Introductory Bioelectronics: For Engineers and Physical Scientists Book

About the Authors Foreward Preface

1. Basic Chemical and Biochemical Concepts
1.1. Chapter Overview
1.2. Energy and Chemical Reactions
1.1.1. Energy
1.1.2. Covalent Chemical Bonds
1.1.3. Chemical Concentrations
1.1.4. Nonpolar, Polar and Ionic Bonds
1.1.5. Van der Waals Attractions
1.1.6. Chemical Reactions
1.1.7. Free-Energy Change ΔG associated with Chemical Reactions
1.2. Water and Hydrogen Bonds
1.2.1. Hydrogen Bonds
1.3. Acids, Bases and pH
1.3.1. The Biological Importance of pH
1.3.2. The Henderson-Hasselbalch Equation
1.3.3. Buffers
1.4. Summary of Key Concepts (1.4 in document)
1.5. Cited References
1.6. Further Reading
1.7. Sample Problems

2. Cells and their Basic Building Blocks
2.1. Chapter Overview
2.2. Lipids and Biomembranes
2.2.1. Fatty Acids
2.3. Carbohydrates and Sugars
2.4. Amino Acids, Polypeptides and Proteins
2.4.1. Amino Acids and Peptide Bonds
2.4.2. Polypeptides and Proteins
2.5. Nucleotides, Nucleic Acids, DNA, RNA and Genes
2.5.1. DNA
2.5.2. Ribonucleic Acid (RNA)
2.5.3. Chromosomes
2.5.4. Central Dogma of Molecular Biology (DNA makes RNA makes Protein)
2.6. Cells and Pathogenic Bioparticles
2.6.1. Prokaryotic and Eukaryotic Cells
2.6.2. The Plasma Membrane
2.6.3. The Cell Cycle
2.6.4. Blood Cells
2.6.5. Bacteria
2.6.6. Plant, Fungal and Protozoal Cells
2.6.7. Viruses
2.6.8. Prions
2.6.9. Cell Culture
2.6.10. Tissue Engineering
2.6.11. Cell-Cell Communication
2.7. Summary of Key Concepts
2.8. Cited References
2.9. Further Reading

3. Basic Biophysical Concepts and Methods
3.1. Chapter Overview
3.2. Electrostatic Interactions
3.2.1. Coulomb’s Law
3.2.2. Ions in Water
3.2.3. The Formation of an Ionic Double Layer
3.2.4. Ion-Dipole and Dipole-Dipole Interactions
3.2.5. Ions in a Membrane or Protein
3.3. Hydrophobic and Hydration forces
3.3.1. Hydrophobic Forces
3.3.2. Hydration Forces
3.4. Osmolarity, Tonicity and Osmotic Pressure
3.4.1. Osmoles
3.4.2. Calculating Osmolarity for Complex Solutions
3.4.3. Osmolarity versus Tonicity
3.5. Transport of Ions and Molecules across Cell Membranes
3.5.1. Diffusion
3.5.2. Osmosis
3.5.3. Facilitated Diffusion
3.5.4. Active Transport
3.6. Electrochemical Gradients and Ion Distributions across Membranes
3.6.1. Donnan Equilibrium
3.7. Osmotic Properties of Cells
3.8. Probing the Electrical Properties of Cells
3.8.1. Passive Electrical Response
3.8.2. Active Electrical Response
3.8.3. Membrane Resistance
3.8.4. Membrane Capacitance
3.8.5. Extent of Ion Transfer associated with the Membrane Resting potential
3.9. Membrane Equilibrium Potentials
3.10. Nernst Potential and Nernst Equation
3.11. The Equilibrium (Resting) Membrane Potential
3.12. Membrane Action Potential
3.12.1. Nerve (axon) Membrane
3.12.2. Heart Muscle Cell Membrane
3.13. Channel Conductance
3.14. The Voltage Clamp
3.15. Patch-Clamp Recording
3.15.1. Application to Drug Discovery
3.16. Electrokinetic Effects
3.16.1. Electrophoresis
3.16.2. Electro-osmosis
3.16.3. Capillary Electrophoresis
3.16.4. Dielectrophoresis (DEP)
3.16.5. Electrowetting on Dielectric (EWOD)
3.17. Cited References

4. Spectroscopic Techniques
4.1. Chapter Overview
4.2. Introduction
4.2.1. Electronic and Molecular Energy Transitions
4.2.2. Luminescence
4.2.3. Chemiluminescence
4.2.4. Fluorescence and Phosphorescence
4.3. Classes of Spectroscopy
4.3.1. Electronic Spectroscopy
4.3.2. Vibrational Spectroscopy
4.3.3. Rotational Spectroscopy
4.3.4. Raman Spectroscopy
4.3.5. Total Internal Reflection Fluorescence (TIRF)
4.3.6. Nuclear Magnetic Resonance (NMR) Spectroscopy
4.3.7. Electron Spin Resonance (ESR) Spectroscopy
4.3.8. Surface Plasmon Resonance (SPR)
4.3.9. Förster Resonance Energy Transfer (FRET)
4.4. The Beer-Lambert Law
4.4.1. Limitations of the Beer-Lambert Law
4.5. Impedance Spectroscopy
4.6. Cited References
4.7. Further Reading
4.8. Problems for Self Study

5. Electrochemical Principles and Electrode Reactions
5.1. Chapter Overview
5.2. Introduction
5.3. Electrochemical Cells and Electrode Reactions
5.3.1. Anodes and Cathodes
5.3.2. Electrode Reactions
5.3.3. Electrode Potential
5.3.4. Standard Reduction Potential and the Standard Hydrogen Electrode
5.3.5. The Relative Reactivities of Metal Electrodes
5.3.6. The Nernst Equation
5.4. Electrical Control of Electron Transfer Reactions
5.4.1. Cyclic Voltammetry
5.4.2. Amperometry
5.4.3. The Ideal Polarized Electrode (5.4.2 in document)
5.4.4. Three-Electrode System (5.4.3 in document)
5.5. Reference Electrodes
5.5.1. The Silver-Silver Chloride Reference Electrode
5.5.2. The Saturated-Calomel Electrode
5.5.3. Liquid Junction Potentials
5.6. Electrochemical Impedance Spectroscopy (EIS)
5.7. Cited References
5.8. Further Reading
5.9. Problems for Self Study
6. Biosensors
6.1. Chapter Overview
6.2. Introduction
6.3. Immobilization of the Biosensing Agent
6.3.1. Physical Methods
6.3.2. Chemical Methods
6.4. Biosensor Parameters
6.4.1. Format
6.4.2. Transfer Function
6.4.3. Sensitivity
6.4.4. Selectivity
6.4.5. Noise
6.4.6. Drift
6.4.7. Precision and Accuracy
6.4.8. Detection Limit and Decision Limit
6.4.9. Dynamic Range
6.4.10. Response Time
6.4.11. Resolution
6.4.12. Bandwidth
6.4.13. Hysteresis
6.4.14. Effects of pH and Temperature
6.4.15. Testing of Anti-interference
6.5. Amperometric Biosensors
6.5.1. Mediated Amperometric Biosensors
6.6. Potentiometric Biosensors
6.6.1. Ion Selective Electrodes (ISEs)
6.7. Conductometric and Impedimetric Biosensors
6.8. Sensors based on Antibody-Antigen interaction
6.9. Photometric Biosensors
6.10. Biomimetic Sensors
6.11. Glucose Sensors
6.12. Biocompatibility of Implantable Sensors
6.12.1. Progression of Wound Healing
6.12.2. Impact of Wound Healing on Implanted Sensors
6.12.3. Controlling the Tissue Response to Sensor Implantation
6.12.4. Regulations for and Testing of Implantable Medical Devices
6.13. Cited References
6.14. Further Reading

7. Basic Sensor Instrumentation and Electrochemical Sensor Interfaces
7.1. Chapter Overview
7.2. Transducer Basics
7.2.1. Transducers
7.2.2. Sensors
7.2.3. Actuators
7.2.4. Transduction in Biosensors
7.2.5. Smart Sensors
7.2.6. Passive vs. Active Sensors
7.3. Sensor Amplification
7.3.1. Equivalent Circuits
7.4. The Operational Amplifier
7.4.1. Op-Amp Basics
7.4.2. Non-Inverting Op-Amp Circuit
7.4.3. Buffer Amplifier Circuit
7.4.4. Inverting Op-Amp Circuit
7.4.5. Differential Amplifier Circuit
7.4.6. Current Follower Amplifier
7.5. Limitations of Operational Amplifiers
7.5.1. Resistor Values
7.5.2. Input Offset Voltage
7.5.3. Input Bias Current
7.5.4. Power Supply
7.5.5. Op-Amp Noise
7.5.6. Frequency Response
7.6. Instrumentation for Electrochemical Sensors
7.6.1. The Electrochemical Cell (Revision)
7.6.2. Equivalent Circuit of an Electrochemical Cell
7.6.3. Potentiostat Circuits
7.6.4. Instrumentation Amplifier
7.6.5. Potentiostat Performance and Design Considerations
7.6.6. Microelectrodes
7.6.7. Low Current Measurement
7.7. Impedance Based Biosensors
7.7.1. ConductometricBiosensors
7.7.2. Electrochemical Impedance Spectroscopy
7.7.3. Complex Impedance Plane Plots and Equivalent Circuits
7.7.4. Biosensing Applications of EIS
7.8. FET Based Biosensors
7.8.1. MOSFET Revision
7.8.2. The Ion Sensitive Field Effect Transistor
7.8.3. ISFET Fabrication
7.8.4. ISFET Instrumentation
7.8.5. The REFET
7.8.6. ISFET Problems
7.8.7. Other FET Based Sensors
7.9. Cited References
7.10. Further Reading
7.11. Problems for Self Study

8. Instrumentation for Other Sensor Technologies
8.1. Chapter Overview
8.2. Temperature Sensors and Instrumentation
8.2.1. Temperature Calibration
8.2.2. Resistance Temperature Detectors
8.2.3. p-n Junction Diode as a Temperature Sensor
8.3. Mechanical Sensor Interfaces
8.3.1. Piezoresistive Effect
8.3.2. Applications of Piezoresistive Sensing
8.3.3. Piezoelectric Effect
8.3.4. Quartz Crystal Microbalance
8.3.5. Surface Acoustic Wave Devices
8.3.6. Capacitive Sensors
8.3.7. Capacitance Measurement
8.3.8. Capacitive Bridge
8.3.9. Switched Capacitor Circuits
8.4. Optical Biosensor Technology
8.4.1. Fluorescence
8.4.2. Optical Fibre Sensors
8.4.3. Optical Detectors
8.4.4. Case Study - Label Free DNA Detection with an Optical Biosensor
8.5. Transducer Technology for Neuroscience and Medicine
8.5.1. The Structure of a Neuron
8.5.2. Measuring and Actuating Neurons
8.5.3. Extra-Cellular Measurements of Neurons
8.6. Cited References
8.7. Further Reading
8.8. Problems for Self Study

9. Microfluidics: Basic Physics and Concepts
9.1. Chapter Overview
9.2. Liquids and Gases
9.2.1. Gases
9.2.2. Liquids
9.3. Fluids treated as a Continuum
9.3.1. Density
9.3.2. Temperature
9.3.3. Pressure
9.3.4. Maxwell Distribution of Molecular Speeds
9.3.5. Viscosity
9.4. Basic Fluidics
9.4.1. Static Fluid Pressure
9.4.2. Pascal’s Law
9.4.3. Laplace’s Law
9.5. Fluid Dynamics
9.5.1. Conservation of Mass Principle (Continuity Equation)
9.5.2. Bernoulli’s Equation (Conservation of Energy)
9.5.3. Poiseuille’s Law (flow resistance)
9.5.4. Laminar Flow (10.5.4 in Document)
9.5.5. Application of Kirchhoff’s Laws (Electrical analogue of fluid flow)
9.6. Navier-Stokes Equations
9.6.1. Conservation of Mass Equation
9.6.2. Conservation of Momentum Equation (Navier-Stokes Equation)
9.6.3. Conservation of Energy Equation
9.7. Continuum versus Molecular Model
9.7.1. Solving Fluid Conservation Equations
9.7.2. Molecular simulations
9.7.3. Meso-scale Physics
9.8. Diffusion
9.9. Surface Tension
9.9.1. Surfactants
9.9.2. Soap Bubble
9.9.3. Contact Wetting Angle
9.9.4. Capillary Action
9.9.5. Practical Aspects of Surface Tension for Lab-on-Chip devices
9.10. Cited References (9.9 in document)
9.11. Further Reading (9.10 in document)
9.12. Problems for Self Study (9.11 in document)

10. Microfluidics: Dimensional Analysis and Scaling
10.1. Chapter Overview
10.2. Dimensional Analysis
10.2.1. Base and Derived Physical Quantities
10.2.2. Buckingham’s π-Theorem
10.3. Dimensionless Parameters
10.3.1. Hydraulic Diameter
10.3.2. The Knudsen Number
10.3.3. The Peclet Number: Transport by Advection or Diffusion?
10.3.4. The Reynolds Number: Laminar or Turbulent Flow?
10.3.5. Reynolds Number as a Ratio of Time Scales
10.3.6. The Bond Number: How Critical is Surface Tension?
10.3.7. Capillary Number: Relative importance of Viscous and Surface Tension Forces
10.3.8. Weber Number: relative effects of Inertia and Surface Tension
10.3.9. Prandtl Number: Relative Thickness of Thermal and Velocity Boundary Layers
10.4. Applying Non-Dimensional Parameters to Practical Flow Problems
10.4.1. Channel filled with Water Vapour
10.4.2. Channel filled with a Dilute Electrolyte at 293 K
10.5. Characteristic Time Scales
10.5.1. Convective Time Scale
10.5.2. Diffusion Time Scale
10.5.3. Capillary Time Scale
10.5.4. Rayleigh Time Scale
10.6. Applying Micro- and Nano-Physics to the Design of Microdevices
10.7. Cited References
10.8. Problems for Self Study

Appendices

Appendix 1: SI Prefixes Appendix 2: Values of Fundamental Physical Constants Appendix 3: Model Answers for Self Study Problems