Molecular, Cellular and Tissue Biomechanics (BE.410J)

Lecture Notes

SES #	TOPICS	LECTURE SLIDES	LECTURE NOTES
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)