Graduate Courses

EN.540.601. Chemical and Biomolecular Engineering Seminar.

Instructor(s): R. Schulman.


EN.540.602. Metabolic Systems Biotechnology.

The aim of this course is to provide a fundamental understanding of the quantitative principles and methodologies of systems biology and biochemical engineering of metabolism. This includes concepts of cellular growth, cellular stoichiometric models, metabolic networks, metabolite fluxes, and genome-scale metabolic models. Quantitative methods and systems biology approaches for metabolic flux analysis and metabolic control theory will be included as well as an analysis of biochemical systems and bioreactors including a consideration of mass transport processes.
Instructor(s): M. Betenbaugh.


EN.540.603. Colloids and Nanoparticles.

Fundamental principles related to interactions, dynamics, and structure in colloidal, nanoparticle, and interfacial systems. Concepts covered include hydrodynamics, Brownian motion, diffusion, sedimentation, electrophoresis, colloidal and surface forces, polymeric forces, aggregation, deposition, and experimental methods. Modern topics related to colloids in nano- science and technology will be discussed throughout the course with frequent references to recent literature. Meets with EN.540.403
Instructor(s): M. Bevan
Area: Engineering.


EN.540.605. The Design of Biomolecular Systems.

This course covers new topics in the design of systems of biomolecules,w both in vitro and in vivo, for decision making and control. The course will begin with an overview of how logical decision making and control with biomolecules as is achieved in biology and then proceed to consider various strategies of engineering similar systems. The focus of the course will be on systems level principles rather than the biochemistry of molecule design. Topics will include engineering of transcriptional networks and genetic control for logically programming of cells, the design of in vitro mimics of genetic controls, molecular computing and systems aspects of metabolic engineering. The course will also cover quantitative and computational techniques for the simulation and analysis of biomolecular systems. Recommended: EN.540.602 Meets with EN.540.405
Instructor(s): R. Schulman.


EN.540.608. Numerical Methods in Chemical & Biomolecular Engineering.

Supervised Graduate Study
Instructor(s): M. Donohue
Area: Engineering, Natural Sciences.


EN.540.610. Fundamentals of Membrane Science for Filtration Applications.

This course focuses on the principles underlying the formation of micro-to-nanostructured membranes applied in a range of modern filtration technologies such as microfiltration, ultrafiltration, nanofiltration, reverse osmosis, pervaporation, gas separation, electrodialysis, hemodialysis, fuel cells, drug delivery, tissue engineering and sensors. Polymeric membranes prepared by phase separation will be examined in detail, while interfacial polymerization and sol-gel processing to prepare thin film composites and ceramic membranes, respectively, will also be studied. The first part of the course will discuss how concepts from thermodynamics, multicomponent diffusion and fluid/solid mechanics are applied to membrane formation theory. The second part will present membrane transport theory, and demonstrate how engineering principles are applied to the various filtration applications and the design of modules.


EN.540.614. Computational Protein Structure Prediction.

This class will introduce the fundamental concepts in protein structure, biophysics, optimization and informatics that have enabled the breakthroughs in computational structure prediction and design. Problems covered will include protein folding and docking, design of ligand-binding sites, design of turns and folds, design of protein interfaces. Class will consist of lectures and hands-on computer workshops. Students will learn to use molecular visualization tools and write programs with the PyRosetta protein structure software suite, including a computational project. Programming experience is recommended.
Instructor(s): J. Gray
Area: Engineering.


EN.540.615. Interfacial Science with Applications to Nanoscale Systems.

Nanostructured materials intrinsically possess large surface area (interface area) to volume ratios. It is this large interfacial area that gives rise to many of the amazing properties and technologies associated with nanotechnology. In this class we will examine how the properties of surfaces, interfaces, and nanoscale features differ from their macroscopic behavior. We will compare and contrast fluid-fluid interfaces with solid-fluid and solid-solid interfaces, discussing fundamental interfacial physics and chemistry, as well as touching on state-of-the-art technologies.
Instructor(s): J. Frechette.


EN.540.616. Current Topics in Protein Structure Prediction.

Permission of instructor required.
Instructor(s): J. Gray.


EN.540.619. Projects in Design: Alternative Energy.

This design project is focused on the role alternative energy will play in our country’s future. About a third of the course will be devoted to understanding the role of energy and alternative energy in the US and world economies. The remainder of the course will be devoted to a technical and economic analysis of the feasibility of making biofuel from algae. Graduate level. Meets with EN.540.401
Instructor(s): M. Donohue.


EN.540.626. Biomacromolecules at the Nanoscale.

This course introduces modern concepts of polymer physics at the nanoscale to describe the conformation and dynamics of biological macromolecules such as filamentous actin, microtubule, and nucleic acids. We will introduce scattering techniques, nano-manipulation techniques, as well as nano-rheology applied to the study of polymers for tissue engineering, nanoparticles, and drug delivery applications.
Instructor(s): D. Wirtz.


EN.540.628. Supramolecular Materials and Nanomedicine.

Nanomedicine is a quickly growing area that exploits the novel chemical, physical, and biological properties of nanostructures and nanostructured materials for medical treatments. This course presents basic design principles of constructing nanomaterials for use in drug delivery, disease diagnosis and imaging, and tissue engineering. Three major topics will be discussed, including 1) nanocarriers for drug delivery that are formed through soft matter assembly (e.g., surfactants, lipids, block copolymers, DNA, polyelectrolytes, peptides), 2) inorganic nanostructures for disease diagnosis and imaging (e.g., nanoparticles of gold and silver, quantum dots and carbon nanotubes), and 3) supramolecular scaffolds for tissue engineering and regenerative medicine. Students are expected to learn the physical, chemical and biological properties of each nanomaterial, the underlying physics and chemistry of fabricating such material, as well as their advantages and potential issues when used for biomedical applications. This course will also provide students opportunities for case studies on commercialized nanomedicine products. After this class, students should gain a deeper understanding of current challenges in translating nanoscience and nanotechnology into medical therapies.
Instructor(s): H. Cui
Area: Engineering, Natural Sciences.


EN.540.630. Thermodynamics, Statistical Mechanics, and Kinetics.

In this course we will aim for understanding the thermodynamics of chemical and bio-molecular systems. We will first review classical, macroscopic thermodynamics covering concepts such as equilibrium, stability and the role of thermodynamic potentials. Our goal will be to gain a feel for the generality of thermodynamics. Statistical mechanics provides a link between the mechanics of atoms and macroscopic thermodynamics. We will introduce this branch in two distinct ways: 1) following standard methods of developing concepts such as ensembles and partition functions, and 2) where we will treat the basis of statistical mechanics as a problem in inference. With this foundation, we will consider concepts relevant to understanding the liquid state. Chemical transformations in a liquid are of importance in much of chemistry and biology; quasi-chemical generalizations of the potential distribution theorem will be introduced to present these ideas. We hope to give an overview of modern developments relating equilibrium work to non-equilibrium work, as these are of increasing importance in studies on single molecule systems. Perm Req’d for undergrads.
Instructor(s): C. Wang.


EN.540.632. Project in Design: Pharmacokinetics.

This course covers pharmacodynamics, i.e. how pharmaceuticals affect biological processes. The course will use MatLab to aid in the design of new drug formulations.
Instructor(s): M. Donohue
Area: Engineering, Natural Sciences.


EN.540.637. Application of Molecular Evolution to Biotechnology.

One of the most promising strategies for successfully designing complex biomolecular functions is to exploit nature’s principles of evolution. This course provides an overview of the basics of molecular evolution as well as its experimental implementation. Current research problems in evolution-based biomolecular engineering will be used to illustrate principles in the design of biomolecules (i.e. protein engineering, RNA/DNA engineering), genetic circuits and complex biological systems including cells. Will meet with EN.540.437. Recommended Course Background: AS.020.305
Instructor(s): M. Ostermeier
Area: Engineering, Natural Sciences.


EN.540.640. Micro/Nanotechnology: The Science and Engineering of Small Structures.

Micro/Nanotechnology is the field of fabrication, characterization and manipulation of extremely small objects (dimensions on the micron to nanometer length scale). Microscale objects, because of their small size are expected to be at the frontier of technological innovation for the next decade. This course will include a description of the materials used in microtechnology, methods employed to fabricate nanoscale objects, techniques involved in characterizing and exploiting the properties of small structures, and examples of how this technology is revolutionizing the areas of Electronics & Medicine. Same class as 540.440
Instructor(s): D. Gracias.


EN.540.641. Micro- and Nanoscale Transport Phenomena.

This course will (1) focus on transport processes that are different or more prominent in microfabricated systems, (2) present practical aspects of experimental and theoretical work in microscale and nanoscale transport processes and (3) develop a working knowledge of the relevant literature. Some topics include Maxwell and Navier-Stokes equations, Couette/Poiseuille flow, Stokes flow, fluid circuits, microfluidic mixing, mass and charge transport, electrodynamics, electrophoresis, electro-osmosis, dielectrophoresis, induced-charge electrokinetics, DNA transport, and zeta potential.
Prerequisites: Prereq: EN.540.304 Transport II OR the equivalent. Instructor permission required.
Instructor(s): Z. Gagnon
Area: Engineering, Natural Sciences.


EN.540.645. Intro to Research in Micro and Nanotechnology.

A class room based learning of all aspects of conducting research in Micro and Nanotechnology including review of state-of-the-art in the field and original research descriptions. In the course, you will learn the state of the art in Micro and Nanotechnology, critical analysis of research including Design of Experiments, research ethics and strategies to deliver effective research presentations. Instructor Approval.
Instructor(s): D. Gracias.


EN.540.647. Advanced Problems in Fluid Mechanics.

A selection of problems in fluid mechanics at low and moderate Reynolds numbers. This is a highly interactive class in which students are expected to choose topics and prepare a presentation at least twice a semester. Therefore, the list of problems will vary depending on student selection. Typically Tuesdays will be an introductory class and Thursdays will be seminars on a specific topic or paper. Meets with 540.447
Instructor(s): G. Drazer
Area: Engineering, Natural Sciences.


EN.540.649. Logic and Decision-making in Biomolecular Systems.

From the smallest change in gene expression to life and death and reproduction, biomolecular decision-making processes govern cellular fate. In this course we explore the design principles by which biomolecules make decisions and orchestrate complex processes such as signal transduction, homeostasis or apoptosis. We will also explore how we can in turn design complex biomolecular networks that can control biological systems and biomolecular materials. Topics will include the design and analysis of molecular logic circuits, transcriptional and translational control, signal transduction cascades, biomolecular oscillators and cycles, DNA nanotechnology and nanobiotechnology, and molecular computing. The course will introduce principles from electrical circuit theory, computing and control theory and show how these tools can be applied to these systems. Students should be familiar with programming and chemical engineering principles.
Instructor(s): R. Schulman.


EN.540.652. Advanced Transport Phenomena.

It is the goal of this course to move the graduate student (and advanced undergraduate student) from the introductory level of transport phenomena (undergraduate) to a level that will allow them to be effective in researching transport-related topics in a variety of biomedical, chemical and biochemical engineering areas. The basic equations that govern mass, momentum, and energy transport will be derived and used to solve problems that demonstrate the physical insight necessary to apply these equations to original situations. Some topics include solution techniques utilizing expansions of harmonic functions, singularity solutions, lubrication theory for flow in confined geometries, boundary layer theory, Stokes flow, forced convection, buoyancy-driven flow, Taylor-Aris dispersion, and reaction-diffusion.
Instructor(s): Z. Gagnon
Area: Engineering, Natural Sciences.


EN.540.659. Bioengineering in Regenerative Medicine.

Introduction and in-depth discussion course focused on tissue and stem cell engineering. The course will focus on principles in tissue engineering, mechanisms of regeneration, and stem cell therapies. Topics will include introduction to regenerative medicine, bioreactors and scaffolds in tissue engineering, adult and pluripotent stem cells, engineering the niche, and two sessions will focus on legal and ethical issues. Selected approaches to analyze tissues and stem cell culture will also be discussed. In addition, the course will be integrated with graduate students’ presentations on selected topics in stem cell engineering. Meets with EN.540.459. Recommended Course Background: AS.020.306 or EN.580.221 or EN.580.440
Instructor(s): S. Gerecht
Area: Engineering.


EN.670.619. Fundamental Physics and Chemistry of Nanomaterials.

This course will cover the physics and chemistry relevant to the design, synthesis, and characterization of nanoparticles. Topics include nanoparticle synthesis, functionalization, surface engineering, and applications in diagnostics and therapeutics. The properties of semiconductor quantum dots and magnetic nanoparticles will be reviewed along with techniques for nanoparticle manipulation, particle tracking, and bio-microrheology. Patterning tools including soft lithography, optical lithography, e-beam lithography, and template lithography will be discussed. Electron and scanning probe microscopy will be reviewed. Cross-listed with Materials Science & Engineering and Chemical & Biomolecular Engineering.
Instructor(s): Staff.


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