CBE Interest Area Electives List

Below you will find a student created list of graduate electives broken down by Interest Area.

Biotechnology and Pharma

Course Code Title Description Course Term
CBE 517 Principles of Genome Engineering This course covers up-to-date techniques in genome engineering and its application in basic research and translational medicine. Genetic engineering techniques including site-directed DNA recombination (Cre-Lox, Phi31 integrase), genome editing (TALEN, CRISPR/Cas-9), next generation sequencing, and molecular imaging will be covered. Key concepts in genomics, epigenetics, gene regulation will be introduced, and application of genetic engineering techniques in the field of developmental biology, stem cell biology, and synthetic biology will be discussed. Spring
CBE 554 Engineering Biotechnology Advanced study of re DNA techniques; bioreactor design for bacteria, mammalian and insect culture; separation methods; chromatography; drug and cell delivery systems; gene therapy; and diagnostics. Spring
CBE/ BE/ MEAM 555 Nanoscale Systems Biology Nano-science and engineering approaches to systems in biology are of growing importance. They extend from novel methods, especially microscopies that invite innovation to mathematical and/or computational modeling which incorporates the physics and chemistry of small scale biology. Proteins and DNA, for example, are highly specialized polymers that interact, catalyze, stretch and bend, move, and/or store information. Membranes are also used extensively by cells to isolate, adhere, deform, and regulate reactions. In this course, students will become familiar with cell & molecular biology and nano-biotechnology through an emphasis on nano-methods, membranes, molecular machines, and ‘polymers’ – from the quantitative perspectives of thermodynamics, statistical physics, and mechanics. We specifically elaborate ideas of energetics, fluctuations and noise, force, kinetics, diffusion, etc. on the nano- thru micro- scale, drawing from very recent examples in the literature. Laboratory experiments will provide hands-on exposure to microscopies in a biological context (eg. fluorescence down to nano-scale, AFM), physical methods (eg. micromanipulation, tracking virus-scale particles or quantum dots), and numerical problems in applied biophysics, chemistry, and engineering. A key goal of the course is to familiarize students with the concepts and technology (plus their limitations) as being employed in current research problems in nanoscale systems biology, extending to nanobiotechnology. Fall
CBE 556 Biochemical Engineering of Wine This course surveys the biochemistry and biochemical unit operations involved in the commercial production of modern wines. Topics will include grape growing, pressing, fermentation , filtration, and packaging/aging. Emphasis will also be placed on yeast microbiology and wine biochemistry. Lectures will be supported by wine tasting sessions to highlight the important characteristics of different wine types. Spring
CBE/ BE 562 Drug Discovery and Development Intro to Drug Discovery; Overview of Pharmaceutical Industry and Drug Development Costs, Timelines; High Throughput Screening (HTS): Assay Design and Sensitivity Solid Phase Synthesis and Combinatorial Chemistry; Enzyme Kinetics; Fluorescence, Linearity, Inner-filter effect, quenching; Time dynamics of a Michaelis-Menton Reaction; Competitive Inhibitor; FLINT, FRET, TRF, FP, SPA, alpha-screen; Enzyme HTS (protease); Cell based screening; Fura-2 ratio, loading signaling; Gfpcalmodulin-gfp integrated calcium response; Estrogen/ERE-Luc HTS; Problems with cell based screening (toxicity, permeability, nonspecificity); Instrumentation, Robotics/Automation; Z-factor; SAR, Positioning Scanning; Microarray HTS; IC50, % Conversion in HTS and IC50, Assay Optimization. Fall
CBE 564 Drug Delivery The topics include drug transport, distribution and interactions in the body, specific challenges for biotherapeutics, pharmacokinetics, drug delivery systems and nanocarriers, gene delivery systems, targeted drug delivery, and translational aspects of new drug delivery systems. Faculty from engineering and medicine will give lectures related to their research interests. The students read current journal articles on drug delivery systems. The major group assignment for the course is a written and oral group proposal on a new drug delivery system. Spring
CBE 580 Masters Biotech Lab The laboratory methods covered include molecular cloning techniques, cell transformation, DNA gel electrophoresis, ImageJ, PCR, DNA sequencing, SDS?PAGE, mammalian cell culture, and enzyme assays. Culture techniques for bacteria, yeast and animal cells are taught and practiced. The students write several individual lab reports and keep a lab notebook during the semester. A group presentation and report on a proposal for a new lab experiment is the final assignment for the lab. Fall
BE 512 Bioengineering III: Biomaterials This course provides a comprehensive background in biomaterials. It covers surface properties, mechanical behavior and tissue response of ceramics, polymers and metals used in the body. It also builds on this knowledge to address aspects of tissue engineering, particularly the substrate component of engineering tissue and organs. Fall
BE 551 Biomicrofluidics The focus of this course is on microfluidics for biomedical applications. Topics to be covered in the first half of this course include microscale phenomena, small-scale fabrication techniques, and sensing technologies that are often leveraged in the development of microfluidic systems for the study of biomolecules, cells, tissues, and organs in living biological systems. In the second half of this course, strong emphasis will be placed on the application of microfluidics in cell biology, bioanalytical chemistry, molecular biology, tissue engineering, and drug discovery. Fall
BE 553 Principles, Methods, and Applications of Tissue Engineering Tissue engineering demonstrates enormous potential for improving human health. This course explores principles of tissue engineering, drawing upon diverse fields such as developmental biology, cell biology, physiology, transport phenomena, material science, and polymer chemistry. Current and developing methods of tissue engineering, as well as specific applications, will be discussed in the context of these principles. A significant component of the course will involve review of current literature within this developing field. Spring
BE 558 Principles of Biological Fabrication Introduces methodological approaches that are currently used for the de novo construction of biological molecules – primarily, nucleic acids and proteins – and how to use these molecules to engineer the properties of cells and intact tissue. By the end of the semester, students should (i) possess a molecular-scale understanding of key biological synthesis (ii) and assembly processes, (ii) gain an intuition for how to create novel (iii) methodologies based on these existing processes, and (iii) appreciate (iv) the drivers of technology adoption (e.g. cost, time, ease, and (v) reproducibility). Throughout the course, we will place the material in context of applications in bioengineering and human health, including protein engineering, drug discovery, synthetic biology & optogenetics, bio-inspired materials, and bio-electronic devices. Spring
BE 561 Musculoskeletal Biology and Bioengineering The goal of this course is to educate students in core principles and expose them to cutting-edge research in musculoskeletal biology and bioengineering through (1) lectures covering the basic engineering principles, biological fundamentals, and clinical practices involved in the function, repair, and regeneration of the musculoskeletal tissues; (2) critical review and presentation by student groups of recent and seminal publications in the field related to the basic science, translation, and clinical practice of musculoskeletal biology and bioengineering, with discussion input by faculty members with relevant expertise. This course will place an emphasis on delivering multidisciplinary knowledge of cell and molecular biology, mechanics, material science, imaging, and clinical medicine as it relates to the field of musculoskeletal bioengineering and science. Fall
BE 565 Developmental Engineering of Tissues This course discusses systems biology approaches to understanding tissue development, homeostasis, and organogenesis. Emphasis is placed on modern technologies, models, and approaches to understanding collective cell behaviors that sculpt tissue form and function, placing developmental principles within an engineering framework. We will consider morphogenetic, mechanobiology, and micro-engineering/sensing analyses. Fall
BE 569 Systems Biology of Cell Signaling Behavior This course discusses the principles of cell signaling and cell decisions. We start from a molecular description of cell signaling components. The course builds towards understanding how their interactions govern cell and tissue behavior and how these processes can breakdown in disease. We conclude with a survey of modern approaches to analyze and manipulate signaling networks to study and control biological systems. Spring
BE 578 Principles of Controlled Release Systems This course provides a basic understanding of the engineering of controlled release systems specifically geared towards the development of formulations for drug delivery, which stands as a 114 billion dollar industry. The course focuses on topics at the interface between engineering and medicine, such as biomaterials, pharmacokinetics, polymer chemistry, reaction kinetics, and transport phenomena. Design of controlled release systems for transdermal, aerosol, oral, gene, and targeted cellular delivery are discussed with emphasis placed on fabrication, US FDA regulatory considerations, and the relevant physiological milieu. The course comprises (1) foundational lectures that provide the basic tools for the student to elaborate a controlled delivery system, (2) an overview of key current research on biomedical controlled release systems for different pathologies and body compartments, (3) an elevator pitch competition for original ideas that use controlled release systems, and (4) a project; plan and presentation to implement the pitched controlled release; system idea to practice design and problem-solving skills and practice basic elements of business proposal. Fall
BIOL 536 Fundamentals of Computational Biology Introductory computational biology course designed for both biology students and computer science, engineering students. The course will cover fundamentals of algorithms, statistics, and mathematics as applied to biological problems. In particular, emphasis will be given to biological problem modeling and understanding the algorithms and mathematical procedures at the “pencil and paper” level. That is, practical implementation of the algorithms is not taught but principles of the algorithms are covered using small sized examples. Topics to be covered are: genome annotation and string algorithms, pattern search and statistical learning, molecular evolution and phylogenetics, functional genomics and systems level analysis. Spring

Catalysis

Course Code Title Description  Course Term
CBE544 Computational Science of Energy and Chemical Transformations This course will introduce students to fundamental concepts and techniques of atomic scale computational modeling. The material will cover electronic structure theory and chemical kinetics. Several well-chosen applications in energy and chemical transformations including study and prediction of properties of chemical systems (heterogeneous, molecular, and biological catalysts) and physical properties of materials will be considered. This course will have modules that will include hands-on computer lab experience and teach the student how to perform electronic structure calculations of energetics which form the basis for the development of a kinetic model for a particular problem, which will be part of a project at the end of the course.
CBE 546 Fundamentals of Industrial Catalytic Processes A survey of heterogeneous catalysis as applied to some of the most important industrial processes. The tools used to synthesize and characterize practical catalysts will be discussed, along with the industrial processes that use them.
CHEM 557 Mechanisms of Biological Catalysis Reaction mechanisms in biological (enzymes, abzymes, ribozymes) and biomimetic systems with emphasis on principles of catalysis, role of coenzymes, kinetics, and allosteric control.

Computational Science in Biological Systems

Course Code Title Description Course Term
CBE 559 Multiscale Modeling of Biological Systems This course provides theoretical, conceptual, and hands-on modeling experience on three different length and time scales – (1) electronic structure (A, ps); (2) molecular mechanics (100A, ns); and (3) deterministic and stochastic approaches for microscale systems (um, sec). Students will gain hands-on experience, i.e., running codes on real applications together with the following theoretical formalisms: molecular dynamics, Monte Carlo, free energy methods, deterministic and stochastic modeling Course not offered every year
BE 567 Mathematical Computation Methods for Modeling Biological Systems This course will cover topics in systems biology at the molecular/cellular scale. The emphasis will be on quantitative aspects of molecular biology, with possible subjects including probabilistic aspects of DNA replication, transcription, translation, as well as gene regulatory networks and signaling. The class will involve analyzing and simulating models of biological behavior using MATLAB.
PHYS 585 Theoretical and Computational Neuroscience This course will develop theoretical and computational approaches to structural and functional organization in the brain. The course will cover: (i) the basic biophysics of neural responses, (ii) neural coding and decoding with an emphasis on sensory systems, (iii) approaches to the study of networks of neurons, (iv) models of adaptation, learning and memory, (v) models of decision making, and (vi) ideas that address why the brain is organized the way that it is. The course will be appropriate for advanced undergraduates and beginning graduate students. A knowledge of multivariable calculus, linear algebra and differential equations is required (except by permission of the instructor). Prior exposure to neuroscience and/or Matlab programming will be helpful
AMCS 567 Mathematical Computation Methods for Modeling Biological Systems This is an introductory course in mathematical biology. The emphasis will be on the use of mathematical and computational tools for modeling physical phenomena which arise in the study biological systems. Possible topics include random walk models of polymers, membrane elasticity, electrodiffusion and excitable systems, single-molecule kinetics, and stochastic models of biochemical networks
BE 504 Biological Data Science II: Data Mining Principles for Epigenomics This course will teach upper level undergraduates and graduate students how to answer biological questions by harnessing the wealth of genomic and epigenomic data sets generated by high-throughput sequencing technologies.
BE 521 Brain-Computer Interfaces The course is geared to advanced undergraduate and graduate students interested in understanding the basics of implantable neuro-devices, their design, practical implementation, approval, and use. Reading will cover the basics of neural signals, recording, analysis, classification, modulation, and fundamental principles of Brain-Machine Interfaces. The course will be based upon twice weekly lectures and “hands-on” weekly assignments that teach basic signal recording, feature extraction, classification and practical implementation in clinical systems. Assignments will build incrementally toward constructing a complete, functional BMI system. Fundamental concepts in neurosignals, hardware and software will be reinforced by practical examples and in-depth study. Guest lecturers and demonstrations will supplement regular lectures.
BE 537 Biomedical Image Analysis This course covers the fundamentals of advanced quantitative image analysis that apply to all of the major and emerging modalities in biological/biomaterials imaging and in vivo biomedical imaging. While traditional image processing techniques will be discussed to provide context, the emphasis will be on cutting edge aspects of all areas of image analysis (including registration, segmentation, and high-dimensional statistical analysis). Significant coverage of state-of-the-art biomedical research and clinical applications will be incorporated to reinforce the theoretical basis of the analysis methods.
BE 566 Network Neuroscience The human brain produces complex functions using a range of system components over varying temporal and spatial scales. These components are couples together by heterogeneous interactions, forming an intricate information-processing network. In this course, we will cover the use of network science in understanding such large-scale and neuronal-level brain circuitry.

Computational Science and Simulation

Course Code Title Description Course Term
CBE 554 Computational Science of Energy and Chemical Transformations

Our theoretical and computational capabilities have reached a point where we can do predictions of materials on the computer. This course will introduce students to fundamental concepts and techniques of atomic scale computational modeling. The material will cover electronic structure theory and chemical kinetics. Several well-chosen applications in energy and chemical transformations including study and prediction of properties of chemical systems (heterogeneous, molecular, and biological catalysts) and physical properties of materials will be considered. This course will have modules that will include hands-on computer lab experience and teach the student how to perform electronic structure calculations of energetics which form the basis for the development of a kinetic model for a particular problem, which will be part of a project at the end of the course.

CBE 525 Molecular Modeling and Simulations Students will explore current topics in thermodynamics through molecular simulations and molecular modeling. The requisite statistical mechanics will be conveyed as well as the essential simulation techniques (molecular dynamics, Monte Carlo, etc.). Various approaches for calculating experimentally measurable properties will be presented and used in student projects.
ENM 531 Data-driven Modeling and Probabilistic Scientific Computing We will revisit classical scientific computing from a statistical learning viewpoint. In this new computing paradigm, differential equations, conservation laws, and data act as complementary agents in a predictive modeling pipeline. This course aims explore the potential of modern machine learning as a unifying computational tool that enables learning models from experimental data, inferring solutions to differential equations, blending information from a hierarchy of models, quantifying uncertainty in computations , and efficiently optimizing complex engineering systems.
AMCS 602 Algebraic Techniques for Applied Mathematics and Computational Science, I We turn to linear algebra and the structural properties of linear systems of equations relevant to their numerical solution. In this context we introduce eigenvalues and the spectral theory of matrices. Methods appropriate to the numerical solution of very large systems are discussed. We discuss modern techniques using randomized algorithms for fast matrix-vector multiplication, and fast direct solvers. Topics covered include the classical Fast Multipole Method, the interpolative decomposition, structured matrix algebra, randomized methods for low-rank approximation, and fast direct solvers for sparse matrices. These techniques are of central importance in applications of linear algebra to the numerical solution of PDE, and in Machine Learning. The theoretical content of this course is illustrated and supplemented throughout the year with substantial computational examples and assignments. Course  not offered every year
AMCS 603 Algebraic Techniques for Applied Mathematics and Computational Science, II We begin with an introduction to group theory. The emphasis is on groups as symmetries and transformations of space. After an introduction to abstract groups, we turn our attention to compact Lie groups, in particular SO(3), and their representations. We explore the connections between orthogonal polynomials, classical transcendental functions and group representations. This unit is completed with a discussion of finite groups and their applications in coding theory Course  not offered every year
CIS 519 Applied Machine Learning Machine learning has been essential to the success of many recent technologies, including autonomous vehicles, search engines, genomics, automated medical diagnosis, image recognition, and social network analysis, among many others. This course will introduce the fundamental concepts and algorithms that enable computers to learn from experience, with an emphasis on their practical application to real problems. This course will introduce supervised learning (decision trees, logistic regression, support vector machines, Bayesian methods, neural networks and deep learning), unsupervised learning (clustering, dimensionality reduction), and reinforcement learning. Additionally, the course will discuss evaluation methodology and recent applications of machine learning, including large scale learning for big data and network analysis.
CIS 520 Machine Learning This course covers the foundations of statistical machine learning. The focus is on probabilistic and statistical methods for prediction and clustering in high dimensions. Topics covered include linear and logistic regression, SVMs, PCA and dimensionality reduction, EM and HMMs, and deep learning
ESE 503 Simulation Modeling and Analysis This course provides a study of discrete-event systems simulation in the areas of queuing, inventory and reliability systems as well as Markov Chains, Random-Walks and Monte-Carlo systems. The course examines many probability distributions used in simulation studies as well as the Poisson process. Fundamental to most simulation studies is the ability to generate reliable random numbers and so the course investigates the basic properties of random numbers and techniques used for the generation and testing of pseudo-random numbers. Random numbers are then used to generate other random variable using the methods of inverse-transform, convolution, composition and acceptance/rejection. Finally, since most inputs to simulation are probabilistic instead of deterministic in nature, the course examines some techniques used for identifying the probabilistic nature of input data. These include identifying distributional families with sample data, using maximum-likelihood methods for parameter estimating within a given family and testing the final choice of distribution using chi-squared goodness-of-fit.
ENM 540 Topics In Computational Science and Engineering This course is focused on techniques for numerical solutions of ordinary and partial differential equations. The content will include: algorithms and their analysis for ODEs; finite element analysis for elliptic, parabolic and hyperbolic PDEs; approximation theory and error estimates for FEM.
MSE 561 Atomic Modeling in Materials Science This course covers two major aspects of atomic level computer modeling in materials. 1. Methods: Molecular statics, Molecular dynamics, Monte Carlo, Kinetic Monte Carlo as well as methods of analysis of the results such as radial distribution function, thermodynamics deduced from the molecular dynamics, fluctuations, correlations and autocorrelations. 2. Semi-empirical descriptions of atomic interactions: pair potentials, embedded atom method, covalent bonding, ionic bonding. Basics of the density functional theory. Mechanics, condensed matter physics, thermodynamics and statistical mechanics needed in interpretations are briefly explained.
MATH 513 Computational Linear Algebra A number of important and interesting problems in a wide range of disciplines within computer science are solved by recourse to techniques from linear algebra. The goal of this course will be to introduce students to some of the most important and widely used algorithms in matrix computation and to illustrate how they are actually used in various settings. Motivating applications will include: the solution of systems of linear equations, applications matrix computations to modeling geometric transformations in graphics, applications of the Discrete Fourier Transform and related techniques in digital signal processing, the solution of linear least squares optimization problems and the analysis of systems of linear differential equations. The course will cover the theoretical underpinnings of these problems and the numerical algorithms that are used to perform important matrix computations such as Gaussian Elimination, LU Decomposition and Singular Value Decomposition.

Energy and Environment

Course Code Title Description Course Term
CBE 545

Electrochemical Energy Conversion and Storage

Fuel cells, electrolysis cells, and batteries are all electrochemical devices for the interconversion between chemical and electrical energy. These devices have inherently high efficiencies and are playing increasingly important roles in both large and small scale electrical power generation, transportation (e.g. hybrid and electric vehicles), and energy storage (e.g. production of H2 via electrolysis). This course will cover the basic electrochemistry and materials science that is needed in order to understand the operation of these devices, their principles of operation, and how they are used in modern applications.

CBE 544 Computational Science of Energy and Chemical Transformations Our theoretical and computational capabilities have reached a point where we can do predictions of materials on the computer. This course will introduce students to fundamenta l concepts and techniques of atomic scale computational modeling. The material will cover electronic structure theory and chemical kinetics. Several well-chosen applications in energy and chemical transformations including study and prediction of properties of chemical systems (heterogeneous, molecular, and biological catalysts) and physical properties of materials will be considered. This course will have modules that will include hands-on computer lab experience and teach the student how to perform electronic structure calculations of energetics which form the basis for the development of a kinetic model for a particular problem, which will be part of a project at the end of the course.
CHEM 764

Materials Chemistry

This course will focus on the structure-property relationships in materials chemistry on length scales from atomic dimension up to the microscale and then core concepts to Chemical design that underpins future, “Energy and Environmental Sustainability.” We will introduce the “12 Principles of Green Chemistry” and “12 Principles of Green Engineering” as a guide to modern materials chemistry design and then follow a trajectory that proceeds with increasing length scales of ordering in the solid state. We will introduce techniques of x-ray, neutron, electron, and ion beam based scattering, real space imaging and spectroscopies and use these to explore non-crystalline materials (amorphous, glasses, and time permitting quasicrystals and aperiodic systems) and crystalline solids. Studies will proceed from atomic scales through nanoscale, mesoscale, and micro-scale discussing the emergence of band structure and delcocalized electronic and optical properties that emerge due tothe finite scale of ordering and influence of the surface. We will then focus on how these foundations of materials chemistry are shaping advances in solar energy utilization with photochemistry and photoelectrochemistry and materials for photovoltaic and enabling advances electrochemical energy conversion and storage.
ESE 518

Battery and Super-Capacitor Systems

This is a senior / graduate course on scientific and technological fundamentals as they apply to electrochemical batteries and super-capacitors. The perspective utilized will be a combination of materials and systems science. The course will introduce the student to the different categories of electrochemical cells and batteries, and their related chemistry, kinds of super-capacitors, charging and discharging profiles, equivalent series resistance (ESR), power capacities, and lifetimes. For super-capacitors, the student will be introduced to double layer capacitance (DLC) and pseudo-capacitance types of energy storage, super-capacitor fundamentals through Faradaic and non-Faradaic processes, pseudo-capacitance of metal oxides and electro-active polymers (EAPs), non-ideal polarizable electrodes, energetics and kinetics of electrode processes, theories of dielectric polarization, inorganic and organic electrol carbonaceous materials, effective surface area (ESA) and functionalizations, as well as the AC impedance behavior of batteries and super-capacitors including the self-discharge characteristics of both. The fundamental electrochemical relations will be discussed, as well as battery / super-caps system modeling, and batteries management systems.
ESE 521 The Physics of Solid State Energy Devices An advanced undergraduate course or graduate level course on the fundamental physical principles underlying the operation of traditional semiconducting electronic and optoelectronic devices and extends these concepts to novel nanoscale electronic and optoelectronic devices. The course assumes an undergraduate level understanding of semiconductors physics, as found in ESE 218 or PHYS 240. The course builds on the physics of solid state semiconductor devices to develop the operation and application of semiconductors and their devices in energy conversion devices such as solar photovoltaics, thermophotovoltaics, and thermoelectrics, to supply energy. The course also considers the importance of the design of modern semiconductor transistor technology to operate at low-power in CMOS.
ESE 555 Electrochemical Engineering of Materials After introducing electrochemical concepts (redox reactions, electrolytic versus galvanic cells, standard oxidation potentials), this course will cover the broad impact of electrochemical phenomena on materials. Topics that will be discussed include: (1) Materials extraction from their ores to finished products by electrowinning, (2) Chemical refining (Mond process) and electrorefining of materials, (3) Materials degradation by destructive electrochemical corrosion, (4) Three-dimensional nanostructured materials by selective electrochemical corrosion, (5) Enhancing the electrochemical performance of materials via nanostructuring – e.g. lithium-ion battery electrodes; (6) Enhancing the electrochemical performance of materials via surface chemistry – e.g. oxygen evolution electrocatalysts; (7) Light-enhanced electrochemical performance of materials – e.g. solar water splitting photoelectrocatalysts. Students will be engaged in interactive classroom activities.
ESE 545 Materials for Energy and Environmental Sustainability This course will cover the fundamental materials science issues central to the design of sustainable energy technology. The goal of this course is to expose students to the emerging advances in materials science and materials chemistry that underpin technologies for energy conversion (fuel cells, thermoelectrics, photovoltaics, wind energy etc..), storage (biofuels, artificial photosynthesis, batteries etc) and distribution (smart grids and hydrogen and methane economy concepts etc..) and to place these in a real world context. This class will emphasize concepts in “green materials and green engineering practices” that are emerging with a global focus on “Sustainable Technology.” “Sustainability is defined as meeting the needs of the present without compromising the ability of future generations to meet their needs.”
EAS 501 Energy and its Impacts: Technology, Environment, Economics, Sustainability The objective is to introduce students to one of the most dominating and compelling areas of human existence and endeavor: energy, with its foundations in technology, from a quantitative sustainability viewpoint with its association to economics and impacts on environment and society. This introduction is intended both for general education and awareness and for preparation for careers related to this field, with emphasis on explaining the technological foundation. The course spans from basic principles to applications. A review of energy consumption, use, and resources; environmental impacts, sustainability and design of sustainable energy systems; introductory aspects of energy economics and carbon trading; methods of energy analysis; forecasting; energy storage; electricity generation and distribution systems (steam and gas turbine based power plans, fuel cells), fossil fuel energy (gas, oil, coal) including nonconventional types (shale gas and oil, oil sands, coalbed and tight-sand gas), nuclear energy wastes: brief introduction to renewable energy use: brief introduction to solar, wind, hydroelectric, geothermal, biomass; energy for buildings, energy for transportation (cars, aircraft, and ships); prospects for future energy systems: fusion power, power generation in space. Students interested in specializing in one or two energy topics can do so by choosing them as their course project assignments.
EAS 502 Renewable Energy and Its Impacts: Technology, Environment, Economics, Sustainability The objective is to introduce students to the major aspects of renewable energy, with its foundations in technology, association to economics, and impacts on ecology and society. This introduction is intended both for general education and awareness and for preparation for careers related to this field. The course spans from basic principles to applications. A review of solar, wind, biomass, hydroelectric, geothermal energy, and prospects for future energy systems such as renewable power generation in space. Spring

EAS 503

Energy Systems and Policy This is a survey course that will examine the current U.S. energy industry, from production to consumption, and its impacts on local, regional, and the global environment. The course will seek to provide a fuller understanding of existing energy systems, ranging from technical overviews of each, a review of industry organization, and an exploration of the well-established policy framework each operates within. Near-term demands upon each energy supply system will be discussed, with particular focus on environmental constraints.
MEAM 690 Advanced Topics in Thermal Fluid Science or Energy This course will be offered when demand permits. The topics will change due to the interest and specialties of the instructor(s). Some topics could include: Computational Fluid Mechanics, Visualization of Computational Results, Free Surface Flows, Fluid Mechanics of the Respiratory System, and transport in Reacting Systems.

Course not offered every year

MEAM 503 Direct Energy Conversion: from Macro to Nano The course focuses on devices that convert thermal, solar, or chemical energy directly to electricity, i.e., without intermediate mechanical machinery such as a turbine or a reciprocating piston engine. A variety of converters with sizes ranging from macro to nano scale will be discussed, with the advantages offered by nanoscale components specifically highlighted. Topics will include thermoelectric energy converters and radioisotope thermoelectric generators (RTGs), thermionic energy converters (TEC), photovoltaic (PV) and thermophotovoltaic (TPV) cells, as well as piezoelectric harvesters. Additional topics may include magnetohydrodynamic (MHD) generators, alkali metal thermal-to-electric converters (AMTEC), and fuel cells

MEAM 502

Energy Engineering in Power Plants and Transportation Systems

Most energy consumed in the U.S. and in the world is produced using thermal-to-mechanical energy conversion. In this course, students will learn the engineering principles that govern how heat is converted to mechanical power in electric power plants, jet aircraft, and internal combustion engines. Topics covered include a review of thermodynamics and basic power cycles, supercritical, combined, and hybrid cycles, cogeneration, jet propulsion, and reciprocating internal combustion engines. A brief introduction to desalination and combustion is also included. The material in this course will provide students a foundation important for industrial and research employment in energy engineering.

Process Control and Design

Course Code Title Description Course Term
MEAM 613 Nonlinear Control Theory The course studies issues in nonlinear control theory, with a particular emphasis on the use of geometric principles. Topics include: controllability, accessibility, and observability, for nonlinear systems; Forbenius’ theorem; feedback and input/outpub linearization for SISO and MIMO systems; dynamic extension; zero dynamics; output tracking and regulation; model matching disturbance decoupling; examples will be taken from mechanical systems, robotic systems, including those involving nonholonomic constraints, and active control of vibrations. Course not offered every year
ESE 505 Feedback Control Design and Analysis Basic methods for analysis and design of feedback control in systems. Applications to practical systems. Methods presented include time response analysis, frequency response analysis, root locus, Nyquist and Bode plots, and the state-space approach.
ESE 518 Battery and Super-Capacitor Systems This is a senior / graduate course on scientific and technological fundamentals as they apply to electrochemical batteries and super-capacitors. The perspective utilized will be a combination of materials and systems science. The course will introduce the student to the different categories of electrochemical cells and batteries, and their related chemistry, kinds of super-capacitors, charging and discharging profiles, equivalent series resistance (ESR), power capacities, and lifetimes. For super-capacitors, the student will be introduced to double layer capacitance (DLC) and pseudo-capacitance types of energy storage, super-capacitor fundamentals through Faradaic and non-Faradaic processes, pseudo-capacitance of metal oxides and electro-active polymers (EAPs), non-ideal polarizable electrodes, energetics and kinetics of electrode processes, theories of dielectric polarization, inorganic and organic electrol carbonaceous materials, effective surface area (ESA) and functionalizations, as well as the AC impedance behavior of batteries and super-capacitors including the self-discharge characteristics of both. The fundamental electrochemical relations will be discussed, as well as battery / super-caps system modeling, and batteries management systems.
ESE 543 Human Systems Engineering This course is an introduction to human systems engineering, examining the various human factors that influence the spectrum of human performance and human systems integration. We will examine both theoretical and practical applications, emphasizing fundamental human cognitive and performance issues. Specific topics include: human performance characteristics related to perception, attention, comprehension, memory, decision making, and the role of automation in human systems integration.

Soft Matter

Course Code Title Description Course Term
CBE 570 Experimental Methods for Polymer Science and Soft Matter – Theory and Practice This course covers the relevant theory and practical application of experimental methods used to study the structure, dynamics and physico-chemical properties of soft matter and macromolecular materials. Systems of interest include self-assembled polymers and (macro)molecular materials, liquid crystals, colloidal suspensions, biological materials, gels, and other complex fluids. Particular emphasis is placed on the development of kinematic theory for X-ray scattering, methods of structure determination by (x-ray/electron) diffraction, microscopy (optical; atomic force; electron), dynamic scattering (light/optical; xray; neutron) and rheology (bulk and microrheology). Thermo-mechanical, electronic and optical property characterization are also addressed. Lectures are complemented by lab exercises and projects. The subject matter is particularly relevant for students conducting experimental research on macromolecular materials, soft matter and complex fluids. Spring

CBE 510/ MSE 580

Introduction to Polymers Polymer is one of the most widely used materials in our daily life, from the rubber tires to clothes, from photoresists in chip manufacturing to flexible electronics and smart sensors, from Scotch tapes to artificial tissues. This course teaches entry-level knowledge in polymer synthesis, characterization, thermodynamics, and structure-property relationship. Emphasis will be on understanding both chemical and physical aspects of polymers, polymer chain size and molecular interactions that drive the microscopic and macroscopic structures and the resulting physical properties. We will discuss how to apply polymer designs to advance nanotechnology, electronics, energy and biotechnology. Case studies include thermodynamics of block copolymer thin films and their applications in nanolithography, shape memory polymers, hydrogels, and elastomeric deformation and applications. Fall
CBE 511 Physical Chemistry of Polymers and Amphiphiles This course deals with static and dynamic properties of two important classes of soft materials: polymers and amphiphiles. Examples of these materials include DNA, proteins, diblock copolymers, surfactants and phospholipids. The fundamental theories of these materials are critical of understanding ploymer processing, nanotechnology, biomembranes and biophysics. Special emphasis will be placedon understanding the chain conformation of polymer chains, thermodynamics of polymer chains, thermodynamics of polymer solutions and melts, dynamics of polymer and statistical thermodynamic principles of self-assembly. Fall
CBE 535

Interfacial Phenomena

This course provides an overview of fundamental concepts in colloid and interface science. Topics include the thermodynamics of interfaces, interfacial interactions (e.g. van der Waal’s interactions, electrostatics, steric interactions), adsorption, the hydrodynamics and stability of interfacial systems, self assembly, etc. Connections to self-assembly and directed assembly of nanomaterials and emerging topics are explored. Pre-requisites: undergraduate thermodynamics, some familiarity with concepts of transport phenomena (including fluid flow and mass transfer) and differential equations Spring
CBE 522 Polymer Rheology and Processing This course focuses on applications of rheology to polymer process technologies. It includes a general review of rheological concepts, including viscoelasticity and the influence of shear rate, temperature and pressure on polymer flow properties. The course covers the elementary processing steps common in various types of polymer manufacturing operations including handling of particulate solids, melting, pressurizing and pumping, mixing and devolatilization. Specific polymer processing operations including extrusion, injection molding, compression molding, fiber spinning and wire coating are covered. Emerging polymer processing applications in microelectronics, biomedical devices and recycling are also discussed. Fall
CBE 557 Stem Cells, Proteomics, Drug Delivery: Soft Matter Fundamentals Lectures on modern topics and methods in cell and molecular biology and biomedicine from the perspective of soft matter science and engineering. Discussions and homeworks will cover soft matter related tools and concepts used to 1) isolate, grow, and physically characterize stem cells, 2) quantify biomolecular profiles, 3) deliver drugs to these cells and other sites (such as tumors with cancer stem cells) will be discussed. Skills in analytical and professional presentations, papers and laboratory work will be developed. Spring
CBE 525 Molecular Modeling and Simulation Students will explore current topics in thermodynamics through molecular simulations and molecular modeling. The requisite statistical mechanics will be conveyed as well as the essential simulation techniques (molecular dynamics, Monte Carlo, etc.). Various approaches for calculating experimentally measurable properties will be presented and used in student projects. Spring
CBE 602 Statistical Mechanics of Liquids The course will focus on advanced concepts and methods in statistical mechanics with a particular emphasis on the liquid state, e.g. aqueous solutions, capillarity, polymers, colloids, glasses, amphiphilic self-assembly, etc. Principles of both equilibrium and non-equilibrium statistical mechanics will be discussed and connections to experimentally measurable quantities will be made wherever possible.
CHEM 723 Polymer Dynamics This course discussed the structure of polymers from a statistical physics point of view as well as dynamical response of polymeric systems such as mechanical response of polymer melts, polymer glass transition, properties of polymers in solutions, and properties of block co-polymers and ionomers. Spring
MSE 500 Experimental Methods in Materials Science This laboratory course introduces students to a variety of experimental methods used in materials science and engineering. Hands-on training will be provided for atomic force microscopy, X-ray diffraction and scattering, mechanical testing with image capture, and dynamic light scattering. Students will use numerous software packages for data collection and analysis, as well as being introduced to LabVIEW as a method for customizing experiments. In addition, students will see demonstrations of scanning electron microscopy, transmission electron microscopy, and electron diffraction and analyze data from these methods. The format for the course will include a weekly lecture (1.5 hours), a weekly lab session (4 hours) and six assignments. Fall
MSE/ MEAM 650 Mechanics of Soft and Biomaterials This course is aimed to expose the students to a variety of topics in mechanic materials via discussion of “classic” problems that have had the widest impact long period of time and have been applied to analyze the mechanical behavior a variety of biological and engineering materials.