| 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 |