Chemistry graduate students may take graduate courses outside the Chemistry Department to fulfill graduate course requirements when the courses serve to advance the student’s research prowess. Examples of interdisciplinary graduate courses taken by our Ph.D. students follow.


ASTR 5010 Astrophysical Processes

An introduction to the basic physics of astronomy and astrophysics organized around learning physical principles and applying them to astrophysical objects. Physics covered will be chosen from fluid mechanics, radiative transfer, statistical mechanics, classical and quantum radiation processes, and quantum mechanics of atomic and molecular structure. This graduate course will involve more complex and difficult assignments than ASTR 4810. Prerequisite: Instructor Permission. Credits 3

ASTR 5340 Introductory Radio Astronomy

Studies the fundamentals of measuring power and power spectra, antennas, interferometers, and radiometers. Topics include thermal radiation, synchrotron radiation, and line frequency radiation; and radio emission from the planets, sun, flare stars, pulsars, supernovae, interstellar gas, galaxies, and quasi-stellar sources. Credits 3

ASTR 5420 Interstellar Medium

Studies the physics of the interstellar gas and grains, the distribution and dynamics of gas, and cosmic radiation and interstellar magnetic fields. Prerequisite: Instructor permission.  Credits 3

Applied Mathematics

APMA 6410 Engineering Mathematics I

Review of ordinary differential equations. Initial value problems, boundary value problems, and various physical applications. Linear algebra, including systems of linear equations, matrices, eigenvalues, eigenvectors, diagonalization, and various applications. Scalar and vector field theory, including the divergence theorem, Green’s theorem, Stokes theorem, and various applications. Partial differential equations that govern physical phenomena in science and engineering. Solutions of partial differential equations by separation of variables, superposition, Fourier series, variations of parameters, d’ Alembert’s solution. Eigenfunction expansion techniques for nonhomogeneous initial-value, boundary-value problems. Particular focus on various physical applications of the heat equation, the potential (Laplace) equation, and the wave equation in rectangular, cylindrical, and spherical coordinates. Cross-listed as MAE 6410. Prerequisite: Graduate standing.  Credits 3

APMA 6420 Engineering Mathematics II

Further and deeper understanding of partial differential equations that govern physical phenomena in science and engineering. Solutions of linear partial differential equations by eigenfunction expansion techniques. Green’s functions for time-independent and time-dependent boundary value problems. Fourier transform methods and Laplace transform methods. Solutions of a variety of initial-value, boundary-value problems. Various physical applications. Study of complex variable theory. Functions of a complex variable, and complex integral calculus, Taylor series, Laurent series, and the residue theorem, and various applications. Serious work and efforts in the further development of analytical skills and expertise. Cross-listed as MAE 6420. Prerequisite: Graduate standing and APMA 6410 or equivalent.  Credits 3

APMA 6430 Statistics for Engineers and Scientists

Analyzes the role of statistics in science; hypothesis tests of significance; confidence intervals; design of experiments; regression; correlation analysis; analysis of variance; and introduction to statistical computing with statistical software libraries. Prerequisite: Admission to graduate studies. Credits 3


BIOC 8140 Applied Genomics

This course will introduce current concepts in genomics, emphasizing the application of the latest approaches (methodology, techniques, tools, or software) to address research questions.  Credits 2

BIOC 8142 Bioinformatics and Protein Structure

The course provides an introduction to strategies for analyzing protein and DNA sequences at the genomic and metagenomic level. The course will focus on practical aspects of genome sequence analysis. Beginning with an introduction to Unix and Perl programming, the course will cover alignment algorithms and statistics, protein function prediction, and preliminary analysis of Next Generation sequence data. Prerequisite: Core Course or permission of instructor. Credits 2

BIOC 8145 Bioinformatics and Functional Analysis of Genomes

The class covers statistical and programming background, as well as an introduction to software tools for analysis of functional genomics datasets and, will focus on the analysis of high throughput sequence data including RNA-Seq and ChIP-Seq. Students will also learn how to further summarize their data from a regulatory network perspective by performing TF-DNA motif, metabolic/signaling pathway, and gene ontology (GO) analysis. Prerequisite: Bioinformatics and Protein Structure or permission of instructor. Credits: 2

Biomedical Engineering

BME 6026 Quantitative Models of Human Perceptual Information Processing

An introduction to the measurement and modeling of human perceptual information processing, with approaches from neurophysiology to psychophysics, for the purposes of system design. Measurement includes classical psychophysics, EEG field potentials, and single-neuron recordings. Modeling includes signal detection theory, neuronal models (leaky integrate-and-fire, Hodgkin-Huxley, and models utilizing regression, probability, and ODEs). Prerequisite: Graduate standing; background courses in ordinary differential equations, statistics and probability; or consent of instructor.  Credits: 3

BME 6280 Motion Biomechanics

Focuses on the study of forces (and their effects) that act on the musculoskeletal structures of the human body. Based on the foundations of functional anatomy and engineering mechanics (rigid body and deformable approaches); students are exposed to clinical problems in orthopedics and rehabilitation. Cross-listed as AM 6280. Prerequisite: BME 6103. Credits: 3

BME 7370 Quantitative Biological Reasoning

Provides students with a quantitative framework for identifying and addressing important biological questions at the molecular, cell, and tissue levels. Focuses on the interplay between methods and logic, with an emphasis on the themes that emerge repeatedly in quantitative experiments. Prerequisites: BME 6101 (or equivalent), SEAS graduate student status, or instructor permission.  Credits: 3

BME 7641 Bioelectricity

Studies the biophysical mechanisms governing production and transmission of bioelectric signals, measurement of these signals and their analysis in basic and clinical electrophysiology. Introduces the principles of design and operation of therapeutic medical devices used in the cardiovascular and nervous systems. Prerequisite: BME 6310 or instructor permission. Credits: 3

BME 7806 Biomedical Applications of Genetic Engineering

Provides biomedical engineers with a grounding in molecular biology and a working knowledge of recombinant DNA technology, thus establishing a basis for the evaluation and application of genetic engineering in whole animal systems. Beginning with the basic principles of genetics, this course examines the use of molecular methods to study gene expression and its critical role in health and disease. Topics include DNA replication, transcription, translation, recombinant DNA methodology, methods for analyzing gene expression (including microarray and genechip analysis), methods for creating genetically-engineered mice, and methods for accomplishing gene therapy by direct in vivo gene transfer. Prerequisite: BME 6103, undergraduate-level cell and/or molecular biology course. (e.g., BME 2104) or instructor permission. Suggested preparation: biochemistry, cell biology, genetics, and physiology.  Credits: 3

Chemical Engineering

CHE 6442 Applied Surface Chemistry

Factors underlying interfacial phenomena, with emphasis on thermodynamics of surfaces, structural aspects, and electrical phenomena; applications such as emulsification, foaming, detergency, sedimentation, flow through porous media, fluidization, nucleation, wetting, adhesion, flotation, electrocapillarity. Prerequisite: Instructor permission.  Credits: 3

CHE 6448 Bioseparations Engineering

Principles of bioseparations engineering including specialized unit operations not normally covered in regular chemical engineering courses. Processing operations downstream of the initial manufacture of biotechnology products, including product recovery, separations, purification, and ancillary operations such as sterile processing, clean-in-place and regulatory aspects. Bioprocess integration and design aspects. Prerequisite: Instructor permission.  Credits: 3

CHE 6615 Advanced Thermodynamics

Development of the thermodynamic laws and derived relations. Application of relations to properties of pure and multicomponent systems at equilibrium in the gaseous, liquid, and solid phases. Prediction and calculation of phase and reaction equilibria in practical systems. Prerequisite: Undergraduate-level thermodynamics or instructor permission.  Credits: 3

CHE 6618 Chemical Reaction Engineering

Fundamentals of chemical reaction kinetics and mechanisms; experimental methods of determining reaction rates; introduction to heterogeneous catalysis; application of chemical kinetics, along with mass-transfer theory, fluid mechanics, and thermodynamics, to the design and operation of chemical reactors. Prerequisite: CHE 6625 and 6665.  Credits: 3

Computer Science

CS 5014 Computation as a Research Tool

This course is an introduction to programming for students who will be using computational methods for their research but are not computer science or computer engineering students. No previous programming experience is required. We use a multi-language/multi-domain approach. The first part of the course covers basic programming concepts for a given language. The last third of the course splits into domain-specific tracks of interest to students.  Credits: 3

CS 6160 Theory of Computation

Analyzes formal languages, the Chomsky hierarchy, formal computation and machine models, finite automata, pushdown automata, Turing machines, Church’s thesis, reductions, decidability and undecidability, and NP-completeness. Prerequisite: CS 3102 or equivalent.  Credits: 3

CS 6161 Design and Analysis of Algorithms

Analyzes concepts in algorithm design, problem solving strategies, proof techniques, complexity analysis, upper and lower bounds, sorting and searching, graph algorithms, geometric algorithms, probabilistic algorithms, intractability and NP-completeness, transformations, and approximation algorithms. Prerequisite: CS 4102 or equivalent.  Credits: 3

CS 6444 Introduction to Parallel Computing

Introduces the basics of parallel computing. Covers parallel computation models, systems, languages, compilers, architectures, and algorithms. Provides a solid foundation on which advanced seminars on different aspects of parallel computation can be based. Emphasizes the practical application of parallel systems. There are several programming assignments. Prerequisite: CS 3330, 4414, and 4610, or instructor permission.  Credits: 3

Material Science & Engineering

MSE 6010 Electronic and Crystal Structure of Materials

Provides a fundamental understanding of the structure of crystalline and non-crystalline engineering materials from electronic to macroscopic properties. Topics include symmetry and crystallography, the reciprocal lattice and diffraction, quantum physics, bonding and band theory. Prerequisite: Instructor permission.  Credits: 3

MSE 6020 Defects and Microstructure in Materials

A basic course designed to provide a foundation for correlating defect structure and microstructure with physical, mechanical and chemical properties of engineering materials. The fundamental properties of point, line and surface defects in ordered media will be formulated. The thermodynamics of point defects in various types of solids will be discussed as well as the geometry and mechanics of crystal dislocations and their role in crystal plasticity elucidated. The essential elements of microstructure will be characterized emphasizing the concepts of phase constitution, microconstituent, polycrystalline aggregate and multiphase materials. The concept of real materials embodying a hierarchy of structures is emphasized. The principles governing the genesis and stability of material structure at various levels will be discussed. Prerequisite: MSE 6010 and MSE 6230.  Credits: 3

MSE 6130 Transmission Electron Microscopy

Emphasizes the fundamental principles of transmission electron microscopy and illustrates its capabilities for characterizing the internal structures of materials by diffraction, imaging, and spectroscopic techniques; includes weekly laboratory exercises. Prerequisite: MSE 6010 or instructor permission. Credits: 3

MSE 6167 Electrical, Magnetic and Optical Properties of Materials

Explore the fundamental physical laws governing electrons in solids, and show how that knowledge can be applied to understanding electronic, optical and magnetic properties. Students will gain an understanding of how these properties vary between different types of materials, and thus why specific materials are optimal for important technological applications. Cross-listed as ECE 6167. Prerequisite: Some background in solid state materials and elementary quantum principles.  Credits: 3

MSE 6230 Thermodynamics and Phase Equilibria of Materials

Emphasizes the understanding of thermal properties such as heat capacity, thermal expansion, and transitions in terms of the entropy and the other thermodynamic functions. Develops the relationships of the Gibbs and Helmholtz functions to equilibrium systems, reactions, and phase diagrams. Atomistic and statistical mechanical interpretations of crystalline and non-crystalline solids are linked to the general thermodynamical laws by the partition function. Nonequilibrium and irreversible processes in solids are discussed. Prerequisite: Instructor permission.  Credits: 3

MSE 6240 Kinetics of Transport and Transformations in Materials

An introduction to basic kinetic processes in materials and develops basic mathematical skills necessary for materials research. Students learn to formulate the partial differential equations and boundary conditions used to describe basic materials phenomena in the solid state including mass and heat diffusion in single- and two-phase systems, the motion of planar phase boundaries, and interfacial reactions. Students develop analytical and numerical techniques for solving these equations and apply them to understanding microstructural evolution. Prerequisite: MSE 6230.  Credits: 3

MSE 6310 Nanomaterials

Introduces relevant concepts governing the synthesis, science, and engineering of nanomaterials. Course modules cover the fundamental scientific principles controlling assembly of nanostructured materials; the types of nanomaterials that are extant; synthesis, measurement and computational tools; new properties at the nanoscale, and existing and emerging applications of nanomaterials.  Credits: 3

MSE 7130 Advanced Electron Microscopy

Emphasis placed on the applications of advanced techniques of transmission and scanning electron microscopy to modern research problems in materials science and engineering. Microdiffraction and microanalysis, lattice imaging, and convergent beam diffraction in TEM and STEM are treated. In SEM, quantitative probe analysis techniques and backscattered electron imaging and channeling are covered. Prerequisite: MSE 6130 or instructor permission.  Credits: 3

MSE 7220 Surface Science

Analyzes the structure and thermodynamics of surfaces, with particular emphasis on the factors controlling chemical reactivity of surfaces; adsorption, catalysis, oxidation, and corrosion are considered from both theoretical and experimental viewpoints.  Modern surface analytical techniques, such as Auger, ESCA, and SIMS are considered.  Prerequiste:  Instructor permission.


MICR 8200 Building Blocks of the Immune System

This module will cover the different components of the adaptive and innate arms of the immune system with a focus on development and molecular pathways regulating these processes. Prerequisite: Previous Immunology class or permission of the instructor.  Credits: 2

MICR 8202 Integration and Diversification of the Immune System

This module will cover how the diverse components of the immune system are integrated and how this integration influences further maturation and differentiation of elements of the immune system under physiological and patho-physiological conditions. This will include responses to different types of pathogens. Prerequisite: Building Blocks of the Immune System.  Credits: 2

Molecular Physiology & Biological Physics

BIOP 8130 Structure and Function of Membrane Proteins

The course will provide the in-depth assessment of the structure and function of biological membranes and membrane proteins. Emphasis will be placed on biophysical and approaches. The primary literature will be the main source of reading. The course will run as a colloquium with the instructors introducing a different topic at each session and students presenting relevant papers. Prerequisite: BIOP 8201/8301, Biophysical Principles.  Credits: 2

BIOP 8401 Membrane Protein Structural Biology

The course will provide the in-depth assessment of the structural biology of membrane proteins. Emphasis will be placed on the methodologies of solving membrane protein structure. The primary literature will be the main source of reading. The course will run as a colloquium with the instructors introducing a different topic at each session and students presenting relevant papers. Prerequisite: BYOP 8130: Structure-Function of Biological Membranes.  Credits: 2

BIOP 8020 Macromolecular Crystallography I

The course offers in-depth coverage of theory and practical applications of X-ray diffraction methods to crystals of biological macromolecules and their complexes. Topics of the first module will cover molecular visualization, crystals and protein crystallization, X-ray diffraction, data collection, data quality, and data reduction. Prerequisite: BIOP 8201/8301, Biophysical Principles.  Credits: 2

BIOP 8101 Biology at Atomic Resolution: Foundations of Crystallography and NMR

The course will introduce students to fundamentals of X-ray crystallography and NMR spectroscopy, two complementary methods that provide insights into the structure and dynamics of biological macromolecules. Both methods can provide 3D structural information and NMR can also be used to understand the role of dynamics in function. Reading of the primary literature will be a significant component of the course. Prerequisites: BIMS 6000, Organic Chemistry, Physics, Calculus.  Credits: 2

BIOP 8201 Biophysical Principles I

This course will introduce students to some of the physical and chemical underpinnings of molecular biophysics. Physical principles will be discussed and related to how they govern biological systems and how they enable important biophysical techniques. Topics: Equilibrium thermodynamics: mean behavior of ensembles at equilibrium, and Biological fluctuations: deviations from the mean Prerequisite: BIMS 6000.  Credits: 2

BIOP 8301 Biophysical Principles II

This course will introduce students to some of the physical and chemical underpinnings of molecular biophysics. Physical principles will be discussed and related to how they govern biological systems and how they enable important biophysical techniques. Topics: Molecules out of equilibrium: kinetic processes, enzymology, and non-equilibrium statistical mechanics, and Statistical physics of heterogeneity Prerequisites: BIOP 8201, Biophysical Principles I. Credits: 2


NESC 7030 Cellular, Molecular and Developmental Neuroscience

Introduces cellular, molecular, and developmental neuroscience.  Includes the cellular and molecular biology of neurons and glia, intercellular signaling in the nervous system, and neuronal development and plasticity.  Lectures and directed readings of primary literature. Credits: 2

NESC 7060 Fundamentals of Neuroscience

Provides a comprehensive and integrated understanding of the structure and function of the central nervous system. Stresses the structural and functional interrelationships of the various regions of the brain and spinal cord, and the cellular, molecular, and developmental biology of the nervous system. Laboratory sessions include brain dissections and examination of microscopic material.  Credits: 2


PHAR 9001 Introduction to Pharmacology

The course will cover the major classes of therapeutically relevant drugs, and how they work at the molecular and cellular levels. The major topics include: general principles, chemical mediators, drugs affecting major organ systems and chemotherapy of infectious and malignant disease. Prerequisite: PHY 8040 and 8041: Physiology A & B recommended.  Credits: 2

PHAR 9002 Introduction to Neuropharmacology

The course will cover the major classes of therapeutically relevant drugs, and how they work at the molecular and cellular levels. The major topics include general principles, chemical mediators, and drugs affecting the central nervous system. Prerequisite: PHY 8040 & 8041: Physiology A & B recommended, PHAR 9001: Introduction to Pharmacology or permission of instructor.  Credits: 2

PHAR 9003 Molecular Targets

Course goals are to instruct students in the molecular targets popular for medicines and the strategies used for target validation and to help students develop effective written and oral presentation skills. Students will prepare and present an NIH R21-style grant proposal integrated with faculty-led case studies, class discussions, mock study sections and lectures.  Credits: 2

PHAR 9004 Discovering Drugs

This course delves into technologies and concepts that guide drug discovery. Students will prepare and present an NIH R21-style grant proposal to develop effective written and oral presentation skills. By integrating faculty-led case studies, class discussions, lectures and mock study sections students will learn how to drug their favorite molecular target.  Credits: 2


PHYS 5190 Electronics Lab

Practical electronics for scientists, from resistors to microprocessors. Prerequisite: Instructor permission.  Credits: 3

PHYS 5310 Optics

Includes reflection and refraction at interfaces, geometrical optics, interference phenomena, diffraction, Gaussian optics, and polarization. Prerequisite: PHYS 2320, 2415, 2610, or an equivalent college-level electromagnetism course; knowledge of vector calculus and previous exposure to Maxwell’s equations.  Credits: 3

PHYS 7410 Electricity and Magnetism I

A consistent mathematical account of the phenomena of electricity and magnetism; electrostatics and magnetostatics; macroscopic media; Maxwell theory; and wave propagation. Prerequisite: PHYS 7250 or instructor permission.  Credits: 3

PHYS 7610 Quantum Theory I

Introduces the physical basis of quantum mechanics, the Schroedinger equation and the quantum mechanics of one-particle systems, and stationary state problem. Prerequisite: Twelve credits of 3000-level physics courses and MATH 5210, 5220, or instructor permission.  Credits: 3

PHYS 5320 Fundamentals of Photonics

This course is designed to provide an understanding of the physics that underlies technologies such as lasers, optical time/frequency standards, laser gyros, and optical telecommunication. Covers the basic physics of lasers and laser beams, nonlinear optics, optical fibers, modulators and optical signal processing, detectors and measurements systems, and optical networks. Prerequisite: PHYS 5310 or instructor permission.  Credits: 3

PHYS 7420 Electricity and Magnetism II

Development of the theory of special relativity, relativistic electrodynamics, radiation from moving charges, classical electron theory, and Lagrangian and Hamiltonian formulations of electrodynamics. Prerequisite: PHYS 7420 or instructor permission.  Credits: 3

PHYS 7620 Quantum Theory II

Includes angular momentum theory, techniques of time-dependent perturbation theory, emission and absorption of radiation, systems of identical particles, second quantization, and Hartree-Fock equations. Prerequisite: PHYS 7610 or instructor permission.  Credits: 3

PHYS 8320 Statistical Mechanics II

Further topics in statistical mechanics. Prerequisite: PHYS 8310.  Credits: 3