Chemical & Biomolecular Engineering (CBE)

CBE 0099 Undergraduate Research and Independent Study

An opportunity for the student to work closely with a professor in a project to develop skills and technique in research and development. To register for this course, the student writes a one-page proposal that is approved by the professor supervising the research and submitted to the undergraduate curriculum chairman during the first week of the term.

Fall or Spring

1-2 Course Units

CBE 1500 Introduction to Biotechnology

The goal of this course is to teach you the fundamentals of biotechnology and introduce you to concepts in Chemical Engineering along the way. Concepts in Biotechnology that will be covered include, DNA, RNA, the Central Dogma, proteins, recombinant technology, RNA silencing, electrophoresis, chromatography, synthetic biology, pull down assays, PCR, hybridization, array technology, DNA machines, DNA sequencing, and forensics. Concepts in Chemical Engineering that will be covered include the mass balance, scaling laws and the Buckingham-Pi theorem, kinetics of enzyme reactions, thermodynamics of molecular binding, the Langmuir isotherm, separations via chromatography. Reserved for Freshmen only.

Fall

1 Course Unit

CBE 1600 Introduction to Chemical Engineering

Students will learn to read and understand a process flow sheet. There is a focus on drawing a process flow sheet, and formulating and solving the material balances for the chemical processes involving chemical reactions (some with recycle streams, some with purge streams, and some with bypass streams). Additionally, students will understand the limits of the ideal gas law, and have a working knowledge of the cubic equations of state and the concept of a compressibility factor. The class will study the basic concepts of gas-liquid phase equilibrium and apply Raoult's Law to solve phase equilibrium problems. A final objective is to design flow sheets and solve material balances for simple chemical processes using ASPEN (chemical engineering simulation program).

Spring

1 Course Unit

CBE 2300 Material and Energy Balances of Chemical Processes

This course introduces the principles of material and energy balances and their applications to the analysis of single- and multiple-phase processes used in the chemical, pharmaceutical, and environmental industries. The course focuses on the conceptual understanding of properties of pure fluids, equations of state, and heat effects accompanying phase changes and chemical reactions, and problem-solving skills needed to solve a wide range of realistic, process-related problems.

Fall

Prerequisite: CBE 1600

1 Course Unit

CBE 2310 Thermodynamics of Fluids

Students will understand, evaluate, and apply different equations of state relating pressure, temperature, and volume for both ideal and non-ideal systems. The course will focus on calculating and applying residual properties and departure functions for thermodynamic analysis of non-ideal gases. Students will apply and describe simple models of vapor-liquid equilibrium in multi-component systems (e.g. Raoult's Law, modified Raoult's Law, Henry's Law). Additionally, the class will analyze and describe properties of non-ideal mixtures and their component species. We will also model and predict reaction equilibria (including non-ideal fluid systems), as well as solve problems related to complex phase equilibria of multi-component systems (find equilibrium compositions for non-ideal phases).

Spring

Prerequisite: CBE 2300

1 Course Unit

CBE 2970 Study Abroad

Fall or Spring

1 Course Unit

CBE 3000 Special Topics in Chemical and Biomolecular Engineering

This course will be offered when necessitated by demand and permitted by schedule. The topics covered by the course will vary depending on the particular interests and expertise of the instructor(s). Topics are generally subjects of contemporary concern in the discipline.

Not Offered Every Year

1 Course Unit

CBE 3200 Basic Chemical Process Safety

Process safety is an important but often overlooked aspect of a chemical engineer's education. When working in chemical engineering, it's simply not possible to learn by trial and error when the error can have catastrophic or dangerous implications. Students will learn the important technical fundamentals to allow them to contribute to a safer future. Chemical process safety is a scientific discipline as important as chemical production. What the students learn here could literally save their life. At the conclusion of the course, the expectation is that students should be able to identify hazards, safety risks and perform inherently safer design for chemical processes. By the end of the course, students will achieve Level I certification from SAChE (Safety and Chemical Engineering Education), a division of AIChE.

Not Offered Every Year

1 Course Unit

CBE 3250 Renewable Energy

This course covers engineering concepts for renewable energy processes. Fundamental engineering calculations for solar, wind, biofuel, geothermal, and hydroelectric energy production in comparison to oil and gas will be covered. Electric vehicles and energy storage will be discussed. Students will consider the specific needs of public health, safety and welfare in addition to global , cultural, social, environmental and economic factors will be in a particular country for a group project.

Spring

Prerequisite: CHEM 1011 AND PHYS 141

1 Course Unit

CBE 3500 Fluid Mechanics

This course is designed for students to understand the fundamental characteristics of fluids. We will develop, starting from first principles, the basic equations for fluid statics, and use them to assess buoyancy forces and determine the pressure variations in fluids with rigid body rotation. Students will understand in detail the basic types of fluid flow line patterns (eg. streamlines and streamtubes) and the different types of interchangeable energy forms (eg. kinetic, potential, and pressure). It is also important to develop, starting from first principles, the formulations for inviscid and viscous flow problems. These include the discussion of a control system and system boundaries, the detailed construction of conservations equations of mass, energy, and momentum for Newtonian fluids, the derivation of the Navier-Stokes equations, and the determination of appropriate initial and boundary conditions. A final objective of the course is to solve various fluid mechanics problems using control systems, dimensional analysis, and developed equations. Such problems include, but are not limited to, the terminal velocity of a falling sphere, Stokes flow, the relation between the friction factor and the Reynolds number, and flow profiles in numerous geometries.

Fall

Prerequisite: CBE 2310

1 Course Unit

CBE 3510 Heat and Mass Transport

Steady-state heat conduction. The energy equation. Fourier's law. Unsteady-state conduction. Convective heat transfer. Radiation. Design of heat transfer equipment. Diffusion, fluxes, and component conservation equations. Convective mass transfer. Interphase mass transport coefficients.

Spring

Prerequisite: CBE 3500

1 Course Unit

CBE 3530 Molecular Thermodynamics and Chemical Kinetics

Applications of physical chemistry to chemical engineering systems. Equilibrium statistical mechanics of ideal gases, dense fluids and interfacial phases. Chemical reaction rates. Collision and transition state theories. Heterogeneous catalysis. Electronic structure and properties of solids.

Fall

Prerequisite: CBE 2310 AND (CHEM 2210 OR MSE 2210)

1 Course Unit

CBE 3540 Societally Significant Soft Matter Solutions

In this course, students will work on case studies for soft matter solutions to problems of societal significance. Examples will be drawn from the pharmaceuticals industry, emerging concepts in carbon capture, process intensification, clean energy, personal care and other fields that exploit our ability to design soft matter systems. The course will take the form of discussions to set societal context, lectures (including guest lecturers who are technical innovators in the field) to provide fundamental underpinnings, and student-led case studies of current approaches in which students critique current solutions and propose competing approaches. This course is designed with students in the junior or senior year in mind. The course is designed to be co-requisite with transport phenomena (CBE 3510 or equivalent), separations (CBE 3710 or equivalent), and thermodynamics (CBE 2310 or equivalent).

1 Course Unit

CBE 3600 Chemical Process Control

Dynamics and control of linear single-input, single output (SISO) systems in chemical processes. Laplace transforms. Dynamic responses of linear systems to various inputs. Frequency domain analysis. Feedback control strategies. Stability. Controller tuning. Advanced control, including cascade and feed forward control. Introduction to multiple-input, multiple-output (MIMO) control. Inverse response.

Spring

Prerequisite: CBE 2300

1 Course Unit

CBE 3710 Separation Processes

The design of industrial methods for separating mixtures. Distillation; liquid-liquid extraction; membranes; absorption. Computer simulations of the processes.

Spring

Prerequisite: CBE 2310

1 Course Unit

CBE 3750 Engineering and the Environment

The course will introduce emerging environmental issues, relevant engineering solutions, and problem-solving techniques to students. The case study approach will be used to assist students to develop and apply the fundamental engineering skills and scientific insights needed to recognize a variety of environmental problems that have profound impacts on all aspects of modern society. Sophomore standing required to enroll.

Spring

1 Course Unit

CBE 3990 Engineering Independent Study

An opportunity for the student to work closely with a professor in a project to develop skills and technique in engineering research and development. To register for this course, the student writes a one-page proposal that is approved by the professor supervising the research and submitted to the undergraduate curriculum chairman during the first week of the term. This course is distinct from CBE 0099 in its emphasis on the engineering aspects of the research topic, and as such it can be used as a CBE elective. In the Project Proposal described on the Application for Independent Study form, the proposal should highlight the engineering aspects of the work. A final report is required to be submitted to the supervising professor and the undergraduate curriculum chair, who will work together to assign a grade.

Fall or Spring

1 Course Unit

CBE 4000 Introduction to Product and Process Design

Introduction to product design, process synthesis, steady-state and batch process simulation, synthesis of separation trains, second-law analysis, heat integration, heat-exchanger design, equipment sizing, and capital cost estimation.

Fall

Prerequisite: CBE 3510 AND CBE 3710

Corequisite: CBE 4510

1 Course Unit

CBE 4100 Chemical Engineering Laboratory

Experimental studies in heat and mass transfer, separations and chemical reactors to verify theoretical concepts and learn laboratory techniques. Methods for analyzing and presenting data. Report preparation and the presentation of an oral technical report.

Fall

Prerequisite: CBE 3510 AND CBE 3710

1 Course Unit

CBE 4300 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

Also Offered As: MSE 4300

Prerequisite: (MSE 2600 OR CBE 2310) AND CHEM 2210 AND MEAM 2030

1 Course Unit

CBE 4510 Chemical Reactor Design

Design of reactors for the production of chemical products. Continuous and batch reactors. Isothermal and non-isothermal operation of reactors. Effects of back-mixing and non-ideal flow in tubular reactors. Mass transfer in heterogeneous reactions.

Fall

Prerequisite: CBE 2310 AND CBE 3510

1 Course Unit

CBE 4590 Product and Process Design Projects

Design of chemical, biochemical, and materials products and processes based on recent advances in chemical and bioengineering technology. Design group weekly meetings with faculty advisor and industrial consultants. Comprehensive design report and formal oral presentation. Heat exchanger design and profitability analysis.

Spring

Prerequisite: CBE 4000

1 Course Unit

CBE 4790 Biotechnology and Biochemical Engineering

The objective of this course is to teach junior CBE students the application of chemical engineering principles to biological systems in order to design biochemical processes. At the end of the course, students should be able to describe a process to produce and isolate a protein from a host cell. Students will work in groups on a current biotechnology topic related to chemical engineering that will be presented to the class and written as a final report. One of the course goals is to prepare students for a successful biotechnology lab experience in CBE 4800. Problem solving, models, open-ended problems, technical communication skills, and teamwork will be emphasized.

Fall

Prerequisite: CBE 2310

1 Course Unit

CBE 4800 Laboratory in Biotechnology and Biochemical Engineering

The laboratory methods covered include CRISPR/Cas9, production of proteins from cells in a bioreactors, purification of proteins by chromatography, and immobilized enzyme reactions. The students write several individual technical memos and submit weekly data analysis assignments. A group presentation and report on a new biotechnology technique is the final assignment for the lab. Oral and written communication skills are emphasized to improve technical communication skills.

Spring

Prerequisite: CBE 4790

1 Course Unit

CBE 5000 Special Topics in Chemical and Biomolecular Engineering

This course will be offered when necessitated by demand and permitted by schedule. The topics covered by the course will vary depending on the particular interests and expertise of the instructor(s). Topics are generally subjects of contemporary concern in the discipline.

Not Offered Every Year

1 Course Unit

CBE 5050 Carbon Capture

Carbon dioxide capture and sequestration has recently emerged as one of the key technologies needed to meeting growing worldwide energy demand while simultaneously reducing carbon dioxide emissions into the atmosphere. The objective of this course is to provide a quantitative introduction into the science and technology of carbon dioxide capture and sequestration. The following topics will be covered. General CO2 chemistry as it applies to capture and sequestration. Applied thermodynamics including minimal work and efficiency calculations for separation. CO2 separation from syngas and flue gas for gasification and combustion processes and the potential for direct air capture. Transportation of CO2 in pipelines and sequestration in deep underground geological formations. Pipeline specifications, monitoring, safety engineering, and costs for long distance transport of CO2. Comparison of options for geological sequestration in oil and gas reservoirs, saline aquifers, and mineral formations. Environmental risk assessment and management. Life cycle analysis

Spring

1 Course Unit

CBE 5060 Introduction to High-Performance Scientific Computing

Research problems in the domain of physical, biological and biomedical sciences and engineering often span multiple time and length-scales from the molecular to the organ/organism, owing to the complexity of information transfer underlying biological mechanisms. Multiscale modeling (MSM) and high-performance scientific computing (HPC) have emerged as indispensable tools for tackling such complex problems. However, a paradigm shift in training is now necessary to leverage the rapid advances, and emerging paradigms in HPC --- GPU, cloud, exascale supercomputing, quantum computing --- that will define the 21st century. This course is a collaboration between Penn, UC Berkeley, and the Extreme Science and Engineering Discovery Environment (XSEDE) which administers several of the federally funded research purpose supercomputing centers in the US. It will be taught as a regular 1 CU course at Penn by adopting a flip-classroom/active learning format. The course is designed to teach students how to program parallel architectures to efficiently solve challenging problems in science and engineering, where very fast computers are required either to perform complex simulations or to analyze enormous datasets. The course is intended to be useful for students from many departments and with different backgrounds, e.g., scholar of Penn Institute for Computational Science, although we will assume reasonable programming skills in a conventional (non-parallel) language, as well as enough mathematical skills to understand the problems and algorithmic solutions presented.

Fall or Spring

Also Offered As: BE 5160

1 Course Unit

CBE 5080 Probability and Statistics for Biotechnology

The course covers topics in probability theories and statistical techniques, with emphases placed on the practical problems relevant to the subject areas of biotechnology. The course provides a rigorous introduction to such topics as elements of probability, random variables and probability functions, random samples, parameter estimations, hypothesis testing, regression, analysis of variance, lifetime testing, and nonparametric tests.

Summer Term

1 Course Unit

CBE 5100 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

Also Offered As: MSE 5800

1 Course Unit

CBE 5110 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

1 Course Unit

CBE 5140 Data Science and Machine Learning in Chemical Engineering

The main objective of this course is to teach concepts and implementation of deep learning techniques for scientific and engineering problems to advanced undergraduate and graduate students. This course entails various methods, including theory and implementation of deep leaning techniques to solve a broad range of computational problems frequently encountered in solid mechanics, fluid mechanics, non destructive evaluation of materials, systems biology, chemistry, and non-linear dynamics. At the end of the course participants will be able to: (1) Understand the underlying theory and mathematics of deep learning; (2) Analyze and synthesize data in order to model physical, chemical, biological, and engineering systems; (3) Apply physics-informed neural networks (PINNs) to model and simulate multiphysics systems. Students should have prior coursework in advanced calculus, linear algebra, probability, and computer programming in Python.

Spring

Prerequisite: MATH 2400 AND MATH 2410

1 Course Unit

CBE 5150 Chemical Product Design

Introduction to product design, molecular and mixture design, functional and formulated product design, design of device products, pharmaceutical product and process design, optimal batch process design strategies, batch process simulation, six-sigma design

1 Course Unit

CBE 5170 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

1 Course Unit

CBE 5220 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 or Spring

1 Course Unit

CBE 5250 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. Students should have basic familiarity with statistical mechanics.

Fall

1 Course Unit

CBE 5350 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

Fall or Spring

1 Course Unit

CBE 5400 Principles of Molecular and Cellular Bioengineering

This course aims to provide theoretical and conceptual principles underlying biomolecular and biological systems. The course will start with basic and advanced concepts in physical chemistry and thermodynamics and introduce statistical mechanics as a tool to understand molecular interactions. The applications will be of relevance to bioengineering and biology disciplines. The course will not shy away from mathematical formulations and will stress the molecular perspective. This course explores physical biology of the cell across several length and timescales, while simultaneously emphasizing molecular specificity and clinical implications such as disease outcome or biomedical applications. The course emphasizes how the basic tools and insights of engineering, physics, chemistry, and mathematics can illuminate the study of molecular and cell biology to make predictive biomedical models and subject them to clinical validation. Drawing on key examples and seminal experiments from the current bioengineering literature, the course demonstrates how quantitative models can help refine our understanding of existing biological data and also be used to make useful clinical predictions. The course blends traditional models in cell biology with the quantitative approach typical in engineering, in order to introduce the student to both the possibilities and boundaries of the emerging field of physical systems biology. While teaching physical model building in cell biology through a practical, case-study approach, the course explores how quantitative modeling based on engineering principles can be used to build a more profound, intuitive understanding of cell biology. Worksheets will be integral to this course. Recitation will comprise of biweekly illustrations of problems and concepts from the worksheets and biweekly quizzes

Fall or Spring

Also Offered As: BE 5400

1 Course Unit

CBE 5410 Engineering and Biological Principles in Cancer

This course provides an integrative framework and provides a quantitative foundation for understanding molecular and cellular mechanisms in cancer. The topics are divided into three classes: (1) the biological basis of cancer; (2) cancer systems biology; and (3) multiscale cancer modeling. Emphasis is placed on quantitative models and paradigms and on integrating bioengineering principles with cancer biology. Prerequisite: Seniors in BE or permission of the instructor.

Spring

Also Offered As: BE 5410

1 Course Unit

CBE 5440 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. Thermodynamics, Kinetics, Physical Chemistry, Quantum Mechanics. Undergraduates should consult and be given permission by the instructor.

Fall or Spring

1 Course Unit

CBE 5450 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. Prerequisite: Introductory chemistry and an undergraduate course in thermodynamics (e.g. CBE 2310, MEAM 2030)

Fall or Spring

1 Course Unit

CBE 5460 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.

Spring

1 Course Unit

CBE 5540 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

Also Offered As: BE 5540

1 Course Unit

CBE 5550 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. Prerequisite: Background in Biology, Physics, Chemistry or Engineering with coursework in Thermodynamics or permission of the instructor.

Fall

Also Offered As: BE 5550, MEAM 5550

1 Course Unit

CBE 5560 The 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

1 Course Unit

CBE 5570 Stem Cells, Proteomics and 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 professiona presentations, papers and laboratory work will be developed. Background in Biology, Physics, Chemistry or Engineering.

Spring

1 Course Unit

CBE 5590 Multiscale Modeling of Chemical and 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, multiscale modeling. Prerequisite: Undergraduate courses in numerical analysis and physical chemistry.

Not Offered Every Year

Also Offered As: BE 5590, SCMP 5590

1 Course Unit

CBE 5620 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

Also Offered As: BE 5620

1 Course Unit

CBE 5640 Drug Delivery Systems: Targeted Therapeutics and Translational Nanomedicine

The topics include the need for new drug delivery systems (DDS), advantages and applications of biotherapeutic drugs, routes for drug transport in the body, pharmacokinetics and biodistribution, nanocarriers as DDS, targeted drug delivery, challenges with developing new DDS, and translational aspects of new DDS. Directors of the course are Miriam Wattenbarger and Vladimir Muzykantov (Pharmacology). In addition to lectures from the course directors, faculty from engineering and medicine will give guest lectures related to their research interests. The students read current journal articles on DDS. The major group assignment for the course is a written and oral group proposal on a new drug delivery system. Technical communication skills and working with students from different disciplines are an important aspects of the course.

Spring

Also Offered As: PHRM 5640

1 Course Unit

CBE 5700 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. Senior standing or permission of the instructor.

Spring

1 Course Unit

CBE 5800 Masters Biotechnology Lab

This lab is an introduction to lab techniques in biochemical engineering and biotechnology for graduate students in SEAS. Students are assumed to have a background in cell and molecular biology or to be co-registered for CBE 5540. Labs will include E. coli gene editing with CRISPR, production of eGFP in E. coli cells and isolation by chromatography, a fed-batch bioreactor to grow yeast cells and determine the growth and yield parameters, analysis of immobilized and soluble enzyme kinetics in a stirred reactor. Each lab will include a data analysis assignment. Three individual technical memos will be assigned, and a group report and presentation will be due at the end of the semester. Oral and written communication skills are emphasized to improve technical communication skills.

Fall or Spring

1 Course Unit

CBE 5970 Master's Thesis Research

Fall or Spring

1-2 Course Units

CBE 5990 Master's Indep Study

Fall or Spring

1-4 Course Units

CBE 6020 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.

Fall or Spring

1 Course Unit

CBE 6180 Advanced Molecular Thermodynamics

This course begins with a brief review of classical thermodynamics, including the development of Maxwell relationships and stability analysis. The remainder of the course develops the fundamental framework of statistical mechanics, then reviews various related topics including ideal and interacting gases, Einstein and Debye models of crystals, lattice models of liquids, and the basis of distribution function theory.

Fall

Also Offered As: BE 6620, MEAM 6620

1 Course Unit

CBE 6210 Advanced Chemical Kinetics and Reactor Design

Mechanisms of chemical reactions. Transition state theory. Langmuir-Hinshelwood Kenetics. Absorption and cataysis. Simple and complex reaction schemes. Design of idealized reactors. Fluidized reactors. Solid-gas reactions. Residence time distributions. Reaction and diffusion in solid catalysts. Reactor stability and control.

Fall

1 Course Unit

CBE 6400 Transport Processes I

This course provides a unified introduction to momentum, energy (heat), and mass transport processes. The basic mechanisms and constitutive laws for the various transport processes will be delineated , and the conservation equations will be derived and applied to internal and external flows. Examples from mechanical, chemical, and biological systems will be used to illustrate fundamental concepts and mathematical methods.

Fall

1 Course Unit

CBE 6410 Transport Processes II (Nanoscale Transport)

A continuation of CBE 6400, with additional emphasis on heat and mass transport. This course aims to teach transport concepts and methods useful in many current CBE laboratory settings. The emphasis will be on microscopic dynamics and transport in both hard and soft systems (e.g. colloids and polymers), of relevance to a variety of biological and biomolecular systems. Wherever possible, will make connections between classical, macroscopic transport, and what is happening microscopically. Will make use of a combination of analytic and algorithmic/numerical methods to facilitate understanding of the material. Physical topics will include stochastic, "single-molecule", non-ideal, hard sphere and frustrated systems, phase transitions, non-equilibrium statistical mechanics and optics. Concepts will include properties of stochastic functions (Gaussian statistics, correlation functions and power spectra), Fourier methods, Convolution, the Central Limit theorem, anomalous diffusion, percolation, and the Fluctuation/Dissipation theorem. Computational methods will concentrate on Monte Carlo simulations of "toy" models.

Spring

1 Course Unit

CBE 8950 Teaching Practicum

This course provides training in the practical aspects of teaching. The students will work with a faculty member to learn and develop teaching and communication skills. As part of the course, students will participate in a range of activities that may include: giving lectures, leading recitations, supervising laboratory experiments, developing instructional laboratories, developing instructional material, preparing and grading homework assignments and solution sets, and preparing examinations. Feedback on the recitations will be provided to the student by the faculty responsible for the course. The course is graded on a Satisfactory/Unsatisfactory basis. The evaluation will be based on comments of the students taking the course and the impressions of the faculty.

Fall or Spring

0 Course Units

CBE 8990 Independent Study

Fall or Spring

1-4 Course Units

CBE 9950 Dissertation

Fall or Spring

0 Course Units

CBE 9990 Thesis/Dissertation Research

For students working on an advanced research program leading to the completion of master's thesis or Ph.D. dissertation requirements.

Fall or Spring

1-4 Course Units