Pritzker School of Molecular Engineering

MENG 30000. Introduction to Emerging Technologies. 100 Units.

This course will examine five emerging technologies (stem cells in regenerative medicine, quantum computing, water purification, new batteries, etc.) over two weeks each. The first of the two weeks will present the basic science underlying the emerging technology; the second of the two weeks will discuss the hurdles that must be addressed successfully to convert a good scientific concept into a commercial product that addresses needs in the market place.

Instructor(s): Terry Johnson     Terms Offered: Autumn
Prerequisite(s): Completion of the general education requirements in mathematics and physical or biological sciences
Note(s): May not be counted toward PME doctoral requirements
Equivalent Course(s): MENG 20000

MENG 30400. Commercializing Products with Molecular Engineering. 100 Units.

Many technologies and products that have been successfully commercialized benefit from engineering at the molecular scale. This course will present case studies of such technologies and products, including those drawn from the fields of pharmaceuticals (e.g., biologics, nanoparticle-based drugs, and excipients for enhanced drug solubility), food products (e.g., Cavamax by Wacker Chemie that applies beta-cyclodextrin for molecular encapsulation to improve flavor solubility), and industrial products (e.g., Febreze Air freshener, sunscreens with UV protection, photographic films, and slurries for polishing surfaces). Each case study will examine: the unmet market need addressed by the product, the science behind the molecular engineering of the technology, the background/history of the technology, and key attributes/decisions made by inventors along the pathway to commercialization. Upon completion of the course, students will be able to understand the overall process for developing a new technology/product, outline the steps to design the key critical-to-quality (CTQ) attributes, describe how to monetize a technology/product, and recognize the avenues available to protect the technology/product or create barriers to entry to the market.

Equivalent Course(s): MENG 20400

MENG 30500. Responsible and Effective Technology Management. 100 Units.

A variety of cases exploring engineering decision making, considering both practical and ethical concerns, in the context of existing and emerging technologies will be discussed. Students will learn how to deal with complex and ambiguous situations, systems, and personalities; and to navigate them responsibly and constructively.

Instructor(s): STAFF     Terms Offered: Winter

MENG 31100. Math Methods in Molecular Engineering. 100 Units.

This course will provide an overview of the general mathematical framework required for the further study of the basic theories (e.g., thermodynamics, statistical mechanics, transport) of molecular engineering. The content of this course mainly includes differential equations, statistics, complex analysis and integral transforms, which will be illustrated in the context of common problems in diffusion, heat conduction, particle transfer, and chemical reactions. This course will lay the mathematical foundations for further study in other thematic core courses for the Materials Systems area, as well as in future research activities.

Instructor(s): Sihong Wang     Terms Offered: Autumn
Prerequisite(s): Required Math Courses in the Core, Algebra, Calculus, Physics

MENG 31200. Thermodynamics and Statistical Mechanics. 100 Units.

This course will present an overview of thermodynamics and statistical mechanics in the context of molecular engineering applications. Such applications will include prediction of the thermophysical properties of multicomponent gases, solids and liquids, prediction of adsorption processes on surfaces or interfaces, and molecular-level descriptions of synthetic and biological macromolecules in solution. Throughout the course, emphasis will be placed on connecting molecular structure and interactions to measurable macroscopic properties.

Instructor(s): Juan de Pablo, Allison Squires     Terms Offered: Autumn
Prerequisite(s): MENG 21400 or CHEM 26100-26200 or PHYS 27900 or equivalent, or the consent of the instructor

MENG 31300. Transport Phenomena. 100 Units.

This course covers essential aspects of molecular transport processes, including fluid dynamics, mass transport and diffusion processes, and energy and heat transport processes. It also discusses the coupling that arises between momentum, mass and energy transport processes.

Instructor(s): Jay Schieber      Terms Offered: Winter

MENG 31400. Advanced Quantum Engineering. 100 Units.

Quantum mechanics underlies many areas of modern engineering, including materials science, photonics, electronics, metrology, and information processing. This course explores both the fundamental physics of quantum systems as well as the tools utilized to engineer and control them. Topics to be discussed may include eigenvalues and eigenstates, harmonic oscillators, operators, symmetries, spin, angular momentum, perturbation theory, and time evolution. We will also explore examples of engineered quantum systems. The course will assume that students have prior exposure to quantum mechanics at the intermediate undergraduate level.

Instructor(s): Tian Zhong      Terms Offered: Autumn
Prerequisite(s): Equivalent to CHEM 26100 or PHYS 23400-23500

MENG 31800-31900. Graduate Engineering Design.

This 200-unit project-based design sequence connects graduate student teams to academic, industrial, and/or clinical mentors with a problem to solve. Available projects, and project areas, will change from year to year. This experiential learning course emphasizes the design process and the application of scientific knowledge to wisely search for and select solutions. It also serves as an opportunity to practice professional conduct and consider responsible engineering in the context of design.

MENG 32200. Cellular Engineering. 100 Units.

Cellular engineering is a field that studies cell and molecule structure-function relationships. It is the development and application of engineering approaches and technologies to biological molecules and cells. This course provides a bridge between engineers and biologists that quantitatively study cells and molecules and develop future clinical applications. Topics include fundamental cell and molecular biology; immunology and biochemistry; receptors, ligands, and their interactions; nanotechnology/biomechanics; enzyme kinetics; molecular probes; cellular and molecular imaging; single-cell genomics and proteomics; genetic and protein engineering; and drug delivery and gene delivery.

Instructor(s): Jun Huang      Terms Offered: Winter
Prerequisite(s): Completion of the first two quarters of a Biological Sciences Fundamentals Sequence
Equivalent Course(s): MOMN 34310, BIOS 21508, MENG 22200

MENG 32300. Quantitative Systems Biology. 100 Units.

This course aims to provide students with knowledge on the use of modern methods for the analysis, manipulation, and modeling of complex biological systems, and to introduce them to some of the most important applications in quantitative and systems biology. We will first survey theoretical concepts and tools for analysis and modeling of biological systems like biomolecules, gene networks, single cells, and multicellular systems. Concepts from information theory, biochemical networks, control theory, and linear systems will be introduced. Mathematical modeling of biological interactions will be discussed. We will then survey quantitative experimental methods currently used in systems biology. These methods include single cell genomic, transcriptomic, and proteomic analysis techniques, in vivo and in vitro quantitative analysis of cellular and molecular interactions, single molecule methods, live cell imaging, high throughput microfluidic analysis, and gene editing. Finally, we will focus on case studies where the quantitative systems approach made a significant difference in the understanding of fundamental phenomena like signaling, immunity, development, and diseases like infection, autoimmunity, and cancer.

Instructor(s): Savas Tay     Terms Offered: Autumn
Prerequisite(s): Completion of the first two quarters of a Biological Sciences Fundamentals Sequence
Equivalent Course(s): MENG 22300, BIOS 28411

MENG 32400. Bioengineering Kinetics. 100 Units.

This course focuses on the kinetics of biochemical reactions at the molecular level and addresses basic questions at the interface between molecular engineering and cell biology. This course will equip students with the knowledge and tools to quantitatively solve problems in biochemical systems and molecular reactions that are dynamic or at equilibrium.

Equivalent Course(s): BIOS 21359, MENG 22400

MENG 33000. Experimental Bioengineering Laboratory. 100 Units.

This course provides a broad knowledge and hands-on experience in bioengineering and biomaterials. The topics to be covered include the design and characterization of materials for biomaterials, cellular engineering, nanomedicine, synthetic vaccines, immunotherapies, drug delivery, tissue engineering, bioimaging, biodiagnostics and biosensors. This course also includes experimental modules for hands-on experience relevant to the topics discussed in the lectures. Students will develop skills and experience relevant to methodologies in bioengineering research. Chromatography, spectroscopy, mechanical testing, particle size analysis, and protein activity assays will be utilized in the laboratory. Students will learn to apply knowledge of bioengineering research tools to design and conduct bioengineering experiments for which they will analyze, interpret, and present the experimental results.

Instructor(s): Mustafa Guler     Terms Offered: Spring
Prerequisite(s): MENG 23100 or MENG 23150
Equivalent Course(s): MENG 23000

MENG 33100. Biological Materials. 100 Units.

In this course, students will gain an understanding of the science and application of biomaterials, a field that utilizes fundamental principles of materials science with cell biology for applications in therapeutics and diagnostics. The course will introduce the basic classes of biomaterials, considering metals used in medicine, ceramics and biological inorganic materials such as hydroxyapatite, and polymers used in medicine. The basis of protein adsorption modulating biological interactions with these materials will be elaborated. Examples to be covered in the course will include polymers used in drug delivery, polymers used in protein therapeutics, polymers used in degradable biomaterial implants, polymers used in biodiagnostics, and hybrid and polymeric nanomaterials used as bioactives and bioactive carriers. An emphasis in the course will be placed on bioactive materials development. Students will be assessed through in-class discussions, take-home assignments and exams, and an end-of-term project on a topic of the student's choice.

Instructor(s): Jeffrey Hubbell, Mustafa Guler     Terms Offered: Autumn
Prerequisite(s): BIOS 20186 and BIOS 20187, or BIOS 20234 and BIOS 20235
Note(s): This course does not meet the requirements for the Biological Sciences major.
Equivalent Course(s): MENG 23100

MENG 33110. Stem Cell Biology, Regeneration, and Disease Modeling. 100 Units.

In this course, students will gain an understanding of the science and application of tissue engineering, a field that seeks to develop technologies for restoring lost function in diseased or damaged tissues and organs. The course will first introduce the underlying cellular and molecular components and processes relevant to tissue engineering: extracellular matrices, cell/matrix interactions such as adhesion and migration, growth factor biology, stem cell biology, inflammation, and innate immunity. The course will then discuss current approaches for engineering a variety of tissues, including bone and musculoskeletal tissues, vascular tissues, skin, nerve, and pancreas. Students will be assessed through in-class discussions, take-home assignments and exams, and an end-of-term project on a topic of the student's choice.

Instructor(s): Huanhuan Chen     Terms Offered: Winter
Prerequisite(s): BIOS 20186 or BIOS 20234
Note(s): CB
Equivalent Course(s): MENG 23110, BIOS 21507, MPMM 34300

MENG 33120. The Structural Basis of Biomolecular Engineering. 100 Units.

In this highly practical course, students will learn different approaches to interrogate the structure-function relationship of proteins. Essential skills in identifying related protein sequences, performing multiple sequence alignments, and visualizing and interpreting conservation in the context of available structures will be acquired. The most basic method of biomolecular engineering is based on rationale design which uses such knowledge of sequence and structure to predict or explore changes in function in a low throughput manner. Advanced methods that employ evolutionary platforms, such as phage-, ribosome-, and yeast display, will also be introduced for screening large libraries of biomolecules to find variants with a specific function of interest. Additional biomolecular engineering topics to be covered may include computational tools to model and design proteins, protein fusions, enzymatic or chemical modifications to change function, and pharmacokinetics. Students will be assessed through in-class discussion, take-home assignments, exams, and an end-of-term project chosen by the student with approval from the instructor(s).

Instructor(s): Juan Mendoza     Terms Offered: Spring
Prerequisite(s): BIOS 20200
Equivalent Course(s): MENG 23120

MENG 33130. Proteomics and Genomics in Biomolecular Engineering. 100 Units.

Modern genomic and proteomic technologies are transforming the analysis and engineering of biological systems. One part of the course will introduce the molecular biology of genomics, including how and why next-generation sequencing is used to measure DNA, RNA, and epigenetic patterns. In addition to experimental tools, it will cover key computational concepts for transforming raw genomic data into biologically meaningful data, as well as the application of those results to analyze biological systems. Specific topics will vary but will include single-cell RNA-sequencing and its analysis in different settings. The other part of the course will focus on technologies that enable the identification of proteins and their dysregulation in disease. Examples include mass spectrometry techniques to determine the exact number of proteins in cells, as well as techniques that identify the types and locations of post-translational protein modifications, such as histone methylation, that are frequently associated with diseases such as cancer. Additionally, the course will review methods to discover protein-protein interactions using computational and experimental screening methods. Student assessments will be made through in-class discussion, take-home assignments, exams, and an end-of-term project chosen by the student with approval from the instructor(s).

Instructor(s): Juan Mendoza, Samantha Riesenfeld     Terms Offered: Autumn
Prerequisite(s): BIOS 20200 or equivalent, and experience with data analysis and computation in R or Python (e.g., MENG 26030, BIOS 20151/20152, STAT/CMSC 11800, or STAT 22000).
Equivalent Course(s): MENG 23130

MENG 33140. Biodiagnostics and Biosensors. 100 Units.

This course focuses on the biological and chemical interactions that are important for the diagnosis of diseases and the design of new assays. The principles and mechanisms of molecular diagnostics and biosensors, as well as their applications in disease diagnosis, will be discussed. Bioanalytical methods including electrochemical, optical, chemical separation, and spectroscopic will be described. Surface functionalization and biomolecular interactions will be presented for the development of protein and DNA based biosensor applications. The goals for the course are to introduce the fundamental mechanisms of bioanalytical methods/tools, examples of specific methods for diagnostic purposes, and analytical methods necessary for developing new precision medicine tools.

Instructor(s): Mustafa Guler      Terms Offered: Spring
Prerequisite(s): Completion of the first two quarters of a Biological Sciences Fundamentals Sequence
Equivalent Course(s): MENG 23140, BIOS 28700

MENG 33150. Nanomedicine. 100 Units.

This course focuses on the applications of nanotechnology in medicine. The chemical, physical and biological features of the nanomaterials will be discussed for applications in medicine. A survey of concepts in therapeutic drug delivery methods, diagnostic imaging agents and cell-materials interactions will be discussed.

Instructor(s): Mustafa Guler     Terms Offered: Winter
Prerequisite(s): Completion of the first two quarters of a Biological Sciences Fundamentals Sequence.
Equivalent Course(s): MENG 23150, BIOS 28410

MENG 33200. Principles of Immunology. 100 Units.

In this course students will gain a comprehensive understanding of the essential principles of immunology. The course will introduce the concept of innate immunity and pattern recognition and how antigen is processed for presentation to the immune system. We will examine how antigen presentation links innate and adaptive immunity. We will then discuss the two arms of adaptive immunity (humoral and cellular) in detail from their development to effector stages. In the last section of the course we will discuss some key aspects of immune system function including immunological memory and vaccination, immunological tolerance and its failure (autoimmunity/allergy), and mucosal immunology and the microbiome. Students will present primary articles related to the topics discussed in class in a weekly discussion section. The course will be graded on class participation, quizzes, a midterm, and a final essay-based exam.

Instructor(s): Cathryn Nagler     Terms Offered: Autumn
Prerequisite(s): BIOS 20186 or BIOS 20234 (or equivalent undergraduate coursework with the permission of the instructor)
Equivalent Course(s): MENG 23200

MENG 33210. Fundamentals and Applications of the Human Microbiota. 100 Units.

Thousands of microbes colonize the human body to collectively establish the human microbiota. Research findings over the past two decades have led to a growing appreciation of the importance of the microbiota in various facets of human health. This course will explore the human microbiota through a critical review of the primary scientific literature. The first portion of the course will cover distinct ways by which the human microbiota impacts mammalian health. The second part of the course will focus on established and developing microbiota-targeting biotechnologies. Students will leave the course with a general understanding of the current state of human microbiota research and its therapeutic and diagnostic applications.

Instructor(s): S. Light, M. Mimee     Terms Offered: Winter
Prerequisite(s): Three quarters of a Biological Sciences Fundamentals Sequence. Third or fourth year standing or consent of instructor.
Note(s): GP.
Equivalent Course(s): MENG 23210, MICR 38000, BIOS 25207

MENG 33300. Quantitative Immunobiology. 100 Units.

The science of immunology was born at the end of the 19th century as a discipline focused on the body's defenses against infection. The following 120+ years has led to the discovery of a myriad of cellular and molecular players in immunity, placing the immune system alongside the most complex systems such as Earth's global climate and the human brain. The functions and malfunctions of the immune system have been implicated in virtually all human diseases. It is thought that cracking the complexity of the immune system will help manipulate and engineer it against some of the most vexing diseases of our times such as AIDS and cancer. To tackle this complexity, immunology in the 21st century - similar to much of the biological sciences - is growing closer to mathematics and data sciences, physics, chemistry and engineering. A central challenge is to use the wealth of large datasets generated by modern day measurement tools in biology to create knowledge, and ultimately predictive models of how the immune system works and can be manipulated. The goal of this course is to introduce motivated students to the quantitative approaches and reasoning applied to fundamental questions in immunology.

Instructor(s): Nicolas Chevrier      Terms Offered: Winter
Prerequisite(s): Completion of the first two quarters of a Biological Sciences Fundamentals Sequence. Knowledge of R is recommended but not required. Courses in immunology and microbiology are an advantage but not required (e.g., BIOS 25256 Immunobiology; BIOS 25206 Fundamentals of Bacterial Physiology).
Note(s): CB
Equivalent Course(s): IMMU 34800, MENG 23300, BIOS 26403

MENG 33310. Immunoengineering Laboratory. 100 Units.

The goal of this laboratory course is to provide students with an original and hands-on research experience in the fields of immunoengineering and synthetic immunology, whereby new molecules will be designed and tested by students in the lab to probe or control immune processes. Specifically, students will study how newly discovered cancer vaccines work. The course will cover wet lab techniques to manipulate and analyze DNA, proteins, and cells, including next-generation sequencing, genome editing, cellular imaging, and nanobodies. In addition, computational tools will be used for processing and analyzing the data generated by students during class. The outcome of students' research during this class will help decipher the inner workings of successful anti-tumor vaccines, which is important to inform future cancer immunotherapies

Instructor(s): Nicolas Chevrier     Terms Offered: Autumn
Prerequisite(s): Completion of the first two quarters of a Biological Sciences Fundamentals Sequence. Prior molecular and cellular biology wet lab work experience is an advantage but not required.
Equivalent Course(s): MENG 23310

MENG 33320. Immunogenomics I. 100 Units.

Our understanding of immune cell function has benefited greatly from advances in next generation sequencing and the genetic characterization of immune cells has become a powerful tool to understand adaptive and innate immunity. This course will train students to tackle immunological questions using quantitative and systems-levels approaches. The topics covered will include: - Introduction of innate and adaptive immunity - Evolution of the different arms of the immune system - Population variation in immune responses - Genomic technologies and applications - Study design in genomic studies - Paper-based discussion of key immunological concepts and how we can study them using systems immunology approaches

Instructor(s): Luis Barreiro Bana Jabri      Terms Offered: Autumn
Note(s): REQUIRED for Students in the CSI Track
Equivalent Course(s): IMMU 48000

MENG 33330. Immunogenomics II: Data Science in Systems Immunology. 100 Units.

This course presents essential concepts in genomic data science and trains students to apply the concepts in immunological contexts. The course encourages students to think independently about genomic analyses. Students will gain an understanding of how to use basic statistics, linear algebra, and computation to explore, analyze, and interpret published RNA-sequencing data (bulk and single-cell) and immune-cell receptor sequencing data. Student performance will be assessed through in-class discussions, take-home assignments and exams, and an end-of-term final project of the student's choice.

Instructor(s): Samantha Riesenfeld, Joshua Weinstein     Terms Offered: Spring
Prerequisite(s): Basic programming skills in R or Python, including control structures, data loading and saving, creating basic plots, and working with data frames. Basic molecular biology, including the central dogma.
Note(s): This course is required for, but not limited to, the Computational and Systems Immunology PhD track in Immunology.
Equivalent Course(s): MENG 23330, IMMU 48900

MENG 33500. Synthetic Biology. 100 Units.

The objective of this course is to provide an overview of the fundamentals of synthetic biology by exploration of published and primary literature. Synthetic biology is an interdisciplinary area that involves the application of engineering principles to biology. It aims at the (re-)design and fabrication of biological components and systems that do not already exist in the natural world. Our goal in the course will be to examine how to apply design principles to biological systems. This will require understanding how biological systems operate, what design principles are successful in biology, and a survey of current approaches in the field to tackle these challenges. Topics will include genetic manipulation, pathway engineering, protein design, cellular engineering, and tools for information input and output in biological systems.

Instructor(s): Aaron Esser-Kahn      Terms Offered: Spring
Prerequisite(s): Completion of the first two quarters of a Biological Sciences Fundamentals Sequence. MENG 21500, BIOS 20236, and BIOS 20200 are recommended but not required.
Equivalent Course(s): MENG 23500

MENG 33510. Microfluidics and Its Applications. 100 Units.

Precision control of fluids at the micrometer scale (hence microfluidics) provides unprecedented capabilities in manipulation and analysis of cells and proteins. Moreover, fluids and particles behave in fundamentally different ways when confined to small dimensions, making microfluidics an interesting topic of basic research. This course aims to provide students with theoretical knowledge and practical skills on the use of microfluidics for the manipulation and analysis of physical, chemical, and biological systems. We will first survey theoretical concepts regarding microfluidics. We will then focus on design considerations and fabrication methods for multi-layer microfluidic chips using PDMS soft-lithography. We will learn how to fabricate, multiplex, and control PDMS membrane valves and integrate them into high-throughput analytical systems. We will survey recent developments in microfluidics and its scientific and industrial applications. Biological systems analysis in cell sorting, culture, cell signaling, single molecule detection, digital nucleic acid and protein quantification, and biosensing are some of the applications we will cover. This course will have a laboratory component where students will design, fabricate, and use microfluidic devices and therefore acquire hands-on skills in microfluidic engineering.

Instructor(s): Savas Tay     Terms Offered: Spring
Prerequisite(s): MATH 13300 (or higher), or MATH 13200 (or higher) plus BIOS 20151 or BIOS 20152 or BIOS 20236
Equivalent Course(s): MENG 23510

MENG 35100. Introduction to Polymer Science. 100 Units.

This course introduces the basics of polymer materials and their behavior and properties. The course will cover a general overview to polymers, basic terminology and definitions, their classification, and their applications. The mechanistic and kinetic behavior of the major classes of polymerization reactions (step-growth, chain addition, and "living" polymerizations) will be introduced with respect to control over polymer structure/architecture, size, and properties. The course will also discuss polymer properties, polymer thermodynamics, and basic structure-property relationships that provide polymers with their unique characteristics compared to small molecules. Techniques for characterizing the chemical and physical properties of polymer solutions will be introduced, including osmometry, viscometry, and gel permeation chromatography.

Instructor(s): Paul Nealey     Terms Offered: Autumn
Prerequisite(s): MENG 21400 or CHEM 26200 or PHYS 27900
Equivalent Course(s): MENG 25100

MENG 35110. Polymer Synthesis. 100 Units.

This course introduces the most important polymerization reactions, focusing on their reaction mechanisms and kinetic aspects. Topics include free radical and ionic chain polymerization, step-growth polymerization, ring-opening, insertion, controlled living polymerization, crosslinking, copolymerization, and chemical modification of preformed polymers.

Instructor(s): Stuart Rowan     Terms Offered: Winter
Prerequisite(s): CHEM 22000 and CHEM 22100
Equivalent Course(s): MENG 25110, CHEM 39100

MENG 35120. Polymer Physics. 100 Units.

This course is an advanced introduction to polymer physics taught at a level suitable for senior undergraduates and graduate students in STEM fields. Topics that will be covered include the statistics and conformations of linear chain molecules; polymer brushes; thermodynamics and dynamics of polymers, polymer blends and polymer solutions; phase equilibria; networks, gels, and rubber elasticity; linear viscoelasticity; and thermal and mechanical properties.

Instructor(s): Paul Nealey     Terms Offered: Spring
Prerequisite(s): MENG 25100
Equivalent Course(s): MENG 25120

MENG 35130. Soft Matter Characterization Laboratory. 100 Units.

The goal of this course is to train students in the fundamental experimental approaches to polymer and soft materials characterization. The course will cover both the theory and practice of techniques focused on three themes: molar mass determination (size exclusion chromatography, laser light scattering, NMR spectroscopy); morphology and structure (x-ray scattering, electron microscopy, atomic force microscopy); and thermo-mechanical properties (calorimetry, thermogravimetry, dynamic mechanical analysis, rheometry, tensile testing). Contextual application of these characterization techniques to modern research problems will be introduced. Through this course, students will develop foundational experimental skills necessary for addressing research challenges in modern polymer and soft materials science and engineering.

Instructor(s): Philip Griffin     Terms Offered: Winter
Prerequisite(s): MENG 25100
Equivalent Course(s): MENG 25130

MENG 35140. Functional Polymers for Electronics, Photonics, and Energy Technology. 100 Units.

In this course, students will learn the fundamental principles of the functional properties of polymers that enable their use in electronics, photonics and energy technology. The topics mainly include electron and ion transport properties, relationships between chemical structures and energy band structures, photo-excitation properties, luminescent properties, thermoelectric property, ferroelectric and ferromagnetic properties, as well as the associated device categories of organic field-effect transistors, organic light-emitting diodes, lasers, electrochromic devices, photovoltaic cells, and photodetectors.

Instructor(s): Sihong Wang     Terms Offered: Spring
Prerequisite(s): MENG 25100 (or MENG 35100), AND CHEM 22000 and CHEM 22100
Equivalent Course(s): MENG 25140

MENG 35200. Solids, Materials, Surfaces. 100 Units.

This course is an introduction to modern materials chemistry. It covers basic chemistry and physics of condensed systems, such as solids, polymers, and nanomaterials. The electronic structure of metals, semiconductors and magnetically ordered phases will be discussed. We will review optical and electronic properties of different classes of materials using examples of hard and soft condensed matter systems and drawing structure-property relationships for conventional solids, polymers, and nanomaterials. Finally, the course will cover the fundamentals of surface science and material synthesis, applying modern understanding of nucleation and growth phenomena.

Instructor(s): D. Talapin     Terms Offered: Autumn
Prerequisite(s): CHEM 26100, CHEM 26200, and CHEM 26300, or equivalent
Equivalent Course(s): CHEM 39000

MENG 35210. Complex Fluids and Non-Newtonian Flows. 100 Units.

Definition of a complex liquid and microrheology. Division of complex fluids into suspensions, solutions, and melts. Suspensions as colloidal and noncolloidal. Extra stress and relation to the stresslet. Suspension rheology including Brownian and non-Brownian fibers. Microhydrodynamics and the Fokker-Planck equation. Linear viscoelasticity and the weak flow limit. Polymer solutions including single mode (dumbbell) and multimode models. Nonlinear viscoelasticity. Intermolecular effects in nondilute solutions and melts and the concept of reptation.

Instructor(s): Eric Shaqfeh     Terms Offered: Autumn
Prerequisite(s): Low Reynolds number hydrodynamics or consent of instructor.

MENG 35220. Molecular Gastronomy and Engineering Food as Soft Matter. 100 Units.

We will focus on understanding and analyzing food as soft matter and molecular gastronomy: the physicochemical basis for designing foods. Imagine bread, butter, wine, cheese, ice cream, chocolates, mayo, frothy beers, milk, yogurt, sushi, meats, cotton candy, burgers, fondue, chips, cookies, cakes, and champagne. We will study the science of cooking and molecular gastronomy, food production, processing, and consumption by highlighting concepts from statistical thermodynamics, macromolecular and soft matter physics, interfacial science, fluid mechanics and rheology (science of deformation & flow). Many food materials are rheologically-complex fluids that can be modeled as multicomponent colloidal dispersions with a continuous liquid phase containing dispersed proteins, polysaccharides, drops, bubbles, particles, and self-assembled structures (like micelles). We will discuss the influence of the dispersed and the continuous phases and of ingredients like salt, sugar, fat, animal proteins, and gluten on stability, microstructure, rheology, and heuristic properties like dispensing behavior, stickiness, thickening, stringiness, softness, creaminess, mouthfeel, texture, foamability, and chewability. Significant emphasis will be on understanding current foods to develop the roadmap for sustainable, cost-effective, healthier, and tasteful alternatives, including meat and dairy alternatives with plant-based ingredients.

Instructor(s): Vivek Sharma     Terms Offered: Spring
Prerequisite(s): MATH 18500 and MENG 21400 and MENG 21500, or equivalents
Equivalent Course(s): MENG 25220

MENG 35300. Molecular Science and Engineering of Water. 100 Units.

This course will cover the properties of the water molecule, hydrogen bonding, clusters, supercritical water, condensed phases, solutions, confined and interfacial water, clathrates, and nucleation. In addition, methods of water purification, water splitting and fuel cells, water in atmospheric and climate science, and water in biology, health and medicine will be discussed.

Instructor(s): Chong Liu     Terms Offered: Autumn
Prerequisite(s): MENG 21400 or CHEM 26200 or PHYS 27900 (or concurrent)
Equivalent Course(s): MENG 25300

MENG 35310. Energy Storage and Conversion Devices. 100 Units.

Addressing the challenges of a sustainable energy future requires a foundational knowledge of current and emerging energy conversion and storage technologies. Energy conversion devices such as solar cells and fuel cells to energy storage systems such as lithium-ion batteries and redox-flow batteries will be covered. Devices related to carbon capture and conversion in addition to 'green fuels' will be introduced as well. Applying basic principles of chemistry, thermodynamics, and transport phenomena, this course will provide a deep understanding of the operational mechanisms, resources, and material properties of each device and the synergies between them.

Instructor(s): Chibueze Amanchukwu     Terms Offered: Winter
Prerequisite(s): MENG 21400 (or CHEM 26200 or PHYS 27900) AND MENG 21500
Equivalent Course(s): MENG 25310

MENG 35320. Electrochemical Principles and Methods. 100 Units.

This course will cover topics related to basic electrochemical principles, methodologies, and systems. In particular, students will be given an overview of fundamental concepts related to electrochemical potential, electric double layer, electrode kinetics, and mass transport processes. In addition, the application of key electrochemical experimental methods will be covered. A few examples include cyclic voltammetry, AC impedance spectroscopy, and the rotating disk electrode. Throughout the course, students will apply basics principles of thermodynamics, kinetics, and transport phenomena. Lastly, a brief overview of traditional electrochemical systems and emerging technologies related to energy storage and conversion (e.g., lithium-ion batteries, flow batteries, and fuel cells) and bioelectronics applications will be discussed.

Instructor(s): Shrayesh Patel      Terms Offered: Spring
Prerequisite(s): MENG 21400 (or CHEM 26200 or PHYS 27900) and MENG 21500
Equivalent Course(s): MENG 25320

MENG 35330. Materials and Characterization Tools to Address Challenges in Energy and Water. 100 Units.

The development of new materials, as well as understanding the materials' structure and dynamics, are at the heart of addressing the challenges in energy and water technologies. This course will introduce students to the design and development of advanced functional materials that enable energy and water related technologies. The importance of all classes of materials spanning metals, alloys, ceramics, polymers, glasses, and their combinations as composite materials will be covered. To understand material properties and function, students will learn about essential characterization tools including microscopy, spectroscopy and mechanical testing techniques. In addition, the course will convey the importance of advanced characterization tools available at X-ray and neutron facilities that are essential in revealing unique physical properties.

Instructor(s): Junhong Chen     Terms Offered: Spring
Prerequisite(s): MENG 21400 (or CHEM 26200 or PHYS 27900)
Equivalent Course(s): MENG 25330

MENG 35500. Classical Molecular and Materials Modeling. 100 Units.

This course will introduce students to the methods of molecular modeling. The topics covered will include an introduction to the origin of molecular forces, a brief introduction to statistical mechanics and ensemble methods, and an introduction to molecular dynamics and Monte Carlo simulations. The course will also cover elements of advanced sampling techniques, including parallel tempering, umbrella sampling, and other common biased sampling approaches. Students will also establish expertise in scientific programming in Python 3.

Instructor(s): Andrew Ferguson      Terms Offered: Winter
Prerequisite(s): MENG 21400 or CHEM 26200 or PHYS 27900, AND MATH 20100 or PHYS 22100. MENG 21300, or prior course work or research experience with elementary programming, is strongly recommended.
Equivalent Course(s): MENG 25500

MENG 35510. Quantum Molecular and Materials Modeling. 100 Units.

Quantum mechanical methods, including quantum chemistry, density functional theory (DFT), and many body perturbation theory, for simulating the properties of molecules and materials will be explored in this course. Numerical algorithms and techniques will be introduced that allow for solution of approximate forms of the Schroedinger and Boltzmann Equations that model structural and transport properties of molecules and materials. The coupling of DFT with molecular dynamics will be detailed for determining finite temperature properties. Coupling of DFT with spin Hamiltonians to study dynamical spin correlations in materials will also be described. Examples of the application of quantum mechanical methods to materials for energy conversion and quantum information technologies will be provided.

Instructor(s): Laura Gagliardi,Giulia Galli     Terms Offered: Spring
Prerequisite(s): MENG 21300 or CHEM 26100 or PHYS 23400 or instructor consent
Equivalent Course(s): MENG 25510, CHEM 26800, CHEM 36800

MENG 35610. Applied Scientific Computing in Molecular Engineering. 100 Units.

This course provides hands-on practical training in scientific computing with a focus on applications to molecular engineering. The first third of the course will provide training in core programming concepts, including a broad introduction to Python programming and use of key scientific libraries. The second third of the course will cover advanced programming topics in CPU and GPU parallel programming and quantum computing, exploring their use through practical examples drawn from a range of scientific and engineering disciplines. The final portion of the class will engage particular applications in computational molecular engineering, including electronic structure calculations of molecules and materials, highlighting the use of modern computing platforms to enable modeling of complex phenomena at unprecedented scales. Students will develop proficiency in making effective use of the diverse landscape of programming models, open-source tools, and computing architectures for high performance computing. Hands-on immersive praxis, mostly using electronic notebooks, will introduce students to the efficient use of several computational resources such as pre-exascale and quantum computers, with the goal of providing them with the confidence and expertise to independently use these tools.

Instructor(s): Marco Govoni     Terms Offered: Spring
Prerequisite(s): Prior programming experience and familiarity with Linux/bash are useful but not required. Prior coursework in quantum mechanics is useful but not required.
Equivalent Course(s): MENG 25610

MENG 35620. Applied Artificial Intelligence for Materials Science and Engineering. 100 Units.

Machine learning and other artificial intelligence tools are quickly becoming commonplace in the computational design of materials. This course is intended to introduce the concepts and practical skills needed to employ machine learning techniques across many areas of computational materials science. The course will cover topics including the management of materials data, the creation of surrogate models for costly computations, building predictive models for material properties without known physical models, and using AI to enhance characterization tools. The content of the course will focus both on the theoretical underpinnings of these technologies, as well as the practical skills needed for successful use of AI in an applied setting. Particular application areas include machine learning tools for atomistic simulations, convolutional neural networks for materials image analysis, Bayesian techniques for material property estimation, and generative methods for molecular design.

Instructor(s): Logan Ward     Terms Offered: Winter
Prerequisite(s): Familiarity in object-oriented programming in Python is preferred. Prior coursework or experience in machine learning is recommended but not required.
Equivalent Course(s): MENG 25620

MENG 35630. Design, Processing, and Scale-Up of Advanced Materials. 100 Units.

The course will cover the scientific background needed to design and optimize advanced materials for scalable synthesis. We will introduce the physics-based understanding needed to simulate the non-equilibrium conditions in reacting gas-phase and complex fluids. The course will use in situ measurement data for validation and acceleration of simulations will allow students to experiment and build the conceptual connections to the background theories and simulations. In particular, we will cover examples of scalable material synthesis such as gas-phase combustion synthesis of lithium ion battery materials, atomic layer deposition (ALD) for porous membranes and coatings, Taylor Vortex Reactors (TVR) for the synthesis of industrial catalysts, additive manufacturing of metals using laser sintering, and microfluidic continuous flow reactors for the synthesis of organic crystals for pharmaceutical applications. Data generated using sensors, imaging cameras, spectroscopic probes, and Argonne APS measurements will be combined with machine-learning approaches for decision making, process optimization and steering of synthesis conditions. This course will include optional hands-on sessions at the Argonne National Laboratory's Materials Engineering and Research Facility, and allow the students to leverage the Manufacturing Data and Machine Learning (MDML) platform and Argonne Leadership Computing Facility (ALCF) supercomputing environment for physics based simulations.

Instructor(s): Santanu Chaudhuri     Terms Offered: Spring
Prerequisite(s): MENG 21400 or CHEM 26200 or PHYS 27900, MENG 24200, and MENG 24400 or CHEM 26300. Some background in a programming language like C, C++ or python, databases, and ability to launch computing jobs in Linux environment is preferred
Equivalent Course(s): MENG 25630

MENG 36400. Quantum Computation. 100 Units.

This course provides an introduction to the fundamentals of quantum information to students who have not had training in quantum computing or quantum information theory. Some knowledge of linear algebra is expected, including matrix multiplication, matrix inversion, and eigenvector-eigenvalue problems. Students will learn how to carry out calculations and gain a fundamental grasp of topics that will include some or all of: entanglement, teleportation, quantum algorithms, cryptography, and error correction.

Instructor(s): Andrew Cleland     Terms Offered: Winter
Prerequisite(s): MATH 19620 or PHYS 22100 or equivalent
Equivalent Course(s): MENG 26400

MENG 36500. Foundations of Quantum Optics. 100 Units.

Quantum optics seeks to illuminate the fundamental quantum mechanics of the interaction of light and matter. These principles can form the basis for quantum technologies in areas such as cryptography, computation, and metrology. This course provides a foundation in the fundamental principles and applications of quantum optics. Topics to be discussed may include Fermi's Golden Rule, interaction of two-level atoms and light, spontaneous emission, Rabi oscillations, classical and non-classical photon statistics, beam splitters, atom cavity interaction, vacuum-Rabi splitting, coherence, entanglement, and teleportation. The course will assume that students are comfortable with single-particle quantum mechanics at the level of a typical introductory graduate-level course.

Instructor(s): Alex High      Terms Offered: Autumn
Prerequisite(s): PHYS 23400-23500 strongly recommended but not required
Equivalent Course(s): MENG 26500

MENG 36600. Electronic and Quantum Materials for Technology. 100 Units.

This is a one-quarter introductory course on the science and engineering of electronic and quantum materials. The intended audience is upper-level undergraduate students and first-year graduate students in Molecular Engineering and other related fields, including Chemistry and Physics. We will learn the basics of electrical and optical properties of electronic materials, including semiconductors, metals, and insulators starting from a simple band picture, and will discuss how these materials enable modern electronic and optoelectronic devices and circuitry. We will also explore the modern synthesis techniques for these materials and the effects of reduced dimensions and emergent quantum properties. No comprehensive exposure to quantum mechanics, thermodynamics, or advanced mathematical skills will be assumed, even though working knowledge of these topics will be helpful.

Instructor(s): Jiwoong Park     Terms Offered: Spring
Prerequisite(s): CHEM 26200 or PHYS 23500 or instructor consent
Equivalent Course(s): CHEM 39300, MENG 26600

MENG 36620. Physics of Solid State Semiconductor Devices. 100 Units.

This course covers the fundamental concepts needed to understand nanoelectronic solid state semiconductor devices. After an overview of the basic properties of semiconductors and electronic transport in semiconductors, we will explore the device physics behind some of the major semiconductor devices that have changed our lives. These include the p-n junction diode, the metal-oxide-semiconductor transistor (MOSFET), the photovoltaics cell (solar cell), the semiconductor light emitting diode (LED) and injection laser, dynamic random access memory (DRAM), and Flash memory. These devices collectively form the backbone behind all computing, communications, and sensing systems used today.

Instructor(s): Supratik Guha     Terms Offered: Autumn
Prerequisite(s): MENG 21300 (or PHYS 23500 or CHEM 26100) or PHYS 22700 or PHYS 23600
Equivalent Course(s): MENG 26620

MENG 36630. Introduction to Nanofabrication. 100 Units.

This course will cover the fundamentals of nanofabrication from a practical viewpoint and will be useful for students planning to pursue research involving semiconductor processing technology, as well as broader topics such as microelectromechanical systems (MEMS), quantum devices, optoelectronics, and microfluidics. This course will cover the theory and practice of lithographic patterning; physical and chemical vapor deposition; reactive plasma etching; wet chemical processing; characterization techniques; and other special topics related to state-of-the-art processes used in the research and development of nanoscale devices. A solid grounding in introductory chemistry and physics is expected.

Instructor(s): Andrew Cleland     Terms Offered: Spring
Prerequisite(s): PHYS 13300 and CHEM 10200, or equivalent
Equivalent Course(s): MENG 26630

MENG 37100. Implementation of Quantum Information Processors. 100 Units.

This course emphasizes the experimental aspects of quantum information focusing on implementations rather than algorithms. Several candidates for quantum information systems will be discussed including ion traps, neutral atoms, superconducting circuits, semiconducting quantum dots, and linear optics. Students will develop an appreciation for the basic physics of these systems, and their relative merits in a variety of quantum information applications.

Instructor(s): Hannes Bernien     Terms Offered: Winter
Prerequisite(s): MENG 31400 or PHYS 34100 or instructor consent

MENG 37200. Quantum Dissipation and Quantum Measurement. 100 Units.

This course introduces the basic tools and concepts used to describe dissipative quantum systems, where a closed quantum system (described by a Hamiltonian) interacts with a dissipative environment. We will also discuss the basic theory of weak continuous quantum measurements and basic quantum limits to measurement. Applications to quantum optics and quantum information processing will be stressed. Topics to be discussed may include quantum master equations, stochastic wavefunction evolution (i.e. quantum trajectories), quantum noise, quantum Langevin equations, and path integral approaches. The course will assume that students are comfortable with single-particle quantum mechanics at the level of a typical introductory graduate-level course.

Instructor(s): Aashish Clerk      Terms Offered: Spring
Prerequisite(s): MENG 31400 or PHYS 34100 or instructor consent

MENG 37300. Experimental Techniques and Advanced Instrumentation. 100 Units.

This course aims to provide students with a knowledge of state-of-the-art experimental measurement techniques and laboratory instrumentation for applications in broad scientific research environments, as well as industrial and general engineering practice. Topics include atomic-scale structural and imaging methods, electronic transport in low dimensional matter, magnetic and optical characterization of materials. Basic concepts in electronic measurement such as lock-in amplifiers, spectrum and network analysis, noise reduction techniques, cryogenics, thermometry, vacuum technology, as well as statistical analysis and fitting of data will also be discussed.

Instructor(s): David Awschalom     Terms Offered: Spring
Equivalent Course(s): MENG 27300

MENG 37400. Advanced Quantum Information and Computation. 100 Units.

This course covers the foundations of quantum theory, quantum communication, quantum metrology, quantum computation, quantum error correction, and topological quantum computation.

Instructor(s): Liang Jiang     Terms Offered: Winter
Prerequisite(s): MENG 31400 or PHYS 34100 or instructor consent

MENG 37500. Quantum Measurements and Metrology. 100 Units.

This course provides an introduction into the concepts and applications of quantum measurements and quantum metrology. We will derive the formal basis of quantum measurements, quantify the information that can be extracted through a measurement and discuss the impact of entanglement. This course will also give a comprehensive overview of different quantum sensing modalities and their technical applications in timekeeping, sensing, imaging and testing of fundamental physics.

Instructor(s): Peter Maurer     Terms Offered: Autumn
Prerequisite(s): MENG 31400 or PHYS 34100 or instructor consent

MENG 40100. Grand Challenges in Molecular Engineering I. 000 Units.

A survey of the research themes in Molecular Engineering for first-year graduate students.

Instructor(s): Staff     Terms Offered: Autumn
Prerequisite(s): Required for all first-year Molecular Engineering graduate students.

MENG 40200. Grand Challenges in Molecular Engineering II. 000 Units.

A survey of the research themes in Molecular Engineering for first-year graduate students.

Instructor(s): Staff     Terms Offered: Winter
Prerequisite(s): Required for all first-year Molecular Engineering graduate students.

MENG 40300. PME Research Professionalization Seminar. 000 Units.

Professionalization involves the development of skills, identities, norms, and values associated with becoming part of an academic or professional community. With the overall goal of positioning first-year doctoral students to function as professionals in the community of engineering researchers, this seminar aims both to build professional competencies and to foster understanding of the roles/responsibilities of researchers. In addition to introducing doctoral students to core principles and practices beyond research and coursework, the seminar will also foster social cohesion and scientific identity. Topics covered will include research ethics, leadership in the lab, freedom of expression, and equity/diversity/inclusion. As a graduate seminar, active participation and discussion will be expected.

Instructor(s): Staff     Terms Offered: Spring
Prerequisite(s): Required for all first-year Molecular Engineering graduate students.

MENG 49700. Research: Related Departments, Institutes, and Industries. 300.00 Units.

For students requiring course registration for internships or similar professional training opportunities. Students must speak to their PI and receive approval from the Dean of Students before they may be enrolled.

Instructor(s): STAFF     Terms Offered: Autumn Spring Summer Winter

MENG 49900. Research: Molecular Engineering. 100-300 Units.

Molecular engineering research

Instructor(s): Faculty     Terms Offered: Autumn Spring Summer Winter
Note(s): Please select desired number of units when registering

MENG 70000. Advanced Study: Molecular Engineering. 300.00 Units.

Advanced Study: Molecular Engineering

MENG 75000. Advanced Research. 300.00 Units.

TBD

Terms Offered: Autumn