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MIT Course Catalog 2014-2015

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Department of Biological Engineering

The mission of the Department of Biological Engineering (BE) is to educate next-generation leaders and to generate and translate new knowledge in a new bioscience-based engineering discipline fusing engineering analysis and synthesis approaches 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; how they respond when perturbed by factors such as medical therapeutics, environmental agents, and genetic variation; and how to manipulate and construct them toward beneficial use. Through this understanding, new technologies can be created to improve human health in a variety of medical applications, and biology-based paradigms can be generated to address many of the diverse challenges facing society across a broad spectrum, including energy, the environment, nutrition, and manufacturing.

The department's premise is that the science of biology is as important to the development of technology and society in the 21st century as physics and chemistry were in the 20th century, and that an increasing ability to measure, model, and manipulate properties of biological systems at the molecular, cellular, and multicellular 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 analytical 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 prosthetics, as well as for applications 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.

Students are encouraged to take the sophomore fall-term subject 20.110 Thermodynamics of Biomolecular Systems. This subject also fulfills an SB degree requirement in Biology. Alternatively, sophomores, or freshmen with advanced standing may take the spring-term 20.111 Physical Chemistry of Biomolecular Systems. Students are also encouraged to take Organic Chemistry I and Differential Equations during their sophomore year in order to prepare for the introductory biological engineering laboratory subject 20.109 that provides context for the lecture subjects and a strong foundation for subsequent undergraduate research in biological engineering through Undergraduate Research Opportunities 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 six thematic areas: systems biology, synthetic biology, biophysics, 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
1.089 Environmental Microbiology
5.07 Biological Chemistry I
7.05 General Biochemistry
7.06 Cell Biology
7.28 Molecular Biology
22.01 Introduction to Ionizing Radiation

 

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, the Whitehead Institute for Biomedical Research, and the Broad Institute, 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.

For both tracks, the written part of the doctoral qualifying examinations—centered on the respective 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. A total of approximately five years in residence is needed to complete the doctoral thesis and other degree requirements.

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 biochemistry has not been taken previously, 7.51 should be selected and will count as one of these graduate-level subjects. If cell biology has not been taken previously, 7.06 should be selected but will not count as one of these graduate-level subjects. In addition, one graduate-level subject from a restricted set of Biological Engineering offerings beyond the core classes, and one additional engineering or science graduate-level subject, are required as electives.

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 systems and synthetic biology, 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. If biochemistry has not been taken previously, 7.51 should be selected and will count as one of these graduate-level subjects. If cell biology has not been taken previously, 7.06 should be selected but will not count as one of these graduate-level subjects. In addition, one graduate-level subject from a restricted set of Biological Engineering offerings beyond the core classes, and one additional engineering or science graduate-level subject, are required as electives.

The applied biosciences track complements the bioengineering track 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 systems and synthetic biology, 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 the BE Academic Office, Room 56-651, be-acad@mit.edu.

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.

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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 six-month internship comprising a research project at one of LGO's partner companies leads to a dual-degree thesis, culminating in two master's degrees—an MBA (or SM in management) and an SM from one of seven MIT engineering programs, some of which have optional or required LGO tracks. For more information, visit http://lgo.mit.edu/.

Faculty and Staff

Faculty and Teaching Staff

Douglas A. Lauffenburger, PhD
Ford Professor of Biological Engineering, Chemical Engineering, and Biology
Department Head

Bruce Tidor, PhD
Professor of Biological Engineering and Electrical Engineering and Computer Science
Associate Department Head

Professors

Angela M. Belcher, PhD
W. M. Keck Professor of Energy, Materials Science and Engineering, and Biological Engineering

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

Arup K. Chakraborty, PhD
Robert T. Haslam (1911) Professor of Chemical Engineering
Professor of Chemistry, Biological Engineering, and Physics
Director, Institute of Medical Engineering and Science

Peter C. Dedon, PhD, MD
Professor of Toxicology and Biological Engineering
Deputy Director, Center for Environmental Health Sciences

Edward F. DeLong, PhD
Martin and Claire Goulder Professor of Civil and Environmental Engineering and Biological Engineering

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

Bevin P. Engelward, DSc
Professor of Biological Engineering

John Martin Essigmann, PhD
William and Betsy Leitch Professor in Residence
Professor of Chemistry, Toxicology, and Biological Engineering
Director, Center for Environmental Health Sciences

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

Linda Griffith, PhD
School of Engineering Professor of Teaching Innovation
Professor of Biological and Mechanical Engineering
Director, Center for Gynepathology Research
MacVicar Faculty Fellow

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

Jongyoon Han, PhD
Professor of Electrical and Biological Engineering

Darrell J. Irvine, PhD
Professor of Biological Engineering and Materials Science
Howard Hughes Medical Institute Investigator
Director, Program in Polymer Science and Technology

Roger D. Kamm, PhD
Cecil and Ida Green Distinguished Professor of Biological and Mechanical Engineering
Director, Center for Emergent Behavior of Integrated Cellular Systems

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

Robert S. Langer, ScD
David H. Koch Institute Professor

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

Scott R. Manalis, PhD
Professor of Biological and Mechanical Engineering, and Media Arts and Sciences

Leona D. Samson, PhD
Professor of Toxicology, Biological Engineering, and Biology

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

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

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

William G. Thilly, ScD
Professor of Toxicology

Christopher A. Voigt, PhD
Professor of Biological Engineering
Codirector, Center for Integrative Synthetic Biology
Associate Member, Broad Institute

Ron Weiss, PhD
Professor of Biological Engineering and Computer Science
Director, Center of Integrative Sythetic Biology

Forest White, PhD
Professor of Biological Engineering

K. Dane Wittrup, PhD
Carbon P. Dubbs Professor of Chemical Engineering and Biological Engineering
Associate Director, Koch Institute for Integrative Cancer Research

Michael B. Yaffe, PHD
Professor of Biology and Biological Engineering
Senior Associate Member, Broad Institute

Ioannis V. Yannas, PhD
Professor of Mechanical and Biological Engineering

Associate Professors

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

Mark Bathe, PhD
Associate Professor of Biological and Mechanical Engineering
Associate Member, Broad Institute

Edward S. Boyden III, PhD
AT&T Career Development Associate Professor of Research and Education
Associate Professor of Media Arts and Sciences, Biological Engineering, and Brain and Cognitive Sciences
Associate Member, Broad Institute

Ernest Fraenkel, PhD
Associate Professor of Biological Engineering
Associate Member, Broad Institute

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

Timothy K. Lu, MD, PhD
Associate Professor of Electrical Engineering and Computer Science and Biological Engineering
Associate Member, Broad Institute

Jacquin C. Niles, PhD, MD
Associate Professor of Biological Engineering

Krystyn Van Vliet, PhD
Paul M. Cook Associate Professor of Materials Science and Engineering and Biological Engineering

Mehmet Fatih Yanik, PhD
Associate Professor of Electrical Engineering and Biological Engineering
Associate Member, Broad Institute

Assistant Professors

Paul Blainey, PhD
Assistant Professor of Biological Engineering
Core Member, Broad Institute

Angela Koehler, PhD
Assistant Professor of Biological Engineering
Associate Member, Broad Institute

Katharina Ribbeck, PhD
Assistant Professor of Biological Engineering

Jonathan Runstadler, DVM
Assistant Professor of Biological Engineering
Associate Member, Broad Institute

Feng Zhang, PhD
Assistant Professor of Brain and Cognitive Sciences and Biological Engineering
Core Member, Broad Institute

Lecturers and Instructors

Noubar Afeyan, PhD
Shannon Hughes, PhD
Maxine Jonas, PhD
Natalie Kuldell, PhD
Mark Murcko, PhD
Steven Nagle, PhD
John Pierce, PhD
Agi Stachowiak, PhD
Steve Wasserman, SM
Alexander Wood, PhD

Research Staff

Senior Research Scientist

John S. Wishnok, PhD

Research Scientists

Jennifer Calvo, PhD
Peter A. Carr, PhD
Murat Cirit, PhD
Robert G. Croy, PhD
Michael DeMott, PhD
Mohammad Reza Ebrahimkhani, PhD
David Gordon
Elena Gostjeva, PhD
Shannon Hughes, PhD
Ramesh Indrakanti, PhD
Vera Koledova, PhD
Rahul Raman, PhD
Vidya Subramanian, PhD
Nevin Summers, PhD
Kannan Tharakaraman, PhD

Theresa Ulrich, PhD
Scientific Program Manager

Dehua Zhao, PhD

Visiting Scientists

Amelia Bailey
Shelley Brown
Rebecca Carrier
Eduardo Fleischer
Emily Marie Florine
Eirini Kefalogianni
Paul Wayne Kopesky
Abigail Koppes
Thomas Long
Megan E. McBee
Rachel Elizabeth Miller
Stefano Perni
Polina Prokopovich
Samuel Senyo
Elba Elisha Serrano
Kathrynn D. Smith
Patrick Stern
Christopher Tape
Hadi Tavakoli Nia
Wen-Han Yu

Professor Emeritus

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

 

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