20.420
Principles of Molecular Bioengineering
Provides an introduction to the mechanistic analysis and engineering of biomolecules and biomolecular systems. Covers methods for measuring, modeling, and manipulating systems, including biophysical experimental tools, computational modeling approaches, and molecular design. Equips students to take systematic and quantitative approaches to the investigation of a wide variety of biological phenomena.
Fall 2004 · Biomolecular Kinetics and Cellular Dynamics (BE.420J)
Topics
- Complex Reactions and Interactions Student Presentations on Assigned Papers
- Protein Lifecycles and Localization Student Presentations on Assigned Papers
- Noise in Biology Student Presentations on Assigned Papers
Readings
- Lauffenburger, Douglas A., and J. Jennifer Linderman. Receptors: Models for Binding, Trafficking, and Signaling . New York, NY: Oxford University Press, 1995. ISBN: 9780195106633.
- Hammes, Gordon G. Thermodynamics and Kinetics for the Biological Sciences . Hoboken, NJ: John Wiley and Sons, 2000. ISBN: 9780471374916.
- Creighton, Thomas E. Proteins: Structures and Molecular Properties . 2nd ed. New York, NY: W.H. Freeman and Company, 1993. ISBN: 9780716723172.
- Bailey, James, and David F. Ollis. Biochemical Engineering Fundamentals . 2nd ed. New York, NY: McGraw Hill Higher Education, 1986. ISBN: 9780070032125.
- Steinfeld, Jeffrey I., J. S. Francisco, and W. L. Hase. Chemical Kinetics and Dynamics . 2nd ed. E. Upper Saddle River, NJ: Prentice Hall PTR, 1998. ISBN: 9780137371235.
- Cantor, Charles R., and Paul R. Schimmel. Biophysical Chemistry . New York, NY: W.H. Freeman, 1980. ISBN: 9780716711889, ISBN: 9780716711902, and ISBN: 9780716711926.
- Blanch, Harvey W., and D. S. Clark, eds. Biochemical Engineering . Boca Raton, FL: CRC, 1997. ISBN: 9780824700997.
- Shargel, Leon, et al. Applied Biopharmaceutics and Pharmacokinetics . New York, NY: McGraw-Hill Professional Publishing, 2004. ISBN: 9780071375504.
- Carberry, James J. Chemical and Catalytic Reaction Engineering . New York, NY: McGraw-Hill, 1976. ISBN: 9780070097902.
- Strogatz, Steven H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering . Cambridge, MA: Perseus Publishing, 2001. ISBN: 9780738204536.
- Lauffenburger, Douglas A., and J. Jennifer Linderman. Receptors: Models for Binding, Trafficking, and Signaling . New York: Oxford University Press, 1995. ISBN: 9780195106633.
- Creighton, Thomas E. Proteins: Structures and Molecular Properties . 2nd ed. New York, NY: W. H. Freeman and Company, 1993. ISBN: 9780716723172.
- Bailey, James, and David F. Ollis. Biochemical Engineering Fundamentals . 2nd ed. Burr Ridge, IL: McGraw Hill Higher Education, 1986. ISBN: 9780070032125.
- Steinfeld, Jeffrey I., J. S. Francisco, and W. L. Hase. Chemical Kinetics and Dynamics . 2nd ed. E. Rutherford, NJ: Prentice Hall PTR, 1998. ISBN: 9780137371235.
- Cantor, Charles R., and Paul R. Schimmel. Biophysical Chemistry . New York, NY: Worth Publishers, 1980. ISBN: 9780716711889, ISBN: 9780716711902, and ISBN: 9780716711926.
- Blanch, Harvey W., and D. S. Clark, eds. Biochemical Engineering . New York, NY: Marcel Dekker, 1997. ISBN: 9780824700997.
- Strogatz, Steven H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering . Cambridge, MA: Perseus Publishing, 2000. ISBN: 9780738204536.
- Noncovalent Biomolecular Interactions
- Protein-Ligand Binding Equilibria
- Multivalent Binding Equilibria
- Multivalent Binding Equilibria (cont.)
- Spectroscopy and Fluorescence
- Measurement of Binding Equilibria SPR
- Diffusion Limits in Association Kinetics
- Temperature and Salt Dependence of Association Kinetics
- Biomolecular Interaction Kinetics Analytical and Pseudo 1 st - Order Solutions
- Biosensor Data Analysis
- Enzyme Kinetics Michaelis-Menten Derivation
- Complex Reactions and Interactions
- * Huang, C. F., and J. E. Ferrell. “Ultrasensitivity in the Mitogen-activated Protein Kinase Cascade.” PNAS 93 (1996): 10078-83.
- Lipschultz, C. A., A. Yee, S. Mohan, Y. Li, and S. J. Smith-Gill. “Temperature Differentially Affects Encounter and Docking Thermodynamics of Antibody-Antigen Association.” J Mol Recognit . 15, no. 1 (January, February 2002): 44-52.
- Kinetics of Protein Synthesis, Turnover, and Localization
- Protein Lifecycles and Localization
- Haugh, J. M. “Mathematical Model of Human Growth Hormone (hGH)-Stimulated Cell Proliferation Explains the Efficacy of hGH Variants as Receptor Agonists or Antagonists.” Biotechnology Progress , in Press 2004.
- * Fallon, E. M., and D. A. Lauffenburger. “Computational Model for Effects of Ligand/Receptor Binding Properties on Interleukin-2 Trafficking Dynamics and T Cell Proliferation Response.” Biotechnology Progress 16 (2000): 905-16.
- Probability Poisson Processes
- * Rao, C. V., and A. P. Arkin. “Stochastic Chemical Kinetics and the Quasi-Steady-State Assumption: Application to the Gillespie Algorithm.” J. Chem Phys 118 (2003): 4999.
- Raser, J. M., and E. K. O’Shea. “Control of Stochasticity in Eukaryotic Gene Expression.” Science 304, no. 5678 (Jun 18, 2004): 1811-14.
- Cell Growth Kinetics and Bioreactors
- Networks and Systems Chemotaxis
- Perelson, A. S., A. U. Neumann, M. Markowitz, J. M. Leonard, and D. D. Ho. “HIV-1 Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time.” Science 271 (1996): 1582-86.
- * Kaplan, E. H., D. L. Craft, and L. M. Wein. “Emergency Response to a Smallpox Attack: The Case for Mass Vaccination.” PNAS 99 (2002): 10935.
- Fundamentals of Nonlinear Dynamics
- Gene Expression - Hysteresis and Switches
- * Gardner, T. S., C. R. Cantor, and J. J. Collins. “Construction of a Genetic Toggle Switch in Escherichia Coli.” Nature 403, no. 339 (2000).
- Xiong, W., and J. E. Ferrell Jr. “A Positive-Feedback-Based Bistable ‘Memory Module’ that governs a Cell Fate Decision.” Nature 426, no. 6965 (November 27, 2003): 460-65.
- Gene Expression: Oscillations
- * Tyson, J. J., C. I. Hong, C. D. Thron, and B. Novak. “A Simple Model of Circadian Rhythms Based on Dimerization and Proteolysis of PER and TIM.” Biophys J . 77, no. 5 (November 1999): 2411-7.
- Gilg, Olivier, Ilkka Hanski, and Benoît Sittler. “Cyclic Dynamics in a Simple Vertebrate Predator-Prey Community.” Science 302 (October 31, 2003): 866-68.
- Spatial heterogeneity: Diffusion and Pharmacokinetics
- Hicks, K. O., F. B. Pruijn, J. R. Sturman, W. A. Denny, and W. R. Wilson. “Multicellular Resistance to Tirapazamine is due to Restricted Extravascular Transport: a Pharmacokinetic/Pharmacodynamic Study in HT29 Multicellular Layer Cultures.” Cancer Res . 63, no. 18 (September 15, 2003): 5970-7.
- Zhu, H., R. K. Jain, and L. T. Baxter. “Tumor Pretargeting for Radioimmunodetection and Radioimmunotherapy.” J Nucl Med . 39, no. 1 (1998): 65-76.
- Pharmacokinetics
- Transport Effects on Biomolecular Interactions
Prerequisites & course information
Same subject as 10.538[J] Prereq: 7.06 and 18.03 G (Fall) 3-0-9 units
Sources
- Course catalogue ↗2026–2027
- MIT OpenCourseWare ↗Fall 2004
- MIT OCW calendar ↗
- MIT OCW syllabus ↗
- MIT OCW readings ↗
- Historical MIT OpenCourseWare offering. Named reading entries and schedule topics are automatically extracted from the linked source pages.