The calendar below provides information on the course’s lecture (L) and exam (E) sessions.
| SES # | TOPICS | KEY DATES |
|---|---|---|
| L1 | Introduction: From Tissue Biomechanics to Molecular Nanomechanics | |
| Molecular Mechanics | ||
| L2 |
Length, Time and Forces in Biology Molecules of Interest: DNA, Proteins, Actin, Peptides, Lipids Molecular Forces: Charges, Dipole, Van der Waals, Hydrogen Bonding kT as Ruler of Molecular Forces Thermal Forces and Brownian Motion Life at Low Reynolds Number |
|
| L3 |
Thermodynamics and Elementary Statistical Mechanics Review of Classical Thermodynamics: Entropy, Equilibrium, Open Systems, Ensembles, Boltzmann Distribution, Entropic Forces |
Assignment 1 out |
| L4 |
Ideal Polymer Chains and Entropic Elasticity Statistics of Random Walks - Freely Jointed Chain - Origins of Elastic Forces Extreme Extension of a FJC and Modeling Force as an Effective Potential Field |
|
| L5 |
Persistent Chain Model and Cooperativity The Worm-like Chain Model - Persistence Length as a Measure of Rigidity - Cooperativity Modeled using Ising Models Examples: Actin Length Fluctuations, Pulling on DNA and Synthetic Polymers |
Assignment 1 due |
| L6 |
Mechano-Chemistry Reactions and Chemical Equilibrium - Kramers/Eyring Rate Theories - Effect of Forces on Chemical Equilibrium Examples: Pulling on Titin, Bond Rupture Experiments |
Assignment 2 out |
| L7 |
Motility at the Macromolecular Level Forces by Polymerization - Concept of Equilibrium Force - Motor Proteins - Molecular Springs Examples: Listeria, Acto-myosin Motors, Kinesin, Vorticellid |
|
| L8 |
Linear Elasticity Continuum Mechanics - Basis of Linear Elasticity: Stress, Strain vs. Strain-rate, Hooke’s Law, Experiments to Measure the Moduli |
|
| Tissue Mechanics | ||
| L9 |
Composition and Structure of the Extracellular Matrix (ECM) Collagens, Proteoglycans, Elastin - Cellular Synthesis and Secretion of ECM Macromolecules Cell-mediated Assembly of ECM |
Assignment 2 due |
| L10 |
Pushing and Pulling on Molecules Guest Lecturer: Prof. Matt Lang |
Assignment 3 out |
| L11 |
Elastic (Time-Independent) Behavior of Tissues Stress and Strain in Tissues Modeled via Hookian Constitutive Law - Homogeneous/NonHomogeneous - Isotropic/Anisotropic - Linear/Nonlinear Behavior of Tissues and Relation to the ECM - Relation between Molecular Constituents and Macroscopic Tensile, Compressive, and Shear Properties of Connective Tissues |
Assignment 4 (Term paper) out |
| L12 |
Examples Isotropic Cross-linked Gels Compared to Fibrous Tissues such as Arterial Wall - Cornea (Relevant to Corneal Dystrophy) - Tendon - Ligament - Cartilage - Bone - Lung |
Assignment 3 due |
| L13 |
Viscoelastic (Time-Dependent) Behavior of Tissues Time-dependent Viscoelastic Behavior of Tissues as Single-phase Materials - Transient Behavior (Creep and Stress Relaxation) - Dynamic Behavior (Storage and Loss Moduli) - Lumped Parameter Models (Advantages and Limitations) Examples |
|
| L14 | Viscoelastic (Time-Dependent) Behavior of Tissues (cont.) | |
| L15 |
Poroelastic (Time-Dependent) Behavior of Tissues The Role of Fluid/Matrix Interactions in Tissue Biomechanics - Darcy’s Law and Hydraulic Permeability, Continuity, Conservation of Momentum - Creep, Stress Relaxation, Dynamic Moduli Revisited - Poro-viscoelastic Behavior Examples: Muscle and Soft Tissues in Health and Disease - e.g., Arthritis and Joint Degeneration |
|
| E1 | Midterm Quiz | Assignment 5 due |
| L16 | Poroelastic (Time-Dependent) Behavior of Tissues (cont.) | Assignment 6 out |
| L17 |
Electromechanical and Physicochemical Properties of Tissues Role of Electrical and Chemical Phenomena in Determining Tissue Biomechanical Behavior - Fluid Convection of Ions During Tissue Deformation and the Resulting “Electrokinetic” Phenomena - Electrostatic Interactions between Charged ECM Molecules: Tissue Swelling and Donnan Osmotic Swelling Pressure Examples: Bone, Muscle, Soft Connective Tissues - Streaming Potentials and Electro-osmosis - Tissue Swelling and Molecular Electromechanical Forces |
|
| L18 |
Muscle Constriction From the Molecular to Macro Scale Characteristics of Contracting Muscle - Hill’s Equation - Force-velocity Curves - Muscle Energetics, Activation - Cross-bridge Dynamics - Models for Muscle Behavior |
Assignment 6 due Assignment 7 out |
| Cell Mechanics | ||
| L19 |
Structure of the Cell Cellular Anatomy, Cytoskeleton, Membrane, Types of Attachment to Neighboring Cells or the ECM, Receptors, Different Cell Types, Experimental Measurements of Mechanical Behavior |
|
| L20 |
Biomembranes Stiffness and Role of Transmembrane Proteins - Equations for a 2-D Elastic Plate - Patch-clamp Experiments - Membrane Cortex - Vesicles: Model Systems |
Assignment 7 due Assignment 8 out |
| L21 |
The Cytoskeleton Fiber Microstructure - Actin and Microtubule Dynamics, Methods of Visualizing Actin Diffusion and Polymerization - Rheology of the Cytoskeleton - Active and Passive Measures of Deformation - Storage and Loss Moduli and their Measurements - Models of the Cytoskeleton: Continuum, Microstructural - Tensegrity, Cellular Solids, Polymer Solution |
|
| L22 |
Cell Peeking and Poking Guest Lecturer: Prof. Peter So |
|
| L23 | The Cytoskeleton (cont.) |
Assignment 8 due Term paper due two days after Lecture 23 |
| L24 |
Cell Adhesion and Aggregation Cell Adhesion Assays, Cell-free Adhesion Assays - Receptor-ligand Interactions Mediated by the Cytoskeleton and the Cell Membrane - Focal Adhesions |
Take-home final exam out |
| L25/E2 |
Cell Migration and Mechanotransduction Measurement of Cell Motility (Speed, Persistence, “Diffusivity”) - Simple Models for Cell Migration - Actin Filament Assembly/Crosslinking and Disassembly - Intracellular Signaling Relating to Physical Force - Molecular Mechanisms of Force Transduction - Force Estimates and Distribution within the Cell |
Take-home final due |
