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Microfluidics: Modeling, Mechanics and Mathematics

Microfluidics: Modeling, Mechanics and Mathematics

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Microfluidics: Modeling, Mechanics and Mathematics

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Dec 13, 2016


This practical, lab-based approach to nano- and microfluidics provides readers with a wealth of practical techniques, protocols, and experiments ready to be put into practice in both research and industrial settings. The practical approach is ideally suited to researchers and R&D staff in industry; additionally the interdisciplinary approach to the science of nano- and microfluidics enables readers from a range of different academic disciplines to broaden their understanding.

Dr Rapp fully engages with the multidisciplinary nature of the subject. Alongside traditional fluid/transport topics, there is a wealth of coverage of materials and manufacturing techniques, chemical modification/surface functionalization, biochemical analysis, and the biosensors involved.

As well as providing a clear and concise overview to get started into the multidisciplinary field of microfluidics and practical guidance on techniques, pitfalls and troubleshooting, this book supplies:

  • A set of hands-on experiments and protocols that will help setting up lab experiments but which will also allow a quick start into practical work.
  • A collection of microfluidic structures, with 3D-CAD and image data that can be used directly (files provided on a companion website).
  • A practical guide to the successful design and implementation of nano- and microfluidic processes (e.g. biosensing) and equipment (e.g., biosensors, such as diabetes blood glucose sensors)
  • Provides techniques, experiments, and protocols ready to be put to use in the lab, in an academic, or industry setting
  • A collection of 3D-CAD and image files is provided on a companion website
Lançado em:
Dec 13, 2016

Sobre o autor

Dr Bastian Rapp is currently employed as Head of Group at the Karlsruhe Institute of Technology (KIT), Institute of Microstructure Technology, Eggenstein-Leopoldshafen, Germany. His research interests are biomechanical engineering, microfluidics, biomaterials and microfabrication.

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Microfluidics - Bastian E. Rapp

Microfluidics: Modeling, Mechanics, and Mathematics

Bastian E. Rapp

Table of Contents

Cover image

Title page





List of Figures

List of Tables

List of Listings

List of Acronyms

List of Abbreviations

List of Symbols

List of Constants

List of Chemicals


I: Fundamentals

Chapter 1: Introduction

1.1 What is Microfluidics?

1.2 A Brief History of Microfluidics

1.3 Commercial Aspects

1.4 About This Book

1.5 Structure of This Book

Chapter 2: Introduction to Maple

2.1 Introduction

2.2 Elementary Maple Commands

2.3 The File Core.txt

2.4 The File Corefunctions.txt

2.5 The Neptunlib

2.6 Summary

Chapter 3: Engineering Mathematics

3.1 Differential Equations

3.2 Important Functions

3.3 Commonly Used Calculus Tricks

3.4 Summary

Chapter 4: Series

4.1 Introduction

4.2 Taylor Series

4.3 Fourier Series

4.4 Fourier-Bessel Series

4.5 Conclusion

Chapter 5: Transforms

5.1 Fourier Transform

5.2 Laplace Transform

5.3 Summary

Chapter 6: Thermodynamics

6.1 Atomic Model

6.2 Weights and Concentrations

6.3 Important Terms and Concepts in Thermodynamics

6.4 Ideal Gases

6.5 Idealized Thermodynamic Processes

6.6 First Law of Thermodynamics

6.7 Second Law of Thermodynamics

6.8 Third Law of Thermodynamics

6.9 Heat and Mass Transfer


Chapter 7: Vector Calculus

7.1 Scalars and Vectors

7.2 Important Theorems in Vector Calculus

7.3 Coordinate System Transformation

7.4 Position, Velocity, and Acceleration

7.5 Jacobian Matrix

7.6 Operators Transformed into the different Coordinate Systems

7.7 Summary

Chapter 8: Differential Equations

8.1 Important Differential Equations

8.2 General Solutions to Selected Ordinary Differential Equations

8.3 General Solutions to Selected Partial Differential Equations

II: Bulk Fluid Flows

Chapter 9: Fluids

9.1 Introduction

9.2 Solids, Liquids, and Gases at the Atomic Scale

9.3 Control Volumes

9.4 Fluid Properties

9.5 Momentum Transport

9.6 Heat Transport

9.7 Mass Transport

9.8 Boundary Conditions

9.9 Dimensionless Numbers

9.10 Summary

Chapter 10: Conservation of Mass: The Continuity Equation

10.1 Fluid Flow in the Bulk

10.2 Continuity Equation

10.3 Integral Representation of the Flowrate

10.4 Mass Balance

10.5 Derivation using Gauss’s Theorem

10.6 Combined Convection and Diffusion: The Convection-Diffusion Equation

10.7 Summary

Chapter 11: Conservation of Momentum: The Navier-Stokes Equation

11.1 Introduction

11.2 Momentum Transfer Into and Out of a Control Volume

11.3 Momentum by in- and Outflowing Mass

11.4 Momentum by Shear Forces

11.5 Momentum by Volume Forces

11.6 Balance of Momentum

11.7 Navier-Stokes Equation for Incompressible Newtonian Fluids

11.8 Dimensional Analysis

11.9 Conclusion

Chapter 12: Conservation of Energy: The Energy Equation and the Thermodynamic Equation of State

12.1 Introduction

12.2 Energy Transfer by Convection

12.3 Heat Flow by Conduction

12.4 Work Flow by Boundary Forces

12.5 Heat Flow by Volume Effects

12.6 Work Flow by Volume Forces

12.7 Balance of Contributions

12.8 Thermodynamic Equation of State

12.9 Summary

Chapter 13: Continuity and Navier-Stokes Equations in Different Coordinate Systems

13.1 Cartesian Coordinates

13.2 Cylindrical Coordinates

13.3 Polar Coordinates

13.4 Spherical Coordinates

13.5 Summary

Chapter 14: The Circular Flow Tube

14.1 Introduction

14.2 Conservation of Mass: The Continuity Equation

14.3 Conservation of Momentum: The Navier-Stokes Equation

14.4 Euler Equation

14.5 Bernoulli Equation

14.6 Conservation of Energy

14.7 Deriving the Euler Equation by a Coordinate System Transformation

14.8 Summary

Chapter 15: Analytical Solutions to the Navier-Stokes Equation

15.1 Hydrostatics and Aerostatics

15.2 Shear Force-Driven Flow: Couette Flow

15.3 Gravity-Driven Flow

15.4 Pressure-Driven Flow: Poiseuille Flow

15.5 Summary

Chapter 16: Analytical Solutions to Poiseuille Flow Problems in Different Geometries

16.1 Elliptical and Circular Profiles

16.2 Planar Infinitesimally Extended Channel Cross-Sections

16.3 Flows in Circular Cross-Sections: Hagen-Poiseuille Flow

16.4 Flows in Rectangular Cross-Sections: Solution to Poisson and Laplace Equations

16.5 Summary

Chapter 17: Hydraulic Resistance

17.1 Introduction

17.2 Viscous Dissipation

17.3 Hydraulic Resistance of Important flow Channel Geometries

17.4 Simplification Approaches to Hydraulic Resistances

17.5 Equivalent Circuit Theory

17.6 Summary

Chapter 18: Analytical Solutions to Transient Flow Problems

18.1 Time-Dependent Transient Effects: Acceleration and Deceleration

18.2 Time-Dependent Couette Flow

18.3 Time-Dependent Hagen-Poiseuille Flow

18.4 Time-Dependent Flow in Rectangular Cross-Sections

18.5 Entrance Effects in Hagen-Poiseuille Flow

18.6 Summary

Chapter 19: Taylor-Aris Dispersion

19.1 Introduction

19.2 Dispersion

19.3 Convection-Diffusion Equation for Cylindrical Cross-Sections

19.4 Mass Concentration Function

19.5 Convection-Diffusion Equation

19.6 Solving for P

19.7 Solving for P

19.8 Validity of the Solution

19.9 Example


III: Fluid Surface Effects

Chapter 20: Surface Tension

20.1 Fluid Effects at Interfaces

20.2 Contact Angle Measurement

20.3 Surfactants

20.4 Marangoni Effect

20.5 Summary

Chapter 21: Capillarity

21.1 Capillary Pressure

21.2 Capillary Length

21.3 Meniscus Formation

21.4 Summary

Chapter 22: Measuring Surface Tension and Free Surface Energy

22.1 Introduction

22.2 Measuring the Surface Tension of Liquids


22.4 Summary

Chapter 23: Plateau-Rayleigh Instability

23.1 Introduction

23.2 Stability Considerations

23.3 Fluid Jets

23.4 Instability

23.5 Standing Waves on a Fluid Jet

23.6 Characteristic Breakup Time

23.7 Applicability of the Plateau-Rayleigh Instability

23.8 Summary

Chapter 24: The Shape of Drops

24.1 Introduction

24.2 Derivation

24.3 Bashforth and Adams: Curvature Expressed as Z (X)

24.4 Brien, Ben, and Van den Brule: Curvature Expressed as Function of θ (Sessile Drops)

24.5 Del Río and Neumann: Curvature Expressed as Function of S (Pendant Drop)

24.6 Comparison With Experimental Data

24.7 Drops Inside of a Fluid

24.8 Historical Development of Drop-Shape Analysis

24.9 Summary

IV: Numerics

Chapter 25: Numerical Methods for Linear Systems of Equations

25.1 Introduction

25.2 Solutions to Linear Systems of Equations

25.3 Numerical Solutions to Linear Systems of Equations

25.4 Summary

Chapter 26: Numerical Solutions to Nonlinear Systems: Newton’s Method

26.1 Introduction

26.2 An Example: The Loran System

26.3 Newton’s Method

26.4 A Solver Implemented in Maple

26.5 Summary

Chapter 27: Numerical Methods for Solving Differential Equations

27.1 Introduction

27.2 Numerical Solutions to Ordinary Differential Equations

27.3 Numerical Solutions to Higher-Order Ordinary Differential Equations and Systems of Coupled Ordinary Differential Equations

27.4 Numerical Solutions to Systems of Ordinary Differential Equations with Boundary Conditions

27.5 Summary

Chapter 28: Numerical Solutions to the Navier-Stokes Equation

28.1 Introduction

28.2 Solution to the Poisson Equation

28.3 Solution to the Poisson Equation Using SOR

28.4 Summary

Chapter 29: Computational Fluid Dynamics

29.1 Introduction

29.2 Galerkin Method

29.3 Summary

Chapter 30: Finite Difference Method

30.1 Introduction

30.2 Advantages and Disadvantages

30.3 FDM in Microsoft Excel

30.4 Summary

Chapter 31: Finite Volume Method

31.1 Introduction

31.2 Conservative form Notation

31.3 Integral form of the Conservative Notation

31.4 Discretization

31.5 Function Reconstruction

31.6 Example: One-Dimensional Heat Equation

31.7 Two-Dimensional Problems of First Order in Time and Space

31.8 Two-Dimensional Problems of First Order in Time and Second-Order in Space

31.9 Summary

Chapter 32: Finite Element Method

32.1 Introduction

32.2 Discretization

32.3 Lagrangian Coordinates

32.4 Basis Functions

32.5 One-Dimensional Example: Flow in Infinitesimally Extended Channels

32.6 Two-Dimensional Example: Flow in Rectangular Channels

32.7 Summary

Chapter 33: Numerical Solutions to Transient Flow Problems

33.1 Introduction

33.2 A Numerical Solver for Two-dimensional Time-Dependent Flow Problems

33.3 A Numerical Solver for Two-Dimensional Entrance Flow Problems

33.4 Summary

Chapter 34: Numerical Solutions to Three-Dimensional Flow Problems

34.1 Introduction

34.2 Derivation

34.3 Implementation of a Stationary Flow Numerical Solver

34.4 Usage of the Numerical Solver

34.5 Summary




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For Anni, Ursula and Karl.


Bastian E. Rapp

Many people have not heard about microfluidics. This is somewhat astonishing as microfluidics surrounds us.

Microfluidics is the scientific disciplines that studies and employs the fluid physics at the micro- and nanometer scale. Fluids do interesting things when probed in such miniaturized systems. Capillarity is one of these effects we are familiar with. If you ever dipped a tissue paper in water and watched the water penetrate it you may have wondered what forces drive it. This is microfluidics. However, nowadays, there is an ample number of technical systems which make use of microfluidics ranging from analytical devices in biomedical engineering and the life sciences all the way to systems such as inkjet printers.

Microfluidics shares many of its fundamentals with classical fluid mechanics. Many students struggled with fluid mechanics during their studies because it is a discipline that requires a quite sound understanding of engineering mathematics. As a consequence, students (as well as established scientists) often take rather heuristic approaches when designing microfluidic systems. A system is characterized and optimized solely on experimental data. Very often, the findings are published omitting pretty much all fluid mechanical fundamentals and (very often) without any theoretical model. Equations are often copied from textbooks and simply applied without real understanding of what the equations actually describe. Whenever a more complex fluidic system is to be designed many researchers default to numerical software packages for providing an assessment of the system prior to device manufacturing. Very often, these extensive calculations are not necessary as there would have been a very simple theoretical model which would have been sufficient to understand the fluid mechanics of the system.

This book is intended for all students and researchers who want to understand the fundamentals of fluid mechanics. The book does not simply state the most important equations, it derives them. I believe that by providing the derivation of an equation, it will be significantly simpler to understand its meaning and its applicability. The reader will require very little prior knowledge when starting with this book. All mathematical concepts, tricks and methods used will be introduced and explained. The book will elucidate analytical techniques as well as numerical methods. It serves as a practical coursebook for those who want to deepen their knowledge, e.g., of numerical methods as well as for those who are already very experienced in fluid mechanics but simply want to understand where a specific formula (such as, e.g., the velocity distribution in a given channel cross-section) actually comes from.

The book comes with a number of worksheets written in Maple. These worksheets serve as templates to experiment with the equations derived and visually check which changes in the fluid mechanics are induced by changing certain variables. They can be used as basis for theoretical assessment of many microfluidic systems. This book contains many listings written in C which elucidate the numerical methods commonly used in fluid mechanics and microfluidics. In the supplementary you will also find a compiled DLL with exports functions that can be used to solve three-dimensional flow problems numerically. These functions are developed within this book together will all necessary numerical fundamentals. By following the book chapter-by-chapter you will gain a very detailed understanding of engineering mechanics, fluid mechanics and numerical methods.

Have fun exploring the fluid mechanics of microfluidics!

November 2016


Bastian E. Rapp

Na gut Kollegen!

Justus Jonas

As anyone who ever wrote a book will agree on, there are many people that help bringing the book to life.

The first and foremost thanks goes out to all the members of my group, the NeptunLab who supported me during the months it took to finish this book. My sincere thanks goes out to my mentor and long-time supporter Volker Saile for all his help and encouragement.

A warm thank you goes out to my dear friend and colleague Matthias Worgull who first encouraged me to write this book and then helped me sticking to this decision. I also want to thank Mohammad for all the Flammkuchen evenings and philosophical discussions.

I would also like to thank my publisher Elsevier and, especially, Simon Holt for his support and his patience despite the fact that (to quote Dave Barry) The deadline is months over and he has still not received what the publishing industry generally refers to as ’the book’.

Most importantly, I want to thank my wife Emily and my family for their everlasting love and support. For my brother Holger, I have hidden something in this book which you are supposed to pick up at the very beginning because it will make your life so much easier at the very end.

List of Figures

1.1 Number of papers and patents published in the field of microfluidics since 1990 5

2.1 The function f (x) = x² 12

3.1 A barrier lake 22

3.2 Graphical representation of differentials and derivatives 26

3.3 Boundary conditions and initial values 30

3.4 Important trigonometric functions 31

3.5 The right triangle 33

3.6 Bessel functions of first kind 36

3.7 Gamma function Γ (x) 38

3.8 Bessel functions of second kind 38

3.9 Approximation of the delta function 41

3.10 Soluble solid as an example for a delta function 41

3.11 Fourier series of the delta function 42

3.12 Shifted delta function 42

3.13 Fourier series of a two-dimensional delta function 44

3.14 Soluble solid as an example for a Heaviside function 45

3.15 Fourier series of the Heaviside function 46

3.16 Error and complementary error function 47

3.17 Curvature of a function 49

3.18 Derivation of the curvature 49

4.1 The Riemann zeta function 52

4.2 Taylor series expansion of the exponential function 55

4.3 Taylor series expansion in wrong interval 55

4.4 Taylor series expansion of the exponential function around a = 3 56

4.5 Taylor series expansion of the sine function 57

4.6 Graphical explanation of the Fourier series weighting factors 63

4.7 Fourier series expansion of the square wave function 65

4.8 Fourier series expansion of the triangular-like function 66

4.9 Approximating a function by a Fourier sine series 68

4.10 Fourier sine series expansion of the constant function 70

4.11 One-dimensional Fourier expansion interpreted in two dimensions 71

4.12 Fourier expansion of a constant to a sine series in two dimensions 72

4.13 Fourier series expansion of the constant function 73

4.14 Fourier expansion of a constant to a cosine series in two dimensions 74

4.15 Fourier expansion of the exponential function 76

4.16 Exponential function expanded to a purely sine or cosine series 76

4.17 Example of a Fourier-Bessel series expansion 79

5.1 Normalized and unnormalized sinc function 84

6.1 Periodic table of the elements 94

6.2 Thermodynamic control volume 99

6.3 Maxwell speed distribution 107

6.4 Reversible and irreversible processes 116

6.5 Fourier’s law of heat conduction 125

6.6 Visualization of diffusion 130

6.7 Output of the digital diffusion experiment 131

6.8 Derivation of the conservation of mass 132

6.9 Diffusion times 134

7.1 Forming the cross product of two vectors 139

7.2 The theorems of Gauß, Stokes and Green 143

7.3 Control volume used for the Reynold’s transport theorem 145

7.4 Common coordinate systems 147

8.1 Derivation of the wave equation 190

8.2 Sine wave function as a solution to the transport equation 206

8.3 Pulse function as a solution to the transport equation 207

8.4 Two waves colliding 208

8.5 Analytical solution of the heat equation 211

8.6 Heat conduction examples 213

8.7 Half-wave sine function 223

8.8 Half-wave sine function with overtone 225

8.9 Limited point source diffusion 228

8.10 Limited plane diffusion 229

8.11 Limited point source diffusion with boundary condition 230

8.12 Laplace transform applied to solving the wave equation on the semi-infinite string 231

8.13 Solution to the one-dimensional wave equation found using the Laplace transform 233

8.14 Solution to the one-dimensional diffusion equation found using the Laplace transform 234

8.15 Limited point source diffusion in two dimensions 237

9.1 Shear stress on solids and liquids 244

9.2 Solids, liquids, and gases 244

9.3 Lennard-Jones potential given as a function of the distance of two rigid particles 245

9.4 Momentum transport in fluids 250

9.5 Thioxotropic and rheopexic fluids 251

9.6 Momentum transport in water 252

9.7 Measurement principles of viscosimeters 252

9.8 Setup of the Ostwald viscosimeter 254

9.9 Momentum transport and heat conduction 255

9.10 Slip and no-slip boundary conditions 256

10.1 Eulerian and Lagrangian frames of reference 266

10.2 Particle trajectories 268

10.3 Continuity equation 269

11.1 Momentum in-/outflux via mass flow 274

11.2 Momentum introduced by shear forces 275

11.3 Laminar and turbulent flow fields 286

11.4 Reynolds’ dye flow experiment 287

11.5 Visualization of the Froude number 288

12.1 Energy in- and outflux by convection 292

12.2 Energy in- and outflux by conduction 293

12.3 Work created by normal and shear forces 295

14.1 The fluid mechanics of the flow tube 309

15.1 Hydrostatics 315

15.2 Atmospheric pressure drop 317

15.3 Couette flow in a slit 317

15.4 Fluid flow under gravity 319

15.5 Flow profiles for gravity driven flow 320

15.6 Microfluidic channel with arbitrary cross-section 320

16.1 Poiseuille flow in elliptical cross-section 324

16.2 Calculated Poiseuille flow profiles for elliptical and circular channel cross-sections 326

16.3 Poiseuille flow in a planar infinitesimally extended channel 327

16.4 Velocity and shear force profile in a channel of 10 µm height 328

16.5 Velocity and shear force profile in a channel of 50 µm height 329

16.6 Hagen-Poiseuille flow in a circular tube 329

16.7 Calculated tube flow profiles 331

16.8 Calculated shear stress profiles 332

16.9 Alternative derivation of the Hagen-Poiseuille profile 333

16.10 Coordinate systems for Poiseuille flow in rectangular channels 337

16.11 Flow profiles in rectangular channel 342

16.12 Normalized flow profiles in rectangular channel cross-sections 344

16.13 Approximations for the flow profiles in rectangular channel cross-sections 345

16.14 Simplified normalized velocity profiles for rectangular cross-sections 346

16.15 Simplification errors for the flow rate 348

17.1 Viscous dissipation 356

17.2 Normalized hydraulic resistance in channels with elliptical and circular cross-sections calculated for water 360

17.3 Pressure drop in infinitesimally extended parallel channels calculated for water 360

17.4 Pressure drop in channels with rectangular and square cross-sections calculated for water 361

17.5 Correction factor α for elliptical cross-sections 364

17.6 Correction factor α for planar infinitesimally extended cross-sections 365

17.7 Correction factor α for rectangular cross-sections 367

17.8 Analogy between hydraulic and electrical resistance 369

18.1 Accelerating and decelerating flow 372

18.2 Fourier series expansion of the steady-state solution 376

18.3 Accelerating Couette flow 377

18.4 Decelerating Couette flow 378

18.5 Dimensionless accelerating and decelerating Couette flow 378

18.6 Dimensionless accelerating and decelerating Hagen-Poiseuille flow 384

18.7 Accelerating and decelerating Hagen-Poiseuille flow in a capillary with radius 1 mm 384

18.8 Dimensionless accelerating and decelerating flow velocity profiles in rectangular cross-sections 391

18.9 Accelerating and decelerating flow in a rectangular channel 392

18.10 Entrance flow 393

18.11 Normalized velocity profiles of the Hagen-Poiseuille entrance flow 398

19.1 Static plug in microfluidic channel 401

19.2 Moving plug in a microfluidic channel 402

19.3 Example of Taylor-Aris dispersion 409

19.4 Balanced rectangular function 411

19.5 Fourier series of the balanced rectangular pulse function fbal.rect. (x) 413

19.6 Effective diffusion Deff. as a function of the pressure drop 414

19.7 Taylor-Aris dispersion at a channel intersection with circular cross-sections 415

20.1 Surface tension 421

20.2 Estimating the free surface energy 423

20.3 Forces originating from surface tension 424

20.4 Photograph of a gerridae walking on a water surface 425

20.5 Contact angle 425

20.6 Young-Laplace equation 428

20.7 Minimal surfaces demonstrated at a soap ring 429

20.8 Fluid flow in a tapered channel 430

20.9 Advancing and receding contact angle 431

20.10 Principle structure of a surfactant 431

20.11 Bilayer and micelle formation 432

20.12 Langmuir-Blodgett films 433

20.13 Saponification reaction 434

20.14 Surfactants based on carboxylic acid 434

20.15 Surfactants based on sulfonic acid 435

20.16 Cationic surfactants 436

20.17 Zwitterionic surfactants 437

20.18 Non-ionic surfactants 439

20.19 Stabilization of suspensions 440

20.20 Marangoni effect 442

20.21 Demonstration of the Maragoni effect using a surfactant 443

21.1 Capillary pressure 445

21.2 Capillary heights 446

21.3 Meniscus formation 447

21.4 Calculated meniscus shape 451

22.1 Wilhelmy plate method 454

22.2 Drop-weight method 455

22.3 Determination of the surface tension using the de/d s 456

22.4 Maximum bubble pressure method 456

22.5 The spinning drop 457

22.6 Geometry of the spinning drop 457

22.7 Example of a Zisman extrapolation on a perfluorinated polyether acrylate surface 463

23.1 Falling fluid jet 468

23.2 Reduction of radius on a falling fluid jet 470

23.3 Plateau-Rayleigh instability on fluid jets 471

23.4 Dispersion relation for the Plateau-Rayleigh instability 475

23.5 Stationary perturbation on a fluid jet 475

23.6 Characteristic breakup time 476

23.7 Typical values for the Ohnesorge numbers 477

24.1 Cut view through a sessile drop 479

24.2 Contour of a sitting water drop 484

24.3 Numerically calculated drop contour of mercury drop on a glass surface 485

24.4 Height convergence of sessile drops 485

24.5 Difficulties using θ as independent variable 487

24.6 Accommodated contact angles at a curved capillary wall 488

24.7 Pendant drop of water 490

24.8 Pendant drop of mercury 491

24.9 Discontinuity of pendant drop 491

24.10 Comparison of the physical drop contour with the numerically derived drop contours 492

26.1 Example of a nonlinear system: the LORAN system 539

26.2 Intersection of the two equidistance lines 539

27.1 Visualization of the Euler method 550

27.2 Example of using Euler’s method to approximate a function 552

27.3 Numerical solution using Euler’s method 554

27.4 Numerical instability of the Euler method 556

27.5 Numerical stability of the backward Euler method 558

27.6 Example of nonlinear ODE solved by the backward Euler method 559

27.7 Numerical stability and precision of the Crank-Nicolson method 562

27.8 Comparison of the forward Euler and the second-order Adams-Bashforth method 567

27.9 Comparison of forward Euler, second-order Adams-Bashforth and second-order Adams-Moulton methods 571

27.10 Comparison of forward Euler, second-order Adams-Bashforth, second-order Adams-Moulton and fourth-order Runge-Kutta methods 575

27.11 Example of damped harmonic oscillation 576

27.12 Over-, under-, and critically-damped oscillation 579

27.13 Numerical output of the forward Euler and the fourth-order Runge-Kutta method 583

27.14 Example of the method of shooting applied to the ODE for the circular channel cross-section 588

27.15 Numerical output of the shooting method applied to the pendant drop ODE 590

28.1 4 × 4 mesh for numerical calculation of the flow profile in rectangular channels 596

28.2 Numerical output of the solution to the Poisson equation 600

28.3 Numerical output of the solution to the Poisson equation using SOR 601

28.4 Numerical output of the SOR solver in C 605

28.5 Application of the numerical SOR solver in C 606

29.1 Example of the Galerkin method used to solve the differential equation for the Hagen-Poiseuille flow 615

29.2 Example of the Galerkin method used to solve the two-dimensional Poisson equation for the rectangular channel flow 618

29.3 The first four Chebyshev polynomials 620

30.1 Spreadsheet for solving the Poisson equation for pressure-driven flow (part 1) 625

30.2 Spreadsheet for solving the Poisson equation for pressure-driven flow (part 2) 627

30.3 Spreadsheet for solving the Poisson equation for pressure-driven flow (part 3) 628

30.4 Use of the spreadsheet to calculate nonzero boundary conditions 628

30.5 Use of the spreadsheet for fluid mechanical problems with Neumann boundary conditions using the Couette flow as example 629

30.6 Use of the spreadsheet to derive the flow profiles in arbitrarily shaped microfluidic channels 630

30.7 Use of the spreadsheet to solve the electric field distribution 631

31.1 Cells used in FVM 637

31.2 Function reconstruction schemes commonly used in FVM 638

31.3 Example of a finite volume method (FVM) using the one-dimensional heat equation 645

31.4 Microsoft Excel spreadsheet used to solve the one-dimensional heat equation using FVM 647

31.5 Numerical output of the Microsoft Excel spreadsheet used to solve the one-dimensional heat equation using FVM 648

31.6 Two-dimensional mesh for FVM 649

32.1 Mesh discretization used in FEM 655

32.2 Lagrangian coordinate system 656

32.3 Common approximation functions in FEM 659

32.4 Numerical solution of the flow profile in infinitesimally extended channels using finite element method (FEM) 666

32.5 Hat functions plotted using the values obtained from listing 32.1 667

32.6 Mesh for solving the Poisson equation for a circular cross-section 669

32.7 Pyramid function supporting the value ĝ(1) in the two-dimensional mesh 670

32.8 Two-dimensional FEM applied to solving the Poisson equation on a circular cross-section 677

33.1 Numerical results for the accelerating flow in rectangular channel profiles 686

33.2 Numerical results for the accelerating flow in circular channel profiles 688

33.3 Numerical results for the space-transient flow in circular channel profiles during entry flow 693

33.4 Numerical results for the space-transient flow in circular channel profiles during entry flow taking convection into account 696

33.5 Comparison of numerical results for the space-transient flow in circular channel profiles during entry flow studying the effects of convection (part 1) 697

33.6 Comparison of numerical results for the space-transient flow in circular channel profiles during entry flow studying the effects of convection (part 2) 698

34.1 Usage of the three-dimensional solver for case 1: channel by-flow 728

34.2 Three-dimensional flow field for case 1: channel by-flow 730

34.3 Usage of the three-dimensional solver for case 2: channel through-flow 731

34.4 Three-dimensional flow field for case 2: channel through-flow 732

34.5 Usage of the three-dimensional solver for case 3: step expansion 733

34.6 Three-dimensional flow field for case 3: step expansion 734

34.7 Usage of the three-dimensional solver for case 4: flow around objects 736

34.8 Three-dimensional flow field for case 4: flow around objects 736

34.9 Usage of the three-dimensional solver for case 5: rectangular channel flow 738

34.10 Three-dimensional flow field for case 5: rectangular channel flow 738

34.11 Comparison of the flow profiles in a rectangular channel cross-section 739

34.12 Derived velocity and pressure profile along the x-axis for case 5 739

34.13 Usage of the three-dimensional solver for case 6: double-fin channel flow 740

34.14 Numerical output for case 6 in the xy-plane 741

34.15 Numerical output for case 6 in the xz-plane 741

34.16 Three-dimensional flow field for case 6: double-fin channel flow 742

List of Tables

3.1 Roots of the Bessel functions and 40

4.1 Important series 52

4.2 Useful Taylor series 61

4.3 The first 16 Bernouilli numbers 62

5.1 Important Fourier transform pairs 83

5.2 Important Laplace transform pairs 88

6.1 Specific gas constants of commonly used gases 101

6.2 Gas molecule diameters of some commonly used gases 102

6.3 Standard formation enthalpy of some compounds 112

6.4 Standard entropy of some compounds 113

6.5 Standard enthalpy of vaporization of some compounds 115

6.6 Free standard enthalpy of formation of important compounds 119

6.7 Boiling points of some gases 124

6.8 Thermal conductivity of selected substances 126

6.9 A selection of diffusion constants 134

8.1 Common approaches for partial fraction expansion 201

8.2 Solutions to differential equations with characteristic polynomials 220

9.1 Some values for calculating the Lennard-Jones potential 246

9.2 Important dimensionless numbers 258

9.3 Some examples for Prandtl values 260

9.4 A selection of Schmidt and Lewis values 260

17.1 Hydraulic resistance of most important geometries 359

17.2 Compactness and correction factor values for elliptical cross-sections 364

17.3 Compactness and correction factor values for planar infinitesimally extended cross-sections 366

17.4 Compactness and correction factor values for rectangular cross-sections 366

20.1 Free surface energy values of the elements 422

20.2 Surface tension of commonly used liquids 423

22.1 Liquids used for determining free surface energies 461

22.2 Critical surface tension values for polymers 464

22.3 Critical surface tension values for modified surfaces 464

26.1 Values obtained from the solver implementing Newton’s method 546

26.2 Second set of values obtained from the solver implementing Newton’s method (instable) 547

27.1 Computational output of the Euler method 551

27.2 Computational results of the Euler method 554

27.3 Family of the Adams-Moulton formulae 565

27.4 Comparison of computational results of forward Euler method, second-order Adams-Moulton, second-order Adams-Bashforth, and fourth-order Runge-Kutta methods 567

27.5 Family of the Adams-Moulton formulae 570

27.6 Family of the Runge-Kutta formulae 573

32.1 Index matrix used in FEM 656

List of Listings

2.1 The file Core.txt 15

2.2 The file CoreFunctions.txt 18

4.1 Listing for Taylor series expansion 57

4.2 Listing for Fourier series expansion of periodic functions 67

4.3 Listing for Fourier series expansion of nonperiodic functions 75

6.1 Listing for the digital diffusion experiment 129

8.1 Listing for the wave equation 224

16.1 Listing for the profile of elliptical Poiseuille flows 325

16.2 Listing for the mechanics of the tube flow 330

16.3 Listing for calculating flow profiles in rectangular channels 343

18.1 Listing for the time-dependent Couette flow 379

18.2 Listing for the time-dependent Hagen-Poiseuille flow 385

18.3 Listing for the time-dependent flow in rectangular cross-sections 392

19.1 Listing for Taylor-Aris dispersion 415

24.1 Listing for the contour of a sessile drop 483

24.2 Listing for the contour of a pendant drop 489

25.1 Listing for the Jacobi method 511

25.2 Listing for the Gauß-Seidel method 513

25.3 Listing for the successive over-relaxation method 515

25.4 Listing for the successive over-relaxation method with pivoting 516

25.5 Listing for LU-decomposition 522

25.6 Listing for LU-substitution without pivoting 524

25.7 Listing for LU-decomposition with pivoting 525

25.8 Listing for LU-substitution with pivoting 526

25.9 Listing for the sequential dense LU-decomposition 529

25.10 Listing for the sequential dense LU-decomposition with pivoting 530

25.11 Listing for sequential dense LU-substitution with pivoting 531

25.12 Listing for solving a linear system of equations using the Thomas algorithm 533

26.1 Listing for matrix/vector multiplication 543

26.2 Listing for matrix evaluation 543

26.3 Listing for vector evaluation 544

26.4 Listing for Newton’s method for solving nonlinear systems of equations 545

26.5 Listing for applying the Newton’s method solver 546

27.1 Listing for Euler’s method for solving ODEs 553

27.2 Listing for the backward Euler method for solving ODEs 557

27.3 Listing for the Crank-Nicolson method for solving ODEs 561

27.4 Listing for the Adams-Bashforth method for solving ODEs 567

27.5 Listing for the Adams-Moulton method for solving ODEs 571

27.6 Listing for the fourth order Runge-Kutta method for solving ODEs 574

27.7 Listing for the Euler method applied to solving higher-order ODEs and systems of ODEs 582

27.8 Listing for the fourth-order Runge-Kutta method applied to solving higher-order ODEs and systems of ODEs 584

27.9 Listing for application examples of the fourth-order Runge-Kutta method applied to solving higher-order ODEs and systems of ODEs 587

27.10 Listing for application examples of the fourth-order Runge-Kutta method applied to solving the pendant drop ODE 589

28.1 Listing for solving a Poisson equation numerically (part 1) 598

28.2 Listing for solving a Poisson equation numerically (part 2) 599

28.3 Listing for solving a Poisson equation numerically (part 3) 600

28.4 Listing for solving a Poisson equation numerically using SOR in C 602

28.5 Listing for solving a Poisson equation numerically (part 4) 604

28.6 Listing for solving a Poisson equation numerically (part 5) 606

29.1 Listing for the Galerkin method (part 1) 614

29.2 Listing for the adapted Galerkin method (part 2) 616

32.1 Listing for solving a linear system of equations using the Thomas algorithm 666

32.2 Mesh definition for two-dimensional FEM 673

32.3 Helper functions for two-dimensional FEM 674

32.4 Function Initialize required for two-dimensional FEM 674

32.5 Single triangle contribution for two-dimensional FEM 676

32.6 Mesh processing for two-dimensional FEM 676

32.7 Solving the mesh in two-dimensional FEM 677

32.8 Applying two-dimensional FEM using the implemented functions 677

33.1 Listing for preparing a rectangular grid 682

33.2 Listing for preparing a circular grid 683

33.3 Listing for solving time-dependent flow problems 683

33.4 Listing for solving transient flow problems numerically (part 1) 685

33.5 Listing for solving transient flow problems numerically (part 2) 687

33.6 Listing for solving a space-transient flow problem while neglecting convection 690

33.7 Listing for solving transient flow problems numerically (part 3) 690

33.8 Listing for solving a space-transient flow problem taking convection into account 691

33.9 Listing for solving transient flow problems numerically (part 4) 692

33.10 Listing for solving transient flow problems numerically (part 5) 698

34.1 Helper structures used for the implementation of the three-dimensional solver 718

34.2 Body of the three-dimensional solver implementation 720

34.3 The macro ABS of the three-dimensional solver implementation 720

34.4 Block 1 of the three-dimensional solver implementation 722

34.5 Block 2 of the three-dimensional solver implementation 722

34.6 Macro UpdateFlowVariableCorrectIndex of the three-dimensional solver implementation 723

34.7 Macros UpdateFlowVariableValuesAll and UpdateFlowVariableValuesSingle of the three-dimensional solver implementation 723

34.8 Macros UpdateFlowVariableValuesDifferenceAll and UpdateFlowVariableValuesDifference of the three-dimensional solver implementation 725

34.9 Block 3 of the three-dimensional solver implementation 726

34.10 Block 4 of the three-dimensional solver implementation 726

34.11 The macros UpdateFlowVariableDoNeumann and UpdateFlowVariableDoNeumannSingle of the three-dimensional solver implementation 726

34.12 Maple worksheet for solving the flow cases using the three-dimensional solver 727

34.13 Maple worksheet for solving case 1 using the three-dimensional solver 729

34.14 Maple worksheet for solving case 2 using the three-dimensional solver 731

34.15 Maple worksheet for solving case 3 using the three-dimensional solver 733

34.16 Maple worksheet for solving case 4 using the three-dimensional solver 735

34.17 Maple worksheet for solving case 5 using the three-dimensional solver 737

34.18 Maple worksheet for solving case 6 using the three-dimensional solver 740

List of Acronyms

List of Abbreviations

List of Symbols

List of Constants

List of Chemicals




Chapter 1


1.1 What is Microfluidics?

Microfluidics is the science of fluids on the micro- and nanometer scale. Academically, it is a subdiscipline of fluid mechanics, as the fundamental equations describing the physics of fluids at larger length scales are identical to the equations underlying microfluidics. However, compared to classical fluid mechanics, the length scales in microfluidic systems are significantly smaller. There is no clear prerequisite as to when a system can be considered as being microfluidic. In general, if one of the characteristic length scales, e.g., the height or width of a fluid system features dimensions in the micrometer range or below, such a system can be considered a microfluidic system. At these length scales, the fluid physics is different from what we are used to seeing in larger scale systems. As an example, microfluidic flows are usually strictly laminar. Laminar flow is rare in macroscopic systems. At an example, consider a river or even a seashore. The water in these systems usually flows under turbulent flow conditions. This is something we rarely see in microfluidic systems.

Another important aspect of microfluidic flows is effects of surface tension. Surface tension is usually an effect not very important for macroscopic fluidic systems. However, in microfluidics, gravitational forces are usually negligible due to the fact that the amount of liquids used is so small. Surface tension becomes predominant, e.g., in systems which transport liquids in the form of single droplets on open surfaces or within closed channels.

As we will see, the fundamental laws of fluid mechanics are valid for microfluidics as well. However, due to the fact that effects such as fluid turbulence, gravity, and the like can often be neglected, the equations describing microfluidic systems are often significantly simplified versions of the equations of fluid physics. This makes microfluidic an attractive discipline for the study of the properties and dynamics of fluid flow where effects, such as, diffusion, can be studied at very high resolution.

1.2 A Brief History of Microfluidics

The development of microfluidics is very closely related to the history of classical microstructure technology. The latter is mainly based on the huge scientific and commercial success of microelectronics that revolutionized electrical engineering and electronics. The term microelectromechanical system (MEMS) was originally defined at the beginning of the 1980s and describes systems that feature both electrically and mechanically actuated or interrogated components. The term was later complemented by the aspect of optical component integration, for which the term microoptoelectromechanical system (MOEMS) was introduced. The first real systems for which the term MEMS is justified were presented by Petersen et al. in 1982 [1] and later by Chen et al. [2] in 1984. These systems consisted mainly of a mechanically movable mass manufactured alongside electronic circuitry on a chip which was used to measure acceleration. It seems like a straightforward implementation of a very basic MEMS system: the electronic components could be produced in complementary metal oxide semiconductor (CMOS) technology which also allowed the creation of bulk mechanical structures such as the acceleratable masses required for these accelerometers. The mass could be made movable by means of sacrificial layers that were etched during manufacturing. Interrogating the position of this mass by means of the electronic circuitry allowed for the creation of the first MEMS systems. As of today, the most commonly used material for semiconductors is still silicon for which decades of extensive research and process optimization have resulted in highly scalable and reproducible processes. The early MEMS systems have profited extensively from this experience which explains why silicon (and its close relative, glass) are still frequently used materials. This also explains the fact that the early microfluidic systems were almost exclusively produced in silicon by means of photolithographically structured resist layers serving as a mask for wet etching, both of which were among the most frequently used processes in MEMS technology at that time. How closely related microfluidic is to MEMS can be seen when looking at early reviews of microfluidic systems and processing techniques, e.g., the review by Gravesen et al. written in 1993 [3]. The manufacturing techniques used were almost exclusively established MEMS processes such as lithography and wet or dry etching.

In contrast to the early MEMS accelerometers, the first microfluidic systems predicted the variety that would later become one of the most important characteristics of the community. Three early contributions are worth noting here.

1.2.1 Inkjet Printing

This has and still is one of the most important commercial applications in the field of microfluidics. The rapid and precise deposition of small amounts of liquids (such as solutions or inks) has been and most likely will always be one of the key advantages and applications in the field of microfluidics. The early work toward these systems has mainly been driven by IBM and the first contributions were presented by Bassous et al. in 1977 [4]. Judging from the commercial success, inkjet printing ranks among the most prominent application examples for microfluidics. Millions of end-user inkjet printers are sold each year, each of which features a (mostly) silicon printing head that is essentially a microfluidic spotting device.

1.2.2 Integrated Circuit Technology

Given the fact that microfluidics can historically be considered as a subdiscipline of MEMS technology, it seems straightforward that early applications would fall into the regime of microelectronics. One of the most important problems to be solved for high-performance integrated circuits (IC) systems was (and still is) heat dissipation and transfer out of the circuit in order to prevent overheating. Using fluids for heat transport seems a logical consequence and as of today, heat pipes and similar systems are still used for processor cooling on high-end graphic cards or high-performance central processing unit (CPU) chips. Tuckerman and Pease presented such systems in 1981, describing a heat sink which was to be used for large-scale IC designs [5]. This heat sink was connected to a microfluidic channel system that was integrated next to the principle heat sources on the chip. This channel system could be purged with a coolant that would transport the heat out of the system for dissipation in the heat sink.

Today microfluidics in IC technology is limited to niche applications. However, for high performance circuits, microfluidic heat transfer is still a viable option.

1.2.3 Analytical Applications

As of today, this class of applications may be considered one of the most important for the development of microfluidics as a scientific discipline. The immense advantages that microfluidics offers over classical macroscopic fluid handling have been the most important driving factor for the development of a wide set of applications that go beyond mere technological development. It has made microfluidics attractive for other scientific disciplines such as chemistry and biochemistry, reaching all the way up to biomedical devices and applications. The first analytical applications of note were presented by Terry et al. in 1979 [6]. This work described an integrated gas chromatography manufactured in silicon. The system consisted of two bonded silicon wafers that integrated monolithic microvalves and a detector implemented in the form of an anemometric heat conductivity detector. The system was able to clearly detect the distinct peaks from the individual components from a mixture consisting of nitrogen gas, n-pentane, and n-hexane. The authors stated in the summary that The application of IC processing techniques was necessary to reduce the size of the sensor from that of a bulky laboratory instrument to a pocket-sized package, while closely retaining the performance of a larger device [...] This miniature analysis system should find wide application in a number of fields including implanted biological monitors, portable air contaminant analyzers, and unmanned planetary probes. [6] (p. 1886).

Looking back from today, it has to be stated that this system was way ahead of its time as the paper went widely unnoticed. It took almost a decade until the beginning of the 1990s, when the field experienced a revival by the work of Manz et al. which put forward the concept of miniaturized total analysis systems (μTAS) [7]. The concept was first suggested and introduced by Widmer in 1983. In one of the most seminal papers for the development of microfluidics he predicted that [...] such sophisticated, integrated [microfluidic] systems, characterized by their exchangeable modular set-up, will have widespread future applications in industry. They will be part of the analytical impact which is changing the face of the chemical and allied industries. [8] (p. 10).

1.2.4 Microfiuidics Today

Today, the microfluidic community is a diverse scientific amalgamation of various disciplines ranging from physics, engineering, material sciences, all the way to biology, biochemistry, and even information technology. Since 1990 the number of papers and patents on microfluidics has increased steadily as the community has grown (see Fig. 1.1). There are several noteworthy annual meetings of the community such as the International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS) and the Microfluidics, BioMEMS, and Medical Microsystems.

Fig. 1.1 Number of journal papers and patents published in the field of microfluidics since 1990. The number of journal papers was determined using Web of Science ( webofknowledge.com , papers containing the term microfluidic as topic). The number of patents published was determined using Espacenet ( worldwide.espacenet.com , patents containing the term microfluidic in title or summary). Data acquired on January 25 th , 2015.

1.3 Commercial Aspects

There have been many studies and reports about the market potential and the most important potential applications for microfluidics. One of the most commonly cited sources of the market potential of MEMS is published annually by Yole Développement (www.yole.fr). The most recent report, dating from 2015, estimates the global MEMS market to double between 2014 and 2020, reaching a worldwide market volume of 22 000MUS$. The share of microfluidic devices is estimated to be around a fifth of this volume [9].

Because the use of microfluidics in inkjet printers has been such a commercial success, the community has often sought the killer application, i.e., a device mainly based on microfluidic concepts and principles that would yield highly selling products. However, until now, such an application has not been found. Despite this, microfluidics is considered to be the key discipline for the development of laboratory test instruments, as well as home care diagnostics. The reason why the technology has not yet found the widespread applications for which it is doubtlessly suitable is difficult to find. This has been noted repeatedly in the literature, see for example, the recent comment by Whitesides [10]. An excellent series of articles has been published over the last two years by Becker, who focused on commercialization aspects of microfluidic devices and tried to elaborate why there are still so few successfully commercialized microfluidic products. The series discusses the question of whether or not there actually is a killer application [11, 12], the factors influencing the manufacturing cost and therefore the industrial producibility of a device [13], the importance of intellectual property [14], and the need for (or the lack) of standardization [15]. It also includes a detailed discussion of the industrial requirements for successful device commercialization [16, 17]. However microfluidics promises such immense advantages, e.g., low sample volume consumption and fast chemical reactions due to short diffusion lengths, strictly laminar flow, etc. that it is one of the most promising evolving technological fields.

1.4 About This Book

The aim of this book is to provide a general and easy-to-follow introduction to the fundamentals and the mathematics of microfluidics. One of the main advantages of microfluidics is the fact that it is comparatively easy to derive theoretical models for experimental data. However, microfluidics is still fluid physics. Thus, students eager to learn about the fundamentals of microfluidics will very quickly find themselves faced with differential equations, vector analysis, thermodynamics, and engineering mathematics. I have found many students struggling with this wide choice of academic disciplines. Some students may even discover that their respective curriculum did not include sufficiently detailed courses on fluid physics, engineering mathematics, or thermodynamics. Thus, some of the most important fundamental concepts of microfluidics will remain a black box for them.

This book intends to cover microfluidics as a multi-disciplinary topic. It contains large introductory sections which will reintroduce and revise most concepts required for understanding the fluid mechanics of microfluidics. The book takes time deriving and explaining the equations. It is not the intention to simply list the most important ones. There are excellent textbooks in the literature which summarize the most important equations of microfluidics and which may serve as a quick lookup if a specific equation is sought. This book is different. It will not only list the equations, it will derive them. It will explain them. And it will show practical examples using the Algebra package Maple which helps in visualizing the equations and their significance. Some of the equations can even be solved and displayed with Microsoft Excel. As it turns out, this is surprisingly easy.

The book comes with a set of Maple worksheets which can be used to experiment with the equations. It will allow students and researchers to quickly adapt the equations to a specific application. Examples include diffusion, dispersion, pressure drop, velocity distribution, and similar effects.

The book is intended for a broad readership. It will start explaining all fundamental concepts required to understand later chapters. You only remember Fourier or Taylor series expansion from the early days of your study? You have never heard of Laplace transforms, operators, or vector calculus? You have never attended a lecture on thermodynamics? Do not worry – this is not a prerequisite for understanding this book. This book will start from scratch, even allowing students who may have had little to no engineering mathematics in their curriculum to understand the mathematical tools required for solving the seemingly complex equations of microfluidics. As we will see, microfluidics is not very complex and, after a proper introduction, most of the tools can be understood and applied quite readily.

1.5 Structure of This Book

This book is divided into

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