About Initiative Knowledge Hubs Projects Lab Education Contact Talks News Wiki
Transport Phenomnea in Biological, Biophysical, and Physiological Systems

Time & Place: TBD

Instructor:
Jun Ni, Ph.D., Associate Professor
Department of Radiology, Carver College of Medicine,
Department of Biomedical Engineering, College of Engineering
Department of Mechanical Engineering, College of Engineering
Department of Computer Science, College of Liberal Arts
The University of Iowa, Iowa City, IA, USA
Tel: (319) 335-9490
E-mail: jun-ni@uiowa.edu

Office Hours and Place:

Textbook:
George A. Truskey, Fan Yuan, David F. Katz , "Transport Phenomena in Biological System ," Second Edition, Pearson Prentice Hall, 2008.

 

 

 

 

Class Lecture Notes:
Additional notes or handouts may be available in classroom.

Course Description: this course addresses the issues of transport phenomena in biological and physiological systems. It presents engineering fundamentals and biological applications, and helps biomedical students learn how to develop and critically analyze models of biological transport and reaction processes. It course covers topics in fluid mechanics, mass transport, and biochemical interactions, with engineering concepts motivated by specific biological and physiological problems. The course is designed for graduate level biomedical students, and thermal science students who are interested in modeling and simulations of transport phenomena in biomedical systems.

Pre-requisites: TBD

Course Contents:

1. Introduction (Lecture I, 1st Week)

1.1. The Role of Transport Processes in Biological Systems
1.2. Definition of Transport Processes

1.2.1. Diffusion
1.2.2. Convection
1.2.3. Transport by Binding Interactions

1.3. Relative Importance of Convection and Diffusion
1.4. Transport Within Cells

1.4.1. Transport Across the Cell Membrane
1.4.2. Transport Within the Cell

1.5. Transcellular Transport

1.5.1. Junctions Between Cells
1.5.2. Epithelial Cells
1.5.3. Endothelial Cells

1.6. Physiological Transport Systems

1.6.1. Cardiovascular System
1.6.2. Respiratory System
1.6.3. Gastrointestinal Tract
1.6.4. Liver
1.6.5. Kidneys
1.6.6. Integrated Organ Function

1.7. Application of Transport Processes in Disease Pathology, Treatment, and Device Development

1.7.1. Transport Processes and Atherosclerosis
1.7.2. Transport Processes and Cancer Treatment
1.7.3. Transport Processes, Artificial Organs, and Tissue Engineering
1.8. Relative Importance of Transport and Reaction Processes

Part I. Introduction to Physiological Fluid Mechanics

2. Conservation Relations and Momentum Balances (Lecture 200, Second Week)

2.1. Introduction
2.2. Fluid Kinematics

2.2.1. Control Volumes
2.2.2. Velocity Field
2.2.3. Flow Rate
2.2.4. Acceleration
2.2.5. Fluid Streamlines
2.3. Conservation Relations and Boundary Conditions
2.3.1. Conservation of Mass
2.3.2. Momentum Balances
2.3.3. Forces
2.3.4. Boundary Conditions
2.4. Fluid Statics
2.4.1. Static Equilibrium
2.4.2. Surface Tension
2.4.3. Membrane and Cortical Tension
2.5. Constitutive Relations
2.5.1. Newton’s Law of Viscosity
2.5.2. Non-Newtonian Rheology
2.5.3. Time-Dependent Viscoelastic Behavior
2.6. Laminar and Turbulent Flow
2.7. Application of Momentum Balances
2.7.1. Flow Induced by a Sliding Plate
2.7.2. Pressure-Driven Flow Through a Narrow Rectangular Channel
2.7.3. Pressure-Driven Flow Through a Cylindrical Tube
2.7.4. Pressure-Driven Flow of a Power Law Fluid in a Cylindrical Tube
2.7.5. Flow Between Rotating Cylinders
2.8. Rheology and Flow of Blood
2.8.1. Measurement of Blood Viscosity
2.8.2. Rheology of Blood Flow in Large Vessels
2.8.3. Blood Flow in Small Tubes
2.8.4. Blood Flow in Capillaries
2.8.5. Regulation of Blood Flow
3. Conservation Relations for Fluid Transport, Dimensional Analysis, and Scaling (Lecture 300, Third Week)
3.1. Introduction
3.2. Differential Form of the Equation of Conservation of Mass in Three Dimensions
3.2.1. General Form of the Equation of Conservation of Mass
3.2.2. Conservation of Mass for Incompressible Fluids
3.3. Differential Form of the Conservation of Linear Momentum and the Navier–Stokes Equations in Three Dimensions
3.3.1. General Form of the Equation of Conservation of Linear Momentum
3.3.2. The Navier–Stokes Equation for an Incompressible Newtonian Fluid
3.4. Fluid Motion with More Than One Dependent Variable
3.4.1. Two-Dimensional Flow in a Channel
3.4.2. Time Required to Establish a Steady Flow in a Rectangular Channel
3.5. Dimensional Analysis and Dimensionless Groups
3.5.1. Dimensional Analysis
3.5.2. Dimensionless Form of the Navier–Stokes Equation
3.5.3. Dimensional Analysis and Dynamic Similarity
3.6. Low-Reynolds-Number Flow
3.6.1. Conservation Relations for Low-Reynolds-Number Flow
3.6.2. Low-Reynolds-Number Flow Around a Sphere
4. Approximate Methods for the Analysis of Complex Physiological Flow (Lecture 400, Fourth Week)
4.1. Introduction
4.2. Integral Form of the Equation of Conservation of Mass
4.3. Integral Form of the Equation of Conservation of Linear Momentum
4.4. Bernoulli’s Equation
4.4.1. Bernoulli’s Equation Applied to Stenotic Heart Valves
4.4.2. The Engineering Bernoulli Equation: The Effects of Viscous Losses and Time-Dependent Energy Changes
4.5. Boundary Layer Theory
4.5.1. Background to Boundary Layer Theory
4.5.2. Derivation of the Boundary Layer Equations
4.5.3. Integral Momentum Equations for Boundary Layer Flows
4.6. Flow Separation
4.7. Lubrication Theory
4.8. Peristaltic Pumping
5. Fluid Flow in the Circulation and Tissues (Lecture500, Fifth Week)
5.1. Introduction
5.2. Oscillating Flow in a Cylindrical Tube
5.3. Entrance Lengths
5.4. Flow in Curved Vessels
5.5. Flow in Branching Vessels
5.6. Flow in Specific Arteries
5.6.1. Carotid Artery
5.6.2. Aorta
5.6.3. Effect of Vessel Wall Elasticity
5.6.4. Coronary Arteries
5.7. Arterial Fluid Dynamics and Atherosclerosis
5.7.1. Hemodynamic Variables Associated with Atherosclerosis
5.7.2. Effect of Hemodynamics upon Endothelial Cell Function
5.8. Heart-Valve Hemodynamics
5.8.1. Artificial Heart Valves
5.8.2. Turbulent Flow Around Heart Valves
5.9. Fluid Dynamic Effects of Reconstructive Surgery for Congenital Heart Defects

Midterm I

Part II. Fundamentals and Applications of Mass Transport in Biological Systems

6. Mass Transport in Biological Systems (Lecture600, Sixth Week)

6.1. Introduction
6.2. Solute Fluxes in Mixtures
6.2.1. The Dilute-Solution Assumption
6.3. Conservation Relations
6.3.1. Equation of Conservation of Mass for a Mixture
6.3.2. Boundary Conditions
6.4. Constitutive Relations
6.4.1. Fick’s Law of Diffusion for Dilute Solutions
6.4.2. Diffusion in Concentrated Solutions
6.5. Diffusion as a Random Walk
6.6. Estimation of Diffusion Coefficients in Solution
6.6.1. Transport Properties of Proteins
6.6.2. The Stokes–Einstein Equation
6.6.3. Estimation of Frictional Drag Coefficients
6.6.4. The Effects of Actual Surface Shape and Hydration
6.6.5. Correlations
6.7. Steady-State Diffusion in One Dimension
6.7.1. Diffusion in Rectangular Coordinates
6.7.2. Radial Diffusion in Cylindrical Coordinates
6.7.3. Radial Diffusion in Spherical Coordinates
6.8. Unsteady Diffusion in One Dimension
6.8.1. One-Dimensional Diffusion in a Semi-Infinite Medium
6.8.2. One-Dimensional Unsteady Diffusion in a Finite Medium
6.8.3. Model of Diffusion of a Solute into a Sphere from a Well-Stirred Bath
6.8.4. Quasi-Steady Transport Across Membranes
6.9. Diffusion-Limited Reactions
6.9.1. Diffusion-Limited Binding and Dissociation in Solution
6.9.2. Diffusion-Limited Binding Between a Cell Surface Protein and a Solute
6.9.3. Diffusion-Limited Binding on a Cell Surface
6.10. A Thermodynamic Derivation of the Stokes–Einstein Equation
7. Diffusion with Convection or Electrical Potentials (Lecture700, Seventh Week)
7.1. Introduction
7.2. Fick’s Law of Diffusion and Solute Flux
7.3. Conservation of Mass for Dilute Solutions
7.3.1. Transport in Multicomponent Mixtures
7.4. Dimensional Analysis
7.5. Electrolyte Transport
7.5.1. Nernst–Planck Equation
7.5.2. Electrolyte Transport Across Membranes
7.6. Diffusion and Convection
7.6.1. Release from the Walls of a Channel: A Short-Contact-Time Solution
7.6.2. Momentum and Concentration Boundary Layers
7.7. Macroscopic Form of Conservation Relations for Dilute Solutions
7.8. Mass Transfer Coefficients
7.9. Mass Transfer Across Membranes: Application to Hemodialysis
7.9.1. Cocurrent Exchange
7.9.2. Countercurrent Exchange
8. Transport in Porous Media (Lecture800, Eighth Week)
8.1. Introduction
8.2. Porosity, Tortuosity, and Available Volume Fraction
8.3. Fluid Flow in Porous Media
8.3.1. Darcy’s Law
8.3.2. Brinkman Equation
8.3.3. Squeeze Flow
8.4. Solute Transport in Porous Media
8.4.1. General Considerations
8.4.2. Effective Diffusion Coefficient in Hydrogels
8.4.3. Effective Diffusion Coefficient in a Liquid-Filled Pore
8.4.4. Effective Diffusion Coefficient in Biological Tissues
8.5. Fluid Transport in Poroelastic Materials
9. Transvascular Transport (Lecture900, Ninth Week)
9.1. Introduction
9.2. Pathways for Transendothelial Transport
9.2.1. Continuous Capillaries
9.2.2. Fenestrated Capillaries
9.2.3. Discontinuous Capillaries
9.3. Rates of Transvascular Transport
9.3.1. Osmotic Pressure
9.3.2. Rate of Fluid Flow and Starling’s Law of Filtration
9.3.3. Rate of Solute Transport and the Kedem–Katchalsky Equation
9.4. Phenomenological Constants in the Analysis of Transvascular Transport
9.5. A Limitation of Starling’s Law
9.5.1. Fluid Filtration in the Steady State
9.5.2. A New View of Starling’s Law

Midterm II

Part III. The Effect of Mass Transport Upon Biochemical Interactions

10. Mass Transport and Biochemical Interactions (Lecture1000, Tenth Week)

10.1. Introduction
10.2. Chemical Kinetics and Reaction Mechanisms
10.2.1. Reaction Rates
10.2.2. Reaction Mechanisms
10.2.3. First-Order Reactions
10.2.4. Second-Order Irreversible Reactions
10.2.5. Reversible Reactions
10.3. Sequential Reactions and the Quasi–Steady-State Assumption
10.4. Enzyme Kinetics
10.4.1. Derivation of Michaelis–Menten Kinetics
10.4.2. Application of the Quasi–Steady-State Assumption to Enzyme Kinetics
10.4.3. Determination of K_m and R_{max}
10.5. Regulation of Enzyme Activity
10.5.1. Competitive Inhibition
10.5.2. Uncompetitive and Noncompetitive Inhibition
10.5.3. Substrate Inhibition
10.6. Effect of Diffusion and Convection on Chemical Reactions
10.6.1. Reaction and Diffusion in Solution
10.6.2. Interphase Mass Transfer and Reaction
10.6.3. Intraphase Chemical Reactions
10.6.4. Interphase and Intraphase Diffusion and Reaction
10.6.5. Observable Quantities and the Effectiveness Factor
10.6.6. Transport Effects on Enzymatic Reactions
11. Cell-Surface Ligand–Receptor Kinetics and Molecular Transport Within Cells (Lecture1100, Eleventh Week)
11.1. Introduction
11.2. Receptor–Ligand Binding Kinetics
11.3. Determination of Rate Constants for Receptor–Ligand Binding
11.4. Deviations from Simple Bimolecular Kinetics
11.4.1. Ligand Depletion
11.4.2. Two or More Receptor Populations
11.4.3. Interconverting Receptor Subpopulations
11.5. Receptor-Mediated Endocytosis
11.5.1. A Kinetic Model for LDL Receptor-Mediated Endocytosis
11.5.2. Receptor Interaction with Coated Pits
11.6. Receptor Regulation During Receptor-Mediated Endocytosis
11.7. Signal Transduction
11.7.1. Qualitative Aspects of Signal Transduction
11.7.2. Quantitative Aspects of Signal Transduction
11.8. Regulation of Gene Expression
11.8.1. Simplified Model for Gene Induction and Expression
12. Cell Adhesion (Lecture1200, Twelve Week)
12.1. Introduction, 582
12.2. Effect of Force on Bond Association and Dissociation
12.2.1. The Influence of Energy Barriers on Molecular Interactions
12.2.2. Bond Disruption in the Presence of an Applied Force
12.2.3. Bond Formation in the Presence of an Applied Force
12.2.4. The Effect of Loading Rates on Bond Forces
12.3. Cell–Matrix Adhesion
12.3.1. Cell Attachment
12.3.2. Cell Detachment
12.4. Biophysics of Leukocyte Rolling and Adhesion
12.4.1. Overview
12.4.2. Modeling Leukocyte–Endothelial Cell Interactions
12.4.3. Effect of Cell Deformation on Leukocyte Adhesion to Endothelium
12.5. Stochastic Effects on Chemical Interactions
12.5.1. Kinetic Analysis of Stochastic Chemical Reactions
12.5.2. Monte Carlo Analysis of Stochastic Chemical Reactions

Part IV. Transport in Organs

13. Transport of Gases Between Blood and Tissues (Lecture1300, Thirteenth Week)

13.1. Introduction
13.2. Oxygen–Hemoglobin Equilibria, 626
13.3. Oxygen–Hemoglobin Binding Kinetics, 631
13.4. Dynamics of Oxygenation of Blood in Lung Capillaries, 632
13.5. Oxygen Delivery to Tissues, 637
13.5.1. The Krogh Cylinder Model of Oxygen Transport in Tissues
13.5.2. Analysis of Assumptions Used in the Krogh Model
13.6. Nitric Oxide Production and Transport in Tissues
13.6.1. NO Formation and Reaction
13.6.2. NO Formation, Diffusion, and Reaction in Tissues
14. Transport in the Kidneys (Lecture1400, Fourth Week)
14.1. Introduction
14.2. Mechanisms of Transmembrane Transport
14.2.1. Direct Diffusion
14.2.2. Facilitated Transport
14.2.3. Active Transport
14.3. Renal Physiology
14.3.1. Renal Blood Flow
14.3.2. Urine Formation
14.4. Quantitative Analysis of Glomerular Filtration
14.4.1. Hydraulic Conductivity of Glomerular Capillaries
14.4.2. Solute Transport Across Glomerular Capillaries
14.5. Quantitative Analysis of Tubular Reabsorption
14.5.1. Mass Balance Equations
14.5.2. Fluxes of Passive Diffusion and Convection
14.5.3. Goldman–Hodgkin–Katz Equation for Ion Channels
14.5.4. Mathematical Modeling of Carrier-Mediated Transport
14.5.5. A Mathematical Model of Na+/K+ ATPase
14.6. A Whole-Organ Approach to Renal Modeling
14.6.1. Filtration
14.6.2. Reabsorption
14.6.3. Secretion
15. Drug Transport in Solid Tumors (Lecture1500, Fifteenth Week)
15.1. Introduction
15.1.1. Drug Delivery in Cancer Treatment
15.1.2. Routes of Drug Administration
15.1.3. Drug Transport Within Solid Tumors
15.2. Quantitative Analysis of Transvascular Transport
15.3. Quantitative Analysis of Interstitial Fluid Transport
15.3.1. Governing Equations
15.3.2. Unidirectional Flow of Fluid at Steady State
15.3.3. Unsteady State Fluid Transport
15.4. Interstitial Hypertension in Solid Tumors
15.4.1. Effects of Interstitial Hypertension on Drug and Gene Delivery
15.4.2. Etiology of Interstitial Hypertension
15.4.3. Strategies for Reducing Interstitial Fluid Pressure
15.5. Quantitative Analysis of Interstitial Transport of Solutes
15.5.1. Governing Equations
15.5.2. Unidirectional Transport in a Solid Tumor
15.5.3. Unidirectional Transport in the Krogh Cylinder
16. Transport in Organs and Organisms (Lecture1600, Sixteen Week)
16.1. Introduction, 736
16.2. General Considerations in Pharmacokinetic Analysis
16.3. Simple Compartment Models in Pharmacokinetic Analysis
16.3.1. One-Compartment Model
16.3.2. Two-Compartment Model
16.4. Physiologically Based Pharmacokinetic Models
16.4.1. Transport in Individual Organs
16.4.2. Physiologically Based Pharmacokinetic Analysis of Methotrexate
16.5. Allometric Scaling Law and Its Application to Transport Properties
16.5.1. Scaling Laws
16.5.2. Applications of the Allometric Scaling Law in Pharmacokinetic Analysis

Part V. Energy and Bioheat Transfer

17. Energy Transport in Biological Systems (Lecture1700, Seventeenth Week)

17.1. Introduction
17.2. First Law of Thermodynamics and Metabolism
17.2.1. Conservation Relations
17.2.2. Differential Forms of the Conservation of Energy
17.2.3. Constitutive Relation and Boundary Conditions
17.2.4. Dimensionless Form of the Conservation Relations
17.3. Steady and Unsteady Heat Conduction
17.3.1. Insulation and Heat Conduction Through Layers of Different Thermal Conductivity
17.3.2. Steady State Conduction and Metabolic Energy Production
17.3.3. Unsteady Heat Conduction
17.3.4. Unsteady Heat Conduction with a Phase Change
17.4. Convective Heat Transfer
17.4.1. Correlations for Forced Convection
17.4.2. Natural Convection
17.5. Energy Transfer Due to Evaporation
17.6. Metabolism and Regulation of Body Temperature
17.6.1. Basal Metabolic Rate and Efficiency
17.6.2. Regulation of Body Temperature
17.6.3. Macroscopic Balance for Energy Transfer in Biological Systems

17.7. The Bioheat-Transfer Equation
17.8. Cryopreservation

Final Project (Eighteenth Week)

 

Hawkeye Radiology Informatics (HRI)
Department of Radiology || Carver College of Medicine || The University of Iowa
Copyright © 2007-2010, All rights reserved. Legal Notices