Biological Engineering:
Science Description :
Biological Engineering [BE] was founded in 1998 as a new MIT departmental academic unit, with the mission of defining and establishing a new discipline fusing molecular life sciences with engineering. The goal of our biological engineering discipline, Course 20, is to advance fundamental understanding of how biological systems operate and to develop effective biology-based technologies for applications across a wide spectrum of societal needs including breakthroughs in diagnosis, treatment, and prevention of disease, in design of novel materials, devices, and processes, and in enhancing environmental health. The innovative educational programs created by BE reflect this emphasis on integrating molecular and cellular biosciences with a quantitative, systems-oriented engineering analysis and synthesis approach, offering opportunities at the undergraduate level for the SB degree in Biological Engineering, and at the graduate level for the Ph.D. in Biological Engineering (with emphasis in either Applied Biosciences or Bioengineering).
Undergraduates Courses:
- Macroepidemiology (BE.102), Spring 2005
Readings Lecture notes Assignment
- Annual Cancer Deaths and Population Sizes as a Function of Age in the United States (1890-1997) and Japan (1952-1995).
- Nordling, C. O. "A New Theory on Cancer-Inducing Mechanism." Br J Cancer 7, no. 1 (Mar 1953): 68-72.
- Armitage, P., and R. Doll. "The Age Distribution of Cancer and a Multi-Stage Theory of Carcinogenesis." Br J Cancer 8, no. 1 (Mar 1954): 1-12.
- "A Two-Stage Theory of Carcinogenesis in Relation to the Age Distribution of Human Cancer." Br J Cancer 11, no. 2 (Jun 1957): 161-9.
- The Age Distribution of Cancer and a Multi-Stage Theory of Carcinogenesis." Br J Cancer 91, no. 12 (Dec 13, 2004A): 1983-9.
- The Age distribution of Cancer and a Multi-Stage Theory of Carcinogenosis." Int J Epidemiol 33, no. 6 (Dec 2004B): 1174-9. Epub Aug 19, 2004.
- Herrero-Jimenez, P., G. Thilly, P. J. Southam, A. Tomita-Mitchell, S. Morgenthaler, E. E. Furth, and W. G. Thilly. "Mutation, Cell Kinetics, and Subpopulations at Risk for Colon Cancer in the United States." Mutat Res 400, nos. 1-2 (May 25, 1998): 553-78.
- Herrero-Jimenez, P., A. Tomita-Mitchell, E. E. Furth, S. Morgenthaler, and W. G. Thilly. "Population Risk and Physiological Rate Parameters for Colon Cancer. The Union of an Explicit Model for Carcinogenesis with the Public Health Records of the United States." Mutat Res 447, no. 1 (Jan 17, 2000): 73-116.
- Hemminki, K., and B. Chen. "Familial Risk for Colorectal Cancers Are Mainly Due to Heritable Causes Cancer Epidemiology." Biomarkers and Prevention 13 (2004A): 1253-1256.
- Hemminki, K., and K. Czene. "Attributable Risks of Familial Cancer from the Family-Cancer Database." Cancer Epidemiol Biomarkers Prev 11, no. 12 (Dec 2002): 1638-44.
- Hemminki, K., I. Lonnstedt, P. Vaittinen, and P. Lichtenstein. "Estimation of Genetic and Environmental Components in Colorectal and Lung Cancer and Melanoma." Genet Epidemiol 20, no. 1 (Jan 2001): 107-116.
1- Introduction: Dimensions of information available to define the unknown causes of common diseases.
2- Public health records and estimation of age-specific risk.
3- Effects of changes in diagnosis, prevention and therapy on historical mortality rates. Sources of differences in reported incidence and mortality.
4- Mathematical models derived from histopathological observations and age-specific mortality/incidence data. Examples: lung and colorectal cancers.
5- Promotion and Progression
6- Multiparametric Analysis of Colon Cancer
7- Multiparametric Analysis of Lung Cancer
8- Role of Gender
9- Sub-populations at Risk
10- National Risk and Community Risk
11- Familial Risk Expectations
12- Familial Risk Observations
13- Population Genetics
14- Population Genetics (cont.)
15- The search for genes carrying mutations conferring risk for common diseases.
16- The search for genes carrying mutations conferring risk for common diseases. (cont.)
17- The search for genes carrying mutations conferring risk for common diseases. (cont.)
18- The search for genes carrying mutations conferring risk for common diseases. (cont.)
19- The origins of somatic and inherited mutations in humans.
1- Problem set1
(PDF)
2- Problem set2
(PDF)
3- Problem set3
(PDF)
Graduates Courses:
- Cell-Matrix Mechanics, Spring 2004
Readings Lecture notes Assignment
- Clinical Examples of the Roles of Mechanical Forces in Tissues and Organs: The Working Paradigms
- Tissue Structures and Unit Cell Processes
- Cell-Matrix Interactions: Extracellular Matrix Molecules, Adhesion Proteins and Integrins
- Models for the Mechanical Behavior of Porous Scaffolds
- Structure-Properties Relationships for Tissues
- Mechanics of Selected Tissues
- Effects of Exogenous Mechanical Forces on Cells
- Response of Cells to Substrate Strain
- Endothelial Cell Response to Flow
- Endogenous Mechanical Force Generation by Cells
- Models for Cell Contraction In Vitro and In Vivo
- Mechanical Coupling of Cells with Matrix
- Cell-matrix Interactions During Wound Closure
- Blockade of Contraction During Induced Organ Regeneration
- Response of Articular Cartilage to Mechanical Loading
- Mechanical Behavior of Ligament, Meniscus and Intervertebral Disc
- Mechanical Behavior of Bone
- Response of Bone to Mechanical Loading
1- Clinical Examples of the Roles of Mechanical Forces in Tissues and Organs: The Working Paradigms
(PDF)
2- Tissue Structures and Unit Cell Processes
(PDF)
3- Cell-Matrix Interactions: Extracellular Matrix Molecules, Adhesion Proteins and Integrins
(PDF)
4- Models for the Mechanical Behavior of Porous Scaffolds
(PDF)
5- Response of Cells to Substrate Strain
(PDF)
6- Measuring Cell Contraction Cell Force Monitor
(PDF)
7- Endogenous Mechanical Force Generation by Cells
(PDF)
8- Models for Cell Contraction In Vitro and In Vivo
(PDF)
9- Mechanical Coupling of Cells with Matrix
(PDF)
10- Cell-matrix Interactions During Wound Closure
(PDF)
1- Problem set1
(PDF)
Solution
(PDF)
2- Problem set2
(PDF)
Solution
(PDF)
3- Problem set3
(PDF)
Undergraduate, and Graduates Courses:
- Molecular Structure of Biological Materials (BE.442), Fall 2005
Readings Lecture notes Assignment
- Important Role of Water Molecule, Hydration of Amino Acids, Protein and other Biological Materials
- Amino Acids: Their Chemical and Physical Properties Influence of Ionic Strength, pH, etc.
- Primary and Secondary Structures of Proteins
Dihedral Angles, Peptide Bonds, Planar Structure, Relationship and Propensity of Amino Acid Sequence, Secondary Structure
Ramachandran Plot
- Alpha-helices, 310 Helix, pi Helix, Beta-helices, etc.
Variation of Helices and their Helical Bundles, Two Strand Coiled-coils, Three or Four Strand Coiled-coils, Supercoils
Various Helical Rich Protein Structure Models
Alpha-helices in Biological Materials
- Helical Coiled-coils
Two-, Three-, Four- Stranded Helical Bundles
Applying Coiled-coils to Nanomaterials, Molecular Springs, Switches, etc.
- Beta Sheets: Antiparallel, Parallel, and Twist
Beta Sheet Rich Proteins
Beta Sheets in Biological Materials
- Practical Aspects of Single Crystal X-ray Crystallography, Part 1 X-ray Single Crystal Diffraction, Fiber Diffraction
Preparation of the Samples for Diffraction Analyses
- NMR (Guest Lecturer: Peter Carr, MIT Media Lab)
- Practical Aspects of Single Crystal X-ray Crystallography, Part 2
- Analytical Approaches and Instrumentation (Guest Lecturer: Sotirus Koutsopoulos, Ph.D)
- Silk
- Biomineralization: Sea Creatures
- Biomineralization: Bones and Teeth
- Bioadhesives
1- Important Role of Water Molecule, Hydration of Amino Acids, Protein and other Biological Materials
(PDF)
2- Amino Acids: Their Chemical and Physical Properties
(PDF)
3- Beta Sheets: Antiparallel, Parallel, and Twist; Beta Sheet Rich Proteins; Beta Sheets in Biological Materials
(PDF)
4- Practical Aspects of Single Crystal X-ray Crystallography, Part 1: X-ray Single Crystal Diffraction, Fiber Diffraction, and Preparation of Samples
(PDF)
5- NMR (Guest Lecturer: Peter Carr, MIT Media Lab)
(PDF)
6- Analytical Approaches and Instrumentation (Guest Lecturer: Sotirus Koutsopoulos, Ph.D)
(PDF)
7- Silk
(PDF)
8- Biomineralization: Sea Creatures
(PDF)
9- Biomineralization: Bones and Teeth
(PDF)
10- Bioadhesives
(PDF)
11- Lipids as Building Materials
(PDF)
12- Polysaccharides and Oligosaccharides
(PDF)
Reaction Coordinates of Amino Acid/Surface Binding by David Appleyard
(PDF)
For more information visit: www.ocw.mit.edu
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