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Browse materialsMIT 20.420J · Fall 2004

Biomolecular Kinetics and Cellular Dynamics (BE.420J)

Subject: Biology

Art: PSM V09 D115 Pasteur apparatus for germ studies, 1876 · Public domain

Instructors: Prof. Bruce Tidor, Prof. Karl Wittrup
Term: Fall 2004
Level: Graduate
What's inside: 1 reading · 4 other files · 4 web pages
Materials open: MIT OCW

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About this course

Source: MIT OpenCourseWare 20.420J Biomolecular Kinetics and Cellular Dynamics (BE.420J), Fall 2004, Prof. Bruce Tidor, Prof. Karl Wittrup — original course page on ocw.mit.edu ↗. License: CC BY-NC-SA 4.0. Study order: MIT's own listing order, section by section. Taken from MIT's published course files, downloaded from ocw.mit.edu on September 23, 2026. How RedLectern is built.

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Syllabus

Grading Scale for Model ImplementationsPDF Download

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Guidelines for Model Implementation AssignmentsPDF Download

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MIT OpenCourseWare, Prof. Bruce Tidor, Prof. Karl Wittrup, 20.420J Biomolecular Kinetics and Cellular Dynamics (BE.420J), Fall 2004.

License: CC BY-NC-SA 4.0 · Edition: Fall 2004 · Open the original course on OCW ↗

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Biomolecular Kinetics and Cellular Dynamics (BE.420J)

Before you start

What's here, and what isn't

Not included here

Materials by section

Syllabus

Assignments

Tools

Lecture 3: Multivalent Binding Equilibria Allostery and Cooperativity Interaction Free Energy Avidity and Effective Concentration (Jencks) Receptor Crosslinking Models

Lecture 4: Multivalent Binding Equilibria (cont.) Immobilized Multivalency (Pluckthun) Soluble Multivalency and Linker Length (Zhou)

Lecture 5: Spectroscopy and Fluorescence Interactions of Light w/Matter, Scatter and Absorb Beer’s Law Fluorescence Theory (Stokes Shift, FRET) Fluorescence Applications (GFP, FRET, Flow Cytometry, Confocal and 2 Photon Microscopy)

Lecture 6: Measurement of Binding Equilibria SPR Optical Spectroscopy Microplate Assays Cell Surface Titration Calorimetry, Ultracentrifugation

Lecture 7: Diffusion Limits in Association Kinetics Shoup/Szabo and Burg/Purcell Surface Diffusion Local Depletion and Recapture Smoluchowski Diffusion Limit Orientation-dependent Interactions

Lecture 8: Temperature and Salt Dependence of Association Kinetics Arrhenius Dependence and Transition State Theory Debye-Hückel Statistics Global Nonlinear Least Squares Confidence Intervals on Fit Parameters

Lecture 9: Biomolecular Interaction Kinetics Analytical and Pseudo 1st - Order Solutions Relaxation (Perturbation, Temperature Jump) Double Jump Approach for Hidden Kinetics

Lecture 10: Biosensor Data Analysis Experimental Method and Design Consistency Checks and Artifacts Mass Transport Effects and Modeling

Lecture 11: Enzyme Kinetics Michaelis-Menten Derivation Reversible Inhibition Receptor Signaling and Kinases

Lecture 12: Complex Reactions and Interactions Student Presentations on Assigned Papers

Lecture 13: Kinetics of Protein Synthesis, Turnover, and Localization General Material Balance and Growth Dilution Steady-state and Kinetics of Intracellular Proteins Receptor Endocytosis and Downregulation Pulse/Chase Internalization and Secretion Rates

Lecture 14: Protein Lifecycles and Localization Student Presentations on Assigned Papers

Lecture 15: Probability Poisson Processes Derivation of Poisson Distribution Exponential Waiting Times Example of Leukocyte Rolling Monte Carlo Simulations Random Number Generation Simulations

Lecture 16: Noise in Biology Student Presentations on Assigned Papers

Lecture 17: Cell Growth Kinetics and Bioreactors Balanced Growth, Stoichiometry, Monod Classifications, Segregated and Structured Chemostat Balance and Washout

Lecture 18: Networks and Systems Chemotaxis Basic Control Theory and Robustness

Lecture 19: Populations Student Presentations on Assigned Papers

Lecture 20: Fundamentals of Nonlinear Dynamics Linear Systems of ODEs Fixed Point Classification Linearization and Local Stability Bifurcations

Lecture 21: Gene Expression - Hysteresis and Switches Student Presentations on Assigned Papers

Lecture 22: Gene Expression: Oscillations Student Presentations on Assigned Papers

Lecture 23: Spatial heterogeneity: Diffusion and Pharmacokinetics Student Presentations on Assigned Papers

Lecture 24: Pharmacokinetics Plasma Clearance Kinetics and Mechanisms One and Two Compartment Models Physiological Models Formulation and Bioavailability

Lecture 25: Transport Effects on Biomolecular Interactions Weisz Analysis, Thiele Modulus, Damkohler # Shrinking Core Model and Tumor Penetration