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Open-Space Microfluidics: Concepts, Implementations, Applications

Open-Space Microfluidics: Concepts, Implementations, Applications

Emmanuel Delamarche (Editor) , Govind V. Kaigala (Editor)

ISBN: 978-3-527-69679-6

Jan 2018

450 pages

$164.99

Description

Summarizing the latest trends and the current state of this research field, this up-to-date book discusses in detail techniques to perform localized alterations on surfaces with great flexibility, including microfluidic probes, multifunctional nanopipettes and various surface patterning techniques, such as dip pen nanolithography. These techniques are also put in perspective in terms of applications and how they can be transformative of numerous (bio)chemical processes involving surfaces.
The editors are from IBM Zurich, the pioneers and pacesetters in the field at the forefront of research in this new and rapidly expanding area.

Foreword xv

Preface xvii

Part I Hydrodynamic Flow Confinement (HFC) 1

1 Hydrodynamic Flow Confinement Using a Microfluidic Probe 3
Emmanuel Delamarche, Robert D. Lovchik, Julien F. Cors, and Govind V. Kaigala

1.1 Introduction 3

1.2 HFC Principle 4

1.3 MFP Heads 7

1.4 Vertical MFP 8

1.5 Advanced MFP Heads and Holders 9

1.6 Surface Processing Using an MFP 11

1.7 MFP Components 15

1.8 Outlook 16

Acknowledgments 17

References 17

2 Hierarchical Hydrodynamic Flow Confinement (hHFC) and Recirculation for Performing Microscale Chemistry on Surfaces 21
Julien F. Cors, Julien Autebert, Aditya Kashyap, David P. Taylor, Robert D. Lovchik, Emmanuel Delamarche, and Govind V. Kaigala

2.1 Introduction 21

2.2 Hierarchical HFC 22

2.2.1 Minimal Dilution of the Processing Liquid 22

2.2.2 Numerical Simulations of Hierarchical HFC 22

2.2.3 Dilution Measurement of hHFC 25

2.2.4 Microscale Chemistry Using hHFC 26

2.3 Recirculation 28

2.3.1 Recirculation of Small Volumes of Liquids within an MFP Head 28

2.3.2 AnalyticalModel: Diffusive Transport between Two Laminar Flows in hHFC 30

2.4 Microscale Deposition 33

2.4.1 Patterning Proteins on Surfaces 33

2.4.2 Protein Deposition Using hHFC and Recirculation 35

2.4.3 AnalyticalModel: Convective Transport between Two Laminar Flows in hHFC 39

2.4.4 Conclusion and Outlook 42

Acknowledgments 43

References 43

3 Design of Hydrodynamically ConfinedMicroflow Devices with Numerical Modeling: Controlling Flow Envelope, Pressure, and Shear Stress 47
Choongbae Park, Kevin V. Christ, and Kevin T. Turner

3.1 Introduction 47

3.2 Theory 48

3.2.1 Pressure, Velocity Distribution, and Nondimensional Quantities 48

3.2.2 Shear Stress 50

3.3 Device and ExperimentalMethods for CFD Validation 50

3.4 Numerical Modeling of HCM devices 52

3.5 Envelope Size and Pressure Drop Across HCMs 54

3.6 Hydrodynamic Loads Generated by HCM Devices 58

3.7 Concluding Remarks 60

References 60

4 Hele-Shaw Flow Theory in the Context of Open Microfluidics: From Dipoles to Quadrupoles 63
Étienne Boulais and Thomas Gervais

4.1 Introduction 63

4.2 Fundamentals of Hele-Shaw Flows 64

4.2.1 Derivation of Hele-Shaw Equation from the Navier–Stokes Equation 64

4.2.2 Hele-Shaw Point Sources, Round Monopoles, and Square Monopoles 68

4.3 Applications to Microfluidic Dipoles and Quadrupoles 69

4.3.1 Velocity Potentials for Dipoles and Quadrupoles 70

4.3.2 Deriving Key Operation Characteristics for Dipoles and Quadrupoles 71

4.3.2.1 Stagnation Points and the Hydrodynamic Flow Confinement Zone 71

4.3.3 Numerical Investigation of Model Accuracy 74

4.4 Diffusion in Hele-Shaw Flows 76

4.4.1 Advection–Diffusion Transport Equations 76

4.4.2 High Péclet Number Asymptotic Solutions Near Stagnation Points 77

4.4.2.1 Floating Gradient Along the Central Line in a Microfluidic Quadrupole 78

4.4.2.2 Diffusion Broadening in the HFC Envelope for Dipoles and Quadrupoles 80

4.4.3 Numerical Investigation of Model Accuracy 80

4.5 Conclusion 81

References 82

5 Implementation and Applications of Microfluidic Quadrupoles 83
Ayoola T. Brimmo andMohammad A. Qasaimeh

5.1 Introduction 83

5.2 Principles and Configurations of MQs 85

5.3 Implementation of MQs 87

5.4 MQ Analysis and Characterization 88

5.4.1 Stagnation Point Visualization 88

5.4.2 Hydrodynamic Flow Confinement 90

5.4.3 Concentration Gradient Measurement 91

5.4.4 Stagnation Point Hydrodynamic Manipulation 92

5.5 Application of MQs in Biology and Life Sciences 94

5.5.1 MQs for Biochemical Concentration Gradient Assays 94

5.5.2 Studying Neutrophil Chemotaxis Using the Lateral MQ 95

5.6 Summary and Outlook 95

References 98

6 Hydrodynamic Flow Confinement-Assisted Immunohistochemistry from Micrometer to Millimeter Scale 101
Robert D. Lovchik, David P. Taylor, Emmanuel Delamarche, And Govind V. Kaigala

6.1 Immunohistochemical Analysis of Tissue Sections 101

6.2 Probe Heads for Multiscale Surface Interactions 102

6.2.1 Probe Design and Operating Conditions for Millimeter-Scale HFCs 103

6.2.2 Slit-Aperture Probes 105

6.2.3 Aperture-Array Probes 105

6.3 Immunohistochemistry with Microfluidic Probes 107

6.4 Micro-IHC on Human Tissue Sections 108

6.4.1 Micro-IHC on Tissue Microarrays 109

6.5 Millimeter-Scale Immunohistochemistry 109

6.6 Outlook 112

Acknowledgments 113

References 113

7 Local Nucleic Acid Analysis of Adherent Cells 115
Aditya Kashyap, Deborah Huber, Julien Autebert, and Govind V. Kaigala

7.1 Introduction 115

7.1.1 Heterogeneity in Cells and Their Microenvironments 115

7.1.2 State of the Art: Microfluidic Devices for Nucleic Acid Analysis 116

7.1.3 Microfluidic Probe for Spatial Probing of Standard Biological Substrates 119

7.2 Methods 121

7.2.1 MFP Platform, Head, and Handling 121

7.2.2 Cell Handling 122

7.2.3 μFISH Protocol 123

7.2.4 Local Lysis and Sample Retrieval Protocol 123

7.2.5 DNA and RNA Quantification 124

7.3 Results 124

7.3.1 Genomic Analysis 126

7.3.1.1 Study of Chromosomal Characteristics of Adherent Cells Using μFISH 124

7.3.1.2 Operational Parameterization for μFISH 126

7.3.1.3 Improved Probe Incubation and Consumption Using μFISH 126

7.3.1.4 μFISH Allows for SpatialMultiplexing of Probes 127

7.3.1.5 Selective Local Lysis for DNA Analysis Using the MFP (Spatialyse) 127

7.3.1.6 Operational Parameterization and Liquid Handling for Spatialyse 127

7.3.1.7 Quantitation of DNA in Local Lysate 129

7.3.2 Transcriptomic Analysis 130

7.3.2.1 Spatially Resolved Probing of Gene Expression in Adherent Cocultures 130

7.4 Discussion 131

7.5 Concluding Remarks 133

Acknowledgments 134

References 134

8 Microfluidic Probe for Neural Organotypic Brain Tissue and Cell Perfusion 139
Donald MacNearney, Mohammad A. Qasaimeh, and David Juncker

8.1 Introduction 139

8.2 Microperfusion of Organotypic Brain Slices Using the Microfluidic Probe 141

8.2.1 Design of Perfusion Chamber for Organotypic Brain Slice Culture 141

8.2.2 Design of PDMS MFP 143

8.2.3 Microscope Setup 147

8.2.4 Microperfusion of Organotypic Brain Slices 148

8.3 Microperfusion of Live Dissociated Neural Cell Cultures Using the Microfluidic Probe 148

8.4 Conclusion 152

Acknowledgments 153

References 153

9 The Multifunctional Pipette 155
Aldo Jesorka and Irep Gözen

9.1 Introduction 155

9.2 Open Volume Probes 157

9.3 Detailed View on the Multifunctional Pipette 159

9.3.1 Chip Concept 159

9.3.2 Device Design and Function 161

9.3.3 Fabrication 165

9.4 Integrated Functions 167

9.4.1 Valveless Switching 168

9.4.2 Control Schematics 169

9.4.3 Operation 170

9.5 Functional Extensions and Applications 172

9.5.1 In-Channel Electrodes 172

9.5.2 Single-Cell Superfusion 173

9.5.3 Optofluidic Thermometer 173

9.5.4 Multiprobe Operation 175

9.5.5 Lab-on-a-Membrane 176

9.6 Future Technology 178

9.6.1 Materials and Fabrication 179

9.6.2 Collection and Integration of Assays and Sensors 181

9.6.3 Automation 182

Acknowledgments 183

References 183

10 Single-Cell Analysis with the BioPen 187
Irep Gözen, Gavin Jeffries, Tatsiana Lobovkina, Emanuele Celauro, Mehrnaz Shaali, Baharan Ali Doosti, and Aldo Jesorka

10.1 Introduction 187

10.2 The Single-Cell Challenge 189

10.2.1 Single-Cell Analysis 189

10.2.2 Technology Overview 190

10.2.3 Adherent Cells 191

10.3 Superfusion Techniques 192

10.3.1 Hydrodynamic Confinement 192

10.4 The BioPen 193

10.5 Application Areas 194

10.5.1 Cell Zeiosis and Ion Channel Activation 194

10.5.2 Single Cell Enzymology 196

10.5.3 Local Temperature Adjustment and Measurement in a Single-Cell Environment 199

10.5.4 Intercellular Communication 202

10.5.5 Single-Cell Viability Test 203

10.5.6 Single Muscle Fiber Physiology 205

10.5.7 Single-Cell Electroporation 208

10.5.8 Local Superfusion of Tissue Slices 210

10.6 Future Technology 213

Acknowledgments 215

References 215

11 Microfluidic Probes for Single-Cell Proteomic Analysis 221
Aniruddh Sarkar, LidanWu, and Jongyoon Han

11.1 Introduction 221

11.2 Technical Requirements of Single-Cell Proteomic Analysis 223

11.3 Methods for Single-Cell Proteomic Analysis 225

11.4 Microfluidics Enabling Next-Generation Single-Cell Proteomics 229

11.5 Open-Ended Microwells for Proteomic and Multiparameter Single-Cell Studies 231

11.6 Microfluidic Probes in In Situ Single-Cell Proteomic Measurement 231

11.7 Outlook for FutureWork with Microfluidic Single-Cell Proteomic Assay 236

11.7.1 Sensitivity 236

11.7.2 Throughput 238

11.7.3 Porting Other Assays to the Microfluidic Probe 240

11.7.4 Applications in Single-Cell Biology 241

11.8 Conclusion 242

References 242

Part II Localized Chemistry 249

12 Aqueous Two-Phase Systems for Micropatterning of Cells and Biomolecules 251
Stephanie L. Ham and Hossein Tavana

12.1 Introduction 251

12.2 Small Molecules Applications 253

12.2.1 Bioreagent Patterning 253

12.2.2 Antibody Assays 253

12.2.3 Collagen Microgels 256

12.3 Cell Patterning 258

12.3.1 Bacterial Cells 258

12.3.2 Mammalian Cells 260

12.3.2.1 Cell Exclusion and Cell Island Patterning 260

12.3.2.2 Cell Co-Culturing 262

12.3.2.3 Heterocellular Stem Cell Niche Engineering 264

12.3.2.4 Skin Tissue Engineering 265

12.3.2.5 Three-Dimensional Cellular Models 266

12.4 Conclusions 269

Acknowledgments 269

References 269

13 Development of Pipettes as Mobile Nanofluidic Devices for Mass Spectrometric Analysis 273
Anumita Saha-Shah and Lane A. Baker

13.1 Introduction 273

13.2 Segmented Flow Analysis 275

13.3 Utility of Nano- and Micropipettes in Mass Spectrometry 276

13.4 Development of Nanopipette Probes for Local Sampling 276

13.5 MALDI-MS Analysis of Analyte Post-Nanopipette Sampling 278

13.5.1 Single Allium cepa Cell Analysis 279

13.5.2 Lipid Analysis in Mouse Brain 280

13.6 Development of Segmented Flow Sampling 282

13.7 Study of Intercellular Heterogeneity 286

13.8 Conclusion and Outlook 288

Acknowledgments 290

References 290

14 FluidFM: Development of the Instrument as well as Its Applications for 2D and 3D Lithography 295
Tomaso Zambelli, Mathias J. Aebersold, Pascal Behr, Hana Han, Luca Hirt, VincentMartinez, Orane Guillaume-Gentil, and János Vörös

14.1 Microchanneled AFM Cantilevers 296

14.1.1 Silicon-Based Hollow Probes 296

14.1.2 Polymer-Based Hollow Probes 297

14.2 Development of the FluidFM 300

14.3 Calibration of Hollow Probes: Stiffness and Flow 303

14.3.1 Stiffness 303

14.3.2 Flow 305

14.4 FluidFM as Lithography Tool in Liquid 308

14.4.1 Patterning Nanoparticles 308

14.4.2 Electrochemical 2D Patterning and 3D Printing 312

14.5 Conclusions and Outlook 316

Acknowledgments 317

References 317

15 FluidFM Applications in Single-Cell Biology 325
Orane Guillaume-Gentil,MaximilianMittelviefhaus, Livie Dorwling-Carter, Tomaso Zambelli and Julia A. Vorholt

15.1 Introduction 325

15.2 Nondestructive Cell Manipulations 326

15.3 Spatial Cell Manipulation 327

15.3.1 Substrate Micropatterning 327

15.3.2 Pick and Place 329

15.3.3 Cell Dispensing/Removal 330

15.4 Controlled Fluid Delivery 331

15.4.1 Extracellular Fluid Delivery 332

15.4.2 Intracellular Fluid Delivery 333

15.5 Mechanical Measurements 335

15.5.1 Quantification of Cell Elasticity 336

15.5.2 Quantification of Single-Cell Adhesion Forces 337

15.6 Ionic Current Measurements 341

15.6.1 Adaptation of the FluidFM Setup for Picoampere Current Measurements 342

15.6.2 Force-Controlled Patch Clamp with the FluidFM 343

15.6.3 Scanning Ion Conductance Microscopy with the FluidFM 346

15.7 Molecular Analyses 348

15.8 Conclusion and Future Perspectives 349

References 350

16 Soft Probes for Scanning ElectrochemicalMicroscopy 355
Tzu-En Lin, Andreas Lesch, Alexandra Bondarenko, Fernando Cortés-Salazar, and Hubert H. Girault

16.1 Introduction 355

16.2 Principles of Scanning Electrochemical Microscopy (SECM) 356

16.2.1 SECM Feedback Mode 356

16.2.2 SECM Generation/Collection Modes 358

16.3 Soft Probes for SECM 358

16.3.1 Fabrication and Characterization 359

16.3.2 Operation Principles 360

16.4 Applications of Soft SECM Probes 360

16.4.1 Reactivity Imaging of Extended Three-Dimensional Samples 362

16.4.2 High-Throughput Patterning and Imaging of Delicate Surfaces 362

16.4.3 Detection of Cancer Biomarkers in Skin Biopsy Sections 364

16.5 Conclusions and Future Perspectives 368

References 368

17 Microfluidic Probes for Scanning Electrochemical Microscopy 373
Alexandra Bondarenko, Fernando Cortés-Salazar, Tzu-En Lin, Andreas Lesch, and Hubert H. Girault

17.1 Introduction 373

17.2 Combining Microfluidics with SECM 374

17.2.1 Fountain Pen Probe 374

17.2.2 Electrochemical Push–Pull Probes 375

17.3 Electrochemical Characterization 377

17.3.1 Cyclic Voltammetry 377

17.3.2 SECM Experiments 378

17.4 Applications 382

17.4.1 SECM Imaging of Human Fingerprints Contaminated with Explosive Traces 382

17.4.2 Monitoring Enzymatic Reactions 384

17.4.3 Local Manipulation of Adherent Live Cell Microenvironments 385

17.5 Conclusions and Outlook 389

References 389

18 Chemistrode for High Temporal- and Spatial-Resolution Chemical Analysis 391
Alexander J. Donovan and Ying Liu

18.1 Introduction 391

18.2 Chemistrode Design and Operation 394

18.2.1 Chemistrode Design and Fabrication 394

18.2.2 Chemistrode Operation 394

18.3 Physical Principles Governing the Transport Processes 395

18.3.1 Non-dimensional Groups 395

18.3.2 Coalescence Dynamics of Incoming Plugs with the Hydrophilic Substrate 396

18.3.3 Mass Transfer at the Hydrophilic Substrate 398

18.4 Multiform Chemical Analysis Independent in Space and Time from Data Acquisition 400

18.4.1 Online Analysis 400

18.4.2 Parallel Offline Analysis 401

18.5 Applicability for Stimuli–Response Surfaces 403

18.5.1 Single Islet Cell Stimulation and Response Analysis 403

18.5.2 Isolation and Incubation of Individual Cells from Multispecies Mixtures 405

18.6 Challenges and Future Directions 406

Acknowledgments 407

References 407

Index 411