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

Calendar / Schedule


The calendar below provides information on the course's lecture (L) and exam (E) sessions.
L1Introduction: From Tissue Biomechanics to Molecular Nanomechanics
Molecular Mechanics
L2Length, 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
L3Thermodynamics and Elementary Statistical Mechanics

Review of Classical Thermodynamics: Entropy, Equilibrium, Open Systems, Ensembles, Boltzmann Distribution, Entropic Forces
Assignment 1 out
L4Ideal 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
L5Persistent 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

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

Examples: Pulling on Titin, Bond Rupture Experiments
Assignment 2 out
L7Motility at the Macromolecular Level

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

Examples: Listeria, Acto-myosin Motors, Kinesin, Vorticellid
L8Linear Elasticity

Continuum Mechanics - Basis of Linear Elasticity: Stress, Strain vs. Strain-rate, Hooke's Law, Experiments to Measure the Moduli
Tissue Mechanics
L9Composition 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
L10Pushing and Pulling on Molecules

Guest Lecturer: Prof. Matt Lang
Assignment 3 out
L11Elastic (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

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
L13Viscoelastic (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)

L14Viscoelastic (Time-Dependent) Behavior of Tissues (cont.)
L15Poroelastic (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
E1Midterm QuizAssignment 5 due
L16Poroelastic (Time-Dependent) Behavior of Tissues (cont.)Assignment 6 out
L17Electromechanical 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
L18Muscle 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
L19Structure 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

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
L21The 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
L22Cell Peeking and Poking

Guest Lecturer: Prof. Peter So
L23The Cytoskeleton (cont.) Assignment 8 due

Term paper due two days after Lecture 23
L24Cell 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/E2Cell 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


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