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Course Criteria
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3.00 Credits
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.
Prerequisite:
Prereq: Biology (GIR); 2.002, 2.006, 6.013, 10.301, or 10.302
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3.00 Credits
Fundamental analysis of biological rate processes using approaches from biomolecular reaction kinetics and dynamical systems engineering. Topics include binding and hybridization interactions, enzyme reactions, metabolic cycles, gene regulation, receptor/ligand trafficking systems, intra- and intercellular signaling, and cell population dynamics.
Prerequisite:
Prereq: 7.05, 7.06, 18.03
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3.00 Credits
Molecular diffusion, diffusion-reaction, conduction, convection in biological systems; fields in heterogeneous media; electrical double layers; Maxwell stress tensor, electrical forces in physiological systems. Fluid and solid continua: equations of motion useful for porous, hydrated biological tissues. Case studies of membrane transport, electrode interfaces, electrical, mechanical, and chemical transduction in tissues, convective-diffusion/reaction, electrophoretic, electroosmotic flows in tissues/MEMs, and ECG. Electromechanical and physicochemical interactions in cells and biomaterials; musculoskeletal, cardiovascular, and other biological and clinical examples.
Prerequisite:
Prereq: 6.013, 2.005, 10.302, or permission of instructor
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3.00 Credits
Covers current models and descriptions of the internal cell dynamics of macromolecules due to reaction and transport. Two major areas will be explored: the process of gene expression, including protein-DNA interactions, chromatin dynamics, and the stochastic nature of gene expression; and cell signaling systems, especially those that lead to or rely on intracellular protein gradients. This class is intended for graduate students or advanced undergraduates with some background in cell biology, transport, and kinetics. An introductory class in probability is recommended.
Prerequisite:
Prereq: 18.03, 7.06, 10.302, or permission of instructor
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6.00 Credits
Comprehensive treatment of the kinetics of basic chemical reactions and biological processes. Subject begins with a foundamental analysis of reaction order in homogeneous reactions and proceeds with the kinetics of heterogeneous systems and catalytic reactions. Methods of measuring and calculating reaction rate constants included. After a basic stoichiometric analysis of biological reaction networks, the subject discusses kinetics of enzymatic reactions and extensions to kinetic characteristics of reaction pathways and bioreaction networks. Similarities and differences between chemical and biological kinetics discussed along with concepts of rate-limiting steps and distribution of control among several reactions in a pathway. Subject concludes with applications to the kinetic analysis of chemical and biological reaction systems in the chemical and bioprocess industries.
Prerequisite:
Prereq: 10.37 or permission of instructor
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3.00 Credits
Interaction of chemical engineering, biochemistry, and microbiology. Mathematical representations of microbial systems. Kinetics of growth, death, and metabolism. Continuous fermentation, agitation, mass transfer, and scale-up in fermentation systems, enzyme technology.
Prerequisite:
Prereq: Permission of instructor
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3.00 Credits
Addresses the multifaceted biochemical problem of protein folding and the surprising ways it affects biological systems. Considers underlying chemistry and cellular biology, folding intermediates and off-pathway reactions, and the roles of chaperones and other folding assistants. Covers the amyloid fold, beneficial amyloid functions, major protein folding diseases (such as Alzheimer's and Prion diseases) and the effects of protein folding on the evolution of novel functions.
Prerequisite:
Prereq: 7.51 or permission of instructor
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3.00 Credits
Presentation of a framework for quantitative understanding of cell functions as integrated molecular systems. Analysis of cell-level processes in terms of underlying molecular mechanisms based on thermodynamics, kinetics, mechanics, and transport principles, emphasizing an engineering, problem-oriented perspective. Objective is to rationalize target selection for genetic engineering and evaluate the physiology of recombinant cells. Topics include cell metabolism and energy production, transport across cell compartment barriers, protein synthesis and secretion, regulation of gene expression, transduction of signals from extracellular environment, cell proliferation, cell adhesion and migration.
Prerequisite:
Prereq: 5.60, 7.05, 10.302, 18.03
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3.00 Credits
Develops classical equilibrium statistical mechanical concepts for application to chemical physics problems. Basic concepts of ensemble theory formulated on the basis of thermodynamic fluctuations. Examples of applications include Ising models, lattice models of binding, ionic and non-ionic solutions, liquid theory, polymer and protein conformations, phase transition, and pattern formation. Introduces computational techniques with examples of liquid and polymer simulations.
Prerequisite:
Prereq: 5.60 or permission of instructor
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3.00 Credits
Description and critical assessment of the major issues and stages of developing a pharmaceutical or biopharmaceutical. Drug discovery, preclinical development, clinical investigation, manufacturing and regulatory issues considered for small and large molecules. Economic and financial considerations of the drug development process. Multidisciplinary perspective from faculty in clinical; life; and management sciences; as well as industry guests.
Prerequisite:
Prereq: Permission of instructor
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