# 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 |