamics of atmospheres, beginning with a phenomenological overview of observed circulations on Earth and other planets and leading to currently unsolved problems. Topics include constraints on atmospheric circulations and zonal winds from angular momentum balance; Rossby wave generation, propagation, and dissipation and their roles in the maintenance of global circulations; Hadley circulations and tropical-extratropical interactions; energy cycle and thermodynamic efficiency of atmospheric circulations. The course focuses on Earth's atmosphere but explores a continuum of possible planetary circulations and relationships among them as parameters such as the planetary rotation rate chance. Not offered 2020-21. Instructor: Staff.
ESE 134. Cloud and Boundary Layer Dynamics. 9 units (3-0-6): third term. Prerequisites: ESE 130 or instructor's permission. Introduction to the dynamics controlling boundary layers and clouds and how they may change with climate, from a phenomenological overview of cloud and boundary layer morphologies to closure theories for turbulence and convection. Topics include similarity theories for boundary layers; mixed-layer models; moist thermodynamics and stability; stratocumulus and trade-cumulus boundary layers; shallow cumulus convection and deep convection. Not offered 2020-21. Instructor: Schneider.
ESE 135. Topics in Atmosphere and Ocean Dynamics. 6 units (2-0-4): third term. Prerequisites: ESE 101/102 or equivalent. A lecture and discussion course on current research in atmosphere and ocean dynamics. Topics covered vary from year to year and may include global circulations of planetary atmospheres, geostrophic turbulence, atmospheric convection and cloud dynamics, wave dynamics and large-scale circulations in the tropics, marine physical-biogeochemical interactions, and dynamics of El Niño and the Southern Oscillation. Not offered 2020-21. Instructor: Callies.
ESE 136. Climate Models. 6 units (2-0-4): third term. Prerequisites: ESE 101 or instructor's permission. Introduction to climate models, from numerical methods for the underlying equations of motion to parameterization schemes for processes such as clouds, sea ice, and land hydrology. The course will move from an overview of modeling concepts to the practice of climate modeling, with hands-on exercises in running a climate model and analyzing and understanding its output. It will enable students to design their own model experiments and to evaluate modeling results critically. Not offered 2020-21. Instructor: Schneider.
ESE 137. Polar Oceanography. 9 units (3-0-6): third term. Prerequisites: ESE 131 or instructor's permission. This course focuses on high latitude processes related to the the Earth's oceans and their interaction with the cryosphere, including glaciers, ice shelves and sea ice. The course starts with introductory lectures related to regional circulation features, water mass modification and ice dynamics. A single topic will be selected to explore in detail through the scientific literature and through individual projects. Given in alternate years; not offered 2020-21. Instructor: Thompson.
ESE 138. Ocean Turbulence and Wave Dynamics. 9 units (3-0-6): third term. Prerequisites: ESE 131 or instructor's permission. Introduction to the dynamics of ocean mixing and transport with a focus on how these processes feedback on large-scale ocean circulation and climate. Topics include: vorticity and potential vorticity dynamics, planetary and topographic Rossby waves, inertia-gravity waves, mesoscale eddies, turbulent transport of tracers, eddy diffusivity in turbulent flows, frontogenesis and submesoscale dynamics, diapycnal mixing. This course will also include a discussion of observational techniques for measuring mesoscale and small-scale processes in the ocean. Not offered 2020-21. Instructor: Staff.
Ge/ESE 139. Introduction to Atmospheric Radiation. 9 units (3-0-6): second term. Prerequisites: Ma 2, Ph 2, or instructor's permission. The basic physics of absorption and scattering of light by molecules, aerosols, and clouds. Theory of radiative transfer. Band models, correlated-k distributions and other approximate methods. Solar insolation, thermal emission, heating rates and radiances. Applications to Earth, Planets and Exoplanets. Given in alternate years; not offered 2020-21. Instructor: Yung.
Ge/ESE 140 c. Stable Isotope Biogeochemistry. 9 units (3-0-6): third term. Prerequisites: Ge 140a or equivalent. An introduction to the use of stable isotopes in biogeochemistry, intended to give interested students the necessary background to understand applications in a variety of fields, from modern carbon cycling to microbial ecology to records of Ancient Earth. Topics include the principles of isotope distribution in reaction networks; isotope effects in enzyme-mediated reactions, and in metabolism and biosynthesis; characteristic fractionations accompanying carbon, nitrogen, and sulfur cycling; and applications of stable isotopes in the biogeosciences. Not offered 2020-21. Instructor: Sessions.
ESE/Ge 142. Aquatic Chemistry of Natural Waters. 9 units (3-0-6): third term. Prerequisites: Ch 1 or instructor's permission. Inorganic chemistry of natural waters with an emphasis on equilibrium solutions to problems in rivers, lakes, and the ocean. Topics will include, acid-base chemistry, precipitation, complexation, redox reactions, and surface chemistry. Examples will largely be drawn from geochemistry and geobiology. Selected topics in kinetics will be covered based on interest and time. Instructor: Adkins.
Ge/ESE 143. Organic Geochemistry. 9 units (3-2-4): third term. Prerequisites: Ch 41 a or equivalent. Main topics include the analysis, properties, sources, and cycling of natural organic materials in the environment, from their production in living organisms to burial and decomposition in sediments and preservation in the rock record. Specific topics include analytical methods for organic geochemistry, lipid structure and biochemistry, composition of organic matter, factors controlling organic preservation, organic climate and CO2 proxies, diagenesis and catagenesis, and biomarkers for ancient life. A laboratory component (three evening labs) teaches the extraction and analysis of modern and ancient organic biomarkers by GC/MS. Class includes a mandatory one-day (weekend) field trip to observe the Monterey Formation. Offered 2020-21. Instructor: Sessions.
ESE 144. Climate from Space. 9 units (3-0-6): third term. Introduction to satellite remote sensing. Earth's energy balance. Atmospherics physics and composition. Ocean dynamics and ice physics from space. The water, energy and carbon cycles. The Earth's biosphere from space. The climate system. Given in alternate years; offered 2020-21. Instructors: Teixeira, Thompson.
Ge/ESE 149. Marine Geochemistry. 9 units (3-0-6): second term. Prerequisites: ESE 102. Introduction to chemical oceanography and sediment geochemistry. We will address the question "Why is the ocean salty?" by examining the processes that determine the major, minor, and trace element distributions of seawater and ocean sediments. Topics include river and estuarine chemistry, air/sea exchange, nutrient uptake by the biota, radioactive tracers, redox processes in the water column and sediments, carbonate chemistry, and ventilation. Given in alternate years; not offered 2020-21. Instructor: Adkins.
Ge/ESE 150. Planetary Atmospheres. 9 units (3-0-6): third term. Prerequisites: Ch 1, Ma 2, Ph 2, or equivalents. Origin of planetary atmospheres, escape, and chemical evolution. Tenuous atmospheres: the moon, Mercury, and outer solar system satellites. Comets. Vapor-pressure atmospheres: Triton, Io, and Mars. Spectrum of dynamical regimes on Mars, Earth, Venus, Titan, and the gas giant planets. Instructor: Knutson.
Ge/ESE 154. Readings in Paleoclimate. 3 units (1-0-2): second term. Prerequisites: instructor's permission. Lectures and readings in areas of current interest in paleoceanography and paleoclimate. Instructor: Adkins.
Ge/ESE 155. Paleoceanography. 9 units (3-0-6): second term. Prerequisites: ESE 102. Evaluation of the data and models that make up our current understanding of past climates. Emphasis will be placed on a historical introduction to the study of the past ten thousand to a few hundred thousand years, with some consideration of longer timescales. Evidence from marine and terrestrial sediments, ice cores, corals, and speleothems will be used to address the mechanisms behind natural climate variability. Models of this variability will be evaluated in light of the data. Topics will include sea level and ice volume, surface temperature evolution, atmospheric composition, deep ocean circulation, tropical climate, ENSO variability, and terrestrial/ocean linkages. Given in alternate years; offered 2020-21. Instructor: Adkins.
ESE 156. Remote Sensing of the Atmosphere and Biosphere. 9 units (3-0-6): first term. An introduction into methods to quantify trace gases as well as vegetation properties remotely (from space, air-borne or ground-based). This course will provide the basic concepts of remote sensing, using hands-on examples to be solved in class and as problem-sets. Topics covered include: Absorption spectroscopy, measurement and modeling techniques, optimal estimation theory and error characterization, applications in global studies of biogeochemical cycles and air pollution/quality. This course is complementary to EE/Ae 157ab and Ge/EE/ESE 157c with stronger emphasis on applications for the atmosphere and biosphere. Students will work with real and synthetic remote sensing data (basic knowledge of Python advantageous, will make use of Jupyter notebooks extensively). Instructor: Frankenberg.
Ge/EE/ESE 157 c. Remote Sensing for Environmental and Geological Applications. 9 units (3-3-3): third term. Analysis of electromagnetic radiation at visible, infrared, and radio wavelengths for interpretation of the physical and chemical characteristics of the surfaces of Earth and other planets. Topics: interaction of light with materials, spectroscopy of minerals and vegetation, atmospheric removal, image analysis, classification, and multi-temporal studies. This course does not require but is complementary to EE 157ab with emphasis on applications for geological and environmental problems, using data acquired from airborne and orbiting remote sensing platforms. Students will work with digital remote sensing datasets in the laboratory and there will be one field trip. Instructor: Ehlmann.
ESE/ChE 158. Aerosol Physics and Chemistry. 9 units (3-0-6): second term. Fundamentals of aerosol physics and chemistry; aerodynamics and diffusion of aerosol particles; condensation and evaporation; thermodynamics of particulate systems; nucleation; coagulation; particle size distributions; optics of small particles. Offered 2020-21. Instructors: Seinfeld, Flagan.
ESE/Bi 166. Microbial Physiology. 9 units (3-1-5): first term. Prerequisites: one year of general biology recommended. A course on growth and functions in the prokaryotic cell. Topics covered: growth, transport of small molecules, protein excretion, membrane bioenergetics, energy metabolism, motility, chemotaxis, global regulators, and metabolic integration. Instructor: Leadbetter.
ESE/Bi 168. Microbial Metabolic Diversity. 9 units (3-0-6): second term. Prerequisites: ESE 142, ESE/Bi 166. A course on the metabolic diversity of microorganisms. Basic thermodynamic principles governing energy conservation will be discussed, with emphasis placed on photosynthesis and respiration. Students will be exposed to genetic, genomic, and biochemical techniques that can be used to elucidate the mechanisms of cellular electron transfer underlying these metabolisms. Given in alternate years; offered 2020-21. Instructor: Newman.
ESE/Ge/Ch 171. Atmospheric Chemistry I. 9 units (3-0-6): third term. Prerequisites: Ch 1 or equivalent. A detailed course about chemical transformation in Earth's atmosphere. Kinetics, spectroscopy, and thermodynamics of gas-phase chemistry of the stratosphere and troposphere; sources, sinks, and lifetimes of trace atmospheric species; stratospheric ozone chemistry; oxidation mechanisms in the troposphere. Instructors: Seinfeld, Wennberg.
ESE/Ge/Ch 172. Atmospheric Chemistry II. 3 units (3-0-0): first term. Prerequisites: ESE/Ge/Ch 171 or equivalent. A lecture and discussion course about active research in atmospheric chemistry. Potential topics include halogen chemistry of the stratosphere and troposphere; aerosol formation in remote environments; coupling of dynamics and photochemistry; development and use of modern remote-sensing and in situ instrumentation. Graded pass/fail. Offered 2020-21. Instructors: Seinfeld, Wennberg.
ESE/Ch 176. Environmental Physical Organic Chemistry Part I. 9 units (3-0-6): second term. Prerequisites: Ch 41 a,b or instructor's permission. This course will cover selected aspects of the chemistry of aquatic systems. Lectures cover basic principles of physical-organic chemistry relevant to the aquatic environment under realistic conditions. Specific topics covered in Part I include the basic principles of equilibrium chemical and physical processes important natural waters. Topics include: chemical potential, fugacity, phase transfer, acid-base chemistry, metal-ligand substitution chemistry, surface chemistry, octanol-water partitioning, air-water partitioning, partitioning to solid organic matter and biomedia, sorption processes, air-water exchange dynamics, and the kinetics and mechanisms of coupled organic and inorganic redox reactions. Thermodynamics, transport, phase transfer and kinetics are emphasized. Instructor: Hoffmann.
ESE/Ch 177. Environmental Physical Organic Chemistry Part II. 9 units (3-0-6): third term. Prerequisites: ESE/Ch 176 or instructor's permission. This course will cover selected aspects of the organic chemistry of aquatic systems and coupled air-water systems. Topics include photochemical transformations, biochemical transformations in sub-surface water, surface water, and sediments, heterogeneous surface reactions and catalysis, hydrolysis reactions, nucleophilic displacement and substitution reactions, elimination reactions, carboxylic acid ester hydrolysis, thiophosphoric acid ester hydrolysis, carbamate ester hydrolysis, and amide ester hydrolysis. The primary goal is to better understand factors controlling the fate and behavior of organic compounds and persistent organic pollutants in the global environment. Case studies will be presented. Instructor: Hoffmann.
Ge/ESE/Bi 178. Microbial Ecology. 9 units (3-2-4): second term. Prerequisites: Either ESE/Bi 166 or ESE/Bi 168. Structural, phylogenetic, and metabolic diversity of microorganisms in nature. The course explores microbial interactions, relationships between diversity and physiology in modern and ancient environments, and influence of microbial community structure on biogeochemical cycles. Introduction to ecological principles and molecular approaches used in microbial ecology and geobiological investigations. Offered in alternate years; offered 2020-21. Instructor: Orphan.
ESE 200. Advanced Topics in Environmental Science and Engineering. Units by arrangement: any term. Course on contemporary topics in environmental science and engineering. Topics covered vary from year to year, depending on the interests of the students and staff.
Ge/Bi/ESE 246. Molecular Geobiology Seminar. 6 units (2-0-4): first term. Critical reviews and discussion of classic papers and current research in microbiology and geomicrobiology. As the topics will vary from year to year, it may be taken multiple times. Instructor: Orphan.
ESE 300. Thesis Research. : .

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