| source MIT (X) |
level |
department Biological Engineering (X) |
20.020 Introduction to Biological Engineering Design ( ) Prereq: None Units: 3-3-3 A project-based introduction to the engineering of synthetic biological systems. Throughout the term, students develop projects that are responsive to real-world problems of their choosing, and whose solutions depend on biological technologies. Lectures, discussions, and studio exercises will introduce (1) components and control of prokaryotic and eukaryotic behavior, (2) DNA synthesis, standards, and abstraction in biological engineering, and (3) issues of human practice, including biological safety; security; ownership, sharing, and innovation; and ethics. Preference to freshmen. N. Kuldell
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20.102 Macroepidemiology and Population Genetics ( ) (Subject meets with 20.215 ) Prereq: Calculus I (GIR) Units: 3-0-9 Lecture: TR1-2.30 ( 56-614 ) Analyses of major causes of mortality in the US since 1900: cancer, cardiovascular and cerebrovascular diseases, diabetes, infectious diseases. Analytical models to derive estimates for historically variant population risk factors and physiological rate parameters. Analysis of familial data to separately estimate inherited and environmental risks. Basic population genetics of dominant, recessive, and non-deleterious inherited risk factors. W. G. Thilly
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20.104J Environmental Risks for Common Disease ( ) (Same subject as 1.081J , ESD.053J ) Prereq: Biology (GIR) , Chemistry (GIR) Units: 3-0-9 Analysis of potentially important risk factors for common diseases in the general environment and the workplace: air-, food- and water-borne chemicals; subclinical infections; diet and lifestyle choices. Analysis of history of changes in common disease rates. General paradigm of environmental sources and exposure of human subpopulations, uptake, internal distribution and metabolism of xenobiotics. Measurement of xenobiotic chemicals and allobiotic life forms in human tissues. Potential pathways of induced pathogenesis: mutagenesis, inflammation, hormonal mimicry. W. Thilly, R. McCunney
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20.106J Systems Microbiology ( ) (Same subject as 1.084J ) Prereq: Chemistry (GIR) , Biology (GIR) Units: 3-0-9 Introductory microbiology from a systems perspective. Considers microbial diversity, population dynamics, and genomics. Emphasize the delicate balance between microbes and humans, and changes that result in the emergence of infectious diseases and antimicrobial resistance. Case study approach covers topics such as vaccines, toxins, biodefense, and infections including Legionnaire's disease, tuberculosis, Helicobacter pylori, and plague. D. B. Schauer, E. DeLong
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20.109 Laboratory Fundamentals in Biological Engineering ( , ) Prereq: Biology (GIR) , Chemistry (GIR) , 6.00 , 18.03 ; 20.110 or 20.111 Units: 2-8-5 Lecture: TR11 ( 66-144 ) Lab: TR1-5 ( 56-322 ) or WF1-5 ( 56-322 ) Introduces experimental biochemical and molecular techniques from a quantitative engineering perspective. Experimental design, data analysis, and scientific communication form the underpinnings of this subject. Examples of discovery-based experimental modules include: DNA Engineering in which students design, construct, and use genetic material; Parts Engineering, which emphasizes protein design and quantitative assessment of protein performance; Systems Engineering, in which students consider genome-wide consequences of genetic perturbations; and Biomaterials Engineering, in which students use biologically-encoded devices to design and build materials. Limited enrollment; priority to BE majors. Fall: A. Belcher, N. Kuldell, B. P. Engelward Spring: A. Jasanoff, J. Niles, A. Stachowiak
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20.110J Thermodynamics of Biomolecular Systems ( ) (Same subject as 2.772J ) Prereq: Calculus II (GIR) , Chemistry (GIR) Units: 5-0-7 Credit cannot also be received for 7.10 Lecture: MWF10 ( 10-250 ) Recitation: TR9 ( 4-159 ) or TR10 ( 4-159 ) or TR1 ( 4-159 ) or TR4 ( 4-159 ) +final Equilibrium properties of macroscopic and microscopic systems. Basic thermodynamics: state of a system, state variables. Work, heat, first law of thermodynamics, thermochemistry. Second and third law of thermodynamics: entropy and its statistical basis, Gibbs function. Chemical equilibrium of reactions in gas and solution phase. Macromolecular structure and interactions in solution. Driving forces for molecular self-assembly. Binding cooperativity, solvation, titration of macromolecules. L. G. Griffith, K. Hamad-Schifferli
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20.111J Physical Chemistry of Biomolecular Systems ( ) (Same subject as 7.10J ) Prereq: Calculus II (GIR) , Chemistry (GIR) , Physics I (GIR) ; Coreq: Physics II (GIR) Units: 5-0-7 Provides a quantitative approach to understanding the physical and chemical laws that govern the behavior of biological macromolecules. Basic thermodynamics, state of a system, state variables. Work, heat, first, second, and third laws of thermodynamics. Entropy and its statistical basis, free energy representations, Legendre transforms, Maxwell relations, Gibbs function, Boltzmann distribution and partition functions. Equilibrium properties of macroscopic and microscopic systems; macromolecular structure and interactions in solution. Driving forces for molecular self-assembly. Binding, cooperativity, solvation, and titration of macromolecules. Applications of introductory quantum mechanics to spectroscopy. Staff
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20.200 Biological Engineering Seminar ( , ) Prereq: Open only to BE graduate students, or by permission of instructor Units: 1-0-2 [P/D/F] Lecture: F12 ( 56-614 ) Weekly one-hour seminars covering graduate student research and presentations by invited speakers. J. S. Wishnok
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20.201 Mechanisms of Drug Actions ( ) Prereq: Permission of instructor Units: 4-0-8 Lecture: MW1.30-3 ( 56-614 ) Recitation: F1.30 ( 56-614 ) Chemical and biological analysis of the metabolism and distribution of drugs and chemicals in animals and humans, and the mechanisms by which they cause therapeutic and toxic responses. Metabolism, pharmacology and toxicity as a basis for drug development. Group project analysis of specific drugs and their role in the market. P. C. Dedon, S. R. Tannenbaum
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20.202 In vivo models: Principles and Practices ( ) Prereq: Permission of instructor Units: 1-1-4 Selected aspects of anatomy, histology, immuno-cytochemistry, in situ hybridization, physiology, and cell biology of mammalian organisms and their pathogens. Subject material integrated with principles of toxicology, in vivo genetic engineering, and molecular biology. A lab/demonstration period each week involves experiments in anatomy (in vivo), physiology, and microscopy to augment the lectures. Offered first half of spring term. J. G. Fox, B. Marini, M. Whary
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20.213 DNA Damage and Genomic Instability ( ) Prereq: 5.07 , 7.05 , permission of instructor Units: 4-0-8 Recent progress has resulted in the identification of dozens of genes that, when mutated, promote tumorigenesis. However, it is not yet clear what causes these mutations. Subject analyzes the chemistry of DNA damaging agents, and continues with analysis of the mutagenic and toxic consequences of modifications to DNA structure. The contrasting perspective that normal DNA processing leads to mutations is also presented. The biochemistry and molecular mechanisms of DNA replication, DNA repair, and recombination form the foundation of the subject. P. C. Dedon, B. P. Engelward
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20.215 Epidemiology, Population Genetics and Cell Biology of Human Cancers ( ) (Subject meets with 20.102 ) Prereq: Calculus II (GIR) , 1.00 Units: 3-0-15 Lecture: TR1-2.30 ( 56-614 ) Logic and technology needed to discover genetic and environmental causes and accelerating factors for common human cancers. Analyses of large organized historical public health databases using quantitative carcinogenesis cascade models. Java-based model construction for mono- and multi-genic inherited risk for late onset (sporadic) cancers. Analyses of historical and clinical data to define role of environmental risk factors. Graduate students complete additional work. W. G. Thilly
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20.219 Selected Topics in Toxicology ( , , , ) Prereq: Permission of Instructor Units arranged Detailed discussion of selected topics of current interest. Classwork in various areas not covered by regular subjects. Staff
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20.309J Instrumentation and Measurement for Biological Systems ( , ) (Same subject as 2.673J , 6.122J , MAS.402J ) (Subject meets with 20.409 ) Prereq: Biology (GIR) , Physics II (GIR) , 6.00 , 18.03 ; 2.001 , 20.310 , or 6.02 ; or permission of instructor; Coreq: 20.330 Units: 3-6-3 Lecture: TR12 ( 4-237 ) Lab: TBA Recitation: F12 ( 4-231 , 4-153 ) Sensing and measurement aimed at quantitative molecular/cell/tissue analysis in terms of genetic, biochemical, and biophysical properties. Methods include light and fluorescence microscopies, electronic circuits, and electro-mechanical probes (atomic force microscopy, optical traps, MEMS devices). Application of statistics, probability, signal and noise analysis, and Fourier techniques to experimental data. Final design project emphasizes utilization of principles underlying biological instrumentation. Preference to juniors and seniors. Fall: S. Manalis, P. T. So, S. Wasserman Spring: E. Boyden, S. Wasserman, M. F. Yanik
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20.310J Molecular, Cellular, and Tissue Biomechanics ( ) (Same subject as 2.797J , 3.053J , 6.024J ) Prereq: 2.370 or 2.772J ; 18.03 or 3.016 ; Biology (GIR) Units: 4-0-8 Develops and applies scaling laws and the methods of continuum mechanics to biomechanical phenomena over a range of length scales. Topics include structure of tissues and the molecular basis for macroscopic properties; chemical and electrical effects on 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
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20.320 Analysis of Biomolecular & Cellular Systems ( ) Prereq: 20.110 , 18.03 , 6.00 ; Coreq: 5.07 Units: 4-0-8 Lecture: TR9.30-11 ( 56-114 ) +final Analysis of molecular and cellular processes across a hierarchy of scales, including genetic, molecular, cellular, and cell population levels. Topics include gene sequence analysis, molecular modeling, metabolic and gene regulation networks, signal transduction pathways and cell populations in tissues. Emphasis on experimental methods, quantitative analysis, and computational modeling. F. White, E. Fraenkel
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20.330J Fields, Forces and Flows in Biological Systems ( ) (Same subject as 2.793J , 6.023J ) Prereq: 2.005 , 6.021 , 20.320 or permission of instructor Units: 4-0-8 Introduction to electric fields, fluid flows, transport phenomena and their application to biological systems. Flux and continuity laws, Maxwell's equations, electro-quasistatics, electro-chemical-mechanical driving forces, conservation of mass and momentum, Navier-Stokes flows, and electrokinetics. Applications include biomolecular transport in tissues, electrophoresis, and microfluidics. J. Han, L. Griffith
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20.340J Materials for Biomedical Applications ( ) (Same subject as 3.051J ) (Subject meets with 3.962J , 20.462J ) Prereq: Chemistry (GIR) , Biology (GIR) , 3.034 , 3.012 or 3.046 ; or permission of instructor Units: 3-0-9 Introduction to the interactions between cells and surfaces of biomaterials. Surface chemistry and physics of selected metals, polymers, and ceramics. Surface characterization methodology. Modification of biomaterials surfaces. Quantitative assays of cell behavior in culture. Biosensors and microarrays. Bulk properties of implants. Acute and chronic response to implanted biomaterials. Topics in biomimetics, drug delivery, and tissue engineering. D. Irvine
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20.342 Molecular Structure of Biological Materials ( ) (Subject meets with 20.442 ) Prereq: 5.07 or 7.05 ; permission of instructor Units: 3-0-9 Lecture: TR1-2.30 ( 56-154 ) Basic molecular structural principles of biological materials. Molecular structures of various materials of biological origin, including collagen, silk, bone, protein adhesives, GFP, self-assembling peptides. Molecular design of new biological materials for nanotechnology, biocomputing and regenerative medicine. Graduate students are expected to complete additional coursework. S. Zhang
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20.360J Tissue Engineering for Analysis, Prevention, and Treatment of Human Disease ( ) (Same subject as 10.499J ) Prereq: 5.07 or 7.05 ; 7.03 ; 18.03 ; 20.110 or 5.60 Units: 3-0-6 Analysis of fundamental processes in tissue engineering with an emphasis on use of comparative animal models and in vitro tissue engineered models to understand human disease and develop therapies for human disease and for regenerating human tissues and organs. using representative examples of metabolic tissue (e.g., liver) and connective tissue (e.g., bone). Design principles and engineering approaches (e.g., use of synthetic materials) for controlling receptor-mediated processes such as cell migration, growth, and differentiation. Mass transfer limitations in design of devices for cell encapsulation and in scaffold-guided regeneration. Guided organization of multicellular structures. Current clinical prospects. Staff
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20.361J Molecular and Engineering Aspects of Biotechnology ( ) (Same subject as 7.37J , 10.441J ) Prereq: 20.110J , 2.005 , 3.012 , or 5.60 ; 7.06 ; or permission of instructor Units: 4-0-8 Biological and bioengineering principles underlying the development and use of recombinant proteins as therapeutic drugs; fundamentals of therapeutic protein action, including cell-cell and cell-matrix interactions and intracellular signaling pathways; classes of protein therapeutics; post-translational processing and secretion of proteins; gene cloning and expression in mammalian cells; physiology of cell growth and in vitro cultivation; site-specific mutation of proteins; protein pharmacology and delivery. H. Lodish, L. G. Griffith
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20.370J Cellular Biophysics ( ) (Same subject as 2.791J , 6.021J ) (Subject meets with 2.794J , 6.521J , 20.470J , HST.541J ) Prereq: Physics II (GIR) ; 18.03 ; 2.005 , 6.002 , 6.003 , 6.071 , 10.301 , or permission of instructor Units: 5-2-5 Lecture: MWF10 ( 4-231 ) Lab: TBA Recitation: TR10 ( 36-713 ) or TR11 ( 36-713 ) +final Integrated overview of the biophysics of cells from prokaryotes to neurons, with a focus on mass transport and electrical signal generation across cell membrane. First half of course focuses on mass transport through membranes: diffusion, osmosis, chemically mediated, and active transport. Second half focuses on electrical properties of cells: ion transport to action potentials in electrically excitable cells. Electrical properties interpreted via kinetic and molecular properties of single voltage-gated ion channels. Laboratory and computer exercises illustrate the concepts. Provides instruction in written and oral communication. Students taking graduate version complete different assignments. Preference to juniors and seniors. D. M. Freeman, J. Han, J. Voldman
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20.371J Quantitative Systems Physiology ( ) (Same subject as 2.792J , 6.022J , HST.542J ) (Subject meets with 2.796J , 6.522J , 20.471J ) Prereq: Physics II (GIR) , 18.03 , or permission of instructor Units: 4-2-6 Application of the principles of energy and mass flow to major human organ systems. Mechanisms of regulation and homeostasis. Anatomical, physiological and pathophysiological features of the cardiovascular, respiratory and renal systems. Systems, features and devices that are most illuminated by the methods of physical sciences. Laboratory work includes some animal studies. R. G. Mark, C. M. Stultz
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20.380 Biological Engineering Design ( ) Prereq: 7.06 , 20.309 , 20.330 Units: 5-0-7 Illustrates how knowledge and principles of biology, biochemistry, and engineering are integrated to create new products for societal benefit. Uses case-study format to examine recently developed products of pharmaceutical and biotechnology industries: how a product evolves from initial idea, through patents, testing, evaluation, production, and marketing. Emphasizes scientific and engineering principles, as well as the responsibility scientists, engineers, and business executives have for the consequences of their technology. Instruction and practice in written and oral communication provided. Enrollment limited; preference to Course 20 undergraduates. J. M. Essigmann, D. J. Irvine
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20.385 Advanced Topics in Synthetic Biology (New) ( ) Prereq: Permission of instructor Units: 3-3-3 Provides an in-depth understanding of the state of research in synthetic biology. Critical evaluation of primary research literature covering a range of approaches to the design, modeling and programming of cellular behaviors. Focuses on developing the skills needed to read, present and discuss primary research literature, and to manage and lead small teams. Students mentor a small undergraduate team of 20.020 students. Open to advanced students with appropriate background in biology. N. Kuldell
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