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2019 - 2020 Graduate Catalog 
    
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2019 - 2020 Graduate Catalog [ARCHIVED CATALOG]

Course Descriptions

Explanation of Course Descriptions

Graduate courses may be taken by persons other than regular or provisional graduate students in Arts and Sciences only with the consent of the chairperson of the department/program committee concerned.

Pairs of numbers (501,502) indicate continuous courses. A hyphen between numbers (501-502) indicates that the courses must be taken in the succession stated.

Courses involving laboratory or studio activity are so labeled. All others are classroom courses.

Semester hour credit for each course is indicated by numbers in parentheses.

 
 

Mathematics
  

  • MATH 514 - Introduction to Numerical Analysis II

    Spring 3 Prerequisite(s): Consent of instructor.

    A discussion of the mathematical theory underlying selected numerical methods and the application of those methods to solving problems of practical importance. Computer programs are used to facilitate calculations. The topics covered are: iterative methods for linear systems, eigenvalue computations and differential equations. Students planning to take MATH 514 are strongly encouraged to take MATH 513  first.

  

  • MATH 524 - Operations Research: Stochastic Models

    Spring 3 Prerequisite(s): Consent of instructor.

    A survey of probabilistic operations research models and applications. Topics include stochastic processes, Markov chains, queuing theory and applications, Markovian decision processes, inventory theory and decision analysis.

  

  • MATH 541 - Nonlinear Dynamics

    Fall (3)

    Linear systems of ODEs. Nonlinear systems; dynamical systems, existence/uniqueness of solutions; phase plane analysis; bifurcation; Poincare-Bendixson theory. Applications in biology, circuit theory, and mechanics. Discrete dynamical systems. Cross-listed with MATH 441 - Ordinary Differential Equations II

  

  • MATH 551 - Probability

    Fall and Spring 3 Prerequisite(s): Consent of instructor.

    Topics include: combinational analysis, discrete and continuous probability distributions and characteristics of distributions, sampling distributions.

  

  • MATH 552 - Mathematical Statistics

    Spring 3 Prerequisite(s): Consent of instructor.

    The mathematical theory of statistical inference. Possible topics include: maximum likelihood, least squares, linear models, methods for estimation and hypothesis testing.

  

  • MATH 559 - Topics in Statistics

    Fall and Spring 1-3 Prerequisite(s): Consent of instructor.

    Statistical topics not covered in other courses. Possible topics include: linear models, nonparametrics, multivariable analysis, computationally intensive methods. This course may be repeated for credit as topics change.

Marine Science
  

  • MSCI 501A - Fundamentals of Marine Science, Physical Oceanography

    Spring (2) Gong

    This course provides an introduction to the various types and scales of motion in the ocean, the global heat budget, major water masses, and processes controlling distributions of temperature and salinity. Discussions on phenomena associated with water motion will include global circulation, wind-driven circulation in ocean basins, tides, coastal upwelling, storm surge, waves, turbulence, and circulation in estuaries. Underlying dynamics governing water motion will be presented, elucidating the role of the rotation of the earth. The El Nino/La Nina oscillation will be examined as a key example of large-scale ocean-atmosphere interactions.

  

  • MSCI 501B - Fundamentals of Marine Science, Chemical Oceanography

    Fall (2) Smith, J.

    This course presents an overview of the chemistry of estuaries and the ocean including chemical processes that occur in marine sediments and at the air/sea interface. Discussion topics will include the chemical properties of seawater, chemical equilibrium and kinetics, the seawater carbonate system and ocean acidification, the global and oceanic carbon and nitrogen cycles, ion speciation, trace metals, and nutrients, sediment diagenesis, and fundamentals of radioisotope and stable isotope biogeochemistry. Interdisciplinary applications are emphasized.

  

  • MSCI 501C - Fundamentals of Marine Geology

    Fall, odd years (2) Hein Note: SMS graduate students with a strong undergraduate geology background can take MSCI 521 instead of MSCI 501C to fulfill a SMS core fundamentals requirement. Contact the instructor for more details.

    This course provides an introduction to the major topics of marine geology without expecting the student to have a background in geology. The course addresses the age and internal structure of the earth, the processes of plate tectonics including the formation of oceanic crust, seamounts, hydrothermal vents, the characteristics and classification of sediments and the distribution of sediments in the deep sea. Also addressed are the interrelationships among and importance of paleoceanography, climate change, and sea-level change, and the processes and characteristics of various marine, estuarine, and coastal sedimentary environments. The course includes discussion of various types of field equipment and logistics and of some economic and societal implications.

  

  • MSCI 501D - Fundamentals of Marine Science, Biological Oceanography

    Fall (2) Steinberg

    This course examines the biology and ecology of marine organisms and how they interact with their environment. Topics include the organisms and their behavior, distribution, and underlying physiology; effects of biology on elemental and nutrient cycles and visa versa; and ecosystem structure and ecological interactions. An interdisciplinary approach will be taken, as biology both depends on and influences ocean chemistry, physics, geology, and climate. The course will emphasize open ocean, pelagic systems, but will include many examples from coastal and estuarine systems, as well as shallow and deep-sea benthic ecosystems.

  

  • MSCI 501E - Fundamentals of Environmental Chemistry, Toxicology and Pathobiology

    Fall (2) Unger, Wargo

    This course emphasizes ongoing and emerging environmental concerns in the Chesapeake Bay and world ocean. Lectures will address basic concepts and mechanisms of contaminant chemistry and toxicology, infectious and noninfectious diseases in aquatic organisms. Case histories will be used to illustrate sources, fate and effects of anthropogenic chemical contaminants, and the important role of environmental change on disease in marine and estuarine ecosystems.

  

  • MSCI 501F - Fundamentals of Marine Fisheries Science

    Spring (2) Graves, Scheld

    This lecture course will introduce the principles and techniques of fishery science. Lecture topics will include the theory and impacts of fishing, description and status of international, North American and regional fisheries, fisheries oceanography, recruitment processes, single-species and ecosystem-based approaches to stock assessment, and fisheries management, and the goals and problems of sustaining an open-access common pool resource.

  

  • MSCI 503 - Interdisciplinary Research in Estuarine and Coastal Systems

    Spring (2) Brush

    This is an interdisciplinary, field-based laboratory course applying concepts from MSCI 501 to a semester-long study of the estuarine and coastal environments of the lower Chesapeake Bay and Virginia’s Eastern Shore. The course is designed to expose students to today’s typical interdisciplinary research process from project conception through presentation of results. Students will organize into crossdisciplinary groups around a particular study site and research topic, and develop and implement a scientifically sound, hypothesis-driven research plan through a series of group cruises and instrument deployments. Particular emphasis will be placed on spatial and temporal patterns of biotic and abiotic processes and their interactions, along with sample design, collection, analysis, and interpretation of data. Students will also be exposed to utilizing historical and ongoing databases as well as synthesizing data from each group member to create an interdisciplinary story. The course culminates with oral presentations and a group poster.

  

  • MSCI 504 - Fundamentals of Statistical Methods and Data Analysis

    Fall (4) Chiu

    In this course, students are introduced to the fundamental statistical methods commonly used for analysis of biological and ecological data. Topics include describing data, probability distributions, statistical inference, hypothesis testing, elementary experimental design, analysis of variance, and regression and correlation. The introductory aspects of categorical data analysis and multivariate techniques will also be covered. Course content will be integrated with a weekly laboratory session using the statistical computing language R.

  

  • MSCI 506 - Scientific Communication Skills

    Spring, even years (2) Hilton, Steinberg. Graded Pass/Fail

    The important elements of oral and written presentation skills for communicating scientific research to diverse audiences will be reviewed in this course. The course addresses topics such as best practices for writing, submitting, and revising scientific papers, proposals, and reports, and developing effective figures and other illustrations. Oral and written presentation skills are emphasized through written exercises and class presentations, with peer review. Other topics include development of effective poster presentations and application materials, such as CVs, cover letters, and research and teaching statements.

  

  • MSCI 507 - Responsible Conduct of Research

    Fall (1) Schaffner

    Students will discuss responsible research and scholarly practices and develop an ability to recognize ethical choices for informed decisions based on key principles of research integrity.  Class attendance and completion of VIMS CITI RCR modules are required.  Grading is pass/fail.

  

  • MSCI 508 - College Science Teaching

    Spring, odd years (1) MacDonald, H.

    Course includes discussion of issues in science teaching and learning, course design, lesson design, teaching and assessment strategies, and teaching statements. Focusing on a course of their own, students develop an assignment, lesson outline, and syllabus. Course is valuable for students who are interested in an academic career and/or other positions that involve teaching and/or outreach. Grading is pass/fail.

  

  • MSCI 515A - Biological Sciences Seminar

    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. Grading is pass/fail.
      Students may repeat seminar registration as required by their respective departments; however, only two (2) credits will be applicable to an SMS degree.
  

  • MSCI 515B - Aquatic Health Sciences 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. Grading is pass/fail. Students may repeat seminar registration as required by their respective departments; however, only two (2) credits will be applicable to an SMS degree.
  

  • MSCI 515C - Fisheries Science Seminar

    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. Grading is pass/fail. Students may repeat seminar registration as required by their respective departments; however, only two (2) credits will be applicable to an SMS degree.
  

  • MSCI 515D - Physical Sciences 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. Grading is pass/fail. Students may repeat seminar registration as required by their respective departments; however, only two (2) credits will be applicable to an SMS degree.
  

  • MSCI 521 - Advanced Marine Geology

    Fall, even years (3) Hein Prerequisite(s): An undergraduate background in geology. Note: SMS graduate students with a geology background can take this course instead of MSCI 501C to fulfill a SMS core fundamentals requirement. This course will cover similar topics as MSCI 501C but be taught at a higher, more advanced level.

    Long Title: Marine Geology: Environments, Processes, and Records. This course is designed as an introduction to the geologic processes which have shaped the world’s oceans and their margins. It is specifically targeted to advanced undergraduates and junior graduate students with a background in geological sciences. It will focus on three key study areas (the Bay of Bengal, the US Atlantic Coast, and the Arctic Ocean), and explore the geology and morphology of each, the key processes responsible for their formation and evolution over timescales ranging from decades to hundreds of millions of years, and the records of past changes in sea level, climate, and physical oceanography contained within their sedimentary deposits.

  

  • MSCI 529 - Fish Physiology

    Spring, odd years (3) Brill

    This course is intended for students interested in incorporating physiological principles and techniques into projects addressing questions in ecology, fishery biology and environmental assessment. It will emphasize basic concepts to make physiological jargon and the published literature understandable.

  

  • MSCI 530 - Microbial Processes in a Changing Coastal Environment

    Spring, odd years (2) Anderson, Reece

    The course will address current topics and societal concerns in coastal and estuarine systems including microbial responses to eutrophication, harmful algal blooms, nutrient enrichment, and roles of bivalve-dominated systems, marshes, seagrasses, groundwater, and photic sediments on microbial nutrient cycling. Cross-listed with BIOL 404 and MSCI 404

  

  • MSCI 548 - Special Topics in Marine Science

    Fall, Spring and Summer (1-3) Staff

    This is the avenue through which subjects not covered in other formal courses are offered. These courses are offered at an introductory or lower level (i.e., below MSCI 550), with content and workload commensurate with other lower level MSCI courses. These courses are offered on an occasional basis as demand warrants. Subjects will be announced prior to registration and after approval by the EPC.

  

  • MSCI 549 - Communicating Ocean Science: Science Education Methods

    As Required (1) Hopper-Brill, Lawrence Note: Instructor permission required.

    Effective science teaching methods for communicating ocean sciences in classroom or informal education settings. Prepares marine science graduate students for interpreting their research to lay audiences via lessons, labs, or field activities.

  

  • MSCI 550 - Rivers: Processes and Problems

    Spring, even years (3) Hein, Staff

    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.

  

  • MSCI 553 - Introduction to Benthic Boundary Layers and Sediment Transport

    Fall, odd 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.

  

  • MSCI 554 - Principles of Numerical Computing

    Spring (3) Harris, Wang

    This course provides students in the marine sciences 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.

  

  • MSCI 555 - Marine Resource Economics

    Fall, odd years (3) Scheld

    This course is designed to introduce students to the economic concepts, tools, and arguments that shape policy and management of living marine resources. Lecture will be supplemented with problem sets and a final project which synthesizes course concepts. Cross-listed with PUBP 614  

  

  • MSCI 559 - Parasitology

    Spring (3) Shields

    Recommended:Invertebrate Zoology or comparable course. This course covers the biology and ecology of protozoan, helminth and crustacean parasites. Focus is on parasites of medical and veterinary importance. Emphasis is placed on life cycles, pathology, control methods and ecological impacts of parasitic infections. Three lecture and three laboratory hours. Cross-listed with (Bio 404 and BIOL 504 )

  

  • MSCI 561 - Statistical & Graphical Analyses in R

    Spring (3) Hoenig

    Use of R to manipulate and graph data and perform statistical analyses. Students will write functions, use debugging facilities, and perform advanced graphical and statistical analyses including bootstrapping, nonlinear regression, and generalized linear mode.

  

  • MSCI 562 - Environmental Pollution

    Fall (2-3) Hale

    This course will introduce students to processes impacting aquatic environments. Emphasis will be on pollution by man-made chemicals and metals. Additional topics include consequences of excessive nutrients, habitat modification and introduction of exotic or elimination of native species.  Students have the option to register for 2 credit hours (lecture only) or 3 credit hours (lecture with an in-class student presentation).

  

  • MSCI 563 - Environmental Chemistry

    Spring (3) Unger

    The fundamental physical, chemical and biological processes controlling the fate of major classes of aquatic contaminants are covered in this course. Topics such as photolysis, biodegradation, sorption and redox chemistry are examined to elucidate the mechanisms controlling chemical degradation and transport. Case studies are used to show how these basic research principals can be integrated and applied to solve real word environmental problems.

  

  • MSCI 565 - Principles of Pathobiology

    Spring, even years (3) Vogelbein, Carnegie, Wargo

    This course focuses on the molecular and cellular mechanisms of pathogenesis in important emerging diseases in the medical, veterinary, and aquacultural fields. Students will learn how current molecular and cellular techniques are being applied to the resolution of a variety of infectious and non-infectious diseases. Mammalian models provide a foundation for application to the diseases of fish and shellfish.

  

  • MSCI 568 - Crustacean Health Issues

    As required (1) Shields

    Crustaceans support major commercial fisheries and aquaculture production. We will explore current topics in crustacean health such as emerging diseases and their impact on fisheries, disease control and prevention, the influence of environmental factors that contribute to health issues, basic aspects of crustacean biology that are affected by pathogens, aspects of animal husbandry and aquaculture, and advances in understanding crustacean immunology. Emphasis will be placed on commercially important crustaceans and their pathogens and diseases, but comparisons will be made among different systems. Students will present papers in topical areas, develop reviews of subject areas, and participate in class discussions. Different topics will be covered each semester. A student may repeat the course up to four times, provided the instructor determines there is no duplication of subject matter. Up to (4) times
  

  • MSCI 571 - Marine Ecology

    Spring (3) Johnson

    The course covers the fundamental processes underlying structure and functioning of marine ecosystems, both pelagic and benthic, and application of those principles to understanding responses of marine ecosystems to anthropogenic and natural global change. Lectures, readings and discussion will emphasize physical processes supporting primary production, planktonic and benthic dynamics, distribution and functional importance of marine biodiversity, biotic interactions structuring communities, and food web structure. The course concludes with a survey of the major marine ecosystem types. A central part of the course involves design, writing, reviewing, and panel discussion of student research proposals.

  

  • MSCI 575 - Aquatic Microbial Ecology

    Fall, odd years (3) Anderson, Song Note: Organic chemistry or biochemistry recommended.

    This course provides an introduction to the role that microorganisms play in the biogeochemical cycling and production of dissolved and particulate inorganic and organic matter in freshwater and marine ecosystems. The approach will be ecological, relating environmental physiochemical properties to regulation of microbial processes, distributions, and biodiversity. Topics will include state of the art methods for detecting distributions, biomass, and activities of microorganisms in the natural environment, the energetics regulating microbial processes, microbial biochemical pathways, biodegradation, microbial interactions, and the role that microorganisms play in the food webs of various ecosystems. Although emphasis will be placed on marine systems, processes in lacustrine, riverine, and groundwater ecosystems will also be discussed. Readings will draw heavily on the primary literature.

  

  • MSCI 583 - Molecular Genetic Data Analysis, Bioinformatics

    Spring, odd years (3) Reece, McDowell

    This is a lecture and computer-based laboratory course covering the principles and practice of analyzing and interpreting population genetic, phylogenetic and genetic mapping datasets. Molecular data sets including DNA sequences, genotypic profiles and genomic data will be exported and processed for analysis by the appropriate suite of computer software programs. Software to be utilized includes DNA sequence analysis, genotyping, population genetic, sequence alignment and phylogenetic programs, as well as standard pipelines for analysis of next generation sequencing data. Phylogenetic programs will include those based on genetic distance, maximum parsimony, maximum likelihood and Bayesian analyses. Population genetics programs include those such as GenePop to perform standard population genetic statistical analyses, Arlequin for doing AMOVAs, and STRUCTURE for doing assignment testing.

  

  • MSCI 599 - Thesis

    Fall, Spring and Summer (1-12) Major or Co-Major Advisor(s)

    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 Associate Dean of Academic Studies.

  

  • MSCI 610 - Effects of Global Change on Modern Marine Systems

    Fall, odd years (2-3) Canuel, Staff

    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.

  

  • MSCI 611 - Estuarine Hydrodynamics I

    Fall (3) Wang

    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.

  

  • MSCI 615 - Hydrodynamic Modeling of Estuarine and Coastal Waters

    Fall, even years as required. (3) Wang.

    This course will survey numerical methods for the solution of partial differential equations describing the 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 the pre- and post-processing for numerical computational models. The course will involve classroom lectures, seminar readings, and application of models for operational environmental prediction.

  

  • MSCI 617 - Estuarine Water Quality Models

    Spring, even years as required (3) Wang. Prerequisite(s): MSCI 611  

    This course examines the principles of mass balance, physical transport processes, diffusion and dispersion in estuarine environments. Water quality processes, representation of biochemical transformations, dissolved oxygen modeling and survey of available models are other topics of discussion.

  

  • MSCI 620A - Coastal Environments I

    Fall, every three years (1) Kuehl. Note: To be offered again in 2021.

    Field experience examining modern and ancient coastal environments. Course rotates annually among three field environments. A 4-5 day field trip during the second half of the semester will be conducted to one of the three field areas each year.

    Barrier Islands and Beaches from Virginia to Georgia: This offering will examine coastal environments along the East Coast from Virginia to Georgia.  A 4-day field trip will highlight barrier-island and beach morphologies encountered along this stretch of the coast, and will also examine dunes, tidal flats, marshes, inlets and deltas.  This stretch of the East Coast is a natural laboratory for investigating the relative roles of physical and biological conditions in creating a remarkable gradient in coastal geomorphology, and also provides many examples of human modification to the natural system.

  

  • MSCI 620B - Coastal Environments II

    Fall, every three years (1) Kuehl. Note: To be offered in 2019.

    Field experience examining modern and ancient coastal environments. Course rotates annually among three field environments. A 4-5 day field trip during the second half of the semester will be conducted to one of the three field areas each year.

    Mississippi Delta: This course will examine the intersection of humans and natural processes at the mouth of the largest river system in North American, the Mississippi Delta.  Students will review the classic and modern literature on deltaic processes and wetlands issues of coastal Louisiana.  A 4-5 day field trip to the delta will examine the range of extant environments from the New River control structure, through the swamps and wetlands to the nascent Atchafalaya delta, the future major lobe of the Mississippi River system.  Class and field discussions will detail the geological and biological processes that conspire to create one of the world’s great delta systems, and explore the results of human modifications in this sensitive and highly dynamic setting.

  

  • MSCI 620C - Coastal Environments III

    Fall, every three years (1) Kuehl. Note: To be offered again in 2020.

    Field experience examining modern and ancient coastal environments. Course rotates annually among three field environments. A 4-5 day field trip during the second half of the semester will be conducted to one of the three field areas each year.

    Paleozoic Coastal Environments - Kentucky and West Virginia: This course will examine Paleozoic fluvial, deltaic and coastal sedimentary rocks.  A 4-day field experience will explore ancient examples of coastal/deltaic environments formed in epicontinental seas of the Paleozoic that are accessible through road and river cuts in West Virginia and Kentucky.  Easy access and extensive outcrop exposures provide a remarkable 3D perspective of preserved coastal sedimentary sequences.

  

  • MSCI 622 - Coastal Evolution

    Spring, odd years (3) Hein Prerequisite(s): MSCI 501C  or MSCI 521   Prereq/Corequisite(s): MSCI 501C  or MSCI 521  

    Long Title: Holocene Coastal Geomorphology and Evolution. This course will review the drivers of, and geomorphic responses to, change along open-ocean coastal sedimentary environments across a range of climatic zones and from the event scale to thousands of years.

  

  • MSCI 626 - Global Ocean Change Biology

    Fall, odd years (2) Rivest

    This course will provide (1) a scientific foundation of physical processes that shape climate (e.g. solar variability, greenhouse gases, atmospheric and oceanic circulation, and volcanic aerosols) and (2) a scientific foundation of biological consequences of global environmental change. Evidence for past and present global environmental change will be discussed, including sea level change, variation in freshwater inputs, and shifts in temperature and acidity. Biological and ecological processes that result from changing ocean conditions will include range shifts, phenological shifts, acclimatization, and local adaptation.

  

  • MSCI 627 - Marine Organic Geochemistry

    Spring, odd years (3) Canuel Prerequisite(s): 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.

  

  • MSCI 631 - Wetland Geomorphology and Ecology

    Spring (3) Kirwan

    This course focuses on the geomorphic and biological processes influencing coastal wetlands. The course examines interactions between sediment transport and plant growth in barrier islands, coastal lagoons, and estuarine headwater and tidal marsh environments.  Through a series of lectures, field trips, assigned readings and an independent project, students will examine geological and biological processes and learn how both natural and anthropogenic factors shape these coastal ecosystems.  One Saturday field trip to the Eastern Shore Laboratory is required.

  

  • MSCI 644 - Aquatic Epidemiology

    Spring, odd years (3) Wargo. Prerequisite(s): MSCI 504  or MSCI 554  

    This course will cover graduate level topics in Epidemiology. Students will gain the ability to critically assess epidemiological literature, design epidemiological studies, and analyze epidemiological data. Where possible, content will focus on aquatic environments and organisms, including human aquatic diseases. A preliminary working knowledge of basic statistics is required. Previous competency in R computing language is expected.

  

  • MSCI 649 - Ecosystem Modeling

    Fall, even years (3) Brush

    This course provides an introduction to quantitative modeling in marine science, with an emphasis on the process of constructing mechanistic models of biological, ecological, and biogeochemical processes. General topics include determination of modeling objectives and assumptions, model formulation and parameter estimation, determination of model accuracy through calibration, validation, and sensitivity analysis, and use of models to address scientific questions through simulation analysis. Types of models covered include compartmental ecosystem models, age/size-structured population models, and food web network analysis, with consideration of deterministic, stochastic, and spatially explicit approaches. Lectures are supplemented with readings from the primary literature and students receive hands-on experience building and using models through in-class lab exercises.

  

  • MSCI 650 - Estuarine Ecology

    Fall, odd years (3) Brush. Prerequisite(s): MSCI 503  

    This survey course will expose students to the key aspects of estuarine ecosystems. Topics covered will include both the abiotic settings of estuaries, including geological, physical, and chemical characteristics, and the biotic components and their interactions, including nutrient dynamics, biogeochemistry, microbial processes, primary production, ecosystem metabolism, secondary production, and food web dynamics. The course will end with overviews of current and emerging issues in estuarine science, including eutrophication and climate change. Bi-weekly class meetings will consist of interactive discussions led by the instructors based on readings from key estuarine ecology texts and the primary literature, supplemented with student-led discussions of primary literature and “virtual field trips” to a variety of well-studied estuaries. Students will work on a semester-long project to develop course materials into an estuary-focused wiki on the William & Mary wiki site. Each student will lead the development of materials for a select number of topics, and be responsible for contributing materials and editing content for all topics. Students will also lead field trips to local systems to illustrate class topics and synthesize existing datasets to conduct a comparative analysis of estuarine ecosystems.

  

  • MSCI 658 - Larval Ecology

    Spring, even years (3) Mann

    The course is based on a broad discussion of the following topics within the marine invertebrates: the concept of the larval form, spawning and developmental patterns, limitations on the fertilization process and embryology, the Reynolds number environment at typical larval size, feeding and nutrition in the larval size range, larval size and parental investment, larval dispersal and supply in maintaining community structure, roles of physical versus biological processes in inducing metamorphosis, early post-metamorphic survival, and larval ecology in extreme environments.

  

  • MSCI 663 - Deep-Sea Biology

    Spring, odd years (2) Vecchione

    Students will receive an introduction to the animals of the deep sea and characteristics of deep-sea and polar ecosystems. Lectures will survey the major metazoan groups found in deep-sea habitats, as well as physical characteristics of the environments and adaptations to life in these cold, dark, hyperbaric regions. An opportunity to participate in a deep-sea trawling cruise may be coordinated with the course.

  

  • MSCI 664 - Marine Conservation Biology

    Spring, even years (3) Lipcius

    This course focuses on the application of multidisciplinary scientific principles to the protection, enhancement and restoration of marine biodiversity (genetic, species, community and ecosystem). Ecological emphasis will be on the conservation of biodiversity threatened by habitat degradation and loss, overexploitation, invasive species, and global change. Social, legal, economic and political influences will be discussed. Also included will be practical application through case studies and training in population viability analysis. (Lecture and laboratory)

  

  • MSCI 666 - Ichthyology

    Fall, odd years (4) Hilton

    Fishes form a large, diverse group of vertebrates that are culturally, economically, and scientifically important, and they offer much for the study of evolutionary biology. This course provides an intensive overview of all aspects of the evolution of fishes, with an emphasis on their morphology and systematic relationships. The lectures cover the diversity and evolutionary history of fossil and living fishes, and discuss the evidence for different hypotheses of their phylogenetic relationships; other topics include the biogeography, functional anatomy, physiology, and behavior of fishes. The mandatory lab section emphasizes dissection-based anatomical study and the global diversity of fishes, and includes some field sampling.

  

  • MSCI 667 - Experimental and Quantitative Ecology

    Spring, odd years (3) Lipcius

    The course addresses the design, conduct, analysis and interpretation of field and laboratory experiments in ecology. The lectures, discussion and supervised field and laboratory projects are designed to illustrate the diversity of experimental and quantitative approaches in use by ecologists. Topics include the scientific method, experimental design, the use and abuse of statistical techniques, modeling and manuscript preparation, with emphasis on topical ecological issues such as those dealing with predatory-prey interactions, recruitment phenomena, environmental science (e.g., dose-response assays) and metapopulation dynamics. (Lecture and laboratory)

  

  • MSCI 668 - Malacology

    Fall, odd years (3) Mann

    The course begins with a discussion of the ancestral mollusc form and the fossil record, proceeds through examination of the structure and function of the molluscan shell. It concludes with reviews of molluscan taxonomy, reproductive biology, physiology, ecology, and feeding mechanisms.

  

  • MSCI 669 - Linear and Generalized Linear Models in Ecology

    Fall (3) Fabrizio Prerequisite(s): Consent of instructor, and ability to program in SAS or R

    This course emphasizes the design and analysis of field data (e.g., retrospective studies, experimental manipulations in the field), rather than design and analysis of controlled laboratory experiments. Students will gain a working knowledge of linear and generalized linear models useful in the analysis of ecological data. Both theoretical development and application of statistical methods will be presented.

  

  • MSCI 670 - Stock Assessment Methods

    Spring, even years (3) Hoenig

    This course will survey methods for assessing the status of exploited populations given various combinations of data types. Emphasis will be placed on deriving statistical methods using maximum likelihood and other analytical techniques, and on computing estimates for a variety of datasets. Population models will be used to integrate information on stock status in order to determine appropriate management measures. Additional topics include analysis of uncertainty in the assessment of results and implications of uncertainty for management, analysis of research surveys, commercial catch, fishing effort, and tagging data.

  

  • MSCI 671 - Fisheries Population Dynamics

    Fall, starting in 2020 (3) Latour

    This course provides an introduction to the fundamental processes governing fish population dynamics, with an emphasis on the theory and practical application of models used to characterize the factors influencing population abundance. Topics include the theory of mortality, growth, stock-recruitment (compensation, depensation), surplus production, VPA, statistical catch-at-age, tagging, and the introductory aspects of multispecies and fisheries ecosystem models. Lectures are supplemented with readings from the primary literature and students receive hands-on experience with nonlinear parameter estimation through computer laboratory sessions using the statistical software package R.

  

  • MSCI 672 - Ecology of Fishes

    Fall, even years (3) Weng

    This course will provide students with an understanding of fish ecology as related to vertebrate evolution and diversity, systematics, feeding and reproductive biology, early life history ecology, and fish community structure and biotic interactions.

  

  • MSCI 673A - Principles of Molecular Biology

    Spring, even years (2) Reece, McDowell, Song Corequisite(s): MSCI 673B  or MSCI 673C  

    This is a lecture, laboratory, and computer laboratory course covering the principles and practice of analyzing and interpreting genomic, metagenomic, population genetic and phylogenetic datasets. Overall, the course will cover the evolutionary processes responsible for the intra- and interspecific genetic relationships among marine organisms, with an emphasis on the application of current molecular methodologies. The course is modular with the first module (MSCI 673A, 2 credits) covering basic molecular genetic principles and molecular biology techniques during the first 6 weeks of the semester. For the second half of the semester students will choose one of two modules (MSCI 673B or MSCI 673C, 2 credits) focusing on molecular genetic studies and bioinformatic analyses of either prokaryotic or eukaryotic organisms.

  

  • MSCI 673B - Metagenomics & Bioinformatics (Prokaryotes)

    Spring, even years (2) Song Corequisite(s): MSCI 673A  

    Refer to MSCI 673A  course description.

  

  • MSCI 673C - Principles of Molecular & Phylo-genetics (Eukaryotes)

    Spring, even years (2) McDowell, Reece Corequisite(s): MSCI 673A  

    Refer to MSCI 673A  course description.

  

  • MSCI 675 - Molecular Microbial Techniques

    Spring, odd years (1-2) Song

    This class will review primary literatures reporting various molecular biological techniques used in microbiome studies. Topics include PCR, FISH, T-RFLP, Real-time PCR, Stable Isotope Probing and Raman microspectroscopy and NanoSIMs.

  

  • MSCI 685 - Coastal Resource Management Clinic

    Fall (1-3) Hershner, Staff. Note: To be offered in 2019 only.

    This course will involve a survey of current issues in coastal resource management and practical engagement in one or more of those issues at the regional level. Through a combination of directed readings and lectures, students will learn about goals and objectives in a number of the large environmental management programs in the United States. The survey of management programs will alternate with a focus on the Chesapeake Bay, the Great Lakes, and the Gulf coast in odd years, and the National Estuary Programs in even years. Management strategies will be reviewed and program designs will be assessed. Students will also learn about the practical aspects of environmental management by observation and engagement in ongoing local, state and regional programs. Students will write background papers, draft legislative proposals, prepare outreach materials, and participate in communication of these products as opportunities allow. Credit, which must be arranged in advance of registration, will depend on the complexity of the student’s engagement in clinic activities. Maximum enrollment is limited to six students. The course may be repeated once, provided the instructor determines there is no duplication of subject matter and clinic activities.
  

  • MSCI 687 - Environmental Policy

    Fall, odd years (3) Chaijaroen

    This course explores policy making for environmental problems and focuses on issues that are local, national, and international. This course will cover the application of welfare economics to environmental problems. Topics include differences in consumer surplus and other measures of economic welfare and techniques to measure the economic value of environmental resources. We examine national environmental policy, and how that policy is implemented at a local and regional level. We examine the U.S. laws and regulations as well as each agency’s approach for quantitatively assessing the benefits and costs of environmental policy. Cross-listed with PUBP 622  

  

  • MSCI 688 - Coastal & Marine Policy Seminar

    Spring (2) Staff

    Students will explore the science-policy interface in a weekly seminar-style course and through 3-day field trips to Virginia’s state capitol in Richmond (state-level) or Washington D.C. (federal-level), in alternative years.  The course is designed to increase student knowledge of state or federal government structure, particularly the coastal, marine, and environmental resource management agencies, but also the General Assembly or Congress; awareness of the nature of the science-policy interface at the state or federal level, including challenges, opportunities, science communication; awareness of the critical professional skills and competencies needed for careers at the science-policy interface, including opportunities to practice professional networking skills and identify one’s strengths and limitations. Grading is pass/fail.

  

  • MSCI 689 - Public Policy for Science & Professions

    Fall (3) Rossiter

    This course examines what governments do and do not do. The class employs an engaging seminar format using provocative materials with practical applications. Students study the assumptions of public policy analysis, markets and government, tools for analysis, and political institutions (e.g., the executive, legislative branches and interest groups).This course is specifically designed for an interdisciplinary class of professional or graduate students from the Schools of Business, Education, Law, and Marine Science, as well as those in the School of Arts and Sciences who are not in a public policy degree program. Students will come to understand public policy as an academic discipline and as a systematic method of thinking about the design, development, and evaluation of public sector policies and programs. Cross-listed with PUBP 614  

  

  • MSCI 693 - Environmental Law

    As required (3) Law School Staff, Wall Prerequisite(s): Consent of instructor

    A study of the nature and causes of environmental pollution and of the main legal techniques for its control. The course will consider the common law, the environmental impact assessment process (e.g., the National Environmental Policy Act), and the basic regulatory framework for air, water and solid and hazardous waste control (the Federal Clean Air Act, Clean Water Act and Resource Conservation and Recovery Act), with attention given under each statute to the basic regulatory framework and the main policy issues presented by it. Cross-listed with LAW 424 .

  

  • MSCI 694 - Land Use Control

    As required (3) Law School Staff, Butler Prerequisite(s): Consent of instructor

    An analysis of the legal principles governing the use and management of land and the fundamental values underlying those principles. While focusing primarily on government regulation of land use, the course also will examine common law rules which affect the way that land is used. Topics that might be considered include judicial control of land use, zoning and the rights of landowners, zoning and the rights of neighbors, land use planning, public regulation of land development, aesthetic regulation, and the preservation of natural and historic resources. Cross-listed with LAW 425 .

  

  • MSCI 695 - Administrative Law

    As required (3) Law School Staff, Bruhl and Larsen Prerequisite(s): Consent of instructor

    Administrative law establishes the legal controls over the operation of government and hence it relates to almost every legal practice, from security regulation to social programs to criminal justice. Indeed, administrative law is essential to justice in a modern society because administrative agencies generate most of the law that actually affects our lives and because administrative agencies adjudicate far more disputes than the traditional judiciary. This course is an introductory examination of the rules and procedures governing agency decision making. It explores (1) how agencies make policy and (2) how businesses, interest groups, and citizens challenge agency policymaking in court. Cross-listed with LAW 453 .

  

  • MSCI 696 - Distributed Courses in Marine Science

    Fall, Spring, and Summer (1-3) Staff

    This is an avenue through which students can participate in distributed courses to gain experience and training in topics not covered through regular catalog courses and not amenable to other special topics courses (MSCI 697 or 698). Distributed courses are those that are conducted on-line or through other distance-learning methods, that contain significant content from faculty outside of VIMS and William & Mary and for which no other mechanism for awarding credit is available (e.g., transfer of credit from another institution). VIMS faculty are responsible for coordinating the approval of the course and agree to take responsibility for delivery of course content, ensuring student participation, providing a mechanism for addressing questions from students, and assessing the student’s learning of the material. Subjects will be announced prior to registration and after approval by the Educational Policy Committee (EPC).

  

  • MSCI 697 - Problems in Marine Science

    Fall, Spring and Summer (1-4) Staff

    This is the avenue through which supervised projects may be selected to suit the needs of the graduate student, including those wishing to perform an internship as part of the Curricular Practical Training Program. Projects are chosen in consultation with the student’s major professor and the instructor. Acceptable research outlines and project reports are required, and the amount of credit depends upon difficulty of course. Examples of projects offered in recent years include management issues in shellfish sanitation; groundwater nutrient processes; bacterioplankton methods and techniques; pesticide analysis in environmental samples; marine molecular population genetics; and law and policy relating to the introduction of non-indigenous plants. Subjects will be announced prior to registration and after approval by the Educational Policy Committee (EPC).

  

  • MSCI 698 - Special Topics in Marine Science

    Fall, Spring and Summer (1-3) Staff

    This is the avenue through which subjects not covered in other formal courses are offered. These advanced courses are offered on an occasional basis as demand warrants. Subjects will be announced prior to registration and after approval by the EPC.

    Examples of courses offered in recent years include:

    • Bayesian Concepts and Methods
    • Coastal and Marine Policy Seminar
    • Contemporary Topics in Ecology
    • Data Analysis using MATLAB
    • Drone Applications for Marine Science
    • Environmental and Aquatic Animal Health
    • Landscape Genetics
    • Project Management
    • Sediment Transport Models
    • SCHISM Modeling for Marshes

    Courses proposed to be offered in the near future:

    • Animal Husbandry
    • Bioavailability
    • Diseases in Molluscs
    • Fine Sediment Processes & Applications
    • HABs
    • Remote Sensing Using Unmanned Systems
    • Water Quality Observ & Data Analysis
  

  • MSCI 699 - Dissertation

    Fall, Spring and Summer (1-12) Major or Co-Major Advisor(s)

    This is the avenue for original research in biological, chemical, geological and physical oceanography, environmental science, marine fisheries science and marine resource management. The doctoral project is chosen in consultation with the student’s major professor and the Associate Dean of Academic Studies.


Physics
  

  • PHYS 566 - Directed Studies

    Fall and Spring variable 3-4 credits Graded Pass/Fail

    No credits earned in this course may be applied to the number of credits required to satisfy graduate degree requirements. This course may be repeated.
  

  • PHYS 581 - Topics in Physics

    Fall and Spring (variable) Staff.

    Special topics of current interest. This course may be repeated for credit when the instructor determines there will not be a duplication of material.
  

  • PHYS 600 - Independent Study

    Fall and Spring (3,3) Staff.

    Course concerning special topics in physics not covered in regular course offerings.  This course may be repeated for credit if instructor determines there will be no duplication of material.
  

  • PHYS 601 - Classical Mechanics

    Fall 4 Qazilbash.

    The mechanics of particles and rigid bodies, methods of Lagrangian and Hamiltonian mechanics, relativistic mechanics, approximation techniques.

  

  • PHYS 603 - Mathematical Physics

    Fall 4 Dudek.

    Complex variables and analytic functions. Vector spaces (finite dimensional and infinite dimensional), operators and matrix representations.

  

  • PHYS 610 - Classical Electricity and Magnetism-I

    Spring 4 Orginos.

    Electrostatics. Solution of boundary value problems. Green’s functions and direct solution of Laplace’s equation. Magnetostatics and steady currents. Maxwell’s equations and plane wave solutions.

  

  • PHYS 611 - Classical Electricity and Magnetism-II

    Fall 3 Rossi. Prerequisite(s): PHYS 610 .

    Waves inside conducting boundaries. Radiation from simple current systems, spherical waves and multipole radiation. Covariant formulation of electromagnetism. Interaction of radiation with matter.

  

  • PHYS 621 - Quantum Mechanics - I

    Fall 4 Krakauer.

    Axiomatic development of wave mechanics and the Schroedinger equation in one and three dimensions; wave packets; spin and angular momentum.

  

  • PHYS 622 - Quantum Mechanics - II

    Spring 4 Rossi. Prerequisite(s):  PHYS 621 .

    Scattering theory; matrix methods; symmetry; perturbation theory and other approximate methods; identical particles; relativistic wave equations and their applications.

  

  • PHYS 630 - Statistical Physics and Thermodynamics

    Spring 4 Vahala. Prerequisite(s): PHYS 601 , PHYS 621 .

    Statistical ensembles and averages, classical equilibrium, thermodynamics and statistical mechanics, quantum statistics, kinetic theory and transport properties.

  

  • PHYS 651 - Teaching Physics

    Fall and Spring 2 Dulli. Graded Pass/Fail.

    Designed for entering students teaching a lab or tutoring one of our undergraduate courses. Respective faculty will instruct students in relevant ways. This course may be repeated for credit.
  

  • PHYS 685 - Colloquium

    Fall and Spring 0-2 Nelson. Graded Pass/Fail.

    Includes presentations by invited speakers on areas of active research in physics. The course also will include an overview of physics research at William and Mary and training in the responsible and ethical conduct of research.  No credits earned in this course may be applied to the number of credits required for a degree. This course may be repeated.
  

  • PHYS 690 - Advanced Topics in Physics

    Fall and Spring Hours and credits to be arranged. Staff.

    Special topics of current interest. This course may be repeated for credit when the instructor determines there will not be a duplication of material.

  

  • PHYS 694 - Directed Research Topics

    Fall and Spring (variable 3-12) Nelson.

    Students design and conduct research on a relevant topic with a faculty advisor.  This course may be repeated, but no more than 12 semester credit hours may be used to satisfy degree requirements.
  

  • PHYS 702 - Advanced Mathematical Physics

    Spring 3 Staff. Prerequisite(s): PHYS 603 .

    Differential equations, Green’s functions, some hypergeometric functions, group theory, representation of groups. 

  

  • PHYS 721 - Quantum Field Theory - I

    Fall 3 Monahan. Prerequisite(s): PHYS 622 .

    Canonical quantization of scalar, spinor and vector fields; interacting field theories and Feynman diagrams; scattering theory; quantum electrodynamics and introduction to radiative corrections.

  

  • PHYS 722 - Quantum Field Theory - II

    Spring 3 Erlich. Prerequisite(s): PHYS 721 .

    Functional integral quantization of field theories. Renormalization. Quantization of gauge theories. Spontaneous Symmetry Breaking and the Higgs mechanism.

  

  • PHYS 741 - Condensed Matter Physics

    Spring 3 Krakauer. Prerequisite(s): PHYS 622 , PHYS 630 .

    Introduction to the frontiers of condensed matter physics research; crystal structure, phonons, electrons, electric, optical, and magnetic properties, impurities, elementary excitations, band theory and experimental methods.

  

  • PHYS 742 - Advanced Condensed Matter Physics

    Spring 3 Prerequisite(s): PHYS 741  

    Selected topics from the frontiers of condensed matter physics research that may include semiconductors, magnetism, superconductivity, topological states of quantum matter.  Discussions of modern experimental and theoretical methods.

  

  • PHYS 761 - Atomic and Molecular Processes

    Fall and Spring 3 Staff. Prerequisite(s): PHYS 622 .

    Theory of atomic structure; emission and absorption of radiation; fine and hyperfine structure; coupling schemes. Molecular structure and intermolecular forces; atomic and molecular collisions. Modern applications.  

  

  • PHYS 762 - Atomic and Molecular Processes

    Fall and Spring 3 Staff. Prerequisite(s): PHYS 622 .

    Theory of atomic structure; emission and absorption of radiation; fine and hyperfine structure; coupling schemes. Molecular structure and intermolecular forces; atomic and molecular collisions. Modern applications. 

 

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