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Machine generated contents note: 1.1. Introduction to BioMEMS -- 1.2. Application Areas -- 1.3. Intersection of Science and Engineering -- 1.4. Evolution of Systems Based on Size -- 1.5. Commercialization, Potential, and Market -- References -- 2.1. Introduction -- 2.2. Metals -- 2.3. Glasses and Ceramics -- 2.4. Silicon and Silicon-Based Surfaces -- 2.5. Polymers -- 2.6. Biopolymers -- 2.7. Organic Molecules (Functional Groups) Involved in the Formation of Self-Assembled Monolayers -- References -- Review Questions -- 3.1. Amino Acids -- 3.2. Polypeptides and Proteins -- 3.3. Lipids -- 3.3.1. Fatty Acids and Their Esters -- 3.3.2. Phospholipids -- 3.3.3. Lipoproteins -- 3.4. Nucleotides and Nucleic Acids -- 3.4.1. Nucleotides -- 3.4.2. Nucleic Acids -- 3.4.3. DNA Sensing Strategies -- 3.5. Carbohydrates -- 3.5.1. Introduction -- 3.5.2. Monosaccharides -- 3.5.3. Oligosaccharides and Polysaccharides -- 3.5.4. Biosensing Applications -- 3.6. Enzymes -- 3.6.1. Definition and Nomenclature
3.6.2. Mechanism of the Enzymatic Catalysis -- 3.6.3. Catalysis by RNA -- 3.6.4. Applications of Enzymes in Biotechnology and Biosensing -- 3.7. Cells -- 3.7.1. Cellular Organization -- 3.7.2. Cell Movement -- 3.7.3. Whole Cell Biosensors: Applications -- 3.8. Bacteria and Viruses -- 3.8.1. Bacterial Cell Structure -- 3.8.2. Virus Structure -- 3.8.3. Biosensors and BioMEMS Sensor Systems for the Detection of Pathogenic Microorganisms and Bacterial Toxins -- References -- Review Questions -- 4.1. Introduction -- 4.2. Plasma Treatment and Plasma-Mediated Surface Modification -- 4.3. Surface Modifications Mediated by Self-Assembled Monolayers (SAMs) -- 4.4. Langmuir-Blodgett and Layer-by-Layer Assembly -- 4.5. Biosmart Hydrogels -- 4.6. Immobilization and Detection of Biomolecules by Using Gold Nanoparticles: Case Studies -- 4.6.1. Gold Nanoparticles Functionalized by Dextran -- 4.6.2. Gold Nanoparticles in Hybridization Experiments -- 4.6.3. Enhanced Biomolecular Binding Sensitivity by Using Gold Nanoislands and Nanoparticles -- 4.6.4. Study of Antigen-Antibody Interactions by Gold Nanoparticle Localized Surface Plasmon Resonance Spectroscopy
4.6.5. Array of Gold Nanoparticles for Binding of Single Biomolecules -- 4.7. Biomimetic Surface Engineering -- 4.8. Attachment of Proteins to Surfaces -- 4.9. Surface Modification of Biomaterials for Tissue Engineering Applications -- 4.10. Temperature-Responsive Intelligent Interfaces -- References -- Review Questions -- 5.1. Contact Angle -- 5.1.1. Introduction to Contact Angle and Surface Science Principles -- 5.1.2. Contact Angle Measurement -- 5.1.3. Evaluation of Hydrophobicity of the Modified Surfaces by Contact Angle Measurements: Case Studies -- 5.1.3.1. Sensitivity of Contact Angle to Surface Treatment -- 5.1.3.2. Contact Angle Measurements of Surfaces Functionalized with Polyethyleneglycol (PEG) -- 5.1.3.3. Study of Surface Wettability of Polypyrrole for Microfluidics Applications -- 5.1.3.4. Wetting Properties of an Open-Channel Microfluidic System -- 5.1.3.5. Contact Angle Analysis of the Interfacial Tension -- 5.2. Atomic Force Microscopy (AFM) -- 5.2.1. Basic Concepts of AFM and Instrumentation -- 5.2.2. AFM Imaging of Biological Sample Surfaces -- 5.2.2.1. Ex Situ and In Situ AFM Characterization of Phospholipid Layers Formed by Solution Spreading (Casting) on a Mica Substrate
5.2.2.2. Study of Bacterial Surfaces in Aqueous Solution -- 5.2.2.3. AFM Study of Native Polysomes of Saccharomyces in a Physiological Buffer Solution -- 5.2.2.4. Single DNA Molecule Stretching Experiments by Using Chemical Force Microscopy -- 5.2.2.5. AFM Measurements of Competitive Binding Interactions between an Enzyme and Two Ligands -- 5.2.2.6. Study of Antigen-Antibody Interactions by Molecular Recognition Force Microscopy (MRFM) -- 5.2.2.7. Study of Cancer Alterations of Single Living Cells by AFM -- 5.3. X-Ray Photoelectron Spectroscopy -- 5.3.1. Introduction -- 5.3.2. X-Ray Photoelectron Spectroscopy of Biologically Important Materials -- 5.3.2.1. Peptide Nucleic Acids on Gold Surfaces as DNA Affinity Biosensors -- 5.3.2.2. Application of XPS to Probing Enzyme-Polymer Interactions at Biosensor Interfaces -- 5.3.2.3. Detection of Adsorbed Protein Films at Interfaces -- 5.4. Confocal Fluorescence Microscopy -- 5.4.1. Introduction -- 5.4.2. Biological Confocal Microscopy: Case Studies -- 5.4.2.1. Bioconjugated Carbon Nanotubes for Biosensor Applications -- 5.5. Attenuated Total Reflection (Internal Reflection) Infrared Spectroscopy
5.5.1. Introduction: ATR-FTIR Basics -- 5.5.2. Applications of ATR-FTIR Spectroscopy to Biomolecules and Biomedical Samples: Case Studies -- 5.5.2.1. Hydration Studies of Surface Adsorbed Layers of Adenosine-5'-Phosphoric Acid and Cytidine-5'-Phosphoric Acid by Freeze-Drying ATR-FTIR Spectroscopy -- 5.5.2.2. Study of the Interaction of Local Anesthetics with Phospholipid Model Membranes -- 5.5.2.3. Assessment of Synthetic and Biologic Membrane Permeability by Using ATR-FTIR Spectroscopy -- 5.5.2.4. ATR Measurement of the Physiological Concentration of Glucose in Blood by Using a Laser Source -- 5.5.2.5. Application of ATR-FTIR Spectroscopic Imaging in Pharmaceutical Research -- 5.6. Mechanical Methods: Use of Micro- and Nanocantilevers for Characterization of Surfaces -- References -- Review Questions -- 6.1. Biosensors -- 6.1.1. Introduction -- 6.1.2. Classification: Case Studies -- 6.1.2.1. Enzyme-Based Biosensors -- 6.1.2.2. Nucleic-Acid-Based Biosensors -- 6.1.2.3. Antibody-Based Biosensors -- 6.1.2.4. Microbial Biosensors -- 6.2. Immunoassays -- 6.2.1. Introduction
6.2.2. Enzyme-Linked Immunosorbent Assay (ELISA) -- 6.2.3. Microfluidic Immunoassay Devices -- 6.2.3.1. A Compact-Disk-Like Microfluidic Platform for Enzyme-Linked Immunosorbent Assay -- 6.2.3.2. Portable Low-Cost Immunoassay for Resource-Poor Settings -- 6.3. Comparison between Biosensors and ELISA Immunoassays -- References -- Review Questions -- 7.1. Basic Microfabrication Processes -- 7.1.1. Introduction -- 7.1.2. Thin-Film Deposition -- 7.1.3. Photolithography -- 7.1.4. Etching -- 7.1.5. Substrate Bonding -- 7.2. Micromachining -- 7.2.1. Bulk Micromachining -- 7.2.2. Surface Micromachining -- 7.2.3. High-Aspect-Ratio Micromachining (LIGA Process) -- 7.3. Soft Micromachining -- 7.3.1. Introduction -- 7.3.2. Molding and Hot Embossing -- 7.3.3. Micro Contact Printing ([]CP) -- 7.3.4. Micro Transfer Molding ([]TM) -- 7.3.5. Micromolding in Capillaries -- 7.4. Microfabrication Techniques for Biodegradable Polymers -- 7.5. Nanofabrication Methods -- 7.5.1. Laser Processing, Ablation, and Deposition -- 7.5.2. High-Precision Milling
7.5.3. Inductively Coupled Plasma (ICP) Reactive Ion Etching -- 7.5.4. Electron Beam Lithography -- 7.5.5. Dip Pen Nanolithography -- 7.5.6. Nanosphere Lithography (Colloid Lithography) -- 7.5.7. Surface Patterning by Microlenses -- 7.5.8. Electrochemical Patterning -- 7.5.9. Electric-Field-Assisted Nanopatterning -- 7.5.10. Large-Area Nanoscale Patterning -- 7.5.11. Selective Molecular Assembly Patterning (SMAP) -- 7.5.12. Site-Selective Assemblies of Gold Nanoparticles on an AFM Tip-Defined Silicon Template -- 7.5.13. Highly Ordered Metal Oxide Nanopatterns Prepared by Template-Assisted Chemical Solution Deposition -- 7.5.14. Wetting-Driven Self-Assembly: A New Approach to Template-Guided Fabrication of Metal Nanopatterns -- 7.5.15. Patterned Gold Films via Site-Selective Deposition of Nanoparticles onto Polymer-Templated Surfaces -- 7.5.16. Nanopatterning by PDMS Relief Structures of Polymer Colloidal Crystals -- References -- Review Questions -- 8.1. Introduction -- 8.2. Fluid Physics at the Microscale -- 8.3. Methods for Enhancing Diffusive Mixing between Two Laminar Flows
8.4. Controlling Flow and Transport in Microfluidic Channels -- 8.4.1. Physical Processes Underlying Electrokinetics in Electroosmosis Systems -- 8.4.2. Droplet Actuation Based on Marangoni Flows -- 8.4.3. Electrowetting -- 8.4.4. Thermocapillary Pumping -- 8.4.5. Surface Electrodeposition -- 8.5. Modeling Microchannel Flow -- 8.5.1. Introduction -- 8.5.2. The Finite Element Method -- 8.5.3. Simulation of Flow in Microfluidic Channels: Case Studies -- 8.5.3.1. Case 1: Silicon Microfluidic Platform for Fluorescence-Based Biosensing -- 8.5.3.2. Case 2: Numerical Simulation of Electroosmotic Flow in Hydrophobic Microchannels: Influence of Electrode's Position -- 8.5.3.3. Case 3: Prediction of Intermittent Flow Microreactor System -- 8.5.3.4. Case 4: Modeling of Electrowetting Flow -- 8.6. Experimental Methods -- 8.6.1. Flow Visualization at Microscale -- 8.6.2. Fluorescent Imaging Method -- 8.6.3. Particle Streak Velocimetry -- 8.6.4. Particle Tracking Velocimetry -- 8.6.5. Micro Particle Imaging Velocimetry (μPIV) -- 8.6.6. Micro-Laser-Induced Fluorescence (μLIF) Method for Shape Measurements
8.6.7. Caged and Bleached Fluorescence -- References -- Review Questions -- 9.1. Introduction to Microarrays -- 9.2. Microarrays Based on DNA -- 9.2.1. Introduction to DNA Chips -- 9.2.2. Principles of DNA Microarray: The Design, Manufacturing, and Data Handling -- 9.2.3. Applications of DNA Microarrays -- 9.3. Polymerase Chain Reaction (PCR) -- 9.3.1. Introduction -- 9.3.2. PCR Process -- 9.3.3. On-Chip Single-Copy Real-Time Reverse Transcription PCR in Isolated Picoliter Droplets: A Case Study
9.4. Protein Microarrays -- 9.4.1. Introduction -- 9.4.2. Fabrication of Protein Microarrays -- 9.4.3. Applications of Protein Arrays -- 9.5. Cell and Tissue-Based Assays on a Chip -- 9.6. Microreactors -- 9.6.1. Introduction -- 9.6.2. Microchannel Enzyme Reactors -- 9.6.3. Enzymatic Conversions: Case Studies -- 9.6.3.1. Glycosidase-Promoted Hydrolysis in Microchannels -- 9.6.3.2. Lactose Hydrolysis by Hyperthermophilic I3-Glycoside Hydrolase with Immobilized Enzyme -- 9.6.3.3. Photopatterning Enzymes inside Microfluidic Channels -- 9.6.3.4. Integrated Microfabricated Device for an Automated Enzymatic Assay -- 9.6.3.5. Silicon Microstructured Enzyme Reactor with Porous Silicon as the Carrier Matrix -- 9.6.3.6. Enzymatic Reactions Using Droplet-Based Microfluidics -- 9.6.4. Synthesis of Nanoparticles and Biomaterials in Microfluidic Devices -- 9.6.5. Microfluidic Devices for Separation
9.6.5.1. Separation of Blood Cells -- 9.6.5.2. Cell or Particle Sorting -- 9.7. Micro Total Analysis Systems (pTAS) and Lab-on-a-Chip (LOC) -- 9.8. Lab-on-a-Chip: Conclusion and Outlook -- 9.9. Microcanti lever BioMEMS -- 9.9.1. Introduction -- 9.9.2. Basic Principles of Sensing Biomechanical Interactions -- 9.9.3. Detection Modes of Biomechanical Interactions -- 9.9.3.1. Static Mode -- 9.9.3.2. Dynamic Mode -- 9.9.4. Location of Interaction in the Case of Mass-Dominant BioMEMS Devices -- 9.9.5. Location of Interaction for Stress-Dominant BioMEMS Devices -- 9.9.6. Fabrication and Functionalization of Microcantilevers -- 9.9.6.1. Case 1: Detection of Interaction between ssDNA and the Thiol Group Using Cantilevers in the Static Mode -- 9.9.6.2. Case 2: Specific Detection of Enzymatic Interactions in the Static Mode -- 9.9.6.3. Case 3: Detection of Enzymatic Interactions in the Dynamic Mode -- References -- Review Questions.
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