# Courses

Faculty in the Materials Science and Engineering doctoral program are committed to providing depth of understanding in their specialty, while recognizing the challenges facing students outside of their home science and engineering disciplines. Instructors in this program welcome the challenge of teaching across disciplines and the opportunities these classrooms present for stimulating questions and widely ranging class discussions.

Under the guidance of the faculty advisor in the host department, **students must select three courses (9 credit hours total) from the following courses approved for the MSE degree**. Two of the three courses must be outside of the student's home department, and only one of those can be cross-listed within the student's home department. Cross-listed means that a course has a course number from two different departments. As an example, Nanoscience and Technology is listed both as CBE60577 and CHEM60577. Each academic department determines whether these credits are electives or additional courses.

MSAE is the attribute used to identify Materials Science and Engineering Courses in the Notre Dame course catalog. To see which of the courses will be offered in the fall, go to **classsearch.nd.edu**, scroll down, click the arrow and select MSAE from the "Attribute" menu. Then click "Search".

### Material Structure – Soft, hard, and heavy matter

**CBE 60561 – Structure of Solids (Instructor: Paul McGinn). **This class seeks to provide students with an understanding of the structure of solids, primarily as found in metals, alloys, and ceramics applied in technological applications. The structure of crystalline solids on the atomic level as well as the microstructural level will be discussed. Imperfections in the arrangements of atoms will be described, especially as regards their impact on properties. The study of structure through X-ray diffraction will be a recurring theme. A sequence of powder diffraction laboratory experiments (four to five class periods) also will be included.

**CHEM 60618 – Chemical Crystallography (Instructor: Allen Oliver). **This course covers the theoretical and practical aspects of Small Molecule X-ray Crystallography. There will be both lecture and laboratory sessions with this course. Topics covered include: crystal growth, the diffraction experiment, space group analysis, symmetry, structure solution and refinement, powder diffraction, use of typical software for diffraction studies. The laboratory session will cover the practical aspects of crystal selection and the use of X-ray diffractometers.

**CHEM 60438 – Polymer: Principle to Practice (Instructor: Haifeng Gao). **This course offers the basic physical and organic chemistry knowledge in polymerization reactions. Topics to be covered include mechanisms of polymerization reactions; polymerization kinetics and thermodynamics; relationship of physical properties to structure and composition; correlations of applications with chemical constitution; functional polymers for medicines and electronics. The course is recommended for students with special interest in polymer materials and future plan on polymer research and professional studies.

**CE 60382 – Actinide Chemistry (Instructor: Amy Hixon). **This course is intended to provide students with a basic understanding of the fundamental chemical and physical properties of actinide elements. Lectures will focus on solution chemistry, bonding, kinetics, and thermodynamics in the context of the behavior of actinides in the environment and within the nuclear fuel cycle. Particular emphasis will be placed on solution chemistry of the actinides and interactions at the solid-water interface.

**CBE 60457 – Polymer Science & Engineering (Instructor: Ruilan Guo). **This course is an intermediate level introduction to the fundamental chemistry and physics of polymer materials. The course is designed to meet the needs of students in all science and engineering disciplines who are interested, or already engaging in polymer related research. The lectures will focus on the underlying concepts and principles in polymer materials, emphasizing the interrelationships between synthesis, structure, processing, properties and performance, and demonstrate them in the context of their everyday use as well as real-world advanced engineering applications. Major topics in polymer chemistry, physics and engineering will be covered including: general introduction of polymers, major classes of polymerization reactions and kinetics, microstructure and morphology, polymer properties (thermal, mechanical, etc.), polymer thermodynamics, polymer characterization techniques, and plastics engineering and processing methods. The successful students will emerge from the course with a current, sound knowledge of polymer concepts and an ability to apply them in career situations.

**CBE 60556 – Polymer Engineering (Instructor: Davide Hill).** A course for seniors and graduate students in science and engineering who are interested in applications of engineering to polymer science and technology. Topics include polymerization reactions, reaction engineering of polymer systems, structure, properties, and processing. Emphasis is placed on the use and extension of fundamental chemical engineering principles and methods of analysis (such as those emerging in reaction engineering, solution thermodynamics, and transport phenomena) to polymer related topics.

**CBE 60667 - Mass Transfer Membrane Systems (Instructor: William Phillip).** Membranes are discrete interfaces that mediate the transfer of chemical species between two adjacent phases. For example, naturally-occurring membranes are central to many of the functions of biology, while engineered membranes can be designed to produce potable water from seawater, to control the release of therapeutic drugs, or to enable energy storage technologies. Regardless of where a membrane is found, elucidating and quantifying the processes that control mass transfer through it is essential to understanding, and potentially enhancing, its function. In this course, the transport phenomena and thermodynamic principles that are used to describe the rates of mass transfer are defined. Subsequently, these principles are used to contemplate the molecular and structural design of materials that can be manufactured to produce next-generation membranes that help to address grand societal challenges.

**CBE 60725 – Principles of Molecular Engineering (Instructor: Matt Webber). **The objective of this course, intended for both upper level undergraduate and graduate students, is to illustrate the emerging field of molecular engineering. By fusing concepts from chemistry and materials science, molecular engineering seeks rational design of chemical building blocks for organized systems and materials. Students will gain a fundamental perspective for how non-covalent interactions and designed molecular motifs can dictate the structure, function, and properties of resulting engineered systems. This will include an appreciation for the role on intermolecular forces in governing the behavior of these molecules as they interact with each other and with their environment (typically a solvent). Additionally, illustrative examples will point to the power of strategies rooted in principles of molecular engineering to create highly controlled and functional materials. topics will include: non-covalent interactions, molecular design, thermodynamic driving forces, solvent effects, molecular self-assembly, supramolecular chemistry, molecular & materials characterization techniques, and applications of molecular engineering for diverse uses in energy, medicine, computing, formulation science, industrial applications, and food sciences.

### Nanostructure Materials

**CBE 60577 – CHEM 60577 – Nanoscience and Technology (Instructor: Nosang Myung).** This course focuses on the unique scientific phenomena that accrue to matter with characteristic nanometer-scale dimensions and on the technologies which can be constructed from them. Special optical, electronic, magnetic, fluidic, structural and dynamic properties characteristic of nanostructures will be addressed. Demonstration of the characterization techniques, including scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive analysis (EDS) and others is an important part of the course.

**AME 60679 – Nanoparticles in Biomedicine (Instructor: Ryan Roeder). **Nanoparticle science and engineering will be introduced including the processing (synthesis and surface modification), structure (physical and molecular), and functional properties (biological, electrical, magnetic, mechanical, optical, X-ray, etc.) that enable biomedical applications in drug delivery, imaging, sensing, and tissue regeneration.

### Solid State Materials

**AME 60733-01 – Solar Energy: Photovoltaic Systems (Instructor: Svetlana Neretina).** This is an interdisciplinary course which covers basic science and engineering applications of solar cell technologies. The course is divided into two modules: the properties of sunlight, which is the source of energy, and solar cells themselves. In the first module the students learn about the sun resources, characteristics of sunlight, tracking the sun, optimizing the tilt of solar panels for different seasons and performing solar site obstacle survey. The second module introduces the students to a solar cell design principles including review on semiconductor properties and p-n junction device operation, optical and electrical design of a solar cell, solar cell interconnection and fabrication of a solar panel. The course will also examine next-generation solar cell concepts.

**EE 60556 – Fundamentals of Semiconductor/Physics (Instructor: Wolfgang Porod). **Treatment of the basic principles of solids. Topics include periodic structures, lattice waves, electron states, static and dynamic properties of solids, electron-electron interaction transport, and optical properties.

**EE 60576 – Electronic and Photonic Materials (Instructor: Chris Hinkle).** Principles of materials science applied to materials issues in fabrication, operation, and reliability of microelectronic devices.

**PHYS 50501 – PHYS 60501 – Intro to Solid State Physics (Instructor: Boldizsar Janko).** The course is intended to introduce the principles of the behavior electrons and phonons in solids, advanced concepts and applications, such as low-dimensional systems and superconductivity, and set the conceptual framework needed for future study and graduate research in condensed matter physics or technology-related industry. Topics will include: crystal structure and diffraction, phonons and heat capacity, free electron gas and elementary band theory, semiconductors, magnetism, and superconductivity.

**PHYS 80501 – Solid State Physics (Instructor: Yi-Ting Hsu).** Free electron theories of solids; Drude and Sommerfeld theory; crystal and reciprocal lattices; diffraction; Bloch electrons; band structure and the Fermi surface; cohesive energy; classical and quantum theory of the harmonic crystal, phonons; dielectric properties of insulators; semiconductors; paramagnetism and diamagnetism, magnetic ordering; superconductivity.

**CBE 60435 – CHEM 60435 – Electrochemistry and Electrochemical Engineering (Instructor: Paul Bohn****). **This course addresses the fundamentals and applications of technologies that rely on heterogeneous electron transfer reactions. The first part of the course addresses fundamental aspects of electron transfer reactions at electrified interfaces, including band structure of metals and semiconductors, electrochemical potentials, electron transfer kinetics and Marcus theory, potential step and potential sweep experiments, hydrodynamic electrochemistry, potentiometry and ion-selective electrodes, impedance measurements, and electrochemical instrumentation. The second part of the course addresses applications to energy storage (batteries, fuel cells, supercapacitors), energy conversion (photovoltaics), bioelectrochemistry, including neurochemistry, corrosion, and electrolysis and electroplating.

**CBE 60535 – Electrochemical Energy (Instructor: Nosang Myung)**. In this class, students learn the fundamental theoretical concepts underlying electrochemical systems, but do not learn how these concepts govern the function of engineered electrochemical systems. This course combines the study of charge transfer at electrode/electrolyte interfaces with the development of practical materials and processes. The development of the technology involves the study of the electrochemical reactors, their voltage and current distribution, mass transport conditions, hydrodynamics, geometry as well as the quantification of overall performance in terms of reaction yield, conversion efficiency, and energy efficiency. This course examines the operational principles of electrochemical energy storage devices (batteries and capacitors), energy conversion devices (fuel cells, electrolyzers), electrodeposition, corrosion, and bioelectrochemical interfaces. The emphasis is on materials and device design based on fundamental chemistry and physics concepts that govern the properties and performance of the materials/devices involved. Specific systems of study will include electrode and electrolyte materials for primary (non-rechargeable) and secondary (rechargeable) batteries including lithium-ion batteries, electrochemical capacitors, proton exchange membrane fuel cells, solid oxide fuel cells, alloy electrocatalysts, mixed ionic-electric conductors, and biosensor development.

**CBE 60623 – Surface Science (Instructor:** **Casey O'Brien) **This course covers the structure and properties of solid surfaces and interfaces and the dynamics of chemical reactions at surfaces. Topics include geometrical structure, surface morphology, electronic structure, surface composition, kinetics and dynamics (adsorption, scattering, vibrations, diffusion, desorption), structure and reactivity of surface molecules, non-thermal excitations of surfaces, and modern ultrahigh vacuum experimental techniques.

**EE 87039 – Quantum Optics and Nanophotonics (Instructor: Anthony Hoffman). **This course will introduce quantum optics and nanophotonics, emphasizing the foundation of these two fields. The material will include quantization of the electromagnetic field, quantum states of light, light-matter interactions, plasmonics, metamaterials, and recent advances that merge the fields of quantum optics and nanophotonics.

**EE 80688 – Advanced Solid State Physics (Instructor: Anthony Hoffman). **This course will provide advanced discussion of interactions that are fundamental to solid state and semiconductor systems for graduate students. Topics that will be covered: free-electron theories, electrons in weak periodic potentials, tight-binding, phonons, semi-classical models for electron dynamics, beyond the relaxation-time approximation, dielectric properties of insulators, and magnetism. While there are no prerequisites for the course, students are expected to have a working knowledge of quantum mechanics and introductory semiconductor or condensed matter physics.

**EE 80656 – Advanced Semiconductor Physics (Instructor: Suman Datta). **The class will provide graduate students with a solid understanding of the basic underlying physics of semiconductors that lead to practical applications. Starting from a review of quantum mechanics and specifically perturbation theory, we will cover electronic bandstructure, electron-photon and electron-phonon interactions, charge scattering by defects and transport, and optical properties of semiconductors. Quantum confinement effects in optical devices, ballistic transistors, and tunneling FETs will be covered. The modern bottom-up approach to electronic properties from the non-equilibrium Green's functions will be covered. Topics 1) Recap of quantum mechanics 2) Formulation of the transport problem: Electric current 3) Ballistic transport and nanoscale FETs 4) Time-independent perturbation theory 5) Electron bandstructure and quantized states 6) Time-dependent perturbation theory 7) Electron-photon interactions, optical properties, LEDs and Lasers 8) Electron-phonon interaction and scattering 9) Electron-defect interaction and scattering 10) Mobility, drift-diffusion, quasi-ballistic FETs 11) High-field phenomena: Tunneling transport and tunnel-FETs 12) Bottom-up approach to transport: Non-Equilibrium Green's Function (NEGF) approach.

**PHYS 90507 – Topology and Dirac Fermions in Condensed Matter (Instructor: Badih Assaf). **This course is an introduction to the burgeoning field of topological and Dirac matter. It covers the following topics: Dirac, Weyl and Majorana fermions, the Jackiw-Bell solution to the Dirac equation, the Berry phase, topological invariants, the band structure of graphene and experimental proofs of its Dirac nature, toy models of topological systems (Kane-Mele, Su-Schrieffer-Heeger, ..., realistic topological materials and their band structure, experimental observables of non-trivial topology (quantum spin Hall effect, band-inversion, ...).

**CHEM 90616 - Solid State Materials and Chemistry (Instructor: Adam Jaffe).** Solid-state materials are the reason we can feed the world, store information in computers, harness solar power, and so much more. This class is designed as an introductory discussion of the physical and electronic structure of solid-state materials with an emphasis on structure-property relationships. The course is aimed at engaging a broad range of scientists and engineers interested in the chemistry and applications of solid-state materials. Perhaps most importantly, the class takes a practical approach with the goal of making participants familiar with a wide variety of materials, methods for materials characterization relevant to students’ research projects, and applications including energy utilization, catalysis, and optoelectronics. We will follow many tangents into the fun and wide world of materials chemistry and how it relates to our modern (and ancient) society.

### Emergent Phenomena at Surfaces and Interfaces

**CBE 60625 – Principles of Heterogeneous Catalysis (Instructor: Jason Hicks).** This course will provide a comprehensive overview of heterogeneous catalysis with particular focus on catalyst synthesis, modern characterization techniques, kinetics, and reaction mechanisms for energy-related applications. Emphasis will be placed on 1) understanding the synthesis and properties of a variety of solid catalysts including carbides, phosphides, zeolites, bimetallic catalysts, tethered catalysts, and metal-organic frameworks, and 2) in-situ/operando techniques to aid in the design of new materials.

**CE 60300**** – Geochemistry (Instructor: Jeremy Fein). **An introduction to the use of chemical thermodynamics and chemical kinetics in modeling geochemical processes. Special emphasis is placed on water-rock interactions of environmental interest.

**CE 60635 – High-Temperature Geochemistry (Instructor: Clive Neal). **This course examines the generation and evolution of magma from a physicochemical standpoint. Using actual geochemical datasets and samples in conjunction with research papers will allow the student to develop the skills for formulating petrogenetic models that are thermodynamically viable. These skills will be used in their individual research projects. The student is evaluated by two exams, weekly homework assignments, and a research paper.

**EE 60568 – Fundamentals of Photonics (Instructor: Doug Hall). **The fundamental physics and engineering of photonic devices will be explored in this class. We will start with Maxwell's equations and study light propagation and interaction with materials, diffraction theory, photon statistics, waveguides, lasers, and optoelectronics. Experience with vector calculus, frequency domain (Fourier) analysis, and previous coursework in electromagnetism are strongly recommended. Appropriate for both graduate students and advanced undergraduate students.

### Biomaterials

**AME 60571 – Structural Aspects of Biomaterials (Instructor: Donny Hanjaya-Putra). **Structure and mechanical functions of load bearing tissues and their replacements. Natural and synthetic load-bearing biomaterials for clinical applications are reviewed. Biocompatibility and host response to structural implants are examined. Quantitative treatment of biomechanical issues related to design of biomaterial replacements for structural function. Material selection for reconstructive surgery is addressed. Directions in tissue engineering are presented.

**AME 60572 – Introduction to Biomechanics. (Instructor: Maria Holland).** This course is an introduction to the application of mechanical engineering analysis to understand topics in biology. Topics will include development, disease, diagnosis, treatment, imaging, and mechanical testing in a variety of biological systems across scales.

**AME 60672 – Cell Mechanics (Instructor: Glen Niebur). **The effects of mechanical loading on cells are examined. Mechanical properties and material structure of cell materials are reviewed. Filaments, filament networks and membranes are examined. Mechanics of flow induced effects, adhesion cell-substrate interactions, and signal transduction are examined. Experimental techniques are reviewed.

**AME 60676 – Cancer Engineering. (Instructor: Meenal Datta). **Applying engineering concepts to cancer biology allows for the design of new models, methods, and technologies for improved diagnostics, monitoring, and treatment. We will explore the barriers in the tumor microenvironment that thwart drug delivery and efficacy and tumor-fighting immune cells. Through didactic lectures, expert seminars, and in-class projects based on the primary literature, we will examine how cutting-edge engineering approaches can be used to overcome these barriers and improve treatment outcomes.

**CBE 60888 – Cellular and Physical Principals of Bioengineering (Instructor: Basar Bilgicer). **This course covers the breakdown of biological systems at molecular, cellular and tissue levels. It evolves to the design and synthesis of biomaterials at a molecular scale used in manipulating and targeting biological systems, including biotechnology and biomedical engineering. For these purposes, we will learn what is inside a cell, molecular machines, nerve impulses, binding thermodynamics and kinetics in biological systems, chemical forces and molecular self-assembly.

### Materials Characterization

**CHEM 60532 – Optical Spectroscopy (Instructor: Greg Hartland). **Principles and applications of spectroscopic measurements and instrumentation. Atomic and molecular absorption, emission, fluorescence, and scattering, emphasizing physical interpretation of experimental data.

**CBE 60727 – CHEM 60727 – Ambient methods for Surface Characterization (Instructor: Merlin Bruening). **This course develops fundamental principles for characterizing surfaces and interfaces, particularly thin films, using infrared spectroscopy, ellipsometry, electrochemistry, and contact angle measurements. The material will cover reflection of light from surfaces, which is relevant to surface infrared spectroscopy, surface plasmon resonance and ellipsometry, surface energies, adsorption isotherms, and some fundamental aspects of electrical double layers, zeta potentials, and mass transport in electrochemistry.

**EE 80603 – Advanced Electron Microscopy (Instructor: Alexander Mukasyan). **Course is an introduction to the fundamental basis and operations of transmission electron microscope and is required for all students who plan using the TEM in their research. Goals: The course goal is for the students to become competent, research-level experts in transmission electron microscopy. They will understand the functions of the TEM and how it works. They will be competent in basic operating techniques, and ready to learn more advanced ones as needed There will be a lectures (2 per week) and laboratory demonstration (3 hours/week). Topics will include: Electro-optics of the TEM - Image formation and imaging modes - Diffraction theory and Diffraction patterns - Dark and bright field imaging - Image interpretation - High resolution microscopy and Lattice imaging - Sample preparation.

### Materials Processing

**EE 60546 – I C Fabrication (Instructor: Alan Seabaugh). **This course introduces the students to the principles of integrated circuit fabrication. Photolithography, impurity deposition and redistribution, metal deposition and definition, and other topics. Students will fabricate a 5000 transistor CMOS LSI circuit.

**CBE 60910 – Materials Processing, CRN 29702 (Instructor: Paul McGinn). **This course covers a limited number of materials processing techniques used by materials researchers as well as industrial manufacturers. The primary areas to be covered include thin film processing, fine ("nanoscale") particle processing, crystal growth, and a few selected ceramics processing techniques. Within each of these areas various techniques will be discussed, with both the theoretical and practical aspects being described.

**CE 60323 – Advanced Physical – Chemical Water Treatment Processes (Instructor: Kyle Doudrick). **The objective of this course is to learn the fundamentals and design principles of advanced water treatment processes, including reactor analysis, redox reactions, adsorption, membrane filtration, ion exchange, air stripping, photolysis, advanced oxidation, and catalysis.

### Computational Modeling

** PHYS 60050 – Computational Physics (Instructor: Zoltan Toroczkai). **This course will provide a basic foundation in the skills and knowledge needed for computational physics. The course has three major parts: (1) Programming basics, with Python; (2) algorithms and methods, frequently used in computational physics and (3) physics projects for turning numerical calculations into solutions to real problems. Topics will include foundations of programming, principles of numerical analysis, interpolation and extrapolation, methods for solving ordinary and partial differential equations, random processes, Markov Chains, basic statistics, graphical representations. Applications include problems from classical physics (mechanics, electrodynamics), statistical mechanics, nuclear physics, basic network science and machine learning. The main goal of this course is to introduce the students to computational thinking in solving physics problems. In that sense this is not a numerical analysis math course but a course about how to tackle a physics problem with a computer, how to perform computational "experiments" to answer questions about a physical system.

** CBE 60501 – Machine Learning for Chemical Engineers (Instructor: Yamil Colon). **Machine Learning (ML) is an important technological tool affecting society in myriad ways. Chemical engineering is not the exception. Students will be exposed to multiple examples within the chemical engineering discipline to appreciate the potential of ML as well as its limitations. The course is structured to provide a practical introduction to machine learning for chemical engineers. Topics to be covered include regression, supervised learning, unsupervised learning, feature extraction and other tools relevant to chemical and molecular engineering (SMILES, RDKit, etc.). The course will emphasize practical programming skills using Python implementations and will use case studies in chemical engineering. Students should have strong math and Python skills. Students who have already taken classes such as Numerical Methods and Statistical Analysis, Linear Algebra, Calculus, and Thermodynamics should have the necessary background to be successful in this course. Materials Science and Engineering students are expected to have a materials topic for the final course project.

** CBE 60547 – Modern Methods in Computational Molecular Thermodynamics and Kinetics (Instructor: William Schneider). **This course will introduce the basis of modern approaches to computing the thermodynamics and kinetics of gas-phase, condensed-phase, and surface chemical reactions from first principles. Quantum chemical wavefunction and density functional approaches for treating the electronic structure of molecules, solids, and surfaces will be described. Optimization methods and statistical mechanical techniques for determining structures, spectroscopies, and thermodynamic and kinetic properties will be covered. Software for calculating these properties will be introduced and applied in hands-on exercises and a class project.

** CBE 60553 – Advanced Chemical Engineering Thermodynamics (Instructor: Jonathan Whitmer). **This course is focused on an advanced treatment of thermodynamic concepts. An introduction to molecular thermodynamics is given, followed by detailed treatments of phase equilibrium, equation-of-state development and activity coefficient models.

** CBE 60642 – Molecular Thermodynamics (Instructor: Jonathan Whitmer). **This course examines advanced topics in thermodynamics and statistical mechanics, including phase transitions, lattice models, renormalization group theory, critical phenomena, physical meaning and interpretation of correlation functions, classical partition functions and collective variables, liquid theory, molecular simulations of fluids and ordered phases, structure and dynamics of complex media, and supercooled and glassy materials.

** AME 70791 – Molecular Level Modeling for Engineering Applications (Instructor: Tengfei Luo). **This graduate level course is intended for engineering graduate students with interests in the simulation of materials and studying their properties at the molecular level using different atomistic simulations techniques. This course will introduce basics of statistical thermodynamics and classical Monte Carlo and molecular dynamics simulations. With the fundamentals, students will learn how to use the knowledge and techniques to study engineering problems such as mass diffusion and heat transfer. It will also emphasize hands-on exercises in which student will use these techniques to model different materials including gas, liquid, solid, the phase transition among these different phases. Structural, flow and thermal properties of materials will also be studied. Students will be required to program their own code for small projects and will be using open source software, such as LAMMPS, for larger projects.

### Quantum Mechanics

** EE 60587 – Introduction to Quantum Mechanics (Instructor: Craig Lent). **The course focuses on those aspects of quantum theory that are of particular relevance to electrical engineering. It is intended to give seniors and first-year graduate students a working knowledge of quantum mechanics at a level sufficient to illuminate the operation of standard and advanced quantum devices. Topics include classical mechanics versus quantum mechanics, early quantum theory, Schrödinger formulation, time-dependent and time-independent Schrödinger equation, Dirac formulation, Bloch theorem, magnetic effects, open quantum systems, and density matrices.

##### Need more information?

For more information on the Materials Science and Engineering Program, please contact us at MSE-list@nd.edu or 574-631-6470.