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MIT Course Catalog 2009-2010

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Department of Biological Engineering

The mission of the Department of Biological Engineering (BE) is to educate leaders and generate and communicate new knowledge fusing engineering with modern molecular-to-genomic biology. Combining quantitative, physical, and integrative principles with advances in mechanistic molecular and cellular bioscience, biological engineering increases understanding of how biological systems function as both physical and chemical mechanisms, and of how they respond when perturbed by factors such as medical therapeutics, environmental agents, and genetic variation. Through this understanding, new technologies can be created to improve human health in a variety of medical and environmental applications, and biology-based paradigms can be generated to address many of the diverse challenges facing society.

The BE Department's central aim is to establish a new, biology-based engineering discipline, alongside well established disciplines such as chemical engineering, electrical engineering, and mechanical engineering. At the same time, the program endeavors to assist these engineering and science disciplines in addressing the impact of new processes and products relating to human health and the environment. To meet these objectives, BE comprises faculty with expertise in key areas of engineering, biology, biochemistry, biophysics, pharmacology, toxicology, and other relevant physical/chemical/computational sciences, and who share a goal of integrating central principles to pioneer innovative research and education direction at this nexus.

The department's premise is that the science of biology is as important to the development of technology and society today as physics and chemistry were in the 20th century, and that the growing ability monitor, assess, and control properties of living organisms at the molecular, cellular, tissue, organ, and systems levels will continue to shape this development. A new generation of engineers and scientists is learning to address problems through their ability to measure, model, and rationally manipulate the technological and environmental factors affecting biological systems. They are applying not only engineering principles to the understanding of how biological systems operate, especially when impacted by genetic, chemical, physical, infectious, or other interventions; but also a synthetic design perspective to creating biology-based technologies for medical diagnostics, therapeutics, and other devices, as well as for application in diverse industries beyond human health care.

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Undergraduate Study

Bachelor of Science in Biological Engineering
[see degree chart]

The Department of Biological Engineering offers an undergraduate curriculum emphasizing quantitative, engineering-based analysis, design, and synthesis in the study of modern biology from the molecular to the systems level. Completion of the curriculum leads to the Bachelor of Science in Biological Engineering and prepares students for careers in diverse fields ranging from the pharmaceutical and biotechnology industries to materials, devices, ecology, and public health. Graduates of the program will be prepared to enter positions in basic research or project-oriented product development, as well as graduate school or further professional study.

The required core curriculum includes a strong foundation in biological and biochemical sciences, which are integrated with quantitative analysis and engineering principles throughout the entire core. Students who wish to pursue the Bachelor of Science in Biological Engineering are encouraged to complete the Biology General Institute Requirement during freshman year and may delay completion of Physics II until the fall term of sophomore year if necessary. The optional subject Introduction to Biological Engineering Design, offered during the spring term of freshman year, provides a framework for understanding the Biological Engineering SB program.

Enrollment in the Biological Engineering SB is limited at the present time, and students who wish to pursue this degree must complete the sophomore fall-term subject 20.110 Thermodynamics of Biomolecular Systems with a passing grade in order to apply for admission. This subject also fulfills an SB degree requirement in Biology. Students are also encouraged to take Organic Chemistry I and Differential Equations by the fall term of sophomore year in order to prepare for spring-term sophomore subjects. The sophomore spring-term curriculum includes an introductory biological engineering laboratory subject that provides context for the lecture subjects and a strong foundation for subsequent undergraduate research in biological engineering through Undergraduate Research Opportunity Program projects or summer internships.

The advanced subjects required in the junior and senior years introduce additional engineering skills through lecture and laboratory subjects and culminate in a senior design project. These advanced subjects maintain the theme of molecular to systems–level analysis, design, and synthesis based on a strong integration with biology fundamentals. They also include a variety of restricted electives that allow students to develop expertise in one of four thematic areas: systems biology, pharmacology/toxicology, cell and tissue engineering, and microbial systems. Many of these advanced subjects are jointly taught with other departments in the School of Engineering or School of Science and may fulfill degree requirements in other programs.

Minor in Biomedical Engineering

An interdepartmental Minor in Biomedical Engineering is available to all undergraduate students outside the BE (Course 20) major. See Interdisciplinary Undergraduate Programs and Minors in Part 3 for detailed information.

Minor in Toxicology and Environmental Health

The Department of Biological Engineering offers an undergraduate Minor in Toxicology and Environmental Health. The goal of this program is to meet the growing demand for undergraduates to acquire the intellectual tools needed to understand and assess the impact of new products and processes on human health, and to provide a perspective on the risks of human exposure to synthetic and natural chemicals, physical agents, and microorganisms.

Given the importance of environmental education at MIT, the program is designed to be accessible to any MIT undergraduate. The program consists of three required didactic core subjects and one laboratory subject, as well as one restricted elective. The prerequisites for the core subjects are 5.111/5.112 Principles of Chemical Science or 3.091 Introduction to Solid State Chemistry plus 7.012/7.013/7.014 Introductory Biology.

Core Subjects

20.102 Macroepidemiology and Population Genetics
20.104J Environmental Risks for Common Diseases
20.106 Systems Microbiology


Laboratory Core

One of the following:
20.109 Laboratory Fundamentals in Biological Engineering
5.310 Laboratory Chemistry
7.02 Introduction to Experimental Biology and Communication
10.702 Introductory Experimental Biology and Communication


Restricted Electives

One of the following:
20.URG Undergraduate Research Opportunities
1.080 Environmental Chemistry and Biology
1.725J Chemicals in the Environment: Fate and Transport
1.89 Environmental Microbiology
5.07 Biological Chemistry I
7.05 General Biochemistry
7.06 Cell Biology
7.28 Molecular Biology
5.23 Atmospheric Chemistry
17.32 Environmental Politics and Policy

 

Inquiries

For further information on the undergraduate programs, please visit the Biological Engineering website at http://web.mit.edu/be/ or contact the BE Academic Office, Room 56-651, 617-253-1712.

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Graduate Study

Doctoral Program in Biological Engineering

The Department of Biological Engineering offers a PhD program—and, in certain cases, an SM degree—with two tracks, one in bioengineering and another in applied biosciences. These tracks complement one another as a reflection of the importance of approaching quantitative biological and biomedical problems from the two perspectives. Students in either track may pursue research projects in any area by agreement with their research supervisor.

Graduate students in the Department of Biological Engineering can carry out their research as part of a number of multi-investigator, multidisciplinary research centers at MIT, including the Center for Biomedical Engineering, the Biotechnology Process Engineering Center, the Center for Environmental Health Sciences, the Division of Comparative Medicine, and the Synthetic Biology Engineering Research Center. These opportunities include collaboration with faculty in the Schools of Engineering and Science, the Koch Institute for Integrative Cancer Research, and the Whitehead Institute for Biomedical Research, along with the Harvard University School of Medicine, Harvard University School of Dental Medicine, Harvard School of Public Health, and Boston University School of Medicine.

Bioengineering Track
Students admitted to the bioengineering track typically have a bachelor's or master's degree in engineering. During that first year, students pursue a unified core curriculum, in which engineering approaches are used to analyze biological systems and technologies over a wide range of length and time scales. The three core bioengineering subjects are:

20.420J Biomolecular Kinetics and Cellular Dynamics
20.430J Fields, Forces, and Flows in Biological Systems
20.440 Analysis of Biological Networks

 

These subjects bring central engineering principles to bear on the operation of biological systems from molecular to cell to tissue/organ/device systems levels. Foundational coursework in biochemistry and molecular cell biology is required, either before admission or during the first year of graduate study.

To enhance depth and breadth, the core subjects are supplemented by electives in the biological sciences and engineering. For doctoral candidates, two of these must be graduate-level biology subjects. The student will be expected to have biochemistry and cell biology as prerequisites and then select two graduate-level subjects in biological science. If cell biology has not been taken previously, it must be selected as one of these two graduate-level subjects. If biochemistry has not been taken previously, it must be taken as a remedial undergraduate subject before selecting the two graduate-level subjects. In addition, one graduate-level subject from Biological Engineering beyond the core classes and one engineering or science graduate-level subject are required as electives. The written part of the doctoral qualifying examinations, centered on the core curriculum, is taken after the second term.

The student selects a research advisor and begins research before the end of the first year. The oral part of the doctoral qualifying exams, which focuses on the student's area of research, is taken during the second year. Approximately five years of total residence are needed to complete the doctoral thesis and other degree requirements.

The bioengineering track educates students to use engineering principles in the analysis and manipulation of biological systems, allowing them to solve problems across a spectrum of important applications. The curriculum is inherently interdisciplinary in that it brings together engineering and biology as fundamentally as possible and cuts across the boundaries of the traditional engineering disciplines.

The faculty members associated with this track possess a wide range of research interests within bioengineering. Areas in which students may specialize include biological and physiological transport phenomena; biological imaging and functional measurement; biomolecular engineering; cell and tissue engineering; computational modeling of biological and physiological systems; bioinformatics; design, discovery and delivery of molecular therapeutics; molecular, cell, and tissue biomechanics; and new tools for genomics, proteomics, and glycomics.

Applied Biosciences Track
Students admitted to the applied biosciences track typically have a bachelor's or master's degree in chemistry, biology, physics, or a related field. During the first year, students pursue a unified core curriculum, in which basic science approaches are applied to problems in the health and disease aspects of biomedical science. The three core subjects are:

20.420J Biomolecular Kinetics and Cellular Dynamics
20.440 Analysis of Biological Networks
20.450 Molecular and Cellular Pathophysiology

 

These subjects bring central scientific principles to bear on the operation of biological systems from molecular to cell to tissue to organismal levels. Foundational coursework in physics, calculus, organic chemistry, biochemistry, physical chemistry/biophysics/engineering, and cell biology/molecular biology/genetics is required, either before admission or during the first year of graduate study.

To enhance depth and breadth, the core subjects are supplemented by elective subjects. Doctoral candidates are expected to take elective subjects in biological science. The student will be expected to have biochemistry and cell biology as prerequisites and then select two graduate-level subjects in biological science. If cell biology has not been taken previously, it must be selected as one of these two graduate-level subjects. If biochemistry has not been taken previously, it must be taken as a remedial undergraduate subject before selecting the two graduate-level subjects. In addition, one graduate-level subject from Biological Engineering beyond the core classes and one engineering or science graduate-level subject are required as electives. The written part of the doctoral qualifying examinations, centered on the core curriculum, is taken after the second term. The students select a research advisor and begin research before the end of the first year. The oral part of the doctoral qualifying examinations, which focuses on the student's area of research, is taken during the second year. Approximately five years of total residence are needed to complete the doctoral thesis and other degree requirements.

The applied biosciences track complements the bioengineering track (and the Computational and Systems Biology graduate program) by focusing on understanding the interactions of organisms with chemical, biological, and physical agents from the molecular to the systems level. The goal here is to apply systems approaches to studying the chemical and molecular pathways by which exogenous and endogenous agents induce toxicity and cause disease in humans; to establishing the molecular mechanisms of drug actions, with the longer-term aim of developing improved therapeutics; to establishing mechanisms of microbial pathogenesis; and to understanding and manipulating immune function.

Systems biology is an emerging field that involves quantitative study of biological processes as integrated systems rather than as isolated parts. This goal of defining the behavior of the myriad of individual molecules requires quantitative models to unify the individual disciplines of physical chemistry, biochemistry, molecular biology, and cell physiology, as well as new tools for the simultaneous measurement of biological components, including small molecules, proteins, nucleic acids and complex carbohydrates.

The applied biosciences track provides rigorous training in the basic sciences, with application of chemistry, mathematics, biochemistry, molecular biology, cell biology, genetics, toxicology, and pharmacology to problems in human health and disease. Students receive preparation for careers in academic institutions, government agencies, and industry involving the application of modern methods of chemical, molecular, biological, and genetic analysis to the characterization of health risks.

Areas of research specialization within the program include development of in vitro models of the immune system and lymphoid tissue; development of molecular methods for direct measurement of mutations in humans; metabolism of foreign compounds; genetic toxicology; the molecular aspects and dosimetry of interactions between mutagens and carcinogens with nucleic acids and proteins; molecular mechanisms of DNA damage and repair; design and mechanisms of action of chemotherapeutic agents; environmental carcinogenesis and epidemiology; molecular mechanisms of carcinogenesis; cell physiology; extracellular regulation and signal transduction; and molecular and pathologic interactions between infectious microbial agents and carcinogens. Interdisciplinary in nature, the program and other programs and departments share an interest in human pathophysiology, molecular pharmacology, and environmental health.

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Master of Engineering in Biomedical Engineering

The Master of Engineering in Biomedical Engineering (MEBE) program is a five-year program leading to a bachelor's degree in a science or engineering discipline along with a Master of Engineering in Biomedical Engineering. The program emphasizes the fusion of engineering with modern molecular-to-genomic biology, as in our SB and PhD degree programs. Admission to the MEBE program is open only to MIT undergraduate students, and requires candidates to demonstrate adequate quantitative and engineering credentials through their undergraduate coursework.

In addition to satisfying the requirements of their departmental program, candidates also are expected to complete subjects in differential equations (18.03); one engineering transport or systems subject (e.g., 2.005, 3.185, 6.002, 10.310); organic chemistry (5.12); biochemistry (7.05 or 5.07); and two of the core subjects from the Biomedical Engineering Minor.

Applications to the MEBE program are accepted from students in any of the departments in the School of Engineering or School of Science. Students interested in applying to the MEBE program should submit a standard MIT graduate application by the end of their junior year and are informed of the decision by the end of that summer.

Additional information on application procedures, objectives, and program requirements can be obtained by contacting Professor Jongyoon Han, jyhan@mit.edu; Professor Darrell Irvine, djirvine@mit.edu; or the BE Academic Office, Room 56-651, 617-253-1712.

Program Requirements

In addition to thesis credits, at least 66 units of coursework are required. At least 42 of these subject units must be from H-level graduate subjects. The remaining units may be satisfied with G-level subjects, or in some cases, with advanced undergraduate subjects. Of the 66 units, a minimum distribution in each of three categories is specified below.

Bioengineering Core

24 units selected from:
20.410J Molecular, Cellular, and Tissue Biomechanics
20.420J Biomolecular Kinetics and Cellular Dynamics
20.430J Fields, Forces, and Flows in Biological Systems


Biomedical Engineering Electives

24 units selected from:
A selection of G- or H-level subjects from various departments in the School of Engineering and HST. A list of suggested subjects is available from the BE Academic Office, Room 56-651.


Bioscience Elective

One biological science subject in addition to organic chemistry and biochemistry. This must be a laboratory subject if one was not taken as part of the student's undergraduate curriculum.


Thesis
The student is required to complete a thesis that must be approved by the program director. The thesis is an original work of research, design, or development. If the supervisor is not a member of the Department of Biological Engineering, a reader who belongs to the BE faculty must also approve and sign the thesis. The student submits a thesis proposal by the end of the fourth year.

Inquiries

For further information on the graduate programs, please visit the Biological Engineering website at http://web.mit.edu/be/ or contact the BE Academic Office, Room 56-651, 617-253-1712.

Leaders for Global Operations Program

The 24-month Leaders for Global Operations (LGO) program combines graduate education in engineering and management for those with two or more years of full-time work experience who aspire to leadership positions in manufacturing or operations companies. A required 6.5-month internship provides opportunity to complete a research project on site at one of LGO’s partner companies. The internship leads to a dual-degree thesis, culminating in two master’s degrees—an SM in management or an MBA, and an SM from a participating engineering department. The program is offered jointly through the MIT Sloan School of Management and the School of Engineering. For more information, see the program description under Engineering Systems Division or visit http://lgo.mit.edu/.

Faculty and Staff

Faculty and Teaching Staff

Douglas A. Lauffenburger, PhD
Whitaker Professor of Biological Engineering, Biology, and Chemical Engineering
Associate Member, Broad Institute
Department Head

Professors

Angela M. Belcher, PhD
Germeshausen Professor of Materials Science and Biological Engineering

Arup Chakraborty, PhD
Haslam Professor of Chemical Engineering, Chemistry, and Biological Engineering

Peter C. Dedon, PhD, MD
Underwood-Prescott Professor of Toxicology and Biological Engineering

Edward F. DeLong, PhD
Professor of Environmental and Biological Engineering
Associate Member, Broad Institute

C. Forbes Dewey, Jr., PhD
Professor of Mechanical Engineering and Bioengineering

John Martin Essigmann, PhD
Professor of Chemistry, Toxicology, and Biological Engineering

James G. Fox, DVM
Professor of Toxicology
Director, Division of Comparative Medicine

Linda Griffith, PhD
S.E.T.I. Professor of Biological and Mechanical Engineering
Director, Biotechnology Process Engineering Center

Alan J. Grodzinsky, PhD
Professor of Electrical, Mechanical, and Biological Engineering
Director, Center for Biomedical Engineering

Roger D. Kamm, PhD
Germeshausen Professor of Biological and Mechanical Engineering

Alexander M. Klibanov, PhD
Novartis Professor of Chemistry and Biological Engineering

Robert S. Langer, ScD
Professor of Chemical and Biomedical Engineering
Institute Professor

Harvey F. Lodish, PhD
Professor of Biology and Biological Engineering
Associate Member, Broad Institute
Member, Whitehead Institute for Biomedical Research

Leona D. Samson, PhD
American Cancer Society Professor
Professor of Toxicology and Biological Engineering
Associate Member, Broad Institute
Director, Center for Environmental Health Sciences

Ram Sasisekharan, PhD
Taplin Professor of Biological Engineering and Health Sciences and Technology

Peter T. So, PhD
Professor of Mechanical and Biological Engineering

Steven R. Tannenbaum, PhD
Underwood-Prescott Professor of Toxicology and Chemistry

William G. Thilly, ScD
Professor of Toxicology

Bruce Tidor, PhD
Professor of Biological Engineering and Computer Science

K. Dane Wittrup, PhD
Mares Professor of Chemical Engineering and Biological Engineering

Michael B. Yaffe, PHD
Professor of Biology and Biological Engineering

Jacquelyn C. Yanch, PhD
Professor of Nuclear Science and Engineering and Biological Engineering

Ioannis V. Yannas, PhD
Professor of Polymer Science and Bioengineering

Associate Professors

Christopher B. Burge, PhD
Whitehead Associate Professor of Biology and Biological Engineering
Associate Member, Broad Institute

Bevin P. Engelward, DSc
Associate Professor of Biological Engineering

Jongyoon Han, PhD
van Tassel Associate Professor of Electrical and Biological Engineering

Darrell J. Irvine, PhD
Associate Professor of Biological Engineering and Materials Science
Howard Hughes Medical Institute Investigator

Alan P. Jasanoff, PhD
Associate Professor of Nuclear Science and Engineering, Biological Engineering, and Brain and Cognitive Sciences

Matthew J. Lang, PhD
Keck Associate Professor of Mechanical and Biological Engineering

Scott R. Manalis, PhD
Associate Professor of Biological and Mechanical Engineering, and Media Arts and Sciences
Associate Member, Broad Institute

Krystyn Van Vliet, PhD
Associate Professor of Materials Science and Engineering and Biological Engineering

Forest White, PhD
Mitsui Associate Professor of Biological Engineering

Assistant Professors

Eric Alm, PhD
Assistant Professor of Biological and Environmental Engineering
Associate Member, Broad Institute

Mark Bathe, PhD
Assistant Professor of Biological Engineering

Ernest Fraenkel, PhD
Bell Assistant Professor of Biological Engineering

Kimberly Hamad-Schifferli, PhD
Burnell Assisant Professor of Mechanical and Biological Engineering

Jacquin C. Niles, PhD, MD
Pfizer-Laubach Assistant Professor of Biological Engineering

Katharina Ribbeck, PhD
Assistant Professor of Biological Engineering

Visiting Professor

Peter K. Sorger, PhD
Visiting Professor of Biological Engineering

Lecturers and Instructors

Noubar Afeyan, PhD
Laura C. Green, PhD
Sean Harriman, PhD
Natalie Kuldell, PhD
Agi Stachowiak, PhD
Nathan Tedford, PhD
Steve Wasserman, SM

Research Staff

Senior Research Scientist

John S. Wishnok, PhD

Principal Research Scientist

Paul L. Skipper, PhD

Principal Research Engineer

Randall Rettberg, MS

Research Scientists

Robert G. Croy, PhD
Michael DeMott, PhD
Karel Domansky, PhD
Elena Gostjeva, PhD
Ramesh Indrakanti, PhD
Vera Koledova, PhD
Rosa Liberman, PhD
Robert McCunney, PhD
Rahul Raman, PhD

Research Associate

Min Young Kim, PhD

Postdoctoral Associates

Shannon Alford, PhD
Neda Bagheri, PhD
Viral Brahmbhatt, PhD
Wan Chan, PhD
Nisanart Charoenlap, PhD
David Clarke
Liang Cui, PhD
Ajit Dash, PhD
Amanda Del Rosario, PhD
Jeannette Fiala, PhD
Alfio Fichera, PhD
Mark Fleury, PhD
Kevin Ford, PhD
Luiz Godoy, PhD
William Grover, PhD
Arthur Goldsipe, PhD
Toomas Haller, PhD
Peyman Honarmandi, PhD
Hannah Johnson, PhD
Pilsoo Kang, PhD
Hyung-Do Kim, PhD
Orsolya Kiraly, PhD
Scott Knudsen, PhD
Charles Knutson, PhD
Jungchul Lee, PhD
Taekwan Lee, PhD
Deyu Li, PhD
Kok Seong Lim, PhD
Pallavi Lonkar, PhD
Megan McBee, PhD
Geeta Mehta, PhD
Shmuel Motola, PhD
Jason Neil, PhD
Dawn Nida, PhD
Gerard Ostheimer, PhD
Ho Seok Park, PhD
Yang Shen, PhD
Peter Slade, PhD
Hsiao-Lan Sun, PhD
Kirill Titievsky, PhD
Lianrong Wang, PhD
Yu Wang, PhD
Courtney Williams, PhD
Wenjie Ye, PhD
Yu Zeng, PhD

Postdoctoral Fellows

Samuel Inman, PhD
Chandrasekhar Kothapalli, PhD
Werner Olipitz, PhD
Shelly Peyton, PhD
Erin Prestwich, PhD
Laura Riva, PhD
Kari Schlicht, PhD
Leslie Woo, PhD

Visiting Scientists

Matthew Lim, PhD
Young Park, PhD
Elba Serrano, PhD

Professor Emeritus

Gerald N. Wogan, PhD
Professor of Chemistry and Biological Engineering, Emeritus

 

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