Biomolecular Sensing Processing and Analysis - Rashid Bashir and Steve Wereley

400

Dielectrophoretic force, 260–262 application of Maxwell’s stress tensor, 167

computation of, at various electric fields, 246–247 Dielectrophoretic microdevice, 259 Dielectrophoretic-field flow fractionation (DEP-FFF),

190

Diffractive optical elements, 349–352 Diffuse layer capacitance, 148

Diverging fringe doppler sensor, 360–363 DNA analysis, novel approach to, 18 DNA biosensors, 9

DNA chips, 16

DNA hybridization, 29–31

DNA microarray detection system, 15 DNA microarrays, case of, 21

DNA multiarray device, use of, 16 DNA pairing, 9

DNA sequencing, 153 DNA–fragments, 9 DNA-ligand interactions, 9 Donnan equilibrium, 123 Donnan exclusion, 123 Doppler pedestal, 354 Doppler shift, 353

DRIE, 111

Drilling molecular-scaled holes, 35

Drug delivery microship. See Therapeutic Microsystems

DS19 murine erythroleukemia cells, 174 Dual velocity sensor, 358–360 Dye-immobilized-gel, use of, 235–236

E. coli detection, 10, 17 EBL-defined pore, 38

Edmund Scientific mini electromagnet, 139, 141 EDTA. See Chemical agent sensing

Elastomeric micromolding, 225 Electrical double layer (EDL), 146, 148 Electrical double layer field (EDL), 279 Electrical double layer

structure of, 306–308

Electrical impedance spectroscopy, 152 Electrochemical detection methods, 12 Electrochemical detection, 13 Electrochemical mmunoassay, 7 Electrofusion of cells, 174

Electrokinetic flow, governing equations for, 308–313

Electron-beam lithography (EBL), 36 Electroosmotic channel flow, 304–306

asymptotic and numerical solutions for electric double layer thickness, 314–317

equilibrium considerations, 318–320 molecular dynamic simulations, 324–328 nano-PIV results in, 342–346

INDEX

Electroosmotic flow, case studies of in a rectangular channel, 290–293

pressure driven flow over heterogeneous surfaces, 293–298

Electrophoresis, 302. See also AC electrokinetic phenomena

application of, 189 definition of, 189

Electroporation of cells, 174 Electro-readout technique, advantages of, 27 Electrothermal stirring, 249–251

use of, 253

Electrothermally driven flow (ETF), 244, 252 ELISA (enzyme linked immunoassay), 239 Ellipsometry, 9

Endoradiosonde, 205

Endoscopic wireless camera-pill, 210, 212–213 Endothelial cells, 374, 385

laminar shear stress effect on, 383, 384t, 393 response to altered flows, 385–386

Engineered bacteria, 57

Engineering transmembrane protein, 35

Enhanced species mixing in electroosmotic flow, case study of

flow simulation, 288–289 mixing simulation, 290

Enzyme immunoassays, 7

Enzyme-linked immunosorbent assay (ELISA), 18 Epoxy group, 97

Ethanol sensing. See Chemical agent sensing Ethylene diamene tetra acetic acid (EDTA), 77–79, 82 Evanescent wave fibre optic biosensor, 10

Evanescent wave illumination, 342 Evanescent wave immunosensor, 12 Evanescent waves, theory of, 334–337 Excitation light, 7

Extracellular based biosensors applications of, 61

Extracellular recording, 55 Extracellular signal spectrum, 55

Fast Fourier transformation (FFT), 73, 354–356, 362 Femlab, 249

Fetal Bovine Serum (FBS), 69–70 FFT analysis, 76

Field effect transistors (FET), 64, 127 Field-flow fractionation (FFF), 155 Flatworm checking valve, 229

Flow devices, non-traditional, 382–383 Fluidic interconnects, 109

general requirements of, 110 types of, 111–112

Fluorescence base cellular biosensors application of, 58

intracellular ionic signals developed by, 58

INDEX

Fluorescence based sensors, applications of, 58 Fluorescence detection techniques, 194 Fluorescent analyte, 7

Fluorophor-labeled antigen, 7

Food and drug administration (FDA), 94 Fourier series, 176

Fourier transform, iterative, 350 Free antigen, 48

Free energy change, advantage of, 22 Free energy reduction, 22, 30

Free ligand, 49

Free-flow electrophoresis (FFE), 156 Frequency modulation, 76

Gamma-butyrolacetone (GBL), 97 Gaussian-shaped microchannels, 107 Gene chips, 223

General purpose interface bus (GPIB), 69 Genosensor, 9

Gerchberg-Saxton algorithm, 350 Gibbs free energy, 119

Glass transition point, 109 Glass, usage, reason for, 95

polymers, types of, 95–96 PDMS, 96

PMMA, 96–97 SU-8, 97

Glucode optodes, 8

Glucose microtransponder. See Therapeutic Microsystems

Glued interconnects, 111 Gold-thiol (Au-S) bonds, 25, 29 Golgi apparatus, 373 Gouy-Chapman model of EDL, 308

Gradient refractive index (GRIN), 15 Green fluorescent protein (GFP), 58 Green’s function, 176

H19-7 cell line, 67

H19-7/IGF-IR cells, 69

Hard bake. See SU-8, process, steps in Hard-baked, 101

Helmholtz layer, 146

Helmholtz plane capacitance, 148 Heterogeneous reactions, 251–253 Hetrotrimeric G proteins, 388 Hexahstidine modified extension, 7 H-filterTM design, 154

High performance liquid chromatography (HPLC), 111

High-density oligonucleotide arrays, 16 Histidine-tagged antibodies, 7

Horizontal tubing interconnects. See process fit interconnects, 113

Horsweradish peroxidase, 7

401

Hot embossing techniques, 225

Hot Embossing, 96-97, 105-106, 225–226 Human serum albumin (HSA), 31 Hydrodynamic off-axis effect, 43, 41

Hydrogel sensors. See Microfluidic tectonics, sensors in

Hydrogel valves, 228

Hydrogels, 119-121, 231, 234, 238 classification of, 119

water uptake, importance of, 121 Hydrogen peroxide sensing, 79 –80 Hydrogen peroxide, 80

Hydrophilic polymeric networks. See Hydrogels Hydrophobic surface patterning, 229

IC microchip-CE system, advantages of, 18 IGF-IR protein, 69

ILS250TLL, 259 iMEDD device, 304 Immobilized ligand, 7

Immunoassay-based sensors, 243 Immunoassays, types of, 44 Immunosensors, 7

Impedance techniques extracellular signal strengths, 59 reliability of, 58–59

use of, 59

Implantable wireless microsystems battery operated, 208

coding scheme, 208 data transmission, 208

degree of protection, 209 design considerations, 207

factors influencing choice of power source, 208–209

hybrid approach designing, 207 sealing techniques, 209–210 transmitter efficiency, 209 wireless communication, 207–208

Infrared spectroscopy, 7, 10 Inhibition assay, 44 Inhibition immunoassay, 50 Injection Molding, 106

Injection molding. See Micromolding In-plane Brownian diffusion, 338, 345

errors due to, 345

Integrated artificial pore on chip, 35 Integrated biosensor arrays, 14 Intelligent polymer networks

advantages of, 119 applications of, 126-129 different polymer systems, 119 major classes of, 119f

Intercellular adhesion molecule(ICAM)-1, 374 Interdigitated electrodes. See n-DEP trap geometries

402

Interspike interval histogram (ISIH), 75 Intracellular based bio sensors

advantages, 60 disadvantages, 60

Intracellular calcium release, 388

Intracellular ionic signals developed by fluorescence based biosensors, 58

Intraocular pressure (IOP) measurement microsystem, 210

Ion sensitive field-effect transistors (ISFET), 198 Isoelectric focusing, 155

Isopropyl alcohol (IPA), 99

Knock down effect, 77

Knudesn number, 302

Kovar, 111–112

L929 fibroblast cells, 174

L-phenylalanine via NADH, indirect detection of, 13 Labeled analyte, 7

Lab-on-a-chip, 187, 193, 228, 243–244, 301, 304 use of, 187

Laminar shear stress effects application to clinical treatment, 391 on endothelial cells, 383-385

on vascular smooth muscle cells, 386–388 Langmuir-Blodgett layers, 11

Laser doppler velocimetry, 332, 352 application of doppler effect, 353

Laser machining, 96, 106 Laser miniaturization, 5 Leaching, 113

Leviation measurements, 181 LIGA, 105

Ligand molecule, 7

Light emitting diodes (LEDs), 17

Light-addressable potentiometric sensors (LAPS), 198 principle of, 198–199

Limit of detection (LOD), 18 Linear PSD, 24

Lipopeptide, 10

Lipophilic carboxylated polyvinyl chloride, 12 Liposome sensors. See Microfluidic tectonics,

sensors in Liquid adhesive, 110

Liquid phase photopolymerization, 235

Liquid phase photopolymerization. See Microfluidic tectonics

Listeria innocua cells, 190

Listeria monocytogenes, detection of, 13

Listeria, 13, 66 Lithography

of thick resists, 98 steps in, 98

SU-8 on PMMA techniques, 98–99

INDEX

Lithography, 97

Living cells, use of, as sensing elements, 55 Lower critical miscibility or solution temperature

(LCST), 121

Low-pressure chemical vapor deposited (LPCVD), 25 LU factorization, 287

Lucite. See PMMA, 98

Mammalian cell death, 172 Mammalian cells, 168 Mammalian cells, use of, 56 Maskless fabrication method, 16 Mass detection methods, 11 Mass-sensitive Techniques,13–14 Matlab script, 26

MatLab, 161, 343

Maxwell-Wagner interfacial polarization, 165 Medical diagnostics, 118

MEMS based biosensors advantages of, 207 disadvantages of, 207

MEMS, 224, 233, 302, 332, 348, 358, 360, 365 MEMS-technology, 97

Metabolism cell stress, 57 METGLAS, 141

MFB biochip device, 17

MHD electrode pairs, 142–143 MHD microfluidic pumps, 138 –139

MHD micropump for sample transport using microchannel parallel electrodes

AC MHD micropump, measurements in, 141 electromagnet field strength, 140–141 fabrication of silicon MHD microfluidic pumps,

138–139

Lorentz force acting on the pump, 138, 144 measurement setup and results, 139–140 MHD microfluidic switch, 142–144

other MHD micropumps and future work, 144–145 principle of operation, 136–138

Micro Coulter particle counter principle, 152 Micro electromechanical systems (MEMS), 93 Micro IEF technique, 156

Micro particle image velocimetry, 261–262 Micro sensor development

micro sensor for flow shear stress measurement, 358–363

micro velosimeter, 356–358

Micro sensor for flow shear stress measurement diverging fringe doppler sensor, 360–363 dual velocity sensor, 358–360

Micro total analysis systems (µTAS), 135, 187 integrated fluids for, 135–136

Microarray of electrochemical biosensors for the detection of glucose on line, 14 for the detection of lactate on line, 14

INDEX

Microcantilever, 21 Microcantilever, use of, 29 Microcantilevers, 21

Microchannel parallel electrodes for sensing biological fluids

MHD based flow sensing, 145–153 MHD based viscosity meter, 146

impedance sensors with microchannel parallel electrodes, 146–153

Microchannel parallel electrodes, impedance sensors with

electrical double layer, 146–147

fabrication of channel electrodes and microfluidic channel, 147–148

flow sensing, 148–149

measurement of particles in solution,151–152 measurement of solution properties, 150–151 particle cytometry using capacitance and

impedance measurements, 152–153 Micro-elctro mechanical systems, 224–225 Microelectrode array technology, 62 Microelectromechanical systems (MEMS), 28,

128

Microfabrication, utilization of, 44

Microfluidic chambers, integration with cantilevers, advantages of, 28

Microfluidic devices, 156, 224

Microfluidic devices, polymeric fabrication methods components used, 228

design considerations, 227–228

laser ablation of polymer surface method, 226 liquid phase photopolymerization. See Microfluidic tectonics

soft lithography, 225–226 system integration, 223–224

Microfluidic devices, traditional fabricating methods micromachining, 224

micromolding, 224–225

Microfluidic electrostatic DNA extractor demonstration, 155

design and experiment, 154–155 principle, 154–156

Microfluidic technology, 93 Microfluidic tectonics, 226, 227–229

advantages of, 229

Microfluidic tectonics, components used in filters, 230–231

mixers, 232–233 pumps, 229–230 valves, 228–229

Microfluidic tectonics, sensors in cell gel sensors, 236

E-gel, 237–238 hydrogels, 235 liposome sensors, 237

403

sensors that change color, 235–236 sensors that change shape, 234–235

Microfluidic transverse isoelectric focusing device, 156

Microfluidics system, 17 Microfluidics, 27–28

Microfluidics, diagnostic techniques in challenges associated with, 349 hot-wire anemometry, 332 laser-doppler velocimetry, 332

micro-particle image velocimetry, 332–334 molecular tagging velocimetry, 333 nano-particle image velocimetry, 334 particle-image velocimetry, 332

Microgripper. See polymeric microgripper Micromachining, 225

Micro-molding techniques, utilization of, 44 Micromolding, 225–226

Micro-PIV, 100

MicroS3TM, 364

Microscale flow and transport simulations, fundamentals of

applied electric field, 279

electrical double layer (EDL), 280–282 inlet/outlet boundary conditions, 247, 249, 279 microscale flow analysis, 278–280 microtransport analysis, 286–287

numeric modeling of, 287, 294

Microscale impedance-based detection systems, 199 Microsystem components

interface components, 207

packaging and encapsulation, 209–210 power source, 208–209

transducers, 208–209

wireless communication, 219, 213 MicroVTM, 331

Mini LDVTM. See Miniature laser doppler velocimeter Miniature laser doppler velocimeter

features of, 351

principle of measurement, 353-355 siganal processing, 355–358

Miniature laser doppler velocimeter, 352 Miniaturized total analysis systems (µ-TAS), 118 Modeling of AC electroosmotic flow in a rectangular

channel, case study of, 290–293 Molecular adsorption, 21

Molecular beacon (MB) detection, 18

Molecular dynamics simulations in electroosmotic flow, 326–328

fluid dynamics, 326–328 fluid statics, 325–326

Molecular light emission, 58 Molecular sensing, 35

Monitoring of phosphorylcholine, 11 Monocyte-derived macrophages, 374

404

Monolayers, activation of 1-ethyl-3-[3-(dimethylamino)propyl] carbodiimide

hydrochloride, 14 N-hydroxysulfosuccinimide, 14

Monolithic horizontal integration, 109 Monte Carlo simulations, 341 Morphine binding, 11

Mouse anti-human antibody (MAH-PSA), 31 Multi-chip module (MCM) concept, 109 Multifunctional biochip (MFB), development of, 16 Multiplexing, 27

Multi-shelled particulate models, 165

N,N -Cystamine-bisacrylamide, 234 Nanochannel systems, 304 Nano-particle image velocimetry

Brownian diffusion effects in, 338–342 generation of evanescent waves, 337–338

Nanopores for molecular sensing, 35 Natural receptors, limitations of, 124 Navier-Stokes equations, 301, 312, 327 n-DEP trap geometries

interdigitated electrodes, 180–181 octopole electrodes, 178

other electrode structures, 178 quadrupole electrodes, 176–177 strip electrodes, 178

n-DEP trapping, 247–248

Negative temperature-sensitive systems, 121 Negatively-charged (carboxyl-coated) latex colloids,

37

Nernst potential, 319

Neuronal networks for biosensor applications, 61 Non-covalent recognition process, 125 Non-enzymatic protein biorecognition, 10 Non-equilibrium molecular dynamics (NEMD),

324

Non-spherical cells, 167

Nucleic acids, use in array chips, 15

Octopole electrodes. See n-DEP trap geometries Oligo amide, 9

On-chip artificial pore for molecular sensing applications, 44–51

fabrication of the pore, 36–37 features of the chip device, 37 pore-measurement, 37–40 PDMS-based pore, 40–44

Optical biosensors, properties of, amplitude, 12

decay time and/or phase, 11 energy, 12

polarization, 12

Optical detection methods, 12

Optical MEMS sensor feasibility study, 365–369

INDEX

Optical transduction, 11 O-rings, 111

Oroglass. See PMMA, 96

Oscillating ferromagnetic micropump, 230 Oscillatory flow patters, 385

Osteoblast cells, 77

Out-of-plane Brownian diffusion, 339

Packaging concepts for biomedical micro devices monolithic horizontal integration, 109 multi-chip module (MCM), concept, 109 stacked modular system, 109

Parallel microchannel electrodes for sample preparation

channel electrodes for isoelectic focusing with field flow fractionation, 155–156

microfluidic electrostatic DNA extractor, 153–155

Parallel plate flow chamber, 378–382 Passive mixers, 232

Passive valves, 229

Patch clamp technique, drawback of, 59–60 PCR amplification, 15

p-DEP trap geometries. See Trap geometries p-DEP trapping, 163

PDMS

application of, 82 properties of, 98–99

PDMS, 195, 209, 225 PDMS-based pore, 40–44

hydrodynamic off-axis, effect of, 41 PDMS mold, 40

PDMS slab, 40 PDMS sealing, 40 pressure usage in, 44

PDMS-based pore, 51 PECVD silicon dioxide, 259

Peptide nucleic acid. See oligo amide Perspex. See PMMA, 96

PGDF-β mRNA, 388 PGMEA developer

Phase-resolved fiberoptic fluoroimmunosensor (PR-FIS), use of, 12

Phosphate buffered saline (PBS), 302, 306, Phosphorylcholine analog, 11 Photodiodes, role of, 17

Photo-induced electron transfer (PET), 58 Photometrics CoolSNAP HQ interline transfer

monochrome camera, 261 Photo-polymerization, 227 Physiocontrol-microsystem, 198 Picornavirus, 10

Piezoelectric bimorph disc. See pump actuator, 101 Piezoelectric crystals, use of, 13

Piezo-electric transducer, 196

406

Signals from microelectrodes sealing of cells, 70–71, 73

signal-to-noise ratios (SNR), 70–71 Signature pattern, 55, 62, 89

Silicon micromachining. See Micromachining Silicon technology, 93, 95

Single channel neuromuscular microstimulator. See Rehabilitative Microsystems

Single linear PSD, 24

Single-stranded DNA (ssDNA), 29–30 Small I/O, 27

Smart pill. See Therapeutic Microsystems Smooth muscle cells, 371

Soft bake. See SU-8, process, steps in, Soft lithography, 225–226 Soft-operator IFT algorithm, 351 Spectrochemical instrumentation, 5

Spin coating. See SU-8, process, steps in SPV (Signature Pattern Vector), 76 Stacked modular system, 11

Star polymer hydrogels, 125–126 Stokes flow, 170

Stokes’ drag, 170–172, 181–182 Stoney’s formula, 23

Streaming current, 148 Streptavidin monolayer, 11

Streptavidin-coated latex colloids, 46

Strip electrodes. See n-DEP trap geometries SU-8 photoresist, components of, 97

SU-8 process, 98, 101 SU-8, 116

SU-8, fabrication of, 105 SU-8, process, steps in, 99 SU-8, use of, 102

Subtler effects, 175

Surface acoustic wave biosensor, inductively coupling of, 14

Surface enhanced Raman scattering (SERS), 9 Surface micromachining, 94

Surface plasmon resonace measurement, 7, 10

Surface plasmon resonance (SPR), 9, 22, 44 Surface roughness effects, 59

Surfactant Tween 20, 37 SV40 T antigen, 69 Swelling, 113

Symptoms of inflammation, 113

Synthetic image method. See Velocity profile extraction process, methods for

Synthetic thioalkane chelator, 7

Therapeutic Microsystems, 213–216

Thermal bimorph effect 26

Thermal direct bonding, 109

Thermal expansion coefficients (TEC)

INDEX

of PMMA, 100 of SU-8, 100

Thermoplastic polymers, 96 Thin-film batteries, use of, 209

Total internal reflection fluorescence, 11

Total internal reflection microscopy (TIRM), 336 Total internal reflection, application of, 334 Toxic heavy metal effects, methods to evaluate,

bioluminescence, 9 cell metabolism, 9 cell respiration, 9

Toxins, different types of, ricin, 15

staphylococcal enterotoxin B (SEB), 15 yersinia pestis, 15

Tranducers, definition of, 206 Transducer classification, techniques of

electrochemical, 7 mass-sensitive measurements, 5 optical measurements, 5

Transducer, 3 Transducers, forms of

electrochemical detection methods, 11–12 mass sensitive detection methods, 13 optical detection methods, 11–12

Transduction pathways, IKK-NF.k B pathway, 391 Ras-MAPK pathways, 389–391

Transduction pathways, 389

Trap design for cells, factors influencing current-induced heating, 172

direct electric-field interactions, 173–175 Trap design

conditions for stability, 160 considerations for, 182–183 finite-element modeling, 161 trapping point, 161

with cell manipulation, 172–175 Trap geometries

comparison of p-DEP and n-DEP approaches, 176t n-DEP trap geometries, 175–178

p-DEP trap geometries, 179

Trap parameters, quantification of, 180–183

Ultrasonic bath treatment

Universal M-300 Laser Platform of Universal Laser Systems Inc., 106

Unlabeled antibody-antigen pairs, 44 Urease, 12

UV-lasers, use of, 106

Vascular cell adhesion molecule(VCAM)-1, 374 Velocity measurement in polymer micro channels

using micro velocitymetry, 365 using mini LDV, 361–363