Biomolecular Kinetics and Cellular Dynamics (BE.420J)

Calendar

LEC #	TOPICS	KEY DATES
1	Noncovalent Biomolecular Interactions Significance in Cell Function Measure, Model, Manipulate at Molecular Level Bonding Forces (HB, VdW, Elec, HE) Solvation and the Role of Water Standard States, Free Energy, Kd Typical Ranges of Affinity, On and Off Rates Free Energy, Enthalpy, and Entropy Characteristics of Interfaces Ala Scan and Double Mutant Cycles
2	Protein-Ligand Binding Equilibria Monovalent Reversible Equilibria Analytic and Pseudo - 1st Order Approx Isotherms Immobilized Protein/Ligand Interactions Graphical Representations of Binding Equilibria Immobilized Protein Binding Data Plotting and Analysis Statistics of Multiple Identical Sites
3	Multivalent Binding Equilibria Allostery and Cooperativity Interaction Free Energy Avidity and Effective Concentration (Jencks) Receptor Crosslinking Models	Homework 1 due
4	Multivalent Binding Equilibria (cont.) Immobilized Multivalency (Pluckthun) Soluble Multivalency and Linker Length (Zhou)
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)	Homework 2 due
6	Measurement of Binding Equilibria SPR Optical Spectroscopy Microplate Assays Cell Surface Titration Calorimetry, Ultracentrifugation
7	Diffusion Limits in Association Kinetics Shoup/Szabo and Burg/Purcell Surface Diffusion Local Depletion and Recapture Smoluchowski Diffusion Limit Orientation-dependent Interactions	Homework 3 due
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
9	Biomolecular Interaction Kinetics Analytical and Pseudo 1st - Order Solutions Relaxation (Perturbation, Temperature Jump) Double Jump Approach for Hidden Kinetics	Homework 4 due
10	Biosensor Data Analysis Experimental Method and Design Consistency Checks and Artifacts Mass Transport Effects and Modeling
11	Enzyme Kinetics Michaelis-Menten Derivation Reversible Inhibition Receptor Signaling and Kinases	Homework 5 due
12	Complex Reactions and Interactions Student Presentations on Assigned Papers
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	Model implementation 1 due
14	Protein Lifecycles and Localization Student Presentations on Assigned Papers
15	Probability Poisson Processes Derivation of Poisson Distribution Exponential Waiting Times Example of Leukocyte Rolling Monte Carlo Simulations Random Number Generation Simulations	Model implementation 2 due
16	Noise in Biology Student Presentations on Assigned Papers
17	Cell Growth Kinetics and Bioreactors Balanced Growth, Stoichiometry, Monod Classifications, Segregated and Structured Chemostat Balance and Washout	Model implementation 3 due
18	Networks and Systems Chemotaxis Basic Control Theory and Robustness	Homework 6 due
19	Populations Student Presentations on Assigned Papers
20	Fundamentals of Nonlinear Dynamics Linear Systems of ODEs Fixed Point Classification Linearization and Local Stability Bifurcations	Model implementation 4 due
21	Gene Expression - Hysteresis and Switches Student Presentations on Assigned Papers
22	Gene Expression: Oscillations Student Presentations on Assigned Papers	Model implementation 5 due
23	Spatial heterogeneity: Diffusion and Pharmacokinetics Student Presentations on Assigned Papers	Model implementation 6 due
24	Pharmacokinetics Plasma Clearance Kinetics and Mechanisms One and Two Compartment Models Physiological Models Formulation and Bioavailability
25	Transport Effects on Biomolecular Interactions Weisz Analysis, Thiele Modulus, Damkohler # Shrinking Core Model and Tumor Penetration