Graduate Study

Preparatory Studies

The Department of Physical Sciences’ education and research programs place a heavy reliance on quantitative skills. Incoming students are expected to have a strong background in physical sciences and mathematics. Undergraduate majors that provide preparation for graduate study in Physical Sciences include physics, applied mathematics, engineering, chemistry, and geology. Biological Sciences majors interested in pursuing graduate work in Physical Sciences are encouraged to take introductory physics and calculus through ordinary differential equations.

Typical Course of Study

All students in the School of Marine Science begin with the core curriculum in Marine Sciences (MS 501, 502, 503, and 505). Upper-level lecture and seminar courses related to the student's area of specialization are selected in consultation with the student's advisor and committee. A weekly departmental seminar during the academic year brings together faculty, students, and staff for updates on current research and informal interaction.

Chemical Oceanography/Marine Geochemistry

Graduate students in chemical oceanography/marine geochemistry may specialize in any of the various aspects of marine and environmental chemistry. Required courses include Principles of Chemical Oceanography (MSCI 524); Advanced Aquatic Chemistry (MSCI 630) is recommended. Specialized course work in other areas of marine and environmental chemistry can be selected through recommendation of the student’s thesis committee. Students interested in geological oceanography may pursue tracks emphasizing sedimentary environments and stratigraphy, sediment geochemistry, or physical transport/morphodynamic processes. Courses include marine sedimentation, coastal morphodynamics, benthic boundary layers, multivariate and time-series analysis, and isotope geochronology.

Geological Oceanography

Geological oceanography students are required to take Geological Oceanography (MSCI 522). In addition, depending on a student’s particular emphasis, he or she may be required to take advanced courses in physical, chemical, or biological oceanography. For students majoring in physical oceanography, required courses include Principles of Coastal and Estuarine Physical Oceanography (MSCI 520). Advanced courses address estuarine hydrodynamics and water quality, providing an in-depth focus on estuarine physics and its influence on biogeochemical processes. Additional courses address other advanced topics in ocean dynamics and apply three-dimensional numerical modeling to estuarine and coastal issues.


506 – Scientific Communication Skills. Spring (2) Milliman. The important elements of oral and written presentation skills for communicating scientific research will be reviewed in this course. The course addresses topics such as the critical evaluation of literature, development of scientific questions and rationale for research, and formulation of conceptual models for developing high-quality scientific research projects. Oral and written presentation skills are emphasized through written exercises and class presentations, with peer review. [top]

515A-D - Marine Science Seminar. Fall and Spring (1) Staff. The departmental seminar course offers a multidisciplinary review of significant areas of marine science. Guest speakers will present a variety of views, and course participants will organize and present talks related to the seminar theme. Students may repeat seminar registration as required by their respective departments; however, only two credits will be applicable to an SMS degree. [top]

520 - Principles of Coastal and Estuarine Physical Oceanography. Spring (3) Brubaker, Friedrichs. Following a review of the governing equations,  lectures and discussions will focus on dynamics of currents and waves on continental shelves and in estuaries. Topics include fundamentals of wind and density-drive flow, and aspects of fronts, mixing, and secondary circulation. Time-dependent motion such as surface gravity waves, internal waves, and coastally trapped waves and tides also will be discussed. [top]

522 – Principles of Geological Oceanography. Fall, even years (3) Kuehl. A brief review of the tectonic history of the oceans will be presented, followed by detailed study of the ocean margins, including sea-level history and near-shore geological processes in the coastal zone and continental shelf regions. The geological effects of bottom currents on ocean sediments will be examined along with ocean basin sediment history and approaches to pale oceanography. [top]

524 - Principles of Chemical Oceanography. Spring (3) Bauer, Canuel. Prerequisite: Instructor’s consent. This course covers in a comprehensive and integrated manner the important factors controlling the chemical composition of seawater. Basic principles of chemical thermodynamics will be applied to the seawater medium and will serve to introduce contemporary, global-scale chemical processes such as the role of the oceans in global climate change. Selected topics include distributions of the bio-limiting elements; chemistry of marine sediments; trace metal chemistry; marine organic chemistry; and ocean-atmosphere interactions. [top]

545 - Marine Sedimentation. Spring, even years (3) Milliman, Staff. This course provides an introduction to continental-margin sedimentary environments with emphasis on physical, biological, and chemical controls on the development of sedimentary strata over a range of spatial and temporal scales. Case studies from modern settings will be used to illustrate concepts of strata formation. Laboratory exercises include petrographic, textural, and mineralogical analysis. [top]

550 - Rivers: Processes and Problems. Spring, odd years (3) Milliman. Rivers form the main link between land and the ocean, discharging more than 35 thousand km3 of water and more than 20 billion tons of suspended and dissolved solids annually to the global ocean. Three central themes are stressed: 1) How do rivers work: the hydrologic cycle and water budget, basin character, physical and chemical erosion; 2) Temporal and spatial variations, ranging from seasonal to millennial, with particular emphasis on catastrophic events; 3) Human interactions: land degradation, river management, future impact of climatic change and anthropogenic activities. Includes a one-week field trip. [top]

552 - Coastal Sedimentary Environments. Fall (3) Staff. This course examines the depositional systems of coastal sedimentary environments such as sand-dominated (barrier islands), mixed (modern deltas), and mud-dominated (wetlands, tidal flats). Modern and ancient examples will be explored in field trips and lectures. Controlling physical and sedimentary processes will be emphasized. Depositional environmental parameters, particularly hydrodynamics, will be interpreted from geomorphology and sedimentary structures. Observational techniques, such as satellite imagery, near-bottom current measurements, seismic profiles, and vibracores will be discussed in lecture and utilized during field-trip exercises. [top]

553 - Introduction to Benthic Boundary Layers and Sediment Transport. Fall, even years (3) Harris. This course addresses the physical and geological aspects of coastal and estuarine benthic boundary layers, their dynamic forcing, and the associated suspension and transport of sediments. Principles of waves, tides and currents are introduced with emphasis on shall-water processes. Boundary layer structure and shear stress on the seabed, wave boundary layers and turbulence are considered in relation to the coastal environment. Forces on sediment particles, initiation of sediment movement, and principles of sediment transport are treated at an intermediate level. [top]

554 – Principles of Numerical Computing. Spring, odd years (3) Harris, Wang. This course provides students with the tools needed to pursue study and research using numerical methods. It will enable them to write programs to solve fairly complex problems, to explore and understand the current literature in which numerical methods are used. Topics include principles of floating-point computation, interpolation, linear and non-linear systems of equations, numerical integration, ordinary and partial differential equations, and optimization. Emphasis is placed on finite difference solutions to conservation of mass and momentum equations. The course consists of three lecture hours per week, assigned problems using MATLAB, and a term project in a topic chosen by the student. [top]

556 - Biogeochemical Modeling. Spring (3) Dickhut. This course will focus on developing mathematical descriptions for biogeochemical processes, as well as on using mathematical models to design experiments to verify specific biogeochemical mechanisms in a system. Equations describing biogeochemical processes will be derived. Discussion will include descriptions of the conditions and assumptions of the models, as well as situations where specific models apply. The course will emphasize mathematical derivations, graphical visualization, and use of model-fitting software. [top]

599 – Thesis. Fall, Spring and Summer (hours to be arranged). This is the avenue for original research in biological, chemical, geological, and physical oceanography; environmental science; marine fisheries science; and marine resource management. The master’s project is chosen in consultation with the student’s major professor and the Dean of Graduate Studies. [top]

610 – Effects of Global Change on Modern Marine Systems. Fall (2-3) Bauer, Canuel, Smith. The course will explore the recent literature highlighting effects of climate and global change on various aspects of marine systems including (but not limited to) biogeochemical cycling, ecosystem structure and function, alterations in ocean chemistry, and physical processes such as polar and glacial ice melting, ocean circulation, and sea-level rise. The course is designed as a 2-credit course. Students will be evaluated primarily on the basis of the quality and organization of the class discussion they lead (including a short introductory background presentation), as well as participation in all other class discussions. In addition, a short (5 pages) critical writing assignment assessing the effectiveness of one or more recently published papers on impacts of global change in marine systems will be required. A 3-credit option may be made available to students who wish to undertake more detailed independent study of a particular topic in the form of additional readings and a research term paper. [top]

611 – Estuarine Hydrodynamics I. Spring, even years (3) Wang. Prerequisite: MS-520. This course examines classification of estuaries, time scales of motions, tidal dynamics in estuaries, non-tidal circulation, mechanism of arrested salt wedge, gravitational circulation, diffusion induced circulation and turbulence in stably stratified flows. [top]

612 – Estuarine Hydrodynamics II. Fall, even years (3) Wang. Prerequisite: MS-611. The contents of the course includes zero-, one-, and two-dimensional descriptions of estuaries, salt intrusion, and pollutant flushing sediment transport through estuaries, field experience in estuaries and model laws for estuarine models. [top]

613 – Ocean Dynamics. Fall (3) Brubaker, Friedrichs. Prerequisite: 520 or Instructor’s consent. In this course, conceptual and analytical models are used to elucidate the effects of the rotation of the earth, stratification, and friction on the dynamics of ocean motion at various scales. Topics include wind-driven gyre circulation, coastal upwelling, turbulence in stratified flows, large-scale waves, internal waves, and climate dynamics. [top]

615 - Hydrodynamic Modeling of Estuarine and Coastal Waters. Spring (3) Wang. Prerequisite: MS-613 or Instructor’s consent. This course will survey numerical methods for the solution of partial differential equations describing estuarine and coastal water motion and transport. Topics include stability, accuracy, consistency, and convergence analysis of numerical scheme, formulation of primitive and scalar transport equations, and pre- and post-processing for numerical computational models. The course will involve classroom lectures, seminar readings, and application of models for operational environmental prediction. [top]

621 – Morphodynamics of Deltaic Coasts and Shelves. Fall, odd years (3) Friedrichs. This course focuses specifically on morphodynamic processes operating on coasts and shelves that receive large inputs of mud from rivers. The term morphodynamics implies the coupled suite of mutually interdependent hydrodynamic processes, coastal and seafloor morphologies, and sequences of change. As in the case of non-deltaic coastal morphodynamic systems, mutual adjustments among coastal physical oceanographic flows, depositional morphologies and sediment transport processes are fundamental and current understandings and data on these phenomena will be presented. [top]

623 – Isotope Geochronology. Fall, odd years (3) Kuehl. The focus of the course is on the principles of radioisotope dating techniques with emphasis on those applicable to marine settings. Equations of radioisotope decay and in growth will be detailed along with the geochemical systematics of each technique. [top]

624 - Ocean Waves: Theory, Measurement and Analysis. Fall, even years (3) Maa. Prerequisite: Instructor’s consent. In this course, students are introduced to linear water wave theory and its applications. Course topics include mechanisms of wave generation (wind waves and tides), the governing equations, wave properties, wave transformation, special cases for tidal wave propagation (e.g., Kelvin waves), wave bottom boundary layer, nonlinear properties (i.e., radiation stress). Practical applications of numerical models for wind wave generation, wave transformation, the spectrum analysis for wave measurements, and harmonic analysis for tides will be introduced and demonstrated. [top]

625 - Multivariate Analysis and Time Series. Fall, odd years (3) Forrest. This course will address the topics of regression and modeling, analysis of residuals; Multivariate regression, eigenvector methods, principal component analysis and factor analysis. Fourier and stochastic models applied to geophysical and other time series data sets will be included. [top]

627 - Marine Organic Geochemistry. Spring, even years (3) Bauer, Canuel. Prerequisite: Organic Chemistry. This course focuses on the characterization of organic carbon, nitrogen, phosphorus and sulfur in the marine environment. Modern methods of organic analysis that enhance our understanding of how organic materials cycle through the oceans will be discussed. Topics include the role of organic matter in the C, N, S and P cycles; chemical composition of marine organic matter; biogeochemistry; diagenetic transformations of organic materials; organic matter decomposition and preservation; and petroleum geochemistry. [top]

627L - Marine Organic Geochemistry Lab. Spring, even years (1) Bauer, Canuel. Prerequisite: Organic Chemistry. In this 1-credit lab module students will conduct an independent lab project that complements the lecture portion of MS-627. [top]

629 - Environmental Organic Chemistry. Fall, odd years (3) Dickhut. This course presents an overview of the partitioning, transport, and transformation processes controlling the environmental fate of organic contaminants. The fundamentals of thermodynamics and chemical kinetics relevant to organic chemical fate and transport, elementary mass transfer equations and their application to chemical transport in the environment is discussed. [top]

630 – Advanced Aquatic Chemistry. Fall, even years (3) Staff. This course describes the principles of chemistry focusing on the chemistry of natural waters. Topics include chemical kinetics and thermodynamics, structure and properties of liquid water, electrolyte solution chemistry; carbonate equilibria, precipitation-dissolution reactions, basic coordination chemistry, and redox reactions with reference to the physical chemistry of biochemical and aquatic systems. [top]

655 - Stable Isotope Biogeochemistry. Fall, even years (2) Anderson, Bronk. This course is a survey of applications that use stable isotopes of carbon, nitrogen, oxygen, and sulfur to define elemental flow through experimental and natural systems. Topics include stable isotope theory; tracer versus natural abundance techniques; quantifying processes of elemental uptake, regeneration, and respiration; and defining trophic relationships using multiple tracers. [top]

688 - Climate Change: Science, Policy, and Law. Spring (3) Ivanova. This seminar will examine climate change as one of the most critical environmental and economic challenges facing humanity. The course will review the interplay among science and policy regarding each discipline’s understanding of the sources and impacts of climate change. It will also focus on the history and future of the legal negotiations and examine the ethical implications of climate change. Topics will include humans as a geophysical force, the science of climate change, measuring the impacts, international legal perspectives and negotiations, market forces, and political constraints. The course will also analyze the energy economies and the rationale for climate change policies in key actors, including the European Union, the United States, Russia, and major developing countries such as India, China, and Brazil. Weekly sessions will include lectures and discussions led by the instructor, invited speakers, and students. Assignments will comprise discussion facilitation, presentations, and written work. Students will participate in small groups that explore in detail a particular aspect of climate change and produce a substantial term paper. (Cross-listed with PUBP 629) [top]