L1

Introduction: From Tissue Biomechanics to Molecular Nanomechanics

(PDF - 1.1 MB)

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

(PDF)

(PDF)

L3

Thermodynamics and Elementary Statistical Mechanics

Review of Classical Thermodynamics: Entropy, Equilibrium, Open Systems, Ensembles, Boltzmann Distribution, Entropic Forces

Tutorial on Statistical Mechanics

(PDF)

(PDF)

(PDF)

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

(PDF)

(PDF)

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

(PDF)

(PDF)

L6

Mechano-Chemistry

Reactions and Chemical Equilibrium - Kramers/Eyring Rate Theories - Effect of Forces on Chemical Equilibrium

Examples: Pulling on Titin, Bond Rupture Experiments

(PDF)

(PDF)

L7

Motility at the Macromolecular Level

Forces by Polymerization - Concept of Equilibrium Force - Motor Proteins - Molecular Springs

Examples: Listeria, Acto-myosin Motors, Kinesin, Vorticellid

(PDF)

L8

Linear Elasticity

Continuum Mechanics - Basis of Linear Elasticity: Stress, Strain vs. Strain-rate, Hooke's Law, Experiments to Measure the Moduli

(PDF - 1.5 MB)

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

(PDF)

(PDF)

L10

Pushing and Pulling on Molecules

Guest Lecturer: Prof. Matt Lang

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

(PDF)

(PDF)

L12

Examples

Isotropic Cross-linked Gels Compared to Fibrous Tissues such as Arterial Wall, Cornea (Relevant to Corneal Dystrophy), Tendon, Ligament, Cartilage, Bone, Lung

(PDF)

(PDF)

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

(PDF)

L14

Viscoelastic (Time-Dependent) Behavior of Tissues (cont.)

(PDF)

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

(PDF)

E1

Midterm Quiz

L16

Poroelastic (Time-Dependent) Behavior of Tissues (cont.)

(PDF)

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

(PDF)

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

(PDF)

(PDF)

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

(PDF)

(PDF)

L20

Biomembranes

Stiffness and Role of Transmembrane Proteins - Equations for a 2-D Elastic Plate - Patch-clamp Experiments - Membrane Cortex - Vesicles: Model Systems

(PDF)

(PDF)

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

(PDF)

(PDF)

L22

Cell Peeking and Poking

Guest Lecturer: Prof. Peter So

L23

The Cytoskeleton (cont.)

(PDF)

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

(PDF)

(PDF)

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

(PDF)

(PDF)