Department of Biological Engineeringcatalog.mit.edu/.../biological-engineering/biological-engineering.pdf · 21st century as physics and chemistry wer e in the 20th century, and that

DEPARTMENT OF BIOLOGICAL ENGINEERING


The mission of the Department of Biological Engineering (BE) isto educate next-generation leaders and to generate and translatenew knowledge in a new bioscience-based engineering disciplinefusing engineering analysis and synthesis approaches with modernmolecular-to-genomic biology. Combining quantitative, physical, andintegrative principles with advances in mechanistic molecular andcellular bioscience, biological engineering increases understandingof how biological systems function as both physical and chemicalmechanisms; how they respond when perturbed by factors such asmedical therapeutics, environmental agents, and genetic variation;and how to manipulate and construct them toward benecial use.Through this understanding, new technologies can be created toimprove human health in a variety of medical applications, andbiology-based paradigms can be generated to address many of thediverse challenges facing society across a broad spectrum, includingenergy, the environment, nutrition, and manufacturing.

The department's premise is that the science of biology is asimportant to the development of technology and society in the21st century as physics and chemistry were in the 20th century,and that an increasing ability to measure, model, and manipulateproperties of biological systems at the molecular, cellular, andmulticellular levels will continue to shape this development. Anew generation of engineers and scientists is learning to addressproblems through their ability to measure, model, and rationallymanipulate the technological and environmental factors aectingbiological systems. They are applying not only engineering principlesto the analytical understanding of how biological systems operate,especially when impacted by genetic, chemical, physical, infectious,or other interventions; but also a synthetic design perspectiveto creating biology-based technologies for medical diagnostics,therapeutics, and prosthetics, as well as for applications in diverseindustries beyond human health care.

Undergraduate Study

Bachelor of Science in Biological Engineering (Course 20)The Department of Biological Engineering (BE) (http://be.mit.edu)oers an undergraduate curriculum emphasizing quantitative,engineering-based analysis, design, and synthesis in the study ofmodern biology from the molecular to the systems level. Completionof the curriculum leads to the Bachelor of Science in BiologicalEngineering and prepares students for careers in diverse eldsranging from the pharmaceutical and biotechnology industries tomaterials, devices, ecology, and public health. Graduates of theprogram will be prepared to enter positions in basic research orproject-oriented product development, as well as graduate school orfurther professional study.

The required core curriculum includes a strong foundation inbiological and biochemical sciences, which are integrated with

quantitative analysis and engineering principles throughout theentire core. Students who wish to pursue the Bachelor of Sciencein Biological Engineering (http://catalog.mit.edu/degree-charts/biological-engineering-course-20) are encouraged to complete theBiology General Institute Requirement during their rst year andmay delay completion of Physics II until the fall term of sophomoreyear if necessary. The optional subject Introduction to BiologicalEngineering Design, oered during the spring term of the rst year,provides a framework for understanding the Biological EngineeringSB program.

Students are encouraged to take the sophomore fall-term subject20.110[J] Thermodynamics of Biomolecular Systems. This subjectalso fullls an SB degree requirement in Biology. Students arealso encouraged to take Organic Chemistry I and DierentialEquations during their sophomore year in order to prepare forthe introductory biological engineering laboratory subject thatprovides context for the lecture subjects and a strong foundationfor subsequent undergraduate research in biological engineeringthrough Undergraduate Research Opportunities Program projects orsummer internships.

The advanced subjects required in the junior and senior yearsintroduce additional engineering skills through lecture andlaboratory subjects and culminate in a senior design project. Theseadvanced subjects maintain the theme of molecular to systems–level analysis, design, and synthesis based on a strong integrationwith biology fundamentals. They also include a variety of restrictedelectives that allow students to develop expertise in one of sixthematic areas: systems biology, synthetic biology, biophysics,pharmacology/toxicology, cell and tissue engineering, and microbialsystems. Many of these advanced subjects are jointly taught withother departments in the School of Engineering or School of Scienceand may fulll degree requirements in other programs.

Minor in Biomedical EngineeringAn interdepartmental Minor in Biomedical Engineering (http://catalog.mit.edu/interdisciplinary/undergraduate-programs/minors/biomedical-engineering) is available to all undergraduate studentsoutside the BE (Course 20) major. See Interdisciplinary Programs(http://catalog.mit.edu/interdisciplinary/undergraduate-programs/minors/biomedical-engineering) for detailed information.

Minor in Toxicology and Environmental HealthThe Department of Biological Engineering oers an undergraduateMinor in Toxicology and Environmental Health. The goal of thisprogram is to meet the growing demand for undergraduates toacquire the intellectual tools needed to understand and assess theimpact of new products and processes on human health, and toprovide a perspective on the risks of human exposure to syntheticand natural chemicals, physical agents, and microorganisms.

Given the importance of environmental education at MIT, theprogram is designed to be accessible to any MIT undergraduate.The program consists of three required didactic core subjects

Department of Biological Engineering | 3


and one laboratory subject, as well as one restricted elective. Theprerequisites for the core subjects are 5.111 /5.112 Principles ofChemical Science or 3.091 Introduction to Solid-State Chemistry plusIntroductory Biology (7.012 / 7.013 / 7.014 / 7.015 / 7.016).

Core Subjects20.102 Metakaryotic Stem Cells in

Carcinogenesis: Origins and Cures12

20.104[J] Environmental Cancer Risks,Prevention, and Therapy

12

20.106[J] Applied Microbiology 12Laboratory CoreSelect one of the following: 12-18

5.310 Laboratory Chemistry20.109 Laboratory Fundamentals in

Biological Engineering7.002& 7.003[J]

Fundamentals of ExperimentalMolecular Biologyand Applied Molecular BiologyLaboratory

Restricted ElectivesSelect one of the following: 12

1.080 Environmental Chemistry1.089 Earth's Microbiomes5.07[J] Introduction to Biological Chemistry7.05 General Biochemistry7.06 Cell Biology7.28 Molecular Biology20.URG Undergraduate Research

Opportunities22.01 Introduction to Nuclear Engineering

and Ionizing Radiation

Total Units 60-66

InquiriesFor further information on the undergraduate programs, see theBiological Engineering website (http://be.mit.edu) or contact the BEAcademic Oce ([email protected]), Room 16-267, 617-452-2465.

Graduate Study

Master of Engineering in Biomedical EngineeringThe Master of Engineering in Biomedical Engineering (MEBE)program is a ve-year program leading to a bachelor's degree in ascience or engineering discipline along with a Master of Engineeringin Biomedical Engineering. The program emphasizes the fusion ofengineering with modern molecular-to-genomic biology, as in ourSB and PhD degree programs. Admission to the MEBE program isopen only to MIT undergraduate students, and requires candidates

to demonstrate adequate quantitative and engineering credentialsthrough their undergraduate coursework.

In addition to satisfying the requirements of their departmentalprogram, candidates also are expected to complete the following:

18.03 Dierential Equations 125.12 Organic Chemistry I 125.07[J] Introduction to Biological Chemistry 12

or 7.05 General BiochemistrySelect one of the following: 12

2.005 Thermal-Fluids Engineering I6.002 Circuits and Electronics

Select two of the following: 241.010 Probability and Causal Inference2.086 Numerical Computation for

Mechanical Engineers6.041 Introduction to Probability18.05 Introduction to Probability and

Statistics

Applications to the MEBE program are accepted from students inany of the departments in the School of Engineering or Schoolof Science. Students interested in applying to the MEBE programshould submit a standard MIT graduate application by the end oftheir junior year; they are informed of the decision by the end of thatsummer.

Additional information on application procedures, objectives,and program requirements can be obtained by contacting the BEAcademic Oce ([email protected]), Room 16-127.

Program RequirementsIn addition to thesis credits, at least 66 units of coursework arerequired. At least 42 of these subject units must be from graduatesubjects. The remaining units may be satised, in some cases, withadvanced undergraduate subjects that are not requirements in MIT'sundergraduate curriculum. Of the 66 units, a minimum distribution ineach of three categories is specied below.

Bioengineering CoreSelect two of the following: 24

20.410[J] Molecular, Cellular, and TissueBiomechanics

20.420[J] Principles of MolecularBioengineering

20.430[J] Fields, Forces, and Flows inBiological Systems

Biomedical Engineering ElectivesSelect 24 units from a selection of graduatesubjects from various departments in the School ofEngineering, including HST. 1

24

4 | Department of Biological Engineering


Bioscience ElectiveSelect one biological science subject in addition toorganic chemistry and biochemistry. This must be alaboratory subject if one was not taken as part of thestudent’s undergraduate curriculum

18

Total Units 66

1 A list of suggested subjects is available from the BE Academic Oce ([email protected]), Room 16-267.

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

Doctoral Program in Biological EngineeringThe Department of Biological Engineering oers a PhD program and,in certain cases, an SM degree. Graduate students in the Departmentof Biological Engineering can carry out their research as part of anumber of multi-investigator, multidisciplinary research centers atMIT, including the Center for Biomedical Engineering, the Center forEnvironmental Health Sciences (http://catalog.mit.edu/mit/research/center-environmental-health-sciences), the Division of ComparativeMedicine (http://catalog.mit.edu/mit/research/division-comparative-medicine), and the Synthetic Biology Engineering Research Center(http://www.synberc.org). These opportunities include collaborationwith faculty in the Schools of Engineering (http://catalog.mit.edu/schools/engineering) and Science (http://catalog.mit.edu/schools/science), the Koch Institute for Integrative Cancer Research (http://catalog.mit.edu/mit/research/koch-institute-integrative-cancer-research), the Whitehead Institute for Biomedical Research (http://catalog.mit.edu/mit/research/whitehead-institute-biomedical-research), and the Broad Institute (http://catalog.mit.edu/mit/research/broad-institute), along with the Harvard University Schoolof Medicine, Harvard University School of Dental Medicine, HarvardSchool of Public Health, and Boston University School of Medicine.

The Biological Engineering graduate program educates studentsto use engineering principles in the analysis and manipulationof biological systems, allowing them to solve problems across aspectrum of important applications. The curriculum is inherentlyinterdisciplinary in that it brings together engineering and biologyas fundamentally as possible and cuts across the boundaries of thetraditional engineering disciplines.

The written part of the doctoral qualifying examinations—focusedon the core curriculum—is taken aer the second term. The studentselects a research advisor, typically by the start of the spring term inthe rst year, and begins research before the end of that year. Theoral part of the doctoral qualifying examinations, which focuses onthe student's area of research, is taken prior to December 1 of the

third year. A total of approximately ve years in residence is neededto complete the doctoral thesis and other degree requirements.

Students admitted to the Biological Engineering graduate programtypically have a bachelor's or master's degree in science orengineering. Foundational coursework in biochemistry andmolecular cell biology is required, either prior to admission orduring the rst year of graduate study. Students who have not takenbiochemistry previously should take 7.05 General Biochemistry or5.07[J] Introduction to Biological Chemistry, and those who have nottaken cell biology previously should take 7.06 Cell Biology, prior totaking the core classes. During their rst year, students pursue aunied core curriculum in which engineering approaches are usedto analyze biological systems and technologies over a wide range oflength and time scales. The subjects in the unied core bring centralengineering principles to bear on the operation of biological systemsfrom molecular to cell to tissue/organ/device systems levels. Theseare then supplemented by electives in the biological sciences andengineering to enhance breadth and depth.

Core20.420[J] Principles of Molecular

Bioengineering12

20.440 Analysis of Biological Networks(Electives)

15

ElectivesOne graduate subject in biological science oered bythe Department of BiologyOne graduate subject from a restricted set ofBiological Engineering oerings beyond the coresubjectsOne graduate subject in Biological EngineeringOne additional graduate engineering or sciencesubject

Faculty members associated with the program possess a widerange of research interests. Areas in which students mayspecialize include systems and synthetic biology; biologicaland physiological transport phenomena; biological imaging andfunctional measurement; biomolecular engineering; cell andtissue engineering; computational modeling of biological andphysiological systems; bioinformatics; design, discovery, anddelivery of molecular therapeutics; molecular, cell, and tissuebiomechanics; development of in vitro models of the immunesystem and lymphoid tissue; development of molecular methodsfor direct measurement of mutations in humans; metabolism offoreign compounds; genetic toxicology; the molecular aspects anddosimetry of interactions between mutagens and carcinogens withnucleic acids and proteins; molecular mechanisms of DNA damageand repair; design and mechanisms of action of chemotherapeuticagents; environmental carcinogenesis and epidemiology; molecularmechanisms of carcinogenesis; cell physiology; extracellularregulation and signal transduction; molecular and pathologic



interactions between infectious microbial agents and carcinogens;and new tools for genomics, proteomics, and glycomics.

Interdisciplinary Programs

Leaders for Global OperationsThe 24-month Leaders for Global Operations (LGO) (http://lgo.mit.edu) program combines graduate degrees in engineering andmanagement for those with previous postgraduate work experienceand strong undergraduate degrees in a technical eld. During thetwo-year program, students complete a six-month internship at oneof LGO's partner companies, where they conduct research that formsthe basis of a dual-degree thesis. Students nish the program withtwo MIT degrees: an MBA (or SM in management) and an SM fromone of seven engineering programs, some of which have optionalor required LGO tracks. Aer graduation, alumni lead strategicinitiatives in high-tech, operations, and manufacturing companies.

Polymers and So MatterThe Program in Polymers and So Matter (PPSM) (http://polymerscience.mit.edu) oers students from participatingdepartments an interdisciplinary core curriculum in polymer scienceand engineering, exposure to the broader polymer communitythrough seminars, contact with visitors from industry and academia,and interdepartmental collaboration while working towards a PhD orScD degree.

Research opportunities include functional polymers, controlleddrug delivery, nanostructured polymers, polymers at interfaces,biomaterials, molecular modeling, polymer synthesis, biomimeticmaterials, polymer mechanics and rheology, self-assembly, andpolymers in energy. The program is described in more detail (http://catalog.mit.edu/interdisciplinary/graduate-programs/polymers-so-matter) under Interdisciplinary Graduate Programs.

InquiriesFor further information on the graduate programs, see the BiologicalEngineering website (http://be.mit.edu) or contact the BE AcademicOce ([email protected]), Room 16-267, 617-253-1712.

Faculty and Teaching Sta

Angela M. Belcher, PhDJames Mason Cras ProfessorProfessor of Biological EngineeringProfessor of Materials Science and EngineeringHead, Department of Biological Engineering

Scott R. Manalis, PhDAndrew (1956) and Erna Viterbi ProfessorProfessor of Biological EngineeringProfessor of Mechanical EngineeringAssociate Head, Department of Biological Engineering

ProfessorsEric J. Alm, PhDProfessor of Biological EngineeringProfessor of Civil and Environmental Engineering

Mark Bathe, PhDProfessor of Biological EngineeringProfessor of Mechanical Engineering

Edward S. Boyden III, PhDY. Eva Tan Professor in NeurotechnologyProfessor of Brain and Cognitive SciencesProfessor of Media Arts and SciencesProfessor of Biological Engineering

Laurie Boyer, PhDProfessor of BiologyProfessor of Biological Engineering

Christopher B. Burge, PhDProfessor of BiologyProfessor of Biological Engineering

James J. Collins, PhDTermeer Professor of Medical Engineering and ScienceProfessor of Biological EngineeringCore Faculty, Institute for Medical Engineering and Science

Peter C. Dedon, MD, PhDUnderwood-Prescott ProfessorProfessor of Toxicology and Biological Engineering

Bevin P. Engelward, DScProfessor of Biological Engineering

John M. Essigmann, PhDWilliam R. (1956) and Betsy P. Leitch Professor in ResidenceProfessor of Toxicology and Biological EngineeringProfessor of Chemistry(On leave, fall)

James G. Fox, DVMProfessor of Biological Engineering

Ernest Fraenkel, PhDProfessor of Biological Engineering

Linda G. Grith, PhDSchool of Engineering Professor of Teaching InnovationProfessor of Biological EngineeringProfessor of Mechanical Engineering

Alan J. Grodzinsky, ScDProfessor of Biological EngineeringProfessor of Electrical EngineeringProfessor of Mechanical Engineering



Jongyoon Han, PhDProfessor of Electrical EngineeringProfessor of Biological Engineering

Darrell J. Irvine, PhDProfessor of Biological EngineeringProfessor of Materials Science

Alan P. Jasano, PhDProfessor of Biological EngineeringProfessor of Nuclear Science and EngineeringProfessor of Brain and Cognitive Sciences

Roger Dale Kamm, PhDCecil H. Green Distinguished Professor Post-TenureProfessor Post-Tenure of Mechanical EngineeringProfessor Post-Tenure of Biological Engineering

Amy E. Keating, PhDProfessor of BiologyProfessor of Biological Engineering

Robert Langer, ScDDavid H. Koch (1962) Institute ProfessorProfessor of Chemical EngineeringProfessor of Mechanical EngineeringProfessor of Biological EngineeringAliate Faculty, Institute for Medical Engineering and Science

Douglas A. Lauenburger, PhDFord Foundation ProfessorProfessor of Biological EngineeringProfessor of Chemical EngineeringProfessor of Biology

Harvey F. Lodish, PhDProfessor of BiologyProfessor of Biological Engineering

Jacquin Niles, MD, PhDProfessor of Biological Engineering

Ram Sasisekharan, PhDAlfred H. Caspary ProfessorProfessor of Biological Engineering

Peter T. C. So, PhDProfessor of Biological EngineeringProfessor of Mechanical Engineering

Steven R. Tannenbaum, PhDUnderwood-Prescott Professor Post-TenureProfessor Post-Tenure of Toxicology and Biological EngineeringProfessor Post-Tenure of Chemistry

William G. Thilly, ScDProfessor of Biological Engineering

Bruce Tidor, PhDProfessor of Electrical Engineering and Computer ScienceProfessor of Biological Engineering

Krystyn J. Van Vliet, PhDMichael (1949) and Sonja Koerner Professor of Materials Science and

EngineeringProfessor of Biological EngineeringAssociate Provost

Christopher A. Voigt, PhDWang ProfessorProfessor of Biological Engineering

Ron Weiss, PhDProfessor of Biological Engineering

Forest M. White, PhDNed C. and Janet Bemis Rice ProfessorProfessor of Biological Engineering

Karl Dane Wittrup, PhDCarbon P. Dubbs Professor of Chemical EngineeringProfessor of Biological Engineering

Michael B. Yae, MD, PhDDavid H. Koch Professor in ScienceProfessor of BiologyProfessor of Biological Engineering

Feng Zhang, PhDJames and Patricia Poitras (1963) Professor of NeuroscienceProfessor of Biological Engineering

Associate ProfessorsPaul C. Blainey, PhDAssociate Professor of Biological Engineering(On leave, spring)

Angela N. Koehler, PhDSamuel Goldblith Career Development ProfessorAssociate Professor of Biological Engineering

Timothy K. Lu, MD, PhDAssociate Professor of Electrical EngineeringAssociate Professor of Biological Engineering

Katharina Ribbeck, PhDMark Hyman, Jr. Career Development Professor of Tissue EngineeringAssociate Professor of Biological Engineering

Assistant ProfessorsMichael Birnbaum, PhDAssistant Professor of Biological Engineering



Bryan Bryson, PhDEsther and Harold Edgerton Career Development ProfessorAssistant Professor of Biological Engineering

Anders Hansen, PhDUnderwood-Prescott Career Development ProfessorAssistant Professor of Biological Engineering

InstructorsJustin Buck, PhDInstructor of Biological Engineering

Sean Aidan Clarke, PhDInstructor of Biological Engineering

Maxine Jonas, PhDInstructor of Biological Engineering

Prerna Bhargava Saluja, PhDInstructor of Biological Engineering

Steven Wasserman, MSLaboratory Instructor of Biological Engineering

Technical InstructorsNoreen L. Lyell, PhDTechnical Instructor of Biological Engineering

Leslie Marie McClain, PhDTechnical Instructor of Biological Engineering

Rebecca Meyer, PhDTechnical Instructor of Biological Engineering

Research Sta

Principal Research EngineersEliot Frank, PhDPrincipal Research Engineer of Biological Engineering

Research EngineersMark Coughlin, PhDResearch Engineer of Biological Engineering

Research ScientistsSupawadee Chawanthayatham, PhDResearch Scientist of Biological Engineering

Swapnil Chhabra, PhDResearch Scientist of Biological Engineering

Robert G. Croy, PhDResearch Scientist of Biological Engineering

Michael S. DeMott, PhDResearch Scientist of Biological Engineering

Yuval Dorfan, PhDResearch Scientist of Biological Engineering

Katya Frois-Moniz, PhDResearch Scientist of Biological Engineering

Benjamin Garcia, PhDResearch Scientist of Biological Engineering

David B. Gordon, PhDResearch Scientist of Biological Engineering

Elena V. Gostjeva, PhDResearch Scientist of Biological Engineering

Jin Hang Huh, PhDResearch Scientist of Biological Engineering

Erez Pery, PhDResearch Scientist of Biological Engineering

Jifa Qi, PhDResearch Scientist of Biological Engineering

Rahul Raman, PhDResearch Scientist of Biological Engineering

Vidya Subramanian, PhDResearch Scientist of Biological Engineering

John Wishnok, PhDResearch Scientist of Biological Engineering

Yu-Xin Xu, PhDResearch Scientist of Biological Engineering

Professors Emeriti

C. Forbes Dewey Jr, PhDProfessor Emeritus of Mechanical EngineeringProfessor Emeritus of Biological Engineering

Alexander M. Klibanov, PhDNovartis Professor EmeritusProfessor Emeritus of ChemistryProfessor Emeritus of Bioengineering

Leona D. Samson, PhDUncas (1923) and Helen Whitaker Professor EmeritaProfessor Emerita of Biological EngineeringProfessor Emerita of Biology

Gerald N. Wogan, PhDProfessor Emeritus of Biological EngineeringProfessor Emeritus of Chemistry



20.001 Introduction to Professional Success and Leadership inBiological EngineeringPrereq: NoneU (Fall)1-0-2 units

Interactive introduction to the discipline of Biological Engineeringthrough presentations by alumni practitioners, with additionalpanels and discussions on skills for professional development.Presentations emphasize the roles of communication through writingand speaking, building and maintaining professional networks, andinterpersonal and leadership skills in building successful careers.Provides practical advice about how to prepare for job searchesand graduate or professional school applications from an informedviewpoint. Prepares students for UROPs, internships, and selectionof BE electives. Subject can count toward the 9-unit discovery-focused credit limit for rst-year students.L. Grith

20.005 Ethics for EngineersSubject meets with 1.082[J], 2.900[J], 6.9041, 6.904[J], 10.01[J],16.676[J], 22.014[J]Prereq: NoneU (Fall, Spring)2-0-7 units

Explores the ethical principles by which an engineer ought to beguided. Integrates foundational texts in ethics with case studiesillustrating ethical problems arising in the practice of engineering.Readings from classic sources including Aristotle, Kant, Locke,Bacon, Franklin, Tocqueville, Arendt and King. Case studies includearticles and lms that address engineering disasters, safety,biotechnology, the internet and AI, and the ultimate scope andaims of engineering. Dierent sections may focus on themes,such as AI or biotechnology. Students taking independent inquiryversion 6.9041 expand the scope of their term project. Studentstaking 20.005 focus their term project on a problem in biologicalengineering in which there are intertwined ethical and technicalissues. In person not required. Limited to 18 per section.D. Lauenburger, B. L. Trout

20.020 Introduction to Biological Engineering Design UsingSynthetic BiologySubject meets with 20.385Prereq: NoneU (Spring)Not oered regularly; consult department3-3-3 units

Project-based introduction to the engineering of synthetic biologicalsystems. Throughout the term, students develop projects that areresponsive to real-world problems of their choosing, and whosesolutions depend on biological technologies. Lectures, discussions,and studio exercises will introduce components and control ofprokaryotic and eukaryotic behavior; DNA synthesis, standards, andabstraction in biological engineering; and issues of human practice,including biological safety, security, ethics, and ownership, sharing,and innovation. Preference to freshmen.N. Kuldell

20.051 Introduction to NEET: Living MachinesPrereq: Biology (GIR), Calculus II (GIR), Chemistry (GIR), and PhysicsI (GIR)U (Spring)2-3-1 units

Focuses on physiomimetics: transforming therapeutic strategy anddevelopment. Overview of development of therapies for complexdiseases, including disease mechanisms in heterogeneous patientpopulations, developing therapeutic strategies, modeling thesein vitro, and testing the therapies. Explores the ve essentialtechnological contributions to this process: computational systemsbiology, synthetic biology, immuno-engineering, microphysiologicalsystems devices/tissue engineering, and device engineering for invitro models and analysis. Introduces disease modeling, patientstratication, and drug development processes, includes extensiveexamples from industry, and provides context for choosing aconcentration track in the Living Machines thread. Weekly lecturesfrom experts in the eld supplemented with structured, shortprojects in each topic area. Preference to students in the NEET LivingMachines thread; open to others with permission of instructor.L. Grith, E. Alm, M. Salek

20.052 NEET Junior Seminar: Living MachinesPrereq: NoneU (Fall, Spring)6-0-6 units

Seminar spanning fall and spring terms for juniors enrolled in theLiving Machines New Engineering Education Transformation (NEET)thread. Focuses on topics around "body-on-a-chip" technology viaguest lectures and research discussions.E. Alm, L. Grith, T. Kassis



20.053 NEET Senior Seminar: Living MachinesPrereq: NoneU (Fall, Spring)6-0-6 units

Seminar spanning fall and spring terms for seniors enrolled in theLiving Machines New Engineering Education Transformation (NEET)thread. Focuses on topics around "body-on-a-chip" technology viaguest lectures and research discussions.E. Alm, L. Grith, T. Kassis

20.054 NEET - Living Machines Research Immersion (New)Prereq: 20.051U (Fall, Spring)Units arrangedCan be repeated for credit.

A structured lab research experience in a specic Living Machinestrack. Students identify a project in a participating research lab, on atopic related to the ve tracks in the NEET Living Machines program,propose a project related to the drug development theme, andprepare interim and nal presentations and reports while conductingthe project. Links to industry-sponsored research projects at MIT areencouraged. Project proposal must be submitted and approved inthe term prior to enrollment. Limited to students in the NEET LivingMachines thread.L. Grith, E. Alm, M. Salek

20.101 Metakaryotic Biology and EpidemiologySubject meets with 20.A02Prereq: NoneU (Fall)2-0-4 units

Introduces non-eukaryotic, "metakaryotic" cells with hollow bell-shaped nuclei that serve as the stem cells of human fetal/juvenilegrowth and development as well as of tumors and atheroscleroticplaques. Studies the relationship of lifetime growth and mutationsof metakaryotic stem cells to age-specic death rates. Considers thebiological bases of treatment protocols found to kill metakaryoticcancer stem cells in vitro and in human pancreatic cancers in vivo.W. G. Thilly

20.102 Metakaryotic Stem Cells in Carcinogenesis: Origins andCuresSubject meets with 20.215Prereq: Biology (GIR), Calculus II (GIR), and Chemistry (GIR)U (Fall)3-0-9 units

Metakaryotic stem cells of organogenesis, wound healing, andthe pathogenic lesions of cancers and atherosclerotic plaques.Metakaryotic cell resistance to x-ray- and chemo-therapies. Commondrug treatment protocols lethal to metakaryotic cancer stem cellsin vivo rst clinical trial against pancreatic cancer. Application of ahypermutable/mutator stem cell model to the age-specic mortalityfrom clonal diseases, and the expected responses to metakaryocidaldrugs in attempted cure and prevention of tumors or atheroscleroticplaques. Students taking 20.215 responsible for de novo computermodeling.E. V. Gostjeva, W. G. Thilly

20.104[J] Environmental Cancer Risks, Prevention, and TherapySame subject as 1.081[J]Prereq: Biology (GIR), Calculus II (GIR), and Chemistry (GIR)U (Spring)3-0-9 units

Analysis of the history of cancer and vascular disease mortalityrates in predominantly European- and African-American US cohorts,1895-2016, to discover specic historical shis. Explored in termsof contemporaneously changing environmental risk factors: air-,food- and water-borne chemicals; subclinical infections; diet andlifestyles. Special section on occupational risk factors. Considersthe hypotheses that genetic and/or environmental factors aectmetakaryotic stem cell mutation rates in fetuses and juveniles and/or their growth rates of preneoplastic in adults.W. Thilly, R. McCunney

20.106[J] Applied MicrobiologySame subject as 1.084[J]Prereq: Biology (GIR) and Chemistry (GIR)Acad Year 2020-2021: Not oeredAcad Year 2021-2022: U (Fall)3-0-9 units

Introductory microbiology from a systems perspective - considersmicrobial diversity and the integration of data from a molecular,cellular, organismal, and ecological context to understand theinteraction of microbial organisms with their environment. Specialemphasis on specic viral, bacterial, and eukaryotic microorganismsand their interaction with animal hosts with focus on contemporaryproblems in areas such as vaccination, emerging disease,antimicrobial drug resistance, and toxicology.J. C. Niles, K. Ribbeck



20.109 Laboratory Fundamentals in Biological EngineeringPrereq: Biology (GIR), Chemistry (GIR), 6.0002, 18.03, and 20.110[J]U (Fall, Spring)2-8-5 units. Institute LAB

Introduces experimental biochemical and molecular techniquesfrom a quantitative engineering perspective. Experimentaldesign, data analysis, and scientic communication form theunderpinnings of this subject. In this, students complete discovery-based experimental modules drawn from current technologies andactive research projects of BE faculty. Generally, topics includeDNA engineering, in which students design, construct, and usegenetic material; parts engineering, emphasizing protein designand quantitative assessment of protein performance; systemsengineering, which considers genome-wide consequences of geneticperturbations; and biomaterials engineering, in which studentsuse biologically-encoded devices to design and build materials.Enrollment limited; priority to Course 20 majors.N. Lyell, A. Koehler, B. Engelward, L. McClain, B. Meyer, S. Clarke, P.Bhargava

20.110[J] Thermodynamics of Biomolecular SystemsSame subject as 2.772[J]Prereq: (Biology (GIR), Calculus II (GIR), Chemistry (GIR), and PhysicsI (GIR)) or permission of instructorU (Fall)5-0-7 units. REST

Equilibrium properties of macroscopic and microscopic systems.Basic thermodynamics: state of a system, state variables. Work,heat, rst law of thermodynamics, thermochemistry. Second andthird law of thermodynamics: entropy and its statistical basis, Gibbsfunction. Chemical equilibrium of reactions in gas and solutionphase. Macromolecular structure and interactions in solution.Driving forces for molecular self-assembly. Binding cooperativity,solvation, titration of macromolecules.M. Birnbaum, C. Voigt

20.129[J] Biological Circuit Engineering Laboratory (New)Same subject as 6.129[J]Prereq: Biology (GIR) and Calculus II (GIR)U (Spring)2-8-2 units. Institute LAB

Students assemble individual genes and regulatory elementsinto larger-scale circuits; they experimentally characterize thesecircuits in yeast cells using quantitative techniques, including flowcytometry, and model their results computationally. Emphasizesconcepts and techniques to perform independent experimentaland computational synthetic biology research. Discusses currentliterature and ongoing research in the eld of synthetic biology.Instruction and practice in oral and written communication provided.Enrollment limited.T. Lu, R. Weiss

20.200 Biological Engineering SeminarPrereq: Permission of instructorG (Fall, Spring)1-0-2 unitsCan be repeated for credit.

Weekly one-hour seminars covering graduate student research andpresentations by invited speakers. Limited to BE graduate students.B. Engelward

20.201 Fundamentals of Drug DevelopmentPrereq: Permission of instructorG (Fall, Spring)4-0-8 units

Team-based exploration of the scientic basis for developingnew drugs. First portion of term covers fundamentals oftarget identication, drug discovery, pharmacokinetics,pharmacodynamics, regulatory policy, and intellectual property.Industry experts and academic entrepreneurs then present casestudies of specic drugs, drug classes, and therapeutic targets. Ina term-long project, student teams develop novel therapeutics tosolve major unmet medical needs, with a trajectory to a "start-up"company. Culminates with team presentations to a panel of industryand scientic leaders.P. C. Dedon, R. Sasisekharan



20.202 In vivo Models: Principles and PracticesPrereq: Permission of instructorAcad Year 2020-2021: G (Spring)Acad Year 2021-2022: Not oered1-1-4 units

Selected aspects of anatomy, histology, immuno-cytochemistry,in situ hybridization, physiology, and cell biology of mammalianorganisms and their pathogens. Subject material integrated withprinciples of toxicology, in vivo genetic engineering, and molecularbiology. A lab/demonstration period each week involves experimentsin anatomy (in vivo), physiology, and microscopy to augment thelectures. Oered rst half of spring term.J. G. Fox, B. Marini, M. Whary

20.203[J] Neurotechnology in ActionSame subject as 9.123[J]Prereq: Permission of instructorG (Spring)3-6-3 units

See description under subject 9.123[J].E. Boyden, M. Jonas

20.205[J] Principles and Applications of Genetic Engineering forBiotechnology and NeuroscienceSame subject as 9.26[J]Prereq: Biology (GIR)U (Spring)3-0-9 units

See description under subject 9.26[J].F. Zhang

20.213 Genome Stability and Engineering in the Context ofDiseases, Drugs, and Public HealthPrereq: 5.07[J], 7.05, or permission of instructorU (Spring; second half of term)4-0-5 units

Studies how DNA damage leads to diseases, and how DNA repairmodulates cancer risk and treatment. Also covers how DNA repairimpacts genetic engineering, whether by targeted gene therapyor CRISPR-mediated genetic changes. Students gain a publichealth perspective by examining how DNA-damaging agents in ourenvironment can lead to downstream cancer. Explores the underlyingchemical, molecular and biochemical processes of DNA damageand repair, and their implications for disease susceptibility andtreatment.B. P. Engelward

20.215 Macroepidemiology, Population Genetics, and Stem CellBiology of Human Clonal DiseasesSubject meets with 20.102Prereq: Calculus II (GIR) and 1.00G (Fall)3-0-15 units

Studies the logic and technology needed to discover genetic andenvironmental risks for common human cancers and vasculardiseases. Includes an introduction to metakaryotic stem cell biology.Analyzes large, organized historical public health databases usingquantitative cascade computer models that include populationstratication of stem cell mutation rates in fetal/juvenile tissues andgrowth rates in preneoplastic colonies and atherosclerotic plaques.Means to test hypotheses (CAST) that certain genes carry mutationsconferring risk for common cancers via genetic analyses in largehuman cohorts. Involves de novo computer modelingof a lifetime disease experience or test of a student-developedhypothesis.W. G. Thilly

20.219 Selected Topics in Biological EngineeringPrereq: Permission of instructorG (Fall, Spring)Units arrangedCan be repeated for credit.

Detailed discussion of selected topics of current interest. Classworkin various areas not covered by regular subjects.Sta

20.230[J] ImmunologySame subject as 7.23[J]Subject meets with 7.63[J], 20.630[J]Prereq: 7.06U (Spring)5-0-7 units

See description under subject 7.23[J].S. Spranger, M. Birnbaum

20.260 Computational Analysis of Biological DataPrereq: Permission of instructorU (Spring; second half of term)3-0-3 units

Presents foundational methods for analysis of complex biologicaldatasets. Covers fundamental concepts in probability, statistics, andlinear algebra underlying computational tools that enable generationof biological insights. Assignments focus on practical examplesspanning basic science and medical applications. Assumes basicknowledge of calculus and programming.E. Alm, D. Lauenburger



20.305[J] Principles of Synthetic BiologySame subject as 6.580[J]Subject meets with 6.589[J], 20.405[J]Prereq: NoneU (Fall)3-0-9 units

Introduces the basics of synthetic biology, including quantitativecellular network characterization and modeling. Considers thediscovery and genetic factoring of useful cellular activities intoreusable functions for design. Emphasizes the principles ofbiomolecular system design and diagnosis of designed systems.Illustrates cutting-edge applications in synthetic biology andenhances skills in analysis and design of synthetic biologicalapplications. Students taking graduate version complete additionalassignments.R. Weiss

20.309[J] Instrumentation and Measurement for BiologicalSystemsSame subject as 2.673[J]Subject meets with 20.409Prereq: (Biology (GIR), Physics II (GIR), 6.0002, and 18.03) orpermission of instructorU (Fall, Spring)3-6-3 units

Sensing and measurement aimed at quantitative molecular/cell/tissue analysis in terms of genetic, biochemical, and biophysicalproperties. Methods include light and fluorescence microscopies,and electro-mechanical probes (atomic force microscopy, opticaltraps, MEMS devices). Application of statistics, probability, signaland noise analysis, and Fourier techniques to experimental data.Enrollment limited; preference to Course 20 undergraduates.P. Blainey, S. Manalis, E. Frank, S. Wasserman, J. Bagnall, E. Boyden,P. So

20.310[J] Molecular, Cellular, and Tissue BiomechanicsSame subject as 2.797[J], 3.053[J], 6.024[J]Prereq: Biology (GIR), (2.370 or 20.110[J]), and (3.016B or 18.03)U (Spring)4-0-8 units

Develops and applies scaling laws and the methods of continuummechanics to biomechanical phenomena over a range of lengthscales. Topics include structure of tissues and the molecularbasis for macroscopic properties; chemical and electrical eectson mechanical behavior; cell mechanics, motility and adhesion;biomembranes; biomolecular mechanics and molecular motors.Experimental methods for probing structures at the tissue, cellular,and molecular levels.M. Bathe, A. Grodzinsky

20.315 Physical BiologySubject meets with 20.415Prereq: 5.60, 20.110[J], or permission of instructorU (Spring)Not oered regularly; consult department3-0-9 unitsCredit cannot also be received for 8.241

Focuses on current major research topics in quantitative, physicalbiology. Covers synthetic structural biology, synthetic cell biology,microbial systems biology and evolution, cellular decision making,neuronal circuits, and development and morphogenesis. Emphasizescurrent motivation and historical background, state-of-the-artmeasurement methodologies and techniques, and quantitativephysical modeling frameworks. Experimental techniques includestructural biology, next-generation sequencing, fluorescenceimaging and spectroscopy, and quantitative biochemistry.Modeling approaches include stochastic rate equations, statisticalthermodynamics, and statistical inference. Students taking graduateversion complete additional assignments. 20.315 and 20.415 meetwith 8.241 when oered concurrently.J. Gore, I. Cisse

20.320 Analysis of Biomolecular and Cellular SystemsPrereq: 6.0002, 18.03, and 20.110[J]; Coreq: 5.07[J] or 7.05U (Fall)4-0-8 units

Analysis of molecular and cellular processes across a hierarchy ofscales, including genetic, molecular, cellular, and cell populationlevels. Topics include gene sequence analysis, molecular modeling,metabolic and gene regulation networks, signal transductionpathways and cell populations in tissues. Emphasis on experimentalmethods, quantitative analysis, and computational modeling.F. White, K. D. Wittrup

20.330[J] Fields, Forces and Flows in Biological SystemsSame subject as 2.793[J], 6.023[J]Prereq: Biology (GIR), Physics II (GIR), and 18.03U (Spring)4-0-8 units

Introduction to electric elds, fluid flows, transport phenomenaand their application to biological systems. Flux and continuitylaws, Maxwell's equations, electro-quasistatics, electro-chemical-mechanical driving forces, conservation of mass and momentum,Navier-Stokes flows, and electrokinetics. Applications includebiomolecular transport in tissues, electrophoresis, and microfluidics.J. Han, S. Manalis



20.334 Biological Systems ModelingPrereq: 20.330[J] or permission of instructorU (Fall; rst half of term)1-0-5 units

Practices the use of modern numerical analysis tools (e.g., COMSOL)for biological systems with multi-physics behavior. Covers modelingof diusion, reaction, convection and other transport mechanisms.Analysis of microfluidic devices as examples. Discusses practicalissues and challenges in numerical modeling. No prior knowledge ofmodeling soware required. Includes weekly modeling homeworkand one nal modeling project.J. Han

20.345[J] Bioinstrumentation Project LabSame subject as 6.123[J]Prereq: 20.309[J], (Biology (GIR) and (2.004 or 6.003)), or permissionof instructorU (Spring)2-7-3 units

In-depth examination of instrumentation design, principles andtechniques for studying biological systems, from single moleculesto entire organisms. Lectures cover optics, advanced microscopytechniques, electronics for biological measurement, magneticresonance imaging, computed tomography, MEMs, microfluidicdevices, and limits of detection. Students select two lab exercisesduring the rst half of the semester and complete a nal designproject in the second half. Lab emphasizes design process andskillful realization of a robust system. Enrollment limited; preferenceto Course 20 majors and minors.E. Boyden, M. Jonas, S. F. Nagle, P. So, S. Wasserman, M. F. Yanik

20.352 Principles of NeuroengineeringSubject meets with 9.422[J], 20.452[J], MAS.881[J]Prereq: Permission of instructorU (Fall)3-0-9 units

Covers how to innovate technologies for brain analysis andengineering, for accelerating the basic understanding of thebrain, and leading to new therapeutic insight and inventions.Focuses on using physical, chemical and biological principles tounderstand technology design criteria governing ability to observeand alter brain structure and function. Topics include optogenetics,noninvasive brain imaging and stimulation, nanotechnologies, stemcells and tissue engineering, and advanced molecular and structuralimaging technologies. Includes design projects. Students takinggraduate version complete additional assignments. Designed forstudents with engineering maturity who are ready for design.E. S. Boyden, III

20.361[J] Molecular and Engineering Aspects of BiotechnologySame subject as 7.37[J], 10.441[J]Prereq: (7.06 and (2.005, 3.012, 5.60, or 20.110[J])) or permission ofinstructorU (Spring)Not oered regularly; consult department4-0-8 unitsCredit cannot also be received for 7.371

See description under subject 7.37[J].Sta

20.363[J] Biomaterials Science and EngineeringSame subject as 3.055[J]Subject meets with 3.963[J], 20.463[J]Prereq: 20.110[J] or permission of instructorU (Fall)3-0-9 units

Covers, at a molecular scale, the analysis and design of materialsused in contact with biological systems, and biomimetic strategiesaimed at creating new materials based on principles found inbiology. Topics include molecular interaction between bio- andsynthetic molecules and surfaces; design, synthesis, and processingapproaches for materials that control cell functions; and applicationof materials science to problems in tissue engineering, drug delivery,vaccines, and cell-guiding surfaces. Students taking graduateversion complete additional assignments.D. Irvine, K. Ribbeck

20.365 Engineering the Immune System in Cancer and BeyondSubject meets with 20.465Prereq: (5.60 or 20.110[J]) and permission of instructorU (Spring)3-0-6 units

Examines strategies in clinical and preclinical development formanipulating the immune system to treat and protect againstdisease. Begins with brief review of immune system. Discussesinteraction of tumors with the immune system, followed byapproaches by which the immune system can be modulated to attackcancer. Also covers strategies based in biotechnology, chemistry,materials science, and molecular biology to induce immuneresponses to treat infection, transplantation, and autoimmunity.Students taking graduate version complete additional assignments.D. Irvine



20.370[J] Cellular Neurophysiology and ComputingSame subject as 2.791[J], 6.021[J], 9.21[J]Subject meets with 2.794[J], 6.521[J], 9.021[J], 20.470[J], HST.541[J]Prereq: (Physics II (GIR), 18.03, and (2.005, 6.002, 6.003, 10.301, or20.110[J])) or permission of instructorU (Fall)5-2-5 units

See description under subject 6.021[J]. Preference to juniors andseniors.J. Han, T. Heldt

20.373 Foundations of Cell Therapy Manufacturing (New)Subject meets with 20.473Prereq: NoneU (Spring)3-0-6 units

Seminar examines cell therapy manufacturing, the ex vivo productionof human cells to be delivered to humans as a product for medicalbenet. Includes a review of cell biology and immunology. Addressestopics such as governmental regulations applying to cell therapyproduction; the manufacture of cell-based therapeutics, includingcell culture unit operations, genetic engineering or editing of cells;process engineering of cell therapy products; and the analytics ofcell therapy manufacturing processes. Students taking graduateversion complete additional assignments.K. Van Vliet

20.375 Applied Developmental Biology and Tissue EngineeringSubject meets with 20.475Prereq: (7.06, 20.320, and (7.003[J] or 20.109)) or permission ofinstructorU (Spring)Not oered regularly; consult department3-0-9 units

Addresses the integration of engineering and biology designprinciples to create human tissues and organs for regenerativemedicine to drug development. Provides an overview ofembryogenesis, how morphogenic phenomena are governed bybiochemical and biophysical cues. Analyzes in vitrogeneration of human brain, gut, and other organoids from stem cells.Studies the roles of biomaterials and microreactors in improvingorganoid formation and function; organoid use in modeling diseaseand physiology in vitro; and engineering and biologicalprinciples of reconstructing tissues and organs from postnatal donorcells using biomaterials scaolds and bioreactors. Includes selectapplications, such as liver disease, brain disorders, and others.Students taking graduate version complete additional assignments.L. Grith

20.380 Biological Engineering DesignPrereq: 7.06, 20.320, and 20.330[J]U (Fall, Spring)5-0-7 units

Illustrates how knowledge and principles of biology, biochemistry,and engineering are integrated to create new products for societalbenet. Uses case study format to examine recently developedproducts of pharmaceutical and biotechnology industries: howa product evolves from initial idea, through patents, testing,evaluation, production, and marketing. Emphasizes scientic andengineering principles, as well as the responsibility scientists,engineers, and business executives have for the consequencesof their technology. Instruction and practice in written and oralcommunication provided. Enrollment limited; preference to Course20 undergraduates.J. Collins, A. Koehler, J. Essigmann, K. Ribbeck

20.381 Biological Engineering Design IIPrereq: 20.380 or permission of instructorU (Spring)0-12-0 units

Continuation of 20.380 that focuses on practical implementation ofdesign proposals. Student teams choose a feasible scope of workrelated to their 20.380 design proposals and execute it in the lab.M. Jonas, J. Sutton, S. Wasserman

20.385 Understanding Current Research in Synthetic BiologySubject meets with 20.020Prereq: (20.109 and 20.320) or permission of instructorU (Spring)Not oered regularly; consult department3-3-3 units

Provides an in-depth understanding of the state of research insynthetic biology. Critical evaluation of primary research literaturecovering a range of approaches to the design, modeling andprogramming of cellular behaviors. Focuses on developing the skillsneeded to read, present and discuss primary research literature,and to manage and lead small teams. Students mentor a smallundergraduate team of 20.020 students. Open to advanced studentswith appropriate background in biology.Sta



20.390[J] Computational Systems Biology: Deep Learning in theLife SciencesSame subject as 6.802[J]Subject meets with 6.874[J], 20.490, HST.506[J]Prereq: (7.05 and (6.0002 or 6.01)) or permission of instructorU (Spring)3-0-9 units

Presents innovative approaches to computational problems in thelife sciences, focusing on deep learning-based approaches withcomparisons to conventional methods. Topics include protein-DNA interaction, chromatin accessibility, regulatory variantinterpretation, medical image understanding, medical recordunderstanding, therapeutic design, and experiment design (thechoice and interpretation of interventions). Focuses on machinelearning model selection, robustness, and interpretation. Teamscomplete a multidisciplinary nal research project using TensorFlowor other framework. Provides a comprehensive introduction to eachlife sciences problem, but relies upon students understandingprobabilistic problem formulations. Students taking graduateversion complete additional assignments.D. K. Giord

20.405[J] Principles of Synthetic BiologySame subject as 6.589[J]Subject meets with 6.580[J], 20.305[J]Prereq: NoneG (Fall)3-0-9 units

Introduces the basics of synthetic biology, including quantitativecellular network characterization and modeling. Considers thediscovery and genetic factoring of useful cellular activities intoreusable functions for design. Emphasizes the principles ofbiomolecular system design and diagnosis of designed systems.Illustrates cutting-edge applications in synthetic biology andenhances skills in analysis and design of synthetic biologicalapplications. Students taking graduate version complete additionalassignments.R. Weiss

20.409 Biological Engineering II: Instrumentation andMeasurementSubject meets with 2.673[J], 20.309[J]Prereq: Permission of instructorG (Fall, Spring)2-7-3 units

Sensing and measurement aimed at quantitative molecular/cell/tissue analysis in terms of genetic, biochemical, and biophysicalproperties. Methods include light and fluorescence microscopies,electronic circuits, and electro-mechanical probes (atomic forcemicroscopy, optical traps, MEMS devices). Application of statistics,probability, signal and noise analysis, and Fourier techniques toexperimental data. Limited to 5 graduate students.P. Blainey, S. Manalis, S. Wasserman, J. Bagnall, E. Frank, E. Boyden,P. So

20.410[J] Molecular, Cellular, and Tissue BiomechanicsSame subject as 2.798[J], 3.971[J], 6.524[J], 10.537[J]Prereq: Biology (GIR) and (2.002, 2.006, 6.013, 10.301, or 10.302)G (Fall)Not oered regularly; consult department3-0-9 units

Develops and applies scaling laws and the methods of continuummechanics to biomechanical phenomena over a range of lengthscales. Topics include structure of tissues and the molecularbasis for macroscopic properties; chemical and electrical eectson mechanical behavior; cell mechanics, motility and adhesion;biomembranes; biomolecular mechanics and molecular motors.Experimental methods for probing structures at the tissue, cellular,and molecular levels.R. D. Kamm, K. J. Van Vliet



20.415 Physical BiologySubject meets with 20.315Prereq: Permission of instructorG (Spring)Not oered regularly; consult department3-0-9 unitsCredit cannot also be received for 8.241

Focuses on current major research topics in quantitative, physicalbiology. Topics include synthetic structural biology, synthetic cellbiology, microbial systems biology and evolution, cellular decisionmaking, neuronal circuits, and development and morphogenesis.Emphasizes current motivation and historical background,state-of-the-art measurement methodologies and techniques,and quantitative physical modeling frameworks. Experimentaltechniques include structural biology, next-generation sequencing,fluorescence imaging and spectroscopy, and quantitativebiochemistry. Modeling approaches include stochastic rateequations, statistical thermodynamics, and statistical inference.Students taking graduate version complete additional assignments.20.315 and 20.415 meet with 8.241 when oered concurrently.J. Gore, I. Cisse

20.416[J] Topics in Biophysics and Physical BiologySame subject as 7.74[J], 8.590[J]Prereq: NoneG (Fall)Not oered regularly; consult department2-0-4 units

Provides broad exposure to research in biophysics and physicalbiology, with emphasis on the critical evaluation of scienticliterature. Weekly meetings include in-depth discussion of scienticliterature led by distinct faculty on active research topics. Eachsession also includes brief discussion of non-research topicsincluding eective presentation skills, writing papers and fellowshipproposals, choosing scientic and technical research topics, timemanagement, and scientic ethics.I. Cisse, N. Fakhri, M. Guo

20.420[J] Principles of Molecular BioengineeringSame subject as 10.538[J]Prereq: 7.06 and 18.03G (Fall)3-0-9 units

Provides an introduction to the mechanistic analysis andengineering of biomolecules and biomolecular systems. Coversmethods for measuring, modeling, and manipulating systems,including biophysical experimental tools, computational modelingapproaches, and molecular design. Equips students to takesystematic and quantitative approaches to the investigation of awide variety of biological phenomena.A. Jasano, E. Fraenkel

20.430[J] Fields, Forces, and Flows in Biological SystemsSame subject as 2.795[J], 6.561[J], 10.539[J]Prereq: Permission of instructorG (Fall)3-0-9 units

Molecular diusion, diusion-reaction, conduction, convection inbiological systems; elds in heterogeneous media; electrical doublelayers; Maxwell stress tensor, electrical forces in physiologicalsystems. Fluid and solid continua: equations of motion useful forporous, hydrated biological tissues. Case studies of membranetransport, electrode interfaces, electrical, mechanical, andchemical transduction in tissues, convective-diusion/reaction,electrophoretic, electroosmotic flows in tissues/MEMs, and ECG.Electromechanical and physicochemical interactions in cells andbiomaterials; musculoskeletal, cardiovascular, and other biologicaland clinical examples. Prior undergraduate coursework in transportrecommended.M. Bathe, A. J. Grodzinsky



20.440 Analysis of Biological NetworksPrereq: 20.420[J] and permission of instructorG (Spring)6-0-9 units

Explores computational and experimental approaches to analyzingcomplex biological networks and systems. Includes genomics,transcriptomics, proteomics, metabolomics and microscopy.Stresses the practical considerations required when designingand performing experiments. Also focuses on selection andimplementation of appropriate computational tools for processing,visualizing, and integrating dierent types of experimental data,including supervised and unsupervised machine learning methods,and multi-omics modelling. Students use statistical methods to testhypotheses and assess the validity of conclusions. In problem sets,students read current literature, develop their skills in Python andR, and interpret quantitative results in a biological manner. In thesecond half of term, students work in groups to complete a project inwhich they apply the computational approaches covered.B. Bryson, P. Blainey

20.445[J] Methods and Problems in MicrobiologySame subject as 1.86[J], 7.492[J]Prereq: NoneG (Fall)3-0-9 units

See description under subject 7.492[J]. Preference to rst-yearMicrobiology and Biology students.M. Laub

20.446[J] Microbial Genetics and EvolutionSame subject as 1.87[J], 7.493[J], 12.493[J]Prereq: 7.03, 7.05, or permission of instructorG (Fall)4-0-8 units

See description under subject 7.493[J].A. D. Grossman, O. Cordero

20.450 Applied MicrobiologyPrereq: (20.420[J] and 20.440) or permission of instructorAcad Year 2020-2021: Not oeredAcad Year 2021-2022: G (Fall)4-0-8 units

Compares the complex molecular and cellular interactions in healthand disease between commensal microbial communities, pathogensand the human or animal host. Special focus is given to currentresearch on microbe/host interactions, infection of signicantimportance to public health, and chronic infectious disease.Classwork will include lecture, but emphasize critical evaluation andclass discussion of recent scientic papers, and the development ofnew research agendas in the elds presented.J. C. Niles, K. Ribbeck

20.452[J] Principles of NeuroengineeringSame subject as 9.422[J], MAS.881[J]Subject meets with 20.352Prereq: Permission of instructorG (Fall)3-0-9 units

See description under subject MAS.881[J].E. S. Boyden, III

20.454[J] Revolutionary Ventures: How to Invent and DeployTransformative TechnologiesSame subject as 9.455[J], 15.128[J], MAS.883[J]Prereq: Permission of instructorG (Fall)2-0-7 units

See description under subject MAS.883[J].E. Boyden, J. Bonsen, J. Jacobson

20.463[J] Biomaterials Science and EngineeringSame subject as 3.963[J]Subject meets with 3.055[J], 20.363[J]Prereq: 20.110[J] or permission of instructorG (Fall)3-0-9 units

Covers, at a molecular scale, the analysis and design of materialsused in contact with biological systems, and biomimetic strategiesaimed at creating new materials based on principles found inbiology. Topics include molecular interaction between bio- andsynthetic molecules and surfaces; design, synthesis, and processingapproaches for materials that control cell functions; and applicationof materials science to problems in tissue engineering, drug delivery,vaccines, and cell-guiding surfaces. Students taking graduateversion complete additional assignments.D. Irvine, K. Ribbeck



20.465 Engineering the Immune System in Cancer and BeyondSubject meets with 20.365Prereq: Permission of instructorG (Spring)3-0-6 units

Examines strategies in clinical and preclinical development formanipulating the immune system to treat and protect againstdisease. Begins with brief review of immune system. Discussesinteraction of tumors with the immune system, followed byapproaches by which the immune system can be modulated to attackcancer. Also covers strategies based in biotechnology, chemistry,materials science, and molecular biology to induce immuneresponses to treat infection, transplantation, and autoimmunity.Students taking graduate version complete additional assignments.D. Irvine

20.470[J] Cellular Neurophysiology and ComputingSame subject as 2.794[J], 6.521[J], 9.021[J], HST.541[J]Subject meets with 2.791[J], 6.021[J], 9.21[J], 20.370[J]Prereq: (Physics II (GIR), 18.03, and (2.005, 6.002, 6.003, 10.301, or20.110[J])) or permission of instructorG (Fall)5-2-5 units

See description under subject 6.521[J].J. Han, T. Heldt

20.473 Foundations of Cell Therapy Manufacturing (New)Subject meets with 20.373Prereq: NoneG (Spring)3-0-6 units

Seminar examines cell therapy manufacturing, the ex vivo productionof human cells to be delivered to humans as a product for medicalbenet. Includes a review of cell biology and immunology. Addressestopics such as governmental regulations applying to cell therapyproduction; the manufacture of cell-based therapeutics, includingcell culture unit operations, genetic engineering or editing of cells;process engineering of cell therapy products; and the analytics ofcell therapy manufacturing processes. Students taking graduateversion complete additional assignments.K. Van Vliet

20.475 Applied Developmental Biology and Tissue EngineeringSubject meets with 20.375Prereq: Permission of instructorG (Spring)Not oered regularly; consult department3-0-9 units

This subject addresses the integration of engineering andbiology design principles to create human tissues and organsfor regenerative medicine to drug development. Overview ofembryogenesis; how morphogenic phenomena are governed bybiochemical and biophysical cues. Analysis of in vitro generationof human brain, gut, and other organoids from stem cells. Roles ofbiomaterials and microreactors in improving organoid formationand function. Organoid use in modeling disease and physiologyin vitro. Engineering and biological principles of reconstructingtissues and organs from postnatal donor cells using biomaterialsscaolds and bioreactors. Select applications such as liver disease,brain disorders, and others. Graduate students will have additionalassignments.L. Grith

20.486[J] Case Studies and Strategies in Drug Discovery andDevelopmentSame subject as 7.549[J], 15.137[J], HST.916[J]Prereq: NoneG (Spring)2-0-4 units

Aims to develop appreciation for the stages of drug discoveryand development, from target identication, to the submission ofpreclinical and clinical data to regulatory authorities for marketingapproval. Following introductory lectures on the process ofdrug development, students working in small teams analyzehow one of four new drugs or drug candidates traversed thediscovery/development landscape. For each case, an outsideexpert from the sponsoring drug company or pivotal clinical trialprincipal investigator provides guidance and critiques the teams'presentations to the class.A. W. Wood

20.487[J] Optical Microscopy and Spectroscopy for Biology andMedicineSame subject as 2.715[J]Prereq: Permission of instructorG (Spring)Not oered regularly; consult department3-0-9 units

See description under subject 2.715[J].P. T. So, C. Sheppard



20.490 Computational Systems Biology: Deep Learning in theLife SciencesSubject meets with 6.802[J], 6.874[J], 20.390[J], HST.506[J]Prereq: Biology (GIR) and (6.041 or 18.600)G (Spring)3-0-9 units

Presents innovative approaches to computational problems in thelife sciences, focusing on deep learning-based approaches withcomparisons to conventional methods. Topics include protein-DNA interaction, chromatin accessibility, regulatory variantinterpretation, medical image understanding, medical recordunderstanding, therapeutic design, and experiment design (thechoice and interpretation of interventions). Focuses on machinelearning model selection, robustness, and interpretation. Teamscomplete a multidisciplinary nal research project using TensorFlowor other framework. Provides a comprehensive introduction to eachlife sciences problem, but relies upon students understandingprobabilistic problem formulations. Students taking graduateversion complete additional assignments.D. K. Giord

20.507[J] Introduction to Biological ChemistrySame subject as 5.07[J]Prereq: 5.12U (Fall)5-0-7 units. RESTCredit cannot also be received for 7.05

See description under subject 5.07[J].A. Krishtal, B. Pentelute

20.535[J] Protein Engineering (New)Same subject as 10.535[J]Prereq: 18.03 and (5.07[J] or 7.05)G (Spring)3-0-9 units

See description under subject 10.535[J].K. D. Wittrup

20.554[J] Frontiers in Chemical BiologySame subject as 5.54[J], 7.540[J]Prereq: 5.07[J], 5.13, 7.06, and permission of instructorG (Fall)3-0-9 units

See description under subject 5.54[J].L. Kiessling, M. Shoulders

20.560 Statistics for Biological EngineeringPrereq: Permission of instructorG (Spring; second half of term)2-0-2 units

Provides basic tools for analyzing experimental data, interpretingstatistical reports in the literature, and reasoning under uncertainsituations. Topics include probability theory, statistical tests, dataexploration, Bayesian statistics, and machine learning. Emphasizesdiscussion and hands-on learning. Experience with MATLAB, Python,or R recommended.S. Olesen

20.561[J] Eukaryotic Cell Biology: Principles and PracticeSame subject as 7.61[J]Prereq: Permission of instructorG (Fall)4-0-8 units

See description under subject 7.61[J]. Enrollment limited.M. Krieger, M. Yae

20.586[J] Science and Business of BiotechnologySame subject as 7.546[J], 15.480[J]Prereq: None. Coreq: 15.401; permission of instructorAcad Year 2020-2021: Not oeredAcad Year 2021-2022: G (Fall)3-0-6 units

See description under subject 15.480[J].A. Lo, H. Lodish

20.630[J] ImmunologySame subject as 7.63[J]Subject meets with 7.23[J], 20.230[J]Prereq: 7.06 and permission of instructorG (Spring)5-0-7 units

See description under subject 7.63[J].S. Spranger, M. Birnbaum

20.902 Independent Study in Biological EngineeringPrereq: Permission of instructorU (Fall, Spring)Units arrangedCan be repeated for credit.

Opportunity for independent study under regular supervision bya faculty member. Projects require prior approval, as well as asubstantive paper. Minimum 12 units required.Sta



20.903 Independent Study in Biological EngineeringPrereq: Permission of instructorU (Fall, Spring, Summer)Units arranged [P/D/F]Can be repeated for credit.

Opportunity for independent study under regular supervision bya faculty member. Projects require prior approval, as well as asubstantive paper. Minimum 6-12 units required.Sta

20.920 Practical Work ExperiencePrereq: NoneU (Fall, IAP, Spring, Summer)0-1-0 units

For Course 20 students participating in o-campus professionalexperiences in biological engineering. Before registering for thissubject, students must have an oer from a company or organizationand must identify a BE supervisor. Upon completion, student mustsubmit a letter from the company or organization describing theexperience, along with a substantive nal report from the studentapproved by the MIT supervisor. Subject to departmental approval.Consult departmental undergraduate oce.Sta

20.930[J] Research Experience in BiopharmaSame subject as 7.930[J]Prereq: NoneG (Spring)2-10-0 units

Provides exposure to industrial science and develops skillsnecessary for success in such an environment. Under the guidanceof an industrial mentor, students participate in on-site researchat a local biopharmaceutical company where they observe andparticipate in industrial science. Serves as a real-time case studyto internalize the factors that shape R&D in industry, including thepurpose and scope of a project, key decision points in the pastand future, and strategies for execution. Students utilize companyresources and work with a scientic team to contribute to the goalsof their assigned project; they then present project results to thecompany and class, emphasizing the logic that dictated their workand their ideas for future directions. Lecture component focuses onprofessional development.S. Clarke

20.950 Research Problems in Biological EngineeringPrereq: Permission of instructorG (Fall, Spring, Summer)Units arrangedCan be repeated for credit.

Directed research in the elds of bioengineering and environmentalhealth. Limited to BE students.Sta

20.951 Thesis ProposalPrereq: Permission of instructorG (Fall, Spring, Summer)0-24-0 units

Thesis proposal research and presentation to the thesis committee.Sta

20.960 Teaching Experience in Biological EngineeringPrereq: Permission of instructorG (Fall, Spring)Units arrangedCan be repeated for credit.

For qualied graduate students interested in teaching. Tutorial,laboratory, or classroom teaching under the supervision of a facultymember. Enrollment limited by availability of suitable teachingassignments.Sta

20.BME Undergraduate Research in Biomedical EngineeringPrereq: NoneU (Fall, Spring)Units arranged [P/D/F]Can be repeated for credit.

Individual research project with biomedical or clinical focus,arranged with appropriate faculty member or approved supervisor.Forms and instructions for the proposal and nal report are availablein the BE Undergraduate Oce.Consult

20.EPE UPOP Engineering Practice ExperienceEngineering School-Wide Elective Subject.Oered under: 1.EPE, 2.EPE, 3.EPE, 6.EPE, 8.EPE, 10.EPE, 15.EPE,16.EPE, 20.EPE, 22.EPEPrereq: 2.EPW or permission of instructorU (Fall, Spring)0-0-1 units

See description under subject 2.EPE.Sta



20.EPW UPOP Engineering Practice WorkshopEngineering School-Wide Elective Subject.Oered under: 1.EPW, 2.EPW, 3.EPW, 6.EPW, 10.EPW, 16.EPW,20.EPW, 22.EPWPrereq: NoneU (Fall, IAP)1-0-0 units

See description under subject 2.EPW. Enrollment limited.Sta

20.S900 Special Subject in Biological EngineeringPrereq: Permission of instructorU (Fall, Spring)Units arranged [P/D/F]Can be repeated for credit.

Detailed discussion of selected topics of current interest. Classworkin various areas not covered by regular subjects.L. Grith, G. McKinley

20.S901 Special Subject in Biological EngineeringPrereq: NoneU (Fall, Spring)Units arranged [P/D/F]Can be repeated for credit.

Detailed discussion of selected topics of current interest. Classworkin various areas not covered by regular subjects.S. Clarke

20.S940 Special Subject in Biological EngineeringPrereq: Permission of instructorU (Fall, Spring)Units arrangedCan be repeated for credit.


20.S947 Special Subject in Biological EngineeringPrereq: Permission of instructorG (Fall, Spring)Units arrangedCan be repeated for credit.






20.S952 Special Subject in Biological EngineeringPrereq: Permission of instructorG (Fall, Spring)Units arranged [P/D/F]Can be repeated for credit.


20.THG Graduate ThesisPrereq: Permission of instructorG (Fall, IAP, Spring, Summer)Units arrangedCan be repeated for credit.

Program of research leading to the writing of an SM or PhD thesis; tobe arranged by the student and the MIT faculty advisor.Sta

20.THU Undergraduate BE ThesisPrereq: NoneU (Fall, IAP, Spring)Units arrangedCan be repeated for credit.

Program of research leading to the writing of an SB thesis; to bearranged by the student under approved supervision.Sta



20.UR Undergraduate Research OpportunitiesPrereq: NoneU (Fall, IAP, Spring, Summer)Units arranged [P/D/F]Can be repeated for credit.

Laboratory research in the elds of bioengineering or environmentalhealth. May be extended over multiple terms.S. Manalis

20.URG Undergraduate Research OpportunitiesPrereq: NoneU (Fall, IAP, Spring, Summer)Units arrangedCan be repeated for credit.

Emphasizes direct and active involvement in laboratory researchin bioengineering or environmental health. May be extended overmultiple terms.Consult S. Manalis

Documents

Department of Biological Engineeringcatalog.mit.edu/.../biological-engineering/biological-engineering.pdf · 21st century as physics and chemistry wer e in the 20th century, and that